Starting phenix.real_space_refine on Sat Mar 23 07:57:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ziy_11231/03_2024/6ziy_11231_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ziy_11231/03_2024/6ziy_11231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ziy_11231/03_2024/6ziy_11231.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ziy_11231/03_2024/6ziy_11231.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ziy_11231/03_2024/6ziy_11231_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ziy_11231/03_2024/6ziy_11231_updated.pdb" } resolution = 4.25 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= 0.045 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 32 7.16 5 P 3 5.49 5 S 180 5.16 5 C 23646 2.51 5 N 6005 2.21 5 O 6235 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 GLU 14": "OE1" <-> "OE2" Residue "1 GLU 24": "OE1" <-> "OE2" Residue "1 TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 56": "OE1" <-> "OE2" Residue "1 PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 82": "OD1" <-> "OD2" Residue "1 TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 94": "OD1" <-> "OD2" Residue "1 GLU 95": "OE1" <-> "OE2" Residue "1 PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 109": "OD1" <-> "OD2" Residue "1 TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 137": "OE1" <-> "OE2" Residue "1 ASP 143": "OD1" <-> "OD2" Residue "1 GLU 151": "OE1" <-> "OE2" Residue "1 TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 170": "OD1" <-> "OD2" Residue "1 GLU 184": "OE1" <-> "OE2" Residue "1 GLU 193": "OE1" <-> "OE2" Residue "1 GLU 222": "OE1" <-> "OE2" Residue "1 GLU 244": "OE1" <-> "OE2" Residue "1 TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 274": "OE1" <-> "OE2" Residue "1 TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 285": "OE1" <-> "OE2" Residue "1 GLU 314": "OE1" <-> "OE2" Residue "1 ASP 339": "OD1" <-> "OD2" Residue "1 GLU 361": "OE1" <-> "OE2" Residue "1 PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 381": "OE1" <-> "OE2" Residue "1 ASP 383": "OD1" <-> "OD2" Residue "1 GLU 385": "OE1" <-> "OE2" Residue "1 GLU 388": "OE1" <-> "OE2" Residue "1 ASP 419": "OD1" <-> "OD2" Residue "1 TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 427": "OE1" <-> "OE2" Residue "2 PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 9": "OD1" <-> "OD2" Residue "2 PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 13": "OE1" <-> "OE2" Residue "2 PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 21": "OE1" <-> "OE2" Residue "2 GLU 38": "OE1" <-> "OE2" Residue "2 GLU 44": "OE1" <-> "OE2" Residue "2 GLU 47": "OE1" <-> "OE2" Residue "2 PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 95": "OE1" <-> "OE2" Residue "2 ASP 98": "OD1" <-> "OD2" Residue "2 TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 123": "OE1" <-> "OE2" Residue "2 ASP 138": "OD1" <-> "OD2" Residue "2 GLU 164": "OE1" <-> "OE2" Residue "2 GLU 167": "OE1" <-> "OE2" Residue "3 GLU 12": "OE1" <-> "OE2" Residue "3 ASP 29": "OD1" <-> "OD2" Residue "3 GLU 36": "OE1" <-> "OE2" Residue "3 ASP 89": "OD1" <-> "OD2" Residue "3 ASP 94": "OD1" <-> "OD2" Residue "3 GLU 102": "OE1" <-> "OE2" Residue "3 ASP 118": "OD1" <-> "OD2" Residue "3 ASP 123": "OD1" <-> "OD2" Residue "3 GLU 129": "OE1" <-> "OE2" Residue "3 ASP 132": "OD1" <-> "OD2" Residue "3 GLU 136": "OE1" <-> "OE2" Residue "3 GLU 141": "OE1" <-> "OE2" Residue "3 TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 177": "OD1" <-> "OD2" Residue "3 GLU 193": "OE1" <-> "OE2" Residue "3 ASP 197": "OD1" <-> "OD2" Residue "3 GLU 198": "OE1" <-> "OE2" Residue "3 ASP 201": "OD1" <-> "OD2" Residue "3 PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 228": "OD1" <-> "OD2" Residue "3 GLU 248": "OE1" <-> "OE2" Residue "3 ASP 268": "OD1" <-> "OD2" Residue "3 GLU 281": "OE1" <-> "OE2" Residue "3 ASP 292": "OD1" <-> "OD2" Residue "3 GLU 299": "OE1" <-> "OE2" Residue "3 GLU 319": "OE1" <-> "OE2" Residue "3 GLU 331": "OE1" <-> "OE2" Residue "3 GLU 335": "OE1" <-> "OE2" Residue "3 ASP 348": "OD1" <-> "OD2" Residue "3 GLU 352": "OE1" <-> "OE2" Residue "3 GLU 353": "OE1" <-> "OE2" Residue "3 GLU 359": "OE1" <-> "OE2" Residue "3 ASP 370": "OD1" <-> "OD2" Residue "3 PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 389": "OD1" <-> "OD2" Residue "3 GLU 404": "OE1" <-> "OE2" Residue "3 ASP 419": "OD1" <-> "OD2" Residue "3 TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 434": "OD1" <-> "OD2" Residue "3 ASP 446": "OD1" <-> "OD2" Residue "3 GLU 466": "OE1" <-> "OE2" Residue "3 GLU 475": "OE1" <-> "OE2" Residue "3 GLU 488": "OE1" <-> "OE2" Residue "3 GLU 498": "OE1" <-> "OE2" Residue "3 ASP 514": "OD1" <-> "OD2" Residue "3 GLU 560": "OE1" <-> "OE2" Residue "3 GLU 574": "OE1" <-> "OE2" Residue "3 GLU 575": "OE1" <-> "OE2" Residue "3 TYR 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 609": "OE1" <-> "OE2" Residue "3 GLU 635": "OE1" <-> "OE2" Residue "3 GLU 646": "OE1" <-> "OE2" Residue "3 GLU 659": "OE1" <-> "OE2" Residue "3 GLU 682": "OE1" <-> "OE2" Residue "3 PHE 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 710": "OE1" <-> "OE2" Residue "3 GLU 721": "OE1" <-> "OE2" Residue "3 GLU 726": "OE1" <-> "OE2" Residue "3 GLU 730": "OE1" <-> "OE2" Residue "3 GLU 737": "OE1" <-> "OE2" Residue "3 PHE 740": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 744": "OE1" <-> "OE2" Residue "4 GLU 51": "OE1" <-> "OE2" Residue "4 GLU 67": "OE1" <-> "OE2" Residue "4 TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 122": "OE1" <-> "OE2" Residue "4 TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 154": "OE1" <-> "OE2" Residue "4 GLU 161": "OE1" <-> "OE2" Residue "4 PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 180": "OE1" <-> "OE2" Residue "4 GLU 189": "OE1" <-> "OE2" Residue "4 GLU 203": "OE1" <-> "OE2" Residue "4 GLU 205": "OE1" <-> "OE2" Residue "4 PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 210": "OE1" <-> "OE2" Residue "4 GLU 227": "OE1" <-> "OE2" Residue "4 ASP 231": "OD1" <-> "OD2" Residue "4 ASP 247": "OD1" <-> "OD2" Residue "4 TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 258": "OE1" <-> "OE2" Residue "4 ASP 263": "OD1" <-> "OD2" Residue "4 ASP 271": "OD1" <-> "OD2" Residue "4 PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 274": "OD1" <-> "OD2" Residue "4 GLU 282": "OE1" <-> "OE2" Residue "4 GLU 285": "OE1" <-> "OE2" Residue "4 ASP 304": "OD1" <-> "OD2" Residue "4 GLU 318": "OE1" <-> "OE2" Residue "4 GLU 322": "OE1" <-> "OE2" Residue "4 PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 341": "OE1" <-> "OE2" Residue "4 TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 347": "OE1" <-> "OE2" Residue "4 TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 392": "OD1" <-> "OD2" Residue "4 ASP 401": "OD1" <-> "OD2" Residue "5 GLU 4": "OE1" <-> "OE2" Residue "5 GLU 18": "OE1" <-> "OE2" Residue "5 GLU 36": "OE1" <-> "OE2" Residue "5 PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 62": "OD1" <-> "OD2" Residue "5 PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 73": "OE1" <-> "OE2" Residue "5 GLU 96": "OE1" <-> "OE2" Residue "5 GLU 115": "OE1" <-> "OE2" Residue "5 GLU 117": "OE1" <-> "OE2" Residue "5 ASP 120": "OD1" <-> "OD2" Residue "5 ASP 131": "OD1" <-> "OD2" Residue "5 GLU 139": "OE1" <-> "OE2" Residue "5 ASP 149": "OD1" <-> "OD2" Residue "5 TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 154": "OE1" <-> "OE2" Residue "5 PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 178": "OD1" <-> "OD2" Residue "5 PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 17": "OE1" <-> "OE2" Residue "6 PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 134": "OD1" <-> "OD2" Residue "6 GLU 145": "OE1" <-> "OE2" Residue "6 TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 165": "OE1" <-> "OE2" Residue "6 GLU 168": "OE1" <-> "OE2" Residue "9 TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 28": "OD1" <-> "OD2" Residue "9 GLU 51": "OE1" <-> "OE2" Residue "9 TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 71": "OE1" <-> "OE2" Residue "9 TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 105": "OE1" <-> "OE2" Residue "9 GLU 106": "OE1" <-> "OE2" Residue "9 PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 120": "OE1" <-> "OE2" Residue "9 ASP 123": "OD1" <-> "OD2" Residue "9 TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 128": "OD1" <-> "OD2" Residue "9 TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 134": "OE1" <-> "OE2" Residue "9 ASP 139": "OD1" <-> "OD2" Residue "9 TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 169": "OE1" <-> "OE2" Residue "9 GLU 171": "OE1" <-> "OE2" Residue "9 GLU 178": "OE1" <-> "OE2" Residue "7 GLU 6": "OE1" <-> "OE2" Residue "7 GLU 8": "OE1" <-> "OE2" Residue "7 TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 11": "OE1" <-> "OE2" Residue "7 GLU 15": "OE1" <-> "OE2" Residue "7 TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 34": "OE1" <-> "OE2" Residue "7 ASP 36": "OD1" <-> "OD2" Residue "7 GLU 45": "OE1" <-> "OE2" Residue "7 ASP 61": "OD1" <-> "OD2" Residue "7 GLU 65": "OE1" <-> "OE2" Residue "7 ASP 71": "OD1" <-> "OD2" Residue "7 GLU 98": "OE1" <-> "OE2" Residue "7 ASP 120": "OD1" <-> "OD2" Residue "7 GLU 124": "OE1" <-> "OE2" Residue "A TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 45": "OE1" <-> "OE2" Residue "A GLU 53": "OE1" <-> "OE2" Residue "A TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 110": "OE1" <-> "OE2" Residue "J PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 80": "OE1" <-> "OE2" Residue "J ASP 112": "OD1" <-> "OD2" Residue "J PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 118": "OD1" <-> "OD2" Residue "J PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 158": "OE1" <-> "OE2" Residue "K TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 88": "OD1" <-> "OD2" Residue "K GLU 92": "OE1" <-> "OE2" Residue "L GLU 26": "OE1" <-> "OE2" Residue "L PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 153": "OD1" <-> "OD2" Residue "L ASP 166": "OD1" <-> "OD2" Residue "L PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 187": "OE1" <-> "OE2" Residue "L GLU 190": "OE1" <-> "OE2" Residue "L ASP 228": "OD1" <-> "OD2" Residue "L TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 290": "OD1" <-> "OD2" Residue "L TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 346": "OE1" <-> "OE2" Residue "L PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 428": "OE1" <-> "OE2" Residue "L GLU 437": "OE1" <-> "OE2" Residue "L TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 470": "OE1" <-> "OE2" Residue "L GLU 490": "OE1" <-> "OE2" Residue "L PHE 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 535": "OD1" <-> "OD2" Residue "L TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 123": "OE1" <-> "OE2" Residue "M TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 178": "OE1" <-> "OE2" Residue "M ASP 179": "OD1" <-> "OD2" Residue "M PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 220": "OE1" <-> "OE2" Residue "M GLU 251": "OE1" <-> "OE2" Residue "M TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 306": "OE1" <-> "OE2" Residue "M TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 334": "OE1" <-> "OE2" Residue "M GLU 416": "OE1" <-> "OE2" Residue "M GLU 417": "OE1" <-> "OE2" Residue "M GLU 429": "OE1" <-> "OE2" Residue "M PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 81": "NH1" <-> "NH2" Residue "N PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 83": "OE1" <-> "OE2" Residue "N GLU 131": "OE1" <-> "OE2" Residue "N PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 168": "OE1" <-> "OE2" Residue "N PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 225": "NH1" <-> "NH2" Residue "N GLU 231": "OE1" <-> "OE2" Residue "N GLU 253": "OE1" <-> "OE2" Residue "N TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 310": "OE1" <-> "OE2" Residue "N ASP 319": "OD1" <-> "OD2" Residue "N PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 388": "OE1" <-> "OE2" Residue "H ASP 8": "OD1" <-> "OD2" Residue "H TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 35": "OE1" <-> "OE2" Residue "H PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 78": "OD1" <-> "OD2" Residue "H PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 130": "OE1" <-> "OE2" Residue "H TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 213": "OE1" <-> "OE2" Residue "H TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 303": "OD1" <-> "OD2" Residue "H ASP 331": "OD1" <-> "OD2" Residue "H TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 36101 Number of models: 1 Model: "" Number of chains: 20 Chain: "1" Number of atoms: 3417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3417 Classifications: {'peptide': 437} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 405} Chain: "2" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1406 Classifications: {'peptide': 178} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 166} Chain: "3" Number of atoms: 5876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 754, 5876 Classifications: {'peptide': 754} Link IDs: {'PTRANS': 53, 'TRANS': 700} Chain breaks: 2 Chain: "4" Number of atoms: 3067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3067 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 353} Chain: "5" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1607 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 16, 'TRANS': 179} Chain: "6" Number of atoms: 1289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1289 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 153} Chain: "9" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 163} Chain: "7" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1031 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 118} Chain: "A" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 910 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "J" Number of atoms: 1183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1183 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "K" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 703 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'TRANS': 94} Chain: "L" Number of atoms: 4604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4604 Classifications: {'peptide': 605} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 575} Chain: "M" Number of atoms: 3489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3489 Classifications: {'peptide': 467} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 443} Chain: "N" Number of atoms: 3154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3154 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 401} Chain: "H" Number of atoms: 2838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2838 Classifications: {'peptide': 353} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 333} Chain: "1" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 28 Unusual residues: {'FES': 1, 'SF4': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "6" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "9" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2772 SG CYS 1 356 112.447 70.668 225.820 1.00 50.00 S ATOM 2792 SG CYS 1 359 116.968 72.842 227.815 1.00 50.00 S ATOM 3102 SG CYS 1 400 111.557 70.732 230.725 1.00 50.00 S ATOM 2753 SG CYS 1 353 115.669 66.764 228.638 1.00 50.00 S ATOM 4091 SG CYS 2 83 127.129 73.877 245.643 1.00 50.00 S ATOM 4123 SG CYS 2 88 128.001 76.134 247.898 1.00 50.00 S ATOM 4394 SG CYS 2 124 122.450 74.150 245.755 1.00 50.00 S ATOM 4418 SG CYS 2 128 122.272 76.914 248.527 1.00 50.00 S ATOM 5640 SG CYS 3 128 119.826 66.759 205.395 1.00 50.00 S ATOM 5584 SG CYS 3 119 124.624 69.285 204.047 1.00 50.00 S ATOM 5604 SG CYS 3 122 124.847 63.347 204.723 1.00 50.00 S ATOM 6083 SG CYS 3 184 114.716 61.249 214.755 1.00 50.00 S ATOM 6059 SG CYS 3 181 120.559 62.365 215.869 1.00 50.00 S ATOM 6109 SG CYS 3 187 116.962 56.821 216.256 1.00 50.00 S ATOM 6445 SG CYS 3 230 118.872 59.448 210.936 1.00 50.00 S ATOM 6652 SG CYS 3 256 110.563 40.981 198.999 1.00 50.00 S ATOM 6918 SG CYS 3 291 112.370 40.978 204.894 1.00 50.00 S ATOM 6695 SG CYS 3 263 106.882 43.048 202.014 1.00 50.00 S ATOM 6671 SG CYS 3 259 108.051 37.016 203.233 1.00 50.00 S ATOM 5085 SG CYS 3 34 108.455 65.630 217.307 1.00 50.00 S ATOM 5163 SG CYS 3 45 110.033 68.960 215.522 1.00 50.00 S ATOM 5188 SG CYS 3 48 104.740 70.246 215.458 1.00 50.00 S ATOM 5320 SG CYS 3 83 104.307 67.157 217.162 1.00 50.00 S ATOM 16119 SG CYS 6 111 124.512 73.316 168.623 1.00 50.00 S ATOM 15614 SG CYS 6 46 129.088 76.164 165.725 1.00 50.00 S ATOM 15608 SG CYS 6 45 124.000 78.349 167.619 1.00 50.00 S ATOM 16328 SG CYS 6 140 128.156 76.570 172.135 1.00 50.00 S ATOM 17432 SG CYS 9 101 128.166 74.739 180.368 1.00 50.00 S ATOM 17407 SG CYS 9 98 131.477 71.468 177.659 1.00 50.00 S ATOM 17450 SG CYS 9 104 131.307 72.888 184.151 1.00 50.00 S ATOM 17129 SG CYS 9 63 127.179 69.311 181.597 1.00 50.00 S ATOM 17479 SG CYS 9 108 134.275 71.374 192.572 1.00 50.00 S ATOM 17108 SG CYS 9 59 131.190 68.295 188.888 1.00 50.00 S ATOM 17070 SG CYS 9 53 136.512 66.140 192.495 1.00 50.00 S ATOM 17088 SG CYS 9 56 130.557 68.129 194.407 1.00 50.00 S Time building chain proxies: 17.29, per 1000 atoms: 0.48 Number of scatterers: 36101 At special positions: 0 Unit cell: (175.44, 132.44, 283.8, 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 32 26.01 S 180 16.00 P 3 15.00 O 6235 8.00 N 6005 7.00 C 23646 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 2 144 " - pdb=" SG CYS 2 172 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.75 Conformation dependent library (CDL) restraints added in 6.