Starting phenix.real_space_refine (version: 1.21rc1) on Sun May 14 22:36:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l7o_0849/05_2023/6l7o_0849_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l7o_0849/05_2023/6l7o_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_0849/05_2023/6l7o_0849.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l7o_0849/05_2023/6l7o_0849.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l7o_0849/05_2023/6l7o_0849_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l7o_0849/05_2023/6l7o_0849_neut_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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: 5 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: 12 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: 2 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: 12 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: 1 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: 13 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: 7 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: 8 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: 21.63, per 1000 atoms: 0.62 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: 15.43 Conformation dependent library (CDL) restraints added in 5.2 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: 2.70 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: 9.78 Time building geometry restraints manager: 16.32 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 - 27.14: 18878 27.14 - 54.28: 923 54.28 - 81.42: 93 81.42 - 108.56: 85 108.56 - 135.71: 115 Dihedral angle restraints: 20094 sinusoidal: 8238 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=" C02 AJP D 604 " pdb=" C85 AJP D 604 " pdb=" O84 AJP D 604 " pdb=" C05 AJP D 604 " ideal model delta sinusoidal sigma weight residual -57.60 78.11 -135.71 1 3.00e+01 1.11e-03 1.83e+01 dihedral pdb=" C02 AJP D 610 " pdb=" C85 AJP D 610 " pdb=" O84 AJP D 610 " pdb=" C05 AJP D 610 " ideal model delta sinusoidal sigma weight residual -57.60 75.77 -133.37 1 3.00e+01 1.11e-03 1.80e+01 ... (remaining 20091 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: 1.710 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: 9.620 Check model and map are aligned: 0.560 Set scattering table: 0.330 Process input model: 95.720 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.150 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: 0.010 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.320 ------------------------------------------------------------------------------- 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 : 19.926 135.706 12512 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 % 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 *********************** 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 : 3.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 860 average time/residue: 0.4979 time to fit residues: 685.2295 Evaluate side-chains 595 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 595 time to evaluate : 3.760 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1081 ------------------------------------------------------------------------------- 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: 0.5980 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: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 349 HIS F 600 GLN I 5 ASN I 76 ASN J 120 GLN ** K 32 ASN ** 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 V 146 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.259 36165 Z= 0.433 Angle : 3.352 51.025 49812 Z= 1.394 Chirality : 0.455 6.675 6080 Planarity : 0.004 0.049 5682 Dihedral : 11.592 122.627 5240 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer Outliers : 2.00 % 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: -1.37 (0.13), residues: 4078 helix: 0.58 (0.11), residues: 2255 sheet: -0.54 (0.32), residues: 244 loop : -3.32 (0.12), residues: 1579 *********************** 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 679 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 611 time to evaluate : 3.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 42 residues processed: 638 average time/residue: 0.4503 time to fit residues: 475.0704 Evaluate side-chains 607 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 565 time to evaluate : 3.604 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.3387 time to fit residues: 30.9262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 204 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 306 optimal weight: 0.8980 chunk 250 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 368 optimal weight: 2.9990 chunk 398 optimal weight: 20.0000 chunk 328 optimal weight: 4.9990 chunk 365 optimal weight: 10.0000 chunk 125 optimal weight: 0.1980 chunk 295 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 GLN B 290 ASN C 99 HIS D 127 GLN D 134 GLN D 486 GLN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 HIS F 71 GLN F 563 GLN ** F 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 114 HIS H 361 ASN J 23 ASN J 137 ASN ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 65 GLN S 64 GLN V 146 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.2966 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= 0.443 Angle : 3.307 50.561 49812 Z= 1.384 Chirality : 0.450 6.353 6080 Planarity : 0.004 0.059 5682 Dihedral : 11.154 124.009 5240 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.35 % Favored : 94.63 % Rotamer Outliers : 1.65 % 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: -0.57 (0.13), residues: 4078 helix: 1.26 (0.11), residues: 2262 sheet: -0.36 (0.32), residues: 242 loop : -3.00 (0.13), residues: 1574 *********************** 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 653 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 597 time to evaluate : 4.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 30 residues processed: 633 average time/residue: 0.4670 time to fit residues: 486.9836 Evaluate side-chains 579 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 549 time to evaluate : 3.923 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.3261 time to fit residues: 23.5931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 364 optimal weight: 0.3980 chunk 277 optimal weight: 3.9990 chunk 191 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 175 optimal weight: 7.9990 chunk 247 optimal weight: 0.9980 chunk 369 optimal weight: 3.9990 chunk 391 optimal weight: 9.9990 chunk 193 optimal weight: 0.9980 chunk 350 optimal weight: 8.