Starting phenix.real_space_refine on Thu Apr 11 23:51:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ow1_17227/04_2024/8ow1_17227.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ow1_17227/04_2024/8ow1_17227.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ow1_17227/04_2024/8ow1_17227.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ow1_17227/04_2024/8ow1_17227.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ow1_17227/04_2024/8ow1_17227.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ow1_17227/04_2024/8ow1_17227.pdb" } resolution = 3.7 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 306 5.49 5 S 293 5.16 5 C 49258 2.51 5 N 13467 2.21 5 O 15347 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 236": "OE1" <-> "OE2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A GLU 265": "OE1" <-> "OE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A GLU 312": "OE1" <-> "OE2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "A GLU 323": "OE1" <-> "OE2" Residue "A GLU 328": "OE1" <-> "OE2" Residue "B GLU 231": "OE1" <-> "OE2" Residue "B ARG 234": "NH1" <-> "NH2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "B GLU 253": "OE1" <-> "OE2" Residue "B GLU 279": "OE1" <-> "OE2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "B GLU 305": "OE1" <-> "OE2" Residue "B GLU 312": "OE1" <-> "OE2" Residue "B GLU 323": "OE1" <-> "OE2" Residue "I GLU 33": "OE1" <-> "OE2" Residue "I GLU 80": "OE1" <-> "OE2" Residue "I GLU 84": "OE1" <-> "OE2" Residue "I ARG 99": "NH1" <-> "NH2" Residue "I ARG 193": "NH1" <-> "NH2" Residue "I GLU 261": "OE1" <-> "OE2" Residue "I TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 328": "NH1" <-> "NH2" Residue "I TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 373": "OE1" <-> "OE2" Residue "I TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 410": "OE1" <-> "OE2" Residue "I GLU 460": "OE1" <-> "OE2" Residue "I ASP 529": "OD1" <-> "OD2" Residue "I ARG 579": "NH1" <-> "NH2" Residue "I PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 654": "OE1" <-> "OE2" Residue "I GLU 668": "OE1" <-> "OE2" Residue "I ARG 712": "NH1" <-> "NH2" Residue "I PHE 717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 16": "OE1" <-> "OE2" Residue "K TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 34": "OD1" <-> "OD2" Residue "K GLU 55": "OE1" <-> "OE2" Residue "K ARG 119": "NH1" <-> "NH2" Residue "K GLU 235": "OE1" <-> "OE2" Residue "H GLU 16": "OE1" <-> "OE2" Residue "H ARG 32": "NH1" <-> "NH2" Residue "H ARG 51": "NH1" <-> "NH2" Residue "H GLU 64": "OE1" <-> "OE2" Residue "H GLU 153": "OE1" <-> "OE2" Residue "H GLU 157": "OE1" <-> "OE2" Residue "H GLU 163": "OE1" <-> "OE2" Residue "LL GLU 30": "OE1" <-> "OE2" Residue "LL GLU 57": "OE1" <-> "OE2" Residue "LL PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LL GLU 82": "OE1" <-> "OE2" Residue "LL GLU 138": "OE1" <-> "OE2" Residue "LL GLU 152": "OE1" <-> "OE2" Residue "LL PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LL GLU 168": "OE1" <-> "OE2" Residue "LL PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NN GLU 8": "OE1" <-> "OE2" Residue "NN ARG 67": "NH1" <-> "NH2" Residue "NN ARG 68": "NH1" <-> "NH2" Residue "NN PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NN GLU 130": "OE1" <-> "OE2" Residue "NN PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NN ARG 158": "NH1" <-> "NH2" Residue "NN PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NN ASP 163": "OD1" <-> "OD2" Residue "NN PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NN PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NN TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NN TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NN GLU 301": "OE1" <-> "OE2" Residue "NN PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NN GLU 317": "OE1" <-> "OE2" Residue "NN PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NN TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NN GLU 392": "OE1" <-> "OE2" Residue "NN ASP 425": "OD1" <-> "OD2" Residue "NN PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CT PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CT PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CT ARG 17": "NH1" <-> "NH2" Residue "CT PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CT PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CT GLU 78": "OE1" <-> "OE2" Residue "CT TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CT GLU 85": "OE1" <-> "OE2" Residue "CT GLU 89": "OE1" <-> "OE2" Residue "CT TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CT TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CT ARG 128": "NH1" <-> "NH2" Residue "CT GLU 146": "OE1" <-> "OE2" Residue "CT TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CT PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CT GLU 159": "OE1" <-> "OE2" Residue "CT GLU 281": "OE1" <-> "OE2" Residue "CT TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CT GLU 373": "OE1" <-> "OE2" Residue "CT GLU 379": "OE1" <-> "OE2" Residue "CT TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CT PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CT ARG 410": "NH1" <-> "NH2" Residue "CT GLU 418": "OE1" <-> "OE2" Residue "CT GLU 466": "OE1" <-> "OE2" Residue "CT TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ce ARG 87": "NH1" <-> "NH2" Residue "ce GLU 