Starting phenix.real_space_refine on Fri Feb 16 02:02:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmg_10520/02_2024/6tmg_10520_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmg_10520/02_2024/6tmg_10520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmg_10520/02_2024/6tmg_10520.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmg_10520/02_2024/6tmg_10520.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmg_10520/02_2024/6tmg_10520_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmg_10520/02_2024/6tmg_10520_trim_updated.pdb" } resolution = 2.8 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= 0.001 sd= 0.007 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: 6 Type Number sf(0) Gaussians P 48 5.49 5 S 306 5.16 5 C 39196 2.51 5 N 10008 2.21 5 O 10990 1.98 5 H 56046 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "q ARG 6": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "q PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "q PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "q ASP 113": "OD1" <-> "OD2" Residue "q TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "q TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "i GLU 150": "OE1" <-> "OE2" Residue "i ARG 178": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "i ASP 187": "OD1" <-> "OD2" Residue "i GLU 192": "OE1" <-> "OE2" Residue "i PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "t TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g GLU 187": "OE1" <-> "OE2" Residue "g ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "o ARG 15": not complete - not flipped Residue "o ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "o TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "o PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "o ARG 59": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "o TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "o PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "o GLU 75": "OE1" <-> "OE2" Residue "o TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "o GLU 101": "OE1" <-> "OE2" Residue "o PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "o ARG 146": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "k ARG 151": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "k PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "k PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "k PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j GLU 81": "OE1" <-> "OE2" Residue "j PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j ASP 113": "OD1" <-> "OD2" Residue "j TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j ARG 142": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "j TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j GLU 179": "OE1" <-> "OE2" Residue "j PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j GLU 208": "OE1" <-> "OE2" Residue "s PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "s TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "s TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "s ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "s GLU 100": "OE1" <-> "OE2" Residue "s ARG 118": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "u TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "u ARG 94": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "u GLU 107": "OE1" <-> "OE2" Residue "u PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h ARG 82": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h ARG 225": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "e TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e GLU 260": "OE1" <-> "OE2" Residue "e GLU 261": "OE1" <-> "OE2" Residue "e GLU 265": "OE1" <-> "OE2" Residue "e ARG 274": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "e GLU 299": "OE1" <-> "OE2" Residue "x GLU 76": "OE1" <-> "OE2" Residue "x TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 152": "OE1" <-> "OE2" Residue "b ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b GLU 168": "OE1" <-> "OE2" Residue "b GLU 196": "OE1" <-> "OE2" Residue "b PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 209": "OE1" <-> "OE2" Residue "b PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 318": "OE1" <-> "OE2" Residue "r PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "r ARG 50": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "r ASP 57": "OD1" <-> "OD2" Residue "r TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "p ASP 20": "OD1" <-> "OD2" Residue "p TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "p PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "p PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "v ARG 14": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "v ARG 26": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "v ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "v ASP 39": "OD1" <-> "OD2" Residue "v ARG 53": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "v TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "l GLU 22": "OE1" <-> "OE2" Residue "l ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "l PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "l ARG 86": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "l GLU 109": "OE1" <-> "OE2" Residue "l PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "l PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c ARG 84": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c ARG 119": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c ASP 142": "OD1" <-> "OD2" Residue "d ARG 117": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "d GLU 162": "OE1" <-> "OE2" Residue "d TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "m TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "m GLU 154": "OE1" <-> "OE2" Residue "m PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "m TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n GLU 47": "OE1" <-> "OE2" Residue "n ARG 129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n GLU 132": "OE1" <-> "OE2" Residue "f PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f GLU 117": "OE1" <-> "OE2" Residue "f ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f ARG 145": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f ARG 180": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f ARG 186": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f ASP 199": "OD1" <-> "OD2" Residue "f PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "w PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a ASP 163": "OD1" <-> "OD2" Residue "a TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 191": "OE1" <-> "OE2" Residue "a PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a ARG 209": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a ARG 245": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 255": "OE1" <-> "OE2" Residue "a ARG 269": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 279": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a ASP 354": "OD1" <-> "OD2" Residue "a PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a ARG 439": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a GLU 448": "OE1" <-> "OE2" Residue "a GLU 456": "OE1" <-> "OE2" Residue "a PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q ARG 6": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q ASP 113": "OD1" <-> "OD2" Residue "Q TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 150": "OE1" <-> "OE2" Residue "I ARG 178": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ASP 187": "OD1" <-> "OD2" Residue "I GLU 192": "OE1" <-> "OE2" Residue "I PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 187": "OE1" <-> "OE2" Residue "G ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 15": not complete - not flipped Residue "O ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O ARG 59": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O GLU 75": "OE1" <-> "OE2" Residue "O TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O GLU 101": "OE1" <-> "OE2" Residue "O PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O ARG 146": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 151": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 81": "OE1" <-> "OE2" Residue "J PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ASP 113": "OD1" <-> "OD2" Residue "J TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 142": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 179": "OE1" <-> "OE2" Residue "J PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 208": "OE1" <-> "OE2" Residue "S PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S GLU 100": "OE1" <-> "OE2" Residue "S ARG 118": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U ARG 94": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U GLU 107": "OE1" <-> "OE2" Residue "U PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 82": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 225": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 260": "OE1" <-> "OE2" Residue "E GLU 261": "OE1" <-> "OE2" Residue "E GLU 265": "OE1" <-> "OE2" Residue "E ARG 274": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 299": "OE1" <-> "OE2" Residue "X GLU 76": "OE1" <-> "OE2" Residue "X TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 152": "OE1" <-> "OE2" Residue "B ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 168": "OE1" <-> "OE2" Residue "B GLU 196": "OE1" <-> "OE2" Residue "B PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 209": "OE1" <-> "OE2" Residue "B PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 318": "OE1" <-> "OE2" Residue "R PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ARG 50": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ASP 57": "OD1" <-> "OD2" Residue "R TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ASP 20": "OD1" <-> "OD2" Residue "P TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V ARG 14": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 26": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ASP 39": "OD1" <-> "OD2" Residue "V ARG 53": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 22": "OE1" <-> "OE2" Residue "L ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 86": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L GLU 109": "OE1" <-> "OE2" Residue "L PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 84": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 119": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 142": "OD1" <-> "OD2" Residue "D ARG 117": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 162": "OE1" <-> "OE2" Residue "D TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 154": "OE1" <-> "OE2" Residue "M PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N GLU 47": "OE1" <-> "OE2" Residue "N ARG 129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N GLU 132": "OE1" <-> "OE2" Residue "F PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 117": "OE1" <-> "OE2" Residue "F ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 145": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 180": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 186": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 199": "OD1" <-> "OD2" Residue "F PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 163": "OD1" <-> "OD2" Residue "A TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 209": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 245": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A ARG 269": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 279": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 354": "OD1" <-> "OD2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 439": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 448": "OE1" <-> "OE2" Residue "A GLU 456": "OE1" <-> "OE2" Residue "A PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 116594 Number of models: 1 Model: "" Number of chains: 68 Chain: "q" Number of atoms: 2119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2119 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 14, 'TRANS': 118} Chain: "i" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 1386 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "t" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1439 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 6, 'TRANS': 85} Chain: "g" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 1732 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 11, 'TRANS': 100} Chain: "o" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 2415 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain: "k" Number of atoms: 1904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1904 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "j" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 2981 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 16, 'TRANS': 159} Chain: "s" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1570 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "u" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1492 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "h" Number of atoms: 3589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3589 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 210} Chain: "e" Number of atoms: 2179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2179 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 11, 'TRANS': 128} Chain: "x" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1298 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 6, 'TRANS': 75} Chain: "b" Number of atoms: 4157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 4157 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 8, 'TRANS': 244} Chain: "r" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 1485 Classifications: {'peptide': 90} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain: "p" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1711 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "v" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1801 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "l" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3273 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain: "c" Number of atoms: 2029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 2029 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "d" Number of atoms: 4046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 4046 Classifications: {'peptide': 254} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 238} Chain breaks: 1 Chain: "m" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1509 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "n" Number of atoms: 2451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 2451 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 145} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "f" Number of atoms: 2867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 2867 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 173} Chain breaks: 1 Chain: "w" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1509 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 9, 'TRANS': 86} Chain breaks: 1 Chain: "a" Number of atoms: 5895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 5895 Classifications: {'peptide': 371} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 2119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2119 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 14, 'TRANS': 118} Chain: "I" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 1386 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "T" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1439 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 6, 'TRANS': 85} Chain: "G" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 1732 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 11, 'TRANS': 100} Chain: "O" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 2415 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain: "K" Number of atoms: 1904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1904 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "J" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 2981 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 16, 'TRANS': 159} Chain: "S" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1570 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "U" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1492 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "H" Number of atoms: 3589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3589 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 210} Chain: "E" Number of atoms: 2179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2179 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 11, 'TRANS': 128} Chain: "X" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1298 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 6, 'TRANS': 75} Chain: "B" Number of atoms: 4157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 4157 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 8, 'TRANS': 244} Chain: "R" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 1485 Classifications: {'peptide': 90} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain: "P" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1711 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "V" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1801 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "L" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3273 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain: "C" Number of atoms: 2029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 2029 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "D" Number of atoms: 4046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 4046 Classifications: {'peptide': 254} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 238} Chain breaks: 1 Chain: "M" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1509 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "N" Number of atoms: 2451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 2451 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 145} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 2867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 2867 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 173} Chain breaks: 1 Chain: "W" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1509 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 9, 'TRANS': 86} Chain breaks: 1 Chain: "A" Number of atoms: 5895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 5895 Classifications: {'peptide': 371} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "o" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 243 Unusual residues: {'CDL': 1, 'LMT': 1, 'PC1': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "j" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "u" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 135 Unusual residues: {'CDL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "e" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "x" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "v" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 154 Unusual residues: {'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 221 Unusual residues: {'CDL': 1, 'LMT': 2, 'PEE': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "d" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 170 Unusual residues: {'CDL': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 243 Unusual residues: {'CDL': 1, 'LMT': 1, 'PC1': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 135 Unusual residues: {'CDL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 200 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 254 Unusual residues: {'CDL': 2, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 221 Unusual residues: {'CDL': 1, 'LMT': 2, 'PEE': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 170 Unusual residues: {'CDL': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 36.46, per 1000 atoms: 0.31 Number of scatterers: 116594 At special positions: 0 Unit cell: (241.53, 183.43, 213.