Starting phenix.real_space_refine on Tue Dec 12 04:04:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wm3_21848/12_2023/6wm3_21848_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wm3_21848/12_2023/6wm3_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_21848/12_2023/6wm3_21848.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wm3_21848/12_2023/6wm3_21848.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wm3_21848/12_2023/6wm3_21848_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wm3_21848/12_2023/6wm3_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: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 27.42, per 1000 atoms: 0.39 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: 22.67 Conformation dependent library (CDL) restraints added in 10.7 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: 11.15 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: 24.72 Time building geometry restraints manager: 24.87 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: 2.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 12.670 Check model and map are aligned: 0.800 Set scattering table: 0.470 Process input model: 146.980 Find NCS groups from input model: 3.280 Set up NCS constraints: 0.460 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:2.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 169.510 ------------------------------------------------------------------------------- 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 : 6.373 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 outliers start: 625 outliers final: 461 residues processed: 1641 average time/residue: 0.6634 time to fit residues: 1854.5885 Evaluate side-chains 1402 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 461 poor density : 941 time to evaluate : 6.238 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 461 outliers final: 1 residues processed: 461 average time/residue: 0.5163 time to fit residues: 457.3240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 382 optimal weight: 3.9990 chunk 235 optimal weight: 10.0000 chunk 465 optimal weight: 3.9990 chunk 368 optimal weight: 2.9990 chunk 713 optimal weight: 3.9990 chunk 276 optimal weight: 0.9980 chunk 433 optimal weight: 7.9990 chunk 530 optimal weight: 0.9990 chunk 826 optimal weight: 20.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 41 ASN R 76 ASN R 85 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 465 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 206 GLN J 221 ASN M 10 GLN M 90 GLN I 122 GLN I 206 GLN L 111 HIS H 49 GLN K 13 GLN K 35 GLN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** V 330 ASN 0 51 ASN 0 148 ASN ** 1 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 81 ASN 7 78 ASN 9 123 GLN Q 88 HIS Q 297 HIS Q 309 GLN ** Q 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 338 GLN C 444 HIS A 140 ASN A 314 ASN ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 ASN B 184 ASN B 231 GLN 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 Z 222 GLN X 19 HIS X 160 GLN ** Y 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 76 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 70970 Z= 0.225 Angle : 0.597 19.343 96108 Z= 0.314 Chirality : 0.042 0.176 11093 Planarity : 0.005 0.049 12396 Dihedral : 5.502 145.334 10084 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.82 % Favored : 95.17 % Rotamer: Outliers : 2.74 % Allowed : 21.38 % Favored : 75.88 % 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: -1.19 (0.09), residues: 9132 helix: 0.54 (0.07), residues: 5157 sheet: -2.20 (0.17), residues: 738 loop : -2.65 (0.10), residues: 3237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 450 HIS 0.005 0.001 HIS U 348 PHE 0.028 0.001 PHE B 196 TYR 0.035 0.001 TYR Y 139 ARG 0.010 0.000 ARG N 32 *********************** 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 1268 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 1074 time to evaluate : 6.365 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 outliers start: 194 outliers final: 85 residues processed: 1216 average time/residue: 0.6732 time to fit residues: 1397.8812 Evaluate side-chains 1034 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 949 time to evaluate : 6.208 Switching outliers to nearest non-outliers outliers start: 85 outliers final: 0 residues processed: 85 average time/residue: 0.5597 time to fit residues: 96.5191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 459 optimal weight: 2.9990 chunk 256 optimal weight: 5.9990 chunk 687 optimal weight: 2.9990 chunk 562 optimal weight: 0.0870 chunk 227 optimal weight: 7.9990 chunk 827 optimal weight: 30.0000 chunk 894 optimal weight: 30.0000 chunk 737 optimal weight: 4.9990 chunk 820 optimal weight: 20.0000 chunk 282 optimal weight: 1.9990 chunk 664 optimal weight: 0.7980 overall best weight: 1.