141": "OE1" <-> "OE2" Residue "ce ASP 145": "OD1" <-> "OD2" Residue "ce ARG 147": "NH1" <-> "NH2" Residue "ce TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ce PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ce TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ce TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ce PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ce ARG 307": "NH1" <-> "NH2" Residue "ce GLU 342": "OE1" <-> "OE2" Residue "ce TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ce GLU 376": "OE1" <-> "OE2" Residue "ce GLU 388": "OE1" <-> "OE2" Residue "ce GLU 389": "OE1" <-> "OE2" Residue "ce PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ce TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ce GLU 478": "OE1" <-> "OE2" Residue "ce GLU 512": "OE1" <-> "OE2" Residue "ce ASP 544": "OD1" <-> "OD2" Residue "ce GLU 549": "OE1" <-> "OE2" Residue "ce ARG 591": "NH1" <-> "NH2" Residue "ce PHE 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ce TYR 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 30": "OE1" <-> "OE2" Residue "L GLU 57": "OE1" <-> "OE2" Residue "L PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 82": "OE1" <-> "OE2" Residue "L GLU 138": "OE1" <-> "OE2" Residue "L GLU 152": "OE1" <-> "OE2" Residue "L PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 168": "OE1" <-> "OE2" Residue "L PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SK GLU 12": "OE1" <-> "OE2" Residue "SK ARG 15": "NH1" <-> "NH2" Residue "SK ARG 25": "NH1" <-> "NH2" Residue "SK GLU 74": "OE1" <-> "OE2" Residue "SK ARG 83": "NH1" <-> "NH2" Residue "SK GLU 92": "OE1" <-> "OE2" Residue "SK ARG 98": "NH1" <-> "NH2" Residue "SK PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SK GLU 105": "OE1" <-> "OE2" Residue "SK ASP 107": "OD1" <-> "OD2" Residue "SK ASP 117": "OD1" <-> "OD2" Residue "SK ARG 121": "NH1" <-> "NH2" Residue "SK ARG 159": "NH1" <-> "NH2" Residue "SK ARG 161": "NH1" <-> "NH2" Residue "SK ARG 168": "NH1" <-> "NH2" Residue "SK PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SK ARG 185": "NH1" <-> "NH2" Residue "SK ARG 186": "NH1" <-> "NH2" Residue "CE ARG 19": "NH1" <-> "NH2" Residue "CE ARG 26": "NH1" <-> "NH2" Residue "CE ARG 36": "NH1" <-> "NH2" Residue "CE GLU 41": "OE1" <-> "OE2" Residue "CE TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE ARG 87": "NH1" <-> "NH2" Residue "CE GLU 120": "OE1" <-> "OE2" Residue "CE TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE GLU 141": "OE1" <-> "OE2" Residue "CE TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE ASP 160": "OD1" <-> "OD2" Residue "CE TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE GLU 177": "OE1" <-> "OE2" Residue "CE ASP 230": "OD1" <-> "OD2" Residue "CE GLU 249": "OE1" <-> "OE2" Residue "CE PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE ASP 354": "OD1" <-> "OD2" Residue "CE ASP 385": "OD1" <-> "OD2" Residue "CE GLU 388": "OE1" <-> "OE2" Residue "CE PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE ARG 392": "NH1" <-> "NH2" Residue "CE TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE GLU 478": "OE1" <-> "OE2" Residue "CE PHE 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE ASP 528": "OD1" <-> "OD2" Residue "CE TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE GLU 549": "OE1" <-> "OE2" Residue "CE PHE 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE ARG 591": "NH1" <-> "NH2" Residue "CE GLU 600": "OE1" <-> "OE2" Residue "P ARG 124": "NH1" <-> "NH2" Residue "P GLU 126": "OE1" <-> "OE2" Residue "P TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 209": "OD1" <-> "OD2" Residue "P TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 246": "OE1" <-> "OE2" Residue "P ARG 267": "NH1" <-> "NH2" Residue "P TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 129": "OE1" <-> "OE2" Residue "Q GLU 137": "OE1" <-> "OE2" Residue "Q GLU 184": "OE1" <-> "OE2" Residue "Q GLU 195": "OE1" <-> "OE2" Residue "Q ARG 226": "NH1" <-> "NH2" Residue "Q ARG 230": "NH1" <-> "NH2" Residue "Q TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 251": "OE1" <-> "OE2" Residue "Q ARG 264": "NH1" <-> "NH2" Residue "Q GLU 265": "OE1" <-> "OE2" Residue "Q ARG 286": "NH1" <-> "NH2" Residue "Q GLU 305": "OE1" <-> "OE2" Residue "Q TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 331": "OE1" <-> "OE2" Residue "Q GLU 385": "OE1" <-> "OE2" Residue "Q GLU 388": "OE1" <-> "OE2" Residue "Q PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "OO GLU 159": "OE1" <-> "OE2" Residue "OO GLU 167": "OE1" <-> "OE2" Residue "OO TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "OO ASP 198": "OD1" <-> "OD2" Residue "OO ARG 212": "NH1" <-> "NH2" Residue "OO PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "OO GLU 217": "OE1" <-> "OE2" Residue "OO TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "OO ARG 227": "NH1" <-> "NH2" Residue "OO PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "OO PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "OO ASP 251": "OD1" <-> "OD2" Residue "OO ASP 252": "OD1" <-> "OD2" Residue "OO GLU 289": "OE1" <-> "OE2" Residue "OO PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "OO ASP 312": "OD1" <-> "OD2" Residue "OO PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "OO GLU 323": "OE1" <-> "OE2" Residue "OO ASP 331": "OD1" <-> "OD2" Residue "OO GLU 345": "OE1" <-> "OE2" Residue "OO GLU 