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES 2 201 " pdb="FE2 FES 2 201 " - pdb=" SG CYS 2 124 " pdb="FE2 FES 2 201 " - pdb=" SG CYS 2 128 " pdb="FE1 FES 2 201 " - pdb=" SG CYS 2 88 " pdb="FE1 FES 2 201 " - pdb=" SG CYS 2 83 " pdb=" FES 3 804 " pdb="FE2 FES 3 804 " - pdb=" SG CYS 3 83 " pdb="FE2 FES 3 804 " - pdb=" SG CYS 3 48 " pdb="FE1 FES 3 804 " - pdb=" SG CYS 3 45 " pdb="FE1 FES 3 804 " - pdb=" SG CYS 3 34 " pdb=" SF4 1 501 " pdb="FE4 SF4 1 501 " - pdb=" SG CYS 1 353 " pdb="FE2 SF4 1 501 " - pdb=" SG CYS 1 359 " pdb="FE3 SF4 1 501 " - pdb=" SG CYS 1 400 " pdb="FE1 SF4 1 501 " - pdb=" SG CYS 1 356 " pdb=" SF4 3 801 " pdb="FE3 SF4 3 801 " - pdb=" NE2 HIS 3 115 " pdb="FE4 SF4 3 801 " - pdb=" SG CYS 3 122 " pdb="FE2 SF4 3 801 " - pdb=" SG CYS 3 119 " pdb="FE1 SF4 3 801 " - pdb=" SG CYS 3 128 " pdb=" SF4 3 802 " pdb="FE4 SF4 3 802 " - pdb=" SG CYS 3 230 " pdb="FE2 SF4 3 802 " - pdb=" SG CYS 3 181 " pdb="FE3 SF4 3 802 " - pdb=" SG CYS 3 187 " pdb="FE1 SF4 3 802 " - pdb=" SG CYS 3 184 " pdb=" SF4 3 803 " pdb="FE4 SF4 3 803 " - pdb=" SG CYS 3 259 " pdb="FE2 SF4 3 803 " - pdb=" SG CYS 3 291 " pdb="FE3 SF4 3 803 " - pdb=" SG CYS 3 263 " pdb="FE1 SF4 3 803 " - pdb=" SG CYS 3 256 " pdb=" SF4 6 201 " pdb="FE4 SF4 6 201 " - pdb=" SG CYS 6 140 " pdb="FE3 SF4 6 201 " - pdb=" SG CYS 6 45 " pdb="FE2 SF4 6 201 " - pdb=" SG CYS 6 46 " pdb="FE1 SF4 6 201 " - pdb=" SG CYS 6 111 " pdb=" SF4 9 201 " pdb="FE4 SF4 9 201 " - pdb=" SG CYS 9 63 " pdb="FE3 SF4 9 201 " - pdb=" SG CYS 9 104 " pdb="FE1 SF4 9 201 " - pdb=" SG CYS 9 101 " pdb="FE2 SF4 9 201 " - pdb=" SG CYS 9 98 " pdb=" SF4 9 202 " pdb="FE4 SF4 9 202 " - pdb=" SG CYS 9 56 " pdb="FE2 SF4 9 202 " - pdb=" SG CYS 9 59 " pdb="FE3 SF4 9 202 " - pdb=" SG CYS 9 53 " pdb="FE1 SF4 9 202 " - pdb=" SG CYS 9 108 " Number of angles added : 93 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8414 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 195 helices and 20 sheets defined 52.6% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.95 Creating SS restraints... Processing helix chain '1' and resid 29 through 35 Processing helix chain '1' and resid 39 through 46 removed outlier: 4.422A pdb=" N LYS 1 46 " --> pdb=" O LYS 1 42 " (cutoff:3.500A) Processing helix chain '1' and resid 50 through 60 removed outlier: 4.148A pdb=" N VAL 1 57 " --> pdb=" O VAL 1 53 " (cutoff:3.500A) Processing helix chain '1' and resid 72 through 76 Processing helix chain '1' and resid 103 through 109 Processing helix chain '1' and resid 111 through 124 Processing helix chain '1' and resid 140 through 155 Processing helix chain '1' and resid 180 through 183 Processing helix chain '1' and resid 185 through 193 removed outlier: 3.514A pdb=" N MET 1 189 " --> pdb=" O GLU 1 185 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN 1 190 " --> pdb=" O THR 1 186 " (cutoff:3.500A) Processing helix chain '1' and resid 211 through 213 No H-bonds generated for 'chain '1' and resid 211 through 213' Processing helix chain '1' and resid 221 through 233 removed outlier: 4.345A pdb=" N VAL 1 228 " --> pdb=" O LEU 1 224 " (cutoff:3.500A) Proline residue: 1 229 - end of helix Processing helix chain '1' and resid 235 through 239 Processing helix chain '1' and resid 272 through 276 Processing helix chain '1' and resid 304 through 307 No H-bonds generated for 'chain '1' and resid 304 through 307' Processing helix chain '1' and resid 317 through 319 No H-bonds generated for 'chain '1' and resid 317 through 319' Processing helix chain '1' and resid 337 through 351 removed outlier: 3.658A pdb=" N HIS 1 350 " --> pdb=" O ARG 1 346 " (cutoff:3.500A) Processing helix chain '1' and resid 357 through 360 No H-bonds generated for 'chain '1' and resid 357 through 360' Processing helix chain '1' and resid 367 through 374 Processing helix chain '1' and resid 381 through 395 removed outlier: 3.814A pdb=" N LEU 1 387 " --> pdb=" O VAL 1 384 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU 1 388 " --> pdb=" O GLU 1 385 " (cutoff:3.500A) Proline residue: 1 392 - end of helix removed outlier: 4.072A pdb=" N GLU 1 395 " --> pdb=" O PRO 1 392 " (cutoff:3.500A) Processing helix chain '1' and resid 402 through 416 Proline residue: 1 409 - end of helix removed outlier: 3.627A pdb=" N LEU 1 414 " --> pdb=" O VAL 1 410 " (cutoff:3.500A) Processing helix chain '1' and resid 418 through 426 removed outlier: 3.599A pdb=" N ALA 1 425 " --> pdb=" O LEU 1 422 " (cutoff:3.500A) Processing helix chain '2' and resid 8 through 16 Processing helix chain '2' and resid 23 through 38 Proline residue: 2 29 - end of helix removed outlier: 3.515A pdb=" N GLN 2 36 " --> pdb=" O ARG 2 33 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU 2 37 " --> pdb=" O VAL 2 34 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU 2 38 " --> pdb=" O GLN 2 35 " (cutoff:3.500A) Processing helix chain '2' and resid 43 through 53 Processing helix chain '2' and resid 57 through 66 removed outlier: 3.553A pdb=" N PHE 2 66 " --> pdb=" O GLY 2 62 " (cutoff:3.500A) Processing helix chain '2' and resid 86 through 90 Processing helix chain '2' and resid 93 through 104 Processing helix chain '2' and resid 128 through 130 No H-bonds generated for 'chain '2' and resid 128 through 130' Processing helix chain '2' and resid 147 through 159 removed outlier: 3.539A pdb=" N ALA 2 159 " --> pdb=" O ALA 2 155 " (cutoff:3.500A) Processing helix chain '3' and resid 19 through 26 Processing helix chain '3' and resid 82 through 84 No H-bonds generated for 'chain '3' and resid 82 through 84' Processing helix chain '3' and resid 98 through 113 Processing helix chain '3' and resid 129 through 137 Processing helix chain '3' and resid 178 through 180 No H-bonds generated for 'chain '3' and resid 178 through 180' Processing helix chain '3' and resid 186 through 193 Processing helix chain '3' and resid 206 through 208 No H-bonds generated for 'chain '3' and resid 206 through 208' Processing helix chain '3' and resid 223 through 229 removed outlier: 3.564A pdb=" N ILE 3 226 " --> pdb=" O SER 3 223 " (cutoff:3.500A) Processing helix chain '3' and resid 238 through 240 No H-bonds generated for 'chain '3' and resid 238 through 240' Processing helix chain '3' and resid 246 through 248 No H-bonds generated for 'chain '3' and resid 246 through 248' Processing helix chain '3' and resid 292 through 295 No H-bonds generated for 'chain '3' and resid 292 through 295' Processing helix chain '3' and resid 299 through 301 No H-bonds generated for 'chain '3' and resid 299 through 301' Processing helix chain '3' and resid 322 through 333 Processing helix chain '3' and resid 351 through 363 Processing helix chain '3' and resid 388 through 391 Processing helix chain '3' and resid 402 through 405 No H-bonds generated for 'chain '3' and resid 402 through 405' Processing helix chain '3' and resid 407 through 417 removed outlier: 3.626A pdb=" N ARG 3 412 " --> pdb=" O LEU 3 409 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL 3 417 " --> pdb=" O SER 3 414 " (cutoff:3.500A) Processing helix chain '3' and resid 457 through 461 removed outlier: 3.734A pdb=" N LYS 3 460 " --> pdb=" O PRO 3 457 " (cutoff:3.500A) Processing helix chain '3' and resid 473 through 481 Processing helix chain '3' and resid 488 through 499 Processing helix chain '3' and resid 515 through 527 removed outlier: 3.888A pdb=" N GLU 3 526 " --> pdb=" O ARG 3 522 " (cutoff:3.500A) Processing helix chain '3' and resid 541 through 546 Processing helix chain '3' and resid 574 through 577 No H-bonds generated for 'chain '3' and resid 574 through 577' Processing helix chain '3' and resid 607 through 609 No H-bonds generated for 'chain '3' and resid 607 through 609' Processing helix chain '3' and resid 637 through 648 removed outlier: 3.517A pdb=" N GLU 3 646 " --> pdb=" O ALA 3 642 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA 3 647 " --> pdb=" O LEU 3 643 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU 3 648 " --> pdb=" O LEU 3 644 " (cutoff:3.500A) Processing helix chain '3' and resid 657 through 667 Processing helix chain '3' and resid 701 through 703 No H-bonds generated for 'chain '3' and resid 701 through 703' Processing helix chain '3' and resid 708 through 711 No H-bonds generated for 'chain '3' and resid 708 through 711' Processing helix chain '3' and resid 720 through 725 Processing helix chain '4' and resid 66 through 72 removed outlier: 3.852A pdb=" N GLU 4 71 " --> pdb=" O GLU 4 67 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N HIS 4 72 " --> pdb=" O LYS 4 68 " (cutoff:3.500A) Processing helix chain '4' and resid 77 through 80 Processing helix chain '4' and resid 82 through 84 No H-bonds generated for 'chain '4' and resid 82 through 84' Processing helix chain '4' and resid 90 through 105 Processing helix chain '4' and resid 111 through 139 Processing helix chain '4' and resid 144 through 164 removed outlier: 3.602A pdb=" N PHE 4 150 " --> pdb=" O PHE 4 147 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU 4 152 " --> pdb=" O ALA 4 149 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR 4 164 " --> pdb=" O GLU 4 161 " (cutoff:3.500A) Processing helix chain '4' and resid 184 through 208 removed outlier: 3.699A pdb=" N VAL 4 187 " --> pdb=" O GLU 4 184 " (cutoff:3.500A) Proline residue: 4 188 - end of helix removed outlier: 4.282A pdb=" N LEU 4 197 " --> pdb=" O LEU 4 194 " (cutoff:3.500A) Proline residue: 4 198 - end of helix removed outlier: 3.696A pdb=" N ASP 4 202 " --> pdb=" O HIS 4 199 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA 4 206 " --> pdb=" O GLU 4 203 " (cutoff:3.500A) Processing helix chain '4' and resid 212 through 218 removed outlier: 3.515A pdb=" N GLU 4 216 " --> pdb=" O PRO 4 212 " (cutoff:3.500A) Processing helix chain '4' and resid 226 through 231 Processing helix chain '4' and resid 239 through 242 Processing helix chain '4' and resid 248 through 251 No H-bonds generated for 'chain '4' and resid 248 through 251' Processing helix chain '4' and resid 257 through 259 No H-bonds generated for 'chain '4' and resid 257 through 259' Processing helix chain '4' and resid 272 through 296 removed outlier: 3.730A pdb=" N ILE 4 280 " --> pdb=" O MET 4 276 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS 4 288 " --> pdb=" O ARG 4 284 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE 4 289 " --> pdb=" O GLU 4 285 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU 4 295 " --> pdb=" O LYS 4 291 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG 4 296 " --> pdb=" O GLN 4 292 " (cutoff:3.500A) Processing helix chain '4' and resid 321 through 332 Processing helix chain '4' and resid 373 through 384 removed outlier: 3.850A pdb=" N GLN 4 379 " --> pdb=" O PHE 4 375 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER 4 380 " --> pdb=" O VAL 4 376 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU 4 381 " --> pdb=" O ASN 4 377 " (cutoff:3.500A) Proline residue: 4 382 - end of helix Processing helix chain '4' and resid 390 through 400 removed outlier: 3.836A pdb=" N VAL 4 394 " --> pdb=" O VAL 4 390 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ALA 4 395 " --> pdb=" O PRO 4 391 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE 4 397 " --> pdb=" O MET 4 393 " (cutoff:3.500A) Processing helix chain '4' and resid 404 through 408 Processing helix chain '5' and resid 2 through 13 removed outlier: 3.768A pdb=" N ARG 5 5 " --> pdb=" O ARG 5 2 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLU 5 8 " --> pdb=" O ARG 5 5 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG 5 11 " --> pdb=" O GLU 5 8 " (cutoff:3.500A) Processing helix chain '5' and resid 34 through 43 Processing helix chain '5' and resid 111 through 121 removed outlier: 3.860A pdb=" N ARG 5 116 " --> pdb=" O ASN 5 112 " (cutoff:3.500A) Processing helix chain '5' and resid 167 through 170 No H-bonds generated for 'chain '5' and resid 167 through 170' Processing helix chain '5' and resid 187 through 190 Processing helix chain '6' and resid 22 through 34 Processing helix chain '6' and resid 45 through 53 removed outlier: 3.708A pdb=" N ILE 6 48 " --> pdb=" O CYS 6 45 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA 6 52 " --> pdb=" O GLU 6 49 " (cutoff:3.500A) Processing helix chain '6' and resid 72 through 74 No H-bonds generated for 'chain '6' and resid 72 through 74' Processing helix chain '6' and resid 86 through 98 Proline residue: 6 90 - end of helix removed outlier: 3.585A pdb=" N ARG 6 93 " --> pdb=" O PRO 6 90 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN 6 98 " --> pdb=" O VAL 6 95 " (cutoff:3.500A) Processing helix chain '6' and resid 110 through 113 No H-bonds generated for 'chain '6' and resid 110 through 113' Processing helix chain '6' and resid 127 through 129 No H-bonds generated for 'chain '6' and resid 127 through 129' Processing helix chain '6' and resid 144 through 158 Processing helix chain '9' and resid 3 through 18 removed outlier: 4.151A pdb=" N SER 9 9 " --> pdb=" O LEU 9 6 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE 9 18 " --> pdb=" O LYS 9 15 " (cutoff:3.500A) Processing helix chain '9' and resid 58 through 62 Processing helix chain '9' and resid 103 through 107 Processing helix chain '9' and resid 126 through 128 No H-bonds generated for 'chain '9' and resid 126 through 128' Processing helix chain '9' and resid 133 through 135 No H-bonds generated for 'chain '9' and resid 133 through 135' Processing helix chain '9' and resid 144 through 152 removed outlier: 3.602A pdb=" N ARG 9 152 " --> pdb=" O ARG 9 148 " (cutoff:3.500A) Processing helix chain '7' and resid 4 through 27 removed outlier: 3.757A pdb=" N GLU 7 11 " --> pdb=" O GLU 7 8 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR 7 23 " --> pdb=" O MET 7 20 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS 7 27 " --> pdb=" O ALA 7 24 " (cutoff:3.500A) Processing helix chain '7' and resid 38 through 41 No H-bonds generated for 'chain '7' and resid 38 through 41' Processing helix chain '7' and resid 112 through 126 Processing helix chain 'A' and resid 4 through 30 removed outlier: 3.520A pdb=" N ILE A 12 " --> pdb=" O GLY A 9 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A 18 " --> pdb=" O GLY A 15 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A 23 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 27 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY A 28 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A 29 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 83 Proline residue: A 80 - end of helix Processing helix chain 'A' and resid 89 through 113 Processing helix chain 'J' and resid 4 through 21 removed outlier: 3.731A pdb=" N VAL J 20 " --> pdb=" O GLY J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 46 Processing helix chain 'J' and resid 49 through 59 Processing helix chain 'J' and resid 63 through 73 Processing helix chain 'J' and resid 85 through 108 removed outlier: 4.068A pdb=" N ARG J 88 " --> pdb=" O PRO J 85 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG J 90 " --> pdb=" O VAL J 87 " (cutoff:3.500A) Proline residue: J 91 - end of helix removed outlier: 3.676A pdb=" N LEU J 96 " --> pdb=" O ALA J 93 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA J 97 " --> pdb=" O ALA J 94 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE J 103 " --> pdb=" O VAL J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 131 Proline residue: J 129 - end of helix Processing helix chain 'J' and resid 136 through 157 removed outlier: 3.501A pdb=" N VAL J 157 " --> pdb=" O ALA J 153 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 20 removed outlier: 3.730A pdb=" N ALA K 8 " --> pdb=" O LEU K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 49 removed outlier: 4.075A pdb=" N ALA K 48 " --> pdb=" O GLY K 44 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 78 Processing helix chain 'L' and resid 2 through 19 removed outlier: 3.579A pdb=" N THR L 6 " --> pdb=" O ALA L 2 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE L 7 " --> pdb=" O LEU L 3 " (cutoff:3.500A) Proline residue: L 10 - end of helix removed outlier: 3.506A pdb=" N PHE L 14 " --> pdb=" O PRO L 10 " (cutoff:3.500A) Processing helix chain 'L' and resid 28 through 49 removed outlier: 3.518A pdb=" N PHE L 41 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LEU L 43 " --> pdb=" O ALA L 39 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU L 47 " --> pdb=" O LEU L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 94 Processing helix chain 'L' and resid 101 through 119 Processing helix chain 'L' and resid 124 through 142 Processing helix chain 'L' and resid 150 through 178 removed outlier: 5.717A pdb=" N ALA L 155 " --> pdb=" O TYR L 151 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG L 163 " --> pdb=" O PHE L 159 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY L 165 " --> pdb=" O VAL L 161 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TRP L 177 " --> pdb=" O MET L 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 192 Processing helix chain 'L' and resid 199 through 216 removed outlier: 3.926A pdb=" N GLY L 215 " --> pdb=" O LEU L 211 " (cutoff:3.500A) Processing helix chain 'L' and resid 224 through 230 removed outlier: 3.689A pdb=" N ASP L 228 " --> pdb=" O VAL L 224 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N MET L 230 " --> pdb=" O LEU L 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 234 through 241 Processing helix chain 'L' and resid 245 through 262 removed outlier: 3.853A pdb=" N LEU L 252 " --> pdb=" O GLY L 249 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG L 255 " --> pdb=" O LEU L 252 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N PHE L 258 " --> pdb=" O ARG L 255 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER L 261 " --> pdb=" O PHE L 258 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL L 262 " --> pdb=" O LEU L 259 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 285 Processing helix chain 'L' and resid 291 through 309 removed outlier: 4.056A pdb=" N SER L 298 " --> pdb=" O ILE L 294 " (cutoff:3.500A) Processing helix chain 'L' and resid 315 through 342 removed outlier: 3.845A