Starting phenix.real_space_refine on Thu Mar 14 10:43:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unf_26623/03_2024/7unf_26623_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unf_26623/03_2024/7unf_26623.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unf_26623/03_2024/7unf_26623.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unf_26623/03_2024/7unf_26623.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unf_26623/03_2024/7unf_26623_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unf_26623/03_2024/7unf_26623_updated.pdb" } resolution = 4.08 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= 0.004 sd= 1.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 11 5.49 5 S 368 5.16 5 C 42729 2.51 5 N 11339 2.21 5 O 12524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 71": "OE1" <-> "OE2" Residue "a GLU 104": "OE1" <-> "OE2" Residue "a GLU 109": "OE1" <-> "OE2" Residue "a PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 126": "OE1" <-> "OE2" Residue "a GLU 180": "OE1" <-> "OE2" Residue "a GLU 186": "OE1" <-> "OE2" Residue "a TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 229": "OE1" <-> "OE2" Residue "a PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 258": "OE1" <-> "OE2" Residue "a GLU 268": "OE1" <-> "OE2" Residue "a ASP 269": "OD1" <-> "OD2" Residue "a GLU 278": "OE1" <-> "OE2" Residue "a GLU 324": "OE1" <-> "OE2" Residue "a GLU 340": "OE1" <-> "OE2" Residue "a PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 390": "OE1" <-> "OE2" Residue "a PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 429": "OE1" <-> "OE2" Residue "a PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 579": "OE1" <-> "OE2" Residue "a PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 712": "OE1" <-> "OE2" Residue "a PHE 716": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 730": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 756": "OE1" <-> "OE2" Residue "a PHE 779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 785": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 797": "OE1" <-> "OE2" Residue "a PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 812": "OE1" <-> "OE2" Residue "a PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 825": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 828": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 19": "OE1" <-> "OE2" Residue "U ASP 25": "OD1" <-> "OD2" Residue "U PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 56": "OE1" <-> "OE2" Residue "U TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 84": "OE1" <-> "OE2" Residue "U GLU 89": "OE1" <-> "OE2" Residue "U PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 105": "OE1" <-> "OE2" Residue "U GLU 118": "OE1" <-> "OE2" Residue "U PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 132": "OD1" <-> "OD2" Residue "U GLU 146": "OE1" <-> "OE2" Residue "U GLU 154": "OE1" <-> "OE2" Residue "U ASP 172": "OD1" <-> "OD2" Residue "U TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 197": "OE1" <-> "OE2" Residue "U PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 226": "OD1" <-> "OD2" Residue "U GLU 233": "OE1" <-> "OE2" Residue "U ASP 237": "OD1" <-> "OD2" Residue "U PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 243": "OE1" <-> "OE2" Residue "U TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 261": "OE1" <-> "OE2" Residue "U PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 273": "OE1" <-> "OE2" Residue "U PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 313": "OE1" <-> "OE2" Residue "U TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 343": "OD1" <-> "OD2" Residue "U TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 407": "OE1" <-> "OE2" Residue "U GLU 432": "OE1" <-> "OE2" Residue "U ARG 450": "NH1" <-> "NH2" Residue "L TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 53": "OE1" <-> "OE2" Residue "L GLU 58": "OE1" <-> "OE2" Residue "L TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 77": "OD1" <-> "OD2" Residue "L PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 193": "OE1" <-> "OE2" Residue "L PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 280": "NH1" <-> "NH2" Residue "L GLU 293": "OE1" <-> "OE2" Residue "L ASP 299": "OD1" <-> "OD2" Residue "L ARG 338": "NH1" <-> "NH2" Residue "L TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 388": "NH1" <-> "NH2" Residue "L ASP 416": "OD1" <-> "OD2" Residue "L ASP 419": "OD1" <-> "OD2" Residue "L ASP 436": "OD1" <-> "OD2" Residue "L PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 466": "OD1" <-> "OD2" Residue "L GLU 485": "OE1" <-> "OE2" Residue "L GLU 487": "OE1" <-> "OE2" Residue "L ASP 488": "OD1" <-> "OD2" Residue "L GLU 491": "OE1" <-> "OE2" Residue "L ASP 517": "OD1" <-> "OD2" Residue "L TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 562": "OD1" <-> "OD2" Residue "L GLU 572": "OE1" <-> "OE2" Residue "L PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 594": "OE1" <-> "OE2" Residue "L ASP 607": "OD1" <-> "OD2" Residue "L GLU 616": "OE1" <-> "OE2" Residue "M TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 58": "OE1" <-> "OE2" Residue "M ASP 60": "OD1" <-> "OD2" Residue "M ASP 77": "OD1" <-> "OD2" Residue "M PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 130": "OD1" <-> "OD2" Residue "M TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 197": "OE1" <-> "OE2" Residue "M GLU 201": "OE1" <-> "OE2" Residue "M PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 219": "OE1" <-> "OE2" Residue "M TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 283": "OE1" <-> "OE2" Residue "M ARG 338": "NH1" <-> "NH2" Residue "M GLU 356": "OE1" <-> "OE2" Residue "M ARG 388": "NH1" <-> "NH2" Residue "M GLU 399": "OE1" <-> "OE2" Residue "M PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 481": "OE1" <-> "OE2" Residue "M ASP 488": "OD1" <-> "OD2" Residue "M ASP 518": "OD1" <-> "OD2" Residue "M ASP 529": "OD1" <-> "OD2" Residue "M TYR 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 552": "NH1" <-> "NH2" Residue "M GLU 594": "OE1" <-> "OE2" Residue "M GLU 606": "OE1" <-> "OE2" Residue "M ASP 607": "OD1" <-> "OD2" Residue "M ARG 613": "NH1" <-> "NH2" Residue "N TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 58": "OE1" <-> "OE2" Residue "N ASP 77": "OD1" <-> "OD2" Residue "N PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 130": "OD1" <-> "OD2" Residue "N ASP 134": "OD1" <-> "OD2" Residue "N ASP 151": "OD1" <-> "OD2" Residue "N TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 195": "OE1" <-> "OE2" Residue "N GLU 219": "OE1" <-> "OE2" Residue "N PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 279": "OE1" <-> "OE2" Residue "N GLU 283": "OE1" <-> "OE2" Residue "N ARG 289": "NH1" <-> "NH2" Residue "N ASP 290": "OD1" <-> "OD2" Residue "N ARG 338": "NH1" <-> "NH2" Residue "N GLU 356": "OE1" <-> "OE2" Residue "N ASP 371": "OD1" <-> "OD2" Residue "N GLU 387": "OE1" <-> "OE2" Residue "N ARG 388": "NH1" <-> "NH2" Residue "N TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 466": "OD1" <-> "OD2" Residue "N GLU 486": "OE1" <-> "OE2" Residue "N GLU 487": "OE1" <-> "OE2" Residue "N GLU 510": "OE1" <-> "OE2" Residue "N ASP 517": "OD1" <-> "OD2" Residue "N PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 556": "OE1" <-> "OE2" Residue "N TYR 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 594": "OE1" <-> "OE2" Residue "N ASP 607": "OD1" <-> "OD2" Residue "O TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 148": "OE1" <-> "OE2" Residue "O PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 221": "OD1" <-> "OD2" Residue "O GLU 224": "OE1" <-> "OE2" Residue "O GLU 239": "OE1" <-> "OE2" Residue "O ASP 247": "OD1" <-> "OD2" Residue "O GLU 250": "OE1" <-> "OE2" Residue "O GLU 283": "OE1" <-> "OE2" Residue "O PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 342": "OE1" <-> "OE2" Residue "O ASP 367": "OD1" <-> "OD2" Residue "O ASP 380": "OD1" <-> "OD2" Residue "O TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 441": "OE1" <-> "OE2" Residue "O GLU 442": "OE1" <-> "OE2" Residue "O GLU 453": "OE1" <-> "OE2" Residue "O ARG 460": "NH1" <-> "NH2" Residue "O PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 469": "OE1" <-> "OE2" Residue "O GLU 490": "OE1" <-> "OE2" Residue "O GLU 502": "OE1" <-> "OE2" Residue "O PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 61": "OD1" <-> "OD2" Residue "P PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 359": "OD1" <-> "OD2" Residue "P ASP 367": "OD1" <-> "OD2" Residue "P TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 431": "OD1" <-> "OD2" Residue "P GLU 442": "OE1" <-> "OE2" Residue "P ASP 447": "OD1" <-> "OD2" Residue "P TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 460": "NH1" <-> "NH2" Residue "P PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 502": "OE1" <-> "OE2" Residue "P PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 506": "NH1" <-> "NH2" Residue "Q ASP 78": "OD1" <-> "OD2" Residue "Q ASP 106": "OD1" <-> "OD2" Residue "Q ASP 126": "OD1" <-> "OD2" Residue "Q ASP 149": "OD1" <-> "OD2" Residue "Q ASP 218": "OD1" <-> "OD2" Residue "Q TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 224": "OE1" <-> "OE2" Residue "Q PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 239": "OE1" <-> "OE2" Residue "Q GLU 249": "OE1" <-> "OE2" Residue "Q PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 283": "OE1" <-> "OE2" Residue "Q PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 290": "OE1" <-> "OE2" Residue "Q TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 408": "OE1" <-> "OE2" Residue "Q TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 431": "OD1" <-> "OD2" Residue "Q ASP 447": "OD1" <-> "OD2" Residue "Q ARG 460": "NH1" <-> "NH2" Residue "Q PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 469": "OE1" <-> "OE2" Residue "Q ASP 478": "OD1" <-> "OD2" Residue "Q PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 490": "OE1" <-> "OE2" Residue "Q GLU 502": "OE1" <-> "OE2" Residue "Q PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 506": "NH1" <-> "NH2" Residue "D GLU 8": "OE1" <-> "OE2" Residue "D GLU 71": "OE1" <-> "OE2" Residue "D PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 120": "OE1" <-> "OE2" Residue "D TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 193": "OE1" <-> "OE2" Residue "D TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 7": "OD1" <-> "OD2" Residue "b PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 20": "OE1" <-> "OE2" Residue "b GLU 22": "OE1" <-> "OE2" Residue "b GLU 28": "OE1" <-> "OE2" Residue "b GLU 29": "OE1" <-> "OE2" Residue "b ASP 31": "OD1" <-> "OD2" Residue "b GLU 35": "OE1" <-> "OE2" Residue "b GLU 41": "OE1" <-> "OE2" Residue "b ARG 44": "NH1" <-> "NH2" Residue "b ARG 50": "NH1" <-> "NH2" Residue "b TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 58": "OE1" <-> "OE2" Residue "b GLU 61": "OE1" <-> "OE2" Residue "b GLU 65": "OE1" <-> "OE2" Residue "b ASP 88": "OD1" <-> "OD2" Residue "b PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 201": "OD1" <-> "OD2" Residue "b PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 37": "OE1" <-> "OE2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "c ARG 50": "NH1" <-> "NH2" Residue "c GLU 55": "OE1" <-> "OE2" Residue "c TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 61": "OE1" <-> "OE2" Residue "c ASP 93": "OD1" <-> "OD2" Residue "c ASP 108": "OD1" <-> "OD2" Residue "c ASP 117": "OD1" <-> "OD2" Residue "c ARG 131": "NH1" <-> "NH2" Residue "c ARG 137": "NH1" <-> "NH2" Residue "c TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 170": "OE1" <-> "OE2" Residue "c GLU 175": "OE1" <-> "OE2" Residue "c TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 187": "OD1" <-> "OD2" Residue "c PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 5": "OD1" <-> "OD2" Residue "d ASP 7": "OD1" <-> "OD2" Residue "d PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 20": "OE1" <-> "OE2" Residue "d GLU 22": "OE1" <-> "OE2" Residue "d GLU 25": "OE1" <-> "OE2" Residue "d ARG 44": "NH1" <-> "NH2" Residue "d GLU 55": "OE1" <-> "OE2" Residue "d TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 88": "OD1" <-> "OD2" Residue "d TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 164": "OD1" <-> "OD2" Residue "d GLU 170": "OE1" <-> "OE2" Residue "d ASP 187": "OD1" <-> "OD2" Residue "d PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 15": "OE1" <-> "OE2" Residue "e ARG 17": "NH1" <-> "NH2" Residue "e ARG 26": "NH1" <-> "NH2" Residue "e ARG 28": "NH1" <-> "NH2" Residue "e ARG 31": "NH1" <-> "NH2" Residue "e ARG 32": "NH1" <-> "NH2" Residue "e GLU 38": "OE1" <-> "OE2" Residue "e GLU 45": "OE1" <-> "OE2" Residue "e ARG 48": "NH1" <-> "NH2" Residue "e ARG 51": "NH1" <-> "NH2" Residue "e GLU 52": "OE1" <-> "OE2" Residue "e PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 66": "NH1" <-> "NH2" Residue "e GLU 72": "OE1" <-> "OE2" Residue "e GLU 79": "OE1" <-> "OE2" Residue "e ARG 89": "NH1" <-> "NH2" Residue "e ASP 97": "OD1" <-> "OD2" Residue "e PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 105": "OD1" <-> "OD2" Residue "f ARG 17": "NH1" <-> "NH2" Residue "f ARG 26": "NH1" <-> "NH2" Residue "f ARG 28": "NH1" <-> "NH2" Residue "f ARG 31": "NH1" <-> "NH2" Residue "f ARG 32": "NH1" <-> "NH2" Residue "f GLU 38": "OE1" <-> "OE2" Residue "f ARG 48": "NH1" <-> "NH2" Residue "f ARG 51": "NH1" <-> "NH2" Residue "f GLU 59": "OE1" <-> "OE2" Residue "f GLU 74": "OE1" <-> "OE2" Residue "f ARG 89": "NH1" <-> "NH2" Residue "f ASP 93": "OD1" <-> "OD2" Residue "f ASP 97": "OD1" <-> "OD2" Residue "f PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 17": "NH1" <-> "NH2" Residue "g GLU 20": "OE1" <-> "OE2" Residue "g GLU 24": "OE1" <-> "OE2" Residue "g ARG 26": "NH1" <-> "NH2" Residue "g ARG 28": "NH1" <-> "NH2" Residue "g ARG 31": "NH1" <-> "NH2" Residue "g GLU 38": "OE1" <-> "OE2" Residue "g GLU 43": "OE1" <-> "OE2" Residue "g TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 48": "NH1" <-> "NH2" Residue "g ARG 51": "NH1" <-> "NH2" Residue "g GLU 52": "OE1" <-> "OE2" Residue "g PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 59": "OE1" <-> "OE2" Residue "g ARG 66": "NH1" <-> "NH2" Residue "g ARG 89": "NH1" <-> "NH2" Residue "g ARG 92": "NH1" <-> "NH2" Residue "g GLU 94": "OE1" <-> "OE2" Residue "g ASP 105": "OD1" <-> "OD2" Residue "g ARG 107": "NH1" <-> "NH2" Residue "g ARG 115": "NH1" <-> "NH2" Residue "F GLU 14": "OE1" <-> "OE2" Residue "F PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 42": "OD1" <-> "OD2" Residue "F ASP 60": "OD1" <-> "OD2" Residue "F GLU 72": "OE1" <-> "OE2" Residue "F ARG 107": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "k TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 12": "OD1" <-> "OD2" Residue "k GLU 40": "OE1" <-> "OE2" Residue "k GLU 43": "OE1" <-> "OE2" Residue "k GLU 61": "OE1" <-> "OE2" Residue "k ARG 73": "NH1" <-> "NH2" Residue "k ASP 98": "OD1" <-> "OD2" Residue "k TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 124": "OE1" <-> "OE2" Residue "k GLU 170": "OE1" <-> "OE2" Residue "k GLU 179": "OE1" <-> "OE2" Residue "k GLU 215": "OE1" <-> "OE2" Residue "k ASP 217": "OD1" <-> "OD2" Residue "k GLU 235": "OE1" <-> "OE2" Residue "k ASP 236": "OD1" <-> "OD2" Residue "k GLU 250": "OE1" <-> "OE2" Residue "k GLU 262": "OE1" <-> "OE2" Residue "k ASP 269": "OD1" <-> "OD2" Residue "k TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 279": "OE1" <-> "OE2" Residue "k ASP 292": "OD1" <-> "OD2" Residue "k GLU 298": "OE1" <-> "OE2" Residue "k PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 334": "OE1" <-> "OE2" Residue "k PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 87": "OE1" <-> "OE2" Residue "n PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 127": "NH1" <-> "NH2" Residue "s ARG 266": "NH1" <-> "NH2" Residue "s TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 417": "OD1" <-> "OD2" Residue "s PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 455": "NH1" <-> "NH2" Residue "s ASP 458": "OD1" <-> "OD2" Residue "r PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 50": "OE1" <-> "OE2" Residue "8 ASP 82": "OD1" <-> "OD2" Residue "9 TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 115": "OD1" <-> "OD2" Residue "1 PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 30": "OD1" <-> "OD2" Residue "1 GLU 116": "OE1" <-> "OE2" Residue "1 PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 50": "OE1" <-> "OE2" Residue "3 GLU 9": "OE1" <-> "OE2" Residue "4 ASP 82": "OD1" <-> "OD2" Residue "6 GLU 9": "OE1" <-> "OE2" Residue "6 GLU 50": "OE1" <-> "OE2" Residue "6 ASP 115": "OD1" <-> "OD2" Residue "7 GLU 9": "OE1" <-> "OE2" Residue "0 GLU 50": "OE1" <-> "OE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 66971 Number of models: 1 Model: "" Number of chains: 40 Chain: "a" Number of atoms: 6127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 6127 Classifications: {'peptide': 752} Link IDs: {'PTRANS': 25, 'TRANS': 726} Chain breaks: 3 Chain: "U" Number of atoms: 3365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3365 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 20, 'TRANS': 406} Chain breaks: 1 Chain: "L" Number of atoms: 4656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4656 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "M" Number of atoms: 4656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4656 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "N" Number of atoms: 4656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4656 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "O" Number of atoms: 3666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3666 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 440} Chain: "P" Number of atoms: 3666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3666 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 440} Chain: "Q" Number of atoms: 3666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3666 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 440} Chain: "D" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1717 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 3, 'TRANS': 209} Chain: "b" Number of atoms: 1809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1809 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 217} Chain: "c" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1782 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 213} Chain: "d" Number of atoms: 1817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1817 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 218} Chain: "e" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 938 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "f" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 938 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "g" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 923 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 1, 'TRANS': 110} Chain: "F" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 856 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "C" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 1770 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 323} Link IDs: {'PTRANS': 9, 'TRANS': 346} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1187 Unresolved non-hydrogen angles: 1517 Unresolved non-hydrogen dihedrals: 993 Unresolved non-hydrogen chiralities: 106 Planarities with less than four sites: {'GLN:plan1': 14, 'ARG:plan': 14, 'TYR:plan': 15, 'ASN:plan1': 23, 'TRP:plan': 6, 'HIS:plan': 6, 'PHE:plan': 14, 'GLU:plan': 25, 'ASP:plan': 24} Unresolved non-hydrogen planarities: 640 Chain: "H" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 2111 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 383} Link IDs: {'PTRANS': 9, 'TRANS': 415} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1448 Unresolved non-hydrogen angles: 1843 Unresolved non-hydrogen dihedrals: 1223 Unresolved non-hydrogen chiralities: 110 Planarities with less than four sites: {'GLN:plan1': 33, 'HIS:plan': 10, 'TYR:plan': 17, 'ASN:plan1': 20, 'TRP:plan': 8, 'ASP:plan': 18, 'PHE:plan': 17, 'GLU:plan': 38, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 851 Chain: "k" Number of atoms: 2836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2836 Classifications: {'peptide': 350} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 336} Chain: "m" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 621 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 6, 'TRANS': 69} Chain: "n" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 658 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain: "s" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1662 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "r" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 377 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "8" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "9" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "1" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1498 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 5, 'TRANS': 198} Chain: "2" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "3" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "4" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "5" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "6" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "7" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "0" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "t" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'GLC': 2, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "w" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'MAN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "s" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 173 Unusual residues: {'NAG': 6, 'POV': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 6 Chain: "r" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 142 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "8" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "1" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 123 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 33 Time building chain proxies: 25.91, per 1000 atoms: 0.39 Number of scatterers: 66971 At special positions: 0 Unit cell: (251.758, 177.662, 244.