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A 168 GLN D 274 HIS E 44 ASN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 600 GLN H 364 GLN I 95 HIS ** 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** O 49 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: 0.7309 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.245 36165 Z= 0.431 Angle : 3.284 50.538 49812 Z= 1.378 Chirality : 0.447 6.402 6080 Planarity : 0.004 0.061 5682 Dihedral : 10.572 114.804 5240 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer Outliers : 1.94 % 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: -0.21 (0.13), residues: 4078 helix: 1.56 (0.11), residues: 2277 sheet: -0.26 (0.32), residues: 260 loop : -2.90 (0.13), residues: 1541 *********************** 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 638 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 572 time to evaluate : 3.982 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 outliers start: 66 outliers final: 34 residues processed: 599 average time/residue: 0.4756 time to fit residues: 470.0352 Evaluate side-chains 567 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 533 time to evaluate : 4.259 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.3377 time to fit residues: 27.1743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 326 optimal weight: 6.9990 chunk 222 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 291 optimal weight: 4.9990 chunk 161 optimal weight: 7.9990 chunk 334 optimal weight: 5.9990 chunk 270 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 199 optimal weight: 3.9990 chunk 351 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN B 130 GLN C 99 HIS E 87 ASN ** H 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 ASN K 104 GLN K 170 HIS P 29 ASN ** 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: 0.7598 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.244 36165 Z= 0.508 Angle : 3.314 50.723 49812 Z= 1.396 Chirality : 0.447 6.684 6080 Planarity : 0.005 0.052 5682 Dihedral : 10.706 122.272 5240 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.50 % Favored : 93.43 % Rotamer Outliers : 2.80 % 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: -0.33 (0.13), residues: 4078 helix: 1.37 (0.11), residues: 2275 sheet: -0.12 (0.33), residues: 256 loop : -2.83 (0.13), residues: 1547 *********************** 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 627 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 532 time to evaluate : 3.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 95 outliers final: 45 residues processed: 590 average time/residue: 0.4713 time to fit residues: 456.3796 Evaluate side-chains 536 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 491 time to evaluate : 3.906 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.3522 time to fit residues: 34.1716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 131 optimal weight: 0.8980 chunk 352 optimal weight: 8.9990 chunk 77 optimal weight: 0.9980 chunk 229 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 391 optimal weight: 5.9990 chunk 325 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 205 optimal weight: 8.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN B 230 GLN C 71 ASN ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 345 HIS F 563 GLN F 600 GLN H 14 ASN H 310 GLN K 32 ASN P 44 HIS 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: 0.7564 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.244 36165 Z= 0.445 Angle : 3.287 50.577 49812 Z= 1.382 Chirality : 0.444 6.352 6080 Planarity : 0.004 0.053 5682 Dihedral : 10.441 116.327 5240 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.25 % Favored : 94.70 % Rotamer Outliers : 1.83 % 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: -0.10 (0.13), residues: 4078 helix: 1.57 (0.11), residues: 2274 sheet: -0.02 (0.33), residues: 264 loop : -2.76 (0.13), residues: 1540 *********************** 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 586 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 524 time to evaluate : 3.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 33 residues processed: 556 average time/residue: 0.4707 time to fit residues: 430.7426 Evaluate side-chains 521 residues out of total 3399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 488 time to evaluate : 3.817 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.3232 time to fit residues: 25.7873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.042 > 50: distance: 27 - 29: 21.359 distance: 29 - 30: 17.425 distance: 30 - 31: 30.505 distance: 30 - 33: 18.049 distance: 31 - 32: 34.224 distance: 31 - 37: 32.563 distance: 33 - 34: 24.783 distance: 34 - 35: 46.857 distance: 34 - 36: 41.781 distance: 37 - 38: 27.235 distance: 38 - 39: 52.964 distance: 38 - 41: 29.799 distance: 39 - 40: 39.443 distance: 39 - 45: 9.676 distance: 41 - 42: 10.524 distance: 42 - 43: 42.454 distance: 42 - 44: 54.029 distance: 45 - 46: 16.180 distance: 46 - 47: 19.269 distance: 46 - 49: 44.582 distance: 47 - 48: 37.219 distance: 47 - 51: 21.406 distance: 49 - 50: 31.851 distance: 51 - 52: 16.038 distance: 51 - 57: 42.028 distance: 52 - 53: 29.086 distance: 52 - 55: 36.047 distance: 53 - 54: 54.155 distance: 53 - 58: 19.621 distance: 54 - 77: 32.441 distance: 55 - 56: 32.294 distance: 56 - 57: 27.153 distance: 58 - 59: 19.998 distance: 59 - 60: 13.020 distance: 59 - 62: 24.273 distance: 60 - 61: 17.647 distance: 60 - 64: 52.552 distance: 61 - 82: 45.318 distance: 62 - 63: 47.181 distance: 64 - 65: 6.821 distance: 65 - 66: 29.782 distance: 65 - 68: 23.070 distance: 66 - 67: 44.649 distance: 66 - 72: 13.173 distance: 67 - 90: 40.675 distance: 68 - 69: 24.620 distance: 69 - 70: 48.371 distance: 69 - 71: 41.220 distance: 70 - 154: 24.335 distance: 72 - 73: 11.925 distance: 73 - 74: 18.608 distance: 73 - 76: 16.252 distance: 74 - 75: 15.531 distance: 74 - 77: 15.903 distance: 75 - 98: 19.904 distance: 77 - 78: 6.952 distance: 78 - 79: 20.663 distance: 78 - 81: 14.869 distance: 79 - 80: 6.237 distance: 79 - 82: 9.162 distance: 80 - 103: 10.786 distance: 82 - 83: 8.687 distance: 83 - 84: 20.808 distance: 83 - 86: 3.057 distance: 84 - 85: 6.185 distance: 84 - 90: 29.514 distance: 85 - 111: 21.675 distance: 86 - 87: 44.059 distance: 86 - 88: 19.241 distance: 87 - 89: 26.114 distance: 90 - 91: 9.788 distance: 91 - 92: 18.946 distance: 91 - 94: 17.153 distance: 92 - 93: 17.956 distance: 92 - 98: 8.704 distance: 93 - 119: 19.373 distance: 94 - 95: 5.666 distance: 95 - 96: 19.770 distance: 95 - 97: 17.111