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 306 16.00 P 48 15.00 O 10990 8.00 N 10008 7.00 C 39196 6.00 H 56046 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS i 193 " - pdb=" SG CYS i 225 " distance=2.03 Simple disulfide: pdb=" SG CYS i 203 " - pdb=" SG CYS i 213 " distance=2.03 Simple disulfide: pdb=" SG CYS g 200 " - pdb=" SG CYS g 212 " distance=2.03 Simple disulfide: pdb=" SG CYS o 125 " - pdb=" SG CYS o 144 " distance=2.03 Simple disulfide: pdb=" SG CYS h 168 " - pdb=" SG CYS h 205 " distance=2.03 Simple disulfide: pdb=" SG CYS l 129 " - pdb=" SG CYS l 165 " distance=2.03 Simple disulfide: pdb=" SG CYS n 14 " - pdb=" SG CYS n 46 " distance=2.03 Simple disulfide: pdb=" SG CYS I 193 " - pdb=" SG CYS I 225 " distance=2.03 Simple disulfide: pdb=" SG CYS I 203 " - pdb=" SG CYS I 213 " distance=2.03 Simple disulfide: pdb=" SG CYS G 200 " - pdb=" SG CYS G 212 " distance=2.03 Simple disulfide: pdb=" SG CYS O 125 " - pdb=" SG CYS O 144 " distance=2.03 Simple disulfide: pdb=" SG CYS H 168 " - pdb=" SG CYS H 205 " distance=2.03 Simple disulfide: pdb=" SG CYS L 129 " - pdb=" SG CYS L 165 " distance=2.03 Simple disulfide: pdb=" SG CYS N 14 " - pdb=" SG CYS N 46 " distance=2.03 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 72.42 Conformation dependent library (CDL) restraints added in 8.4 seconds 14020 Ramachandran restraints generated. 7010 Oldfield, 0 Emsley, 7010 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13560 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 290 helices and 22 sheets defined 64.8% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 30.39 Creating SS restraints... Processing helix chain 'q' and resid 11 through 17 removed outlier: 5.108A pdb=" N ILE q 15 " --> pdb=" O PRO q 11 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE q 16 " --> pdb=" O VAL q 12 " (cutoff:3.500A) Processing helix chain 'q' and resid 48 through 65 Processing helix chain 'q' and resid 68 through 95 removed outlier: 4.243A pdb=" N VAL q 72 " --> pdb=" O GLY q 68 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL q 86 " --> pdb=" O CYS q 82 " (cutoff:3.500A) Processing helix chain 'q' and resid 96 through 104 removed outlier: 4.503A pdb=" N GLN q 100 " --> pdb=" O PRO q 96 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA q 101 " --> pdb=" O ALA q 97 " (cutoff:3.500A) Processing helix chain 'q' and resid 107 through 114 Processing helix chain 'q' and resid 116 through 121 removed outlier: 4.035A pdb=" N LEU q 120 " --> pdb=" O ARG q 116 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N GLN q 121 " --> pdb=" O TYR q 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 116 through 121' Processing helix chain 'q' and resid 127 through 133 removed outlier: 4.602A pdb=" N LYS q 131 " --> pdb=" O SER q 127 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N TYR q 132 " --> pdb=" O ILE q 128 " (cutoff:3.500A) Processing helix chain 'Q' and resid 11 through 17 removed outlier: 5.108A pdb=" N ILE Q 15 " --> pdb=" O PRO Q 11 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE Q 16 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) Processing helix chain 'Q' and resid 48 through 65 Processing helix chain 'Q' and resid 68 through 95 removed outlier: 4.242A pdb=" N VAL Q 72 " --> pdb=" O GLY Q 68 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL Q 86 " --> pdb=" O CYS Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 96 through 104 removed outlier: 4.503A pdb=" N GLN Q 100 " --> pdb=" O PRO Q 96 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA Q 101 " --> pdb=" O ALA Q 97 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 114 Processing helix chain 'Q' and resid 116 through 121 removed outlier: 4.036A pdb=" N LEU Q 120 " --> pdb=" O ARG Q 116 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N GLN Q 121 " --> pdb=" O TYR Q 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 116 through 121' Processing helix chain 'Q' and resid 127 through 133 removed outlier: 4.602A pdb=" N LYS Q 131 " --> pdb=" O SER Q 127 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N TYR Q 132 " --> pdb=" O ILE Q 128 " (cutoff:3.500A) Processing helix chain 'i' and resid 147 through 166 Processing helix chain 'i' and resid 169 through 174 Processing helix chain 'i' and resid 175 through 193 Processing helix chain 'i' and resid 194 through 207 Processing helix chain 'i' and resid 216 through 234 removed outlier: 4.267A pdb=" N LEU i 222 " --> pdb=" O ALA i 218 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 166 Processing helix chain 'I' and resid 169 through 174 Processing helix chain 'I' and resid 175 through 193 Processing helix chain 'I' and resid 194 through 207 Processing helix chain 'I' and resid 216 through 234 removed outlier: 4.267A pdb=" N LEU I 222 " --> pdb=" O ALA I 218 " (cutoff:3.500A) Processing helix chain 't' and resid 18 through 31 removed outlier: 5.040A pdb=" N TRP t 23 " --> pdb=" O ARG t 19 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N MET t 24 " --> pdb=" O SER t 20 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS t 31 " --> pdb=" O PHE t 27 " (cutoff:3.500A) Processing helix chain 't' and resid 35 through 40 removed outlier: 4.662A pdb=" N CYS t 39 " --> pdb=" O THR t 35 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ALA t 40 " --> pdb=" O ALA t 36 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 35 through 40' Processing helix chain 't' and resid 65 through 92 removed outlier: 5.985A pdb=" N LYS t 71 " --> pdb=" O HIS t 67 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TYR t 72 " --> pdb=" O ILE t 68 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR t 74 " --> pdb=" O GLU t 70 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU t 75 " --> pdb=" O LYS t 71 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLN t 76 " --> pdb=" O TYR t 72 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N THR t 77 " --> pdb=" O ASP t 73 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS t 91 " --> pdb=" O SER t 87 " (cutoff:3.500A) Processing helix chain 't' and resid 96 through 103 Processing helix chain 'T' and resid 18 through 31 removed outlier: 5.040A pdb=" N TRP T 23 " --> pdb=" O ARG T 19 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N MET T 24 " --> pdb=" O SER T 20 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS T 31 " --> pdb=" O PHE T 27 " (cutoff:3.500A) Processing helix chain 'T' and resid 35 through 40 removed outlier: 4.661A pdb=" N CYS T 39 " --> pdb=" O THR T 35 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ALA T 40 " --> pdb=" O ALA T 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 35 through 40' Processing helix chain 'T' and resid 65 through 92 removed outlier: 5.985A pdb=" N LYS T 71 " --> pdb=" O HIS T 67 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TYR T 72 " --> pdb=" O ILE T 68 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR T 74 " --> pdb=" O GLU T 70 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU T 75 " --> pdb=" O LYS T 71 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLN T 76 " --> pdb=" O TYR T 72 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N THR T 77 " --> pdb=" O ASP T 73 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS T 91 " --> pdb=" O SER T 87 " (cutoff:3.500A) Processing helix chain 'T' and resid 96 through 103 Processing helix chain 'g' and resid 120 through 130 removed outlier: 3.920A pdb=" N TRP g 124 " --> pdb=" O PRO g 120 " (cutoff:3.500A) Proline residue: g 125 - end of helix removed outlier: 3.762A pdb=" N TYR g 129 " --> pdb=" O PRO g 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 139 through 144 Proline residue: g 144 - end of helix Processing helix chain 'g' and resid 151 through 164 Processing helix chain 'g' and resid 166 through 174 Processing helix chain 'g' and resid 184 through 190 removed outlier: 4.312A pdb=" N LYS g 188 " --> pdb=" O ASN g 184 " (cutoff:3.500A) Processing helix chain 'g' and resid 191 through 205 Processing helix chain 'g' and resid 212 through 225 Processing helix chain 'G' and resid 120 through 130 removed outlier: 3.920A pdb=" N TRP G 124 " --> pdb=" O PRO G 120 " (cutoff:3.500A) Proline residue: G 125 - end of helix removed outlier: 3.763A pdb=" N TYR G 129 " --> pdb=" O PRO G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 144 Proline residue: G 144 - end of helix Processing helix chain 'G' and resid 151 through 164 Processing helix chain 'G' and resid 166 through 174 Processing helix chain 'G' and resid 184 through 190 removed outlier: 4.313A pdb=" N LYS G 188 " --> pdb=" O ASN G 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 205 Processing helix chain 'G' and resid 212 through 225 Processing helix chain 'o' and resid 16 through 39 removed outlier: 3.923A pdb=" N SER o 39 " --> pdb=" O SER o 35 " (cutoff:3.500A) Processing helix chain 'o' and resid 41 through 64 removed outlier: 4.336A pdb=" N TYR o 45 " --> pdb=" O SER o 41 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N VAL o 46 " --> pdb=" O SER o 42 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N PHE o 51 " --> pdb=" O MET o 47 " (cutoff:3.500A) Proline residue: o 52 - end of helix Processing helix chain 'o' and resid 74 through 79 removed outlier: 3.862A pdb=" N TYR o 78 " --> pdb=" O GLU o 74 " (cutoff:3.500A) Proline residue: o 79 - end of helix No H-bonds generated for 'chain 'o' and resid 74 through 79' Processing helix chain 'o' and resid 103 through 113 Processing helix chain 'o' and resid 135 through 144 Processing helix chain 'O' and resid 16 through 39 removed outlier: 3.924A pdb=" N SER O 39 " --> pdb=" O SER O 35 " (cutoff:3.500A) Processing helix chain 'O' and resid 41 through 64 removed outlier: 4.335A pdb=" N TYR O 45 " --> pdb=" O SER O 41 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N VAL O 46 " --> pdb=" O SER O 42 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N PHE O 51 " --> pdb=" O MET O 47 " (cutoff:3.500A) Proline residue: O 52 - end of helix Processing helix chain 'O' and resid 74 through 79 removed outlier: 3.862A pdb=" N TYR O 78 " --> pdb=" O GLU O 74 " (cutoff:3.500A) Proline residue: O 79 - end of helix No H-bonds generated for 'chain 'O' and resid 74 through 79' Processing helix chain 'O' and resid 103 through 113 Processing helix chain 'O' and resid 135 through 144 Processing helix chain 'k' and resid 110 through 118 removed outlier: 4.241A pdb=" N GLN k 116 " --> pdb=" O GLY k 112 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE k 117 " --> pdb=" O SER k 113 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N GLN k 118 " --> pdb=" O ASN k 114 " (cutoff:3.500A) Processing helix chain 'k' and resid 120 through 130 Processing helix chain 'k' and resid 135 through 185 removed outlier: 4.034A pdb=" N PHE k 150 " --> pdb=" O PHE k 146 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ARG k 151 " --> pdb=" O LEU k 147 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N PHE k 152 " --> pdb=" O LEU k 148 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N TYR k 153 " --> pdb=" O ASN k 149 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE k 154 " --> pdb=" O PHE k 150 " (cutoff:3.500A) Proline residue: k 167 - end of helix removed outlier: 4.250A pdb=" N PHE k 174 " --> pdb=" O ALA k 170 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY k 175 " --> pdb=" O PHE k 171 " (cutoff:3.500A) Processing helix chain 'k' and resid 188 through 220 removed outlier: 4.252A pdb=" N PHE k 196 " --> pdb=" O PHE k 192 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL k 197 " --> pdb=" O LEU k 193 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 118 removed outlier: 4.241A pdb=" N GLN K 116 " --> pdb=" O GLY K 112 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE K 117 " --> pdb=" O SER K 113 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N GLN K 118 " --> pdb=" O ASN K 114 " (cutoff:3.500A) Processing helix chain 'K' and resid 120 through 130 Processing helix chain 'K' and resid 135 through 185 removed outlier: 4.033A pdb=" N PHE K 150 " --> pdb=" O PHE K 146 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ARG K 151 " --> pdb=" O LEU K 147 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N PHE K 152 " --> pdb=" O LEU K 148 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N TYR K 153 " --> pdb=" O ASN K 149 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE K 154 " --> pdb=" O PHE K 150 " (cutoff:3.500A) Proline residue: K 167 - end of helix removed outlier: 4.250A pdb=" N PHE K 174 " --> pdb=" O ALA K 170 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY K 175 " --> pdb=" O PHE K 171 " (cutoff:3.500A) Processing helix chain 'K' and resid 188 through 220 removed outlier: 4.252A pdb=" N PHE K 196 " --> pdb=" O PHE K 192 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL K 197 " --> pdb=" O LEU K 193 " (cutoff:3.500A) Processing helix chain 'j' and resid 54 through 59 removed outlier: 4.392A pdb=" N ILE j 58 " --> pdb=" O PRO j 54 " (cutoff:3.500A) Processing helix chain 'j' and resid 74 through 86 removed outlier: 4.105A pdb=" N PHE j 84 " --> pdb=" O TRP j 80 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA j 85 " --> pdb=" O GLU j 81 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ASN j 86 " --> pdb=" O ALA j 82 " (cutoff:3.500A) Processing helix chain 'j' and resid 95 through 110 removed outlier: 4.977A pdb=" N ARG j 110 " --> pdb=" O ILE j 106 " (cutoff:3.500A) Processing helix chain 'j' and resid 116 through 124 removed outlier: 5.020A pdb=" N ASP j 121 " --> pdb=" O LYS j 117 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ARG j 122 " --> pdb=" O GLU j 118 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TYR j 123 " --> pdb=" O ARG j 119 " (cutoff:3.500A) Processing helix chain 'j' and resid 127 through 139 Proline residue: j 139 - end of helix Processing helix chain 'j' and resid 143 through 157 Processing helix chain 'j' and resid 166 through 187 removed outlier: 4.718A pdb=" N GLU j 187 " --> pdb=" O VAL j 183 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 59 removed outlier: 4.392A pdb=" N ILE J 58 " --> pdb=" O PRO J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 86 removed outlier: 4.105A pdb=" N PHE J 84 " --> pdb=" O TRP J 80 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA J 85 " --> pdb=" O GLU J 81 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ASN J 86 " --> pdb=" O ALA J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 110 removed outlier: 4.977A pdb=" N ARG J 110 " --> pdb=" O ILE J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 116 through 124 removed outlier: 5.019A pdb=" N ASP J 121 " --> pdb=" O LYS J 117 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG J 122 " --> pdb=" O GLU J 118 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TYR J 123 " --> pdb=" O ARG J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 139 Proline residue: J 139 - end of helix Processing helix chain 'J' and resid 143 through 157 Processing helix chain 'J' and resid 166 through 187 removed outlier: 4.717A pdb=" N GLU J 187 " --> pdb=" O VAL J 183 " (cutoff:3.500A) Processing helix chain 's' and resid 34 through 40 Processing helix chain 's' and resid 41 through 46 Processing helix chain 's' and resid 50 through 109 Proline residue: s 61 - end of helix removed outlier: 3.973A pdb=" N GLU s 107 " --> pdb=" O ARG s 103 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLN s 108 " --> pdb=" O VAL s 104 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL s 109 " --> pdb=" O LEU s 105 " (cutoff:3.500A) Processing helix chain 'S' and resid 34 through 40 Processing helix chain 'S' and resid 41 through 46 Processing helix chain 'S' and resid 50 through 109 Proline residue: S 61 - end of helix removed outlier: 3.972A pdb=" N GLU S 107 " --> pdb=" O ARG S 103 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLN S 108 " --> pdb=" O VAL S 104 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL S 109 " --> pdb=" O LEU S 105 " (cutoff:3.500A) Processing helix chain 'u' and resid 38 through 67 Processing helix chain 'u' and resid 69 through 115 removed outlier: 5.632A pdb=" N VAL u 73 " --> pdb=" O ASP u 69 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU u 104 " --> pdb=" O HIS u 100 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL u 105 " --> pdb=" O ILE u 101 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA u 106 " --> pdb=" O ALA u 102 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLU u 107 " --> pdb=" O SER u 103 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ASP u 109 " --> pdb=" O VAL u 105 " (cutoff:3.500A) Proline residue: u 110 - end of helix removed outlier: 4.295A pdb=" N THR u 113 " --> pdb=" O ASP u 109 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG u 114 " --> pdb=" O PRO u 110 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LEU u 115 " --> pdb=" O VAL u 111 " (cutoff:3.500A) Processing helix chain 'U' and resid 38 through 67 Processing helix chain 'U' and resid 69 through 115 removed outlier: 5.631A pdb=" N VAL U 73 " --> pdb=" O ASP U 69 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU U 104 " --> pdb=" O HIS U 100 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL U 105 " --> pdb=" O ILE U 101 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA U 106 " --> pdb=" O ALA U 102 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLU U 107 " --> pdb=" O SER U 103 