Starting phenix.real_space_refine on Sat Mar 23 00:40:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l7o_0849/03_2024/6l7o_0849_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l7o_0849/03_2024/6l7o_0849.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l7o_0849/03_2024/6l7o_0849.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l7o_0849/03_2024/6l7o_0849.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l7o_0849/03_2024/6l7o_0849_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l7o_0849/03_2024/6l7o_0849_neut_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 14 7.16 5 P 9 5.49 5 S 184 5.16 5 C 23515 2.51 5 N 5205 2.21 5 O 6110 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 2": "OE1" <-> "OE2" Residue "A ASP 23": "OD1" <-> "OD2" Residue "A ARG 62": "NH1" <-> "NH2" Residue "A GLU 66": "OE1" <-> "OE2" Residue "A ASP 79": "OD1" <-> "OD2" Residue "A PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 88": "OD1" <-> "OD2" Residue "A PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A ASP 233": "OD1" <-> "OD2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "A GLU 248": "OE1" <-> "OE2" Residue "A TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 287": "OE1" <-> "OE2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A ASP 338": "OD1" <-> "OD2" Residue "A ASP 342": "OD1" <-> "OD2" Residue "B ASP 2": "OD1" <-> "OD2" Residue "B ASP 40": "OD1" <-> "OD2" Residue "B PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 100": "NH1" <-> "NH2" Residue "B GLU 103": "OE1" <-> "OE2" Residue "B PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 155": "NH1" <-> "NH2" Residue "B TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 204": "OE1" <-> "OE2" Residue "B PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 272": "OD1" <-> "OD2" Residue "B PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 353": "NH1" <-> "NH2" Residue "B PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 427": "NH1" <-> "NH2" Residue "B GLU 436": "OE1" <-> "OE2" Residue "B GLU 442": "OE1" <-> "OE2" Residue "B ASP 491": "OD1" <-> "OD2" Residue "C TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 85": "OD1" <-> "OD2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "C ARG 125": "NH1" <-> "NH2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "D PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 26": "OD1" <-> "OD2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 58": "OD1" <-> "OD2" Residue "D ASP 85": "OD1" <-> "OD2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 205": "OD1" <-> "OD2" Residue "D PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 237": "OD1" <-> "OD2" Residue "D ARG 264": "NH1" <-> "NH2" Residue "D TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 356": "NH1" <-> "NH2" Residue "D GLU 363": "OE1" <-> "OE2" Residue "D GLU 398": "OE1" <-> "OE2" Residue "D PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 440": "OE1" <-> "OE2" Residue "D ASP 458": "OD1" <-> "OD2" Residue "D ARG 462": "NH1" <-> "NH2" Residue "D PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 489": "OD1" <-> "OD2" Residue "D ARG 498": "NH1" <-> "NH2" Residue "D ARG 500": "NH1" <-> "NH2" Residue "E ARG 25": "NH1" <-> "NH2" Residue "E ARG 29": "NH1" <-> "NH2" Residue "E TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ASP 92": "OD1" <-> "OD2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "F GLU 2": "OE1" <-> "OE2" Residue "F PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "F TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 112": "OD1" <-> "OD2" Residue "F ASP 118": "OD1" <-> "OD2" Residue "F ARG 123": "NH1" <-> "NH2" Residue "F PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 152": "OE1" <-> "OE2" Residue "F TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 204": "OD1" <-> "OD2" Residue "F ASP 210": "OD1" <-> "OD2" Residue "F PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 255": "OE1" <-> "OE2" Residue "F PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 368": "OE1" <-> "OE2" Residue "F ASP 376": "OD1" <-> "OD2" Residue "F ASP 418": "OD1" <-> "OD2" Residue "F GLU 419": "OE1" <-> "OE2" Residue "F PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 448": "NH1" <-> "NH2" Residue "F PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 459": "NH1" <-> "NH2" Residue "F GLU 481": "OE1" <-> "OE2" Residue "F PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 512": "OE1" <-> "OE2" Residue "F PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 529": "OD1" <-> "OD2" Residue "F PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 583": "OD1" <-> "OD2" Residue "F TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 596": "NH1" <-> "NH2" Residue "F ASP 610": "OD1" <-> "OD2" Residue "F PHE 637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 85": "OE1" <-> "OE2" Residue "G ASP 142": "OD1" <-> "OD2" Residue "G GLU 148": "OE1" <-> "OE2" Residue "G GLU 168": "OE1" <-> "OE2" Residue "G GLU 172": "OE1" <-> "OE2" Residue "G GLU 179": "OE1" <-> "OE2" Residue "G GLU 193": "OE1" <-> "OE2" Residue "H GLU 5": "OE1" <-> "OE2" Residue "H TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 71": "OD1" <-> "OD2" Residue "H PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 87": "OE1" <-> "OE2" Residue "H ARG 110": "NH1" <-> "NH2" Residue "H ASP 124": "OD1" <-> "OD2" Residue "H TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 137": "OE1" <-> "OE2" Residue "H GLU 139": "OE1" <-> "OE2" Residue "H ASP 143": "OD1" <-> "OD2" Residue "H PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 146": "OE1" <-> "OE2" Residue "H PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 192": "NH1" <-> "NH2" Residue "H PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 213": "OE1" <-> "OE2" Residue "H ASP 233": "OD1" <-> "OD2" Residue "H ARG 235": "NH1" <-> "NH2" Residue "H ASP 238": "OD1" <-> "OD2" Residue "H TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 261": "NH1" <-> "NH2" Residue "H GLU 268": "OE1" <-> "OE2" Residue "H ARG 270": "NH1" <-> "NH2" Residue "H GLU 271": "OE1" <-> "OE2" Residue "H ASP 281": "OD1" <-> "OD2" Residue "H GLU 289": "OE1" <-> "OE2" Residue "H GLU 298": "OE1" <-> "OE2" Residue "H GLU 303": "OE1" <-> "OE2" Residue "H PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 345": "OD1" <-> "OD2" Residue "H ASP 346": "OD1" <-> "OD2" Residue "H ARG 352": "NH1" <-> "NH2" Residue "H ASP 377": "OD1" <-> "OD2" Residue "I PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 13": "OE1" <-> "OE2" Residue "I ARG 35": "NH1" <-> "NH2" Residue "I GLU 50": "OE1" <-> "OE2" Residue "I PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 67": "OE1" <-> "OE2" Residue "I ASP 81": "OD1" <-> "OD2" Residue "I GLU 87": "OE1" <-> "OE2" Residue "I GLU 92": "OE1" <-> "OE2" Residue "I TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 122": "OE1" <-> "OE2" Residue "I GLU 123": "OE1" <-> "OE2" Residue "I TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 130": "OD1" <-> "OD2" Residue "I ARG 131": "NH1" <-> "NH2" Residue "I TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 151": "OD1" <-> "OD2" Residue "I ASP 172": "OD1" <-> "OD2" Residue "I GLU 182": "OE1" <-> "OE2" Residue "I GLU 185": "OE1" <-> "OE2" Residue "J ARG 43": "NH1" <-> "NH2" Residue "J ARG 45": "NH1" <-> "NH2" Residue "J ARG 62": "NH1" <-> "NH2" Residue "J TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 74": "OD1" <-> "OD2" Residue "J ASP 89": "OD1" <-> "OD2" Residue "J PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 102": "NH1" <-> "NH2" Residue "J ASP 104": "OD1" <-> "OD2" Residue "J ASP 118": "OD1" <-> "OD2" Residue "J GLU 123": "OE1" <-> "OE2" Residue "J ASP 146": "OD1" <-> "OD2" Residue "J ARG 153": "NH1" <-> "NH2" Residue "J ASP 155": "OD1" <-> "OD2" Residue "K GLU 17": "OE1" <-> "OE2" Residue "K ARG 69": "NH1" <-> "NH2" Residue "K ARG 75": "NH1" <-> "NH2" Residue "K ARG 79": "NH1" <-> "NH2" Residue "K ASP 82": "OD1" <-> "OD2" Residue "K ARG 133": "NH1" <-> "NH2" Residue "K ASP 142": "OD1" <-> "OD2" Residue "K TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 153": "OE1" <-> "OE2" Residue "K ARG 207": "NH1" <-> "NH2" Residue "L PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 72": "NH1" <-> "NH2" Residue "M TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 27": "OE1" <-> "OE2" Residue "M GLU 38": "OE1" <-> "OE2" Residue "M GLU 55": "OE1" <-> "OE2" Residue "M ASP 76": "OD1" <-> "OD2" Residue "M GLU 78": "OE1" <-> "OE2" Residue "M PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 14": "OE1" <-> "OE2" Residue "N PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 26": "OE1" <-> "OE2" Residue "N TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "N ARG 107": "NH1" <-> "NH2" Residue "N GLU 141": "OE1" <-> "OE2" Residue "N ASP 145": "OD1" <-> "OD2" Residue "O ASP 7": "OD1" <-> "OD2" Residue "O ASP 26": "OD1" <-> "OD2" Residue "O ARG 28": "NH1" <-> "NH2" Residue "O ARG 37": "NH1" <-> "NH2" Residue "O ASP 42": "OD1" <-> "OD2" Residue "O ARG 44": "NH1" <-> "NH2" Residue "O ASP 46": "OD1" <-> "OD2" Residue "O ARG 62": "NH1" <-> "NH2" Residue "O GLU 67": "OE1" <-> "OE2" Residue "P ARG 28": "NH1" <-> "NH2" Residue "P PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 35": "OD1" <-> "OD2" Residue "Q PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 21": "OE1" <-> "OE2" Residue "R ASP 22": "OD1" <-> "OD2" Residue "R GLU 23": "OE1" <-> "OE2" Residue "R ASP 27": "OD1" <-> "OD2" Residue "R GLU 30": "OE1" <-> "OE2" Residue "R GLU 31": "OE1" <-> "OE2" Residue "R ASP 35": "OD1" <-> "OD2" Residue "R GLU 54": "OE1" <-> "OE2" Residue "R GLU 56": "OE1" <-> "OE2" Residue "R ASP 58": "OD1" <-> "OD2" Residue "R ASP 61": "OD1" <-> "OD2" Residue "R PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 68": "OD1" <-> "OD2" Residue "R GLU 71": "OE1" <-> "OE2" Residue "R GLU 93": "OE1" <-> "OE2" Residue "R TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 40": "OD1" <-> "OD2" Residue "S PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 69": "NH1" <-> "NH2" Residue "S ASP 85": "OD1" <-> "OD2" Residue "S GLU 94": "OE1" <-> "OE2" Residue "S GLU 96": "OE1" <-> "OE2" Residue "V GLU 46": "OE1" <-> "OE2" Residue "V PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 50": "OE1" <-> "OE2" Residue "V ASP 66": "OD1" <-> "OD2" Residue "V ARG 70": "NH1" <-> "NH2" Residue "V GLU 72": "OE1" <-> "OE2" Residue "V GLU 79": "OE1" <-> "OE2" Residue "V PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 121": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 35037 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 2859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2859 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 3732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3732 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 18, 'TRANS': 474} Chain: "C" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 978 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "D" Number of atoms: 3896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3896 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 26, 'TRANS': 477} Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 783 Classifications: {'peptide': 101} Link IDs: {'TRANS': 100} Chain: "F" Number of atoms: 5004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5004 Classifications: {'peptide': 647} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 32, 'TRANS': 614} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1463 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 13, 'TRANS': 178} Chain: "H" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3177 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 22, 'TRANS': 370} Chain: "I" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1525 Classifications: {'peptide': 190} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 177} Chain: "J" Number of atoms: 1278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1278 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 11, 'TRANS': 144} Chain: "K" Number of atoms: 1597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1597 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 184} Chain: "L" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 590 