Starting phenix.real_space_refine on Sun Apr 14 08:57:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eza_28732/04_2024/8eza_28732_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eza_28732/04_2024/8eza_28732.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eza_28732/04_2024/8eza_28732.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eza_28732/04_2024/8eza_28732.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eza_28732/04_2024/8eza_28732_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eza_28732/04_2024/8eza_28732_updated.pdb" } resolution = 4.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 128 5.49 5 S 562 5.16 5 C 59453 2.51 5 N 15900 2.21 5 O 17545 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "S ARG 179": "NH1" <-> "NH2" Residue "S PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 35": "NH1" <-> "NH2" Residue "J ARG 80": "NH1" <-> "NH2" Residue "J ARG 115": "NH1" <-> "NH2" Residue "J ARG 130": "NH1" <-> "NH2" Residue "J ARG 165": "NH1" <-> "NH2" Residue "J PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 185": "NH1" <-> "NH2" Residue "J ARG 187": "NH1" <-> "NH2" Residue "J ARG 194": "NH1" <-> "NH2" Residue "J ARG 218": "NH1" <-> "NH2" Residue "J ARG 244": "NH1" <-> "NH2" Residue "J ARG 247": "NH1" <-> "NH2" Residue "J ARG 252": "NH1" <-> "NH2" Residue "J ARG 254": "NH1" <-> "NH2" Residue "J ARG 258": "NH1" <-> "NH2" Residue "J ARG 290": "NH1" <-> "NH2" Residue "J ARG 301": "NH1" <-> "NH2" Residue "J ARG 318": "NH1" <-> "NH2" Residue "J ARG 325": "NH1" <-> "NH2" Residue "J ARG 339": "NH1" <-> "NH2" Residue "J ARG 363": "NH1" <-> "NH2" Residue "J ARG 399": "NH1" <-> "NH2" Residue "J ARG 403": "NH1" <-> "NH2" Residue "J ARG 404": "NH1" <-> "NH2" Residue "J ARG 444": "NH1" <-> "NH2" Residue "J ARG 470": "NH1" <-> "NH2" Residue "J ARG 474": "NH1" <-> "NH2" Residue "J ARG 488": "NH1" <-> "NH2" Residue "J ARG 517": "NH1" <-> "NH2" Residue "J TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 35": "NH1" <-> "NH2" Residue "A ARG 80": "NH1" <-> "NH2" Residue "A ARG 115": "NH1" <-> "NH2" Residue "A ARG 130": "NH1" <-> "NH2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 185": "NH1" <-> "NH2" Residue "A ARG 187": "NH1" <-> "NH2" Residue "A ARG 194": "NH1" <-> "NH2" Residue "A ARG 218": "NH1" <-> "NH2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A ARG 254": "NH1" <-> "NH2" Residue "A ARG 258": "NH1" <-> "NH2" Residue "A ARG 290": "NH1" <-> "NH2" Residue "A ARG 301": "NH1" <-> "NH2" Residue "A ARG 318": "NH1" <-> "NH2" Residue "A ARG 325": "NH1" <-> "NH2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A ARG 399": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A ARG 404": "NH1" <-> "NH2" Residue "A ARG 444": "NH1" <-> "NH2" Residue "A ARG 470": "NH1" <-> "NH2" Residue "A ARG 474": "NH1" <-> "NH2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "A ARG 517": "NH1" <-> "NH2" Residue "A TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 44": "NH1" <-> "NH2" Residue "K ARG 81": "NH1" <-> "NH2" Residue "K ARG 130": "NH1" <-> "NH2" Residue "K ARG 141": "NH1" <-> "NH2" Residue "K ARG 232": "NH1" <-> "NH2" Residue "K ARG 242": "NH1" <-> "NH2" Residue "K ARG 250": "NH1" <-> "NH2" Residue "K ARG 260": "NH1" <-> "NH2" Residue "K ARG 271": "NH1" <-> "NH2" Residue "K ARG 315": "NH1" <-> "NH2" Residue "K ARG 353": "NH1" <-> "NH2" Residue "K ARG 354": "NH1" <-> "NH2" Residue "K ARG 368": "NH1" <-> "NH2" Residue "K ARG 394": "NH1" <-> "NH2" Residue "K ARG 400": "NH1" <-> "NH2" Residue "K ARG 431": "NH1" <-> "NH2" Residue "K ARG 486": "NH1" <-> "NH2" Residue "K ARG 489": "NH1" <-> "NH2" Residue "K ARG 497": "NH1" <-> "NH2" Residue "K ARG 502": "NH1" <-> "NH2" Residue "L ARG 9": "NH1" <-> "NH2" Residue "L ARG 14": "NH1" <-> "NH2" Residue "L ARG 24": "NH1" <-> "NH2" Residue "L ARG 36": "NH1" <-> "NH2" Residue "L ARG 61": "NH1" <-> "NH2" Residue "L ARG 70": "NH1" <-> "NH2" Residue "L ARG 79": "NH1" <-> "NH2" Residue "L ARG 82": "NH1" <-> "NH2" Residue "L ARG 119": "NH1" <-> "NH2" Residue "L ARG 139": "NH1" <-> "NH2" Residue "L ARG 142": "NH1" <-> "NH2" Residue "L ARG 198": "NH1" <-> "NH2" Residue "L ARG 213": "NH1" <-> "NH2" Residue "L ARG 246": "NH1" <-> "NH2" Residue "L ARG 257": "NH1" <-> "NH2" Residue "L ARG 264": "NH1" <-> "NH2" Residue "L ARG 273": "NH1" <-> "NH2" Residue "L TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 350": "NH1" <-> "NH2" Residue "L ARG 364": "NH1" <-> "NH2" Residue "L ARG 391": "NH1" <-> "NH2" Residue "L ARG 406": "NH1" <-> "NH2" Residue "L ARG 459": "NH1" <-> "NH2" Residue "L ARG 476": "NH1" <-> "NH2" Residue "L ARG 489": "NH1" <-> "NH2" Residue "L ARG 532": "NH1" <-> "NH2" Residue "L ARG 631": "NH1" <-> "NH2" Residue "L ARG 659": "NH1" <-> "NH2" Residue "L ARG 675": "NH1" <-> "NH2" Residue "L ARG 746": "NH1" <-> "NH2" Residue "L ARG 782": "NH1" <-> "NH2" Residue "L ARG 820": "NH1" <-> "NH2" Residue "L ARG 852": "NH1" <-> "NH2" Residue "L ARG 854": "NH1" <-> "NH2" Residue "L ARG 888": "NH1" <-> "NH2" Residue "L ARG 891": "NH1" <-> "NH2" Residue "L ARG 899": "NH1" <-> "NH2" Residue "L ARG 913": "NH1" <-> "NH2" Residue "L ARG 924": "NH1" <-> "NH2" Residue "L ARG 964": "NH1" <-> "NH2" Residue "L ARG 971": "NH1" <-> "NH2" Residue "L ARG 981": "NH1" <-> "NH2" Residue "L ARG 1026": "NH1" <-> "NH2" Residue "L ARG 1031": "NH1" <-> "NH2" Residue "L ARG 1034": "NH1" <-> "NH2" Residue "L ARG 1062": "NH1" <-> "NH2" Residue "L ARG 1075": "NH1" <-> "NH2" Residue "L ARG 1087": "NH1" <-> "NH2" Residue "L ARG 1090": "NH1" <-> "NH2" Residue "L ARG 1136": "NH1" <-> "NH2" Residue "L ARG 1151": "NH1" <-> "NH2" Residue "L ARG 1152": "NH1" <-> "NH2" Residue "L ARG 1155": "NH1" <-> "NH2" Residue "L ARG 1178": "NH1" <-> "NH2" Residue "L ARG 1184": "NH1" <-> "NH2" Residue "L ARG 1202": "NH1" <-> "NH2" Residue "L ARG 1274": "NH1" <-> "NH2" Residue "L ARG 1329": "NH1" <-> "NH2" Residue "L ARG 1340": "NH1" <-> "NH2" Residue "L ARG 1370": "NH1" <-> "NH2" Residue "L ARG 1420": "NH1" <-> "NH2" Residue "L ARG 1445": "NH1" <-> "NH2" Residue "L ARG 1447": "NH1" <-> "NH2" Residue "L ARG 1460": "NH1" <-> "NH2" Residue "L ARG 1497": "NH1" <-> "NH2" Residue "L ARG 1527": "NH1" <-> "NH2" Residue "L ARG 1606": "NH1" <-> "NH2" Residue "L ARG 1608": "NH1" <-> "NH2" Residue "L ASP 1656": "OD1" <-> "OD2" Residue "L ARG 1711": "NH1" <-> "NH2" Residue "L ARG 1712": "NH1" <-> "NH2" Residue "L ARG 1727": "NH1" <-> "NH2" Residue "L ARG 1735": "NH1" <-> "NH2" Residue "L ARG 1768": "NH1" <-> "NH2" Residue "L ARG 1783": "NH1" <-> "NH2" Residue "L ARG 1784": "NH1" <-> "NH2" Residue "L ARG 1787": "NH1" <-> "NH2" Residue "L ARG 1788": "NH1" <-> "NH2" Residue "L ARG 1806": "NH1" <-> "NH2" Residue "L ARG 1811": "NH1" <-> "NH2" Residue "L ARG 1816": "NH1" <-> "NH2" Residue "L ARG 1822": "NH1" <-> "NH2" Residue "L ARG 1837": "NH1" <-> "NH2" Residue "L ARG 1854": "NH1" <-> "NH2" Residue "L ARG 1883": "NH1" <-> "NH2" Residue "L ARG 1936": "NH1" <-> "NH2" Residue "L ARG 1937": "NH1" <-> "NH2" Residue "L ARG 1938": "NH1" <-> "NH2" Residue "L ARG 1986": "NH1" <-> "NH2" Residue "L ARG 1987": "NH1" <-> "NH2" Residue "L ARG 2090": "NH1" <-> "NH2" Residue "L ARG 2106": "NH1" <-> "NH2" Residue "L ARG 2120": "NH1" <-> "NH2" Residue "L ARG 2143": "NH1" <-> "NH2" Residue "L ARG 2158": "NH1" <-> "NH2" Residue "L ARG 2214": "NH1" <-> "NH2" Residue "L ARG 2228": "NH1" <-> "NH2" Residue "L ARG 2232": "NH1" <-> "NH2" Residue "L ARG 2254": "NH1" <-> "NH2" Residue "L ARG 2311": "NH1" <-> "NH2" Residue "L ARG 2328": "NH1" <-> "NH2" Residue "L ARG 2333": "NH1" <-> "NH2" Residue "L ARG 2377": "NH1" <-> "NH2" Residue "L ARG 2404": "NH1" <-> "NH2" Residue "L ARG 2425": "NH1" <-> "NH2" Residue "L ARG 2427": "NH1" <-> "NH2" Residue "L ARG 2431": "NH1" <-> "NH2" Residue "L ARG 2452": "NH1" <-> "NH2" Residue "L ARG 2470": "NH1" <-> "NH2" Residue "L ARG 2485": "NH1" <-> "NH2" Residue "L ARG 2522": "NH1" <-> "NH2" Residue "L ARG 2530": "NH1" <-> "NH2" Residue "L ARG 2538": "NH1" <-> "NH2" Residue "L ARG 2596": "NH1" <-> "NH2" Residue "L ARG 2598": "NH1" <-> "NH2" Residue "L ARG 2722": "NH1" <-> "NH2" Residue "L ARG 2727": "NH1" <-> "NH2" Residue "L ARG 2729": "NH1" <-> "NH2" Residue "L ARG 2730": "NH1" <-> "NH2" Residue "L ARG 2731": "NH1" <-> "NH2" Residue "L ARG 2734": "NH1" <-> "NH2" Residue "L ARG 2745": "NH1" <-> "NH2" Residue "L ARG 2753": "NH1" <-> "NH2" Residue "L ARG 2773": "NH1" <-> "NH2" Residue "L ARG 2776": "NH1" <-> "NH2" Residue "L ARG 2800": "NH1" <-> "NH2" Residue "L ARG 2842": "NH1" <-> "NH2" Residue "L ARG 2891": "NH1" <-> "NH2" Residue "L ARG 2899": "NH1" <-> "NH2" Residue "L ARG 2915": "NH1" <-> "NH2" Residue "L ARG 2922": "NH1" <-> "NH2" Residue "L ARG 2931": "NH1" <-> "NH2" Residue "L ARG 2940": "NH1" <-> "NH2" Residue "L ARG 2962": "NH1" <-> "NH2" Residue "L ARG 3046": "NH1" <-> "NH2" Residue "L ARG 3098": "NH1" <-> "NH2" Residue "L ARG 3125": "NH1" <-> "NH2" Residue "L ARG 3159": "NH1" <-> "NH2" Residue "L ARG 3167": "NH1" <-> "NH2" Residue "L ARG 3186": "NH1" <-> "NH2" Residue "L ARG 3232": "NH1" <-> "NH2" Residue "L ARG 3247": "NH1" <-> "NH2" Residue "L ARG 3269": "NH1" <-> "NH2" Residue "L ARG 3282": "NH1" <-> "NH2" Residue "L ARG 3287": "NH1" <-> "NH2" Residue "L ARG 3289": "NH1" <-> "NH2" Residue "L ARG 3324": "NH1" <-> "NH2" Residue "L ARG 3335": "NH1" <-> "NH2" Residue "L ARG 3357": "NH1" <-> "NH2" Residue "L ARG 3358": "NH1" <-> "NH2" Residue "L ARG 3380": "NH1" <-> "NH2" Residue "L ARG 3425": "NH1" <-> "NH2" Residue "L ARG 3462": "NH1" <-> "NH2" Residue "L ARG 3467": "NH1" <-> "NH2" Residue "L ARG 3474": "NH1" <-> "NH2" Residue "L ARG 3557": "NH1" <-> "NH2" Residue "L ARG 3593": "NH1" <-> "NH2" Residue "L ARG 3612": "NH1" <-> "NH2" Residue "L ARG 3629": "NH1" <-> "NH2" Residue "L ARG 3630": "NH1" <-> "NH2" Residue "L ARG 3653": "NH1" <-> "NH2" Residue "L ARG 3696": "NH1" <-> "NH2" Residue "L ARG 3708": "NH1" <-> "NH2" Residue "L ARG 3718": "NH1" <-> "NH2" Residue "L ARG 3725": "NH1" <-> "NH2" Residue "L ARG 3733": "NH1" <-> "NH2" Residue "L ARG 3734": "NH1" <-> "NH2" Residue "L ARG 3737": "NH1" <-> "NH2" Residue "L ARG 3741": "NH1" <-> "NH2" Residue "L ARG 3746": "NH1" <-> "NH2" Residue "L ARG 3759": "NH1" <-> "NH2" Residue "L ARG 3763": "NH1" <-> "NH2" Residue "L ARG 3784": "NH1" <-> "NH2" Residue "L ARG 3789": "NH1" <-> "NH2" Residue "L ARG 3799": "NH1" <-> "NH2" Residue "L ARG 3833": "NH1" <-> "NH2" Residue "L ARG 3864": "NH1" <-> "NH2" Residue "L ARG 3872": "NH1" <-> "NH2" Residue "L ARG 3874": "NH1" <-> "NH2" Residue "L ARG 3885": "NH1" <-> "NH2" Residue "L ARG 3889": "NH1" <-> "NH2" Residue "L ARG 3901": "NH1" <-> "NH2" Residue "L ARG 3923": "NH1" <-> "NH2" Residue "L ARG 3962": "NH1" <-> "NH2" Residue "L ARG 3965": "NH1" <-> "NH2" Residue "L ARG 3989": "NH1" <-> "NH2" Residue "L ARG 3992": "NH1" <-> "NH2" Residue "L ARG 4041": "NH1" <-> "NH2" Residue "L ARG 4049": "NH1" <-> "NH2" Residue "L ARG 4075": "NH1" <-> "NH2" Residue "L ARG 4082": "NH1" <-> "NH2" Residue "L ARG 4090": "NH1" <-> "NH2" Residue "L ARG 4119": "NH1" <-> "NH2" Residue "H ARG 57": "NH1" <-> "NH2" Residue "H ARG 64": "NH1" <-> "NH2" Residue "H ARG 81": "NH1" <-> "NH2" Residue "H ARG 107": "NH1" <-> "NH2" Residue "H ARG 109": "NH1" <-> "NH2" Residue "H ARG 137": "NH1" <-> "NH2" Residue "H ARG 151": "NH1" <-> "NH2" Residue "H ARG 176": "NH1" <-> "NH2" Residue "H ARG 178": "NH1" <-> "NH2" Residue "H ARG 295": "NH1" <-> "NH2" Residue "I ARG 57": "NH1" <-> "NH2" Residue "I ARG 64": "NH1" <-> "NH2" Residue "I PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 107": "NH1" <-> "NH2" Residue "I ARG 109": "NH1" <-> "NH2" Residue "I ARG 137": "NH1" <-> "NH2" Residue "I ARG 151": "NH1" <-> "NH2" Residue "I ARG 176": "NH1" <-> "NH2" Residue "I ARG 178": "NH1" <-> "NH2" Residue "I ARG 295": "NH1" <-> "NH2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 81": "NH1" <-> "NH2" Residue "B ARG 130": "NH1" <-> "NH2" Residue "B ARG 141": "NH1" <-> "NH2" Residue "B ARG 232": "NH1" <-> "NH2" Residue "B ARG 242": "NH1" <-> "NH2" Residue "B ARG 250": "NH1" <-> "NH2" Residue "B ARG 260": "NH1" <-> "NH2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B ARG 315": "NH1" <-> "NH2" Residue "B ARG 353": "NH1" <-> "NH2" Residue "B ARG 354": "NH1" <-> "NH2" Residue "B ARG 368": "NH1" <-> "NH2" Residue "B ARG 394": "NH1" <-> "NH2" Residue "B ARG 400": "NH1" <-> "NH2" Residue "B ARG 431": "NH1" <-> "NH2" Residue "B ARG 486": "NH1" <-> "NH2" Residue "B ARG 489": "NH1" <-> "NH2" Residue "B ARG 497": "NH1" <-> "NH2" Residue "B ARG 502": "NH1" <-> "NH2" Residue "B ASP 726": "OD1" <-> "OD2" Residue "C ARG 9": "NH1" <-> "NH2" Residue "C ARG 14": "NH1" <-> "NH2" Residue "C ARG 24": "NH1" <-> "NH2" Residue "C ARG 36": "NH1" <-> "NH2" Residue "C ARG 61": "NH1" <-> "NH2" Residue "C ARG 70": "NH1" <-> "NH2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C ARG 82": "NH1" <-> "NH2" Residue "C ARG 119": "NH1" <-> "NH2" Residue "C ARG 139": "NH1" <-> "NH2" Residue "C ARG 142": "NH1" <-> "NH2" Residue "C ARG 198": "NH1" <-> "NH2" Residue "C ARG 213": "NH1" <-> "NH2" Residue "C ARG 246": "NH1" <-> "NH2" Residue "C ARG 257": "NH1" <-> "NH2" Residue "C ARG 264": "NH1" <-> "NH2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "C TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 350": "NH1" <-> "NH2" Residue "C ARG 364": "NH1" <-> "NH2" Residue "C ARG 391": "NH1" <-> "NH2" Residue "C ARG 406": "NH1" <-> "NH2" Residue "C ARG 459": "NH1" <-> "NH2" Residue "C ARG 476": "NH1" <-> "NH2" Residue "C ARG 489": "NH1" <-> "NH2" Residue "C ARG 532": "NH1" <-> "NH2" Residue "C ARG 631": "NH1" <-> "NH2" Residue "C ARG 659": "NH1" <-> "NH2" Residue "C ARG 675": "NH1" <-> "NH2" Residue "C ARG 746": "NH1" <-> "NH2" Residue "C ARG 782": "NH1" <-> "NH2" Residue "C ARG 820": "NH1" <-> "NH2" Residue "C ARG 852": "NH1" <-> "NH2" Residue "C ARG 854": "NH1" <-> "NH2" Residue "C ARG 888": "NH1" <-> "NH2" Residue "C ARG 891": "NH1" <-> "NH2" Residue "C ARG 899": "NH1" <-> "NH2" Residue "C ARG 913": "NH1" <-> "NH2" Residue "C ARG 924": "NH1" <-> "NH2" Residue "C ARG 964": "NH1" <-> "NH2" Residue "C ARG 971": "NH1" <-> "NH2" Residue "C ARG 981": "NH1" <-> "NH2" Residue "C ARG 1026": "NH1" <-> "NH2" Residue "C ARG 1031": "NH1" <-> "NH2" Residue "C ARG 1034": "NH1" <-> "NH2" Residue "C ARG 1062": "NH1" <-> "NH2" Residue "C ARG 1075": "NH1" <-> "NH2" Residue "C ARG 1087": "NH1" <-> "NH2" Residue "C ARG 1090": "NH1" <-> "NH2" Residue "C ARG 1136": "NH1" <-> "NH2" Residue "C ARG 1151": "NH1" <-> "NH2" Residue "C ARG 1152": "NH1" <-> "NH2" Residue "C ARG 1155": "NH1" <-> "NH2" Residue "C ARG 1178": "NH1" <-> "NH2" Residue "C ARG 1184": "NH1" <-> "NH2" Residue "C ARG 1202": "NH1" <-> "NH2" Residue "C ARG 1274": "NH1" <-> "NH2" Residue "C ARG 1329": "NH1" <-> "NH2" Residue "C ARG 1340": "NH1" <-> "NH2" Residue "C ARG 1370": "NH1" <-> "NH2" Residue "C ARG 1420": "NH1" <-> "NH2" Residue "C ARG 1445": "NH1" <-> "NH2" Residue "C ARG 1447": "NH1" <-> "NH2" Residue "C ARG 1460": "NH1" <-> "NH2" Residue "C ARG 1497": "NH1" <-> "NH2" Residue "C ARG 1527": "NH1" <-> "NH2" Residue "C ARG 1606": "NH1" <-> "NH2" Residue "C ARG 1608": "NH1" <-> "NH2" Residue "C ASP 1656": "OD1" <-> "OD2" Residue "C ARG 1711": "NH1" <-> "NH2" Residue "C ARG 1712": "NH1" <-> "NH2" Residue "C ARG 1727": "NH1" <-> "NH2" Residue "C ARG 1735": "NH1" <-> "NH2" Residue "C ARG 1768": "NH1" <-> "NH2" Residue "C ARG 1783": "NH1" <-> "NH2" Residue "C ARG 1784": "NH1" <-> "NH2" Residue "C ARG 1787": "NH1" <-> "NH2" Residue "C ARG 1788": "NH1" <-> "NH2" Residue "C ARG 1806": "NH1" <-> "NH2" Residue "C ARG 1811": "NH1" <-> "NH2" Residue "C ARG 1816": "NH1" <-> "NH2" Residue "C ARG 1822": "NH1" <-> "NH2" Residue "C ARG 1837": "NH1" <-> "NH2" Residue "C ARG 1854": "NH1" <-> "NH2" Residue "C ARG 1883": "NH1" <-> "NH2" Residue "C ARG 1936": "NH1" <-> "NH2" Residue "C ARG 1937": "NH1" <-> "NH2" Residue "C ARG 1938": "NH1" <-> "NH2" Residue "C ARG 1986": "NH1" <-> "NH2" Residue "C ARG 1987": "NH1" <-> "NH2" Residue "C ARG 2090": "NH1" <-> "NH2" Residue "C ARG 2106": "NH1" <-> "NH2" Residue "C ARG 2120": "NH1" <-> "NH2" Residue "C ARG 2143": "NH1" <-> "NH2" Residue "C ARG 2158": "NH1" <-> "NH2" Residue "C ARG 2214": "NH1" <-> "NH2" Residue "C ARG 2228": "NH1" <-> "NH2" Residue "C ARG 2232": "NH1" <-> "NH2" Residue "C ARG 2254": "NH1" <-> "NH2" Residue "C ARG 2311": "NH1" <-> "NH2" Residue "C ARG 2328": "NH1" <-> "NH2" Residue "C ARG 2333": "NH1" <-> "NH2" Residue "C ARG 2377": "NH1" <-> "NH2" Residue "C ARG 2404": "NH1" <-> "NH2" Residue "C ARG 2425": "NH1" <-> "NH2" Residue "C ARG 2427": "NH1" <-> "NH2" Residue "C ARG 2431": "NH1" <-> "NH2" Residue "C ARG 2452": "NH1" <-> "NH2" Residue "C ARG 2470": "NH1" <-> "NH2" Residue "C ARG 2485": "NH1" <-> "NH2" Residue "C ARG 2522": "NH1" <-> "NH2" Residue "C ARG 2530": "NH1" <-> "NH2" Residue "C ARG 2538": "NH1" <-> "NH2" Residue "C ARG 2596": "NH1" <-> "NH2" Residue "C ARG 2598": "NH1" <-> "NH2" Residue "C ARG 2722": "NH1" <-> "NH2" Residue "C ARG 2727": "NH1" <-> "NH2" Residue "C ARG 2729": "NH1" <-> "NH2" Residue "C ARG 2730": "NH1" <-> "NH2" Residue "C ARG 2731": "NH1" <-> "NH2" Residue "C ARG 2734": "NH1" <-> "NH2" Residue "C ARG 2745": "NH1" <-> "NH2" Residue "C ARG 2753": "NH1" <-> "NH2" Residue "C ARG 2773": "NH1" <-> "NH2" Residue "C ARG 2776": "NH1" <-> "NH2" Residue "C ARG 2800": "NH1" <-> "NH2" Residue "C ARG 2842": "NH1" <-> "NH2" Residue "C ARG 2891": "NH1" <-> "NH2" Residue "C ARG 2899": "NH1" <-> "NH2" Residue "C ARG 2915": "NH1" <-> "NH2" Residue "C ARG 2922": "NH1" <-> "NH2" Residue "C ARG 2931": "NH1" <-> "NH2" Residue "C ARG 2940": "NH1" <-> "NH2" Residue "C ARG 2962": "NH1" <-> "NH2" Residue "C ARG 3046": "NH1" <-> "NH2" Residue "C ARG 3098": "NH1" <-> "NH2" Residue "C ARG 3125": "NH1" <-> "NH2" Residue "C ARG 3159": "NH1" <-> "NH2" Residue "C ARG 3167": "NH1" <-> "NH2" Residue "C ARG 3186": "NH1" <-> "NH2" Residue "C ARG 3232": "NH1" <-> "NH2" Residue "C ARG 3247": "NH1" <-> "NH2" Residue "C ARG 3269": "NH1" <-> "NH2" Residue "C ARG 3282": "NH1" <-> "NH2" Residue "C ARG 3287": "NH1" <-> "NH2" Residue "C ARG 3289": "NH1" <-> "NH2" Residue "C ARG 3324": "NH1" <-> "NH2" Residue "C ARG 3335": "NH1" <-> "NH2" Residue "C ARG 3357": "NH1" <-> "NH2" Residue "C ARG 3358": "NH1" <-> "NH2" Residue "C ARG 3380": "NH1" <-> "NH2" Residue "C ARG 3425": "NH1" <-> "NH2" Residue "C ARG 3462": "NH1" <-> "NH2" Residue "C ARG 3467": "NH1" <-> "NH2" Residue "C ARG 3474": "NH1" <-> "NH2" Residue "C ARG 3557": "NH1" <-> "NH2" Residue "C ARG 3593": "NH1" <-> "NH2" Residue "C ARG 3612": "NH1" <-> "NH2" Residue "C ARG 3629": "NH1" <-> "NH2" Residue "C ARG 3630": "NH1" <-> "NH2" Residue "C ARG 3653": "NH1" <-> "NH2" Residue "C ARG 3696": "NH1" <-> "NH2" Residue "C ARG 3708": "NH1" <-> "NH2" Residue "C ARG 3718": "NH1" <-> "NH2" Residue "C ARG 3725": "NH1" <-> "NH2" Residue "C ARG 3733": "NH1" <-> "NH2" Residue "C ARG 3734": "NH1" <-> "NH2" Residue "C ARG 3737": "NH1" <-> "NH2" Residue "C ARG 3741": "NH1" <-> "NH2" Residue "C ARG 3746": "NH1" <-> "NH2" Residue "C ARG 3759": "NH1" <-> "NH2" Residue "C ARG 3763": "NH1" <-> "NH2" Residue "C ARG 3784": "NH1" <-> "NH2" Residue "C ARG 3789": "NH1" <-> "NH2" Residue "C ARG 3799": "NH1" <-> "NH2" Residue "C ARG 3833": "NH1" <-> "NH2" Residue "C ARG 3864": "NH1" <-> "NH2" Residue "C ARG 3872": "NH1" <-> "NH2" Residue "C ARG 3874": "NH1" <-> "NH2" Residue "C ARG 3885": "NH1" <-> "NH2" Residue "C ARG 3889": "NH1" <-> "NH2" Residue "C ARG 3901": "NH1" <-> "NH2" Residue "C ARG 3923": "NH1" <-> "NH2" Residue "C ARG 3962": "NH1" <-> "NH2" Residue "C ARG 3965": "NH1" <-> "NH2" Residue "C ARG 3989": "NH1" <-> "NH2" Residue "C ARG 3992": "NH1" <-> "NH2" Residue "C ARG 4041": "NH1" <-> "NH2" Residue "C ARG 4049": "NH1" <-> "NH2" Residue "C ARG 4075": "NH1" <-> "NH2" Residue "C ARG 4082": "NH1" <-> "NH2" Residue "C ARG 4090": "NH1" <-> "NH2" Residue "C ARG 4119": "NH1" <-> "NH2" Residue "F ARG 3": "NH1" <-> "NH2" Residue "F ARG 7": "NH1" <-> "NH2" Residue "F ARG 71": "NH1" <-> "NH2" Residue "F ARG 107": "NH1" <-> "NH2" Residue "F ARG 124": "NH1" <-> "NH2" Residue "F ARG 150": "NH1" <-> "NH2" Residue "F ARG 153": "NH1" <-> "NH2" Residue "F ARG 161": "NH1" <-> "NH2" Residue "F ARG 179": "NH1" <-> "NH2" Residue "F ARG 192": "NH1" <-> "NH2" Residue "F ARG 270": "NH1" <-> "NH2" Residue "F ARG 272": "NH1" <-> "NH2" Residue "F ARG 273": "NH1" <-> "NH2" Residue "F ARG 275": "NH1" <-> "NH2" Residue "F ARG 278": "NH1" <-> "NH2" Residue "X ARG 681": "NH1" <-> "NH2" Residue "X ARG 708": "NH1" <-> "NH2" Residue "X ARG 741": "NH1" <-> "NH2" Residue "X ARG 756": "NH1" <-> "NH2" Residue "X ARG 802": "NH1" <-> "NH2" Residue "X ARG 814": "NH1" <-> "NH2" Residue "X ARG 815": "NH1" <-> "NH2" Residue "X ARG 837": "NH1" <-> "NH2" Residue "X ARG 846": "NH1" <-> "NH2" Residue "X ARG 871": "NH1" <-> "NH2" Residue "X ARG 879": "NH1" <-> "NH2" Residue "X ARG 880": "NH1" <-> "NH2" Residue "X ARG 884": "NH1" <-> "NH2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G ARG 7": "NH1" <-> "NH2" Residue "G ARG 71": "NH1" <-> "NH2" Residue "G ARG 107": "NH1" <-> "NH2" Residue "G ARG 124": "NH1" <-> "NH2" Residue "G ARG 150": "NH1" <-> "NH2" Residue "G ARG 153": "NH1" <-> "NH2" Residue "G ARG 161": "NH1" <-> "NH2" Residue "G ARG 179": "NH1" <-> "NH2" Residue "G ARG 192": "NH1" <-> "NH2" Residue "T ARG 179": "NH1" <-> "NH2" Residue "T PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 3": "NH1" <-> "NH2" Residue "O ARG 7": "NH1" <-> "NH2" Residue "O ARG 71": "NH1" <-> "NH2" Residue "O ARG 107": "NH1" <-> "NH2" Residue "O ARG 124": "NH1" <-> "NH2" Residue "O ARG 150": "NH1" <-> "NH2" Residue "O ARG 153": "NH1" <-> "NH2" Residue "O ARG 161": "NH1" <-> "NH2" Residue "O ARG 179": "NH1" <-> "NH2" Residue "O ARG 192": "NH1" <-> "NH2" Residue "O ARG 270": "NH1" <-> "NH2" Residue "O ARG 272": "NH1" <-> "NH2" Residue "O ARG 273": "NH1" <-> "NH2" Residue "O ARG 275": "NH1" <-> "NH2" Residue "O ARG 278": "NH1" <-> "NH2" Residue "Y ARG 681": "NH1" <-> "NH2" Residue "Y ARG 708": "NH1" <-> "NH2" Residue "Y ARG 741": "NH1" <-> "NH2" Residue "Y ARG 756": "NH1" <-> "NH2" Residue "Y ARG 802": "NH1" <-> "NH2" Residue "Y ARG 814": "NH1" <-> "NH2" Residue "Y ARG 815": "NH1" <-> "NH2" Residue "Y ARG 837": "NH1" <-> "NH2" Residue "Y ARG 846": "NH1" <-> "NH2" Residue "Y ARG 871": "NH1" <-> "NH2" Residue "Y ARG 879": "NH1" <-> "NH2" Residue "Y ARG 880": "NH1" <-> "NH2" Residue "Y ARG 884": "NH1" <-> "NH2" Residue "P ARG 3": "NH1" <-> "NH2" Residue "P ARG 7": "NH1" <-> "NH2" Residue "P ARG 71": "NH1" <-> "NH2" Residue "P ARG 107": "NH1" <-> "NH2" Residue "P ARG 124": "NH1" <-> "NH2" Residue "P ARG 150": "NH1" <-> "NH2" Residue "P ARG 153": "NH1" <-> "NH2" Residue "P ARG 161": "NH1" <-> "NH2" Residue "P ARG 179": "NH1" <-> "NH2" Residue "P ARG 192": "NH1" <-> "NH2" Time to flip residues: 0.25s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 93588 Number of models: 1 Model: "" Number of chains: 24 Chain: "S" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 168 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 3, 'TRANS': 19} Chain: "J" Number of atoms: 4021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 4021 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 27, 'TRANS': 469} Chain breaks: 1 Chain: "A" Number of atoms: 4021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 4021 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 27, 'TRANS': 469} Chain breaks: 1 Chain: "K" Number of atoms: 4259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4259 Classifications: {'peptide': 531} Link IDs: {'PTRANS': 23, 'TRANS': 507} Chain breaks: 2 Chain: "L" Number of atoms: 29811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3720, 29811 Classifications: {'peptide': 3720} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 159, 'TRANS': 3560} Chain breaks: 16 Chain: "R" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 101 Classifications: {'peptide': 20} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'TRANS': 19} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "M" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 634 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "N" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 616 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "H" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1779 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 211} Chain breaks: 2 Chain: "I" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1737 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 207} Chain breaks: 2 Chain: "B" Number of atoms: 4259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4259 Classifications: {'peptide': 531} Link IDs: {'PTRANS': 23, 'TRANS': 507} Chain breaks: 2 Chain: "C" Number of atoms: 29811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3720, 29811 Classifications: {'peptide': 3720} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 159, 'TRANS': 3560} Chain breaks: 16 Chain: "Q" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 101 Classifications: {'peptide': 20} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'TRANS': 19} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "D" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 634 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "E" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 616 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "F" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1736 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 4, 'TRANS': 208} Chain breaks: 1 Chain: "X" Number of atoms: 2064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2064 Classifications: {'peptide': 254} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 243} Chain breaks: 1 Chain: "G" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1595 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 2, 'TRANS': 192} Chain breaks: 1 Chain: "T" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 168 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 3, 'TRANS': 19} Chain: "O" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1736 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 4, 'TRANS': 208} Chain breaks: 1 Chain: "Y" Number of atoms: 2064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2064 Classifications: {'peptide': 254} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 243} Chain breaks: 1 Chain: "P" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1595 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 2, 'TRANS': 192} Chain breaks: 1 Chain: "L" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 35.56, per 1000 atoms: 0.38 Number of scatterers: 93588 At special positions: 0 Unit cell: (316.147, 235.222, 247.091, 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 562 16.00 P 128 15.00 O 17545 8.00 N 15900 7.00 C 59453 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 29.26 Conformation dependent library (CDL) restraints added in 12.3 seconds 22358 Ramachandran restraints generated. 