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 85 ASN ** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 106 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 748 HIS J 66 GLN ** J 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 78 GLN L 6 GLN ** K 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 51 ASN ** 6 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 78 ASN 9 51 GLN 9 123 GLN ** Q 60 ASN ** 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 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN B 123 ASN F 421 GLN D 421 GLN ** E 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 165 GLN Y 19 HIS N 83 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1742 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= 0.203 Angle : 0.567 19.279 96108 Z= 0.294 Chirality : 0.041 0.247 11093 Planarity : 0.004 0.046 12396 Dihedral : 5.210 143.437 10084 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.10 % Favored : 94.89 % Rotamer: Outliers : 2.57 % Allowed : 22.59 % Favored : 74.83 % 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: -0.60 (0.09), residues: 9132 helix: 1.02 (0.07), residues: 5139 sheet: -1.88 (0.18), residues: 748 loop : -2.40 (0.10), residues: 3245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 567 HIS 0.005 0.001 HIS B 444 PHE 0.023 0.001 PHE R 578 TYR 0.038 0.001 TYR Y 139 ARG 0.009 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 1212 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1030 time to evaluate : 7.091 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 outliers start: 182 outliers final: 106 residues processed: 1147 average time/residue: 0.6749 time to fit residues: 1330.4748 Evaluate side-chains 1050 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 944 time to evaluate : 6.229 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 106 outliers final: 1 residues processed: 106 average time/residue: 0.5157 time to fit residues: 112.3948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 817 optimal weight: 8.9990 chunk 622 optimal weight: 0.8980 chunk 429 optimal weight: 9.9990 chunk 91 optimal weight: 0.7980 chunk 395 optimal weight: 0.8980 chunk 555 optimal weight: 5.9990 chunk 830 optimal weight: 4.9990 chunk 879 optimal weight: 20.0000 chunk 434 optimal weight: 6.9990 chunk 787 optimal weight: 0.0070 chunk 237 optimal weight: 6.9990 overall best weight: 1.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 85 ASN ** R 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 365 ASN ** R 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 66 GLN ** K 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 327 ASN ** 6 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 51 GLN ** Q 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 430 GLN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN B 123 ASN B 397 ASN F 421 GLN F 456 GLN E 54 ASN Z 165 GLN N 83 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 70970 Z= 0.185 Angle : 0.554 19.385 96108 Z= 0.286 Chirality : 0.040 0.175 11093 Planarity : 0.004 0.045 12396 Dihedral : 5.018 141.246 10084 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.79 % Favored : 95.20 % Rotamer: Outliers : 1.95 % Allowed : 24.13 % Favored : 73.91 % 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: -0.26 (0.09), residues: 9132 helix: 1.26 (0.07), residues: 5134 sheet: -1.58 (0.18), residues: 727 loop : -2.22 (0.10), residues: 3271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 52 HIS 0.005 0.001 HIS B 444 PHE 0.024 0.001 PHE B 196 TYR 0.029 0.001 TYR Y 139 ARG 0.011 0.000 ARG 7 126 *********************** 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 1173 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1035 time to evaluate : 6.420 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 outliers start: 138 outliers final: 59 residues processed: 1127 average time/residue: 0.6724 time to fit residues: 1301.0690 Evaluate side-chains 1008 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 949 time to evaluate : 7.382 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 0 residues processed: 59 average time/residue: 0.5473 time to fit residues: 67.9915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 12 optimal weight: 30.0000 chunk 654 optimal weight: 8.9990 chunk 362 optimal weight: 10.0000 chunk 750 optimal weight: 5.9990 chunk 