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 5, 'TRANS': 67} Chain: "M" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 879 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "N" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1165 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 11, 'TRANS': 136} Chain: "O" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 538 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 5, 'TRANS': 62} Chain: "P" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 321 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "Q" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 332 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "R" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 748 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "S" Number of atoms: 485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 485 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "V" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 797 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "A" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 381 Unusual residues: {'AJP': 5, 'BCR': 1, 'DGD': 2, 'LHG': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 290 Unresolved non-hydrogen angles: 435 Unresolved non-hydrogen dihedrals: 625 Unresolved non-hydrogen chiralities: 120 Chain: "B" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 618 Unusual residues: {'AJP': 12, 'LHG': 3, 'PQN': 1, 'SQD': 1} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 696 Unresolved non-hydrogen angles: 1044 Unresolved non-hydrogen dihedrals: 1500 Unresolved non-hydrogen chiralities: 288 Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'AJP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 48 Chain: "D" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 482 Unusual residues: {'AJP': 12, 'LHG': 2} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 696 Unresolved non-hydrogen angles: 1044 Unresolved non-hydrogen dihedrals: 1500 Unresolved non-hydrogen chiralities: 288 Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'AJP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 24 Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 662 Unusual residues: {'AJP': 13, 'BCR': 1, 'LHG': 2, 'SQD': 2} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 754 Unresolved non-hydrogen angles: 1131 Unresolved non-hydrogen dihedrals: 1625 Unresolved non-hydrogen chiralities: 312 Chain: "G" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 224 Unusual residues: {'AJP': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 406 Unresolved non-hydrogen angles: 609 Unresolved non-hydrogen dihedrals: 875 Unresolved non-hydrogen chiralities: 168 Chain: "H" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'SQD': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 256 Unusual residues: {'AJP': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 464 Unresolved non-hydrogen angles: 696 Unresolved non-hydrogen dihedrals: 1000 Unresolved non-hydrogen chiralities: 192 Chain: "R" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 22739 SG CYS I 103 55.643 52.477 50.265 1.00 39.26 S ATOM 22783 SG CYS I 109 51.527 46.691 47.807 1.00 50.41 S ATOM 22488 SG CYS I 73 54.151 45.896 53.644 1.00 48.74 S ATOM 22416 SG CYS I 63 39.311 45.723 49.087 1.00 71.75 S ATOM 22435 SG CYS I 66 41.935 40.175 49.035 1.00 61.84 S ATOM 25567 SG CYS K 117 67.001 54.779 55.928 1.00 33.34 S ATOM 25069 SG CYS K 53 68.736 57.832 51.380 1.00 42.53 S ATOM 25063 SG CYS K 52 70.759 53.458 49.683 1.00 47.63 S ATOM 25793 SG CYS K 148 63.834 52.389 51.092 1.00 42.59 S ATOM 30707 SG CYS R 78 40.720 28.949 44.847 1.00117.98 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N CYS R 86 " occ=0.50 ... (4 atoms not shown) pdb=" SG CYS R 86 " occ=0.50 Time building chain proxies: 17.80, per 1000 atoms: 0.51 Number of scatterers: 35037 At special positions: 0 Unit cell: (237.62, 138.43, 182.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 14 26.01 S 184 16.00 P 9 15.00 O 6110 8.00 N 5205 7.00 C 23515 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=28, symmetry=0 Number of additional bonds: simple=28, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.54 Conformation dependent library (CDL) restraints added in 6.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES R 101 " pdb="FE2 FES R 101 " - pdb=" SG CYS R 78 " pdb="FE2 FES R 101 " - pdb=" SG CYS R 48 " pdb="FE1 FES R 101 " - pdb=" SG CYS R 40 " pdb=" SF4 I 201 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 109 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 73 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 103 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 106 " pdb=" SF4 I 202 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 66 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 63 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 69 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 113 " pdb=" SF4 K 301 " pdb="FE1 SF4 K 301 " - pdb=" SG CYS K 117 " pdb="FE4 SF4 K 301 " - pdb=" SG CYS K 148 " pdb="FE2 SF4 K 301 " - pdb=" SG CYS K 53 " pdb="FE3 SF4 K 301 " - pdb=" SG CYS K 52 " Number of angles added : 40 8156 Ramachandran restraints generated. 4078 Oldfield, 0 Emsley, 4078 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7582 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 154 helices and 15 sheets defined 54.3% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.14 Creating SS restraints... Processing helix chain 'A' and resid 7 through 18 Processing helix chain 'A' and resid 24 through 27 No H-bonds generated for 'chain 'A' and resid 24 through 27' Processing helix chain 'A' and resid 30 through 59 removed outlier: 3.783A pdb=" N LEU A 38 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 82 Processing helix chain 'A' and resid 96 through 115 Proline residue: A 103 - end of helix Proline residue: A 109 - end of helix removed outlier: 4.471A pdb=" N TYR A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ILE A 115 " --> pdb=" O PHE A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 136 removed outlier: 3.597A pdb=" N ILE A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 153 Processing helix chain 'A' and resid 156 through 187 removed outlier: 3.834A pdb=" N LEU A 160 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 171 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TYR A 172 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU A 173 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ILE A 174 " --> pdb=" O ILE A 170 " (cutoff:3.500A) Proline residue: A 175 - end of helix removed outlier: 3.578A pdb=" N VAL A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N MET A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 200 Processing helix chain 'A' and resid 204 through 206 No H-bonds generated for 'chain 'A' and resid 204 through 206' Processing helix chain 'A' and resid 208 through 211 No H-bonds generated for 'chain 'A' and resid 208 through 211' Processing helix chain 'A' and resid 213 through 227 Processing helix chain 'A' and resid 251 through 275 removed outlier: 3.649A pdb=" N SER A 273 " --> pdb=" O ALA A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 293 Processing helix chain 'A' and resid 300 through 329 removed outlier: 3.601A pdb=" N ALA A 305 " --> pdb=" O PHE A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 365 removed outlier: 4.546A pdb=" N LEU A 349 " --> pdb=" O TRP A 345 " (cutoff:3.500A) Proline residue: A 350 - end of helix Processing helix chain 'B' and resid 4 through 10 Processing helix chain 'B' and resid 16 through 34 Processing helix chain 'B' and resid 43 through 62 removed outlier: 3.504A pdb=" N THR B 57 " --> pdb=" O GLY B 53 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N MET B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ILE B 59 " --> pdb=" O ILE B 55 " (cutoff:3.500A) Proline residue: B 60 - end of helix Processing helix chain 'B' and resid 78 through 105 removed outlier: 5.332A pdb=" N ARG B 100 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N TYR B 101 " --> pdb=" O MET B 97 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU B 103 " --> pdb=" O ILE B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 126 removed outlier: 3.696A pdb=" N ILE B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 150 Processing helix chain 'B' and resid 159 through 187 removed outlier: 3.804A pdb=" N LYS B 165 " --> pdb=" O GLU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 200 removed outlier: 3.893A pdb=" N GLN B 199 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ALA B 200 " --> pdb=" O ALA B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 223 removed outlier: 3.916A pdb=" N GLY B 218 " --> pdb=" O PHE B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 228 No H-bonds generated for 'chain 'B' and resid 226 through 228' Processing helix chain 'B' and resid 232 through 238 removed outlier: 4.361A pdb=" N GLU B 237 " --> pdb=" O PRO B 233 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY B 238 " --> pdb=" O ASP B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 247 Processing helix chain 'B' and resid 250 through 266 Processing helix chain 'B' and resid 271 through 294 removed outlier: 4.101A pdb=" N LEU B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ILE B 277 " --> pdb=" O GLN B 273 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 287 " --> pdb=" O ILE B 283 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LEU B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 319 removed outlier: 3.822A pdb=" N GLY B 312 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE B 313 " --> pdb=" O GLY B 309 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL B 314 " --> pdb=" O GLN B 310 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N MET B 315 " --> pdb=" O ALA B 311 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE B 316 " --> pdb=" O GLY B 312 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY B 317 " --> pdb=" O PHE B 313 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B 318 " --> pdb=" O VAL B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 353 removed outlier: 3.816A pdb=" N ALA B 327 " --> pdb=" O GLU B 323 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE B 338 " --> pdb=" O LEU B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 362 No H-bonds generated for 'chain 'B' and resid 360 through 362' Processing helix chain 'B' and resid 370 through 384 Processing helix chain 'B' and resid 390 through 405 Processing helix chain 'B' and resid 408 through 425 removed outlier: 4.298A pdb=" N TYR B 423 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N TYR B 424 " --> pdb=" O ILE B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 433 Processing helix chain 'B' and resid 457 through 476 removed outlier: 3.541A pdb=" N LEU B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLY B 475 " --> pdb=" O THR B 471 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE B 476 " --> pdb=" O SER B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 489 removed outlier: 3.718A pdb=" N ASN B 483 " --> pdb=" O ASN B 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 42 Proline residue: C 33 - end of helix Processing helix chain 'C' and resid 73 through 96 Proline residue: C 93 - end of helix Processing helix chain 'C' and resid 104 through 125 Processing helix chain 'D' and resid 7 through 19 Proline residue: D 14 - end of helix removed outlier: 3.949A pdb=" N LEU D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 56 removed outlier: 3.539A pdb=" N ALA D 40 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN D 55 " --> pdb=" O TYR D 51 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE D 56 " --> pdb=" O ALA D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 104 Proline residue: D 90 - end of helix removed outlier: 3.564A pdb=" N LEU D 93 " --> pdb=" O MET D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 132 removed outlier: 3.697A pdb=" N PHE D 131 " --> pdb=" O GLN D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 156 removed outlier: 3.840A pdb=" N GLU D 146 " --> pdb=" O ALA D 142 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU D 147 " --> pdb=" O TRP D 143 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ILE D 148 " --> pdb=" O GLU D 144 " (cutoff:3.500A) Proline residue: D 149 - end of helix Processing helix chain 'D' and resid 163 through 188 removed outlier: 4.303A pdb=" N PHE D 179 " --> pdb=" O GLY D 175 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ILE D 180 " --> pdb=" O SER D 176 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU D 181 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL D 182 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET D 187 " --> pdb=" O ALA D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 201 No H-bonds generated for 'chain 'D' and resid 198 through 201' Processing helix chain 'D' and resid 208 through 225 removed outlier: 3.546A pdb=" N ALA D 221 " --> pdb=" O GLY D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 240 removed outlier: 4.412A pdb=" N ASP D 237 " --> pdb=" O THR D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 251 removed outlier: 4.294A pdb=" N LEU D 249 " --> pdb=" O PRO D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 268 removed outlier: 4.092A pdb=" N GLY D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY D 259 " --> pdb=" O LEU D 255 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU D 262 " --> pdb=" O GLY D 258 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP D 268 " --> pdb=" O ARG D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 276 removed outlier: 4.143A pdb=" N LYS D 276 " --> pdb=" O ALA D 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 272 through 276' Processing helix chain 'D' and resid 278 through 296 removed outlier: 3.641A pdb=" N ALA D 293 " --> pdb=" O ILE D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 323 removed outlier: 3.904A pdb=" N ILE D 306 " --> pdb=" O LEU D 302 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER D 309 " --> pdb=" O LYS D 305 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE D 311 " --> pdb=" O ALA D 307 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE D 316 " --> pdb=" O SER D 312 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL D 317 " --> pdb=" O HIS D 313 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ALA D 322 " --> pdb=" O LEU D 318 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER D 323 " --> pdb=" O ILE D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 354 removed outlier: 3.782A pdb=" N ALA D 332 " --> pdb=" O GLY D 328 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VAL D 333 " --> pdb=" O MET D 329 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU D 334 " --> pdb=" O SER D 330 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER D 345 " --> pdb=" O LEU D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 387 Processing helix chain 'D' and resid 393 through 406 Processing helix chain 'D' and resid 414 through 441 Proline residue: D 431 - end of helix removed outlier: 4.536A pdb=" N LEU D 434 " --> pdb=" O THR D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 453 Processing helix chain 'D' and resid 461 through 479 removed outlier: 3.514A pdb=" N ILE D 467 " --> pdb=" O GLU D 463 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL D 472 " --> pdb=" O ALA D 468 " (cutoff:3.500A) Proline residue: D 473 - end of helix Processing helix chain 'D' and resid 482 through 502 removed outlier: 3.899A pdb=" N GLN D 486 " --> pdb=" O LYS D 482 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE D 487 " --> pdb=" O LEU D 483 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N TYR D 488 " --> pdb=" O LEU D 484 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ALA D 490 " --> pdb=" O GLN D 486 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N THR D 491 " --> pdb=" O ILE D 487 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 22 Processing helix chain 'E' and resid 29 through 51 removed outlier: 3.731A pdb=" N VAL E 41 " --> pdb=" O LEU E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 87 removed outlier: 3.819A pdb=" N ALA E 83 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE E 84 " --> pdb=" O ILE E 80 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR E 85 " --> pdb=" O ILE E 81 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG E 86 " --> pdb=" O LEU E 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 6 Processing helix chain 'F' and resid 11 through 26 Proline residue: F 15 - end of helix Processing helix chain 'F' and resid 32 through 35 No H-bonds generated for 'chain 'F' and resid 32 through 35' Processing helix chain 'F' and resid 38 through 65 removed outlier: 3.659A pdb=" N ILE F 44 " --> pdb=" O SER F 40 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY F 65 " --> pdb=" O SER F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 114 removed outlier: 3.512A pdb=" N ILE F 99 " --> pdb=" O LEU F 95 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLY F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 139 Processing helix chain 'F' and resid 144 through 162 Processing helix chain 'F' and resid 170 through 199 removed outlier: 3.615A pdb=" N GLN F 176 " --> pdb=" O ALA F 172 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL F 180 " --> pdb=" O GLN F 176 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY F 185 " --> pdb=" O THR F 181 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA F 199 " --> pdb=" O GLY F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 217 Processing helix chain 'F' and resid 223 through 240 removed outlier: 3.932A pdb=" N GLY F 236 " --> pdb=" O LEU F 232 " (cutoff:3.500A) Proline residue: F 237 - end of helix Processing helix chain 'F' and resid 249 through 254 Processing helix chain 'F' and resid 258 through 266 removed outlier: 3.587A pdb=" N ALA F 266 " --> pdb=" O ALA F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 284 removed outlier: 4.092A pdb=" N VAL F 274 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE F 277 " --> pdb=" O GLY F 273 " (cutoff:3.500A) Proline residue: F 282 - end of helix Processing helix chain 'F' and resid 288 through 308 Processing helix chain 'F' and resid 315 through 336 Processing helix chain 'F' and resid 339 through 370 removed outlier: 3.835A pdb=" N MET F 355 " --> pdb=" O TYR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 375 through 378 No H-bonds generated for 'chain 'F' and resid 375 through 378' Processing helix chain 'F' and resid 392 through 406 removed outlier: 3.800A pdb=" N SER F 406 " --> pdb=" O CYS F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 427 removed outlier: 4.108A pdb=" N SER F 416 " --> pdb=" O ALA F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 453 removed outlier: 3.569A pdb=" N TYR F 445 " --> pdb=" O LEU F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 485 through 492 Proline residue: F 489 - end of helix Processing helix chain 'F' and resid 495 through 503 removed outlier: 4.027A pdb=" N GLY F 501 " --> pdb=" O SER F 497 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE F 502 " --> pdb=" O THR F 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 510 through 514 Processing helix chain 'F' and resid 531 through 553 removed outlier: 4.036A pdb=" N LEU F 553 " --> pdb=" O THR F 549 " (cutoff:3.500A) Processing helix chain 'F' and resid 562 through 568 Processing helix chain 'F' and resid 571 through 577 removed outlier: 3.913A pdb=" N SER F 576 " --> pdb=" O LEU F 572 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 586 No H-bonds generated for 'chain 'F' and resid 583 through 586' Processing helix chain 'F' and resid 588 through 628 removed outlier: 4.580A pdb=" N VAL F 609 " --> pdb=" O ASP F 605 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ASP F 610 " --> pdb=" O TYR F 606 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL F 612 " --> pdb=" O VAL F 608 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N VAL F 613 " --> pdb=" O VAL F 609 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN F 614 " --> pdb=" O ASP F 610 " (cutoff:3.500A) Processing helix chain 'F' and resid 635 through 655 removed outlier: 3.517A pdb=" N ALA F 639 " --> pdb=" O ALA F 635 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 28 removed outlier: 3.621A pdb=" N VAL G 27 " --> pdb=" O ALA G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 53 removed outlier: 3.533A pdb=" N MET G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 68 Processing helix chain 'G' and resid 70 through 80 Processing helix chain 'G' and resid 94 through 117 Processing helix chain 'G' and resid 133 through 138 Processing helix chain 'G' and resid 145 through 164 removed outlier: 3.997A pdb=" N SER G 151 " --> pdb=" O PHE G 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 70 Processing helix chain 'H' and resid 76 through 90 Proline residue: H 86 - end of helix Processing helix chain 'H' and resid 96 through 115 Processing helix chain 'H' and resid 118 through 123 Processing helix chain 'H' and resid 129 through 148 removed outlier: 3.628A pdb=" N TYR H 133 " --> pdb=" O THR H 129 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR H 140 " --> pdb=" O ARG H 136 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE H 141 " --> pdb=" O GLU H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 195 removed outlier: 3.987A pdb=" N LEU H 184 " --> pdb=" O CYS H 180 " (cutoff:3.500A) Proline residue: H 185 - end of helix removed outlier: 3.788A pdb=" N ILE H 194 " --> pdb=" O TYR H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 200 through 205 removed outlier: 3.669A pdb=" N LEU H 204 " --> pdb=" O PHE H 200 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLN H 205 " --> pdb=" O VAL H 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 200 through 205' Processing helix chain 'H' and resid 212 through 218 Processing helix chain 'H' and resid 223 through 228 Processing helix chain 'H' and resid 234 through 237 No H-bonds generated for 'chain 'H' and resid 234 through 237' Processing helix chain 'H' and resid 258 through 281 removed outlier: 3.575A pdb=" N ARG H 270 " --> pdb=" O ILE H 266 " (cutoff:3.500A) Processing helix chain 'H' and resid 288 through 297 Processing helix chain 'H' and resid 358 through 369 removed outlier: 3.642A pdb=" N ASN H 362 " --> pdb=" O PRO H 358 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLN H 364 " --> pdb=" O PHE H 360 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N VAL H 365 " --> pdb=" O ASN H 361 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU H 366 " --> pdb=" O ASN H 362 " (cutoff:3.500A) Proline residue: H 367 - end of helix Processing helix chain 'H' and resid 377 through 384 Processing helix chain 'H' and resid 389 through 393 Processing helix chain 'I' and resid 3 through 30 removed outlier: 3.604A pdb=" N GLY I 24 " --> pdb=" O TYR I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 72 No H-bonds generated for 'chain 'I' and resid 69 through 72' Processing helix chain 'I' and resid 184 through 190 Processing helix chain 'J' and resid 14 through 22 removed outlier: 4.064A pdb=" N GLN J 22 " --> pdb=" O LEU J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 56 removed outlier: 3.679A pdb=" N ALA J 55 " --> pdb=" O GLN J 51 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ASP J 56 " --> pdb=" O THR J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 116 through 118 No H-bonds generated for 'chain 'J' and resid 116 through 118' Processing helix chain 'J' and resid 120 through 127 Processing helix chain 'K' and resid 26 through 42 Processing helix chain 'K' and resid 52 through 61 removed outlier: 3.640A pdb=" N MET K 60 " --> pdb=" O GLU K 56 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE K 61 " --> pdb=" O PHE K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 70 removed outlier: 3.958A pdb=" N PHE K 70 " --> pdb=" O PHE K 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 67 through 70' Processing helix chain 'K' and resid 92 through 103 Proline residue: K 96 - end of helix Processing helix chain 'K' and resid 116 through 119 No H-bonds generated for 'chain 'K' and resid 116 through 119' Processing helix chain 'K' and resid 152 through 168 removed outlier: 3.607A pdb=" N ALA K 167 " --> pdb=" O