11179 Oldfield, 0 Emsley, 11179 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 21762 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 534 helices and 38 sheets defined 57.7% alpha, 5.8% beta 34 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 45.52 Creating SS restraints... Processing helix chain 'S' and resid 180 through 182 No H-bonds generated for 'chain 'S' and resid 180 through 182' Processing helix chain 'J' and resid 46 through 49 No H-bonds generated for 'chain 'J' and resid 46 through 49' Processing helix chain 'J' and resid 59 through 77 removed outlier: 3.598A pdb=" N ILE J 76 " --> pdb=" O ILE J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 122 removed outlier: 4.446A pdb=" N PHE J 122 " --> pdb=" O GLU J 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 130 No H-bonds generated for 'chain 'J' and resid 127 through 130' Processing helix chain 'J' and resid 143 through 156 Processing helix chain 'J' and resid 180 through 195 removed outlier: 4.451A pdb=" N ARG J 185 " --> pdb=" O ALA J 181 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA J 186 " --> pdb=" O LYS J 182 " (cutoff:3.500A) Processing helix chain 'J' and resid 239 through 243 Processing helix chain 'J' and resid 313 through 315 No H-bonds generated for 'chain 'J' and resid 313 through 315' Processing helix chain 'J' and resid 333 through 335 No H-bonds generated for 'chain 'J' and resid 333 through 335' Processing helix chain 'J' and resid 378 through 392 removed outlier: 3.510A pdb=" N ALA J 384 " --> pdb=" O THR J 380 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU J 390 " --> pdb=" O LEU J 386 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU J 391 " --> pdb=" O ILE J 387 " (cutoff:3.500A) Processing helix chain 'J' and resid 440 through 442 No H-bonds generated for 'chain 'J' and resid 440 through 442' Processing helix chain 'J' and resid 456 through 468 removed outlier: 3.568A pdb=" N ALA J 464 " --> pdb=" O GLY J 460 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU J 467 " --> pdb=" O LYS J 463 " (cutoff:3.500A) Processing helix chain 'J' and resid 475 through 477 No H-bonds generated for 'chain 'J' and resid 475 through 477' Processing helix chain 'J' and resid 481 through 495 removed outlier: 3.594A pdb=" N ARG J 488 " --> pdb=" O GLN J 484 " (cutoff:3.500A) Processing helix chain 'J' and resid 511 through 518 removed outlier: 3.709A pdb=" N LEU J 518 " --> pdb=" O MET J 514 " (cutoff:3.500A) Processing helix chain 'J' and resid 520 through 528 removed outlier: 3.779A pdb=" N GLU J 527 " --> pdb=" O GLU J 524 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU J 528 " --> pdb=" O PHE J 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 49 No H-bonds generated for 'chain 'A' and resid 46 through 49' Processing helix chain 'A' and resid 59 through 77 removed outlier: 3.597A pdb=" N ILE A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 122 removed outlier: 4.446A pdb=" N PHE A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 130 No H-bonds generated for 'chain 'A' and resid 127 through 130' Processing helix chain 'A' and resid 143 through 156 Processing helix chain 'A' and resid 180 through 195 removed outlier: 4.452A pdb=" N ARG A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA A 186 " --> pdb=" O LYS A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 243 Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 333 through 335 No H-bonds generated for 'chain 'A' and resid 333 through 335' Processing helix chain 'A' and resid 378 through 392 removed outlier: 3.510A pdb=" N ALA A 384 " --> pdb=" O THR A 380 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 390 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU A 391 " --> pdb=" O ILE A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 442 No H-bonds generated for 'chain 'A' and resid 440 through 442' Processing helix chain 'A' and resid 456 through 469 removed outlier: 3.568A pdb=" N ALA A 464 " --> pdb=" O GLY A 460 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU A 467 " --> pdb=" O LYS A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 477 No H-bonds generated for 'chain 'A' and resid 475 through 477' Processing helix chain 'A' and resid 481 through 495 removed outlier: 3.595A pdb=" N ARG A 488 " --> pdb=" O GLN A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 518 removed outlier: 3.709A pdb=" N LEU A 518 " --> pdb=" O MET A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 528 removed outlier: 3.778A pdb=" N GLU A 527 " --> pdb=" O GLU A 524 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 528 " --> pdb=" O PHE A 525 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 21 No H-bonds generated for 'chain 'K' and resid 19 through 21' Processing helix chain 'K' and resid 30 through 47 removed outlier: 4.576A pdb=" N ARG K 44 " --> pdb=" O MET K 40 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLN K 45 " --> pdb=" O PHE K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 96 Processing helix chain 'K' and resid 107 through 124 removed outlier: 4.819A pdb=" N ILE K 123 " --> pdb=" O GLN K 119 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLY K 124 " --> pdb=" O HIS K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 156 Processing helix chain 'K' and resid 199 through 223 removed outlier: 8.711A pdb=" N GLU K 218 " --> pdb=" O SER K 214 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N ASP K 219 " --> pdb=" O LEU K 215 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY K 220 " --> pdb=" O GLU K 216 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU K 221 " --> pdb=" O GLY K 217 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ASP K 222 " --> pdb=" O GLU K 218 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU K 223 " --> pdb=" O ASP K 219 " (cutoff:3.500A) Processing helix chain 'K' and resid 227 through 231 Processing helix chain 'K' and resid 306 through 309 No H-bonds generated for 'chain 'K' and resid 306 through 309' Processing helix chain 'K' and resid 325 through 331 removed outlier: 3.552A pdb=" N GLU K 329 " --> pdb=" O LYS K 325 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLN K 330 " --> pdb=" O VAL K 326 " (cutoff:3.500A) Processing helix chain 'K' and resid 348 through 350 No H-bonds generated for 'chain 'K' and resid 348 through 350' Processing helix chain 'K' and resid 371 through 382 Processing helix chain 'K' and resid 441 through 443 No H-bonds generated for 'chain 'K' and resid 441 through 443' Processing helix chain 'K' and resid 448 through 460 removed outlier: 4.734A pdb=" N ALA K 456 " --> pdb=" O ASN K 452 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU K 457 " --> pdb=" O ALA K 453 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE K 458 " --> pdb=" O VAL K 454 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP K 459 " --> pdb=" O ASP K 455 " (cutoff:3.500A) Processing helix chain 'K' and resid 479 through 481 No H-bonds generated for 'chain 'K' and resid 479 through 481' Processing helix chain 'K' and resid 485 through 499 Processing helix chain 'K' and resid 510 through 516 Processing helix chain 'K' and resid 520 through 536 removed outlier: 3.711A pdb=" N THR K 524 " --> pdb=" O ALA K 520 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN K 527 " --> pdb=" O THR K 523 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ILE K 528 " --> pdb=" O THR K 524 " (cutoff:3.500A) Proline residue: K 529 - end of helix removed outlier: 4.243A pdb=" N THR K 535 " --> pdb=" O SER K 531 " (cutoff:3.500A) Processing helix chain 'K' and resid 548 through 551 Processing helix chain 'L' and resid 8 through 20 removed outlier: 3.589A pdb=" N GLN L 16 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU L 17 " --> pdb=" O LEU L 13 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER L 20 " --> pdb=" O GLN L 16 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 44 removed outlier: 3.856A pdb=" N ALA L 28 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU L 29 " --> pdb=" O CYS L 25 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA L 30 " --> pdb=" O GLY L 26 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN L 40 " --> pdb=" O ARG L 36 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS L 42 " --> pdb=" O LEU L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 58 Processing helix chain 'L' and resid 64 through 71 Processing helix chain 'L' and resid 77 through 117 removed outlier: 4.262A pdb=" N GLU L 80 " --> pdb=" O GLU L 77 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU L 83 " --> pdb=" O GLU L 80 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE L 85 " --> pdb=" O ARG L 82 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU L 93 " --> pdb=" O CYS L 90 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N MET L 96 " --> pdb=" O LEU L 93 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY L 97 " --> pdb=" O GLU L 94 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N GLN L 98 " --> pdb=" O LYS L 95 " (cutoff:3.500A) Proline residue: L 102 - end of helix removed outlier: 4.862A pdb=" N VAL L 105 " --> pdb=" O PRO L 102 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR L 112 " --> pdb=" O ASN L 109 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS L 117 " --> pdb=" O VAL L 114 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 137 Proline residue: L 126 - end of helix Processing helix chain 'L' and resid 142 through 144 No H-bonds generated for 'chain 'L' and resid 142 through 144' Processing helix chain 'L' and resid 149 through 165 removed outlier: 3.586A pdb=" N PHE L 153 " --> pdb=" O ILE L 149 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU L 159 " --> pdb=" O LYS L 155 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU L 160 " --> pdb=" O PHE L 156 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA L 161 " --> pdb=" O TYR L 157 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LEU L 162 " --> pdb=" O GLY L 158 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS L 163 " --> pdb=" O GLU L 159 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LYS L 164 " --> pdb=" O LEU L 160 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N LYS L 165 " --> pdb=" O ALA L 161 " (cutoff:3.500A) Processing helix chain 'L' and resid 168 through 184 removed outlier: 3.816A pdb=" N LYS L 173 " --> pdb=" O THR L 169 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR L 175 " --> pdb=" O LEU L 171 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY L 182 " --> pdb=" O LEU L 178 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU L 183 " --> pdb=" O GLY L 179 " (cutoff:3.500A) Processing helix chain 'L' and resid 186 through 189 Processing helix chain 'L' and resid 193 through 209 Processing helix chain 'L' and resid 217 through 230 removed outlier: 3.613A pdb=" N SER L 229 " --> pdb=" O LYS L 225 " (cutoff:3.500A) Processing helix chain 'L' and resid 242 through 256 Processing helix chain 'L' and resid 266 through 282 removed outlier: 5.833A pdb=" N SER L 280 " --> pdb=" O ALA L 276 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLN L 281 " --> pdb=" O LEU L 277 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE L 282 " --> pdb=" O HIS L 278 " (cutoff:3.500A) Processing helix chain 'L' and resid 285 through 288 No H-bonds generated for 'chain 'L' and resid 285 through 288' Processing helix chain 'L' and resid 290 through 302 removed outlier: 3.812A pdb=" N ALA L 302 " --> pdb=" O LEU L 298 " (cutoff:3.500A) Processing helix chain 'L' and resid 306 through 328 removed outlier: 3.755A pdb=" N GLU L 317 " --> pdb=" O LEU L 313 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER L 318 " --> pdb=" O SER L 314 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL L 327 " --> pdb=" O VAL L 323 " (cutoff:3.500A) Processing helix chain 'L' and resid 332 through 349 removed outlier: 4.154A pdb=" N ASN L 336 " --> pdb=" O MET L 333 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN L 339 " --> pdb=" O ASN L 336 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N MET L 342 " --> pdb=" O GLN L 339 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N PHE L 345 " --> pdb=" O MET L 342 " (cutoff:3.500A) Processing helix chain 'L' and resid 356 through 376 removed outlier: 3.616A pdb=" N PHE L 369 " --> pdb=" O GLY L 365 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA L 370 " --> pdb=" O TYR L 366 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N GLY L 371 " --> pdb=" O GLY L 367 " (cutoff:3.500A) Proline residue: L 372 - end of helix removed outlier: 4.254A pdb=" N VAL L 375 " --> pdb=" O GLY L 371 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE L 376 " --> pdb=" O PRO L 372 " (cutoff:3.500A) Processing helix chain 'L' and resid 378 through 395 removed outlier: 3.777A pdb=" N ASP L 382 " --> pdb=" O ALA L 378 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N PHE L 383 " --> pdb=" O LYS L 379 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU L 388 " --> pdb=" O MET L 384 " (cutoff:3.500A) Processing helix chain 'L' and resid 409 through 423 removed outlier: 3.669A pdb=" N PHE L 413 " --> pdb=" O GLN L 409 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER L 419 " --> pdb=" O GLN L 415 " (cutoff:3.500A) Processing helix chain 'L' and resid 429 through 443 Proline residue: L 433 - end of helix Processing helix chain 'L' and resid 446 through 448 No H-bonds generated for 'chain 'L' and resid 446 through 448' Processing helix chain 'L' and resid 451 through 471 removed outlier: 3.674A pdb=" N PHE L 465 " --> pdb=" O ILE L 461 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU L 466 " --> pdb=" O VAL L 462 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS L 471 " --> pdb=" O ALA L 467 " (cutoff:3.500A) Processing helix chain 'L' and resid 473 through 491 removed outlier: 3.757A pdb=" N ASN L 477 " --> pdb=" O PRO L 473 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N CYS L 478 " --> pdb=" O VAL L 474 " (cutoff:3.500A) Processing helix chain 'L' and resid 524 through 526 No H-bonds generated for 'chain 'L' and resid 524 through 526' Processing helix chain 'L' and resid 528 through 536 Processing helix chain 'L' and resid 538 through 540 No H-bonds generated for 'chain 'L' and resid 538 through 540' Processing helix chain 'L' and resid 558 through 578 removed outlier: 3.672A pdb=" N LEU L 573 " --> pdb=" O VAL L 569 " (cutoff:3.500A) Processing helix chain 'L' and resid 617 through 633 removed outlier: 4.534A pdb=" N ALA L 622 " --> pdb=" O LYS L 618 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE L 623 " --> pdb=" O ASP L 619 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU L 632 " --> pdb=" O GLU L 628 " (cutoff:3.500A) Processing helix chain 'L' and resid 643 through 659 removed outlier: 3.766A pdb=" N VAL L 646 " --> pdb=" O GLU L 643 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N TYR L 647 " --> pdb=" O PRO L 644 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE L 649 " --> pdb=" O VAL L 646 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER L 650 " --> pdb=" O TYR L 647 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR L 651 " --> pdb=" O SER L 648 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU L 652 " --> pdb=" O PHE L 649 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU L 655 " --> pdb=" O GLU L 652 " (cutoff:3.500A) Processing helix chain 'L' and resid 664 through 680 Processing helix chain 'L' and resid 700 through 720 removed outlier: 3.534A pdb=" N ALA L 705 " --> pdb=" O TYR L 701 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LYS L 719 " --> pdb=" O ALA L 715 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLN L 720 " --> pdb=" O VAL L 716 " (cutoff:3.500A) Processing helix chain 'L' and resid 723 through 735 removed outlier: 3.579A pdb=" N SER L 735 " --> pdb=" O THR L 731 " (cutoff:3.500A) Processing helix chain 'L' and resid 738 through 741 No H-bonds generated for 'chain 'L' and resid 738 through 741' Processing helix chain 'L' and resid 745 through 761 removed outlier: 3.838A pdb=" N VAL L 749 " --> pdb=" O ARG L 746 " (cutoff:3.500A) Proline residue: L 750 - end of helix removed outlier: 4.047A pdb=" N GLN L 753 " --> pdb=" O PRO L 750 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU L 760 " --> pdb=" O LYS L 757 " (cutoff:3.500A) Processing helix chain 'L' and resid 763 through 779 Processing helix chain 'L' and resid 782 through 800 Proline residue: L 787 - end of helix removed outlier: 4.522A pdb=" N LYS L 790 " --> pdb=" O GLN L 786 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ASP L 791 " --> pdb=" O PRO L 787 " (cutoff:3.500A) Proline residue: L 794 - end of helix removed outlier: 4.433A pdb=" N ASP L 797 " --> pdb=" O LEU L 793 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N GLY L 798 " --> pdb=" O PRO L 794 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N TYR L 799 " --> pdb=" O CYS L 795 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU L 800 " --> pdb=" O LEU L 796 " (cutoff:3.500A) Processing helix chain 'L' and resid 817 through 824 removed outlier: 3.553A pdb=" N LYS L 824 " --> pdb=" O ARG L 820 " (cutoff:3.500A) Processing helix chain 'L' and resid 828 through 837 Processing helix chain 'L' and resid 848 through 862 Processing helix chain 'L' and resid 864 through 870 removed outlier: 3.670A pdb=" N LYS L 868 " --> pdb=" O GLY L 864 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ASN L 869 " --> pdb=" O GLN L 865 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LEU L 870 " --> pdb=" O ILE L 866 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 864 through 870' Processing helix chain 'L' and resid 877 through 882 removed outlier: 4.318A pdb=" N SER L 882 " --> pdb=" O GLU L 878 " (cutoff:3.500A) Processing helix chain 'L' and resid 907 through 909 No H-bonds generated for 'chain 'L' and resid 907 through 909' Processing helix chain 'L' and resid 911 through 920 removed outlier: 4.009A pdb=" N GLU L 916 " --> pdb=" O PRO L 912 " (cutoff:3.500A) Processing helix chain 'L' and resid 924 through 946 removed outlier: 3.507A pdb=" N ALA L 929 " --> pdb=" O GLN L 925 " (cutoff:3.500A) Processing helix chain 'L' and resid 959 through 973 removed outlier: 3.669A pdb=" N ARG L 964 " --> pdb=" O GLN L 960 " (cutoff:3.500A) Proline residue: L 967 - end of helix Processing helix chain 'L' and resid 978 through 994 removed outlier: 3.673A pdb=" N LEU L 983 " --> pdb=" O VAL L 979 " (cutoff:3.500A) Proline residue: L 986 - end of helix Processing helix chain 'L' and resid 1000 through 1002 No H-bonds generated for 'chain 'L' and resid 1000 through 1002' Processing helix chain 'L' and resid 1004 through 1018 removed outlier: 4.856A pdb=" N VAL L1018 " --> pdb=" O LEU L1014 " (cutoff:3.500A) Processing helix chain 'L' and resid 1023 through 1042 removed outlier: 3.794A pdb=" N ASP L1027 " --> pdb=" O SER L1023 " (cutoff:3.500A) Processing helix chain 'L' and resid 1046 through 1049 No H-bonds generated for 'chain 'L' and resid 1046 through 1049' Processing helix chain 'L' and resid 1056 through 1068 removed outlier: 3.988A pdb=" N PHE L1060 " --> pdb=" O THR L1056 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER L1065 " --> pdb=" O LYS L1061 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU L1066 " --> pdb=" O ARG L1062 " (cutoff:3.500A) Processing helix chain 'L' and resid 1072 through 1089 removed outlier: 3.516A pdb=" N PHE L1082 " --> pdb=" O ALA L1078 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ARG L1087 " --> pdb=" O ASN L1083 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N GLU L1088 " --> pdb=" O ASN L1084 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE L1089 " --> pdb=" O ILE L1085 " (cutoff:3.500A) Processing helix chain 'L' and resid 1096 through 1112 removed outlier: 3.513A pdb=" N VAL L1100 " --> pdb=" O GLU L1097 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU L1104 " --> pdb=" O PHE L1101 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR L1107 " --> pdb=" O LEU L1104 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU L1109 " --> pdb=" O ILE L1106 " (cutoff:3.500A) Processing helix chain 'L' and resid 1124 through 1144 removed outlier: 4.355A pdb=" N ASP L1129 " --> pdb=" O GLN L1125 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ALA L1130 " --> pdb=" O GLN L1126 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ILE L1131 " --> pdb=" O CYS L1127 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASP L1132 " --> pdb=" O CYS L1128 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N HIS L1133 " --> pdb=" O ASP L1129 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU L1134 " --> pdb=" O ALA L1130 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ILE L1138 " --> pdb=" O LEU L1134 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL L1143 " --> pdb=" O GLU L1139 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N SER L1144 " --> pdb=" O LYS L1140 " (cutoff:3.500A) Processing helix chain 'L' and resid 1164 through 1174 removed outlier: 4.615A pdb=" N VAL L1169 " --> pdb=" O LEU L1165 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS L1170 " --> pdb=" O LEU L1166 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU L1172 " --> pdb=" O LEU L1168 " (cutoff:3.500A) Processing helix chain 'L' and resid 1181 through 1196 Proline residue: L1196 - end of helix Processing helix chain 'L' and resid 1204 through 1214 removed outlier: 4.253A pdb=" N ASP L1210 " --> pdb=" O LEU L1206 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL L1211 " --> pdb=" O TRP L1207 " (cutoff:3.500A) Processing helix chain 'L' and resid 1216 through 1224 Processing helix chain 'L' and resid 1238 through 1242 Processing helix chain 'L' and resid 1251 through 1265 removed outlier: 3.504A pdb=" N ASP L1258 " --> pdb=" O CYS L1255 " (cutoff:3.500A) Processing helix chain 'L' and resid 1267 through 1270 No H-bonds generated for 'chain 'L' and resid 1267 through 1270' Processing helix chain 'L' and resid 1278 through 1281 No H-bonds generated for 'chain 'L' and resid 1278 through 1281' Processing helix chain 'L' and resid 1288 through 1300 removed outlier: 4.542A pdb=" N VAL L1294 " --> pdb=" O LEU L1290 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ALA L1295 " --> pdb=" O LEU L1291 " (cutoff:3.500A) Processing helix chain 'L' and resid 1324 through 1347 removed outlier: 4.759A pdb=" N ASN L1331 " --> pdb=" O GLY L1327 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR L1346 " --> pdb=" O MET L1342 " (cutoff:3.500A) Processing helix chain 'L' and resid 1356 through 1359 No H-bonds generated for 'chain 'L' and resid 1356 through 