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ASP U 109 " --> pdb=" O VAL U 105 " (cutoff:3.500A) Proline residue: U 110 - end of helix removed outlier: 4.295A pdb=" N THR U 113 " --> pdb=" O ASP U 109 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG U 114 " --> pdb=" O PRO U 110 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N LEU U 115 " --> pdb=" O VAL U 111 " (cutoff:3.500A) Processing helix chain 'h' and resid 21 through 27 removed outlier: 4.161A pdb=" N LYS h 27 " --> pdb=" O GLU h 23 " (cutoff:3.500A) Processing helix chain 'h' and resid 31 through 39 Processing helix chain 'h' and resid 51 through 56 Processing helix chain 'h' and resid 98 through 107 removed outlier: 4.161A pdb=" N SER h 104 " --> pdb=" O SER h 100 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP h 105 " --> pdb=" O ASN h 101 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER h 106 " --> pdb=" O MET h 102 " (cutoff:3.500A) Processing helix chain 'h' and resid 120 through 131 removed outlier: 3.886A pdb=" N ARG h 124 " --> pdb=" O SER h 120 " (cutoff:3.500A) Processing helix chain 'h' and resid 134 through 139 Processing helix chain 'h' and resid 144 through 163 Processing helix chain 'h' and resid 168 through 183 Processing helix chain 'h' and resid 187 through 215 removed outlier: 3.612A pdb=" N LYS h 194 " --> pdb=" O GLY h 190 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N LYS h 197 " --> pdb=" O THR h 193 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N TRP h 198 " --> pdb=" O LYS h 194 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY h 215 " --> pdb=" O LYS h 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 27 removed outlier: 4.161A pdb=" N LYS H 27 " --> pdb=" O GLU H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 39 Processing helix chain 'H' and resid 51 through 56 Processing helix chain 'H' and resid 98 through 107 removed outlier: 4.162A pdb=" N SER H 104 " --> pdb=" O SER H 100 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ASP H 105 " --> pdb=" O ASN H 101 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER H 106 " --> pdb=" O MET H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 120 through 131 removed outlier: 3.887A pdb=" N ARG H 124 " --> pdb=" O SER H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 139 Processing helix chain 'H' and resid 144 through 163 Processing helix chain 'H' and resid 168 through 183 Processing helix chain 'H' and resid 187 through 215 removed outlier: 3.611A pdb=" N LYS H 194 " --> pdb=" O GLY H 190 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N LYS H 197 " --> pdb=" O THR H 193 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N TRP H 198 " --> pdb=" O LYS H 194 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY H 215 " --> pdb=" O LYS H 211 " (cutoff:3.500A) Processing helix chain 'e' and resid 187 through 192 removed outlier: 5.056A pdb=" N GLN e 192 " --> pdb=" O ALA e 188 " (cutoff:3.500A) Processing helix chain 'e' and resid 196 through 208 Processing helix chain 'e' and resid 212 through 217 removed outlier: 4.826A pdb=" N GLU e 216 " --> pdb=" O PRO e 212 " (cutoff:3.500A) Proline residue: e 217 - end of helix No H-bonds generated for 'chain 'e' and resid 212 through 217' Processing helix chain 'e' and resid 261 through 266 removed outlier: 4.485A pdb=" N GLU e 265 " --> pdb=" O GLU e 261 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N THR e 266 " --> pdb=" O THR e 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 261 through 266' Processing helix chain 'e' and resid 267 through 275 Processing helix chain 'e' and resid 276 through 302 Processing helix chain 'E' and resid 187 through 192 removed outlier: 5.056A pdb=" N GLN E 192 " --> pdb=" O ALA E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 208 Processing helix chain 'E' and resid 212 through 217 removed outlier: 4.826A pdb=" N GLU E 216 " --> pdb=" O PRO E 212 " (cutoff:3.500A) Proline residue: E 217 - end of helix No H-bonds generated for 'chain 'E' and resid 212 through 217' Processing helix chain 'E' and resid 261 through 266 removed outlier: 4.484A pdb=" N GLU E 265 " --> pdb=" O GLU E 261 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N THR E 266 " --> pdb=" O THR E 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 261 through 266' Processing helix chain 'E' and resid 267 through 275 Processing helix chain 'E' and resid 276 through 302 Processing helix chain 'x' and resid 4 through 45 removed outlier: 3.883A pdb=" N ALA x 8 " --> pdb=" O SER x 4 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N PHE x 9 " --> pdb=" O PRO x 5 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ALA x 10 " --> pdb=" O GLY x 6 " (cutoff:3.500A) Proline residue: x 19 - end of helix Proline residue: x 22 - end of helix Processing helix chain 'X' and resid 4 through 45 removed outlier: 3.884A pdb=" N ALA X 8 " --> pdb=" O SER X 4 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N PHE X 9 " --> pdb=" O PRO X 5 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ALA X 10 " --> pdb=" O GLY X 6 " (cutoff:3.500A) Proline residue: X 19 - end of helix Proline residue: X 22 - end of helix Processing helix chain 'b' and resid 116 through 121 Processing helix chain 'b' and resid 123 through 128 removed outlier: 5.501A pdb=" N ALA b 128 " --> pdb=" O LYS b 124 " (cutoff:3.500A) Processing helix chain 'b' and resid 135 through 149 removed outlier: 4.011A pdb=" N PHE b 140 " --> pdb=" O LEU b 136 " (cutoff:3.500A) Processing helix chain 'b' and resid 150 through 162 removed outlier: 4.301A pdb=" N PHE b 154 " --> pdb=" O ARG b 150 " (cutoff:3.500A) Processing helix chain 'b' and resid 174 through 186 Processing helix chain 'b' and resid 188 through 199 Processing helix chain 'b' and resid 206 through 215 Processing helix chain 'b' and resid 217 through 233 removed outlier: 3.784A pdb=" N THR b 232 " --> pdb=" O GLN b 228 " (cutoff:3.500A) Proline residue: b 233 - end of helix Processing helix chain 'b' and resid 246 through 262 Processing helix chain 'b' and resid 269 through 291 removed outlier: 5.097A pdb=" N PHE b 277 " --> pdb=" O TYR b 273 " (cutoff:3.500A) Proline residue: b 278 - end of helix Processing helix chain 'b' and resid 292 through 328 removed outlier: 5.102A pdb=" N GLU b 301 " --> pdb=" O LYS b 297 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLU b 302 " --> pdb=" O LEU b 298 " (cutoff:3.500A) Processing helix chain 'b' and resid 331 through 337 removed outlier: 4.289A pdb=" N ASP b 335 " --> pdb=" O THR b 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 123 through 128 removed outlier: 5.500A pdb=" N ALA B 128 " --> pdb=" O LYS B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 149 removed outlier: 4.010A pdb=" N PHE B 140 " --> pdb=" O LEU B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 162 removed outlier: 4.301A pdb=" N PHE B 154 " --> pdb=" O ARG B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 188 through 199 Processing helix chain 'B' and resid 206 through 215 Processing helix chain 'B' and resid 217 through 233 removed outlier: 3.784A pdb=" N THR B 232 " --> pdb=" O GLN B 228 " (cutoff:3.500A) Proline residue: B 233 - end of helix Processing helix chain 'B' and resid 246 through 262 Processing helix chain 'B' and resid 269 through 291 removed outlier: 5.097A pdb=" N PHE B 277 " --> pdb=" O TYR B 273 " (cutoff:3.500A) Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 292 through 328 removed outlier: 5.102A pdb=" N GLU B 301 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLU B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 337 removed outlier: 4.289A pdb=" N ASP B 335 " --> pdb=" O THR B 331 " (cutoff:3.500A) Processing helix chain 'r' and resid 36 through 48 removed outlier: 4.444A pdb=" N ILE r 43 " --> pdb=" O THR r 39 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N TYR r 44 " --> pdb=" O ILE r 40 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU r 45 " --> pdb=" O GLU r 41 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLY r 46 " --> pdb=" O LYS r 42 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ASP r 48 " --> pdb=" O TYR r 44 " (cutoff:3.500A) Processing helix chain 'r' and resid 62 through 83 removed outlier: 4.834A pdb=" N GLU r 83 " --> pdb=" O ALA r 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 36 through 48 removed outlier: 4.443A pdb=" N ILE R 43 " --> pdb=" O THR R 39 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N TYR R 44 " --> pdb=" O ILE R 40 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU R 45 " --> pdb=" O GLU R 41 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLY R 46 " --> pdb=" O LYS R 42 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ASP R 48 " --> pdb=" O TYR R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 83 removed outlier: 4.834A pdb=" N GLU R 83 " --> pdb=" O ALA R 79 " (cutoff:3.500A) Processing helix chain 'p' and resid 16 through 39 Processing helix chain 'p' and resid 40 through 51 Processing helix chain 'p' and resid 55 through 66 Proline residue: p 63 - end of helix Processing helix chain 'p' and resid 70 through 84 Processing helix chain 'p' and resid 92 through 113 Processing helix chain 'P' and resid 16 through 39 Processing helix chain 'P' and resid 40 through 51 Processing helix chain 'P' and resid 55 through 66 Proline residue: P 63 - end of helix Processing helix chain 'P' and resid 70 through 84 Processing helix chain 'P' and resid 92 through 113 Processing helix chain 'v' and resid 4 through 18 Proline residue: v 18 - end of helix Processing helix chain 'v' and resid 19 through 29 removed outlier: 3.959A pdb=" N GLU v 29 " --> pdb=" O TRP v 25 " (cutoff:3.500A) Processing helix chain 'v' and resid 32 through 58 removed outlier: 4.346A pdb=" N GLN v 56 " --> pdb=" O SER v 52 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TYR v 57 " --> pdb=" O ARG v 53 " (cutoff:3.500A) Processing helix chain 'v' and resid 67 through 99 removed outlier: 4.124A pdb=" N VAL v 71 " --> pdb=" O GLY v 67 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL v 85 " --> pdb=" O MET v 81 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ARG v 86 " --> pdb=" O ILE v 82 " (cutoff:3.500A) Processing helix chain 'V' and resid 4 through 18 Proline residue: V 18 - end of helix Processing helix chain 'V' and resid 19 through 29 removed outlier: 3.960A pdb=" N GLU V 29 " --> pdb=" O TRP V 25 " (cutoff:3.500A) Processing helix chain 'V' and resid 32 through 58 removed outlier: 4.347A pdb=" N GLN V 56 " --> pdb=" O SER V 52 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TYR V 57 " --> pdb=" O ARG V 53 " (cutoff:3.500A) Processing helix chain 'V' and resid 67 through 99 removed outlier: 4.124A pdb=" N VAL V 71 " --> pdb=" O GLY V 67 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL V 85 " --> pdb=" O MET V 81 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ARG V 86 " --> pdb=" O ILE V 82 " (cutoff:3.500A) Processing helix chain 'l' and resid 25 through 70 Processing helix chain 'l' and resid 82 through 94 Processing helix chain 'l' and resid 104 through 124 removed outlier: 4.735A pdb=" N ASP l 124 " --> pdb=" O LYS l 120 " (cutoff:3.500A) Processing helix chain 'l' and resid 129 through 144 Processing helix chain 'l' and resid 147 through 205 removed outlier: 4.059A pdb=" N SER l 153 " --> pdb=" O SER l 149 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER l 154 " --> pdb=" O ALA l 150 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ASN l 157 " --> pdb=" O SER l 153 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ALA l 158 " --> pdb=" O SER l 154 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N SER l 161 " --> pdb=" O ASN l 157 " (cutoff:3.500A) Processing helix chain 'L' and resid 25 through 70 Processing helix chain 'L' and resid 82 through 94 Processing helix chain 'L' and resid 104 through 124 removed outlier: 4.736A pdb=" N ASP L 124 " --> pdb=" O LYS L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 129 through 144 Processing helix chain 'L' and resid 147 through 205 removed outlier: 4.059A pdb=" N SER L 153 " --> pdb=" O SER L 149 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER L 154 " --> pdb=" O ALA L 150 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ASN L 157 " --> pdb=" O SER L 153 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ALA L 158 " --> pdb=" O SER L 154 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER L 161 " --> pdb=" O ASN L 157 " (cutoff:3.500A) Processing helix chain 'c' and resid 32 through 66 removed outlier: 5.080A pdb=" N ASP c 63 " --> pdb=" O GLN c 59 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ARG c 64 " --> pdb=" O LEU c 60 " (cutoff:3.500A) Processing helix chain 'c' and resid 77 through 85 Processing helix chain 'c' and resid 97 through 107 removed outlier: 4.061A pdb=" N ARG c 103 " --> pdb=" O GLN c 99 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N LEU c 104 " --> pdb=" O GLU c 100 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ALA c 105 " --> pdb=" O GLN c 101 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N HIS c 107 " --> pdb=" O ARG c 103 " (cutoff:3.500A) Processing helix chain 'c' and resid 112 through 123 removed outlier: 4.001A pdb=" N LYS c 121 " --> pdb=" O GLU c 117 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N PHE c 122 " --> pdb=" O GLU c 118 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG c 123 " --> pdb=" O ARG c 119 " (cutoff:3.500A) Processing helix chain 'c' and resid 126 through 144 Processing helix chain 'C' and resid 32 through 66 removed outlier: 5.079A pdb=" N ASP C 63 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ARG C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 85 Processing helix chain 'C' and resid 97 through 107 removed outlier: 4.060A pdb=" N ARG C 103 " --> pdb=" O GLN C 99 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LEU C 104 " --> pdb=" O GLU C 100 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ALA C 105 " --> pdb=" O GLN C 101 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N HIS C 107 " --> pdb=" O ARG C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 123 removed outlier: 4.002A pdb=" N LYS C 121 " --> pdb=" O GLU C 117 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N PHE C 122 " --> pdb=" O GLU C 118 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG C 123 " --> pdb=" O ARG C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 144 Processing helix chain 'd' and resid 58 through 63 removed outlier: 4.168A pdb=" N TYR d 62 " --> pdb=" O PRO d 58 " (cutoff:3.500A) Processing helix chain 'd' and resid 70 through 111 Proline residue: d 81 - end of helix Proline residue: d 104 - end of helix Processing helix chain 'd' and resid 115 through 161 Processing helix chain 'd' and resid 167 through 201 Processing helix chain 'd' and resid 202 through 213 removed outlier: 4.312A pdb=" N LEU d 206 " --> pdb=" O ASN d 202 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU d 210 " --> pdb=" O LEU d 206 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ASN d 211 " --> pdb=" O VAL d 207 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N HIS d 212 " --> pdb=" O SER d 208 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N GLY d 213 " --> pdb=" O TYR d 209 " (cutoff:3.500A) Processing helix chain 'd' and resid 249 through 254 removed outlier: 4.195A pdb=" N LYS d 253 " --> pdb=" O ASN d 249 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N THR d 254 " --> pdb=" O PRO d 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 249 through 254' Processing helix chain 'd' and resid 258 through 263 Proline residue: d 263 - end of helix Processing helix chain 'd' and resid 291 through 296 Proline residue: d 296 - end of helix Processing helix chain 'd' and resid 297 through 303 removed outlier: 4.038A pdb=" N PHE d 301 " --> pdb=" O ALA d 297 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THR d 302 " --> pdb=" O ARG d 298 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ASP d 303 " --> pdb=" O MET d 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 297 through 303' Processing helix chain 'D' and resid 58 through 63 removed outlier: 4.168A pdb=" N TYR D 62 " --> pdb=" O PRO D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 111 Proline residue: D 81 - end of helix Proline residue: D 104 - end of helix Processing helix chain 'D' and resid 115 through 161 Processing helix chain 'D' and resid 167 through 201 Processing helix chain 'D' and resid 202 through 213 removed outlier: 4.311A pdb=" N LEU D 206 " --> pdb=" O ASN D 202 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU D 210 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ASN D 211 " --> pdb=" O VAL D 207 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N HIS D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N GLY D 213 " --> pdb=" O TYR D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 254 removed outlier: 4.195A pdb=" N LYS D 253 " --> pdb=" O ASN D 249 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N THR D 254 " --> pdb=" O PRO D 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 249 through 254' Processing helix chain 'D' and resid 258 through 263 Proline residue: D 263 - end of helix Processing helix chain 'D' and resid 291 through 296 Proline residue: D 296 - end of helix Processing helix chain 'D' and resid 297 through 303 removed outlier: 4.037A pdb=" N PHE D 301 " --> pdb=" O ALA D 297 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR D 302 " --> pdb=" O ARG D 298 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ASP D 303 " --> pdb=" O MET D 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 297 through 303' Processing helix chain 'm' and resid 113 through 129 removed outlier: 4.482A pdb=" N MET m 117 " --> pdb=" O GLU m 113 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ALA m 118 " --> pdb=" O LEU m 114 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N GLY m 119 " --> pdb=" O ILE m 115 " (cutoff:3.500A) Processing helix chain 'm' and resid 132 through 171 removed outlier: 3.723A pdb=" N HIS m 166 " --> pdb=" O TRP m 162 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N THR m 170 " --> pdb=" O HIS m 166 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ASN m 171 " --> pdb=" O LEU m 167 " (cutoff:3.500A) Processing helix chain 'm' and resid 177 through 185 removed outlier: 3.726A pdb=" N ALA m 181 " --> pdb=" O HIS m 177 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N TYR m 182 " --> pdb=" O PRO m 178 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ALA m 183 " --> pdb=" O ARG m 179 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU m 184 " --> pdb=" O TYR m 180 " (cutoff:3.500A) Proline residue: m 185 - end of helix No H-bonds generated for 'chain 'm' and resid 177 through 185' Processing helix chain 'M' and resid 113 through 