356": "OE1" <-> "OE2" Residue "N GLU 4": "OE1" <-> "OE2" Residue "N GLU 8": "OE1" <-> "OE2" Residue "N GLU 63": "OE1" <-> "OE2" Residue "N TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 91": "OE1" <-> "OE2" Residue "N PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 158": "NH1" <-> "NH2" Residue "N PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 304": "OD1" <-> "OD2" Residue "N GLU 320": "OE1" <-> "OE2" Residue "N PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 392": "OE1" <-> "OE2" Residue "N GLU 415": "OE1" <-> "OE2" Residue "N GLU 450": "OE1" <-> "OE2" Residue "T GLU 303": "OE1" <-> "OE2" Residue "T GLU 342": "OE1" <-> "OE2" Residue "T GLU 357": "OE1" <-> "OE2" Residue "U PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 191": "OD1" <-> "OD2" Residue "U GLU 201": "OE1" <-> "OE2" Residue "U TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 212": "NH1" <-> "NH2" Residue "U GLU 214": "OE1" <-> "OE2" Residue "U GLU 229": "OE1" <-> "OE2" Residue "U GLU 242": "OE1" <-> "OE2" Residue "U ASP 300": "OD1" <-> "OD2" Residue "PP ARG 124": "NH1" <-> "NH2" Residue "PP ASP 173": "OD1" <-> "OD2" Residue "PP GLU 181": "OE1" <-> "OE2" Residue "PP TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "PP GLU 198": "OE1" <-> "OE2" Residue "PP GLU 246": "OE1" <-> "OE2" Residue "PP ARG 267": "NH1" <-> "NH2" Residue "PP ASP 278": "OD1" <-> "OD2" Residue "PP ARG 284": "NH1" <-> "NH2" Residue "PP ARG 287": "NH1" <-> "NH2" Residue "PP PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "PP GLU 307": "OE1" <-> "OE2" Residue "PP GLU 330": "OE1" <-> "OE2" Residue "PP ASP 336": "OD1" <-> "OD2" Residue "PP TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 68": "OE1" <-> "OE2" Residue "W GLU 79": "OE1" <-> "OE2" Residue "W PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 200": "OE1" <-> "OE2" Residue "O GLU 211": "OE1" <-> "OE2" Residue "O ARG 212": "NH1" <-> "NH2" Residue "O TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 252": "OD1" <-> "OD2" Residue "O ASP 263": "OD1" <-> "OD2" Residue "O PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 296": "OD1" <-> "OD2" Residue "O PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 354": "OD1" <-> "OD2" Residue "Y TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 50": "NH1" <-> "NH2" Residue "Y ASP 68": "OD1" <-> "OD2" Residue "Y TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 161": "OE1" <-> "OE2" Residue "Y GLU 183": "OE1" <-> "OE2" Residue "Y TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 4": "OE1" <-> "OE2" Residue "Z TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 49": "NH1" <-> "NH2" Residue "Z ARG 52": "NH1" <-> "NH2" Residue "Z PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 109": "OD1" <-> "OD2" Residue "UU GLU 147": "OE1" <-> "OE2" Residue "UU PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "UU PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "UU ARG 212": "NH1" <-> "NH2" Residue "UU GLU 226": "OE1" <-> "OE2" Residue "UU GLU 242": "OE1" <-> "OE2" Residue "UU ASP 286": "OD1" <-> "OD2" Residue "UU PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "UU ASP 300": "OD1" <-> "OD2" Residue "YY TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "YY ARG 50": "NH1" <-> "NH2" Residue "YY ASP 68": "OD1" <-> "OD2" Residue "YY TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "YY GLU 161": "OE1" <-> "OE2" Residue "YY GLU 183": "OE1" <-> "OE2" Residue "YY TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ZZ TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ZZ ARG 49": "NH1" <-> "NH2" Residue "ZZ ARG 52": "NH1" <-> "NH2" Residue "ZZ GLU 79": "OE1" <-> "OE2" Residue "ZZ TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ZZ GLU 118": "OE1" <-> "OE2" Residue "ZZ GLU 123": "OE1" <-> "OE2" Residue "II ARG 18": "NH1" <-> "NH2" Residue "II GLU 54": "OE1" <-> "OE2" Residue "II ARG 99": "NH1" <-> "NH2" Residue "II ARG 127": "NH1" <-> "NH2" Residue "II PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "II ARG 193": "NH1" <-> "NH2" Residue "II ARG 240": "NH1" <-> "NH2" Residue "II ASP 313": "OD1" <-> "OD2" Residue "II TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "II ARG 328": "NH1" <-> "NH2" Residue "II TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "II GLU 373": "OE1" <-> "OE2" Residue "II PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "II GLU 427": "OE1" <-> "OE2" Residue "II ARG 449": "NH1" <-> "NH2" Residue "II PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "II ASP 476": "OD1" <-> "OD2" Residue "II TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "II TYR 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "II PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "II ARG 579": "NH1" <-> "NH2" Residue "II PHE 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "II GLU 651": "OE1" <-> "OE2" Residue "II GLU 668": "OE1" <-> "OE2" Residue "II PHE 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "II ARG 712": "NH1" <-> "NH2" Residue "II PHE 717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "II TYR 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "KK TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "KK GLU 44": "OE1" <-> "OE2" Residue "KK GLU 51": "OE1" <-> "OE2" Residue "KK PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "KK ARG 58": "NH1" <-> "NH2" Residue "KK PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "KK PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "KK ASP 68": "OD1" <-> "OD2" Residue "KK GLU 88": "OE1" <-> "OE2" Residue "KK ARG 119": "NH1" <-> "NH2" Residue "KK GLU 218": "OE1" <-> "OE2" Residue "KK GLU 235": "OE1" <-> "OE2" Residue "HH ARG 32": "NH1" <-> "NH2" Residue "HH TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HH ARG 51": "NH1" <-> "NH2" Residue "HH GLU 64": "OE1" <-> "OE2" Residue "HH GLU 92": "OE1" <-> "OE2" Residue "HH GLU 99": "OE1" <-> "OE2" Residue "HH PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "QQ GLU 195": "OE1" <-> "OE2" Residue "QQ ARG 226": "NH1" <-> "NH2" Residue "QQ ARG 230": "NH1" <-> "NH2" Residue "QQ GLU 259": "OE1" <-> "OE2" Residue "QQ ARG 264": "NH1" <-> "NH2" Residue "QQ GLU 265": "OE1" <-> "OE2" Residue "QQ ASP 328": "OD1" <-> "OD2" Residue "QQ GLU 331": "OE1" <-> "OE2" Residue "QQ ASP 349": "OD1" <-> "OD2" Residue "QQ GLU 369": "OE1" <-> "OE2" Residue "QQ GLU 385": "OE1" <-> "OE2" Residue "b TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 64": "OE1" <-> "OE2" Residue "b TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 97": "OE1" <-> "OE2" Residue "d GLU 109": "OE1" <-> "OE2" Residue "d TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 167": "OD1" <-> "OD2" Residue "e PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 54": "OE1" <-> "OE2" Residue "f ASP 69": "OD1" <-> "OD2" Residue "f TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 86": "OD1" <-> "OD2" Residue "f TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 63": "OE1" <-> "OE2" Residue "g GLU 94": "OE1" <-> "OE2" Residue "h TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 80": "OE1" <-> "OE2" Residue "c ARG 38": "NH1" <-> "NH2" Residue "c TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 93": "OD1" <-> "OD2" Residue "a TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 167": "OD1" <-> "OD2" Residue "a PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "TT GLU 351": "OE1" <-> "OE2" Residue "WW ASP 2": "OD1" <-> "OD2" Residue "WW TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "WW TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "WW GLU 72": "OE1" <-> "OE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 78671 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 898 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 1, 'TRANS': 108} Chain: "B" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 957 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 1, 'TRANS': 114} Chain: "I" Number of atoms: 5337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5337 Classifications: {'peptide': 659} Link IDs: {'CIS': 2, 'PTRANS': 27, 'TRANS': 629} Chain breaks: 4 Chain: "K" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1762 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1412 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 167} Chain breaks: 1 Chain: "LL" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1941 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 9, 'TRANS': 231} Chain: "NN" Number of atoms: 3121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3121 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 363} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "CT" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3298 Classifications: {'peptide': 391} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 382} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "ce" Number of atoms: 4352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4352 Classifications: {'peptide': 524} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 506} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1941 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 9, 'TRANS': 231} Chain: "SK" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1230 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain breaks: 1 Chain: "CE" Number of atoms: 4608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4608 Classifications: {'peptide': 557} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 536} Chain breaks: 3 Chain: "P" Number of atoms: 2098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2098 Classifications: {'peptide': 255} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 248} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Q" Number of atoms: 2193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2193 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 9, 'TRANS': 251} Chain breaks: 1 Chain: "OO" Number of atoms: 1967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1967 Classifications: {'peptide': 240} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 234} Chain breaks: 1 Chain: "N" Number of atoms: 3129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3129 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 364} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "T" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 761 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain: "U" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1485 Classifications: {'peptide': 184} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 181} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "PP" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2094 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 6, 'TRANS': 247} Chain breaks: 2 