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 368 16.00 P 11 15.00 O 12524 8.00 N 11339 7.00 C 42729 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS s 371 " - pdb=" SG CYS s 418 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied ALPHA1-2 " MAN t 4 " - " MAN t 5 " " MAN t 5 " - " MAN t 6 " ALPHA1-3 " BMA t 3 " - " MAN t 4 " " MAN t 6 " - " GLC t 7 " " GLC t 7 " - " GLC t 8 " ALPHA1-6 " MAN w 1 " - " MAN w 2 " BETA1-4 " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " NAG-ASN " NAG s 501 " - " ASN s 273 " " NAG s 502 " - " ASN s 296 " " NAG s 503 " - " ASN s 303 " " NAG s 504 " - " ASN s 350 " " NAG s 505 " - " ASN s 357 " " NAG s 506 " - " ASN s 261 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 19.11 Conformation dependent library (CDL) restraints added in 9.2 seconds 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16326 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 320 helices and 47 sheets defined 49.2% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.46 Creating SS restraints... Processing helix chain 'a' and resid 20 through 22 No H-bonds generated for 'chain 'a' and resid 20 through 22' Processing helix chain 'a' and resid 25 through 30 Processing helix chain 'a' and resid 50 through 73 removed outlier: 4.551A pdb=" N ASN a 53 " --> pdb=" O LYS a 50 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU a 54 " --> pdb=" O PHE a 51 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL a 55 " --> pdb=" O VAL a 52 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG a 57 " --> pdb=" O GLU a 54 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS a 58 " --> pdb=" O VAL a 55 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N SER a 60 " --> pdb=" O ARG a 57 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG a 66 " --> pdb=" O ARG a 63 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP a 70 " --> pdb=" O PHE a 67 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU a 71 " --> pdb=" O LEU a 68 " (cutoff:3.500A) Processing helix chain 'a' and resid 90 through 138 removed outlier: 3.710A pdb=" N ILE a 94 " --> pdb=" O PRO a 90 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR a 95 " --> pdb=" O ARG a 91 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU a 96 " --> pdb=" O GLU a 92 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR a 98 " --> pdb=" O ILE a 94 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL a 99 " --> pdb=" O THR a 95 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS a 102 " --> pdb=" O THR a 98 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU a 107 " --> pdb=" O LEU a 103 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN a 112 " --> pdb=" O GLN a 108 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN a 115 " --> pdb=" O ASN a 111 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU a 126 " --> pdb=" O LEU a 122 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS a 128 " --> pdb=" O LEU a 124 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR a 129 " --> pdb=" O THR a 125 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP a 136 " --> pdb=" O LYS a 132 " (cutoff:3.500A) Processing helix chain 'a' and resid 185 through 193 removed outlier: 4.241A pdb=" N LEU a 189 " --> pdb=" O PHE a 185 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N TRP a 190 " --> pdb=" O GLU a 186 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE a 192 " --> pdb=" O LEU a 188 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS a 193 " --> pdb=" O LEU a 189 " (cutoff:3.500A) Processing helix chain 'a' and resid 235 through 239 Processing helix chain 'a' and resid 253 through 288 removed outlier: 3.529A pdb=" N ILE a 271 " --> pdb=" O LEU a 267 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR a 272 " --> pdb=" O GLU a 268 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER a 279 " --> pdb=" O THR a 275 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS a 280 " --> pdb=" O GLN a 276 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU a 284 " --> pdb=" O HIS a 280 " (cutoff:3.500A) Processing helix chain 'a' and resid 293 through 311 removed outlier: 4.556A pdb=" N ILE a 297 " --> pdb=" O HIS a 293 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS a 298 " --> pdb=" O SER a 294 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN a 310 " --> pdb=" O TYR a 306 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET a 311 " --> pdb=" O HIS a 307 " (cutoff:3.500A) Processing helix chain 'a' and resid 329 through 346 removed outlier: 5.253A pdb=" N THR a 333 " --> pdb=" O ALA a 330 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG a 334 " --> pdb=" O ASP a 331 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE a 335 " --> pdb=" O ALA a 332 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG a 337 " --> pdb=" O ARG a 334 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN a 341 " --> pdb=" O ALA a 338 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY a 342 " --> pdb=" O LEU a 339 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU a 344 " --> pdb=" O GLN a 341 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU a 345 " --> pdb=" O GLY a 342 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER a 346 " --> pdb=" O MET a 343 " (cutoff:3.500A) Processing helix chain 'a' and resid 374 through 381 removed outlier: 3.734A pdb=" N ILE a 379 " --> pdb=" O GLY a 375 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL a 380 " --> pdb=" O PHE a 376 " (cutoff:3.500A) Processing helix chain 'a' and resid 400 through 408 removed outlier: 3.756A pdb=" N MET a 408 " --> pdb=" O LEU a 404 " (cutoff:3.500A) Processing helix chain 'a' and resid 412 through 427 removed outlier: 3.757A pdb=" N VAL a 417 " --> pdb=" O GLY a 413 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET a 425 " --> pdb=" O ALA a 421 " (cutoff:3.500A) Processing helix chain 'a' and resid 429 through 434 Processing helix chain 'a' and resid 440 through 447 removed outlier: 3.552A pdb=" N HIS a 447 " --> pdb=" O ASN a 443 " (cutoff:3.500A) Processing helix chain 'a' and resid 449 through 465 removed outlier: 3.689A pdb=" N LEU a 454 " --> pdb=" O TYR a 450 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER a 459 " --> pdb=" O MET a 455 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE a 460 " --> pdb=" O GLY a 456 " (cutoff:3.500A) Processing helix chain 'a' and resid 484 through 488 Processing helix chain 'a' and resid 494 through 499 removed outlier: 3.555A pdb=" N GLU a 498 " --> pdb=" O THR a 494 " (cutoff:3.500A) Processing helix chain 'a' and resid 532 through 566 removed outlier: 3.605A pdb=" N ASN a 537 " --> pdb=" O LEU a 533 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER a 538 " --> pdb=" O THR a 534 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS a 542 " --> pdb=" O SER a 538 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL a 545 " --> pdb=" O MET a 541 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN a 551 " --> pdb=" O LEU a 547 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL a 556 " --> pdb=" O MET a 552 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER a 559 " --> pdb=" O GLY a 555 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N HIS a 563 " --> pdb=" O SER a 559 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR a 565 " --> pdb=" O PHE a 561 " (cutoff:3.500A) Processing helix chain 'a' and resid 569 through 574 removed outlier: 3.870A pdb=" N ILE a 573 " --> pdb=" O THR a 569 " (cutoff:3.500A) Processing helix chain 'a' and resid 579 through 585 removed outlier: 4.182A pdb=" N LEU a 584 " --> pdb=" O MET a 580 " (cutoff:3.500A) Processing helix chain 'a' and resid 587 through 599 removed outlier: 3.636A pdb=" N VAL a 591 " --> pdb=" O PHE a 587 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS a 597 " --> pdb=" O MET a 593 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N CYS a 599 " --> pdb=" O ILE a 595 " (cutoff:3.500A) Processing helix chain 'a' and resid 603 through 608 removed outlier: 5.110A pdb=" N GLN a 607 " --> pdb=" O HIS a 604 " (cutoff:3.500A) Processing helix chain 'a' and resid 612 through 621 removed outlier: 3.888A pdb=" N PHE a 620 " --> pdb=" O PHE a 616 " (cutoff:3.500A) Processing helix chain 'a' and resid 636 through 655 removed outlier: 3.674A pdb=" N PHE a 642 " --> pdb=" O GLU a 638 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE a 643 " --> pdb=" O VAL a 639 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL a 645 " --> pdb=" O SER a 641 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER a 650 " --> pdb=" O MET a 646 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL a 651 " --> pdb=" O ALA a 647 " (cutoff:3.500A) Proline residue: a 652 - end of helix removed outlier: 3.520A pdb=" N LEU a 655 " --> pdb=" O VAL a 651 " (cutoff:3.500A) Processing helix chain 'a' and resid 657 through 667 Processing helix chain 'a' and resid 717 through 761 removed outlier: 3.901A pdb=" N HIS a 722 " --> pdb=" O ASP a 718 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLN a 723 " --> pdb=" O VAL a 719 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE a 728 " --> pdb=" O ALA a 724 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU a 732 " --> pdb=" O ILE a 728 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE a 735 " --> pdb=" O CYS a 731 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER a 736 " --> pdb=" O LEU a 732 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR a 738 " --> pdb=" O CYS a 734 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA a 739 " --> pdb=" O ILE a 735 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU a 742 " --> pdb=" O THR a 738 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ARG a 743 " --> pdb=" O ALA a 739 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N LEU a 744 " --> pdb=" O SER a 740 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TRP a 745 " --> pdb=" O TYR a 741 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER a 748 " --> pdb=" O LEU a 744 " (cutoff:3.500A) Processing helix chain 'a' and resid 763 through 766 No H-bonds generated for 'chain 'a' and resid 763 through 766' Processing helix chain 'a' and resid 772 through 791 removed outlier: 3.962A pdb=" N ILE a 775 " --> pdb=" O TRP a 772 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL a 776 " --> pdb=" O GLY a 773 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL a 778 " --> pdb=" O ILE a 775 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE a 779 " --> pdb=" O VAL a 776 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ILE a 780 " --> pdb=" O GLY a 777 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE a 781 " --> pdb=" O VAL a 778 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE a 782 " --> pdb=" O PHE a 779 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL a 784 " --> pdb=" O ILE a 781 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA a 786 " --> pdb=" O ALA a 783 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL a 787 " --> pdb=" O VAL a 784 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU a 788 " --> pdb=" O PHE a 785 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR a 789 " --> pdb=" O ALA a 786 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL a 790 " --> pdb=" O VAL a 787 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA a 791 " --> pdb=" O LEU a 788 " (cutoff:3.500A) Processing helix chain 'a' and resid 796 through 810 removed outlier: 3.814A pdb=" N LEU a 808 " --> pdb=" O HIS a 804 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N HIS a 809 " --> pdb=" O ALA a 805 " (cutoff:3.500A) Processing helix chain 'U' and resid 22 through 31 removed outlier: 3.671A pdb=" N GLN U 26 " --> pdb=" O ALA U 22 " (cutoff:3.500A) Processing helix chain 'U' and resid 47 through 50 No H-bonds generated for 'chain 'U' and resid 47 through 50' Processing helix chain 'U' and resid 60 through 68 removed outlier: 3.709A pdb=" N THR U 64 " --> pdb=" O PRO U 60 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG U 65 " --> pdb=" O GLU U 61 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP U 68 " --> pdb=" O THR U 64 " (cutoff:3.500A) Processing helix chain 'U' and resid 89 through 92 No H-bonds generated for 'chain 'U' and resid 89 through 92' Processing helix chain 'U' and resid 95 through 98 No H-bonds generated for 'chain 'U' and resid 95 through 98' Processing helix chain 'U' and resid 106 through 113 removed outlier: 3.723A pdb=" N ILE U 110 " --> pdb=" O LYS U 106 " (cutoff:3.500A) Processing helix chain 'U' and resid 123 through 134 removed outlier: 3.859A pdb=" N LYS U 128 " --> pdb=" O ARG U 124 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU U 131 " --> pdb=" O GLN U 127 " (cutoff:3.500A) Processing helix chain 'U' and resid 136 through 143 removed outlier: 3.679A pdb=" N LEU U 141 " --> pdb=" O VAL U 137 " (cutoff:3.500A) Processing helix chain 'U' and resid 160 through 171 removed outlier: 3.565A pdb=" N VAL U 164 " --> pdb=" O PRO U 160 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU U 165 " --> pdb=" O ARG U 161 " (cutoff:3.500A) Processing helix chain 'U' and resid 196 through 202 removed outlier: 3.627A pdb=" N VAL U 200 " --> pdb=" O ILE U 196 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE U 201 " --> pdb=" O GLU U 197 " (cutoff:3.500A) Processing helix chain 'U' and resid 204 through 212 removed outlier: 3.902A pdb=" N SER U 211 " --> pdb=" O ALA U 207 " (cutoff:3.500A) Processing helix chain 'U' and resid 214 through 217 No H-bonds generated for 'chain 'U' and resid 214 through 217' Processing helix chain 'U' and resid 248 through 254 removed outlier: 3.604A pdb=" N MET U 252 " --> pdb=" O VAL U 248 " (cutoff:3.500A) Processing helix chain 'U' and resid 260 through 262 No H-bonds generated for 'chain 'U' and resid 260 through 262' Processing helix chain 'U' and resid 279 through 286 removed outlier: 3.745A pdb=" N GLY U 284 " --> pdb=" O SER U 280 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE U 286 " --> pdb=" O LEU U 282 " (cutoff:3.500A) Processing helix chain 'U' and resid 431 through 437 removed outlier: 3.823A pdb=" N ALA U 435 " --> pdb=" O PRO U 431 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 112 removed outlier: 4.124A pdb=" N SER L 110 " --> pdb=" O LEU L 106 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER L 111 " --> pdb=" O SER L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 256 through 260 Processing helix chain 'L' and resid 262 through 265 No H-bonds generated for 'chain 'L' and resid 262 through 265' Processing helix chain 'L' and resid 281 through 290 removed outlier: 3.559A pdb=" N GLU L 286 " --> pdb=" O ASN L 282 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL L 287 " --> pdb=" O GLU L 283 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU L 288 " --> pdb=" O MET L 284 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG L 289 " --> pdb=" O SER L 285 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP L 290 " --> pdb=" O GLU L 286 " (cutoff:3.500A) Processing helix chain 'L' and resid 305 through 307 No H-bonds generated for 'chain 'L' and resid 305 through 307' Processing helix chain 'L' and resid 320 through 340 removed outlier: 4.678A pdb=" N ILE L 327 " --> pdb=" O ARG L 323 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N TYR L 328 " --> pdb=" O GLU L 324 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR L 329 " --> pdb=" O ALA L 325 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE L 337 " --> pdb=" O LEU L 333 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET L 340 " --> pdb=" O TYR L 336 " (cutoff:3.500A) Processing helix chain 'L' and resid 351 through 364 removed outlier: 3.501A pdb=" N GLU L 360 " --> pdb=" O GLU L 356 " (cutoff:3.500A) Processing helix chain 'L' and resid 379 through 388 removed outlier: 5.076A pdb=" N ARG L 388 " --> pdb=" O SER L 384 " (cutoff:3.500A) Processing helix chain 'L' and resid 420 through 428 removed outlier: 3.605A pdb=" N GLY L 427 " --> pdb=" O SER L 423 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE L 428 " --> pdb=" O ALA L 424 " (cutoff:3.500A) Processing helix chain 'L' and resid 438 through 442 removed outlier: 3.624A pdb=" N ARG L 442 " --> pdb=" O LYS L 438 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 438 through 442' Processing helix chain 'L' and resid 459 through 468 removed outlier: 3.760A pdb=" N ASP L 462 " --> pdb=" O ARG L 459 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLU L 463 " --> pdb=" O ALA L 460 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TYR L 465 " --> pdb=" O ASP L 462 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP L 466 " --> pdb=" O GLU L 463 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N HIS L 468 " --> pdb=" O TYR L 465 " (cutoff:3.500A) Processing helix chain 'L' and resid 472 through 496 removed outlier: 3.645A pdb=" N LYS L 478 " --> pdb=" O PRO L 474 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA L 479 " --> pdb=" O LEU L 475 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU L 481 " --> pdb=" O THR L 477 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU L 483 " --> pdb=" O ALA L 479 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU L 491 " --> pdb=" O GLU L 487 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE L 492 " --> pdb=" O ASP L 488 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN L 494 " --> pdb=" O ALA L 490 " (cutoff:3.500A) Processing helix chain 'L' and resid 504 through 518 removed outlier: 3.585A pdb=" N THR L 508 " --> pdb=" O THR L 504 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU L 510 " --> pdb=" O LYS L 506 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS L 513 " --> pdb=" O LEU L 509 " (cutoff:3.500A) Processing helix chain 'L' and resid 534 through 558 removed outlier: 3.552A pdb=" N ASN L 543 " --> pdb=" O GLY L 539 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE L 547 " --> pdb=" O ASN L 543 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR L 548 " --> pdb=" O MET L 544 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET L 550 " --> pdb=" O ALA L 546 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL L 555 " --> pdb=" O ALA L 551 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N THR L 558 " --> pdb=" O ALA L 554 " (cutoff:3.500A) Processing helix chain 'L' and resid 567 through 573 Processing helix chain 'L' and resid 575 through 581 Processing helix chain 'L' and resid 584 through 586 No H-bonds generated for 'chain 'L' and resid 584 through 586' Processing helix chain 'L' and resid 594 through 615 removed outlier: 3.601A pdb=" N LYS L 598 " --> pdb=" O GLU L 594 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU L 605 " --> pdb=" O TYR L 601 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU L 606 " --> pdb=" O ALA L 602 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA L 611 " --> pdb=" O ASP L 607 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER L 614 " --> pdb=" O ASN L 610 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 112 removed outlier: 3.625A pdb=" N SER M 110 " --> pdb=" O LEU M 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 256 through 264 removed outlier: 3.773A pdb=" N SER M 262 " --> pdb=" O VAL M 258 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER M 264 " --> pdb=" O SER M 260 " (cutoff:3.500A) Processing helix chain 'M' and resid 281 through 293 removed outlier: 3.735A pdb=" N SER M 285 " --> pdb=" O GLY M 281 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU M 286 " --> pdb=" O ASN M 282 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL M 287 " --> pdb=" O GLU M 283 " (cutoff:3.500A) Proline residue: M 292 - end of helix Processing helix chain 'M' and resid 305 through 307 No H-bonds generated for 'chain 'M' and resid 305 through 307' Processing helix chain 'M' and resid 320 through 338 removed outlier: 3.603A pdb=" N GLU M 324 " --> pdb=" O VAL M 320 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA M 325 " --> pdb=" O ALA M 321 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE M 327 " --> pdb=" O ARG M 323 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N TYR M 328 " --> pdb=" O GLU M 324 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY M 330 " --> pdb=" O SER M 326 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE M 337 " --> pdb=" O LEU M 333 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG M 338 " --> pdb=" O SER M 334 " (cutoff:3.500A) Processing helix chain 'M' and resid 351 through 364 removed outlier: 3.535A pdb=" N ARG M 359 " --> pdb=" O ALA M 355 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU M 360 " --> pdb=" O GLU M 356 " (cutoff:3.500A) Processing helix chain 'M' and resid 378 through 388 removed outlier: 3.558A pdb=" N PHE M 385 " --> pdb=" O ARG M 381 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ARG M 388 " --> pdb=" O SER M 384 " (cutoff:3.500A) Processing helix chain 'M' and resid 413 through 415 No H-bonds generated for 'chain 'M' and resid 413 through 415' Processing helix chain 'M' and resid 438 through 440 No H-bonds generated for 'chain 'M' and resid 438 through 440' Processing helix chain 'M' and resid 462 through 468 Processing helix chain 'M' and resid 472 through 493 removed outlier: 3.662A pdb=" N LEU M 483 " --> pdb=" O ALA M 479 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU M 487 " --> pdb=" O LEU M 483 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASP M 488 " --> pdb=" O GLN M 484 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU M 491 " --> pdb=" O GLU M 487 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE M 492 " --> pdb=" O ASP M 488 " (cutoff:3.500A) Processing helix chain 'M' and resid 503 through 518 removed outlier: 3.587A pdb=" N LEU M 509 " --> pdb=" O ASP M 505 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS M 513 " --> pdb=" O LEU M 509 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU M 514 " --> pdb=" O GLU M 510 " (cutoff:3.500A) Processing helix chain 'M' and resid 534 through 551 removed outlier: 3.650A pdb=" N ASN M 543 " --> pdb=" O GLY M 539 " (cutoff:3.500A) Processing helix chain 'M' and resid 553 through 556 No H-bonds generated for 'chain 'M' and resid 553 through 556' Processing helix chain 'M' and resid 567 through 573 Processing helix chain 'M' and resid 575 through 580 removed outlier: 3.771A pdb=" N TYR M 579 " --> pdb=" O GLY M 575 " (cutoff:3.500A) Processing helix chain 'M' and resid 582 through 584 No H-bonds generated for 'chain 'M' and resid 582 through 584' Processing helix chain 'M' and resid 594 through 612 removed outlier: 3.580A pdb=" N LYS M 598 " --> pdb=" O GLU M 594 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA M 602 " --> pdb=" O LYS M 598 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLN M 603 " --> pdb=" O SER M 599 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU M 604 " --> pdb=" O ASP M 600 " (cutoff:3.500A) Processing helix chain 'N' and resid 106 through 112 removed outlier: 4.234A pdb=" N SER N 111 " --> pdb=" O SER N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 260 through 263 No H-bonds generated for 'chain 'N' and resid 260 through 263' Processing helix chain 'N' and resid 281 through 284 No H-bonds generated for 'chain 'N' and resid 281 through 284' Processing helix chain 'N' and resid 320 through 324 Processing helix chain 'N' and resid 326 through 339 removed outlier: 3.628A pdb=" N PHE N 337 " --> pdb=" O LEU N 333 " (cutoff:3.500A) Processing helix chain 'N' and resid 351 through 364 removed outlier: 3.694A pdb=" N ALA N 357 " --> pdb=" O ARG N 353 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU N 360 " --> pdb=" O GLU N 356 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG N 364 " --> pdb=" O GLU N 360 " (cutoff:3.500A) Processing helix chain 'N' and resid 378 through 388 removed outlier: 3.608A pdb=" N ALA N 383 " --> pdb=" O GLY N 379 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE N 385 " --> pdb=" O ARG N 381 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU N 387 " --> pdb=" O ALA N 383 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ARG N 388 " --> pdb=" O SER N 384 " (cutoff:3.500A) Processing helix chain 'N' and resid 422 through 425 No H-bonds generated for 'chain 'N' and resid 422 through 425' Processing helix chain 'N' and resid 438 through 440 No H-bonds generated for 'chain 'N' and resid 438 through 440' Processing helix chain 'N' and resid 462 through 468 Processing helix chain 'N' and resid 472 through 493 removed outlier: 3.709A pdb=" N LEU N 483 " --> pdb=" O ALA N 479 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN N 484 " --> pdb=" O LYS N 480 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLU N 487 " --> pdb=" O LEU N 483 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP N 488 " --> pdb=" O GLN N 484 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU N 491 " --> pdb=" O GLU N 487 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ILE N 492 " --> pdb=" O ASP N 488 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL N 493 " --> pdb=" O LEU N 489 " (cutoff:3.500A) Processing helix chain 'N' and resid 505 through 518 removed outlier: 3.700A pdb=" N ALA N 512 " --> pdb=" O THR N 508 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP N 518 " --> pdb=" O LEU N 514 " (cutoff:3.500A) Processing helix chain 'N' and resid 534 through 557 removed outlier: 3.757A pdb=" N ASN N 543 " --> pdb=" O GLY N 539 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET N 544 " --> pdb=" O MET N 540 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE N 545 " --> pdb=" O LEU N 541 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR N 548 " --> pdb=" O MET N 544 " (cutoff:3.500A) Processing helix chain 'N' and resid 568 through 571 No H-bonds generated for 'chain 'N' and resid 568 through 571' Processing helix chain 'N' and resid 577 through 580 No H-bonds generated for 'chain 'N' and resid 577 through 580' Processing helix chain 'N' and resid 594 through 613 removed outlier: 3.758A pdb=" N LYS N 598 " --> pdb=" O GLU N 594 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR N 601 " --> pdb=" O ILE N 597 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU N 605 " --> pdb=" O TYR N 601 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU N 606 " --> pdb=" O ALA N 602 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN N 610 " --> pdb=" O GLU N 606 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA N 611 " --> pdb=" O ASP N 607 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE N 612 " --> pdb=" O MET N 608 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG N 613 " --> pdb=" O GLN N 609 " (cutoff:3.500A) Processing helix chain 'O' and resid 160 through 162 No H-bonds generated for 'chain 'O' and resid 160 through 162' Processing helix chain 'O' and resid 175 through 179 Processing helix chain 'O' and resid 199 through 209 Processing helix chain 'O' and resid 219 through 222 Processing helix chain 'O' and resid 238 through 247 removed outlier: 3.793A pdb=" N PHE O 244 " --> pdb=" O THR O 240 " (cutoff:3.500A) Processing helix chain 'O' and resid 254 through 256 No H-bonds generated for 'chain 'O' and resid 254 through 256' Processing helix chain 'O' and resid 274 through 287 removed outlier: 3.726A pdb=" N LEU O 279 " --> pdb=" O PRO O 275 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR O 281 " --> pdb=" O LEU O 277 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR O 287 " --> pdb=" O GLU O 283 " (cutoff:3.500A) Processing helix chain 'O' and resid 300 through 304 Processing helix chain 'O' and resid 307 through 313 Processing helix chain 'O' and resid 320 through 322 No H-bonds generated for 'chain 'O' and resid 320 through 322' Processing helix chain 'O' and resid 327 through 335 removed outlier: 3.638A pdb=" N THR O 333 " --> pdb=" O THR O 329 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE O 334 " --> pdb=" O ASP O 330 " (cutoff:3.500A) Processing