ARG K 163 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASN K 168 " --> pdb=" O LYS K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 205 through 208 No H-bonds generated for 'chain 'K' and resid 205 through 208' Processing helix chain 'L' and resid 5 through 21 Processing helix chain 'L' and resid 23 through 34 removed outlier: 3.525A pdb=" N ASN L 33 " --> pdb=" O TYR L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 53 Processing helix chain 'L' and resid 55 through 61 removed outlier: 3.652A pdb=" N LEU L 60 " --> pdb=" O PRO L 56 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 59 Processing helix chain 'M' and resid 67 through 86 Processing helix chain 'N' and resid 9 through 15 Processing helix chain 'N' and resid 30 through 40 Processing helix chain 'N' and resid 55 through 59 Processing helix chain 'N' and resid 83 through 89 Processing helix chain 'N' and resid 112 through 122 removed outlier: 3.508A pdb=" N GLN N 121 " --> pdb=" O ALA N 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 143 through 148 Processing helix chain 'O' and resid 20 through 22 No H-bonds generated for 'chain 'O' and resid 20 through 22' Processing helix chain 'O' and resid 31 through 34 No H-bonds generated for 'chain 'O' and resid 31 through 34' Processing helix chain 'P' and resid 8 through 12 Processing helix chain 'P' and resid 15 through 26 removed outlier: 4.202A pdb=" N LEU P 23 " --> pdb=" O ILE P 19 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE P 24 " --> pdb=" O LEU P 20 " (cutoff:3.500A) Processing helix chain 'Q' and resid 18 through 42 removed outlier: 4.040A pdb=" N ILE Q 23 " --> pdb=" O ALA Q 19 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 32 Processing helix chain 'R' and resid 67 through 72 Processing helix chain 'R' and resid 77 through 79 No H-bonds generated for 'chain 'R' and resid 77 through 79' Processing helix chain 'R' and resid 93 through 96 No H-bonds generated for 'chain 'R' and resid 93 through 96' Processing helix chain 'V' and resid 45 through 62 removed outlier: 3.864A pdb=" N LEU V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) Proline residue: V 54 - end of helix removed outlier: 3.912A pdb=" N ALA V 59 " --> pdb=" O ALA V 55 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER V 61 " --> pdb=" O LYS V 57 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA V 62 " --> pdb=" O ASN V 58 " (cutoff:3.500A) Processing helix chain 'V' and resid 126 through 137 Processing sheet with id= A, first strand: chain 'D' and resid 67 through 70 Processing sheet with id= B, first strand: chain 'F' and resid 69 through 74 Processing sheet with id= C, first strand: chain 'H' and resid 11 through 15 Processing sheet with id= D, first strand: chain 'H' and resid 325 through 332 removed outlier: 3.685A pdb=" N VAL H 329 " --> pdb=" O ILE H 340 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE H 340 " --> pdb=" O VAL H 329 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY H 339 " --> pdb=" O ARG H 356 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG H 352 " --> pdb=" O ILE H 343 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'I' and resid 55 through 58 Processing sheet with id= F, first strand: chain 'J' and resid 38 through 40 removed outlier: 8.634A pdb=" N ILE J 39 " --> pdb=" O GLU J 93 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ARG J 95 " --> pdb=" O ILE J 39 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N CYS J 63 " --> pdb=" O HIS J 80 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE J 82 " --> pdb=" O LEU J 61 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LEU J 61 " --> pdb=" O ILE J 82 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 106 through 108 removed outlier: 6.386A pdb=" N VAL J 131 " --> pdb=" O VAL J 107 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'K' and resid 45 through 47 removed outlier: 7.588A pdb=" N LEU K 83 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N TYR K 110 " --> pdb=" O ILE K 84 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N THR K 86 " --> pdb=" O TYR K 110 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE K 112 " --> pdb=" O THR K 86 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL K 143 " --> pdb=" O ALA K 113 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'M' and resid 4 through 6 removed outlier: 3.833A pdb=" N SER M 5 " --> pdb=" O ILE M 12 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE M 12 " --> pdb=" O SER M 5 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 139 through 142 removed outlier: 3.698A pdb=" N ARG N 139 " --> pdb=" O PHE N 22 " (cutoff:3.500A) removed outlier: 9.251A pdb=" N LEU N 19 " --> pdb=" O PHE N 126 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL N 128 " --> pdb=" O LEU N 19 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N LEU N 21 " --> pdb=" O VAL N 128 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL N 130 " --> pdb=" O LEU N 21 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU N 98 " --> pdb=" O LYS N 127 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL N 129 " --> pdb=" O LEU N 98 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU N 100 " --> pdb=" O VAL N 129 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N GLU N 131 " --> pdb=" O LEU N 100 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N LEU N 102 " --> pdb=" O GLU N 131 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'N' and resid 63 through 65 Processing sheet with id= L, first strand: chain 'O' and resid 38 through 40 Processing sheet with id= M, first strand: chain 'R' and resid 14 through 20 removed outlier: 6.690A pdb=" N CYS R 86 " --> pdb=" O THR R 6 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL R 8 " --> pdb=" O CYS R 86 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE R 88 " --> pdb=" O VAL R 8 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU R 54 " --> pdb=" O LYS R 87 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU R 89 " --> pdb=" O LEU R 52 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LEU R 52 " --> pdb=" O LEU R 89 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'S' and resid 95 through 97 removed outlier: 7.602A pdb=" N GLN S 64 " --> pdb=" O GLU S 80 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLU S 80 " --> pdb=" O GLN S 64 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY S 81 " --> pdb=" O TRP S 84 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP S 84 " --> pdb=" O GLY S 81 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'V' and resid 67 through 72 removed outlier: 3.755A pdb=" N TYR V 85 " --> pdb=" O TRP V 80 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN V 86 " --> pdb=" O SER V 105 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER V 105 " --> pdb=" O GLN V 86 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL V 101 " --> pdb=" O TYR V 90 " (cutoff:3.500A) 1513 hydrogen bonds defined for protein. 4500 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: 10.98 Time building geometry restraints manager: 15.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.44: 14564 1.44 - 1.66: 21253 1.66 - 1.88: 308 1.88 - 2.11: 0 2.11 - 2.33: 40 Bond restraints: 36165 Sorted by residual: bond pdb=" C12 PQN B 601 " pdb=" C13 PQN B 601 " ideal model delta sigma weight residual 1.334 1.523 -0.189 2.00e-02 2.50e+03 8.92e+01 bond pdb=" C4 PQN B 601 " pdb=" O4 PQN B 601 " ideal model delta sigma weight residual 1.214 1.401 -0.187 2.00e-02 2.50e+03 8.70e+01 bond pdb=" C1 PQN B 601 " pdb=" O1 PQN B 601 " ideal model delta sigma weight residual 1.214 1.399 -0.185 2.00e-02 2.50e+03 8.56e+01 bond pdb=" C1 PQN B 601 " pdb=" C2 PQN B 601 " ideal model delta sigma weight residual 1.488 1.385 0.103 2.00e-02 2.50e+03 2.63e+01 bond pdb=" C1 SQD F 704 " pdb=" O5 SQD F 704 " ideal model delta sigma weight residual 1.500 1.404 0.096 2.00e-02 2.50e+03 2.30e+01 ... (remaining 36160 not shown) Histogram of bond angle deviations from ideal: 69.54 - 82.43: 36 82.43 - 95.32: 58 95.32 - 108.21: 2704 108.21 - 121.10: 38544 121.10 - 133.99: 8470 Bond angle restraints: 49812 Sorted by residual: angle pdb="FE1 FES R 101 " pdb=" S2 FES R 101 " pdb="FE2 FES R 101 " ideal model delta sigma weight residual 75.66 88.93 -13.27 1.14e+00 7.69e-01 1.36e+02 angle pdb=" S1 FES R 101 " pdb="FE2 FES R 101 " pdb=" S2 FES R 101 " ideal model delta sigma weight residual 104.33 91.06 13.27 1.14e+00 7.69e-01 1.36e+02 angle pdb="FE1 FES R 101 " pdb=" S1 FES R 101 " pdb="FE2 FES R 101 " ideal model delta sigma weight residual 75.66 89.01 -13.35 1.20e+00 6.94e-01 1.24e+02 angle pdb=" S1 FES R 101 " pdb="FE1 FES R 101 " pdb=" S2 FES R 101 " ideal model delta sigma weight residual 104.33 90.99 13.34 1.20e+00 6.94e-01 1.24e+02 angle pdb=" N ILE V 96 " pdb=" CA ILE V 96 " pdb=" C ILE V 96 " ideal model delta sigma weight residual 113.71 107.51 6.20 9.50e-01 1.11e+00 4.26e+01 ... (remaining 49807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 21475 35.99 - 71.98: 1595 71.98 - 107.97: 714 107.97 - 143.96: 1715 143.96 - 179.95: 298 Dihedral angle restraints: 25797 sinusoidal: 13941 harmonic: 11856 Sorted by residual: dihedral pdb=" CA HIS F 578 " pdb=" C HIS F 578 " pdb=" N LYS F 579 " pdb=" CA LYS F 579 " ideal model delta harmonic sigma weight residual 180.00 156.72 23.28 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" C12 AJP F 711 " pdb=" C10 AJP F 711 " pdb=" C11 AJP F 711 " pdb=" O82 AJP F 711 " ideal model delta sinusoidal sigma weight residual 287.38 107.43 179.95 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C12 AJP D 607 " pdb=" C10 AJP D 607 " pdb=" C11 AJP D 607 " pdb=" O82 AJP D 607 " ideal model delta sinusoidal sigma weight residual 287.38 107.45 179.93 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 25794 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.290: 5348 4.290 - 8.581: 720 8.581 - 12.871: 0 12.871 - 17.161: 0 17.161 - 21.451: 12 Chirality restraints: 6080 Sorted by residual: chirality pdb="FE3 SF4 I 202 " pdb=" S1 SF4 I 202 " pdb=" S2 SF4 I 202 " pdb=" S4 SF4 I 202 " both_signs ideal model delta sigma weight residual False -10.55 10.90 -21.45 2.00e-01 2.50e+01 1.15e+04 chirality pdb="FE4 SF4 I 201 " pdb=" S1 SF4 I 201 " pdb=" S2 SF4 I 201 " pdb=" S3 SF4 I 201 " both_signs ideal model delta sigma weight residual False 10.55 -10.83 21.38 2.00e-01 2.50e+01 1.14e+04 chirality pdb="FE3 SF4 I 201 " pdb=" S1 SF4 I 201 " pdb=" S2 SF4 I 201 " pdb=" S4 SF4 I 201 " both_signs ideal model delta sigma weight residual False -10.55 10.75 -21.31 2.00e-01 2.50e+01 1.13e+04 ... (remaining 6077 not shown) Planarity restraints: 5682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 PQN B 601 " -0.081 2.00e-02 2.50e+03 2.10e-01 5.50e+02 pdb=" C12 PQN B 601 " 0.237 2.00e-02 2.50e+03 pdb=" C13 PQN B 601 " -0.363 2.00e-02 2.50e+03 pdb=" C14 PQN B 601 " 0.147 2.00e-02 2.50e+03 pdb=" C15 PQN B 601 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C20 BCR P 101 " 0.197 2.00e-02 2.50e+03 1.64e-01 3.36e+02 pdb=" C21 BCR P 101 " -0.258 2.00e-02 2.50e+03 pdb=" C22 BCR P 101 " -0.077 2.00e-02 2.50e+03 pdb=" C23 BCR P 101 " 0.150 2.00e-02 2.50e+03 pdb=" C37 BCR P 101 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BCR P 101 " -0.118 2.00e-02 2.50e+03 1.25e-01 1.56e+02 pdb=" C11 BCR P 101 " 0.099 2.00e-02 2.50e+03 pdb=" C12 BCR P 101 " 0.148 2.00e-02 2.50e+03 pdb=" C13 BCR P 101 " -0.129 2.00e-02 2.50e+03 ... (remaining 5679 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.06: 6 2.06 - 2.77: 6521 2.77 - 3.48: 47069 3.48 - 4.19: 78604 4.19 - 4.90: 139853 Nonbonded interactions: 272053 Sorted by model distance: nonbonded pdb=" OH TYR F 629 " pdb=" C18 AJP F 712 " model vdw 1.354 3.440 nonbonded pdb=" OH TYR F 629 " pdb=" C19 AJP F 712 " model vdw 1.525 3.470 nonbonded pdb=" CZ TYR F 629 " pdb=" C19 AJP F 712 " model vdw 1.851 3.690 nonbonded pdb=" CD2 LEU D 413 " pdb=" C80 AJP D 608 " model vdw 2.025 3.880 nonbonded pdb=" CZ TYR F 629 " pdb=" C18 AJP F 712 " model vdw 2.042 2.928 ... (remaining 272048 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 1.450 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: 0.030 Extract box with map and model: 8.110 Check model and map are aligned: 0.510 Set scattering table: 0.340 Process input model: 95.070 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.120 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: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.189 36165 Z= 0.452 Angle : 1.351 14.990 49812 Z= 0.522 Chirality : 2.044 21.451 6080 Planarity : 0.007 0.210 5682 Dihedral : 50.049 179.955 18215 Min Nonbonded Distance : 1.354 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.12), residues: 4078 helix: -0.50 (0.10), residues: 2244 sheet: -1.06 (0.31), residues: 244 loop : -3.71 (0.12), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.000 TRP H 248 HIS 0.003 0.000 HIS N 63 PHE 0.025 0.001 PHE C 112 TYR 0.015 0.001 TYR F 445 ARG 0.003 0.000 ARG O 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8156 Ramachandran restraints generated. 