1359' Processing helix chain 'L' and resid 1367 through 1377 Processing helix chain 'L' and resid 1379 through 1381 No H-bonds generated for 'chain 'L' and resid 1379 through 1381' Processing helix chain 'L' and resid 1384 through 1386 No H-bonds generated for 'chain 'L' and resid 1384 through 1386' Processing helix chain 'L' and resid 1389 through 1407 removed outlier: 3.576A pdb=" N HIS L1394 " --> pdb=" O GLN L1390 " (cutoff:3.500A) Proline residue: L1396 - end of helix removed outlier: 3.511A pdb=" N CYS L1399 " --> pdb=" O LEU L1395 " (cutoff:3.500A) Processing helix chain 'L' and resid 1412 through 1416 Processing helix chain 'L' and resid 1427 through 1434 removed outlier: 3.546A pdb=" N CYS L1432 " --> pdb=" O GLU L1429 " (cutoff:3.500A) Processing helix chain 'L' and resid 1446 through 1461 removed outlier: 3.505A pdb=" N VAL L1451 " --> pdb=" O ARG L1447 " (cutoff:3.500A) Processing helix chain 'L' and resid 1463 through 1467 Processing helix chain 'L' and resid 1477 through 1485 removed outlier: 3.641A pdb=" N LEU L1484 " --> pdb=" O GLY L1480 " (cutoff:3.500A) Processing helix chain 'L' and resid 1505 through 1520 Processing helix chain 'L' and resid 1525 through 1532 removed outlier: 4.644A pdb=" N SER L1530 " --> pdb=" O GLU L1526 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU L1531 " --> pdb=" O ARG L1527 " (cutoff:3.500A) Processing helix chain 'L' and resid 1555 through 1562 Processing helix chain 'L' and resid 1564 through 1572 removed outlier: 4.407A pdb=" N GLU L1570 " --> pdb=" O THR L1566 " (cutoff:3.500A) Processing helix chain 'L' and resid 1575 through 1583 Processing helix chain 'L' and resid 1590 through 1607 removed outlier: 5.320A pdb=" N ALA L1595 " --> pdb=" O LYS L1591 " (cutoff:3.500A) Processing helix chain 'L' and resid 1614 through 1624 Processing helix chain 'L' and resid 1626 through 1631 removed outlier: 4.026A pdb=" N SER L1631 " --> pdb=" O LYS L1627 " (cutoff:3.500A) Processing helix chain 'L' and resid 1639 through 1656 removed outlier: 4.293A pdb=" N LEU L1646 " --> pdb=" O LYS L1642 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA L1647 " --> pdb=" O MET L1643 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU L1648 " --> pdb=" O ALA L1644 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU L1649 " --> pdb=" O VAL L1645 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLN L1654 " --> pdb=" O ALA L1650 " (cutoff:3.500A) Processing helix chain 'L' and resid 1668 through 1678 removed outlier: 3.652A pdb=" N TYR L1675 " --> pdb=" O VAL L1671 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ILE L1676 " --> pdb=" O PHE L1672 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER L1677 " --> pdb=" O THR L1673 " (cutoff:3.500A) Processing helix chain 'L' and resid 1686 through 1699 removed outlier: 3.695A pdb=" N THR L1694 " --> pdb=" O GLY L1690 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU L1696 " --> pdb=" O ALA L1692 " (cutoff:3.500A) Proline residue: L1697 - end of helix Processing helix chain 'L' and resid 1707 through 1721 removed outlier: 3.854A pdb=" N VAL L1713 " --> pdb=" O GLU L1709 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA L1720 " --> pdb=" O GLN L1716 " (cutoff:3.500A) Processing helix chain 'L' and resid 1726 through 1728 No H-bonds generated for 'chain 'L' and resid 1726 through 1728' Processing helix chain 'L' and resid 1734 through 1753 removed outlier: 4.150A pdb=" N LEU L1752 " --> pdb=" O ASP L1748 " (cutoff:3.500A) Processing helix chain 'L' and resid 1756 through 1766 removed outlier: 3.605A pdb=" N GLU L1764 " --> pdb=" O GLU L1760 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL L1765 " --> pdb=" O LEU L1761 " (cutoff:3.500A) Processing helix chain 'L' and resid 1775 through 1787 removed outlier: 4.143A pdb=" N SER L1780 " --> pdb=" O GLU L1776 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER L1781 " --> pdb=" O LEU L1777 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE L1782 " --> pdb=" O PHE L1778 " (cutoff:3.500A) Processing helix chain 'L' and resid 1791 through 1806 Processing helix chain 'L' and resid 1813 through 1821 removed outlier: 4.202A pdb=" N VAL L1820 " --> pdb=" O ARG L1816 " (cutoff:3.500A) Processing helix chain 'L' and resid 1824 through 1828 Processing helix chain 'L' and resid 1836 through 1851 removed outlier: 3.678A pdb=" N PHE L1840 " --> pdb=" O LEU L1836 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N VAL L1845 " --> pdb=" O SER L1841 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASP L1846 " --> pdb=" O THR L1842 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ALA L1847 " --> pdb=" O ILE L1843 " (cutoff:3.500A) Processing helix chain 'L' and resid 1855 through 1857 No H-bonds generated for 'chain 'L' and resid 1855 through 1857' Processing helix chain 'L' and resid 1861 through 1875 removed outlier: 4.271A pdb=" N THR L1868 " --> pdb=" O THR L1865 " (cutoff:3.500A) Processing helix chain 'L' and resid 1878 through 1881 No H-bonds generated for 'chain 'L' and resid 1878 through 1881' Processing helix chain 'L' and resid 1886 through 1889 No H-bonds generated for 'chain 'L' and resid 1886 through 1889' Processing helix chain 'L' and resid 1911 through 1915 Processing helix chain 'L' and resid 1917 through 1924 Processing helix chain 'L' and resid 1934 through 1955 Processing helix chain 'L' and resid 1959 through 1963 Processing helix chain 'L' and resid 2094 through 2106 removed outlier: 3.575A pdb=" N ARG L2106 " --> pdb=" O LYS L2102 " (cutoff:3.500A) Processing helix chain 'L' and resid 2120 through 2132 removed outlier: 3.617A pdb=" N TRP L2125 " --> pdb=" O ASP L2121 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N MET L2126 " --> pdb=" O LEU L2122 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE L2128 " --> pdb=" O SER L2124 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LEU L2129 " --> pdb=" O TRP L2125 " (cutoff:3.500A) Processing helix chain 'L' and resid 2140 through 2156 removed outlier: 3.573A pdb=" N LEU L2149 " --> pdb=" O PHE L2145 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL L2150 " --> pdb=" O LEU L2146 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR L2153 " --> pdb=" O LEU L2149 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLU L2155 " --> pdb=" O ILE L2151 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL L2156 " --> pdb=" O ASN L2152 " (cutoff:3.500A) Processing helix chain 'L' and resid 2158 through 2173 removed outlier: 5.182A pdb=" N LYS L2162 " --> pdb=" O PRO L2159 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU L2165 " --> pdb=" O LYS L2162 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER L2166 " --> pdb=" O HIS L2163 " (cutoff:3.500A) Proline residue: L2167 - end of helix removed outlier: 3.503A pdb=" N LEU L2171 " --> pdb=" O LEU L2168 " (cutoff:3.500A) Processing helix chain 'L' and resid 2184 through 2200 removed outlier: 3.708A pdb=" N THR L2197 " --> pdb=" O ILE L2193 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N GLY L2198 " --> pdb=" O LEU L2194 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N LEU L2199 " --> pdb=" O SER L2195 " (cutoff:3.500A) Processing helix chain 'L' and resid 2206 through 2221 removed outlier: 4.543A pdb=" N VAL L2210 " --> pdb=" O PRO L2206 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG L2214 " --> pdb=" O VAL L2210 " (cutoff:3.500A) Processing helix chain 'L' and resid 2228 through 2243 removed outlier: 3.569A pdb=" N ILE L2238 " --> pdb=" O ASN L2234 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR L2240 " --> pdb=" O GLU L2236 " (cutoff:3.500A) Processing helix chain 'L' and resid 2253 through 2261 removed outlier: 4.242A pdb=" N GLU L2258 " --> pdb=" O ARG L2254 " (cutoff:3.500A) Processing helix chain 'L' and resid 2271 through 2282 Processing helix chain 'L' and resid 2296 through 2308 removed outlier: 4.930A pdb=" N GLN L2301 " --> pdb=" O SER L2297 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N MET L2307 " --> pdb=" O LEU L2303 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N SER L2308 " --> pdb=" O VAL L2304 " (cutoff:3.500A) Processing helix chain 'L' and resid 2313 through 2332 removed outlier: 4.430A pdb=" N ALA L2318 " --> pdb=" O GLU L2314 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA L2319 " --> pdb=" O VAL L2315 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA L2320 " --> pdb=" O TYR L2316 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU L2325 " --> pdb=" O GLU L2321 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ARG L2328 " --> pdb=" O GLY L2324 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU L2332 " --> pdb=" O ARG L2328 " (cutoff:3.500A) Processing helix chain 'L' and resid 2336 through 2353 removed outlier: 4.069A pdb=" N LEU L2341 " --> pdb=" O GLU L2338 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N CYS L2342 " --> pdb=" O GLU L2339 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL L2345 " --> pdb=" O CYS L2342 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS L2350 " --> pdb=" O LYS L2347 " (cutoff:3.500A) Processing helix chain 'L' and resid 2357 through 2368 Processing helix chain 'L' and resid 2373 through 2385 removed outlier: 4.413A pdb=" N MET L2379 " --> pdb=" O ASP L2376 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASN L2380 " --> pdb=" O ARG L2377 " (cutoff:3.500A) Processing helix chain 'L' and resid 2391 through 2402 removed outlier: 3.759A pdb=" N GLU L2399 " --> pdb=" O LEU L2396 " (cutoff:3.500A) Processing helix chain 'L' and resid 2411 through 2417 Processing helix chain 'L' and resid 2420 through 2425 removed outlier: 3.945A pdb=" N ARG L2425 " --> pdb=" O VAL L2421 " (cutoff:3.500A) Processing helix chain 'L' and resid 2429 through 2445 Proline residue: L2444 - end of helix Processing helix chain 'L' and resid 2448 through 2463 removed outlier: 3.653A pdb=" N GLU L2453 " --> pdb=" O VAL L2449 " (cutoff:3.500A) Proline residue: L2457 - end of helix removed outlier: 3.689A pdb=" N GLU L2460 " --> pdb=" O ASN L2456 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE L2461 " --> pdb=" O PRO L2457 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N VAL L2462 " --> pdb=" O VAL L2458 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N SER L2463 " --> pdb=" O VAL L2459 " (cutoff:3.500A) Processing helix chain 'L' and resid 2467 through 2484 removed outlier: 3.557A pdb=" N ASP L2482 " --> pdb=" O MET L2478 " (cutoff:3.500A) Processing helix chain 'L' and resid 2493 through 2511 removed outlier: 3.509A pdb=" N ILE L2498 " --> pdb=" O ASP L2494 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN L2508 " --> pdb=" O ASP L2504 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU L2510 " --> pdb=" O LEU L2506 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE L2511 " --> pdb=" O ILE L2507 " (cutoff:3.500A) Processing helix chain 'L' and resid 2515 through 2526 Processing helix chain 'L' and resid 2535 through 2544 removed outlier: 4.132A pdb=" N ASN L2543 " --> pdb=" O LEU L2539 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N SER L2544 " --> pdb=" O LEU L2540 " (cutoff:3.500A) Processing helix chain 'L' and resid 2548 through 2568 removed outlier: 5.624A pdb=" N VAL L2552 " --> pdb=" O LYS L2549 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LEU L2555 " --> pdb=" O VAL L2552 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA L2558 " --> pdb=" O LEU L2555 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR L2559 " --> pdb=" O SER L2556 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU L2563 " --> pdb=" O ASN L2560 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU L2564 " --> pdb=" O PHE L2561 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N MET L2568 " --> pdb=" O MET L2565 " (cutoff:3.500A) Processing helix chain 'L' and resid 2725 through 2728 Processing helix chain 'L' and resid 2736 through 2767 removed outlier: 3.673A pdb=" N ASP L2766 " --> pdb=" O LYS L2762 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA L2767 " --> pdb=" O MET L2763 " (cutoff:3.500A) Processing helix chain 'L' and resid 2787 through 2798 Proline residue: L2793 - end of helix Processing helix chain 'L' and resid 2802 through 2822 removed outlier: 4.613A pdb=" N ASP L2821 " --> pdb=" O LEU L2817 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N LYS L2822 " --> pdb=" O LYS L2818 " (cutoff:3.500A) Processing helix chain 'L' and resid 2826 through 2846 removed outlier: 3.909A pdb=" N ASN L2831 " --> pdb=" O SER L2827 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG L2842 " --> pdb=" O GLN L2838 " (cutoff:3.500A) Processing helix chain 'L' and resid 2852 through 2863 removed outlier: 3.940A pdb=" N GLN L2859 " --> pdb=" O VAL L2855 " (cutoff:3.500A) Processing helix chain 'L' and resid 2868 through 2870 No H-bonds generated for 'chain 'L' and resid 2868 through 2870' Processing helix chain 'L' and resid 2873 through 2882 Processing helix chain 'L' and resid 2886 through 2899 Processing helix chain 'L' and resid 2920 through 2932 Processing helix chain 'L' and resid 2936 through 2943 removed outlier: 4.016A pdb=" N ARG L2940 " --> pdb=" O TYR L2936 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N GLY L2941 " --> pdb=" O ASP L2937 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE L2942 " --> pdb=" O VAL L2938 " (cutoff:3.500A) Processing helix chain 'L' and resid 2952 through 2961 Processing helix chain 'L' and resid 2965 through 2977 Processing helix chain 'L' and resid 2988 through 3004 Processing helix chain 'L' and resid 3008 through 3017 Processing helix chain 'L' and resid 3027 through 3032 removed outlier: 4.105A pdb=" N TRP L3031 " --> pdb=" O ASN L3028 " (cutoff:3.500A) Processing helix chain 'L' and resid 3034 through 3053 removed outlier: 4.576A pdb=" N LEU L3041 " --> pdb=" O GLN L3037 " (cutoff:3.500A) Proline residue: L3042 - end of helix Processing helix chain 'L' and resid 3060 through 3070 removed outlier: 3.947A pdb=" N HIS L3070 " --> pdb=" O ASP L3066 " (cutoff:3.500A) Processing helix chain 'L' and resid 3072 through 3081 removed outlier: 3.594A pdb=" N LEU L3080 " --> pdb=" O ALA L3076 " (cutoff:3.500A) Processing helix chain 'L' and resid 3083 through 3092 removed outlier: 3.523A pdb=" N LEU L3091 " --> pdb=" O SER L3087 " (cutoff:3.500A) Processing helix chain 'L' and resid 3096 through 3116 Processing helix chain 'L' and resid 3122 through 3146 removed outlier: 3.585A pdb=" N GLN L3130 " --> pdb=" O LEU L3126 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N SER L3131 " --> pdb=" O THR L3127 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL L3132 " --> pdb=" O LYS L3128 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLN L3133 " --> pdb=" O LEU L3129 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ALA L3134 " --> pdb=" O GLN L3130 " (cutoff:3.500A) Processing helix chain 'L' and resid 3148 through 3151 No H-bonds generated for 'chain 'L' and resid 3148 through 3151' Processing helix chain 'L' and resid 3155 through 3166 removed outlier: 3.825A pdb=" N ARG L3159 " --> pdb=" O VAL L3155 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN L3166 " --> pdb=" O ASN L3162 " (cutoff:3.500A) Processing helix chain 'L' and resid 3176 through 3196 removed outlier: 3.691A pdb=" N ASP L3181 " --> pdb=" O ASN L3177 " (cutoff:3.500A) Processing helix chain 'L' and resid 3228 through 3248 removed outlier: 4.006A pdb=" N SER L3233 " --> pdb=" O SER L3229 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET L3242 " --> pdb=" O MET L3238 " (cutoff:3.500A) Processing helix chain 'L' and resid 3252 through 3268 removed outlier: 3.584A pdb=" N GLU L3261 " --> pdb=" O LYS L3257 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LYS L3264 " --> pdb=" O LYS L3260 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLU L3265 " --> pdb=" O GLU L3261 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N THR L3268 " --> pdb=" O LYS L3264 " (cutoff:3.500A) Processing helix chain 'L' and resid 3270 through 3290 removed outlier: 4.730A pdb=" N SER L3290 " --> pdb=" O CYS L3286 " (cutoff:3.500A) Processing helix chain 'L' and resid 3295 through 3301 Processing helix chain 'L' and resid 3304 through 3307 No H-bonds generated for 'chain 'L' and resid 3304 through 3307' Processing helix chain 'L' and resid 3311 through 3313 No H-bonds generated for 'chain 'L' and resid 3311 through 3313' Processing helix chain 'L' and resid 3320 through 3343 removed outlier: 4.600A pdb=" N GLY L3331 " --> pdb=" O ASN L3327 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU L3341 " --> pdb=" O ILE L3337 " (cutoff:3.500A) Processing helix chain 'L' and resid 3348 through 3351 No H-bonds generated for 'chain 'L' and resid 3348 through 3351' Processing helix chain 'L' and resid 3357 through 3363 Processing helix chain 'L' and resid 3372 through 3392 removed outlier: 3.570A pdb=" N VAL L3389 " --> pdb=" O LEU L3385 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN L3390 " --> pdb=" O SER L3386 " (cutoff:3.500A) Processing helix chain 'L' and resid 3409 through 3429 removed outlier: 3.757A pdb=" N GLU L3429 " --> pdb=" O ARG L3425 " (cutoff:3.500A) Processing helix chain 'L' and resid 3433 through 3455 removed outlier: 4.382A pdb=" N ALA L3441 " --> pdb=" O ALA L3437 " (cutoff:3.500A) Proline residue: L3443 - end of helix removed outlier: 3.806A pdb=" N LYS L3449 " --> pdb=" O LEU L3445 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA L3453 " --> pdb=" O LYS L3449 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LEU L3454 " --> pdb=" O MET L3450 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LYS L3455 " --> pdb=" O LEU L3451 " (cutoff:3.500A) Processing helix chain 'L' and resid 3459 through 3474 Proline residue: L3466 - end of helix removed outlier: 4.874A pdb=" N LEU L3469 " --> pdb=" O PHE L3465 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N GLN L3470 " --> pdb=" O PRO L3466 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU L3473 " --> pdb=" O LEU L3469 " (cutoff:3.500A) Processing helix chain 'L' and resid 3477 through 3483 removed outlier: 3.769A pdb=" N MET L3483 " --> pdb=" O LEU L3480 " (cutoff:3.500A) Processing helix chain 'L' and resid 3487 through 3489 No H-bonds generated for 'chain 'L' and resid 3487 through 3489' Processing helix chain 'L' and resid 3492 through 3496 removed outlier: 3.787A pdb=" N ILE L3496 " --> pdb=" O TRP L3493 " (cutoff:3.500A) Processing helix chain 'L' and resid 3499 through 3505 Processing helix chain 'L' and resid 3509 through 3524 removed outlier: 3.789A pdb=" N GLN L3515 " --> pdb=" O VAL L3512 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N HIS L3516 " --> pdb=" O ALA L3513 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU L3519 " --> pdb=" O HIS L3516 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASN L3524 " --> pdb=" O ILE L3521 " (cutoff:3.500A) Processing helix chain 'L' and resid 3526 through 3537 removed outlier: 4.888A pdb=" N TYR L3531 " --> pdb=" O GLN L3527 " (cutoff:3.500A) Proline residue: L3532 - end of helix removed outlier: 4.299A pdb=" N ILE L3535 " --> pdb=" O TYR L3531 " (cutoff:3.500A) Processing helix chain 'L' and resid 3546 through 3561 removed outlier: 3.954A pdb=" N LYS L3550 " --> pdb=" O SER L3546 " (cutoff:3.500A) Processing helix chain 'L' and resid 3567 through 3579 removed outlier: 3.541A pdb=" N SER L3579 " --> pdb=" O LEU L3575 " (cutoff:3.500A) Processing helix chain 'L' and resid 3582 through 3597 removed outlier: 3.690A pdb=" N SER L3589 " --> pdb=" O LYS L3586 " (cutoff:3.500A) Processing helix chain 'L' and resid 3600 through 3616 removed outlier: 4.165A pdb=" N LYS L3604 " --> pdb=" O VAL L3601 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU L3611 " --> pdb=" O LYS L3608 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG L3612 " --> pdb=" O MET L3609 " (cutoff:3.500A) Processing helix chain 'L' and resid 3627 through 3636 Processing helix chain 'L' and resid 3638 through 3643 Processing helix chain 'L' and resid 3646 through 3652 removed outlier: 3.573A pdb=" N SER L3649 " --> pdb=" O LYS L3646 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LYS L3650 " --> pdb=" O GLY L3647 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU L3651 " --> pdb=" O GLY L3648 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU L3652 " --> pdb=" O SER L3649 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 3646 through 3652' Processing helix chain 'L' and resid 3658 through 3671 removed outlier: 3.790A pdb=" N LEU L3668 " --> pdb=" O MET L3665 " (cutoff:3.500A) Processing helix chain 'L' and resid 3685 through 3689 Processing helix chain 'L' and resid 3713 through 3715 No H-bonds generated for 'chain 'L' and resid 3713 through 3715' Processing helix chain 'L' and resid 3758 through 3777 removed outlier: 3.589A pdb=" N PHE L3768 " --> pdb=" O VAL L3764 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN L3777 " --> pdb=" O GLY L3773 " (cutoff:3.500A) Processing helix chain 'L' and resid 3779 through 3782 No H-bonds generated for 'chain 'L' and resid 3779 through 3782' Processing helix chain 'L' and resid 3812 through 3819 Processing helix chain 'L' and resid 3822 through 3829 removed outlier: 4.451A pdb=" N ALA L3827 " --> pdb=" O GLU L3823 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TYR L3828 " --> pdb=" O GLU L3824 " (cutoff:3.500A) Processing helix chain 'L' and resid 3838 through 3844 removed outlier: 3.851A pdb=" N LEU L3843 " --> pdb=" O LYS L3840 " (cutoff:3.500A) Processing helix chain 'L' and resid 3854 through 3861 removed outlier: 4.943A pdb=" N TYR L3859 " --> pdb=" O MET L3856 " (cutoff:3.500A) Processing helix chain 'L' and resid 3864 through 3875 Processing helix chain 'L' and resid 3882 through 3890 Processing helix chain 'L' and resid 3894 through 3917 Processing helix chain 'L' and resid 3948 through 3951 No H-bonds generated for 'chain 'L' and resid 3948 through 3951' Processing helix chain 'L' and resid 3965 through 3970 Processing helix chain 'L' and resid 3979 through 4004 removed outlier: 3.877A pdb=" N ALA L3990 " --> pdb=" O HIS L3986 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE L3991 " --> pdb=" O ALA L3987 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ASP L3994 " --> pdb=" O ALA L3990 " (cutoff:3.500A) Proline residue: L3995 - end of helix removed outlier: 4.603A pdb=" N LEU L3998 " --> pdb=" O ASP L3994 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR L4001 " --> pdb=" O LEU L3997 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N VAL L4004 " --> pdb=" O ASN L4000 " (cutoff:3.500A) Processing helix chain 'L' and resid 4039 through 4051 removed outlier: 3.672A pdb=" N TYR L4046 " --> pdb=" O GLN L4042 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG L4049 " --> pdb=" O CYS L4045 " (cutoff:3.500A) Processing helix chain 'L' and resid 4056 through 4065 Processing helix chain 'L' and resid 4068 through 4070 No H-bonds generated for 'chain 'L' and resid 4068 through 4070' Processing helix chain 'L' and resid 4072 through 4081 removed outlier: 4.293A pdb=" N ARG L4075 " --> pdb=" O PRO L4072 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL L4078 " --> pdb=" O ARG L4075 " (cutoff:3.500A) Processing helix chain 'L' and resid 4100 through 4112 removed outlier: 3.620A pdb=" N ASP L4109 " --> pdb=" O LYS L4105 " (cutoff:3.500A) Processing helix chain 'L' and resid 4114 through 4117 No H-bonds generated for 'chain 'L' and resid 4114 through 4117' Processing helix chain 'R' and resid 6006 through 6016 removed outlier: 3.517A pdb=" N UNK R6012 " --> pdb=" O UNK R6008 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N UNK R6015 " --> pdb=" O UNK R6011 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 10 removed outlier: 3.682A pdb=" N MET H 10 " --> pdb=" O GLN H 6 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 61 Processing helix chain 'H' and resid 69 through 83 Proline residue: H 82 - end of helix Processing helix chain 'H' and resid 128 through 134 Processing helix chain 'H' and resid 136 through 169 Processing helix chain 'H' and resid 186 through 196 Processing helix chain 'H' and resid 198 through 201 No H-bonds generated for 'chain 'H' and resid 198 through 201' Processing helix chain 'H' and resid 208 through 213 Processing helix chain 'H' and resid 215 through 223 Processing helix chain 'H' and resid 296 through 298 No H-bonds generated for 'chain 'H' and resid 296 through 298' Processing helix chain 'I' and resid 2 through 10 removed outlier: 3.783A pdb=" N MET I 10 " --> pdb=" O GLN I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 61 Processing helix chain 'I' and resid 69 through 78 Processing helix chain 'I' and resid 128 through 134 Processing helix chain 'I' and resid 136 through 168 removed outlier: 3.537A pdb=" N TYR I 167 " --> pdb=" O GLU I 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 196 Processing helix chain 'I' and resid 198 through 202 Processing helix chain 'I' and resid 208 through 213 Processing helix chain 'I' and resid 215 through 223 Processing helix chain 'I' and resid 296 through 298 No H-bonds generated for 'chain 'I' and resid 296 through 298' Processing helix chain 'B' and resid 19 through 21 No H-bonds generated for 'chain 'B' and resid 19 through 21' Processing helix chain 'B' and resid 30 through 47 removed outlier: 4.575A pdb=" N ARG B 44 " --> pdb=" O MET B 40 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLN B 45 " --> pdb=" O PHE B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 96 Processing helix chain 'B' and resid 107 through 124 removed outlier: 4.821A pdb=" N ILE B 123 " --> pdb=" O GLN B 119 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLY B 124 " --> pdb=" O HIS B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 156 Processing helix chain 'B' and resid 199 through 223 removed outlier: 8.712A pdb=" N GLU B 218 " --> pdb=" O SER B 214 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N ASP B 219 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY B 220 " --> pdb=" O GLU B 216 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU B 221 " --> pdb=" O GLY B 217 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ASP B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU B 223 " --> pdb=" O ASP B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 231 Processing helix chain 'B' and resid 306 through 309 No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 325 through 331 removed outlier: 3.550A pdb=" N GLU B 329 " --> pdb=" O LYS B 325 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLN B 330 " --> pdb=" O VAL B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 350 No H-bonds generated for 'chain 'B' and resid 348 through 350' Processing helix chain 'B' and resid 371 through 382 Processing helix chain 'B' and resid 441 through 443 No H-bonds generated for 'chain 'B' and resid 441 through 443' Processing helix chain 'B' and resid 448 through 460 removed outlier: 4.733A pdb=" N ALA B 456 " --> pdb=" O ASN B 452 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 457 " --> pdb=" O ALA B 453 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 458 " --> pdb=" O VAL B 454 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ASP B 459 " --> pdb=" O ASP B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 481 No H-bonds generated for 'chain 'B' and resid 479 through 481' Processing helix chain 'B' and resid 485 through 499 Processing helix chain 'B' and resid 510 through 516 Processing helix chain 'B' and resid 520 through 536 removed outlier: 3.711A pdb=" N THR B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN B 527 " --> pdb=" O THR B 523 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ILE B 528 " --> pdb=" O THR B 524 " (cutoff:3.500A) Proline residue: B 529 - end of helix removed outlier: 4.243A pdb=" N THR B 535 " --> pdb=" O SER B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 551 Processing helix chain 'C' and resid 8 through 20 removed outlier: 3.589A pdb=" N GLN C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU C 17 " --> pdb=" O LEU C 13 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER C 20 " --> pdb=" O GLN C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 44 removed outlier: 3.855A pdb=" N ALA C 28 " --> pdb=" O ARG C 24 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU C 29 " --> pdb=" O CYS C 25 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA C 30 " --> pdb=" O GLY C 26 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLN C 40 " --> pdb=" O ARG C 36 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS C 42 " --> pdb=" O LEU C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 58 Processing helix chain 'C' and resid 64 through 71 Processing helix chain 'C' and resid 77 through 117 removed outlier: 4.259A pdb=" N GLU C 80 " --> pdb=" O GLU C 77 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU C 83 " --> pdb=" O GLU C 80 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE C 85 " --> pdb=" O ARG C 82 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU C 93 " --> pdb=" O CYS C 90 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N MET C 96 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY C 97 " --> pdb=" O GLU C 94 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N GLN C 98 " --> pdb=" O LYS C 95 " (cutoff:3.500A) Proline residue: C 102 - end of helix removed outlier: 4.862A pdb=" N VAL C 105 " --> pdb=" O PRO C 102 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR C 112 " --> pdb=" O ASN C 109 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS C 117 " --> pdb=" O VAL C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 137 Proline residue: C 126 - end of helix Processing helix chain 'C' and resid 142 through 144 No H-bonds generated for 'chain 'C' and resid 142 through 144' Processing helix chain 'C' and resid 149 through 165 removed outlier: 3.586A pdb=" N PHE C 153 " --> pdb=" O ILE C 149 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU C 159 " --> pdb=" O LYS C 155 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU C 160 " --> pdb=" O PHE C 156 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA C 161 " --> pdb=" O TYR C 157 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LEU C 162 " --> pdb=" O GLY C 158 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS C 163 " --> pdb=" O GLU C 159 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N LYS C 164 " --> pdb=" O LEU C 160 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N LYS C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 184 removed outlier: 3.816A pdb=" N LYS C 173 " --> pdb=" O THR C 169 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR C 175 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY C 182 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU C 183 " --> pdb=" O GLY C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 189 Processing helix chain 'C' and resid 193 through 209 Processing helix chain 'C' and resid 217 through 230 removed outlier: 3.613A pdb=" N SER C 229 " --> pdb=" O LYS C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 256 Processing helix chain 'C' and resid 266 through 282 removed outlier: 5.834A pdb=" N SER C 280 " --> pdb=" O ALA C 276 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLN C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE C 282 " --> pdb=" O HIS C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 288 No H-bonds generated for 'chain 'C' and resid 285 through 288' Processing helix chain 'C' and resid 290 through 302 removed outlier: 3.813A pdb=" N ALA C 302 " --> pdb=" O LEU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 328 removed outlier: 3.755A pdb=" N GLU C 317 " --> pdb=" O LEU C 313 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER C 318 " --> pdb=" O SER C 314 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL C 327 " --> pdb=" O VAL C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 349 removed outlier: 4.154A pdb=" N ASN C 336 " --> pdb=" O MET C 333 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN C 339 " --> pdb=" O ASN C 336 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N MET C 342 " --> pdb=" O GLN C 339 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N PHE C 345 " --> pdb=" O MET C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 376 removed outlier: 3.616A pdb=" N PHE C 369 " --> pdb=" O GLY C 365 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA C 370 " --> pdb=" O TYR C 366 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N GLY C 371 " --> pdb=" O GLY C 367 " (cutoff:3.500A) Proline residue: C 372 - end of helix removed outlier: 4.254A pdb=" N VAL C 375 " --> pdb=" O GLY C 371 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE C 376 " --> pdb=" O PRO C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 395 removed outlier: 3.777A pdb=" N ASP C 382 " --> pdb=" O ALA C 378 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N PHE C 383 " --> pdb=" O LYS C 379 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU C 388 " --> pdb=" O MET C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 423 removed outlier: 3.670A pdb=" N PHE C 413 " --> pdb=" O GLN C 409 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER C 419 " --> pdb=" O GLN C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 443 Proline residue: C 433 - end of helix Processing helix chain 'C' and resid 446 through 448 No H-bonds generated for 'chain 'C' and resid 446 through 448' Processing helix chain 'C' and resid 451 through 471 removed outlier: 3.674A pdb=" N PHE C 465 " --> pdb=" O ILE C 461 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU C 466 " --> pdb=" O VAL C 462 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS C 471 " --> pdb=" O ALA C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 491 removed outlier: 3.756A pdb=" N ASN C 477 " --> pdb=" O PRO C 473 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N CYS C 478 " --> pdb=" O VAL C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 526 No H-bonds generated for 'chain 'C' and resid 524 through 526' Processing helix chain 'C' and resid 528 through 536 Processing helix chain 'C' and resid 538 through 540 No H-bonds generated for 'chain 'C' and resid 538 through 540' Processing helix chain 'C' and resid 558 through 578 removed outlier: 3.673A pdb=" N LEU C 573 " --> pdb=" O VAL C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 617 through 633 removed outlier: 4.534A pdb=" N ALA C 622 " --> pdb=" O LYS C 618 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE C 623 " --> pdb=" O ASP C 619 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU C 632 " --> pdb=" O GLU C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 643 through 659 removed outlier: 3.764A pdb=" N VAL C 646 " --> pdb=" O GLU C 643 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N TYR C 647 " --> pdb=" O PRO C 644 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE C 649 " --> pdb=" O VAL C 646 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER C 650 " --> pdb=" O TYR C 647 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU C 652 " --> pdb=" O PHE C 649 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU C 655 " --> pdb=" O GLU C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 680 Processing helix chain 'C' and resid 700 through 720 removed outlier: 3.535A pdb=" N ALA C 705 " --> pdb=" O TYR C 701 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LYS C 719 " --> pdb=" O ALA C 715 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLN C 720 " --> pdb=" O VAL C 716 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 735 removed outlier: 3.580A pdb=" N SER C 735 " --> pdb=" O THR C 731 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 741 No H-bonds generated for 'chain 'C' and resid 738 through 741' Processing helix chain 'C' and resid 745 through 761 removed outlier: 3.836A pdb=" N VAL C 749 " --> pdb=" O ARG C 746 " (cutoff:3.500A) Proline residue: C 750 - end of helix removed outlier: 4.047A pdb=" N GLN C 753 " --> pdb=" O PRO C 750 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU C 760 " --> pdb=" O LYS C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 763 through 779 Processing helix chain 'C' and resid 782 through 800 Proline residue: C 787 - end of helix removed outlier: 4.523A pdb=" N LYS C 790 " --> pdb=" O GLN C 786 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ASP C 791 " --> pdb=" O PRO C 787 " (cutoff:3.500A) Proline residue: C 794 - end of helix removed outlier: 4.433A pdb=" N ASP C 797 " --> pdb=" O LEU C 793 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N GLY C 798 " --> pdb=" O PRO C 794 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N TYR C 799 " --> pdb=" O CYS C 795 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU C 800 " --> pdb=" O LEU C 796 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 824 removed outlier: 3.553A pdb=" N LYS C 824 " --> pdb=" O ARG C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 828 through 837 Processing helix chain 'C' and resid 848 through 862 Processing helix chain 'C' and resid 864 through 870 removed outlier: 3.670A pdb=" N LYS C 868 " --> pdb=" O GLY C 864 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ASN C 869 " --> pdb=" O GLN C 865 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N LEU C 870 " --> pdb=" O ILE C 866 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 864 through 870' Processing helix chain 'C' and resid 877 through 882 removed outlier: 4.316A pdb=" N SER C 882 " --> pdb=" O GLU C 878 " (cutoff:3.500A) Processing helix chain 'C' and resid 907 through 909 No H-bonds generated for 'chain 'C' and resid 907 through 909' Processing helix chain 'C' and resid 911 through 920 removed outlier: 4.009A pdb=" N GLU C 916 " --> pdb=" O PRO C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 946 removed outlier: 3.506A pdb=" N ALA C 929 " --> pdb=" O GLN C 925 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 973 removed outlier: 3.668A pdb=" N ARG C 964 " --> pdb=" O GLN C 960 " (cutoff:3.500A) Proline residue: C 967 - end of helix Processing helix chain 'C' and resid 978 through 994 removed outlier: 3.673A pdb=" N LEU C 983 " --> pdb=" O VAL C 979 " (cutoff:3.500A) Proline residue: C 986 - end of helix Processing helix chain 'C' and resid 1000 through 1002 No H-bonds generated for 'chain 'C' and resid 1000 through 1002' Processing helix chain 'C' and resid 1004 through 1018 removed outlier: 4.856A pdb=" N VAL C1018 " --> pdb=" O LEU C1014 " (cutoff:3.500A) Processing helix chain 'C' and resid 1023 through 1042 removed outlier: 3.794A pdb=" N ASP C1027 " --> pdb=" O SER C1023 " (cutoff:3.500A) Processing helix chain 'C' and resid 1046 through 1049 No H-bonds generated for 'chain 'C' and resid 1046 through 1049' Processing helix chain 'C' and resid 1056 through 1068 removed outlier: 3.987A pdb=" N PHE C1060 " --> pdb=" O THR C1056 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER C1065 " --> pdb=" O LYS C1061 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU C1066 " --> pdb=" O ARG C1062 " (cutoff:3.500A) Processing helix chain 'C' and resid 1072 through 1089 removed outlier: 3.515A pdb=" N PHE C1082 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ARG C1087 " --> pdb=" O ASN C1083 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N GLU C1088 " --> pdb=" O ASN C1084 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE C1089 " --> pdb=" O ILE C1085 " (cutoff:3.500A) Processing helix chain 'C' and resid 1096 through 1112 removed outlier: 3.513A pdb=" N VAL C1100 " --> pdb=" O GLU C1097 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU C1104 " --> pdb=" O PHE C1101 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR C1107 " --> pdb=" O LEU C1104 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU C1109 " --> pdb=" O ILE C1106 " (cutoff:3.500A) Processing helix chain 'C' and resid 1124 through 1144 removed outlier: 4.355A pdb=" N ASP C1129 " --> pdb=" O GLN C1125 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ALA C1130 " --> pdb=" O GLN C1126 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ILE C1131 " --> pdb=" O CYS C1127 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASP C1132 " --> pdb=" O CYS C1128 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N HIS C1133 " --> pdb=" O ASP C1129 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ILE C1138 " --> pdb=" O LEU C1134 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL C1143 " --> pdb=" O GLU C1139 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N SER C1144 " --> pdb=" O LYS C1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 1164 through 1174 removed outlier: 4.613A pdb=" N VAL C1169 " --> pdb=" O LEU C1165 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS C1170 " --> pdb=" O LEU C1166 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU C1172 " --> pdb=" O LEU C1168 " (cutoff:3.500A) Processing helix chain 'C' and resid 1181 through 1196 Proline residue: C1196 - end of helix Processing helix chain 'C' and resid 1204 through 1214 removed outlier: 4.252A pdb=" N ASP C1210 " --> pdb=" O LEU C1206 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL C1211 " --> pdb=" O TRP C1207 " (cutoff:3.500A) Processing helix chain 'C' and resid 1216 through 1224 Processing helix chain 'C' and resid 1238 through 1242 Processing helix chain 'C' and resid 1251 through 1265 removed outlier: 3.504A pdb=" N ASP C1258 " --> pdb=" O CYS C1255 " (cutoff:3.500A) Processing helix chain 'C' and resid 1267 through 1270 No H-bonds generated for 'chain 'C' and resid 1267 through 1270' Processing helix chain 'C' and resid 1278 through 1281 No H-bonds generated for 'chain 'C' and resid 1278 through 1281' Processing helix chain 'C' and resid 1288 through 1300 removed outlier: 4.542A pdb=" N VAL C1294 " --> pdb=" O LEU C1290 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ALA C1295 " --> pdb=" O LEU C1291 " (cutoff:3.500A) Processing helix chain 'C' and resid 1324 through 1347 removed outlier: 4.758A pdb=" N ASN C1331 " --> pdb=" O GLY C1327 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR C1346 " --> pdb=" O MET C1342 " (cutoff:3.500A) Processing helix chain 'C' and resid 1356 through 1359 No H-bonds generated for 'chain 'C' and resid 1356 through 1359' Processing helix chain 'C' and resid 1367 through 1377 Processing helix chain 'C' and resid 1379 through 1381 No H-bonds generated for 'chain 'C' and resid 1379 through 1381' Processing helix chain 'C' and resid 1384 through 1386 No H-bonds generated for 'chain 'C' and resid 1384 through 1386' Processing helix chain 'C' and resid 1389 through 1407 removed outlier: 3.576A pdb=" N HIS C1394 " --> pdb=" O GLN C1390 " (cutoff:3.500A) Proline residue: C1396 - end of helix removed outlier: 3.512A pdb=" N CYS C1399 " --> pdb=" O LEU C1395 " (cutoff:3.500A) Processing helix chain 'C' and resid 1412 through 1416 Processing helix chain 'C' and resid 1427 through 1434 removed outlier: 3.548A pdb=" N CYS C1432 " --> pdb=" O GLU C1429 " (cutoff:3.500A) Processing helix chain 'C' and resid 1446 through 1461 removed outlier: 3.505A pdb=" N VAL C1451 " --> pdb=" O ARG C1447 " (cutoff:3.500A) Processing helix chain 'C' and resid 1463 through 1467 Processing helix chain 'C' and resid 1477 through 1485 removed outlier: 3.640A pdb=" N LEU C1484 " --> pdb=" O GLY C1480 " (cutoff:3.500A) Processing helix chain 'C' and resid 1505 through 1520 Processing helix chain 'C' and resid 1525 through 1532 removed outlier: 4.644A pdb=" N SER C1530 " --> pdb=" O GLU C1526 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU C1531 " --> pdb=" O ARG C1527 " (cutoff:3.500A) Processing helix chain 'C' and resid 1555 through 1562 Processing helix chain 'C' and resid 1564 through 1572 removed outlier: 4.407A pdb=" N GLU C1570 " --> pdb=" O THR C1566 " (cutoff:3.500A) Processing helix chain 'C' and resid 1575 through 1583 Processing helix chain 'C' and resid 1590 through 1607 removed outlier: 5.320A pdb=" N ALA C1595 " --> pdb=" O LYS C1591 " (cutoff:3.500A) Processing helix chain 'C' and resid 1614 through 1624 Processing helix chain 'C' and resid 1626 through 1631 removed outlier: 4.026A pdb=" N SER C1631 " --> pdb=" O LYS C1627 " (cutoff:3.500A) Processing helix chain 'C' and resid 1639 through 1656 removed outlier: 4.294A pdb=" N LEU C1646 " --> pdb=" O LYS C1642 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA C1647 " --> pdb=" O MET C1643 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU C1648 " --> pdb=" O ALA C1644 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU C1649 " --> pdb=" O VAL C1645 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLN C1654 " --> pdb=" O ALA C1650 " (cutoff:3.500A) Processing helix chain 'C' and resid 1668 through 1678 removed outlier: 3.654A pdb=" N TYR C1675 " --> pdb=" O VAL C1671 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILE C1676 " --> pdb=" O PHE C1672 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER C1677 " --> pdb=" O THR C1673 " (cutoff:3.500A) Processing helix chain 'C' and resid 1686 through 1699 removed outlier: 3.694A pdb=" N THR C1694 " --> pdb=" O GLY C1690 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU C1696 " --> pdb=" O ALA C1692 " (cutoff:3.500A) Proline residue: C1697 - end of helix Processing helix chain 'C' and resid 1707 through 1721 removed outlier: 3.854A pdb=" N VAL C1713 " --> pdb=" O GLU C1709 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA C1720 " --> pdb=" O GLN C1716 " (cutoff:3.500A) Processing helix chain 'C' and resid 1726 through 1728 No H-bonds generated for 'chain 'C' and resid 1726 through 1728' Processing helix chain 'C' and resid 1734 through 1753 removed outlier: 4.150A pdb=" N LEU C1752 " --> pdb=" O ASP C1748 " (cutoff:3.500A) Processing helix chain 'C' and resid 1756 through 1766 removed outlier: 3.606A pdb=" N GLU C1764 " --> pdb=" O GLU C1760 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL C1765 " --> pdb=" O LEU C1761 " (cutoff:3.500A) Processing helix chain 'C' and resid 1775 through 1787 removed outlier: 4.142A pdb=" N SER C1780 " --> pdb=" O GLU C1776 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER C1781 " --> pdb=" O LEU C1777 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE C1782 " --> pdb=" O PHE C1778 " (cutoff:3.500A) Processing helix chain 'C' and resid 1791 through 1806 Processing helix chain 'C' and resid 1813 through 1821 removed outlier: 4.200A pdb=" N VAL C1820 " --> pdb=" O ARG C1816 " (cutoff:3.500A) Processing helix chain 'C' and resid 1824 through 1828 Processing helix chain 'C' and resid 1836 through 1851 removed outlier: 3.678A pdb=" N PHE C1840 " --> pdb=" O LEU C1836 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N VAL C1845 " --> pdb=" O SER C1841 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASP C1846 " --> pdb=" O THR C1842 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ALA C1847 " --> pdb=" O ILE C1843 " (cutoff:3.500A) Processing helix chain 'C' and resid 1855 through 1857 No H-bonds generated for 'chain 'C' and resid 1855 through 1857' Processing helix chain 'C' and resid 1861 through 1875 removed outlier: 4.270A pdb=" N THR C1868 " --> pdb=" O THR C1865 " (cutoff:3.500A) Processing helix chain 'C' and resid 1878 through 1881 No H-bonds generated for 'chain 'C' and resid 1878 through 1881' Processing helix chain 'C' and resid 1886 through 1889 No H-bonds generated for 'chain 'C' and resid 1886 through 1889' Processing helix chain 'C' and resid 1911 through 1915 Processing helix chain 'C' and resid 1917 through 1924 Processing helix chain 'C' and resid 1934 through 1955 Processing helix chain 'C' and resid 1959 through 1963 Processing helix chain 'C' and resid 2094 through 2106 removed outlier: 3.576A pdb=" N ARG C2106 " --> pdb=" O LYS C2102 " (cutoff:3.500A) Processing helix chain 'C' and resid 2120 through 2132 removed outlier: 3.617A pdb=" N TRP C2125 " --> pdb=" O ASP C2121 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N MET C2126 " --> pdb=" O LEU C2122 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE C2128 " --> pdb=" O SER C2124 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LEU C2129 " --> pdb=" O TRP C2125 " (cutoff:3.500A) Processing helix chain 'C' and resid 2140 through 2156 removed outlier: 3.573A pdb=" N LEU C2149 " --> pdb=" O PHE C2145 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL C2150 " --> pdb=" O LEU C2146 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N THR C2153 " --> pdb=" O LEU C2149 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLU C2155 " --> pdb=" O ILE C2151 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL C2156 " --> pdb=" O ASN C2152 " (cutoff:3.500A) Processing helix chain 'C' and resid 2158 through 2173 removed outlier: 5.181A pdb=" N LYS C2162 " --> pdb=" O PRO C2159 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU C2165 " --> pdb=" O LYS C2162 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER C2166 " --> pdb=" O HIS C2163 " (cutoff:3.500A) Proline residue: C2167 - end of helix removed outlier: 3.503A pdb=" N LEU C2171 " --> pdb=" O LEU C2168 " (cutoff:3.500A) Processing helix chain 'C' and resid 2184 through 2200 removed outlier: 3.708A pdb=" N THR C2197 " --> pdb=" O ILE C2193 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N GLY C2198 " --> pdb=" O LEU C2194 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N LEU C2199 " --> pdb=" O SER C2195 " (cutoff:3.500A) Processing helix chain 'C' and resid 2206 through 2221 removed outlier: 4.544A pdb=" N VAL C2210 " --> pdb=" O PRO C2206 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG C2214 " --> pdb=" O VAL C2210 " (cutoff:3.500A) Processing helix chain 'C' and resid 2228 through 2243 removed outlier: 3.568A pdb=" N ILE C2238 " --> pdb=" O ASN C2234 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR C2240 " --> pdb=" O GLU C2236 " (cutoff:3.500A) Processing helix chain 'C' and resid 2253 through 2261 removed outlier: 4.243A pdb=" N GLU C2258 " --> pdb=" O ARG C2254 " (cutoff:3.500A) Processing helix chain 'C' and resid 2271 through 2282 Processing helix chain 'C' and resid 2296 through 2308 removed outlier: 4.930A pdb=" N GLN C2301 " --> pdb=" O SER C2297 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N MET C2307 " --> pdb=" O LEU C2303 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N SER C2308 " --> pdb=" O VAL C2304 " (cutoff:3.500A) Processing helix chain 'C' and resid 2313 through 2332 removed outlier: 4.431A pdb=" N ALA C2318 " --> pdb=" O GLU C2314 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALA C2319 " --> pdb=" O VAL C2315 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA C2320 " --> pdb=" O TYR C2316 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU C2325 " --> pdb=" O GLU C2321 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ARG C2328 " --> pdb=" O GLY C2324 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU C2332 " --> pdb=" O ARG C2328 " (cutoff:3.500A) Processing helix chain 'C' and resid 2336 through 2353 removed outlier: 4.069A pdb=" N LEU C2341 " --> pdb=" O GLU C2338 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N CYS C2342 " --> pdb=" O GLU C2339 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C2345 " --> pdb=" O CYS C2342 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS C2350 " --> pdb=" O LYS C2347 " (cutoff:3.500A) Processing helix chain 'C' and resid 2357 through 2368 Processing helix chain 'C' and resid 2373 through 2385 removed outlier: 4.413A pdb=" N MET C2379 " --> pdb=" O ASP C2376 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASN C2380 " --> pdb=" O ARG C2377 " (cutoff:3.500A) Processing helix chain 'C' and resid 2391 through 2402 removed outlier: 3.760A pdb=" N GLU C2399 " --> pdb=" O LEU C2396 " (cutoff:3.500A) Processing helix chain 'C' and resid 2411 through 2417 Processing helix chain 'C' and resid 2420 through 2425 removed outlier: 3.944A pdb=" N ARG C2425 " --> pdb=" O VAL C2421 " (cutoff:3.500A) Processing helix chain 'C' and resid 2429 through 2445 Proline residue: C2444 - end of helix Processing helix chain 'C' and resid 2448 through 2463 removed outlier: 3.653A pdb=" N GLU C2453 " --> pdb=" O VAL C2449 " (cutoff:3.500A) Proline residue: C2457 - end of helix removed outlier: 3.689A pdb=" N GLU C2460 " --> pdb=" O ASN C2456 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE C2461 " --> pdb=" O PRO C2457 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N VAL C2462 " --> pdb=" O VAL C2458 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N SER C2463 " --> pdb=" O VAL C2459 " (cutoff:3.500A) Processing helix chain 'C' and resid 2467 through 2484 removed outlier: 3.558A pdb=" N ASP C2482 " --> pdb=" O MET C2478 " (cutoff:3.500A) Processing helix chain 'C' and resid 2493 through 2511 removed outlier: 3.508A pdb=" N ILE C2498 " --> pdb=" O ASP C2494 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN C2508 " --> pdb=" O ASP C2504 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU C2510 " --> pdb=" O LEU C2506 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE C2511 " --> pdb=" O ILE C2507 " (cutoff:3.500A) Processing helix chain 'C' and resid 2515 through 2526 Processing helix chain 'C' and resid 2535 through 2544 removed outlier: 4.132A pdb=" N ASN C2543 " --> pdb=" O LEU C2539 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N SER C2544 " --> pdb=" O LEU C2540 " (cutoff:3.500A) Processing helix chain 'C' and resid 2548 through 2568 removed outlier: 5.625A pdb=" N VAL C2552 " --> pdb=" O LYS C2549 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N LEU C2555 " --> pdb=" O VAL C2552 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA C2558 " --> pdb=" O LEU C2555 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR C2559 " --> pdb=" O SER C2556 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU C2563 " --> pdb=" O ASN C2560 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU C2564 " --> pdb=" O PHE C2561 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET C2568 " --> pdb=" O MET C2565 " (cutoff:3.500A) Processing helix chain 'C' and resid 2725 through 2728 Processing helix chain 'C' and resid 2736 through 2767 removed outlier: 3.672A pdb=" N ASP C2766 " --> pdb=" O LYS C2762 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA C2767 " --> pdb=" O MET C2763 " (cutoff:3.500A) Processing helix chain 'C' and resid 2787 through 2798 Proline residue: C2793 - end of helix Processing helix chain 'C' and resid 2802 through 2822 removed outlier: 4.613A pdb=" N ASP C2821 " --> pdb=" O LEU C2817 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N LYS C2822 " --> pdb=" O LYS C2818 " (cutoff:3.500A) Processing helix chain 'C' and resid 2826 through 2846 removed outlier: 3.909A pdb=" N ASN C2831 " --> pdb=" O SER C2827 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG C2842 " --> pdb=" O GLN C2838 " (cutoff:3.500A) Processing helix chain 'C' and resid 2852 through 2863 removed outlier: 3.939A pdb=" N GLN C2859 " --> pdb=" O VAL C2855 " (cutoff:3.500A) Processing helix chain 'C' and resid 2868 through 2870 No H-bonds generated for 'chain 'C' and resid 2868 through 2870' Processing helix chain 'C' and resid 2873 through 2882 Processing helix chain 'C' and resid 2886 through 2899 Processing helix chain 'C' and resid 2920 through 2932 Processing helix chain 'C' and resid 2936 through 2943 removed outlier: 4.016A pdb=" N ARG C2940 " --> pdb=" O TYR C2936 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N GLY C2941 " --> pdb=" O ASP C2937 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE C2942 " --> pdb=" O VAL C2938 " (cutoff:3.500A) Processing helix chain 'C' and resid 2952 through 2961 Processing helix chain 'C' and resid 2965 through 2977 Processing helix chain 'C' and resid 2988 through 3004 Processing helix chain 'C' and resid 3008 through 3017 Processing helix chain 'C' and resid 3027 through 3032 removed outlier: 4.106A pdb=" N TRP C3031 " --> pdb=" O ASN C3028 " (cutoff:3.500A) Processing helix chain 'C' and resid 3034 through 3053 removed outlier: 4.576A pdb=" N LEU C3041 " --> pdb=" O GLN C3037 " (cutoff:3.500A) Proline residue: C3042 - end of helix Processing helix chain 'C' and resid 3060 through 3070 removed outlier: 3.947A pdb=" N HIS C3070 " --> pdb=" O ASP C3066 " (cutoff:3.500A) Processing helix chain 'C' and resid 3072 through 3081 removed outlier: 3.593A pdb=" N LEU C3080 " --> pdb=" O ALA C3076 " (cutoff:3.500A) Processing helix chain 'C' and resid 3083 through 3092 removed outlier: 3.523A pdb=" N LEU C3091 " --> pdb=" O SER C3087 " (cutoff:3.500A) Processing helix chain 'C' and resid 3096 through 3116 Processing helix chain 'C' and resid 3122 through 3146 removed outlier: 3.584A pdb=" N GLN C3130 " --> pdb=" O LEU C3126 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N SER C3131 " --> pdb=" O THR C3127 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL C3132 " --> pdb=" O LYS C3128 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLN C3133 " --> pdb=" O LEU C3129 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ALA C3134 " --> pdb=" O GLN C3130 " (cutoff:3.500A) Processing helix chain 'C' and resid 3148 through 3151 No H-bonds generated for 'chain 'C' and resid 3148 through 3151' Processing helix chain 'C' and resid 3155 through 3166 removed outlier: 3.825A pdb=" N ARG C3159 " --> pdb=" O VAL C3155 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN C3166 " --> pdb=" O ASN C3162 " (cutoff:3.500A) Processing helix chain 'C' and resid 3176 through 3196 removed outlier: 3.691A pdb=" N ASP C3181 " --> pdb=" O ASN C3177 " (cutoff:3.500A) Processing helix chain 'C' and resid 3228 through 3248 removed outlier: 4.005A pdb=" N SER C3233 " --> pdb=" O SER C3229 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET C3242 " --> pdb=" O MET C3238 " (cutoff:3.500A) Processing helix chain 'C' and resid 3252 through 3268 removed outlier: 3.585A pdb=" N GLU C3261 " --> pdb=" O LYS C3257 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N LYS C3264 " --> pdb=" O LYS C3260 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLU C3265 " --> pdb=" O GLU C3261 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N THR C3268 " --> pdb=" O LYS C3264 " (cutoff:3.500A) Processing helix chain 'C' and resid 3270 through 3290 removed outlier: 4.730A pdb=" N SER C3290 " --> pdb=" O CYS C3286 " (cutoff:3.500A) Processing helix chain 'C' and resid 3295 through 3301 Processing helix chain 'C' and resid 3304 through 3307 No H-bonds generated for 'chain 'C' and resid 3304 through 3307' Processing helix chain 'C' and resid 3311 through 3313 No H-bonds generated for 'chain 'C' and resid 3311 through 3313' Processing helix chain 'C' and resid 3320 through 3343 removed outlier: 4.600A pdb=" N GLY C3331 " --> pdb=" O ASN C3327 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU C3341 " --> pdb=" O ILE C3337 " (cutoff:3.500A) Processing helix chain 'C' and resid 3348 through 3351 No H-bonds generated for 'chain 'C' and resid 3348 through 3351' Processing helix chain 'C' and resid 3357 through 3363 Processing helix chain 'C' and resid 3372 through 3392 removed outlier: 3.570A pdb=" N VAL C3389 " --> pdb=" O LEU C3385 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN C3390 " --> pdb=" O SER C3386 " (cutoff:3.500A) Processing helix chain 'C' and resid 3409 through 3429 removed outlier: 3.757A pdb=" N GLU C3429 " --> pdb=" O ARG C3425 " (cutoff:3.500A) Processing helix chain 'C' and resid 3433 through 3455 removed outlier: 4.381A pdb=" N ALA C3441 " --> pdb=" O ALA C3437 " (cutoff:3.500A) Proline residue: C3443 - end of helix removed outlier: 3.805A pdb=" N LYS C3449 " --> pdb=" O LEU C3445 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA C3453 " --> pdb=" O LYS C3449 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU C3454 " --> pdb=" O MET C3450 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LYS C3455 " --> pdb=" O LEU C3451 " (cutoff:3.500A) Processing helix chain 'C' and resid 3459 through 3474 Proline residue: C3466 - end of helix removed outlier: 4.874A pdb=" N LEU C3469 " --> pdb=" O PHE C3465 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N GLN C3470 " --> pdb=" O PRO C3466 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU C3473 " --> pdb=" O LEU C3469 " (cutoff:3.500A) Processing helix chain 'C' and resid 3477 through 3483 removed outlier: 3.770A pdb=" N MET C3483 " --> pdb=" O LEU C3480 " (cutoff:3.500A) Processing helix chain 'C' and resid 3487 through 3489 No H-bonds generated for 'chain 'C' and resid 3487 through 3489' Processing helix chain 'C' and resid 3492 through 3496 removed outlier: 3.786A pdb=" N ILE C3496 " --> pdb=" O TRP C3493 " (cutoff:3.500A) Processing helix chain 'C' and resid 3499 through 3505 Processing helix chain 'C' and resid 3509 through 3524 removed outlier: 3.789A pdb=" N GLN C3515 " --> pdb=" O VAL C3512 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N HIS C3516 " --> pdb=" O ALA C3513 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU C3519 " --> pdb=" O HIS C3516 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASN C3524 " --> pdb=" O ILE C3521 " (cutoff:3.500A) Processing helix chain 'C' and resid 3526 through 3537 removed outlier: 4.888A pdb=" N TYR C3531 " --> pdb=" O GLN C3527 " (cutoff:3.500A) Proline residue: C3532 - end of helix removed outlier: 4.299A pdb=" N ILE C3535 " --> pdb=" O TYR C3531 " (cutoff:3.500A) Processing helix chain 'C' and resid 3546 through 3561 removed outlier: 3.953A pdb=" N LYS C3550 " --> pdb=" O SER C3546 " (cutoff:3.500A) Processing helix chain 'C' and resid 3567 through 3579 removed outlier: 3.541A pdb=" N SER C3579 " --> pdb=" O LEU C3575 " (cutoff:3.500A) Processing helix chain 'C' and resid 3582 through 3597 removed outlier: 3.690A pdb=" N SER C3589 " --> pdb=" O LYS C3586 " (cutoff:3.500A) Processing helix chain 'C' and resid 3600 through 3616 removed outlier: 4.165A pdb=" N LYS C3604 " --> pdb=" O VAL C3601 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU C3611 " --> pdb=" O LYS C3608 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG C3612 " --> pdb=" O MET C3609 " (cutoff:3.500A) Processing helix chain 'C' and resid 3627 through 3636 Processing helix chain 'C' and resid 3638 through 3643 Processing helix chain 'C' and resid 3646 through 3652 removed outlier: 3.574A pdb=" N SER C3649 " --> pdb=" O LYS C3646 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LYS C3650 " --> pdb=" O GLY C3647 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU C3651 " --> pdb=" O GLY C3648 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU C3652 " --> pdb=" O SER C3649 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3646 through 3652' Processing helix chain 'C' and resid 3658 through 3671 removed outlier: 3.790A pdb=" N LEU C3668 " --> pdb=" O MET C3665 " (cutoff:3.500A) Processing helix chain 'C' and resid 3685 through 3689 Processing helix chain 'C' and resid 3713 through 3715 No H-bonds generated for 'chain 'C' and resid 3713 through 3715' Processing helix chain 'C' and resid 3758 through 3777 removed outlier: 3.589A pdb=" N PHE C3768 " --> pdb=" O VAL C3764 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN C3777 " --> pdb=" O GLY C3773 " (cutoff:3.500A) Processing helix chain 'C' and resid 3779 through 3782 No H-bonds generated for 'chain 'C' and resid 3779 through 3782' Processing helix chain 'C' and resid 3812 through 3819 Processing helix chain 'C' and resid 3822 through 3829 removed outlier: 4.452A pdb=" N ALA C3827 " --> pdb=" O GLU C3823 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR C3828 " --> pdb=" O GLU C3824 " (cutoff:3.500A) Processing helix chain 'C' and resid 3838 through 3844 removed outlier: 3.851A pdb=" N LEU C3843 " --> pdb=" O LYS C3840 " (cutoff:3.500A) Processing helix chain 'C' and resid 3854 through 3861 removed outlier: 4.943A pdb=" N TYR C3859 " --> pdb=" O MET C3856 " (cutoff:3.500A) Processing helix chain 'C' and resid 3864 through 3875 Processing helix chain 'C' and resid 3882 through 3890 Processing helix chain 'C' and resid 3894 through 3917 Processing helix chain 'C' and resid 3948 through 3951 No H-bonds generated for 'chain 'C' and resid 3948 through 3951' Processing helix chain 'C' and resid 3965 through 3970 Processing helix chain 'C' and resid 3979 through 4004 removed outlier: 3.876A pdb=" N ALA C3990 " --> pdb=" O HIS C3986 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE C3991 " --> pdb=" O ALA C3987 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ASP C3994 " --> pdb=" O ALA C3990 " (cutoff:3.500A) Proline residue: C3995 - end of helix removed outlier: 4.604A pdb=" N LEU C3998 " --> pdb=" O ASP C3994 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR C4001 " --> pdb=" O LEU C3997 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL C4004 " --> pdb=" O ASN C4000 " (cutoff:3.500A) Processing helix chain 'C' and resid 4039 through 4051 removed outlier: 3.672A pdb=" N TYR C4046 " --> pdb=" O GLN C4042 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG C4049 " --> pdb=" O CYS C4045 " (cutoff:3.500A) Processing helix chain 'C' and resid 4056 through 4065 Processing helix chain 'C' and resid 4068 through 4070 No H-bonds generated for 'chain 'C' and resid 4068 through 4070' Processing helix chain 'C' and resid 4072 through 4081 removed outlier: 4.293A pdb=" N ARG C4075 " --> pdb=" O PRO C4072 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL C4078 " --> pdb=" O ARG C4075 " (cutoff:3.500A) Processing helix chain 'C' and resid 4100 through 4112 removed outlier: 3.622A pdb=" N ASP C4109 " --> pdb=" O LYS C4105 " (cutoff:3.500A) Processing helix chain 'C' and resid 4114 through 4117 No H-bonds generated for 'chain 'C' and resid 4114 through 4117' Processing helix chain 'Q' and resid 6006 through 6016 removed outlier: 3.517A pdb=" N UNK Q6012 " --> pdb=" O UNK Q6008 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N UNK Q6015 " --> pdb=" O UNK Q6011 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 30 No H-bonds generated for 'chain 'F' and resid 28 through 30' Processing helix chain 'F' and resid 49 through 59 Processing helix chain 'F' and resid 65 through 74 Processing helix chain 'F' and resid 119 through 200 removed outlier: 4.122A pdb=" N GLU F 173 " --> pdb=" O LYS F 169 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N THR F 174 " --> pdb=" O GLU F 170 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU F 182 " --> pdb=" O LYS F 178 " (cutoff:3.500A) Processing helix chain 'X' and resid 675 through 684 removed outlier: 3.732A pdb=" N GLU X 679 " --> pdb=" O LYS X 675 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN X 680 " --> pdb=" O PRO X 676 " (cutoff:3.500A) Processing helix chain 'X' and resid 707 through 714 Processing helix chain 'X' and resid 723 through 731 removed outlier: 3.805A pdb=" N LEU X 727 " --> pdb=" O PRO X 723 " (cutoff:3.500A) Processing helix chain 'X' and resid 740 through 742 No H-bonds generated for 'chain 'X' and resid 740 through 742' Processing helix chain 'X' and resid 748 through 757 removed outlier: 4.183A pdb=" N ARG X 756 " --> pdb=" O GLU X 752 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU X 757 " --> pdb=" O HIS X 753 " (cutoff:3.500A) Processing helix chain 'X' and resid 771 through 780 Processing helix chain 'X' and resid 789 through 802 Processing helix chain 'X' and resid 805 through 807 No H-bonds generated for 'chain 'X' and resid 805 through 807' Processing helix chain 'X' and resid 809 through 811 No H-bonds generated for 'chain 'X' and resid 809 through 811' Processing helix chain 'X' and resid 837 through 847 Processing helix chain 'X' and resid 872 through 881 removed outlier: 3.504A pdb=" N ARG X 880 " --> pdb=" O LYS X 876 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR X 881 " --> pdb=" O ALA X 877 " (cutoff:3.500A) Processing helix chain 'X' and resid 891 through 899 removed outlier: 3.589A pdb=" N ASP X 896 " --> pdb=" O TRP X 893 " (cutoff:3.500A) Processing helix chain 'X' and resid 906 through 909 Processing helix chain 'G' and resid 11 through 13 No H-bonds generated for 'chain 'G' and resid 11 through 13' Processing helix chain 'G' and resid 49 through 58 removed outlier: 3.692A pdb=" N GLN G 54 " --> pdb=" O SER G 50 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA G 56 " --> pdb=" O ILE G 52 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASP G 57 " --> pdb=" O SER G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 73 Processing helix chain 'G' and resid 119 through 200 Processing helix chain 'T' and resid 180 through 182 No H-bonds generated for 'chain 'T' and resid 180 through 182' Processing helix chain 'O' and resid 28 through 30 No H-bonds generated for 'chain 'O' and resid 28 through 30' Processing helix chain 'O' and resid 49 through 58 Processing helix chain 'O' and resid 65 through 74 Processing helix chain 'O' and resid 119 through 200 removed outlier: 4.123A pdb=" N GLU O 173 " --> pdb=" O LYS O 169 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N THR O 174 " --> pdb=" O GLU O 170 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU O 182 " --> pdb=" O LYS O 178 " (cutoff:3.500A) Processing helix chain 'Y' and resid 675 through 684 removed outlier: 3.732A pdb=" N GLU Y 679 " --> pdb=" O LYS Y 675 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN Y 680 " --> pdb=" O PRO Y 676 " (cutoff:3.500A) Processing helix chain 'Y' and resid 707 through 714 Processing helix chain 'Y' and resid 723 through 731 removed outlier: 3.804A pdb=" N LEU Y 727 " --> pdb=" O PRO Y 723 " (cutoff:3.500A) Processing helix chain 'Y' and resid 740 through 742 No H-bonds generated for 'chain 'Y' and resid 740 through 742' Processing helix chain 'Y' and resid 748 through 757 removed outlier: 4.183A pdb=" N ARG Y 756 " --> pdb=" O GLU Y 752 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU Y 757 " --> pdb=" O HIS Y 753 " (cutoff:3.500A) Processing helix chain 'Y' and resid 771 through 780 Processing helix chain 'Y' and resid 789 through 802 Processing helix chain 'Y' and resid 805 through 807 No H-bonds generated for 'chain 'Y' and resid 805 through 807' Processing helix chain 'Y' and resid 809 through 811 No H-bonds generated for 'chain 'Y' and resid 809 through 811' Processing helix chain 'Y' and resid 837 through 847 Processing helix chain 'Y' and resid 872 through 881 removed outlier: 3.503A pdb=" N ARG Y 880 " --> pdb=" O LYS Y 876 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR Y 881 " --> pdb=" O ALA Y 877 " (cutoff:3.500A) Processing helix chain 'Y' and resid 891 through 899 removed outlier: 3.590A pdb=" N ASP Y 896 " --> pdb=" O TRP Y 893 " (cutoff:3.500A) Processing helix chain 'Y' and resid 906 through 909 Processing helix chain 'P' and resid 11 through 13 No H-bonds generated for 'chain 'P' and resid 11 through 13' Processing helix chain 'P' and resid 49 through 58 removed outlier: 3.692A pdb=" N GLN P 54 " --> pdb=" O SER P 50 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA P 56 " --> pdb=" O ILE P 52 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASP P 57 " --> pdb=" O SER P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 73 Processing helix chain 'P' and resid 119 through 200 Processing sheet with id= A, first strand: chain 'J' and resid 82 through 88 removed outlier: 7.368A pdb=" N SER J 37 " --> pdb=" O SER J 162 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LYS J 164 " --> pdb=" O SER J 37 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ILE J 39 " --> pdb=" O LYS J 164 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ILE J 166 " --> pdb=" O ILE J 39 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N LEU J 41 " --> pdb=" O ILE J 166 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N LEU J 168 " --> pdb=" O LEU J 41 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ASP J 43 " --> pdb=" O LEU J 168 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N PHE J 199 " --> pdb=" O ILE J 166 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N LEU J 168 " --> pdb=" O PHE J 199 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ASP J 201 " --> pdb=" O LEU J 168 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'J' and resid 257 through 262 removed outlier: 3.821A pdb=" N SER J 257 " --> pdb=" O ILE J 273 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE J 273 " --> pdb=" O SER J 257 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE J 269 " --> pdb=" O LEU J 261 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR J 369 " --> pdb=" O GLY J 272 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY J 344 " --> pdb=" O THR J 401 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'J' and resid 318 through 322 Processing sheet with id= D, first strand: chain 'J' and resid 350 through 352 removed outlier: 3.559A pdb=" N ALA J 395 " --> pdb=" O LYS J 351 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 82 through 88 removed outlier: 7.370A pdb=" N SER A 37 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LYS A 164 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ILE A 39 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ILE A 166 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N LEU A 41 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N LEU A 168 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ASP A 43 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N PHE A 199 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N LEU A 168 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ASP A 201 " --> pdb=" O LEU A 168 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 257 through 262 removed outlier: 3.822A pdb=" N SER A 257 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A 273 " --> pdb=" O SER A 257 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 269 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR A 369 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY A 344 " --> pdb=" O THR A 401 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 318 through 322 Processing sheet with id= H, first strand: chain 'A' and resid 350 through 352 removed outlier: 3.561A pdb=" N ALA A 395 " --> pdb=" O LYS A 351 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'K' and resid 53 through 59 removed outlier: 7.534A pdb=" N HIS K 131 " --> pdb=" O VAL K 11 