129 removed outlier: 4.482A pdb=" N MET M 117 " --> pdb=" O GLU M 113 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ALA M 118 " --> pdb=" O LEU M 114 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N GLY M 119 " --> pdb=" O ILE M 115 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 171 removed outlier: 3.723A pdb=" N HIS M 166 " --> pdb=" O TRP M 162 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N THR M 170 " --> pdb=" O HIS M 166 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ASN M 171 " --> pdb=" O LEU M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 185 removed outlier: 3.726A pdb=" N ALA M 181 " --> pdb=" O HIS M 177 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N TYR M 182 " --> pdb=" O PRO M 178 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ALA M 183 " --> pdb=" O ARG M 179 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU M 184 " --> pdb=" O TYR M 180 " (cutoff:3.500A) Proline residue: M 185 - end of helix No H-bonds generated for 'chain 'M' and resid 177 through 185' Processing helix chain 'n' and resid 7 through 29 Processing helix chain 'n' and resid 36 through 51 removed outlier: 4.733A pdb=" N HIS n 40 " --> pdb=" O CYS n 36 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N SER n 41 " --> pdb=" O THR n 37 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LYS n 42 " --> pdb=" O ASP n 38 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA n 45 " --> pdb=" O SER n 41 " (cutoff:3.500A) Processing helix chain 'n' and resid 55 through 69 removed outlier: 3.725A pdb=" N LYS n 67 " --> pdb=" O MET n 63 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN n 68 " --> pdb=" O LYS n 64 " (cutoff:3.500A) Proline residue: n 69 - end of helix Processing helix chain 'n' and resid 74 through 86 removed outlier: 3.932A pdb=" N ARG n 86 " --> pdb=" O ARG n 82 " (cutoff:3.500A) Processing helix chain 'n' and resid 107 through 115 removed outlier: 4.709A pdb=" N HIS n 112 " --> pdb=" O PRO n 108 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU n 113 " --> pdb=" O GLU n 109 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR n 114 " --> pdb=" O VAL n 110 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ASN n 115 " --> pdb=" O LYS n 111 " (cutoff:3.500A) Processing helix chain 'n' and resid 130 through 146 Processing helix chain 'N' and resid 7 through 29 Processing helix chain 'N' and resid 36 through 51 removed outlier: 4.732A pdb=" N HIS N 40 " --> pdb=" O CYS N 36 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N SER N 41 " --> pdb=" O THR N 37 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LYS N 42 " --> pdb=" O ASP N 38 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA N 45 " --> pdb=" O SER N 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 69 removed outlier: 3.725A pdb=" N LYS N 67 " --> pdb=" O MET N 63 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN N 68 " --> pdb=" O LYS N 64 " (cutoff:3.500A) Proline residue: N 69 - end of helix Processing helix chain 'N' and resid 74 through 86 removed outlier: 3.932A pdb=" N ARG N 86 " --> pdb=" O ARG N 82 " (cutoff:3.500A) Processing helix chain 'N' and resid 107 through 115 removed outlier: 4.710A pdb=" N HIS N 112 " --> pdb=" O PRO N 108 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU N 113 " --> pdb=" O GLU N 109 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR N 114 " --> pdb=" O VAL N 110 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ASN N 115 " --> pdb=" O LYS N 111 " (cutoff:3.500A) Processing helix chain 'N' and resid 130 through 146 Processing helix chain 'f' and resid 78 through 83 Processing helix chain 'f' and resid 93 through 99 removed outlier: 4.102A pdb=" N GLU f 97 " --> pdb=" O PRO f 93 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ALA f 98 " --> pdb=" O PRO f 94 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N VAL f 99 " --> pdb=" O VAL f 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 93 through 99' Processing helix chain 'f' and resid 121 through 136 removed outlier: 4.206A pdb=" N SER f 133 " --> pdb=" O VAL f 129 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N PHE f 134 " --> pdb=" O TYR f 130 " (cutoff:3.500A) Processing helix chain 'f' and resid 147 through 165 removed outlier: 3.857A pdb=" N LYS f 151 " --> pdb=" O SER f 147 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLN f 155 " --> pdb=" O LYS f 151 " (cutoff:3.500A) Proline residue: f 156 - end of helix Processing helix chain 'f' and resid 174 through 179 Proline residue: f 179 - end of helix Processing helix chain 'f' and resid 180 through 186 Processing helix chain 'f' and resid 198 through 203 removed outlier: 6.329A pdb=" N PHE f 202 " --> pdb=" O GLY f 198 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ARG f 203 " --> pdb=" O ASP f 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 198 through 203' Processing helix chain 'f' and resid 214 through 236 removed outlier: 5.210A pdb=" N GLU f 236 " --> pdb=" O LEU f 232 " (cutoff:3.500A) Processing helix chain 'f' and resid 244 through 249 removed outlier: 4.581A pdb=" N TYR f 248 " --> pdb=" O GLY f 244 " (cutoff:3.500A) Processing helix chain 'f' and resid 257 through 263 removed outlier: 3.939A pdb=" N ARG f 261 " --> pdb=" O LEU f 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 83 Processing helix chain 'F' and resid 93 through 99 removed outlier: 4.102A pdb=" N GLU F 97 " --> pdb=" O PRO F 93 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ALA F 98 " --> pdb=" O PRO F 94 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N VAL F 99 " --> pdb=" O VAL F 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 93 through 99' Processing helix chain 'F' and resid 121 through 136 removed outlier: 4.205A pdb=" N SER F 133 " --> pdb=" O VAL F 129 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N PHE F 134 " --> pdb=" O TYR F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 165 removed outlier: 3.857A pdb=" N LYS F 151 " --> pdb=" O SER F 147 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLN F 155 " --> pdb=" O LYS F 151 " (cutoff:3.500A) Proline residue: F 156 - end of helix Processing helix chain 'F' and resid 174 through 179 Proline residue: F 179 - end of helix Processing helix chain 'F' and resid 180 through 186 Processing helix chain 'F' and resid 198 through 203 removed outlier: 6.329A pdb=" N PHE F 202 " --> pdb=" O GLY F 198 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ARG F 203 " --> pdb=" O ASP F 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 198 through 203' Processing helix chain 'F' and resid 214 through 236 removed outlier: 5.209A pdb=" N GLU F 236 " --> pdb=" O LEU F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 249 removed outlier: 4.582A pdb=" N TYR F 248 " --> pdb=" O GLY F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 263 removed outlier: 3.938A pdb=" N ARG F 261 " --> pdb=" O LEU F 257 " (cutoff:3.500A) Processing helix chain 'w' and resid 4 through 9 removed outlier: 4.412A pdb=" N ALA w 9 " --> pdb=" O TRP w 5 " (cutoff:3.500A) Processing helix chain 'w' and resid 14 through 20 removed outlier: 4.034A pdb=" N PHE w 18 " --> pdb=" O VAL w 14 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA w 19 " --> pdb=" O PRO w 15 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N SER w 20 " --> pdb=" O SER w 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 14 through 20' Processing helix chain 'w' and resid 39 through 46 removed outlier: 4.981A pdb=" N SER w 43 " --> pdb=" O SER w 39 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU w 44 " --> pdb=" O ASN w 40 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N SER w 45 " --> pdb=" O SER w 41 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N VAL w 46 " --> pdb=" O GLU w 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 39 through 46' Processing helix chain 'w' and resid 74 through 79 removed outlier: 4.711A pdb=" N LEU w 78 " --> pdb=" O PRO w 74 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LYS w 79 " --> pdb=" O SER w 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 74 through 79' Processing helix chain 'w' and resid 90 through 95 removed outlier: 5.576A pdb=" N PHE w 94 " --> pdb=" O ASN w 90 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N THR w 95 " --> pdb=" O LEU w 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 90 through 95' Processing helix chain 'w' and resid 97 through 102 Processing helix chain 'W' and resid 4 through 9 removed outlier: 4.412A pdb=" N ALA W 9 " --> pdb=" O TRP W 5 " (cutoff:3.500A) Processing helix chain 'W' and resid 14 through 20 removed outlier: 4.034A pdb=" N PHE W 18 " --> pdb=" O VAL W 14 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA W 19 " --> pdb=" O PRO W 15 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N SER W 20 " --> pdb=" O SER W 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 14 through 20' Processing helix chain 'W' and resid 39 through 46 removed outlier: 4.980A pdb=" N SER W 43 " --> pdb=" O SER W 39 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU W 44 " --> pdb=" O ASN W 40 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N SER W 45 " --> pdb=" O SER W 41 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N VAL W 46 " --> pdb=" O GLU W 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 39 through 46' Processing helix chain 'W' and resid 74 through 79 removed outlier: 4.710A pdb=" N LEU W 78 " --> pdb=" O PRO W 74 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LYS W 79 " --> pdb=" O SER W 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 74 through 79' Processing helix chain 'W' and resid 90 through 95 removed outlier: 5.576A pdb=" N PHE W 94 " --> pdb=" O ASN W 90 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR W 95 " --> pdb=" O LEU W 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 90 through 95' Processing helix chain 'W' and resid 97 through 102 Processing helix chain 'a' and resid 122 through 148 Processing helix chain 'a' and resid 150 through 155 removed outlier: 5.335A pdb=" N ASN a 155 " --> pdb=" O VAL a 151 " (cutoff:3.500A) Processing helix chain 'a' and resid 156 through 164 removed outlier: 4.694A pdb=" N GLN a 164 " --> pdb=" O LEU a 160 " (cutoff:3.500A) Processing helix chain 'a' and resid 165 through 174 removed outlier: 3.545A pdb=" N HIS a 173 " --> pdb=" O PHE a 169 " (cutoff:3.500A) Processing helix chain 'a' and resid 188 through 208 Processing helix chain 'a' and resid 223 through 232 removed outlier: 3.888A pdb=" N ARG a 232 " --> pdb=" O TYR a 228 " (cutoff:3.500A) Processing helix chain 'a' and resid 233 through 246 Processing helix chain 'a' and resid 249 through 254 removed outlier: 4.052A pdb=" N PHE a 253 " --> pdb=" O ASP a 249 " (cutoff:3.500A) Proline residue: a 254 - end of helix No H-bonds generated for 'chain 'a' and resid 249 through 254' Processing helix chain 'a' and resid 258 through 287 removed outlier: 4.322A pdb=" N LEU a 285 " --> pdb=" O SER a 281 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ALA a 286 " --> pdb=" O GLN a 282 " (cutoff:3.500A) Processing helix chain 'a' and resid 304 through 331 removed outlier: 3.862A pdb=" N TYR a 308 " --> pdb=" O HIS a 304 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N HIS a 330 " --> pdb=" O ARG a 326 " (cutoff:3.500A) Processing helix chain 'a' and resid 343 through 355 removed outlier: 3.826A pdb=" N VAL a 353 " --> pdb=" O ALA a 349 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP a 354 " --> pdb=" O VAL a 350 " (cutoff:3.500A) Processing helix chain 'a' and resid 375 through 380 removed outlier: 5.166A pdb=" N ASP a 380 " --> pdb=" O GLN a 376 " (cutoff:3.500A) Processing helix chain 'a' and resid 383 through 399 Processing helix chain 'a' and resid 403 through 422 removed outlier: 4.025A pdb=" N ARG a 420 " --> pdb=" O VAL a 416 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLY a 421 " --> pdb=" O LEU a 417 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N GLU a 422 " --> pdb=" O GLU a 418 " (cutoff:3.500A) Processing helix chain 'a' and resid 431 through 440 Processing helix chain 'a' and resid 446 through 464 removed outlier: 4.121A pdb=" N GLY a 463 " --> pdb=" O GLU a 459 " (cutoff:3.500A) Processing helix chain 'a' and resid 473 through 494 removed outlier: 3.951A pdb=" N THR a 478 " --> pdb=" O LYS a 474 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY a 491 " --> pdb=" O ALA a 487 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU a 492 " --> pdb=" O ALA a 488 " (cutoff:3.500A) Processing helix chain 'a' and resid 499 through 507 Processing helix chain 'A' and resid 122 through 148 Processing helix chain 'A' and resid 150 through 155 removed outlier: 5.335A pdb=" N ASN A 155 " --> pdb=" O VAL A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 164 removed outlier: 4.694A pdb=" N GLN A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 174 removed outlier: 3.545A pdb=" N HIS A 173 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 208 Processing helix chain 'A' and resid 223 through 232 removed outlier: 3.888A pdb=" N ARG A 232 " --> pdb=" O TYR A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 246 Processing helix chain 'A' and resid 249 through 254 removed outlier: 4.052A pdb=" N PHE A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) Proline residue: A 254 - end of helix No H-bonds generated for 'chain 'A' and resid 249 through 254' Processing helix chain 'A' and resid 258 through 287 removed outlier: 4.323A pdb=" N LEU A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ALA A 286 " --> pdb=" O GLN A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 331 removed outlier: 3.862A pdb=" N TYR A 308 " --> pdb=" O HIS A 304 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N HIS A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 355 removed outlier: 3.825A pdb=" N VAL A 353 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP A 354 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 380 removed outlier: 5.166A pdb=" N ASP A 380 " --> pdb=" O GLN A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 399 Processing helix chain 'A' and resid 403 through 422 removed outlier: 4.025A pdb=" N ARG A 420 " --> pdb=" O VAL A 416 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLY A 421 " --> pdb=" O LEU A 417 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N GLU A 422 " --> pdb=" O GLU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 440 Processing helix chain 'A' and resid 446 through 464 removed outlier: 4.121A pdb=" N GLY A 463 " --> pdb=" O GLU A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 494 removed outlier: 3.951A pdb=" N THR A 478 " --> pdb=" O LYS A 474 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY A 491 " --> pdb=" O ALA A 487 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 507 Processing sheet with id= 1, first strand: chain 't' and resid 41 through 47 removed outlier: 6.125A pdb=" N ALA t 41 " --> pdb=" O ARG t 59 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LYS t 53 " --> pdb=" O ASN t 47 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'T' and resid 41 through 47 removed outlier: 6.126A pdb=" N ALA T 41 " --> pdb=" O ARG T 59 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LYS T 53 " --> pdb=" O ASN T 47 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'o' and resid 94 through 97 removed outlier: 4.030A pdb=" N HIS o 69 " --> pdb=" O PRO o 148 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N GLN o 154 " --> pdb=" O ASN o 73 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'O' and resid 94 through 97 removed outlier: 4.031A pdb=" N HIS O 69 " --> pdb=" O PRO O 148 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N GLN O 154 " --> pdb=" O ASN O 73 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'h' and resid 59 through 62 removed outlier: 6.372A pdb=" N ARG h 59 " --> pdb=" O VAL h 73 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU h 71 " --> pdb=" O ASN h 61 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'H' and resid 59 through 62 removed outlier: 6.373A pdb=" N ARG H 59 " --> pdb=" O VAL H 73 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU H 71 " --> pdb=" O ASN H 61 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'e' and resid 225 through 231 removed outlier: 5.544A pdb=" N ILE e 236 " --> pdb=" O PHE e 231 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'E' and resid 225 through 231 removed outlier: 5.544A pdb=" N ILE E 236 " --> pdb=" O PHE E 231 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'b' and resid 112 through 115 Processing sheet with id= 10, first strand: chain 'b' and resid 130 through 133 Processing sheet with id= 11, first strand: chain 'B' and resid 112 through 115 Processing sheet with id= 12, first strand: chain 'B' and resid 130 through 133 Processing sheet with id= 13, first strand: chain 'r' and resid 4 through 7 removed outlier: 7.873A pdb=" N ASP r 57 " --> pdb=" O LYS r 7 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'r' and resid 22 through 26 Processing sheet with id= 15, first strand: chain 'R' and resid 4 through 7 removed outlier: 7.873A pdb=" N ASP R 57 " --> pdb=" O LYS R 7 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'R' and resid 22 through 26 Processing sheet with id= 17, first strand: chain 'n' and resid 92 through 95 removed outlier: 4.575A pdb=" N HIS n 103 " --> pdb=" O SER n 95 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'N' and resid 92 through 95 removed outlier: 4.575A pdb=" N HIS N 103 " --> pdb=" O SER N 95 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'f' and resid 116 through 119 Processing sheet with id= 20, first strand: chain 'F' and resid 116 through 119 Processing sheet with id= 21, first strand: chain 'a' and resid 338 through 342 Processing sheet with id= 22, first strand: chain 'A' and resid 338 through 342 3126 hydrogen bonds defined for protein. 9342 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 36.56 Time building geometry restraints manager: 76.