4078 Oldfield, 0 Emsley, 4078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8156 Ramachandran restraints generated. 4078 Oldfield, 0 Emsley, 4078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 860 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 860 time to evaluate : 3.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.6001 (m-30) cc_final: 0.5739 (m-30) REVERT: A 204 ILE cc_start: 0.7426 (mm) cc_final: 0.7065 (mm) REVERT: D 311 ILE cc_start: 0.8291 (mt) cc_final: 0.7936 (mt) REVERT: E 81 ILE cc_start: 0.6785 (mm) cc_final: 0.6545 (mt) REVERT: E 91 VAL cc_start: 0.6878 (p) cc_final: 0.6601 (p) REVERT: F 60 TRP cc_start: 0.5934 (t-100) cc_final: 0.5151 (t60) REVERT: F 421 LEU cc_start: 0.7780 (mt) cc_final: 0.7553 (mt) REVERT: F 546 MET cc_start: 0.7719 (ttp) cc_final: 0.7456 (ttm) REVERT: F 586 TYR cc_start: 0.7010 (t80) cc_final: 0.6247 (t80) REVERT: F 605 ASP cc_start: 0.7866 (t70) cc_final: 0.7572 (t0) REVERT: F 649 PHE cc_start: 0.7246 (m-80) cc_final: 0.6983 (m-80) REVERT: H 3 LYS cc_start: 0.7131 (mtmt) cc_final: 0.6680 (pttt) REVERT: H 320 PHE cc_start: 0.7119 (p90) cc_final: 0.6657 (p90) REVERT: I 116 ASN cc_start: 0.7991 (p0) cc_final: 0.7593 (m-40) REVERT: I 168 MET cc_start: 0.3870 (mmp) cc_final: 0.3374 (mmp) REVERT: J 123 GLU cc_start: 0.7383 (tm-30) cc_final: 0.6873 (tt0) REVERT: K 169 GLU cc_start: 0.7017 (mt-10) cc_final: 0.6662 (mt-10) REVERT: M 4 LYS cc_start: 0.7806 (pttp) cc_final: 0.7472 (pttp) REVERT: O 10 LYS cc_start: 0.7308 (tttt) cc_final: 0.6934 (ttmm) outliers start: 0 outliers final: 0 residues processed: 860 average time/residue: 0.4700 time to fit residues: 645.1768 Evaluate side-chains 600 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 600 time to evaluate : 3.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 341 optimal weight: 7.9990 chunk 306 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 317 optimal weight: 0.5980 chunk 122 optimal weight: 0.9990 chunk 193 optimal weight: 4.9990 chunk 236 optimal weight: 0.8980 chunk 367 optimal weight: 0.4980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 GLN A 208 ASN A 291 ASN B 9 GLN B 310 GLN B 340 ASN B 358 GLN C 69 GLN C 99 HIS D 60 ASN D 65 GLN D 127 GLN D 288 ASN D 339 HIS ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN F 62 GLN F 66 HIS F 146 GLN F 312 GLN F 563 GLN I 5 ASN I 76 ASN J 120 GLN ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 ASN N 8 GLN N 69 HIS N 94 ASN N 118 GLN O 49 GLN O 65 GLN P 40 ASN S 55 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.287 36165 Z= 0.486 Angle : 3.400 51.387 49812 Z= 1.410 Chirality : 0.437 6.491 6080 Planarity : 0.004 0.049 5682 Dihedral : 45.277 179.937 10943 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.15 % Allowed : 11.72 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.13), residues: 4078 helix: 0.62 (0.11), residues: 2261 sheet: -0.50 (0.32), residues: 244 loop : -3.30 (0.13), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP V 80 HIS 0.010 0.001 HIS C 99 PHE 0.026 0.001 PHE F 352 TYR 0.018 0.001 TYR G 50 ARG 0.005 0.000 ARG J 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8156 Ramachandran restraints generated. 4078 Oldfield, 0 Emsley, 4078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8156 Ramachandran restraints generated. 4078 Oldfield, 0 Emsley, 4078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 620 time to evaluate : 3.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 PHE cc_start: 0.7539 (OUTLIER) cc_final: 0.7085 (t80) REVERT: A 204 ILE cc_start: 0.7791 (mm) cc_final: 0.7375 (mm) REVERT: B 336 TYR cc_start: 0.8523 (t80) cc_final: 0.8125 (t80) REVERT: D 248 MET cc_start: 0.8628 (mtp) cc_final: 0.8186 (mtp) REVERT: D 384 LEU cc_start: 0.8890 (mt) cc_final: 0.8500 (mm) REVERT: E 44 ASN cc_start: 0.8042 (t0) cc_final: 0.7445 (t0) REVERT: E 81 ILE cc_start: 0.7328 (mm) cc_final: 0.7111 (mt) REVERT: E 91 VAL cc_start: 0.7318 (p) cc_final: 0.6944 (p) REVERT: F 60 TRP cc_start: 0.6179 (t-100) cc_final: 0.5313 (t60) REVERT: F 64 GLN cc_start: 0.6208 (tp40) cc_final: 0.5559 (tt0) REVERT: F 280 MET cc_start: 0.8539 (mmm) cc_final: 0.8275 (mmm) REVERT: F 381 MET cc_start: 0.8259 (mmm) cc_final: 0.8013 (mmm) REVERT: F 384 MET cc_start: 0.6853 (mmt) cc_final: 0.6634 (mmt) REVERT: F 546 MET cc_start: 0.7659 (ttp) cc_final: 0.7390 (ttm) REVERT: F 586 TYR cc_start: 0.7115 (t80) cc_final: 0.6418 (t80) REVERT: G 142 ASP cc_start: 0.7924 (m-30) cc_final: 0.7652 (m-30) REVERT: H 320 PHE cc_start: 0.7314 (p90) cc_final: 0.6877 (p90) REVERT: I 116 ASN cc_start: 0.8407 (p0) cc_final: 0.7776 (m-40) REVERT: J 73 GLN cc_start: 0.7180 (mm-40) cc_final: 0.6938 (mm-40) REVERT: J 123 GLU cc_start: 0.7463 (tm-30) cc_final: 0.7004 (tm-30) REVERT: M 4 LYS cc_start: 0.8107 (pttp) cc_final: 0.7777 (pttp) REVERT: N 139 ARG cc_start: 0.7009 (ptt90) cc_final: 0.6720 (ptt-90) REVERT: O 10 LYS cc_start: 0.7546 (tttt) cc_final: 0.7174 (ttmm) REVERT: V 80 TRP cc_start: 0.6748 (t60) cc_final: 0.6318 (t60) outliers start: 73 outliers final: 43 residues processed: 652 average time/residue: 0.4372 time to fit residues: 467.9873 Evaluate side-chains 608 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 564 time to evaluate : 3.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain D residue 172 TYR Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 480 HIS Chi-restraints excluded: chain F residue 549 THR Chi-restraints excluded: chain F residue 589 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain N residue 140 TRP Chi-restraints excluded: chain P residue 29 ASN Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain V residue 53 LEU Chi-restraints excluded: chain V residue 56 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 204 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 chunk 306 optimal weight: 0.7980 chunk 250 optimal weight: 0.0470 chunk 101 optimal weight: 1.9990 chunk 368 optimal weight: 10.0000 chunk 398 optimal weight: 10.0000 chunk 328 optimal weight: 0.8980 chunk 365 optimal weight: 0.0050 chunk 125 optimal weight: 0.9980 chunk 295 optimal weight: 0.9980 overall best weight: 0.5492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 GLN B 230 GLN B 290 ASN C 99 HIS D 127 GLN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 486 GLN E 44 ASN ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 71 GLN F 600 GLN H 114 HIS H 368 GLN ** I 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 23 ASN ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 170 HIS S 64 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.248 36165 Z= 0.431 Angle : 3.325 50.504 49812 Z= 1.387 Chirality : 0.443 6.344 6080 Planarity : 0.004 0.064 5682 Dihedral : 44.716 179.786 10943 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.50 % Allowed : 13.84 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % 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: -0.63 (0.13), residues: 4078 helix: 1.23 (0.11), residues: 2259 sheet: -0.36 (0.32), residues: 251 loop : -3.06 (0.13), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 330 HIS 0.011 0.001 HIS C 99 PHE 0.034 0.001 PHE F 29 TYR 0.032 0.001 TYR F 629 ARG 0.003 0.000 ARG H 136 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8156 Ramachandran restraints generated. 4078 Oldfield, 0 Emsley, 4078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8156 Ramachandran restraints generated. 4078 Oldfield, 0 Emsley, 4078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 580 time to evaluate : 3.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.7029 (mtt) REVERT: A 111 PHE cc_start: 0.7671 (OUTLIER) cc_final: 0.7234 (t80) REVERT: A 327 LEU cc_start: 0.7888 (tp) cc_final: 0.7685 (tp) REVERT: B 168 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7890 (tt) REVERT: B 315 MET cc_start: 0.8216 (mmm) cc_final: 0.7644 (mtt) REVERT: B 366 TYR cc_start: 0.8359 (t80) cc_final: 0.7994 (t80) REVERT: D 384 LEU cc_start: 0.8888 (mt) cc_final: 0.8508 (mm) REVERT: E 44 ASN cc_start: 0.7868 (t0) cc_final: 0.7362 (t0) REVERT: E 91 VAL cc_start: 0.7518 (p) cc_final: 0.7168 (p) REVERT: F 60 TRP cc_start: 0.6233 (t-100) cc_final: 0.5286 (t60) REVERT: F 64 GLN cc_start: 0.6487 (tp40) cc_final: 0.5827 (tt0) REVERT: F 586 TYR cc_start: 0.7082 (t80) cc_final: 0.6483 (t80) REVERT: G 142 ASP cc_start: 0.7879 (m-30) cc_final: 0.7616 (m-30) REVERT: H 320 PHE cc_start: 0.7576 (p90) cc_final: 0.7117 (p90) REVERT: I 116 ASN cc_start: 0.8462 (p0) cc_final: 0.7703 (m-40) REVERT: I 168 MET cc_start: 0.4539 (mmp) cc_final: 0.4199 (mmp) REVERT: I 171 HIS cc_start: 0.7017 (OUTLIER) cc_final: 0.6617 (t-90) REVERT: J 73 GLN cc_start: 0.7177 (mm-40) cc_final: 0.6921 (mm-40) REVERT: J 123 GLU cc_start: 0.7417 (tm-30) cc_final: 0.6930 (tm-30) REVERT: J 139 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.8125 (mttp) REVERT: K 169 GLU cc_start: 0.6966 (mt-10) cc_final: 0.6739 (mt-10) REVERT: M 4 LYS cc_start: 0.8266 (pttp) cc_final: 0.7916 (pttp) REVERT: N 11 LYS cc_start: 0.8207 (mttt) cc_final: 0.7988 (mttp) REVERT: O 10 LYS cc_start: 0.7539 (tttt) cc_final: 0.7278 (ttmm) REVERT: P 24 PHE cc_start: 0.7476 (t80) cc_final: 0.6926 (t80) REVERT: P 28 ARG cc_start: 0.8095 (mmm-85) cc_final: 0.7786 (mmm-85) REVERT: V 80 TRP cc_start: 0.6732 (t60) cc_final: 0.6509 (t60) outliers start: 85 outliers final: 52 residues processed: 624 average time/residue: 0.4382 time to fit residues: 457.5945 Evaluate side-chains 605 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 548 time to evaluate : 3.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 172 TYR Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 480 HIS Chi-restraints excluded: chain F residue 585 LEU Chi-restraints excluded: chain F residue 589 VAL Chi-restraints excluded: chain F residue 629 TYR Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 243 TYR Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain I residue 131 ARG Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain I residue 171 HIS Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 93 GLU Chi-restraints excluded: chain J residue 139 LYS Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 128 VAL Chi-restraints excluded: chain P residue 29 ASN Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain V residue 53 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 364 optimal weight: 5.9990 chunk 277 optimal weight: 1.9990 chunk 191 optimal weight: 0.0270 chunk 40 optimal weight: 9.9990 chunk 175 optimal weight: 7.9990 chunk 247 optimal weight: 0.8980 chunk 369 optimal weight: 8.9990 chunk 391 optimal weight: 5.9990 chunk 193 optimal weight: 2.9990 chunk 350 optimal weight: 10.0000 chunk 105 optimal weight: 0.9980 overall best weight: 1.3842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 GLN B 130 GLN D 274 HIS E 44 ASN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 HIS F 563 GLN H 78 ASN H 361 ASN H 364 GLN H 368 GLN ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 64 GLN ** V 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.260 36165 Z= 0.448 Angle : 3.326 50.701 49812 Z= 1.391 Chirality : 0.439 6.441 6080 Planarity : 0.004 0.052 5682 Dihedral : 44.761 179.995 10943 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.18 % Allowed : 15.48 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.13), residues: 4078 helix: 1.47 (0.11), residues: 2273 sheet: -0.23 (0.33), residues: 244 loop : -2.89 (0.13), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 330 HIS 0.010 0.001 HIS C 99 PHE 0.023 0.002 PHE F 352 TYR 0.032 0.002 TYR F 629 ARG 0.009 0.000 ARG D 439 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8156 Ramachandran restraints generated. 