pdb=" N PHE L 327 " --> pdb=" O PHE L 323 " (cutoff:3.500A) Processing helix chain 'L' and resid 349 through 351 No H-bonds generated for 'chain 'L' and resid 349 through 351' Processing helix chain 'L' and resid 355 through 357 No H-bonds generated for 'chain 'L' and resid 355 through 357' Processing helix chain 'L' and resid 362 through 374 Processing helix chain 'L' and resid 380 through 394 removed outlier: 3.845A pdb=" N LEU L 393 " --> pdb=" O LEU L 389 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 425 removed outlier: 3.536A pdb=" N VAL L 404 " --> pdb=" O VAL L 400 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY L 405 " --> pdb=" O GLY L 401 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU L 408 " --> pdb=" O VAL L 404 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL L 411 " --> pdb=" O LEU L 407 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ALA L 417 " --> pdb=" O THR L 413 " (cutoff:3.500A) Processing helix chain 'L' and resid 440 through 455 Proline residue: L 445 - end of helix removed outlier: 3.529A pdb=" N VAL L 454 " --> pdb=" O ALA L 450 " (cutoff:3.500A) Processing helix chain 'L' and resid 457 through 459 No H-bonds generated for 'chain 'L' and resid 457 through 459' Processing helix chain 'L' and resid 470 through 474 Processing helix chain 'L' and resid 489 through 511 removed outlier: 3.658A pdb=" N LEU L 493 " --> pdb=" O ALA L 489 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU L 502 " --> pdb=" O ALA L 498 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TRP L 506 " --> pdb=" O LEU L 502 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLY L 508 " --> pdb=" O GLY L 504 " (cutoff:3.500A) Processing helix chain 'L' and resid 519 through 530 removed outlier: 3.712A pdb=" N SER L 528 " --> pdb=" O GLU L 525 " (cutoff:3.500A) Processing helix chain 'L' and resid 534 through 541 removed outlier: 3.573A pdb=" N LEU L 541 " --> pdb=" O ALA L 537 " (cutoff:3.500A) Processing helix chain 'L' and resid 543 through 579 removed outlier: 3.576A pdb=" N GLU L 551 " --> pdb=" O LYS L 547 " (cutoff:3.500A) Processing helix chain 'L' and resid 586 through 603 Processing helix chain 'M' and resid 2 through 17 Proline residue: M 9 - end of helix Processing helix chain 'M' and resid 23 through 42 removed outlier: 3.774A pdb=" N LEU M 27 " --> pdb=" O ALA M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 59 No H-bonds generated for 'chain 'M' and resid 57 through 59' Processing helix chain 'M' and resid 69 through 88 removed outlier: 4.450A pdb=" N LEU M 73 " --> pdb=" O GLY M 69 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE M 74 " --> pdb=" O LEU M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 96 through 111 Processing helix chain 'M' and resid 115 through 134 removed outlier: 4.449A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) Proline residue: M 128 - end of helix Processing helix chain 'M' and resid 141 through 168 Proline residue: M 158 - end of helix removed outlier: 4.329A pdb=" N ALA M 161 " --> pdb=" O LEU M 157 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA M 162 " --> pdb=" O PRO M 158 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG M 167 " --> pdb=" O VAL M 163 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 182 Processing helix chain 'M' and resid 190 through 202 removed outlier: 4.017A pdb=" N ALA M 200 " --> pdb=" O GLY M 196 " (cutoff:3.500A) Processing helix chain 'M' and resid 208 through 210 No H-bonds generated for 'chain 'M' and resid 208 through 210' Processing helix chain 'M' and resid 213 through 220 Processing helix chain 'M' and resid 226 through 232 removed outlier: 3.531A pdb=" N GLY M 231 " --> pdb=" O ALA M 227 " (cutoff:3.500A) Processing helix chain 'M' and resid 237 through 243 Processing helix chain 'M' and resid 245 through 248 No H-bonds generated for 'chain 'M' and resid 245 through 248' Processing helix chain 'M' and resid 250 through 277 removed outlier: 4.121A pdb=" N GLN M 255 " --> pdb=" O GLU M 251 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLY M 258 " --> pdb=" O ALA M 254 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LEU M 259 " --> pdb=" O GLN M 255 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA M 268 " --> pdb=" O ALA M 264 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE M 276 " --> pdb=" O ALA M 272 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA M 277 " --> pdb=" O TRP M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 281 through 302 Processing helix chain 'M' and resid 305 through 336 removed outlier: 3.719A pdb=" N VAL M 320 " --> pdb=" O ALA M 316 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY M 323 " --> pdb=" O GLY M 319 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU M 325 " --> pdb=" O TYR M 321 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG M 335 " --> pdb=" O ARG M 331 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR M 336 " --> pdb=" O LEU M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 347 through 350 No H-bonds generated for 'chain 'M' and resid 347 through 350' Processing helix chain 'M' and resid 354 through 366 Processing helix chain 'M' and resid 373 through 387 Processing helix chain 'M' and resid 389 through 414 removed outlier: 3.680A pdb=" N PHE M 396 " --> pdb=" O ALA M 392 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU M 397 " --> pdb=" O ALA M 393 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N SER M 398 " --> pdb=" O LEU M 394 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL M 399 " --> pdb=" O ALA M 395 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ILE M 400 " --> pdb=" O PHE M 396 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA M 401 " --> pdb=" O LEU M 397 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR M 413 " --> pdb=" O ALA M 409 " (cutoff:3.500A) Processing helix chain 'M' and resid 427 through 445 removed outlier: 4.018A pdb=" N GLY M 431 " --> pdb=" O GLY M 427 " (cutoff:3.500A) Processing helix chain 'M' and resid 447 through 449 No H-bonds generated for 'chain 'M' and resid 447 through 449' Processing helix chain 'M' and resid 451 through 463 Proline residue: M 456 - end of helix Processing helix chain 'N' and resid 2 through 18 removed outlier: 3.880A pdb=" N LEU N 15 " --> pdb=" O VAL N 11 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N PHE N 18 " --> pdb=" O THR N 14 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 43 removed outlier: 3.808A pdb=" N THR N 43 " --> pdb=" O SER N 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 57 through 76 removed outlier: 3.511A pdb=" N LEU N 76 " --> pdb=" O TRP N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 99 removed outlier: 5.587A pdb=" N LEU N 87 " --> pdb=" O PHE N 84 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR N 90 " --> pdb=" O LEU N 87 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU N 97 " --> pdb=" O GLY N 94 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 122 Proline residue: N 117 - end of helix removed outlier: 3.634A pdb=" N ALA N 120 " --> pdb=" O LEU N 116 " (cutoff:3.500A) Processing helix chain 'N' and resid 128 through 158 removed outlier: 4.070A pdb=" N ALA N 133 " --> pdb=" O GLY N 129 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY N 156 " --> pdb=" O ALA N 152 " (cutoff:3.500A) Processing helix chain 'N' and resid 170 through 187 removed outlier: 3.574A pdb=" N GLY N 177 " --> pdb=" O ALA N 173 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU N 179 " --> pdb=" O ALA N 175 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU N 180 " --> pdb=" O LEU N 176 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY N 182 " --> pdb=" O LEU N 178 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU N 183 " --> pdb=" O LEU N 179 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA N 187 " --> pdb=" O LEU N 183 " (cutoff:3.500A) Processing helix chain 'N' and resid 194 through 202 removed outlier: 4.311A pdb=" N ASP N 198 " --> pdb=" O PHE N 194 " (cutoff:3.500A) Processing helix chain 'N' and resid 205 through 212 Processing helix chain 'N' and resid 214 through 225 removed outlier: 3.958A pdb=" N ARG N 225 " --> pdb=" O ALA N 221 " (cutoff:3.500A) Processing helix chain 'N' and resid 232 through 250 removed outlier: 4.052A pdb=" N LEU N 249 " --> pdb=" O ASN N 245 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ALA N 250 " --> pdb=" O LEU N 246 " (cutoff:3.500A) Processing helix chain 'N' and resid 254 through 272 removed outlier: 3.518A pdb=" N ALA N 266 " --> pdb=" O SER N 262 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU N 271 " --> pdb=" O GLY N 267 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA N 272 " --> pdb=" O TYR N 268 " (cutoff:3.500A) Processing helix chain 'N' and resid 280 through 302 Processing helix chain 'N' and resid 309 through 312 Processing helix chain 'N' and resid 315 through 318 No H-bonds generated for 'chain 'N' and resid 315 through 318' Processing helix chain 'N' and resid 320 through 334 Processing helix chain 'N' and resid 340 through 355 removed outlier: 3.519A pdb=" N ALA N 348 " --> pdb=" O GLY N 344 " (cutoff:3.500A) Processing helix chain 'N' and resid 359 through 379 removed outlier: 3.517A pdb=" N ALA N 369 " --> pdb=" O LEU N 365 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA N 372 " --> pdb=" O SER N 368 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TYR N 373 " --> pdb=" O ALA N 369 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N TYR N 374 " --> pdb=" O VAL N 370 " (cutoff:3.500A) Processing helix chain 'N' and resid 381 through 383 No H-bonds generated for 'chain 'N' and resid 381 through 383' Processing helix chain 'N' and resid 396 through 414 Processing helix chain 'N' and resid 416 through 418 No H-bonds generated for 'chain 'N' and resid 416 through 418' Processing helix chain 'N' and resid 420 through 422 No H-bonds generated for 'chain 'N' and resid 420 through 422' Processing helix chain 'H' and resid 10 through 42 removed outlier: 3.576A pdb=" N LEU H 33 " --> pdb=" O ALA H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 66 Processing helix chain 'H' and resid 79 through 94 Proline residue: H 86 - end of helix removed outlier: 3.724A pdb=" N SER H 89 " --> pdb=" O ALA H 85 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA H 93 " --> pdb=" O SER H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 143 removed outlier: 3.572A pdb=" N LEU H 131 " --> pdb=" O ALA H 127 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA H 132 " --> pdb=" O VAL H 128 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL H 133 " --> pdb=" O SER H 129 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N TYR H 134 " --> pdb=" O GLU H 130 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY H 135 " --> pdb=" O LEU H 131 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE H 137 " --> pdb=" O VAL H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 146 through 177 removed outlier: 3.517A pdb=" N LEU H 164 " --> pdb=" O ILE H 160 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY H 165 " --> pdb=" O SER H 161 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY H 167 " --> pdb=" O GLU H 163 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU H 168 " --> pdb=" O LEU H 164 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ALA H 172 " --> pdb=" O LEU H 168 " (cutoff:3.500A) Proline residue: H 173 - end of helix removed outlier: 3.730A pdb=" N LEU H 176 " --> pdb=" O ALA H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 191 Processing helix chain 'H' and resid 195 through 198 No H-bonds generated for 'chain 'H' and resid 195 through 198' Processing helix chain 'H' and resid 200 through 213 removed outlier: 3.603A pdb=" N VAL H 205 " --> pdb=" O PRO H 201 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ALA H 212 " --> pdb=" O ILE H 208 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU H 213 " --> pdb=" O ALA H 209 " (cutoff:3.500A) Processing helix chain 'H' and resid 239 through 263 Proline residue: H 260 - end of helix Processing helix chain 'H' and resid 277 through 296 Processing helix chain 'H' and resid 303 through 311 Processing helix chain 'H' and resid 313 through 330 Processing helix chain 'H' and resid 335 through 352 removed outlier: 3.724A pdb=" N LEU H 340 " --> pdb=" O TYR H 336 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N VAL H 352 " --> pdb=" O LEU H 348 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain '1' and resid 216 through 220 removed outlier: 6.529A pdb=" N TYR 1 88 " --> pdb=" O THR 1 217 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N ASN 1 219 " --> pdb=" O TYR 1 88 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE 1 90 " --> pdb=" O ASN 1 219 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR 1 128 " --> pdb=" O HIS 1 87 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N LEU 1 89 " --> pdb=" O THR 1 128 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLY 1 130 " --> pdb=" O LEU 1 89 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N CYS 1 91 " --> pdb=" O GLY 1 130 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ILE 1 132 " --> pdb=" O CYS 1 91 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ALA 1 93 " --> pdb=" O ILE 1 132 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N VAL 1 134 " --> pdb=" O ALA 1 93 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL 1 134 " --> pdb=" O HIS 1 174 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '1' and resid 262 through 267 removed outlier: 3.505A pdb=" N GLY 1 262 " --> pdb=" O ILE 1 254 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR 1 252 " --> pdb=" O TYR 1 264 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '2' and resid 117 through 122 removed outlier: 6.294A pdb=" N TYR 2 78 " --> pdb=" O SER 2 118 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N GLN 2 120 " --> pdb=" O TYR 2 78 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LEU 2 80 " --> pdb=" O GLN 2 120 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL 2 122 " --> pdb=" O LEU 2 80 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N VAL 2 82 " --> pdb=" O VAL 2 122 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '3' and resid 9 through 12 removed outlier: 6.944A pdb=" N MET 3 91 " --> pdb=" O LYS 3 5 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '3' and resid 235 through 237 removed outlier: 3.724A pdb=" N SER 3 171 " --> pdb=" O VAL 3 174 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU 3 176 " --> pdb=" O PRO 3 169 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '3' and resid 250 through 255 removed outlier: 6.998A pdb=" N ARG 3 270 " --> pdb=" O LEU 3 274 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N LEU 3 274 " --> pdb=" O ARG 3 270 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '3' and resid 310 through 312 Processing sheet with id= H, first strand: chain '3' and resid 369 through 371 removed outlier: 9.599A pdb=" N ASP 3 370 " --> pdb=" O VAL 3 341 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N LEU 3 343 " --> pdb=" O ASP 3 370 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N TYR 3 565 " --> pdb=" O GLY 3 342 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N TYR 3 344 " --> pdb=" O TYR 3 565 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N TYR 3 567 " --> pdb=" O TYR 3 344 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL 3 600 " --> pdb=" O MET 3 585 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LEU 3 587 " --> pdb=" O VAL 3 600 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N LEU 3 602 " --> pdb=" O LEU 3 587 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '3' and resid 448 through 451 removed outlier: 6.514A pdb=" N ALA 3 396 " --> pdb=" O ALA 3 449 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N PHE 3 451 " --> pdb=" O ALA 3 396 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL 3 398 " --> pdb=" O PHE 3 451 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL 3 504 " --> pdb=" O LEU 3 397 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N LEU 3 399 " --> pdb=" O VAL 3 504 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ILE 3 506 " --> pdb=" O LEU 3 399 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '3' and resid 612 through 615 Processing sheet with id= K, first strand: chain '3' and resid 692 through 696 removed outlier: 5.845A pdb=" N LEU 3 758 " --> pdb=" O TYR 3 693 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ARG 3 695 " --> pdb=" O LEU 3 758 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU 3 760 " --> pdb=" O ARG 3 695 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain '3' and resid 714 through 718 removed outlier: 3.905A pdb=" N ALA 3 714 " --> pdb=" O GLU 3 744 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '4' and resid 27 through 30 removed outlier: 3.678A pdb=" N GLU 4 54 " --> pdb=" O THR 4 46 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N SER 4 48 " --> pdb=" O VAL 4 52 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N VAL 4 52 " --> pdb=" O SER 4 48 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain '4' and resid 345 through 348 removed outlier: 4.087A pdb=" N GLY 4 354 " --> pdb=" O ARG 4 371 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '5' and resid 88 through 94 removed outlier: 3.636A pdb=" N VAL 5 70 " --> pdb=" O VAL 5 92 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP 5 51 " --> pdb=" O GLU 5 73 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL 5 75 " --> pdb=" O LEU 5 49 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LEU 5 49 " --> pdb=" O VAL 5 75 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain '6' and resid 38 through 42 removed outlier: 5.657A pdb=" N VAL 6 77 " --> pdb=" O ALA 6 39 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE 6 41 " --> pdb=" O VAL 6 77 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ILE 6 79 " --> pdb=" O PHE 6 41 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TRP 6 104 " --> pdb=" O MET 6 78 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL 6 80 " --> pdb=" O TRP 6 104 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE 6 106 " --> pdb=" O VAL 6 80 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL 6 135 " --> pdb=" O SER 6 107 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain '9' and resid 130 through 132 removed outlier: 6.658A pdb=" N GLU 9 71 " --> pdb=" O LYS 9 89 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N TYR 9 91 " --> pdb=" O TYR 9 69 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TYR 9 69 " --> pdb=" O TYR 9 91 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain '7' and resid 102 through 105 removed outlier: 6.764A pdb=" N LEU 7 59 " --> pdb=" O PHE 7 67 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LEU 7 69 " --> pdb=" O ALA 7 57 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ALA 7 57 " --> pdb=" O LEU 7 69 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR 7 56 " --> pdb=" O ALA 7 35 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N SER 7 58 " --> pdb=" O LYS 7 33 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N LYS 7 33 " --> pdb=" O SER 7 58 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N SER 7 60 " --> pdb=" O PHE 7 31 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N PHE 7 31 " --> pdb=" O SER 7 60 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'L' and resid 53 through 57 Processing sheet with id= T, first strand: chain 'M' and resid 50 through 56 removed outlier: 3.622A pdb=" N LEU M 55 " --> pdb=" O VAL M 61 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL M 61 " --> pdb=" O LEU M 55 " (cutoff:3.500A) 1587 hydrogen bonds defined for protein. 4191 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: 11.98 Time building geometry restraints manager: 14.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.44: 17687 1.44 - 1.67: 19065 1.67 - 1.91: 256 1.91 - 2.14: 0 2.14 - 2.38: 92 Bond restraints: 37100 Sorted by residual: bond pdb=" CD GLU 3 192 " pdb=" OE2 GLU 3 192 " ideal model delta sigma weight residual 1.249 1.398 -0.149 1.90e-02 2.77e+03 6.14e+01 bond pdb=" CG ASP L 386 " pdb=" OD2 ASP L 386 " ideal model delta sigma weight residual 1.249 1.397 -0.148 1.90e-02 2.77e+03 6.07e+01 bond pdb=" CD GLU H 225 " pdb=" OE2 GLU H 225 " ideal model delta sigma weight residual 1.249 1.394 -0.145 1.90e-02 2.77e+03 5.84e+01 bond pdb=" CD GLU A 110 " pdb=" OE1 GLU A 110 " ideal model delta sigma weight residual 1.249 1.393 -0.144 1.90e-02 2.77e+03 5.76e+01 bond pdb=" CD GLU K 32 " pdb=" OE2 GLU K 32 " ideal model delta sigma weight residual 1.249 1.393 -0.144 1.90e-02 2.77e+03 5.75e+01 ... (remaining 37095 not shown) Histogram of bond angle deviations from ideal: 62.33 - 76.45: 88 76.45 - 90.57: 3 90.57 - 104.70: 1490 104.70 - 118.82: 28250 118.82 - 132.94: 20706 Bond angle restraints: 50537 Sorted by residual: angle pdb=" C THR 1 72 " pdb=" CA THR 1 72 " pdb=" CB THR 1 72 " ideal model delta sigma weight residual 110.74 91.60 19.14 1.66e+00 3.63e-01 1.33e+02 angle pdb=" CA PHE H 286 " pdb=" CB PHE H 286 " pdb=" CG PHE H 286 " ideal model delta sigma weight residual 113.80 103.22 10.58 1.00e+00 1.00e+00 1.12e+02 angle pdb=" CA PHE 9 100 " pdb=" CB PHE 9 100 " pdb=" CG PHE 9 100 " ideal model delta sigma weight residual 113.80 103.93 9.87 1.00e+00 1.00e+00 9.75e+01 angle pdb=" CA ALA N 165 " pdb=" C ALA N 165 " pdb=" N PRO N 166 " ideal model delta sigma weight residual 117.69 126.26 -8.57 9.30e-01 1.16e+00 8.50e+01 angle pdb=" C ILE 1 331 " pdb=" N PRO 1 332 " pdb=" CA PRO 1 332 " ideal model delta sigma weight residual 120.31 129.11 -8.80 9.80e-01 1.04e+00 8.07e+01 ... (remaining 50532 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.00: 21035 34.00 - 68.00: 572 68.00 - 102.00: 98 102.00 - 136.00: 0 136.00 - 170.00: 1 Dihedral angle restraints: 21706 sinusoidal: 8479 harmonic: 13227 Sorted by residual: dihedral pdb=" C THR 1 72 " pdb=" N THR 1 72 " pdb=" CA THR 1 72 " pdb=" CB THR 1 72 " ideal model delta harmonic sigma weight residual -122.00 -98.94 -23.06 0 2.50e+00 1.60e-01 8.51e+01 dihedral pdb=" CA THR H 217 " pdb=" C THR H 217 " pdb=" N PRO H 218 " pdb=" CA PRO H 218 " ideal model delta harmonic sigma weight residual 180.00 137.44 42.56 0 5.00e+00 4.00e-02 7.25e+01 dihedral pdb=" N CYS 9 104 " pdb=" C CYS 9 104 " pdb=" CA CYS 9 104 " pdb=" CB CYS 9 104 " ideal model delta harmonic sigma weight residual 122.80 143.66 -20.86 0 2.50e+00 1.60e-01 6.96e+01 ... (remaining 21703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.213: 5644 4.213 - 8.426: 0 8.426 - 12.639: 0 12.639 - 16.852: 0 16.852 - 21.065: 28 Chirality restraints: 5672 Sorted by residual: chirality pdb="FE3 SF4 3 801 " pdb=" S1 SF4 3 801 " pdb=" S2 SF4 3 801 " pdb=" S4 SF4 3 801 " both_signs ideal model delta sigma weight residual False -10.55 10.51 -21.06 2.00e-01 2.50e+01 1.11e+04 chirality pdb="FE3 SF4 9 202 " pdb=" S1 SF4 9 202 " pdb=" S2 SF4 9 202 " pdb=" S4 SF4 9 202 " both_signs ideal model delta sigma weight residual False -10.55 10.23 -20.78 2.00e-01 2.50e+01 1.08e+04 chirality pdb="FE3 SF4 3 803 " pdb=" S1 SF4 3 803 " pdb=" S2 SF4 3 803 " pdb=" S4 SF4 3 803 " both_signs ideal model delta sigma weight residual False -10.55 10.20 -20.75 2.00e-01 2.50e+01 1.08e+04 ... (remaining 5669 not shown) Planarity restraints: 6377 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR M 344 " -0.276 2.00e-02 2.50e+03 1.44e-01 4.13e+02 pdb=" CG TYR M 344 " 0.098 2.00e-02 2.50e+03 pdb=" CD1 TYR M 344 " 0.141 2.00e-02 2.50e+03 pdb=" CD2 TYR M 344 " 0.122 2.00e-02 2.50e+03 pdb=" CE1 TYR M 344 " 0.056 2.00e-02 2.50e+03 pdb=" CE2 TYR M 344 " 0.066 2.00e-02 2.50e+03 pdb=" CZ TYR M 344 " -0.014 2.00e-02 2.50e+03 pdb=" OH TYR M 344 " -0.192 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR M 449 " 0.275 2.00e-02 2.50e+03 1.42e-01 4.03e+02 pdb=" CG TYR M 449 " -0.105 2.00e-02 2.50e+03 pdb=" CD1 TYR M 449 " -0.134 2.00e-02 2.50e+03 pdb=" CD2 TYR M 449 " -0.122 2.00e-02 2.50e+03 pdb=" CE1 TYR M 449 " -0.052 2.00e-02 2.50e+03 pdb=" CE2 TYR M 449 " -0.063 2.00e-02 2.50e+03 pdb=" CZ TYR M 449 " 0.015 2.00e-02 2.50e+03 pdb=" OH TYR M 449 " 0.187 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 81 " 0.270 2.00e-02 2.50e+03 1.40e-01 3.91e+02 pdb=" CG TYR A 81 " -0.104 2.00e-02 2.50e+03 pdb=" CD1 TYR A 81 " -0.127 2.00e-02 2.50e+03 pdb=" CD2 TYR A 81 " -0.117 2.00e-02 2.50e+03 pdb=" CE1 TYR A 81 " -0.065 2.00e-02 2.50e+03 pdb=" CE2 TYR A 81 " -0.054 2.00e-02 2.50e+03 pdb=" CZ TYR A 81 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR A 81 " 0.190 2.00e-02 2.50e+03 ... (remaining 6374 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 184 2.52 - 3.11: 27694 3.11 - 3.71: 52399 3.71 - 4.30: 80860 4.30 - 4.90: 131592 Nonbonded interactions: 292729 Sorted by model distance: nonbonded pdb=" CG ARG 1 65 " pdb=" OG1 THR 1 223 " model vdw 1.919 3.440 nonbonded pdb=" CB ARG 1 65 " pdb=" OG1 THR 1 223 " model vdw 1.979 3.440 nonbonded pdb=" O2' FMN 1 502 " pdb=" O4' FMN 1 502 " model vdw 2.101 2.440 nonbonded pdb=" O1P FMN 1 502 " pdb=" O4' FMN 1 502 " model vdw 2.257 2.440 nonbonded pdb=" OG SER 1 100 " pdb=" OG1 THR 1 325 " model vdw 2.295 2.440 ... (remaining 292724 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.800 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: 30.690 Check model and map are aligned: 0.580 Set scattering table: 0.340 Process input model: 96.920 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.160 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:3.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 141.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 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 : 0.021 0.149 37100 Z= 1.383 Angle : 2.367 19.141 50537 Z= 1.575 Chirality : 1.393 21.065 5672 Planarity : 0.023 0.263 6377 Dihedral : 16.058 169.997 13289 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 3.45 % Allowed : 9.89 % Favored : 86.67 % Rotamer: Outliers : 3.34 % Allowed : 6.78 % Favored : 89.88 % Cbeta Deviations : 0.88 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.37 % 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: -4.76 (0.10), residues: 4612 helix: -3.09 (0.07), residues: 2383 sheet: -2.36 (0.28), residues: 236 loop : -3.23 (0.12), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.207 0.030 TRP H 194 HIS 0.008 0.002 HIS 3 183 PHE 0.150 0.020 PHE 4 208 TYR 0.276 0.034 TYR M 344 ARG 0.015 0.001 ARG 9 86 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1551 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 1429 time to evaluate : 3.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 14 GLU cc_start: 0.4974 (pt0) cc_final: 0.3519 (pm20) REVERT: 1 79 MET cc_start: 0.8741 (mmm) cc_final: 0.8027 (mmt) REVERT: 1 102 LYS cc_start: 0.8484 (pttp) cc_final: 0.7832 (pttp) REVERT: 1 110 VAL cc_start: 0.8899 (m) cc_final: 0.8668 (m) REVERT: 1 215 PRO cc_start: 0.8963 (OUTLIER) cc_final: 0.8329 (Cg_endo) REVERT: 1 251 LEU cc_start: 0.9086 (mt) cc_final: 0.8673 (mt) REVERT: 1 268 MET cc_start: 0.6616 (mtp) cc_final: 0.5807 (mtp) REVERT: 1 337 MET cc_start: 0.8211 (mmm) cc_final: 0.7964 (mmm) REVERT: 1 342 TRP cc_start: 0.7726 (OUTLIER) cc_final: 0.7378 (t60) REVERT: 1 351 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8436 (mm-30) REVERT: 1 407 VAL cc_start: 0.9385 (m) cc_final: 0.9178 (p) REVERT: 1 408 TRP cc_start: 0.7626 (m-10) cc_final: 0.7164 (m-10) REVERT: 2 3 PHE cc_start: 0.5934 (m-80) cc_final: 0.5425 (m-10) REVERT: 2 9 ASP cc_start: 0.6973 (m-30) cc_final: 0.6355 (t0) REVERT: 2 35 GLN cc_start: 0.8737 (tp40) cc_final: 0.8451 (tp40) REVERT: 2 36 GLN cc_start: 0.9210 (mt0) cc_final: 0.8659 (mt0) REVERT: 2 49 ILE cc_start: 0.8329 (mt) cc_final: 0.7854 (tp) REVERT: 2 71 GLN cc_start: 0.7394 (mm-40) cc_final: 0.7129 (tp40) REVERT: 2 97 TRP cc_start: 0.8304 (t-100) cc_final: 0.7912 (t60) REVERT: 2 101 THR cc_start: 0.7374 (m) cc_final: 0.7015 (t) REVERT: 2 141 TYR cc_start: 0.7316 (m-80) cc_final: 0.6265 (m-80) REVERT: 3 37 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8179 (mtmm) REVERT: 3 47 MET cc_start: 0.8789 (mmm) cc_final: 0.8566 (tpp) REVERT: 3 82 SER cc_start: 0.9448 (m) cc_final: 0.9194 (t) REVERT: 3 109 GLU cc_start: 0.8539 (tt0) cc_final: 0.8263 (tt0) REVERT: 3 114 ASN cc_start: 0.8735 (m110) cc_final: 0.8301 (m110) REVERT: 3 133 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8612 (mmp80) REVERT: 3 184 CYS cc_start: 0.9268 (OUTLIER) cc_final: 0.8859 (p) REVERT: 3 189 ARG cc_start: 0.9269 (ttm170) cc_final: 0.8871 (mtm110) REVERT: 3 228 ASP cc_start: 0.8188 (m-30) cc_final: 0.7945 (t0) REVERT: 3 237 ASP cc_start: 0.9013 (p0) cc_final: 0.8703 (p0) REVERT: 3 251 GLU cc_start: 0.7320 (mp0) cc_final: 0.7049 (mp0) REVERT: 3 255 THR cc_start: 0.9538 (m) cc_final: 0.9329 (t) REVERT: 3 284 GLU cc_start: 0.8045 (pt0) cc_final: 0.7475 (pt0) REVERT: 3 351 LEU cc_start: 0.8517 (mt) cc_final: 0.7735 (mp) REVERT: 3 387 LEU cc_start: 0.8077 (mt) cc_final: 0.7548 (mt) REVERT: 3 404 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7504 (mp0) REVERT: 3 459 MET cc_start: 0.8198 (mtt) cc_final: 0.7730 (mtm) REVERT: 3 535 MET cc_start: 0.6596 (mtm) cc_final: 0.6370 (mtm) REVERT: 3 558 TRP cc_start: 0.8760 (OUTLIER) cc_final: 0.6998 (p-90) REVERT: 3 567 TYR cc_start: 0.5301 (OUTLIER) cc_final: 0.4289 (t80) REVERT: 3 624 LEU cc_start: 0.9126 (mp) cc_final: 0.8875 (mp) REVERT: 3 655 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.6770 (ptm160) REVERT: 3 760 LEU cc_start: 0.7950 (tp) cc_final: 0.7337 (tt) REVERT: 4 40 VAL cc_start: 0.8710 (p) cc_final: 0.8484 (p) REVERT: 4 71 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8127 (mt-10) REVERT: 4 87 TYR cc_start: 0.8945 (OUTLIER) cc_final: 0.8642 (m-80) REVERT: 4 121 ASN cc_start: 0.8776 (t0) cc_final: 0.8147 (t0) REVERT: 4 171 ASN cc_start: 0.8693 (m-40) cc_final: 0.7716 (p0) REVERT: 4 194 LEU cc_start: 0.9177 (mt) cc_final: 0.8930 (mm) REVERT: 4 271 ASP cc_start: 0.7622 (m-30) cc_final: 0.7238 (m-30) REVERT: 4 315 HIS cc_start: 0.8139 (OUTLIER) cc_final: 0.7844 (m170) REVERT: 4 364 MET cc_start: 0.9177 (mtm) cc_final: 0.8858 (mtm) REVERT: 4 380 SER cc_start: 0.9276 (m) cc_final: 0.9064 (t) REVERT: 5 105 THR cc_start: 0.8799 (p) cc_final: 0.8572 (p) REVERT: 5 115 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8787 (mt-10) REVERT: 5 122 PHE cc_start: 0.8121 (m-80) cc_final: 0.7718 (m-80) REVERT: 5 136 LEU cc_start: 0.8874 (mt) cc_final: 0.8669 (mp) REVERT: 5 170 PHE cc_start: 0.8145 (OUTLIER) cc_final: 0.7220 (t80) REVERT: 6 94 ARG cc_start: 0.7991 (mtm-85) cc_final: 0.7615 (mtm-85) REVERT: 6 97 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8298 (mt-10) REVERT: 6 103 LYS cc_start: 0.8715 (pttt) cc_final: 0.8256 (ptpt) REVERT: 6 155 GLN cc_start: 0.8516 (tt0) cc_final: 0.8277 (tt0) REVERT: 9 14 LEU cc_start: 0.9077 (tp) cc_final: 0.8817 (tp) REVERT: 9 44 THR cc_start: 0.9168 (p) cc_final: 0.8450 (t) REVERT: 9 91 TYR cc_start: 0.8655 (t80) cc_final: 0.7355 (t80) REVERT: 9 95 MET cc_start: 0.9340 (mmt) cc_final: 0.8904 (mmm) REVERT: 9 128 ASP cc_start: 0.7034 (m-30) cc_final: 0.6694 (m-30) REVERT: 9 131 TYR cc_start: 0.8466 (m-80) cc_final: 0.7819 (m-80) REVERT: 9 149 GLU cc_start: 0.8174 (tt0) cc_final: 0.7690 (mt-10) REVERT: 7 11 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6718 (mm-30) REVERT: 7 16 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.8980 (tt) REVERT: 7 21 ARG cc_start: 0.8274 (mtt90) cc_final: 0.7929 (mtt180) REVERT: 7 25 GLN cc_start: 0.7093 (pt0) cc_final: 0.5329 (tp40) REVERT: A 56 ARG cc_start: 0.8076 (tpp-160) cc_final: 0.7738 (ptt180) REVERT: A 57 PHE cc_start: 0.8332 (m-80) cc_final: 0.8076 (m-80) REVERT: A 67 LEU cc_start: 0.8305 (tp) cc_final: 0.8070 (tt) REVERT: A 72 ASP cc_start: 0.8831 (t0) cc_final: 0.8607 (t0) REVERT: A 108 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8271 (tp) REVERT: J 1 MET cc_start: 0.4261 (mmm) cc_final: 0.3722 (mmt) REVERT: J 20 VAL cc_start: 0.8729 (m) cc_final: 0.8475 (p) REVERT: J 39 LEU cc_start: 0.9349 (tp) cc_final: 0.9053 (tp) REVERT: J 43 TYR cc_start: 0.8834 (m-80) cc_final: 0.8425 (m-80) REVERT: J 96 LEU cc_start: 0.8200 (mt) cc_final: 0.7997 (mp) REVERT: J 120 LYS cc_start: 0.8514 (mtmm) cc_final: 0.7800 (mmtt) REVERT: J 135 TRP cc_start: 0.8343 (m100) cc_final: 0.8135 (m100) REVERT: K 43 VAL cc_start: 0.8918 (t) cc_final: 0.8699 (t) REVERT: K 70 VAL cc_start: 0.9433 (t) cc_final: 0.9205 (t) REVERT: K 94 ARG cc_start: 0.6296 (ptt180) cc_final: 0.4974 (ptm-80) REVERT: L 25 ARG cc_start: 0.5827 (mtm180) cc_final: 0.5538 (mmt180) REVERT: L 28 LEU cc_start: 0.6778 (tp) cc_final: 0.6340 (tp) REVERT: L 36 LEU cc_start: 0.7667 (mt) cc_final: 0.7165 (tt) REVERT: L 63 ILE cc_start: 0.7593 (mp) cc_final: 0.6944 (mp) REVERT: L 75 PHE cc_start: 0.7264 (t80) cc_final: 0.6708 (t80) REVERT: L 104 PHE cc_start: 0.8339 (t80) cc_final: 0.7790 (t80) REVERT: L 108 PHE cc_start: 0.8685 (t80) cc_final: 0.8269 (t80) REVERT: L 114 MET cc_start: 0.7898 (mmt) cc_final: 0.7423 (mmm) REVERT: L 127 MET cc_start: 0.8233 (mtp) cc_final: 0.7923 (mmt) REVERT: L 138 SER cc_start: 0.8514 (m) cc_final: 0.8243 (p) REVERT: L 225 TRP cc_start: 0.7782 (p-90) cc_final: 0.7436 (p-90) REVERT: L 333 PHE cc_start: 0.7353 (OUTLIER) cc_final: 0.7116 (t80) REVERT: L 355 LEU cc_start: 0.7622 (mt) cc_final: 0.7266 (tp) REVERT: L 377 PRO cc_start: 0.6026 (Cg_exo) cc_final: 0.5659 (Cg_endo) REVERT: M 1 MET cc_start: 0.5371 (tpt) cc_final: 0.5088 (mmm) REVERT: M 33 PHE cc_start: 0.8254 (t80) cc_final: 0.7970 (t80) REVERT: M 78 ILE cc_start: 0.8604 (mt) cc_final: 0.8319 (mt) REVERT: M 98 LEU cc_start: 0.9416 (mt) cc_final: 0.8343 (mp) REVERT: M 100 LEU cc_start: 0.8866 (mt) cc_final: 0.8349 (tp) REVERT: M 109 LEU cc_start: 0.8782 (tp) cc_final: 0.8434 (tp) REVERT: M 123 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8292 (mm-30) REVERT: M 132 MET cc_start: 0.8949 (ptp) cc_final: 0.8608 (ptp) REVERT: M 208 PHE cc_start: 0.8156 (t80) cc_final: 0.7825 (t80) REVERT: M 211 HIS cc_start: 0.6785 (p90) cc_final: 0.6134 (p-80) REVERT: M 281 PHE cc_start: 0.6275 (m-80) cc_final: 0.5879 (m-80) REVERT: M 302 SER cc_start: 0.9147 (m) cc_final: 0.8789 (p) REVERT: N 114 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8262 (tt) REVERT: N 116 LEU cc_start: 0.9192 (mt) cc_final: 0.8958 (mp) REVERT: N 119 TYR cc_start: 0.8412 (m-80) cc_final: 0.8198 (m-80) REVERT: N 171 LEU cc_start: 0.9392 (tp) cc_final: 0.9010 (tp) REVERT: N 255 LYS cc_start: 0.9186 (mttt) cc_final: 0.8766 (mttt) REVERT: N 258 LEU cc_start: 0.8844 (mt) cc_final: 0.8462 (mm) REVERT: N 260 TYR cc_start: 0.8757 (m-80) cc_final: 0.8547 (m-80) REVERT: N 296 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.8325 (m-80) REVERT: N 318 LYS cc_start: 0.7778 (mttm) cc_final: 0.7244 (tptp) REVERT: N 326 PHE cc_start: 0.9101 (t80) cc_final: 0.8436 (t80) REVERT: N 363 LEU cc_start: 0.8394 (mt) cc_final: 0.7829 (tt) REVERT: H 74 VAL cc_start: 0.8601 (OUTLIER) cc_final: 0.8332 (t) REVERT: H 137 PHE cc_start: 0.8652 (p90) cc_final: 0.7946 (p90) REVERT: H 149 LEU cc_start: 0.8497 (tp) cc_final: 0.8196 (tp) REVERT: H 163 GLU cc_start: 0.6795 (tp30) cc_final: 0.6260 (tp30) REVERT: H 223 GLU cc_start: 0.6691 (tt0) cc_final: 0.6414 (tt0) REVERT: H 250 ILE cc_start: 0.9249 (mt) cc_final: 0.8974 (mm) REVERT: H 262 LEU cc_start: 0.9078 (mt) cc_final: 0.8801 (mt) REVERT: H 299 ARG cc_start: 0.7945 (ptp-170) cc_final: 0.6477 (ptp-170) REVERT: H 335 THR cc_start: 0.7747 (p) cc_final: 0.7445 (p) outliers start: 122 outliers final: 41 residues processed: 1506 average time/residue: 0.4979 time to fit residues: 1210.6258 Evaluate side-chains 982 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 923 time to evaluate : 3.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 385 optimal weight: 3.9990 chunk 346 optimal weight: 1.9990 chunk 192 optimal weight: 7.9990 chunk 118 optimal weight: 20.0000 chunk 233 optimal weight: 2.9990 chunk 185 optimal weight: 0.9980 chunk 358 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 217 optimal weight: 0.1980 chunk 266 optimal weight: 0.9980 chunk 415 optimal weight: 7.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 92 ASN 1 174 HIS 2 129 HIS 3 7 ASN 3 163 HIS ** 3 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 639 GLN 4 33 GLN 4 72 HIS 4 78 ASN 4 93 HIS ** 4 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 315 HIS 4 377 ASN 6 125 GLN 9 41 HIS 7 76 HIS K 36 ASN ** L 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 361 GLN ** L 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 436 HIS L 544 ASN M 36 ASN M 186 GLN M 211 HIS M 222 HIS N 60 GLN N 103 HIS N 245 ASN N 279 GLN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.290 37100 Z= 0.795 Angle : 2.272 50.829 50537 Z= 1.479 Chirality : 0.444 6.394 5672 Planarity : 0.007 0.105 6377 Dihedral : 7.637 167.373 5149 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.68 % Favored : 93.97 % Rotamer: Outliers : 0.16 % Allowed : 4.02 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.07 % 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: -2.12 (0.11), residues: 4612 helix: -0.49 (0.10), residues: 2405 sheet: -1.30 (0.29), residues: 259 loop : -2.60 (0.13), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP H 310 HIS 0.012 0.002 HIS H 233 PHE 0.053 0.002 PHE L 328 TYR 0.046 0.002 TYR H 147 ARG 0.011 0.001 ARG L 587 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1207 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1201 time to evaluate : 3.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 14 GLU cc_start: 0.4767 (pt0) cc_final: 0.3998 (pm20) REVERT: 1 201 LEU cc_start: 0.8166 (mt) cc_final: 0.7832 (mt) REVERT: 1 270 THR cc_start: 0.8219 (p) cc_final: 0.7971 (t) REVERT: 1 311 MET cc_start: 0.8709 (mtm) cc_final: 0.8501 (mtm) REVERT: 2 8 GLN cc_start: 0.6976 (mm-40) cc_final: 0.6772 (mm110) REVERT: 2 9 ASP cc_start: 0.6478 (m-30) cc_final: 0.6058 (t0) REVERT: 2 35 GLN cc_start: 0.8591 (tp40) cc_final: 0.7874 (tm-30) REVERT: 2 36 GLN cc_start: 0.8833 (mt0) cc_final: 0.8185 (mt0) REVERT: 2 41 ILE cc_start: 0.8629 (mt) cc_final: 0.8410 (mp) REVERT: 2 61 MET cc_start: 0.8060 (tpt) cc_final: 0.7640 (tpt) REVERT: 2 69 TYR cc_start: 0.7791 (t80) cc_final: 0.7431 (t80) REVERT: 2 75 THR cc_start: 0.8362 (m) cc_final: 0.8134 (p) REVERT: 2 141 TYR cc_start: 0.7310 (m-80) cc_final: 0.5952 (m-80) REVERT: 3 47 MET cc_start: 0.8633 (mmm) cc_final: 0.8336 (tpp) REVERT: 3 82 SER cc_start: 0.9226 (m) cc_final: 0.8848 (p) REVERT: 3 228 ASP cc_start: 0.8727 (m-30) cc_final: 0.8187 (t0) REVERT: 3 284 GLU cc_start: 0.7956 (pt0) cc_final: 0.7737 (pt0) REVERT: 3 437 ILE cc_start: 0.8436 (pt) cc_final: 0.7981 (pt) REVERT: 3 448 MET cc_start: 0.6412 (ptm) cc_final: 0.6154 (ttp) REVERT: 3 459 MET cc_start: 0.8071 (mtt) cc_final: 0.7839 (mtt) REVERT: 3 477 LEU cc_start: 0.8572 (mt) cc_final: 0.8324 (tp) REVERT: 3 531 LYS cc_start: 0.7522 (mppt) cc_final: 0.7207 (mmtt) REVERT: 3 655 ARG cc_start: 0.7878 (mpp-170) cc_final: 0.7501 (mtp-110) REVERT: 4 71 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8093 (mt-10) REVERT: 4 102 GLU cc_start: 0.6980 (mt-10) cc_final: 0.6596 (mt-10) REVERT: 4 109 VAL cc_start: 0.9074 (p) cc_final: 0.8710 (m) REVERT: 4 119 ILE cc_start: 0.8902 (mt) cc_final: 0.8695 (mp) REVERT: 4 158 ASP cc_start: 0.8772 (m-30) cc_final: 0.8386 (t0) REVERT: 4 238 SER cc_start: 0.8847 (m) cc_final: 0.8464 (p) REVERT: 4 247 ASP cc_start: 0.8681 (t70) cc_final: 0.8252 (t70) REVERT: 4 282 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7497 (mt-10) REVERT: 4 286 SER cc_start: 0.8528 (m) cc_final: 0.8320 (p) REVERT: 4 364 MET cc_start: 0.8992 (mtm) cc_final: 0.8571 (mtm) REVERT: 4 378 LEU cc_start: 0.8598 (tp) cc_final: 0.8312 (tt) REVERT: 4 380 SER cc_start: 0.9446 (m) cc_final: 0.9204 (t) REVERT: 5 17 ILE cc_start: 0.8940 (pt) cc_final: 0.8381 (mt) REVERT: 5 56 ASP cc_start: 0.8540 (t0) cc_final: 0.8211 (t0) REVERT: 5 75 VAL cc_start: 0.9009 (t) cc_final: 0.8760 (t) REVERT: 5 105 THR cc_start: 0.9069 (p) cc_final: 0.8848 (p) REVERT: 5 106 ASP cc_start: 0.8259 (m-30) cc_final: 0.7607 (p0) REVERT: 5 122 PHE cc_start: 0.7769 (m-80) cc_final: 0.7241 (m-80) REVERT: 5 177 LYS cc_start: 0.8301 (tttm) cc_final: 0.8076 (tptm) REVERT: 6 27 LEU cc_start: 0.8737 (tp) cc_final: 0.8274 (tp) REVERT: 6 41 PHE cc_start: 0.8476 (t80) cc_final: 0.7938 (t80) REVERT: 6 86 LYS cc_start: 0.8892 (tptt) cc_final: 0.8519 (tttt) REVERT: 6 92 MET cc_start: 0.8850 (tpp) cc_final: 0.8212 (tpp) REVERT: 6 103 LYS cc_start: 0.8662 (pttt) cc_final: 0.8354 (ptpt) REVERT: 9 14 LEU cc_start: 0.9067 (tp) cc_final: 0.8860 (tp) REVERT: 9 23 THR cc_start: 0.9119 (m) cc_final: 0.8809 (t) REVERT: 9 44 THR cc_start: 0.9031 (p) cc_final: 0.8582 (t) REVERT: 9 149 GLU cc_start: 0.8178 (tt0) cc_final: 0.7608 (mm-30) REVERT: 7 25 GLN cc_start: 0.6638 (pt0) cc_final: 0.5077 (tp40) REVERT: 7 90 HIS cc_start: 0.6859 (p90) cc_final: 0.6302 (t70) REVERT: 7 107 LYS cc_start: 0.7506 (ptpp) cc_final: 0.7148 (mttm) REVERT: A 55 LYS cc_start: 0.5544 (pttt) cc_final: 0.5197 (pptt) REVERT: A 56 ARG cc_start: 0.7991 (tpp-160) cc_final: 0.7491 (ptt180) REVERT: J 73 LEU cc_start: 0.8868 (tp) cc_final: 0.8158 (mt) REVERT: J 120 LYS cc_start: 0.8302 (mtmm) cc_final: 0.7353 (mmtt) REVERT: J 135 TRP cc_start: 0.8133 (m100) cc_final: 0.7760 (m100) REVERT: J 144 PHE cc_start: 0.8552 (t80) cc_final: 0.8192 (t80) REVERT: K 36 ASN cc_start: 0.8453 (m110) cc_final: 0.7150 (m110) REVERT: L 25 ARG cc_start: 0.6359 (mtm180) cc_final: 0.5340 (mmt180) REVERT: L 75 PHE cc_start: 0.6769 (t80) cc_final: 0.6186 (t80) REVERT: L 131 TRP cc_start: 0.7391 (m-10) cc_final: 0.6943 (m100) REVERT: L 134 VAL cc_start: 0.9229 (t) cc_final: 0.8666 (m) REVERT: L 138 SER cc_start: 0.8742 (m) cc_final: 0.8404 (p) REVERT: L 216 LYS cc_start: 0.7719 (mmtt) cc_final: 0.7457 (mmtt) REVERT: L 225 TRP cc_start: 0.7385 (p-90) cc_final: 0.6851 (p-90) REVERT: L 265 ASP cc_start: 0.7494 (p0) cc_final: 0.6016 (t70) REVERT: L 334 LEU cc_start: 0.8573 (mp) cc_final: 0.7600 (mp) REVERT: L 355 LEU cc_start: 0.7865 (mt) cc_final: 0.7027 (tp) REVERT: L 377 PRO cc_start: 0.6409 (Cg_exo) cc_final: 0.5980 (Cg_endo) REVERT: L 576 GLN cc_start: 0.7713 (mt0) cc_final: 0.6278 (tm-30) REVERT: M 31 LEU cc_start: 0.8425 (tp) cc_final: 0.7997 (mm) REVERT: M 67 LEU cc_start: 0.8805 (mt) cc_final: 0.8541 (mt) REVERT: M 100 LEU cc_start: 0.8812 (mt) cc_final: 0.8485 (mm) REVERT: M 109 LEU cc_start: 0.9184 (tp) cc_final: 0.8805 (tp) REVERT: M 246 ILE cc_start: 0.7921 (mp) cc_final: 0.7646 (mm) REVERT: M 282 LYS cc_start: 0.8375 (mtpp) cc_final: 0.7940 (mttm) REVERT: M 283 THR cc_start: 0.7720 (m) cc_final: 0.7235 (t) REVERT: M 284 LEU cc_start: 0.7569 (tp) cc_final: 0.7356 (tp) REVERT: M 285 LEU cc_start: 0.9116 (mp) cc_final: 0.8358 (mp) REVERT: M 359 LEU cc_start: 0.8508 (tp) cc_final: 0.8270 (tp) REVERT: M 363 LEU cc_start: 0.8642 (mt) cc_final: 0.8333 (mt) REVERT: M 377 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7785 (mm-30) REVERT: M 443 MET cc_start: 0.8452 (mtt) cc_final: 0.8068 (mtp) REVERT: N 3 LEU cc_start: 0.8744 (tp) cc_final: 0.8423 (tp) REVERT: N 39 SER cc_start: 0.8800 (t) cc_final: 0.8303 (p) REVERT: N 40 LEU cc_start: 0.6949 (tp) cc_final: 0.6583 (tp) REVERT: N 95 MET cc_start: 0.8845 (mtp) cc_final: 0.8520 (mtp) REVERT: N 103 HIS cc_start: 0.7685 (t-90) cc_final: 0.7329 (t-170) REVERT: N 126 ARG cc_start: 0.7089 (mtt180) cc_final: 0.6600 (mtt-85) REVERT: N 137 PHE cc_start: 0.8545 (t80) cc_final: 0.7382 (t80) REVERT: N 198 ASP cc_start: 0.8406 (m-30) cc_final: 0.8161 (m-30) REVERT: N 201 GLN cc_start: 0.8961 (tt0) cc_final: 0.8722 (tt0) REVERT: N 326 PHE cc_start: 0.8901 (t80) cc_final: 0.7954 (t80) REVERT: N 330 MET cc_start: 0.8753 (mmp) cc_final: 0.8498 (mmp) REVERT: N 333 LEU cc_start: 0.8693 (mt) cc_final: 0.8396 (tp) REVERT: N 363 LEU cc_start: 0.7677 (mt) cc_final: 0.7048 (tp) REVERT: H 137 PHE cc_start: 0.8186 (p90) cc_final: 0.7116 (p90) REVERT: H 149 LEU cc_start: 0.8575 (tp) cc_final: 0.8272 (tp) REVERT: H 223 GLU cc_start: 0.6761 (tt0) cc_final: 0.6395 (tt0) REVERT: H 246 MET cc_start: 0.7683 (ttm) cc_final: 0.7366 (ttt) REVERT: H 279 MET cc_start: 0.8561 (tpt) cc_final: 0.8162 (tpt) REVERT: H 302 TYR cc_start: 0.8654 (t80) cc_final: 0.8449 (t80) outliers start: 6 outliers final: 3 residues processed: 1205 average time/residue: 0.4556 time to fit residues: 912.2042 Evaluate side-chains 827 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 824 time to evaluate : 3.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 230 optimal weight: 5.9990 chunk 128 optimal weight: 0.7980 chunk 345 optimal weight: 7.9990 chunk 282 optimal weight: 4.9990 chunk 114 optimal weight: 9.9990 chunk 415 optimal weight: 9.9990 chunk 449 optimal weight: 10.0000 chunk 370 optimal weight: 5.9990 chunk 412 optimal weight: 6.9990 chunk 141 optimal weight: 5.9990 chunk 333 optimal weight: 10.0000 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 35 HIS 1 147 GLN 1 190 ASN 1 288 GLN 1 315 HIS ** 2 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 114 ASN ** 3 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 168 HIS 3 368 HIS ** 3 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 465 HIS 3 703 GLN 4 63 HIS 4 306 ASN ** 6 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 119 ASN 6 125 GLN 6 155 GLN ** K 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 433 HIS L 467 ASN ** M 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 255 GLN M 455 HIS N 245 ASN H 187 ASN ** H 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 233 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.249 37100 Z= 0.817 Angle : 2.302 51.195 50537 Z= 1.490 Chirality : 0.444 6.595 5672 Planarity : 0.007 0.074 6377 Dihedral : 7.337 173.672 5149 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.16 % Favored : 92.48 % Rotamer: Outliers : 0.14 % Allowed : 5.25 % Favored : 94.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.12), residues: 4612 helix: 0.08 (0.10), residues: 2400 sheet: -1.17 (0.31), residues: 262 loop : -2.27 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 310 HIS 0.011 0.002 HIS 3 591 PHE 0.028 0.003 PHE L 333 TYR 0.037 0.003 TYR 4 87 ARG 0.010 0.001 ARG 6 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 987 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 982 time to evaluate : 3.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 102 LYS cc_start: 0.8559 (pttt) cc_final: 0.8218 (pttt) REVERT: 1 201 LEU cc_start: 0.8567 (mt) cc_final: 0.8273 (mt) REVERT: 1 268 MET cc_start: 0.6710 (ttm) cc_final: 0.6383 (ttm) REVERT: 1 270 THR cc_start: 0.8674 (p) cc_final: 0.8251 (t) REVERT: 1 272 PHE cc_start: 0.7861 (m-80) cc_final: 0.7326 (m-10) REVERT: 1 311 MET cc_start: 0.8641 (mtm) cc_final: 0.7948 (mtm) REVERT: 1 367 MET cc_start: 0.8405 (tmm) cc_final: 0.7941 (tmm) REVERT: 2 9 ASP cc_start: 0.6755 (m-30) cc_final: 0.6273 (t0) REVERT: 2 35 GLN cc_start: 0.8870 (tp40) cc_final: 0.7746 (tm-30) REVERT: 2 36 GLN cc_start: 0.9016 (mt0) cc_final: 0.8273 (mt0) REVERT: 2 61 MET cc_start: 0.8364 (tpt) cc_final: 0.7149 (tpt) REVERT: 2 69 TYR cc_start: 0.8452 (t80) cc_final: 0.8027 (t80) REVERT: 3 47 MET cc_start: 0.8629 (mmm) cc_final: 0.8385 (tpp) REVERT: 3 82 SER cc_start: 0.9426 (m) cc_final: 0.8930 (p) REVERT: 3 113 LEU cc_start: 0.9459 (tp) cc_final: 0.9258 (tp) REVERT: 3 197 ASP cc_start: 0.8225 (m-30) cc_final: 0.8017 (m-30) REVERT: 3 227 THR cc_start: 0.9579 (p) cc_final: 0.9369 (p) REVERT: 3 228 ASP cc_start: 0.8569 (m-30) cc_final: 0.8353 (p0) REVERT: 3 448 MET cc_start: 0.6369 (ptm) cc_final: 0.6155 (ttp) REVERT: 3 459 MET cc_start: 0.8096 (mtt) cc_final: 0.7572 (mtm) REVERT: 3 519 GLU cc_start: 0.6845 (tp30) cc_final: 0.6317 (pp20) REVERT: 3 531 LYS cc_start: 0.7689 (mppt) cc_final: 0.7267 (mmtt) REVERT: 3 655 ARG cc_start: 0.8329 (mpp-170) cc_final: 0.7821 (mtp85) REVERT: 4 50 GLU cc_start: 0.6233 (tt0) cc_final: 0.5092 (mp0) REVERT: 4 71 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8211 (mt-10) REVERT: 4 121 ASN cc_start: 0.8893 (t0) cc_final: 0.8182 (t0) REVERT: 4 138 LEU cc_start: 0.8429 (tp) cc_final: 0.8133 (tp) REVERT: 4 247 ASP cc_start: 0.8827 (t70) cc_final: 0.8316 (t70) REVERT: 4 271 ASP cc_start: 0.7449 (m-30) cc_final: 0.7213 (m-30) REVERT: 4 364 MET cc_start: 0.9016 (mtm) cc_final: 0.8717 (mtm) REVERT: 5 55 LEU cc_start: 0.9064 (mt) cc_final: 0.8854 (mp) REVERT: 5 56 ASP cc_start: 0.8486 (t0) cc_final: 0.8068 (t0) REVERT: 5 73 GLU cc_start: 0.7470 (tt0) cc_final: 0.6675 (tm-30) REVERT: 5 75 VAL cc_start: 0.8830 (t) cc_final: 0.8408 (t) REVERT: 5 105 THR cc_start: 0.9079 (p) cc_final: 0.8869 (p) REVERT: 5 106 ASP cc_start: 0.8164 (m-30) cc_final: 0.7669 (p0) REVERT: 5 122 PHE cc_start: 0.8013 (m-80) cc_final: 0.7561 (m-80) REVERT: 5 136 LEU cc_start: 0.8692 (mp) cc_final: 0.8418 (mt) REVERT: 5 177 LYS cc_start: 0.8389 (tttm) cc_final: 0.8162 (tptm) REVERT: 6 27 LEU cc_start: 0.9105 (tp) cc_final: 0.8723 (tp) REVERT: 6 50 MET cc_start: 0.8453 (tpt) cc_final: 0.8126 (tpt) REVERT: 6 86 LYS cc_start: 0.8842 (tptt) cc_final: 0.8344 (tttt) REVERT: 6 92 MET cc_start: 0.8595 (tpp) cc_final: 0.8384 (tpp) REVERT: 9 44 THR cc_start: 0.8872 (p) cc_final: 0.8362 (t) REVERT: 9 79 ASN cc_start: 0.8193 (m-40) cc_final: 0.7186 (m110) REVERT: 9 105 GLU cc_start: 0.9059 (tt0) cc_final: 0.8757 (tt0) REVERT: 9 106 GLU cc_start: 0.7829 (tp30) cc_final: 0.7529 (tp30) REVERT: 7 21 ARG cc_start: 0.8173 (mtt-85) cc_final: 0.7850 (mtt180) REVERT: 7 25 GLN cc_start: 0.6978 (pt0) cc_final: 0.4720 (tp40) REVERT: 7 86 LEU cc_start: 0.8448 (mp) cc_final: 0.8186 (mp) REVERT: 7 90 HIS cc_start: 0.7486 (p90) cc_final: 0.6429 (t70) REVERT: 7 107 LYS cc_start: 0.7912 (ptpp) cc_final: 0.7603 (mttm) REVERT: A 35 LYS cc_start: 0.5479 (tptt) cc_final: 0.5231 (tptm) REVERT: A 56 ARG cc_start: 0.8232 (tpp-160) cc_final: 0.7701 (ptt180) REVERT: A 66 MET cc_start: 0.8242 (tmm) cc_final: 0.7798 (tmm) REVERT: A 67 LEU cc_start: 0.8873 (tp) cc_final: 0.8107 (tp) REVERT: A 99 PHE cc_start: 0.9226 (t80) cc_final: 0.8774 (t80) REVERT: J 39 LEU cc_start: 0.9114 (tp) cc_final: 0.8791 (tp) REVERT: J 96 LEU cc_start: 0.8378 (mt) cc_final: 0.8159 (mt) REVERT: J 132 TYR cc_start: 0.8562 (m-80) cc_final: 0.8261 (m-10) REVERT: J 144 PHE cc_start: 0.8634 (t80) cc_final: 0.8291 (t80) REVERT: K 54 GLN cc_start: 0.8623 (mt0) cc_final: 0.8224 (pm20) REVERT: L 25 ARG cc_start: 0.6521 (mtm180) cc_final: 0.5316 (mmt-90) REVERT: L 75 PHE cc_start: 0.6858 (t80) cc_final: 0.6127 (t80) REVERT: L 214 VAL cc_start: 0.8548 (t) cc_final: 0.8346 (t) REVERT: L 225 TRP cc_start: 0.8254 (p-90) cc_final: 0.7610 (p-90) REVERT: L 265 ASP cc_start: 0.7750 (p0) cc_final: 0.6461 (t70) REVERT: L 334 LEU cc_start: 0.8818 (mp) cc_final: 0.8108 (mp) REVERT: L 382 PHE cc_start: 0.5790 (t80) cc_final: 0.5538 (t80) REVERT: L 415 MET cc_start: 0.7871 (mmm) cc_final: 0.7666 (mmm) REVERT: L 416 TYR cc_start: 0.8197 (p90) cc_final: 0.7796 (p90) REVERT: L 576 GLN cc_start: 0.8192 (mt0) cc_final: 0.7279 (tm-30) REVERT: M 31 LEU cc_start: 0.8622 (tp) cc_final: 0.8330 (tp) REVERT: M 36 ASN cc_start: 0.9101 (m-40) cc_final: 0.8545 (m110) REVERT: M 100 LEU cc_start: 0.8884 (mt) cc_final: 0.8580 (mm) REVERT: M 109 LEU cc_start: 0.9146 (tp) cc_final: 0.8749 (tp) REVERT: M 235 LYS cc_start: 0.8813 (mttt) cc_final: 0.8515 (mttm) REVERT: M 246 ILE cc_start: 0.7961 (mp) cc_final: 0.7464 (mm) REVERT: M 282 LYS cc_start: 0.8023 (mtpp) cc_final: 0.7698 (mttm) REVERT: M 285 LEU cc_start: 0.8965 (mp) cc_final: 0.8557 (mp) REVERT: M 325 LEU cc_start: 0.8836 (tp) cc_final: 0.8593 (tp) REVERT: M 326 PHE cc_start: 0.7520 (m-10) cc_final: 0.7226 (m-80) REVERT: M 412 LYS cc_start: 0.9156 (mttt) cc_final: 0.8886 (mtmt) REVERT: M 455 HIS cc_start: 0.6089 (t70) cc_final: 0.5514 (t-170) REVERT: N 3 LEU cc_start: 0.9156 (tp) cc_final: 0.8674 (tp) REVERT: N 39 SER cc_start: 0.9176 (t) cc_final: 0.8856 (p) REVERT: N 40 LEU cc_start: 0.8066 (tp) cc_final: 0.7640 (tp) REVERT: N 103 HIS cc_start: 0.8114 (t-90) cc_final: 0.7522 (t-170) REVERT: N 171 LEU cc_start: 0.9472 (tp) cc_final: 0.9247 (tp) REVERT: N 216 LYS cc_start: 0.8821 (mttp) cc_final: 0.8572 (mttt) REVERT: N 318 LYS cc_start: 0.8056 (mttm) cc_final: 0.7169 (tptt) REVERT: N 326 PHE cc_start: 0.9238 (t80) cc_final: 0.8426 (t80) REVERT: N 330 MET cc_start: 0.8862 (mmp) cc_final: 0.8640 (mmp) REVERT: N 363 LEU cc_start: 0.7827 (mt) cc_final: 0.7244 (tt) REVERT: H 35 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7550 (tm-30) REVERT: H 46 MET cc_start: 0.8977 (mtp) cc_final: 0.8770 (mtm) REVERT: H 95 LEU cc_start: 0.8885 (mm) cc_final: 0.8639 (mm) REVERT: H 137 PHE cc_start: 0.8694 (p90) cc_final: 0.7936 (p90) REVERT: H 149 LEU cc_start: 0.8722 (tp) cc_final: 0.8225 (tp) REVERT: H 195 LEU cc_start: 0.9041 (mt) cc_final: 0.8763 (mt) REVERT: H 213 GLU cc_start: 0.8293 (tt0) cc_final: 0.8068 (tt0) REVERT: H 235 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7585 (mm-30) REVERT: H 250 ILE cc_start: 0.9354 (mm) cc_final: 0.9101 (mm) REVERT: H 281 LEU cc_start: 0.8431 (mt) cc_final: 0.8111 (mt) REVERT: H 282 LYS cc_start: 0.7797 (mtmm) cc_final: 0.7550 (mttp) REVERT: H 304 GLN cc_start: 0.7757 (tp-100) cc_final: 0.7551 (tp-100) outliers start: 5 outliers final: 2 residues processed: 986 average time/residue: 0.4286 time to fit residues: 709.0446 Evaluate side-chains 760 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 758 time to evaluate : 4.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 410 optimal weight: 8.9990 chunk 312 optimal weight: 10.0000 chunk 215 optimal weight: 0.5980 chunk 46 optimal weight: 6.9990 chunk 198 optimal weight: 9.9990 chunk 279 optimal weight: 9.9990 chunk 417 optimal weight: 2.9990 chunk 441 optimal weight: 7.9990 chunk 217 optimal weight: 7.9990 chunk 395 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 591 HIS 4 306 ASN ** 4 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 120 ASN 6 155 GLN 7 92 HIS ** L 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 432 HIS L 434 HIS ** M 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.5478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.253 37100 Z= 0.819 Angle : 2.302 51.134 50537 Z= 1.489 Chirality : 0.445 6.489 5672 Planarity : 0.006 0.065 6377 Dihedral : 7.301 178.190 5149 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.16 % Favored : 92.56 % Rotamer: Outliers : 0.05 % Allowed : 4.46 % Favored : 95.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.35 % 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: -1.43 (0.12), residues: 4612 helix: 0.03 (0.10), residues: 2385 sheet: -1.20 (0.29), residues: 300 loop : -2.17 (0.13), residues: 1927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 506 HIS 0.010 0.002 HIS 4 93 PHE 0.037 0.003 PHE L 111 TYR 0.039 0.003 TYR H 147 ARG 0.008 0.001 ARG L 419 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 912 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 910 time to evaluate : 4.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 89 LEU cc_start: 0.9084 (tt) cc_final: 0.8840 (tt) REVERT: 1 102 LYS cc_start: 0.8675 (pttt) cc_final: 0.8215 (pttt) REVERT: 1 189 MET cc_start: 0.6826 (mtm) cc_final: 0.6512 (mtp) REVERT: 1 272 PHE cc_start: 0.7933 (m-80) cc_final: 0.7590 (m-10) REVERT: 1 311 MET cc_start: 0.8597 (mtm) cc_final: 0.7977 (mtm) REVERT: 1 367 MET cc_start: 0.8490 (tmm) cc_final: 0.7992 (tmm) REVERT: 2 9 ASP cc_start: 0.6789 (m-30) cc_final: 0.6362 (t0) REVERT: 2 35 GLN cc_start: 0.8944 (tp40) cc_final: 0.8324 (tm-30) REVERT: 2 81 GLN cc_start: 0.7045 (mt0) cc_final: 0.6797 (mt0) REVERT: 2 151 GLU cc_start: 0.7523 (mt-10) cc_final: 0.6724 (mt-10) REVERT: 3 36 GLU cc_start: 0.8984 (tm-30) cc_final: 0.8533 (tm-30) REVERT: 3 47 MET cc_start: 0.8806 (mmm) cc_final: 0.8150 (tpp) REVERT: 3 82 SER cc_start: 0.9336 (m) cc_final: 0.8868 (p) REVERT: 3 228 ASP cc_start: 0.8623 (m-30) cc_final: 0.8233 (p0) REVERT: 3 448 MET cc_start: 0.6494 (ptm) cc_final: 0.6096 (ttp) REVERT: 3 459 MET cc_start: 0.8226 (mtt) cc_final: 0.7616 (mtm) REVERT: 3 519 GLU cc_start: 0.7164 (tp30) cc_final: 0.6255 (pp20) REVERT: 3 531 LYS cc_start: 0.7559 (mppt) cc_final: 0.6880 (mmtt) REVERT: 3 533 LEU cc_start: 0.8797 (mt) cc_final: 0.8500 (mt) REVERT: 3 585 MET cc_start: 0.8301 (mmm) cc_final: 0.7502 (mmm) REVERT: 4 67 GLU cc_start: 0.8422 (pm20) cc_final: 0.7970 (pm20) REVERT: 4 121 ASN cc_start: 0.8991 (t0) cc_final: 0.8130 (t0) REVERT: 4 138 LEU cc_start: 0.8356 (tp) cc_final: 0.7964 (tp) REVERT: 4 238 SER cc_start: 0.8868 (m) cc_final: 0.8501 (p) REVERT: 4 247 ASP cc_start: 0.8967 (t70) cc_final: 0.8586 (t70) REVERT: 4 364 MET cc_start: 0.9010 (mtm) cc_final: 0.8612 (mtm) REVERT: 5 55 LEU cc_start: 0.9175 (mt) cc_final: 0.8925 (mp) REVERT: 5 56 ASP cc_start: 0.8381 (t0) cc_final: 0.8125 (t0) REVERT: 5 73 GLU cc_start: 0.7505 (tt0) cc_final: 0.6635 (tm-30) REVERT: 5 106 ASP cc_start: 0.8202 (m-30) cc_final: 0.7792 (p0) REVERT: 5 122 PHE cc_start: 0.7834 (m-80) cc_final: 0.7528 (m-80) REVERT: 5 177 LYS cc_start: 0.8410 (tttm) cc_final: 0.8078 (tppt) REVERT: 6 50 MET cc_start: 0.8387 (tpt) cc_final: 0.8157 (tpp) REVERT: 6 92 MET cc_start: 0.8712 (tpp) cc_final: 0.8442 (tpp) REVERT: 6 94 ARG cc_start: 0.8862 (ttp80) cc_final: 0.8368 (ttp80) REVERT: 6 97 GLU cc_start: 0.8461 (mt-10) cc_final: 0.7619 (tp30) REVERT: 6 165 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7216 (tm-30) REVERT: 9 14 LEU cc_start: 0.8750 (tp) cc_final: 0.8411 (tp) REVERT: 9 79 ASN cc_start: 0.8129 (m-40) cc_final: 0.7152 (m110) REVERT: 9 91 TYR cc_start: 0.9230 (t80) cc_final: 0.7572 (t80) REVERT: 9 105 GLU cc_start: 0.8905 (tt0) cc_final: 0.8624 (tm-30) REVERT: 9 126 TYR cc_start: 0.7847 (t80) cc_final: 0.7536 (t80) REVERT: 7 86 LEU cc_start: 0.8521 (mp) cc_final: 0.8307 (mp) REVERT: A 42 MET cc_start: 0.5529 (pmm) cc_final: 0.5277 (pmm) REVERT: A 56 ARG cc_start: 0.7958 (tpp-160) cc_final: 0.7509 (ptt180) REVERT: A 67 LEU cc_start: 0.8892 (tp) cc_final: 0.8513 (tt) REVERT: A 72 ASP cc_start: 0.8896 (t70) cc_final: 0.8374 (t70) REVERT: J 36 PHE cc_start: 0.8109 (m-10) cc_final: 0.7822 (m-10) REVERT: J 39 LEU cc_start: 0.9115 (tp) cc_final: 0.8810 (tp) REVERT: J 144 PHE cc_start: 0.8683 (t80) cc_final: 0.8332 (t80) REVERT: K 36 ASN cc_start: 0.7573 (m110) cc_final: 0.7216 (m110) REVERT: K 41 SER cc_start: 0.8475 (p) cc_final: 0.8205 (p) REVERT: L 1 MET cc_start: 0.5649 (tmm) cc_final: 0.5413 (mmm) REVERT: L 25 ARG cc_start: 0.5785 (mtm180) cc_final: 0.5411 (mmt-90) REVERT: L 75 PHE cc_start: 0.6847 (t80) cc_final: 0.6305 (t80) REVERT: L 114 MET cc_start: 0.8324 (tpt) cc_final: 0.8015 (tpt) REVERT: L 148 ASN cc_start: 0.7054 (m110) cc_final: 0.6661 (m110) REVERT: L 222 LEU cc_start: 0.8451 (pp) cc_final: 0.8169 (pp) REVERT: L 225 TRP cc_start: 0.8397 (p-90) cc_final: 0.7876 (p-90) REVERT: L 265 ASP cc_start: 0.7710 (p0) cc_final: 0.6509 (t70) REVERT: L 334 LEU cc_start: 0.8604 (mp) cc_final: 0.7796 (mp) REVERT: L 603 VAL cc_start: 0.8794 (p) cc_final: 0.8559 (m) REVERT: M 100 LEU cc_start: 0.8931 (mt) cc_final: 0.8712 (mm) REVERT: M 102 MET cc_start: 0.9046 (tpp) cc_final: 0.8358 (tpp) REVERT: M 103 GLU cc_start: 0.8418 (tt0) cc_final: 0.8086 (tp30) REVERT: M 132 MET cc_start: 0.8859 (ptm) cc_final: 0.8606 (ptm) REVERT: M 150 LEU cc_start: 0.8732 (tp) cc_final: 0.8271 (tp) REVERT: M 282 LYS cc_start: 0.8564 (mtpp) cc_final: 0.8096 (mttm) REVERT: M 285 LEU cc_start: 0.8773 (mp) cc_final: 0.8323 (mp) REVERT: M 293 MET cc_start: 0.7988 (mmp) cc_final: 0.7655 (mpp) REVERT: M 325 LEU cc_start: 0.8646 (tp) cc_final: 0.8332 (tp) REVERT: M 326 PHE cc_start: 0.7547 (m-10) cc_final: 0.6812 (m-80) REVERT: M 363 LEU cc_start: 0.8687 (mt) cc_final: 0.8467 (mt) REVERT: N 3 LEU cc_start: 0.9174 (tp) cc_final: 0.8727 (tp) REVERT: N 103 HIS cc_start: 0.8466 (t-90) cc_final: 0.7860 (t-170) REVERT: N 216 LYS cc_start: 0.8721 (mttp) cc_final: 0.8392 (mttp) REVERT: N 269 MET cc_start: 0.8949 (mtp) cc_final: 0.8721 (ttm) REVERT: N 326 PHE cc_start: 0.9305 (t80) cc_final: 0.8889 (t80) REVERT: N 328 VAL cc_start: 0.9247 (t) cc_final: 0.8850 (p) REVERT: N 363 LEU cc_start: 0.8481 (mt) cc_final: 0.7735 (tt) REVERT: N 387 GLU cc_start: 0.8330 (tp30) cc_final: 0.8028 (tm-30) REVERT: N 420 LEU cc_start: 0.8625 (tp) cc_final: 0.8394 (tt) REVERT: H 18 LEU cc_start: 0.9296 (tp) cc_final: 0.9062 (tp) REVERT: H 35 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7388 (tm-30) REVERT: H 163 GLU cc_start: 0.6577 (tp30) cc_final: 0.5944 (tp30) REVERT: H 196 PHE cc_start: 0.7343 (p90) cc_final: 0.7082 (p90) REVERT: H 208 ILE cc_start: 0.9497 (mm) cc_final: 0.9257 (mt) REVERT: H 213 GLU cc_start: 0.8441 (tt0) cc_final: 0.7956 (tt0) REVERT: H 235 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7650 (mm-30) REVERT: H 281 LEU cc_start: 0.8421 (mt) cc_final: 0.8161 (mt) REVERT: H 304 GLN cc_start: 0.8033 (tp-100) cc_final: 0.7687 (tp40) outliers start: 2 outliers final: 1 residues processed: 912 average time/residue: 0.4825 time to fit residues: 747.6294 Evaluate side-chains 706 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 705 time to evaluate : 3.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 367 optimal weight: 10.0000 chunk 250 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 328 optimal weight: 8.9990 chunk 182 optimal weight: 4.9990 chunk 376 optimal weight: 8.9990 chunk 305 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 225 optimal weight: 5.9990 chunk 396 optimal weight: 0.0470 chunk 111 optimal weight: 9.9990 overall best weight: 4.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 86 GLN 1 147 GLN 1 198 ASN ** 3 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 347 HIS ** 3 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 155 GLN 7 90 HIS ** L 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 434 HIS ** L 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.5864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.241 37100 Z= 0.796 Angle : 2.281 50.901 50537 Z= 1.481 Chirality : 0.443 6.441 5672 Planarity : 0.006 0.075 6377 Dihedral : 7.145 179.583 5149 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.35 % Favored : 92.39 % Rotamer: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.35 % 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: -1.28 (0.12), residues: 4612 helix: 0.14 (0.10), residues: 2381 sheet: -1.15 (0.32), residues: 258 loop : -2.05 (0.13), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP L 131 HIS 0.011 0.002 HIS H 192 PHE 0.044 0.002 PHE A 71 TYR 0.039 0.002 TYR H 147 ARG 0.005 0.001 ARG H 216 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 882 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 882 time to evaluate : 4.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 102 LYS cc_start: 0.8668 (pttt) cc_final: 0.8206 (pttt) REVERT: 1 189 MET cc_start: 0.6694 (mtm) cc_final: 0.6233 (mtm) REVERT: 1 270 THR cc_start: 0.8524 (p) cc_final: 0.8320 (t) REVERT: 1 272 PHE cc_start: 0.7947 (m-80) cc_final: 0.7570 (m-10) REVERT: 1 367 MET cc_start: 0.8565 (tmm) cc_final: 0.8120 (tmm) REVERT: 1 397 ARG cc_start: 0.8722 (mpt180) cc_final: 0.8475 (mpt180) REVERT: 2 9 ASP cc_start: 0.6597 (m-30) cc_final: 0.6251 (t0) REVERT: 2 35 GLN cc_start: 0.8915 (tp40) cc_final: 0.8315 (tm-30) REVERT: 2 61 MET cc_start: 0.8296 (tpt) cc_final: 0.7844 (tpt) REVERT: 2 81 GLN cc_start: 0.7275 (mt0) cc_final: 0.6629 (mt0) REVERT: 3 47 MET cc_start: 0.8659 (mmm) cc_final: 0.8140 (tpp) REVERT: 3 177 ASP cc_start: 0.7067 (m-30) cc_final: 0.6866 (m-30) REVERT: 3 459 MET cc_start: 0.8213 (mtt) cc_final: 0.7606 (mtm) REVERT: 3 531 LYS cc_start: 0.7453 (mppt) cc_final: 0.6747 (mmtt) REVERT: 3 533 LEU cc_start: 0.9005 (mt) cc_final: 0.8681 (mt) REVERT: 3 585 MET cc_start: 0.7839 (mmm) cc_final: 0.7312 (mmm) REVERT: 4 121 ASN cc_start: 0.8941 (t0) cc_final: 0.8071 (t0) REVERT: 4 138 LEU cc_start: 0.8162 (tp) cc_final: 0.7800 (tp) REVERT: 4 238 SER cc_start: 0.8753 (m) cc_final: 0.8428 (p) REVERT: 4 247 ASP cc_start: 0.8921 (t70) cc_final: 0.8548 (t70) REVERT: 4 364 MET cc_start: 0.8957 (mtm) cc_final: 0.8593 (mtm) REVERT: 5 17 ILE cc_start: 0.8955 (pt) cc_final: 0.8743 (pt) REVERT: 5 56 ASP cc_start: 0.8522 (t0) cc_final: 0.8169 (t0) REVERT: 5 73 GLU cc_start: 0.7467 (tt0) cc_final: 0.6820 (tm-30) REVERT: 5 75 VAL cc_start: 0.9006 (m) cc_final: 0.8369 (p) REVERT: 5 106 ASP cc_start: 0.8063 (m-30) cc_final: 0.7704 (p0) REVERT: 5 170 PHE cc_start: 0.7773 (m-10) cc_final: 0.7551 (m-10) REVERT: 5 177 LYS cc_start: 0.8480 (tttm) cc_final: 0.7986 (tppt) REVERT: 6 92 MET cc_start: 0.8669 (tpp) cc_final: 0.8437 (tpp) REVERT: 6 123 ILE cc_start: 0.9306 (tt) cc_final: 0.8929 (tt) REVERT: 6 134 ASP cc_start: 0.9243 (m-30) cc_final: 0.9032 (m-30) REVERT: 6 165 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7469 (tp30) REVERT: 9 14 LEU cc_start: 0.8503 (tp) cc_final: 0.8244 (tp) REVERT: 9 44 THR cc_start: 0.8934 (p) cc_final: 0.8521 (t) REVERT: 9 79 ASN cc_start: 0.7794 (m-40) cc_final: 0.7030 (m110) REVERT: 9 105 GLU cc_start: 0.8853 (tt0) cc_final: 0.8301 (tp30) REVERT: 9 126 TYR cc_start: 0.7969 (t80) cc_final: 0.7639 (t80) REVERT: 7 86 LEU cc_start: 0.8604 (mp) cc_final: 0.8349 (mp) REVERT: A 56 ARG cc_start: 0.7985 (tpp-160) cc_final: 0.7512 (ptt180) REVERT: A 67 LEU cc_start: 0.8826 (tp) cc_final: 0.8525 (tp) REVERT: A 72 ASP cc_start: 0.8910 (t70) cc_final: 0.8508 (t70) REVERT: J 36 PHE cc_start: 0.8248 (m-10) cc_final: 0.8009 (m-10) REVERT: J 144 PHE cc_start: 0.8692 (t80) cc_final: 0.8363 (t80) REVERT: K 41 SER cc_start: 0.8431 (p) cc_final: 0.8197 (p) REVERT: L 34 SER cc_start: 0.6937 (m) cc_final: 0.6715 (p) REVERT: L 75 PHE cc_start: 0.7163 (t80) cc_final: 0.6615 (t80) REVERT: L 148 ASN cc_start: 0.6910 (m110) cc_final: 0.6541 (m110) REVERT: L 153 ASP cc_start: 0.7584 (m-30) cc_final: 0.7158 (t0) REVERT: L 192 MET cc_start: 0.7769 (ttp) cc_final: 0.7521 (ttp) REVERT: L 222 LEU cc_start: 0.8732 (pp) cc_final: 0.8501 (pp) REVERT: L 265 ASP cc_start: 0.7308 (p0) cc_final: 0.6263 (t70) REVERT: L 334 LEU cc_start: 0.8817 (mp) cc_final: 0.8446 (mp) REVERT: L 603 VAL cc_start: 0.8894 (p) cc_final: 0.8649 (m) REVERT: M 100 LEU cc_start: 0.8982 (mt) cc_final: 0.8650 (mm) REVERT: M 102 MET cc_start: 0.9068 (tpp) cc_final: 0.8794 (tpp) REVERT: M 103 GLU cc_start: 0.8470 (tt0) cc_final: 0.8095 (tp30) REVERT: M 228 ASP cc_start: 0.8464 (m-30) cc_final: 0.7835 (m-30) REVERT: M 282 LYS cc_start: 0.8639 (mtpp) cc_final: 0.8174 (mttm) REVERT: M 285 LEU cc_start: 0.9154 (mp) cc_final: 0.8792 (mp) REVERT: M 293 MET cc_start: 0.8025 (mmp) cc_final: 0.7688 (mpp) REVERT: M 325 LEU cc_start: 0.8730 (tp) cc_final: 0.8503 (tp) REVERT: M 326 PHE cc_start: 0.7854 (m-80) cc_final: 0.6809 (m-80) REVERT: M 391 LEU cc_start: 0.9032 (tp) cc_final: 0.8817 (tt) REVERT: N 3 LEU cc_start: 0.9079 (tp) cc_final: 0.8698 (tp) REVERT: N 95 MET cc_start: 0.9192 (mtp) cc_final: 0.8907 (mtp) REVERT: N 103 HIS cc_start: 0.8380 (t-90) cc_final: 0.7767 (t-170) REVERT: N 125 ARG cc_start: 0.7318 (tpt90) cc_final: 0.7115 (tpt90) REVERT: N 136 TYR cc_start: 0.8876 (t80) cc_final: 0.8666 (t80) REVERT: N 216 LYS cc_start: 0.8712 (mttp) cc_final: 0.8276 (mttp) REVERT: N 269 MET cc_start: 0.8709 (mtp) cc_final: 0.8370 (ttm) REVERT: N 271 LEU cc_start: 0.9067 (mt) cc_final: 0.8783 (mt) REVERT: N 326 PHE cc_start: 0.9321 (t80) cc_final: 0.8891 (t80) REVERT: N 328 VAL cc_start: 0.9175 (t) cc_final: 0.8743 (p) REVERT: N 333 LEU cc_start: 0.9004 (mt) cc_final: 0.8561 (tp) REVERT: N 363 LEU cc_start: 0.8662 (mt) cc_final: 0.7820 (tt) REVERT: H 35 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7604 (tm-30) REVERT: H 163 GLU cc_start: 0.6474 (tp30) cc_final: 0.5910 (tp30) REVERT: H 181 ASN cc_start: 0.7884 (m-40) cc_final: 0.7502 (t0) REVERT: H 196 PHE cc_start: 0.7286 (p90) cc_final: 0.7054 (p90) REVERT: H 235 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7577 (mm-30) REVERT: H 281 LEU cc_start: 0.8406 (mt) cc_final: 0.8098 (mt) outliers start: 0 outliers final: 0 residues processed: 882 average time/residue: 0.4358 time to fit residues: 644.5840 Evaluate side-chains 698 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 698 time to evaluate : 3.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 148 optimal weight: 0.6980 chunk 397 optimal weight: 6.9990 chunk 87 optimal weight: 0.0670 chunk 259 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 chunk 442 optimal weight: 0.8980 chunk 367 optimal weight: 9.9990 chunk 204 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 146 optimal weight: 10.0000 chunk 232 optimal weight: 10.0000 overall best weight: 1.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 86 GLN ** 2 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 78 ASN ** 6 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 90 HIS 7 92 HIS 7 94 HIS L 88 HIS ** L 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 434 HIS ** M 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 211 HIS H 49 ASN H 183 ASN ** H 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.6196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.258 37100 Z= 0.765 Angle : 2.245 51.165 50537 Z= 1.467 Chirality : 0.442 6.374 5672 Planarity : 0.005 0.070 6377 Dihedral : 6.666 178.890 5149 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.92 % Favored : 93.84 % Rotamer: Outliers : 0.03 % Allowed : 2.41 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.35 % 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: -0.78 (0.12), residues: 4612 helix: 0.55 (0.11), residues: 2398 sheet: -0.97 (0.31), residues: 278 loop : -1.82 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP 3 558 HIS 0.007 0.001 HIS 7 90 PHE 0.029 0.002 PHE N 220 TYR 0.026 0.002 TYR H 147 ARG 0.006 0.000 ARG 6 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 927 time to evaluate : 3.998 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: 1 102 LYS cc_start: 0.8642 (pttt) cc_final: 0.8168 (pttt) REVERT: 1 189 MET cc_start: 0.6359 (mtm) cc_final: 0.5949 (mtm) REVERT: 1 270 THR cc_start: 0.8339 (p) cc_final: 0.8028 (t) REVERT: 1 311 MET cc_start: 0.8381 (mtm) cc_final: 0.7999 (mtm) REVERT: 1 367 MET cc_start: 0.8472 (tmm) cc_final: 0.8247 (tmm) REVERT: 1 397 ARG cc_start: 0.8558 (mpt180) cc_final: 0.8239 (mpt180) REVERT: 2 9 ASP cc_start: 0.6738 (m-30) cc_final: 0.6357 (t0) REVERT: 2 35 GLN cc_start: 0.8787 (tp40) cc_final: 0.7718 (tm-30) REVERT: 2 69 TYR cc_start: 0.8491 (t80) cc_final: 0.8034 (t80) REVERT: 3 36 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8372 (tm-30) REVERT: 3 47 MET cc_start: 0.8230 (mmm) cc_final: 0.8021 (tpp) REVERT: 3 78 LYS cc_start: 0.9110 (mttt) cc_final: 0.8877 (mtpp) REVERT: 3 177 ASP cc_start: 0.6727 (m-30) cc_final: 0.6464 (m-30) REVERT: 3 250 GLU cc_start: 0.6811 (tt0) cc_final: 0.6579 (tt0) REVERT: 3 331 GLU cc_start: 0.7126 (tm-30) cc_final: 0.6624 (tp30) REVERT: 3 459 MET cc_start: 0.8122 (mtt) cc_final: 0.7531 (mtm) REVERT: 3 531 LYS cc_start: 0.7200 (mppt) cc_final: 0.6573 (mmtt) REVERT: 3 533 LEU cc_start: 0.8976 (mt) cc_final: 0.8684 (mp) REVERT: 3 585 MET cc_start: 0.7894 (mmm) cc_final: 0.7649 (mmm) REVERT: 4 74 THR cc_start: 0.8996 (m) cc_final: 0.8759 (m) REVERT: 4 238 SER cc_start: 0.8881 (m) cc_final: 0.8639 (p) REVERT: 4 247 ASP cc_start: 0.8842 (t70) cc_final: 0.8488 (t70) REVERT: 4 274 ASP cc_start: 0.8216 (m-30) cc_final: 0.7964 (m-30) REVERT: 4 364 MET cc_start: 0.8928 (mtm) cc_final: 0.8496 (mtm) REVERT: 5 56 ASP cc_start: 0.8398 (t0) cc_final: 0.8163 (t0) REVERT: 5 115 GLU cc_start: 0.9201 (mp0) cc_final: 0.8770 (mp0) REVERT: 5 170 PHE cc_start: 0.7786 (m-10) cc_final: 0.7541 (m-10) REVERT: 5 177 LYS cc_start: 0.8423 (tttm) cc_final: 0.7923 (tppt) REVERT: 6 50 MET cc_start: 0.8164 (tpt) cc_final: 0.7344 (tpp) REVERT: 6 86 LYS cc_start: 