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 55954 1.01 - 1.21: 188 1.21 - 1.41: 25830 1.41 - 1.61: 35608 1.61 - 1.81: 588 Bond restraints: 118168 Sorted by residual: bond pdb=" CB7 CDL V 202 " pdb=" OB8 CDL V 202 " ideal model delta sigma weight residual 1.334 1.405 -0.071 1.10e-02 8.26e+03 4.18e+01 bond pdb=" CB7 CDL v 201 " pdb=" OB8 CDL v 201 " ideal model delta sigma weight residual 1.334 1.405 -0.071 1.10e-02 8.26e+03 4.16e+01 bond pdb=" CA7 CDL C 404 " pdb=" OA8 CDL C 404 " ideal model delta sigma weight residual 1.334 1.403 -0.069 1.10e-02 8.26e+03 3.98e+01 bond pdb=" CB7 CDL u 201 " pdb=" OB8 CDL u 201 " ideal model delta sigma weight residual 1.334 1.403 -0.069 1.10e-02 8.26e+03 3.89e+01 bond pdb=" CA7 CDL c 404 " pdb=" OA8 CDL c 404 " ideal model delta sigma weight residual 1.334 1.403 -0.069 1.10e-02 8.26e+03 3.89e+01 ... (remaining 118163 not shown) Histogram of bond angle deviations from ideal: 79.02 - 90.04: 4 90.04 - 101.06: 158 101.06 - 112.08: 130311 112.08 - 123.09: 69279 123.09 - 134.11: 11106 Bond angle restraints: 210858 Sorted by residual: angle pdb="HD11 LEU Q 17 " pdb=" CD1 LEU Q 17 " pdb="HD13 LEU Q 17 " ideal model delta sigma weight residual 110.00 79.88 30.12 3.00e+00 1.11e-01 1.01e+02 angle pdb=" CG LEU Q 17 " pdb=" CD1 LEU Q 17 " pdb="HD13 LEU Q 17 " ideal model delta sigma weight residual 109.00 79.02 29.98 3.00e+00 1.11e-01 9.99e+01 angle pdb="HD11 LEU Q 17 " pdb=" CD1 LEU Q 17 " pdb="HD12 LEU Q 17 " ideal model delta sigma weight residual 110.00 81.33 28.67 3.00e+00 1.11e-01 9.13e+01 angle pdb=" CG LEU Q 17 " pdb=" CD1 LEU Q 17 " pdb="HD12 LEU Q 17 " ideal model delta sigma weight residual 109.00 81.65 27.35 3.00e+00 1.11e-01 8.31e+01 angle pdb="HD12 LEU Q 17 " pdb=" CD1 LEU Q 17 " pdb="HD13 LEU Q 17 " ideal model delta sigma weight residual 110.00 133.18 -23.18 3.00e+00 1.11e-01 5.97e+01 ... (remaining 210853 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 55959 36.00 - 71.99: 1883 71.99 - 107.99: 154 107.99 - 143.98: 38 143.98 - 179.98: 14 Dihedral angle restraints: 58048 sinusoidal: 32222 harmonic: 25826 Sorted by residual: dihedral pdb=" CD ARG O 15 " pdb=" NE ARG O 15 " pdb=" CZ ARG O 15 " pdb=" NH1 ARG O 15 " ideal model delta sinusoidal sigma weight residual 0.00 179.98 -179.98 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD ARG o 15 " pdb=" NE ARG o 15 " pdb=" CZ ARG o 15 " pdb=" NH1 ARG o 15 " ideal model delta sinusoidal sigma weight residual 0.00 179.95 -179.95 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" N PEE J 302 " pdb=" C4 PEE J 302 " pdb=" C5 PEE J 302 " pdb=" O4P PEE J 302 " ideal model delta sinusoidal sigma weight residual 303.03 135.26 167.77 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 58045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 6563 0.042 - 0.084: 1558 0.084 - 0.126: 380 0.126 - 0.168: 23 0.168 - 0.210: 20 Chirality restraints: 8544 Sorted by residual: chirality pdb=" C1B LMT D 403 " pdb=" C2B LMT D 403 " pdb=" O1B LMT D 403 " pdb=" O5B LMT D 403 " both_signs ideal model delta sigma weight residual False -2.20 -2.41 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" C1B LMT d 403 " pdb=" C2B LMT d 403 " pdb=" O1B LMT d 403 " pdb=" O5B LMT d 403 " both_signs ideal model delta sigma weight residual False -2.20 -2.41 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" C1B LMT c 403 " pdb=" C2B LMT c 403 " pdb=" O1B LMT c 403 " pdb=" O5B LMT c 403 " both_signs ideal model delta sigma weight residual False -2.20 -2.40 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 8541 not shown) Planarity restraints: 17194 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN J 83 " -0.066 2.00e-02 2.50e+03 8.89e-02 1.19e+02 pdb=" CD GLN J 83 " 0.044 2.00e-02 2.50e+03 pdb=" OE1 GLN J 83 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 GLN J 83 " 0.144 2.00e-02 2.50e+03 pdb="HE21 GLN J 83 " 0.018 2.00e-02 2.50e+03 pdb="HE22 GLN J 83 " -0.142 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN j 83 " 0.064 2.00e-02 2.50e+03 8.59e-02 1.11e+02 pdb=" CD GLN j 83 " -0.043 2.00e-02 2.50e+03 pdb=" OE1 GLN j 83 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 GLN j 83 " -0.139 2.00e-02 2.50e+03 pdb="HE21 GLN j 83 " -0.016 2.00e-02 2.50e+03 pdb="HE22 GLN j 83 " 0.137 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 257 " -0.037 5.00e-02 4.00e+02 5.60e-02 5.02e+00 pdb=" N PRO A 258 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 258 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 258 " -0.031 5.00e-02 4.00e+02 ... (remaining 17191 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.10: 2143 2.10 - 2.72: 191575 2.72 - 3.35: 328995 3.35 - 3.97: 423424 3.97 - 4.60: 685259 Nonbonded interactions: 1631396 Sorted by model distance: nonbonded pdb="HH12 ARG U 94 " pdb=" OE2 GLU W 42 " model vdw 1.473 1.850 nonbonded pdb=" OD2 ASP J 162 " pdb=" HH TYR U 81 " model vdw 1.509 1.850 nonbonded pdb="HH12 ARG u 94 " pdb=" OE2 GLU w 42 " model vdw 1.511 1.850 nonbonded pdb=" O HIS U 100 " pdb=" HG SER U 103 " model vdw 1.530 1.850 nonbonded pdb=" O HIS u 100 " pdb=" HG SER u 103 " model vdw 1.544 1.850 ... (remaining 1631391 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'a' } ncs_group { reference = (chain 'B' and (resid 85 through 337 or resid 601)) selection = chain 'b' } ncs_group { reference = chain 'C' selection = chain 'c' } ncs_group { reference = chain 'D' selection = chain 'd' } ncs_group { reference = chain 'E' selection = chain 'e' } ncs_group { reference = chain 'F' selection = chain 'f' } ncs_group { reference = chain 'G' selection = chain 'g' } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'I' selection = chain 'i' } ncs_group { reference = chain 'J' selection = chain 'j' } ncs_group { reference = chain 'K' selection = chain 'k' } ncs_group { reference = chain 'L' selection = chain 'l' } ncs_group { reference = chain 'M' selection = chain 'm' } ncs_group { reference = chain 'N' selection = chain 'n' } ncs_group { reference = chain 'O' selection = chain 'o' } ncs_group { reference = chain 'P' selection = chain 'p' } ncs_group { reference = chain 'Q' selection = chain 'q' } ncs_group { reference = chain 'R' selection = chain 'r' } ncs_group { reference = chain 'S' selection = chain 's' } ncs_group { reference = chain 'T' selection = chain 't' } ncs_group { reference = chain 'U' selection = chain 'u' } ncs_group { reference = (chain 'V' and (resid 2 through 111 or resid 201)) selection = (chain 'v' and (resid 2 through 111 or resid 201)) } ncs_group { reference = chain 'W' selection = chain 'w' } ncs_group { reference = chain 'X' selection = chain 'x' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.510 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: 1.220 Extract box with map and model: 36.080 Check model and map are aligned: 1.290 Set scattering table: 0.820 Process input model: 291.850 Find NCS groups from input model: 3.700 Set up NCS constraints: 1.210 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:9.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 352.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 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 : 0.008 0.109 62122 Z= 0.501 Angle : 0.938 17.014 83572 Z= 0.443 Chirality : 0.039 0.210 8544 Planarity : 0.004 0.056 10550 Dihedral : 17.834 179.977 24948 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.69 % Allowed : 2.20 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % 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: -0.62 (0.09), residues: 7010 helix: 0.60 (0.08), residues: 3846 sheet: -1.34 (0.30), residues: 246 loop : -1.71 (0.11), residues: 2918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 96 HIS 0.004 0.001 HIS a 174 PHE 0.018 0.001 PHE D 53 TYR 0.011 0.001 TYR m 147 ARG 0.004 0.001 ARG V 111 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14020 Ramachandran restraints generated. 7010 Oldfield, 0 Emsley, 7010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14020 Ramachandran restraints generated. 7010 Oldfield, 0 Emsley, 7010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 107 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue THR 351 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue THR 351 is missing expected H atoms. Skipping. Evaluate side-chains 1520 residues out of total 6102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 1478 time to evaluate : 7.219 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: i 153 SER cc_start: 0.8488 (OUTLIER) cc_final: 0.7919 (m) REVERT: i 174 CYS cc_start: 0.7529 (m) cc_final: 0.6628 (m) REVERT: i 183 GLN cc_start: 0.8004 (tp40) cc_final: 0.7339 (tp-100) REVERT: i 187 ASP cc_start: 0.7378 (m-30) cc_final: 0.7141 (m-30) REVERT: g 211 GLN cc_start: 0.8075 (mt0) cc_final: 0.7863 (mt0) REVERT: o 63 ASP cc_start: 0.7399 (m-30) cc_final: 0.7192 (m-30) REVERT: o 84 ASN cc_start: 0.8193 (p0) cc_final: 0.7836 (p0) REVERT: o 87 ASP cc_start: 0.6801 (p0) cc_final: 0.6426 (p0) REVERT: k 180 LEU cc_start: 0.8229 (mt) cc_final: 0.8027 (tp) REVERT: j 200 ARG cc_start: 0.7807 (mmt180) cc_final: 0.7545 (mpt90) REVERT: h 35 ASP cc_start: 0.8391 (t70) cc_final: 0.8082 (t0) REVERT: h 71 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7393 (mt-10) REVERT: r 72 ASP cc_start: 0.7298 (m-30) cc_final: 0.7049 (m-30) REVERT: c 58 ASN cc_start: 0.8807 (m-40) cc_final: 0.8487 (m110) REVERT: c 86 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8860 (m) REVERT: d 277 SER cc_start: 0.8396 (p) cc_final: 0.7894 (t) REVERT: m 111 LYS cc_start: 0.7912 (mtmm) cc_final: 0.7488 (mmtm) REVERT: f 167 ASN cc_start: 0.8576 (m-40) cc_final: 0.8259 (m110) REVERT: I 153 SER cc_start: 0.8280 (OUTLIER) cc_final: 0.7716 (m) REVERT: I 174 CYS cc_start: 0.7635 (m) cc_final: 0.6645 (m) REVERT: I 183 GLN cc_start: 0.7956 (tp40) cc_final: 0.7439 (tp-100) REVERT: G 204 ARG cc_start: 0.7949 (mmt180) cc_final: 0.7746 (mpt180) REVERT: O 63 ASP cc_start: 0.7403 (m-30) cc_final: 0.7190 (m-30) REVERT: O 84 ASN cc_start: 0.8166 (p0) cc_final: 0.7824 (p0) REVERT: O 87 ASP cc_start: 0.6836 (p0) cc_final: 0.6414 (p0) REVERT: J 200 ARG cc_start: 0.7872 (mmt180) cc_final: 0.7564 (mpt90) REVERT: H 35 ASP cc_start: 0.8384 (t70) cc_final: 0.8085 (t0) REVERT: D 229 GLN cc_start: 0.7384 (mt0) cc_final: 0.7173 (mt0) REVERT: M 111 LYS cc_start: 0.8043 (mtmm) cc_final: 0.7752 (mmtt) outliers start: 42 outliers final: 22 residues processed: 1504 average time/residue: 3.3101 time to fit residues: 6221.0640 Evaluate side-chains 1064 residues out of total 6102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 1039 time to evaluate : 6.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 17 LEU Chi-restraints excluded: chain q residue 82 CYS Chi-restraints excluded: chain i residue 153 SER Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain j residue 91 PHE Chi-restraints excluded: chain j residue 190 GLN Chi-restraints excluded: chain j residue 203 THR Chi-restraints excluded: chain h residue 15 ILE Chi-restraints excluded: chain h residue 80 ASP Chi-restraints excluded: chain c residue 86 THR Chi-restraints excluded: chain d residue 73 VAL Chi-restraints excluded: chain f residue 209 SER Chi-restraints excluded: chain a residue 354 ASP Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 82 CYS Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 190 GLN Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain N residue 38 ASP Chi-restraints excluded: chain F residue 209 SER Chi-restraints excluded: chain A residue 354 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 586 optimal weight: 0.6980 chunk 526 optimal weight: 8.9990 chunk 291 optimal weight: 2.9990 chunk 179 optimal weight: 7.9990 chunk 354 optimal weight: 4.9990 chunk 281 optimal weight: 2.9990 chunk 543 optimal weight: 0.7980 chunk 210 optimal weight: 1.9990 chunk 330 optimal weight: 3.9990 chunk 404 optimal weight: 9.9990 chunk 630 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: q 25 GLN q 77 ASN t 76 GLN o 40 GLN o 69 HIS k 208 GLN j 216 GLN u 118 GLN h 41 ASN h 61 ASN h 180 GLN h 209 GLN b 163 ASN v 6 GLN v 7 GLN l 121 GLN c 125 GLN d 171 GLN d 229 GLN m 106 ASN n 23 GLN a 321 GLN Q 77 ASN I 179 GLN T 76 GLN G 211 GLN O 40 GLN O 69 HIS ** K 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 ASN H 61 ASN H 209 GLN B 163 ASN L 121 GLN C 125 GLN N 10 GLN N 23 GLN N 28 ASN F 167 ASN F 234 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 62122 Z= 0.261 Angle : 0.568 9.345 83572 Z= 0.282 Chirality : 0.039 0.172 8544 Planarity : 0.005 0.072 10550 Dihedral : 17.534 179.807 11019 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.74 % Allowed : 11.86 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % 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: 0.80 (0.10), residues: 7010 helix: 1.77 (0.08), residues: 3832 sheet: -0.84 (0.31), residues: 232 loop : -1.07 (0.11), residues: 2946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP a 159 HIS 0.008 0.001 HIS H 130 PHE 0.014 0.001 PHE d 53 TYR 0.025 0.001 TYR q 55 ARG 0.011 0.001 ARG A 352 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14020 Ramachandran restraints generated. 7010 Oldfield, 0 Emsley, 7010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14020 Ramachandran restraints generated. 7010 Oldfield, 0 Emsley, 7010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 107 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue THR 351 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue THR 351 is missing expected H atoms. Skipping. Evaluate side-chains 1233 residues out of total 6102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 1127 time to evaluate : 7.140 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: i 183 GLN cc_start: 0.8165 (tp40) cc_final: 0.7428 (tp-100) REVERT: t 25 GLN cc_start: 0.7511 (OUTLIER) cc_final: 0.7300 (mp-120) REVERT: g 117 SER cc_start: 0.8957 (m) cc_final: 0.8745 (m) REVERT: g 208 LYS cc_start: 0.8473 (ttpp) cc_final: 0.8199 (ttpp) REVERT: g 211 GLN cc_start: 0.8183 (mt0) cc_final: 0.7912 (mt0) REVERT: o 63 ASP cc_start: 0.7514 (m-30) cc_final: 0.7305 (m-30) REVERT: o 84 ASN cc_start: 0.8156 (p0) cc_final: 0.7949 (p0) REVERT: o 87 ASP cc_start: 0.6845 (p0) cc_final: 0.6499 (p0) REVERT: j 200 ARG cc_start: 0.7972 (mmt180) cc_final: 0.7740 (mpt90) REVERT: h 35 ASP cc_start: 0.8580 (t70) cc_final: 0.8200 (t0) REVERT: h 146 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7319 (m-30) REVERT: b 125 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6926 (mp0) REVERT: r 32 GLN cc_start: 0.8669 (mt0) cc_final: 0.8331 (mt0) REVERT: m 111 LYS cc_start: 0.8072 (mtmm) cc_final: 0.7733 (mmtt) REVERT: f 234 GLN cc_start: 0.8126 (mp10) cc_final: 0.7902 (mp10) REVERT: I 183 GLN cc_start: 0.8041 (tp40) cc_final: 0.7766 (tp-100) REVERT: O 63 ASP cc_start: 0.7503 (m-30) cc_final: 0.7299 (m-30) REVERT: O 84 ASN cc_start: 0.8117 (p0) cc_final: 0.7697 (p0) REVERT: O 87 ASP cc_start: 0.6834 (p0) cc_final: 0.6382 (p0) REVERT: J 200 ARG cc_start: 0.8005 (mmt180) cc_final: 0.7735 (mpt90) REVERT: H 35 ASP cc_start: 0.8563 (t70) cc_final: 0.8198 (t0) REVERT: H 146 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7295 (m-30) REVERT: D 65 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8448 (pt0) REVERT: D 277 SER cc_start: 0.8488 (p) cc_final: 0.7991 (t) REVERT: M 111 LYS cc_start: 0.8110 (mtmm) cc_final: 0.7802 (mmtt) outliers start: 106 outliers final: 44 residues processed: 1169 average time/residue: 3.3617 time to fit residues: 4988.6760 Evaluate side-chains 1094 residues out of total 6102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 1045 time to evaluate : 7.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 17 LEU Chi-restraints excluded: chain q residue 48 CYS Chi-restraints excluded: chain q residue 82 CYS Chi-restraints excluded: chain t residue 25 GLN Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 91 THR Chi-restraints excluded: chain k residue 212 SER Chi-restraints excluded: chain j residue 77 LYS Chi-restraints excluded: chain j residue 91 PHE Chi-restraints excluded: chain j residue 203 THR Chi-restraints excluded: chain j residue 218 GLN Chi-restraints excluded: chain j residue 220 HIS Chi-restraints excluded: chain j residue 222 HIS Chi-restraints excluded: chain s residue 83 GLU Chi-restraints excluded: chain u residue 95 GLU Chi-restraints excluded: chain h residue 80 ASP Chi-restraints excluded: chain h residue 146 ASP Chi-restraints excluded: chain h residue 181 SER Chi-restraints excluded: chain x residue 46 THR Chi-restraints excluded: chain b residue 125 GLU Chi-restraints excluded: chain p residue 39 GLN Chi-restraints excluded: chain v residue 71 VAL Chi-restraints excluded: chain d residue 46 HIS Chi-restraints excluded: chain d residue 73 VAL Chi-restraints excluded: chain d residue 199 LEU Chi-restraints excluded: chain f residue 166 ASN Chi-restraints excluded: chain f residue 209 SER Chi-restraints excluded: chain a residue 354 ASP Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 82 CYS Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 220 HIS Chi-restraints excluded: chain J residue 222 HIS Chi-restraints excluded: chain S residue 83 GLU Chi-restraints excluded: chain U residue 95 GLU Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 146 ASP Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain F residue 209 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 350 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 524 optimal weight: 2.9990 chunk 429 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 chunk 631 optimal weight: 0.9990 chunk 682 optimal weight: 7.9990 chunk 562 optimal weight: 4.9990 chunk 626 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 506 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 179 GLN i 202 GLN u 118 GLN h 41 ASN h 98 GLN b 314 ASN v 7 GLN n 23 GLN f 78 ASN I 202 GLN I 226 GLN T 88 GLN K 208 GLN J 216 GLN H 41 ASN H 98 GLN H 189 GLN X 34 ASN B 163 ASN V 7 GLN D 138 ASN D 229 GLN M 106 ASN N 23 GLN F 78 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 62122 Z= 0.364 Angle : 0.575 9.570 83572 Z= 0.294 Chirality : 0.040 0.199 8544 Planarity : 0.005 0.055 10550 Dihedral : 16.216 178.758 11004 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.23 % Allowed : 12.53 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.10), residues: 7010 helix: 1.94 (0.08), residues: 3854 sheet: -0.60 (0.32), residues: 238 loop : -0.82 (0.11), residues: 2918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP N 157 HIS 0.007 0.001 HIS H 130 PHE 0.017 0.002 PHE h 138 TYR 0.019 0.002 TYR U 54 ARG 0.011 0.001 ARG A 352 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14020 Ramachandran restraints generated. 7010 Oldfield, 0 Emsley, 7010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14020 Ramachandran restraints generated. 