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N CYS K 13 " --> pdb=" O HIS K 131 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLU K 133 " --> pdb=" O CYS K 13 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ASP K 15 " --> pdb=" O GLU K 133 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N PHE K 135 " --> pdb=" O ASP K 15 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N SER K 160 " --> pdb=" O ILE K 132 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ILE K 134 " --> pdb=" O SER K 160 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLN K 162 " --> pdb=" O ILE K 134 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'K' and resid 247 through 251 removed outlier: 4.245A pdb=" N TRP K 247 " --> pdb=" O ALA K 263 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA K 263 " --> pdb=" O TRP K 247 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'K' and resid 313 through 316 Processing sheet with id= L, first strand: chain 'K' and resid 416 through 423 removed outlier: 3.860A pdb=" N ALA K 391 " --> pdb=" O ALA K 408 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N MET K 389 " --> pdb=" O PRO K 410 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY K 344 " --> pdb=" O ILE K 392 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ARG K 394 " --> pdb=" O VAL K 342 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N VAL K 342 " --> pdb=" O ARG K 394 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'L' and resid 893 through 895 Processing sheet with id= N, first strand: chain 'L' and resid 3800 through 3804 removed outlier: 3.897A pdb=" N ARG L3746 " --> pdb=" O GLY L3742 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'L' and resid 3928 through 3931 removed outlier: 4.078A pdb=" N GLY L3936 " --> pdb=" O ALA L3931 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 14 through 18 Processing sheet with id= Q, first strand: chain 'H' and resid 94 through 100 Processing sheet with id= R, first strand: chain 'I' and resid 13 through 17 Processing sheet with id= S, first strand: chain 'I' and resid 94 through 100 Processing sheet with id= T, first strand: chain 'B' and resid 53 through 59 removed outlier: 7.536A pdb=" N HIS B 131 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N CYS B 13 " --> pdb=" O HIS B 131 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLU B 133 " --> pdb=" O CYS B 13 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASP B 15 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N PHE B 135 " --> pdb=" O ASP B 15 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N SER B 160 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ILE B 134 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLN B 162 " --> pdb=" O ILE B 134 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 247 through 251 removed outlier: 4.246A pdb=" N TRP B 247 " --> pdb=" O ALA B 263 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA B 263 " --> pdb=" O TRP B 247 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 313 through 316 Processing sheet with id= W, first strand: chain 'B' and resid 416 through 423 removed outlier: 3.861A pdb=" N ALA B 391 " --> pdb=" O ALA B 408 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N MET B 389 " --> pdb=" O PRO B 410 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY B 344 " --> pdb=" O ILE B 392 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ARG B 394 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N VAL B 342 " --> pdb=" O ARG B 394 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 893 through 895 Processing sheet with id= Y, first strand: chain 'C' and resid 3800 through 3804 removed outlier: 3.896A pdb=" N ARG C3746 " --> pdb=" O GLY C3742 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 3928 through 3931 removed outlier: 4.077A pdb=" N GLY C3936 " --> pdb=" O ALA C3931 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 2 through 8 Processing sheet with id= AB, first strand: chain 'F' and resid 83 through 88 removed outlier: 4.424A pdb=" N VAL F 83 " --> pdb=" O ASN F 100 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY F 109 " --> pdb=" O PHE F 97 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N LYS F 99 " --> pdb=" O ARG F 107 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ARG F 107 " --> pdb=" O LYS F 99 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU F 101 " --> pdb=" O SER F 105 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N SER F 105 " --> pdb=" O LEU F 101 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'X' and resid 688 through 690 removed outlier: 4.000A pdb=" N VAL X 666 " --> pdb=" O VAL X 690 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N CYS X 699 " --> pdb=" O CYS X 665 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET X 667 " --> pdb=" O CYS X 699 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ILE X 701 " --> pdb=" O MET X 667 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'X' and resid 851 through 853 removed outlier: 4.368A pdb=" N LEU X 820 " --> pdb=" O VAL X 853 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N HIS X 862 " --> pdb=" O TYR X 819 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LYS X 887 " --> pdb=" O VAL X 863 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ILE X 865 " --> pdb=" O LYS X 887 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU X 889 " --> pdb=" O ILE X 865 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 2 through 8 Processing sheet with id= AF, first strand: chain 'G' and resid 83 through 88 removed outlier: 3.749A pdb=" N THR G 85 " --> pdb=" O GLU G 98 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N LYS G 99 " --> pdb=" O ARG G 107 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ARG G 107 " --> pdb=" O LYS G 99 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'O' and resid 2 through 8 Processing sheet with id= AH, first strand: chain 'O' and resid 84 through 88 removed outlier: 3.503A pdb=" N GLY O 109 " --> pdb=" O PHE O 97 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LYS O 99 " --> pdb=" O ARG O 107 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ARG O 107 " --> pdb=" O LYS O 99 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU O 101 " --> pdb=" O SER O 105 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N SER O 105 " --> pdb=" O LEU O 101 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'Y' and resid 688 through 690 removed outlier: 4.000A pdb=" N VAL Y 666 " --> pdb=" O VAL Y 690 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N CYS Y 699 " --> pdb=" O CYS Y 665 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET Y 667 " --> pdb=" O CYS Y 699 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE Y 701 " --> pdb=" O MET Y 667 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'Y' and resid 851 through 853 removed outlier: 4.367A pdb=" N LEU Y 820 " --> pdb=" O VAL Y 853 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N HIS Y 862 " --> pdb=" O TYR Y 819 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LYS Y 887 " --> pdb=" O VAL Y 863 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ILE Y 865 " --> pdb=" O LYS Y 887 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU Y 889 " --> pdb=" O ILE Y 865 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'P' and resid 2 through 8 Processing sheet with id= AL, first strand: chain 'P' and resid 83 through 88 removed outlier: 3.749A pdb=" N THR P 85 " --> pdb=" O GLU P 98 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N LYS P 99 " --> pdb=" O ARG P 107 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ARG P 107 " --> pdb=" O LYS P 99 " (cutoff:3.500A) 4074 hydrogen bonds defined for protein. 10836 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 78 hydrogen bonds 148 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 54.86 Time building geometry restraints manager: 32.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.44: 40234 1.44 - 1.79: 54609 1.79 - 2.13: 858 2.13 - 2.48: 0 2.48 - 2.82: 2 Bond restraints: 95703 Sorted by residual: bond pdb=" N THR J 334 " pdb=" CA THR J 334 " ideal model delta sigma weight residual 1.458 2.076 -0.618 1.42e-02 4.96e+03 1.90e+03 bond pdb=" N THR A 334 " pdb=" CA THR A 334 " ideal model delta sigma weight residual 1.458 2.076 -0.618 1.42e-02 4.96e+03 1.89e+03 bond pdb=" CB THR A 334 " pdb=" CG2 THR A 334 " ideal model delta sigma weight residual 1.521 2.824 -1.303 3.30e-02 9.18e+02 1.56e+03 bond pdb=" CB THR J 334 " pdb=" CG2 THR J 334 " ideal model delta sigma weight residual 1.521 2.823 -1.302 3.30e-02 9.18e+02 1.56e+03 bond pdb=" CB THR J 334 " pdb=" OG1 THR J 334 " ideal model delta sigma weight residual 1.433 1.775 -0.342 1.60e-02 3.91e+03 4.57e+02 ... (remaining 95698 not shown) Histogram of bond angle deviations from ideal: 84.64 - 95.56: 15 95.56 - 106.48: 4201 106.48 - 117.40: 62560 117.40 - 128.32: 62228 128.32 - 139.24: 711 Bond angle restraints: 129715 Sorted by residual: angle pdb=" PB ATP L4201 " pdb=" O3B ATP L4201 " pdb=" PG ATP L4201 " ideal model delta sigma weight residual 139.87 121.03 18.84 1.00e+00 1.00e+00 3.55e+02 angle pdb=" PB ATP C4201 " pdb=" O3B ATP C4201 " pdb=" PG ATP C4201 " ideal model delta sigma weight residual 139.87 121.62 18.25 1.00e+00 1.00e+00 3.33e+02 angle pdb=" CA THR J 334 " pdb=" CB THR J 334 " pdb=" OG1 THR J 334 " ideal model delta sigma weight residual 109.60 84.73 24.87 1.50e+00 4.44e-01 2.75e+02 angle pdb=" CA THR A 334 " pdb=" CB THR A 334 " pdb=" OG1 THR A 334 " ideal model delta sigma weight residual 109.60 84.76 24.84 1.50e+00 4.44e-01 2.74e+02 angle pdb=" CA GLU J 333 " pdb=" CB GLU J 333 " pdb=" CG GLU J 333 " ideal model delta sigma weight residual 114.10 84.64 29.46 2.00e+00 2.50e-01 2.17e+02 ... (remaining 129710 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 51291 17.99 - 35.99: 5273 35.99 - 53.98: 1250 53.98 - 71.98: 362 71.98 - 89.97: 139 Dihedral angle restraints: 58315 sinusoidal: 24940 harmonic: 33375 Sorted by residual: dihedral pdb=" C GLU J 333 " pdb=" N GLU J 333 " pdb=" CA GLU J 333 " pdb=" CB GLU J 333 " ideal model delta harmonic sigma weight residual -122.60 -88.41 -34.19 0 2.50e+00 1.60e-01 1.87e+02 dihedral pdb=" C GLU A 333 " pdb=" N GLU A 333 " pdb=" CA GLU A 333 " pdb=" CB GLU A 333 " ideal model delta harmonic sigma weight residual -122.60 -88.44 -34.16 0 2.50e+00 1.60e-01 1.87e+02 dihedral pdb=" N GLU J 333 " pdb=" C GLU J 333 " pdb=" CA GLU J 333 " pdb=" CB GLU J 333 " ideal model delta harmonic sigma weight residual 122.80 92.70 30.10 0 2.50e+00 1.60e-01 1.45e+02 ... (remaining 58312 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.722: 14584 0.722 - 1.443: 28 1.443 - 2.165: 0 2.165 - 2.887: 2 2.887 - 3.609: 2 Chirality restraints: 14616 Sorted by residual: chirality pdb=" CB THR J 334 " pdb=" CA THR J 334 " pdb=" OG1 THR J 334 " pdb=" CG2 THR J 334 " both_signs ideal model delta sigma weight residual False 2.55 6.16 -3.61 2.00e-01 2.50e+01 3.26e+02 chirality pdb=" CB THR A 334 " pdb=" CA THR A 334 " pdb=" OG1 THR A 334 " pdb=" CG2 THR A 334 " both_signs ideal model delta sigma weight residual False 2.55 6.16 -3.60 2.00e-01 2.50e+01 3.25e+02 chirality pdb=" CA GLU J 333 " pdb=" N GLU J 333 " pdb=" C GLU J 333 " pdb=" CB GLU J 333 " both_signs ideal model delta sigma weight residual False 2.51 5.11 -2.60 2.00e-01 2.50e+01 1.69e+02 ... (remaining 14613 not shown) Planarity restraints: 16087 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT N 17 " 0.562 2.00e-02 2.50e+03 3.15e-01 2.48e+03 pdb=" N1 DT N 17 " 0.056 2.00e-02 2.50e+03 pdb=" C2 DT N 17 " -0.129 2.00e-02 2.50e+03 pdb=" O2 DT N 17 " -0.537 2.00e-02 2.50e+03 pdb=" N3 DT N 17 " 0.071 2.00e-02 2.50e+03 pdb=" C4 DT N 17 " 0.143 2.00e-02 2.50e+03 pdb=" O4 DT N 17 " 0.432 2.00e-02 2.50e+03 pdb=" C5 DT N 17 " -0.121 2.00e-02 2.50e+03 pdb=" C7 DT N 17 " -0.355 2.00e-02 2.50e+03 pdb=" C6 DT N 17 " -0.123 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT E 17 " -0.561 2.00e-02 2.50e+03 3.14e-01 2.47e+03 pdb=" N1 DT E 17 " -0.056 2.00e-02 2.50e+03 pdb=" C2 DT E 17 " 0.129 2.00e-02 2.50e+03 pdb=" O2 DT E 17 " 0.536 2.00e-02 2.50e+03 pdb=" N3 DT E 17 " -0.072 2.00e-02 2.50e+03 pdb=" C4 DT E 17 " -0.143 2.00e-02 2.50e+03 pdb=" O4 DT E 17 " -0.431 2.00e-02 2.50e+03 pdb=" C5 DT E 17 " 0.121 2.00e-02 2.50e+03 pdb=" C7 DT E 17 " 0.354 2.00e-02 2.50e+03 pdb=" C6 DT E 17 " 0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA M 7 " -0.335 2.00e-02 2.50e+03 1.55e-01 6.61e+02 pdb=" N9 DA M 7 " -0.004 2.00e-02 2.50e+03 pdb=" C8 DA M 7 " 0.103 2.00e-02 2.50e+03 pdb=" N7 DA M 7 " 0.140 2.00e-02 2.50e+03 pdb=" C5 DA M 7 " 0.107 2.00e-02 2.50e+03 pdb=" C6 DA M 7 " -0.028 2.00e-02 2.50e+03 pdb=" N6 DA M 7 " -0.269 2.00e-02 2.50e+03 pdb=" N1 DA M 7 " -0.036 2.00e-02 2.50e+03 pdb=" C2 DA M 7 " 0.075 2.00e-02 2.50e+03 pdb=" N3 DA M 7 " 0.128 2.00e-02 2.50e+03 pdb=" C4 DA M 7 " 0.119 2.00e-02 2.50e+03 ... (remaining 16084 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 37 2.53 - 3.12: 69675 3.12 - 3.71: 145322 3.71 - 4.31: 200493 4.31 - 4.90: 322153 Nonbonded interactions: 737680 Sorted by model distance: nonbonded pdb=" O ALA S 196 " pdb=" O SER A 477 " model vdw 1.932 3.040 nonbonded pdb=" O SER J 477 " pdb=" O ALA T 196 " model vdw 1.933 3.040 nonbonded pdb=" O THR I 66 " pdb=" CE1 PHE F 106 " model vdw 2.260 3.340 nonbonded pdb=" N ASN C1897 " pdb=" OE1 GLN C1898 " model vdw 2.284 2.520 nonbonded pdb=" N ASN L1897 " pdb=" OE1 GLN L1898 " model vdw 2.284 2.520 ... (remaining 737675 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'L' } ncs_group { reference = chain 'D' selection = chain 'M' } ncs_group { reference = chain 'E' selection = chain 'N' } ncs_group { reference = (chain 'F' and (resid 1 through 76 or resid 83 through 201)) selection = chain 'G' selection = (chain 'O' and (resid 1 through 76 or resid 83 through 201)) selection = chain 'P' } ncs_group { reference = (chain 'H' and (resid 1 through 79 or resid 93 through 299)) selection = chain 'I' } ncs_group { reference = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 6.970 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: 0.070 Extract box with map and model: 24.880 Check model and map are aligned: 1.060 Set scattering table: 0.660 Process input model: 227.080 Find NCS groups from input model: 4.290 Set up NCS constraints: 0.650 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: 0.020 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 268.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5851 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 : 0.015 1.303 95703 Z= 0.953 Angle : 2.002 30.374 129715 Z= 1.324 Chirality : 0.128 3.609 14616 Planarity : 0.021 0.338 16087 Dihedral : 16.512 89.971 36553 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.48 % Favored : 93.32 % Rotamer: Outliers : 1.57 % Allowed : 8.57 % Favored : 89.86 % Cbeta Deviations : 1.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.07), residues: 11179 helix: -2.09 (0.05), residues: 6192 sheet: -0.73 (0.20), residues: 584 loop : -1.70 (0.09), residues: 4403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.216 0.033 TRP C3179 HIS 0.029 0.004 HIS A 359 PHE 0.172 0.018 PHE C1956 TYR 0.272 0.027 TYR L3791 ARG 0.028 0.002 ARG L 9 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22358 Ramachandran restraints generated. 11179 Oldfield, 0 Emsley, 11179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22358 Ramachandran restraints generated. 11179 Oldfield, 0 Emsley, 11179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1399 residues out of total 10141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1240 time to evaluate : 8.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 101 ASN cc_start: 0.8095 (m-40) cc_final: 0.7886 (p0) REVERT: A 483 LEU cc_start: 0.9522 (tt) cc_final: 0.8972 (mm) REVERT: K 212 MET cc_start: 0.9698 (mtt) cc_final: 0.9496 (mtt) REVERT: L 87 LYS cc_start: 0.8364 (mttp) cc_final: 0.7971 (tppp) REVERT: L 342 MET cc_start: 0.8041 (mmp) cc_final: 0.7764 (mmm) REVERT: L 384 MET cc_start: 0.5479 (ptm) cc_final: 0.4510 (ptm) REVERT: L 395 MET cc_start: 0.7938 (mmm) cc_final: 0.7071 (tpt) REVERT: L 653 LEU cc_start: 0.8888 (tp) cc_final: 0.8453 (tp) REVERT: L 878 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7026 (tm-30) REVERT: L 937 MET cc_start: 0.7941 (ttm) cc_final: 0.7709 (ttm) REVERT: L 941 MET cc_start: 0.7750 (mtp) cc_final: 0.6807 (mtp) REVERT: L 958 MET cc_start: 0.7629 (mtp) cc_final: 0.6915 (mtp) REVERT: L 1085 ILE cc_start: 0.8040 (pt) cc_final: 0.7804 (pt) REVERT: L 1120 SER cc_start: 0.8702 (t) cc_final: 0.8456 (p) REVERT: L 1369 MET cc_start: 0.8798 (mmm) cc_final: 0.8473 (mmm) REVERT: L 1640 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8128 (tp30) REVERT: L 1871 MET cc_start: 0.8827 (ttm) cc_final: 0.8437 (tmm) REVERT: L 1934 LEU cc_start: 0.8125 (mm) cc_final: 0.7915 (mm) REVERT: L 2398 LEU cc_start: 0.8940 (mt) cc_final: 0.8522 (tt) REVERT: L 2473 MET cc_start: 0.8808 (tmt) cc_final: 0.8519 (tmm) REVERT: L 2526 SER cc_start: 0.8442 (t) cc_final: 0.7873 (p) REVERT: L 3066 ASP cc_start: 0.8717 (m-30) cc_final: 0.8514 (m-30) REVERT: L 3083 SER cc_start: 0.8990 (p) cc_final: 0.8763 (t) REVERT: L 3136 THR cc_start: 0.9156 (m) cc_final: 0.8860 (p) REVERT: L 3238 MET cc_start: 0.9175 (ttm) cc_final: 0.8897 (ttm) REVERT: L 3242 MET cc_start: 0.9065 (ttp) cc_final: 0.8784 (tpp) REVERT: L 3251 ASN cc_start: 0.8336 (t0) cc_final: 0.7858 (p0) REVERT: L 3283 LEU cc_start: 0.9055 (tp) cc_final: 0.8831 (tp) REVERT: L 3414 MET cc_start: 0.9307 (tpt) cc_final: 0.8941 (tpp) REVERT: L 3613 MET cc_start: 0.6274 (ppp) cc_final: 0.5462 (tpt) REVERT: L 3959 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7164 (pp-130) REVERT: H 169 GLU cc_start: 0.0492 (OUTLIER) cc_final: -0.1450 (mp0) REVERT: B 212 MET cc_start: 0.9588 (mtt) cc_final: 0.9282 (mtt) REVERT: B 330 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.6992 (tt0) REVERT: B 427 MET cc_start: 0.7353 (ppp) cc_final: 0.6840 (ppp) REVERT: C 40 GLN cc_start: 0.7040 (mt0) cc_final: 0.6388 (mt0) REVERT: C 96 MET cc_start: 0.8949 (mmm) cc_final: 0.8743 (mmm) REVERT: C 219 VAL cc_start: 0.9537 (t) cc_final: 0.9277 (p) REVERT: C 384 MET cc_start: 0.5981 (ptm) cc_final: 0.4988 (ptm) REVERT: C 395 MET cc_start: 0.8067 (mmm) cc_final: 0.7159 (tpt) REVERT: C 479 ILE cc_start: 0.9167 (mt) cc_final: 0.8556 (tp) REVERT: C 524 TYR cc_start: 0.8264 (p90) cc_final: 0.7946 (p90) REVERT: C 670 LEU cc_start: 0.9274 (tp) cc_final: 0.8999 (tp) REVERT: C 718 MET cc_start: 0.8600 (ppp) cc_final: 0.8071 (ppp) REVERT: C 785 MET cc_start: 0.7796 (tpp) cc_final: 0.7550 (tpp) REVERT: C 826 PHE cc_start: 0.6566 (m-80) cc_final: 0.5832 (m-10) REVERT: C 827 ASN cc_start: 0.7921 (m110) cc_final: 0.7649 (m110) REVERT: C 883 TYR cc_start: 0.7393 (m-80) cc_final: 0.6948 (m-80) REVERT: C 916 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7705 (mm-30) REVERT: C 1342 MET cc_start: 0.8893 (mtm) cc_final: 0.8571 (ttt) REVERT: C 1871 MET cc_start: 0.8791 (ttm) cc_final: 0.8405 (tmm) REVERT: C 1934 LEU cc_start: 0.8230 (mm) cc_final: 0.8025 (mm) REVERT: C 2504 ASP cc_start: 0.8173 (t0) cc_final: 0.7664 (t70) REVERT: C 2513 GLU cc_start: 0.6983 (tt0) cc_final: 0.6773 (tt0) REVERT: C 2884 LEU cc_start: 0.7828 (tp) cc_final: 0.7547 (tp) REVERT: C 3066 ASP cc_start: 0.8076 (m-30) cc_final: 0.7807 (m-30) REVERT: C 3251 ASN cc_start: 0.7906 (t0) cc_final: 0.7156 (p0) REVERT: C 3654 MET cc_start: 0.3247 (mmp) cc_final: 0.1243 (mmt) REVERT: C 4002 MET cc_start: 0.7838 (tpt) cc_final: 0.7554 (tpp) REVERT: F 1 MET cc_start: 0.0098 (ttt) cc_final: -0.1226 (tpt) REVERT: F 23 SER cc_start: 0.1375 (OUTLIER) cc_final: 0.0844 (p) REVERT: F 61 MET cc_start: -0.0499 (ttm) cc_final: -0.0992 (ptp) REVERT: X 667 MET cc_start: 0.6149 (ttm) cc_final: 0.5716 (tpp) REVERT: O 1 MET cc_start: -0.0177 (ttt) cc_final: -0.1323 (tpt) REVERT: O 23 SER cc_start: 0.1185 (OUTLIER) cc_final: 0.0876 (p) REVERT: O 59 MET cc_start: -0.0079 (mtm) cc_final: -0.0430 (ttt) REVERT: O 76 SER cc_start: -0.1074 (OUTLIER) cc_final: -0.1593 (m) REVERT: O 276 MET cc_start: 0.7481 (mmt) cc_final: 0.7258 (mmm) REVERT: Y 667 MET cc_start: 0.7192 (ttm) cc_final: 0.6881 (tpp) outliers start: 159 outliers final: 39 residues processed: 1376 average time/residue: 0.8664 time to fit residues: 2052.7930 Evaluate side-chains 689 residues out of total 10141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 643 time to evaluate : 8.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1141 random chunks: chunk 963 optimal weight: 9.9990 chunk 864 optimal weight: 1.9990 chunk 479 optimal weight: 40.0000 chunk 295 optimal weight: 6.9990 chunk 583 optimal weight: 30.0000 chunk 462 optimal weight: 6.9990 chunk 894 optimal weight: 0.8980 chunk 346 optimal weight: 5.9990 chunk 543 optimal weight: 30.0000 chunk 665 optimal weight: 2.9990 chunk 1036 optimal weight: 8.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 187 ASN J 68 GLN J 204 HIS J 326 GLN ** J 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 405 ASN J 433 GLN A 68 GLN A 121 GLN A 204 HIS A 326 GLN ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 ASN A 433 GLN K 246 HIS L 185 HIS ** L1687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1866 GLN L2177 ASN ** L2183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L2306 ASN ** L2380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L2456 ASN L2508 GLN L2543 ASN ** L2560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L2830 ASN ** L2865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L3150 ASN ** L3154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L3515 GLN L3573 ASN L3969 ASN L4068 HIS H 42 GLN H 62 ASN H 78 ASN H 213 ASN I 56 GLN B 246 HIS C 185 HIS C 437 HIS ** C 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1866 GLN C2177 ASN ** C2183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2306 ASN ** C2380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2543 ASN ** C2579 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2736 GLN C2865 HIS C3150 ASN C3515 GLN C3573 ASN C3903 HIS ** C3969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4068 HIS ** F 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN ** F 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 833 ASN G 21 GLN ** G 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 187 ASN ** O 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 100 ASN ** O 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 277 GLN Y 833 ASN P 21 GLN P 100 ASN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6097 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 95703 Z= 0.349 Angle : 0.806 11.814 129715 Z= 0.428 Chirality : 0.047 0.266 14616 Planarity : 0.006 0.080 16087 Dihedral : 12.431 85.330 13622 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.96 % Favored : 95.96 % Rotamer: Outliers : 0.27 % Allowed : 3.99 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.35 (0.08), residues: 11179 helix: -0.58 (0.06), residues: 6227 sheet: -0.56 (0.18), residues: 708 loop : -1.23 (0.10), residues: 4244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP G 155 HIS 0.021 0.002 HIS F 40 PHE 0.044 0.003 PHE L1082 TYR 0.025 0.002 TYR C 799 ARG 0.011 0.001 ARG C1936 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22358 Ramachandran restraints generated. 11179 Oldfield, 0 Emsley, 11179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22358 Ramachandran restraints generated. 11179 Oldfield, 0 Emsley, 11179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 10141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 718 time to evaluate : 8.