helix chain 'O' and resid 357 through 359 No H-bonds generated for 'chain 'O' and resid 357 through 359' Processing helix chain 'O' and resid 364 through 370 Processing helix chain 'O' and resid 382 through 385 No H-bonds generated for 'chain 'O' and resid 382 through 385' Processing helix chain 'O' and resid 402 through 405 No H-bonds generated for 'chain 'O' and resid 402 through 405' Processing helix chain 'O' and resid 415 through 439 removed outlier: 3.680A pdb=" N SER O 419 " --> pdb=" O HIS O 415 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASN O 420 " --> pdb=" O ALA O 416 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP O 431 " --> pdb=" O ALA O 427 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA O 437 " --> pdb=" O GLN O 433 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL O 438 " --> pdb=" O ALA O 434 " (cutoff:3.500A) Processing helix chain 'O' and resid 449 through 461 removed outlier: 3.752A pdb=" N GLN O 456 " --> pdb=" O LEU O 452 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG O 460 " --> pdb=" O GLN O 456 " (cutoff:3.500A) Processing helix chain 'O' and resid 473 through 482 removed outlier: 3.619A pdb=" N LEU O 477 " --> pdb=" O VAL O 473 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN O 482 " --> pdb=" O ASP O 478 " (cutoff:3.500A) Processing helix chain 'O' and resid 497 through 503 removed outlier: 3.563A pdb=" N SER O 501 " --> pdb=" O GLN O 497 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU O 502 " --> pdb=" O SER O 498 " (cutoff:3.500A) Processing helix chain 'P' and resid 160 through 162 No H-bonds generated for 'chain 'P' and resid 160 through 162' Processing helix chain 'P' and resid 176 through 179 No H-bonds generated for 'chain 'P' and resid 176 through 179' Processing helix chain 'P' and resid 199 through 209 removed outlier: 3.666A pdb=" N CYS P 207 " --> pdb=" O ALA P 203 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG P 208 " --> pdb=" O ALA P 204 " (cutoff:3.500A) Processing helix chain 'P' and resid 220 through 223 No H-bonds generated for 'chain 'P' and resid 220 through 223' Processing helix chain 'P' and resid 238 through 250 removed outlier: 3.586A pdb=" N PHE P 248 " --> pdb=" O PHE P 244 " (cutoff:3.500A) Processing helix chain 'P' and resid 268 through 287 removed outlier: 3.897A pdb=" N THR P 274 " --> pdb=" O ARG P 271 " (cutoff:3.500A) Proline residue: P 275 - end of helix removed outlier: 3.970A pdb=" N ALA P 278 " --> pdb=" O PRO P 275 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU P 279 " --> pdb=" O ARG P 276 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR P 280 " --> pdb=" O LEU P 277 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR P 281 " --> pdb=" O ALA P 278 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU P 283 " --> pdb=" O THR P 280 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU P 285 " --> pdb=" O ALA P 282 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA P 286 " --> pdb=" O GLU P 283 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N TYR P 287 " --> pdb=" O PHE P 284 " (cutoff:3.500A) Processing helix chain 'P' and resid 301 through 314 removed outlier: 3.623A pdb=" N ALA P 306 " --> pdb=" O SER P 302 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL P 310 " --> pdb=" O ALA P 306 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER P 311 " --> pdb=" O LEU P 307 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA P 313 " --> pdb=" O GLU P 309 " (cutoff:3.500A) Processing helix chain 'P' and resid 325 through 335 removed outlier: 4.349A pdb=" N TYR P 328 " --> pdb=" O GLY P 325 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR P 329 " --> pdb=" O TYR P 326 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU P 331 " --> pdb=" O TYR P 328 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ALA P 332 " --> pdb=" O THR P 329 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR P 333 " --> pdb=" O ASP P 330 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR P 335 " --> pdb=" O ALA P 332 " (cutoff:3.500A) Processing helix chain 'P' and resid 357 through 359 No H-bonds generated for 'chain 'P' and resid 357 through 359' Processing helix chain 'P' and resid 364 through 370 removed outlier: 3.599A pdb=" N LEU P 368 " --> pdb=" O PRO P 364 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY P 370 " --> pdb=" O PRO P 366 " (cutoff:3.500A) Processing helix chain 'P' and resid 382 through 385 No H-bonds generated for 'chain 'P' and resid 382 through 385' Processing helix chain 'P' and resid 415 through 439 removed outlier: 3.586A pdb=" N TYR P 423 " --> pdb=" O SER P 419 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA P 424 " --> pdb=" O ASN P 420 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA P 434 " --> pdb=" O LYS P 430 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA P 437 " --> pdb=" O GLN P 433 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL P 438 " --> pdb=" O ALA P 434 " (cutoff:3.500A) Processing helix chain 'P' and resid 441 through 443 No H-bonds generated for 'chain 'P' and resid 441 through 443' Processing helix chain 'P' and resid 449 through 461 removed outlier: 3.637A pdb=" N GLN P 456 " --> pdb=" O LEU P 452 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG P 460 " --> pdb=" O GLN P 456 " (cutoff:3.500A) Processing helix chain 'P' and resid 473 through 484 removed outlier: 3.920A pdb=" N ASP P 478 " --> pdb=" O PHE P 474 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY P 480 " --> pdb=" O THR P 476 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN P 482 " --> pdb=" O ASP P 478 " (cutoff:3.500A) Processing helix chain 'P' and resid 497 through 503 removed outlier: 3.866A pdb=" N GLU P 502 " --> pdb=" O SER P 498 " (cutoff:3.500A) Processing helix chain 'Q' and resid 160 through 162 No H-bonds generated for 'chain 'Q' and resid 160 through 162' Processing helix chain 'Q' and resid 175 through 177 No H-bonds generated for 'chain 'Q' and resid 175 through 177' Processing helix chain 'Q' and resid 199 through 209 Processing helix chain 'Q' and resid 238 through 245 removed outlier: 3.684A pdb=" N ARG Q 242 " --> pdb=" O MET Q 238 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE Q 243 " --> pdb=" O GLU Q 239 " (cutoff:3.500A) Processing helix chain 'Q' and resid 270 through 285 Proline residue: Q 275 - end of helix removed outlier: 3.529A pdb=" N LEU Q 279 " --> pdb=" O PRO Q 275 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR Q 281 " --> pdb=" O LEU Q 277 " (cutoff:3.500A) Processing helix chain 'Q' and resid 301 through 313 removed outlier: 3.769A pdb=" N ALA Q 306 " --> pdb=" O SER Q 302 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU Q 309 " --> pdb=" O GLU Q 305 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA Q 313 " --> pdb=" O GLU Q 309 " (cutoff:3.500A) Processing helix chain 'Q' and resid 320 through 322 No H-bonds generated for 'chain 'Q' and resid 320 through 322' Processing helix chain 'Q' and resid 325 through 335 removed outlier: 4.525A pdb=" N TYR Q 328 " --> pdb=" O GLY Q 325 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP Q 330 " --> pdb=" O MET Q 327 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU Q 331 " --> pdb=" O TYR Q 328 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA Q 332 " --> pdb=" O THR Q 329 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TYR Q 335 " --> pdb=" O ALA Q 332 " (cutoff:3.500A) Processing helix chain 'Q' and resid 357 through 359 No H-bonds generated for 'chain 'Q' and resid 357 through 359' Processing helix chain 'Q' and resid 364 through 370 Processing helix chain 'Q' and resid 415 through 435 removed outlier: 4.246A pdb=" N ASN Q 420 " --> pdb=" O ALA Q 416 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN Q 421 " --> pdb=" O ASP Q 417 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA Q 424 " --> pdb=" O ASN Q 420 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP Q 431 " --> pdb=" O ALA Q 427 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN Q 433 " --> pdb=" O GLY Q 429 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA Q 434 " --> pdb=" O LYS Q 430 " (cutoff:3.500A) Processing helix chain 'Q' and resid 450 through 461 removed outlier: 3.640A pdb=" N GLN Q 456 " --> pdb=" O LEU Q 452 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU Q 459 " --> pdb=" O LEU Q 455 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG Q 460 " --> pdb=" O GLN Q 456 " (cutoff:3.500A) Processing helix chain 'Q' and resid 473 through 481 removed outlier: 3.680A pdb=" N LEU Q 477 " --> pdb=" O VAL Q 473 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASP Q 478 " --> pdb=" O PHE Q 474 " (cutoff:3.500A) Processing helix chain 'Q' and resid 489 through 491 No H-bonds generated for 'chain 'Q' and resid 489 through 491' Processing helix chain 'Q' and resid 497 through 503 removed outlier: 3.569A pdb=" N GLU Q 502 " --> pdb=" O SER Q 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 64 removed outlier: 3.626A pdb=" N MET D 19 " --> pdb=" O ALA D 15 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY D 29 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN D 31 " --> pdb=" O GLN D 27 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU D 33 " --> pdb=" O GLY D 29 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU D 53 " --> pdb=" O LYS D 49 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N MET D 56 " --> pdb=" O ILE D 52 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU D 60 " --> pdb=" O MET D 56 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG D 63 " --> pdb=" O GLY D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 76 removed outlier: 3.834A pdb=" N THR D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'D' and resid 129 through 165 removed outlier: 3.566A pdb=" N ARG D 136 " --> pdb=" O ALA D 132 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA D 141 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU D 147 " --> pdb=" O GLU D 143 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER D 154 " --> pdb=" O SER D 150 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N THR D 157 " --> pdb=" O THR D 153 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS D 163 " --> pdb=" O ASP D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 174 Processing helix chain 'D' and resid 177 through 215 removed outlier: 3.575A pdb=" N THR D 183 " --> pdb=" O ARG D 179 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR D 186 " --> pdb=" O ARG D 182 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N THR D 189 " --> pdb=" O ALA D 185 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU D 195 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR D 200 " --> pdb=" O ARG D 196 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ILE D 205 " --> pdb=" O ARG D 201 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS D 208 " --> pdb=" O LYS D 204 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS D 210 " --> pdb=" O GLN D 206 " (cutoff:3.500A) Processing helix chain 'b' and resid 5 through 107 removed outlier: 3.782A pdb=" N LYS b 10 " --> pdb=" O ALA b 6 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS b 26 " --> pdb=" O GLU b 22 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA b 27 " --> pdb=" O ALA b 23 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU b 29 " --> pdb=" O GLU b 25 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA b 34 " --> pdb=" O ILE b 30 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU b 36 " --> pdb=" O ALA b 32 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU b 37 " --> pdb=" O LYS b 33 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE b 40 " --> pdb=" O GLU b 36 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU b 41 " --> pdb=" O GLU b 37 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU b 45 " --> pdb=" O GLU b 41 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLN b 47 " --> pdb=" O GLY b 43 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR b 48 " --> pdb=" O ARG b 44 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU b 51 " --> pdb=" O GLN b 47 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE b 64 " --> pdb=" O LYS b 60 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN b 67 " --> pdb=" O GLN b 63 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS b 69 " --> pdb=" O GLU b 65 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN b 71 " --> pdb=" O GLN b 67 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU b 81 " --> pdb=" O ASN b 77 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS b 82 " --> pdb=" O GLN b 78 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL b 83 " --> pdb=" O ALA b 79 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN b 100 " --> pdb=" O ASN b 96 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL b 105 " --> pdb=" O ARG b 101 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL b 106 " --> pdb=" O LEU b 102 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS b 107 " --> pdb=" O SER b 103 " (cutoff:3.500A) Processing helix chain 'b' and resid 110 through 127 removed outlier: 4.343A pdb=" N VAL b 114 " --> pdb=" O THR b 110 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU b 115 " --> pdb=" O ARG b 111 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY b 118 " --> pdb=" O VAL b 114 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU b 121 " --> pdb=" O ASP b 117 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY b 123 " --> pdb=" O LEU b 119 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN b 126 " --> pdb=" O GLN b 122 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU b 127 " --> pdb=" O GLY b 123 " (cutoff:3.500A) Processing helix chain 'b' and resid 141 through 158 removed outlier: 3.682A pdb=" N LYS b 150 " --> pdb=" O ALA b 146 " (cutoff:3.500A) Proline residue: b 153 - end of helix removed outlier: 3.568A pdb=" N ILE b 157 " --> pdb=" O PRO b 153 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA b 158 " --> pdb=" O MET b 154 " (cutoff:3.500A) Processing helix chain 'b' and resid 196 through 206 removed outlier: 3.811A pdb=" N LEU b 200 " --> pdb=" O LEU b 196 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP b 201 " --> pdb=" O GLU b 197 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLN b 205 " --> pdb=" O ASP b 201 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN b 206 " --> pdb=" O LEU b 202 " (cutoff:3.500A) Processing helix chain 'b' and resid 208 through 215 removed outlier: 3.611A pdb=" N GLY b 213 " --> pdb=" O PRO b 209 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 20 removed outlier: 3.690A pdb=" N MET c 15 " --> pdb=" O GLN c 11 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLU c 20 " --> pdb=" O MET c 16 " (cutoff:3.500A) Processing helix chain 'c' and resid 26 through 103 removed outlier: 3.778A pdb=" N ASP c 31 " --> pdb=" O ALA c 27 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU c 41 " --> pdb=" O GLU c 37 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL c 46 " --> pdb=" O LYS c 42 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN c 47 " --> pdb=" O GLY c 43 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ARG c 50 " --> pdb=" O VAL c 46 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU c 51 " --> pdb=" O GLN c 47 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU c 55 " --> pdb=" O LEU c 51 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU c 58 " --> pdb=" O MET c 54 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU c 61 " --> pdb=" O TYR c 57 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN c 63 " --> pdb=" O LYS c 59 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS c 69 " --> pdb=" O GLU c 65 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG c 80 " --> pdb=" O MET c 76 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL c 83 " --> pdb=" O ALA c 79 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU c 90 " --> pdb=" O ALA c 86 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE c 91 " --> pdb=" O ARG c 87 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU c 97 " --> pdb=" O ASP c 93 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 126 Processing helix chain 'c' and resid 139 through 157 Proline residue: c 142 - end of helix removed outlier: 3.695A pdb=" N LYS c 145 " --> pdb=" O PRO c 142 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL c 148 " --> pdb=" O LYS c 145 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN c 149 " --> pdb=" O ALA c 146 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS c 150 " --> pdb=" O ALA c 147 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE c 152 " --> pdb=" O GLN c 149 " (cutoff:3.500A) Proline residue: c 153 - end of helix removed outlier: 3.703A pdb=" N ILE c 157 " --> pdb=" O MET c 154 " (cutoff:3.500A) Processing helix chain 'c' and resid 198 through 215 removed outlier: 3.605A pdb=" N ILE c 203 " --> pdb=" O ARG c 199 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN c 205 " --> pdb=" O ASP c 201 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN c 206 " --> pdb=" O LEU c 202 " (cutoff:3.500A) Proline residue: c 209 - end of helix Processing helix chain 'd' and resid 6 through 15 removed outlier: 3.569A pdb=" N LYS d 10 " --> pdb=" O ALA d 6 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN d 11 " --> pdb=" O ASP d 7 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS d 14 " --> pdb=" O LYS d 10 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET d 15 " --> pdb=" O GLN d 11 " (cutoff:3.500A) Processing helix chain 'd' and resid 19 through 53 removed outlier: 3.504A pdb=" N GLU d 29 " --> pdb=" O GLU d 25 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ILE d 30 " --> pdb=" O LYS d 26 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASP d 31 " --> pdb=" O ALA d 27 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA d 32 " --> pdb=" O GLU d 28 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS d 33 " --> pdb=" O GLU d 29 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU d 36 " --> pdb=" O ALA d 32 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE d 38 " --> pdb=" O ALA d 34 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N THR d 48 " --> pdb=" O ARG d 44 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN d 49 " --> pdb=" O LEU d 45 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU d 51 " --> pdb=" O GLN d 47 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LYS d 52 " --> pdb=" O THR d 48 " (cutoff:3.500A) Processing helix chain 'd' and resid 55 through 71 removed outlier: 3.614A pdb=" N ILE d 64 " --> pdb=" O LYS d 60 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLU d 65 " --> pdb=" O GLU d 61 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN d 66 " --> pdb=" O LYS d 62 " (cutoff:3.500A) Processing helix chain 'd' and resid 76 through 105 removed outlier: 3.699A pdb=" N LEU d 81 " --> pdb=" O ASN d 77 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL d 83 " --> pdb=" O ALA d 79 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG d 85 " --> pdb=" O LEU d 81 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA d 86 " --> pdb=" O LYS d 82 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP d 88 " --> pdb=" O LEU d 84 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP d 89 " --> pdb=" O ARG d 85 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER d 103 " --> pdb=" O LYS d 99 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL d 105 " --> pdb=" O ARG d 101 " (cutoff:3.500A) Processing helix chain 'd' and resid 112 through 127 removed outlier: 3.511A pdb=" N GLY d 118 " --> pdb=" O VAL d 114 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL d 120 " --> pdb=" O LEU d 116 " (cutoff:3.500A) Processing helix chain 'd' and resid 141 through 159 removed outlier: 3.828A pdb=" N GLN d 149 " --> pdb=" O LYS d 145 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS d 150 " --> pdb=" O ALA d 146 " (cutoff:3.500A) Proline residue: d 153 - end of helix removed outlier: 3.986A pdb=" N ALA d 158 " --> pdb=" O MET d 154 " (cutoff:3.500A) Processing helix chain 'd' and resid 196 through 206 removed outlier: 4.241A pdb=" N GLN d 205 " --> pdb=" O ASP d 201 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN d 206 " --> pdb=" O LEU d 202 " (cutoff:3.500A) Processing helix chain 'd' and resid 208 through 215 Processing helix chain 'e' and resid 5 through 21 removed outlier: 3.793A pdb=" N GLN e 9 " --> pdb=" O SER e 5 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN e 10 " --> pdb=" O GLN e 6 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU e 11 " --> pdb=" O GLY e 7 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN e 13 " --> pdb=" O GLN e 9 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA e 14 " --> pdb=" O GLN e 10 " (cutoff:3.500A) Processing helix chain 'e' and resid 27 through 50 removed outlier: 3.593A pdb=" N ARG e 31 " --> pdb=" O LYS e 27 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ARG e 32 " --> pdb=" O ARG e 28 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU e 33 " --> pdb=" O LYS e 29 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS e 34 " --> pdb=" O ASN e 30 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS e 37 " --> pdb=" O LEU e 33 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU e 38 " --> pdb=" O LYS e 34 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA e 40 " --> pdb=" O ALA e 36 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU e 45 " --> pdb=" O GLN e 41 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN e 46 " --> pdb=" O ALA e 42 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR e 47 " --> pdb=" O GLU e 43 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU e 49 " --> pdb=" O GLU e 45 " (cutoff:3.500A) Processing helix chain 'e' and resid 53 through 60 Processing helix chain 'e' and resid 62 through 65 No H-bonds generated for 'chain 'e' and resid 62 through 65' Processing helix chain 'e' and resid 67 through 103 removed outlier: 3.646A pdb=" N THR e 71 " --> pdb=" O GLY e 67 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU e 72 " --> pdb=" O SER e 68 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL e 73 " --> pdb=" O CYS e 69 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS e 75 " --> pdb=" O THR e 71 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU e 76 " --> pdb=" O GLU e 72 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU e 79 " --> pdb=" O LYS e 75 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR e 82 " --> pdb=" O GLN e 78 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE e 83 " --> pdb=" O GLU e 79 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR e 86 " --> pdb=" O THR e 82 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR e 87 " --> pdb=" O ILE e 83 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG e 89 " --> pdb=" O GLN e 85 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN e 91 " --> pdb=" O TYR e 87 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ASP e 93 " --> pdb=" O ARG e 89 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N GLU e 94 " --> pdb=" O GLN e 90 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL e 95 " --> pdb=" O ASN e 91 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA e 101 " --> pdb=" O ASP e 97 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE e 102 " --> pdb=" O ASN e 98 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL e 103 " --> pdb=" O LEU e 99 " (cutoff:3.500A) Processing helix chain 'f' and resid 5 through 37 removed outlier: 3.910A pdb=" N GLN f 9 " --> pdb=" O SER f 5 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN f 10 " --> pdb=" O GLN f 6 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU f 11 " --> pdb=" O GLY f 7 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER f 23 " --> pdb=" O ALA f 19 " (cutoff:3.500A) Processing helix chain 'f' and resid 42 through 45 No H-bonds generated for 'chain 'f' and resid 42 through 45' Processing helix chain 'f' and resid 48 through 81 removed outlier: 3.708A pdb=" N ALA f 57 " --> pdb=" O LYS f 53 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA f 61 " --> pdb=" O ALA f 57 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER f 65 " --> pdb=" O ALA f 61 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY f 67 " --> pdb=" O LEU f 63 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR f 71 " --> pdb=" O GLY f 67 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS f 75 " --> pdb=" O THR f 71 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN f 78 " --> pdb=" O GLU f 74 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS f 80 " --> pdb=" O GLU f 76 " (cutoff:3.500A) Processing helix chain 'f' and resid 83 through 102 removed outlier: 3.598A pdb=" N GLN f 90 " --> pdb=" O THR f 86 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ASP f 93 " --> pdb=" O ARG f 89 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N GLU f 94 " --> pdb=" O GLN f 90 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL f 95 " --> pdb=" O ASN f 91 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU f 96 " --> pdb=" O ARG f 92 