Chain: "W" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 551 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain breaks: 1 Chain: "O" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 2015 Classifications: {'peptide': 245} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 238} Chain breaks: 1 Chain: "Y" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1663 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 217} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "Z" Number of atoms: 1180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1180 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 2, 'TRANS': 148} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 2, 'ASN%COO:plan1': 1} Unresolved non-hydrogen planarities: 35 Chain: "UU" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1445 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 176} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "YY" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1663 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 217} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "ZZ" Number of atoms: 1180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1180 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 2, 'TRANS': 148} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 2, 'ASN%COO:plan1': 1} Unresolved non-hydrogen planarities: 35 Chain: "II" Number of atoms: 5705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5705 Classifications: {'peptide': 704} Link IDs: {'PTRANS': 30, 'TRANS': 673} Chain breaks: 3 Chain: "KK" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1805 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "HH" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1449 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 5, 'TRANS': 170} Chain breaks: 1 Chain: "QQ" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2060 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 239} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 3139 Classifications: {'DNA': 153} Link IDs: {'rna3p': 152} Chain: "E" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 3134 Classifications: {'DNA': 153} Link IDs: {'rna3p': 152} Chain: "b" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 625 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 735 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "e" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 781 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 94} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "f" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "g" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 751 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "h" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 745 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 94} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "c" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 742 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 92} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "a" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 781 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 94} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "TT" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 761 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain: "WW" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 550 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain breaks: 1 Time building chain proxies: 29.57, per 1000 atoms: 0.38 Number of scatterers: 78671 At special positions: 0 Unit cell: (214.92, 250.56, 299.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 293 16.00 P 306 15.00 O 15347 8.00 N 13467 7.00 C 49258 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYSce 99 " - pdb=" SG CYSce 215 " distance=2.03 Simple disulfide: pdb=" SG CYSCE 14 " - pdb=" SG CYSCE 17 " 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: 28.92 Conformation dependent library (CDL) restraints added in 9.2 seconds 17524 Ramachandran restraints generated. 8762 Oldfield, 0 Emsley, 8762 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17264 Finding SS restraints... Secondary structure from input PDB file: 380 helices and 32 sheets defined 66.5% alpha, 5.2% beta 132 base pairs and 264 stacking pairs defined. Time for finding SS restraints: 19.89 Creating SS restraints... Processing helix chain 'A' and resid 226 through 248 removed outlier: 3.563A pdb=" N GLU A 231 " --> pdb=" O HIS A 227 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU A 248 " --> pdb=" O VAL A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 324 removed outlier: 3.756A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A 320 " --> pdb=" O MET A 316 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG A 321 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS A 322 " --> pdb=" O ARG A 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 249 removed outlier: 3.507A pdb=" N ILE B 238 " --> pdb=" O ARG B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 324 removed outlier: 3.604A pdb=" N GLU B 289 " --> pdb=" O LYS B 285 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 39 Processing helix chain 'I' and resid 41 through 55 Processing helix chain 'I' and resid 59 through 69 Processing helix chain 'I' and resid 78 through 90 removed outlier: 3.672A pdb=" N