4078 Oldfield, 0 Emsley, 4078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8156 Ramachandran restraints generated. 4078 Oldfield, 0 Emsley, 4078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 573 time to evaluate : 3.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.7444 (mtt) cc_final: 0.7069 (mtm) REVERT: A 79 ASP cc_start: 0.7113 (m-30) cc_final: 0.6683 (m-30) REVERT: B 315 MET cc_start: 0.8217 (mmm) cc_final: 0.7978 (mtt) REVERT: D 237 ASP cc_start: 0.7688 (m-30) cc_final: 0.7452 (m-30) REVERT: D 254 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7952 (mp) REVERT: D 379 PHE cc_start: 0.8989 (OUTLIER) cc_final: 0.8508 (t80) REVERT: E 44 ASN cc_start: 0.8103 (t0) cc_final: 0.7401 (t0) REVERT: E 100 LYS cc_start: 0.7370 (mttt) cc_final: 0.7006 (mmtt) REVERT: F 60 TRP cc_start: 0.6884 (t-100) cc_final: 0.5600 (t60) REVERT: F 64 GLN cc_start: 0.7015 (tp40) cc_final: 0.6286 (tt0) REVERT: F 280 MET cc_start: 0.8658 (mmm) cc_final: 0.8457 (mmt) REVERT: F 553 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7732 (pp) REVERT: F 586 TYR cc_start: 0.7149 (t80) cc_final: 0.6550 (t80) REVERT: G 166 ARG cc_start: 0.7544 (mtm180) cc_final: 0.7306 (mtm-85) REVERT: I 19 LYS cc_start: 0.6412 (tttt) cc_final: 0.5882 (tttt) REVERT: I 116 ASN cc_start: 0.8649 (p0) cc_final: 0.7699 (m-40) REVERT: I 171 HIS cc_start: 0.7215 (OUTLIER) cc_final: 0.6690 (t-90) REVERT: J 123 GLU cc_start: 0.7461 (tm-30) cc_final: 0.7000 (tm-30) REVERT: J 137 ASN cc_start: 0.8418 (t0) cc_final: 0.8004 (t0) REVERT: O 10 LYS cc_start: 0.7654 (tttt) cc_final: 0.7188 (ttmm) REVERT: P 20 LEU cc_start: 0.8300 (mm) cc_final: 0.8086 (mp) REVERT: V 141 LYS cc_start: 0.8050 (mttt) cc_final: 0.7806 (mtmm) outliers start: 108 outliers final: 66 residues processed: 632 average time/residue: 0.4500 time to fit residues: 472.2730 Evaluate side-chains 593 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 523 time to evaluate : 3.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 172 TYR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 257 MET Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 379 PHE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 101 TRP Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 315 ILE Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 553 LEU Chi-restraints excluded: chain F residue 585 LEU Chi-restraints excluded: chain F residue 589 VAL Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain H residue 5 GLU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 316 LEU Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain I residue 131 ARG Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain I residue 171 HIS Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 93 GLU Chi-restraints excluded: chain J residue 146 ASP Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain K residue 119 ILE Chi-restraints excluded: chain K residue 200 GLN Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain N residue 128 VAL Chi-restraints excluded: chain N residue 140 TRP Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain V residue 53 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 326 optimal weight: 5.9990 chunk 222 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 291 optimal weight: 1.9990 chunk 161 optimal weight: 0.4980 chunk 334 optimal weight: 4.9990 chunk 270 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 199 optimal weight: 3.9990 chunk 351 optimal weight: 2.9990 chunk 98 optimal weight: 0.0770 overall best weight: 1.0742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 ASN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 563 GLN ** H 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN K 32 ASN K 104 GLN O 49 GLN O 65 GLN ** V 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 140 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.250 36165 Z= 0.429 Angle : 3.314 50.692 49812 Z= 1.386 Chirality : 0.436 6.380 6080 Planarity : 0.004 0.050 5682 Dihedral : 44.872 179.999 10943 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.91 % Allowed : 17.43 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.04 (0.14), residues: 4078 helix: 1.69 (0.11), residues: 2273 sheet: -0.13 (0.32), residues: 260 loop : -2.83 (0.13), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP V 80 HIS 0.011 0.001 HIS C 99 PHE 0.035 0.001 PHE F 29 TYR 0.050 0.001 TYR F 629 ARG 0.004 0.000 ARG P 28 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8156 Ramachandran restraints generated. 4078 Oldfield, 0 Emsley, 4078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8156 Ramachandran restraints generated. 4078 Oldfield, 0 Emsley, 4078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 549 time to evaluate : 3.522 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: A 34 MET cc_start: 0.7289 (mtt) cc_final: 0.6905 (mtm) REVERT: A 79 ASP cc_start: 0.7220 (m-30) cc_final: 0.6871 (m-30) REVERT: D 64 MET cc_start: 0.7069 (mtt) cc_final: 0.6598 (mtt) REVERT: D 237 ASP cc_start: 0.7677 (m-30) cc_final: 0.7458 (m-30) REVERT: E 1 MET cc_start: 0.7469 (tpp) cc_final: 0.6647 (ttp) REVERT: E 100 LYS cc_start: 0.7488 (mttt) cc_final: 0.7075 (mmtt) REVERT: F 45 MET cc_start: 0.7718 (mmp) cc_final: 0.7300 (mmm) REVERT: F 60 TRP cc_start: 0.7156 (t-100) cc_final: 0.5873 (t60) REVERT: F 64 GLN cc_start: 0.7193 (tp40) cc_final: 0.6365 (tt0) REVERT: F 334 MET cc_start: 0.8461 (ttm) cc_final: 0.8052 (ttm) REVERT: F 586 TYR cc_start: 0.7059 (t80) cc_final: 0.6397 (t80) REVERT: G 24 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8005 (mm) REVERT: G 166 ARG cc_start: 0.7622 (mtm180) cc_final: 0.7367 (mtm-85) REVERT: G 186 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7354 (mm-30) REVERT: I 19 LYS cc_start: 0.6555 (tttt) cc_final: 0.6052 (tttt) REVERT: I 116 ASN cc_start: 0.8614 (p0) cc_final: 0.7771 (m-40) REVERT: I 171 HIS cc_start: 0.7366 (OUTLIER) cc_final: 0.6689 (t-90) REVERT: J 123 GLU cc_start: 0.7533 (tm-30) cc_final: 0.6937 (tm-30) REVERT: J 145 GLU cc_start: 0.7357 (mp0) cc_final: 0.7081 (mp0) REVERT: O 10 LYS cc_start: 0.7674 (tttt) cc_final: 0.7236 (ttmm) REVERT: V 141 LYS cc_start: 0.8055 (mttt) cc_final: 0.7826 (mtmm) outliers start: 99 outliers final: 65 residues processed: 604 average time/residue: 0.4872 time to fit residues: 492.3162 Evaluate side-chains 587 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 520 time to evaluate : 3.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 480 HIS Chi-restraints excluded: chain F residue 585 LEU Chi-restraints excluded: chain F residue 589 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain H residue 5 GLU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 238 ASP Chi-restraints excluded: chain H residue 316 LEU Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 131 ARG Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain I residue 171 HIS Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 93 GLU Chi-restraints excluded: chain J residue 146 ASP Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 114 MET Chi-restraints excluded: chain K residue 200 GLN Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain N residue 128 VAL Chi-restraints excluded: chain P residue 14 MET Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain S residue 41 LEU Chi-restraints excluded: chain V residue 53 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 131 optimal weight: 4.9990 chunk 352 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 229 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 391 optimal weight: 9.9990 chunk 325 optimal weight: 0.7980 chunk 181 optimal weight: 0.0980 chunk 32 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 205 optimal weight: 9.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 ASN D 127 GLN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN F 345 HIS F 563 GLN ** H 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 49 GLN ** V 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.4840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.246 36165 Z= 0.441 Angle : 3.315 50.651 49812 Z= 1.389 Chirality : 0.435 6.364 6080 Planarity : 0.004 0.050 5682 Dihedral : 44.997 179.991 10943 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.98 % Favored : 93.99 % Rotamer: Outliers : 3.47 % Allowed : 17.60 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.14), residues: 4078 helix: 1.76 (0.11), residues: 2272 sheet: 0.12 (0.33), residues: 258 loop : -2.73 (0.13), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 330 HIS 0.010 0.001 HIS C 99 PHE 0.024 0.002 PHE E 62 TYR 0.039 0.002 TYR F 629 ARG 0.004 0.000 ARG N 139 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8156 Ramachandran restraints generated. 4078 Oldfield, 0 Emsley, 4078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8156 Ramachandran restraints generated. 4078 Oldfield, 0 Emsley, 4078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 535 time to evaluate : 3.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 VAL cc_start: 0.8599 (t) cc_final: 0.8379 (t) REVERT: A 79 ASP cc_start: 0.7381 (m-30) cc_final: 0.6952 (m-30) REVERT: A 114 TYR cc_start: 0.9047 (m-80) cc_final: 0.8670 (m-80) REVERT: A 258 TYR cc_start: 0.6448 (OUTLIER) cc_final: 0.4828 (m-80) REVERT: B 35 GLN cc_start: 0.7514 (mm110) cc_final: 0.7272 (mm110) REVERT: C 92 TYR cc_start: 0.8521 (OUTLIER) cc_final: 0.7405 (t80) REVERT: D 64 MET cc_start: 0.7431 (mtt) cc_final: 0.6882 (mtt) REVERT: D 254 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8071 (mp) REVERT: D 265 MET cc_start: 0.7869 (mmt) cc_final: 0.7645 (mmm) REVERT: D 379 PHE cc_start: 0.9056 (OUTLIER) cc_final: 0.8565 (t80) REVERT: E 1 MET cc_start: 0.7592 (tpp) cc_final: 0.6921 (ttp) REVERT: E 100 LYS cc_start: 0.7711 (mttt) cc_final: 0.7164 (mmtt) REVERT: F 45 MET cc_start: 0.7917 (mmp) cc_final: 0.7540 (mmm) REVERT: F 64 GLN cc_start: 0.7401 (tp40) cc_final: 0.6647 (tt0) REVERT: F 280 MET cc_start: 0.8571 (mmm) cc_final: 0.8269 (mmt) REVERT: F 334 MET cc_start: 0.8449 (ttm) cc_final: 0.8079 (ttm) REVERT: F 586 TYR cc_start: 0.7088 (t80) cc_final: 0.6384 (t80) REVERT: G 24 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.7973 (mm) REVERT: G 166 ARG cc_start: 0.7850 (mtm180) cc_final: 0.7599 (mtm-85) REVERT: I 19 LYS cc_start: 0.6614 (tttt) cc_final: 0.6160 (tttt) REVERT: I 168 MET cc_start: 0.6386 (mmp) cc_final: 0.6167 (mmp) REVERT: I 171 HIS cc_start: 0.7504 (OUTLIER) cc_final: 0.6767 (t-90) REVERT: J 123 GLU cc_start: 0.7603 (tm-30) cc_final: 0.6994 (tm-30) REVERT: K 48 TYR cc_start: 0.8271 (t80) cc_final: 0.7073 (t80) REVERT: N 136 ARG cc_start: 0.7363 (ttt90) cc_final: 0.7043 (mtp85) REVERT: O 10 LYS cc_start: 0.7773 (tttt) cc_final: 0.7368 (ttmm) REVERT: V 93 GLU cc_start: 0.6214 (OUTLIER) cc_final: 0.5843 (mm-30) REVERT: V 141 LYS cc_start: 0.8188 (mttt) cc_final: 0.7908 (mtmm) outliers start: 118 outliers final: 82 residues processed: 607 average time/residue: 0.4367 time to fit residues: 435.4273 Evaluate side-chains 585 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 496 time to evaluate : 3.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 379 PHE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 315 ILE Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 446 MET Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain F residue 585 LEU Chi-restraints excluded: chain F residue 589 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain H residue 5 GLU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 316 LEU Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain I residue 171 HIS Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 93 GLU Chi-restraints excluded: chain J residue 146 ASP Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 114 MET Chi-restraints excluded: chain K residue 119 ILE Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain N residue 128 VAL Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain P residue 14 MET Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain S residue 71 THR Chi-restraints excluded: chain V residue 53 LEU Chi-restraints excluded: chain V residue 93 GLU Chi-restraints excluded: chain V residue 124 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 377 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 223 optimal weight: 0.7980 chunk 286 optimal weight: 3.9990 chunk 221 optimal weight: 4.9990 chunk 329 optimal weight: 0.9990 chunk 218 optimal weight: 5.9990 chunk 390 optimal weight: 4.9990 chunk 244 optimal weight: 6.9990 chunk 237 optimal weight: 2.9990 chunk 180 optimal weight: 8.