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP f 97 " --> pdb=" O ASP f 93 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE f 102 " --> pdb=" O ASN f 98 " (cutoff:3.500A) Processing helix chain 'g' and resid 6 through 19 removed outlier: 4.113A pdb=" N LEU g 12 " --> pdb=" O ILE g 8 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN g 13 " --> pdb=" O GLN g 9 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG g 17 " --> pdb=" O GLN g 13 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA g 18 " --> pdb=" O ALA g 14 " (cutoff:3.500A) Processing helix chain 'g' and resid 23 through 26 No H-bonds generated for 'chain 'g' and resid 23 through 26' Processing helix chain 'g' and resid 29 through 37 removed outlier: 3.597A pdb=" N ALA g 36 " --> pdb=" O ARG g 32 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS g 37 " --> pdb=" O LEU g 33 " (cutoff:3.500A) Processing helix chain 'g' and resid 42 through 45 No H-bonds generated for 'chain 'g' and resid 42 through 45' Processing helix chain 'g' and resid 51 through 69 removed outlier: 3.928A pdb=" N ALA g 60 " --> pdb=" O LYS g 56 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA g 62 " --> pdb=" O LYS g 58 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU g 63 " --> pdb=" O GLU g 59 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLY g 64 " --> pdb=" O ALA g 60 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER g 65 " --> pdb=" O ALA g 61 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG g 66 " --> pdb=" O ALA g 62 " (cutoff:3.500A) Processing helix chain 'g' and resid 73 through 80 Processing helix chain 'g' and resid 84 through 90 removed outlier: 3.838A pdb=" N ARG g 89 " --> pdb=" O GLN g 85 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN g 90 " --> pdb=" O THR g 86 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 103 removed outlier: 3.537A pdb=" N LEU g 96 " --> pdb=" O ARG g 92 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP g 97 " --> pdb=" O ASP g 93 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN g 98 " --> pdb=" O GLU g 94 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE g 102 " --> pdb=" O ASN g 98 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL g 103 " --> pdb=" O LEU g 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 23 removed outlier: 4.076A pdb=" N GLY F 19 " --> pdb=" O ASP F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 57 removed outlier: 3.695A pdb=" N GLU F 49 " --> pdb=" O ILE F 45 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR F 51 " --> pdb=" O GLU F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 73 removed outlier: 3.697A pdb=" N MET F 73 " --> pdb=" O TYR F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 78 No H-bonds generated for 'chain 'F' and resid 75 through 78' Processing helix chain 'F' and resid 100 through 102 No H-bonds generated for 'chain 'F' and resid 100 through 102' Processing helix chain 'C' and resid 14 through 19 removed outlier: 3.770A pdb=" N GLN C 17 " --> pdb=" O THR C 14 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TRP C 19 " --> pdb=" O GLN C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 77 removed outlier: 3.919A pdb=" N GLU C 57 " --> pdb=" O GLY C 53 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS C 60 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA C 73 " --> pdb=" O VAL C 69 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N MET C 76 " --> pdb=" O VAL C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 103 No H-bonds generated for 'chain 'C' and resid 100 through 103' Processing helix chain 'C' and resid 118 through 156 removed outlier: 4.329A pdb=" N ILE C 124 " --> pdb=" O ASN C 120 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER C 141 " --> pdb=" O LYS C 137 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR C 143 " --> pdb=" O ARG C 139 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU C 146 " --> pdb=" O ALA C 142 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN C 149 " --> pdb=" O ASN C 145 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU C 154 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG C 155 " --> pdb=" O GLN C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 168 No H-bonds generated for 'chain 'C' and resid 166 through 168' Processing helix chain 'C' and resid 193 through 198 Processing helix chain 'C' and resid 234 through 243 removed outlier: 3.666A pdb=" N LYS C 240 " --> pdb=" O ASP C 236 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA C 241 " --> pdb=" O PHE C 237 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG C 242 " --> pdb=" O ARG C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 308 removed outlier: 3.890A pdb=" N LYS C 262 " --> pdb=" O MET C 258 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN C 266 " --> pdb=" O LYS C 262 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER C 269 " --> pdb=" O MET C 265 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) Proline residue: C 278 - end of helix removed outlier: 4.103A pdb=" N ARG C 281 " --> pdb=" O GLY C 277 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL C 285 " --> pdb=" O ARG C 281 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN C 286 " --> pdb=" O TRP C 282 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE C 287 " --> pdb=" O LEU C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 338 removed outlier: 3.753A pdb=" N VAL C 334 " --> pdb=" O LYS C 330 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 25 Processing helix chain 'H' and resid 63 through 65 No H-bonds generated for 'chain 'H' and resid 63 through 65' Processing helix chain 'H' and resid 75 through 83 removed outlier: 4.352A pdb=" N THR H 82 " --> pdb=" O ILE H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 95 Processing helix chain 'H' and resid 98 through 103 removed outlier: 4.101A pdb=" N GLU H 103 " --> pdb=" O ASP H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 108 No H-bonds generated for 'chain 'H' and resid 106 through 108' Processing helix chain 'H' and resid 136 through 144 removed outlier: 3.539A pdb=" N ALA H 142 " --> pdb=" O VAL H 138 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG H 143 " --> pdb=" O HIS H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 208 removed outlier: 3.659A pdb=" N GLN H 199 " --> pdb=" O SER H 195 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N CYS H 200 " --> pdb=" O GLN H 196 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA H 202 " --> pdb=" O VAL H 198 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU H 207 " --> pdb=" O GLY H 203 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N MET H 208 " --> pdb=" O CYS H 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 217 through 220 No H-bonds generated for 'chain 'H' and resid 217 through 220' Processing helix chain 'H' and resid 224 through 232 Processing helix chain 'H' and resid 239 through 250 removed outlier: 3.563A pdb=" N LEU H 250 " --> pdb=" O SER H 246 " (cutoff:3.500A) Processing helix chain 'H' and resid 256 through 262 removed outlier: 4.059A pdb=" N LEU H 260 " --> pdb=" O MET H 256 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ARG H 261 " --> pdb=" O CYS H 257 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG H 262 " --> pdb=" O GLU H 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 256 through 262' Processing helix chain 'H' and resid 266 through 273 removed outlier: 3.708A pdb=" N ILE H 272 " --> pdb=" O VAL H 268 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 289 Processing helix chain 'H' and resid 291 through 294 No H-bonds generated for 'chain 'H' and resid 291 through 294' Processing helix chain 'H' and resid 302 through 306 removed outlier: 3.699A pdb=" N TYR H 305 " --> pdb=" O ARG H 302 " (cutoff:3.500A) Processing helix chain 'H' and resid 315 through 321 removed outlier: 3.643A pdb=" N GLU H 319 " --> pdb=" O LEU H 315 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN H 320 " --> pdb=" O LYS H 316 " (cutoff:3.500A) Processing helix chain 'H' and resid 329 through 349 removed outlier: 4.002A pdb=" N LYS H 336 " --> pdb=" O SER H 332 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS H 341 " --> pdb=" O PHE H 337 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU H 342 " --> pdb=" O LEU H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 354 through 361 Processing helix chain 'H' and resid 386 through 399 removed outlier: 3.557A pdb=" N GLU H 389 " --> pdb=" O LYS H 386 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU H 390 " --> pdb=" O ASN H 387 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU H 391 " --> pdb=" O TYR H 388 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE H 393 " --> pdb=" O LEU H 390 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU H 394 " --> pdb=" O LEU H 391 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR H 395 " --> pdb=" O LYS H 392 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS H 396 " --> pdb=" O ILE H 393 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU H 397 " --> pdb=" O LEU H 394 " (cutoff:3.500A) Processing helix chain 'H' and resid 406 through 414 Processing helix chain 'H' and resid 416 through 419 No H-bonds generated for 'chain 'H' and resid 416 through 419' Processing helix chain 'H' and resid 422 through 430 removed outlier: 3.647A pdb=" N LYS H 425 " --> pdb=" O PRO H 422 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG H 426 " --> pdb=" O ARG H 423 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL H 427 " --> pdb=" O GLY H 424 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU H 429 " --> pdb=" O ARG H 426 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN H 430 " --> pdb=" O VAL H 427 " (cutoff:3.500A) Processing helix chain 'H' and resid 433 through 440 removed outlier: 4.026A pdb=" N MET H 438 " --> pdb=" O LYS H 434 " (cutoff:3.500A) Processing helix chain 'H' and resid 446 through 455 removed outlier: 3.682A pdb=" N ASN H 451 " --> pdb=" O GLN H 447 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU H 453 " --> pdb=" O ARG H 449 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU H 454 " --> pdb=" O TYR H 450 " (cutoff:3.500A) Processing helix chain 'k' and resid 9 through 12 No H-bonds generated for 'chain 'k' and resid 9 through 12' Processing helix chain 'k' and resid 15 through 25 removed outlier: 3.708A pdb=" N ALA k 25 " --> pdb=" O ARG k 21 " (cutoff:3.500A) Processing helix chain 'k' and resid 30 through 36 Processing helix chain 'k' and resid 42 through 50 removed outlier: 3.559A pdb=" N GLN k 50 " --> pdb=" O LYS k 46 " (cutoff:3.500A) Processing helix chain 'k' and resid 67 through 88 removed outlier: 3.531A pdb=" N LYS k 75 " --> pdb=" O ASP k 71 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL k 79 " --> pdb=" O LYS k 75 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU k 81 " --> pdb=" O LYS k 77 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS k 84 " --> pdb=" O VAL k 80 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN k 87 " --> pdb=" O ARG k 83 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N HIS k 88 " --> pdb=" O HIS k 84 " (cutoff:3.500A) Processing helix chain 'k' and resid 91 through 100 removed outlier: 4.044A pdb=" N PHE k 96 " --> pdb=" O PRO k 92 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE k 100 " --> pdb=" O PHE k 96 " (cutoff:3.500A) Processing helix chain 'k' and resid 102 through 112 removed outlier: 3.986A pdb=" N ASP k 107 " --> pdb=" O SER k 103 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU k 111 " --> pdb=" O ASP k 107 " (cutoff:3.500A) Processing helix chain 'k' and resid 126 through 128 No H-bonds generated for 'chain 'k' and resid 126 through 128' Processing helix chain 'k' and resid 147 through 157 removed outlier: 3.514A pdb=" N ALA k 153 " --> pdb=" O GLU k 149 " (cutoff:3.500A) Processing helix chain 'k' and resid 159 through 163 removed outlier: 4.273A pdb=" N ALA k 162 " --> pdb=" O PRO k 159 " (cutoff:3.500A) Processing helix chain 'k' and resid 172 through 175 No H-bonds generated for 'chain 'k' and resid 172 through 175' Processing helix chain 'k' and resid 178 through 199 removed outlier: 4.161A pdb=" N ASN k 183 " --> pdb=" O GLU k 179 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS k 187 " --> pdb=" O ASN k 183 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS k 195 " --> pdb=" O GLU k 191 " (cutoff:3.500A) Processing helix chain 'k' and resid 204 through 207 No H-bonds generated for 'chain 'k' and resid 204 through 207' Processing helix chain 'k' and resid 209 through 225 removed outlier: 3.908A pdb=" N PHE k 214 " --> pdb=" O PRO k 210 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP k 217 " --> pdb=" O GLU k 213 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG k 219 " --> pdb=" O GLU k 215 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA k 220 " --> pdb=" O ALA k 216 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE k 223 " --> pdb=" O ARG k 219 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR k 224 " --> pdb=" O ALA k 220 " (cutoff:3.500A) Processing helix chain 'k' and resid 238 through 240 No H-bonds generated for 'chain 'k' and resid 238 through 240' Processing helix chain 'k' and resid 261 through 265 Processing helix chain 'k' and resid 272 through 278 removed outlier: 3.790A pdb=" N LEU k 276 " --> pdb=" O PRO k 272 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU k 277 " --> pdb=" O GLU k 273 " (cutoff:3.500A) Processing helix chain 'k' and resid 290 through 306 removed outlier: 3.706A pdb=" N PHE k 295 " --> pdb=" O GLU k 291 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS k 297 " --> pdb=" O ARG k 293 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA k 305 " --> pdb=" O LEU k 301 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N PHE k 306 " --> pdb=" O ASN k 302 " (cutoff:3.500A) Processing helix chain 'k' and resid 312 through 337 removed outlier: 3.685A pdb=" N TYR k 316 " --> pdb=" O GLY k 313 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA k 317 " --> pdb=" O VAL k 314 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE k 318 " --> pdb=" O PHE k 315 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS k 320 " --> pdb=" O ALA k 317 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU k 321 " --> pdb=" O PHE k 318 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS k 322 " --> pdb=" O VAL k 319 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU k 323 " --> pdb=" O LYS k 320 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS k 326 " --> pdb=" O GLU k 323 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE k 329 " --> pdb=" O CYS k 326 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL k 330 " --> pdb=" O ARG k 327 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TRP k 331 " --> pdb=" O ASN k 328 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU k 334 " --> pdb=" O TRP k 331 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE k 336 " --> pdb=" O ALA k 333 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA k 337 " --> pdb=" O GLU k 334 " (cutoff:3.500A) Processing helix chain 'k' and resid 344 through 346 No H-bonds generated for 'chain 'k' and resid 344 through 346' Processing helix chain 'm' and resid 8 through 22 removed outlier: 3.620A pdb=" N VAL m 12 " --> pdb=" O VAL m 8 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL m 20 " --> pdb=" O PHE m 16 " (cutoff:3.500A) Processing helix chain 'm' and resid 34 through 40 removed outlier: 3.903A pdb=" N THR m 39 " --> pdb=" O GLY m 35 " (cutoff:3.500A) Processing helix chain 'm' and resid 42 through 59 removed outlier: 3.523A pdb=" N CYS m 47 " --> pdb=" O THR m 43 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU m 50 " --> pdb=" O VAL m 46 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA m 55 " --> pdb=" O PHE m 51 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN m 59 " --> pdb=" O ALA m 55 " (cutoff:3.500A) Processing helix chain 'm' and resid 70 through 77 removed outlier: 4.169A pdb=" N TYR m 75 " --> pdb=" O GLU m 71 " (cutoff:3.500A) Processing helix chain 'n' and resid 48 through 73 removed outlier: 3.615A pdb=" N CYS n 53 " --> pdb=" O LYS n 49 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE n 55 " --> pdb=" O ALA n 51 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE n 63 " --> pdb=" O ALA n 59 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN n 73 " --> pdb=" O GLY n 69 " (cutoff:3.500A) Processing helix chain 'n' and resid 98 through 127 removed outlier: 3.557A pdb=" N GLU n 102 " --> pdb=" O TYR n 98 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN n 103 " --> pdb=" O ASN n 99 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE n 110 " --> pdb=" O TYR n 106 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA n 112 " --> pdb=" O CYS n 108 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR n 115 " --> pdb=" O ALA n 111 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU n 116 " --> pdb=" O ALA n 112 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU n 117 " --> pdb=" O GLY n 113 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL n 126 " --> pdb=" O SER n 122 " (cutoff:3.500A) Processing helix chain 's' and resid 424 through 447 removed outlier: 3.631A pdb=" N MET s 428 " --> pdb=" O PRO s 424 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER s 433 " --> pdb=" O GLY s 429 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE s 435 " --> pdb=" O LEU s 431 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE s 438 " --> pdb=" O LEU s 434 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE s 439 " --> pdb=" O PHE s 435 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET s 446 " --> pdb=" O TYR s 442 " (cutoff:3.500A) Processing helix chain 'r' and resid 298 through 324 removed outlier: 3.834A pdb=" N ASN r 303 " --> pdb=" O SER r 299 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL r 305 " --> pdb=" O VAL r 301 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE r 308 " --> pdb=" O MET r 304 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA r 311 " --> pdb=" O TRP r 307 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL r 316 " --> pdb=" O LEU r 312 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASN r 322 " --> pdb=" O ILE r 318 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE r 323 " --> pdb=" O THR r 319 " (cutoff:3.500A) Processing helix chain '8' and resid 13 through 44 removed outlier: 3.787A pdb=" N GLY 8 18 " --> pdb=" O PHE 8 14 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA 8 21 " --> pdb=" O MET 8 17 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N MET 8 23 " --> pdb=" O ALA 8 19 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER 8 26 " --> pdb=" O ALA 8 22 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR 8 32 " --> pdb=" O LEU 8 28 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY 8 33 " --> pdb=" O GLY 8 29 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER 8 37 " --> pdb=" O GLY 8 33 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR 8 39 " --> pdb=" O ALA 8 35 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE 8 41 " --> pdb=" O SER 8 37 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA 8 42 " --> pdb=" O GLY 8 38 " (cutoff:3.500A) Processing helix chain '8' and resid 49 through 51 No H-bonds generated for 'chain '8' and resid 49 through 51' Processing helix chain '8' and resid 57 through 60 No H-bonds generated for 'chain '8' and resid 57 through 60' Processing helix chain '8' and resid 65 through 76 removed outlier: 3.579A pdb=" N VAL 8 72 " --> pdb=" O TYR 8 68 " (cutoff:3.500A) Processing helix chain '8' and resid 90 through 119 removed outlier: 3.669A pdb=" N SER 8 98 " --> pdb=" O GLY 8 94 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER 8 102 " --> pdb=" O SER 8 98 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE 8 110 " --> pdb=" O ALA 8 106 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY 8 111 " --> pdb=" O GLY 8 107 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL 8 113 " --> pdb=" O ALA 8 109 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL 8 118 " --> pdb=" O GLY 8 114 " (cutoff:3.500A) Processing helix chain '8' and resid 125 through 153 removed outlier: 3.728A pdb=" N PHE 8 128 " --> pdb=" O PRO 8 125 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N VAL 8 129 " --> pdb=" O ARG 8 126 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE 8 132 " --> pdb=" O VAL 8 129 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU 8 133 " --> pdb=" O GLY 8 130 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE 8 136 " --> pdb=" O LEU 8 133 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA 8 138 " --> pdb=" O LEU 8 135 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL 8 140 " --> pdb=" O PHE 8 137 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU 8 141 " --> pdb=" O ALA 8 138 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYR 8 144 " --> pdb=" O LEU 8 141 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY 8 145 " --> pdb=" O GLY 8 142 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE 8 147 " --> pdb=" O TYR 8 144 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA 8 149 " --> pdb=" O LEU 8 146 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE 8 151 " --> pdb=" O VAL 8 148 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU 8 152 " --> pdb=" O ALA 8 149 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER 8 153 " --> pdb=" O LEU 8 150 " (cutoff:3.500A) Processing helix chain '9' and resid 12 through 20 removed outlier: 3.622A pdb=" N GLY 9 18 " --> pdb=" O PHE 9 14 " (cutoff:3.500A) Processing helix chain '9' and resid 24 through 35 removed outlier: 3.514A pdb=" N LEU 9 28 " --> pdb=" O VAL 9 24 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY 9 29 " --> pdb=" O PHE 9 25 " (cutoff:3.500A) Processing helix chain '9' and resid 38 through 44 Processing helix chain '9' and resid 49 through 51 No H-bonds generated for 'chain '9' and resid 49 through 51' Processing helix chain '9' and resid 54 through 78 removed outlier: 4.133A pdb=" N ILE 9 57 " --> pdb=" O LYS 9 54 " (cutoff:3.500A) Proline residue: 9 58 - end of helix removed outlier: 3.831A pdb=" N MET 9 61 " --> pdb=" O PRO 9 58 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE 9 64 " --> pdb=" O MET 9 61 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE 9 65 " --> pdb=" O ALA 9 62 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA 9 66 " --> pdb=" O GLY 9 63 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL 9 71 " --> pdb=" O TYR 9 68 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL 9 72 " --> pdb=" O GLY 9 69 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA 9 73 " --> pdb=" O LEU 9 70 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL 9 74 " --> pdb=" O VAL 9 71 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE 9 76 " --> pdb=" O ALA 9 73 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN 9 78 " --> pdb=" O LEU 9 75 " (cutoff:3.500A) Processing helix chain '9' and resid 88 through 121 removed outlier: 3.580A pdb=" N VAL 9 99 " --> pdb=" O ALA 9 95 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER 9 102 " --> pdb=" O SER 9 98 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA 9 105 " --> pdb=" O LEU 9 101 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE 9 110 " --> pdb=" O ALA 9 106 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP 9 115 " --> pdb=" O GLY 9 111 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA 9 116 " --> pdb=" O ILE 9 112 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL 9 118 " --> pdb=" O GLY 9 114 " (cutoff:3.500A) Processing helix chain '9' and resid 128 through 154 removed outlier: 3.871A pdb=" N LEU 9 133 " --> pdb=" O VAL 9 129 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE 9 134 " --> pdb=" O GLY 9 130 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LEU 9 141 " --> pdb=" O PHE 9 137 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLY 9 142 " --> pdb=" O ALA 9 138 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY 9 145 " --> pdb=" O LEU 9 141 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR 9 154 " --> pdb=" O LEU 9 150 " (cutoff:3.500A) Processing helix chain '1' and resid 3 through 8 Processing helix chain '1' and resid 10 through 16 removed outlier: 3.579A pdb=" N PHE 1 15 " --> pdb=" O VAL 1 11 " (cutoff:3.500A) Processing helix chain '1' and resid 19 through 28 removed outlier: 4.018A pdb=" N THR 1 27 " --> pdb=" O GLY 1 23 " (cutoff:3.500A) Processing helix chain '1' and resid 37 through 43 removed outlier: 3.520A pdb=" N THR 1 42 " --> pdb=" O ALA 1 38 " (cutoff:3.500A) Processing helix chain '1' and resid 46 through 77 removed outlier: 3.831A pdb=" N GLY 1 53 " --> pdb=" O TRP 1 49 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE 1 54 " --> pdb=" O SER 1 50 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY 1 55 " --> pdb=" O ASN 1 51 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU 1 56 " --> pdb=" O LEU 1 52 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE 1 58 " --> pdb=" O ILE 1 54 