608 optimal weight: 20.0000 chunk 1 optimal weight: 50.0000 chunk 449 optimal weight: 10.0000 chunk 789 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 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 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 216 HIS ** R 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 365 ASN ** R 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 66 GLN L 35 GLN ** K 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 330 ASN ** 1 51 GLN ** 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 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 311 HIS C 449 ASN ** 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** B 123 ASN F 200 ASN N 83 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 70970 Z= 0.454 Angle : 0.676 20.835 96108 Z= 0.352 Chirality : 0.045 0.233 11093 Planarity : 0.005 0.081 12396 Dihedral : 5.400 143.326 10084 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.53 % Favored : 93.46 % Rotamer: Outliers : 2.60 % Allowed : 25.11 % Favored : 72.29 % 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: -0.46 (0.09), residues: 9132 helix: 0.99 (0.07), residues: 5173 sheet: -1.44 (0.19), residues: 710 loop : -2.20 (0.10), residues: 3249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP S 52 HIS 0.009 0.001 HIS Q 340 PHE 0.027 0.002 PHE Q 3 TYR 0.041 0.002 TYR 6 68 ARG 0.006 0.001 ARG C 364 *********************** 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 1117 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 933 time to evaluate : 6.303 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 outliers start: 184 outliers final: 118 residues processed: 1057 average time/residue: 0.6820 time to fit residues: 1238.5598 Evaluate side-chains 1015 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 897 time to evaluate : 6.213 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 118 outliers final: 1 residues processed: 118 average time/residue: 0.5237 time to fit residues: 125.8635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 295 optimal weight: 0.7980 chunk 792 optimal weight: 9.9990 chunk 173 optimal weight: 30.0000 chunk 516 optimal weight: 0.9980 chunk 217 optimal weight: 3.9990 chunk 880 optimal weight: 5.9990 chunk 730 optimal weight: 2.9990 chunk 407 optimal weight: 2.9990 chunk 73 optimal weight: 20.0000 chunk 291 optimal weight: 4.9990 chunk 462 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 85 ASN ** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 365 ASN ** R 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 614 ASN J 66 GLN ** K 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** Q 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 311 HIS C 449 ASN ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 ASN B 65 GLN B 123 ASN B 397 ASN F 421 GLN N 83 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 70970 Z= 0.223 Angle : 0.579 21.118 96108 Z= 0.299 Chirality : 0.041 0.193 11093 Planarity : 0.004 0.047 12396 Dihedral : 5.128 141.273 10084 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.89 % Favored : 95.09 % Rotamer: Outliers : 1.37 % Allowed : 26.09 % Favored : 72.54 % 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: -0.14 (0.09), residues: 9132 helix: 1.25 (0.07), residues: 5155 sheet: -1.35 (0.19), residues: 723 loop : -2.03 (0.10), residues: 3254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP S 52 HIS 0.006 0.001 HIS 0 132 PHE 0.034 0.001 PHE R 240 TYR 0.044 0.001 TYR J 56 ARG 0.008 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 1081 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 984 time to evaluate : 6.304 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 outliers start: 97 outliers final: 39 residues processed: 1051 average time/residue: 0.6835 time to fit residues: 1237.6537 Evaluate side-chains 991 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 952 time to evaluate : 6.287 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 39 outliers final: 1 residues processed: 39 average time/residue: 0.5560 time to fit residues: 48.8158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 848 optimal weight: 8.9990 chunk 99 optimal weight: 50.0000 chunk 501 optimal weight: 3.9990 chunk 642 optimal weight: 1.9990 chunk 498 optimal weight: 10.0000 chunk 741 optimal weight: 3.9990 chunk 491 optimal weight: 8.9990 chunk 877 optimal weight: 9.9990 chunk 548 optimal weight: 3.9990 chunk 534 optimal weight: 2.9990 chunk 404 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 85 ASN ** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 365 ASN ** R 