7010 Oldfield, 0 Emsley, 7010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 107 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue THR 351 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue THR 351 is missing expected H atoms. Skipping. Evaluate side-chains 1212 residues out of total 6102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1076 time to evaluate : 7.269 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: t 43 THR cc_start: 0.9152 (OUTLIER) cc_final: 0.8933 (t) REVERT: o 63 ASP cc_start: 0.7611 (m-30) cc_final: 0.7376 (m-30) REVERT: o 84 ASN cc_start: 0.8226 (p0) cc_final: 0.7850 (p0) REVERT: o 87 ASP cc_start: 0.6933 (p0) cc_final: 0.6544 (p0) REVERT: o 105 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7242 (mm-30) REVERT: o 147 ASP cc_start: 0.8022 (t70) cc_final: 0.7784 (t0) REVERT: k 180 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8417 (tp) REVERT: j 56 LYS cc_start: 0.8711 (pttt) cc_final: 0.8473 (pttm) REVERT: j 200 ARG cc_start: 0.8087 (mmt180) cc_final: 0.7850 (mpt90) REVERT: s 81 GLU cc_start: 0.7694 (tt0) cc_final: 0.7488 (tm-30) REVERT: h 35 ASP cc_start: 0.8724 (t70) cc_final: 0.8368 (t0) REVERT: h 223 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7347 (ttp80) REVERT: b 121 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.7932 (mp10) REVERT: b 125 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7107 (mp0) REVERT: m 111 LYS cc_start: 0.8157 (mtmm) cc_final: 0.7764 (mmtm) REVERT: n 63 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.8326 (mtm) REVERT: a 396 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6956 (mp0) REVERT: Q 19 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7205 (tt0) REVERT: I 183 GLN cc_start: 0.8194 (tp40) cc_final: 0.7965 (tp-100) REVERT: T 43 THR cc_start: 0.9116 (OUTLIER) cc_final: 0.8901 (t) REVERT: T 53 LYS cc_start: 0.8517 (mmmm) cc_final: 0.8315 (mmmt) REVERT: O 63 ASP cc_start: 0.7603 (m-30) cc_final: 0.7358 (m-30) REVERT: O 74 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.7157 (mt-10) REVERT: O 84 ASN cc_start: 0.8159 (p0) cc_final: 0.7702 (p0) REVERT: O 87 ASP cc_start: 0.6967 (p0) cc_final: 0.6479 (p0) REVERT: J 169 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8379 (mt-10) REVERT: J 200 ARG cc_start: 0.8113 (mmt180) cc_final: 0.7852 (mpt90) REVERT: H 35 ASP cc_start: 0.8708 (t70) cc_final: 0.8348 (t0) REVERT: H 223 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7410 (ttp80) REVERT: D 290 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.7955 (mmpt) REVERT: M 111 LYS cc_start: 0.8135 (mtmm) cc_final: 0.7815 (mmtm) REVERT: A 255 GLU cc_start: 0.7844 (tt0) cc_final: 0.7580 (tt0) outliers start: 136 outliers final: 61 residues processed: 1143 average time/residue: 3.3237 time to fit residues: 4762.3349 Evaluate side-chains 1085 residues out of total 6102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 1012 time to evaluate : 7.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 17 LEU Chi-restraints excluded: chain q residue 63 HIS Chi-restraints excluded: chain t residue 43 THR Chi-restraints excluded: chain t residue 55 THR Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 91 THR Chi-restraints excluded: chain k residue 180 LEU Chi-restraints excluded: chain k residue 212 SER Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 88 SER Chi-restraints excluded: chain j residue 91 PHE Chi-restraints excluded: chain j residue 203 THR Chi-restraints excluded: chain j residue 218 GLN Chi-restraints excluded: chain j residue 220 HIS Chi-restraints excluded: chain j residue 222 HIS Chi-restraints excluded: chain s residue 83 GLU Chi-restraints excluded: chain u residue 95 GLU Chi-restraints excluded: chain h residue 223 ARG Chi-restraints excluded: chain x residue 46 THR Chi-restraints excluded: chain b residue 121 GLN Chi-restraints excluded: chain b residue 125 GLU Chi-restraints excluded: chain r residue 13 SER Chi-restraints excluded: chain r residue 47 VAL Chi-restraints excluded: chain r residue 88 SER Chi-restraints excluded: chain v residue 71 VAL Chi-restraints excluded: chain l residue 9 SER Chi-restraints excluded: chain c residue 86 THR Chi-restraints excluded: chain c residue 118 GLU Chi-restraints excluded: chain d residue 46 HIS Chi-restraints excluded: chain d residue 56 THR Chi-restraints excluded: chain d residue 73 VAL Chi-restraints excluded: chain d residue 199 LEU Chi-restraints excluded: chain n residue 63 MET Chi-restraints excluded: chain f residue 166 ASN Chi-restraints excluded: chain f residue 209 SER Chi-restraints excluded: chain w residue 78 LEU Chi-restraints excluded: chain a residue 353 VAL Chi-restraints excluded: chain a residue 396 GLU Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 19 GLU Chi-restraints excluded: chain I residue 170 TRP Chi-restraints excluded: chain T residue 43 THR Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain O residue 74 GLU Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 218 GLN Chi-restraints excluded: chain J residue 220 HIS Chi-restraints excluded: chain J residue 222 HIS Chi-restraints excluded: chain S residue 83 GLU Chi-restraints excluded: chain U residue 95 GLU Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 223 ARG Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain V residue 3 PHE Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 290 LYS Chi-restraints excluded: chain M residue 140 MET Chi-restraints excluded: chain N residue 38 ASP Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain F residue 209 SER Chi-restraints excluded: chain W residue 78 LEU Chi-restraints excluded: chain A residue 482 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 623 optimal weight: 3.9990 chunk 474 optimal weight: 1.9990 chunk 327 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 301 optimal weight: 1.9990 chunk 423 optimal weight: 0.5980 chunk 633 optimal weight: 0.0870 chunk 670 optimal weight: 0.0020 chunk 331 optimal weight: 6.9990 chunk 600 optimal weight: 0.7980 chunk 180 optimal weight: 2.9990 overall best weight: 0.4366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: j 216 GLN u 118 GLN h 41 ASN x 34 ASN b 185 ASN v 7 GLN m 120 ASN n 23 GLN f 78 ASN ** J 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 118 GLN H 41 ASN H 189 GLN X 34 ASN B 163 ASN V 7 GLN C 99 GLN M 120 ASN N 23 GLN F 78 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 62122 Z= 0.149 Angle : 0.495 9.157 83572 Z= 0.250 Chirality : 0.035 0.182 8544 Planarity : 0.004 0.070 10550 Dihedral : 15.034 178.529 10998 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.67 % Allowed : 14.17 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.10), residues: 7010 helix: 2.29 (0.08), residues: 3848 sheet: -0.54 (0.30), residues: 258 loop : -0.56 (0.11), residues: 2904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP d 190 HIS 0.004 0.001 HIS H 130 PHE 0.010 0.001 PHE B 255 TYR 0.013 0.001 TYR q 55 ARG 0.013 0.000 ARG p 69 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14020 Ramachandran restraints generated. 7010 Oldfield, 0 Emsley, 7010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14020 Ramachandran restraints generated. 7010 Oldfield, 0 Emsley, 7010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 107 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue THR 351 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue THR 351 is missing expected H atoms. Skipping. Evaluate side-chains 1150 residues out of total 6102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 1048 time to evaluate : 7.137 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: t 25 GLN cc_start: 0.7994 (mm-40) cc_final: 0.7781 (mm110) REVERT: t 88 GLN cc_start: 0.8591 (tp40) cc_final: 0.8316 (mt0) REVERT: o 84 ASN cc_start: 0.8163 (p0) cc_final: 0.7942 (p0) REVERT: o 87 ASP cc_start: 0.6856 (p0) cc_final: 0.6522 (p0) REVERT: k 180 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8458 (tp) REVERT: j 56 LYS cc_start: 0.8672 (pttt) cc_final: 0.8452 (pttm) REVERT: j 200 ARG cc_start: 0.7973 (mmt180) cc_final: 0.7724 (mpt90) REVERT: u 120 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7685 (ttp) REVERT: h 35 ASP cc_start: 0.8636 (t70) cc_final: 0.8238 (t0) REVERT: h 223 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7405 (ttp80) REVERT: b 125 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7016 (mp0) REVERT: b 245 LYS cc_start: 0.8499 (mttp) cc_final: 0.8207 (mmtm) REVERT: l 47 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7320 (m-30) REVERT: d 170 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7292 (mt-10) REVERT: m 111 LYS cc_start: 0.8111 (mtmm) cc_final: 0.7725 (mmtm) REVERT: a 396 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6950 (mp0) REVERT: I 183 GLN cc_start: 0.8152 (tp40) cc_final: 0.7921 (tp-100) REVERT: O 84 ASN cc_start: 0.8162 (p0) cc_final: 0.7718 (p0) REVERT: O 87 ASP cc_start: 0.6867 (p0) cc_final: 0.6414 (p0) REVERT: O 105 GLU cc_start: 0.7331 (mm-30) cc_final: 0.6915 (mm-30) REVERT: J 200 ARG cc_start: 0.8009 (mmt180) cc_final: 0.7721 (mpt90) REVERT: H 35 ASP cc_start: 0.8632 (t70) cc_final: 0.8249 (t0) REVERT: H 223 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7456 (ttp80) REVERT: R 50 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.7301 (mtp85) REVERT: L 26 ARG cc_start: 0.6664 (mmm-85) cc_final: 0.6457 (mmt-90) REVERT: L 47 ASP cc_start: 0.7621 (OUTLIER) cc_final: 0.7295 (m-30) REVERT: M 111 LYS cc_start: 0.8087 (mtmm) cc_final: 0.7797 (mmtm) REVERT: N 117 ASP cc_start: 0.7746 (OUTLIER) cc_final: 0.7484 (m-30) REVERT: F 177 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7629 (ttp-170) REVERT: A 396 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6789 (mp0) outliers start: 102 outliers final: 63 residues processed: 1095 average time/residue: 3.3212 time to fit residues: 4608.5154 Evaluate side-chains 1082 residues out of total 6102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 1006 time to evaluate : 7.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 17 LEU Chi-restraints excluded: chain q residue 63 HIS Chi-restraints excluded: chain q residue 82 CYS Chi-restraints excluded: chain q residue 107 ASP Chi-restraints excluded: chain g residue 212 CYS Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 89 LYS Chi-restraints excluded: chain o residue 91 THR Chi-restraints excluded: chain k residue 180 LEU Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 91 PHE Chi-restraints excluded: chain j residue 203 THR Chi-restraints excluded: chain j residue 218 GLN Chi-restraints excluded: chain j residue 220 HIS Chi-restraints excluded: chain j residue 222 HIS Chi-restraints excluded: chain s residue 83 GLU Chi-restraints excluded: chain u residue 69 ASP Chi-restraints excluded: chain u residue 120 MET Chi-restraints excluded: chain h residue 80 ASP Chi-restraints excluded: chain h residue 223 ARG Chi-restraints excluded: chain e residue 262 THR Chi-restraints excluded: chain b residue 125 GLU Chi-restraints excluded: chain r residue 47 VAL Chi-restraints excluded: chain r residue 69 LEU Chi-restraints excluded: chain p residue 45 GLU Chi-restraints excluded: chain v residue 71 VAL Chi-restraints excluded: chain l residue 47 ASP Chi-restraints excluded: chain c residue 118 GLU Chi-restraints excluded: chain d residue 46 HIS Chi-restraints excluded: chain d residue 56 THR Chi-restraints excluded: chain d residue 73 VAL Chi-restraints excluded: chain d residue 170 GLU Chi-restraints excluded: chain d residue 199 LEU Chi-restraints excluded: chain m residue 117 MET Chi-restraints excluded: chain m residue 140 MET Chi-restraints excluded: chain n residue 63 MET Chi-restraints excluded: chain f residue 166 ASN Chi-restraints excluded: chain w residue 78 LEU Chi-restraints excluded: chain a residue 357 LYS Chi-restraints excluded: chain a residue 396 GLU Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 82 CYS Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain G residue 212 CYS Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain J residue 56 LYS Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 220 HIS Chi-restraints excluded: chain J residue 222 HIS Chi-restraints excluded: chain S residue 83 GLU Chi-restraints excluded: chain U residue 95 GLU Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 223 ARG Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 50 ARG Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 94 GLN Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain M residue 117 MET Chi-restraints excluded: chain N residue 38 ASP Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain F residue 177 ARG Chi-restraints excluded: chain F residue 209 SER Chi-restraints excluded: chain W residue 78 LEU Chi-restraints excluded: chain A residue 396 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 558 optimal weight: 3.9990 chunk 380 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 499 optimal weight: 0.7980 chunk 276 optimal weight: 0.3980 chunk 572 optimal weight: 2.9990 chunk 463 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 342 optimal weight: 6.9990 chunk 602 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: u 118 GLN h 41 ASN b 163 ASN v 7 GLN n 23 GLN f 78 ASN ** T 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 216 GLN H 41 ASN H 189 GLN B 163 ASN L 121 GLN M 106 ASN N 23 GLN F 78 ASN F 234 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 62122 Z= 0.242 Angle : 0.514 8.853 83572 Z= 0.261 Chirality : 0.037 0.176 8544 Planarity : 0.004 0.043 10550 Dihedral : 14.732 178.657 10997 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.77 % Allowed : 14.73 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.10), residues: 7010 helix: 2.33 (0.08), residues: 3872 sheet: -0.48 (0.30), residues: 258 loop : -0.49 (0.11), residues: 2880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 190 HIS 0.006 0.001 HIS h 130 PHE 0.013 0.001 PHE h 138 TYR 0.016 0.001 TYR U 54 ARG 0.005 0.000 ARG c 64 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14020 Ramachandran restraints generated. 7010 Oldfield, 0 Emsley, 7010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14020 Ramachandran restraints generated. 7010 Oldfield, 0 Emsley, 7010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 107 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue THR 351 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue THR 351 is missing expected H atoms. Skipping. Evaluate side-chains 1146 residues out of total 6102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1038 time to evaluate : 7.202 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: t 43 THR cc_start: 0.9162 (OUTLIER) cc_final: 0.8930 (t) REVERT: o 87 ASP cc_start: 0.6894 (p0) cc_final: 0.6571 (p0) REVERT: o 105 GLU cc_start: 0.7362 (mm-30) cc_final: 0.6979 (mm-30) REVERT: k 180 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8391 (tp) REVERT: j 56 LYS cc_start: 0.8692 (pttt) cc_final: 0.8470 (pttm) REVERT: j 200 ARG cc_start: 0.8074 (mmt180) cc_final: 0.7828 (mpt90) REVERT: h 35 ASP cc_start: 0.8686 (t70) cc_final: 0.8307 (t0) REVERT: h 223 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7434 (ttp80) REVERT: b 125 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7123 (mp0) REVERT: b 245 LYS cc_start: 0.8520 (mttp) cc_final: 0.8221 (mmtm) REVERT: l 47 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.7336 (m-30) REVERT: d 170 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7416 (mt-10) REVERT: m 111 LYS cc_start: 0.8164 (mtmm) cc_final: 0.7778 (mmtm) REVERT: a 396 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6956 (mp0) REVERT: Q 19 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7152 (tt0) REVERT: I 183 GLN cc_start: 0.8213 (tp40) cc_final: 0.7991 (tp-100) REVERT: T 43 THR cc_start: 0.9124 (OUTLIER) cc_final: 0.8900 (t) REVERT: T 53 LYS cc_start: 0.8530 (mmmm) cc_final: 0.8325 (mmmt) REVERT: O 84 ASN cc_start: 0.8151 (p0) cc_final: 0.7664 (p0) REVERT: O 87 ASP cc_start: 0.6902 (p0) cc_final: 0.6401 (p0) REVERT: J 200 ARG cc_start: 0.8077 (mmt180) cc_final: 0.7798 (mpt90) REVERT: H 35 ASP cc_start: 0.8686 (t70) cc_final: 0.8325 (t0) REVERT: H 223 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7499 (ttp80) REVERT: M 111 LYS cc_start: 0.8117 (mtmm) cc_final: 0.7828 (mmtt) REVERT: F 177 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7599 (ttp-170) REVERT: A 255 GLU cc_start: 0.7860 (tt0) cc_final: 0.7586 (tt0) REVERT: A 396 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6918 (mp0) outliers start: 108 outliers final: 68 residues processed: 1086 average time/residue: 3.4901 time to fit residues: 4836.7602 Evaluate side-chains 1105 residues out of total 6102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1025 time to evaluate : 7.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 17 LEU Chi-restraints excluded: chain q residue 63 HIS Chi-restraints excluded: chain t residue 43 THR Chi-restraints excluded: chain g residue 204 ARG Chi-restraints excluded: chain g residue 212 CYS Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 89 LYS Chi-restraints excluded: chain o residue 91 THR Chi-restraints excluded: chain k residue 180 LEU Chi-restraints excluded: chain k residue 212 SER Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 91 PHE Chi-restraints excluded: chain j residue 203 THR Chi-restraints excluded: chain j residue 218 GLN Chi-restraints excluded: chain j residue 220 HIS Chi-restraints excluded: chain j residue 222 HIS Chi-restraints excluded: chain s residue 83 GLU Chi-restraints excluded: chain u residue 95 GLU Chi-restraints excluded: chain h residue 223 ARG Chi-restraints excluded: chain e residue 262 THR Chi-restraints excluded: chain b residue 125 GLU Chi-restraints excluded: chain r residue 47 VAL Chi-restraints excluded: chain r residue 71 LEU Chi-restraints excluded: chain v residue 3 PHE Chi-restraints excluded: chain v residue 71 VAL Chi-restraints excluded: chain l residue 47 ASP Chi-restraints excluded: chain c residue 118 GLU Chi-restraints excluded: chain d residue 46 HIS Chi-restraints excluded: chain d residue 56 THR Chi-restraints excluded: chain d residue 73 VAL Chi-restraints excluded: chain d residue 170 GLU Chi-restraints excluded: chain d residue 199 LEU Chi-restraints excluded: chain d residue 212 HIS Chi-restraints excluded: chain d residue 282 ASP Chi-restraints excluded: chain m residue 140 MET Chi-restraints excluded: chain n residue 63 MET Chi-restraints excluded: chain n residue 66 THR Chi-restraints excluded: chain f residue 89 THR Chi-restraints excluded: chain f residue 166 ASN Chi-restraints excluded: chain f residue 209 SER Chi-restraints excluded: chain w residue 78 LEU Chi-restraints excluded: chain a residue 357 LYS Chi-restraints excluded: chain a residue 396 GLU Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 19 GLU Chi-restraints excluded: chain Q residue 82 CYS Chi-restraints excluded: chain I residue 170 TRP Chi-restraints excluded: chain T residue 43 THR Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain G residue 212 CYS Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain J residue 56 LYS Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 220 HIS Chi-restraints excluded: chain J residue 222 HIS Chi-restraints excluded: chain S residue 83 GLU Chi-restraints excluded: chain U residue 95 GLU Chi-restraints excluded: chain H residue 223 ARG Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain V residue 3 PHE Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain L residue 94 GLN Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain N residue 38 ASP Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain F residue 177 ARG Chi-restraints excluded: chain W residue 78 LEU Chi-restraints excluded: chain A residue 396 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 225 optimal weight: 2.9990 chunk 604 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 393 optimal weight: 2.9990 chunk 165 optimal weight: 0.7980 chunk 671 optimal weight: 3.9990 chunk 557 optimal weight: 1.9990 chunk 310 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 222 optimal weight: 10.0000 chunk 352 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** t 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 118 GLN h 41 ASN b 163 ASN v 7 GLN l 77 ASN n 133 GLN f 78 ASN w 21 GLN ** T 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 216 GLN H 41 ASN H 189 GLN B 163 ASN V 7 GLN L 77 ASN F 78 ASN F 234 GLN W 21 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 62122 Z= 0.231 Angle : 0.512 8.784 83572 Z= 0.260 Chirality : 0.037 0.163 8544 Planarity : 0.004 0.088 10550 Dihedral : 14.386 178.910 10994 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.80 % Allowed : 14.81 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.10), residues: 7010 helix: 2.39 (0.08), residues: 3872 sheet: -0.47 (0.30), residues: 258 loop : -0.42 (0.11), residues: 2880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP d 190 HIS 0.005 0.001 HIS h 130 PHE 0.012 0.001 PHE H 138 TYR 0.014 0.001 TYR U 54 ARG 0.012 0.000 ARG P 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14020 Ramachandran restraints generated. 7010 Oldfield, 0 Emsley, 7010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14020 Ramachandran restraints generated. 7010 Oldfield, 0 Emsley, 7010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 107 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue THR 351 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue THR 351 is missing expected H atoms. Skipping. Evaluate side-chains 1154 residues out of total 6102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 1044 time to evaluate : 7.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: t 43 THR cc_start: 0.9172 (OUTLIER) cc_final: 0.8937 (t) REVERT: o 105 GLU cc_start: 0.7295 (mm-30) cc_final: 0.7002 (mm-30) REVERT: k 180 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8457 (tp) REVERT: j 56 LYS cc_start: 0.8693 (pttt) cc_final: 0.8473 (pttm) REVERT: j 200 ARG cc_start: 0.8067 (mmt180) cc_final: 0.7834 (mpt90) REVERT: u 120 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7848 (ttp) REVERT: h 35 ASP cc_start: 0.8694 (t70) cc_final: 0.8328 (t0) REVERT: b 125 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7108 (mp0) REVERT: b 245 LYS cc_start: 0.8517 (mttp) cc_final: 0.8222 (mmtm) REVERT: r 50 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7160 (mtp85) REVERT: l 47 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7323 (m-30) REVERT: d 290 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8110 (mmpt) REVERT: m 111 LYS cc_start: 0.8165 (mtmm) cc_final: 0.7820 (mmtm) REVERT: n 63 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8291 (mtm) REVERT: a 396 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6964 (mp0) REVERT: Q 51 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8175 (mm-40) REVERT: I 183 GLN cc_start: 0.8285 (tp40) cc_final: 0.8073 (tp-100) REVERT: T 43 THR cc_start: 0.9145 (OUTLIER) cc_final: 0.8914 (t) REVERT: O 84 ASN cc_start: 0.8153 (p0) cc_final: 0.7661 (p0) REVERT: O 87 ASP cc_start: 0.6871 (p0) cc_final: 0.6375 (p0) REVERT: J 200 ARG cc_start: 0.8099 (mmt180) cc_final: 0.7832 (mpt90) REVERT: H 35 ASP cc_start: 0.8694 (t70) cc_final: 0.8335 (t0) REVERT: H 223 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7532 (ttp80) REVERT: M 111 LYS cc_start: 0.8118 (mtmm) cc_final: 0.7831 (mmtt) REVERT: N 117 ASP cc_start: 0.7792 (OUTLIER) cc_final: 0.7563 (m-30) REVERT: F 177 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7590 (ttp-170) REVERT: A 255 GLU cc_start: 0.7858 (tt0) cc_final: 0.7587 (tt0) REVERT: A 396 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6953 (mp0) outliers start: 110 outliers final: 73 residues processed: 1095 average time/residue: 3.2213 time to fit residues: 4420.3228 Evaluate side-chains 1112 residues out of total 6102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1024 time to evaluate : 7.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 17 LEU Chi-restraints excluded: chain q residue 40 LEU Chi-restraints excluded: chain q residue 63 HIS Chi-restraints excluded: chain q residue 82 CYS Chi-restraints excluded: chain t residue 43 THR Chi-restraints excluded: chain g residue 212 CYS Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 89 LYS Chi-restraints excluded: chain o residue 91 THR Chi-restraints excluded: chain k residue 180 LEU Chi-restraints excluded: chain k residue 212 SER Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 91 PHE Chi-restraints excluded: chain j residue 203 THR Chi-restraints excluded: chain j residue 218 GLN Chi-restraints excluded: chain j residue 220 HIS Chi-restraints excluded: chain j residue 222 HIS Chi-restraints excluded: chain s residue 83 GLU Chi-restraints excluded: chain s residue 87 ASP Chi-restraints excluded: chain u residue 120 MET Chi-restraints excluded: chain h residue 80 ASP Chi-restraints excluded: chain e residue 262 THR Chi-restraints excluded: chain x residue 46 THR Chi-restraints excluded: chain b residue 125 GLU Chi-restraints excluded: chain r residue 47 VAL Chi-restraints excluded: chain r residue 50 ARG Chi-restraints excluded: chain r residue 71 LEU Chi-restraints excluded: chain v residue 3 PHE Chi-restraints excluded: chain v residue 71 VAL Chi-restraints excluded: chain l residue 47 ASP Chi-restraints excluded: chain c residue 107 HIS Chi-restraints excluded: chain c residue 118 GLU Chi-restraints excluded: chain d residue 46 HIS Chi-restraints excluded: chain d residue 56 THR Chi-restraints excluded: chain d residue 73 VAL Chi-restraints excluded: chain d residue 199 LEU Chi-restraints excluded: chain d residue 212 HIS Chi-restraints excluded: chain d residue 282 ASP Chi-restraints excluded: chain d residue 290 LYS Chi-restraints excluded: chain m residue 140 MET Chi-restraints excluded: chain n residue 63 MET Chi-restraints excluded: chain n residue 66 THR Chi-restraints excluded: chain f residue 89 THR Chi-restraints excluded: chain f residue 166 ASN Chi-restraints excluded: chain f residue 209 SER Chi-restraints excluded: chain w residue 78 LEU Chi-restraints excluded: chain a residue 396 GLU Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 51 GLN Chi-restraints excluded: chain Q residue 82 CYS Chi-restraints excluded: chain T residue 43 THR Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain G residue 212 CYS Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain J residue 56 LYS Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 220 HIS Chi-restraints excluded: chain J residue 222 HIS Chi-restraints excluded: chain S residue 83 GLU Chi-restraints excluded: chain U residue 95 GLU Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 223 ARG Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain V residue 3 PHE Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain L residue 22 GLU Chi-restraints excluded: chain L residue 94 GLN Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 212 HIS Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain M residue 117 MET Chi-restraints excluded: chain M residue 140 MET Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain F residue 177 ARG Chi-restraints excluded: chain W residue 78 LEU Chi-restraints excluded: chain A residue 396 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 647 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 382 optimal weight: 2.9990 chunk 490 optimal weight: 1.9990 chunk 379 optimal weight: 0.3980 chunk 565 optimal weight: 2.9990 chunk 374 optimal weight: 2.9990 chunk 668 optimal weight: 1.9990 chunk 418 optimal weight: 2.9990 chunk 407 optimal weight: 1.9990 chunk 308 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** t 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 118 GLN h 41 ASN b 163 ASN v 7 GLN n 23 GLN f 78 ASN I 179 GLN ** T 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 216 GLN H 41 ASN H 121 ASN H 189 GLN B 163 ASN V 7 GLN N 23 GLN F 78 ASN ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 234 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 62122 Z= 0.259 Angle : 0.522 8.495 83572 Z= 0.266 Chirality : 0.037 0.170 8544 Planarity : 0.004 0.069 10550 Dihedral : 14.218 179.632 10994 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.98 % Allowed : 14.94 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.10), residues: 7010 helix: 2.42 (0.08), residues: 3870 sheet: -0.45 (0.30), residues: 258 loop : -0.38 (0.11), residues: 2882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP I 170 HIS 0.006 0.001 HIS h 130 PHE 0.013 0.001 PHE H 138 TYR 0.015 0.001 TYR U 54 ARG 0.009 0.000 ARG A 352 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14020 Ramachandran restraints generated. 7010 Oldfield, 0 Emsley, 7010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14020 Ramachandran restraints generated. 7010 Oldfield, 0 Emsley, 7010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 107 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue THR 351 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue THR 351 is missing expected H atoms. Skipping. Evaluate side-chains 1164 residues out of total 6102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 1043 time to evaluate : 7.317 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: t 43 THR cc_start: 0.9180 (OUTLIER) cc_final: 0.8940 (t) REVERT: k 180 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8450 (tp) REVERT: j 56 LYS cc_start: 0.8693 (pttt) cc_final: 0.8468 (pttm) REVERT: j 200 ARG cc_start: 0.8062 (mmt180) cc_final: 0.7813 (mpt90) REVERT: h 223 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7357 (ttp-170) REVERT: b 125 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7131 (mp0) REVERT: b 245 LYS cc_start: 0.8529 (mttp) cc_final: 0.8230 (mmtm) REVERT: r 50 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.7197 (mtp85) REVERT: c 92 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7785 (m-30) REVERT: d 290 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8115 (mmpt) REVERT: m 111 LYS cc_start: 0.8158 (mtmm) cc_final: 0.7769 (mmtm) REVERT: n 63 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8295 (mtm) REVERT: a 396 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6962 (mp0) REVERT: Q 19 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7370 (tt0) REVERT: I 183 GLN cc_start: 0.8306 (tp40) cc_final: 0.8101 (tp-100) REVERT: T 43 THR cc_start: 0.9173 (OUTLIER) cc_final: 0.8934 (t) REVERT: O 84 ASN cc_start: 0.8156 (p0) cc_final: 0.7651 (p0) REVERT: O 87 ASP cc_start: 0.6933 (p0) cc_final: 0.6443 (p0) REVERT: J 200 ARG cc_start: 0.8114 (mmt180) cc_final: 0.7859 (mpt90) REVERT: H 223 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7476 (ttp-170) REVERT: R 50 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7252 (mtp85) REVERT: C 92 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7776 (m-30) REVERT: M 111 LYS cc_start: 0.8124 (mtmm) cc_final: 0.7837 (mmtt) REVERT: N 65 CYS cc_start: 0.7170 (m) cc_final: 0.6921 (m) REVERT: F 177 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7546 (ttp-170) REVERT: A 255 GLU cc_start: 0.7858 (tt0) cc_final: 0.7575 (tt0) REVERT: A 396 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6970 (mp0) outliers start: 121 outliers final: 83 residues processed: 1102 average time/residue: 3.2818 time to fit residues: 4557.4641 Evaluate side-chains 1127 residues out of total 6102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 1028 time to evaluate : 7.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 17 LEU Chi-restraints excluded: chain q residue 40 LEU Chi-restraints excluded: chain q residue 63 HIS Chi-restraints excluded: chain q residue 82 CYS Chi-restraints excluded: chain t residue 43 THR Chi-restraints excluded: chain t residue 55 THR Chi-restraints excluded: chain g residue 212 CYS Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 89 LYS Chi-restraints excluded: chain o residue 91 THR Chi-restraints excluded: chain k residue 180 LEU Chi-restraints excluded: chain k residue 212 SER Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 91 PHE Chi-restraints excluded: chain j residue 203 THR Chi-restraints excluded: chain j residue 218 GLN Chi-restraints excluded: chain j residue 220 HIS Chi-restraints excluded: chain j residue 222 HIS Chi-restraints excluded: chain s residue 83 GLU Chi-restraints excluded: chain u residue 95 GLU Chi-restraints excluded: chain h residue 80 ASP Chi-restraints excluded: chain h residue 223 ARG Chi-restraints excluded: chain e residue 262 THR Chi-restraints excluded: chain x residue 46 THR Chi-restraints excluded: chain b residue 125 GLU Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 47 VAL Chi-restraints excluded: chain r residue 50 ARG Chi-restraints excluded: chain r residue 69 LEU Chi-restraints excluded: chain r residue 71 LEU Chi-restraints excluded: chain v residue 3 PHE Chi-restraints excluded: chain v residue 71 VAL Chi-restraints excluded: chain l residue 9 SER Chi-restraints excluded: chain l residue 22 GLU Chi-restraints excluded: chain l residue 94 GLN Chi-restraints excluded: chain c residue 86 THR Chi-restraints excluded: chain c residue 92 ASP Chi-restraints excluded: chain c residue 107 HIS Chi-restraints excluded: chain c residue 118 GLU Chi-restraints excluded: chain d residue 46 HIS Chi-restraints excluded: chain d residue 56 THR Chi-restraints excluded: chain d residue 73 VAL Chi-restraints excluded: chain d residue 199 LEU Chi-restraints excluded: chain d residue 212 HIS Chi-restraints excluded: chain d residue 282 ASP Chi-restraints excluded: chain d residue 290 LYS Chi-restraints excluded: chain n residue 63 MET Chi-restraints excluded: chain n residue 66 THR Chi-restraints excluded: chain f residue 89 THR Chi-restraints excluded: chain f residue 166 ASN Chi-restraints excluded: chain f residue 209 SER Chi-restraints excluded: chain w residue 78 LEU Chi-restraints excluded: chain a residue 396 GLU Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 19 GLU Chi-restraints excluded: chain Q residue 82 CYS Chi-restraints excluded: chain T residue 43 THR Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain G residue 212 CYS Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain J residue 56 LYS Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 220 HIS Chi-restraints excluded: chain J residue 222 HIS Chi-restraints excluded: chain S residue 83 GLU Chi-restraints excluded: chain U residue 95 GLU Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 223 ARG Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain X residue 46 THR Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 50 ARG Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain V residue 3 PHE Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 22 GLU Chi-restraints excluded: chain L residue 94 GLN Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain N residue 105 GLU Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 177 ARG Chi-restraints excluded: chain W residue 78 LEU Chi-restraints excluded: chain A residue 396 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 413 optimal weight: 2.9990 chunk 267 optimal weight: 6.9990 chunk 399 optimal weight: 0.2980 chunk 201 optimal weight: 2.9990 chunk 131 optimal weight: 0.5980 chunk 129 optimal weight: 1.9990 chunk 425 optimal weight: 0.9980 chunk 455 optimal weight: 0.3980 chunk 330 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 525 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** t 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 118 GLN h 41 ASN b 163 ASN v 7 GLN n 32 HIS f 78 ASN J 216 GLN H 41 ASN H 189 GLN V 7 GLN N 23 GLN F 78 ASN ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 234 GLN ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 62122 Z= 0.184 Angle : 0.500 8.659 83572 Z= 0.255 Chirality : 0.036 0.160 8544 Planarity : 0.004 0.070 10550 Dihedral : 13.787 179.189 10994 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.66 % Allowed : 15.58 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.10), residues: 7010 helix: 2.54 (0.08), residues: 3864 sheet: -0.40 (0.30), residues: 258 loop : -0.30 (0.11), residues: 2888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP d 190 HIS 0.005 0.001 HIS h 130 PHE 0.010 0.001 PHE b 255 TYR 0.014 0.001 TYR q 55 ARG 0.013 0.000 ARG A 352 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14020 Ramachandran restraints generated. 7010 Oldfield, 0 Emsley, 7010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14020 Ramachandran restraints generated. 7010 Oldfield, 0 Emsley, 7010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 107 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue THR 351 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue THR 351 is missing expected H atoms. Skipping. Evaluate side-chains 1150 residues out of total 6102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 1049 time to evaluate : 6.642 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: k 180 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8443 (tp) REVERT: j 56 LYS cc_start: 0.8675 (pttt) cc_final: 0.8452 (pttm) REVERT: j 200 ARG cc_start: 0.8019 (mmt180) cc_final: 0.7757 (mpt90) REVERT: b 125 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7077 (mp0) REVERT: b 245 LYS cc_start: 0.8509 (mttp) cc_final: 0.8232 (mmtm) REVERT: r 50 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7182 (mtp85) REVERT: m 111 LYS cc_start: 0.8142 (mtmm) cc_final: 0.7805 (mmtm) REVERT: a 396 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6940 (mp0) REVERT: Q 19 GLU cc_start: 0.7869 (tt0) cc_final: 0.7385 (tt0) REVERT: T 43 THR cc_start: 0.9178 (OUTLIER) cc_final: 0.8943 (t) REVERT: G 205 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7247 (tm-30) REVERT: O 84 ASN cc_start: 0.8162 (p0) cc_final: 0.7657 (p0) REVERT: O 87 ASP cc_start: 0.6868 (p0) cc_final: 0.6393 (p0) REVERT: J 200 ARG cc_start: 0.8068 (mmt180) cc_final: 0.7806 (mpt90) REVERT: R 50 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7241 (mtp85) REVERT: M 111 LYS cc_start: 0.8110 (mtmm) cc_final: 0.7827 (mmtt) REVERT: N 65 CYS cc_start: 0.7190 (m) cc_final: 0.6962 (m) REVERT: N 117 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7505 (m-30) REVERT: A 396 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6974 (mp0) outliers start: 101 outliers final: 75 residues processed: 1098 average time/residue: 3.2926 time to fit residues: 4559.2028 Evaluate side-chains 1114 residues out of total 6102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1031 time to evaluate : 7.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 17 LEU Chi-restraints excluded: chain q residue 63 HIS Chi-restraints excluded: chain q residue 82 CYS Chi-restraints excluded: chain g residue 212 CYS Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 89 LYS Chi-restraints excluded: chain o residue 91 THR Chi-restraints excluded: chain k residue 180 LEU Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 91 PHE Chi-restraints excluded: chain j residue 203 THR Chi-restraints excluded: chain j residue 218 GLN Chi-restraints excluded: chain j residue 220 HIS Chi-restraints excluded: chain j residue 222 HIS Chi-restraints excluded: chain s residue 83 GLU Chi-restraints excluded: chain h residue 80 ASP Chi-restraints excluded: chain e residue 262 THR Chi-restraints excluded: chain x residue 82 SER Chi-restraints excluded: chain b residue 125 GLU Chi-restraints excluded: chain r residue 50 ARG Chi-restraints excluded: chain r residue 69 LEU Chi-restraints excluded: chain r residue 71 LEU Chi-restraints excluded: chain v residue 3 PHE Chi-restraints excluded: chain v residue 71 VAL Chi-restraints excluded: chain l residue 9 SER Chi-restraints excluded: chain l residue 22 GLU Chi-restraints excluded: chain l residue 94 GLN Chi-restraints excluded: chain c residue 86 THR Chi-restraints excluded: chain c residue 107 HIS Chi-restraints excluded: chain c residue 118 GLU Chi-restraints excluded: chain d residue 46 HIS Chi-restraints excluded: chain d residue 56 THR Chi-restraints excluded: chain d residue 73 VAL Chi-restraints excluded: chain d residue 199 LEU Chi-restraints excluded: chain d residue 212 HIS Chi-restraints excluded: chain d residue 282 ASP Chi-restraints excluded: chain m residue 140 MET Chi-restraints excluded: chain n residue 66 THR Chi-restraints excluded: chain f residue 166 ASN Chi-restraints excluded: chain f residue 209 SER Chi-restraints excluded: chain w residue 78 LEU Chi-restraints excluded: chain a residue 396 GLU Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 82 CYS Chi-restraints excluded: chain T residue 43 THR Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain G residue 212 CYS Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain J residue 56 LYS Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 220 HIS Chi-restraints excluded: chain J residue 222 HIS Chi-restraints excluded: chain U residue 95 GLU Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 50 ARG Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain V residue 3 PHE Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain L residue 22 GLU Chi-restraints excluded: chain L residue 94 GLN Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain M residue 117 MET Chi-restraints excluded: chain M residue 140 MET Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain N residue 105 GLU Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 177 ARG Chi-restraints excluded: chain W residue 78 LEU Chi-restraints excluded: chain A residue 396 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 608 optimal weight: 0.7980 chunk 640 optimal weight: 1.9990 chunk 584 optimal weight: 1.9990 chunk 623 optimal weight: 3.9990 chunk 375 optimal weight: 2.9990 chunk 271 optimal weight: 8.9990 chunk 489 optimal weight: 0.9990 chunk 191 optimal weight: 1.9990 chunk 563 optimal weight: 2.9990 chunk 589 optimal weight: 2.9990 chunk 621 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 179 GLN ** t 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 118 GLN h 41 ASN b 163 ASN v 7 GLN n 32 HIS f 78 ASN ** T 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 216 GLN H 41 ASN H 189 GLN V 7 GLN N 23 GLN F 78 ASN F 234 GLN ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 62122 Z= 0.276 Angle : 0.530 8.613 83572 Z= 0.271 Chirality : 0.037 0.194 8544 Planarity : 0.004 0.078 10550 Dihedral : 13.883 179.960 10994 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.80 % Allowed : 15.58 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.10), residues: 7010 helix: 2.49 (0.08), residues: 3864 sheet: -0.39 (0.30), residues: 258 loop : -0.31 (0.11), residues: 2888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 157 HIS 0.007 0.001 HIS h 130 PHE 0.015 0.001 PHE h 138 TYR 0.016 0.001 TYR U 54 ARG 0.016 0.000 ARG A 352 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14020 Ramachandran restraints generated. 7010 Oldfield, 0 Emsley, 7010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14020 Ramachandran restraints generated. 7010 Oldfield, 0 Emsley, 7010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 107 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue THR 351 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue THR 351 is missing expected H atoms. Skipping. Evaluate side-chains 1148 residues out of total 6102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 1038 time to evaluate : 7.842 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: t 43 THR cc_start: 0.9202 (OUTLIER) cc_final: 0.8972 (t) REVERT: k 180 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8469 (tp) REVERT: j 56 LYS cc_start: 0.8689 (pttt) cc_final: 0.8467 (pttm) REVERT: j 200 ARG cc_start: 0.8073 (mmt180) cc_final: 0.7824 (mpt90) REVERT: b 125 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7195 (mp0) REVERT: b 245 LYS cc_start: 0.8525 (mttp) cc_final: 0.8231 (mmtm) REVERT: r 50 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.7213 (mtp85) REVERT: c 92 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7716 (m-30) REVERT: m 111 LYS cc_start: 0.8146 (mtmm) cc_final: 0.7848 (mmtt) REVERT: a 396 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6983 (mp0) REVERT: Q 19 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7405 (tt0) REVERT: T 43 THR cc_start: 0.9204 (OUTLIER) cc_final: 0.8968 (t) REVERT: G 205 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7256 (tm-30) REVERT: O 84 ASN cc_start: 0.8164 (p0) cc_final: 0.7641 (p0) REVERT: O 87 ASP cc_start: 0.6942 (p0) cc_final: 0.6435 (p0) REVERT: J 200 ARG cc_start: 0.8112 (mmt180) cc_final: 0.7846 (mpt90) REVERT: R 32 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.7970 (mt0) REVERT: R 50 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7285 (mtp85) REVERT: C 92 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7685 (m-30) REVERT: M 111 LYS cc_start: 0.8146 (mtmm) cc_final: 0.7870 (mmtt) REVERT: N 65 CYS cc_start: 0.7169 (m) cc_final: 0.6943 (m) REVERT: A 255 GLU cc_start: 0.7851 (tt0) cc_final: 0.7573 (tt0) REVERT: A 396 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6994 (mp0) outliers start: 110 outliers final: 79 residues processed: 1097 average time/residue: 3.3442 time to fit residues: 4618.9691 Evaluate side-chains 1118 residues out of total 6102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 1027 time to evaluate : 6.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 17 LEU Chi-restraints excluded: chain q residue 63 HIS Chi-restraints excluded: chain q residue 82 CYS Chi-restraints excluded: chain t residue 43 THR Chi-restraints excluded: chain t residue 55 THR Chi-restraints excluded: chain g residue 212 CYS Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 89 LYS Chi-restraints excluded: chain o residue 91 THR Chi-restraints excluded: chain k residue 180 LEU Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 91 PHE Chi-restraints excluded: chain j residue 203 THR Chi-restraints excluded: chain j residue 218 GLN Chi-restraints excluded: chain j residue 220 HIS Chi-restraints excluded: chain j residue 222 HIS Chi-restraints excluded: chain s residue 83 GLU Chi-restraints excluded: chain u residue 95 GLU Chi-restraints excluded: chain e residue 262 THR Chi-restraints excluded: chain x residue 46 THR Chi-restraints excluded: chain x residue 82 SER Chi-restraints excluded: chain b residue 125 GLU Chi-restraints excluded: chain r residue 47 VAL Chi-restraints excluded: chain r residue 50 ARG Chi-restraints excluded: chain r residue 69 LEU Chi-restraints excluded: chain r residue 71 LEU Chi-restraints excluded: chain r residue 88 SER Chi-restraints excluded: chain v residue 3 PHE Chi-restraints excluded: chain v residue 71 VAL Chi-restraints excluded: chain l residue 9 SER Chi-restraints excluded: chain l residue 17 THR Chi-restraints excluded: chain l residue 22 GLU Chi-restraints excluded: chain l residue 94 GLN Chi-restraints excluded: chain c residue 86 THR Chi-restraints excluded: chain c residue 92 ASP Chi-restraints excluded: chain c residue 107 HIS Chi-restraints excluded: chain c residue 118 GLU Chi-restraints excluded: chain d residue 46 HIS Chi-restraints excluded: chain d residue 56 THR Chi-restraints excluded: chain d residue 73 VAL Chi-restraints excluded: chain d residue 199 LEU Chi-restraints excluded: chain d residue 212 HIS Chi-restraints excluded: chain d residue 282 ASP Chi-restraints excluded: chain n residue 66 THR Chi-restraints excluded: chain f residue 89 THR Chi-restraints excluded: chain f residue 166 ASN Chi-restraints excluded: chain f residue 209 SER Chi-restraints excluded: chain w residue 78 LEU Chi-restraints excluded: chain a residue 396 GLU Chi-restraints excluded: chain Q residue 19 GLU Chi-restraints excluded: chain Q residue 82 CYS Chi-restraints excluded: chain T residue 43 THR Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain G residue 212 CYS Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain J residue 56 LYS Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 220 HIS Chi-restraints excluded: chain J residue 222 HIS Chi-restraints excluded: chain S residue 83 GLU Chi-restraints excluded: chain U residue 95 GLU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain X residue 82 SER Chi-restraints excluded: chain R residue 32 GLN Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 50 ARG Chi-restraints excluded: chain V residue 3 PHE Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 22 GLU Chi-restraints excluded: chain L residue 94 GLN Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain N residue 105 GLU Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 177 ARG Chi-restraints excluded: chain W residue 78 LEU Chi-restraints excluded: chain A residue 396 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 409 optimal weight: 2.9990 chunk 659 optimal weight: 1.9990 chunk 402 optimal weight: 0.6980 chunk 312 optimal weight: 0.9980 chunk 458 optimal weight: 1.9990 chunk 691 optimal weight: 1.9990 chunk 636 optimal weight: 2.9990 chunk 550 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 425 optimal weight: 0.6980 chunk 337 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 65 GLN u 118 GLN h 41 ASN b 163 ASN v 7 GLN n 32 HIS f 78 ASN ** T 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 216 GLN H 41 ASN H 189 GLN V 7 GLN N 23 GLN F 78 ASN F 234 GLN ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 62122 Z= 0.208 Angle : 0.514 8.634 83572 Z= 0.262 Chirality : 0.036 0.152 8544 Planarity : 0.004 0.095 10550 Dihedral : 13.566 179.599 10992 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.53 % Allowed : 16.01 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.10), residues: 7010 helix: 2.56 (0.08), residues: 3866 sheet: -0.37 (0.30), residues: 258 loop : -0.27 (0.11), residues: 2886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 159 HIS 0.005 0.001 HIS h 130 PHE 0.011 0.001 PHE H 138 TYR 0.015 0.001 TYR q 55 ARG 0.018 0.000 ARG P 69 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14020 Ramachandran restraints generated. 7010 Oldfield, 0 Emsley, 7010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14020 Ramachandran restraints generated. 7010 Oldfield, 0 Emsley, 7010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 107 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue THR 351 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue THR 351 is missing expected H atoms. Skipping. Evaluate side-chains 1137 residues out of total 6102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 1044 time to evaluate : 7.327 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: t 101 ASN cc_start: 0.8912 (m-40) cc_final: 0.8702 (m-40) REVERT: g 205 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7358 (tm-30) REVERT: k 180 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8452 (tp) REVERT: j 56 LYS cc_start: 0.8682 (pttt) cc_final: 0.8458 (pttm) REVERT: j 200 ARG cc_start: 0.8046 (mmt180) cc_final: 0.7795 (mpt90) REVERT: b 125 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7116 (mp0) REVERT: b 245 LYS cc_start: 0.8523 (mttp) cc_final: 0.8241 (mmtm) REVERT: r 50 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7191 (mtp85) REVERT: m 111 LYS cc_start: 0.8136 (mtmm) cc_final: 0.7841 (mmtt) REVERT: a 396 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6983 (mp0) REVERT: Q 19 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7434 (tt0) REVERT: T 43 THR cc_start: 0.9199 (OUTLIER) cc_final: 0.8959 (t) REVERT: G 205 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7197 (tm-30) REVERT: O 84 ASN cc_start: 0.8148 (p0) cc_final: 0.7640 (p0) REVERT: O 87 ASP cc_start: 0.6884 (p0) cc_final: 0.6392 (p0) REVERT: J 200 ARG cc_start: 0.8096 (mmt180) cc_final: 0.7823 (mpt90) REVERT: R 32 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.7973 (mt0) REVERT: R 50 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.7301 (mtp85) REVERT: M 111 LYS cc_start: 0.8129 (mtmm) cc_final: 0.7840 (mmtt) REVERT: N 65 CYS cc_start: 0.7185 (m) cc_final: 0.6944 (m) REVERT: A 255 GLU cc_start: 0.7835 (tt0) cc_final: 0.7558 (tt0) REVERT: A 396 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6975 (mp0) outliers start: 93 outliers final: 75 residues processed: 1090 average time/residue: 3.4615 time to fit residues: 4799.7293 Evaluate side-chains 1119 residues out of total 6102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 1035 time to evaluate : 7.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 17 LEU Chi-restraints excluded: chain q residue 63 HIS Chi-restraints excluded: chain q residue 82 CYS Chi-restraints excluded: chain t residue 55 THR Chi-restraints excluded: chain g residue 212 CYS Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 89 LYS Chi-restraints excluded: chain o residue 91 THR Chi-restraints excluded: chain k residue 180 LEU Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 91 PHE Chi-restraints excluded: chain j residue 203 THR Chi-restraints excluded: chain j residue 218 GLN Chi-restraints excluded: chain j residue 220 HIS Chi-restraints excluded: chain j residue 222 HIS Chi-restraints excluded: chain s residue 83 GLU Chi-restraints excluded: chain u residue 95 GLU Chi-restraints excluded: chain e residue 262 THR Chi-restraints excluded: chain x residue 82 SER Chi-restraints excluded: chain b residue 125 GLU Chi-restraints excluded: chain r residue 47 VAL Chi-restraints excluded: chain r residue 50 ARG Chi-restraints excluded: chain r residue 69 LEU Chi-restraints excluded: chain r residue 71 LEU Chi-restraints excluded: chain v residue 3 PHE Chi-restraints excluded: chain v residue 71 VAL Chi-restraints excluded: chain l residue 9 SER Chi-restraints excluded: chain l residue 94 GLN Chi-restraints excluded: chain c residue 86 THR Chi-restraints excluded: chain c residue 107 HIS Chi-restraints excluded: chain c residue 118 GLU Chi-restraints excluded: chain d residue 46 HIS Chi-restraints excluded: chain d residue 56 THR Chi-restraints excluded: chain d residue 73 VAL Chi-restraints excluded: chain d residue 199 LEU Chi-restraints excluded: chain d residue 212 HIS Chi-restraints excluded: chain d residue 282 ASP Chi-restraints excluded: chain n residue 66 THR Chi-restraints excluded: chain f residue 89 THR Chi-restraints excluded: chain f residue 166 ASN Chi-restraints excluded: chain w residue 78 LEU Chi-restraints excluded: chain a residue 396 GLU Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 19 GLU Chi-restraints excluded: chain Q residue 82 CYS Chi-restraints excluded: chain T residue 43 THR Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain G residue 212 CYS Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain J residue 56 LYS Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 220 HIS Chi-restraints excluded: chain J residue 222 HIS Chi-restraints excluded: chain U residue 95 GLU Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain X residue 82 SER Chi-restraints excluded: chain R residue 32 GLN Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 50 ARG Chi-restraints excluded: chain V residue 3 PHE Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 22 GLU Chi-restraints excluded: chain L residue 94 GLN Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 212 HIS Chi-restraints excluded: chain N residue 38 ASP Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain N residue 105 GLU Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 177 ARG Chi-restraints excluded: chain W residue 78 LEU Chi-restraints excluded: chain A residue 396 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 437 optimal weight: 1.9990 chunk 586 optimal weight: 0.8980 chunk 168 optimal weight: 0.5980 chunk 507 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 152 optimal weight: 2.9990 chunk 551 optimal weight: 0.6980 chunk 230 optimal weight: 1.9990 chunk 566 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 179 GLN ** t 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 65 GLN u 118 GLN h 41 ASN b 163 ASN v 7 GLN n 32 HIS n 48 ASN f 78 ASN w 21 GLN ** T 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 216 GLN H 41 ASN H 189 GLN V 7 GLN ** M 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 23 GLN F 78 ASN F 234 GLN W 21 GLN ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.119541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.087531 restraints weight = 217336.879| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 1.48 r_work: 0.2776 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 62122 Z= 0.186 Angle : 0.508 8.652 83572 Z= 0.259 Chirality : 0.036 0.146 8544 Planarity : 0.004 0.088 10550 Dihedral : 13.390 179.478 10992 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.53 % Allowed : 16.19 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % 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: 2.02 (0.10), residues: 7010 helix: 2.59 (0.08), residues: 3866 sheet: -0.36 (0.30), residues: 258 loop : -0.24 (0.12), residues: 2886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP d 190 HIS 0.004 0.001 HIS N 9 PHE 0.011 0.001 PHE D 53 TYR 0.014 0.001 TYR U 54 ARG 0.017 0.000 ARG A 352 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 59513.67 seconds wall clock time: 1013 minutes 0.66 seconds (60780.66 seconds total)