GLY I 90 " --> pdb=" O ILE I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 117 Processing helix chain 'I' and resid 131 through 141 removed outlier: 3.512A pdb=" N GLN I 141 " --> pdb=" O LEU I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 157 removed outlier: 3.754A pdb=" N THR I 150 " --> pdb=" O GLN I 146 " (cutoff:3.500A) Proline residue: I 151 - end of helix removed outlier: 3.510A pdb=" N ILE I 154 " --> pdb=" O THR I 150 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 163 Processing helix chain 'I' and resid 164 through 177 Processing helix chain 'I' and resid 182 through 199 Processing helix chain 'I' and resid 204 through 210 Processing helix chain 'I' and resid 215 through 223 Processing helix chain 'I' and resid 227 through 241 removed outlier: 3.531A pdb=" N SER I 232 " --> pdb=" O ALA I 228 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE I 233 " --> pdb=" O HIS I 229 " (cutoff:3.500A) Processing helix chain 'I' and resid 247 through 267 Processing helix chain 'I' and resid 295 through 302 removed outlier: 3.717A pdb=" N GLN I 301 " --> pdb=" O GLU I 297 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN I 302 " --> pdb=" O GLN I 298 " (cutoff:3.500A) Processing helix chain 'I' and resid 303 through 306 Processing helix chain 'I' and resid 311 through 317 Processing helix chain 'I' and resid 332 through 348 removed outlier: 4.188A pdb=" N LEU I 336 " --> pdb=" O SER I 332 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N HIS I 338 " --> pdb=" O ASP I 334 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU I 339 " --> pdb=" O SER I 335 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER I 342 " --> pdb=" O HIS I 338 " (cutoff:3.500A) Processing helix chain 'I' and resid 354 through 369 Processing helix chain 'I' and resid 378 through 387 Processing helix chain 'I' and resid 389 through 401 removed outlier: 3.533A pdb=" N SER I 394 " --> pdb=" O ASN I 390 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ARG I 395 " --> pdb=" O LYS I 391 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE I 396 " --> pdb=" O LEU I 392 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE I 400 " --> pdb=" O ILE I 396 " (cutoff:3.500A) Processing helix chain 'I' and resid 402 through 409 removed outlier: 3.918A pdb=" N LEU I 406 " --> pdb=" O ASN I 402 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU I 408 " --> pdb=" O LYS I 404 " (cutoff:3.500A) Processing helix chain 'I' and resid 409 through 419 removed outlier: 3.702A pdb=" N LEU I 413 " --> pdb=" O ASP I 409 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS I 415 " --> pdb=" O LEU I 411 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY I 419 " --> pdb=" O LYS I 415 " (cutoff:3.500A) Processing helix chain 'I' and resid 432 through 444 Processing helix chain 'I' and resid 446 through 451 Processing helix chain 'I' and resid 457 through 475 removed outlier: 3.579A pdb=" N MET I 468 " --> pdb=" O TYR I 464 " (cutoff:3.500A) Processing helix chain 'I' and resid 478 through 494 removed outlier: 3.583A pdb=" N GLY I 482 " --> pdb=" O LEU I 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 506 through 523 removed outlier: 3.593A pdb=" N ILE I 518 " --> pdb=" O SER I 514 " (cutoff:3.500A) Processing helix chain 'I' and resid 543 through 548 Processing helix chain 'I' and resid 550 through 569 removed outlier: 3.631A pdb=" N ALA I 556 " --> pdb=" O LEU I 552 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA I 557 " --> pdb=" O LEU I 553 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET I 569 " --> pdb=" O LYS I 565 " (cutoff:3.500A) Processing helix chain 'I' and resid 575 through 592 removed outlier: 3.913A pdb=" N LEU I 588 " --> pdb=" O TYR I 584 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU I 592 " --> pdb=" O LEU I 588 " (cutoff:3.500A) Processing helix chain 'I' and resid 612 through 618 removed outlier: 3.501A pdb=" N LEU I 618 " --> pdb=" O ILE I 614 " (cutoff:3.500A) Processing helix chain 'I' and resid 625 through 630 removed outlier: 3.764A pdb=" N LYS I 629 " --> pdb=" O PHE I 625 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE I 630 " --> pdb=" O LYS I 626 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 625 through 630' Processing helix chain 'I' and resid 636 through 654 removed outlier: 4.144A pdb=" N TYR I 641 " --> pdb=" O PRO I 637 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE I 642 " --> pdb=" O ALA I 638 " (cutoff:3.500A) Processing helix chain 'I' and resid 666 through 675 Processing helix chain 'I' and resid 692 through 705 removed outlier: 3.501A pdb=" N LEU I 696 " --> pdb=" O ASN I 692 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N HIS I 703 " --> pdb=" O LYS I 699 " (cutoff:3.500A) Processing helix chain 'I' and resid 711 through 721 removed outlier: 3.670A pdb=" N ALA I 715 " --> pdb=" O TYR I 711 " (cutoff:3.500A) Processing helix chain 'I' and resid 722 through 727 removed outlier: 3.710A pdb=" N LYS I 727 " --> pdb=" O LYS I 723 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 40 removed outlier: 3.617A pdb=" N TYR K 11 " --> pdb=" O VAL K 7 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN K 18 " --> pdb=" O ASN K 14 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR K 24 " --> pdb=" O GLY K 20 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE K 25 " --> pdb=" O ASN K 21 