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 66 GLN H 49 GLN ** K 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 330 ASN ** 0 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 132 HIS 7 78 ASN ** 9 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 ASN B 397 ASN F 421 GLN ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 83 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 70970 Z= 0.259 Angle : 0.591 22.369 96108 Z= 0.304 Chirality : 0.042 0.234 11093 Planarity : 0.004 0.047 12396 Dihedral : 5.079 140.134 10084 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.63 % Favored : 94.36 % Rotamer: Outliers : 1.43 % Allowed : 27.00 % Favored : 71.57 % 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: -0.09 (0.09), residues: 9132 helix: 1.31 (0.07), residues: 5150 sheet: -1.22 (0.19), residues: 713 loop : -2.08 (0.10), residues: 3269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP S 52 HIS 0.005 0.001 HIS 0 132 PHE 0.030 0.001 PHE R 578 TYR 0.036 0.001 TYR 6 68 ARG 0.011 0.000 ARG N 75 *********************** 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 1055 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 954 time to evaluate : 6.306 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 outliers start: 101 outliers final: 57 residues processed: 1017 average time/residue: 0.6827 time to fit residues: 1194.2759 Evaluate side-chains 984 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 927 time to evaluate : 6.332 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 0 residues processed: 57 average time/residue: 0.5465 time to fit residues: 67.3034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 542 optimal weight: 0.9980 chunk 350 optimal weight: 0.7980 chunk 523 optimal weight: 0.9990 chunk 264 optimal weight: 2.9990 chunk 172 optimal weight: 5.9990 chunk 169 optimal weight: 7.9990 chunk 557 optimal weight: 7.9990 chunk 597 optimal weight: 7.9990 chunk 433 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 689 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 85 ASN ** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 365 ASN ** R 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 66 GLN H 49 GLN ** K 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 ASN F 421 GLN D 421 GLN ** Z 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 GLN G 206 GLN N 83 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 70970 Z= 0.180 Angle : 0.564 21.002 96108 Z= 0.288 Chirality : 0.040 0.204 11093 Planarity : 0.004 0.046 12396 Dihedral : 4.885 136.961 10084 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.54 % Favored : 95.44 % Rotamer: Outliers : 0.51 % Allowed : 27.44 % Favored : 72.05 % 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: 0.12 (0.09), residues: 9132 helix: 1.50 (0.07), residues: 5124 sheet: -1.17 (0.19), residues: 716 loop : -1.98 (0.10), residues: 3292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP S 52 HIS 0.012 0.001 HIS A 573 PHE 0.026 0.001 PHE I 38 TYR 0.040 0.001 TYR U 373 ARG 0.008 0.000 ARG N 75 *********************** 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 1051 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 1015 time to evaluate : 6.480 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 outliers start: 36 outliers final: 14 residues processed: 1037 average time/residue: 0.7159 time to fit residues: 1278.9454 Evaluate side-chains 972 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 958 time to evaluate : 6.216 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 14 outliers final: 1 residues processed: 14 average time/residue: 0.5299 time to fit residues: 22.6541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 797 optimal weight: 2.9990 chunk 840 optimal weight: 9.9990 chunk 766 optimal weight: 3.9990 chunk 817 optimal weight: 8.9990 chunk 491 optimal weight: 9.9990 chunk 356 optimal weight: 10.0000 chunk 641 optimal weight: 2.9990 chunk 250 optimal weight: 10.0000 chunk 738 optimal weight: 6.9990 chunk 773 optimal weight: 4.9990 chunk 814 optimal weight: 0.0470 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 348 HIS ** U 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 330 ASN ** 0 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 51 GLN ** Q 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 GLN ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN B 123 ASN F 421 GLN D 421 GLN ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 67 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 70970 Z= 0.274 Angle : 0.603 20.887 96108 Z= 0.309 Chirality : 0.042 0.321 11093 