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 127 GLN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 460 ASN H 14 ASN H 290 ASN J 64 GLN ** J 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 49 GLN P 44 HIS S 64 GLN ** V 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.5240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.247 36165 Z= 0.463 Angle : 3.319 50.628 49812 Z= 1.392 Chirality : 0.435 6.347 6080 Planarity : 0.004 0.052 5682 Dihedral : 45.006 179.978 10943 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.76 % Favored : 94.19 % Rotamer: Outliers : 3.71 % Allowed : 18.31 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.08 (0.13), residues: 4078 helix: 1.71 (0.11), residues: 2268 sheet: 0.18 (0.33), residues: 262 loop : -2.67 (0.13), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 330 HIS 0.009 0.001 HIS C 99 PHE 0.027 0.002 PHE E 62 TYR 0.046 0.002 TYR F 629 ARG 0.007 0.000 ARG J 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8156 Ramachandran restraints generated. 4078 Oldfield, 0 Emsley, 4078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8156 Ramachandran restraints generated. 4078 Oldfield, 0 Emsley, 4078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 515 time to evaluate : 3.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 MET cc_start: 0.6722 (OUTLIER) cc_final: 0.6510 (ttm) REVERT: A 45 VAL cc_start: 0.7120 (OUTLIER) cc_final: 0.6860 (t) REVERT: A 47 VAL cc_start: 0.8604 (t) cc_final: 0.8377 (t) REVERT: A 79 ASP cc_start: 0.7361 (m-30) cc_final: 0.7005 (m-30) REVERT: A 258 TYR cc_start: 0.6456 (OUTLIER) cc_final: 0.4833 (m-80) REVERT: B 35 GLN cc_start: 0.7664 (mm110) cc_final: 0.7429 (mm110) REVERT: C 92 TYR cc_start: 0.8548 (OUTLIER) cc_final: 0.7300 (t80) REVERT: D 24 ILE cc_start: 0.7757 (mm) cc_final: 0.7510 (mm) REVERT: D 64 MET cc_start: 0.7570 (mtt) cc_final: 0.7025 (mtt) REVERT: D 254 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8179 (mp) REVERT: D 265 MET cc_start: 0.7988 (mmt) cc_final: 0.7765 (mmm) REVERT: D 379 PHE cc_start: 0.9060 (OUTLIER) cc_final: 0.8554 (t80) REVERT: E 1 MET cc_start: 0.7554 (tpp) cc_final: 0.7136 (ttp) REVERT: E 100 LYS cc_start: 0.7779 (mttt) cc_final: 0.7229 (mmtt) REVERT: F 45 MET cc_start: 0.7983 (mmp) cc_final: 0.7672 (mmm) REVERT: F 60 TRP cc_start: 0.7259 (t-100) cc_final: 0.5733 (t60) REVERT: F 64 GLN cc_start: 0.7654 (tp40) cc_final: 0.6840 (tt0) REVERT: F 381 MET cc_start: 0.8346 (mmm) cc_final: 0.8116 (mtt) REVERT: F 586 TYR cc_start: 0.7120 (OUTLIER) cc_final: 0.6445 (t80) REVERT: G 24 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.7966 (mm) REVERT: G 166 ARG cc_start: 0.7997 (mtm180) cc_final: 0.7753 (mtm-85) REVERT: I 19 LYS cc_start: 0.6634 (tttt) cc_final: 0.6159 (tttt) REVERT: I 171 HIS cc_start: 0.7543 (OUTLIER) cc_final: 0.6738 (t-90) REVERT: J 22 GLN cc_start: 0.7368 (OUTLIER) cc_final: 0.6226 (mt0) REVERT: J 123 GLU cc_start: 0.7571 (tm-30) cc_final: 0.6998 (tm-30) REVERT: K 161 LYS cc_start: 0.8536 (mmtp) cc_final: 0.8219 (mmtm) REVERT: L 36 TRP cc_start: 0.6270 (t-100) cc_final: 0.5801 (t-100) REVERT: O 10 LYS cc_start: 0.7786 (tttt) cc_final: 0.7420 (ttmm) REVERT: S 80 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7374 (tp30) REVERT: V 52 PHE cc_start: 0.6393 (OUTLIER) cc_final: 0.5486 (m-80) REVERT: V 80 TRP cc_start: 0.7042 (t60) cc_final: 0.6786 (t60) REVERT: V 141 LYS cc_start: 0.8281 (mttt) cc_final: 0.7948 (mtmm) outliers start: 126 outliers final: 86 residues processed: 592 average time/residue: 0.4170 time to fit residues: 408.7939 Evaluate side-chains 588 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 491 time to evaluate : 3.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 247 HIS Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 379 PHE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 315 ILE Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 446 MET Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain F residue 586 TYR Chi-restraints excluded: chain F residue 589 VAL Chi-restraints excluded: chain F residue 630 LEU Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain H residue 5 GLU Chi-restraints excluded: chain H residue 14 ASN Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 236 LYS Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain H residue 316 LEU Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain I residue 171 HIS Chi-restraints excluded: chain J residue 22 GLN Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 93 GLU Chi-restraints excluded: chain J residue 146 ASP Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 114 MET Chi-restraints excluded: chain K residue 136 ASP Chi-restraints excluded: chain K residue 180 THR Chi-restraints excluded: chain K residue 200 GLN Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain N residue 128 VAL Chi-restraints excluded: chain N residue 140 TRP Chi-restraints excluded: chain P residue 14 MET Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain S residue 71 THR Chi-restraints excluded: chain V residue 52 PHE Chi-restraints excluded: chain V residue 53 LEU Chi-restraints excluded: chain V residue 124 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 241 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 233 optimal weight: 0.9990 chunk 117 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 248 optimal weight: 2.9990 chunk 265 optimal weight: 6.9990 chunk 192 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 306 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN B 230 GLN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 GLN H 14 ASN ** H 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 364 GLN ** I 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN ** J 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 49 GLN S 64 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.5852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.246 36165 Z= 0.511 Angle : 3.339 50.683 49812 Z= 1.402 Chirality : 0.436 6.362 6080 Planarity : 0.005 0.053 5682 Dihedral : 45.108 179.965 10943 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.84 % Favored : 93.08 % Rotamer: Outliers : 4.00 % Allowed : 18.69 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.13), residues: 4078 helix: 1.52 (0.11), residues: 2270 sheet: 0.10 (0.33), residues: 264 loop : -2.67 (0.14), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 330 HIS 0.008 0.001 HIS C 99 PHE 0.037 0.002 PHE E 62 TYR 0.092 0.002 TYR F 629 ARG 0.008 0.001 ARG H 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8156 Ramachandran restraints generated. 4078 Oldfield, 0 Emsley, 4078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8156 Ramachandran restraints generated. 4078 Oldfield, 0 Emsley, 4078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 501 time to evaluate : 3.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASP cc_start: 0.7486 (m-30) cc_final: 0.7121 (m-30) REVERT: A 114 TYR cc_start: 0.9057 (m-80) cc_final: 0.8773 (m-80) REVERT: A 258 TYR cc_start: 0.6520 (OUTLIER) cc_final: 0.4934 (m-80) REVERT: B 335 VAL cc_start: 0.8569 (t) cc_final: 0.8174 (m) REVERT: D 64 MET cc_start: 0.7819 (mtt) cc_final: 0.7241 (mtt) REVERT: D 254 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8441 (mp) REVERT: D 265 MET cc_start: 0.7979 (mmt) cc_final: 0.7761 (mmm) REVERT: D 379 PHE cc_start: 0.9074 (OUTLIER) cc_final: 0.8560 (t80) REVERT: E 1 MET cc_start: 0.7603 (tpp) cc_final: 0.7301 (ttp) REVERT: E 100 LYS cc_start: 0.7879 (mttt) cc_final: 0.7336 (mmtt) REVERT: F 45 MET cc_start: 0.8008 (mmp) cc_final: 0.7752 (mmm) REVERT: F 64 GLN cc_start: 0.7756 (tp40) cc_final: 0.7104 (tt0) REVERT: F 367 MET cc_start: 0.7738 (tpp) cc_final: 0.6988 (mmm) REVERT: F 376 ASP cc_start: 0.8099 (t70) cc_final: 0.7640 (t70) REVERT: F 449 MET cc_start: 0.8022 (ttm) cc_final: 0.7757 (ttm) REVERT: F 586 TYR cc_start: 0.7171 (OUTLIER) cc_final: 0.6303 (t80) REVERT: G 24 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.7934 (mm) REVERT: G 166 ARG cc_start: 0.8262 (mtm180) cc_final: 0.8056 (mtm-85) REVERT: H 238 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.7299 (p0) REVERT: H 310 GLN cc_start: 0.7368 (mm-40) cc_final: 0.6942 (mm-40) REVERT: I 19 LYS cc_start: 0.6677 (tttt) cc_final: 0.6130 (tttt) REVERT: I 168 MET cc_start: 0.7359 (mmp) cc_final: 0.6530 (mmm) REVERT: I 171 HIS cc_start: 0.7722 (OUTLIER) cc_final: 0.6686 (t-90) REVERT: J 22 GLN cc_start: 0.7382 (OUTLIER) cc_final: 0.6238 (mt0) REVERT: J 123 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7058 (tm-30) REVERT: K 161 LYS cc_start: 0.8557 (mmtp) cc_final: 0.8238 (mmtm) REVERT: M 34 ASP cc_start: 0.7943 (t0) cc_final: 0.7699 (t0) REVERT: O 10 LYS cc_start: 0.7875 (tttt) cc_final: 0.7471 (ttmm) REVERT: R 6 THR cc_start: 0.5801 (OUTLIER) cc_final: 0.5398 (t) REVERT: S 52 LYS cc_start: 0.7525 (tttm) cc_final: 0.7293 (tttm) REVERT: S 80 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7350 (tp30) REVERT: V 52 PHE cc_start: 0.6598 (OUTLIER) cc_final: 0.5686 (m-80) REVERT: V 80 TRP cc_start: 0.6851 (t60) cc_final: 0.6594 (t60) REVERT: V 141 LYS cc_start: 0.8422 (mttt) cc_final: 0.7982 (mtmm) outliers start: 136 outliers final: 96 residues processed: 587 average time/residue: 0.4410 time to fit residues: 431.9631 Evaluate side-chains 592 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 486 time to evaluate : 3.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 446 ASN Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 247 HIS Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 379 PHE Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 437 MET Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 315 ILE Chi-restraints excluded: chain F residue 330 MET Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 446 MET Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 585 LEU Chi-restraints excluded: chain F residue 586 TYR Chi-restraints excluded: chain F residue 589 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain H residue 3 LYS Chi-restraints excluded: chain H residue 5 GLU Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 238 ASP Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 69 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain I residue 171 HIS Chi-restraints excluded: chain J residue 22 GLN Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 146 ASP Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 114 MET Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 180 THR Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain N residue 23 VAL Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 128 VAL Chi-restraints excluded: chain N residue 140 TRP Chi-restraints excluded: chain P residue 14 MET Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain S residue 71 THR Chi-restraints excluded: chain V residue 52 PHE Chi-restraints excluded: chain V residue 53 LEU Chi-restraints excluded: chain V residue 105 SER Chi-restraints excluded: chain V residue 124 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 355 optimal weight: 3.9990 chunk 373 optimal weight: 4.9990 chunk 341 optimal weight: 5.9990 chunk 363 optimal weight: 4.9990 chunk 218 optimal weight: 2.9990 chunk 158 optimal weight: 0.0970 chunk 285 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 328 optimal weight: 2.9990 chunk 344 optimal weight: 4.9990 chunk 362 optimal weight: 1.