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU 1 60 " --> pdb=" O LEU 1 56 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER 1 61 " --> pdb=" O ALA 1 57 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY 1 64 " --> pdb=" O LEU 1 60 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY 1 68 " --> pdb=" O GLY 1 64 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR 1 70 " --> pdb=" O ALA 1 66 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE 1 71 " --> pdb=" O TRP 1 67 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR 1 72 " --> pdb=" O GLY 1 68 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER 1 75 " --> pdb=" O ILE 1 71 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE 1 77 " --> pdb=" O GLY 1 73 " (cutoff:3.500A) Processing helix chain '1' and resid 84 through 112 removed outlier: 3.501A pdb=" N LYS 1 87 " --> pdb=" O PRO 1 84 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N THR 1 88 " --> pdb=" O ARG 1 85 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS 1 89 " --> pdb=" O ILE 1 86 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ASN 1 90 " --> pdb=" O LYS 1 87 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU 1 91 " --> pdb=" O THR 1 88 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL 1 92 " --> pdb=" O LYS 1 89 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE 1 95 " --> pdb=" O VAL 1 92 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE 1 96 " --> pdb=" O SER 1 93 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N CYS 1 97 " --> pdb=" O ILE 1 94 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL 1 100 " --> pdb=" O CYS 1 97 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE 1 102 " --> pdb=" O ALA 1 99 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE 1 105 " --> pdb=" O ILE 1 102 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE 1 106 " --> pdb=" O TYR 1 103 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET 1 107 " --> pdb=" O GLY 1 104 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA 1 108 " --> pdb=" O ILE 1 105 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL 1 110 " --> pdb=" O MET 1 107 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE 1 111 " --> pdb=" O ALA 1 108 " (cutoff:3.500A) Processing helix chain '1' and resid 130 through 168 removed outlier: 3.638A pdb=" N MET 1 137 " --> pdb=" O ALA 1 133 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE 1 138 " --> pdb=" O GLY 1 134 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN 1 148 " --> pdb=" O VAL 1 144 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL 1 153 " --> pdb=" O LEU 1 149 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY 1 159 " --> pdb=" O VAL 1 155 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA 1 167 " --> pdb=" O ALA 1 163 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN 1 168 " --> pdb=" O LEU 1 164 " (cutoff:3.500A) Processing helix chain '1' and resid 173 through 176 No H-bonds generated for 'chain '1' and resid 173 through 176' Processing helix chain '1' and resid 178 through 185 removed outlier: 3.670A pdb=" N GLY 1 183 " --> pdb=" O VAL 1 179 " (cutoff:3.500A) Processing helix chain '1' and resid 188 through 197 removed outlier: 3.951A pdb=" N VAL 1 193 " --> pdb=" O PHE 1 189 " (cutoff:3.500A) Processing helix chain '2' and resid 11 through 19 removed outlier: 4.108A pdb=" N PHE 2 14 " --> pdb=" O ALA 2 11 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA 2 15 " --> pdb=" O SER 2 12 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL 2 16 " --> pdb=" O PHE 2 13 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N MET 2 17 " --> pdb=" O PHE 2 14 " (cutoff:3.500A) Processing helix chain '2' and resid 21 through 46 removed outlier: 3.565A pdb=" N PHE 2 25 " --> pdb=" O ALA 2 21 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER 2 26 " --> pdb=" O ALA 2 22 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU 2 28 " --> pdb=" O VAL 2 24 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR 2 32 " --> pdb=" O LEU 2 28 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER 2 37 " --> pdb=" O GLY 2 33 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR 2 39 " --> pdb=" O ALA 2 35 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY 2 40 " --> pdb=" O LYS 2 36 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL 2 46 " --> pdb=" O ALA 2 42 " (cutoff:3.500A) Processing helix chain '2' and resid 57 through 78 removed outlier: 3.969A pdb=" N ILE 2 65 " --> pdb=" O MET 2 61 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ALA 2 66 " --> pdb=" O ALA 2 62 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE 2 67 " --> pdb=" O GLY 2 63 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY 2 69 " --> pdb=" O ILE 2 65 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU 2 70 " --> pdb=" O ALA 2 66 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL 2 72 " --> pdb=" O TYR 2 68 " (cutoff:3.500A) Processing helix chain '2' and resid 88 through 121 removed outlier: 3.578A pdb=" N GLN 2 92 " --> pdb=" O LYS 2 88 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU 2 93 " --> pdb=" O SER 2 89 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER 2 98 " --> pdb=" O GLY 2 94 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL 2 99 " --> pdb=" O ALA 2 95 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER 2 102 " --> pdb=" O SER 2 98 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY 2 107 " --> pdb=" O GLY 2 103 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE 2 108 " --> pdb=" O LEU 2 104 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA 2 109 " --> pdb=" O ALA 2 105 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG 2 119 " --> pdb=" O ASP 2 115 " (cutoff:3.500A) Processing helix chain '2' and resid 125 through 153 removed outlier: 3.943A pdb=" N PHE 2 128 " --> pdb=" O PRO 2 125 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N VAL 2 129 " --> pdb=" O ARG 2 126 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY 2 130 " --> pdb=" O LEU 2 127 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU 2 133 " --> pdb=" O GLY 2 130 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU 2 139 " --> pdb=" O ILE 2 136 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL 2 140 " --> pdb=" O PHE 2 137 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR 2 144 " --> pdb=" O LEU 2 141 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY 2 145 " --> pdb=" O GLY 2 142 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL 2 148 " --> pdb=" O GLY 2 145 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU 2 152 " --> pdb=" O ALA 2 149 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER 2 153 " --> pdb=" O LEU 2 150 " (cutoff:3.500A) Processing helix chain '3' and resid 11 through 19 removed outlier: 3.507A pdb=" N VAL 3 16 " --> pdb=" O PHE 3 13 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N MET 3 17 " --> pdb=" O PHE 3 14 " (cutoff:3.500A) Processing helix chain '3' and resid 21 through 24 No H-bonds generated for 'chain '3' and resid 21 through 24' Processing helix chain '3' and resid 29 through 44 removed outlier: 3.678A pdb=" N THR 3 34 " --> pdb=" O ALA 3 30 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR 3 39 " --> pdb=" O ALA 3 35 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE 3 41 " --> pdb=" O SER 3 37 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA 3 42 " --> pdb=" O GLY 3 38 " (cutoff:3.500A) Processing helix chain '3' and resid 57 through 61 Processing helix chain '3' and resid 65 through 79 removed outlier: 3.513A pdb=" N LEU 3 70 " --> pdb=" O ALA 3 66 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER 3 79 " --> pdb=" O LEU 3 75 " (cutoff:3.500A) Processing helix chain '3' and resid 88 through 121 removed outlier: 3.912A pdb=" N LEU 3 93 " --> pdb=" O SER 3 89 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL 3 99 " --> pdb=" O ALA 3 95 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER 3 102 " --> pdb=" O SER 3 98 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA 3 105 " --> pdb=" O LEU 3 101 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE 3 112 " --> pdb=" O PHE 3 108 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL 3 118 " --> pdb=" O GLY 3 114 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG 3 119 " --> pdb=" O ASP 3 115 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY 3 120 " --> pdb=" O ALA 3 116 " (cutoff:3.500A) Processing helix chain '3' and resid 125 through 139 removed outlier: 3.866A pdb=" N PHE 3 128 " --> pdb=" O PRO 3 125 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N VAL 3 129 " --> pdb=" O ARG 3 126 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET 3 131 " --> pdb=" O PHE 3 128 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE 3 132 " --> pdb=" O VAL 3 129 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE 3 136 " --> pdb=" O LEU 3 133 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA 3 138 " --> pdb=" O LEU 3 135 " (cutoff:3.500A) Processing helix chain '3' and resid 141 through 154 removed outlier: 3.694A pdb=" N GLY 3 145 " --> pdb=" O LEU 3 141 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU 3 146 " --> pdb=" O GLY 3 142 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL 3 148 " --> pdb=" O TYR 3 144 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR 3 154 " --> pdb=" O LEU 3 150 " (cutoff:3.500A) Processing helix chain '4' and resid 12 through 27 removed outlier: 3.968A pdb=" N MET 4 23 " --> pdb=" O ALA 4 19 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER 4 26 " --> pdb=" O ALA 4 22 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA 4 27 " --> pdb=" O MET 4 23 " (cutoff:3.500A) Processing helix chain '4' and resid 29 through 46 removed outlier: 3.504A pdb=" N THR 4 34 " --> pdb=" O ALA 4 30 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER 4 37 " --> pdb=" O GLY 4 33 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY 4 40 " --> pdb=" O LYS 4 36 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA 4 42 " --> pdb=" O GLY 4 38 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N VAL 4 46 " --> pdb=" O ALA 4 42 " (cutoff:3.500A) Processing helix chain '4' and resid 57 through 63 removed outlier: 3.792A pdb=" N ALA 4 62 " --> pdb=" O PRO 4 58 " (cutoff:3.500A) Processing helix chain '4' and resid 65 through 78 removed outlier: 3.650A pdb=" N VAL 4 72 " --> pdb=" O TYR 4 68 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA 4 77 " --> pdb=" O ALA 4 73 " (cutoff:3.500A) Processing helix chain '4' and resid 88 through 121 removed outlier: 3.510A pdb=" N LEU 4 101 " --> pdb=" O LEU 4 97 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER 4 102 " --> pdb=" O SER 4 98 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA 4 105 " --> pdb=" O LEU 4 101 " (cutoff:3.500A) Processing helix chain '4' and resid 125 through 137 removed outlier: 3.911A pdb=" N PHE 4 128 " --> pdb=" O PRO 4 125 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL 4 129 " --> pdb=" O ARG 4 126 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE 4 132 " --> pdb=" O VAL 4 129 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE 4 137 " --> pdb=" O ILE 4 134 " (cutoff:3.500A) Processing helix chain '4' and resid 140 through 153 removed outlier: 3.820A pdb=" N VAL 4 148 " --> pdb=" O TYR 4 144 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER 4 153 " --> pdb=" O ALA 4 149 " (cutoff:3.500A) Processing helix chain '5' and resid 13 through 24 removed outlier: 4.143A pdb=" N MET 5 23 " --> pdb=" O ALA 5 19 " (cutoff:3.500A) Processing helix chain '5' and resid 26 through 46 removed outlier: 3.544A pdb=" N ALA 5 31 " --> pdb=" O ALA 5 27 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA 5 35 " --> pdb=" O ALA 5 31 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N VAL 5 46 " --> pdb=" O ALA 5 42 " (cutoff:3.500A) Processing helix chain '5' and resid 49 through 51 No H-bonds generated for 'chain '5' and resid 49 through 51' Processing helix chain '5' and resid 57 through 63 Processing helix chain '5' and resid 65 through 79 removed outlier: 3.540A pdb=" N ALA 5 77 " --> pdb=" O ALA 5 73 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER 5 79 " --> pdb=" O LEU 5 75 " (cutoff:3.500A) Processing helix chain '5' and resid 90 through 121 removed outlier: 3.618A pdb=" N SER 5 98 " --> pdb=" O GLY 5 94 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL 5 99 " --> pdb=" O ALA 5 95 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER 5 102 " --> pdb=" O SER 5 98 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY 5 103 " --> pdb=" O VAL 5 99 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE 5 110 " --> pdb=" O ALA 5 106 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE 5 112 " --> pdb=" O PHE 5 108 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL 5 118 " --> pdb=" O GLY 5 114 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG 5 119 " --> pdb=" O ASP 5 115 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY 5 120 " --> pdb=" O ALA 5 116 " (cutoff:3.500A) Processing helix chain '5' and resid 125 through 154 removed outlier: 3.781A pdb=" N PHE 5 128 " --> pdb=" O PRO 5 125 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL 5 129 " --> pdb=" O ARG 5 126 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET 5 131 " --> pdb=" O PHE 5 128 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE 5 132 " --> pdb=" O VAL 5 129 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE 5 136 " --> pdb=" O LEU 5 133 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N VAL 5 140 " --> pdb=" O PHE 5 137 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU 5 141 " --> pdb=" O ALA 5 138 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR 5 144 " --> pdb=" O LEU 5 141 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY 5 145 " --> pdb=" O GLY 5 142 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE 5 147 " --> pdb=" O TYR 5 144 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL 5 148 " --> pdb=" O GLY 5 145 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU 5 152 " --> pdb=" O ALA 5 149 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER 5 153 " --> pdb=" O LEU 5 150 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR 5 154 " --> pdb=" O ILE 5 151 " (cutoff:3.500A) Processing helix chain '6' and resid 11 through 43 removed outlier: 3.622A pdb=" N ALA 6 15 " --> pdb=" O SER 6 12 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL 6 16 " --> pdb=" O PHE 6 13 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET 6 17 " --> pdb=" O PHE 6 14 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY 6 18 " --> pdb=" O ALA 6 15 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER 6 20 " --> pdb=" O MET 6 17 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA 6 21 " --> pdb=" O GLY 6 18 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA 6 22 " --> pdb=" O ALA 6 19 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL 6 24 " --> pdb=" O ALA 6 21 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N PHE 6 25 " --> pdb=" O ALA 6 22 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER 6 26 " --> pdb=" O MET 6 23 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU 6 28 " --> pdb=" O PHE 6 25 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA 6 30 " --> pdb=" O ALA 6 27 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA 6 31 " --> pdb=" O LEU 6 28 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR 6 32 " --> pdb=" O GLY 6 29 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLY 6 33 " --> pdb=" O ALA 6 30 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA 6 35 " --> pdb=" O TYR 6 32 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LYS 6 36 " --> pdb=" O GLY 6 33 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY 6 38 " --> pdb=" O ALA 6 35 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR 6 39 " --> pdb=" O LYS 6 36 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE 6 41 " --> pdb=" O GLY 6 38 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA 6 42 " --> pdb=" O THR 6 39 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA 6 43 " --> pdb=" O GLY 6 40 " (cutoff:3.500A) Processing helix chain '6' and resid 49 through 51 No H-bonds generated for 'chain '6' and resid 49 through 51' Processing helix chain '6' and resid 57 through 79 removed outlier: 4.286A pdb=" N ILE 6 65 " --> pdb=" O MET 6 61 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA 6 66 " --> pdb=" O ALA 6 62 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE 6 67 " --> pdb=" O GLY 6 63 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL 6 72 " --> pdb=" O TYR 6 68 " (cutoff:3.500A) Processing helix chain '6' and resid 88 through 121 removed outlier: 3.796A pdb=" N GLN 6 92 " --> pdb=" O LYS 6 88 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER 6 98 " --> pdb=" O GLY 6 94 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY 6 103 " --> pdb=" O VAL 6 99 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE 6 110 " --> pdb=" O ALA 6 106 " (cutoff:3.500A) Processing helix chain '6' and resid 128 through 153 removed outlier: 4.050A pdb=" N PHE 6 137 " --> pdb=" O LEU 6 133 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU 6 141 " --> pdb=" O PHE 6 137 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY 6 142 " --> pdb=" O ALA 6 138 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL 6 148 " --> pdb=" O TYR 6 144 " (cutoff:3.500A) Processing helix chain '7' and resid 11 through 19 removed outlier: 3.624A pdb=" N PHE 7 14 " --> pdb=" O ALA 7 11 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL 7 16 " --> pdb=" O PHE 7 13 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET 7 17 " --> pdb=" O PHE 7 14 " (cutoff:3.500A) Processing helix chain '7' and resid 21 through 46 removed outlier: 3.979A pdb=" N SER 7 26 " --> pdb=" O ALA 7 22 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR 7 32 " --> pdb=" O LEU 7 28 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA 7 35 " --> pdb=" O ALA 7 31 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER 7 37 " --> pdb=" O GLY 7 33 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY 7 40 " --> pdb=" O LYS 7 36 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET 7 44 " --> pdb=" O GLY 7 40 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N VAL 7 46 " --> pdb=" O ALA 7 42 " (cutoff:3.500A) Processing helix chain '7' and resid 57 through 78 removed outlier: 3.569A pdb=" N ILE 7 64 " --> pdb=" O VAL 7 60 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE 7 65 " --> pdb=" O MET 7 61 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ALA 7 66 " --> pdb=" O ALA 7 62 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY 7 69 " --> pdb=" O ILE 7 65 " (cutoff:3.500A) Processing helix chain '7' and resid 88 through 120 removed outlier: 3.532A pdb=" N SER 7 98 " --> pdb=" O GLY 7 94 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL 7 99 " --> pdb=" O ALA 7 95 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER 7 102 " --> pdb=" O SER 7 98 " (cutoff:3.500A) Processing helix chain '7' and resid 125 through 153 removed outlier: 3.971A pdb=" N PHE 7 128 " --> pdb=" O PRO 7 125 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL 7 129 " --> pdb=" O ARG 7 126 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET 7 131 " --> pdb=" O PHE 7 128 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE 7 132 " --> pdb=" O VAL 7 129 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE 7 134 " --> pdb=" O MET 7 131 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE 7 136 " --> pdb=" O LEU 7 133 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA 7 138 " --> pdb=" O LEU 7 135 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL 7 140 " --> pdb=" O PHE 7 137 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU 7 141 " --> pdb=" O ALA 7 138 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR 7 144 " --> pdb=" O LEU 7 141 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU 7 146 " --> pdb=" O LEU 7 143 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE 7 147 " --> pdb=" O TYR 7 144 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA 7 149 " --> pdb=" O LEU 7 146 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE 7 151 " --> pdb=" O VAL 7 148 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU 7 152 " --> pdb=" O ALA 7 149 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER 7 153 " --> pdb=" O LEU 7 150 " (cutoff:3.500A) Processing helix chain '0' and resid 12 through 44 removed outlier: 4.122A pdb=" N MET 0 23 " --> pdb=" O ALA 0 19 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE 0 25 " --> pdb=" O ALA 0 21 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N SER 0 26 " --> pdb=" O ALA 0 22 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY 0 29 " --> pdb=" O PHE 0 25 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR 0 34 " --> pdb=" O ALA 0 30 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER 0 37 " --> pdb=" O GLY 0 33 " (cutoff:3.500A) Processing helix chain '0' and resid 57 through 62 Processing helix chain '0' and resid 65 through 78 removed outlier: 3.833A pdb=" N VAL 0 72 " --> pdb=" O TYR 0 68 " (cutoff:3.500A) Processing helix chain '0' and resid 88 through 123 removed outlier: 3.595A pdb=" N VAL 0 99 " --> pdb=" O ALA 0 95 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY 0 103 " --> pdb=" O VAL 0 99 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA 0 105 " --> pdb=" O LEU 0 101 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE 0 110 " --> pdb=" O ALA 0 106 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY 0 111 " --> pdb=" O GLY 0 107 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA 0 122 " --> pdb=" O VAL 0 118 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLN 0 123 " --> pdb=" O ARG 0 119 " (cutoff:3.500A) Processing helix chain '0' and resid 125 through 154 removed outlier: 3.866A pdb=" N PHE 0 128 " --> pdb=" O PRO 0 125 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL 0 129 " --> pdb=" O ARG 0 126 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE 0 132 " --> pdb=" O VAL 0 129 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE 0 137 " --> pdb=" O ILE 0 134 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL 0 140 " --> pdb=" O PHE 0 137 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU 0 141 " --> pdb=" O ALA 0 138 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR 0 144 " --> pdb=" O LEU 0 141 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL 0 148 " --> pdb=" O GLY 0 145 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA 0 149 " --> pdb=" O LEU 0 146 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE 0 151 " --> pdb=" O VAL 0 148 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU 0 152 " --> pdb=" O ALA 0 149 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER 0 153 " --> pdb=" O LEU 0 150 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR 0 154 " --> pdb=" O ILE 0 151 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'a' and resid 353 through 356 removed outlier: 4.588A pdb=" N GLU a 324 " --> pdb=" O LYS a 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'a' and resid 174 through 177 Processing sheet with id= C, first strand: chain 'a' and resid 313 through 315 removed outlier: 3.652A pdb=" N ASP a 315 " --> pdb=" O CYS a 320 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N CYS a 320 " --> pdb=" O ASP a 315 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'U' and resid 233 through 235 removed outlier: 3.562A pdb=" N LEU U 268 " --> pdb=" O GLN U 235 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL U 408 " --> pdb=" O LEU U 269 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER U 271 " --> pdb=" O MET U 406 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N MET U 406 " --> pdb=" O SER U 271 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP U 404 " --> pdb=" O GLU U 297 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N GLU U 297 " --> pdb=" O ASP U 404 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N MET U 406 " --> pdb=" O VAL U 295 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL U 295 " --> pdb=" O MET U 406 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL U 408 " --> pdb=" O VAL U 293 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL U 293 " --> pdb=" O VAL U 408 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE U 325 " --> pdb=" O PHE U 307 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'U' and resid 358 through 361 Processing sheet with id= F, first strand: chain 'L' and resid 78 through 80 removed outlier: 6.472A pdb=" N THR L 30 " --> pdb=" O HIS L 22 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL L 24 " --> pdb=" O VAL L 28 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL L 28 " --> pdb=" O VAL L 24 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG L 56 " --> pdb=" O THR L 63 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLN L 65 " --> pdb=" O ILE L 54 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ILE L 54 " --> pdb=" O GLN L 65 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY L 52 " --> pdb=" O VAL L 43 