Planarity : 0.004 0.087 12396 Dihedral : 4.968 136.790 10084 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.41 % Favored : 94.58 % Rotamer: Outliers : 0.69 % Allowed : 27.85 % Favored : 71.45 % 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: 0.10 (0.09), residues: 9132 helix: 1.43 (0.07), residues: 5144 sheet: -1.04 (0.19), residues: 717 loop : -1.96 (0.10), residues: 3271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP S 52 HIS 0.010 0.001 HIS 0 132 PHE 0.030 0.001 PHE R 578 TYR 0.035 0.001 TYR 6 68 ARG 0.010 0.000 ARG B 553 *********************** 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 1009 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 960 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 outliers start: 49 outliers final: 34 residues processed: 980 average time/residue: 0.6982 time to fit residues: 1169.2835 Evaluate side-chains 965 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 931 time to evaluate : 6.284 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.5203 time to fit residues: 42.0556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 536 optimal weight: 0.9980 chunk 864 optimal weight: 3.9990 chunk 527 optimal weight: 1.9990 chunk 410 optimal weight: 0.0050 chunk 600 optimal weight: 4.9990 chunk 906 optimal weight: 20.0000 chunk 834 optimal weight: 50.0000 chunk 721 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 chunk 557 optimal weight: 7.9990 chunk 442 optimal weight: 0.6980 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 ASN F 421 GLN D 421 GLN D 433 GLN ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 83 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 70970 Z= 0.172 Angle : 0.571 19.489 96108 Z= 0.292 Chirality : 0.041 0.291 11093 Planarity : 0.004 0.046 12396 Dihedral : 4.785 133.317 10084 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.38 % Favored : 95.61 % Rotamer: Outliers : 0.28 % Allowed : 27.99 % Favored : 71.72 % 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: 0.26 (0.09), residues: 9132 helix: 1.58 (0.07), residues: 5115 sheet: -1.00 (0.19), residues: 732 loop : -1.88 (0.11), residues: 3285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP S 52 HIS 0.009 0.001 HIS 0 132 PHE 0.024 0.001 PHE 5 128 TYR 0.038 0.001 TYR U 373 ARG 0.008 0.000 ARG B 553 ********************** 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 1029 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 1009 time to evaluate : 6.369 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 outliers start: 20 outliers final: 12 residues processed: 1018 average time/residue: 0.7117 time to fit residues: 1238.5970 Evaluate side-chains 973 residues out of total 7804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 961 time to evaluate : 6.356 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.5774 time to fit residues: 21.5459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 573 optimal weight: 6.9990 chunk 769 optimal weight: 10.0000 chunk 221 optimal weight: 0.9980 chunk 665 optimal weight: 0.9990 chunk 106 optimal weight: 50.0000 chunk 200 optimal weight: 5.9990 chunk 723 optimal weight: 5.9990 chunk 302 optimal weight: 10.0000 chunk 742 optimal weight: 4.9990 chunk 91 optimal weight: 50.0000 chunk 133 optimal weight: 9.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 46 GLN ** U 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 330 ASN ** 0 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 56 ASN ** Q 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 ASN F 421 GLN D 421 GLN E 181 ASN ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.146815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.114364 restraints weight = 123374.221| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.13 r_work: 0.3226 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 70970 Z= 0.330 Angle : 0.639 19.377 96108 Z= 0.329 Chirality : 0.043 0.309 11093 Planarity : 0.005 0.102 12396 Dihedral : 5.028 135.014 10084 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.80 % Favored : 94.19 % Rotamer: Outliers : 0.41 % Allowed : 28.39 % Favored : 71.20 % 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: 0.15 (0.09), residues: 9132 helix: 1.44 (0.07), residues: 5139 sheet: -0.96 (0.19), residues: 742 loop : -1.90 (0.11), residues: 3251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP S 52 HIS 0.021 0.001 HIS R 801 PHE 0.044 0.002 PHE 6 13 TYR 0.049 0.002 TYR J 56 ARG 0.019 0.000 ARG 8 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21241.13 seconds wall clock time: 370 minutes 25.28 seconds (22225.28 seconds total)