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 GLN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 GLN H 14 ASN H 310 GLN H 364 GLN J 64 GLN ** J 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 64 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.5952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.246 36165 Z= 0.467 Angle : 3.325 50.623 49812 Z= 1.395 Chirality : 0.435 6.352 6080 Planarity : 0.004 0.053 5682 Dihedral : 45.104 179.991 10943 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.20 % Favored : 93.75 % Rotamer: Outliers : 3.59 % Allowed : 19.72 % Favored : 76.69 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.03 (0.13), residues: 4078 helix: 1.62 (0.11), residues: 2267 sheet: 0.26 (0.34), residues: 256 loop : -2.61 (0.14), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 70 HIS 0.008 0.001 HIS C 99 PHE 0.028 0.002 PHE R 64 TYR 0.068 0.002 TYR F 629 ARG 0.005 0.000 ARG H 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8156 Ramachandran restraints generated. 4078 Oldfield, 0 Emsley, 4078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8156 Ramachandran restraints generated. 4078 Oldfield, 0 Emsley, 4078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 490 time to evaluate : 3.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.7667 (mtt) cc_final: 0.7269 (mtt) REVERT: A 47 VAL cc_start: 0.8569 (t) cc_final: 0.8358 (t) REVERT: A 79 ASP cc_start: 0.7491 (m-30) cc_final: 0.7107 (m-30) REVERT: A 258 TYR cc_start: 0.6420 (OUTLIER) cc_final: 0.4778 (m-80) REVERT: B 335 VAL cc_start: 0.8478 (t) cc_final: 0.8120 (m) REVERT: D 64 MET cc_start: 0.7839 (mtt) cc_final: 0.7313 (mtt) REVERT: D 254 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8386 (mp) REVERT: D 265 MET cc_start: 0.7959 (mmt) cc_final: 0.7755 (mmm) REVERT: D 379 PHE cc_start: 0.9052 (OUTLIER) cc_final: 0.8540 (t80) REVERT: E 1 MET cc_start: 0.7646 (tpp) cc_final: 0.7390 (ttp) REVERT: E 94 GLU cc_start: 0.7012 (tp30) cc_final: 0.6792 (tp30) REVERT: E 100 LYS cc_start: 0.7884 (mttt) cc_final: 0.7511 (mttm) REVERT: F 45 MET cc_start: 0.7907 (mmp) cc_final: 0.7672 (mmm) REVERT: F 64 GLN cc_start: 0.7773 (tp40) cc_final: 0.7393 (tp40) REVERT: F 187 PHE cc_start: 0.8248 (t80) cc_final: 0.7960 (t80) REVERT: F 367 MET cc_start: 0.7758 (tpp) cc_final: 0.7036 (mmm) REVERT: F 376 ASP cc_start: 0.8091 (t70) cc_final: 0.7656 (t70) REVERT: F 449 MET cc_start: 0.7976 (ttm) cc_final: 0.7719 (ttm) REVERT: F 486 MET cc_start: 0.7346 (mtt) cc_final: 0.7075 (mtt) REVERT: F 586 TYR cc_start: 0.7123 (OUTLIER) cc_final: 0.6262 (t80) REVERT: G 24 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.7862 (mm) REVERT: G 153 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8146 (tp) REVERT: I 19 LYS cc_start: 0.6717 (tttt) cc_final: 0.6170 (tttt) REVERT: I 168 MET cc_start: 0.7432 (mmp) cc_final: 0.6544 (mmm) REVERT: I 171 HIS cc_start: 0.7743 (OUTLIER) cc_final: 0.6695 (t-90) REVERT: J 22 GLN cc_start: 0.7332 (OUTLIER) cc_final: 0.6215 (mt0) REVERT: J 37 GLU cc_start: 0.8061 (pm20) cc_final: 0.7835 (pm20) REVERT: J 123 GLU cc_start: 0.7625 (tm-30) cc_final: 0.7027 (tm-30) REVERT: K 161 LYS cc_start: 0.8515 (mmtp) cc_final: 0.8217 (mmtm) REVERT: M 34 ASP cc_start: 0.7923 (t0) cc_final: 0.7679 (t0) REVERT: N 58 TYR cc_start: 0.8149 (m-80) cc_final: 0.7831 (m-80) REVERT: Q 20 MET cc_start: 0.7442 (tpp) cc_final: 0.7167 (tpt) REVERT: R 6 THR cc_start: 0.5805 (OUTLIER) cc_final: 0.5389 (t) REVERT: S 52 LYS cc_start: 0.7485 (tttm) cc_final: 0.7201 (tttm) REVERT: S 80 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7363 (tp30) REVERT: V 52 PHE cc_start: 0.6640 (OUTLIER) cc_final: 0.5632 (m-80) REVERT: V 80 TRP cc_start: 0.6796 (t60) cc_final: 0.6450 (t60) REVERT: V 141 LYS cc_start: 0.8420 (mttt) cc_final: 0.7965 (mtmm) outliers start: 122 outliers final: 92 residues processed: 566 average time/residue: 0.4242 time to fit residues: 401.5048 Evaluate side-chains 574 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 472 time to evaluate : 3.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 446 ASN Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 247 HIS Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 379 PHE Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 437 MET Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 315 ILE Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 446 MET Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 585 LEU Chi-restraints excluded: chain F residue 586 TYR Chi-restraints excluded: chain F residue 589 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain H residue 3 LYS Chi-restraints excluded: chain H residue 5 GLU Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 69 CYS Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain I residue 171 HIS Chi-restraints excluded: chain J residue 22 GLN Chi-restraints excluded: chain J residue 93 GLU Chi-restraints excluded: chain J residue 146 ASP Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 114 MET Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 180 THR Chi-restraints excluded: chain M residue 5 SER Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 128 VAL Chi-restraints excluded: chain N residue 140 TRP Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain P residue 14 MET Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain Q residue 26 VAL Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain S residue 71 THR Chi-restraints excluded: chain V residue 52 PHE Chi-restraints excluded: chain V residue 53 LEU Chi-restraints excluded: chain V residue 105 SER Chi-restraints excluded: chain V residue 124 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 238 optimal weight: 0.2980 chunk 384 optimal weight: 6.9990 chunk 234 optimal weight: 10.0000 chunk 182 optimal weight: 0.8980 chunk 267 optimal weight: 4.9990 chunk 403 optimal weight: 9.9990 chunk 371 optimal weight: 1.9990 chunk 321 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 248 optimal weight: 0.8980 chunk 197 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN G 117 GLN H 14 ASN H 78 ASN H 196 ASN H 364 GLN S 64 GLN ** V 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.5935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.247 36165 Z= 0.429 Angle : 3.312 50.559 49812 Z= 1.388 Chirality : 0.433 6.341 6080 Planarity : 0.004 0.052 5682 Dihedral : 45.137 179.994 10943 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.15 % Favored : 93.80 % Rotamer: Outliers : 2.83 % Allowed : 20.55 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.14), residues: 4078 helix: 1.80 (0.11), residues: 2273 sheet: 0.32 (0.34), residues: 259 loop : -2.51 (0.14), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 60 HIS 0.008 0.001 HIS C 99 PHE 0.025 0.001 PHE F 352 TYR 0.063 0.001 TYR F 629 ARG 0.004 0.000 ARG H 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8156 Ramachandran restraints generated. 4078 Oldfield, 0 Emsley, 4078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8156 Ramachandran restraints generated. 4078 Oldfield, 0 Emsley, 4078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 505 time to evaluate : 3.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 VAL cc_start: 0.8559 (t) cc_final: 0.8348 (t) REVERT: A 79 ASP cc_start: 0.7473 (m-30) cc_final: 0.7089 (m-30) REVERT: A 258 TYR cc_start: 0.6341 (OUTLIER) cc_final: 0.4758 (m-80) REVERT: D 24 ILE cc_start: 0.8135 (mm) cc_final: 0.7918 (mm) REVERT: D 44 ILE cc_start: 0.8165 (pt) cc_final: 0.7801 (mt) REVERT: D 64 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.7171 (mtt) REVERT: D 265 MET cc_start: 0.7999 (mmt) cc_final: 0.7789 (mmm) REVERT: D 379 PHE cc_start: 0.9046 (OUTLIER) cc_final: 0.8513 (t80) REVERT: E 1 MET cc_start: 0.7686 (tpp) cc_final: 0.7404 (ttp) REVERT: E 94 GLU cc_start: 0.7138 (tp30) cc_final: 0.6874 (tp30) REVERT: E 100 LYS cc_start: 0.7831 (mttt) cc_final: 0.7277 (mmtt) REVERT: F 64 GLN cc_start: 0.7744 (tp40) cc_final: 0.7130 (tt0) REVERT: F 187 PHE cc_start: 0.8248 (t80) cc_final: 0.8034 (t80) REVERT: F 367 MET cc_start: 0.7680 (tpp) cc_final: 0.7032 (mmm) REVERT: F 376 ASP cc_start: 0.8083 (t70) cc_final: 0.7613 (t70) REVERT: F 586 TYR cc_start: 0.7110 (OUTLIER) cc_final: 0.6156 (t80) REVERT: G 24 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.7781 (mm) REVERT: G 28 LEU cc_start: 0.8068 (mt) cc_final: 0.7868 (mt) REVERT: I 19 LYS cc_start: 0.6665 (tttt) cc_final: 0.6133 (tttt) REVERT: I 168 MET cc_start: 0.7341 (mmp) cc_final: 0.6406 (mmm) REVERT: I 171 HIS cc_start: 0.7540 (OUTLIER) cc_final: 0.6486 (t-90) REVERT: J 106 ARG cc_start: 0.7039 (mtp85) cc_final: 0.6779 (mtm110) REVERT: J 123 GLU cc_start: 0.7542 (tm-30) cc_final: 0.7036 (tm-30) REVERT: K 161 LYS cc_start: 0.8431 (mmtp) cc_final: 0.8166 (mmtm) REVERT: O 5 LYS cc_start: 0.8400 (mttm) cc_final: 0.8081 (mttm) REVERT: Q 20 MET cc_start: 0.7407 (tpp) cc_final: 0.7105 (tpt) REVERT: R 6 THR cc_start: 0.5871 (OUTLIER) cc_final: 0.5482 (t) REVERT: S 52 LYS cc_start: 0.7454 (tttm) cc_final: 0.7156 (tttm) REVERT: S 80 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7321 (tp30) REVERT: V 52 PHE cc_start: 0.6627 (OUTLIER) cc_final: 0.5733 (m-80) REVERT: V 80 TRP cc_start: 0.6907 (t60) cc_final: 0.6606 (t60) REVERT: V 141 LYS cc_start: 0.8360 (mttt) cc_final: 0.7940 (mtmm) outliers start: 96 outliers final: 72 residues processed: 560 average time/residue: 0.4473 time to fit residues: 415.9406 Evaluate side-chains 569 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 489 time to evaluate : 3.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 446 ASN Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain D residue 64 MET Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 247 HIS Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 379 PHE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 437 MET Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 315 ILE Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 446 MET Chi-restraints excluded: chain F residue 461 VAL Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 585 LEU Chi-restraints excluded: chain F residue 586 TYR Chi-restraints excluded: chain F residue 589 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain I residue 171 HIS Chi-restraints excluded: chain J residue 146 ASP Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 180 THR Chi-restraints excluded: chain M residue 5 SER Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 128 VAL Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain P residue 14 MET Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain Q residue 26 VAL Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain S residue 71 THR Chi-restraints excluded: chain V residue 52 PHE Chi-restraints excluded: chain V residue 53 LEU Chi-restraints excluded: chain V residue 105 SER Chi-restraints excluded: chain V residue 124 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 255 optimal weight: 2.9990 chunk 342 optimal weight: 0.9990 chunk 98 optimal weight: 0.3980 chunk 296 optimal weight: 0.4980 chunk 47 optimal weight: 0.8980 chunk 89 optimal weight: 0.0170 chunk 321 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 330 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 127 GLN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 GLN H 14 ASN H 196 ASN H 364 GLN ** V 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.159941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.125476 restraints weight = 43493.166| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.98 r_work: 0.3230 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3211 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3211 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.5875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.246 36165 Z= 0.417 Angle : 3.305 50.542 49812 Z= 1.384 Chirality : 0.432 6.324 6080 Planarity : 0.004 0.052 5682 Dihedral : 45.171 179.974 10943 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.89 % Favored : 94.07 % Rotamer: Outliers : 2.56 % Allowed : 21.02 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.49 (0.14), residues: 4078 helix: 1.98 (0.11), residues: 2268 sheet: 0.44 (0.34), residues: 259 loop : -2.38 (0.14), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP F 60 HIS 0.007 0.001 HIS C 99 PHE 0.025 0.001 PHE F 352 TYR 0.059 0.001 TYR F 629 ARG 0.005 0.000 ARG H 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9515.25 seconds wall clock time: 170 minutes 17.81 seconds (10217.81 seconds total)