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'L' and resid 87 through 90 Processing sheet with id= H, first strand: chain 'L' and resid 183 through 185 removed outlier: 5.389A pdb=" N ASP L 134 " --> pdb=" O SER L 157 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER L 157 " --> pdb=" O ASP L 134 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE L 166 " --> pdb=" O TYR L 153 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ILE L 155 " --> pdb=" O HIS L 164 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N HIS L 164 " --> pdb=" O ILE L 155 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'L' and resid 199 through 203 removed outlier: 3.803A pdb=" N VAL L 199 " --> pdb=" O PHE L 196 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLU L 195 " --> pdb=" O VAL L 176 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N VAL L 176 " --> pdb=" O GLU L 195 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'L' and resid 245 through 249 removed outlier: 8.519A pdb=" N THR L 246 " --> pdb=" O VAL L 404 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE L 406 " --> pdb=" O THR L 246 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ILE L 248 " --> pdb=" O ILE L 406 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLY L 408 " --> pdb=" O ILE L 248 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA L 409 " --> pdb=" O ALA L 348 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL L 271 " --> pdb=" O SER L 345 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N MET L 347 " --> pdb=" O VAL L 271 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ILE L 273 " --> pdb=" O MET L 347 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ASP L 349 " --> pdb=" O ILE L 273 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL L 275 " --> pdb=" O ASP L 349 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'L' and resid 295 through 298 Processing sheet with id= L, first strand: chain 'M' and resid 20 through 24 removed outlier: 6.614A pdb=" N THR M 30 " --> pdb=" O HIS M 22 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N VAL M 24 " --> pdb=" O VAL M 28 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL M 28 " --> pdb=" O VAL M 24 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET M 61 " --> pdb=" O GLU M 58 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG M 56 " --> pdb=" O THR M 63 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLN M 65 " --> pdb=" O ILE M 54 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ILE M 54 " --> pdb=" O GLN M 65 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'M' and resid 87 through 90 Processing sheet with id= N, first strand: chain 'M' and resid 200 through 203 removed outlier: 6.050A pdb=" N GLU M 195 " --> pdb=" O VAL M 176 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL M 176 " --> pdb=" O GLU M 195 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'M' and resid 406 through 408 removed outlier: 8.730A pdb=" N VAL M 407 " --> pdb=" O VAL M 344 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N MET M 346 " --> pdb=" O VAL M 407 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL M 271 " --> pdb=" O SER M 345 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N MET M 347 " --> pdb=" O VAL M 271 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ILE M 273 " --> pdb=" O MET M 347 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ASP M 349 " --> pdb=" O ILE M 273 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL M 275 " --> pdb=" O ASP M 349 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'M' and resid 295 through 297 Processing sheet with id= Q, first strand: chain 'M' and resid 152 through 157 removed outlier: 6.810A pdb=" N ILE M 166 " --> pdb=" O TYR M 153 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ILE M 155 " --> pdb=" O HIS M 164 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N HIS M 164 " --> pdb=" O ILE M 155 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'N' and resid 18 through 20 removed outlier: 6.714A pdb=" N THR N 63 " --> pdb=" O ILE N 55 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LEU N 57 " --> pdb=" O MET N 61 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N MET N 61 " --> pdb=" O LEU N 57 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N CYS N 32 " --> pdb=" O VAL N 21 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL N 21 " --> pdb=" O CYS N 32 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'N' and resid 87 through 90 Processing sheet with id= T, first strand: chain 'N' and resid 200 through 203 removed outlier: 3.575A pdb=" N GLU N 193 " --> pdb=" O TYR N 178 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLU N 195 " --> pdb=" O VAL N 176 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N VAL N 176 " --> pdb=" O GLU N 195 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'N' and resid 245 through 247 removed outlier: 8.468A pdb=" N THR N 246 " --> pdb=" O VAL N 404 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE N 406 " --> pdb=" O THR N 246 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL N 271 " --> pdb=" O SER N 345 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N MET N 347 " --> pdb=" O VAL N 271 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE N 273 " --> pdb=" O MET N 347 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ASP N 349 " --> pdb=" O ILE N 273 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N VAL N 275 " --> pdb=" O ASP N 349 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'N' and resid 295 through 297 Processing sheet with id= W, first strand: chain 'N' and resid 152 through 157 removed outlier: 3.513A pdb=" N TYR N 153 " --> pdb=" O ILE N 166 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE N 166 " --> pdb=" O TYR N 153 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE N 155 " --> pdb=" O HIS N 164 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N HIS N 164 " --> pdb=" O ILE N 155 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'O' and resid 57 through 59 removed outlier: 3.648A pdb=" N GLU O 88 " --> pdb=" O VAL O 95 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLN O 97 " --> pdb=" O VAL O 86 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N VAL O 86 " --> pdb=" O GLN O 97 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'O' and resid 120 through 123 removed outlier: 3.574A pdb=" N ASP O 149 " --> pdb=" O VAL O 123 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'O' and resid 131 through 133 removed outlier: 8.723A pdb=" N PHE O 132 " --> pdb=" O VAL O 257 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU O 259 " --> pdb=" O PHE O 132 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N CYS O 258 " --> pdb=" O PHE O 227 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE O 229 " --> pdb=" O CYS O 258 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N PHE O 260 " --> pdb=" O ILE O 229 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N PHE O 231 " --> pdb=" O PHE O 260 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N ASN O 262 " --> pdb=" O PHE O 231 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ALA O 233 " --> pdb=" O ASN O 262 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N HIS O 292 " --> pdb=" O ALA O 228 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL O 230 " --> pdb=" O HIS O 292 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU O 294 " --> pdb=" O VAL O 230 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ALA O 232 " --> pdb=" O LEU O 294 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE O 296 " --> pdb=" O ALA O 232 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET O 234 " --> pdb=" O ILE O 296 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N THR O 298 " --> pdb=" O MET O 234 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL O 236 " --> pdb=" O THR O 298 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N SER O 347 " --> pdb=" O VAL O 293 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL O 295 " --> pdb=" O SER O 347 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N THR O 349 " --> pdb=" O VAL O 295 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU O 297 " --> pdb=" O THR O 349 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE O 351 " --> pdb=" O LEU O 297 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'P' and resid 57 through 59 removed outlier: 3.856A pdb=" N GLU P 88 " --> pdb=" O VAL P 95 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLN P 97 " --> pdb=" O VAL P 86 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N VAL P 86 " --> pdb=" O GLN P 97 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'P' and resid 120 through 123 removed outlier: 3.618A pdb=" N ASP P 149 " --> pdb=" O VAL P 123 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'P' and resid 376 through 378 Processing sheet with id= AD, first strand: chain 'P' and resid 347 through 352 removed outlier: 3.506A pdb=" N LEU P 297 " --> pdb=" O ILE P 351 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA P 228 " --> pdb=" O LEU P 294 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ILE P 296 " --> pdb=" O ALA P 228 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL P 230 " --> pdb=" O ILE P 296 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N THR P 298 " --> pdb=" O VAL P 230 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA P 232 " --> pdb=" O THR P 298 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'Q' and resid 57 through 61 removed outlier: 3.685A pdb=" N ALA Q 94 " --> pdb=" O LEU Q 60 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU Q 88 " --> pdb=" O VAL Q 95 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN Q 97 " --> pdb=" O VAL Q 86 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N VAL Q 86 " --> pdb=" O GLN Q 97 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'Q' and resid 72 through 75 Processing sheet with id= AG, first strand: chain 'Q' and resid 120 through 123 Processing sheet with id= AH, first strand: chain 'Q' and resid 347 through 352 removed outlier: 3.522A pdb=" N LEU Q 297 " --> pdb=" O ILE Q 351 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'D' and resid 92 through 101 Processing sheet with id= AJ, first strand: chain 'b' and resid 133 through 135 removed outlier: 3.634A pdb=" N VAL b 181 " --> pdb=" O ASN b 194 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE b 183 " --> pdb=" O VAL b 192 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'c' and resid 131 through 134 removed outlier: 6.130A pdb=" N ASP c 164 " --> pdb=" O MET c 132 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N VAL c 134 " --> pdb=" O ASP c 164 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLN c 166 " --> pdb=" O VAL c 134 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK Processing sheet with id= AL, first strand: chain 'c' and resid 180 through 184 Processing sheet with id= AM, first strand: chain 'd' and resid 164 through 168 removed outlier: 3.712A pdb=" N ILE d 133 " --> pdb=" O TYR d 184 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU d 182 " --> pdb=" O ARG d 135 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL d 181 " --> pdb=" O ASN d 194 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'F' and resid 36 through 38 removed outlier: 7.124A pdb=" N VAL F 10 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ALA F 87 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ILE F 66 " --> pdb=" O ALA F 87 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N LEU F 89 " --> pdb=" O ILE F 66 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'C' and resid 373 through 375 Processing sheet with id= AP, first strand: chain 'C' and resid 247 through 249 removed outlier: 4.021A pdb=" N LEU C 186 " --> pdb=" O ARG C 249 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL C 187 " --> pdb=" O CYS C 225 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N CYS C 225 " --> pdb=" O VAL C 187 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL C 189 " --> pdb=" O TYR C 223 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER C 217 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ASN C 226 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL C 215 " --> pdb=" O ASN C 226 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 's' and resid 258 through 260 removed outlier: 3.535A pdb=" N GLN s 403 " --> pdb=" O LEU s 268 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N HIS s 370 " --> pdb=" O SER s 416 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 's' and resid 282 through 284 Processing sheet with id= AS, first strand: chain 's' and resid 306 through 313 removed outlier: 3.532A pdb=" N ILE s 326 " --> pdb=" O ARG s 344 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG s 344 " --> pdb=" O ILE s 326 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ALA s 328 " --> pdb=" O MET s 342 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N MET s 342 " --> pdb=" O ALA s 328 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 's' and resid 330 through 332 removed outlier: 3.555A pdb=" N TRP s 339 " --> pdb=" O ARG s 330 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG s 337 " --> pdb=" O TYR s 332 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 's' and resid 356 through 358 2457 hydrogen bonds defined for protein. 6741 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 22.94 Time building geometry restraints manager: 20.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 11211 1.28 - 1.42: 16526 1.42 - 1.56: 39738 1.56 - 1.70: 29 1.70 - 1.84: 640 Bond restraints: 68144 Sorted by residual: bond pdb=" C29 POV 1 301 " pdb="C210 POV 1 301 " ideal model delta sigma weight residual 1.333 1.532 -0.199 2.00e-02 2.50e+03 9.88e+01 bond pdb=" C29 POV 1 303 " pdb="C210 POV 1 303 " ideal model delta sigma weight residual 1.333 1.530 -0.197 2.00e-02 2.50e+03 9.68e+01 bond pdb=" C29 POV r 401 " pdb="C210 POV r 401 " ideal model delta sigma weight residual 1.333 1.528 -0.195 2.00e-02 2.50e+03 9.49e+01 bond pdb=" C29 POV 1 302 " pdb="C210 POV 1 302 " ideal model delta sigma weight residual 1.333 1.527 -0.194 2.00e-02 2.50e+03 9.42e+01 bond pdb=" C29 POV r 402 " pdb="C210 POV r 402 " ideal model delta sigma weight residual 1.333 1.526 -0.193 2.00e-02 2.50e+03 9.36e+01 ... (remaining 68139 not shown) Histogram of bond angle deviations from ideal: 97.84 - 105.32: 1310 105.32 - 112.81: 35560 112.81 - 120.29: 29311 120.29 - 127.78: 25634 127.78 - 135.26: 433 Bond angle restraints: 92248 Sorted by residual: angle pdb=" N ASN a 178 " pdb=" CA ASN a 178 " pdb=" C ASN a 178 " ideal model delta sigma weight residual 111.03 122.98 -11.95 1.11e+00 8.12e-01 1.16e+02 angle pdb=" N ASP s 417 " pdb=" CA ASP s 417 " pdb=" C ASP s 417 " ideal model delta sigma weight residual 110.41 120.03 -9.62 1.23e+00 6.61e-01 6.12e+01 angle pdb=" N SER Q 501 " pdb=" CA SER Q 501 " pdb=" C SER Q 501 " ideal model delta sigma weight residual 112.93 121.64 -8.71 1.12e+00 7.97e-01 6.04e+01 angle pdb=" N GLN Q 497 " pdb=" CA GLN Q 497 " pdb=" C GLN Q 497 " ideal model delta sigma weight residual 111.28 119.52 -8.24 1.09e+00 8.42e-01 5.71e+01 angle pdb=" O13 POV r 401 " pdb=" P POV r 401 " pdb=" O14 POV r 401 " ideal model delta sigma weight residual 121.11 100.70 20.41 3.00e+00 1.11e-01 4.63e+01 ... (remaining 92243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.62: 40162 33.62 - 67.24: 999 67.24 - 100.86: 161 100.86 - 134.48: 8 134.48 - 168.10: 3 Dihedral angle restraints: 41333 sinusoidal: 15951 harmonic: 25382 Sorted by residual: dihedral pdb=" O2A ADP M 701 " pdb=" O3A ADP M 701 " pdb=" PA ADP M 701 " pdb=" PB ADP M 701 " ideal model delta sinusoidal sigma weight residual -60.00 91.27 -151.26 1 2.00e+01 2.50e-03 4.50e+01 dihedral pdb=" O1B ADP M 701 " pdb=" O3A ADP M 701 " pdb=" PB ADP M 701 " pdb=" PA ADP M 701 " ideal model delta sinusoidal sigma weight residual -60.00 80.25 -140.25 1 2.00e+01 2.50e-03 4.25e+01 dihedral pdb=" CA ILE 2 84 " pdb=" C ILE 2 84 " pdb=" N SER 2 85 " pdb=" CA SER 2 85 " ideal model delta harmonic sigma weight residual 180.00 -152.02 -27.98 0 5.00e+00 4.00e-02 3.13e+01 ... (remaining 41330 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 10346 0.126 - 0.252: 253 0.252 - 0.378: 14 0.378 - 0.504: 1 0.504 - 0.630: 2 Chirality restraints: 10616 Sorted by residual: chirality pdb=" C1 NAG s 505 " pdb=" ND2 ASN s 357 " pdb=" C2 NAG s 505 " pdb=" O5 NAG s 505 " both_signs ideal model delta sigma weight residual False -2.40 -3.03 0.63 2.00e-01 2.50e+01 9.93e+00 chirality pdb=" CA SER Q 501 " pdb=" N SER Q 501 " pdb=" C SER Q 501 " pdb=" CB SER Q 501 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.39e+00 chirality pdb=" CA GLN Q 497 " pdb=" N GLN Q 497 " pdb=" C GLN Q 497 " pdb=" CB GLN Q 497 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.86e+00 ... (remaining 10613 not shown) Planarity restraints: 11865 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV s 507 " 0.302 2.00e-02 2.50e+03 3.35e-01 1.12e+03 pdb=" C29 POV s 507 " -0.558 2.00e-02 2.50e+03 pdb="C210 POV s 507 " 0.207 2.00e-02 2.50e+03 pdb="C211 POV s 507 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV 1 302 " -0.145 2.00e-02 2.50e+03 2.63e-01 6.93e+02 pdb=" C29 POV 1 302 " 0.341 2.00e-02 2.50e+03 pdb="C210 POV 1 302 " -0.344 2.00e-02 2.50e+03 pdb="C211 POV 1 302 " 0.147 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN s 261 " -0.171 2.00e-02 2.50e+03 2.08e-01 5.40e+02 pdb=" CG ASN s 261 " 0.072 2.00e-02 2.50e+03 pdb=" OD1 ASN s 261 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN s 261 " 0.354 2.00e-02 2.50e+03 pdb=" C1 NAG s 506 " -0.237 2.00e-02 2.50e+03 ... (remaining 11862 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 443 2.59 - 3.17: 51178 3.17 - 3.74: 98425 3.74 - 4.32: 140276 4.32 - 4.90: 229854 Nonbonded interactions: 520176 Sorted by model distance: nonbonded pdb=" NH2 ARG P 400 " pdb=" O1B ADP M 701 " model vdw 2.011 2.496 nonbonded pdb=" O ILE O 71 " pdb=" OG1 THR O 115 " model vdw 2.262 2.440 nonbonded pdb=" O ALA 9 11 " pdb=" OG SER 9 89 " model vdw 2.264 2.440 nonbonded pdb=" CE1 TYR U 367 " pdb=" O ARG U 382 " model vdw 2.264 3.340 nonbonded pdb=" OG SER U 103 " pdb=" O GLU U 197 " model vdw 2.267 2.440 ... (remaining 520171 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 '0' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = (chain '8' and resid 6 through 155) selection = chain '9' } ncs_group { reference = chain 'L' selection = (chain 'M' and resid 17 through 616) selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' } ncs_group { reference = (chain 'b' and resid 8 through 226) selection = chain 'c' selection = (chain 'd' and resid 8 through 226) } ncs_group { reference = (chain 'e' and resid 5 through 116) selection = (chain 'f' and resid 5 through 116) selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 24.440 Check model and map are aligned: 0.790 Set scattering table: 0.490 Process input model: 133.380 Find NCS groups from input model: 3.110 Set up NCS constraints: 0.510 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 168.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 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 : 0.007 0.199 68144 Z= 0.470 Angle : 0.981 20.414 92248 Z= 0.530 Chirality : 0.054 0.630 10616 Planarity : 0.008 0.335 11859 Dihedral : 15.889 168.098 25004 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.27 % Allowed : 8.21 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.90 (0.06), residues: 8727 helix: -4.67 (0.03), residues: 4540 sheet: -2.37 (0.16), residues: 799 loop : -2.86 (0.09), residues: 3388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP 1 67 HIS 0.012 0.001 HIS M 47 PHE 0.030 0.002 PHE s 274 TYR 0.031 0.002 TYR a 741 ARG 0.011 0.001 ARG P 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1285 residues out of total 7420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 1267 time to evaluate : 6.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 71 GLU cc_start: 0.7561 (tp30) cc_final: 0.7094 (tm-30) REVERT: a 199 LEU cc_start: 0.5928 (OUTLIER) cc_final: 0.5374 (mm) REVERT: a 236 LYS cc_start: 0.6566 (tptt) cc_final: 0.5957 (mmtp) REVERT: a 247 TYR cc_start: 0.3692 (m-80) cc_final: 0.3490 (m-80) REVERT: a 266 ARG cc_start: 0.5393 (mtt180) cc_final: 0.5090 (ttt180) REVERT: a 350 MET cc_start: 0.4876 (mtp) cc_final: 0.4047 (mtp) REVERT: a 451 LEU cc_start: 0.8372 (tt) cc_final: 0.7964 (tt) REVERT: a 486 MET cc_start: 0.7659 (mmt) cc_final: 0.7378 (mmt) REVERT: a 646 MET cc_start: 0.7772 (mmm) cc_final: 0.7545 (tpt) REVERT: a 728 ILE cc_start: 0.9235 (pt) cc_final: 0.8431 (mt) REVERT: U 333 MET cc_start: 0.7629 (mtt) cc_final: 0.7317 (mtt) REVERT: L 95 MET cc_start: 0.8994 (mmt) cc_final: 0.8684 (mmt) REVERT: L 301 LYS cc_start: 0.7698 (pttt) cc_final: 0.7121 (ptmt) REVERT: L 303 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7340 (mp0) REVERT: L 442 ARG cc_start: 0.7350 (mtt180) cc_final: 0.7055 (mtm-85) REVERT: L 544 MET cc_start: 0.7912 (mtt) cc_final: 0.7619 (mtm) REVERT: L 574 MET cc_start: 0.5737 (mtt) cc_final: 0.5245 (mtp) REVERT: L 577 ILE cc_start: 0.7658 (mm) cc_final: 0.7434 (tp) REVERT: L 597 ILE cc_start: 0.8995 (mt) cc_final: 0.8706 (tt) REVERT: L 607 ASP cc_start: 0.8203 (m-30) cc_final: 0.7946 (m-30) REVERT: M 613 ARG cc_start: 0.7024 (mtm180) cc_final: 0.6485 (tpm170) REVERT: N 114 GLN cc_start: 0.8262 (mm-40) cc_final: 0.8011 (tp-100) REVERT: N 139 LYS cc_start: 0.7661 (pptt) cc_final: 0.7440 (ptmt) REVERT: N 279 GLU cc_start: 0.6840 (mm-30) cc_final: 0.6408 (mt-10) REVERT: N 506 LYS cc_start: 0.5660 (mttt) cc_final: 0.5346 (mttt) REVERT: N 541 LEU cc_start: 0.8491 (tp) cc_final: 0.8151 (tt) REVERT: N 574 MET cc_start: 0.4686 (mtm) cc_final: 0.4233 (mmm) REVERT: O 54 ASN cc_start: 0.8833 (t0) cc_final: 0.8585 (t0) REVERT: P 39 TYR cc_start: 0.5826 (m-10) cc_final: 0.5353 (m-10) REVERT: P 265 ASN cc_start: 0.8064 (p0) cc_final: 0.7858 (m-40) REVERT: P 433 GLN cc_start: 0.8522 (tm-30) cc_final: 0.8158 (tm-30) REVERT: P 435 MET cc_start: 0.7748 (mmm) cc_final: 0.7345 (mmt) REVERT: Q 54 ASN cc_start: 0.8601 (t0) cc_final: 0.8203 (t0) REVERT: Q 249 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7871 (mt-10) REVERT: D 85 GLN cc_start: 0.8285 (mm-40) cc_final: 0.7813 (mm-40) REVERT: D 86 ASN cc_start: 0.7396 (t0) cc_final: 0.7048 (t0) REVERT: b 68 LYS cc_start: 0.8778 (mttt) cc_final: 0.8299 (mtpp) REVERT: c 72 MET cc_start: 0.8183 (tpp) cc_final: 0.7804 (tpp) REVERT: c 112 TYR cc_start: 0.9045 (t80) cc_final: 0.8718 (t80) REVERT: d 26 LYS cc_start: 0.7306 (mmtt) cc_final: 0.6919 (mtmt) REVERT: d 39 ASN cc_start: 0.8641 (m-40) cc_final: 0.8349 (m-40) REVERT: d 72 MET cc_start: 0.7460 (mmm) cc_final: 0.6912 (ptt) REVERT: d 77 ASN cc_start: 0.8382 (t0) cc_final: 0.8109 (t0) REVERT: d 125 TYR cc_start: 0.8808 (m-10) cc_final: 0.8526 (m-80) REVERT: e 53 LYS cc_start: 0.6397 (mtpt) cc_final: 0.5981 (ptpp) REVERT: e 80 LYS cc_start: 0.8136 (mtmt) cc_final: 0.7591 (mtpt) REVERT: F 53 ARG cc_start: 0.8131 (ttp-110) cc_final: 0.7888 (mtm110) REVERT: F 82 GLN cc_start: 0.8571 (mm-40) cc_final: 0.8324 (mm110) REVERT: k 78 MET cc_start: 0.7944 (ttp) cc_final: 0.7680 (ttp) REVERT: k 150 LEU cc_start: 0.8615 (tp) cc_final: 0.8256 (tp) REVERT: k 154 ILE cc_start: 0.8337 (mm) cc_final: 0.8106 (mt) REVERT: k 209 CYS cc_start: 0.7812 (m) cc_final: 0.7479 (m) REVERT: m 13 MET cc_start: 0.8164 (mmm) cc_final: 0.7860 (mmt) REVERT: m 27 PHE cc_start: 0.7963 (m-80) cc_final: 0.7671 (m-10) REVERT: m 56 ILE cc_start: 0.9237 (tt) cc_final: 0.9012 (tt) REVERT: n 67 MET cc_start: 0.7489 (ttp) cc_final: 0.7269 (ttp) REVERT: s 398 GLN cc_start: 0.8141 (tt0) cc_final: 0.7866 (tt0) REVERT: s 453 MET cc_start: 0.8219 (pmm) cc_final: 0.7992 (pmm) REVERT: 8 139 GLU cc_start: 0.7820 (tt0) cc_final: 0.7541 (tt0) REVERT: 9 54 LYS cc_start: 0.8184 (pttt) cc_final: 0.7935 (ptpt) REVERT: 9 64 ILE cc_start: 0.8590 (mt) cc_final: 0.8066 (mm) REVERT: 9 68 TYR cc_start: 0.8499 (m-10) cc_final: 0.8245 (m-10) REVERT: 9 134 ILE cc_start: 0.9335 (mm) cc_final: 0.9034 (mm) REVERT: 1 82 LYS cc_start: 0.8597 (mmmm) cc_final: 0.7916 (tppt) REVERT: 1 107 MET cc_start: 0.8357 (mmm) cc_final: 0.8134 (tpt) REVERT: 1 113 ASN cc_start: 0.8047 (m-40) cc_final: 0.7672 (t0) REVERT: 1 114 MET cc_start: 0.8139 (mtt) cc_final: 0.7893 (mpp) REVERT: 1 116 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7906 (mt-10) REVERT: 4 127 LEU cc_start: 0.8877 (tp) cc_final: 0.8656 (tp) REVERT: 4 139 GLU cc_start: 0.8912 (tp30) cc_final: 0.8711 (tp30) REVERT: 5 92 GLN cc_start: 0.9248 (mm-40) cc_final: 0.8983 (mm-40) REVERT: 6 83 ASP cc_start: 0.8062 (p0) cc_final: 0.7263 (p0) REVERT: 6 124 GLN cc_start: 0.8602 (tp-100) cc_final: 0.8342 (tm-30) REVERT: 7 23 MET cc_start: 0.8211 (tpt) cc_final: 0.7883 (tpp) REVERT: 0 54 LYS cc_start: 0.8315 (ttpp) cc_final: 0.7693 (mttt) REVERT: 0 68 TYR cc_start: 0.8452 (m-10) cc_final: 0.8243 (m-10) REVERT: 0 132 ILE cc_start: 0.8989 (mm) cc_final: 0.8761 (mm) outliers start: 18 outliers final: 6 residues processed: 1283 average time/residue: 0.7373 time to fit residues: 1577.2369 Evaluate side-chains 889 residues out of total 7420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 882 time to evaluate : 5.