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN K 30 " --> pdb=" O LEU K 26 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLU K 35 " --> pdb=" O GLY K 31 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LYS K 38 " --> pdb=" O ASP K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 57 Processing helix chain 'K' and resid 70 through 85 removed outlier: 3.708A pdb=" N SER K 76 " --> pdb=" O PHE K 72 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG K 82 " --> pdb=" O PHE K 78 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA K 83 " --> pdb=" O LEU K 79 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER K 85 " --> pdb=" O LEU K 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 130 removed outlier: 4.067A pdb=" N SER K 91 " --> pdb=" O SER K 87 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU K 92 " --> pdb=" O GLU K 88 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP K 113 " --> pdb=" O ASN K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 138 through 159 Processing helix chain 'K' and resid 159 through 165 Processing helix chain 'K' and resid 170 through 187 removed outlier: 3.546A pdb=" N ASN K 176 " --> pdb=" O ASP K 172 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU K 177 " --> pdb=" O SER K 173 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL K 178 " --> pdb=" O LEU K 174 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU K 180 " --> pdb=" O ASN K 176 " (cutoff:3.500A) Processing helix chain 'K' and resid 200 through 211 removed outlier: 4.641A pdb=" N ILE K 204 " --> pdb=" O LYS K 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 39 removed outlier: 3.581A pdb=" N ILE H 36 " --> pdb=" O ARG H 32 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ARG H 37 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N HIS H 39 " --> pdb=" O LEU H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 68 Processing helix chain 'H' and resid 83 through 135 removed outlier: 3.768A pdb=" N TYR H 98 " --> pdb=" O ASN H 94 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU H 99 " --> pdb=" O SER H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 173 Processing helix chain 'LL' and resid 48 through 52 removed outlier: 3.997A pdb=" N ASPLL 51 " --> pdb=" O THRLL 48 " (cutoff:3.500A) Processing helix chain 'LL' and resid 93 through 96 Processing helix chain 'LL' and resid 97 through 103 Processing helix chain 'LL' and resid 103 through 108 removed outlier: 3.885A pdb=" N TYRLL 107 " --> pdb=" O LEULL 103 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLYLL 108 " --> pdb=" O LYSLL 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'LL' and resid 103 through 108' Processing helix chain 'LL' and resid 117 through 129 removed outlier: 3.939A pdb=" N ILELL 122 " --> pdb=" O GLNLL 118 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N LYSLL 123 " --> pdb=" O LYSLL 119 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALALL 125 " --> pdb=" O METLL 121 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASPLL 126 " --> pdb=" O ILELL 122 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALALL 127 " --> pdb=" O LYSLL 123 " (cutoff:3.500A) Processing helix chain 'LL' and resid 153 through 157 removed outlier: 3.805A pdb=" N LYSLL 156 " --> pdb=" O THRLL 153 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASNLL 157 " --> pdb=" O GLNLL 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'LL' and resid 153 through 157' Processing helix chain 'LL' and resid 166 through 178 removed outlier: 3.657A pdb=" N GLYLL 176 " --> pdb=" O GLYLL 172 " (cutoff:3.500A) Processing helix chain 'LL' and resid 182 through 187 removed outlier: 3.639A pdb=" N ASPLL 186 " --> pdb=" O HISLL 182 " (cutoff:3.500A) Processing helix chain 'LL' and resid 188 through 196 Processing helix chain 'LL' and resid 229 through 241 removed outlier: 4.143A pdb=" N LEULL 233 " --> pdb=" O ARGLL 229 " (cutoff:3.500A) Processing helix chain 'NN' and resid 16 through 26 removed outlier: 3.621A pdb=" N VALNN 20 " --> pdb=" O ASPNN 16 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYSNN 26 " --> pdb=" O LYSNN 22 " (cutoff:3.500A) Processing helix chain 'NN' and resid 28 through 44 removed outlier: 3.805A pdb=" N ASPNN 34 " --> pdb=" O THRNN 30 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEUNN 35 " --> pdb=" O VALNN 31 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THRNN 36 " --> pdb=" O LEUNN 32 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEUNN 37 " --> pdb=" O TYRNN 33 " (cutoff:3.500A) Processing helix chain 'NN' and resid 50 through 64 removed outlier: 3.735A pdb=" N GLUNN 56 " --> pdb=" O TYRNN 52 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEUNN 61 " --> pdb=" O THRNN 57 " (cutoff:3.500A) Processing helix chain 'NN' and resid 67 through 78 removed outlier: 4.383A pdb=" N ILENN 71 " --> pdb=" O ARGNN 67 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VALNN 72 " --> pdb=" O ARGNN 68 " (cutoff:3.500A) Processing helix chain 'NN' and resid 85 through 100 removed outlier: 3.557A pdb=" N ILENN 92 " --> pdb=" O GLNNN 88 " (cutoff:3.500A) Processing helix chain 'NN' and resid 124 through 138 removed outlier: 3.847A pdb=" N GLUNN 130 " --> pdb=" O ALANN 126 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYSNN 138 " --> pdb=" O THRNN 134 " (cutoff:3.500A) Processing helix chain 'NN' and resid 218 through 