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 79 ASP cc_start: 0.7886 (p0) cc_final: 0.7459 (t0) REVERT: J 346 MET cc_start: 0.7675 (tpt) cc_final: 0.7255 (tpp) REVERT: J 348 MET cc_start: 0.7787 (mmm) cc_final: 0.6589 (mmm) REVERT: A 346 MET cc_start: 0.7714 (tpt) cc_final: 0.7281 (tpp) REVERT: A 348 MET cc_start: 0.7302 (mmm) cc_final: 0.6266 (mmm) REVERT: A 366 LEU cc_start: 0.9463 (tp) cc_final: 0.8836 (mp) REVERT: K 115 MET cc_start: 0.9022 (mmp) cc_final: 0.8742 (mmm) REVERT: L 13 LEU cc_start: 0.8972 (mt) cc_final: 0.8535 (mt) REVERT: L 273 ARG cc_start: 0.8577 (mtt90) cc_final: 0.7717 (mtt90) REVERT: L 384 MET cc_start: 0.5447 (ptm) cc_final: 0.5233 (ptm) REVERT: L 395 MET cc_start: 0.8024 (mmm) cc_final: 0.7240 (tpt) REVERT: L 653 LEU cc_start: 0.9123 (tp) cc_final: 0.8864 (tp) REVERT: L 828 LYS cc_start: 0.8508 (tttp) cc_final: 0.7956 (mmmt) REVERT: L 858 MET cc_start: 0.8791 (tmm) cc_final: 0.8543 (tmm) REVERT: L 948 MET cc_start: 0.8344 (tmm) cc_final: 0.8091 (tmm) REVERT: L 977 ASP cc_start: 0.8570 (t70) cc_final: 0.8081 (p0) REVERT: L 1120 SER cc_start: 0.8597 (t) cc_final: 0.8392 (p) REVERT: L 1871 MET cc_start: 0.8534 (ttm) cc_final: 0.8299 (tmm) REVERT: L 1934 LEU cc_start: 0.8117 (mm) cc_final: 0.7870 (mm) REVERT: L 2094 MET cc_start: 0.6255 (mtt) cc_final: 0.6038 (mtp) REVERT: L 2456 ASN cc_start: 0.8953 (OUTLIER) cc_final: 0.8531 (t0) REVERT: L 2497 GLU cc_start: 0.8434 (tp30) cc_final: 0.8182 (tt0) REVERT: L 2581 LEU cc_start: 0.9093 (mt) cc_final: 0.8879 (mp) REVERT: L 2943 PHE cc_start: 0.7469 (m-10) cc_final: 0.7172 (m-10) REVERT: L 3083 SER cc_start: 0.9049 (p) cc_final: 0.8782 (t) REVERT: L 3104 GLN cc_start: 0.8302 (tm-30) cc_final: 0.8045 (tm-30) REVERT: L 3238 MET cc_start: 0.9233 (ttm) cc_final: 0.8925 (ttm) REVERT: L 3251 ASN cc_start: 0.8370 (t0) cc_final: 0.7903 (t0) REVERT: L 3414 MET cc_start: 0.9312 (tpt) cc_final: 0.8997 (tpp) REVERT: L 3613 MET cc_start: 0.6023 (ppp) cc_final: 0.5552 (tpt) REVERT: L 3654 MET cc_start: 0.3839 (mmm) cc_final: 0.3161 (mmm) REVERT: L 4002 MET cc_start: 0.8031 (tpp) cc_final: 0.7816 (tpp) REVERT: L 4108 MET cc_start: 0.8768 (tmm) cc_final: 0.8507 (tmm) REVERT: H 194 MET cc_start: -0.1966 (mmt) cc_final: -0.2950 (mmt) REVERT: I 159 MET cc_start: 0.1858 (ptt) cc_final: 0.1426 (ptt) REVERT: B 89 ASP cc_start: 0.9368 (OUTLIER) cc_final: 0.8695 (p0) REVERT: B 92 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8631 (pp20) REVERT: B 212 MET cc_start: 0.9472 (mtt) cc_final: 0.9228 (mtt) REVERT: C 282 PHE cc_start: 0.8599 (m-80) cc_final: 0.8398 (m-80) REVERT: C 384 MET cc_start: 0.5601 (ptm) cc_final: 0.5349 (ptm) REVERT: C 395 MET cc_start: 0.7992 (mmm) cc_final: 0.7191 (tpt) REVERT: C 670 LEU cc_start: 0.9092 (tp) cc_final: 0.8838 (tp) REVERT: C 785 MET cc_start: 0.8298 (tpp) cc_final: 0.8057 (tpp) REVERT: C 901 MET cc_start: 0.7620 (ptm) cc_final: 0.7251 (ptm) REVERT: C 1342 MET cc_start: 0.8915 (mtm) cc_final: 0.8634 (ttm) REVERT: C 1871 MET cc_start: 0.8545 (ttm) cc_final: 0.8126 (tmm) REVERT: C 2094 MET cc_start: 0.5715 (mtt) cc_final: 0.5434 (mtp) REVERT: C 2473 MET cc_start: 0.8880 (tmm) cc_final: 0.8640 (tmm) REVERT: C 2980 ASP cc_start: 0.6362 (m-30) cc_final: 0.6063 (m-30) REVERT: C 3066 ASP cc_start: 0.8451 (m-30) cc_final: 0.8106 (m-30) REVERT: C 3654 MET cc_start: 0.2707 (mmp) cc_final: 0.2452 (mmp) REVERT: C 3687 MET cc_start: 0.6467 (mmt) cc_final: 0.5971 (mmt) REVERT: C 3932 MET cc_start: 0.7113 (tmm) cc_final: 0.6450 (tmm) REVERT: C 3980 MET cc_start: 0.8223 (mtp) cc_final: 0.7635 (mtp) REVERT: F 1 MET cc_start: -0.1509 (ttt) cc_final: -0.1767 (tpt) REVERT: F 61 MET cc_start: -0.0423 (ttm) cc_final: -0.1244 (ptp) REVERT: G 1 MET cc_start: 0.2818 (tpt) cc_final: 0.2365 (tpp) REVERT: O 59 MET cc_start: -0.0631 (mtm) cc_final: -0.0869 (tpt) REVERT: P 1 MET cc_start: 0.1115 (tpt) cc_final: -0.2008 (ptt) outliers start: 27 outliers final: 5 residues processed: 745 average time/residue: 0.8601 time to fit residues: 1121.6369 Evaluate side-chains 516 residues out of total 10141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 508 time to evaluate : 8.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1141 random chunks: chunk 575 optimal weight: 8.9990 chunk 321 optimal weight: 40.0000 chunk 862 optimal weight: 0.9990 chunk 705 optimal weight: 0.6980 chunk 285 optimal weight: 10.0000 chunk 1038 optimal weight: 20.0000 chunk 1121 optimal weight: 40.0000 chunk 924 optimal weight: 20.0000 chunk 1029 optimal weight: 0.0670 chunk 353 optimal weight: 5.9990 chunk 832 optimal weight: 20.0000 overall best weight: 3.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 405 ASN J 485 GLN A 278 GLN ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 ASN A 485 GLN K 33 GLN K 382 HIS ** K 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 16 GLN ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1325 GLN L1625 HIS L1725 GLN ** L1738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L2574 ASN L2579 HIS L2736 GLN ** L2859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L3577 GLN L3660 ASN L3903 HIS ** L3927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L3969 ASN L4000 ASN H 149 GLN I 147 GLN B 33 GLN B 382 HIS C 16 GLN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 HIS C 676 ASN ** C 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1325 GLN C1350 ASN C1625 HIS C1725 GLN ** C1738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2560 ASN C2830 ASN C2859 GLN C3112 GLN C3577 GLN C3660 ASN C3927 ASN ** C3969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4000 ASN ** F 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 ASN O 137 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6166 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 95703 Z= 0.308 Angle : 0.699 12.403 129715 Z= 0.367 Chirality : 0.043 0.210 14616 Planarity : 0.005 0.067 16087 Dihedral : 12.008 86.275 13622 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.00 % Favored : 95.97 % Rotamer: Outliers : 0.14 % Allowed : 4.27 % Favored : 95.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.08), residues: 11179 helix: -0.06 (0.06), residues: 6257 sheet: -0.46 (0.18), residues: 761 loop : -1.03 (0.10), residues: 4161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP L2196 HIS 0.013 0.001 HIS F 40 PHE 0.039 0.002 PHE C3236 TYR 0.024 0.002 TYR C2772 ARG 0.010 0.001 ARG I 107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22358 Ramachandran restraints generated. 11179 Oldfield, 0 Emsley, 11179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22358 Ramachandran restraints generated. 11179 Oldfield, 0 Emsley, 11179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 10141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 625 time to evaluate : 8.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 366 LEU cc_start: 0.9503 (tp) cc_final: 0.8973 (mp) REVERT: K 84 MET cc_start: 0.9508 (mpp) cc_final: 0.9249 (mpp) REVERT: K 115 MET cc_start: 0.8965 (mmp) cc_final: 0.8668 (mmp) REVERT: K 389 MET cc_start: 0.8722 (mmp) cc_final: 0.8381 (mmm) REVERT: L 13 LEU cc_start: 0.9078 (mt) cc_final: 0.8664 (mt) REVERT: L 395 MET cc_start: 0.8020 (mmm) cc_final: 0.7481 (tmm) REVERT: L 653 LEU cc_start: 0.9087 (tp) cc_final: 0.8863 (tp) REVERT: L 754 MET cc_start: 0.8252 (tpt) cc_final: 0.8045 (tmm) REVERT: L 828 LYS cc_start: 0.8607 (tttp) cc_final: 0.8131 (mmmt) REVERT: L 858 MET cc_start: 0.8801 (tmm) cc_final: 0.8407 (tmm) REVERT: L 880 MET cc_start: 0.8337 (tpt) cc_final: 0.8018 (tpp) REVERT: L 901 MET cc_start: 0.8509 (ptm) cc_final: 0.8254 (ptm) REVERT: L 1085 ILE cc_start: 0.8577 (pt) cc_final: 0.8335 (pt) REVERT: L 1120 SER cc_start: 0.8698 (t) cc_final: 0.8439 (p) REVERT: L 1871 MET cc_start: 0.8585 (ttm) cc_final: 0.8377 (tmm) REVERT: L 1934 LEU cc_start: 0.8163 (mm) cc_final: 0.7893 (mm) REVERT: L 3079 GLU cc_start: 0.8516 (pt0) cc_final: 0.8243 (pt0) REVERT: L 3104 GLN cc_start: 0.8376 (tm-30) cc_final: 0.8068 (tm-30) REVERT: L 3238 MET cc_start: 0.9231 (ttm) cc_final: 0.8947 (ttm) REVERT: L 3251 ASN cc_start: 0.8670 (t0) cc_final: 0.8057 (t0) REVERT: L 3414 MET cc_start: 0.9223 (tpt) cc_final: 0.8865 (tpp) REVERT: L 3613 MET cc_start: 0.6204 (ppp) cc_final: 0.5734 (tpt) REVERT: L 3654 MET cc_start: 0.3530 (mmm) cc_final: 0.3019 (mmm) REVERT: L 4108 MET cc_start: 0.8610 (tmm) cc_final: 0.8316 (tmm) REVERT: H 50 ASP cc_start: 0.3075 (m-30) cc_final: 0.2834 (m-30) REVERT: H 194 MET cc_start: -0.1676 (mmt) cc_final: -0.2775 (mmt) REVERT: I 159 MET cc_start: 0.2067 (ptt) cc_final: 0.1793 (ptt) REVERT: B 212 MET cc_start: 0.9640 (mtt) cc_final: 0.9284 (mmm) REVERT: C 368 LEU cc_start: 0.8638 (pp) cc_final: 0.8410 (mm) REVERT: C 384 MET cc_start: 0.6222 (ptm) cc_final: 0.6021 (ptm) REVERT: C 392 CYS cc_start: 0.8997 (m) cc_final: 0.8718 (m) REVERT: C 395 MET cc_start: 0.7999 (mmm) cc_final: 0.7396 (tmm) REVERT: C 670 LEU cc_start: 0.9100 (tp) cc_final: 0.8892 (tp) REVERT: C 718 MET cc_start: 0.8456 (tmm) cc_final: 0.8218 (tmm) REVERT: C 827 ASN cc_start: 0.7766 (m110) cc_final: 0.7347 (m-40) REVERT: C 828 LYS cc_start: 0.8589 (tttp) cc_final: 0.8084 (mmmt) REVERT: C 858 MET cc_start: 0.8679 (tmm) cc_final: 0.8360 (tmm) REVERT: C 948 MET cc_start: 0.8081 (tmm) cc_final: 0.7836 (tmm) REVERT: C 1001 PHE cc_start: 0.7184 (t80) cc_final: 0.6745 (t80) REVERT: C 1342 MET cc_start: 0.8837 (mtm) cc_final: 0.8355 (ttm) REVERT: C 1871 MET cc_start: 0.8616 (ttm) cc_final: 0.8214 (tmm) REVERT: C 2094 MET cc_start: 0.5977 (mtt) cc_final: 0.5496 (mtt) REVERT: C 2408 MET cc_start: 0.7702 (ttt) cc_final: 0.7407 (tmm) REVERT: C 2584 CYS cc_start: 0.6867 (t) cc_final: 0.6349 (p) REVERT: C 3066 ASP cc_start: 0.8472 (m-30) cc_final: 0.8155 (m-30) REVERT: C 3687 MET cc_start: 0.6679 (mmt) cc_final: 0.6281 (mmt) REVERT: C 3816 LEU cc_start: 0.9530 (mt) cc_final: 0.9325 (mt) REVERT: F 1 MET cc_start: -0.1262 (ttt) cc_final: -0.1945 (tpt) REVERT: F 61 MET cc_start: -0.0436 (ttm) cc_final: -0.1823 (mtt) REVERT: X 792 MET cc_start: -0.2402 (ttt) cc_final: -0.3067 (ttt) REVERT: G 1 MET cc_start: 0.2635 (tpt) cc_final: 0.2051 (tpp) REVERT: O 61 MET cc_start: -0.1745 (mtm) cc_final: -0.2507 (mtt) REVERT: Y 667 MET cc_start: 0.7404 (ttt) cc_final: 0.6907 (tpt) REVERT: Y 792 MET cc_start: -0.2278 (ttt) cc_final: -0.2741 (ttt) REVERT: P 1 MET cc_start: 0.1398 (tpt) cc_final: -0.1637 (ptt) outliers start: 14 outliers final: 1 residues processed: 637 average time/residue: 0.8424 time to fit residues: 943.0676 Evaluate side-chains 477 residues out of total 10141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 476 time to evaluate : 8.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1141 random chunks: chunk 1025 optimal weight: 50.0000 chunk 780 optimal weight: 4.9990 chunk 538 optimal weight: 50.0000 chunk 114 optimal weight: 10.0000 chunk 495 optimal weight: 7.9990 chunk 697 optimal weight: 0.8980 chunk 1041 optimal weight: 4.9990 chunk 1102 optimal weight: 9.9990 chunk 544 optimal weight: 30.0000 chunk 987 optimal weight: 0.0970 chunk 297 optimal weight: 30.0000 overall best weight: 3.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 16 GLN ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 322 GLN ** L 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1304 HIS L1738 ASN ** L1754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L2233 HIS ** L2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L2574 ASN L2859 GLN ** L2865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L3105 ASN L3590 ASN ** L3927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L3966 GLN L3969 ASN ** L4000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 16 GLN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 869 ASN ** C1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1738 ASN ** C1754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2233 HIS ** C2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3590 ASN ** C3969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 HIS O 21 GLN O 40 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6233 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 95703 Z= 0.330 Angle : 0.688 14.642 129715 Z= 0.357 Chirality : 0.043 0.307 14616 Planarity : 0.005 0.083 16087 Dihedral : 11.871 88.312 13622 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.20 % Favored : 95.77 % Rotamer: Outliers : 0.11 % Allowed : 3.96 % Favored : 95.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.08), residues: 11179 helix: 0.14 (0.07), residues: 6219 sheet: -0.31 (0.18), residues: 744 loop : -0.89 (0.10), residues: 4216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP L2196 HIS 0.010 0.001 HIS L 833 PHE 0.042 0.002 PHE C 710 TYR 0.031 0.002 TYR C2772 ARG 0.010 0.001 ARG C1527 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22358 Ramachandran restraints generated. 11179 Oldfield, 0 Emsley, 11179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22358 Ramachandran restraints generated. 11179 Oldfield, 0 Emsley, 11179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 10141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 571 time to evaluate : 8.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 446 MET cc_start: 0.7020 (pmm) cc_final: 0.6549 (pmm) REVERT: A 62 MET cc_start: 0.9265 (mmm) cc_final: 0.9019 (mtt) REVERT: A 346 MET cc_start: 0.7811 (tpt) cc_final: 0.7239 (tpp) REVERT: A 348 MET cc_start: 0.6928 (mmm) cc_final: 0.5695 (mmm) REVERT: A 514 MET cc_start: 0.8366 (mpp) cc_final: 0.8155 (mpp) REVERT: K 84 MET cc_start: 0.9489 (mpp) cc_final: 0.9242 (mpp) REVERT: K 115 MET cc_start: 0.8985 (mmp) cc_final: 0.8749 (mmp) REVERT: K 212 MET cc_start: 0.9466 (mtp) cc_final: 0.9160 (ttm) REVERT: L 13 LEU cc_start: 0.9239 (mt) cc_final: 0.9039 (mt) REVERT: L 395 MET cc_start: 0.7950 (mmm) cc_final: 0.7399 (tmm) REVERT: L 828 LYS cc_start: 0.8612 (tttp) cc_final: 0.8300 (mptt) REVERT: L 858 MET cc_start: 0.8847 (tmm) cc_final: 0.8407 (tmm) REVERT: L 880 MET cc_start: 0.8527 (tpt) cc_final: 0.8251 (tpp) REVERT: L 932 GLU cc_start: 0.6634 (mt-10) cc_final: 0.6331 (mp0) REVERT: L 1045 THR cc_start: 0.7233 (m) cc_final: 0.6714 (p) REVERT: L 1066 LEU cc_start: 0.9019 (mm) cc_final: 0.8618 (tp) REVERT: L 1085 ILE cc_start: 0.8720 (pt) cc_final: 0.8492 (pt) REVERT: L 1120 SER cc_start: 0.8811 (t) cc_final: 0.8559 (p) REVERT: L 1261 LEU cc_start: 0.9109 (mt) cc_final: 0.8764 (mt) REVERT: L 1342 MET cc_start: 0.7637 (tmm) cc_final: 0.7258 (tmm) REVERT: L 1934 LEU cc_start: 0.8234 (mm) cc_final: 0.7992 (mm) REVERT: L 3079 GLU cc_start: 0.8714 (pt0) cc_final: 0.8336 (pt0) REVERT: L 3238 MET cc_start: 0.9234 (ttm) cc_final: 0.9030 (ttm) REVERT: L 3251 ASN cc_start: 0.8806 (t0) cc_final: 0.8307 (t0) REVERT: L 3256 MET cc_start: 0.8413 (mtm) cc_final: 0.8162 (mpp) REVERT: L 3414 MET cc_start: 0.9216 (tpt) cc_final: 0.8624 (tpp) REVERT: L 3613 MET cc_start: 0.6340 (ppp) cc_final: 0.6003 (tpt) REVERT: L 3654 MET cc_start: 0.3323 (mmm) cc_final: 0.3103 (mmm) REVERT: L 4108 MET cc_start: 0.8567 (tmm) cc_final: 0.8344 (tmm) REVERT: H 50 ASP cc_start: 0.3754 (m-30) cc_final: 0.3398 (m-30) REVERT: H 194 MET cc_start: -0.1544 (mmt) cc_final: -0.2854 (mmt) REVERT: B 389 MET cc_start: 0.8786 (mmp) cc_final: 0.8518 (mmm) REVERT: C 238 MET cc_start: 0.7678 (pmm) cc_final: 0.7383 (pmm) REVERT: C 368 LEU cc_start: 0.8626 (pp) cc_final: 0.8418 (mm) REVERT: C 392 CYS cc_start: 0.9019 (m) cc_final: 0.8753 (m) REVERT: C 395 MET cc_start: 0.8038 (mmm) cc_final: 0.7577 (tmm) REVERT: C 827 ASN cc_start: 0.7545 (m110) cc_final: 0.7105 (m-40) REVERT: C 828 LYS cc_start: 0.8579 (tttp) cc_final: 0.8172 (mmmt) REVERT: C 858 MET cc_start: 0.8654 (tmm) cc_final: 0.8308 (tmm) REVERT: C 948 MET cc_start: 0.8112 (tmm) cc_final: 0.7904 (tmm) REVERT: C 1001 PHE cc_start: 0.7374 (t80) cc_final: 0.7071 (t80) REVERT: C 1342 MET cc_start: 0.8916 (mtm) cc_final: 0.8418 (ttm) REVERT: C 1871 MET cc_start: 0.8638 (ttm) cc_final: 0.8244 (tmm) REVERT: C 2094 MET cc_start: 0.6061 (mtt) cc_final: 0.5660 (mtt) REVERT: C 2584 CYS cc_start: 0.7423 (t) cc_final: 0.6879 (p) REVERT: C 2813 PHE cc_start: 0.7912 (t80) cc_final: 0.7502 (t80) REVERT: C 2830 ASN cc_start: 0.8254 (m110) cc_final: 0.7821 (t0) REVERT: C 3000 ASP cc_start: 0.8517 (t70) cc_final: 0.8263 (t70) REVERT: C 3043 TYR cc_start: 0.9216 (m-80) cc_final: 0.8994 (m-80) REVERT: C 3654 MET cc_start: 0.2951 (mmp) cc_final: 0.2275 (mmt) REVERT: C 3687 MET cc_start: 0.6671 (mmt) cc_final: 0.6339 (mmt) REVERT: F 61 MET cc_start: -0.0556 (ttm) cc_final: -0.1546 (mtt) REVERT: X 792 MET cc_start: -0.2516 (ttt) cc_final: -0.3362 (ttt) REVERT: G 1 MET cc_start: 0.2703 (tpt) cc_final: 0.1688 (tpp) REVERT: O 21 GLN cc_start: 0.2699 (OUTLIER) cc_final: 0.1922 (pm20) REVERT: O 61 MET cc_start: -0.1954 (mtm) cc_final: -0.2227 (mtt) REVERT: Y 667 MET cc_start: 0.7438 (ttt) cc_final: 0.6638 (tpt) REVERT: Y 792 MET cc_start: -0.2590 (ttt) cc_final: -0.3244 (ttt) REVERT: P 1 MET cc_start: 0.1684 (tpt) cc_final: -0.1398 (ptt) outliers start: 11 outliers final: 1 residues processed: 582 average time/residue: 0.8453 time to fit residues: 868.7054 Evaluate side-chains 463 residues out of total 10141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 461 time to evaluate : 10.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1141 random chunks: chunk 918 optimal weight: 8.9990 chunk 626 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 821 optimal weight: 0.0170 chunk 455 optimal weight: 20.0000 chunk 941 optimal weight: 9.9990 chunk 762 optimal weight: 30.0000 chunk 1 optimal weight: 5.9990 chunk 563 optimal weight: 50.0000 chunk 989 optimal weight: 3.9990 chunk 278 optimal weight: 3.9990 overall best weight: 4.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1350 ASN ** L1754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L3969 ASN L4000 ASN H 149 GLN B 119 GLN ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1946 ASN ** C2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3105 ASN C3926 ASN ** C3969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4000 ASN ** O 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6265 moved from start: 0.5214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 95703 Z= 0.332 Angle : 0.676 13.873 129715 Z= 0.351 Chirality : 0.043 0.203 14616 Planarity : 0.005 0.070 16087 Dihedral : 11.866 89.968 13622 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.54 % Favored : 95.45 % Rotamer: Outliers : 0.04 % Allowed : 3.19 % Favored : 96.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.08), residues: 11179 helix: 0.18 (0.06), residues: 6281 sheet: -0.19 (0.19), residues: 746 loop : -0.90 (0.10), residues: 4152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP L2196 HIS 0.008 0.001 HIS C2865 PHE 0.030 0.002 PHE L3946 TYR 0.021 0.002 TYR L 799 ARG 0.010 0.001 ARG L2734 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22358 Ramachandran restraints generated. 11179 Oldfield, 0 Emsley, 11179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22358 Ramachandran restraints generated. 11179 Oldfield, 0 Emsley, 11179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 10141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 536 time to evaluate : 8.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 446 MET cc_start: 0.6982 (pmm) cc_final: 0.6637 (pmm) REVERT: J 514 MET cc_start: 0.8404 (mpp) cc_final: 0.8185 (mpp) REVERT: K 84 MET cc_start: 0.9465 (mpp) cc_final: 0.9223 (mpp) REVERT: K 115 MET cc_start: 0.8897 (mmp) cc_final: 0.8666 (mmp) REVERT: K 212 MET cc_start: 0.9477 (mtp) cc_final: 0.9146 (mtp) REVERT: L 342 MET cc_start: 0.8518 (mpp) cc_final: 0.8253 (mpp) REVERT: L 395 MET cc_start: 0.8015 (mmm) cc_final: 0.7493 (tmm) REVERT: L 828 LYS cc_start: 0.8616 (tttp) cc_final: 0.8236 (mptt) REVERT: L 849 GLU cc_start: 0.8187 (tp30) cc_final: 0.7976 (tm-30) REVERT: L 858 MET cc_start: 0.8887 (tmm) cc_final: 0.8430 (tmm) REVERT: L 932 GLU cc_start: 0.6289 (mt-10) cc_final: 0.6076 (mp0) REVERT: L 1066 LEU cc_start: 0.9003 (mm) cc_final: 0.8547 (tp) REVERT: L 1085 ILE cc_start: 0.8778 (pt) cc_final: 0.8530 (pt) REVERT: L 1120 SER cc_start: 0.8826 (t) cc_final: 0.8593 (p) REVERT: L 1261 LEU cc_start: 0.9204 (mt) cc_final: 0.8917 (mt) REVERT: L 1927 MET cc_start: 0.8452 (pmm) cc_final: 0.8054 (pmm) REVERT: L 1934 LEU cc_start: 0.8203 (mm) cc_final: 0.7915 (mm) REVERT: L 2126 MET cc_start: 0.7818 (mpp) cc_final: 0.7589 (mpp) REVERT: L 2281 MET cc_start: 0.8678 (ttt) cc_final: 0.8131 (tmm) REVERT: L 3079 GLU cc_start: 0.8782 (pt0) cc_final: 0.8446 (pt0) REVERT: L 3238 MET cc_start: 0.9199 (ttm) cc_final: 0.8967 (ttm) REVERT: L 3414 MET cc_start: 0.9200 (tpt) cc_final: 0.8618 (tpp) REVERT: L 3613 MET cc_start: 0.6422 (ppp) cc_final: 0.6092 (tpt) REVERT: L 3654 MET cc_start: 0.3398 (mmm) cc_final: 0.2836 (mmm) REVERT: L 3929 MET cc_start: 0.8818 (mmp) cc_final: 0.8609 (mmm) REVERT: H 50 ASP cc_start: 0.3987 (m-30) cc_final: 0.3528 (m-30) REVERT: H 194 MET cc_start: -0.1607 (mmt) cc_final: -0.2278 (mmt) REVERT: C 238 MET cc_start: 0.7691 (pmm) cc_final: 0.7252 (pmm) REVERT: C 368 LEU cc_start: 0.8683 (pp) cc_final: 0.8429 (mm) REVERT: C 384 MET cc_start: 0.6986 (ptm) cc_final: 0.6729 (ptm) REVERT: C 395 MET cc_start: 0.8042 (mmm) cc_final: 0.7324 (tmm) REVERT: C 827 ASN cc_start: 0.7534 (m110) cc_final: 0.7138 (m-40) REVERT: C 828 LYS cc_start: 0.8579 (tttp) cc_final: 0.8173 (mmmt) REVERT: C 858 MET cc_start: 0.8589 (tmm) cc_final: 0.8178 (tmm) REVERT: C 948 MET cc_start: 0.8195 (tmm) cc_final: 0.7930 (tmm) REVERT: C 1342 MET cc_start: 0.8946 (mtm) cc_final: 0.8411 (ttm) REVERT: C 1871 MET cc_start: 0.8598 (ttp) cc_final: 0.8312 (tmm) REVERT: C 1927 MET cc_start: 0.8345 (pmm) cc_final: 0.7965 (pmm) REVERT: C 2094 MET cc_start: 0.6221 (mtt) cc_final: 0.5757 (mtp) REVERT: C 2126 MET cc_start: 0.7756 (mpp) cc_final: 0.7484 (mpp) REVERT: C 2584 CYS cc_start: 0.7424 (t) cc_final: 0.6906 (p) REVERT: C 2813 PHE cc_start: 0.7921 (t80) cc_final: 0.7577 (t80) REVERT: C 2830 ASN cc_start: 0.8255 (m110) cc_final: 0.7891 (t0) REVERT: C 3043 TYR cc_start: 0.9213 (m-80) cc_final: 0.8942 (m-80) REVERT: C 3687 MET cc_start: 0.6693 (mmt) cc_final: 0.6366 (mmt) REVERT: C 3816 LEU cc_start: 0.9567 (mt) cc_final: 0.9354 (mt) REVERT: C 3929 MET cc_start: 0.7625 (tpp) cc_final: 0.6765 (tpp) REVERT: F 1 MET cc_start: 0.0199 (tpt) cc_final: -0.0131 (tpt) REVERT: F 61 MET cc_start: -0.0678 (ttm) cc_final: -0.1899 (mtt) REVERT: G 1 MET cc_start: 0.2776 (tpt) cc_final: 0.1710 (tpp) REVERT: O 61 MET cc_start: -0.2385 (mtm) cc_final: -0.2737 (mtt) REVERT: Y 667 MET cc_start: 0.7461 (ttt) cc_final: 0.6753 (tpt) REVERT: Y 792 MET cc_start: -0.2933 (ttt) cc_final: -0.3593 (ttt) REVERT: P 1 MET cc_start: 0.1873 (tpt) cc_final: -0.1334 (ptt) outliers start: 4 outliers final: 0 residues processed: 540 average time/residue: 0.8953 time to fit residues: 857.6034 Evaluate side-chains 448 residues out of total 10141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 448 time to evaluate : 8.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1141 random chunks: chunk 371 optimal weight: 0.7980 chunk 993 optimal weight: 30.0000 chunk 218 optimal weight: 0.7980 chunk 647 optimal weight: 8.9990 chunk 272 optimal weight: 0.0980 chunk 1103 optimal weight: 8.9990 chunk 916 optimal weight: 0.9990 chunk 511 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 365 optimal weight: 10.0000 chunk 579 optimal weight: 30.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 738 HIS ** L 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1946 ASN ** L2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L2560 ASN L2795 GLN L2830 ASN L2865 HIS L3379 GLN ** L3470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L3969 ASN L4000 ASN ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN B 514 ASN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 738 HIS ** C 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1721 HIS ** C2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2496 GLN C2830 ASN C3379 GLN ** C3969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4000 ASN ** X 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6201 moved from start: 0.5392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 95703 Z= 0.188 Angle : 0.597 11.364 129715 Z= 0.305 Chirality : 0.040 0.294 14616 Planarity : 0.004 0.056 16087 Dihedral : 11.666 89.497 13622 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.94 % Favored : 96.05 % Rotamer: Outliers : 0.01 % Allowed : 1.95 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.08), residues: 11179 helix: 0.47 (0.07), residues: 6307 sheet: -0.02 (0.19), residues: 740 loop : -0.84 (0.10), residues: 4132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP C2196 HIS 0.006 0.001 HIS C1687 PHE 0.033 0.001 PHE C3946 TYR 0.028 0.001 TYR L3315 ARG 0.012 0.000 ARG C1184 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22358 Ramachandran restraints generated. 11179 Oldfield, 0 Emsley, 11179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22358 Ramachandran restraints generated. 11179 Oldfield, 0 Emsley, 11179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 10141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 554 time to evaluate : 8.