0.8747 (tptt) cc_final: 0.8422 (tttt) REVERT: 6 92 MET cc_start: 0.8635 (tpp) cc_final: 0.8412 (tpp) REVERT: 6 94 ARG cc_start: 0.8830 (ttp80) cc_final: 0.8343 (ttp80) REVERT: 6 152 MET cc_start: 0.8656 (mtp) cc_final: 0.8452 (mtm) REVERT: 6 165 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7571 (tp30) REVERT: 9 14 LEU cc_start: 0.8414 (tp) cc_final: 0.8160 (tp) REVERT: 9 44 THR cc_start: 0.8809 (p) cc_final: 0.8501 (t) REVERT: 9 79 ASN cc_start: 0.8432 (m-40) cc_final: 0.7618 (m110) REVERT: 9 105 GLU cc_start: 0.8857 (tt0) cc_final: 0.8323 (tp30) REVERT: 9 126 TYR cc_start: 0.7837 (t80) cc_final: 0.7523 (t80) REVERT: 7 25 GLN cc_start: 0.6957 (pt0) cc_final: 0.4960 (tp-100) REVERT: 7 55 MET cc_start: 0.8655 (ttt) cc_final: 0.8303 (ttt) REVERT: 7 86 LEU cc_start: 0.8521 (mp) cc_final: 0.8181 (mp) REVERT: 7 90 HIS cc_start: 0.6725 (p90) cc_final: 0.5902 (t-170) REVERT: 7 104 VAL cc_start: 0.8264 (m) cc_final: 0.7973 (p) REVERT: A 56 ARG cc_start: 0.7906 (tpp-160) cc_final: 0.7478 (ptt180) REVERT: A 67 LEU cc_start: 0.9286 (tp) cc_final: 0.8633 (mt) REVERT: A 68 PHE cc_start: 0.8439 (t80) cc_final: 0.7896 (t80) REVERT: A 72 ASP cc_start: 0.8755 (t70) cc_final: 0.8539 (t70) REVERT: A 109 TYR cc_start: 0.9075 (t80) cc_final: 0.8743 (t80) REVERT: J 36 PHE cc_start: 0.7978 (m-10) cc_final: 0.7730 (m-10) REVERT: J 57 ILE cc_start: 0.8920 (tt) cc_final: 0.8718 (tt) REVERT: J 138 VAL cc_start: 0.9160 (t) cc_final: 0.8881 (p) REVERT: J 139 LEU cc_start: 0.9207 (tp) cc_final: 0.8893 (tt) REVERT: L 34 SER cc_start: 0.6824 (m) cc_final: 0.6472 (p) REVERT: L 75 PHE cc_start: 0.6981 (t80) cc_final: 0.6697 (t80) REVERT: L 79 ILE cc_start: 0.8530 (mt) cc_final: 0.8321 (mt) REVERT: L 150 GLN cc_start: 0.7814 (pm20) cc_final: 0.7434 (pm20) REVERT: L 153 ASP cc_start: 0.7538 (m-30) cc_final: 0.7124 (t0) REVERT: L 170 MET cc_start: 0.8405 (mtm) cc_final: 0.8126 (mtm) REVERT: L 192 MET cc_start: 0.7718 (ttp) cc_final: 0.7513 (ttp) REVERT: L 222 LEU cc_start: 0.8430 (pp) cc_final: 0.8098 (pp) REVERT: L 225 TRP cc_start: 0.7933 (p-90) cc_final: 0.7503 (p-90) REVERT: L 265 ASP cc_start: 0.7466 (p0) cc_final: 0.6597 (t70) REVERT: L 286 PHE cc_start: 0.5116 (p90) cc_final: 0.4237 (p90) REVERT: L 442 MET cc_start: 0.5871 (mtt) cc_final: 0.4667 (mtp) REVERT: L 561 LEU cc_start: 0.8337 (tp) cc_final: 0.8063 (pp) REVERT: M 3 VAL cc_start: 0.8367 (t) cc_final: 0.8056 (p) REVERT: M 100 LEU cc_start: 0.8938 (mt) cc_final: 0.8628 (mm) REVERT: M 103 GLU cc_start: 0.8449 (tt0) cc_final: 0.8136 (tp30) REVERT: M 133 LEU cc_start: 0.8240 (tp) cc_final: 0.8028 (tp) REVERT: M 282 LYS cc_start: 0.8466 (mtpp) cc_final: 0.7822 (mttm) REVERT: M 285 LEU cc_start: 0.9091 (mp) cc_final: 0.8886 (mp) REVERT: M 293 MET cc_start: 0.7628 (mmp) cc_final: 0.7335 (mpp) REVERT: M 326 PHE cc_start: 0.7715 (m-80) cc_final: 0.7056 (m-80) REVERT: M 391 LEU cc_start: 0.9007 (tp) cc_final: 0.8792 (tt) REVERT: M 396 PHE cc_start: 0.7871 (m-80) cc_final: 0.7390 (m-80) REVERT: N 3 LEU cc_start: 0.8502 (tp) cc_final: 0.8042 (tp) REVERT: N 95 MET cc_start: 0.9070 (mtp) cc_final: 0.8827 (mtp) REVERT: N 103 HIS cc_start: 0.8575 (t-90) cc_final: 0.8123 (t-170) REVERT: N 171 LEU cc_start: 0.9330 (tp) cc_final: 0.9096 (tp) REVERT: N 216 LYS cc_start: 0.8550 (mttp) cc_final: 0.8218 (mttp) REVERT: N 286 LEU cc_start: 0.9557 (tt) cc_final: 0.9343 (tt) REVERT: N 326 PHE cc_start: 0.9275 (t80) cc_final: 0.8561 (t80) REVERT: N 330 MET cc_start: 0.8998 (mmp) cc_final: 0.8663 (mmp) REVERT: N 333 LEU cc_start: 0.8946 (mt) cc_final: 0.8525 (tp) REVERT: N 363 LEU cc_start: 0.8685 (mt) cc_final: 0.7764 (tt) REVERT: H 18 LEU cc_start: 0.9259 (tp) cc_final: 0.9043 (tp) REVERT: H 130 GLU cc_start: 0.8183 (tp30) cc_final: 0.7677 (tp30) REVERT: H 137 PHE cc_start: 0.8599 (p90) cc_final: 0.7817 (p90) REVERT: H 163 GLU cc_start: 0.6552 (tp30) cc_final: 0.6031 (tp30) REVERT: H 181 ASN cc_start: 0.7926 (m-40) cc_final: 0.7721 (t0) REVERT: H 190 LYS cc_start: 0.8860 (tmmt) cc_final: 0.8555 (tmmt) REVERT: H 235 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7626 (mm-30) REVERT: H 281 LEU cc_start: 0.8109 (mt) cc_final: 0.7852 (mt) REVERT: H 304 GLN cc_start: 0.8330 (tp40) cc_final: 0.8122 (tp40) outliers start: 1 outliers final: 0 residues processed: 928 average time/residue: 0.4386 time to fit residues: 685.2243 Evaluate side-chains 706 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 706 time to evaluate : 3.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 426 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 251 optimal weight: 7.9990 chunk 322 optimal weight: 10.0000 chunk 250 optimal weight: 0.9990 chunk 372 optimal weight: 10.0000 chunk 246 optimal weight: 0.0470 chunk 440 optimal weight: 8.9990 chunk 275 optimal weight: 10.0000 chunk 268 optimal weight: 2.9990 chunk 203 optimal weight: 4.9990 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 86 GLN 1 147 GLN ** 3 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 92 HIS ** L 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 434 HIS ** M 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 219 GLN ** N 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.6372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.246 37100 Z= 0.776 Angle : 2.260 50.934 50537 Z= 1.472 Chirality : 0.443 6.406 5672 Planarity : 0.005 0.053 6377 Dihedral : 6.689 178.669 5149 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.70 % Favored : 93.04 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.35 % 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: -0.75 (0.12), residues: 4612 helix: 0.56 (0.11), residues: 2374 sheet: -0.79 (0.33), residues: 256 loop : -1.79 (0.14), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP M 273 HIS 0.007 0.001 HIS H 251 PHE 0.040 0.002 PHE L 382 TYR 0.044 0.002 TYR M 321 ARG 0.012 0.001 ARG 6 180 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 875 time to evaluate : 3.962 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: 1 102 LYS cc_start: 0.8676 (pttt) cc_final: 0.8189 (pttt) REVERT: 1 189 MET cc_start: 0.6373 (mtm) cc_final: 0.5931 (mtm) REVERT: 1 270 THR cc_start: 0.8424 (p) cc_final: 0.8219 (t) REVERT: 1 311 MET cc_start: 0.8453 (mtm) cc_final: 0.8206 (mtm) REVERT: 1 334 ARG cc_start: 0.6431 (mtm-85) cc_final: 0.5924 (ttm110) REVERT: 1 367 MET cc_start: 0.8673 (tmm) cc_final: 0.8302 (tmm) REVERT: 2 9 ASP cc_start: 0.6614 (m-30) cc_final: 0.6242 (t0) REVERT: 2 35 GLN cc_start: 0.8708 (tp40) cc_final: 0.7472 (tm-30) REVERT: 2 69 TYR cc_start: 0.8412 (t80) cc_final: 0.7973 (t80) REVERT: 3 36 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8414 (tm-30) REVERT: 3 47 MET cc_start: 0.8401 (mmm) cc_final: 0.8048 (tpp) REVERT: 3 78 LYS cc_start: 0.8950 (mttt) cc_final: 0.8750 (mtpp) REVERT: 3 113 LEU cc_start: 0.9550 (tp) cc_final: 0.9337 (tp) REVERT: 3 177 ASP cc_start: 0.6728 (m-30) cc_final: 0.6459 (m-30) REVERT: 3 331 GLU cc_start: 0.7242 (tm-30) cc_final: 0.6558 (tm-30) REVERT: 3 459 MET cc_start: 0.8145 (mtt) cc_final: 0.7736 (mtm) REVERT: 3 489 MET cc_start: 0.6046 (mmm) cc_final: 0.5024 (mmt) REVERT: 3 531 LYS cc_start: 0.7315 (mppt) cc_final: 0.6562 (mmtt) REVERT: 3 533 LEU cc_start: 0.8998 (mt) cc_final: 0.8755 (mt) REVERT: 4 67 GLU cc_start: 0.8509 (pm20) cc_final: 0.8258 (pm20) REVERT: 4 138 LEU cc_start: 0.8316 (tp) cc_final: 0.8053 (tp) REVERT: 4 238 SER cc_start: 0.9012 (m) cc_final: 0.8649 (p) REVERT: 4 364 MET cc_start: 0.8901 (mtm) cc_final: 0.8546 (mtm) REVERT: 5 56 ASP cc_start: 0.8367 (t0) cc_final: 0.8137 (t0) REVERT: 5 106 ASP cc_start: 0.8382 (p0) cc_final: 0.8161 (p0) REVERT: 5 115 GLU cc_start: 0.9155 (mp0) cc_final: 0.8732 (mp0) REVERT: 5 170 PHE cc_start: 0.7804 (m-10) cc_final: 0.7555 (m-10) REVERT: 5 177 LYS cc_start: 0.8429 (tttm) cc_final: 0.7938 (tppt) REVERT: 6 50 MET cc_start: 0.8254 (tpt) cc_final: 0.7415 (tpp) REVERT: 6 63 PHE cc_start: 0.8181 (m-80) cc_final: 0.7963 (m-80) REVERT: 6 86 LYS cc_start: 0.8750 (tptt) cc_final: 0.8427 (tttt) REVERT: 6 92 MET cc_start: 0.8676 (tpp) cc_final: 0.8452 (tpp) REVERT: 6 94 ARG cc_start: 0.8884 (ttp80) cc_final: 0.8365 (ttp80) REVERT: 6 120 ASN cc_start: 0.8797 (p0) cc_final: 0.8523 (p0) REVERT: 6 165 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7549 (tp30) REVERT: 9 14 LEU cc_start: 0.8452 (tp) cc_final: 0.8160 (tp) REVERT: 9 44 THR cc_start: 0.8803 (p) cc_final: 0.8479 (t) REVERT: 9 79 ASN cc_start: 0.8434 (m-40) cc_final: 0.7603 (m110) REVERT: 9 105 GLU cc_start: 0.8854 (tt0) cc_final: 0.8317 (tp30) REVERT: 9 126 TYR cc_start: 0.7905 (t80) cc_final: 0.7587 (t80) REVERT: 7 25 GLN cc_start: 0.6972 (pt0) cc_final: 0.4948 (tp-100) REVERT: 7 86 LEU cc_start: 0.8597 (mp) cc_final: 0.8281 (mp) REVERT: 7 90 HIS cc_start: 0.6521 (p90) cc_final: 0.5526 (t70) REVERT: A 56 ARG cc_start: 0.7928 (tpp-160) cc_final: 0.7462 (ptt180) REVERT: A 67 LEU cc_start: 0.9254 (tp) cc_final: 0.8895 (mt) REVERT: A 68 PHE cc_start: 0.8560 (t80) cc_final: 0.8037 (t80) REVERT: A 72 ASP cc_start: 0.8802 (t70) cc_final: 0.8555 (t70) REVERT: A 109 TYR cc_start: 0.8939 (t80) cc_final: 0.8600 (t80) REVERT: J 36 PHE cc_start: 0.8083 (m-10) cc_final: 0.7817 (m-10) REVERT: J 139 LEU cc_start: 0.9222 (tp) cc_final: 0.8946 (tt) REVERT: L 75 PHE cc_start: 0.6928 (t80) cc_final: 0.6703 (t80) REVERT: L 153 ASP cc_start: 0.7572 (m-30) cc_final: 0.7107 (t0) REVERT: L 167 LEU cc_start: 0.7684 (tp) cc_final: 0.7329 (tp) REVERT: L 170 MET cc_start: 0.8509 (mtm) cc_final: 0.8184 (mtm) REVERT: L 192 MET cc_start: 0.7666 (ttp) cc_final: 0.7434 (ttp) REVERT: L 222 LEU cc_start: 0.8374 (pp) cc_final: 0.8095 (pp) REVERT: L 225 TRP cc_start: 0.7960 (p-90) cc_final: 0.7421 (p-90) REVERT: L 265 ASP cc_start: 0.7454 (p0) cc_final: 0.6628 (t70) REVERT: L 442 MET cc_start: 0.5891 (mtt) cc_final: 0.4891 (mtp) REVERT: L 601 LEU cc_start: 0.8345 (mm) cc_final: 0.8138 (mt) REVERT: M 3 VAL cc_start: 0.8290 (t) cc_final: 0.7999 (p) REVERT: M 100 LEU cc_start: 0.8900 (mt) cc_final: 0.8628 (mm) REVERT: M 103 GLU cc_start: 0.8495 (tt0) cc_final: 0.8128 (tp30) REVERT: M 118 PHE cc_start: 0.9268 (t80) cc_final: 0.9001 (t80) REVERT: M 282 LYS cc_start: 0.8514 (mtpp) cc_final: 0.7899 (mttm) REVERT: M 321 TYR cc_start: 0.9054 (p90) cc_final: 0.8609 (p90) REVERT: M 396 PHE cc_start: 0.7950 (m-80) cc_final: 0.7425 (m-80) REVERT: M 443 MET cc_start: 0.8735 (mtp) cc_final: 0.8099 (mtp) REVERT: N 3 LEU cc_start: 0.9088 (tp) cc_final: 0.8701 (tp) REVERT: N 103 HIS cc_start: 0.8402 (t-90) cc_final: 0.7901 (t-170) REVERT: N 124 TRP cc_start: 0.4498 (t-100) cc_final: 0.3862 (t60) REVERT: N 131 GLU cc_start: 0.7949 (mp0) cc_final: 0.7500 (mp0) REVERT: N 216 LYS cc_start: 0.8626 (mttp) cc_final: 0.8272 (mttp) REVERT: N 330 MET cc_start: 0.8980 (mmp) cc_final: 0.8731 (mmp) REVERT: N 333 LEU cc_start: 0.8906 (mt) cc_final: 0.8401 (tp) REVERT: N 363 LEU cc_start: 0.8722 (mt) cc_final: 0.7891 (tt) REVERT: N 409 LEU cc_start: 0.8467 (tp) cc_final: 0.8241 (tp) REVERT: N 410 LEU cc_start: 0.8908 (pt) cc_final: 0.7897 (tt) REVERT: H 18 LEU cc_start: 0.9291 (tp) cc_final: 0.9091 (tp) REVERT: H 35 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7619 (tm-30) REVERT: H 130 GLU cc_start: 0.8260 (tp30) cc_final: 0.7898 (tp30) REVERT: H 137 PHE cc_start: 0.8680 (p90) cc_final: 0.7888 (p90) REVERT: H 163 GLU cc_start: 0.6502 (tp30) cc_final: 0.6114 (tp30) REVERT: H 181 ASN cc_start: 0.7867 (m-40) cc_final: 0.7640 (t0) REVERT: H 190 LYS cc_start: 0.8914 (tmmt) cc_final: 0.8532 (tmmt) REVERT: H 213 GLU cc_start: 0.8504 (tt0) cc_final: 0.8285 (tt0) REVERT: H 235 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7541 (mm-30) REVERT: H 250 ILE cc_start: 0.9365 (mm) cc_final: 0.9125 (mm) REVERT: H 281 LEU cc_start: 0.8361 (mt) cc_final: 0.8044 (mt) outliers start: 0 outliers final: 0 residues processed: 875 average time/residue: 0.4424 time to fit residues: 651.8011 Evaluate side-chains 674 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 674 time to evaluate : 3.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 272 optimal weight: 0.9980 chunk 175 optimal weight: 3.9990 chunk 263 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 280 optimal weight: 0.0980 chunk 300 optimal weight: 10.0000 chunk 217 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 346 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 86 GLN ** 3 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 589 HIS ** L 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 201 GLN N 245 ASN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.6626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.264 37100 Z= 0.762 Angle : 2.239 50.787 50537 Z= 1.463 Chirality : 0.443 6.374 5672 Planarity : 0.005 0.069 6377 Dihedral : 6.369 179.038 5149 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.36 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.35 % 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: -0.50 (0.13), residues: 4612 helix: 0.75 (0.11), residues: 2379 sheet: -0.75 (0.32), residues: 272 loop : -1.64 (0.14), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 420 HIS 0.007 0.001 HIS 3 115 PHE 0.039 0.002 PHE L 328 TYR 0.042 0.001 TYR M 321 ARG 0.007 0.000 ARG L 587 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 938 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 938 time to evaluate : 4.163 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: 1 102 LYS cc_start: 0.8573 (pttt) cc_final: 0.8122 (pttt) REVERT: 1 189 MET cc_start: 0.6054 (mtm) cc_final: 0.5767 (mtm) REVERT: 1 367 MET cc_start: 0.8682 (tmm) cc_final: 0.8247 (tmm) REVERT: 2 35 GLN cc_start: 0.8620 (tp40) cc_final: 0.7614 (tm-30) REVERT: 2 120 GLN cc_start: 0.8183 (tp-100) cc_final: 0.7911 (tp40) REVERT: 3 36 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8448 (tm-30) REVERT: 3 47 MET cc_start: 0.8295 (mmm) cc_final: 0.8021 (tpp) REVERT: 3 113 LEU cc_start: 0.9498 (tp) cc_final: 0.9249 (tp) REVERT: 3 197 ASP cc_start: 0.8266 (m-30) cc_final: 0.8063 (m-30) REVERT: 3 250 GLU cc_start: 0.6718 (tt0) cc_final: 0.6375 (tt0) REVERT: 3 331 GLU cc_start: 0.7158 (tm-30) cc_final: 0.6489 (tm-30) REVERT: 3 459 MET cc_start: 0.8142 (mtt) cc_final: 0.7679 (mtm) REVERT: 3 489 MET cc_start: 0.5718 (mmm) cc_final: 0.4726 (mmt) REVERT: 3 531 LYS cc_start: 0.7396 (mppt) cc_final: 0.6825 (mmtt) REVERT: 3 533 LEU cc_start: 0.8972 (mt) cc_final: 0.8695 (mt) REVERT: 4 50 GLU cc_start: 0.6533 (tp30) cc_final: 0.5126 (pm20) REVERT: 4 67 GLU cc_start: 0.8525 (pm20) cc_final: 0.8183 (pm20) REVERT: 4 130 LEU cc_start: 0.9257 (mm) cc_final: 0.8966 (mt) REVERT: 4 238 SER cc_start: 0.9030 (m) cc_final: 0.8799 (p) REVERT: 4 247 ASP cc_start: 0.8811 (t70) cc_final: 0.8388 (t70) REVERT: 4 276 MET cc_start: 0.8470 (mtt) cc_final: 0.8111 (mtt) REVERT: 4 364 MET cc_start: 0.8935 (mtm) cc_final: 0.8548 (mtm) REVERT: 5 48 PHE cc_start: 0.8315 (t80) cc_final: 0.7852 (t80) REVERT: 5 75 VAL cc_start: 0.8727 (m) cc_final: 0.7985 (m) REVERT: 5 106 ASP cc_start: 0.8353 (p0) cc_final: 0.8149 (p0) REVERT: 5 115 GLU cc_start: 0.9098 (mp0) cc_final: 0.8759 (mp0) REVERT: 5 136 LEU cc_start: 0.8963 (mt) cc_final: 0.8740 (mt) REVERT: 5 177 LYS cc_start: 0.8349 (tttm) cc_final: 0.7863 (tppt) REVERT: 6 27 LEU cc_start: 0.8818 (tp) cc_final: 0.8392 (tp) REVERT: 6 50 MET cc_start: 0.8012 (tpt) cc_final: 0.7125 (tpp) REVERT: 6 73 ARG cc_start: 0.7777 (mmm-85) cc_final: 0.6603 (mmm-85) REVERT: 6 86 LYS cc_start: 0.8617 (tptt) cc_final: 0.8265 (tttt) REVERT: 6 92 MET cc_start: 0.8624 (tpp) cc_final: 0.8350 (tpp) REVERT: 6 97 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7796 (mt-10) REVERT: 6 108 MET cc_start: 0.8127 (ttm) cc_final: 0.7558 (ttp) REVERT: 6 120 ASN cc_start: 0.8811 (p0) cc_final: 0.8598 (p0) REVERT: 6 133 VAL cc_start: 0.8764 (t) cc_final: 0.8492 (t) REVERT: 6 147 LEU cc_start: 0.8812 (tp) cc_final: 0.8568 (tp) REVERT: 9 44 THR cc_start: 0.9008 (p) cc_final: 0.8657 (t) REVERT: 9 79 ASN cc_start: 0.8520 (m-40) cc_final: 0.7759 (m110) REVERT: 9 91 TYR cc_start: 0.9211 (t80) cc_final: 0.7729 (t80) REVERT: 9 105 GLU cc_start: 0.8800 (tt0) cc_final: 0.8291 (tp30) REVERT: 9 113 ILE cc_start: 0.9295 (tt) cc_final: 0.8893 (tt) REVERT: 9 126 TYR cc_start: 0.7705 (t80) cc_final: 0.7351 (t80) REVERT: 7 25 GLN cc_start: 0.7340 (pt0) cc_final: 0.5824 (tp40) REVERT: 7 86 LEU cc_start: 0.8436 (mp) cc_final: 0.8106 (mp) REVERT: 7 90 HIS cc_start: 0.6270 (p90) cc_final: 0.5535 (t70) REVERT: 7 104 VAL cc_start: 0.7994 (m) cc_final: 0.7789 (p) REVERT: A 56 ARG cc_start: 0.7919 (tpp-160) cc_final: 0.7434 (ptt180) REVERT: A 67 LEU cc_start: 0.9208 (tp) cc_final: 0.8958 (mt) REVERT: A 109 TYR cc_start: 0.8969 (t80) cc_final: 0.8298 (t80) REVERT: K 34 MET cc_start: 0.8660 (mmt) cc_final: 0.7967 (mmt) REVERT: L 75 PHE cc_start: 0.6759 (t80) cc_final: 0.6472 (t80) REVERT: L 79 ILE cc_start: 0.9162 (mt) cc_final: 0.8773 (mt) REVERT: L 119 VAL cc_start: 0.9498 (m) cc_final: 0.9296 (m) REVERT: L 127 MET cc_start: 0.8211 (mmm) cc_final: 0.7916 (mmm) REVERT: L 153 ASP cc_start: 0.7368 (m-30) cc_final: 0.7054 (t0) REVERT: L 170 MET cc_start: 0.8439 (mtm) cc_final: 0.8025 (mtm) REVERT: L 192 MET cc_start: 0.7612 (ttp) cc_final: 0.7378 (ttp) REVERT: L 222 LEU cc_start: 0.8160 (pp) cc_final: 0.7856 (pp) REVERT: L 225 TRP cc_start: 0.7774 (p-90) cc_final: 0.7199 (p-90) REVERT: L 265 ASP cc_start: 0.7455 (p0) cc_final: 0.6618 (t70) REVERT: L 286 PHE cc_start: 0.4971 (p90) cc_final: 0.4211 (p90) REVERT: L 442 MET cc_start: 0.5672 (mtt) cc_final: 0.4651 (mtp) REVERT: M 3 VAL cc_start: 0.8135 (t) cc_final: 0.7922 (p) REVERT: M 8 LEU cc_start: 0.8762 (tp) cc_final: 0.8299 (tp) REVERT: M 39 LEU cc_start: 0.7633 (mm) cc_final: 0.6580 (tp) REVERT: M 100 LEU cc_start: 0.8932 (mt) cc_final: 0.8670 (mm) REVERT: M 282 LYS cc_start: 0.8452 (mtpp) cc_final: 0.7912 (mttm) REVERT: M 285 LEU cc_start: 0.8923 (mp) cc_final: 0.8542 (mt) REVERT: M 321 TYR cc_start: 0.8953 (p90) cc_final: 0.8611 (p90) REVERT: M 325 LEU cc_start: 0.8604 (tp) cc_final: 0.8336 (tp) REVERT: M 396 PHE cc_start: 0.7723 (m-80) cc_final: 0.7315 (m-80) REVERT: M 443 MET cc_start: 0.8784 (mtp) cc_final: 0.8265 (mtp) REVERT: N 3 LEU cc_start: 0.9078 (tp) cc_final: 0.8712 (tp) REVERT: N 13 LEU cc_start: 0.9000 (mm) cc_final: 0.8527 (mm) REVERT: N 95 MET cc_start: 0.8945 (mtp) cc_final: 0.8639 (mtp) REVERT: N 103 HIS cc_start: 0.8486 (t-90) cc_final: 0.7643 (t-170) REVERT: N 131 GLU cc_start: 0.7946 (mp0) cc_final: 0.7526 (mp0) REVERT: N 216 LYS cc_start: 0.8535 (mttp) cc_final: 0.8143 (mttp) REVERT: N 326 PHE cc_start: 0.9266 (t80) cc_final: 0.8560 (t80) REVERT: N 330 MET cc_start: 0.8911 (mmp) cc_final: 0.8643 (mmp) REVERT: N 333 LEU cc_start: 0.8686 (mt) cc_final: 0.8301 (tp) REVERT: N 363 LEU cc_start: 0.8575 (mt) cc_final: 0.7962 (tt) REVERT: N 407 VAL cc_start: 0.7842 (t) cc_final: 0.7487 (p) REVERT: N 410 LEU cc_start: 0.8821 (pt) cc_final: 0.7901 (tt) REVERT: H 18 LEU cc_start: 0.9218 (tp) cc_final: 0.8989 (tp) REVERT: H 35 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7168 (tm-30) REVERT: H 43 GLN cc_start: 0.9218 (mt0) cc_final: 0.8883 (pt0) REVERT: H 130 GLU cc_start: 0.8088 (tp30) cc_final: 0.7774 (tp30) REVERT: H 137 PHE cc_start: 0.8291 (p90) cc_final: 0.7441 (p90) REVERT: H 163 GLU cc_start: 0.6471 (tp30) cc_final: 0.6033 (tp30) REVERT: H 170 LEU cc_start: 0.9047 (mt) cc_final: 0.8732 (mt) REVERT: H 235 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7682 (mm-30) REVERT: H 250 ILE cc_start: 0.9261 (mm) cc_final: 0.9034 (mm) REVERT: H 281 LEU cc_start: 0.8267 (mt) cc_final: 0.8024 (mt) outliers start: 0 outliers final: 0 residues processed: 938 average time/residue: 0.4309 time to fit residues: 681.9281 Evaluate side-chains 725 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 725 time to evaluate : 4.