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 870 random chunks: chunk 734 optimal weight: 4.9990 chunk 659 optimal weight: 0.9990 chunk 365 optimal weight: 5.9990 chunk 225 optimal weight: 9.9990 chunk 444 optimal weight: 6.9990 chunk 352 optimal weight: 0.8980 chunk 681 optimal weight: 0.9990 chunk 263 optimal weight: 7.9990 chunk 414 optimal weight: 0.9980 chunk 507 optimal weight: 0.8980 chunk 790 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 282 GLN a 300 GLN ** a 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 435 GLN a 443 ASN a 495 HIS a 516 ASN ** a 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 764 ASN a 768 GLN a 814 GLN U 90 GLN U 97 HIS U 143 HIS U 159 ASN U 380 HIS L 314 ASN L 449 ASN L 468 HIS L 573 HIS M 172 ASN M 261 GLN M 397 ASN M 430 GLN M 449 ASN M 484 GLN M 603 GLN N 573 HIS N 603 GLN O 199 HIS O 205 GLN O 251 ASN O 292 HIS O 382 GLN ** O 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 42 GLN ** P 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 421 GLN P 497 GLN Q 181 ASN Q 199 HIS Q 209 GLN Q 256 ASN Q 292 HIS ** Q 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 421 GLN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 HIS b 21 GLN b 39 ASN b 77 ASN c 66 GLN c 77 ASN c 122 GLN c 161 ASN d 14 HIS d 24 ASN d 126 GLN d 139 GLN d 206 GLN d 221 ASN ** e 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 50 GLN f 35 GLN f 111 HIS f 113 ASN g 85 GLN ** g 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 50 GLN ** k 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 183 ASN m 67 GLN n 103 GLN s 255 HIS s 329 ASN ** s 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 398 GLN s 403 GLN 9 51 GLN 1 128 HIS 1 148 ASN 2 51 GLN 2 123 GLN 6 51 GLN Total number of N/Q/H flips: 74 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 68144 Z= 0.167 Angle : 0.581 9.556 92248 Z= 0.306 Chirality : 0.042 0.423 10616 Planarity : 0.005 0.083 11859 Dihedral : 9.310 174.838 10104 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.21 % Favored : 96.78 % Rotamer: Outliers : 0.03 % Allowed : 3.90 % Favored : 96.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.07 (0.07), residues: 8727 helix: -2.85 (0.06), residues: 4539 sheet: -1.91 (0.17), residues: 799 loop : -2.42 (0.09), residues: 3389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP a 292 HIS 0.005 0.001 HIS d 14 PHE 0.025 0.001 PHE N 547 TYR 0.024 0.001 TYR 1 70 ARG 0.007 0.000 ARG N 552 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1106 residues out of total 7420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1104 time to evaluate : 5.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 236 LYS cc_start: 0.6726 (tptt) cc_final: 0.6259 (tppt) REVERT: a 247 TYR cc_start: 0.3644 (m-80) cc_final: 0.3432 (m-80) REVERT: a 261 GLU cc_start: 0.5767 (pp20) cc_final: 0.5391 (pm20) REVERT: a 266 ARG cc_start: 0.5251 (mtt180) cc_final: 0.4986 (ttt180) REVERT: a 350 MET cc_start: 0.4246 (mtp) cc_final: 0.4034 (mtp) REVERT: a 486 MET cc_start: 0.7622 (mmt) cc_final: 0.7366 (mmt) REVERT: a 728 ILE cc_start: 0.9087 (pt) cc_final: 0.8440 (mt) REVERT: a 732 LEU cc_start: 0.8535 (tp) cc_final: 0.8316 (tt) REVERT: U 150 TRP cc_start: 0.7882 (m100) cc_final: 0.7540 (m100) REVERT: U 253 TYR cc_start: 0.8345 (t80) cc_final: 0.7975 (t80) REVERT: U 333 MET cc_start: 0.7572 (mtt) cc_final: 0.7343 (mtt) REVERT: U 424 LYS cc_start: 0.5682 (tttt) cc_final: 0.5227 (mtpt) REVERT: L 303 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7404 (mp0) REVERT: L 574 MET cc_start: 0.5416 (mtt) cc_final: 0.5135 (mtp) REVERT: L 577 ILE cc_start: 0.7522 (mm) cc_final: 0.7263 (tp) REVERT: L 597 ILE cc_start: 0.9042 (mt) cc_final: 0.8815 (tt) REVERT: M 196 PHE cc_start: 0.6183 (t80) cc_final: 0.5880 (t80) REVERT: M 613 ARG cc_start: 0.7063 (mtm180) cc_final: 0.5776 (tpm170) REVERT: N 114 GLN cc_start: 0.8236 (mm-40) cc_final: 0.8016 (tp-100) REVERT: N 405 SER cc_start: 0.9499 (m) cc_final: 0.9161 (t) REVERT: N 506 LYS cc_start: 0.4963 (mttt) cc_final: 0.4572 (mttt) REVERT: N 553 ARG cc_start: 0.7036 (ttp80) cc_final: 0.6811 (ptt90) REVERT: N 574 MET cc_start: 0.4519 (mtm) cc_final: 0.4199 (mmm) REVERT: O 54 ASN cc_start: 0.8658 (t0) cc_final: 0.8449 (t0) REVERT: P 433 GLN cc_start: 0.8336 (tm-30) cc_final: 0.8062 (tm-30) REVERT: P 435 MET cc_start: 0.7635 (mmm) cc_final: 0.7424 (mmt) REVERT: Q 54 ASN cc_start: 0.8456 (t0) cc_final: 0.8118 (t0) REVERT: Q 249 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7819 (mt-10) REVERT: D 85 GLN cc_start: 0.8225 (mm-40) cc_final: 0.7742 (mm-40) REVERT: D 86 ASN cc_start: 0.7232 (t0) cc_final: 0.6987 (t0) REVERT: b 68 LYS cc_start: 0.8856 (mttt) cc_final: 0.8336 (mtpp) REVERT: c 40 ILE cc_start: 0.8011 (mm) cc_final: 0.7713 (mm) REVERT: c 72 MET cc_start: 0.8238 (tpp) cc_final: 0.7792 (tpp) REVERT: d 26 LYS cc_start: 0.7369 (mmtt) cc_final: 0.7005 (mttp) REVERT: d 55 GLU cc_start: 0.6689 (tp30) cc_final: 0.6338 (mm-30) REVERT: d 72 MET cc_start: 0.7491 (mmm) cc_final: 0.7018 (ptt) REVERT: e 80 LYS cc_start: 0.7954 (mtmt) cc_final: 0.7704 (mtpt) REVERT: k 120 ARG cc_start: 0.7780 (tpp80) cc_final: 0.7283 (ttm110) REVERT: k 150 LEU cc_start: 0.8513 (tp) cc_final: 0.7997 (tp) REVERT: k 154 ILE cc_start: 0.8271 (mm) cc_final: 0.7926 (mt) REVERT: k 209 CYS cc_start: 0.7793 (m) cc_final: 0.7478 (m) REVERT: m 23 LEU cc_start: 0.7999 (mp) cc_final: 0.7602 (tp) REVERT: m 46 VAL cc_start: 0.9359 (p) cc_final: 0.9131 (t) REVERT: m 56 ILE cc_start: 0.9175 (tt) cc_final: 0.8892 (tt) REVERT: s 398 GLN cc_start: 0.7759 (tt0) cc_final: 0.7424 (tt0) REVERT: s 453 MET cc_start: 0.8200 (pmm) cc_final: 0.7745 (ptp) REVERT: 8 144 TYR cc_start: 0.8775 (m-10) cc_final: 0.8562 (m-10) REVERT: 9 54 LYS cc_start: 0.8222 (pttt) cc_final: 0.8022 (pttt) REVERT: 1 36 ASP cc_start: 0.8703 (t0) cc_final: 0.8503 (t0) REVERT: 1 82 LYS cc_start: 0.8566 (mmmm) cc_final: 0.8064 (tppt) REVERT: 1 113 ASN cc_start: 0.7764 (m-40) cc_final: 0.7411 (t0) REVERT: 1 116 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7962 (mt-10) REVERT: 4 23 MET cc_start: 0.8624 (tpt) cc_final: 0.8336 (tpp) REVERT: 4 44 MET cc_start: 0.8085 (ppp) cc_final: 0.7871 (tmm) REVERT: 4 139 GLU cc_start: 0.8940 (tp30) cc_final: 0.8723 (tp30) REVERT: 5 61 MET cc_start: 0.8043 (ttm) cc_final: 0.7174 (ttm) REVERT: 5 84 ILE cc_start: 0.9034 (mm) cc_final: 0.8700 (mt) REVERT: 5 139 GLU cc_start: 0.8262 (tp30) cc_final: 0.8036 (tp30) REVERT: 6 83 ASP cc_start: 0.7981 (p0) cc_final: 0.7114 (p0) REVERT: 6 139 GLU cc_start: 0.8654 (tp30) cc_final: 0.8387 (mm-30) REVERT: 7 84 ILE cc_start: 0.8499 (mt) cc_final: 0.8201 (mt) REVERT: 0 54 LYS cc_start: 0.8148 (ttpp) cc_final: 0.7762 (tttt) REVERT: 0 57 ILE cc_start: 0.9097 (mp) cc_final: 0.8675 (mp) outliers start: 2 outliers final: 0 residues processed: 1106 average time/residue: 0.6423 time to fit residues: 1212.0550 Evaluate side-chains 870 residues out of total 7420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 870 time to evaluate : 5.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 870 random chunks: chunk 439 optimal weight: 8.9990 chunk 245 optimal weight: 7.9990 chunk 657 optimal weight: 10.0000 chunk 537 optimal weight: 20.0000 chunk 217 optimal weight: 8.9990 chunk 791 optimal weight: 1.9990 chunk 855 optimal weight: 10.0000 chunk 704 optimal weight: 6.9990 chunk 784 optimal weight: 2.9990 chunk 269 optimal weight: 5.9990 chunk 634 optimal weight: 40.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 495 HIS ** a 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 737 ASN U 97 HIS U 264 HIS L 207 GLN L 449 ASN L 573 HIS ** L 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 65 GLN M 468 HIS ** O 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 HIS Q 350 GLN ** Q 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 421 GLN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN D 206 GLN b 14 HIS ** c 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 49 GLN d 139 GLN d 161 ASN ** f 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 35 GLN ** g 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 HIS k 84 HIS ** k 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 67 GLN ** s 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 123 GLN 6 124 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 68144 Z= 0.422 Angle : 0.677 10.733 92248 Z= 0.349 Chirality : 0.047 0.412 10616 Planarity : 0.005 0.082 11859 Dihedral : 9.111 158.250 10104 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.07 % Allowed : 5.02 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.08), residues: 8727 helix: -1.94 (0.07), residues: 4555 sheet: -1.74 (0.17), residues: 770 loop : -2.24 (0.10), residues: 3402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 450 HIS 0.008 0.001 HIS Q 415 PHE 0.027 0.002 PHE c 18 TYR 0.032 0.002 TYR O 371 ARG 0.024 0.001 ARG 5 119 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1003 residues out of total 7420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 998 time to evaluate : 6.038 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: a 236 LYS cc_start: 0.6769 (tptt) cc_final: 0.6245 (tppt) REVERT: a 247 TYR cc_start: 0.3849 (m-80) cc_final: 0.3592 (m-80) REVERT: a 266 ARG cc_start: 0.5315 (mtt180) cc_final: 0.4958 (ttt180) REVERT: a 728 ILE cc_start: 0.9096 (pt) cc_final: 0.8447 (mt) REVERT: a 732 LEU cc_start: 0.8480 (tp) cc_final: 0.8238 (tt) REVERT: a 821 ASP cc_start: 0.7631 (m-30) cc_final: 0.7340 (m-30) REVERT: U 97 HIS cc_start: 0.2043 (OUTLIER) cc_final: 0.1675 (m-70) REVERT: U 113 MET cc_start: 0.6972 (mtp) cc_final: 0.6450 (ttp) REVERT: U 253 TYR cc_start: 0.8500 (t80) cc_final: 0.8121 (t80) REVERT: U 333 MET cc_start: 0.7665 (mtt) cc_final: 0.7399 (mtt) REVERT: U 424 LYS cc_start: 0.5746 (tttt) cc_final: 0.5281 (mtpt) REVERT: L 95 MET cc_start: 0.8979 (mmt) cc_final: 0.8578 (mmt) REVERT: L 131 ILE cc_start: 0.9033 (mm) cc_final: 0.8727 (mm) REVERT: L 178 TYR cc_start: 0.8009 (t80) cc_final: 0.7754 (t80) REVERT: L 574 MET cc_start: 0.5754 (mtt) cc_final: 0.5472 (mtp) REVERT: M 488 ASP cc_start: 0.7638 (m-30) cc_final: 0.7304 (m-30) REVERT: M 613 ARG cc_start: 0.7095 (mtm180) cc_final: 0.5989 (tpm170) REVERT: N 405 SER cc_start: 0.9527 (m) cc_final: 0.9201 (t) REVERT: N 481 GLU cc_start: 0.7774 (tp30) cc_final: 0.7417 (tp30) REVERT: N 506 LYS cc_start: 0.5068 (mttt) cc_final: 0.4725 (mttt) REVERT: N 535 TYR cc_start: 0.7611 (p90) cc_final: 0.7321 (p90) REVERT: N 552 ARG cc_start: 0.7752 (tpp-160) cc_final: 0.7528 (tpp-160) REVERT: N 574 MET cc_start: 0.4461 (mtm) cc_final: 0.3874 (mmp) REVERT: Q 54 ASN cc_start: 0.8586 (t0) cc_final: 0.8183 (t0) REVERT: Q 321 ARG cc_start: 0.8098 (mtt180) cc_final: 0.7855 (mtp85) REVERT: D 86 ASN cc_start: 0.7459 (t0) cc_final: 0.7156 (t0) REVERT: b 54 MET cc_start: 0.7020 (ttt) cc_final: 0.6814 (ttt) REVERT: b 68 LYS cc_start: 0.8828 (mttt) cc_final: 0.8356 (mtpp) REVERT: d 26 LYS cc_start: 0.7680 (mmtt) cc_final: 0.7106 (mtmt) REVERT: d 44 ARG cc_start: 0.7218 (ttp-170) cc_final: 0.7016 (tmm160) REVERT: d 53 ILE cc_start: 0.8427 (pt) cc_final: 0.8059 (mt) REVERT: d 72 MET cc_start: 0.7778 (mmm) cc_final: 0.7274 (ptt) REVERT: e 10 GLN cc_start: 0.7963 (mm110) cc_final: 0.7732 (tp40) REVERT: e 80 LYS cc_start: 0.8034 (mtmt) cc_final: 0.7674 (mtpt) REVERT: k 150 LEU cc_start: 0.8603 (tp) cc_final: 0.8254 (tp) REVERT: k 209 CYS cc_start: 0.8023 (m) cc_final: 0.7555 (m) REVERT: m 27 PHE cc_start: 0.7993 (m-80) cc_final: 0.7738 (m-10) REVERT: m 56 ILE cc_start: 0.9228 (tt) cc_final: 0.8952 (tt) REVERT: s 360 GLN cc_start: 0.8133 (mp10) cc_final: 0.7679 (mp10) REVERT: s 398 GLN cc_start: 0.7882 (tt0) cc_final: 0.7650 (tt0) REVERT: s 399 ASP cc_start: 0.8628 (m-30) cc_final: 0.8387 (m-30) REVERT: s 453 MET cc_start: 0.8251 (pmm) cc_final: 0.7582 (ptp) REVERT: 1 82 LYS cc_start: 0.8537 (mmmm) cc_final: 0.7998 (tppt) REVERT: 1 113 ASN cc_start: 0.7712 (m-40) cc_final: 0.7500 (t0) REVERT: 1 116 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8042 (mt-10) REVERT: 4 23 MET cc_start: 0.8612 (tpt) cc_final: 0.8180 (tpp) REVERT: 5 61 MET cc_start: 0.8259 (ttm) cc_final: 0.8019 (ttm) REVERT: 6 83 ASP cc_start: 0.8082 (p0) cc_final: 0.7193 (p0) REVERT: 0 132 ILE cc_start: 0.8803 (mm) cc_final: 0.8520 (mm) outliers start: 5 outliers final: 1 residues processed: 1000 average time/residue: 0.6454 time to fit residues: 1094.7112 Evaluate side-chains 824 residues out of total 7420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 822 time to evaluate : 5.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 870 random chunks: chunk 781 optimal weight: 2.9990 chunk 595 optimal weight: 9.9990 chunk 410 optimal weight: 7.9990 chunk 87 optimal weight: 20.0000 chunk 377 optimal weight: 5.9990 chunk 531 optimal weight: 7.9990 chunk 794 optimal weight: 0.9980 chunk 840 optimal weight: 0.9990 chunk 414 optimal weight: 1.9990 chunk 752 optimal weight: 5.9990 chunk 226 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 640 GLN U 97 HIS U 277 HIS L 314 ASN L 573 HIS M 172 ASN ** N 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 205 GLN ** Q 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 421 GLN D 46 GLN D 113 HIS D 206 GLN b 11 GLN b 14 HIS ** c 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 206 GLN d 39 ASN d 139 GLN d 161 ASN ** f 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 ASN k 84 HIS ** k 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 67 GLN s 370 HIS 6 124 GLN 0 123 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 68144 Z= 0.170 Angle : 0.531 9.086 92248 Z= 0.274 Chirality : 0.042 0.442 10616 Planarity : 0.004 0.081 11859 Dihedral : 8.399 147.053 10104 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.03 % Allowed : 2.93 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.08), residues: 8727 helix: -1.24 (0.07), residues: 4535 sheet: -1.50 (0.18), residues: 773 loop : -1.99 (0.10), residues: 3419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 481 HIS 0.010 0.001 HIS b 14 PHE 0.026 0.001 PHE c 18 TYR 0.021 0.001 TYR L 535 ARG 0.005 0.000 ARG P 400 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1062 residues out of total 7420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1060 time to evaluate : 6.046 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: a 236 LYS cc_start: 0.6757 (tptt) cc_final: 0.6214 (tppt) REVERT: a 247 TYR cc_start: 0.3785 (m-80) cc_final: 0.3538 (m-80) REVERT: a 266 ARG cc_start: 0.5334 (mtt180) cc_final: 0.5026 (ttt180) REVERT: a 350 MET cc_start: 0.4810 (mmm) cc_final: 0.4443 (mmt) REVERT: a 451 LEU cc_start: 0.8204 (tt) cc_final: 0.7409 (tt) REVERT: a 486 MET cc_start: 0.8003 (mmt) cc_final: 0.7476 (mmt) REVERT: a 728 ILE cc_start: 0.9002 (pt) cc_final: 0.8482 (mt) REVERT: a 732 LEU cc_start: 0.8404 (tp) cc_final: 0.8135 (tt) REVERT: U 19 GLU cc_start: 0.5784 (tp30) cc_final: 0.5470 (tp30) REVERT: U 333 MET cc_start: 0.7561 (mtt) cc_final: 0.7303 (mtt) REVERT: U 424 LYS cc_start: 0.5641 (tttt) cc_final: 0.5209 (mtpt) REVERT: L 131 ILE cc_start: 0.9039 (mm) cc_final: 0.8832 (mm) REVERT: L 574 MET cc_start: 0.5630 (mtt) cc_final: 0.5384 (mtp) REVERT: M 488 ASP cc_start: 0.7535 (m-30) cc_final: 0.7208 (m-30) REVERT: M 574 MET cc_start: 0.7965 (mmt) cc_final: 0.7031 (mmt) REVERT: M 610 ASN cc_start: 0.8664 (m-40) cc_final: 0.8222 (m-40) REVERT: M 613 ARG cc_start: 0.6989 (mtm180) cc_final: 0.5974 (tpm170) REVERT: N 114 GLN cc_start: 0.8258 (mm-40) cc_final: 0.8017 (tp-100) REVERT: N 306 MET cc_start: 0.8245 (mmm) cc_final: 0.7542 (tpp) REVERT: N 405 SER cc_start: 0.9531 (m) cc_final: 0.9171 (t) REVERT: N 506 LYS cc_start: 0.5075 (mttt) cc_final: 0.4682 (mttt) REVERT: N 552 ARG cc_start: 0.7756 (tpp-160) cc_final: 0.7517 (tpp-160) REVERT: N 574 MET cc_start: 0.4588 (mtm) cc_final: 0.4229 (mmp) REVERT: O 135 SER cc_start: 0.8474 (p) cc_final: 0.7658 (t) REVERT: O 164 ILE cc_start: 0.8676 (mt) cc_final: 0.8313 (mm) REVERT: Q 54 ASN cc_start: 0.8387 (t0) cc_final: 0.8099 (t0) REVERT: Q 249 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7809 (mt-10) REVERT: D 86 ASN cc_start: 0.7330 (t0) cc_final: 0.7007 (t0) REVERT: b 68 LYS cc_start: 0.8791 (mttt) cc_final: 0.8309 (mtpp) REVERT: b 159 THR cc_start: 0.8937 (p) cc_final: 0.8506 (p) REVERT: b 161 ASN cc_start: 0.7376 (m110) cc_final: 0.7078 (m110) REVERT: c 66 GLN cc_start: 0.7810 (tt0) cc_final: 0.7474 (tt0) REVERT: c 72 MET cc_start: 0.8353 (tpp) cc_final: 0.7774 (tpp) REVERT: d 26 LYS cc_start: 0.7722 (mmtt) cc_final: 0.7061 (mttp) REVERT: d 53 ILE cc_start: 0.8402 (pt) cc_final: 0.8058 (mt) REVERT: d 72 MET cc_start: 0.7901 (mmm) cc_final: 0.7406 (ptt) REVERT: e 10 GLN cc_start: 0.8008 (mm110) cc_final: 0.7788 (tp40) REVERT: F 75 ARG cc_start: 0.6951 (tpt-90) cc_final: 0.6578 (tpt-90) REVERT: k 298 GLU cc_start: 0.6445 (tt0) cc_final: 0.6173 (tp30) REVERT: m 23 LEU cc_start: 0.8034 (mp) cc_final: 0.7677 (tp) REVERT: s 360 GLN cc_start: 0.8067 (mp10) cc_final: 0.7696 (mp10) REVERT: 1 82 LYS cc_start: 0.8559 (mmmm) cc_final: 0.7999 (tppt) REVERT: 1 113 ASN cc_start: 0.7703 (m-40) cc_final: 0.7377 (t0) REVERT: 1 116 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7966 (mt-10) REVERT: 1 197 GLN cc_start: 0.8397 (mt0) cc_final: 0.8031 (mt0) REVERT: 4 23 MET cc_start: 0.8558 (tpt) cc_final: 0.8129 (tpp) REVERT: 4 81 ASN cc_start: 0.7294 (t0) cc_final: 0.7046 (t0) REVERT: 5 83 ASP cc_start: 0.7019 (m-30) cc_final: 0.6802 (p0) REVERT: 6 48 ARG cc_start: 0.7578 (mtp-110) cc_final: 0.6823 (mtp-110) REVERT: 6 83 ASP cc_start: 0.8008 (p0) cc_final: 0.7049 (p0) REVERT: 0 23 MET cc_start: 0.8046 (tpt) cc_final: 0.7778 (tpt) REVERT: 0 57 ILE cc_start: 0.9192 (mp) cc_final: 0.8585 (mp) REVERT: 0 132 ILE cc_start: 0.8839 (mm) cc_final: 0.8426 (mm) outliers start: 2 outliers final: 0 residues processed: 1061 average time/residue: 0.6257 time to fit residues: 1145.2890 Evaluate side-chains 838 residues out of total 7420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 838 time to evaluate : 5.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 870 random chunks: chunk 700 optimal weight: 10.0000 chunk 477 optimal weight: 10.0000 chunk 12 optimal weight: 30.0000 chunk 626 optimal weight: 30.0000 chunk 346 optimal weight: 6.9990 chunk 717 optimal weight: 10.0000 chunk 581 optimal weight: 0.0050 chunk 0 optimal weight: 10.0000 chunk 429 optimal weight: 9.9990 chunk 754 optimal weight: 5.9990 chunk 212 optimal weight: 8.9990 overall best weight: 6.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 135 GLN ** a 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 318 GLN a 367 ASN a 737 ASN a 768 GLN U 434 GLN ** L 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 573 HIS M 65 GLN ** N 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 256 ASN P 387 GLN P 421 GLN ** Q 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 421 GLN D 46 GLN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 39 ASN d 63 GLN d 139 GLN d 161 ASN ** f 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 HIS F 67 ASN k 119 GLN ** k 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 346 ASN m 67 GLN ** s 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 401 GLN ** 6 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 123 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.118 68144 Z= 0.515 Angle : 0.736 11.387 92248 Z= 0.376 Chirality : 0.050 0.612 10616 Planarity : 0.005 0.086 11859 Dihedral : 8.813 167.701 10104 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.04 % Allowed : 4.29 % Favored : 95.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.08), residues: 8727 helix: -1.29 (0.07), residues: 4550 sheet: -1.58 (0.18), residues: 768 loop : -2.10 (0.10), residues: 3409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP P 481 HIS 0.010 0.001 HIS N 444 PHE 0.038 0.002 PHE n 109 TYR 0.028 0.002 TYR 1 70 ARG 0.009 0.001 ARG 5 119 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 968 residues out of total 7420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 965 time to evaluate : 6.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 247 TYR cc_start: 0.4043 (m-80) cc_final: 0.3830 (m-80) REVERT: a 259 MET cc_start: 0.3551 (ttt) cc_final: 0.3272 (ttp) REVERT: a 266 ARG cc_start: 0.5459 (mtt180) cc_final: 0.5014 (ttt180) REVERT: a 728 ILE cc_start: 0.9083 (pt) cc_final: 0.8423 (mt) REVERT: a 732 LEU cc_start: 0.8479 (tp) cc_final: 0.8227 (tt) REVERT: U 333 MET cc_start: 0.7690 (mtt) cc_final: 0.7416 (mtt) REVERT: U 424 LYS cc_start: 0.5759 (tttt) cc_final: 0.5276 (mtpt) REVERT: L 95 MET cc_start: 0.9018 (mmt) cc_final: 0.8563 (mmt) REVERT: L 131 ILE cc_start: 0.9115 (mm) cc_final: 0.8836 (mm) REVERT: L 178 TYR cc_start: 0.7964 (t80) cc_final: 0.7593 (t80) REVERT: L 544 MET cc_start: 0.7838 (mmm) cc_final: 0.7441 (mmm) REVERT: L 574 MET cc_start: 0.5726 (mtt) cc_final: 0.5353 (mtp) REVERT: L 577 ILE cc_start: 0.7645 (mm) cc_final: 0.7417 (tp) REVERT: L 584 MET cc_start: 0.8395 (mtm) cc_final: 0.8192 (mtm) REVERT: M 443 LYS cc_start: 0.7354 (pttm) cc_final: 0.6882 (pptt) REVERT: M 488 ASP cc_start: 0.7439 (m-30) cc_final: 0.7158 (m-30) REVERT: M 574 MET cc_start: 0.7790 (mmt) cc_final: 0.6818 (mmt) REVERT: M 588 ASP cc_start: 0.8389 (t70) cc_final: 0.8090 (t0) REVERT: N 405 SER cc_start: 0.9543 (m) cc_final: 0.9183 (t) REVERT: N 481 GLU cc_start: 0.7689 (tp30) cc_final: 0.7325 (tp30) REVERT: N 506 LYS cc_start: 0.5085 (mttt) cc_final: 0.4720 (mtmt) REVERT: N 507 ILE cc_start: 0.5171 (mt) cc_final: 0.4946 (mt) REVERT: N 573 HIS cc_start: 0.5649 (t-170) cc_final: 0.5405 (t-170) REVERT: Q 54 ASN cc_start: 0.8525 (t0) cc_final: 0.8240 (t0) REVERT: D 86 ASN cc_start: 0.7653 (t0) cc_final: 0.7325 (t0) REVERT: b 68 LYS cc_start: 0.8745 (mttt) cc_final: 0.8319 (mtpp) REVERT: b 159 THR cc_start: 0.8885 (p) cc_final: 0.8471 (p) REVERT: b 161 ASN cc_start: 0.7428 (m110) cc_final: 0.7053 (m110) REVERT: d 26 LYS cc_start: 0.7869 (mmtt) cc_final: 0.7099 (mtmt) REVERT: d 53 ILE cc_start: 0.8523 (pt) cc_final: 0.8161 (mt) REVERT: d 72 MET cc_start: 0.7970 (mmm) cc_final: 0.7447 (ptt) REVERT: e 9 GLN cc_start: 0.7831 (mp-120) cc_final: 0.7359 (mp10) REVERT: e 13 GLN cc_start: 0.6688 (pt0) cc_final: 0.6330 (pt0) REVERT: e 79 GLU cc_start: 0.8170 (pp20) cc_final: 0.7967 (pp20) REVERT: g 93 ASP cc_start: 0.7589 (p0) cc_final: 0.7352 (p0) REVERT: F 47 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7556 (mm-30) REVERT: F 102 LYS cc_start: 0.7866 (ttmt) cc_final: 0.7595 (ttmm) REVERT: m 27 PHE cc_start: 0.8054 (m-80) cc_final: 0.7780 (m-10) REVERT: s 360 GLN cc_start: 0.8128 (mp10) cc_final: 0.7586 (mp10) REVERT: s 395 MET cc_start: 0.8268 (mtp) cc_final: 0.7824 (mtt) REVERT: s 399 ASP cc_start: 0.8632 (m-30) cc_final: 0.8401 (m-30) REVERT: 1 30 ASP cc_start: 0.7590 (t0) cc_final: 0.7277 (t0) REVERT: 1 36 ASP cc_start: 0.8867 (t0) cc_final: 0.8659 (t0) REVERT: 1 82 LYS cc_start: 0.8542 (mmmm) cc_final: 0.8038 (tppt) REVERT: 1 113 ASN cc_start: 0.7812 (m-40) cc_final: 0.7527 (t0) REVERT: 1 116 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8106 (mt-10) REVERT: 1 197 GLN cc_start: 0.8527 (mt0) cc_final: 0.8255 (mt0) REVERT: 4 23 MET cc_start: 0.8503 (tpt) cc_final: 0.8132 (tpp) REVERT: 6 83 ASP cc_start: 0.8077 (p0) cc_final: 0.7100 (p0) outliers start: 3 outliers final: 1 residues processed: 965 average time/residue: 0.6476 time to fit residues: 1062.5943 Evaluate side-chains 792 residues out of total 7420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 791 time to evaluate : 5.