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 MET cc_start: 0.4660 (ptt) cc_final: 0.4359 (ptt) REVERT: K 84 MET cc_start: 0.9470 (mpp) cc_final: 0.9195 (mpp) REVERT: K 115 MET cc_start: 0.8862 (mmp) cc_final: 0.8641 (mmp) REVERT: K 212 MET cc_start: 0.9465 (mtp) cc_final: 0.9156 (mtp) REVERT: L 395 MET cc_start: 0.8000 (mmm) cc_final: 0.7692 (tmm) REVERT: L 828 LYS cc_start: 0.8520 (tttp) cc_final: 0.8203 (mmtt) REVERT: L 858 MET cc_start: 0.8767 (tmm) cc_final: 0.8306 (tmm) REVERT: L 1066 LEU cc_start: 0.8928 (mm) cc_final: 0.8490 (tp) REVERT: L 1085 ILE cc_start: 0.8639 (pt) cc_final: 0.8385 (pt) REVERT: L 1120 SER cc_start: 0.8684 (t) cc_final: 0.8400 (p) REVERT: L 1261 LEU cc_start: 0.9150 (mt) cc_final: 0.8857 (mt) REVERT: L 1934 LEU cc_start: 0.8199 (mm) cc_final: 0.7912 (mm) REVERT: L 2126 MET cc_start: 0.7759 (mpp) cc_final: 0.7535 (mpp) REVERT: L 2281 MET cc_start: 0.8551 (ttt) cc_final: 0.8240 (tmm) REVERT: L 2331 MET cc_start: 0.8435 (tpp) cc_final: 0.8039 (tpp) REVERT: L 3079 GLU cc_start: 0.8664 (pt0) cc_final: 0.8393 (pt0) REVERT: L 3238 MET cc_start: 0.9141 (ttm) cc_final: 0.8932 (ttm) REVERT: L 3414 MET cc_start: 0.9213 (tpt) cc_final: 0.8654 (tpp) REVERT: L 3613 MET cc_start: 0.6402 (ppp) cc_final: 0.6066 (tpt) REVERT: L 3654 MET cc_start: 0.3403 (mmm) cc_final: 0.2856 (mmm) REVERT: L 4108 MET cc_start: 0.8470 (tmm) cc_final: 0.8267 (tmm) REVERT: H 50 ASP cc_start: 0.4241 (m-30) cc_final: 0.3723 (m-30) REVERT: H 194 MET cc_start: -0.1783 (mmt) cc_final: -0.2466 (mmt) REVERT: I 159 MET cc_start: 0.5229 (ppp) cc_final: 0.3114 (ptt) REVERT: B 212 MET cc_start: 0.9560 (mtt) cc_final: 0.9320 (mmt) REVERT: B 389 MET cc_start: 0.8643 (mmm) cc_final: 0.8436 (mmm) REVERT: C 238 MET cc_start: 0.7812 (pmm) cc_final: 0.7316 (pmm) REVERT: C 368 LEU cc_start: 0.8745 (pp) cc_final: 0.8474 (mm) REVERT: C 384 MET cc_start: 0.6802 (ptm) cc_final: 0.6581 (ptm) REVERT: C 395 MET cc_start: 0.8070 (mmm) cc_final: 0.7388 (tmm) REVERT: C 858 MET cc_start: 0.8471 (tmm) cc_final: 0.8096 (tmm) REVERT: C 948 MET cc_start: 0.8093 (tmm) cc_final: 0.7793 (tmm) REVERT: C 1342 MET cc_start: 0.8895 (mtm) cc_final: 0.8343 (ttm) REVERT: C 1871 MET cc_start: 0.8608 (ttp) cc_final: 0.8282 (tmm) REVERT: C 1927 MET cc_start: 0.8290 (pmm) cc_final: 0.7884 (pmm) REVERT: C 2126 MET cc_start: 0.7700 (mpp) cc_final: 0.7470 (mpp) REVERT: C 2584 CYS cc_start: 0.7280 (t) cc_final: 0.6745 (p) REVERT: C 2813 PHE cc_start: 0.7889 (t80) cc_final: 0.7551 (t80) REVERT: C 3043 TYR cc_start: 0.9088 (m-80) cc_final: 0.8752 (m-80) REVERT: C 3238 MET cc_start: 0.9087 (ttm) cc_final: 0.8867 (ttm) REVERT: C 3687 MET cc_start: 0.6603 (mmt) cc_final: 0.5899 (mmt) REVERT: C 3816 LEU cc_start: 0.9576 (mt) cc_final: 0.9354 (mt) REVERT: F 1 MET cc_start: 0.0004 (tpt) cc_final: -0.0301 (tpt) REVERT: F 61 MET cc_start: -0.0445 (ttm) cc_final: -0.1694 (mtt) REVERT: X 667 MET cc_start: 0.7086 (mmp) cc_final: 0.5607 (ttp) REVERT: X 792 MET cc_start: -0.3168 (ttt) cc_final: -0.3593 (ttt) REVERT: G 1 MET cc_start: 0.2808 (tpt) cc_final: 0.1722 (tpp) REVERT: O 61 MET cc_start: -0.2414 (mtm) cc_final: -0.2773 (mtt) REVERT: Y 667 MET cc_start: 0.7315 (ttt) cc_final: 0.6606 (tpt) REVERT: Y 792 MET cc_start: -0.3082 (ttt) cc_final: -0.3592 (ttt) REVERT: P 1 MET cc_start: 0.1762 (tpt) cc_final: -0.1398 (ptt) outliers start: 1 outliers final: 0 residues processed: 555 average time/residue: 0.8311 time to fit residues: 815.2014 Evaluate side-chains 446 residues out of total 10141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 446 time to evaluate : 8.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1141 random chunks: chunk 1064 optimal weight: 50.0000 chunk 124 optimal weight: 20.0000 chunk 628 optimal weight: 4.9990 chunk 806 optimal weight: 8.9990 chunk 624 optimal weight: 0.9980 chunk 929 optimal weight: 10.0000 chunk 616 optimal weight: 9.9990 chunk 1099 optimal weight: 1.9990 chunk 688 optimal weight: 10.0000 chunk 670 optimal weight: 1.9990 chunk 507 optimal weight: 9.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 119 GLN ** K 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L3470 GLN ** L3927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L3969 ASN L4000 ASN ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1049 GLN ** C1687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4000 ASN G 9 HIS G 145 GLN ** O 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 9 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6280 moved from start: 0.5755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 95703 Z= 0.320 Angle : 0.660 13.866 129715 Z= 0.339 Chirality : 0.042 0.261 14616 Planarity : 0.004 0.056 16087 Dihedral : 11.636 89.580 13622 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.08), residues: 11179 helix: 0.41 (0.07), residues: 6310 sheet: -0.02 (0.19), residues: 758 loop : -0.86 (0.10), residues: 4111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP C2196 HIS 0.008 0.001 HIS C3850 PHE 0.032 0.002 PHE L1344 TYR 0.036 0.002 TYR C2930 ARG 0.008 0.001 ARG L 888 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22358 Ramachandran restraints generated. 11179 Oldfield, 0 Emsley, 11179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22358 Ramachandran restraints generated. 11179 Oldfield, 0 Emsley, 11179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 10141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 520 time to evaluate : 8.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 514 MET cc_start: 0.8581 (mpp) cc_final: 0.8346 (mpp) REVERT: A 346 MET cc_start: 0.7832 (tpt) cc_final: 0.7631 (tpp) REVERT: A 348 MET cc_start: 0.7131 (mmt) cc_final: 0.5466 (mmt) REVERT: A 453 MET cc_start: 0.4459 (ptt) cc_final: 0.3091 (pmm) REVERT: A 514 MET cc_start: 0.8394 (mpp) cc_final: 0.8179 (mpp) REVERT: K 84 MET cc_start: 0.9413 (mpp) cc_final: 0.9146 (mpp) REVERT: K 115 MET cc_start: 0.8862 (mmp) cc_final: 0.8637 (mmp) REVERT: K 212 MET cc_start: 0.9485 (mtp) cc_final: 0.9107 (mtp) REVERT: L 395 MET cc_start: 0.8077 (mmm) cc_final: 0.7552 (tpt) REVERT: L 540 MET cc_start: 0.6409 (tpp) cc_final: 0.6089 (tpp) REVERT: L 828 LYS cc_start: 0.8562 (tttp) cc_final: 0.8231 (mptt) REVERT: L 858 MET cc_start: 0.8839 (tmm) cc_final: 0.8337 (tmm) REVERT: L 948 MET cc_start: 0.8240 (mtt) cc_final: 0.7843 (tmm) REVERT: L 1085 ILE cc_start: 0.8851 (pt) cc_final: 0.8595 (pt) REVERT: L 1120 SER cc_start: 0.8705 (t) cc_final: 0.8491 (p) REVERT: L 1934 LEU cc_start: 0.8239 (mm) cc_final: 0.7941 (mm) REVERT: L 3079 GLU cc_start: 0.8729 (pt0) cc_final: 0.8488 (pt0) REVERT: L 3414 MET cc_start: 0.9199 (tpt) cc_final: 0.8640 (tpp) REVERT: L 3613 MET cc_start: 0.6401 (ppp) cc_final: 0.6078 (tpt) REVERT: L 3654 MET cc_start: 0.3559 (mmm) cc_final: 0.3130 (mmm) REVERT: L 3929 MET cc_start: 0.8805 (mmp) cc_final: 0.8492 (mmp) REVERT: L 4108 MET cc_start: 0.8500 (tmm) cc_final: 0.8284 (tmm) REVERT: H 50 ASP cc_start: 0.4133 (m-30) cc_final: 0.3604 (m-30) REVERT: H 194 MET cc_start: -0.1653 (mmt) cc_final: -0.2353 (mmt) REVERT: B 84 MET cc_start: 0.9292 (mpp) cc_final: 0.9053 (mpp) REVERT: C 238 MET cc_start: 0.7835 (pmm) cc_final: 0.7234 (pmm) REVERT: C 368 LEU cc_start: 0.8763 (pp) cc_final: 0.8449 (mm) REVERT: C 384 MET cc_start: 0.7049 (ptm) cc_final: 0.6792 (ptm) REVERT: C 395 MET cc_start: 0.8149 (mmm) cc_final: 0.7515 (tmm) REVERT: C 540 MET cc_start: 0.6374 (tpt) cc_final: 0.6170 (mmm) REVERT: C 828 LYS cc_start: 0.8462 (tttp) cc_final: 0.8232 (tppt) REVERT: C 858 MET cc_start: 0.8586 (tmm) cc_final: 0.8146 (tmm) REVERT: C 1342 MET cc_start: 0.8961 (mtm) cc_final: 0.8443 (ttm) REVERT: C 1871 MET cc_start: 0.8678 (ttp) cc_final: 0.8308 (tmm) REVERT: C 2094 MET cc_start: 0.6948 (mmp) cc_final: 0.6543 (mtp) REVERT: C 2408 MET cc_start: 0.7952 (tmm) cc_final: 0.7703 (tmm) REVERT: C 2813 PHE cc_start: 0.8009 (t80) cc_final: 0.7631 (t80) REVERT: C 3043 TYR cc_start: 0.9167 (m-80) cc_final: 0.8819 (m-80) REVERT: C 3238 MET cc_start: 0.9151 (ttm) cc_final: 0.8925 (ttm) REVERT: C 3816 LEU cc_start: 0.9593 (mt) cc_final: 0.9299 (mt) REVERT: F 1 MET cc_start: -0.0157 (tpt) cc_final: -0.0410 (tpt) REVERT: F 61 MET cc_start: -0.0085 (ttm) cc_final: -0.1469 (mtt) REVERT: X 667 MET cc_start: 0.7116 (mmp) cc_final: 0.5645 (ttp) REVERT: G 1 MET cc_start: 0.2882 (tpt) cc_final: 0.1650 (tpp) REVERT: O 61 MET cc_start: -0.2363 (mtm) cc_final: -0.2761 (mtt) REVERT: Y 792 MET cc_start: -0.3113 (ttt) cc_final: -0.3585 (ttt) REVERT: P 1 MET cc_start: 0.1780 (tpt) cc_final: -0.1401 (ptt) outliers start: 0 outliers final: 0 residues processed: 520 average time/residue: 0.8449 time to fit residues: 777.3023 Evaluate side-chains 432 residues out of total 10141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 432 time to evaluate : 8.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1141 random chunks: chunk 680 optimal weight: 8.9990 chunk 439 optimal weight: 3.9990 chunk 656 optimal weight: 10.0000 chunk 331 optimal weight: 4.9990 chunk 216 optimal weight: 0.5980 chunk 213 optimal weight: 2.9990 chunk 699 optimal weight: 0.5980 chunk 749 optimal weight: 9.9990 chunk 543 optimal weight: 8.9990 chunk 102 optimal weight: 8.9990 chunk 864 optimal weight: 0.8980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 HIS ** K 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1721 HIS ** L2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L4000 ASN ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1049 GLN ** C2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3969 ASN C4000 ASN ** O 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6228 moved from start: 0.5875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 95703 Z= 0.197 Angle : 0.597 11.548 129715 Z= 0.304 Chirality : 0.040 0.222 14616 Planarity : 0.004 0.053 16087 Dihedral : 11.533 87.293 13622 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.08), residues: 11179 helix: 0.57 (0.07), residues: 6326 sheet: 0.09 (0.19), residues: 755 loop : -0.81 (0.10), residues: 4098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP C2196 HIS 0.011 0.001 HIS C1367 PHE 0.031 0.001 PHE C3946 TYR 0.025 0.001 TYR C2772 ARG 0.017 0.000 ARG C1184 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22358 Ramachandran restraints generated. 11179 Oldfield, 0 Emsley, 11179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22358 Ramachandran restraints generated. 11179 Oldfield, 0 Emsley, 11179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 10141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 539 time to evaluate : 8.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 203 MET cc_start: 0.8190 (pmm) cc_final: 0.7929 (pmm) REVERT: J 514 MET cc_start: 0.8500 (mpp) cc_final: 0.8269 (mpp) REVERT: A 346 MET cc_start: 0.7662 (tpt) cc_final: 0.7441 (tpp) REVERT: A 348 MET cc_start: 0.7105 (mmt) cc_final: 0.5413 (mmt) REVERT: A 514 MET cc_start: 0.8455 (mpp) cc_final: 0.8233 (mpp) REVERT: K 84 MET cc_start: 0.9424 (mpp) cc_final: 0.9161 (mpp) REVERT: K 212 MET cc_start: 0.9482 (mtp) cc_final: 0.9099 (mtp) REVERT: L 395 MET cc_start: 0.8029 (mmm) cc_final: 0.7401 (tpt) REVERT: L 828 LYS cc_start: 0.8525 (tttp) cc_final: 0.8196 (mptt) REVERT: L 858 MET cc_start: 0.8736 (tmm) cc_final: 0.8312 (tmm) REVERT: L 941 MET cc_start: 0.7398 (mtp) cc_final: 0.7193 (ttm) REVERT: L 1066 LEU cc_start: 0.9042 (mm) cc_final: 0.8507 (tp) REVERT: L 1085 ILE cc_start: 0.8772 (pt) cc_final: 0.8507 (pt) REVERT: L 1120 SER cc_start: 0.8639 (t) cc_final: 0.8420 (p) REVERT: L 1392 MET cc_start: 0.7842 (tpp) cc_final: 0.7573 (tpp) REVERT: L 1934 LEU cc_start: 0.8286 (mm) cc_final: 0.8042 (mm) REVERT: L 2126 MET cc_start: 0.7785 (mpp) cc_final: 0.7564 (mpp) REVERT: L 2408 MET cc_start: 0.7804 (tmm) cc_final: 0.7559 (tmm) REVERT: L 3079 GLU cc_start: 0.8662 (pt0) cc_final: 0.8453 (pt0) REVERT: L 3238 MET cc_start: 0.9253 (mtp) cc_final: 0.8885 (ttm) REVERT: L 3414 MET cc_start: 0.9197 (tpt) cc_final: 0.8661 (tpp) REVERT: L 3613 MET cc_start: 0.6426 (ppp) cc_final: 0.6084 (tpt) REVERT: L 3654 MET cc_start: 0.3488 (mmm) cc_final: 0.2949 (mmt) REVERT: L 3856 MET cc_start: 0.7044 (ptt) cc_final: 0.6831 (ttm) REVERT: L 3929 MET cc_start: 0.8862 (mmp) cc_final: 0.8589 (mmp) REVERT: L 4108 MET cc_start: 0.8451 (tmm) cc_final: 0.8233 (tmm) REVERT: H 50 ASP cc_start: 0.4253 (m-30) cc_final: 0.3689 (m-30) REVERT: H 194 MET cc_start: -0.1629 (mmt) cc_final: -0.2322 (mmt) REVERT: I 159 MET cc_start: 0.5248 (ppp) cc_final: 0.3170 (ptt) REVERT: B 84 MET cc_start: 0.9313 (mpp) cc_final: 0.9036 (mpp) REVERT: C 238 MET cc_start: 0.7867 (pmm) cc_final: 0.7242 (pmm) REVERT: C 368 LEU cc_start: 0.8778 (pp) cc_final: 0.8408 (mm) REVERT: C 384 MET cc_start: 0.6925 (ptm) cc_final: 0.6691 (ptm) REVERT: C 395 MET cc_start: 0.8065 (mmm) cc_final: 0.7815 (tpt) REVERT: C 540 MET cc_start: 0.6144 (tpt) cc_final: 0.5890 (tpp) REVERT: C 858 MET cc_start: 0.8437 (tmm) cc_final: 0.8024 (tmm) REVERT: C 932 GLU cc_start: 0.6136 (mt-10) cc_final: 0.5719 (mp0) REVERT: C 1261 LEU cc_start: 0.9465 (tp) cc_final: 0.9251 (tt) REVERT: C 1342 MET cc_start: 0.8953 (mtm) cc_final: 0.8428 (ttm) REVERT: C 1871 MET cc_start: 0.8598 (ttp) cc_final: 0.8307 (tmm) REVERT: C 2408 MET cc_start: 0.7985 (tmm) cc_final: 0.7755 (tmm) REVERT: C 2813 PHE cc_start: 0.7921 (t80) cc_final: 0.7618 (t80) REVERT: C 3043 TYR cc_start: 0.9072 (m-80) cc_final: 0.8686 (m-80) REVERT: C 3238 MET cc_start: 0.9159 (ttm) cc_final: 0.8947 (ttm) REVERT: C 3816 LEU cc_start: 0.9598 (mt) cc_final: 0.9278 (mt) REVERT: C 3929 MET cc_start: 0.7645 (tpp) cc_final: 0.7048 (tpp) REVERT: F 61 MET cc_start: -0.0042 (ttm) cc_final: -0.1435 (mtt) REVERT: X 792 MET cc_start: -0.3112 (ttt) cc_final: -0.3401 (ttt) REVERT: O 61 MET cc_start: -0.2457 (mtm) cc_final: -0.2825 (mtt) REVERT: Y 667 MET cc_start: 0.7001 (ttt) cc_final: 0.6134 (mmm) REVERT: Y 792 MET cc_start: -0.3340 (ttt) cc_final: -0.3698 (ttt) REVERT: P 1 MET cc_start: 0.1806 (tpt) cc_final: -0.1405 (ptt) outliers start: 0 outliers final: 0 residues processed: 539 average time/residue: 0.8326 time to fit residues: 795.7321 Evaluate side-chains 441 residues out of total 10141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 441 time to evaluate : 8.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1141 random chunks: chunk 1000 optimal weight: 6.9990 chunk 1053 optimal weight: 50.0000 chunk 961 optimal weight: 4.9990 chunk 1024 optimal weight: 50.0000 chunk 616 optimal weight: 0.9990 chunk 446 optimal weight: 0.0000 chunk 804 optimal weight: 10.0000 chunk 314 optimal weight: 8.9990 chunk 926 optimal weight: 0.8980 chunk 969 optimal weight: 10.0000 chunk 1021 optimal weight: 50.0000 overall best weight: 2.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L3926 ASN ** L3927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L4000 ASN I 32 GLN B 80 HIS ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 833 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1043 GLN ** C2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3054 GLN C3969 ASN C4000 ASN ** O 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6260 moved from start: 0.6076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 95703 Z= 0.251 Angle : 0.621 12.730 129715 Z= 0.317 Chirality : 0.041 0.216 14616 Planarity : 0.004 0.051 16087 Dihedral : 11.508 85.438 13622 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.08), residues: 11179 helix: 0.58 (0.07), residues: 6312 sheet: 0.03 (0.19), residues: 781 loop : -0.82 (0.10), residues: 4086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP L2196 HIS 0.009 0.001 HIS C1367 PHE 0.030 0.002 PHE C1194 TYR 0.025 0.001 TYR C2772 ARG 0.009 0.000 ARG C1184 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22358 Ramachandran restraints generated. 11179 Oldfield, 0 Emsley, 11179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22358 Ramachandran restraints generated. 11179 Oldfield, 0 Emsley, 11179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 10141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 513 time to evaluate : 8.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 62 MET cc_start: 0.9358 (mmm) cc_final: 0.9120 (mtt) REVERT: J 514 MET cc_start: 0.8535 (mpp) cc_final: 0.8310 (mpp) REVERT: A 453 MET cc_start: 0.3081 (ptt) cc_final: 0.1721 (pmm) REVERT: A 514 MET cc_start: 0.8574 (mpp) cc_final: 0.8335 (mpp) REVERT: K 84 MET cc_start: 0.9410 (mpp) cc_final: 0.9149 (mpp) REVERT: K 115 MET cc_start: 0.8879 (mmp) cc_final: 0.8647 (mmm) REVERT: K 212 MET cc_start: 0.9477 (mtp) cc_final: 0.9094 (mtp) REVERT: L 395 MET cc_start: 0.8064 (mmm) cc_final: 0.7703 (tpt) REVERT: L 453 MET cc_start: 0.8520 (mmm) cc_final: 0.8276 (mmm) REVERT: L 828 LYS cc_start: 0.8521 (tttp) cc_final: 0.8212 (mptt) REVERT: L 858 MET cc_start: 0.8790 (tmm) cc_final: 0.8315 (tmm) REVERT: L 1085 ILE cc_start: 0.8808 (pt) cc_final: 0.8524 (pt) REVERT: L 1120 SER cc_start: 0.8651 (t) cc_final: 0.8437 (p) REVERT: L 1934 LEU cc_start: 0.8298 (mm) cc_final: 0.8042 (mm) REVERT: L 2126 MET cc_start: 0.7869 (mpp) cc_final: 0.7643 (mpp) REVERT: L 2331 MET cc_start: 0.8406 (tpp) cc_final: 0.7901 (tpp) REVERT: L 3414 MET cc_start: 0.9205 (tpt) cc_final: 0.8671 (tpp) REVERT: L 3450 MET cc_start: 0.9042 (ppp) cc_final: 0.8821 (ppp) REVERT: L 3613 MET cc_start: 0.6304 (ppp) cc_final: 0.5973 (tpt) REVERT: L 3654 MET cc_start: 0.3360 (mmm) cc_final: 0.2889 (mmt) REVERT: L 3856 MET cc_start: 0.7103 (ptt) cc_final: 0.6772 (tpt) REVERT: L 3929 MET cc_start: 0.8845 (mmp) cc_final: 0.8620 (mmp) REVERT: L 4108 MET cc_start: 0.8483 (tmm) cc_final: 0.8265 (tmm) REVERT: H 50 ASP cc_start: 0.4210 (m-30) cc_final: 0.3629 (m-30) REVERT: H 194 MET cc_start: -0.1691 (mmt) cc_final: -0.2375 (mmt) REVERT: I 142 MET cc_start: -0.1245 (ppp) cc_final: -0.3384 (ptt) REVERT: I 159 MET cc_start: 0.5250 (ppp) cc_final: 0.3194 (ptt) REVERT: B 40 MET cc_start: 0.8257 (ptt) cc_final: 0.7929 (ppp) REVERT: B 84 MET cc_start: 0.9312 (mpp) cc_final: 0.9061 (mpp) REVERT: C 238 MET cc_start: 0.7935 (pmm) cc_final: 0.7278 (pmm) REVERT: C 368 LEU cc_start: 0.8780 (pp) cc_final: 0.8468 (mm) REVERT: C 395 MET cc_start: 0.8096 (mmm) cc_final: 0.7865 (tpt) REVERT: C 540 MET cc_start: 0.6181 (tpt) cc_final: 0.5927 (tpp) REVERT: C 785 MET cc_start: 0.8333 (tpp) cc_final: 0.8036 (tpp) REVERT: C 858 MET cc_start: 0.8478 (tmm) cc_final: 0.8003 (tmm) REVERT: C 932 GLU cc_start: 0.6144 (mt-10) cc_final: 0.5724 (mp0) REVERT: C 1342 MET cc_start: 0.8840 (mtm) cc_final: 0.8365 (ttm) REVERT: C 1871 MET cc_start: 0.8565 (ttp) cc_final: 0.8210 (tmm) REVERT: C 2126 MET cc_start: 0.7702 (mpp) cc_final: 0.7480 (mpp) REVERT: C 2408 MET cc_start: 0.8034 (tmm) cc_final: 0.7795 (tmm) REVERT: C 2770 VAL cc_start: 0.8186 (p) cc_final: 0.7981 (p) REVERT: C 2813 PHE cc_start: 0.7919 (t80) cc_final: 0.7623 (t80) REVERT: C 3043 TYR cc_start: 0.9111 (m-80) cc_final: 0.8736 (m-80) REVERT: C 3238 MET cc_start: 0.9156 (ttm) cc_final: 0.8947 (ttm) REVERT: C 3816 LEU cc_start: 0.9602 (mt) cc_final: 0.9267 (mt) REVERT: C 3929 MET cc_start: 0.7611 (tpp) cc_final: 0.7012 (tpp) REVERT: C 3932 MET cc_start: 0.7098 (ppp) cc_final: 0.6744 (tmm) REVERT: F 61 MET cc_start: 0.0034 (ttm) cc_final: -0.1449 (mtt) REVERT: X 792 MET cc_start: -0.2989 (ttt) cc_final: -0.3362 (ttt) REVERT: G 59 MET cc_start: -0.1606 (mpp) cc_final: -0.1843 (ptp) REVERT: O 61 MET cc_start: -0.2437 (mtm) cc_final: -0.2909 (mtt) REVERT: Y 792 MET cc_start: -0.3277 (ttt) cc_final: -0.3660 (ttt) REVERT: P 1 MET cc_start: 0.1888 (tpt) cc_final: -0.1369 (ptt) outliers start: 0 outliers final: 0 residues processed: 513 average time/residue: 0.8564 time to fit residues: 779.9697 Evaluate side-chains 427 residues out of total 10141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 427 time to evaluate : 8.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1141 random chunks: chunk 672 optimal weight: 2.9990 chunk 1083 optimal weight: 40.0000 chunk 661 optimal weight: 8.9990 chunk 514 optimal weight: 10.0000 chunk 753 optimal weight: 8.9990 chunk 1136 optimal weight: 40.0000 chunk 1046 optimal weight: 5.9990 chunk 905 optimal weight: 0.6980 chunk 93 optimal weight: 7.9990 chunk 699 optimal weight: 0.4980 chunk 555 optimal weight: 20.0000 overall best weight: 3.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1738 ASN ** L1754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L3054 GLN ** L3927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L4000 ASN H 56 GLN ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 GLN ** C 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 833 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3969 ASN C4000 ASN ** O 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 787 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6295 moved from start: 0.6359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 95703 Z= 0.308 Angle : 0.655 13.848 129715 Z= 0.335 Chirality : 0.042 0.212 14616 Planarity : 0.004 0.055 16087 Dihedral : 11.537 83.544 13622 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.08), residues: 11179 helix: 0.49 (0.07), residues: 6322 sheet: -0.05 (0.18), residues: 797 loop : -0.89 (0.10), residues: 4060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.002 TRP L2196 HIS 0.010 0.001 HIS C3384 PHE 0.041 0.002 PHE C1194 TYR 0.025 0.001 TYR L3442 ARG 0.013 0.001 ARG C1184 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22358 Ramachandran restraints generated. 11179 Oldfield, 0 Emsley, 11179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22358 Ramachandran restraints generated. 11179 Oldfield, 0 Emsley, 11179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 10141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 498 time to evaluate : 8.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 62 MET cc_start: 0.9344 (mmm) cc_final: 0.9105 (mtt) REVERT: J 203 MET cc_start: 0.8275 (pmm) cc_final: 0.8051 (pmm) REVERT: J 346 MET cc_start: 0.6898 (tmm) cc_final: 0.6487 (tmm) REVERT: J 348 MET cc_start: 0.7607 (mmt) cc_final: 0.6059 (mmt) REVERT: J 514 MET cc_start: 0.8597 (mpp) cc_final: 0.8389 (mpp) REVERT: A 346 MET cc_start: 0.7641 (tpt) cc_final: 0.7416 (tpp) REVERT: A 348 MET cc_start: 0.7098 (mmt) cc_final: 0.5588 (mmt) REVERT: A 453 MET cc_start: 0.3300 (ptt) cc_final: 0.2260 (pmm) REVERT: A 514 MET cc_start: 0.8662 (mpp) cc_final: 0.8436 (mpp) REVERT: K 84 MET cc_start: 0.9400 (mpp) cc_final: 0.9141 (mpp) REVERT: K 115 MET cc_start: 0.8856 (mmp) cc_final: 0.8616 (mmm) REVERT: K 212 MET cc_start: 0.9469 (mtp) cc_final: 0.9100 (mtp) REVERT: L 395 MET cc_start: 0.8110 (mmm) cc_final: 0.7793 (tpt) REVERT: L 828 LYS cc_start: 0.8559 (tttp) cc_final: 0.8207 (mptt) REVERT: L 858 MET cc_start: 0.8856 (tmm) cc_final: 0.8382 (tmm) REVERT: L 1085 ILE cc_start: 0.8851 (pt) cc_final: 0.8577 (pt) REVERT: L 1261 LEU cc_start: 0.9360 (tp) cc_final: 0.9133 (tp) REVERT: L 1804 MET cc_start: 0.8075 (mpp) cc_final: 0.7823 (mpp) REVERT: L 1934 LEU cc_start: 0.8349 (mm) cc_final: 0.8081 (mm) REVERT: L 2126 MET cc_start: 0.7832 (mpp) cc_final: 0.7630 (mpp) REVERT: L 3414 MET cc_start: 0.9179 (tpt) cc_final: 0.8726 (tpp) REVERT: L 3450 MET cc_start: 0.9107 (ppp) cc_final: 0.8860 (ppp) REVERT: L 3613 MET cc_start: 0.6395 (ppp) cc_final: 0.6062 (tpt) REVERT: L 3654 MET cc_start: 0.2532 (mmm) cc_final: 0.2078 (mmt) REVERT: L 3856 MET cc_start: 0.7206 (ptt) cc_final: 0.6821 (tpt) REVERT: L 4108 MET cc_start: 0.8502 (tmm) cc_final: 0.8277 (tmm) REVERT: H 50 ASP cc_start: 0.4342 (m-30) cc_final: 0.3762 (m-30) REVERT: H 194 MET cc_start: -0.1534 (mmt) cc_final: -0.2181 (mmt) REVERT: B 40 MET cc_start: 0.8431 (ptt) cc_final: 0.8102 (ppp) REVERT: B 84 MET cc_start: 0.9327 (mpp) cc_final: 0.9055 (mpp) REVERT: C 275 PHE cc_start: 0.8566 (t80) cc_final: 0.8340 (t80) REVERT: C 368 LEU cc_start: 0.8753 (pp) cc_final: 0.8456 (mm) REVERT: C 395 MET cc_start: 0.8173 (mmm) cc_final: 0.7935 (tpt) REVERT: C 858 MET cc_start: 0.8547 (tmm) cc_final: 0.8045 (tmm) REVERT: C 932 GLU cc_start: 0.6219 (mt-10) cc_final: 0.5837 (mp0) REVERT: C 1342 MET cc_start: 0.8963 (mtm) cc_final: 0.8448 (ttm) REVERT: C 1871 MET cc_start: 0.8586 (ttp) cc_final: 0.8207 (tmm) REVERT: C 2094 MET cc_start: 0.7068 (mmp) cc_final: 0.6705 (mtt) REVERT: C 2126 MET cc_start: 0.7794 (mpp) cc_final: 0.7579 (mpp) REVERT: C 2408 MET cc_start: 0.8074 (tmm) cc_final: 0.7832 (tmm) REVERT: C 3043 TYR cc_start: 0.9127 (m-80) cc_final: 0.8787 (m-80) REVERT: C 3238 MET cc_start: 0.9120 (ttm) cc_final: 0.8894 (ttm) REVERT: C 3816 LEU cc_start: 0.9605 (mt) cc_final: 0.9272 (mt) REVERT: C 3929 MET cc_start: 0.7764 (tpp) cc_final: 0.7165 (tpp) REVERT: F 61 MET cc_start: 0.0199 (ttm) cc_final: -0.1283 (mtt) REVERT: X 792 MET cc_start: -0.3196 (ttt) cc_final: -0.3572 (ttt) REVERT: O 61 MET cc_start: -0.2320 (mtm) cc_final: -0.2676 (mtt) REVERT: Y 792 MET cc_start: -0.3260 (ttt) cc_final: -0.3620 (ttt) REVERT: P 1 MET cc_start: 0.1874 (tpt) cc_final: -0.1326 (ptt) outliers start: 0 outliers final: 0 residues processed: 498 average time/residue: 0.8563 time to fit residues: 757.3754 Evaluate side-chains 417 residues out of total 10141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 417 time to evaluate : 8.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1141 random chunks: chunk 718 optimal weight: 0.4980 chunk 964 optimal weight: 0.6980 chunk 277 optimal weight: 10.0000 chunk 834 optimal weight: 9.9990 chunk 133 optimal weight: 10.0000 chunk 251 optimal weight: 0.6980 chunk 906 optimal weight: 0.9990 chunk 379 optimal weight: 2.9990 chunk 930 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 166 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: