Starting phenix.real_space_refine on Fri Mar 15 19:29:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wm3_21848/03_2024/6wm3_21848_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wm3_21848/03_2024/6wm3_21848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wm3_21848/03_2024/6wm3_21848.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wm3_21848/03_2024/6wm3_21848.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wm3_21848/03_2024/6wm3_21848_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wm3_21848/03_2024/6wm3_21848_updated.pdb" } resolution = 3.4 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= 0.016 sd= 1.165 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 375 5.16 5 C 44467 2.51 5 N 11852 2.21 5 O 13059 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 31": "OE1" <-> "OE2" Residue "R ARG 38": "NH1" <-> "NH2" Residue "R ASP 39": "OD1" <-> "OD2" Residue "R PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 49": "NH1" <-> "NH2" Residue "R PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 56": "NH1" <-> "NH2" Residue "R ARG 57": "NH1" <-> "NH2" Residue "R ARG 63": "NH1" <-> "NH2" Residue "R ARG 66": "NH1" <-> "NH2" Residue "R GLU 71": "OE1" <-> "OE2" Residue "R ARG 73": "NH1" <-> "NH2" Residue "R GLU 84": "OE1" <-> "OE2" Residue "R PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 92": "NH1" <-> "NH2" Residue "R ASP 93": "OD1" <-> "OD2" Residue "R GLU 98": "OE1" <-> "OE2" Residue "R GLU 105": "OE1" <-> "OE2" Residue "R GLU 110": "OE1" <-> "OE2" Residue "R ARG 120": "NH1" <-> "NH2" Residue "R ARG 133": "NH1" <-> "NH2" Residue "R PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 177": "NH1" <-> "NH2" Residue "R ARG 179": "NH1" <-> "NH2" Residue "R PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 185": "NH1" <-> "NH2" Residue "R ARG 189": "NH1" <-> "NH2" Residue "R ARG 198": "NH1" <-> "NH2" Residue "R GLU 201": "OE1" <-> "OE2" Residue "R GLU 203": "OE1" <-> "OE2" Residue "R GLU 207": "OE1" <-> "OE2" Residue "R ASP 208": "OD1" <-> "OD2" Residue "R PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 232": "NH1" <-> "NH2" Residue "R ARG 241": "NH1" <-> "NH2" Residue "R TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 254": "NH1" <-> "NH2" Residue "R ARG 264": "NH1" <-> "NH2" Residue "R ARG 279": "NH1" <-> "NH2" Residue "R ARG 281": "NH1" <-> "NH2" Residue "R ARG 291": "NH1" <-> "NH2" Residue "R PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 298": "NH1" <-> "NH2" Residue "R GLU 322": "OE1" <-> "OE2" Residue "R ARG 338": "NH1" <-> "NH2" Residue "R ARG 339": "NH1" <-> "NH2" Residue "R ARG 354": "NH1" <-> "NH2" Residue "R ASP 379": "OD1" <-> "OD2" Residue "R GLU 388": "OE1" <-> "OE2" Residue "R PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 409": "OD1" <-> "OD2" Residue "R GLU 427": "OE1" <-> "OE2" Residue "R PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 466": "OD1" <-> "OD2" Residue "R PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 491": "OE1" <-> "OE2" Residue "R ARG 495": "NH1" <-> "NH2" Residue "R PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 622": "OE1" <-> "OE2" Residue "R TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 660": "NH1" <-> "NH2" Residue "R TYR 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 665": "NH1" <-> "NH2" Residue "R ASP 712": "OD1" <-> "OD2" Residue "R ASP 715": "OD1" <-> "OD2" Residue "R PHE 779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 794": "OE1" <-> "OE2" Residue "R PHE 799": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 820": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 5": "OD1" <-> "OD2" Residue "J PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 20": "OE1" <-> "OE2" Residue "J GLU 25": "OE1" <-> "OE2" Residue "J GLU 28": "OE1" <-> "OE2" Residue "J GLU 36": "OE1" <-> "OE2" Residue "J PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 41": "OE1" <-> "OE2" Residue "J ARG 44": "NH1" <-> "NH2" Residue "J ARG 50": "NH1" <-> "NH2" Residue "J GLU 55": "OE1" <-> "OE2" Residue "J TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 61": "OE1" <-> "OE2" Residue "J ASP 89": "OD1" <-> "OD2" Residue "J TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 162": "OD1" <-> "OD2" Residue "J GLU 170": "OE1" <-> "OE2" Residue "J TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 187": "OD1" <-> "OD2" Residue "J GLU 197": "OE1" <-> "OE2" Residue "J PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 15": "OE1" <-> "OE2" Residue "M ARG 17": "NH1" <-> "NH2" Residue "M GLU 24": "OE1" <-> "OE2" Residue "M ARG 26": "NH1" <-> "NH2" Residue "M ARG 28": "NH1" <-> "NH2" Residue "M ARG 31": "NH1" <-> "NH2" Residue "M ARG 32": "NH1" <-> "NH2" Residue "M GLU 39": "OE1" <-> "OE2" Residue "M ARG 48": "NH1" <-> "NH2" Residue "M ARG 51": "NH1" <-> "NH2" Residue "M GLU 52": "OE1" <-> "OE2" Residue "M PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 66": "NH1" <-> "NH2" Residue "M GLU 79": "OE1" <-> "OE2" Residue "M ARG 89": "NH1" <-> "NH2" Residue "M ASP 93": "OD1" <-> "OD2" Residue "M PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 105": "OD1" <-> "OD2" Residue "M GLU 109": "OE1" <-> "OE2" Residue "M ARG 115": "NH1" <-> "NH2" Residue "I GLU 22": "OE1" <-> "OE2" Residue "I GLU 28": "OE1" <-> "OE2" Residue "I GLU 29": "OE1" <-> "OE2" Residue "I PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 44": "NH1" <-> "NH2" Residue "I ARG 50": "NH1" <-> "NH2" Residue "I TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 93": "OD1" <-> "OD2" Residue "I ASP 108": "OD1" <-> "OD2" Residue "I ARG 131": "NH1" <-> "NH2" Residue "I ARG 137": "NH1" <-> "NH2" Residue "I TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 162": "OD1" <-> "OD2" Residue "I ASP 164": "OD1" <-> "OD2" Residue "I GLU 170": "OE1" <-> "OE2" Residue "I ASP 176": "OD1" <-> "OD2" Residue "I TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 197": "OE1" <-> "OE2" Residue "I PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 17": "NH1" <-> "NH2" Residue "L GLU 24": "OE1" <-> "OE2" Residue "L ARG 26": "NH1" <-> "NH2" Residue "L ARG 28": "NH1" <-> "NH2" Residue "L ARG 31": "NH1" <-> "NH2" Residue "L ARG 32": "NH1" <-> "NH2" Residue "L GLU 38": "OE1" <-> "OE2" Residue "L GLU 39": "OE1" <-> "OE2" Residue "L GLU 45": "OE1" <-> "OE2" Residue "L ARG 48": "NH1" <-> "NH2" Residue "L ARG 51": "NH1" <-> "NH2" Residue "L GLU 54": "OE1" <-> "OE2" Residue "L ARG 66": "NH1" <-> "NH2" Residue "L GLU 74": "OE1" <-> "OE2" Residue "L GLU 79": "OE1" <-> "OE2" Residue "L ARG 89": "NH1" <-> "NH2" Residue "L GLU 94": "OE1" <-> "OE2" Residue "L ASP 97": "OD1" <-> "OD2" Residue "H ASP 5": "OD1" <-> "OD2" Residue "H PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 36": "OE1" <-> "OE2" Residue "H PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 41": "OE1" <-> "OE2" Residue "H ARG 44": "NH1" <-> "NH2" Residue "H ARG 50": "NH1" <-> "NH2" Residue "H TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 58": "OE1" <-> "OE2" Residue "H GLU 61": "OE1" <-> "OE2" Residue "H GLU 65": "OE1" <-> "OE2" Residue "H ASP 93": "OD1" <-> "OD2" Residue "H TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 164": "OD1" <-> "OD2" Residue "H GLU 170": "OE1" <-> "OE2" Residue "H TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 175": "OE1" <-> "OE2" Residue "H ASP 201": "OD1" <-> "OD2" Residue "H PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 17": "NH1" <-> "NH2" Residue "K GLU 20": "OE1" <-> "OE2" Residue "K GLU 24": "OE1" <-> "OE2" Residue "K ARG 26": "NH1" <-> "NH2" Residue "K ARG 28": "NH1" <-> "NH2" Residue "K ARG 31": "NH1" <-> "NH2" Residue "K ARG 32": "NH1" <-> "NH2" Residue "K GLU 39": "OE1" <-> "OE2" Residue "K ARG 48": "NH1" <-> "NH2" Residue "K ARG 51": "NH1" <-> "NH2" Residue "K GLU 52": "OE1" <-> "OE2" Residue "K GLU 54": "OE1" <-> "OE2" Residue "K PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 66": "NH1" <-> "NH2" Residue "K GLU 74": "OE1" <-> "OE2" Residue "K GLU 79": "OE1" <-> "OE2" Residue "K ARG 89": "NH1" <-> "NH2" Residue "K GLU 94": "OE1" <-> "OE2" Residue "K GLU 109": "OE1" <-> "OE2" Residue "K GLU 112": "OE1" <-> "OE2" Residue "S GLU 71": "OE1" <-> "OE2" Residue "S TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 81": "OE1" <-> "OE2" Residue "T PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 127": "NH1" <-> "NH2" Residue "U ARG 266": "NH1" <-> "NH2" Residue "U PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 280": "OD1" <-> "OD2" Residue "U PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 294": "OE1" <-> "OE2" Residue "U PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 410": "OE1" <-> "OE2" Residue "U TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 455": "NH1" <-> "NH2" Residue "U ASP 458": "OD1" <-> "OD2" Residue "V TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 302": "OE1" <-> "OE2" Residue "V TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 332": "OD1" <-> "OD2" Residue "V TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 336": "OD1" <-> "OD2" Residue "0 PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 116": "OE1" <-> "OE2" Residue "0 PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ASP 122": "OD1" <-> "OD2" Residue "0 TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 50": "OE1" <-> "OE2" Residue "1 ASP 115": "OD1" <-> "OD2" Residue "1 GLU 139": "OE1" <-> "OE2" Residue "2 GLU 9": "OE1" <-> "OE2" Residue "2 TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 50": "OE1" <-> "OE2" Residue "2 ASP 82": "OD1" <-> "OD2" Residue "2 ASP 83": "OD1" <-> "OD2" Residue "3 GLU 9": "OE1" <-> "OE2" Residue "3 GLU 50": "OE1" <-> "OE2" Residue "3 GLU 139": "OE1" <-> "OE2" Residue "4 GLU 9": "OE1" <-> "OE2" Residue "4 GLU 50": "OE1" <-> "OE2" Residue "4 ASP 83": "OD1" <-> "OD2" Residue "5 GLU 50": "OE1" <-> "OE2" Residue "5 ASP 83": "OD1" <-> "OD2" Residue "6 GLU 50": "OE1" <-> "OE2" Residue "7 TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 50": "OE1" <-> "OE2" Residue "7 GLU 139": "OE1" <-> "OE2" Residue "8 PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 50": "OE1" <-> "OE2" Residue "8 ASP 82": "OD1" <-> "OD2" Residue "9 GLU 50": "OE1" <-> "OE2" Residue "9 ASP 82": "OD1" <-> "OD2" Residue "9 GLU 139": "OE1" <-> "OE2" Residue "Q PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 40": "OE1" <-> "OE2" Residue "Q GLU 43": "OE1" <-> "OE2" Residue "Q ASP 44": "OD1" <-> "OD2" Residue "Q ASP 53": "OD1" <-> "OD2" Residue "Q GLU 61": "OE1" <-> "OE2" Residue "Q ASP 72": "OD1" <-> "OD2" Residue "Q ARG 73": "NH1" <-> "NH2" Residue "Q GLU 76": "OE1" <-> "OE2" Residue "Q PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 98": "OD1" <-> "OD2" Residue "Q TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 124": "OE1" <-> "OE2" Residue "Q GLU 136": "OE1" <-> "OE2" Residue "Q GLU 149": "OE1" <-> "OE2" Residue "Q PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 175": "OE1" <-> "OE2" Residue "Q GLU 215": "OE1" <-> "OE2" Residue "Q GLU 231": "OE1" <-> "OE2" Residue "Q ASP 260": "OD1" <-> "OD2" Residue "Q TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 269": "OD1" <-> "OD2" Residue "Q GLU 273": "OE1" <-> "OE2" Residue "Q GLU 298": "OE1" <-> "OE2" Residue "Q PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 334": "OE1" <-> "OE2" Residue "Q PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C ASP 60": "OD1" <-> "OD2" Residue "C TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 68": "OE1" <-> "OE2" Residue "C ASP 77": "OD1" <-> "OD2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 130": "OD1" <-> "OD2" Residue "C TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 286": "OE1" <-> "OE2" Residue "C ASP 290": "OD1" <-> "OD2" Residue "C PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 299": "OD1" <-> "OD2" Residue "C ARG 338": "NH1" <-> "NH2" Residue "C ASP 349": "OD1" <-> "OD2" Residue "C GLU 356": "OE1" <-> "OE2" Residue "C ASP 371": "OD1" <-> "OD2" Residue "C GLU 387": "OE1" <-> "OE2" Residue "C ARG 388": "NH1" <-> "NH2" Residue "C ASP 416": "OD1" <-> "OD2" Residue "C ASP 419": "OD1" <-> "OD2" Residue "C ASP 436": "OD1" <-> "OD2" Residue "C TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 485": "OE1" <-> "OE2" Residue "C GLU 503": "OE1" <-> "OE2" Residue "C ASP 505": "OD1" <-> "OD2" Residue "C ASP 517": "OD1" <-> "OD2" Residue "C ASP 518": "OD1" <-> "OD2" Residue "C TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 529": "OD1" <-> "OD2" Residue "C PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 572": "OE1" <-> "OE2" Residue "C TYR 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 53": "OE1" <-> "OE2" Residue "A GLU 58": "OE1" <-> "OE2" Residue "A ASP 60": "OD1" <-> "OD2" Residue "A TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 77": "OD1" <-> "OD2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 100": "OD1" <-> "OD2" Residue "A TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 193": "OE1" <-> "OE2" Residue "A ASP 235": "OD1" <-> "OD2" Residue "A PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A GLU 286": "OE1" <-> "OE2" Residue "A ASP 290": "OD1" <-> "OD2" Residue "A GLU 303": "OE1" <-> "OE2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A ASP 349": "OD1" <-> "OD2" Residue "A GLU 356": "OE1" <-> "OE2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "A ARG 388": "NH1" <-> "NH2" Residue "A GLU 401": "OE1" <-> "OE2" Residue "A GLU 463": "OE1" <-> "OE2" Residue "A TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 529": "OD1" <-> "OD2" Residue "A PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 562": "OD1" <-> "OD2" Residue "A GLU 572": "OE1" <-> "OE2" Residue "A ASP 576": "OD1" <-> "OD2" Residue "A PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 588": "OD1" <-> "OD2" Residue "A GLU 594": "OE1" <-> "OE2" Residue "A ASP 600": "OD1" <-> "OD2" Residue "A GLU 606": "OE1" <-> "OE2" Residue "B PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 58": "OE1" <-> "OE2" Residue "B GLU 68": "OE1" <-> "OE2" Residue "B ASP 77": "OD1" <-> "OD2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 197": "OE1" <-> "OE2" Residue "B PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 279": "OE1" <-> "OE2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B ASP 349": "OD1" <-> "OD2" Residue "B GLU 356": "OE1" <-> "OE2" Residue "B ARG 388": "NH1" <-> "NH2" Residue "B GLU 463": "OE1" <-> "OE2" Residue "B PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B GLU 491": "OE1" <-> "OE2" Residue "B ASP 518": "OD1" <-> "OD2" Residue "B ASP 529": "OD1" <-> "OD2" Residue "B PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 562": "OD1" <-> "OD2" Residue "B GLU 594": "OE1" <-> "OE2" Residue "B ASP 607": "OD1" <-> "OD2" Residue "F ASP 106": "OD1" <-> "OD2" Residue "F GLU 148": "OE1" <-> "OE2" Residue "F ASP 218": "OD1" <-> "OD2" Residue "F ASP 221": "OD1" <-> "OD2" Residue "F TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 224": "OE1" <-> "OE2" Residue "F PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 247": "OD1" <-> "OD2" Residue "F GLU 250": "OE1" <-> "OE2" Residue "F GLU 283": "OE1" <-> "OE2" Residue "F GLU 290": "OE1" <-> "OE2" Residue "F TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 336": "OE1" <-> "OE2" Residue "F ASP 360": "OD1" <-> "OD2" Residue "F TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 417": "OD1" <-> "OD2" Residue "F ASP 431": "OD1" <-> "OD2" Residue "F GLU 441": "OE1" <-> "OE2" Residue "F GLU 442": "OE1" <-> "OE2" Residue "F GLU 453": "OE1" <-> "OE2" Residue "F ARG 460": "NH1" <-> "NH2" Residue "F PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 469": "OE1" <-> "OE2" Residue "F PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 490": "OE1" <-> "OE2" Residue "F PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 88": "OE1" <-> "OE2" Residue "D ASP 140": "OD1" <-> "OD2" Residue "D GLU 148": "OE1" <-> "OE2" Residue "D ASP 149": "OD1" <-> "OD2" Residue "D GLU 201": "OE1" <-> "OE2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D GLU 225": "OE1" <-> "OE2" Residue "D PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 247": "OD1" <-> "OD2" Residue "D GLU 250": "OE1" <-> "OE2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "D PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 330": "OD1" <-> "OD2" Residue "D ASP 360": "OD1" <-> "OD2" Residue "D ASP 367": "OD1" <-> "OD2" Residue "D TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 380": "OD1" <-> "OD2" Residue "D ASP 417": "OD1" <-> "OD2" Residue "D TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 448": "OD1" <-> "OD2" Residue "D GLU 453": "OE1" <-> "OE2" Residue "D ARG 460": "NH1" <-> "NH2" Residue "D PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 469": "OE1" <-> "OE2" Residue "D GLU 490": "OE1" <-> "OE2" Residue "D PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 61": "OD1" <-> "OD2" Residue "E ASP 78": "OD1" <-> "OD2" Residue "E GLU 224": "OE1" <-> "OE2" Residue "E GLU 225": "OE1" <-> "OE2" Residue "E PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 239": "OE1" <-> "OE2" Residue "E PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 247": "OD1" <-> "OD2" Residue "E GLU 250": "OE1" <-> "OE2" Residue "E GLU 290": "OE1" <-> "OE2" Residue "E TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 374": "OE1" <-> "OE2" Residue "E TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 447": "OD1" <-> "OD2" Residue "E TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 453": "OE1" <-> "OE2" Residue "E ARG 460": "NH1" <-> "NH2" Residue "E PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 469": "OE1" <-> "OE2" Residue "E ASP 478": "OD1" <-> "OD2" Residue "E PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 39": "OE1" <-> "OE2" Residue "Z TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 77": "OD1" <-> "OD2" Residue "Z GLU 109": "OE1" <-> "OE2" Residue "Z TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 171": "OD1" <-> "OD2" Residue "Z ASP 194": "OD1" <-> "OD2" Residue "Z TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 206": "OD1" <-> "OD2" Residue "Z GLU 210": "OE1" <-> "OE2" Residue "Z ASP 221": "OD1" <-> "OD2" Residue "Z ASP 231": "OD1" <-> "OD2" Residue "Z ASP 244": "OD1" <-> "OD2" Residue "Z ASP 253": "OD1" <-> "OD2" Residue "Z ASP 261": "OD1" <-> "OD2" Residue "X ASP 37": "OD1" <-> "OD2" Residue "X GLU 47": "OE1" <-> "OE2" Residue "X PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 77": "OD1" <-> "OD2" Residue "X ASP 138": "OD1" <-> "OD2" Residue "X TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 170": "OE1" <-> "OE2" Residue "X GLU 173": "OE1" <-> "OE2" Residue "X GLU 191": "OE1" <-> "OE2" Residue "X ASP 194": "OD1" <-> "OD2" Residue "X GLU 214": "OE1" <-> "OE2" Residue "X ASP 221": "OD1" <-> "OD2" Residue "X GLU 269": "OE1" <-> "OE2" Residue "X GLU 271": "OE1" <-> "OE2" Residue "Y TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 37": "OD1" <-> "OD2" Residue "Y GLU 39": "OE1" <-> "OE2" Residue "Y TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 67": "OE1" <-> "OE2" Residue "Y ASP 77": "OD1" <-> "OD2" Residue "Y ASP 79": "OD1" <-> "OD2" Residue "Y GLU 113": "OE1" <-> "OE2" Residue "Y ASP 125": "OD1" <-> "OD2" Residue "Y TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 170": "OE1" <-> "OE2" Residue "Y GLU 191": "OE1" <-> "OE2" Residue "Y TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 206": "OD1" <-> "OD2" Residue "Y ASP 221": "OD1" <-> "OD2" Residue "Y ASP 231": "OD1" <-> "OD2" Residue "Y ASP 244": "OD1" <-> "OD2" Residue "Y ASP 264": "OD1" <-> "OD2" Residue "Y GLU 269": "OE1" <-> "OE2" Residue "Y GLU 271": "OE1" <-> "OE2" Residue "G ASP 5": "OD1" <-> "OD2" Residue "G GLU 8": "OE1" <-> "OE2" Residue "G PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G ASP 78": "OD1" <-> "OD2" Residue "G PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 120": "OE1" <-> "OE2" Residue "G TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 143": "OE1" <-> "OE2" Residue "G PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 160": "OE1" <-> "OE2" Residue "G GLU 173": "OE1" <-> "OE2" Residue "G TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 192": "OD1" <-> "OD2" Residue "G GLU 193": "OE1" <-> "OE2" Residue "G GLU 195": "OE1" <-> "OE2" Residue "G GLU 197": "OE1" <-> "OE2" Residue "G PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 13": "OD1" <-> "OD2" Residue "N GLU 14": "OE1" <-> "OE2" Residue "N PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 40": "OE1" <-> "OE2" Residue "N ASP 50": "OD1" <-> "OD2" Residue "N PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 79": "OD1" <-> "OD2" Residue "N ARG 107": "NH1" <-> "NH2" Residue "N ARG 110": "NH1" <-> "NH2" Time to flip residues: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 69755 Number of models: 1 Model: "" Number of chains: 39 Chain: "R" Number of atoms: 6147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 753, 6147 Classifications: {'peptide': 753} Link IDs: {'PTRANS': 32, 'TRANS': 720} Chain breaks: 2 Chain: "O" Number of atoms: 1864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 1864 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 337} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 363} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1229 Unresolved non-hydrogen angles: 1571 Unresolved non-hydrogen dihedrals: 1025 Unresolved non-hydrogen chiralities: 111 Planarities with less than four sites: {'GLN:plan1': 16, 'ARG:plan': 14, 'TYR:plan': 15, 'ASN:plan1': 24, 'TRP:plan': 6, 'HIS:plan': 6, 'PHE:plan': 14, 'GLU:plan': 25, 'ASP:plan': 26} Unresolved non-hydrogen planarities: 657 Chain: "J" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1822 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 219} Chain: "M" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 938 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "I" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1822 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 219} Chain: "L" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 938 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "H" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1822 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 219} Chain: "K" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 938 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "S" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 631 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 6, 'TRANS': 70} Chain: "T" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 658 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain: "U" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1662 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "V" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 411 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 1, 'TRANS': 47} Chain: "0" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1498 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 5, 'TRANS': 198} Chain: "1" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "2" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "3" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "4" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "5" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "6" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "7" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "8" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "9" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "Q" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2844 Classifications: {'peptide': 351} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 337} Chain: "C" Number of atoms: 4656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4656 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "A" Number of atoms: 4656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4656 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "B" Number of atoms: 4656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4656 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "F" Number of atoms: 3666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3666 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 440} Chain: "D" Number of atoms: 3666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3666 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 440} Chain: "E" Number of atoms: 3666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3666 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 440} Chain: "Z" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2110 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 252} Unresolved chain links: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 2136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2136 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 257} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Y" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2111 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 252} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "G" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1717 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 3, 'TRANS': 209} Chain: "N" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 875 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "P" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 2121 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 385} Link IDs: {'PTRANS': 9, 'TRANS': 417} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1457 Unresolved non-hydrogen angles: 1855 Unresolved non-hydrogen dihedrals: 1231 Unresolved non-hydrogen chiralities: 110 Planarities with less than four sites: {'GLN:plan1': 33, 'HIS:plan': 11, 'TYR:plan': 17, 'ASN:plan1': 21, 'TRP:plan': 8, 'ASP:plan': 18, 'PHE:plan': 17, 'GLU:plan': 38, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 859 Chain: "R" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 27.64, per 1000 atoms: 0.40 Number of scatterers: 69755 At special positions: 0 Unit cell: (222.48, 271.08, 221.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 375 16.00 P 2 15.00 O 13059 8.00 N 11852 7.00 C 44467 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS U 371 " - pdb=" SG CYS U 418 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG R 901 " - " ASN R 488 " " NAG S 101 " - " ASN S 70 " " NAG U 501 " - " ASN U 350 " " NAG U 502 " - " ASN U 296 " " NAG U 503 " - " ASN U 261 " " NAG U 504 " - " ASN U 303 " " NAG U 505 " - " ASN U 357 " " NAG U 506 " - " ASN U 273 " Time building additional restraints: 21.07 Conformation dependent library (CDL) restraints added in 10.5 seconds 18264 Ramachandran restraints generated. 9132 Oldfield, 0 Emsley, 9132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17134 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 312 helices and 46 sheets defined 56.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.46 Creating SS restraints... Processing helix chain 'R' and resid 19 through 32 removed outlier: 4.542A pdb=" N CYS R 24 " --> pdb=" O GLU R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 75 Processing helix chain 'R' and resid 85 through 87 No H-bonds generated for 'chain 'R' and resid 85 through 87' Processing helix chain 'R' and resid 92 through 133 removed outlier: 3.982A pdb=" N GLU R 116 " --> pdb=" O THR R 113 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE R 131 " --> pdb=" O LEU R 128 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU R 132 " --> pdb=" O LYS R 129 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ARG R 133 " --> pdb=" O PHE R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 190 removed outlier: 3.927A pdb=" N VAL R 190 " --> pdb=" O MET R 186 " (cutoff:3.500A) Processing helix chain 'R' and resid 227 through 239 removed outlier: 3.821A pdb=" N ARG R 232 " --> pdb=" O GLN R 228 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL R 233 " --> pdb=" O LEU R 229 " (cutoff:3.500A) Processing helix chain 'R' and resid 253 through 308 removed outlier: 3.797A pdb=" N ARG R 264 " --> pdb=" O GLY R 260 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN R 274 " --> pdb=" O MET R 270 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU R 276 " --> pdb=" O LEU R 272 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN R 284 " --> pdb=" O GLN R 280 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASN R 289 " --> pdb=" O ALA R 285 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG R 291 " --> pdb=" O ALA R 287 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL R 292 " --> pdb=" O LYS R 288 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE R 295 " --> pdb=" O ARG R 291 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA R 302 " --> pdb=" O ARG R 298 " (cutoff:3.500A) Processing helix chain 'R' and resid 330 through 343 Processing helix chain 'R' and resid 372 through 381 removed outlier: 3.734A pdb=" N VAL R 378 " --> pdb=" O PHE R 374 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N TYR R 381 " --> pdb=" O ILE R 377 " (cutoff:3.500A) Processing helix chain 'R' and resid 392 through 395 No H-bonds generated for 'chain 'R' and resid 392 through 395' Processing helix chain 'R' and resid 398 through 406 removed outlier: 4.070A pdb=" N ALA R 404 " --> pdb=" O PRO R 400 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL R 405 " --> pdb=" O PHE R 401 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET R 406 " --> pdb=" O LEU R 402 " (cutoff:3.500A) Processing helix chain 'R' and resid 410 through 425 removed outlier: 3.552A pdb=" N LEU R 415 " --> pdb=" O GLY R 411 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU R 418 " --> pdb=" O ILE R 414 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N PHE R 419 " --> pdb=" O LEU R 415 " (cutoff:3.500A) Processing helix chain 'R' and resid 427 through 431 Processing helix chain 'R' and resid 438 through 464 removed outlier: 3.831A pdb=" N THR R 442 " --> pdb=" O GLU R 438 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL R 443 " --> pdb=" O MET R 439 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER R 445 " --> pdb=" O SER R 441 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY R 446 " --> pdb=" O THR R 442 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG R 447 " --> pdb=" O VAL R 443 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N TYR R 448 " --> pdb=" O PHE R 444 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE R 449 " --> pdb=" O SER R 445 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE R 463 " --> pdb=" O TYR R 459 " (cutoff:3.500A) Processing helix chain 'R' and resid 482 through 487 removed outlier: 3.653A pdb=" N TYR R 487 " --> pdb=" O MET R 484 " (cutoff:3.500A) Processing helix chain 'R' and resid 493 through 496 No H-bonds generated for 'chain 'R' and resid 493 through 496' Processing helix chain 'R' and resid 528 through 553 removed outlier: 4.595A pdb=" N ASN R 533 " --> pdb=" O LEU R 529 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS R 536 " --> pdb=" O LEU R 532 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET R 537 " --> pdb=" O ASN R 533 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER R 540 " --> pdb=" O LYS R 536 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL R 541 " --> pdb=" O MET R 537 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS R 547 " --> pdb=" O LEU R 543 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY R 551 " --> pdb=" O HIS R 547 " (cutoff:3.500A) Processing helix chain 'R' and resid 555 through 562 Processing helix chain 'R' and resid 565 through 569 removed outlier: 3.795A pdb=" N TYR R 569 " --> pdb=" O LEU R 566 " (cutoff:3.500A) Processing helix chain 'R' and resid 572 through 596 removed outlier: 3.600A pdb=" N LEU R 582 " --> pdb=" O PHE R 578 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR R 585 " --> pdb=" O SER R 581 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU R 586 " --> pdb=" O LEU R 582 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL R 587 " --> pdb=" O PHE R 583 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILE R 588 " --> pdb=" O GLY R 584 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU R 589 " --> pdb=" O TYR R 585 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE R 590 " --> pdb=" O LEU R 586 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE R 591 " --> pdb=" O VAL R 587 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR R 595 " --> pdb=" O PHE R 591 " (cutoff:3.500A) Processing helix chain 'R' and resid 602 through 604 No H-bonds generated for 'chain 'R' and resid 602 through 604' Processing helix chain 'R' and resid 610 through 617 removed outlier: 3.916A pdb=" N PHE R 616 " --> pdb=" O PHE R 612 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU R 617 " --> pdb=" O ILE R 613 " (cutoff:3.500A) Processing helix chain 'R' and resid 632 through 665 removed outlier: 3.782A pdb=" N VAL R 647 " --> pdb=" O ALA R 643 " (cutoff:3.500A) Proline residue: R 648 - end of helix removed outlier: 3.599A pdb=" N PHE R 653 " --> pdb=" O TRP R 649 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N LYS R 654 " --> pdb=" O MET R 650 " (cutoff:3.500A) Proline residue: R 655 - end of helix Processing helix chain 'R' and resid 713 through 758 removed outlier: 3.523A pdb=" N HIS R 723 " --> pdb=" O HIS R 719 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR R 735 " --> pdb=" O CYS R 731 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA R 736 " --> pdb=" O ILE R 732 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR R 738 " --> pdb=" O ASN R 734 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N LEU R 739 " --> pdb=" O THR R 735 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ARG R 740 " --> pdb=" O ALA R 736 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N LEU R 741 " --> pdb=" O SER R 737 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N TRP R 742 " --> pdb=" O TYR R 738 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU R 753 " --> pdb=" O ALA R 749 " (cutoff:3.500A) Processing helix chain 'R' and resid 760 through 763 No H-bonds generated for 'chain 'R' and resid 760 through 763' Processing helix chain 'R' and resid 768 through 788 removed outlier: 3.562A pdb=" N GLY R 772 " --> pdb=" O SER R 768 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU R 775 " --> pdb=" O GLY R 771 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N PHE R 776 " --> pdb=" O GLY R 772 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE R 777 " --> pdb=" O LEU R 773 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL R 787 " --> pdb=" O ALA R 783 " (cutoff:3.500A) Processing helix chain 'R' and resid 793 through 808 removed outlier: 4.328A pdb=" N PHE R 799 " --> pdb=" O GLY R 795 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA R 802 " --> pdb=" O ALA R 798 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS R 806 " --> pdb=" O ALA R 802 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TRP R 807 " --> pdb=" O LEU R 803 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL R 808 " --> pdb=" O ARG R 804 " (cutoff:3.500A) Processing helix chain 'R' and resid 811 through 813 No H-bonds generated for 'chain 'R' and resid 811 through 813' Processing helix chain 'O' and resid 14 through 22 removed outlier: 3.626A pdb=" N GLN O 17 " --> pdb=" O THR O 14 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TRP O 19 " --> pdb=" O GLN O 16 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N GLU O 20 " --> pdb=" O GLN O 17 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS O 21 " --> pdb=" O THR O 18 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU O 22 " --> pdb=" O TRP O 19 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 78 removed outlier: 3.895A pdb=" N ASP O 56 " --> pdb=" O VAL O 52 " (cutoff:3.500A) Processing helix chain 'O' and resid 98 through 103 Processing helix chain 'O' and resid 118 through 156 Processing helix chain 'O' and resid 194 through 200 Processing helix chain 'O' and resid 232 through 244 removed outlier: 4.437A pdb=" N ASP O 235 " --> pdb=" O LYS O 232 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLU O 243 " --> pdb=" O LYS O 240 " (cutoff:3.500A) Processing helix chain 'O' and resid 255 through 310 Proline residue: O 278 - end of helix removed outlier: 4.296A pdb=" N ARG O 281 " --> pdb=" O GLY O 277 " (cutoff:3.500A) Processing helix chain 'O' and resid 328 through 339 Processing helix chain 'J' and resid 3 through 15 removed outlier: 3.704A pdb=" N ASP J 7 " --> pdb=" O LEU J 3 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL J 8 " --> pdb=" O SER J 4 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N MET J 15 " --> pdb=" O GLN J 11 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 106 removed outlier: 3.787A pdb=" N ASN J 24 " --> pdb=" O GLU J 20 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU J 29 " --> pdb=" O GLU J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 127 removed outlier: 3.896A pdb=" N VAL J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY J 123 " --> pdb=" O LEU J 119 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN J 126 " --> pdb=" O GLN J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 141 through 159 removed outlier: 3.726A pdb=" N ALA J 146 " --> pdb=" O PRO J 142 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN J 149 " --> pdb=" O LYS J 145 " (cutoff:3.500A) Proline residue: J 153 - end of helix Processing helix chain 'J' and resid 196 through 206 Processing helix chain 'J' and resid 208 through 216 Processing helix chain 'M' and resid 4 through 103 removed outlier: 3.701A pdb=" N ARG M 31 " --> pdb=" O LYS M 27 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU M 54 " --> pdb=" O GLN M 50 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN M 90 " --> pdb=" O THR M 86 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN M 91 " --> pdb=" O TYR M 87 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ASP M 93 " --> pdb=" O ARG M 89 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLU M 94 " --> pdb=" O GLN M 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 106 removed outlier: 3.945A pdb=" N LYS I 13 " --> pdb=" O GLN I 9 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS I 14 " --> pdb=" O LYS I 10 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET I 15 " --> pdb=" O GLN I 11 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N MET I 16 " --> pdb=" O ILE I 12 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA I 17 " --> pdb=" O LYS I 13 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N PHE I 18 " --> pdb=" O HIS I 14 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL I 105 " --> pdb=" O ARG I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 126 Processing helix chain 'I' and resid 141 through 157 removed outlier: 4.121A pdb=" N ALA I 146 " --> pdb=" O PRO I 142 " (cutoff:3.500A) Proline residue: I 153 - end of helix Processing helix chain 'I' and resid 198 through 206 Processing helix chain 'I' and resid 208 through 215 Processing helix chain 'L' and resid 4 through 99 Processing helix chain 'H' and resid 5 through 107 removed outlier: 3.704A pdb=" N LYS H 107 " --> pdb=" O SER H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 127 Processing helix chain 'H' and resid 138 through 159 removed outlier: 3.600A pdb=" N PHE H 141 " --> pdb=" O LYS H 138 " (cutoff:3.500A) Proline residue: H 142 - end of helix removed outlier: 4.059A pdb=" N ILE H 152 " --> pdb=" O GLN H 149 " (cutoff:3.500A) Proline residue: H 153 - end of helix removed outlier: 4.143A pdb=" N THR H 159 " --> pdb=" O LYS H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 204 Processing helix chain 'H' and resid 208 through 216 Processing helix chain 'K' and resid 5 through 104 removed outlier: 4.734A pdb=" N LYS K 37 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU K 38 " --> pdb=" O LYS K 34 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN K 41 " --> pdb=" O LYS K 37 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA K 42 " --> pdb=" O GLU K 38 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU K 43 " --> pdb=" O GLU K 39 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG K 51 " --> pdb=" O TYR K 47 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LYS K 53 " --> pdb=" O LEU K 49 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N GLU K 54 " --> pdb=" O GLN K 50 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU K 63 " --> pdb=" O GLU K 59 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY K 64 " --> pdb=" O ALA K 60 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY K 67 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER K 68 " --> pdb=" O GLY K 64 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER K 70 " --> pdb=" O ARG K 66 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR K 71 " --> pdb=" O GLY K 67 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU K 76 " --> pdb=" O GLU K 72 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR K 82 " --> pdb=" O GLN K 78 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ASP K 93 " --> pdb=" O ARG K 89 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N GLU K 94 " --> pdb=" O GLN K 90 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS K 104 " --> pdb=" O LEU K 100 " (cutoff:3.500A) Processing helix chain 'S' and resid 7 through 21 Processing helix chain 'S' and resid 25 through 27 No H-bonds generated for 'chain 'S' and resid 25 through 27' Processing helix chain 'S' and resid 34 through 59 removed outlier: 3.630A pdb=" N ILE S 38 " --> pdb=" O ARG S 34 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR S 39 " --> pdb=" O GLY S 35 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA S 58 " --> pdb=" O ILE S 54 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN S 59 " --> pdb=" O ALA S 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 70 through 79 removed outlier: 3.511A pdb=" N LYS S 77 " --> pdb=" O ILE S 73 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TYR S 78 " --> pdb=" O TRP S 74 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS S 79 " --> pdb=" O TYR S 75 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 73 removed outlier: 4.062A pdb=" N CYS T 53 " --> pdb=" O LYS T 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 97 through 128 removed outlier: 3.621A pdb=" N ASN T 107 " --> pdb=" O GLN T 103 " (cutoff:3.500A) Processing helix chain 'U' and resid 424 through 448 Processing helix chain 'V' and resid 303 through 329 Processing helix chain '0' and resid 3 through 28 Processing helix chain '0' and resid 31 through 34 Processing helix chain '0' and resid 37 through 43 Processing helix chain '0' and resid 46 through 79 removed outlier: 4.232A pdb=" N SER 0 75 " --> pdb=" O ILE 0 71 " (cutoff:3.500A) Processing helix chain '0' and resid 84 through 89 removed outlier: 3.627A pdb=" N LYS 0 87 " --> pdb=" O PRO 0 84 " (cutoff:3.500A) Processing helix chain '0' and resid 91 through 114 removed outlier: 4.079A pdb=" N ALA 0 101 " --> pdb=" O CYS 0 97 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N MET 0 114 " --> pdb=" O VAL 0 110 " (cutoff:3.500A) Processing helix chain '0' and resid 131 through 166 removed outlier: 3.651A pdb=" N GLY 0 161 " --> pdb=" O ILE 0 157 " (cutoff:3.500A) Processing helix chain '0' and resid 173 through 176 No H-bonds generated for 'chain '0' and resid 173 through 176' Processing helix chain '0' and resid 178 through 197 removed outlier: 4.017A pdb=" N ILE 0 186 " --> pdb=" O PHE 0 182 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY 0 187 " --> pdb=" O GLY 0 183 " (cutoff:3.500A) Processing helix chain '1' and resid 11 through 44 removed outlier: 3.599A pdb=" N PHE 1 14 " --> pdb=" O ALA 1 11 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER 1 20 " --> pdb=" O MET 1 17 " (cutoff:3.500A) Processing helix chain '1' and resid 49 through 51 No H-bonds generated for 'chain '1' and resid 49 through 51' Processing helix chain '1' and resid 53 through 55 No H-bonds generated for 'chain '1' and resid 53 through 55' Processing helix chain '1' and resid 57 through 77 Processing helix chain '1' and resid 88 through 123 removed outlier: 4.153A pdb=" N GLN 1 123 " --> pdb=" O ARG 1 119 " (cutoff:3.500A) Processing helix chain '1' and resid 125 through 152 removed outlier: 4.210A pdb=" N PHE 1 128 " --> pdb=" O PRO 1 125 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N VAL 1 129 " --> pdb=" O ARG 1 126 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL 1 140 " --> pdb=" O PHE 1 137 " (cutoff:3.500A) Processing helix chain '2' and resid 11 through 45 removed outlier: 3.577A pdb=" N SER 2 20 " --> pdb=" O MET 2 17 " (cutoff:3.500A) Processing helix chain '2' and resid 49 through 51 No H-bonds generated for 'chain '2' and resid 49 through 51' Processing helix chain '2' and resid 55 through 78 Proline residue: 2 58 - end of helix removed outlier: 3.501A pdb=" N ALA 2 77 " --> pdb=" O VAL 2 74 " (cutoff:3.500A) Processing helix chain '2' and resid 88 through 121 Processing helix chain '2' and resid 128 through 153 removed outlier: 3.830A pdb=" N LEU 2 141 " --> pdb=" O PHE 2 137 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY 2 142 " --> pdb=" O ALA 2 138 " (cutoff:3.500A) Processing helix chain '3' and resid 12 through 44 Processing helix chain '3' and resid 57 through 79 Processing helix chain '3' and resid 87 through 121 removed outlier: 3.717A pdb=" N LEU 3 91 " --> pdb=" O TYR 3 87 " (cutoff:3.500A) Processing helix chain '3' and resid 125 through 153 removed outlier: 3.766A pdb=" N PHE 3 128 " --> pdb=" O PRO 3 125 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N VAL 3 129 " --> pdb=" O ARG 3 126 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER 3 153 " --> pdb=" O LEU 3 150 " (cutoff:3.500A) Processing helix chain '4' and resid 12 through 44 Processing helix chain '4' and resid 49 through 51 No H-bonds generated for 'chain '4' and resid 49 through 51' Processing helix chain '4' and resid 57 through 79 removed outlier: 3.858A pdb=" N ILE 4 65 " --> pdb=" O MET 4 61 " (cutoff:3.500A) Processing helix chain '4' and resid 87 through 121 Processing helix chain '4' and resid 128 through 154 removed outlier: 4.031A pdb=" N LEU 4 141 " --> pdb=" O PHE 4 137 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLY 4 142 " --> pdb=" O ALA 4 138 " (cutoff:3.500A) Processing helix chain '5' and resid 11 through 44 removed outlier: 3.596A pdb=" N SER 5 20 " --> pdb=" O MET 5 17 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA 5 42 " --> pdb=" O THR 5 39 " (cutoff:3.500A) Processing helix chain '5' and resid 49 through 51 No H-bonds generated for 'chain '5' and resid 49 through 51' Processing helix chain '5' and resid 53 through 78 removed outlier: 5.135A pdb=" N ILE 5 57 " --> pdb=" O LYS 5 54 " (cutoff:3.500A) Proline residue: 5 58 - end of helix Processing helix chain '5' and resid 88 through 121 Processing helix chain '5' and resid 128 through 153 removed outlier: 4.142A pdb=" N LEU 5 141 " --> pdb=" O PHE 5 137 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLY 5 142 " --> pdb=" O ALA 5 138 " (cutoff:3.500A) Processing helix chain '6' and resid 12 through 45 Processing helix chain '6' and resid 49 through 51 No H-bonds generated for 'chain '6' and resid 49 through 51' Processing helix chain '6' and resid 57 through 78 removed outlier: 3.628A pdb=" N ILE 6 65 " --> pdb=" O MET 6 61 " (cutoff:3.500A) Processing helix chain '6' and resid 88 through 121 Processing helix chain '6' and resid 125 through 153 removed outlier: 3.907A pdb=" N PHE 6 128 " --> pdb=" O PRO 6 125 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N VAL 6 129 " --> pdb=" O ARG 6 126 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL 6 140 " --> pdb=" O PHE 6 137 " (cutoff:3.500A) Processing helix chain '7' and resid 11 through 47 removed outlier: 3.977A pdb=" N ALA 7 15 " --> pdb=" O ALA 7 11 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N VAL 7 46 " --> pdb=" O ALA 7 42 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N MET 7 47 " --> pdb=" O ALA 7 43 " (cutoff:3.500A) Processing helix chain '7' and resid 53 through 55 No H-bonds generated for 'chain '7' and resid 53 through 55' Processing helix chain '7' and resid 57 through 78 removed outlier: 4.255A pdb=" N ILE 7 65 " --> pdb=" O MET 7 61 " (cutoff:3.500A) Processing helix chain '7' and resid 88 through 121 Processing helix chain '7' and resid 125 through 154 removed outlier: 4.005A pdb=" N PHE 7 128 " --> pdb=" O PRO 7 125 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N VAL 7 129 " --> pdb=" O ARG 7 126 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL 7 140 " --> pdb=" O PHE 7 137 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER 7 153 " --> pdb=" O LEU 7 150 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR 7 154 " --> pdb=" O ILE 7 151 " (cutoff:3.500A) Processing helix chain '8' and resid 11 through 45 removed outlier: 3.693A pdb=" N ALA 8 15 " --> pdb=" O ALA 8 11 " (cutoff:3.500A) Processing helix chain '8' and resid 56 through 79 removed outlier: 4.288A pdb=" N ILE 8 64 " --> pdb=" O MET 8 61 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE 8 76 " --> pdb=" O ALA 8 73 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA 8 77 " --> pdb=" O VAL 8 74 " (cutoff:3.500A) Processing helix chain '8' and resid 88 through 121 Processing helix chain '8' and resid 128 through 154 removed outlier: 3.659A pdb=" N LEU 8 141 " --> pdb=" O PHE 8 137 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLY 8 142 " --> pdb=" O ALA 8 138 " (cutoff:3.500A) Processing helix chain '9' and resid 11 through 44 removed outlier: 4.171A pdb=" N ALA 9 15 " --> pdb=" O ALA 9 11 " (cutoff:3.500A) Processing helix chain '9' and resid 49 through 51 No H-bonds generated for 'chain '9' and resid 49 through 51' Processing helix chain '9' and resid 57 through 79 Processing helix chain '9' and resid 88 through 122 Processing helix chain '9' and resid 125 through 154 removed outlier: 3.693A pdb=" N PHE 9 128 " --> pdb=" O PRO 9 125 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N VAL 9 129 " --> pdb=" O ARG 9 126 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL 9 140 " --> pdb=" O PHE 9 137 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR 9 154 " --> pdb=" O ILE 9 151 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 26 removed outlier: 6.805A pdb=" N TYR Q 15 " --> pdb=" O VAL Q 11 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU Q 16 " --> pdb=" O ASP Q 12 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY Q 26 " --> pdb=" O GLY Q 22 " (cutoff:3.500A) Processing helix chain 'Q' and resid 30 through 36 Processing helix chain 'Q' and resid 42 through 49 Processing helix chain 'Q' and resid 68 through 88 removed outlier: 4.030A pdb=" N MET Q 78 " --> pdb=" O LEU Q 74 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N HIS Q 88 " --> pdb=" O HIS Q 84 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 112 removed outlier: 4.051A pdb=" N PHE Q 96 " --> pdb=" O PRO Q 92 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N SER Q 103 " --> pdb=" O PHE Q 99 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TYR Q 104 " --> pdb=" O ILE Q 100 " (cutoff:3.500A) Processing helix chain 'Q' and resid 122 through 128 Proline residue: Q 127 - end of helix Processing helix chain 'Q' and resid 147 through 157 removed outlier: 3.785A pdb=" N ASP Q 157 " --> pdb=" O ALA Q 153 " (cutoff:3.500A) Processing helix chain 'Q' and resid 159 through 164 removed outlier: 3.783A pdb=" N ALA Q 162 " --> pdb=" O PRO Q 159 " (cutoff:3.500A) Processing helix chain 'Q' and resid 172 through 175 No H-bonds generated for 'chain 'Q' and resid 172 through 175' Processing helix chain 'Q' and resid 178 through 199 Processing helix chain 'Q' and resid 203 through 227 Proline residue: Q 210 - end of helix Processing helix chain 'Q' and resid 234 through 240 removed outlier: 3.855A pdb=" N LEU Q 240 " --> pdb=" O ASP Q 236 " (cutoff:3.500A) Processing helix chain 'Q' and resid 252 through 255 No H-bonds generated for 'chain 'Q' and resid 252 through 255' Processing helix chain 'Q' and resid 261 through 268 Processing helix chain 'Q' and resid 272 through 279 Processing helix chain 'Q' and resid 290 through 307 removed outlier: 3.877A pdb=" N ALA Q 305 " --> pdb=" O LEU Q 301 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE Q 306 " --> pdb=" O ASN Q 302 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LEU Q 307 " --> pdb=" O LYS Q 303 " (cutoff:3.500A) Processing helix chain 'Q' and resid 313 through 337 Processing helix chain 'Q' and resid 343 through 346 Processing helix chain 'C' and resid 106 through 112 Processing helix chain 'C' and resid 256 through 266 Processing helix chain 'C' and resid 283 through 290 Processing helix chain 'C' and resid 320 through 340 removed outlier: 4.812A pdb=" N ILE C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TYR C 328 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET C 340 " --> pdb=" O TYR C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 365 Processing helix chain 'C' and resid 376 through 388 removed outlier: 4.706A pdb=" N GLY C 379 " --> pdb=" O ALA C 376 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA C 380 " --> pdb=" O TYR C 377 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLU C 387 " --> pdb=" O SER C 384 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG C 388 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 428 Processing helix chain 'C' and resid 438 through 441 No H-bonds generated for 'chain 'C' and resid 438 through 441' Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 473 through 495 removed outlier: 3.955A pdb=" N ILE C 492 " --> pdb=" O ASP C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 518 Processing helix chain 'C' and resid 534 through 559 removed outlier: 3.606A pdb=" N THR C 558 " --> pdb=" O ALA C 554 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA C 559 " --> pdb=" O VAL C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 573 Processing helix chain 'C' and resid 575 through 586 removed outlier: 5.476A pdb=" N LYS C 585 " --> pdb=" O LEU C 581 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N PHE C 586 " --> pdb=" O SER C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 615 Processing helix chain 'A' and resid 106 through 113 Processing helix chain 'A' and resid 256 through 265 removed outlier: 3.870A pdb=" N SER A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 307 No H-bonds generated for 'chain 'A' and resid 305 through 307' Processing helix chain 'A' and resid 320 through 324 Processing helix chain 'A' and resid 326 through 340 removed outlier: 3.901A pdb=" N MET A 340 " --> pdb=" O TYR A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 364 Processing helix chain 'A' and resid 378 through 388 removed outlier: 4.298A pdb=" N ARG A 388 " --> pdb=" O SER A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 428 Processing helix chain 'A' and resid 437 through 441 Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 472 through 496 removed outlier: 3.722A pdb=" N ILE A 492 " --> pdb=" O ASP A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 518 Processing helix chain 'A' and resid 534 through 561 removed outlier: 4.551A pdb=" N GLN A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N SER A 561 " --> pdb=" O THR A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 573 Processing helix chain 'A' and resid 575 through 581 Processing helix chain 'A' and resid 584 through 586 No H-bonds generated for 'chain 'A' and resid 584 through 586' Processing helix chain 'A' and resid 594 through 614 Processing helix chain 'B' and resid 106 through 112 Processing helix chain 'B' and resid 256 through 265 Processing helix chain 'B' and resid 281 through 293 removed outlier: 3.601A pdb=" N SER B 285 " --> pdb=" O GLY B 281 " (cutoff:3.500A) Proline residue: B 292 - end of helix Processing helix chain 'B' and resid 322 through 338 removed outlier: 3.894A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR B 328 " --> pdb=" O GLU B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 365 Processing helix chain 'B' and resid 378 through 385 Processing helix chain 'B' and resid 413 through 415 No H-bonds generated for 'chain 'B' and resid 413 through 415' Processing helix chain 'B' and resid 420 through 426 Processing helix chain 'B' and resid 438 through 441 No H-bonds generated for 'chain 'B' and resid 438 through 441' Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 473 through 495 removed outlier: 3.797A pdb=" N ILE B 492 " --> pdb=" O ASP B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 518 Processing helix chain 'B' and resid 534 through 557 Processing helix chain 'B' and resid 567 through 573 Processing helix chain 'B' and resid 575 through 586 removed outlier: 4.788A pdb=" N LYS B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N PHE B 586 " --> pdb=" O SER B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 615 Processing helix chain 'F' and resid 125 through 127 No H-bonds generated for 'chain 'F' and resid 125 through 127' Processing helix chain 'F' and resid 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 175 through 179 Processing helix chain 'F' and resid 199 through 209 Processing helix chain 'F' and resid 217 through 225 removed outlier: 4.073A pdb=" N GLU F 224 " --> pdb=" O VAL F 220 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLU F 225 " --> pdb=" O ASP F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 249 Processing helix chain 'F' and resid 270 through 288 removed outlier: 3.914A pdb=" N THR F 274 " --> pdb=" O ARG F 271 " (cutoff:3.500A) Proline residue: F 275 - end of helix removed outlier: 3.564A pdb=" N TYR F 287 " --> pdb=" O PHE F 284 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLN F 288 " --> pdb=" O LEU F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 314 removed outlier: 3.610A pdb=" N ARG F 314 " --> pdb=" O VAL F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 322 No H-bonds generated for 'chain 'F' and resid 320 through 322' Processing helix chain 'F' and resid 327 through 335 Processing helix chain 'F' and resid 357 through 359 No H-bonds generated for 'chain 'F' and resid 357 through 359' Processing helix chain 'F' and resid 364 through 372 Processing helix chain 'F' and resid 382 through 385 No H-bonds generated for 'chain 'F' and resid 382 through 385' Processing helix chain 'F' and resid 400 through 405 removed outlier: 4.224A pdb=" N LYS F 403 " --> pdb=" O ARG F 400 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N SER F 404 " --> pdb=" O LEU F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 439 Processing helix chain 'F' and resid 446 through 461 Processing helix chain 'F' and resid 473 through 485 Processing helix chain 'F' and resid 489 through 491 No H-bonds generated for 'chain 'F' and resid 489 through 491' Processing helix chain 'F' and resid 497 through 502 Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 199 through 209 Processing helix chain 'D' and resid 219 through 226 removed outlier: 4.216A pdb=" N GLU D 224 " --> pdb=" O VAL D 220 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU D 225 " --> pdb=" O ASP D 221 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ASN D 226 " --> pdb=" O TYR D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 250 Processing helix chain 'D' and resid 268 through 289 Proline residue: D 275 - end of helix Processing helix chain 'D' and resid 300 through 314 Processing helix chain 'D' and resid 320 through 322 No H-bonds generated for 'chain 'D' and resid 320 through 322' Processing helix chain 'D' and resid 327 through 335 Processing helix chain 'D' and resid 357 through 359 No H-bonds generated for 'chain 'D' and resid 357 through 359' Processing helix chain 'D' and resid 364 through 372 Processing helix chain 'D' and resid 381 through 385 Processing helix chain 'D' and resid 402 through 405 No H-bonds generated for 'chain 'D' and resid 402 through 405' Processing helix chain 'D' and resid 415 through 439 Processing helix chain 'D' and resid 446 through 461 Processing helix chain 'D' and resid 473 through 486 removed outlier: 4.845A pdb=" N ILE D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 503 Processing helix chain 'E' and resid 160 through 162 No H-bonds generated for 'chain 'E' and resid 160 through 162' Processing helix chain 'E' and resid 175 through 179 Processing helix chain 'E' and resid 199 through 209 Processing helix chain 'E' and resid 219 through 225 removed outlier: 3.923A pdb=" N GLU E 224 " --> pdb=" O VAL E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 249 Processing helix chain 'E' and resid 269 through 287 Proline residue: E 275 - end of helix Processing helix chain 'E' and resid 300 through 314 Processing helix chain 'E' and resid 320 through 322 No H-bonds generated for 'chain 'E' and resid 320 through 322' Processing helix chain 'E' and resid 327 through 335 Processing helix chain 'E' and resid 357 through 359 No H-bonds generated for 'chain 'E' and resid 357 through 359' Processing helix chain 'E' and resid 364 through 372 Processing helix chain 'E' and resid 415 through 439 Processing helix chain 'E' and resid 446 through 461 Processing helix chain 'E' and resid 473 through 484 Processing helix chain 'E' and resid 489 through 491 No H-bonds generated for 'chain 'E' and resid 489 through 491' Processing helix chain 'E' and resid 498 through 503 Processing helix chain 'Z' and resid 16 through 36 Processing helix chain 'Z' and resid 43 through 57 removed outlier: 5.434A pdb=" N ASP Z 51 " --> pdb=" O GLU Z 47 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL Z 52 " --> pdb=" O ASP Z 48 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N TRP Z 55 " --> pdb=" O ASP Z 51 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA Z 56 " --> pdb=" O VAL Z 52 " (cutoff:3.500A) Processing helix chain 'Z' and resid 62 through 71 Processing helix chain 'Z' and resid 78 through 96 Processing helix chain 'Z' and resid 105 through 116 Processing helix chain 'Z' and resid 121 through 123 No H-bonds generated for 'chain 'Z' and resid 121 through 123' Processing helix chain 'Z' and resid 125 through 141 Processing helix chain 'Z' and resid 147 through 166 Processing helix chain 'Z' and resid 174 through 186 Processing helix chain 'Z' and resid 194 through 205 Processing helix chain 'Z' and resid 219 through 234 Processing helix chain 'Z' and resid 240 through 251 removed outlier: 3.620A pdb=" N LEU Z 249 " --> pdb=" O LYS Z 245 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER Z 250 " --> pdb=" O LEU Z 246 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N SER Z 251 " --> pdb=" O SER Z 247 " (cutoff:3.500A) Processing helix chain 'Z' and resid 257 through 272 removed outlier: 3.557A pdb=" N LYS Z 272 " --> pdb=" O LYS Z 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 15 through 36 Processing helix chain 'X' and resid 43 through 55 removed outlier: 5.037A pdb=" N ASP X 51 " --> pdb=" O GLU X 47 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL X 52 " --> pdb=" O ASP X 48 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N TRP X 55 " --> pdb=" O ASP X 51 " (cutoff:3.500A) Processing helix chain 'X' and resid 64 through 70 Processing helix chain 'X' and resid 78 through 96 Processing helix chain 'X' and resid 105 through 117 removed outlier: 4.280A pdb=" N GLN X 117 " --> pdb=" O GLU X 113 " (cutoff:3.500A) Processing helix chain 'X' and resid 121 through 123 No H-bonds generated for 'chain 'X' and resid 121 through 123' Processing helix chain 'X' and resid 126 through 139 Processing helix chain 'X' and resid 147 through 166 Processing helix chain 'X' and resid 174 through 186 Processing helix chain 'X' and resid 194 through 206 Processing helix chain 'X' and resid 219 through 236 Proline residue: X 235 - end of helix Processing helix chain 'X' and resid 240 through 251 removed outlier: 3.781A pdb=" N LEU X 249 " --> pdb=" O LYS X 245 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER X 250 " --> pdb=" O LEU X 246 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N SER X 251 " --> pdb=" O SER X 247 " (cutoff:3.500A) Processing helix chain 'X' and resid 257 through 273 removed outlier: 3.814A pdb=" N LYS X 272 " --> pdb=" O LYS X 268 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU X 273 " --> pdb=" O GLU X 269 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 36 Processing helix chain 'Y' and resid 43 through 48 Processing helix chain 'Y' and resid 50 through 53 No H-bonds generated for 'chain 'Y' and resid 50 through 53' Processing helix chain 'Y' and resid 62 through 70 Processing helix chain 'Y' and resid 78 through 96 removed outlier: 3.671A pdb=" N LEU Y 88 " --> pdb=" O ARG Y 84 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU Y 91 " --> pdb=" O ILE Y 87 " (cutoff:3.500A) Processing helix chain 'Y' and resid 105 through 116 Processing helix chain 'Y' and resid 125 through 140 Processing helix chain 'Y' and resid 147 through 166 Processing helix chain 'Y' and resid 173 through 187 Processing helix chain 'Y' and resid 193 through 204 Processing helix chain 'Y' and resid 219 through 235 Proline residue: Y 235 - end of helix Processing helix chain 'Y' and resid 240 through 251 removed outlier: 4.391A pdb=" N SER Y 251 " --> pdb=" O SER Y 247 " (cutoff:3.500A) Processing helix chain 'Y' and resid 257 through 273 removed outlier: 3.801A pdb=" N LYS Y 272 " --> pdb=" O LYS Y 268 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU Y 273 " --> pdb=" O GLU Y 269 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 75 removed outlier: 3.775A pdb=" N GLU G 60 " --> pdb=" O MET G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 84 Processing helix chain 'G' and resid 129 through 174 Processing helix chain 'G' and resid 176 through 215 removed outlier: 3.775A pdb=" N LYS G 215 " --> pdb=" O ILE G 211 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 23 Processing helix chain 'N' and resid 45 through 57 Processing helix chain 'N' and resid 68 through 80 removed outlier: 5.805A pdb=" N HIS N 76 " --> pdb=" O GLU N 72 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ALA N 77 " --> pdb=" O MET N 73 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 102 No H-bonds generated for 'chain 'N' and resid 100 through 102' Processing helix chain 'N' and resid 105 through 107 No H-bonds generated for 'chain 'N' and resid 105 through 107' Processing helix chain 'P' and resid 18 through 28 removed outlier: 3.541A pdb=" N ALA P 24 " --> pdb=" O ALA P 20 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA P 28 " --> pdb=" O ALA P 24 " (cutoff:3.500A) Processing helix chain 'P' and resid 34 through 36 No H-bonds generated for 'chain 'P' and resid 34 through 36' Processing helix chain 'P' and resid 59 through 61 No H-bonds generated for 'chain 'P' and resid 59 through 61' Processing helix chain 'P' and resid 64 through 68 Processing helix chain 'P' and resid 79 through 83 Processing helix chain 'P' and resid 92 through 103 removed outlier: 3.871A pdb=" N ASP P 99 " --> pdb=" O THR P 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 108 No H-bonds generated for 'chain 'P' and resid 106 through 108' Processing helix chain 'P' and resid 112 through 114 No H-bonds generated for 'chain 'P' and resid 112 through 114' Processing helix chain 'P' and resid 127 through 129 No H-bonds generated for 'chain 'P' and resid 127 through 129' Processing helix chain 'P' and resid 136 through 145 Processing helix chain 'P' and resid 147 through 149 No H-bonds generated for 'chain 'P' and resid 147 through 149' Processing helix chain 'P' and resid 158 through 161 No H-bonds generated for 'chain 'P' and resid 158 through 161' Processing helix chain 'P' and resid 168 through 171 Processing helix chain 'P' and resid 195 through 210 removed outlier: 4.813A pdb=" N CYS P 200 " --> pdb=" O GLN P 196 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY P 203 " --> pdb=" O GLN P 199 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET P 208 " --> pdb=" O CYS P 204 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG P 210 " --> pdb=" O GLN P 206 " (cutoff:3.500A) Processing helix chain 'P' and resid 212 through 220 removed outlier: 3.649A pdb=" N ALA P 217 " --> pdb=" O GLU P 213 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL P 219 " --> pdb=" O ARG P 215 " (cutoff:3.500A) Processing helix chain 'P' and resid 224 through 232 Processing helix chain 'P' and resid 237 through 250 Processing helix chain 'P' and resid 254 through 261 removed outlier: 3.721A pdb=" N HIS P 259 " --> pdb=" O GLN P 255 " (cutoff:3.500A) Processing helix chain 'P' and resid 266 through 274 Processing helix chain 'P' and resid 281 through 295 Processing helix chain 'P' and resid 301 through 309 removed outlier: 4.104A pdb=" N GLU P 304 " --> pdb=" O THR P 301 " (cutoff:3.500A) Processing helix chain 'P' and resid 315 through 323 Processing helix chain 'P' and resid 329 through 349 Processing helix chain 'P' and resid 352 through 361 Processing helix chain 'P' and resid 374 through 378 Processing helix chain 'P' and resid 380 through 383 No H-bonds generated for 'chain 'P' and resid 380 through 383' Processing helix chain 'P' and resid 386 through 399 removed outlier: 5.547A pdb=" N LEU P 390 " --> pdb=" O ASN P 387 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE P 393 " --> pdb=" O LEU P 390 " (cutoff:3.500A) Processing helix chain 'P' and resid 404 through 419 removed outlier: 4.326A pdb=" N VAL P 409 " --> pdb=" O GLN P 405 " (cutoff:3.500A) Processing helix chain 'P' and resid 423 through 431 removed outlier: 3.737A pdb=" N ARG P 426 " --> pdb=" O ARG P 423 " (cutoff:3.500A) Processing helix chain 'P' and resid 433 through 441 Processing helix chain 'P' and resid 446 through 460 removed outlier: 4.021A pdb=" N ASN P 451 " --> pdb=" O GLN P 447 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU P 453 " --> pdb=" O ARG P 449 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEU P 454 " --> pdb=" O TYR P 450 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'R' and resid 318 through 326 Processing sheet with id= B, first strand: chain 'R' and resid 197 through 202 removed outlier: 3.646A pdb=" N ILE R 221 " --> pdb=" O ARG R 198 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'O' and resid 373 through 375 Processing sheet with id= D, first strand: chain 'O' and resid 247 through 249 removed outlier: 4.162A pdb=" N LEU O 186 " --> pdb=" O ARG O 249 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL O 187 " --> pdb=" O CYS O 225 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N CYS O 225 " --> pdb=" O VAL O 187 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU O 224 " --> pdb=" O SER O 217 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER O 217 " --> pdb=" O LEU O 224 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ASN O 226 " --> pdb=" O VAL O 215 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL O 215 " --> pdb=" O ASN O 226 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'J' and resid 131 through 134 removed outlier: 6.424A pdb=" N ASP J 164 " --> pdb=" O MET J 132 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N VAL J 134 " --> pdb=" O ASP J 164 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N GLN J 166 " --> pdb=" O VAL J 134 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'J' and resid 180 through 184 Processing sheet with id= G, first strand: chain 'I' and resid 164 through 167 removed outlier: 3.599A pdb=" N ILE I 133 " --> pdb=" O TYR I 184 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 164 through 167 removed outlier: 3.736A pdb=" N VAL H 181 " --> pdb=" O ASN H 194 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'U' and resid 268 through 270 Processing sheet with id= J, first strand: chain 'U' and resid 282 through 284 removed outlier: 3.548A pdb=" N ASN U 273 " --> pdb=" O GLN U 398 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU U 397 " --> pdb=" O VAL U 374 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'U' and resid 306 through 313 removed outlier: 3.576A pdb=" N ALA U 307 " --> pdb=" O LEU U 327 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU U 346 " --> pdb=" O LYS U 324 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE U 326 " --> pdb=" O ARG U 344 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ARG U 344 " --> pdb=" O ILE U 326 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU U 345 " --> pdb=" O PHE U 356 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'U' and resid 329 through 332 removed outlier: 3.994A pdb=" N ARG U 330 " --> pdb=" O TRP U 339 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR U 332 " --> pdb=" O ARG U 337 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG U 337 " --> pdb=" O TYR U 332 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 61 through 66 removed outlier: 3.500A pdb=" N MET C 61 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU C 58 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG C 56 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLN C 65 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ILE C 54 " --> pdb=" O GLN C 65 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL C 43 " --> pdb=" O GLY C 52 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR C 30 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N VAL C 24 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N VAL C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 87 through 90 Processing sheet with id= O, first strand: chain 'C' and resid 133 through 135 Processing sheet with id= P, first strand: chain 'C' and resid 146 through 148 removed outlier: 6.393A pdb=" N GLU C 193 " --> pdb=" O THR C 177 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 245 through 247 removed outlier: 6.763A pdb=" N ILE C 406 " --> pdb=" O THR C 246 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N MET C 346 " --> pdb=" O VAL C 407 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ALA C 409 " --> pdb=" O MET C 346 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ALA C 348 " --> pdb=" O ALA C 409 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE C 273 " --> pdb=" O MET C 347 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ASP C 349 " --> pdb=" O ILE C 273 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL C 275 " --> pdb=" O ASP C 349 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 295 through 297 Processing sheet with id= S, first strand: chain 'C' and resid 152 through 157 removed outlier: 6.638A pdb=" N ILE C 166 " --> pdb=" O TYR C 153 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ILE C 155 " --> pdb=" O HIS C 164 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N HIS C 164 " --> pdb=" O ILE C 155 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'A' and resid 79 through 81 removed outlier: 3.584A pdb=" N GLU A 53 " --> pdb=" O GLN A 65 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'A' and resid 87 through 90 Processing sheet with id= V, first strand: chain 'A' and resid 183 through 185 removed outlier: 5.488A pdb=" N ASP A 134 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER A 157 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE A 166 " --> pdb=" O TYR A 153 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE A 155 " --> pdb=" O HIS A 164 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N HIS A 164 " --> pdb=" O ILE A 155 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'A' and resid 245 through 249 removed outlier: 6.593A pdb=" N ILE A 406 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ILE A 248 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLY A 408 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N MET A 346 " --> pdb=" O VAL A 407 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N ALA A 409 " --> pdb=" O MET A 346 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N ALA A 348 " --> pdb=" O ALA A 409 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE A 273 " --> pdb=" O MET A 347 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ASP A 349 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL A 275 " --> pdb=" O ASP A 349 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'A' and resid 295 through 298 Processing sheet with id= Y, first strand: chain 'A' and resid 175 through 179 removed outlier: 6.641A pdb=" N GLU A 193 " --> pdb=" O THR A 177 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 18 through 20 removed outlier: 6.524A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL B 28 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N CYS B 32 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N VAL B 21 " --> pdb=" O CYS B 32 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'B' and resid 87 through 90 Processing sheet with id= AB, first strand: chain 'B' and resid 183 through 185 removed outlier: 5.306A pdb=" N ASP B 134 " --> pdb=" O SER B 157 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER B 157 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'B' and resid 200 through 203 removed outlier: 5.771A pdb=" N GLU B 195 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N VAL B 176 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'B' and resid 245 through 247 removed outlier: 8.653A pdb=" N THR B 246 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE B 406 " --> pdb=" O THR B 246 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER B 405 " --> pdb=" O VAL B 344 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA B 348 " --> pdb=" O VAL B 407 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ILE B 273 " --> pdb=" O MET B 347 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ASP B 349 " --> pdb=" O ILE B 273 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL B 275 " --> pdb=" O ASP B 349 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'B' and resid 295 through 297 Processing sheet with id= AF, first strand: chain 'F' and resid 111 through 114 removed outlier: 3.778A pdb=" N SER F 111 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ASP F 61 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL F 50 " --> pdb=" O ASP F 61 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 120 through 123 Processing sheet with id= AH, first strand: chain 'F' and resid 130 through 133 removed outlier: 3.838A pdb=" N ARG F 130 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE F 229 " --> pdb=" O CYS F 258 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N PHE F 260 " --> pdb=" O ILE F 229 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE F 231 " --> pdb=" O PHE F 260 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ASN F 262 " --> pdb=" O PHE F 231 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA F 233 " --> pdb=" O ASN F 262 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU F 294 " --> pdb=" O VAL F 230 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ALA F 232 " --> pdb=" O LEU F 294 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE F 296 " --> pdb=" O ALA F 232 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N MET F 234 " --> pdb=" O ILE F 296 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR F 298 " --> pdb=" O MET F 234 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL F 236 " --> pdb=" O THR F 298 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'F' and resid 191 through 193 Processing sheet with id= AJ, first strand: chain 'D' and resid 93 through 97 removed outlier: 3.909A pdb=" N ALA D 94 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ASP D 61 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N VAL D 50 " --> pdb=" O ASP D 61 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'D' and resid 81 through 85 removed outlier: 3.524A pdb=" N VAL D 72 " --> pdb=" O GLY D 84 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER D 111 " --> pdb=" O THR D 75 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'D' and resid 120 through 123 removed outlier: 3.550A pdb=" N ASP D 149 " --> pdb=" O VAL D 123 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'D' and resid 191 through 193 Processing sheet with id= AN, first strand: chain 'D' and resid 347 through 350 removed outlier: 3.559A pdb=" N MET D 234 " --> pdb=" O THR D 298 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'E' and resid 57 through 59 Processing sheet with id= AP, first strand: chain 'E' and resid 120 through 123 Processing sheet with id= AQ, first strand: chain 'E' and resid 130 through 133 removed outlier: 3.755A pdb=" N ARG E 130 " --> pdb=" O VAL E 257 " (cutoff:3.500A) removed outlier: 9.106A pdb=" N CYS E 258 " --> pdb=" O PHE E 227 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE E 229 " --> pdb=" O CYS E 258 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N PHE E 260 " --> pdb=" O ILE E 229 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N PHE E 231 " --> pdb=" O PHE E 260 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ASN E 262 " --> pdb=" O PHE E 231 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA E 233 " --> pdb=" O ASN E 262 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N HIS E 292 " --> pdb=" O ALA E 228 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N VAL E 230 " --> pdb=" O HIS E 292 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU E 294 " --> pdb=" O VAL E 230 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ALA E 232 " --> pdb=" O LEU E 294 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE E 296 " --> pdb=" O ALA E 232 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N MET E 234 " --> pdb=" O ILE E 296 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N THR E 298 " --> pdb=" O MET E 234 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL E 236 " --> pdb=" O THR E 298 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N SER E 347 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL E 295 " --> pdb=" O SER E 347 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N THR E 349 " --> pdb=" O VAL E 295 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N LEU E 297 " --> pdb=" O THR E 349 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'E' and resid 191 through 193 Processing sheet with id= AS, first strand: chain 'G' and resid 92 through 101 Processing sheet with id= AT, first strand: chain 'N' and resid 36 through 38 removed outlier: 6.941A pdb=" N VAL N 10 " --> pdb=" O LEU N 37 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N LEU N 89 " --> pdb=" O ILE N 66 " (cutoff:3.500A) 3930 hydrogen bonds defined for protein. 10626 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: 24.76 Time building geometry restraints manager: 23.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 23034 1.34 - 1.47: 16236 1.47 - 1.60: 31038 1.60 - 1.72: 3 1.72 - 1.85: 659 Bond restraints: 70970 Sorted by residual: bond pdb=" CA ARG B 442 " pdb=" C ARG B 442 " ideal model delta sigma weight residual 1.522 1.465 0.057 1.72e-02 3.38e+03 1.10e+01 bond pdb=" C LEU P 127 " pdb=" N PRO P 128 " ideal model delta sigma weight residual 1.337 1.312 0.025 9.80e-03 1.04e+04 6.27e+00 bond pdb=" CA LEU P 148 " pdb=" C LEU P 148 " ideal model delta sigma weight residual 1.523 1.485 0.039 1.80e-02 3.09e+03 4.62e+00 bond pdb=" C THR L 86 " pdb=" O THR L 86 " ideal model delta sigma weight residual 1.236 1.258 -0.022 1.15e-02 7.56e+03 3.56e+00 bond pdb=" C1 NAG R 901 " pdb=" O5 NAG R 901 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.41e+00 ... (remaining 70965 not shown) Histogram of bond angle deviations from ideal: 96.78 - 104.52: 1118 104.52 - 112.27: 36130 112.27 - 120.02: 28308 120.02 - 127.77: 30119 127.77 - 135.52: 433 Bond angle restraints: 96108 Sorted by residual: angle pdb=" N VAL A 287 " pdb=" CA VAL A 287 " pdb=" C VAL A 287 " ideal model delta sigma weight residual 113.53 106.75 6.78 9.80e-01 1.04e+00 4.79e+01 angle pdb=" C ILE 8 56 " pdb=" N ILE 8 57 " pdb=" CA ILE 8 57 " ideal model delta sigma weight residual 120.43 124.81 -4.38 9.60e-01 1.09e+00 2.09e+01 angle pdb=" CA CYS U 418 " pdb=" CB CYS U 418 " pdb=" SG CYS U 418 " ideal model delta sigma weight residual 114.40 124.66 -10.26 2.30e+00 1.89e-01 1.99e+01 angle pdb=" N VAL 4 46 " pdb=" CA VAL 4 46 " pdb=" C VAL 4 46 " ideal model delta sigma weight residual 112.80 107.92 4.88 1.15e+00 7.56e-01 1.80e+01 angle pdb=" N ILE R 568 " pdb=" CA ILE R 568 " pdb=" C ILE R 568 " ideal model delta sigma weight residual 112.96 108.72 4.24 1.00e+00 1.00e+00 1.80e+01 ... (remaining 96103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.51: 40719 29.51 - 59.01: 2072 59.01 - 88.52: 209 88.52 - 118.03: 8 118.03 - 147.53: 1 Dihedral angle restraints: 43009 sinusoidal: 16387 harmonic: 26622 Sorted by residual: dihedral pdb=" CA PHE F 487 " pdb=" C PHE F 487 " pdb=" N PRO F 488 " pdb=" CA PRO F 488 " ideal model delta harmonic sigma weight residual -180.00 -138.02 -41.98 0 5.00e+00 4.00e-02 7.05e+01 dihedral pdb=" CA ASP A 33 " pdb=" C ASP A 33 " pdb=" N MET A 34 " pdb=" CA MET A 34 " ideal model delta harmonic sigma weight residual 180.00 144.52 35.48 0 5.00e+00 4.00e-02 5.04e+01 dihedral pdb=" CA PHE I 224 " pdb=" C PHE I 224 " pdb=" N LEU I 225 " pdb=" CA LEU I 225 " ideal model delta harmonic sigma weight residual -180.00 -146.20 -33.80 0 5.00e+00 4.00e-02 4.57e+01 ... (remaining 43006 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 7369 0.041 - 0.082: 2871 0.082 - 0.123: 740 0.123 - 0.164: 107 0.164 - 0.205: 6 Chirality restraints: 11093 Sorted by residual: chirality pdb=" C1 NAG U 506 " pdb=" ND2 ASN U 273 " pdb=" C2 NAG U 506 " pdb=" O5 NAG U 506 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA TYR E 451 " pdb=" N TYR E 451 " pdb=" C TYR E 451 " pdb=" CB TYR E 451 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.80e-01 chirality pdb=" CA ASP U 417 " pdb=" N ASP U 417 " pdb=" C ASP U 417 " pdb=" CB ASP U 417 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.18e-01 ... (remaining 11090 not shown) Planarity restraints: 12404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU P 94 " -0.014 2.00e-02 2.50e+03 2.89e-02 8.33e+00 pdb=" C LEU P 94 " 0.050 2.00e-02 2.50e+03 pdb=" O LEU P 94 " -0.019 2.00e-02 2.50e+03 pdb=" N THR P 95 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE L 88 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.25e+00 pdb=" C PHE L 88 " 0.047 2.00e-02 2.50e+03 pdb=" O PHE L 88 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG L 89 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE F 495 " -0.036 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO F 496 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO F 496 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 496 " -0.030 5.00e-02 4.00e+02 ... (remaining 12401 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 817 2.60 - 3.18: 64589 3.18 - 3.75: 106845 3.75 - 4.33: 144548 4.33 - 4.90: 240609 Nonbonded interactions: 557408 Sorted by model distance: nonbonded pdb=" O LEU C 263 " pdb=" OG SER C 267 " model vdw 2.026 2.440 nonbonded pdb=" O SER 7 98 " pdb=" OG SER 7 102 " model vdw 2.045 2.440 nonbonded pdb=" OG SER E 498 " pdb=" OE2 GLU E 502 " model vdw 2.059 2.440 nonbonded pdb=" O GLN 7 51 " pdb=" OG SER 7 55 " model vdw 2.100 2.440 nonbonded pdb=" O GLN 5 51 " pdb=" OG SER 5 55 " model vdw 2.108 2.440 ... (remaining 557403 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 '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' } ncs_group { reference = chain 'A' selection = (chain 'B' and resid 17 through 616) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' } ncs_group { reference = (chain 'X' and (resid 14 through 235 or (resid 236 and (name CA or name C or nam \ e O or name CB or name CG or name CD or name CE or name NZ )) or resid 237 throu \ gh 275)) selection = (chain 'Y' and (resid 14 through 219 or (resid 220 and (name N or name CA or nam \ e C or name O or name CB )) or resid 221 through 222 or (resid 223 and (name N o \ r name CA or name C or name O or name CB )) or resid 224 through 235 or (resid 2 \ 36 and (name CA or name C or name O or name CB or name CG or name CD or name CE \ or name NZ )) or resid 237 through 275)) selection = (chain 'Z' and (resid 14 through 219 or (resid 220 and (name N or name CA or nam \ e C or name O or name CB )) or resid 221 through 222 or (resid 223 and (name N o \ r name CA or name C or name O or name CB )) or resid 224 through 275)) } 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: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 12.670 Check model and map are aligned: 0.780 Set scattering table: 0.500 Process input model: 144.230 Find NCS groups from input model: 3.150 Set up NCS constraints: 0.490 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 166.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 70970 Z= 0.480 Angle : 0.714 10.261 96108 Z= 0.403 Chirality : 0.045 0.205 11093 Planarity : 0.004 0.055 12396 Dihedral : 16.946 147.534 25872 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.79 % Favored : 92.18 % Rotamer: Outliers : 8.84 % Allowed : 16.51 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.08), residues: 9132 helix: -0.80 (0.06), residues: 5123 sheet: -2.75 (0.16), residues: 732 loop : -3.31 (0.09), residues: 3277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 567 HIS 0.006 0.001 HIS B 444 PHE 0.021 0.002 PHE I 224 TYR 0.027 0.002 TYR 0 70 ARG 0.013 0.001 ARG C 364 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18264 Ramachandran restraints generated. 9132 Oldfield, 0 Emsley, 9132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18264 Ramachandran restraints generated. 9132 Oldfield, 0 Emsley, 9132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1729 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 625 poor density : 1104 time to evaluate : 6.196 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 TARDY: cannot create tardy model for: "LYS Z 236 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: R 96 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7685 (p0) REVERT: R 214 TYR cc_start: 0.7078 (m-80) cc_final: 0.6757 (m-80) REVERT: R 270 MET cc_start: 0.7769 (tmm) cc_final: 0.7464 (tmm) REVERT: R 503 ASN cc_start: 0.7432 (OUTLIER) cc_final: 0.7050 (p0) REVERT: R 573 ILE cc_start: 0.7885 (OUTLIER) cc_final: 0.7300 (mm) REVERT: R 579 MET cc_start: 0.7884 (ttm) cc_final: 0.7401 (mtp) REVERT: R 767 LYS cc_start: 0.4471 (tttp) cc_final: 0.4172 (mmmt) REVERT: J 56 TYR cc_start: 0.6929 (OUTLIER) cc_final: 0.5746 (m-80) REVERT: J 74 ASN cc_start: 0.8717 (m-40) cc_final: 0.8400 (m-40) REVERT: M 47 TYR cc_start: 0.5656 (OUTLIER) cc_final: 0.4069 (p90) REVERT: M 93 ASP cc_start: 0.7556 (t70) cc_final: 0.7222 (t0) REVERT: M 97 ASP cc_start: 0.8241 (m-30) cc_final: 0.7890 (m-30) REVERT: I 55 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8469 (mm-30) REVERT: I 78 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8244 (mp10) REVERT: L 54 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.6889 (mp0) REVERT: L 92 ARG cc_start: 0.7094 (OUTLIER) cc_final: 0.6851 (tmm-80) REVERT: H 38 PHE cc_start: 0.8489 (t80) cc_final: 0.8100 (t80) REVERT: H 69 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8016 (tttt) REVERT: H 161 ASN cc_start: 0.8057 (m-40) cc_final: 0.7826 (m-40) REVERT: H 226 ASP cc_start: 0.8145 (t0) cc_final: 0.7942 (t0) REVERT: K 92 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.6608 (ttm170) REVERT: S 78 TYR cc_start: 0.8723 (m-80) cc_final: 0.8460 (m-10) REVERT: T 65 LEU cc_start: 0.8550 (mm) cc_final: 0.8071 (mt) REVERT: T 114 LEU cc_start: 0.8101 (mt) cc_final: 0.7801 (mm) REVERT: U 284 ASP cc_start: 0.7278 (t70) cc_final: 0.6917 (t0) REVERT: U 430 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8523 (mt) REVERT: 0 52 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8629 (tt) REVERT: 0 177 LEU cc_start: 0.8676 (tp) cc_final: 0.8446 (tt) REVERT: 3 61 MET cc_start: 0.7313 (mtp) cc_final: 0.6719 (mtp) REVERT: 4 54 LYS cc_start: 0.7561 (mmtt) cc_final: 0.7196 (pttt) REVERT: 4 104 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8587 (tp) REVERT: 6 44 MET cc_start: 0.7471 (mmm) cc_final: 0.7188 (mmm) REVERT: 7 115 ASP cc_start: 0.7866 (OUTLIER) cc_final: 0.7620 (t0) REVERT: 7 143 LEU cc_start: 0.8289 (tp) cc_final: 0.8063 (tt) REVERT: 8 154 THR cc_start: 0.7977 (OUTLIER) cc_final: 0.7775 (p) REVERT: C 40 TYR cc_start: 0.9062 (m-80) cc_final: 0.8852 (m-80) REVERT: C 201 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.5275 (tt0) REVERT: C 283 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7970 (mm-30) REVERT: C 439 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8458 (mp) REVERT: C 513 LYS cc_start: 0.8238 (ttmt) cc_final: 0.7349 (mmtp) REVERT: C 540 MET cc_start: 0.8136 (mtp) cc_final: 0.7611 (mtm) REVERT: C 612 PHE cc_start: 0.7837 (OUTLIER) cc_final: 0.7495 (t80) REVERT: A 57 LEU cc_start: 0.4981 (OUTLIER) cc_final: 0.4332 (mp) REVERT: A 485 GLU cc_start: 0.7876 (tp30) cc_final: 0.7651 (tp30) REVERT: A 503 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6818 (mm-30) REVERT: A 506 LYS cc_start: 0.7842 (mttt) cc_final: 0.7521 (mtpt) REVERT: A 565 ILE cc_start: 0.7011 (OUTLIER) cc_final: 0.6784 (pt) REVERT: A 585 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8354 (pttp) REVERT: B 129 ARG cc_start: 0.7790 (mmt90) cc_final: 0.7403 (mmt90) REVERT: B 142 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7595 (mtt90) REVERT: B 151 ASP cc_start: 0.7998 (m-30) cc_final: 0.7624 (m-30) REVERT: B 195 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7249 (pt0) REVERT: B 263 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8967 (tt) REVERT: B 347 MET cc_start: 0.7742 (mtp) cc_final: 0.7408 (mtp) REVERT: B 397 ASN cc_start: 0.7222 (m110) cc_final: 0.6656 (m110) REVERT: B 459 ARG cc_start: 0.7888 (mmp80) cc_final: 0.7615 (mmp80) REVERT: B 540 MET cc_start: 0.8869 (mtp) cc_final: 0.8560 (mtp) REVERT: F 97 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8669 (tt0) REVERT: F 161 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8079 (tm-30) REVERT: F 249 GLU cc_start: 0.7774 (tt0) cc_final: 0.7490 (mt-10) REVERT: F 380 ASP cc_start: 0.8342 (t0) cc_final: 0.8100 (t0) REVERT: F 382 GLN cc_start: 0.8645 (mp10) cc_final: 0.8356 (mm-40) REVERT: F 402 MET cc_start: 0.9035 (ttt) cc_final: 0.8602 (ttt) REVERT: F 491 MET cc_start: 0.4490 (mtm) cc_final: 0.3966 (mtm) REVERT: D 40 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8743 (mt) REVERT: D 433 GLN cc_start: 0.7988 (mm-40) cc_final: 0.7575 (tp-100) REVERT: E 177 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.8882 (pt) REVERT: E 316 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8098 (mt-10) REVERT: E 495 ILE cc_start: 0.5829 (OUTLIER) cc_final: 0.5302 (mm) REVERT: X 10 MET cc_start: 0.6588 (mtp) cc_final: 0.5852 (ttt) REVERT: X 201 LYS cc_start: 0.8150 (ptmt) cc_final: 0.7791 (mmtt) REVERT: X 234 MET cc_start: 0.8276 (ttp) cc_final: 0.7757 (tpp) REVERT: X 236 LYS cc_start: 0.6813 (mmtp) cc_final: 0.6482 (mttm) REVERT: Y 93 ARG cc_start: 0.7224 (OUTLIER) cc_final: 0.6843 (ttm170) REVERT: Y 130 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8422 (mm) REVERT: G 67 PHE cc_start: 0.8649 (t80) cc_final: 0.8409 (t80) REVERT: N 29 ASN cc_start: 0.8500 (t0) cc_final: 0.7162 (t0) REVERT: N 99 ASP cc_start: 0.7202 (t0) cc_final: 0.6656 (t0) outliers start: 625 outliers final: 461 residues processed: 1641 average time/residue: 0.6397 time to fit residues: 1781.6755 Evaluate side-chains 1439 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 495 poor density : 944 time to evaluate : 6.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 47 PHE Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 80 MET Chi-restraints excluded: chain R residue 96 ASP Chi-restraints excluded: chain R residue 100 ASN Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 250 THR Chi-restraints excluded: chain R residue 283 LEU Chi-restraints excluded: chain R residue 312 ILE Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 325 CYS Chi-restraints excluded: chain R residue 363 THR Chi-restraints excluded: chain R residue 368 ASN Chi-restraints excluded: chain R residue 371 THR Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 437 ASN Chi-restraints excluded: chain R residue 471 SER Chi-restraints excluded: chain R residue 503 ASN Chi-restraints excluded: chain R residue 535 PHE Chi-restraints excluded: chain R residue 549 LEU Chi-restraints excluded: chain R residue 552 VAL Chi-restraints excluded: chain R residue 573 ILE Chi-restraints excluded: chain R residue 581 SER Chi-restraints excluded: chain R residue 582 LEU Chi-restraints excluded: chain R residue 598 ASP Chi-restraints excluded: chain R residue 607 SER Chi-restraints excluded: chain R residue 613 ILE Chi-restraints excluded: chain R residue 644 LEU Chi-restraints excluded: chain R residue 746 LEU Chi-restraints excluded: chain R residue 830 ILE Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 56 TYR Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 104 LYS Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 139 GLN Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 171 SER Chi-restraints excluded: chain J residue 177 ILE Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 193 SER Chi-restraints excluded: chain J residue 194 ASN Chi-restraints excluded: chain J residue 201 ASP Chi-restraints excluded: chain J residue 202 LEU Chi-restraints excluded: chain J residue 211 VAL Chi-restraints excluded: chain M residue 47 TYR Chi-restraints excluded: chain M residue 83 ILE Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 107 ARG Chi-restraints excluded: chain M residue 110 ILE Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 76 MET Chi-restraints excluded: chain I residue 78 GLN Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 139 GLN Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 169 GLN Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain I residue 208 MET Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 54 GLU Chi-restraints excluded: chain L residue 56 LYS Chi-restraints excluded: chain L residue 80 LYS Chi-restraints excluded: chain L residue 92 ARG Chi-restraints excluded: chain H residue 14 HIS Chi-restraints excluded: chain H residue 37 GLU Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain H residue 71 GLN Chi-restraints excluded: chain K residue 85 GLN Chi-restraints excluded: chain K residue 92 ARG Chi-restraints excluded: chain K residue 112 GLU Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 36 VAL Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain T residue 79 LEU Chi-restraints excluded: chain T residue 96 ASN Chi-restraints excluded: chain T residue 116 LEU Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain U residue 258 VAL Chi-restraints excluded: chain U residue 310 SER Chi-restraints excluded: chain U residue 311 LEU Chi-restraints excluded: chain U residue 320 THR Chi-restraints excluded: chain U residue 334 VAL Chi-restraints excluded: chain U residue 340 PHE Chi-restraints excluded: chain U residue 341 THR Chi-restraints excluded: chain U residue 347 VAL Chi-restraints excluded: chain U residue 365 SER Chi-restraints excluded: chain U residue 374 VAL Chi-restraints excluded: chain U residue 385 VAL Chi-restraints excluded: chain U residue 407 VAL Chi-restraints excluded: chain U residue 423 SER Chi-restraints excluded: chain U residue 427 TRP Chi-restraints excluded: chain U residue 430 LEU Chi-restraints excluded: chain U residue 447 ILE Chi-restraints excluded: chain U residue 458 ASP Chi-restraints excluded: chain V residue 306 VAL Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 313 ILE Chi-restraints excluded: chain V residue 315 ILE Chi-restraints excluded: chain V residue 338 ILE Chi-restraints excluded: chain 0 residue 2 THR Chi-restraints excluded: chain 0 residue 22 VAL Chi-restraints excluded: chain 0 residue 26 TYR Chi-restraints excluded: chain 0 residue 28 ILE Chi-restraints excluded: chain 0 residue 45 SER Chi-restraints excluded: chain 0 residue 52 LEU Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 0 residue 69 ILE Chi-restraints excluded: chain 0 residue 70 TYR Chi-restraints excluded: chain 0 residue 72 THR Chi-restraints excluded: chain 0 residue 122 ASP Chi-restraints excluded: chain 0 residue 149 LEU Chi-restraints excluded: chain 0 residue 151 CYS Chi-restraints excluded: chain 0 residue 154 CYS Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 0 residue 198 THR Chi-restraints excluded: chain 1 residue 39 THR Chi-restraints excluded: chain 1 residue 45 SER Chi-restraints excluded: chain 1 residue 56 ILE Chi-restraints excluded: chain 1 residue 74 VAL Chi-restraints excluded: chain 1 residue 98 SER Chi-restraints excluded: chain 1 residue 115 ASP Chi-restraints excluded: chain 1 residue 121 THR Chi-restraints excluded: chain 1 residue 127 LEU Chi-restraints excluded: chain 1 residue 136 ILE Chi-restraints excluded: chain 1 residue 140 VAL Chi-restraints excluded: chain 1 residue 151 ILE Chi-restraints excluded: chain 2 residue 20 SER Chi-restraints excluded: chain 2 residue 24 VAL Chi-restraints excluded: chain 2 residue 28 LEU Chi-restraints excluded: chain 2 residue 45 SER Chi-restraints excluded: chain 2 residue 56 ILE Chi-restraints excluded: chain 2 residue 61 MET Chi-restraints excluded: chain 2 residue 67 ILE Chi-restraints excluded: chain 2 residue 71 VAL Chi-restraints excluded: chain 2 residue 92 GLN Chi-restraints excluded: chain 2 residue 102 SER Chi-restraints excluded: chain 2 residue 118 VAL Chi-restraints excluded: chain 2 residue 121 THR Chi-restraints excluded: chain 2 residue 124 GLN Chi-restraints excluded: chain 2 residue 129 VAL Chi-restraints excluded: chain 2 residue 132 ILE Chi-restraints excluded: chain 2 residue 140 VAL Chi-restraints excluded: chain 3 residue 9 GLU Chi-restraints excluded: chain 3 residue 44 MET Chi-restraints excluded: chain 3 residue 52 ILE Chi-restraints excluded: chain 3 residue 56 ILE Chi-restraints excluded: chain 3 residue 84 ILE Chi-restraints excluded: chain 3 residue 102 SER Chi-restraints excluded: chain 3 residue 110 ILE Chi-restraints excluded: chain 3 residue 121 THR Chi-restraints excluded: chain 3 residue 132 ILE Chi-restraints excluded: chain 3 residue 139 GLU Chi-restraints excluded: chain 3 residue 140 VAL Chi-restraints excluded: chain 4 residue 41 ILE Chi-restraints excluded: chain 4 residue 44 MET Chi-restraints excluded: chain 4 residue 55 SER Chi-restraints excluded: chain 4 residue 56 ILE Chi-restraints excluded: chain 4 residue 67 ILE Chi-restraints excluded: chain 4 residue 72 VAL Chi-restraints excluded: chain 4 residue 80 LEU Chi-restraints excluded: chain 4 residue 93 LEU Chi-restraints excluded: chain 4 residue 99 VAL Chi-restraints excluded: chain 4 residue 104 LEU Chi-restraints excluded: chain 4 residue 118 VAL Chi-restraints excluded: chain 4 residue 121 THR Chi-restraints excluded: chain 4 residue 129 VAL Chi-restraints excluded: chain 4 residue 132 ILE Chi-restraints excluded: chain 4 residue 133 LEU Chi-restraints excluded: chain 4 residue 140 VAL Chi-restraints excluded: chain 4 residue 151 ILE Chi-restraints excluded: chain 5 residue 28 LEU Chi-restraints excluded: chain 5 residue 37 SER Chi-restraints excluded: chain 5 residue 55 SER Chi-restraints excluded: chain 5 residue 56 ILE Chi-restraints excluded: chain 5 residue 93 LEU Chi-restraints excluded: chain 5 residue 115 ASP Chi-restraints excluded: chain 5 residue 121 THR Chi-restraints excluded: chain 5 residue 129 VAL Chi-restraints excluded: chain 5 residue 132 ILE Chi-restraints excluded: chain 5 residue 133 LEU Chi-restraints excluded: chain 5 residue 140 VAL Chi-restraints excluded: chain 6 residue 9 GLU Chi-restraints excluded: chain 6 residue 26 SER Chi-restraints excluded: chain 6 residue 37 SER Chi-restraints excluded: chain 6 residue 39 THR Chi-restraints excluded: chain 6 residue 41 ILE Chi-restraints excluded: chain 6 residue 46 VAL Chi-restraints excluded: chain 6 residue 72 VAL Chi-restraints excluded: chain 6 residue 86 LEU Chi-restraints excluded: chain 6 residue 121 THR Chi-restraints excluded: chain 6 residue 140 VAL Chi-restraints excluded: chain 7 residue 37 SER Chi-restraints excluded: chain 7 residue 44 MET Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 74 VAL Chi-restraints excluded: chain 7 residue 84 ILE Chi-restraints excluded: chain 7 residue 93 LEU Chi-restraints excluded: chain 7 residue 102 SER Chi-restraints excluded: chain 7 residue 115 ASP Chi-restraints excluded: chain 7 residue 121 THR Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 139 GLU Chi-restraints excluded: chain 8 residue 41 ILE Chi-restraints excluded: chain 8 residue 44 MET Chi-restraints excluded: chain 8 residue 46 VAL Chi-restraints excluded: chain 8 residue 60 VAL Chi-restraints excluded: chain 8 residue 67 ILE Chi-restraints excluded: chain 8 residue 74 VAL Chi-restraints excluded: chain 8 residue 98 SER Chi-restraints excluded: chain 8 residue 112 ILE Chi-restraints excluded: chain 8 residue 115 ASP Chi-restraints excluded: chain 8 residue 118 VAL Chi-restraints excluded: chain 8 residue 121 THR Chi-restraints excluded: chain 8 residue 132 ILE Chi-restraints excluded: chain 8 residue 140 VAL Chi-restraints excluded: chain 8 residue 153 SER Chi-restraints excluded: chain 8 residue 154 THR Chi-restraints excluded: chain 9 residue 9 GLU Chi-restraints excluded: chain 9 residue 56 ILE Chi-restraints excluded: chain 9 residue 60 VAL Chi-restraints excluded: chain 9 residue 67 ILE Chi-restraints excluded: chain 9 residue 72 VAL Chi-restraints excluded: chain 9 residue 79 SER Chi-restraints excluded: chain 9 residue 82 ASP Chi-restraints excluded: chain 9 residue 99 VAL Chi-restraints excluded: chain 9 residue 132 ILE Chi-restraints excluded: chain 9 residue 140 VAL Chi-restraints excluded: chain 9 residue 150 LEU Chi-restraints excluded: chain Q residue 36 LEU Chi-restraints excluded: chain Q residue 52 THR Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 132 LEU Chi-restraints excluded: chain Q residue 155 LEU Chi-restraints excluded: chain Q residue 166 ASP Chi-restraints excluded: chain Q residue 169 SER Chi-restraints excluded: chain Q residue 197 CYS Chi-restraints excluded: chain Q residue 199 LEU Chi-restraints excluded: chain Q residue 200 LEU Chi-restraints excluded: chain Q residue 230 THR Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 532 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 612 PHE Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 585 LYS Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 592 ASP Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 161 GLN Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 200 ASN Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 234 MET Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 340 ARG Chi-restraints excluded: chain F residue 359 ASP Chi-restraints excluded: chain F residue 403 LYS Chi-restraints excluded: chain F residue 404 SER Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 371 TYR Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 270 GLU Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 316 GLU Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 359 ASP Chi-restraints excluded: chain E residue 397 SER Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 495 ILE Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain E residue 506 ARG Chi-restraints excluded: chain Z residue 14 THR Chi-restraints excluded: chain Z residue 15 SER Chi-restraints excluded: chain Z residue 35 THR Chi-restraints excluded: chain Z residue 99 SER Chi-restraints excluded: chain Z residue 125 ASP Chi-restraints excluded: chain Z residue 146 THR Chi-restraints excluded: chain Z residue 181 LEU Chi-restraints excluded: chain Z residue 241 VAL Chi-restraints excluded: chain Z residue 260 LEU Chi-restraints excluded: chain X residue 17 GLN Chi-restraints excluded: chain X residue 35 THR Chi-restraints excluded: chain X residue 36 ILE Chi-restraints excluded: chain X residue 52 VAL Chi-restraints excluded: chain X residue 74 CYS Chi-restraints excluded: chain X residue 119 VAL Chi-restraints excluded: chain X residue 163 ILE Chi-restraints excluded: chain X residue 196 GLN Chi-restraints excluded: chain X residue 217 LEU Chi-restraints excluded: chain X residue 221 ASP Chi-restraints excluded: chain X residue 247 SER Chi-restraints excluded: chain X residue 256 THR Chi-restraints excluded: chain X residue 267 VAL Chi-restraints excluded: chain Y residue 51 ASP Chi-restraints excluded: chain Y residue 93 ARG Chi-restraints excluded: chain Y residue 95 VAL Chi-restraints excluded: chain Y residue 108 ILE Chi-restraints excluded: chain Y residue 119 VAL Chi-restraints excluded: chain Y residue 130 LEU Chi-restraints excluded: chain Y residue 136 LEU Chi-restraints excluded: chain Y residue 146 THR Chi-restraints excluded: chain Y residue 179 PHE Chi-restraints excluded: chain Y residue 241 VAL Chi-restraints excluded: chain Y residue 274 ASN Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain N residue 14 GLU Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 48 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 768 optimal weight: 5.9990 chunk 689 optimal weight: 0.6980 chunk 382 optimal weight: 0.9980 chunk 235 optimal weight: 8.9990 chunk 465 optimal weight: 4.9990 chunk 368 optimal weight: 3.9990 chunk 713 optimal weight: 1.9990 chunk 276 optimal weight: 0.8980 chunk 433 optimal weight: 7.9990 chunk 530 optimal weight: 0.9980 chunk 826 optimal weight: 20.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 41 ASN R 194 ASN ** R 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 252 GLN ** R 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 365 ASN ** R 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 523 ASN R 547 HIS R 734 ASN J 21 GLN J 66 GLN J 78 GLN J 139 GLN J 166 GLN J 194 ASN J 206 GLN J 221 ASN M 10 GLN M 90 GLN I 122 GLN I 169 GLN I 206 GLN L 111 HIS H 49 GLN H 161 ASN K 111 HIS S 59 GLN U 329 ASN U 370 HIS ** U 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 401 GLN U 403 GLN U 406 ASN V 330 ASN 0 51 ASN 0 148 ASN ** 1 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 81 ASN 6 92 GLN 7 78 ASN 9 123 GLN Q 88 HIS Q 297 HIS ** Q 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 338 GLN A 314 ASN ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 ASN B 184 ASN B 231 GLN B 397 ASN B 441 GLN B 468 HIS B 560 GLN B 573 HIS F 199 HIS F 421 GLN D 161 GLN D 199 HIS D 345 ASN D 363 HIS D 421 GLN E 54 ASN E 181 ASN E 199 HIS E 251 ASN E 382 GLN E 421 GLN E 456 GLN Z 34 GLN Z 50 GLN Z 176 ASN Z 177 GLN X 19 HIS X 160 GLN ** X 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 19 HIS Y 76 ASN Y 135 GLN Y 142 ASN Y 150 ASN Y 162 GLN G 31 ASN G 85 GLN N 81 HIS Total number of N/Q/H flips: 78 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 70970 Z= 0.185 Angle : 0.580 18.265 96108 Z= 0.306 Chirality : 0.041 0.179 11093 Planarity : 0.005 0.057 12396 Dihedral : 9.982 145.205 10924 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.66 % Favored : 95.32 % Rotamer: Outliers : 5.70 % Allowed : 21.21 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.09), residues: 9132 helix: 0.58 (0.07), residues: 5151 sheet: -2.18 (0.17), residues: 718 loop : -2.69 (0.10), residues: 3263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 324 HIS 0.005 0.001 HIS B 444 PHE 0.021 0.001 PHE F 487 TYR 0.037 0.001 TYR Y 139 ARG 0.014 0.000 ARG N 110 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18264 Ramachandran restraints generated. 9132 Oldfield, 0 Emsley, 9132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18264 Ramachandran restraints generated. 9132 Oldfield, 0 Emsley, 9132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1478 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 403 poor density : 1075 time to evaluate : 6.177 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: R 94 MET cc_start: 0.8426 (ppp) cc_final: 0.7684 (mtt) REVERT: R 214 TYR cc_start: 0.6859 (m-80) cc_final: 0.6532 (m-80) REVERT: R 257 MET cc_start: 0.6302 (tmm) cc_final: 0.6093 (tmm) REVERT: R 270 MET cc_start: 0.7592 (tmm) cc_final: 0.7359 (tmm) REVERT: R 471 SER cc_start: 0.5838 (OUTLIER) cc_final: 0.5571 (t) REVERT: R 484 MET cc_start: 0.8052 (mmm) cc_final: 0.7549 (tpp) REVERT: J 56 TYR cc_start: 0.7010 (OUTLIER) cc_final: 0.5717 (m-80) REVERT: J 62 LYS cc_start: 0.8361 (mmtm) cc_final: 0.7978 (mmtp) REVERT: J 132 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8097 (mpt) REVERT: J 145 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8488 (ttpm) REVERT: J 225 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8506 (mt) REVERT: M 93 ASP cc_start: 0.7692 (t70) cc_final: 0.7292 (t0) REVERT: M 97 ASP cc_start: 0.8165 (m-30) cc_final: 0.7825 (m-30) REVERT: I 55 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8234 (mp0) REVERT: I 63 GLN cc_start: 0.8209 (mt0) cc_final: 0.7980 (mm-40) REVERT: I 202 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8541 (mp) REVERT: L 54 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7094 (mp0) REVERT: L 81 MET cc_start: 0.8531 (mtm) cc_final: 0.8284 (mtt) REVERT: H 38 PHE cc_start: 0.8419 (t80) cc_final: 0.8132 (t80) REVERT: K 102 PHE cc_start: 0.7946 (OUTLIER) cc_final: 0.7129 (t80) REVERT: K 109 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7041 (pt0) REVERT: S 71 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8239 (mm-30) REVERT: S 78 TYR cc_start: 0.8686 (m-80) cc_final: 0.8429 (m-10) REVERT: T 65 LEU cc_start: 0.8526 (mm) cc_final: 0.8024 (mt) REVERT: T 114 LEU cc_start: 0.8104 (mt) cc_final: 0.7801 (mm) REVERT: U 373 TYR cc_start: 0.6871 (m-80) cc_final: 0.5678 (m-10) REVERT: U 397 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8270 (mt) REVERT: U 408 MET cc_start: 0.6748 (mmt) cc_final: 0.6493 (mmt) REVERT: 0 26 TYR cc_start: 0.8130 (OUTLIER) cc_final: 0.6433 (t80) REVERT: 0 52 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8444 (tt) REVERT: 2 61 MET cc_start: 0.7068 (OUTLIER) cc_final: 0.6855 (mmm) REVERT: 4 54 LYS cc_start: 0.7480 (mmtt) cc_final: 0.7105 (ptmt) REVERT: 4 75 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8286 (tt) REVERT: 4 134 ILE cc_start: 0.7897 (mm) cc_final: 0.7560 (mt) REVERT: 5 47 MET cc_start: 0.7755 (mmm) cc_final: 0.7547 (mmp) REVERT: 6 56 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8494 (tp) REVERT: C 194 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8645 (pt) REVERT: C 486 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7985 (tm-30) REVERT: C 513 LYS cc_start: 0.8165 (ttmt) cc_final: 0.7249 (mmtm) REVERT: C 540 MET cc_start: 0.8048 (mtp) cc_final: 0.7628 (mtm) REVERT: A 57 LEU cc_start: 0.4711 (OUTLIER) cc_final: 0.4192 (mp) REVERT: A 81 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8548 (ptt180) REVERT: A 485 GLU cc_start: 0.7755 (tp30) cc_final: 0.7511 (tp30) REVERT: A 503 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6615 (mm-30) REVERT: A 506 LYS cc_start: 0.7742 (mttt) cc_final: 0.7424 (mtpt) REVERT: A 525 TYR cc_start: 0.7595 (OUTLIER) cc_final: 0.7157 (p90) REVERT: B 60 ASP cc_start: 0.7857 (m-30) cc_final: 0.7599 (m-30) REVERT: B 129 ARG cc_start: 0.7766 (mmt90) cc_final: 0.7559 (mmt90) REVERT: B 231 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8338 (mm110) REVERT: B 284 MET cc_start: 0.8292 (mmm) cc_final: 0.8070 (mmp) REVERT: B 360 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6722 (tt0) REVERT: B 459 ARG cc_start: 0.7858 (mmp80) cc_final: 0.7611 (mmp80) REVERT: B 540 MET cc_start: 0.8809 (mtp) cc_final: 0.8489 (mtp) REVERT: F 178 ASP cc_start: 0.8818 (OUTLIER) cc_final: 0.8419 (m-30) REVERT: F 249 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7477 (mt-10) REVERT: F 250 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8131 (pp20) REVERT: F 402 MET cc_start: 0.9024 (ttt) cc_final: 0.8571 (ttt) REVERT: F 435 MET cc_start: 0.4825 (OUTLIER) cc_final: 0.4143 (mmp) REVERT: F 487 PHE cc_start: 0.5159 (OUTLIER) cc_final: 0.4951 (m-80) REVERT: D 310 VAL cc_start: 0.8807 (t) cc_final: 0.8569 (t) REVERT: D 433 GLN cc_start: 0.7849 (mm-40) cc_final: 0.7505 (tp-100) REVERT: E 177 ILE cc_start: 0.9197 (pt) cc_final: 0.8931 (pt) REVERT: E 435 MET cc_start: 0.5180 (mmm) cc_final: 0.4380 (mtt) REVERT: E 479 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8721 (mt) REVERT: Z 166 TYR cc_start: 0.7969 (m-80) cc_final: 0.7675 (m-80) REVERT: X 10 MET cc_start: 0.6407 (mtp) cc_final: 0.5855 (ttt) REVERT: X 234 MET cc_start: 0.8104 (ttp) cc_final: 0.7626 (tpp) REVERT: X 236 LYS cc_start: 0.6819 (mmtp) cc_final: 0.6466 (mttm) REVERT: Y 93 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.7119 (ttm170) REVERT: G 67 PHE cc_start: 0.8604 (t80) cc_final: 0.8358 (t80) REVERT: N 50 ASP cc_start: 0.8439 (t0) cc_final: 0.7489 (t0) REVERT: N 81 HIS cc_start: 0.7015 (OUTLIER) cc_final: 0.6727 (t-90) outliers start: 403 outliers final: 267 residues processed: 1389 average time/residue: 0.6503 time to fit residues: 1542.9755 Evaluate side-chains 1265 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 297 poor density : 968 time to evaluate : 6.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 47 PHE Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 96 ASP Chi-restraints excluded: chain R residue 100 ASN Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 194 ASN Chi-restraints excluded: chain R residue 250 THR Chi-restraints excluded: chain R residue 283 LEU Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 308 ASN Chi-restraints excluded: chain R residue 312 ILE Chi-restraints excluded: chain R residue 357 THR Chi-restraints excluded: chain R residue 363 THR Chi-restraints excluded: chain R residue 396 ILE Chi-restraints excluded: chain R residue 437 ASN Chi-restraints excluded: chain R residue 471 SER Chi-restraints excluded: chain R residue 549 LEU Chi-restraints excluded: chain R residue 556 LEU Chi-restraints excluded: chain R residue 572 PHE Chi-restraints excluded: chain R residue 573 ILE Chi-restraints excluded: chain R residue 607 SER Chi-restraints excluded: chain R residue 613 ILE Chi-restraints excluded: chain R residue 716 THR Chi-restraints excluded: chain R residue 726 GLU Chi-restraints excluded: chain R residue 729 LEU Chi-restraints excluded: chain R residue 746 LEU Chi-restraints excluded: chain R residue 830 ILE Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 56 TYR Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 104 LYS Chi-restraints excluded: chain J residue 132 MET Chi-restraints excluded: chain J residue 139 GLN Chi-restraints excluded: chain J residue 145 LYS Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 177 ILE Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 201 ASP Chi-restraints excluded: chain J residue 202 LEU Chi-restraints excluded: chain J residue 225 LEU Chi-restraints excluded: chain M residue 102 PHE Chi-restraints excluded: chain M residue 107 ARG Chi-restraints excluded: chain M residue 110 ILE Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 202 LEU Chi-restraints excluded: chain L residue 54 GLU Chi-restraints excluded: chain L residue 80 LYS Chi-restraints excluded: chain H residue 14 HIS Chi-restraints excluded: chain H residue 71 GLN Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain H residue 198 SER Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 50 GLN Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 85 GLN Chi-restraints excluded: chain K residue 87 TYR Chi-restraints excluded: chain K residue 102 PHE Chi-restraints excluded: chain K residue 109 GLU Chi-restraints excluded: chain K residue 112 GLU Chi-restraints excluded: chain S residue 36 VAL Chi-restraints excluded: chain T residue 79 LEU Chi-restraints excluded: chain T residue 116 LEU Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain U residue 258 VAL Chi-restraints excluded: chain U residue 323 PHE Chi-restraints excluded: chain U residue 334 VAL Chi-restraints excluded: chain U residue 340 PHE Chi-restraints excluded: chain U residue 347 VAL Chi-restraints excluded: chain U residue 362 THR Chi-restraints excluded: chain U residue 374 VAL Chi-restraints excluded: chain U residue 385 VAL Chi-restraints excluded: chain U residue 397 LEU Chi-restraints excluded: chain U residue 407 VAL Chi-restraints excluded: chain U residue 427 TRP Chi-restraints excluded: chain U residue 447 ILE Chi-restraints excluded: chain U residue 458 ASP Chi-restraints excluded: chain V residue 313 ILE Chi-restraints excluded: chain V residue 338 ILE Chi-restraints excluded: chain 0 residue 2 THR Chi-restraints excluded: chain 0 residue 26 TYR Chi-restraints excluded: chain 0 residue 45 SER Chi-restraints excluded: chain 0 residue 52 LEU Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 0 residue 69 ILE Chi-restraints excluded: chain 0 residue 70 TYR Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 0 residue 191 VAL Chi-restraints excluded: chain 1 residue 67 ILE Chi-restraints excluded: chain 1 residue 85 SER Chi-restraints excluded: chain 1 residue 97 LEU Chi-restraints excluded: chain 1 residue 110 ILE Chi-restraints excluded: chain 1 residue 115 ASP Chi-restraints excluded: chain 1 residue 121 THR Chi-restraints excluded: chain 1 residue 140 VAL Chi-restraints excluded: chain 2 residue 28 LEU Chi-restraints excluded: chain 2 residue 56 ILE Chi-restraints excluded: chain 2 residue 57 ILE Chi-restraints excluded: chain 2 residue 61 MET Chi-restraints excluded: chain 2 residue 67 ILE Chi-restraints excluded: chain 2 residue 140 VAL Chi-restraints excluded: chain 3 residue 44 MET Chi-restraints excluded: chain 3 residue 56 ILE Chi-restraints excluded: chain 3 residue 84 ILE Chi-restraints excluded: chain 3 residue 102 SER Chi-restraints excluded: chain 3 residue 110 ILE Chi-restraints excluded: chain 3 residue 140 VAL Chi-restraints excluded: chain 4 residue 55 SER Chi-restraints excluded: chain 4 residue 75 LEU Chi-restraints excluded: chain 4 residue 80 LEU Chi-restraints excluded: chain 4 residue 110 ILE Chi-restraints excluded: chain 4 residue 113 VAL Chi-restraints excluded: chain 4 residue 129 VAL Chi-restraints excluded: chain 4 residue 140 VAL Chi-restraints excluded: chain 5 residue 24 VAL Chi-restraints excluded: chain 5 residue 37 SER Chi-restraints excluded: chain 5 residue 93 LEU Chi-restraints excluded: chain 5 residue 115 ASP Chi-restraints excluded: chain 5 residue 118 VAL Chi-restraints excluded: chain 5 residue 129 VAL Chi-restraints excluded: chain 5 residue 133 LEU Chi-restraints excluded: chain 5 residue 140 VAL Chi-restraints excluded: chain 5 residue 143 LEU Chi-restraints excluded: chain 6 residue 46 VAL Chi-restraints excluded: chain 6 residue 56 ILE Chi-restraints excluded: chain 6 residue 81 ASN Chi-restraints excluded: chain 6 residue 127 LEU Chi-restraints excluded: chain 6 residue 140 VAL Chi-restraints excluded: chain 7 residue 44 MET Chi-restraints excluded: chain 7 residue 59 VAL Chi-restraints excluded: chain 7 residue 93 LEU Chi-restraints excluded: chain 7 residue 102 SER Chi-restraints excluded: chain 7 residue 112 ILE Chi-restraints excluded: chain 8 residue 28 LEU Chi-restraints excluded: chain 8 residue 45 SER Chi-restraints excluded: chain 8 residue 60 VAL Chi-restraints excluded: chain 8 residue 93 LEU Chi-restraints excluded: chain 8 residue 115 ASP Chi-restraints excluded: chain 8 residue 118 VAL Chi-restraints excluded: chain 8 residue 148 VAL Chi-restraints excluded: chain 9 residue 9 GLU Chi-restraints excluded: chain 9 residue 39 THR Chi-restraints excluded: chain 9 residue 44 MET Chi-restraints excluded: chain 9 residue 67 ILE Chi-restraints excluded: chain 9 residue 110 ILE Chi-restraints excluded: chain 9 residue 112 ILE Chi-restraints excluded: chain 9 residue 123 GLN Chi-restraints excluded: chain 9 residue 140 VAL Chi-restraints excluded: chain 9 residue 150 LEU Chi-restraints excluded: chain Q residue 6 GLU Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 52 THR Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 122 ILE Chi-restraints excluded: chain Q residue 155 LEU Chi-restraints excluded: chain Q residue 166 ASP Chi-restraints excluded: chain Q residue 344 ILE Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 525 TYR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 231 GLN Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 592 ASP Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain F residue 234 MET Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 340 ARG Chi-restraints excluded: chain F residue 359 ASP Chi-restraints excluded: chain F residue 403 LYS Chi-restraints excluded: chain F residue 435 MET Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 487 PHE Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 161 GLN Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 344 ARG Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 371 TYR Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 359 ASP Chi-restraints excluded: chain E residue 397 SER Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain Z residue 228 THR Chi-restraints excluded: chain Z residue 241 VAL Chi-restraints excluded: chain X residue 17 GLN Chi-restraints excluded: chain X residue 52 VAL Chi-restraints excluded: chain X residue 74 CYS Chi-restraints excluded: chain X residue 199 LEU Chi-restraints excluded: chain X residue 209 GLU Chi-restraints excluded: chain X residue 217 LEU Chi-restraints excluded: chain X residue 221 ASP Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Y residue 51 ASP Chi-restraints excluded: chain Y residue 93 ARG Chi-restraints excluded: chain Y residue 95 VAL Chi-restraints excluded: chain Y residue 119 VAL Chi-restraints excluded: chain Y residue 130 LEU Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain Y residue 179 PHE Chi-restraints excluded: chain Y residue 204 VAL Chi-restraints excluded: chain Y residue 241 VAL Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain G residue 85 GLN Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain N residue 14 GLU Chi-restraints excluded: chain N residue 30 LYS Chi-restraints excluded: chain N residue 81 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 459 optimal weight: 0.2980 chunk 256 optimal weight: 5.9990 chunk 687 optimal weight: 2.9990 chunk 562 optimal weight: 2.9990 chunk 227 optimal weight: 7.9990 chunk 827 optimal weight: 20.0000 chunk 894 optimal weight: 10.0000 chunk 737 optimal weight: 4.9990 chunk 820 optimal weight: 4.9990 chunk 282 optimal weight: 0.9980 chunk 664 optimal weight: 0.7980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 365 ASN R 465 ASN ** R 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 66 GLN I 78 GLN L 6 GLN K 13 GLN ** U 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 327 ASN 0 51 ASN 2 51 GLN ** 7 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 78 ASN 9 51 GLN ** 9 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 HIS B 65 GLN B 123 ASN F 421 GLN D 421 GLN ** E 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 165 GLN G 85 GLN N 83 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 70970 Z= 0.193 Angle : 0.555 19.081 96108 Z= 0.289 Chirality : 0.040 0.169 11093 Planarity : 0.004 0.046 12396 Dihedral : 8.062 143.202 10441 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.98 % Favored : 95.01 % Rotamer: Outliers : 5.57 % Allowed : 22.03 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.09), residues: 9132 helix: 1.05 (0.07), residues: 5137 sheet: -1.85 (0.18), residues: 718 loop : -2.43 (0.10), residues: 3277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 52 HIS 0.013 0.001 HIS N 81 PHE 0.024 0.001 PHE R 578 TYR 0.035 0.001 TYR Y 139 ARG 0.010 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18264 Ramachandran restraints generated. 9132 Oldfield, 0 Emsley, 9132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18264 Ramachandran restraints generated. 9132 Oldfield, 0 Emsley, 9132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1418 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 394 poor density : 1024 time to evaluate : 6.250 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: R 94 MET cc_start: 0.8445 (ppp) cc_final: 0.7800 (mtt) REVERT: R 214 TYR cc_start: 0.6959 (m-80) cc_final: 0.6668 (m-80) REVERT: R 257 MET cc_start: 0.6280 (tmm) cc_final: 0.6036 (ppp) REVERT: J 16 MET cc_start: 0.6033 (tpp) cc_final: 0.5828 (tpt) REVERT: J 56 TYR cc_start: 0.6935 (OUTLIER) cc_final: 0.5455 (m-80) REVERT: J 62 LYS cc_start: 0.8381 (mmtm) cc_final: 0.7997 (mmtp) REVERT: J 132 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8117 (mpt) REVERT: J 145 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8466 (ttpm) REVERT: M 93 ASP cc_start: 0.7831 (t70) cc_final: 0.7376 (t0) REVERT: M 97 ASP cc_start: 0.8068 (m-30) cc_final: 0.7615 (m-30) REVERT: I 63 GLN cc_start: 0.8208 (mt0) cc_final: 0.7974 (mm-40) REVERT: L 54 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7160 (mp0) REVERT: L 81 MET cc_start: 0.8543 (mtm) cc_final: 0.7618 (mtt) REVERT: L 85 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7415 (mp10) REVERT: H 38 PHE cc_start: 0.8431 (t80) cc_final: 0.8168 (t80) REVERT: H 54 MET cc_start: 0.8179 (tmm) cc_final: 0.7910 (tmm) REVERT: H 206 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8471 (mt0) REVERT: K 102 PHE cc_start: 0.7907 (OUTLIER) cc_final: 0.7155 (t80) REVERT: K 109 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.7084 (pt0) REVERT: S 71 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8082 (mm-30) REVERT: T 65 LEU cc_start: 0.8584 (mm) cc_final: 0.8077 (mt) REVERT: T 114 LEU cc_start: 0.8177 (mt) cc_final: 0.7873 (mm) REVERT: U 373 TYR cc_start: 0.7341 (m-80) cc_final: 0.6973 (m-10) REVERT: U 397 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7851 (mt) REVERT: 0 26 TYR cc_start: 0.8210 (OUTLIER) cc_final: 0.6562 (t80) REVERT: 0 52 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8491 (tt) REVERT: 2 61 MET cc_start: 0.6953 (OUTLIER) cc_final: 0.6632 (mmm) REVERT: 4 54 LYS cc_start: 0.7447 (mmtt) cc_final: 0.7127 (ptmt) REVERT: 4 75 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8324 (tt) REVERT: 4 134 ILE cc_start: 0.7996 (mm) cc_final: 0.7744 (mt) REVERT: 5 131 MET cc_start: 0.7100 (ttp) cc_final: 0.6784 (ttp) REVERT: 6 56 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8431 (tp) REVERT: 8 131 MET cc_start: 0.6812 (tmm) cc_final: 0.6568 (ttp) REVERT: 9 9 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6723 (tp30) REVERT: C 194 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8460 (pt) REVERT: C 235 ASP cc_start: 0.8029 (t0) cc_final: 0.7771 (t0) REVERT: C 268 ASN cc_start: 0.8766 (OUTLIER) cc_final: 0.8396 (p0) REVERT: C 419 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7546 (p0) REVERT: C 486 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7995 (tm-30) REVERT: C 513 LYS cc_start: 0.8232 (ttmt) cc_final: 0.7283 (mmtp) REVERT: C 540 MET cc_start: 0.8035 (mtp) cc_final: 0.7646 (mtm) REVERT: A 57 LEU cc_start: 0.4749 (OUTLIER) cc_final: 0.4299 (mp) REVERT: A 81 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8358 (ptt180) REVERT: A 201 GLU cc_start: 0.7039 (tt0) cc_final: 0.6465 (tt0) REVERT: A 485 GLU cc_start: 0.7793 (tp30) cc_final: 0.7566 (tp30) REVERT: A 503 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6620 (mm-30) REVERT: A 506 LYS cc_start: 0.7817 (mttt) cc_final: 0.7499 (mtpt) REVERT: A 525 TYR cc_start: 0.7543 (OUTLIER) cc_final: 0.7103 (p90) REVERT: B 60 ASP cc_start: 0.7790 (m-30) cc_final: 0.7502 (m-30) REVERT: B 172 ASN cc_start: 0.9145 (OUTLIER) cc_final: 0.8856 (m-40) REVERT: B 284 MET cc_start: 0.8304 (mmm) cc_final: 0.8050 (mmp) REVERT: B 360 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6669 (tt0) REVERT: B 459 ARG cc_start: 0.7848 (mmp80) cc_final: 0.7619 (mmp80) REVERT: B 540 MET cc_start: 0.8809 (mtp) cc_final: 0.8354 (mtp) REVERT: F 224 GLU cc_start: 0.2762 (OUTLIER) cc_final: 0.2028 (mm-30) REVERT: F 249 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7473 (mt-10) REVERT: F 250 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8187 (pp20) REVERT: F 340 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.7820 (mtm110) REVERT: F 402 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.8566 (ttt) REVERT: F 435 MET cc_start: 0.4770 (OUTLIER) cc_final: 0.4251 (tpp) REVERT: F 487 PHE cc_start: 0.5266 (OUTLIER) cc_final: 0.4886 (m-80) REVERT: D 161 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.7513 (tt0) REVERT: D 310 VAL cc_start: 0.8808 (t) cc_final: 0.8569 (t) REVERT: D 433 GLN cc_start: 0.7850 (mm-40) cc_final: 0.7448 (tp-100) REVERT: E 435 MET cc_start: 0.5095 (mmm) cc_final: 0.4327 (mtt) REVERT: E 479 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8719 (mt) REVERT: X 10 MET cc_start: 0.6322 (mtp) cc_final: 0.5913 (ttt) REVERT: X 126 TYR cc_start: 0.8556 (m-10) cc_final: 0.8309 (m-10) REVERT: X 234 MET cc_start: 0.8116 (ttp) cc_final: 0.7638 (tpp) REVERT: X 236 LYS cc_start: 0.6852 (mmtp) cc_final: 0.6477 (mttm) REVERT: Y 93 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.7260 (ttm170) REVERT: G 67 PHE cc_start: 0.8542 (t80) cc_final: 0.8310 (t80) REVERT: N 29 ASN cc_start: 0.8252 (t0) cc_final: 0.7417 (t0) REVERT: N 50 ASP cc_start: 0.8087 (t0) cc_final: 0.7813 (t0) REVERT: N 81 HIS cc_start: 0.6929 (OUTLIER) cc_final: 0.5927 (t70) outliers start: 394 outliers final: 267 residues processed: 1317 average time/residue: 0.6466 time to fit residues: 1463.5108 Evaluate side-chains 1246 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 302 poor density : 944 time to evaluate : 6.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 47 PHE Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 96 ASP Chi-restraints excluded: chain R residue 100 ASN Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 250 THR Chi-restraints excluded: chain R residue 312 ILE Chi-restraints excluded: chain R residue 334 GLN Chi-restraints excluded: chain R residue 363 THR Chi-restraints excluded: chain R residue 396 ILE Chi-restraints excluded: chain R residue 397 ILE Chi-restraints excluded: chain R residue 437 ASN Chi-restraints excluded: chain R residue 458 MET Chi-restraints excluded: chain R residue 471 SER Chi-restraints excluded: chain R residue 549 LEU Chi-restraints excluded: chain R residue 556 LEU Chi-restraints excluded: chain R residue 572 PHE Chi-restraints excluded: chain R residue 607 SER Chi-restraints excluded: chain R residue 613 ILE Chi-restraints excluded: chain R residue 644 LEU Chi-restraints excluded: chain R residue 726 GLU Chi-restraints excluded: chain R residue 830 ILE Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 56 TYR Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 104 LYS Chi-restraints excluded: chain J residue 132 MET Chi-restraints excluded: chain J residue 145 LYS Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 193 SER Chi-restraints excluded: chain J residue 201 ASP Chi-restraints excluded: chain J residue 202 LEU Chi-restraints excluded: chain M residue 107 ARG Chi-restraints excluded: chain M residue 110 ILE Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 54 GLU Chi-restraints excluded: chain L residue 80 LYS Chi-restraints excluded: chain L residue 85 GLN Chi-restraints excluded: chain H residue 14 HIS Chi-restraints excluded: chain H residue 71 GLN Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 198 SER Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain H residue 207 MET Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 87 TYR Chi-restraints excluded: chain K residue 102 PHE Chi-restraints excluded: chain K residue 109 GLU Chi-restraints excluded: chain K residue 112 GLU Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 36 VAL Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 70 ASN Chi-restraints excluded: chain T residue 79 LEU Chi-restraints excluded: chain T residue 116 LEU Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain U residue 258 VAL Chi-restraints excluded: chain U residue 323 PHE Chi-restraints excluded: chain U residue 340 PHE Chi-restraints excluded: chain U residue 347 VAL Chi-restraints excluded: chain U residue 362 THR Chi-restraints excluded: chain U residue 385 VAL Chi-restraints excluded: chain U residue 397 LEU Chi-restraints excluded: chain U residue 407 VAL Chi-restraints excluded: chain U residue 447 ILE Chi-restraints excluded: chain V residue 314 MET Chi-restraints excluded: chain V residue 331 MET Chi-restraints excluded: chain V residue 338 ILE Chi-restraints excluded: chain 0 residue 2 THR Chi-restraints excluded: chain 0 residue 26 TYR Chi-restraints excluded: chain 0 residue 45 SER Chi-restraints excluded: chain 0 residue 52 LEU Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 0 residue 69 ILE Chi-restraints excluded: chain 0 residue 149 LEU Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 1 residue 67 ILE Chi-restraints excluded: chain 1 residue 85 SER Chi-restraints excluded: chain 1 residue 110 ILE Chi-restraints excluded: chain 1 residue 113 VAL Chi-restraints excluded: chain 1 residue 115 ASP Chi-restraints excluded: chain 1 residue 121 THR Chi-restraints excluded: chain 1 residue 140 VAL Chi-restraints excluded: chain 2 residue 28 LEU Chi-restraints excluded: chain 2 residue 57 ILE Chi-restraints excluded: chain 2 residue 61 MET Chi-restraints excluded: chain 2 residue 67 ILE Chi-restraints excluded: chain 2 residue 118 VAL Chi-restraints excluded: chain 2 residue 129 VAL Chi-restraints excluded: chain 3 residue 56 ILE Chi-restraints excluded: chain 3 residue 140 VAL Chi-restraints excluded: chain 4 residue 55 SER Chi-restraints excluded: chain 4 residue 67 ILE Chi-restraints excluded: chain 4 residue 75 LEU Chi-restraints excluded: chain 4 residue 80 LEU Chi-restraints excluded: chain 4 residue 99 VAL Chi-restraints excluded: chain 4 residue 113 VAL Chi-restraints excluded: chain 4 residue 129 VAL Chi-restraints excluded: chain 4 residue 133 LEU Chi-restraints excluded: chain 4 residue 140 VAL Chi-restraints excluded: chain 5 residue 24 VAL Chi-restraints excluded: chain 5 residue 28 LEU Chi-restraints excluded: chain 5 residue 93 LEU Chi-restraints excluded: chain 5 residue 115 ASP Chi-restraints excluded: chain 5 residue 118 VAL Chi-restraints excluded: chain 5 residue 133 LEU Chi-restraints excluded: chain 5 residue 140 VAL Chi-restraints excluded: chain 6 residue 39 THR Chi-restraints excluded: chain 6 residue 46 VAL Chi-restraints excluded: chain 6 residue 56 ILE Chi-restraints excluded: chain 6 residue 59 VAL Chi-restraints excluded: chain 6 residue 81 ASN Chi-restraints excluded: chain 6 residue 121 THR Chi-restraints excluded: chain 6 residue 127 LEU Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 59 VAL Chi-restraints excluded: chain 7 residue 60 VAL Chi-restraints excluded: chain 7 residue 93 LEU Chi-restraints excluded: chain 7 residue 112 ILE Chi-restraints excluded: chain 8 residue 28 LEU Chi-restraints excluded: chain 8 residue 45 SER Chi-restraints excluded: chain 8 residue 60 VAL Chi-restraints excluded: chain 8 residue 93 LEU Chi-restraints excluded: chain 8 residue 115 ASP Chi-restraints excluded: chain 8 residue 118 VAL Chi-restraints excluded: chain 8 residue 148 VAL Chi-restraints excluded: chain 9 residue 9 GLU Chi-restraints excluded: chain 9 residue 44 MET Chi-restraints excluded: chain 9 residue 60 VAL Chi-restraints excluded: chain 9 residue 67 ILE Chi-restraints excluded: chain 9 residue 99 VAL Chi-restraints excluded: chain 9 residue 110 ILE Chi-restraints excluded: chain 9 residue 112 ILE Chi-restraints excluded: chain 9 residue 150 LEU Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 52 THR Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 122 ILE Chi-restraints excluded: chain Q residue 132 LEU Chi-restraints excluded: chain Q residue 166 ASP Chi-restraints excluded: chain Q residue 230 THR Chi-restraints excluded: chain Q residue 335 CYS Chi-restraints excluded: chain Q residue 344 ILE Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 466 ASP Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 525 TYR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 573 HIS Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain B residue 592 ASP Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 234 MET Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 340 ARG Chi-restraints excluded: chain F residue 359 ASP Chi-restraints excluded: chain F residue 402 MET Chi-restraints excluded: chain F residue 403 LYS Chi-restraints excluded: chain F residue 410 MET Chi-restraints excluded: chain F residue 435 MET Chi-restraints excluded: chain F residue 482 GLN Chi-restraints excluded: chain F residue 487 PHE Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 161 GLN Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 344 ARG Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 371 TYR Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 270 GLU Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 359 ASP Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 482 GLN Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain Z residue 140 LEU Chi-restraints excluded: chain Z residue 146 THR Chi-restraints excluded: chain Z residue 241 VAL Chi-restraints excluded: chain X residue 17 GLN Chi-restraints excluded: chain X residue 52 VAL Chi-restraints excluded: chain X residue 74 CYS Chi-restraints excluded: chain X residue 89 GLN Chi-restraints excluded: chain X residue 209 GLU Chi-restraints excluded: chain X residue 217 LEU Chi-restraints excluded: chain X residue 267 VAL Chi-restraints excluded: chain Y residue 93 ARG Chi-restraints excluded: chain Y residue 119 VAL Chi-restraints excluded: chain Y residue 136 LEU Chi-restraints excluded: chain Y residue 146 THR Chi-restraints excluded: chain Y residue 156 THR Chi-restraints excluded: chain Y residue 179 PHE Chi-restraints excluded: chain Y residue 204 VAL Chi-restraints excluded: chain Y residue 241 VAL Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain G residue 85 GLN Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 14 GLU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 81 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 817 optimal weight: 9.9990 chunk 622 optimal weight: 0.2980 chunk 429 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 395 optimal weight: 4.9990 chunk 555 optimal weight: 5.9990 chunk 830 optimal weight: 30.0000 chunk 879 optimal weight: 20.0000 chunk 434 optimal weight: 5.9990 chunk 787 optimal weight: 0.2980 chunk 237 optimal weight: 0.7980 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 76 ASN R 106 ASN ** R 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 365 ASN ** R 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 66 GLN ** U 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 330 ASN 0 51 ASN 2 51 GLN ** 7 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 HIS B 65 GLN B 123 ASN F 421 GLN D 161 GLN E 54 ASN E 456 GLN Z 165 GLN Z 222 GLN ** X 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 134 ASN G 85 GLN N 83 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 70970 Z= 0.237 Angle : 0.562 19.400 96108 Z= 0.291 Chirality : 0.041 0.235 11093 Planarity : 0.004 0.046 12396 Dihedral : 7.606 142.032 10366 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.15 % Favored : 94.84 % Rotamer: Outliers : 6.02 % Allowed : 22.30 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.09), residues: 9132 helix: 1.21 (0.07), residues: 5120 sheet: -1.65 (0.18), residues: 762 loop : -2.29 (0.10), residues: 3250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 52 HIS 0.005 0.001 HIS 0 132 PHE 0.019 0.001 PHE A 337 TYR 0.030 0.001 TYR Y 139 ARG 0.009 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18264 Ramachandran restraints generated. 9132 Oldfield, 0 Emsley, 9132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18264 Ramachandran restraints generated. 9132 Oldfield, 0 Emsley, 9132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1418 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 426 poor density : 992 time to evaluate : 6.295 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: R 94 MET cc_start: 0.8441 (ppp) cc_final: 0.7855 (mtt) REVERT: R 214 TYR cc_start: 0.6935 (m-80) cc_final: 0.6560 (m-80) REVERT: R 240 PHE cc_start: 0.4473 (OUTLIER) cc_final: 0.4211 (t80) REVERT: R 257 MET cc_start: 0.6314 (tmm) cc_final: 0.6085 (ppp) REVERT: R 368 ASN cc_start: 0.6710 (OUTLIER) cc_final: 0.6353 (p0) REVERT: R 586 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.7004 (tt) REVERT: J 16 MET cc_start: 0.5946 (tpp) cc_final: 0.5736 (tpt) REVERT: J 56 TYR cc_start: 0.6965 (OUTLIER) cc_final: 0.5484 (m-80) REVERT: J 62 LYS cc_start: 0.8379 (mmtm) cc_final: 0.8042 (mmtp) REVERT: J 132 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.8161 (mpt) REVERT: J 145 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8489 (ttpm) REVERT: M 93 ASP cc_start: 0.7849 (t70) cc_final: 0.7386 (t0) REVERT: M 97 ASP cc_start: 0.8140 (m-30) cc_final: 0.7698 (m-30) REVERT: I 63 GLN cc_start: 0.8211 (mt0) cc_final: 0.7978 (mm-40) REVERT: L 54 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7150 (mp0) REVERT: L 81 MET cc_start: 0.8565 (mtm) cc_final: 0.7670 (mtt) REVERT: L 85 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7452 (mp10) REVERT: H 38 PHE cc_start: 0.8426 (t80) cc_final: 0.8178 (t80) REVERT: H 54 MET cc_start: 0.8129 (tmm) cc_final: 0.7857 (tmm) REVERT: H 103 SER cc_start: 0.9122 (t) cc_final: 0.8494 (p) REVERT: H 206 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8493 (mt0) REVERT: K 102 PHE cc_start: 0.7935 (OUTLIER) cc_final: 0.7185 (t80) REVERT: K 109 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7082 (pt0) REVERT: T 65 LEU cc_start: 0.8591 (mm) cc_final: 0.8016 (mt) REVERT: T 114 LEU cc_start: 0.8196 (mt) cc_final: 0.7900 (mm) REVERT: U 373 TYR cc_start: 0.7059 (m-80) cc_final: 0.6824 (m-10) REVERT: U 397 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8075 (mt) REVERT: 0 26 TYR cc_start: 0.8225 (OUTLIER) cc_final: 0.6553 (t80) REVERT: 2 61 MET cc_start: 0.7003 (OUTLIER) cc_final: 0.6666 (mmm) REVERT: 4 54 LYS cc_start: 0.7437 (mmtt) cc_final: 0.7120 (ptmt) REVERT: 4 75 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8365 (tt) REVERT: 4 134 ILE cc_start: 0.8041 (mm) cc_final: 0.7739 (mt) REVERT: 6 56 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8441 (tp) REVERT: 7 51 GLN cc_start: 0.7653 (pp30) cc_final: 0.7099 (pp30) REVERT: 8 131 MET cc_start: 0.6822 (tmm) cc_final: 0.6560 (ttp) REVERT: Q 181 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8585 (mt) REVERT: C 194 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8572 (pt) REVERT: C 268 ASN cc_start: 0.8760 (OUTLIER) cc_final: 0.8383 (p0) REVERT: C 419 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.7609 (p0) REVERT: C 486 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7987 (tm-30) REVERT: C 513 LYS cc_start: 0.8173 (ttmt) cc_final: 0.7304 (mmtp) REVERT: C 540 MET cc_start: 0.8021 (mtp) cc_final: 0.7599 (mtm) REVERT: A 57 LEU cc_start: 0.4844 (OUTLIER) cc_final: 0.4361 (mp) REVERT: A 81 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8438 (ptt180) REVERT: A 201 GLU cc_start: 0.7192 (tt0) cc_final: 0.6405 (tt0) REVERT: A 347 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.7664 (ttt) REVERT: A 485 GLU cc_start: 0.7834 (tp30) cc_final: 0.7613 (tp30) REVERT: A 503 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6662 (mm-30) REVERT: A 506 LYS cc_start: 0.7838 (mttt) cc_final: 0.7519 (mtpt) REVERT: A 525 TYR cc_start: 0.7516 (OUTLIER) cc_final: 0.7103 (p90) REVERT: B 172 ASN cc_start: 0.9188 (OUTLIER) cc_final: 0.8900 (m-40) REVERT: B 284 MET cc_start: 0.8337 (mmm) cc_final: 0.7927 (mmt) REVERT: B 459 ARG cc_start: 0.7816 (mmp80) cc_final: 0.7599 (mmp80) REVERT: B 540 MET cc_start: 0.8820 (mtp) cc_final: 0.8353 (mtp) REVERT: F 97 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8444 (tt0) REVERT: F 224 GLU cc_start: 0.2511 (OUTLIER) cc_final: 0.1922 (mm-30) REVERT: F 249 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7490 (mt-10) REVERT: F 297 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9027 (mt) REVERT: F 340 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8045 (mtm180) REVERT: F 402 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8568 (ttt) REVERT: F 435 MET cc_start: 0.4980 (OUTLIER) cc_final: 0.4435 (tpp) REVERT: D 310 VAL cc_start: 0.8814 (t) cc_final: 0.8578 (t) REVERT: D 344 ARG cc_start: 0.9127 (OUTLIER) cc_final: 0.6648 (mtt180) REVERT: D 433 GLN cc_start: 0.7838 (mm-40) cc_final: 0.7416 (tp-100) REVERT: E 435 MET cc_start: 0.5117 (mmm) cc_final: 0.4466 (mtt) REVERT: E 479 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8725 (mt) REVERT: X 10 MET cc_start: 0.6350 (mtp) cc_final: 0.5862 (ttt) REVERT: X 234 MET cc_start: 0.8151 (ttp) cc_final: 0.7619 (tpp) REVERT: X 236 LYS cc_start: 0.6796 (mmtp) cc_final: 0.6425 (mttm) REVERT: Y 207 GLN cc_start: 0.5652 (OUTLIER) cc_final: 0.5170 (pt0) REVERT: G 67 PHE cc_start: 0.8548 (t80) cc_final: 0.8308 (t80) REVERT: N 29 ASN cc_start: 0.8362 (t0) cc_final: 0.8149 (t0) REVERT: N 81 HIS cc_start: 0.7206 (OUTLIER) cc_final: 0.5620 (t70) outliers start: 426 outliers final: 316 residues processed: 1319 average time/residue: 0.6341 time to fit residues: 1442.6713 Evaluate side-chains 1296 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 353 poor density : 943 time to evaluate : 6.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 47 PHE Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 96 ASP Chi-restraints excluded: chain R residue 100 ASN Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 240 PHE Chi-restraints excluded: chain R residue 250 THR Chi-restraints excluded: chain R residue 283 LEU Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 312 ILE Chi-restraints excluded: chain R residue 334 GLN Chi-restraints excluded: chain R residue 363 THR Chi-restraints excluded: chain R residue 368 ASN Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 396 ILE Chi-restraints excluded: chain R residue 397 ILE Chi-restraints excluded: chain R residue 437 ASN Chi-restraints excluded: chain R residue 458 MET Chi-restraints excluded: chain R residue 471 SER Chi-restraints excluded: chain R residue 549 LEU Chi-restraints excluded: chain R residue 556 LEU Chi-restraints excluded: chain R residue 572 PHE Chi-restraints excluded: chain R residue 586 LEU Chi-restraints excluded: chain R residue 607 SER Chi-restraints excluded: chain R residue 613 ILE Chi-restraints excluded: chain R residue 644 LEU Chi-restraints excluded: chain R residue 716 THR Chi-restraints excluded: chain R residue 726 GLU Chi-restraints excluded: chain R residue 729 LEU Chi-restraints excluded: chain R residue 796 LEU Chi-restraints excluded: chain R residue 830 ILE Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 56 TYR Chi-restraints excluded: chain J residue 85 ARG Chi-restraints excluded: chain J residue 104 LYS Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 132 MET Chi-restraints excluded: chain J residue 145 LYS Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 193 SER Chi-restraints excluded: chain J residue 201 ASP Chi-restraints excluded: chain J residue 202 LEU Chi-restraints excluded: chain M residue 107 ARG Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 54 GLU Chi-restraints excluded: chain L residue 80 LYS Chi-restraints excluded: chain L residue 85 GLN Chi-restraints excluded: chain H residue 14 HIS Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 198 SER Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 87 TYR Chi-restraints excluded: chain K residue 102 PHE Chi-restraints excluded: chain K residue 109 GLU Chi-restraints excluded: chain K residue 112 GLU Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 36 VAL Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain T residue 79 LEU Chi-restraints excluded: chain T residue 96 ASN Chi-restraints excluded: chain T residue 116 LEU Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain U residue 258 VAL Chi-restraints excluded: chain U residue 323 PHE Chi-restraints excluded: chain U residue 334 VAL Chi-restraints excluded: chain U residue 340 PHE Chi-restraints excluded: chain U residue 341 THR Chi-restraints excluded: chain U residue 347 VAL Chi-restraints excluded: chain U residue 362 THR Chi-restraints excluded: chain U residue 385 VAL Chi-restraints excluded: chain U residue 396 MET Chi-restraints excluded: chain U residue 397 LEU Chi-restraints excluded: chain U residue 407 VAL Chi-restraints excluded: chain U residue 430 LEU Chi-restraints excluded: chain U residue 447 ILE Chi-restraints excluded: chain V residue 314 MET Chi-restraints excluded: chain V residue 315 ILE Chi-restraints excluded: chain V residue 331 MET Chi-restraints excluded: chain V residue 338 ILE Chi-restraints excluded: chain 0 residue 2 THR Chi-restraints excluded: chain 0 residue 26 TYR Chi-restraints excluded: chain 0 residue 45 SER Chi-restraints excluded: chain 0 residue 51 ASN Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 0 residue 70 TYR Chi-restraints excluded: chain 0 residue 72 THR Chi-restraints excluded: chain 0 residue 144 VAL Chi-restraints excluded: chain 0 residue 149 LEU Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 0 residue 191 VAL Chi-restraints excluded: chain 1 residue 24 VAL Chi-restraints excluded: chain 1 residue 67 ILE Chi-restraints excluded: chain 1 residue 85 SER Chi-restraints excluded: chain 1 residue 113 VAL Chi-restraints excluded: chain 1 residue 115 ASP Chi-restraints excluded: chain 1 residue 121 THR Chi-restraints excluded: chain 1 residue 132 ILE Chi-restraints excluded: chain 1 residue 140 VAL Chi-restraints excluded: chain 2 residue 28 LEU Chi-restraints excluded: chain 2 residue 44 MET Chi-restraints excluded: chain 2 residue 57 ILE Chi-restraints excluded: chain 2 residue 61 MET Chi-restraints excluded: chain 2 residue 67 ILE Chi-restraints excluded: chain 2 residue 102 SER Chi-restraints excluded: chain 2 residue 118 VAL Chi-restraints excluded: chain 2 residue 129 VAL Chi-restraints excluded: chain 3 residue 9 GLU Chi-restraints excluded: chain 3 residue 44 MET Chi-restraints excluded: chain 3 residue 56 ILE Chi-restraints excluded: chain 3 residue 110 ILE Chi-restraints excluded: chain 3 residue 132 ILE Chi-restraints excluded: chain 3 residue 140 VAL Chi-restraints excluded: chain 4 residue 67 ILE Chi-restraints excluded: chain 4 residue 75 LEU Chi-restraints excluded: chain 4 residue 80 LEU Chi-restraints excluded: chain 4 residue 97 LEU Chi-restraints excluded: chain 4 residue 118 VAL Chi-restraints excluded: chain 4 residue 129 VAL Chi-restraints excluded: chain 4 residue 133 LEU Chi-restraints excluded: chain 4 residue 140 VAL Chi-restraints excluded: chain 5 residue 24 VAL Chi-restraints excluded: chain 5 residue 28 LEU Chi-restraints excluded: chain 5 residue 93 LEU Chi-restraints excluded: chain 5 residue 115 ASP Chi-restraints excluded: chain 5 residue 118 VAL Chi-restraints excluded: chain 5 residue 129 VAL Chi-restraints excluded: chain 5 residue 133 LEU Chi-restraints excluded: chain 5 residue 140 VAL Chi-restraints excluded: chain 5 residue 143 LEU Chi-restraints excluded: chain 6 residue 39 THR Chi-restraints excluded: chain 6 residue 46 VAL Chi-restraints excluded: chain 6 residue 56 ILE Chi-restraints excluded: chain 6 residue 59 VAL Chi-restraints excluded: chain 6 residue 81 ASN Chi-restraints excluded: chain 6 residue 121 THR Chi-restraints excluded: chain 6 residue 127 LEU Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 59 VAL Chi-restraints excluded: chain 7 residue 60 VAL Chi-restraints excluded: chain 7 residue 67 ILE Chi-restraints excluded: chain 7 residue 93 LEU Chi-restraints excluded: chain 7 residue 112 ILE Chi-restraints excluded: chain 7 residue 148 VAL Chi-restraints excluded: chain 8 residue 28 LEU Chi-restraints excluded: chain 8 residue 60 VAL Chi-restraints excluded: chain 8 residue 93 LEU Chi-restraints excluded: chain 8 residue 115 ASP Chi-restraints excluded: chain 8 residue 118 VAL Chi-restraints excluded: chain 8 residue 123 GLN Chi-restraints excluded: chain 8 residue 133 LEU Chi-restraints excluded: chain 9 residue 9 GLU Chi-restraints excluded: chain 9 residue 44 MET Chi-restraints excluded: chain 9 residue 60 VAL Chi-restraints excluded: chain 9 residue 67 ILE Chi-restraints excluded: chain 9 residue 99 VAL Chi-restraints excluded: chain 9 residue 110 ILE Chi-restraints excluded: chain 9 residue 112 ILE Chi-restraints excluded: chain 9 residue 123 GLN Chi-restraints excluded: chain 9 residue 150 LEU Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 52 THR Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 122 ILE Chi-restraints excluded: chain Q residue 132 LEU Chi-restraints excluded: chain Q residue 166 ASP Chi-restraints excluded: chain Q residue 181 ILE Chi-restraints excluded: chain Q residue 230 THR Chi-restraints excluded: chain Q residue 344 ILE Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 466 ASP Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 516 LYS Chi-restraints excluded: chain A residue 525 TYR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain B residue 592 ASP Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 162 CYS Chi-restraints excluded: chain F residue 188 LYS Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 234 MET Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 340 ARG Chi-restraints excluded: chain F residue 350 GLN Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 359 ASP Chi-restraints excluded: chain F residue 402 MET Chi-restraints excluded: chain F residue 403 LYS Chi-restraints excluded: chain F residue 435 MET Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 482 GLN Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 161 GLN Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 344 ARG Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 371 TYR Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 359 ASP Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 482 GLN Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain Z residue 140 LEU Chi-restraints excluded: chain Z residue 146 THR Chi-restraints excluded: chain Z residue 241 VAL Chi-restraints excluded: chain X residue 17 GLN Chi-restraints excluded: chain X residue 35 THR Chi-restraints excluded: chain X residue 74 CYS Chi-restraints excluded: chain X residue 89 GLN Chi-restraints excluded: chain X residue 106 ASP Chi-restraints excluded: chain X residue 209 GLU Chi-restraints excluded: chain X residue 217 LEU Chi-restraints excluded: chain X residue 221 ASP Chi-restraints excluded: chain X residue 267 VAL Chi-restraints excluded: chain Y residue 51 ASP Chi-restraints excluded: chain Y residue 95 VAL Chi-restraints excluded: chain Y residue 119 VAL Chi-restraints excluded: chain Y residue 136 LEU Chi-restraints excluded: chain Y residue 146 THR Chi-restraints excluded: chain Y residue 156 THR Chi-restraints excluded: chain Y residue 179 PHE Chi-restraints excluded: chain Y residue 204 VAL Chi-restraints excluded: chain Y residue 207 GLN Chi-restraints excluded: chain Y residue 241 VAL Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain G residue 85 GLN Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 14 GLU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 51 THR Chi-restraints excluded: chain N residue 81 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 732 optimal weight: 8.9990 chunk 499 optimal weight: 4.9990 chunk 12 optimal weight: 20.0000 chunk 654 optimal weight: 3.9990 chunk 362 optimal weight: 10.0000 chunk 750 optimal weight: 4.9990 chunk 608 optimal weight: 5.9990 chunk 1 optimal weight: 50.0000 chunk 449 optimal weight: 7.9990 chunk 789 optimal weight: 10.0000 chunk 221 optimal weight: 30.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 194 ASN ** R 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 365 ASN ** R 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 748 HIS J 66 GLN ** K 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 330 ASN ** 6 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 GLN ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 ASN F 421 GLN F 456 GLN D 161 GLN E 54 ASN ** X 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 70970 Z= 0.452 Angle : 0.659 20.701 96108 Z= 0.343 Chirality : 0.045 0.264 11093 Planarity : 0.005 0.048 12396 Dihedral : 7.776 143.841 10347 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.63 % Favored : 93.36 % Rotamer: Outliers : 7.01 % Allowed : 22.42 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.09), residues: 9132 helix: 0.99 (0.07), residues: 5170 sheet: -1.51 (0.18), residues: 714 loop : -2.27 (0.10), residues: 3248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP S 52 HIS 0.005 0.001 HIS 0 132 PHE 0.024 0.002 PHE R 578 TYR 0.031 0.002 TYR Y 139 ARG 0.010 0.001 ARG 3 119 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18264 Ramachandran restraints generated. 9132 Oldfield, 0 Emsley, 9132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18264 Ramachandran restraints generated. 9132 Oldfield, 0 Emsley, 9132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1434 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 496 poor density : 938 time to evaluate : 6.488 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: R 94 MET cc_start: 0.8459 (ppp) cc_final: 0.7829 (mtt) REVERT: R 214 TYR cc_start: 0.7062 (m-80) cc_final: 0.6603 (m-80) REVERT: R 257 MET cc_start: 0.6413 (tmm) cc_final: 0.6169 (ppp) REVERT: R 586 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7159 (tt) REVERT: J 56 TYR cc_start: 0.7020 (OUTLIER) cc_final: 0.5383 (m-80) REVERT: J 132 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8193 (mpt) REVERT: J 145 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8566 (ttpm) REVERT: J 225 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8526 (mt) REVERT: M 93 ASP cc_start: 0.7824 (t70) cc_final: 0.7369 (t0) REVERT: M 97 ASP cc_start: 0.8106 (m-30) cc_final: 0.7626 (m-30) REVERT: I 38 PHE cc_start: 0.5332 (OUTLIER) cc_final: 0.4490 (t80) REVERT: I 63 GLN cc_start: 0.8281 (mt0) cc_final: 0.8020 (mm-40) REVERT: L 54 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7190 (mp0) REVERT: L 81 MET cc_start: 0.8556 (mtm) cc_final: 0.7642 (mtt) REVERT: L 85 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7442 (mp10) REVERT: H 38 PHE cc_start: 0.8446 (t80) cc_final: 0.8146 (t80) REVERT: H 103 SER cc_start: 0.9184 (t) cc_final: 0.8551 (p) REVERT: H 206 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8511 (mt0) REVERT: H 212 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8092 (ttt-90) REVERT: K 109 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7129 (pt0) REVERT: T 65 LEU cc_start: 0.8666 (mm) cc_final: 0.8117 (mt) REVERT: T 114 LEU cc_start: 0.8221 (mt) cc_final: 0.7931 (mm) REVERT: U 373 TYR cc_start: 0.7128 (m-80) cc_final: 0.6606 (m-10) REVERT: U 397 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8344 (mt) REVERT: U 428 MET cc_start: 0.8660 (mtm) cc_final: 0.8444 (mtm) REVERT: 0 26 TYR cc_start: 0.8254 (OUTLIER) cc_final: 0.6492 (t80) REVERT: 0 52 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8540 (tt) REVERT: 4 54 LYS cc_start: 0.7480 (mmtt) cc_final: 0.7136 (pttt) REVERT: 4 104 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8594 (tp) REVERT: 4 134 ILE cc_start: 0.8058 (mm) cc_final: 0.7755 (mt) REVERT: 6 56 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8549 (tp) REVERT: 8 17 MET cc_start: 0.7344 (mmm) cc_final: 0.7072 (mmm) REVERT: Q 181 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8622 (mt) REVERT: C 194 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8666 (pt) REVERT: C 268 ASN cc_start: 0.8765 (OUTLIER) cc_final: 0.8376 (p0) REVERT: C 486 GLU cc_start: 0.8317 (tm-30) cc_final: 0.8100 (tm-30) REVERT: C 513 LYS cc_start: 0.8288 (ttmt) cc_final: 0.7375 (mmtm) REVERT: C 540 MET cc_start: 0.8096 (mtp) cc_final: 0.7689 (mtm) REVERT: A 57 LEU cc_start: 0.4920 (OUTLIER) cc_final: 0.4293 (mp) REVERT: A 201 GLU cc_start: 0.7450 (tt0) cc_final: 0.6811 (tt0) REVERT: A 347 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.7733 (ttt) REVERT: A 485 GLU cc_start: 0.7903 (tp30) cc_final: 0.7677 (tp30) REVERT: A 503 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6920 (mm-30) REVERT: A 506 LYS cc_start: 0.7934 (mttt) cc_final: 0.7602 (mtpt) REVERT: A 525 TYR cc_start: 0.7589 (OUTLIER) cc_final: 0.7165 (p90) REVERT: B 65 GLN cc_start: 0.8318 (mt0) cc_final: 0.7812 (mt0) REVERT: B 459 ARG cc_start: 0.7887 (mmp80) cc_final: 0.7672 (mmp80) REVERT: B 540 MET cc_start: 0.8878 (mtp) cc_final: 0.8545 (mtp) REVERT: F 97 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8519 (tt0) REVERT: F 224 GLU cc_start: 0.2724 (OUTLIER) cc_final: 0.1944 (mm-30) REVERT: F 249 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7534 (mt-10) REVERT: F 250 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8236 (pp20) REVERT: F 297 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9039 (mt) REVERT: F 402 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.8560 (ttt) REVERT: F 435 MET cc_start: 0.5376 (OUTLIER) cc_final: 0.4767 (tpp) REVERT: F 487 PHE cc_start: 0.5649 (OUTLIER) cc_final: 0.4499 (m-80) REVERT: D 310 VAL cc_start: 0.8802 (t) cc_final: 0.8583 (t) REVERT: D 344 ARG cc_start: 0.9171 (OUTLIER) cc_final: 0.6714 (mtt180) REVERT: D 433 GLN cc_start: 0.7958 (mm-40) cc_final: 0.7479 (tp-100) REVERT: E 294 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8949 (tt) REVERT: E 435 MET cc_start: 0.5485 (mmm) cc_final: 0.5074 (mtt) REVERT: E 479 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8791 (mt) REVERT: X 10 MET cc_start: 0.6442 (mtp) cc_final: 0.5815 (ttt) REVERT: X 126 TYR cc_start: 0.8605 (OUTLIER) cc_final: 0.8362 (m-10) REVERT: X 234 MET cc_start: 0.8146 (ttp) cc_final: 0.7528 (tpp) REVERT: X 236 LYS cc_start: 0.6797 (mmtp) cc_final: 0.6424 (mttm) REVERT: Y 207 GLN cc_start: 0.5615 (OUTLIER) cc_final: 0.5317 (pt0) REVERT: G 67 PHE cc_start: 0.8612 (t80) cc_final: 0.8376 (t80) REVERT: N 37 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8351 (mt) REVERT: N 81 HIS cc_start: 0.7059 (OUTLIER) cc_final: 0.5498 (t70) outliers start: 496 outliers final: 378 residues processed: 1328 average time/residue: 0.6346 time to fit residues: 1445.8683 Evaluate side-chains 1329 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 416 poor density : 913 time to evaluate : 6.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 47 PHE Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 96 ASP Chi-restraints excluded: chain R residue 100 ASN Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 250 THR Chi-restraints excluded: chain R residue 283 LEU Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 308 ASN Chi-restraints excluded: chain R residue 312 ILE Chi-restraints excluded: chain R residue 334 GLN Chi-restraints excluded: chain R residue 360 THR Chi-restraints excluded: chain R residue 363 THR Chi-restraints excluded: chain R residue 368 ASN Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 396 ILE Chi-restraints excluded: chain R residue 437 ASN Chi-restraints excluded: chain R residue 458 MET Chi-restraints excluded: chain R residue 471 SER Chi-restraints excluded: chain R residue 549 LEU Chi-restraints excluded: chain R residue 556 LEU Chi-restraints excluded: chain R residue 568 ILE Chi-restraints excluded: chain R residue 572 PHE Chi-restraints excluded: chain R residue 586 LEU Chi-restraints excluded: chain R residue 607 SER Chi-restraints excluded: chain R residue 613 ILE Chi-restraints excluded: chain R residue 644 LEU Chi-restraints excluded: chain R residue 716 THR Chi-restraints excluded: chain R residue 726 GLU Chi-restraints excluded: chain R residue 729 LEU Chi-restraints excluded: chain R residue 830 ILE Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 56 TYR Chi-restraints excluded: chain J residue 104 LYS Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 132 MET Chi-restraints excluded: chain J residue 145 LYS Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 193 SER Chi-restraints excluded: chain J residue 201 ASP Chi-restraints excluded: chain J residue 202 LEU Chi-restraints excluded: chain J residue 225 LEU Chi-restraints excluded: chain M residue 107 ARG Chi-restraints excluded: chain M residue 110 ILE Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain I residue 164 ASP Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 54 GLU Chi-restraints excluded: chain L residue 80 LYS Chi-restraints excluded: chain L residue 85 GLN Chi-restraints excluded: chain L residue 87 TYR Chi-restraints excluded: chain H residue 14 HIS Chi-restraints excluded: chain H residue 71 GLN Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 198 SER Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain H residue 212 ARG Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 87 TYR Chi-restraints excluded: chain K residue 109 GLU Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 112 GLU Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 36 VAL Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 70 ASN Chi-restraints excluded: chain T residue 46 CYS Chi-restraints excluded: chain T residue 79 LEU Chi-restraints excluded: chain T residue 95 GLN Chi-restraints excluded: chain T residue 96 ASN Chi-restraints excluded: chain T residue 116 LEU Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain U residue 258 VAL Chi-restraints excluded: chain U residue 323 PHE Chi-restraints excluded: chain U residue 334 VAL Chi-restraints excluded: chain U residue 340 PHE Chi-restraints excluded: chain U residue 341 THR Chi-restraints excluded: chain U residue 347 VAL Chi-restraints excluded: chain U residue 385 VAL Chi-restraints excluded: chain U residue 396 MET Chi-restraints excluded: chain U residue 397 LEU Chi-restraints excluded: chain U residue 407 VAL Chi-restraints excluded: chain U residue 408 MET Chi-restraints excluded: chain U residue 416 SER Chi-restraints excluded: chain U residue 430 LEU Chi-restraints excluded: chain U residue 447 ILE Chi-restraints excluded: chain V residue 313 ILE Chi-restraints excluded: chain V residue 315 ILE Chi-restraints excluded: chain V residue 331 MET Chi-restraints excluded: chain V residue 338 ILE Chi-restraints excluded: chain 0 residue 2 THR Chi-restraints excluded: chain 0 residue 22 VAL Chi-restraints excluded: chain 0 residue 26 TYR Chi-restraints excluded: chain 0 residue 45 SER Chi-restraints excluded: chain 0 residue 51 ASN Chi-restraints excluded: chain 0 residue 52 LEU Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 0 residue 69 ILE Chi-restraints excluded: chain 0 residue 70 TYR Chi-restraints excluded: chain 0 residue 72 THR Chi-restraints excluded: chain 0 residue 122 ASP Chi-restraints excluded: chain 0 residue 144 VAL Chi-restraints excluded: chain 0 residue 149 LEU Chi-restraints excluded: chain 0 residue 151 CYS Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 0 residue 184 SER Chi-restraints excluded: chain 0 residue 191 VAL Chi-restraints excluded: chain 1 residue 23 MET Chi-restraints excluded: chain 1 residue 24 VAL Chi-restraints excluded: chain 1 residue 39 THR Chi-restraints excluded: chain 1 residue 67 ILE Chi-restraints excluded: chain 1 residue 85 SER Chi-restraints excluded: chain 1 residue 97 LEU Chi-restraints excluded: chain 1 residue 110 ILE Chi-restraints excluded: chain 1 residue 113 VAL Chi-restraints excluded: chain 1 residue 115 ASP Chi-restraints excluded: chain 1 residue 121 THR Chi-restraints excluded: chain 1 residue 127 LEU Chi-restraints excluded: chain 1 residue 132 ILE Chi-restraints excluded: chain 1 residue 140 VAL Chi-restraints excluded: chain 2 residue 24 VAL Chi-restraints excluded: chain 2 residue 44 MET Chi-restraints excluded: chain 2 residue 57 ILE Chi-restraints excluded: chain 2 residue 59 VAL Chi-restraints excluded: chain 2 residue 61 MET Chi-restraints excluded: chain 2 residue 64 ILE Chi-restraints excluded: chain 2 residue 67 ILE Chi-restraints excluded: chain 2 residue 102 SER Chi-restraints excluded: chain 2 residue 118 VAL Chi-restraints excluded: chain 2 residue 129 VAL Chi-restraints excluded: chain 2 residue 140 VAL Chi-restraints excluded: chain 3 residue 44 MET Chi-restraints excluded: chain 3 residue 56 ILE Chi-restraints excluded: chain 3 residue 84 ILE Chi-restraints excluded: chain 3 residue 93 LEU Chi-restraints excluded: chain 3 residue 110 ILE Chi-restraints excluded: chain 3 residue 121 THR Chi-restraints excluded: chain 3 residue 132 ILE Chi-restraints excluded: chain 3 residue 140 VAL Chi-restraints excluded: chain 4 residue 67 ILE Chi-restraints excluded: chain 4 residue 80 LEU Chi-restraints excluded: chain 4 residue 97 LEU Chi-restraints excluded: chain 4 residue 99 VAL Chi-restraints excluded: chain 4 residue 104 LEU Chi-restraints excluded: chain 4 residue 113 VAL Chi-restraints excluded: chain 4 residue 118 VAL Chi-restraints excluded: chain 4 residue 129 VAL Chi-restraints excluded: chain 4 residue 133 LEU Chi-restraints excluded: chain 4 residue 137 PHE Chi-restraints excluded: chain 4 residue 140 VAL Chi-restraints excluded: chain 5 residue 24 VAL Chi-restraints excluded: chain 5 residue 28 LEU Chi-restraints excluded: chain 5 residue 55 SER Chi-restraints excluded: chain 5 residue 93 LEU Chi-restraints excluded: chain 5 residue 115 ASP Chi-restraints excluded: chain 5 residue 118 VAL Chi-restraints excluded: chain 5 residue 121 THR Chi-restraints excluded: chain 5 residue 129 VAL Chi-restraints excluded: chain 5 residue 133 LEU Chi-restraints excluded: chain 5 residue 140 VAL Chi-restraints excluded: chain 5 residue 143 LEU Chi-restraints excluded: chain 6 residue 39 THR Chi-restraints excluded: chain 6 residue 46 VAL Chi-restraints excluded: chain 6 residue 56 ILE Chi-restraints excluded: chain 6 residue 81 ASN Chi-restraints excluded: chain 6 residue 121 THR Chi-restraints excluded: chain 6 residue 127 LEU Chi-restraints excluded: chain 7 residue 37 SER Chi-restraints excluded: chain 7 residue 41 ILE Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 60 VAL Chi-restraints excluded: chain 7 residue 67 ILE Chi-restraints excluded: chain 7 residue 74 VAL Chi-restraints excluded: chain 7 residue 93 LEU Chi-restraints excluded: chain 7 residue 102 SER Chi-restraints excluded: chain 7 residue 112 ILE Chi-restraints excluded: chain 7 residue 148 VAL Chi-restraints excluded: chain 8 residue 28 LEU Chi-restraints excluded: chain 8 residue 37 SER Chi-restraints excluded: chain 8 residue 60 VAL Chi-restraints excluded: chain 8 residue 67 ILE Chi-restraints excluded: chain 8 residue 93 LEU Chi-restraints excluded: chain 8 residue 115 ASP Chi-restraints excluded: chain 8 residue 118 VAL Chi-restraints excluded: chain 8 residue 121 THR Chi-restraints excluded: chain 8 residue 148 VAL Chi-restraints excluded: chain 9 residue 9 GLU Chi-restraints excluded: chain 9 residue 34 THR Chi-restraints excluded: chain 9 residue 44 MET Chi-restraints excluded: chain 9 residue 59 VAL Chi-restraints excluded: chain 9 residue 60 VAL Chi-restraints excluded: chain 9 residue 67 ILE Chi-restraints excluded: chain 9 residue 99 VAL Chi-restraints excluded: chain 9 residue 112 ILE Chi-restraints excluded: chain 9 residue 150 LEU Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 52 THR Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 122 ILE Chi-restraints excluded: chain Q residue 132 LEU Chi-restraints excluded: chain Q residue 155 LEU Chi-restraints excluded: chain Q residue 166 ASP Chi-restraints excluded: chain Q residue 181 ILE Chi-restraints excluded: chain Q residue 200 LEU Chi-restraints excluded: chain Q residue 230 THR Chi-restraints excluded: chain Q residue 335 CYS Chi-restraints excluded: chain Q residue 344 ILE Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 466 ASP Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 516 LYS Chi-restraints excluded: chain A residue 525 TYR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain B residue 592 ASP Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 162 CYS Chi-restraints excluded: chain F residue 188 LYS Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 234 MET Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 340 ARG Chi-restraints excluded: chain F residue 350 GLN Chi-restraints excluded: chain F residue 359 ASP Chi-restraints excluded: chain F residue 402 MET Chi-restraints excluded: chain F residue 403 LYS Chi-restraints excluded: chain F residue 410 MET Chi-restraints excluded: chain F residue 435 MET Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 482 GLN Chi-restraints excluded: chain F residue 487 PHE Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain D residue 39 TYR Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 161 GLN Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 344 ARG Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 371 TYR Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 359 ASP Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 482 GLN Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain E residue 506 ARG Chi-restraints excluded: chain Z residue 35 THR Chi-restraints excluded: chain Z residue 146 THR Chi-restraints excluded: chain Z residue 228 THR Chi-restraints excluded: chain Z residue 241 VAL Chi-restraints excluded: chain X residue 17 GLN Chi-restraints excluded: chain X residue 35 THR Chi-restraints excluded: chain X residue 45 ILE Chi-restraints excluded: chain X residue 74 CYS Chi-restraints excluded: chain X residue 89 GLN Chi-restraints excluded: chain X residue 106 ASP Chi-restraints excluded: chain X residue 119 VAL Chi-restraints excluded: chain X residue 126 TYR Chi-restraints excluded: chain X residue 199 LEU Chi-restraints excluded: chain X residue 209 GLU Chi-restraints excluded: chain X residue 217 LEU Chi-restraints excluded: chain X residue 221 ASP Chi-restraints excluded: chain X residue 256 THR Chi-restraints excluded: chain X residue 264 ASP Chi-restraints excluded: chain X residue 267 VAL Chi-restraints excluded: chain Y residue 22 VAL Chi-restraints excluded: chain Y residue 51 ASP Chi-restraints excluded: chain Y residue 95 VAL Chi-restraints excluded: chain Y residue 119 VAL Chi-restraints excluded: chain Y residue 136 LEU Chi-restraints excluded: chain Y residue 146 THR Chi-restraints excluded: chain Y residue 156 THR Chi-restraints excluded: chain Y residue 179 PHE Chi-restraints excluded: chain Y residue 204 VAL Chi-restraints excluded: chain Y residue 207 GLN Chi-restraints excluded: chain Y residue 241 VAL Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain G residue 188 ILE Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 14 GLU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 51 THR Chi-restraints excluded: chain N residue 81 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 295 optimal weight: 0.8980 chunk 792 optimal weight: 8.9990 chunk 173 optimal weight: 30.0000 chunk 516 optimal weight: 0.9990 chunk 217 optimal weight: 30.0000 chunk 880 optimal weight: 5.9990 chunk 730 optimal weight: 0.7980 chunk 407 optimal weight: 3.9990 chunk 73 optimal weight: 20.0000 chunk 291 optimal weight: 1.9990 chunk 462 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 194 ASN ** R 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 365 ASN ** R 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 66 GLN ** K 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 51 ASN 0 132 HIS ** 6 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN B 123 ASN F 421 GLN D 161 GLN E 54 ASN ** Z 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 70970 Z= 0.194 Angle : 0.559 20.836 96108 Z= 0.288 Chirality : 0.041 0.267 11093 Planarity : 0.004 0.046 12396 Dihedral : 7.355 141.286 10339 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.89 % Favored : 95.09 % Rotamer: Outliers : 5.77 % Allowed : 24.18 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.09), residues: 9132 helix: 1.32 (0.07), residues: 5138 sheet: -1.43 (0.19), residues: 705 loop : -2.06 (0.10), residues: 3289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP S 52 HIS 0.005 0.001 HIS A 573 PHE 0.018 0.001 PHE R 419 TYR 0.031 0.001 TYR Y 139 ARG 0.009 0.000 ARG N 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18264 Ramachandran restraints generated. 9132 Oldfield, 0 Emsley, 9132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18264 Ramachandran restraints generated. 9132 Oldfield, 0 Emsley, 9132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1422 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 408 poor density : 1014 time to evaluate : 6.596 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: R 94 MET cc_start: 0.8409 (ppp) cc_final: 0.7888 (mtt) REVERT: R 214 TYR cc_start: 0.6855 (m-80) cc_final: 0.6464 (m-80) REVERT: R 257 MET cc_start: 0.6368 (tmm) cc_final: 0.6126 (ppp) REVERT: R 368 ASN cc_start: 0.6703 (OUTLIER) cc_final: 0.6352 (p0) REVERT: R 586 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.7050 (tt) REVERT: J 56 TYR cc_start: 0.7020 (OUTLIER) cc_final: 0.5396 (m-80) REVERT: J 62 LYS cc_start: 0.8250 (mmtp) cc_final: 0.8007 (ptpp) REVERT: J 132 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8175 (mpt) REVERT: M 87 TYR cc_start: 0.7910 (OUTLIER) cc_final: 0.7030 (m-10) REVERT: M 93 ASP cc_start: 0.7820 (t70) cc_final: 0.7313 (t0) REVERT: M 97 ASP cc_start: 0.8083 (m-30) cc_final: 0.7592 (m-30) REVERT: M 116 ILE cc_start: 0.7667 (mm) cc_final: 0.7278 (mm) REVERT: I 38 PHE cc_start: 0.5381 (OUTLIER) cc_final: 0.4718 (t80) REVERT: I 63 GLN cc_start: 0.8175 (mt0) cc_final: 0.7936 (mm-40) REVERT: L 54 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: L 81 MET cc_start: 0.8555 (mtm) cc_final: 0.7650 (mtt) REVERT: L 85 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7423 (mp10) REVERT: H 38 PHE cc_start: 0.8432 (t80) cc_final: 0.8167 (t80) REVERT: H 103 SER cc_start: 0.9140 (t) cc_final: 0.8470 (p) REVERT: H 206 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8421 (mt0) REVERT: K 43 GLU cc_start: 0.8160 (tp30) cc_final: 0.7941 (pp20) REVERT: K 102 PHE cc_start: 0.7922 (OUTLIER) cc_final: 0.7148 (t80) REVERT: K 109 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7073 (pt0) REVERT: T 65 LEU cc_start: 0.8626 (mm) cc_final: 0.8072 (mt) REVERT: T 114 LEU cc_start: 0.8199 (mt) cc_final: 0.7906 (mm) REVERT: U 373 TYR cc_start: 0.6995 (m-80) cc_final: 0.6462 (m-10) REVERT: U 397 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8195 (mt) REVERT: 0 26 TYR cc_start: 0.8209 (OUTLIER) cc_final: 0.6625 (t80) REVERT: 0 116 GLU cc_start: 0.6901 (mp0) cc_final: 0.6497 (mp0) REVERT: 2 61 MET cc_start: 0.7043 (OUTLIER) cc_final: 0.6701 (mmm) REVERT: 4 54 LYS cc_start: 0.7461 (mmtt) cc_final: 0.7115 (pttt) REVERT: 4 104 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8549 (tp) REVERT: 4 134 ILE cc_start: 0.8019 (mm) cc_final: 0.7707 (mt) REVERT: 5 17 MET cc_start: 0.8097 (mmm) cc_final: 0.7863 (mmt) REVERT: 6 56 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8465 (tp) REVERT: 6 67 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8684 (mp) REVERT: Q 181 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8467 (mt) REVERT: C 235 ASP cc_start: 0.7980 (t0) cc_final: 0.7725 (t0) REVERT: C 268 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8322 (p0) REVERT: C 513 LYS cc_start: 0.8198 (ttmt) cc_final: 0.7315 (mmtp) REVERT: C 540 MET cc_start: 0.7992 (mtp) cc_final: 0.7576 (mtm) REVERT: A 34 MET cc_start: 0.2604 (mmm) cc_final: 0.2396 (mmm) REVERT: A 201 GLU cc_start: 0.7304 (tt0) cc_final: 0.6418 (tt0) REVERT: A 347 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7648 (ttt) REVERT: A 485 GLU cc_start: 0.7892 (tp30) cc_final: 0.7677 (tp30) REVERT: A 503 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6765 (mm-30) REVERT: A 506 LYS cc_start: 0.7823 (mttt) cc_final: 0.7580 (mtpt) REVERT: A 525 TYR cc_start: 0.7500 (OUTLIER) cc_final: 0.7054 (p90) REVERT: B 58 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7625 (tp30) REVERT: B 172 ASN cc_start: 0.9189 (OUTLIER) cc_final: 0.8925 (m-40) REVERT: B 284 MET cc_start: 0.8313 (mmm) cc_final: 0.7876 (mmt) REVERT: B 360 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6668 (tt0) REVERT: B 540 MET cc_start: 0.8816 (mtp) cc_final: 0.8336 (mtp) REVERT: F 97 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8440 (tt0) REVERT: F 224 GLU cc_start: 0.2561 (OUTLIER) cc_final: 0.1812 (mm-30) REVERT: F 249 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7568 (mt-10) REVERT: F 250 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8179 (pp20) REVERT: F 297 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9012 (mt) REVERT: F 340 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8242 (mtm180) REVERT: F 402 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8587 (ttt) REVERT: F 435 MET cc_start: 0.5202 (OUTLIER) cc_final: 0.4553 (tpp) REVERT: F 487 PHE cc_start: 0.5254 (OUTLIER) cc_final: 0.4351 (m-80) REVERT: D 310 VAL cc_start: 0.8815 (t) cc_final: 0.8580 (t) REVERT: D 344 ARG cc_start: 0.9140 (OUTLIER) cc_final: 0.6623 (mtt180) REVERT: D 433 GLN cc_start: 0.7805 (mm-40) cc_final: 0.7408 (tp-100) REVERT: E 177 ILE cc_start: 0.9178 (pt) cc_final: 0.8949 (pt) REVERT: E 435 MET cc_start: 0.5210 (mmm) cc_final: 0.4884 (mtt) REVERT: E 479 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8717 (mt) REVERT: E 491 MET cc_start: 0.1602 (ptm) cc_final: 0.1295 (mtm) REVERT: X 10 MET cc_start: 0.6377 (mtp) cc_final: 0.5916 (ttt) REVERT: X 126 TYR cc_start: 0.8436 (OUTLIER) cc_final: 0.8087 (m-10) REVERT: X 229 MET cc_start: 0.8412 (tpp) cc_final: 0.8152 (mmm) REVERT: X 234 MET cc_start: 0.8056 (ttp) cc_final: 0.7516 (tpp) REVERT: X 236 LYS cc_start: 0.6731 (mmtp) cc_final: 0.6360 (mttm) REVERT: Y 161 MET cc_start: 0.7002 (ppp) cc_final: 0.6770 (ppp) REVERT: Y 188 MET cc_start: 0.7792 (mmm) cc_final: 0.7236 (mmm) REVERT: G 67 PHE cc_start: 0.8526 (t80) cc_final: 0.8297 (t80) REVERT: N 37 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8353 (mt) REVERT: N 81 HIS cc_start: 0.7018 (OUTLIER) cc_final: 0.6276 (t70) outliers start: 408 outliers final: 305 residues processed: 1322 average time/residue: 0.6395 time to fit residues: 1459.1340 Evaluate side-chains 1300 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 344 poor density : 956 time to evaluate : 6.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 47 PHE Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 96 ASP Chi-restraints excluded: chain R residue 100 ASN Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 194 ASN Chi-restraints excluded: chain R residue 250 THR Chi-restraints excluded: chain R residue 283 LEU Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 312 ILE Chi-restraints excluded: chain R residue 334 GLN Chi-restraints excluded: chain R residue 363 THR Chi-restraints excluded: chain R residue 368 ASN Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 396 ILE Chi-restraints excluded: chain R residue 437 ASN Chi-restraints excluded: chain R residue 471 SER Chi-restraints excluded: chain R residue 549 LEU Chi-restraints excluded: chain R residue 572 PHE Chi-restraints excluded: chain R residue 586 LEU Chi-restraints excluded: chain R residue 609 LEU Chi-restraints excluded: chain R residue 613 ILE Chi-restraints excluded: chain R residue 716 THR Chi-restraints excluded: chain R residue 726 GLU Chi-restraints excluded: chain R residue 729 LEU Chi-restraints excluded: chain R residue 830 ILE Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 56 TYR Chi-restraints excluded: chain J residue 104 LYS Chi-restraints excluded: chain J residue 132 MET Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 177 ILE Chi-restraints excluded: chain J residue 193 SER Chi-restraints excluded: chain J residue 201 ASP Chi-restraints excluded: chain J residue 202 LEU Chi-restraints excluded: chain M residue 87 TYR Chi-restraints excluded: chain M residue 107 ARG Chi-restraints excluded: chain M residue 110 ILE Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 54 GLU Chi-restraints excluded: chain L residue 80 LYS Chi-restraints excluded: chain L residue 85 GLN Chi-restraints excluded: chain L residue 87 TYR Chi-restraints excluded: chain H residue 14 HIS Chi-restraints excluded: chain H residue 71 GLN Chi-restraints excluded: chain H residue 198 SER Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 87 TYR Chi-restraints excluded: chain K residue 102 PHE Chi-restraints excluded: chain K residue 109 GLU Chi-restraints excluded: chain K residue 112 GLU Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain S residue 70 ASN Chi-restraints excluded: chain T residue 79 LEU Chi-restraints excluded: chain T residue 96 ASN Chi-restraints excluded: chain T residue 116 LEU Chi-restraints excluded: chain T residue 123 PHE Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain U residue 258 VAL Chi-restraints excluded: chain U residue 334 VAL Chi-restraints excluded: chain U residue 340 PHE Chi-restraints excluded: chain U residue 341 THR Chi-restraints excluded: chain U residue 347 VAL Chi-restraints excluded: chain U residue 362 THR Chi-restraints excluded: chain U residue 385 VAL Chi-restraints excluded: chain U residue 397 LEU Chi-restraints excluded: chain U residue 407 VAL Chi-restraints excluded: chain U residue 408 MET Chi-restraints excluded: chain U residue 447 ILE Chi-restraints excluded: chain V residue 313 ILE Chi-restraints excluded: chain V residue 314 MET Chi-restraints excluded: chain V residue 315 ILE Chi-restraints excluded: chain V residue 331 MET Chi-restraints excluded: chain V residue 338 ILE Chi-restraints excluded: chain 0 residue 2 THR Chi-restraints excluded: chain 0 residue 26 TYR Chi-restraints excluded: chain 0 residue 28 ILE Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 0 residue 69 ILE Chi-restraints excluded: chain 0 residue 70 TYR Chi-restraints excluded: chain 0 residue 144 VAL Chi-restraints excluded: chain 0 residue 149 LEU Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 1 residue 23 MET Chi-restraints excluded: chain 1 residue 67 ILE Chi-restraints excluded: chain 1 residue 85 SER Chi-restraints excluded: chain 1 residue 110 ILE Chi-restraints excluded: chain 1 residue 113 VAL Chi-restraints excluded: chain 1 residue 115 ASP Chi-restraints excluded: chain 1 residue 121 THR Chi-restraints excluded: chain 1 residue 140 VAL Chi-restraints excluded: chain 2 residue 24 VAL Chi-restraints excluded: chain 2 residue 28 LEU Chi-restraints excluded: chain 2 residue 44 MET Chi-restraints excluded: chain 2 residue 57 ILE Chi-restraints excluded: chain 2 residue 59 VAL Chi-restraints excluded: chain 2 residue 61 MET Chi-restraints excluded: chain 2 residue 64 ILE Chi-restraints excluded: chain 2 residue 102 SER Chi-restraints excluded: chain 2 residue 129 VAL Chi-restraints excluded: chain 3 residue 44 MET Chi-restraints excluded: chain 3 residue 56 ILE Chi-restraints excluded: chain 3 residue 110 ILE Chi-restraints excluded: chain 3 residue 132 ILE Chi-restraints excluded: chain 3 residue 140 VAL Chi-restraints excluded: chain 4 residue 80 LEU Chi-restraints excluded: chain 4 residue 93 LEU Chi-restraints excluded: chain 4 residue 97 LEU Chi-restraints excluded: chain 4 residue 99 VAL Chi-restraints excluded: chain 4 residue 104 LEU Chi-restraints excluded: chain 4 residue 129 VAL Chi-restraints excluded: chain 4 residue 137 PHE Chi-restraints excluded: chain 4 residue 140 VAL Chi-restraints excluded: chain 5 residue 6 SER Chi-restraints excluded: chain 5 residue 24 VAL Chi-restraints excluded: chain 5 residue 93 LEU Chi-restraints excluded: chain 5 residue 115 ASP Chi-restraints excluded: chain 5 residue 118 VAL Chi-restraints excluded: chain 5 residue 129 VAL Chi-restraints excluded: chain 5 residue 133 LEU Chi-restraints excluded: chain 5 residue 140 VAL Chi-restraints excluded: chain 5 residue 143 LEU Chi-restraints excluded: chain 6 residue 46 VAL Chi-restraints excluded: chain 6 residue 56 ILE Chi-restraints excluded: chain 6 residue 59 VAL Chi-restraints excluded: chain 6 residue 67 ILE Chi-restraints excluded: chain 6 residue 81 ASN Chi-restraints excluded: chain 6 residue 121 THR Chi-restraints excluded: chain 6 residue 127 LEU Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 59 VAL Chi-restraints excluded: chain 7 residue 60 VAL Chi-restraints excluded: chain 7 residue 67 ILE Chi-restraints excluded: chain 7 residue 93 LEU Chi-restraints excluded: chain 7 residue 112 ILE Chi-restraints excluded: chain 7 residue 148 VAL Chi-restraints excluded: chain 8 residue 28 LEU Chi-restraints excluded: chain 8 residue 60 VAL Chi-restraints excluded: chain 8 residue 93 LEU Chi-restraints excluded: chain 8 residue 115 ASP Chi-restraints excluded: chain 8 residue 118 VAL Chi-restraints excluded: chain 8 residue 123 GLN Chi-restraints excluded: chain 8 residue 133 LEU Chi-restraints excluded: chain 8 residue 148 VAL Chi-restraints excluded: chain 9 residue 44 MET Chi-restraints excluded: chain 9 residue 59 VAL Chi-restraints excluded: chain 9 residue 60 VAL Chi-restraints excluded: chain 9 residue 67 ILE Chi-restraints excluded: chain 9 residue 99 VAL Chi-restraints excluded: chain 9 residue 110 ILE Chi-restraints excluded: chain 9 residue 112 ILE Chi-restraints excluded: chain 9 residue 150 LEU Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 52 THR Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 122 ILE Chi-restraints excluded: chain Q residue 166 ASP Chi-restraints excluded: chain Q residue 181 ILE Chi-restraints excluded: chain Q residue 230 THR Chi-restraints excluded: chain Q residue 335 CYS Chi-restraints excluded: chain Q residue 344 ILE Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 466 ASP Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 516 LYS Chi-restraints excluded: chain A residue 525 TYR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 592 ASP Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 188 LYS Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 234 MET Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 340 ARG Chi-restraints excluded: chain F residue 350 GLN Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 359 ASP Chi-restraints excluded: chain F residue 402 MET Chi-restraints excluded: chain F residue 403 LYS Chi-restraints excluded: chain F residue 410 MET Chi-restraints excluded: chain F residue 435 MET Chi-restraints excluded: chain F residue 482 GLN Chi-restraints excluded: chain F residue 487 PHE Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 161 GLN Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 344 ARG Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 371 TYR Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 359 ASP Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 506 ARG Chi-restraints excluded: chain Z residue 146 THR Chi-restraints excluded: chain Z residue 228 THR Chi-restraints excluded: chain Z residue 241 VAL Chi-restraints excluded: chain X residue 17 GLN Chi-restraints excluded: chain X residue 74 CYS Chi-restraints excluded: chain X residue 89 GLN Chi-restraints excluded: chain X residue 106 ASP Chi-restraints excluded: chain X residue 126 TYR Chi-restraints excluded: chain X residue 163 ILE Chi-restraints excluded: chain X residue 196 GLN Chi-restraints excluded: chain X residue 199 LEU Chi-restraints excluded: chain X residue 209 GLU Chi-restraints excluded: chain X residue 217 LEU Chi-restraints excluded: chain X residue 221 ASP Chi-restraints excluded: chain X residue 256 THR Chi-restraints excluded: chain X residue 264 ASP Chi-restraints excluded: chain X residue 267 VAL Chi-restraints excluded: chain Y residue 51 ASP Chi-restraints excluded: chain Y residue 95 VAL Chi-restraints excluded: chain Y residue 119 VAL Chi-restraints excluded: chain Y residue 146 THR Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain Y residue 156 THR Chi-restraints excluded: chain Y residue 179 PHE Chi-restraints excluded: chain Y residue 241 VAL Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 85 GLN Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain G residue 172 ILE Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 14 GLU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 51 THR Chi-restraints excluded: chain N residue 81 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 848 optimal weight: 0.9990 chunk 99 optimal weight: 50.0000 chunk 501 optimal weight: 0.5980 chunk 642 optimal weight: 3.9990 chunk 498 optimal weight: 9.9990 chunk 741 optimal weight: 4.9990 chunk 491 optimal weight: 0.8980 chunk 877 optimal weight: 0.0070 chunk 548 optimal weight: 30.0000 chunk 534 optimal weight: 8.9990 chunk 404 optimal weight: 0.6980 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 365 ASN R 614 ASN J 66 GLN L 85 GLN ** H 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN S 61 ASN ** U 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 51 ASN ** 6 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 78 ASN ** 9 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 ASN ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN B 123 ASN F 421 GLN D 161 GLN D 421 GLN ** E 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 165 GLN G 85 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 70970 Z= 0.155 Angle : 0.544 18.586 96108 Z= 0.279 Chirality : 0.040 0.269 11093 Planarity : 0.004 0.045 12396 Dihedral : 6.943 137.951 10324 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.53 % Favored : 95.46 % Rotamer: Outliers : 4.65 % Allowed : 25.46 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % 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: 0.16 (0.09), residues: 9132 helix: 1.55 (0.07), residues: 5124 sheet: -1.13 (0.19), residues: 728 loop : -2.00 (0.10), residues: 3280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP S 52 HIS 0.006 0.000 HIS A 573 PHE 0.028 0.001 PHE R 578 TYR 0.032 0.001 TYR X 112 ARG 0.008 0.000 ARG 3 119 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18264 Ramachandran restraints generated. 9132 Oldfield, 0 Emsley, 9132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18264 Ramachandran restraints generated. 9132 Oldfield, 0 Emsley, 9132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1372 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 329 poor density : 1043 time to evaluate : 6.258 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: R 94 MET cc_start: 0.8404 (ppp) cc_final: 0.7960 (mtt) REVERT: R 214 TYR cc_start: 0.6726 (m-80) cc_final: 0.6356 (m-80) REVERT: R 368 ASN cc_start: 0.6668 (OUTLIER) cc_final: 0.6312 (p0) REVERT: R 586 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.7019 (tt) REVERT: J 15 MET cc_start: 0.4130 (mmp) cc_final: 0.2945 (mtm) REVERT: J 56 TYR cc_start: 0.7007 (OUTLIER) cc_final: 0.5374 (m-80) REVERT: J 57 TYR cc_start: 0.5700 (m-80) cc_final: 0.5428 (m-80) REVERT: J 62 LYS cc_start: 0.8316 (mmtp) cc_final: 0.8089 (ptpp) REVERT: J 132 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8151 (mpt) REVERT: M 87 TYR cc_start: 0.7813 (OUTLIER) cc_final: 0.6998 (m-80) REVERT: M 93 ASP cc_start: 0.7730 (t70) cc_final: 0.7215 (t0) REVERT: M 97 ASP cc_start: 0.8019 (m-30) cc_final: 0.7537 (m-30) REVERT: M 116 ILE cc_start: 0.7406 (OUTLIER) cc_final: 0.6841 (mm) REVERT: I 38 PHE cc_start: 0.5337 (OUTLIER) cc_final: 0.4769 (t80) REVERT: I 57 TYR cc_start: 0.8165 (m-10) cc_final: 0.6773 (m-10) REVERT: I 63 GLN cc_start: 0.8142 (mt0) cc_final: 0.7910 (mm-40) REVERT: L 54 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7282 (mp0) REVERT: L 81 MET cc_start: 0.8549 (mtm) cc_final: 0.7717 (mtt) REVERT: L 85 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7449 (mp-120) REVERT: H 54 MET cc_start: 0.8289 (tmm) cc_final: 0.7697 (tmm) REVERT: H 103 SER cc_start: 0.9034 (t) cc_final: 0.8324 (p) REVERT: K 102 PHE cc_start: 0.7867 (OUTLIER) cc_final: 0.7207 (t80) REVERT: T 65 LEU cc_start: 0.8613 (mm) cc_final: 0.8057 (mt) REVERT: T 106 TYR cc_start: 0.6650 (m-80) cc_final: 0.6443 (m-80) REVERT: T 114 LEU cc_start: 0.8142 (mt) cc_final: 0.7890 (mm) REVERT: U 297 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7716 (tt) REVERT: U 373 TYR cc_start: 0.6863 (m-80) cc_final: 0.6521 (m-10) REVERT: U 397 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8168 (mt) REVERT: V 325 SER cc_start: 0.8104 (t) cc_final: 0.7901 (m) REVERT: 0 26 TYR cc_start: 0.8165 (OUTLIER) cc_final: 0.6873 (t80) REVERT: 0 116 GLU cc_start: 0.6867 (mp0) cc_final: 0.6449 (mp0) REVERT: 2 61 MET cc_start: 0.7040 (OUTLIER) cc_final: 0.6725 (mmm) REVERT: 3 144 TYR cc_start: 0.6994 (m-10) cc_final: 0.6656 (m-80) REVERT: 4 54 LYS cc_start: 0.7311 (mmtt) cc_final: 0.7084 (pttt) REVERT: 4 134 ILE cc_start: 0.7903 (mm) cc_final: 0.7603 (mt) REVERT: 5 17 MET cc_start: 0.8145 (mmm) cc_final: 0.7903 (mmt) REVERT: 6 48 ARG cc_start: 0.7367 (mtt180) cc_final: 0.7106 (mtm-85) REVERT: 6 56 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8357 (tp) REVERT: 6 67 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8497 (mp) REVERT: 8 131 MET cc_start: 0.6821 (tmm) cc_final: 0.6530 (ttp) REVERT: 9 143 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7559 (tp) REVERT: Q 181 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8361 (mt) REVERT: C 235 ASP cc_start: 0.7901 (t0) cc_final: 0.7665 (t0) REVERT: C 268 ASN cc_start: 0.8732 (OUTLIER) cc_final: 0.8281 (p0) REVERT: C 368 MET cc_start: 0.8624 (tpp) cc_final: 0.8417 (tpp) REVERT: C 486 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7925 (tm-30) REVERT: C 513 LYS cc_start: 0.8194 (ttmt) cc_final: 0.7276 (mmtp) REVERT: C 540 MET cc_start: 0.7927 (mtp) cc_final: 0.7505 (mtm) REVERT: C 608 MET cc_start: 0.7981 (ttm) cc_final: 0.7671 (ttp) REVERT: A 201 GLU cc_start: 0.7017 (tt0) cc_final: 0.6040 (tt0) REVERT: A 347 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7326 (tpt) REVERT: A 485 GLU cc_start: 0.7914 (tp30) cc_final: 0.7695 (tp30) REVERT: A 506 LYS cc_start: 0.7756 (mttt) cc_final: 0.7485 (mtpt) REVERT: A 525 TYR cc_start: 0.7432 (OUTLIER) cc_final: 0.7022 (p90) REVERT: B 172 ASN cc_start: 0.9141 (OUTLIER) cc_final: 0.8883 (m-40) REVERT: B 284 MET cc_start: 0.8183 (mmm) cc_final: 0.7955 (mmp) REVERT: B 360 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6663 (tt0) REVERT: B 540 MET cc_start: 0.8798 (mtp) cc_final: 0.8451 (mtp) REVERT: F 88 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7428 (tt0) REVERT: F 97 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8391 (tt0) REVERT: F 224 GLU cc_start: 0.2742 (OUTLIER) cc_final: 0.2126 (mm-30) REVERT: F 249 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7554 (mt-10) REVERT: F 250 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8137 (pp20) REVERT: F 380 ASP cc_start: 0.8289 (t0) cc_final: 0.8032 (t0) REVERT: F 402 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.8600 (ttt) REVERT: F 403 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8505 (pttm) REVERT: F 435 MET cc_start: 0.5256 (OUTLIER) cc_final: 0.4497 (tpp) REVERT: F 456 GLN cc_start: 0.7682 (mp10) cc_final: 0.7420 (mp10) REVERT: F 487 PHE cc_start: 0.5038 (OUTLIER) cc_final: 0.4377 (m-80) REVERT: D 310 VAL cc_start: 0.8802 (t) cc_final: 0.8576 (t) REVERT: D 344 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.6606 (mtt180) REVERT: D 433 GLN cc_start: 0.7707 (mm-40) cc_final: 0.7354 (tp-100) REVERT: E 435 MET cc_start: 0.5068 (mmm) cc_final: 0.4735 (mtt) REVERT: E 479 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8713 (mt) REVERT: E 491 MET cc_start: 0.1405 (ptm) cc_final: 0.1139 (mtm) REVERT: E 497 GLN cc_start: 0.5970 (pm20) cc_final: 0.5639 (pm20) REVERT: Z 229 MET cc_start: 0.7397 (ptp) cc_final: 0.6662 (tpt) REVERT: X 10 MET cc_start: 0.6201 (mtp) cc_final: 0.5933 (ttt) REVERT: X 234 MET cc_start: 0.8021 (ttp) cc_final: 0.7338 (tpp) REVERT: X 236 LYS cc_start: 0.6712 (mmtp) cc_final: 0.6379 (mttm) REVERT: Y 188 MET cc_start: 0.7550 (mmm) cc_final: 0.7271 (mmm) REVERT: G 67 PHE cc_start: 0.8497 (t80) cc_final: 0.8233 (t80) REVERT: N 37 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8184 (mt) REVERT: N 68 GLN cc_start: 0.8663 (tm-30) cc_final: 0.7898 (tt0) REVERT: N 81 HIS cc_start: 0.7172 (OUTLIER) cc_final: 0.6810 (t70) REVERT: N 83 GLN cc_start: 0.7983 (tt0) cc_final: 0.7750 (tt0) outliers start: 329 outliers final: 244 residues processed: 1285 average time/residue: 0.6403 time to fit residues: 1409.8358 Evaluate side-chains 1259 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 280 poor density : 979 time to evaluate : 6.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 47 PHE Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 96 ASP Chi-restraints excluded: chain R residue 100 ASN Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 250 THR Chi-restraints excluded: chain R residue 283 LEU Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 312 ILE Chi-restraints excluded: chain R residue 334 GLN Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain R residue 363 THR Chi-restraints excluded: chain R residue 368 ASN Chi-restraints excluded: chain R residue 396 ILE Chi-restraints excluded: chain R residue 437 ASN Chi-restraints excluded: chain R residue 549 LEU Chi-restraints excluded: chain R residue 572 PHE Chi-restraints excluded: chain R residue 586 LEU Chi-restraints excluded: chain R residue 613 ILE Chi-restraints excluded: chain R residue 644 LEU Chi-restraints excluded: chain R residue 716 THR Chi-restraints excluded: chain R residue 830 ILE Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 56 TYR Chi-restraints excluded: chain J residue 104 LYS Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 132 MET Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 202 LEU Chi-restraints excluded: chain M residue 87 TYR Chi-restraints excluded: chain M residue 107 ARG Chi-restraints excluded: chain M residue 110 ILE Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain I residue 20 GLU Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain L residue 54 GLU Chi-restraints excluded: chain L residue 80 LYS Chi-restraints excluded: chain L residue 85 GLN Chi-restraints excluded: chain H residue 14 HIS Chi-restraints excluded: chain H residue 71 GLN Chi-restraints excluded: chain H residue 198 SER Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 87 TYR Chi-restraints excluded: chain K residue 102 PHE Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 70 ASN Chi-restraints excluded: chain T residue 46 CYS Chi-restraints excluded: chain T residue 79 LEU Chi-restraints excluded: chain T residue 116 LEU Chi-restraints excluded: chain T residue 123 PHE Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain U residue 258 VAL Chi-restraints excluded: chain U residue 297 LEU Chi-restraints excluded: chain U residue 340 PHE Chi-restraints excluded: chain U residue 347 VAL Chi-restraints excluded: chain U residue 362 THR Chi-restraints excluded: chain U residue 385 VAL Chi-restraints excluded: chain U residue 396 MET Chi-restraints excluded: chain U residue 397 LEU Chi-restraints excluded: chain U residue 407 VAL Chi-restraints excluded: chain U residue 408 MET Chi-restraints excluded: chain U residue 447 ILE Chi-restraints excluded: chain V residue 315 ILE Chi-restraints excluded: chain V residue 331 MET Chi-restraints excluded: chain 0 residue 2 THR Chi-restraints excluded: chain 0 residue 26 TYR Chi-restraints excluded: chain 0 residue 51 ASN Chi-restraints excluded: chain 0 residue 69 ILE Chi-restraints excluded: chain 0 residue 70 TYR Chi-restraints excluded: chain 0 residue 144 VAL Chi-restraints excluded: chain 0 residue 149 LEU Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 1 residue 23 MET Chi-restraints excluded: chain 1 residue 67 ILE Chi-restraints excluded: chain 1 residue 85 SER Chi-restraints excluded: chain 1 residue 97 LEU Chi-restraints excluded: chain 1 residue 110 ILE Chi-restraints excluded: chain 1 residue 115 ASP Chi-restraints excluded: chain 1 residue 140 VAL Chi-restraints excluded: chain 2 residue 24 VAL Chi-restraints excluded: chain 2 residue 28 LEU Chi-restraints excluded: chain 2 residue 44 MET Chi-restraints excluded: chain 2 residue 61 MET Chi-restraints excluded: chain 2 residue 64 ILE Chi-restraints excluded: chain 2 residue 129 VAL Chi-restraints excluded: chain 3 residue 56 ILE Chi-restraints excluded: chain 4 residue 80 LEU Chi-restraints excluded: chain 4 residue 93 LEU Chi-restraints excluded: chain 4 residue 97 LEU Chi-restraints excluded: chain 4 residue 129 VAL Chi-restraints excluded: chain 4 residue 133 LEU Chi-restraints excluded: chain 4 residue 137 PHE Chi-restraints excluded: chain 4 residue 140 VAL Chi-restraints excluded: chain 5 residue 24 VAL Chi-restraints excluded: chain 5 residue 93 LEU Chi-restraints excluded: chain 5 residue 112 ILE Chi-restraints excluded: chain 5 residue 115 ASP Chi-restraints excluded: chain 5 residue 129 VAL Chi-restraints excluded: chain 5 residue 133 LEU Chi-restraints excluded: chain 5 residue 140 VAL Chi-restraints excluded: chain 5 residue 143 LEU Chi-restraints excluded: chain 6 residue 46 VAL Chi-restraints excluded: chain 6 residue 47 MET Chi-restraints excluded: chain 6 residue 56 ILE Chi-restraints excluded: chain 6 residue 67 ILE Chi-restraints excluded: chain 6 residue 81 ASN Chi-restraints excluded: chain 6 residue 127 LEU Chi-restraints excluded: chain 7 residue 37 SER Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 59 VAL Chi-restraints excluded: chain 7 residue 60 VAL Chi-restraints excluded: chain 7 residue 118 VAL Chi-restraints excluded: chain 7 residue 148 VAL Chi-restraints excluded: chain 8 residue 60 VAL Chi-restraints excluded: chain 8 residue 115 ASP Chi-restraints excluded: chain 8 residue 123 GLN Chi-restraints excluded: chain 8 residue 133 LEU Chi-restraints excluded: chain 9 residue 60 VAL Chi-restraints excluded: chain 9 residue 67 ILE Chi-restraints excluded: chain 9 residue 99 VAL Chi-restraints excluded: chain 9 residue 112 ILE Chi-restraints excluded: chain 9 residue 143 LEU Chi-restraints excluded: chain 9 residue 150 LEU Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 52 THR Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 132 LEU Chi-restraints excluded: chain Q residue 166 ASP Chi-restraints excluded: chain Q residue 181 ILE Chi-restraints excluded: chain Q residue 230 THR Chi-restraints excluded: chain Q residue 335 CYS Chi-restraints excluded: chain Q residue 344 ILE Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 466 ASP Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 516 LYS Chi-restraints excluded: chain A residue 525 TYR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 592 ASP Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 188 LYS Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 234 MET Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 359 ASP Chi-restraints excluded: chain F residue 402 MET Chi-restraints excluded: chain F residue 403 LYS Chi-restraints excluded: chain F residue 410 MET Chi-restraints excluded: chain F residue 435 MET Chi-restraints excluded: chain F residue 482 GLN Chi-restraints excluded: chain F residue 487 PHE Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 161 GLN Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 344 ARG Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 359 ASP Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain Z residue 140 LEU Chi-restraints excluded: chain Z residue 146 THR Chi-restraints excluded: chain Z residue 228 THR Chi-restraints excluded: chain Z residue 241 VAL Chi-restraints excluded: chain X residue 74 CYS Chi-restraints excluded: chain X residue 89 GLN Chi-restraints excluded: chain X residue 196 GLN Chi-restraints excluded: chain X residue 199 LEU Chi-restraints excluded: chain X residue 209 GLU Chi-restraints excluded: chain X residue 217 LEU Chi-restraints excluded: chain X residue 221 ASP Chi-restraints excluded: chain X residue 256 THR Chi-restraints excluded: chain X residue 264 ASP Chi-restraints excluded: chain X residue 267 VAL Chi-restraints excluded: chain Y residue 51 ASP Chi-restraints excluded: chain Y residue 95 VAL Chi-restraints excluded: chain Y residue 119 VAL Chi-restraints excluded: chain Y residue 146 THR Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain Y residue 156 THR Chi-restraints excluded: chain Y residue 179 PHE Chi-restraints excluded: chain Y residue 204 VAL Chi-restraints excluded: chain Y residue 241 VAL Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain N residue 14 GLU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 46 ASN Chi-restraints excluded: chain N residue 51 THR Chi-restraints excluded: chain N residue 81 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 542 optimal weight: 7.9990 chunk 350 optimal weight: 0.9990 chunk 523 optimal weight: 0.0050 chunk 264 optimal weight: 1.9990 chunk 172 optimal weight: 30.0000 chunk 169 optimal weight: 6.9990 chunk 557 optimal weight: 10.0000 chunk 597 optimal weight: 2.9990 chunk 433 optimal weight: 30.0000 chunk 81 optimal weight: 6.9990 chunk 689 optimal weight: 0.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 194 ASN ** R 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 365 ASN J 66 GLN L 85 GLN ** H 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN ** K 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 348 HIS ** U 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 430 GLN C 603 GLN ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 ASN F 421 GLN D 161 GLN D 421 GLN E 54 ASN G 85 GLN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 70970 Z= 0.179 Angle : 0.551 17.837 96108 Z= 0.281 Chirality : 0.040 0.272 11093 Planarity : 0.004 0.045 12396 Dihedral : 6.668 135.701 10289 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.66 % Favored : 95.32 % Rotamer: Outliers : 4.68 % Allowed : 25.82 % Favored : 69.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % 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: 0.27 (0.09), residues: 9132 helix: 1.62 (0.07), residues: 5119 sheet: -1.00 (0.19), residues: 733 loop : -1.94 (0.10), residues: 3280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP R 594 HIS 0.005 0.000 HIS B 444 PHE 0.027 0.001 PHE H 38 TYR 0.031 0.001 TYR X 112 ARG 0.009 0.000 ARG B 553 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18264 Ramachandran restraints generated. 9132 Oldfield, 0 Emsley, 9132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18264 Ramachandran restraints generated. 9132 Oldfield, 0 Emsley, 9132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1338 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 331 poor density : 1007 time to evaluate : 6.290 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: R 94 MET cc_start: 0.8386 (ppp) cc_final: 0.7927 (mtt) REVERT: R 214 TYR cc_start: 0.6702 (m-80) cc_final: 0.6345 (m-80) REVERT: R 368 ASN cc_start: 0.6671 (OUTLIER) cc_final: 0.6311 (p0) REVERT: R 586 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7053 (tt) REVERT: J 15 MET cc_start: 0.4007 (mmp) cc_final: 0.2947 (mtm) REVERT: J 56 TYR cc_start: 0.6865 (OUTLIER) cc_final: 0.5206 (m-80) REVERT: J 57 TYR cc_start: 0.5627 (m-80) cc_final: 0.5375 (m-80) REVERT: J 62 LYS cc_start: 0.8333 (mmtp) cc_final: 0.8121 (ptpp) REVERT: J 132 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8167 (mpt) REVERT: J 145 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8359 (ttpm) REVERT: M 87 TYR cc_start: 0.7816 (OUTLIER) cc_final: 0.7039 (m-80) REVERT: M 93 ASP cc_start: 0.7720 (t70) cc_final: 0.7216 (t0) REVERT: M 97 ASP cc_start: 0.7997 (m-30) cc_final: 0.7546 (m-30) REVERT: M 116 ILE cc_start: 0.7282 (OUTLIER) cc_final: 0.6755 (mm) REVERT: I 38 PHE cc_start: 0.5224 (OUTLIER) cc_final: 0.4676 (t80) REVERT: I 63 GLN cc_start: 0.8138 (mt0) cc_final: 0.7902 (mm-40) REVERT: L 54 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7311 (mp0) REVERT: L 80 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8070 (mptm) REVERT: H 54 MET cc_start: 0.8261 (tmm) cc_final: 0.7677 (tmm) REVERT: H 103 SER cc_start: 0.8998 (t) cc_final: 0.8303 (p) REVERT: K 102 PHE cc_start: 0.7882 (OUTLIER) cc_final: 0.7236 (t80) REVERT: T 65 LEU cc_start: 0.8618 (mm) cc_final: 0.8072 (mt) REVERT: T 114 LEU cc_start: 0.8134 (mt) cc_final: 0.7887 (mm) REVERT: U 297 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7725 (tt) REVERT: U 397 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8189 (mt) REVERT: V 325 SER cc_start: 0.8132 (t) cc_final: 0.7911 (m) REVERT: 0 26 TYR cc_start: 0.8178 (OUTLIER) cc_final: 0.6865 (t80) REVERT: 0 116 GLU cc_start: 0.6857 (mp0) cc_final: 0.6389 (mp0) REVERT: 2 61 MET cc_start: 0.6985 (OUTLIER) cc_final: 0.6646 (mmm) REVERT: 4 54 LYS cc_start: 0.7320 (mmtt) cc_final: 0.7066 (pttt) REVERT: 4 134 ILE cc_start: 0.7958 (mm) cc_final: 0.7619 (mt) REVERT: 5 17 MET cc_start: 0.8161 (mmm) cc_final: 0.7833 (mmt) REVERT: 5 131 MET cc_start: 0.7085 (ttp) cc_final: 0.6716 (ttp) REVERT: 6 56 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8341 (tp) REVERT: 6 67 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8592 (mp) REVERT: 6 139 GLU cc_start: 0.7355 (tm-30) cc_final: 0.7110 (tm-30) REVERT: 8 131 MET cc_start: 0.6719 (tmm) cc_final: 0.6431 (ttp) REVERT: Q 181 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8363 (mt) REVERT: C 235 ASP cc_start: 0.7925 (t0) cc_final: 0.7473 (t0) REVERT: C 268 ASN cc_start: 0.8742 (OUTLIER) cc_final: 0.8301 (p0) REVERT: C 306 MET cc_start: 0.8277 (mmt) cc_final: 0.7682 (mmt) REVERT: C 486 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7952 (tm-30) REVERT: C 513 LYS cc_start: 0.8188 (ttmt) cc_final: 0.7337 (mmtp) REVERT: C 540 MET cc_start: 0.7956 (mtp) cc_final: 0.7550 (mtm) REVERT: A 201 GLU cc_start: 0.6988 (tt0) cc_final: 0.6315 (tt0) REVERT: A 347 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7672 (ttt) REVERT: A 485 GLU cc_start: 0.7940 (tp30) cc_final: 0.7730 (tp30) REVERT: A 506 LYS cc_start: 0.7776 (mttt) cc_final: 0.7453 (mtpt) REVERT: A 525 TYR cc_start: 0.7440 (OUTLIER) cc_final: 0.7064 (p90) REVERT: B 172 ASN cc_start: 0.9165 (OUTLIER) cc_final: 0.8921 (m-40) REVERT: B 284 MET cc_start: 0.8228 (mmm) cc_final: 0.7905 (mmt) REVERT: B 540 MET cc_start: 0.8829 (mtp) cc_final: 0.8469 (mtp) REVERT: F 88 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7547 (tt0) REVERT: F 224 GLU cc_start: 0.2787 (OUTLIER) cc_final: 0.2197 (mm-30) REVERT: F 249 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7561 (mt-10) REVERT: F 250 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8130 (pp20) REVERT: F 380 ASP cc_start: 0.8304 (t0) cc_final: 0.8054 (t0) REVERT: F 402 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8596 (ttt) REVERT: F 435 MET cc_start: 0.5319 (OUTLIER) cc_final: 0.4556 (tpp) REVERT: F 487 PHE cc_start: 0.4958 (OUTLIER) cc_final: 0.4293 (m-80) REVERT: D 300 MET cc_start: 0.8443 (mmm) cc_final: 0.8102 (mmm) REVERT: D 310 VAL cc_start: 0.8810 (t) cc_final: 0.8574 (t) REVERT: D 344 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.6623 (mtt180) REVERT: D 433 GLN cc_start: 0.7710 (mm-40) cc_final: 0.7347 (tp-100) REVERT: E 294 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8911 (tt) REVERT: E 435 MET cc_start: 0.5142 (mmm) cc_final: 0.4834 (mtt) REVERT: E 497 GLN cc_start: 0.5991 (pm20) cc_final: 0.5703 (pm20) REVERT: X 10 MET cc_start: 0.6221 (mtp) cc_final: 0.5925 (ttt) REVERT: X 234 MET cc_start: 0.8009 (ttp) cc_final: 0.7325 (tpp) REVERT: X 236 LYS cc_start: 0.6695 (mmtp) cc_final: 0.6389 (mttm) REVERT: Y 188 MET cc_start: 0.7546 (mmm) cc_final: 0.7345 (mmm) REVERT: Y 207 GLN cc_start: 0.5712 (OUTLIER) cc_final: 0.5413 (pt0) REVERT: G 67 PHE cc_start: 0.8468 (t80) cc_final: 0.8246 (t80) REVERT: N 37 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8181 (mt) REVERT: N 83 GLN cc_start: 0.7962 (tt0) cc_final: 0.7723 (tt0) outliers start: 331 outliers final: 265 residues processed: 1251 average time/residue: 0.6491 time to fit residues: 1401.8286 Evaluate side-chains 1269 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 298 poor density : 971 time to evaluate : 6.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 96 ASP Chi-restraints excluded: chain R residue 100 ASN Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 194 ASN Chi-restraints excluded: chain R residue 250 THR Chi-restraints excluded: chain R residue 283 LEU Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 312 ILE Chi-restraints excluded: chain R residue 334 GLN Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain R residue 363 THR Chi-restraints excluded: chain R residue 368 ASN Chi-restraints excluded: chain R residue 396 ILE Chi-restraints excluded: chain R residue 437 ASN Chi-restraints excluded: chain R residue 549 LEU Chi-restraints excluded: chain R residue 556 LEU Chi-restraints excluded: chain R residue 586 LEU Chi-restraints excluded: chain R residue 613 ILE Chi-restraints excluded: chain R residue 644 LEU Chi-restraints excluded: chain R residue 716 THR Chi-restraints excluded: chain R residue 729 LEU Chi-restraints excluded: chain R residue 796 LEU Chi-restraints excluded: chain R residue 830 ILE Chi-restraints excluded: chain J residue 56 TYR Chi-restraints excluded: chain J residue 104 LYS Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 132 MET Chi-restraints excluded: chain J residue 145 LYS Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 177 ILE Chi-restraints excluded: chain J residue 201 ASP Chi-restraints excluded: chain M residue 87 TYR Chi-restraints excluded: chain M residue 107 ARG Chi-restraints excluded: chain M residue 110 ILE Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain I residue 20 GLU Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain L residue 54 GLU Chi-restraints excluded: chain L residue 80 LYS Chi-restraints excluded: chain L residue 85 GLN Chi-restraints excluded: chain H residue 14 HIS Chi-restraints excluded: chain H residue 71 GLN Chi-restraints excluded: chain H residue 198 SER Chi-restraints excluded: chain H residue 207 MET Chi-restraints excluded: chain K residue 87 TYR Chi-restraints excluded: chain K residue 102 PHE Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain S residue 70 ASN Chi-restraints excluded: chain T residue 46 CYS Chi-restraints excluded: chain T residue 79 LEU Chi-restraints excluded: chain T residue 116 LEU Chi-restraints excluded: chain T residue 123 PHE Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain U residue 258 VAL Chi-restraints excluded: chain U residue 297 LEU Chi-restraints excluded: chain U residue 340 PHE Chi-restraints excluded: chain U residue 341 THR Chi-restraints excluded: chain U residue 347 VAL Chi-restraints excluded: chain U residue 362 THR Chi-restraints excluded: chain U residue 385 VAL Chi-restraints excluded: chain U residue 396 MET Chi-restraints excluded: chain U residue 397 LEU Chi-restraints excluded: chain U residue 407 VAL Chi-restraints excluded: chain U residue 447 ILE Chi-restraints excluded: chain V residue 315 ILE Chi-restraints excluded: chain V residue 331 MET Chi-restraints excluded: chain V residue 338 ILE Chi-restraints excluded: chain 0 residue 2 THR Chi-restraints excluded: chain 0 residue 26 TYR Chi-restraints excluded: chain 0 residue 28 ILE Chi-restraints excluded: chain 0 residue 51 ASN Chi-restraints excluded: chain 0 residue 69 ILE Chi-restraints excluded: chain 0 residue 70 TYR Chi-restraints excluded: chain 0 residue 144 VAL Chi-restraints excluded: chain 0 residue 149 LEU Chi-restraints excluded: chain 0 residue 151 CYS Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 0 residue 160 SER Chi-restraints excluded: chain 1 residue 23 MET Chi-restraints excluded: chain 1 residue 67 ILE Chi-restraints excluded: chain 1 residue 85 SER Chi-restraints excluded: chain 1 residue 97 LEU Chi-restraints excluded: chain 1 residue 110 ILE Chi-restraints excluded: chain 1 residue 113 VAL Chi-restraints excluded: chain 1 residue 115 ASP Chi-restraints excluded: chain 1 residue 140 VAL Chi-restraints excluded: chain 2 residue 24 VAL Chi-restraints excluded: chain 2 residue 44 MET Chi-restraints excluded: chain 2 residue 61 MET Chi-restraints excluded: chain 2 residue 64 ILE Chi-restraints excluded: chain 2 residue 118 VAL Chi-restraints excluded: chain 2 residue 129 VAL Chi-restraints excluded: chain 3 residue 44 MET Chi-restraints excluded: chain 3 residue 56 ILE Chi-restraints excluded: chain 3 residue 132 ILE Chi-restraints excluded: chain 3 residue 134 ILE Chi-restraints excluded: chain 4 residue 59 VAL Chi-restraints excluded: chain 4 residue 80 LEU Chi-restraints excluded: chain 4 residue 93 LEU Chi-restraints excluded: chain 4 residue 97 LEU Chi-restraints excluded: chain 4 residue 129 VAL Chi-restraints excluded: chain 4 residue 133 LEU Chi-restraints excluded: chain 4 residue 137 PHE Chi-restraints excluded: chain 4 residue 140 VAL Chi-restraints excluded: chain 5 residue 24 VAL Chi-restraints excluded: chain 5 residue 28 LEU Chi-restraints excluded: chain 5 residue 112 ILE Chi-restraints excluded: chain 5 residue 115 ASP Chi-restraints excluded: chain 5 residue 129 VAL Chi-restraints excluded: chain 5 residue 133 LEU Chi-restraints excluded: chain 5 residue 140 VAL Chi-restraints excluded: chain 5 residue 143 LEU Chi-restraints excluded: chain 6 residue 37 SER Chi-restraints excluded: chain 6 residue 46 VAL Chi-restraints excluded: chain 6 residue 47 MET Chi-restraints excluded: chain 6 residue 56 ILE Chi-restraints excluded: chain 6 residue 67 ILE Chi-restraints excluded: chain 6 residue 81 ASN Chi-restraints excluded: chain 6 residue 127 LEU Chi-restraints excluded: chain 7 residue 37 SER Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 59 VAL Chi-restraints excluded: chain 7 residue 60 VAL Chi-restraints excluded: chain 7 residue 112 ILE Chi-restraints excluded: chain 7 residue 118 VAL Chi-restraints excluded: chain 7 residue 148 VAL Chi-restraints excluded: chain 8 residue 60 VAL Chi-restraints excluded: chain 8 residue 115 ASP Chi-restraints excluded: chain 9 residue 60 VAL Chi-restraints excluded: chain 9 residue 67 ILE Chi-restraints excluded: chain 9 residue 99 VAL Chi-restraints excluded: chain 9 residue 150 LEU Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 6 GLU Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 52 THR Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 132 LEU Chi-restraints excluded: chain Q residue 166 ASP Chi-restraints excluded: chain Q residue 181 ILE Chi-restraints excluded: chain Q residue 230 THR Chi-restraints excluded: chain Q residue 335 CYS Chi-restraints excluded: chain Q residue 344 ILE Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 466 ASP Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 516 LYS Chi-restraints excluded: chain A residue 525 TYR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 592 ASP Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 188 LYS Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 234 MET Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 350 GLN Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 359 ASP Chi-restraints excluded: chain F residue 402 MET Chi-restraints excluded: chain F residue 410 MET Chi-restraints excluded: chain F residue 435 MET Chi-restraints excluded: chain F residue 482 GLN Chi-restraints excluded: chain F residue 487 PHE Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 161 GLN Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 344 ARG Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 359 ASP Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain Z residue 140 LEU Chi-restraints excluded: chain Z residue 146 THR Chi-restraints excluded: chain Z residue 228 THR Chi-restraints excluded: chain Z residue 241 VAL Chi-restraints excluded: chain X residue 74 CYS Chi-restraints excluded: chain X residue 89 GLN Chi-restraints excluded: chain X residue 106 ASP Chi-restraints excluded: chain X residue 199 LEU Chi-restraints excluded: chain X residue 209 GLU Chi-restraints excluded: chain X residue 217 LEU Chi-restraints excluded: chain X residue 221 ASP Chi-restraints excluded: chain X residue 256 THR Chi-restraints excluded: chain X residue 264 ASP Chi-restraints excluded: chain X residue 267 VAL Chi-restraints excluded: chain Y residue 51 ASP Chi-restraints excluded: chain Y residue 95 VAL Chi-restraints excluded: chain Y residue 119 VAL Chi-restraints excluded: chain Y residue 146 THR Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain Y residue 156 THR Chi-restraints excluded: chain Y residue 179 PHE Chi-restraints excluded: chain Y residue 204 VAL Chi-restraints excluded: chain Y residue 207 GLN Chi-restraints excluded: chain Y residue 241 VAL Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain N residue 14 GLU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 46 ASN Chi-restraints excluded: chain N residue 51 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 797 optimal weight: 6.9990 chunk 840 optimal weight: 10.0000 chunk 766 optimal weight: 4.9990 chunk 817 optimal weight: 7.9990 chunk 491 optimal weight: 10.0000 chunk 356 optimal weight: 6.9990 chunk 641 optimal weight: 0.4980 chunk 250 optimal weight: 10.0000 chunk 738 optimal weight: 8.9990 chunk 773 optimal weight: 20.0000 chunk 814 optimal weight: 7.9990 overall best weight: 5.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 194 ASN ** R 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 365 ASN L 85 GLN K 35 GLN ** U 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 330 ASN ** 0 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 ASN ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 ASN F 421 GLN D 161 GLN E 54 ASN E 181 ASN ** Z 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 70970 Z= 0.439 Angle : 0.679 19.939 96108 Z= 0.352 Chirality : 0.045 0.316 11093 Planarity : 0.005 0.057 12396 Dihedral : 6.997 138.742 10273 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.40 % Favored : 93.59 % Rotamer: Outliers : 5.17 % Allowed : 25.56 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.09), residues: 9132 helix: 1.27 (0.07), residues: 5160 sheet: -1.08 (0.19), residues: 710 loop : -1.98 (0.10), residues: 3262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP S 52 HIS 0.007 0.001 HIS G 111 PHE 0.022 0.002 PHE R 578 TYR 0.091 0.002 TYR U 373 ARG 0.019 0.001 ARG H 50 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18264 Ramachandran restraints generated. 9132 Oldfield, 0 Emsley, 9132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18264 Ramachandran restraints generated. 9132 Oldfield, 0 Emsley, 9132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1309 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 366 poor density : 943 time to evaluate : 6.362 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: R 94 MET cc_start: 0.8438 (ppp) cc_final: 0.7969 (mtt) REVERT: R 214 TYR cc_start: 0.6921 (m-80) cc_final: 0.6509 (m-80) REVERT: R 368 ASN cc_start: 0.6740 (OUTLIER) cc_final: 0.6380 (p0) REVERT: R 438 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7671 (tm-30) REVERT: R 586 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7094 (tt) REVERT: J 15 MET cc_start: 0.4190 (mmp) cc_final: 0.3142 (mtm) REVERT: J 16 MET cc_start: 0.5598 (mmm) cc_final: 0.5332 (mmm) REVERT: J 56 TYR cc_start: 0.7026 (OUTLIER) cc_final: 0.5628 (m-80) REVERT: J 132 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8229 (mpt) REVERT: J 145 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8539 (ttpm) REVERT: M 87 TYR cc_start: 0.7961 (OUTLIER) cc_final: 0.7168 (m-80) REVERT: M 93 ASP cc_start: 0.7792 (t70) cc_final: 0.7410 (t70) REVERT: M 97 ASP cc_start: 0.8034 (m-30) cc_final: 0.7628 (m-30) REVERT: M 116 ILE cc_start: 0.7644 (OUTLIER) cc_final: 0.7239 (mm) REVERT: I 63 GLN cc_start: 0.8245 (mt0) cc_final: 0.7967 (mm-40) REVERT: L 54 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7087 (mp0) REVERT: L 81 MET cc_start: 0.8625 (mtm) cc_final: 0.7992 (mtp) REVERT: L 85 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7711 (mp-120) REVERT: H 54 MET cc_start: 0.8337 (tmm) cc_final: 0.7762 (tmm) REVERT: H 103 SER cc_start: 0.9140 (t) cc_final: 0.8476 (p) REVERT: H 212 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8067 (ttt-90) REVERT: K 35 GLN cc_start: 0.3198 (OUTLIER) cc_final: 0.2056 (pp30) REVERT: K 109 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7177 (pt0) REVERT: T 65 LEU cc_start: 0.8661 (mm) cc_final: 0.8132 (mt) REVERT: T 114 LEU cc_start: 0.8193 (mt) cc_final: 0.7928 (mm) REVERT: U 297 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7765 (tt) REVERT: 0 26 TYR cc_start: 0.8242 (OUTLIER) cc_final: 0.6719 (t80) REVERT: 4 134 ILE cc_start: 0.8027 (mm) cc_final: 0.7713 (mt) REVERT: 5 17 MET cc_start: 0.8244 (mmm) cc_final: 0.8034 (mmt) REVERT: 6 56 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8549 (tp) REVERT: 6 67 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8682 (mp) REVERT: 7 54 LYS cc_start: 0.8577 (ttpp) cc_final: 0.8222 (ttpt) REVERT: Q 176 MET cc_start: 0.8041 (ptp) cc_final: 0.7837 (ptt) REVERT: Q 181 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8622 (mt) REVERT: C 196 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7782 (t80) REVERT: C 513 LYS cc_start: 0.8315 (ttmt) cc_final: 0.7430 (mmtm) REVERT: C 540 MET cc_start: 0.8135 (mtp) cc_final: 0.7561 (mtm) REVERT: A 201 GLU cc_start: 0.7216 (tt0) cc_final: 0.6408 (tt0) REVERT: A 347 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.7717 (ttt) REVERT: A 485 GLU cc_start: 0.7981 (tp30) cc_final: 0.7769 (tp30) REVERT: A 506 LYS cc_start: 0.7818 (mttt) cc_final: 0.7491 (mtpt) REVERT: A 525 TYR cc_start: 0.7444 (OUTLIER) cc_final: 0.7014 (p90) REVERT: B 58 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7617 (tp30) REVERT: B 65 GLN cc_start: 0.8228 (mt0) cc_final: 0.7851 (mt0) REVERT: B 172 ASN cc_start: 0.9280 (OUTLIER) cc_final: 0.9016 (m-40) REVERT: B 540 MET cc_start: 0.8881 (mtp) cc_final: 0.8533 (mtp) REVERT: F 224 GLU cc_start: 0.2542 (OUTLIER) cc_final: 0.2063 (mm-30) REVERT: F 249 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7601 (mt-10) REVERT: F 250 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8277 (pp20) REVERT: F 297 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9010 (mt) REVERT: F 380 ASP cc_start: 0.8343 (t0) cc_final: 0.8053 (t0) REVERT: F 402 MET cc_start: 0.9056 (OUTLIER) cc_final: 0.8589 (ttt) REVERT: F 435 MET cc_start: 0.5647 (OUTLIER) cc_final: 0.5040 (tpp) REVERT: F 456 GLN cc_start: 0.7704 (mp10) cc_final: 0.7478 (mp10) REVERT: D 300 MET cc_start: 0.8598 (mmm) cc_final: 0.8253 (mmm) REVERT: D 310 VAL cc_start: 0.8795 (t) cc_final: 0.8571 (t) REVERT: D 344 ARG cc_start: 0.9222 (OUTLIER) cc_final: 0.6851 (mtt180) REVERT: D 433 GLN cc_start: 0.7881 (mm-40) cc_final: 0.7436 (tp-100) REVERT: E 294 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8948 (tt) REVERT: X 10 MET cc_start: 0.6398 (mtp) cc_final: 0.5869 (ttt) REVERT: X 234 MET cc_start: 0.8158 (ttp) cc_final: 0.7403 (tpp) REVERT: Y 207 GLN cc_start: 0.5787 (OUTLIER) cc_final: 0.5559 (pt0) REVERT: G 67 PHE cc_start: 0.8557 (t80) cc_final: 0.8350 (t80) REVERT: N 37 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8158 (mt) REVERT: N 83 GLN cc_start: 0.8060 (tt0) cc_final: 0.7826 (tt0) REVERT: N 84 SER cc_start: 0.8258 (m) cc_final: 0.7642 (p) outliers start: 366 outliers final: 301 residues processed: 1228 average time/residue: 0.6609 time to fit residues: 1401.3946 Evaluate side-chains 1248 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 334 poor density : 914 time to evaluate : 6.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 47 PHE Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 96 ASP Chi-restraints excluded: chain R residue 100 ASN Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 250 THR Chi-restraints excluded: chain R residue 283 LEU Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 312 ILE Chi-restraints excluded: chain R residue 334 GLN Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain R residue 363 THR Chi-restraints excluded: chain R residue 365 ASN Chi-restraints excluded: chain R residue 368 ASN Chi-restraints excluded: chain R residue 396 ILE Chi-restraints excluded: chain R residue 437 ASN Chi-restraints excluded: chain R residue 438 GLU Chi-restraints excluded: chain R residue 539 MET Chi-restraints excluded: chain R residue 549 LEU Chi-restraints excluded: chain R residue 556 LEU Chi-restraints excluded: chain R residue 568 ILE Chi-restraints excluded: chain R residue 572 PHE Chi-restraints excluded: chain R residue 586 LEU Chi-restraints excluded: chain R residue 609 LEU Chi-restraints excluded: chain R residue 613 ILE Chi-restraints excluded: chain R residue 628 LEU Chi-restraints excluded: chain R residue 716 THR Chi-restraints excluded: chain R residue 729 LEU Chi-restraints excluded: chain R residue 796 LEU Chi-restraints excluded: chain R residue 830 ILE Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 56 TYR Chi-restraints excluded: chain J residue 104 LYS Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 132 MET Chi-restraints excluded: chain J residue 145 LYS Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 177 ILE Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 193 SER Chi-restraints excluded: chain J residue 201 ASP Chi-restraints excluded: chain M residue 84 LEU Chi-restraints excluded: chain M residue 87 TYR Chi-restraints excluded: chain M residue 107 ARG Chi-restraints excluded: chain M residue 110 ILE Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain I residue 20 GLU Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 54 GLU Chi-restraints excluded: chain L residue 80 LYS Chi-restraints excluded: chain L residue 85 GLN Chi-restraints excluded: chain H residue 14 HIS Chi-restraints excluded: chain H residue 71 GLN Chi-restraints excluded: chain H residue 198 SER Chi-restraints excluded: chain H residue 212 ARG Chi-restraints excluded: chain K residue 35 GLN Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 87 TYR Chi-restraints excluded: chain K residue 109 GLU Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 70 ASN Chi-restraints excluded: chain T residue 46 CYS Chi-restraints excluded: chain T residue 79 LEU Chi-restraints excluded: chain T residue 98 TYR Chi-restraints excluded: chain T residue 116 LEU Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain U residue 258 VAL Chi-restraints excluded: chain U residue 297 LEU Chi-restraints excluded: chain U residue 334 VAL Chi-restraints excluded: chain U residue 340 PHE Chi-restraints excluded: chain U residue 341 THR Chi-restraints excluded: chain U residue 347 VAL Chi-restraints excluded: chain U residue 362 THR Chi-restraints excluded: chain U residue 385 VAL Chi-restraints excluded: chain U residue 396 MET Chi-restraints excluded: chain U residue 407 VAL Chi-restraints excluded: chain U residue 408 MET Chi-restraints excluded: chain U residue 430 LEU Chi-restraints excluded: chain U residue 441 THR Chi-restraints excluded: chain U residue 447 ILE Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 315 ILE Chi-restraints excluded: chain V residue 331 MET Chi-restraints excluded: chain V residue 338 ILE Chi-restraints excluded: chain 0 residue 2 THR Chi-restraints excluded: chain 0 residue 26 TYR Chi-restraints excluded: chain 0 residue 28 ILE Chi-restraints excluded: chain 0 residue 69 ILE Chi-restraints excluded: chain 0 residue 70 TYR Chi-restraints excluded: chain 0 residue 144 VAL Chi-restraints excluded: chain 0 residue 149 LEU Chi-restraints excluded: chain 0 residue 151 CYS Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 1 residue 23 MET Chi-restraints excluded: chain 1 residue 24 VAL Chi-restraints excluded: chain 1 residue 67 ILE Chi-restraints excluded: chain 1 residue 85 SER Chi-restraints excluded: chain 1 residue 97 LEU Chi-restraints excluded: chain 1 residue 98 SER Chi-restraints excluded: chain 1 residue 110 ILE Chi-restraints excluded: chain 1 residue 113 VAL Chi-restraints excluded: chain 1 residue 115 ASP Chi-restraints excluded: chain 1 residue 140 VAL Chi-restraints excluded: chain 2 residue 24 VAL Chi-restraints excluded: chain 2 residue 44 MET Chi-restraints excluded: chain 2 residue 57 ILE Chi-restraints excluded: chain 2 residue 59 VAL Chi-restraints excluded: chain 2 residue 61 MET Chi-restraints excluded: chain 2 residue 64 ILE Chi-restraints excluded: chain 2 residue 102 SER Chi-restraints excluded: chain 2 residue 118 VAL Chi-restraints excluded: chain 2 residue 129 VAL Chi-restraints excluded: chain 3 residue 26 SER Chi-restraints excluded: chain 3 residue 44 MET Chi-restraints excluded: chain 3 residue 56 ILE Chi-restraints excluded: chain 3 residue 121 THR Chi-restraints excluded: chain 3 residue 132 ILE Chi-restraints excluded: chain 4 residue 67 ILE Chi-restraints excluded: chain 4 residue 80 LEU Chi-restraints excluded: chain 4 residue 93 LEU Chi-restraints excluded: chain 4 residue 97 LEU Chi-restraints excluded: chain 4 residue 129 VAL Chi-restraints excluded: chain 4 residue 133 LEU Chi-restraints excluded: chain 4 residue 137 PHE Chi-restraints excluded: chain 4 residue 140 VAL Chi-restraints excluded: chain 5 residue 6 SER Chi-restraints excluded: chain 5 residue 24 VAL Chi-restraints excluded: chain 5 residue 45 SER Chi-restraints excluded: chain 5 residue 115 ASP Chi-restraints excluded: chain 5 residue 118 VAL Chi-restraints excluded: chain 5 residue 129 VAL Chi-restraints excluded: chain 5 residue 133 LEU Chi-restraints excluded: chain 5 residue 140 VAL Chi-restraints excluded: chain 5 residue 143 LEU Chi-restraints excluded: chain 6 residue 37 SER Chi-restraints excluded: chain 6 residue 39 THR Chi-restraints excluded: chain 6 residue 46 VAL Chi-restraints excluded: chain 6 residue 47 MET Chi-restraints excluded: chain 6 residue 56 ILE Chi-restraints excluded: chain 6 residue 67 ILE Chi-restraints excluded: chain 6 residue 81 ASN Chi-restraints excluded: chain 6 residue 127 LEU Chi-restraints excluded: chain 7 residue 37 SER Chi-restraints excluded: chain 7 residue 41 ILE Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 60 VAL Chi-restraints excluded: chain 7 residue 118 VAL Chi-restraints excluded: chain 7 residue 148 VAL Chi-restraints excluded: chain 7 residue 153 SER Chi-restraints excluded: chain 8 residue 60 VAL Chi-restraints excluded: chain 8 residue 93 LEU Chi-restraints excluded: chain 8 residue 115 ASP Chi-restraints excluded: chain 8 residue 121 THR Chi-restraints excluded: chain 8 residue 135 LEU Chi-restraints excluded: chain 9 residue 60 VAL Chi-restraints excluded: chain 9 residue 67 ILE Chi-restraints excluded: chain 9 residue 99 VAL Chi-restraints excluded: chain 9 residue 150 LEU Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 52 THR Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 122 ILE Chi-restraints excluded: chain Q residue 132 LEU Chi-restraints excluded: chain Q residue 155 LEU Chi-restraints excluded: chain Q residue 166 ASP Chi-restraints excluded: chain Q residue 181 ILE Chi-restraints excluded: chain Q residue 230 THR Chi-restraints excluded: chain Q residue 335 CYS Chi-restraints excluded: chain Q residue 344 ILE Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 466 ASP Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 516 LYS Chi-restraints excluded: chain A residue 525 TYR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 592 ASP Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 188 LYS Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 234 MET Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 359 ASP Chi-restraints excluded: chain F residue 402 MET Chi-restraints excluded: chain F residue 410 MET Chi-restraints excluded: chain F residue 435 MET Chi-restraints excluded: chain F residue 482 GLN Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 161 GLN Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 344 ARG Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 359 ASP Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain Z residue 146 THR Chi-restraints excluded: chain Z residue 228 THR Chi-restraints excluded: chain Z residue 241 VAL Chi-restraints excluded: chain X residue 35 THR Chi-restraints excluded: chain X residue 74 CYS Chi-restraints excluded: chain X residue 89 GLN Chi-restraints excluded: chain X residue 106 ASP Chi-restraints excluded: chain X residue 196 GLN Chi-restraints excluded: chain X residue 199 LEU Chi-restraints excluded: chain X residue 209 GLU Chi-restraints excluded: chain X residue 217 LEU Chi-restraints excluded: chain X residue 221 ASP Chi-restraints excluded: chain X residue 256 THR Chi-restraints excluded: chain X residue 264 ASP Chi-restraints excluded: chain X residue 267 VAL Chi-restraints excluded: chain Y residue 51 ASP Chi-restraints excluded: chain Y residue 95 VAL Chi-restraints excluded: chain Y residue 119 VAL Chi-restraints excluded: chain Y residue 146 THR Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain Y residue 156 THR Chi-restraints excluded: chain Y residue 179 PHE Chi-restraints excluded: chain Y residue 204 VAL Chi-restraints excluded: chain Y residue 207 GLN Chi-restraints excluded: chain Y residue 241 VAL Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 172 ILE Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain N residue 14 GLU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 46 ASN Chi-restraints excluded: chain N residue 51 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 536 optimal weight: 0.8980 chunk 864 optimal weight: 7.9990 chunk 527 optimal weight: 2.9990 chunk 410 optimal weight: 5.9990 chunk 600 optimal weight: 0.9980 chunk 906 optimal weight: 30.0000 chunk 834 optimal weight: 7.9990 chunk 721 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 557 optimal weight: 10.0000 chunk 442 optimal weight: 0.5980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 194 ASN ** R 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 365 ASN ** K 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 330 ASN ** 0 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 309 GLN ** Q 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 ASN F 421 GLN E 456 GLN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.291 70970 Z= 0.336 Angle : 0.760 59.200 96108 Z= 0.409 Chirality : 0.043 0.502 11093 Planarity : 0.005 0.105 12396 Dihedral : 7.009 138.671 10273 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.29 % Favored : 93.70 % Rotamer: Outliers : 4.81 % Allowed : 26.07 % Favored : 69.12 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 2.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.06 (0.09), residues: 9132 helix: 1.28 (0.07), residues: 5152 sheet: -1.08 (0.19), residues: 720 loop : -1.99 (0.10), residues: 3260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP S 52 HIS 0.011 0.001 HIS C 573 PHE 0.023 0.002 PHE A 337 TYR 0.088 0.002 TYR U 373 ARG 0.058 0.001 ARG R 179 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18264 Ramachandran restraints generated. 9132 Oldfield, 0 Emsley, 9132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18264 Ramachandran restraints generated. 9132 Oldfield, 0 Emsley, 9132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1260 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 340 poor density : 920 time to evaluate : 6.285 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: R 94 MET cc_start: 0.8434 (ppp) cc_final: 0.7964 (mtt) REVERT: R 214 TYR cc_start: 0.6918 (m-80) cc_final: 0.6508 (m-80) REVERT: R 368 ASN cc_start: 0.6648 (OUTLIER) cc_final: 0.6275 (p0) REVERT: R 586 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.7084 (tt) REVERT: J 15 MET cc_start: 0.4193 (mmp) cc_final: 0.3140 (mtm) REVERT: J 16 MET cc_start: 0.5597 (mmm) cc_final: 0.5329 (mmm) REVERT: J 56 TYR cc_start: 0.7074 (OUTLIER) cc_final: 0.5624 (m-80) REVERT: J 132 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8224 (mpt) REVERT: J 145 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8531 (ttpm) REVERT: M 87 TYR cc_start: 0.7948 (OUTLIER) cc_final: 0.7154 (m-80) REVERT: M 93 ASP cc_start: 0.7782 (t70) cc_final: 0.7397 (t70) REVERT: M 97 ASP cc_start: 0.8025 (m-30) cc_final: 0.7620 (m-30) REVERT: M 116 ILE cc_start: 0.7627 (OUTLIER) cc_final: 0.7199 (mm) REVERT: I 38 PHE cc_start: 0.5164 (OUTLIER) cc_final: 0.4529 (t80) REVERT: I 63 GLN cc_start: 0.8241 (mt0) cc_final: 0.7958 (mm-40) REVERT: L 54 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7082 (mp0) REVERT: H 54 MET cc_start: 0.8331 (tmm) cc_final: 0.7758 (tmm) REVERT: H 103 SER cc_start: 0.9136 (t) cc_final: 0.8483 (p) REVERT: H 212 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8052 (ttt-90) REVERT: K 109 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7168 (pt0) REVERT: T 65 LEU cc_start: 0.8661 (mm) cc_final: 0.8123 (mt) REVERT: T 114 LEU cc_start: 0.8187 (mt) cc_final: 0.7922 (mm) REVERT: U 297 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7759 (tt) REVERT: 0 26 TYR cc_start: 0.8232 (OUTLIER) cc_final: 0.6707 (t80) REVERT: 4 134 ILE cc_start: 0.8008 (mm) cc_final: 0.7682 (mt) REVERT: 5 17 MET cc_start: 0.8228 (mmm) cc_final: 0.8021 (mmt) REVERT: 6 56 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8537 (tp) REVERT: 6 67 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8657 (mp) REVERT: Q 181 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8589 (mt) REVERT: C 196 PHE cc_start: 0.8087 (OUTLIER) cc_final: 0.7771 (t80) REVERT: C 486 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7978 (tm-30) REVERT: C 513 LYS cc_start: 0.8211 (ttmt) cc_final: 0.7421 (mmtm) REVERT: C 540 MET cc_start: 0.8134 (mtp) cc_final: 0.7702 (mtm) REVERT: A 201 GLU cc_start: 0.7316 (tt0) cc_final: 0.6541 (tt0) REVERT: A 347 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7701 (ttt) REVERT: A 485 GLU cc_start: 0.7970 (tp30) cc_final: 0.7757 (tp30) REVERT: A 506 LYS cc_start: 0.7818 (mttt) cc_final: 0.7484 (mtpt) REVERT: A 525 TYR cc_start: 0.7431 (OUTLIER) cc_final: 0.7006 (p90) REVERT: B 65 GLN cc_start: 0.8207 (mt0) cc_final: 0.7839 (mt0) REVERT: B 540 MET cc_start: 0.8843 (mtp) cc_final: 0.8521 (mtp) REVERT: F 224 GLU cc_start: 0.2528 (OUTLIER) cc_final: 0.2055 (mm-30) REVERT: F 249 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7599 (mt-10) REVERT: F 250 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8272 (pp20) REVERT: F 297 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9014 (mt) REVERT: F 380 ASP cc_start: 0.8326 (t0) cc_final: 0.8033 (t0) REVERT: F 402 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.8590 (ttt) REVERT: F 435 MET cc_start: 0.5638 (OUTLIER) cc_final: 0.5030 (tpp) REVERT: F 456 GLN cc_start: 0.7746 (mp10) cc_final: 0.7503 (mp10) REVERT: D 300 MET cc_start: 0.8595 (mmm) cc_final: 0.8255 (mmm) REVERT: D 310 VAL cc_start: 0.8780 (t) cc_final: 0.8554 (t) REVERT: D 344 ARG cc_start: 0.9201 (OUTLIER) cc_final: 0.6840 (mtt180) REVERT: D 433 GLN cc_start: 0.7867 (mm-40) cc_final: 0.7422 (tp-100) REVERT: E 294 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8932 (tt) REVERT: X 10 MET cc_start: 0.6391 (mtp) cc_final: 0.5866 (ttt) REVERT: X 126 TYR cc_start: 0.8507 (OUTLIER) cc_final: 0.8166 (m-10) REVERT: X 234 MET cc_start: 0.8154 (ttp) cc_final: 0.7397 (tpp) REVERT: Y 207 GLN cc_start: 0.5787 (OUTLIER) cc_final: 0.5553 (pt0) REVERT: G 67 PHE cc_start: 0.8547 (t80) cc_final: 0.8340 (t80) REVERT: N 37 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8162 (mt) REVERT: N 83 GLN cc_start: 0.8062 (tt0) cc_final: 0.7819 (tt0) REVERT: N 84 SER cc_start: 0.8243 (m) cc_final: 0.7636 (p) outliers start: 340 outliers final: 304 residues processed: 1183 average time/residue: 0.6323 time to fit residues: 1289.0682 Evaluate side-chains 1247 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 334 poor density : 913 time to evaluate : 6.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 47 PHE Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 96 ASP Chi-restraints excluded: chain R residue 100 ASN Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 250 THR Chi-restraints excluded: chain R residue 283 LEU Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 312 ILE Chi-restraints excluded: chain R residue 334 GLN Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain R residue 357 THR Chi-restraints excluded: chain R residue 363 THR Chi-restraints excluded: chain R residue 368 ASN Chi-restraints excluded: chain R residue 396 ILE Chi-restraints excluded: chain R residue 437 ASN Chi-restraints excluded: chain R residue 549 LEU Chi-restraints excluded: chain R residue 556 LEU Chi-restraints excluded: chain R residue 568 ILE Chi-restraints excluded: chain R residue 572 PHE Chi-restraints excluded: chain R residue 586 LEU Chi-restraints excluded: chain R residue 609 LEU Chi-restraints excluded: chain R residue 613 ILE Chi-restraints excluded: chain R residue 628 LEU Chi-restraints excluded: chain R residue 716 THR Chi-restraints excluded: chain R residue 729 LEU Chi-restraints excluded: chain R residue 830 ILE Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 56 TYR Chi-restraints excluded: chain J residue 104 LYS Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 132 MET Chi-restraints excluded: chain J residue 145 LYS Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 177 ILE Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 193 SER Chi-restraints excluded: chain J residue 201 ASP Chi-restraints excluded: chain M residue 84 LEU Chi-restraints excluded: chain M residue 87 TYR Chi-restraints excluded: chain M residue 107 ARG Chi-restraints excluded: chain M residue 110 ILE Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain I residue 20 GLU Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 54 GLU Chi-restraints excluded: chain L residue 80 LYS Chi-restraints excluded: chain H residue 14 HIS Chi-restraints excluded: chain H residue 71 GLN Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 198 SER Chi-restraints excluded: chain H residue 212 ARG Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 87 TYR Chi-restraints excluded: chain K residue 109 GLU Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 70 ASN Chi-restraints excluded: chain T residue 46 CYS Chi-restraints excluded: chain T residue 79 LEU Chi-restraints excluded: chain T residue 98 TYR Chi-restraints excluded: chain T residue 116 LEU Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain U residue 258 VAL Chi-restraints excluded: chain U residue 297 LEU Chi-restraints excluded: chain U residue 340 PHE Chi-restraints excluded: chain U residue 341 THR Chi-restraints excluded: chain U residue 347 VAL Chi-restraints excluded: chain U residue 362 THR Chi-restraints excluded: chain U residue 385 VAL Chi-restraints excluded: chain U residue 396 MET Chi-restraints excluded: chain U residue 407 VAL Chi-restraints excluded: chain U residue 408 MET Chi-restraints excluded: chain U residue 430 LEU Chi-restraints excluded: chain U residue 441 THR Chi-restraints excluded: chain U residue 447 ILE Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 313 ILE Chi-restraints excluded: chain V residue 315 ILE Chi-restraints excluded: chain V residue 331 MET Chi-restraints excluded: chain V residue 338 ILE Chi-restraints excluded: chain 0 residue 2 THR Chi-restraints excluded: chain 0 residue 26 TYR Chi-restraints excluded: chain 0 residue 28 ILE Chi-restraints excluded: chain 0 residue 69 ILE Chi-restraints excluded: chain 0 residue 70 TYR Chi-restraints excluded: chain 0 residue 144 VAL Chi-restraints excluded: chain 0 residue 149 LEU Chi-restraints excluded: chain 0 residue 151 CYS Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 1 residue 23 MET Chi-restraints excluded: chain 1 residue 67 ILE Chi-restraints excluded: chain 1 residue 85 SER Chi-restraints excluded: chain 1 residue 97 LEU Chi-restraints excluded: chain 1 residue 98 SER Chi-restraints excluded: chain 1 residue 110 ILE Chi-restraints excluded: chain 1 residue 113 VAL Chi-restraints excluded: chain 1 residue 115 ASP Chi-restraints excluded: chain 1 residue 140 VAL Chi-restraints excluded: chain 2 residue 24 VAL Chi-restraints excluded: chain 2 residue 44 MET Chi-restraints excluded: chain 2 residue 57 ILE Chi-restraints excluded: chain 2 residue 61 MET Chi-restraints excluded: chain 2 residue 64 ILE Chi-restraints excluded: chain 2 residue 102 SER Chi-restraints excluded: chain 2 residue 118 VAL Chi-restraints excluded: chain 2 residue 129 VAL Chi-restraints excluded: chain 3 residue 26 SER Chi-restraints excluded: chain 3 residue 44 MET Chi-restraints excluded: chain 3 residue 56 ILE Chi-restraints excluded: chain 3 residue 132 ILE Chi-restraints excluded: chain 3 residue 140 VAL Chi-restraints excluded: chain 4 residue 67 ILE Chi-restraints excluded: chain 4 residue 80 LEU Chi-restraints excluded: chain 4 residue 93 LEU Chi-restraints excluded: chain 4 residue 97 LEU Chi-restraints excluded: chain 4 residue 99 VAL Chi-restraints excluded: chain 4 residue 129 VAL Chi-restraints excluded: chain 4 residue 133 LEU Chi-restraints excluded: chain 4 residue 137 PHE Chi-restraints excluded: chain 4 residue 140 VAL Chi-restraints excluded: chain 5 residue 6 SER Chi-restraints excluded: chain 5 residue 24 VAL Chi-restraints excluded: chain 5 residue 45 SER Chi-restraints excluded: chain 5 residue 115 ASP Chi-restraints excluded: chain 5 residue 129 VAL Chi-restraints excluded: chain 5 residue 133 LEU Chi-restraints excluded: chain 5 residue 140 VAL Chi-restraints excluded: chain 5 residue 143 LEU Chi-restraints excluded: chain 6 residue 37 SER Chi-restraints excluded: chain 6 residue 46 VAL Chi-restraints excluded: chain 6 residue 47 MET Chi-restraints excluded: chain 6 residue 56 ILE Chi-restraints excluded: chain 6 residue 67 ILE Chi-restraints excluded: chain 6 residue 81 ASN Chi-restraints excluded: chain 6 residue 127 LEU Chi-restraints excluded: chain 7 residue 37 SER Chi-restraints excluded: chain 7 residue 41 ILE Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 7 residue 60 VAL Chi-restraints excluded: chain 7 residue 118 VAL Chi-restraints excluded: chain 7 residue 148 VAL Chi-restraints excluded: chain 7 residue 153 SER Chi-restraints excluded: chain 8 residue 55 SER Chi-restraints excluded: chain 8 residue 60 VAL Chi-restraints excluded: chain 8 residue 93 LEU Chi-restraints excluded: chain 8 residue 115 ASP Chi-restraints excluded: chain 8 residue 121 THR Chi-restraints excluded: chain 8 residue 123 GLN Chi-restraints excluded: chain 8 residue 135 LEU Chi-restraints excluded: chain 9 residue 34 THR Chi-restraints excluded: chain 9 residue 60 VAL Chi-restraints excluded: chain 9 residue 67 ILE Chi-restraints excluded: chain 9 residue 99 VAL Chi-restraints excluded: chain 9 residue 150 LEU Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 52 THR Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 122 ILE Chi-restraints excluded: chain Q residue 132 LEU Chi-restraints excluded: chain Q residue 155 LEU Chi-restraints excluded: chain Q residue 166 ASP Chi-restraints excluded: chain Q residue 181 ILE Chi-restraints excluded: chain Q residue 230 THR Chi-restraints excluded: chain Q residue 335 CYS Chi-restraints excluded: chain Q residue 344 ILE Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 466 ASP Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 516 LYS Chi-restraints excluded: chain A residue 525 TYR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 592 ASP Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 188 LYS Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 234 MET Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 359 ASP Chi-restraints excluded: chain F residue 402 MET Chi-restraints excluded: chain F residue 410 MET Chi-restraints excluded: chain F residue 435 MET Chi-restraints excluded: chain F residue 482 GLN Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 161 GLN Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 344 ARG Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 359 ASP Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain Z residue 146 THR Chi-restraints excluded: chain Z residue 228 THR Chi-restraints excluded: chain Z residue 241 VAL Chi-restraints excluded: chain X residue 35 THR Chi-restraints excluded: chain X residue 74 CYS Chi-restraints excluded: chain X residue 89 GLN Chi-restraints excluded: chain X residue 106 ASP Chi-restraints excluded: chain X residue 126 TYR Chi-restraints excluded: chain X residue 163 ILE Chi-restraints excluded: chain X residue 196 GLN Chi-restraints excluded: chain X residue 199 LEU Chi-restraints excluded: chain X residue 209 GLU Chi-restraints excluded: chain X residue 217 LEU Chi-restraints excluded: chain X residue 221 ASP Chi-restraints excluded: chain X residue 246 LEU Chi-restraints excluded: chain X residue 256 THR Chi-restraints excluded: chain X residue 264 ASP Chi-restraints excluded: chain X residue 267 VAL Chi-restraints excluded: chain Y residue 51 ASP Chi-restraints excluded: chain Y residue 95 VAL Chi-restraints excluded: chain Y residue 119 VAL Chi-restraints excluded: chain Y residue 136 LEU Chi-restraints excluded: chain Y residue 146 THR Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain Y residue 156 THR Chi-restraints excluded: chain Y residue 179 PHE Chi-restraints excluded: chain Y residue 204 VAL Chi-restraints excluded: chain Y residue 207 GLN Chi-restraints excluded: chain Y residue 241 VAL Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 85 GLN Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 172 ILE Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain N residue 14 GLU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 46 ASN Chi-restraints excluded: chain N residue 51 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 573 optimal weight: 7.9990 chunk 769 optimal weight: 9.9990 chunk 221 optimal weight: 10.0000 chunk 665 optimal weight: 6.9990 chunk 106 optimal weight: 40.0000 chunk 200 optimal weight: 0.0270 chunk 723 optimal weight: 3.9990 chunk 302 optimal weight: 8.9990 chunk 742 optimal weight: 1.9990 chunk 91 optimal weight: 40.0000 chunk 133 optimal weight: 10.0000 overall best weight: 4.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 194 ASN ** R 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 GLN ** K 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 330 ASN ** 0 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 ASN F 421 GLN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.144570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.111837 restraints weight = 123305.010| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.10 r_work: 0.3187 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.291 70970 Z= 0.336 Angle : 0.760 59.197 96108 Z= 0.409 Chirality : 0.043 0.502 11093 Planarity : 0.005 0.105 12396 Dihedral : 7.009 138.671 10273 Min Nonbonded Distance : 1.032 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.29 % Favored : 93.70 % Rotamer: Outliers : 4.74 % Allowed : 26.17 % Favored : 69.09 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 2.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.06 (0.09), residues: 9132 helix: 1.28 (0.07), residues: 5152 sheet: -1.08 (0.19), residues: 720 loop : -1.99 (0.10), residues: 3260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP S 52 HIS 0.011 0.001 HIS C 573 PHE 0.023 0.002 PHE A 337 TYR 0.088 0.002 TYR U 373 ARG 0.058 0.001 ARG R 179 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21849.42 seconds wall clock time: 380 minutes 51.45 seconds (22851.45 seconds total)