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 870 random chunks: chunk 282 optimal weight: 4.9990 chunk 757 optimal weight: 9.9990 chunk 166 optimal weight: 6.9990 chunk 493 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 841 optimal weight: 0.9980 chunk 698 optimal weight: 0.5980 chunk 389 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 278 optimal weight: 4.9990 chunk 441 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 310 ASN a 318 GLN a 443 ASN ** a 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 302 HIS L 449 ASN L 573 HIS ** N 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 205 GLN P 209 GLN P 251 ASN P 421 GLN ** Q 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 421 GLN D 46 GLN ** c 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 139 GLN d 161 ASN ** e 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 145 GLN ** k 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 67 GLN 6 124 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 68144 Z= 0.205 Angle : 0.551 9.688 92248 Z= 0.284 Chirality : 0.043 0.383 10616 Planarity : 0.004 0.092 11859 Dihedral : 8.246 155.630 10104 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.09), residues: 8727 helix: -0.81 (0.08), residues: 4562 sheet: -1.44 (0.18), residues: 751 loop : -1.94 (0.10), residues: 3414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP L 450 HIS 0.012 0.001 HIS a 293 PHE 0.014 0.001 PHE Q 454 TYR 0.021 0.001 TYR L 535 ARG 0.006 0.000 ARG 6 48 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 995 residues out of total 7420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 995 time to evaluate : 6.263 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: a 266 ARG cc_start: 0.5418 (mtt180) cc_final: 0.5016 (ttt180) REVERT: a 367 ASN cc_start: 0.7807 (m110) cc_final: 0.7528 (m-40) REVERT: a 728 ILE cc_start: 0.8997 (pt) cc_final: 0.8484 (mt) REVERT: a 732 LEU cc_start: 0.8434 (tp) cc_final: 0.8170 (tt) REVERT: U 173 MET cc_start: 0.7239 (mmt) cc_final: 0.6636 (tpp) REVERT: U 253 TYR cc_start: 0.8458 (t80) cc_final: 0.8039 (t80) REVERT: U 333 MET cc_start: 0.7609 (mtt) cc_final: 0.7299 (mtt) REVERT: U 345 TYR cc_start: 0.8713 (m-80) cc_final: 0.8452 (m-80) REVERT: L 131 ILE cc_start: 0.9100 (mm) cc_final: 0.8850 (mm) REVERT: L 574 MET cc_start: 0.5362 (mtt) cc_final: 0.5074 (mtp) REVERT: M 488 ASP cc_start: 0.7573 (m-30) cc_final: 0.7117 (m-30) REVERT: M 574 MET cc_start: 0.7863 (mmt) cc_final: 0.7035 (mmt) REVERT: M 588 ASP cc_start: 0.8368 (t70) cc_final: 0.8117 (t0) REVERT: M 613 ARG cc_start: 0.7188 (ttm110) cc_final: 0.6370 (tpm170) REVERT: N 405 SER cc_start: 0.9535 (m) cc_final: 0.9146 (t) REVERT: N 506 LYS cc_start: 0.5057 (mttt) cc_final: 0.4804 (mtmt) REVERT: N 574 MET cc_start: 0.5010 (mmm) cc_final: 0.4763 (mmm) REVERT: O 135 SER cc_start: 0.8369 (p) cc_final: 0.7543 (t) REVERT: O 433 GLN cc_start: 0.8042 (tp-100) cc_final: 0.7606 (tt0) REVERT: P 433 GLN cc_start: 0.8404 (tm-30) cc_final: 0.8017 (tm-30) REVERT: Q 54 ASN cc_start: 0.8320 (t0) cc_final: 0.8112 (t0) REVERT: D 86 ASN cc_start: 0.7473 (t0) cc_final: 0.7141 (t0) REVERT: b 68 LYS cc_start: 0.8697 (mttt) cc_final: 0.8271 (mtpp) REVERT: b 159 THR cc_start: 0.8908 (p) cc_final: 0.8444 (p) REVERT: b 161 ASN cc_start: 0.7427 (m110) cc_final: 0.7055 (m110) REVERT: c 72 MET cc_start: 0.8373 (tpp) cc_final: 0.7872 (tpp) REVERT: d 26 LYS cc_start: 0.7859 (mmtt) cc_final: 0.7078 (mttp) REVERT: d 53 ILE cc_start: 0.8452 (pt) cc_final: 0.8074 (mt) REVERT: e 10 GLN cc_start: 0.7953 (tp40) cc_final: 0.7004 (tp40) REVERT: g 93 ASP cc_start: 0.7510 (p0) cc_final: 0.7303 (p0) REVERT: F 75 ARG cc_start: 0.6924 (tpt-90) cc_final: 0.6298 (tpt-90) REVERT: F 102 LYS cc_start: 0.7903 (ttmt) cc_final: 0.7658 (ttmm) REVERT: k 60 ASN cc_start: 0.6854 (t0) cc_final: 0.6644 (t0) REVERT: m 23 LEU cc_start: 0.8042 (mp) cc_final: 0.7750 (tp) REVERT: s 360 GLN cc_start: 0.8087 (mp10) cc_final: 0.7622 (mp10) REVERT: s 395 MET cc_start: 0.8190 (mtp) cc_final: 0.7751 (mtt) REVERT: s 399 ASP cc_start: 0.8598 (m-30) cc_final: 0.8350 (m-30) REVERT: 1 30 ASP cc_start: 0.7557 (t0) cc_final: 0.7224 (t0) REVERT: 1 36 ASP cc_start: 0.8732 (t0) cc_final: 0.8447 (t0) REVERT: 1 82 LYS cc_start: 0.8528 (mmmm) cc_final: 0.8139 (tptt) REVERT: 1 113 ASN cc_start: 0.7716 (m-40) cc_final: 0.7463 (t0) REVERT: 1 116 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8006 (mt-10) REVERT: 1 197 GLN cc_start: 0.8409 (mt0) cc_final: 0.8124 (mt0) REVERT: 2 134 ILE cc_start: 0.8984 (mm) cc_final: 0.8766 (mm) REVERT: 4 23 MET cc_start: 0.8471 (tpt) cc_final: 0.8108 (tpp) REVERT: 6 83 ASP cc_start: 0.7968 (p0) cc_final: 0.7047 (p0) outliers start: 0 outliers final: 0 residues processed: 995 average time/residue: 0.6280 time to fit residues: 1072.4421 Evaluate side-chains 813 residues out of total 7420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 813 time to evaluate : 5.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 870 random chunks: chunk 811 optimal weight: 8.9990 chunk 94 optimal weight: 0.9990 chunk 479 optimal weight: 20.0000 chunk 614 optimal weight: 50.0000 chunk 476 optimal weight: 4.9990 chunk 708 optimal weight: 5.9990 chunk 470 optimal weight: 7.9990 chunk 838 optimal weight: 0.6980 chunk 524 optimal weight: 7.9990 chunk 511 optimal weight: 5.9990 chunk 387 optimal weight: 0.8980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 108 GLN ** a 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 318 GLN a 319 GLN a 443 ASN ** a 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 449 ASN ** N 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 573 HIS O 363 HIS ** O 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 205 GLN P 209 GLN ** Q 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 421 GLN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 139 GLN ** e 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 67 GLN ** 6 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 68144 Z= 0.246 Angle : 0.560 9.631 92248 Z= 0.287 Chirality : 0.044 0.558 10616 Planarity : 0.004 0.079 11859 Dihedral : 8.021 152.793 10104 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.01 % Allowed : 1.50 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.09), residues: 8727 helix: -0.53 (0.08), residues: 4511 sheet: -1.41 (0.18), residues: 784 loop : -1.81 (0.10), residues: 3432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP a 190 HIS 0.009 0.001 HIS a 293 PHE 0.027 0.001 PHE k 193 TYR 0.022 0.001 TYR L 535 ARG 0.013 0.000 ARG Q 321 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 977 residues out of total 7420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 976 time to evaluate : 5.953 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: a 182 MET cc_start: 0.5406 (tmm) cc_final: 0.4430 (ppp) REVERT: a 266 ARG cc_start: 0.5422 (mtt180) cc_final: 0.5046 (ttt180) REVERT: a 367 ASN cc_start: 0.7765 (m110) cc_final: 0.7493 (m-40) REVERT: a 728 ILE cc_start: 0.8982 (pt) cc_final: 0.8493 (mt) REVERT: a 732 LEU cc_start: 0.8348 (tp) cc_final: 0.8123 (tt) REVERT: U 333 MET cc_start: 0.7609 (mtt) cc_final: 0.7365 (mtt) REVERT: U 345 TYR cc_start: 0.8718 (m-80) cc_final: 0.8490 (m-80) REVERT: L 95 MET cc_start: 0.8953 (mmt) cc_final: 0.8624 (mmt) REVERT: L 131 ILE cc_start: 0.9093 (mm) cc_final: 0.8839 (mm) REVERT: M 39 MET cc_start: 0.8029 (mmm) cc_final: 0.7748 (mtp) REVERT: M 488 ASP cc_start: 0.7566 (m-30) cc_final: 0.7111 (m-30) REVERT: M 574 MET cc_start: 0.7773 (mmt) cc_final: 0.6929 (mmt) REVERT: M 588 ASP cc_start: 0.8354 (t70) cc_final: 0.8123 (t0) REVERT: M 613 ARG cc_start: 0.7149 (ttm110) cc_final: 0.6574 (tpm170) REVERT: N 405 SER cc_start: 0.9538 (m) cc_final: 0.9122 (t) REVERT: N 506 LYS cc_start: 0.5175 (mttt) cc_final: 0.4881 (mtmt) REVERT: N 565 ILE cc_start: 0.5627 (pt) cc_final: 0.5352 (pt) REVERT: O 135 SER cc_start: 0.8336 (p) cc_final: 0.7546 (t) REVERT: O 433 GLN cc_start: 0.8084 (tp-100) cc_final: 0.7653 (tt0) REVERT: P 433 GLN cc_start: 0.8421 (tm-30) cc_final: 0.8021 (tm-30) REVERT: Q 54 ASN cc_start: 0.8378 (t0) cc_final: 0.8113 (t0) REVERT: D 86 ASN cc_start: 0.7503 (t0) cc_final: 0.7181 (t0) REVERT: b 68 LYS cc_start: 0.8701 (mttt) cc_final: 0.8266 (mtpp) REVERT: b 159 THR cc_start: 0.8927 (p) cc_final: 0.8459 (p) REVERT: b 161 ASN cc_start: 0.7476 (m110) cc_final: 0.7126 (m110) REVERT: d 53 ILE cc_start: 0.8453 (pt) cc_final: 0.8065 (mt) REVERT: e 13 GLN cc_start: 0.6626 (pt0) cc_final: 0.6112 (pt0) REVERT: g 93 ASP cc_start: 0.7594 (p0) cc_final: 0.7330 (p0) REVERT: m 23 LEU cc_start: 0.8040 (mp) cc_final: 0.7745 (tp) REVERT: m 56 ILE cc_start: 0.9165 (tt) cc_final: 0.8958 (tt) REVERT: s 360 GLN cc_start: 0.8089 (mp10) cc_final: 0.7691 (mp10) REVERT: 1 30 ASP cc_start: 0.7610 (t0) cc_final: 0.7276 (t0) REVERT: 1 36 ASP cc_start: 0.8765 (t0) cc_final: 0.8448 (t0) REVERT: 1 82 LYS cc_start: 0.8521 (mmmm) cc_final: 0.7992 (tppt) REVERT: 1 113 ASN cc_start: 0.7722 (m-40) cc_final: 0.7462 (t0) REVERT: 1 116 GLU cc_start: 0.8325 (mt-10) cc_final: 0.8026 (mt-10) REVERT: 1 197 GLN cc_start: 0.8391 (mt0) cc_final: 0.8105 (mt0) REVERT: 2 134 ILE cc_start: 0.9019 (mm) cc_final: 0.8799 (mm) REVERT: 4 23 MET cc_start: 0.8430 (tpt) cc_final: 0.8066 (tpp) REVERT: 5 61 MET cc_start: 0.8309 (ttm) cc_final: 0.7782 (ttm) REVERT: 6 83 ASP cc_start: 0.7992 (p0) cc_final: 0.7061 (p0) outliers start: 1 outliers final: 0 residues processed: 977 average time/residue: 0.6172 time to fit residues: 1036.5288 Evaluate side-chains 813 residues out of total 7420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 813 time to evaluate : 5.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 870 random chunks: chunk 518 optimal weight: 10.0000 chunk 334 optimal weight: 9.9990 chunk 500 optimal weight: 20.0000 chunk 252 optimal weight: 0.9980 chunk 164 optimal weight: 0.4980 chunk 162 optimal weight: 8.9990 chunk 533 optimal weight: 7.9990 chunk 571 optimal weight: 50.0000 chunk 414 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 659 optimal weight: 4.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 318 GLN L 449 ASN L 573 HIS ** N 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 205 GLN P 209 GLN P 421 GLN ** P 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 71 GLN d 139 GLN ** e 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 GLN k 145 GLN ** k 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 67 GLN 6 123 GLN ** 6 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 68144 Z= 0.267 Angle : 0.575 9.761 92248 Z= 0.295 Chirality : 0.044 0.504 10616 Planarity : 0.004 0.078 11859 Dihedral : 7.939 154.679 10104 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.09), residues: 8727 helix: -0.39 (0.08), residues: 4494 sheet: -1.35 (0.18), residues: 789 loop : -1.77 (0.10), residues: 3444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP a 190 HIS 0.016 0.001 HIS N 573 PHE 0.023 0.001 PHE c 18 TYR 0.026 0.001 TYR a 741 ARG 0.007 0.000 ARG 6 48 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 963 residues out of total 7420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 963 time to evaluate : 5.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 182 MET cc_start: 0.5414 (tmm) cc_final: 0.4499 (ppp) REVERT: a 266 ARG cc_start: 0.5510 (mtt180) cc_final: 0.5100 (ttt180) REVERT: a 350 MET cc_start: 0.4142 (mmm) cc_final: 0.3340 (mmt) REVERT: a 367 ASN cc_start: 0.7769 (m110) cc_final: 0.7512 (m-40) REVERT: a 728 ILE cc_start: 0.8953 (pt) cc_final: 0.8493 (mt) REVERT: a 732 LEU cc_start: 0.8400 (tp) cc_final: 0.8082 (tt) REVERT: U 113 MET cc_start: 0.5957 (ttp) cc_final: 0.5710 (ttp) REVERT: U 333 MET cc_start: 0.7665 (mtt) cc_final: 0.7399 (mtt) REVERT: U 345 TYR cc_start: 0.8746 (m-80) cc_final: 0.8507 (m-80) REVERT: L 95 MET cc_start: 0.8977 (mmt) cc_final: 0.8637 (mmt) REVERT: M 205 MET cc_start: 0.8168 (mtm) cc_final: 0.7791 (mtm) REVERT: M 488 ASP cc_start: 0.7561 (m-30) cc_final: 0.7061 (m-30) REVERT: M 574 MET cc_start: 0.7814 (mmt) cc_final: 0.7020 (mmt) REVERT: M 588 ASP cc_start: 0.8372 (t70) cc_final: 0.8119 (t0) REVERT: N 405 SER cc_start: 0.9528 (m) cc_final: 0.9129 (t) REVERT: N 481 GLU cc_start: 0.7596 (tp30) cc_final: 0.7262 (tp30) REVERT: N 506 LYS cc_start: 0.4953 (mttt) cc_final: 0.4659 (mtmt) REVERT: N 507 ILE cc_start: 0.4962 (mt) cc_final: 0.4656 (mt) REVERT: O 135 SER cc_start: 0.8297 (p) cc_final: 0.7498 (t) REVERT: O 164 ILE cc_start: 0.8818 (mt) cc_final: 0.8409 (mm) REVERT: O 433 GLN cc_start: 0.8092 (tp-100) cc_final: 0.7794 (tt0) REVERT: P 250 GLU cc_start: 0.7407 (tt0) cc_final: 0.7199 (tt0) REVERT: P 433 GLN cc_start: 0.8448 (tm-30) cc_final: 0.8052 (tm-30) REVERT: Q 54 ASN cc_start: 0.8385 (t0) cc_final: 0.8110 (t0) REVERT: D 86 ASN cc_start: 0.7581 (t0) cc_final: 0.7206 (t0) REVERT: b 68 LYS cc_start: 0.8697 (mttt) cc_final: 0.8260 (mtpp) REVERT: b 159 THR cc_start: 0.8944 (p) cc_final: 0.8461 (p) REVERT: b 161 ASN cc_start: 0.7483 (m110) cc_final: 0.7157 (m110) REVERT: c 207 MET cc_start: 0.7736 (ttt) cc_final: 0.7491 (ttm) REVERT: d 53 ILE cc_start: 0.8400 (pt) cc_final: 0.8048 (mt) REVERT: e 10 GLN cc_start: 0.7795 (tp40) cc_final: 0.7323 (tp40) REVERT: e 13 GLN cc_start: 0.6585 (pt0) cc_final: 0.6004 (pt0) REVERT: e 81 MET cc_start: 0.8168 (mtm) cc_final: 0.7837 (mtm) REVERT: m 23 LEU cc_start: 0.8035 (mp) cc_final: 0.7751 (tp) REVERT: s 360 GLN cc_start: 0.8082 (mp10) cc_final: 0.7676 (mp10) REVERT: s 395 MET cc_start: 0.8267 (mtp) cc_final: 0.7800 (mtt) REVERT: s 399 ASP cc_start: 0.8485 (m-30) cc_final: 0.8239 (m-30) REVERT: s 436 MET cc_start: 0.8273 (mmm) cc_final: 0.7752 (mtm) REVERT: 8 44 MET cc_start: 0.8151 (tmm) cc_final: 0.7947 (ttp) REVERT: 1 30 ASP cc_start: 0.7651 (t0) cc_final: 0.7317 (t0) REVERT: 1 36 ASP cc_start: 0.8691 (t0) cc_final: 0.8352 (t0) REVERT: 1 82 LYS cc_start: 0.8490 (mmmm) cc_final: 0.7967 (tppt) REVERT: 1 113 ASN cc_start: 0.7728 (m-40) cc_final: 0.7480 (t0) REVERT: 1 116 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8034 (mt-10) REVERT: 4 23 MET cc_start: 0.8407 (tpt) cc_final: 0.8044 (tpp) REVERT: 6 83 ASP cc_start: 0.7992 (p0) cc_final: 0.7078 (p0) REVERT: 0 41 ILE cc_start: 0.9051 (mt) cc_final: 0.8730 (mm) outliers start: 0 outliers final: 0 residues processed: 963 average time/residue: 0.6288 time to fit residues: 1047.6023 Evaluate side-chains 814 residues out of total 7420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 814 time to evaluate : 5.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 870 random chunks: chunk 762 optimal weight: 3.9990 chunk 803 optimal weight: 0.7980 chunk 732 optimal weight: 8.9990 chunk 781 optimal weight: 6.9990 chunk 470 optimal weight: 0.6980 chunk 340 optimal weight: 1.9990 chunk 613 optimal weight: 40.0000 chunk 239 optimal weight: 0.1980 chunk 706 optimal weight: 1.9990 chunk 739 optimal weight: 2.9990 chunk 778 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 443 ASN L 449 ASN L 573 HIS M 65 GLN N 261 GLN N 543 ASN ** O 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 421 GLN ** P 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 421 GLN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 139 GLN ** e 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 145 GLN ** k 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 295 ASN 6 123 GLN 6 124 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 68144 Z= 0.151 Angle : 0.524 9.449 92248 Z= 0.268 Chirality : 0.042 0.358 10616 Planarity : 0.004 0.076 11859 Dihedral : 7.495 141.567 10104 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.01 % Allowed : 0.49 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.09), residues: 8727 helix: -0.07 (0.08), residues: 4492 sheet: -1.24 (0.18), residues: 769 loop : -1.69 (0.10), residues: 3466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP a 190 HIS 0.010 0.001 HIS N 573 PHE 0.026 0.001 PHE a 67 TYR 0.031 0.001 TYR O 371 ARG 0.008 0.000 ARG 6 48 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1024 residues out of total 7420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1023 time to evaluate : 6.089 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: a 182 MET cc_start: 0.5374 (tmm) cc_final: 0.4454 (ppp) REVERT: a 266 ARG cc_start: 0.5439 (mtt180) cc_final: 0.5020 (ttt180) REVERT: a 350 MET cc_start: 0.4021 (mmm) cc_final: 0.3692 (mmt) REVERT: a 367 ASN cc_start: 0.7787 (m110) cc_final: 0.7554 (m-40) REVERT: a 728 ILE cc_start: 0.8900 (pt) cc_final: 0.8494 (mt) REVERT: a 732 LEU cc_start: 0.8348 (tp) cc_final: 0.7984 (tt) REVERT: U 113 MET cc_start: 0.5837 (ttp) cc_final: 0.5564 (ttp) REVERT: U 333 MET cc_start: 0.7586 (mtt) cc_final: 0.7311 (mtt) REVERT: U 345 TYR cc_start: 0.8753 (m-80) cc_final: 0.8504 (m-80) REVERT: L 95 MET cc_start: 0.8933 (mmt) cc_final: 0.8708 (mmt) REVERT: L 306 MET cc_start: 0.8473 (mmm) cc_final: 0.8261 (mmm) REVERT: M 205 MET cc_start: 0.8077 (mtm) cc_final: 0.7671 (mtm) REVERT: M 488 ASP cc_start: 0.7500 (m-30) cc_final: 0.6933 (m-30) REVERT: M 574 MET cc_start: 0.7772 (mmt) cc_final: 0.7062 (mmt) REVERT: M 588 ASP cc_start: 0.8354 (t70) cc_final: 0.8125 (t0) REVERT: N 114 GLN cc_start: 0.8299 (mm-40) cc_final: 0.7985 (tp-100) REVERT: N 356 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6969 (mt-10) REVERT: N 405 SER cc_start: 0.9536 (m) cc_final: 0.9100 (t) REVERT: N 481 GLU cc_start: 0.7597 (tp30) cc_final: 0.7224 (tp30) REVERT: N 506 LYS cc_start: 0.4915 (mttt) cc_final: 0.4710 (mtmt) REVERT: O 135 SER cc_start: 0.8332 (p) cc_final: 0.7582 (t) REVERT: O 164 ILE cc_start: 0.8822 (mt) cc_final: 0.8412 (mm) REVERT: O 433 GLN cc_start: 0.8047 (tp-100) cc_final: 0.7769 (tt0) REVERT: P 433 GLN cc_start: 0.8429 (tm-30) cc_final: 0.8027 (tm-30) REVERT: Q 54 ASN cc_start: 0.8289 (t0) cc_final: 0.8059 (t0) REVERT: D 35 LYS cc_start: 0.8169 (pttt) cc_final: 0.7759 (mttt) REVERT: D 86 ASN cc_start: 0.7425 (t0) cc_final: 0.7062 (t0) REVERT: D 200 TYR cc_start: 0.7251 (t80) cc_final: 0.7047 (t80) REVERT: b 68 LYS cc_start: 0.8665 (mttt) cc_final: 0.8238 (mtpp) REVERT: b 159 THR cc_start: 0.8931 (p) cc_final: 0.8458 (p) REVERT: b 161 ASN cc_start: 0.7467 (m110) cc_final: 0.7158 (m110) REVERT: c 207 MET cc_start: 0.7779 (ttt) cc_final: 0.7543 (ttm) REVERT: d 39 ASN cc_start: 0.8365 (m-40) cc_final: 0.8122 (m-40) REVERT: d 53 ILE cc_start: 0.8343 (pt) cc_final: 0.8013 (mt) REVERT: e 10 GLN cc_start: 0.7805 (tp40) cc_final: 0.7214 (tp40) REVERT: e 13 GLN cc_start: 0.6347 (pt0) cc_final: 0.5639 (pt0) REVERT: e 81 MET cc_start: 0.8059 (mtm) cc_final: 0.7742 (mtm) REVERT: g 47 TYR cc_start: 0.7396 (t80) cc_final: 0.7060 (t80) REVERT: g 93 ASP cc_start: 0.7547 (p0) cc_final: 0.7284 (p0) REVERT: k 298 GLU cc_start: 0.6428 (tt0) cc_final: 0.6156 (tp30) REVERT: s 360 GLN cc_start: 0.8007 (mp10) cc_final: 0.7648 (mp10) REVERT: s 399 ASP cc_start: 0.8482 (m-30) cc_final: 0.8238 (m-30) REVERT: s 436 MET cc_start: 0.8293 (mmm) cc_final: 0.7766 (mtm) REVERT: 1 30 ASP cc_start: 0.7643 (t0) cc_final: 0.7315 (t0) REVERT: 1 82 LYS cc_start: 0.8488 (mmmm) cc_final: 0.8070 (tptt) REVERT: 1 113 ASN cc_start: 0.7657 (m-40) cc_final: 0.7388 (t0) REVERT: 1 116 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7896 (mt-10) REVERT: 1 179 VAL cc_start: 0.9092 (m) cc_final: 0.8703 (p) REVERT: 1 197 GLN cc_start: 0.8308 (mt0) cc_final: 0.7960 (mt0) REVERT: 2 134 ILE cc_start: 0.8972 (mm) cc_final: 0.8770 (mm) REVERT: 4 23 MET cc_start: 0.8413 (tpt) cc_final: 0.8026 (tpp) REVERT: 5 83 ASP cc_start: 0.7027 (m-30) cc_final: 0.6666 (p0) REVERT: 6 83 ASP cc_start: 0.7987 (p0) cc_final: 0.7047 (p0) outliers start: 1 outliers final: 0 residues processed: 1023 average time/residue: 0.6294 time to fit residues: 1101.2142 Evaluate side-chains 832 residues out of total 7420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 832 time to evaluate : 5.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 870 random chunks: chunk 513 optimal weight: 5.9990 chunk 826 optimal weight: 10.0000 chunk 504 optimal weight: 0.9990 chunk 391 optimal weight: 0.6980 chunk 574 optimal weight: 3.9990 chunk 866 optimal weight: 7.9990 chunk 797 optimal weight: 6.9990 chunk 690 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 533 optimal weight: 4.9990 chunk 423 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 443 ASN L 449 ASN L 573 HIS M 65 GLN ** N 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 497 GLN ** Q 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 421 GLN c 113 GLN d 39 ASN d 139 GLN ** e 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 297 HIS 6 123 GLN ** 6 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 68144 Z= 0.195 Angle : 0.538 10.916 92248 Z= 0.274 Chirality : 0.042 0.364 10616 Planarity : 0.004 0.079 11859 Dihedral : 7.384 140.626 10104 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.09), residues: 8727 helix: 0.02 (0.08), residues: 4530 sheet: -1.23 (0.18), residues: 796 loop : -1.63 (0.10), residues: 3401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP a 190 HIS 0.011 0.001 HIS N 573 PHE 0.024 0.001 PHE N 547 TYR 0.024 0.001 TYR L 535 ARG 0.017 0.000 ARG Q 321 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 979 residues out of total 7420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 979 time to evaluate : 5.935 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: a 182 MET cc_start: 0.5430 (tmm) cc_final: 0.4532 (ppp) REVERT: a 266 ARG cc_start: 0.5453 (mtt180) cc_final: 0.4975 (ttt180) REVERT: a 367 ASN cc_start: 0.7767 (m110) cc_final: 0.7510 (m-40) REVERT: a 728 ILE cc_start: 0.8902 (pt) cc_final: 0.8494 (mt) REVERT: a 732 LEU cc_start: 0.8249 (tp) cc_final: 0.7937 (tt) REVERT: U 111 MET cc_start: 0.4259 (mmm) cc_final: 0.3932 (tpt) REVERT: U 113 MET cc_start: 0.5843 (ttp) cc_final: 0.5484 (ttp) REVERT: U 333 MET cc_start: 0.7607 (mtt) cc_final: 0.7327 (mtt) REVERT: U 345 TYR cc_start: 0.8755 (m-80) cc_final: 0.8441 (m-80) REVERT: L 95 MET cc_start: 0.8951 (mmt) cc_final: 0.8661 (mmt) REVERT: L 608 MET cc_start: 0.7312 (tmm) cc_final: 0.7110 (tmm) REVERT: M 39 MET cc_start: 0.7958 (mmm) cc_final: 0.7725 (mtp) REVERT: M 205 MET cc_start: 0.8114 (mtm) cc_final: 0.7697 (mtm) REVERT: M 488 ASP cc_start: 0.7484 (m-30) cc_final: 0.6932 (m-30) REVERT: M 574 MET cc_start: 0.7908 (mmt) cc_final: 0.7160 (mmt) REVERT: M 588 ASP cc_start: 0.8374 (t70) cc_final: 0.8134 (t0) REVERT: N 356 GLU cc_start: 0.7319 (mt-10) cc_final: 0.7116 (mt-10) REVERT: N 405 SER cc_start: 0.9539 (m) cc_final: 0.9094 (t) REVERT: N 481 GLU cc_start: 0.7618 (tp30) cc_final: 0.7251 (tp30) REVERT: N 506 LYS cc_start: 0.4955 (mttt) cc_final: 0.4746 (mtmt) REVERT: O 135 SER cc_start: 0.8301 (p) cc_final: 0.7594 (t) REVERT: O 164 ILE cc_start: 0.8824 (mt) cc_final: 0.8426 (mm) REVERT: O 433 GLN cc_start: 0.8090 (tp-100) cc_final: 0.7789 (tt0) REVERT: P 433 GLN cc_start: 0.8405 (tm-30) cc_final: 0.8040 (tm-30) REVERT: Q 54 ASN cc_start: 0.8329 (t0) cc_final: 0.8074 (t0) REVERT: D 35 LYS cc_start: 0.8171 (pttt) cc_final: 0.7781 (mttt) REVERT: D 86 ASN cc_start: 0.7468 (t0) cc_final: 0.7084 (t0) REVERT: D 200 TYR cc_start: 0.7281 (t80) cc_final: 0.7057 (t80) REVERT: b 68 LYS cc_start: 0.8677 (mttt) cc_final: 0.8248 (mtpp) REVERT: b 159 THR cc_start: 0.8925 (p) cc_final: 0.8475 (p) REVERT: b 161 ASN cc_start: 0.7464 (m110) cc_final: 0.7173 (m110) REVERT: c 207 MET cc_start: 0.7812 (ttt) cc_final: 0.7597 (ttm) REVERT: d 39 ASN cc_start: 0.8488 (m110) cc_final: 0.8101 (m-40) REVERT: d 53 ILE cc_start: 0.8347 (pt) cc_final: 0.8029 (mt) REVERT: e 10 GLN cc_start: 0.7810 (tp40) cc_final: 0.7413 (tp40) REVERT: e 81 MET cc_start: 0.8103 (mtm) cc_final: 0.7770 (mtm) REVERT: e 93 ASP cc_start: 0.6950 (m-30) cc_final: 0.6506 (p0) REVERT: f 46 GLN cc_start: 0.6755 (pt0) cc_final: 0.6149 (tm-30) REVERT: k 298 GLU cc_start: 0.6432 (tt0) cc_final: 0.6159 (tp30) REVERT: s 360 GLN cc_start: 0.8029 (mp10) cc_final: 0.7683 (mp10) REVERT: s 395 MET cc_start: 0.8219 (mtp) cc_final: 0.7764 (mtt) REVERT: s 399 ASP cc_start: 0.8528 (m-30) cc_final: 0.8251 (m-30) REVERT: s 436 MET cc_start: 0.8295 (mmm) cc_final: 0.7770 (mtm) REVERT: 1 30 ASP cc_start: 0.7627 (t0) cc_final: 0.7303 (t0) REVERT: 1 82 LYS cc_start: 0.8458 (mmmm) cc_final: 0.8078 (tptt) REVERT: 1 113 ASN cc_start: 0.7663 (m-40) cc_final: 0.7422 (t0) REVERT: 1 116 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7908 (mt-10) REVERT: 1 179 VAL cc_start: 0.9047 (m) cc_final: 0.8697 (p) REVERT: 2 50 GLU cc_start: 0.7362 (pm20) cc_final: 0.7139 (mp0) REVERT: 4 23 MET cc_start: 0.8393 (tpt) cc_final: 0.8010 (tpp) REVERT: 5 83 ASP cc_start: 0.6948 (m-30) cc_final: 0.6672 (p0) REVERT: 6 83 ASP cc_start: 0.7993 (p0) cc_final: 0.7033 (p0) outliers start: 0 outliers final: 0 residues processed: 979 average time/residue: 0.6348 time to fit residues: 1070.9379 Evaluate side-chains 821 residues out of total 7420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 821 time to evaluate : 5.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 870 random chunks: chunk 548 optimal weight: 8.9990 chunk 735 optimal weight: 4.9990 chunk 211 optimal weight: 2.9990 chunk 636 optimal weight: 40.0000 chunk 101 optimal weight: 10.0000 chunk 191 optimal weight: 10.0000 chunk 691 optimal weight: 6.9990 chunk 289 optimal weight: 10.0000 chunk 709 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 127 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 443 ASN L 172 ASN L 207 GLN L 449 ASN L 573 HIS ** O 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 421 GLN ** P 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 497 GLN Q 181 ASN Q 497 GLN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 122 GLN d 139 GLN ** f 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 HIS k 145 GLN ** k 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 67 GLN ** s 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 295 ASN 6 123 GLN 6 124 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.115799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.090210 restraints weight = 116692.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.089357 restraints weight = 170155.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.090839 restraints weight = 134789.343| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 68144 Z= 0.336 Angle : 0.619 10.149 92248 Z= 0.316 Chirality : 0.046 0.445 10616 Planarity : 0.004 0.078 11859 Dihedral : 7.745 158.463 10104 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.03 % Allowed : 0.37 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.09), residues: 8727 helix: -0.12 (0.08), residues: 4518 sheet: -1.26 (0.18), residues: 777 loop : -1.70 (0.10), residues: 3432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP a 190 HIS 0.011 0.001 HIS N 573 PHE 0.027 0.002 PHE c 38 TYR 0.029 0.002 TYR O 371 ARG 0.013 0.000 ARG f 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16833.07 seconds wall clock time: 294 minutes 42.18 seconds (17682.18 seconds total)