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 400 optimal weight: 1.9990 chunk 421 optimal weight: 0.8980 chunk 385 optimal weight: 0.9980 chunk 410 optimal weight: 0.0060 chunk 247 optimal weight: 0.9980 chunk 178 optimal weight: 2.9990 chunk 322 optimal weight: 0.0570 chunk 125 optimal weight: 4.9990 chunk 370 optimal weight: 0.0770 chunk 388 optimal weight: 1.9990 chunk 409 optimal weight: 7.9990 overall best weight: 0.4072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 86 GLN 1 147 GLN 1 386 ASN ** 3 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 428 HIS 3 513 GLN 3 749 HIS L 288 GLN ** L 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 219 GLN M 455 HIS ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.6867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.258 37100 Z= 0.764 Angle : 2.236 50.771 50537 Z= 1.461 Chirality : 0.443 6.357 5672 Planarity : 0.005 0.052 6377 Dihedral : 6.180 179.668 5149 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.18 % Favored : 94.62 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.35 % 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: -0.34 (0.13), residues: 4612 helix: 0.85 (0.11), residues: 2363 sheet: -0.68 (0.32), residues: 270 loop : -1.50 (0.14), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 195 HIS 0.007 0.001 HIS M 292 PHE 0.022 0.001 PHE J 137 TYR 0.038 0.001 TYR M 321 ARG 0.010 0.000 ARG 6 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 938 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 938 time to evaluate : 4.052 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: 1 95 GLU cc_start: 0.6728 (tt0) cc_final: 0.6482 (tt0) REVERT: 1 102 LYS cc_start: 0.8556 (pttt) cc_final: 0.7914 (pttt) REVERT: 1 189 MET cc_start: 0.6006 (mtm) cc_final: 0.5702 (mtm) REVERT: 1 240 GLN cc_start: 0.6731 (mp10) cc_final: 0.5770 (tm-30) REVERT: 1 334 ARG cc_start: 0.6561 (mtm-85) cc_final: 0.6150 (ttm110) REVERT: 1 367 MET cc_start: 0.8129 (tmm) cc_final: 0.7840 (tmm) REVERT: 2 35 GLN cc_start: 0.8162 (tp40) cc_final: 0.7661 (tm-30) REVERT: 3 36 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8312 (tm-30) REVERT: 3 47 MET cc_start: 0.8329 (mmm) cc_final: 0.8013 (tpp) REVERT: 3 197 ASP cc_start: 0.8284 (m-30) cc_final: 0.8074 (m-30) REVERT: 3 331 GLU cc_start: 0.7098 (tm-30) cc_final: 0.6482 (tm-30) REVERT: 3 353 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8107 (mm-30) REVERT: 3 459 MET cc_start: 0.8232 (mtt) cc_final: 0.7724 (mtm) REVERT: 3 489 MET cc_start: 0.5657 (mmm) cc_final: 0.4607 (mmt) REVERT: 3 531 LYS cc_start: 0.7273 (mppt) cc_final: 0.6761 (mmtt) REVERT: 3 533 LEU cc_start: 0.9069 (mt) cc_final: 0.8805 (mt) REVERT: 4 50 GLU cc_start: 0.6514 (tp30) cc_final: 0.5066 (pm20) REVERT: 4 67 GLU cc_start: 0.8515 (pm20) cc_final: 0.8231 (pm20) REVERT: 4 71 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8281 (mt-10) REVERT: 4 159 LEU cc_start: 0.8596 (tt) cc_final: 0.8323 (mm) REVERT: 4 238 SER cc_start: 0.8840 (m) cc_final: 0.8524 (p) REVERT: 4 247 ASP cc_start: 0.8830 (t70) cc_final: 0.8444 (t70) REVERT: 4 269 ARG cc_start: 0.7860 (ptt-90) cc_final: 0.7209 (ptt-90) REVERT: 4 364 MET cc_start: 0.8924 (mtm) cc_final: 0.8642 (mtm) REVERT: 5 48 PHE cc_start: 0.8338 (t80) cc_final: 0.8083 (t80) REVERT: 5 115 GLU cc_start: 0.9101 (mp0) cc_final: 0.8701 (mp0) REVERT: 5 136 LEU cc_start: 0.8845 (mt) cc_final: 0.8546 (mt) REVERT: 5 177 LYS cc_start: 0.8317 (tttm) cc_final: 0.7834 (tppt) REVERT: 6 27 LEU cc_start: 0.8869 (tp) cc_final: 0.8482 (tp) REVERT: 6 35 SER cc_start: 0.9069 (t) cc_final: 0.7949 (t) REVERT: 6 36 LEU cc_start: 0.9035 (mt) cc_final: 0.8831 (mt) REVERT: 6 50 MET cc_start: 0.7802 (tpt) cc_final: 0.7174 (tpp) REVERT: 6 86 LYS cc_start: 0.8687 (tptt) cc_final: 0.8219 (tttt) REVERT: 6 92 MET cc_start: 0.8558 (tpp) cc_final: 0.8310 (tpp) REVERT: 6 98 GLN cc_start: 0.8179 (mp-120) cc_final: 0.7939 (mm-40) REVERT: 6 108 MET cc_start: 0.7953 (ttm) cc_final: 0.7631 (tpp) REVERT: 6 126 ASN cc_start: 0.7881 (t0) cc_final: 0.7667 (t0) REVERT: 9 44 THR cc_start: 0.9047 (p) cc_final: 0.8701 (t) REVERT: 9 79 ASN cc_start: 0.8497 (m-40) cc_final: 0.7710 (m110) REVERT: 9 105 GLU cc_start: 0.8884 (tt0) cc_final: 0.8424 (tt0) REVERT: 9 126 TYR cc_start: 0.7802 (t80) cc_final: 0.7381 (t80) REVERT: 9 149 GLU cc_start: 0.8011 (tt0) cc_final: 0.7322 (mm-30) REVERT: 7 25 GLN cc_start: 0.7334 (pt0) cc_final: 0.5879 (tp40) REVERT: 7 86 LEU cc_start: 0.8390 (mp) cc_final: 0.8093 (mp) REVERT: 7 90 HIS cc_start: 0.6442 (p90) cc_final: 0.5830 (t70) REVERT: A 56 ARG cc_start: 0.7880 (tpp-160) cc_final: 0.7351 (ptt180) REVERT: A 67 LEU cc_start: 0.9146 (tp) cc_final: 0.8889 (mt) REVERT: A 109 TYR cc_start: 0.8956 (t80) cc_final: 0.8558 (t80) REVERT: J 113 LEU cc_start: 0.7378 (mt) cc_final: 0.7103 (mt) REVERT: K 34 MET cc_start: 0.8490 (mmt) cc_final: 0.8256 (mmt) REVERT: L 24 MET cc_start: 0.3299 (tpp) cc_final: 0.3048 (mmp) REVERT: L 79 ILE cc_start: 0.9023 (mt) cc_final: 0.8544 (mt) REVERT: L 127 MET cc_start: 0.8075 (mmm) cc_final: 0.7785 (mmm) REVERT: L 167 LEU cc_start: 0.7786 (tp) cc_final: 0.7549 (tp) REVERT: L 192 MET cc_start: 0.7648 (ttp) cc_final: 0.7428 (ttp) REVERT: L 216 LYS cc_start: 0.7992 (mmtt) cc_final: 0.7570 (mttt) REVERT: L 225 TRP cc_start: 0.7613 (p-90) cc_final: 0.7001 (p-90) REVERT: L 265 ASP cc_start: 0.7498 (p0) cc_final: 0.6635 (t70) REVERT: L 286 PHE cc_start: 0.4845 (p90) cc_final: 0.4237 (p90) REVERT: L 442 MET cc_start: 0.6392 (mtt) cc_final: 0.5048 (mtp) REVERT: L 533 TYR cc_start: 0.5783 (m-80) cc_final: 0.5433 (m-10) REVERT: M 39 LEU cc_start: 0.7519 (mm) cc_final: 0.6613 (tp) REVERT: M 132 MET cc_start: 0.8542 (mtm) cc_final: 0.8022 (mtm) REVERT: M 285 LEU cc_start: 0.8873 (mp) cc_final: 0.8505 (mt) REVERT: M 293 MET cc_start: 0.8310 (mpp) cc_final: 0.8067 (mpp) REVERT: M 325 LEU cc_start: 0.8597 (tp) cc_final: 0.8333 (tp) REVERT: M 396 PHE cc_start: 0.7620 (m-80) cc_final: 0.7152 (m-80) REVERT: N 3 LEU cc_start: 0.8945 (tp) cc_final: 0.8529 (tp) REVERT: N 13 LEU cc_start: 0.9020 (mm) cc_final: 0.8585 (mm) REVERT: N 93 LEU cc_start: 0.9425 (mp) cc_final: 0.9131 (mm) REVERT: N 95 MET cc_start: 0.8889 (mtp) cc_final: 0.8625 (mtp) REVERT: N 103 HIS cc_start: 0.8498 (t-90) cc_final: 0.7628 (t-170) REVERT: N 131 GLU cc_start: 0.7989 (mp0) cc_final: 0.7462 (mp0) REVERT: N 153 LEU cc_start: 0.9287 (mm) cc_final: 0.9076 (mm) REVERT: N 326 PHE cc_start: 0.9249 (t80) cc_final: 0.8493 (t80) REVERT: N 330 MET cc_start: 0.8916 (mmp) cc_final: 0.8642 (mmp) REVERT: N 333 LEU cc_start: 0.8820 (mt) cc_final: 0.8194 (tp) REVERT: N 363 LEU cc_start: 0.8576 (mt) cc_final: 0.7988 (tt) REVERT: N 374 TYR cc_start: 0.8755 (p90) cc_final: 0.8534 (p90) REVERT: N 397 TRP cc_start: 0.6178 (t-100) cc_final: 0.5331 (t60) REVERT: N 407 VAL cc_start: 0.7866 (t) cc_final: 0.7513 (p) REVERT: N 410 LEU cc_start: 0.8811 (pt) cc_final: 0.7952 (tt) REVERT: H 35 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7234 (tm-30) REVERT: H 130 GLU cc_start: 0.8042 (tp30) cc_final: 0.7660 (tp30) REVERT: H 137 PHE cc_start: 0.8184 (p90) cc_final: 0.7291 (p90) REVERT: H 163 GLU cc_start: 0.6395 (tp30) cc_final: 0.5982 (tp30) REVERT: H 250 ILE cc_start: 0.9225 (mm) cc_final: 0.8950 (mm) REVERT: H 281 LEU cc_start: 0.8255 (mt) cc_final: 0.8023 (mt) outliers start: 0 outliers final: 0 residues processed: 938 average time/residue: 0.4482 time to fit residues: 705.5209 Evaluate side-chains 737 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 737 time to evaluate : 3.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 269 optimal weight: 0.9990 chunk 434 optimal weight: 0.8980 chunk 264 optimal weight: 1.9990 chunk 205 optimal weight: 0.8980 chunk 301 optimal weight: 10.0000 chunk 455 optimal weight: 4.9990 chunk 419 optimal weight: 0.7980 chunk 362 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 280 optimal weight: 0.9990 chunk 222 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 86 GLN ** 3 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 315 HIS J 125 GLN ** K 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 GLN N 193 HIS ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 251 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.7018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.256 37100 Z= 0.763 Angle : 2.241 50.787 50537 Z= 1.463 Chirality : 0.442 6.363 5672 Planarity : 0.005 0.059 6377 Dihedral : 6.085 179.283 5149 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.33 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.35 % 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: -0.28 (0.13), residues: 4612 helix: 0.83 (0.11), residues: 2368 sheet: -0.57 (0.32), residues: 260 loop : -1.38 (0.14), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP N 124 HIS 0.018 0.001 HIS H 192 PHE 0.032 0.002 PHE M 12 TYR 0.025 0.001 TYR J 59 ARG 0.010 0.000 ARG 6 94 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9224 Ramachandran restraints generated. 4612 Oldfield, 0 Emsley, 4612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 896 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 896 time to evaluate : 4.041 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: 1 79 MET cc_start: 0.8490 (tpt) cc_final: 0.7603 (tpp) REVERT: 1 95 GLU cc_start: 0.6781 (tt0) cc_final: 0.6454 (tt0) REVERT: 1 102 LYS cc_start: 0.8433 (pttt) cc_final: 0.7970 (pttt) REVERT: 1 189 MET cc_start: 0.5948 (mtm) cc_final: 0.5671 (mtm) REVERT: 1 240 GLN cc_start: 0.6515 (mp10) cc_final: 0.5526 (tm-30) REVERT: 1 241 MET cc_start: 0.5302 (mtm) cc_final: 0.4776 (ptp) REVERT: 1 334 ARG cc_start: 0.6704 (mtm-85) cc_final: 0.6344 (ttm110) REVERT: 1 367 MET cc_start: 0.8231 (tmm) cc_final: 0.7856 (tmm) REVERT: 2 35 GLN cc_start: 0.8349 (tp40) cc_final: 0.7737 (tm-30) REVERT: 3 36 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8466 (tm-30) REVERT: 3 47 MET cc_start: 0.8234 (mmm) cc_final: 0.7929 (tpt) REVERT: 3 113 LEU cc_start: 0.9481 (tp) cc_final: 0.9226 (tp) REVERT: 3 331 GLU cc_start: 0.7112 (tm-30) cc_final: 0.6540 (tm-30) REVERT: 3 353 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8270 (mm-30) REVERT: 3 459 MET cc_start: 0.8114 (mtt) cc_final: 0.7665 (mtm) REVERT: 3 489 MET cc_start: 0.5301 (mmm) cc_final: 0.4348 (mmt) REVERT: 3 531 LYS cc_start: 0.7315 (mppt) cc_final: 0.6832 (mmtt) REVERT: 3 533 LEU cc_start: 0.8931 (mt) cc_final: 0.8683 (mt) REVERT: 4 67 GLU cc_start: 0.8279 (pm20) cc_final: 0.7993 (pm20) REVERT: 4 238 SER cc_start: 0.8835 (m) cc_final: 0.8553 (p) REVERT: 4 269 ARG cc_start: 0.8007 (ptt-90) cc_final: 0.7291 (ptt-90) REVERT: 4 285 GLU cc_start: 0.7383 (tp30) cc_final: 0.7173 (tp30) REVERT: 4 364 MET cc_start: 0.8906 (mtm) cc_final: 0.8647 (ttm) REVERT: 5 115 GLU cc_start: 0.9091 (mp0) cc_final: 0.8575 (mp0) REVERT: 5 136 LEU cc_start: 0.8826 (mt) cc_final: 0.8568 (mt) REVERT: 5 177 LYS cc_start: 0.8321 (tttm) cc_final: 0.7835 (tppt) REVERT: 6 50 MET cc_start: 0.7519 (tpt) cc_final: 0.6792 (tpp) REVERT: 6 68 PHE cc_start: 0.6086 (m-10) cc_final: 0.5425 (m-10) REVERT: 6 86 LYS cc_start: 0.8659 (tptt) cc_final: 0.8204 (tttt) REVERT: 6 133 VAL cc_start: 0.8704 (t) cc_final: 0.8469 (t) REVERT: 9 44 THR cc_start: 0.9010 (p) cc_final: 0.8659 (t) REVERT: 9 79 ASN cc_start: 0.8499 (m-40) cc_final: 0.7722 (m110) REVERT: 9 105 GLU cc_start: 0.8912 (tt0) cc_final: 0.8576 (tt0) REVERT: 9 126 TYR cc_start: 0.7735 (t80) cc_final: 0.7359 (t80) REVERT: 9 149 GLU cc_start: 0.7969 (tt0) cc_final: 0.7278 (mm-30) REVERT: 7 50 LEU cc_start: 0.7966 (mm) cc_final: 0.7631 (mt) REVERT: 7 86 LEU cc_start: 0.8293 (mp) cc_final: 0.7899 (mp) REVERT: 7 90 HIS cc_start: 0.6349 (p90) cc_final: 0.5875 (t70) REVERT: A 56 ARG cc_start: 0.7899 (tpp-160) cc_final: 0.7339 (ptt180) REVERT: A 67 LEU cc_start: 0.9200 (tp) cc_final: 0.8902 (mt) REVERT: A 103 LEU cc_start: 0.9174 (mm) cc_final: 0.8565 (tt) REVERT: A 109 TYR cc_start: 0.8949 (t80) cc_final: 0.8543 (t80) REVERT: J 120 LYS cc_start: 0.8132 (mtmm) cc_final: 0.7868 (mptt) REVERT: L 75 PHE cc_start: 0.6770 (t80) cc_final: 0.6510 (t80) REVERT: L 79 ILE cc_start: 0.9108 (mt) cc_final: 0.8789 (mt) REVERT: L 107 TYR cc_start: 0.8268 (m-10) cc_final: 0.7981 (m-80) REVERT: L 128 PHE cc_start: 0.8315 (t80) cc_final: 0.6979 (t80) REVERT: L 192 MET cc_start: 0.7723 (ttp) cc_final: 0.7489 (ttp) REVERT: L 216 LYS cc_start: 0.7944 (mmtt) cc_final: 0.7396 (mttt) REVERT: L 222 LEU cc_start: 0.7759 (pp) cc_final: 0.7555 (pp) REVERT: L 225 TRP cc_start: 0.7373 (p-90) cc_final: 0.6723 (p-90) REVERT: L 265 ASP cc_start: 0.7524 (p0) cc_final: 0.6656 (t70) REVERT: L 286 PHE cc_start: 0.4758 (p90) cc_final: 0.4251 (p90) REVERT: L 442 MET cc_start: 0.6327 (mtt) cc_final: 0.5094 (mtp) REVERT: L 529 ARG cc_start: 0.7165 (ttp-110) cc_final: 0.6861 (ttp-110) REVERT: M 39 LEU cc_start: 0.7502 (mm) cc_final: 0.6586 (tp) REVERT: M 94 ARG cc_start: 0.6981 (pmt170) cc_final: 0.6460 (pmt-80) REVERT: M 246 ILE cc_start: 0.7926 (mp) cc_final: 0.7474 (mt) REVERT: M 293 MET cc_start: 0.8371 (mpp) cc_final: 0.8075 (mpp) REVERT: M 396 PHE cc_start: 0.7664 (m-80) cc_final: 0.7320 (m-80) REVERT: N 3 LEU cc_start: 0.8964 (tp) cc_final: 0.8518 (tp) REVERT: N 95 MET cc_start: 0.9004 (mtp) cc_final: 0.8628 (mtp) REVERT: N 103 HIS cc_start: 0.8463 (t-90) cc_final: 0.7521 (t-170) REVERT: N 131 GLU cc_start: 0.7980 (mp0) cc_final: 0.7474 (mp0) REVERT: N 326 PHE cc_start: 0.9221 (t80) cc_final: 0.8508 (t80) REVERT: N 330 MET cc_start: 0.8915 (mmp) cc_final: 0.8678 (mmp) REVERT: N 333 LEU cc_start: 0.8878 (mt) cc_final: 0.8332 (tp) REVERT: N 363 LEU cc_start: 0.8596 (mt) cc_final: 0.7931 (tt) REVERT: N 397 TRP cc_start: 0.6219 (t-100) cc_final: 0.5460 (t60) REVERT: N 410 LEU cc_start: 0.8815 (pt) cc_final: 0.7978 (tt) REVERT: H 35 GLU cc_start: 0.7368 (tm-30) cc_final: 0.7000 (tm-30) REVERT: H 130 GLU cc_start: 0.8119 (tp30) cc_final: 0.7719 (tp30) REVERT: H 137 PHE cc_start: 0.8256 (p90) cc_final: 0.7404 (p90) REVERT: H 149 LEU cc_start: 0.8924 (tp) cc_final: 0.8722 (tp) REVERT: H 182 LEU cc_start: 0.9344 (mt) cc_final: 0.9067 (mm) REVERT: H 235 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7116 (mm-30) REVERT: H 250 ILE cc_start: 0.9257 (mm) cc_final: 0.8973 (mm) REVERT: H 281 LEU cc_start: 0.8252 (mt) cc_final: 0.8000 (mt) REVERT: H 304 GLN cc_start: 0.8028 (tp40) cc_final: 0.7809 (tp40) outliers start: 0 outliers final: 0 residues processed: 896 average time/residue: 0.4205 time to fit residues: 633.9954 Evaluate side-chains 710 residues out of total 3657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 710 time to evaluate : 4.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 287 optimal weight: 6.9990 chunk 386 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 334 optimal weight: 0.9990 chunk 53 optimal weight: 0.3980 chunk 100 optimal weight: 0.1980 chunk 363 optimal weight: 1.9990 chunk 151 optimal weight: 0.1980 chunk 372 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 86 GLN 1 147 GLN 1 420 GLN ** 3 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 410 HIS 4 129 HIS ** L 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.119271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.106676 restraints weight = 83585.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.107560 restraints weight = 59570.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.109124 restraints weight = 46619.419| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.7151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.257 37100 Z= 0.764 Angle : 2.240 50.781 50537 Z= 1.462 Chirality : 0.443 6.356 5672 Planarity : 0.005 0.061 6377 Dihedral : 6.050 179.164 5149 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.10 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.87 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.13), residues: 4612 helix: 0.85 (0.11), residues: 2368 sheet: -0.52 (0.32), residues: 260 loop : -1.37 (0.14), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 6 176 HIS 0.020 0.001 HIS H 192 PHE 0.054 0.002 PHE L 328 TYR 0.034 0.001 TYR M 449 ARG 0.010 0.000 ARG 6 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11208.12 seconds wall clock time: 200 minutes 6.17 seconds (12006.17 seconds total)