233 Processing helix chain 'NN' and resid 250 through 259 Processing helix chain 'NN' and resid 267 through 269 No H-bonds generated for 'chain 'NN' and resid 267 through 269' Processing helix chain 'NN' and resid 270 through 276 removed outlier: 3.925A pdb=" N ALANN 274 " --> pdb=" O TRPNN 270 " (cutoff:3.500A) Processing helix chain 'NN' and resid 289 through 294 Processing helix chain 'NN' and resid 318 through 335 removed outlier: 3.524A pdb=" N ARGNN 323 " --> pdb=" O PRONN 319 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEUNN 324 " --> pdb=" O GLUNN 320 " (cutoff:3.500A) Processing helix chain 'NN' and resid 408 through 419 removed outlier: 3.831A pdb=" N GLUNN 415 " --> pdb=" O GLYNN 411 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEUNN 416 " --> pdb=" O GLYNN 412 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N CYSNN 417 " --> pdb=" O LEUNN 413 " (cutoff:3.500A) Processing helix chain 'NN' and resid 428 through 433 removed outlier: 3.564A pdb=" N GLYNN 433 " --> pdb=" O GLYNN 429 " (cutoff:3.500A) Processing helix chain 'CT' and resid 5 through 11 removed outlier: 3.607A pdb=" N PHECT 9 " --> pdb=" O ASNCT 5 " (cutoff:3.500A) Processing helix chain 'CT' and resid 13 through 25 removed outlier: 3.597A pdb=" N ASPCT 25 " --> pdb=" O TYRCT 21 " (cutoff:3.500A) Processing helix chain 'CT' and resid 61 through 70 removed outlier: 4.065A pdb=" N TYRCT 67 " --> pdb=" O LEUCT 63 " (cutoff:3.500A) Proline residue: CT 68 - end of helix Processing helix chain 'CT' and resid 75 through 79 removed outlier: 3.531A pdb=" N GLUCT 78 " --> pdb=" O ASNCT 75 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N TYRCT 79 " --> pdb=" O ILECT 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'CT' and resid 75 through 79' Processing helix chain 'CT' and resid 80 through 92 removed outlier: 3.552A pdb=" N ILECT 84 " --> pdb=" O SERCT 80 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHECT 92 " --> pdb=" O LEUCT 88 " (cutoff:3.500A) Processing helix chain 'CT' and resid 97 through 110 Processing helix chain 'CT' and resid 143 through 151 removed outlier: 3.657A pdb=" N TRPCT 150 " --> pdb=" O GLUCT 146 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VALCT 151 " --> pdb=" O TYRCT 147 " (cutoff:3.500A) Processing helix chain 'CT' and resid 176 through 189 removed outlier: 3.525A pdb=" N ASPCT 181 " --> pdb=" O PROCT 177 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYSCT 182 " --> pdb=" O GLNCT 178 " (cutoff:3.500A) Processing helix chain 'CT' and resid 257 through 264 removed outlier: 3.580A pdb=" N THRCT 263 " --> pdb=" O SERCT 259 " (cutoff:3.500A) Processing helix chain 'CT' and resid 280 through 288 removed outlier: 3.883A pdb=" N TYRCT 284 " --> pdb=" O GLYCT 280 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLUCT 285 " --> pdb=" O GLUCT 281 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEUCT 286 " --> pdb=" O LYSCT 282 " (cutoff:3.500A) Processing helix chain 'CT' and resid 304 through 309 removed outlier: 4.316A pdb=" N ARGCT 308 " --> pdb=" O ILECT 304 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILECT 309 " --> pdb=" O VALCT 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'CT' and resid 304 through 309' Processing helix chain 'CT' and resid 372 through 381 removed outlier: 3.580A pdb=" N ILECT 376 " --> pdb=" O ILECT 372 " (cutoff:3.500A) Processing helix chain 'CT' and resid 383 through 388 Processing helix chain 'CT' and resid 400 through 404 Processing helix chain 'CT' and resid 420 through 434 removed outlier: 3.999A pdb=" N SERCT 434 " --> pdb=" O ILECT 430 " (cutoff:3.500A) Processing helix chain 'CT' and resid 457 through 462 removed outlier: 3.565A pdb=" N SERCT 462 " --> pdb=" O ALACT 458 " (cutoff:3.500A) Processing helix chain 'ce' and resid 57 through 73 removed outlier: 3.511A pdb=" N LEUce 63 " --> pdb=" O PROce 59 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHEce 64 " --> pdb=" O ASPce 60 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TRPce 65 " --> pdb=" O LEUce 61 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLNce 66 " --> pdb=" O LEUce 62 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASNce 67 " --> pdb=" O LEUce 63 " (cutoff:3.500A) Processing helix chain 'ce' and resid 96 through 104 removed outlier: 3.642A pdb=" N ASNce 104 " --> pdb=" O METce 100 " (cutoff:3.500A) Processing helix chain 'ce' and resid 109 through 122 removed outlier: 3.687A pdb=" N GLNce 113 " --> pdb=" O ASPce 109 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLUce 120 " --> pdb=" O ASNce 116 " (cutoff:3.500A) Processing helix chain 'ce' and resid 123 through 129 removed outlier: 3.536A pdb=" N TYRce 126 " --> pdb=" O GLYce 123 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N PHEce 127 " --> pdb=" O ALAce 124 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLYce 128 " --> pdb=" O LEUce 125 " (cutoff:3.500A) Processing helix chain 'ce' and resid 133 through 146 removed outlier: 3.530A pdb=" N TYRce 137 " --> pdb=" O ILEce 133 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEUce 138 " --> pdb=" O SERce 134 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARGce 139 " --> pdb=" O GLUce 135 " (cutoff:3.500A) Processing helix chain 'ce' and resid 153 through 174 removed outlier: 3.693A pdb=" N TRPce 159 " --> pdb=" O ASPce 155 " (cutoff:3.500A) Processing helix chain 'ce' and resid 175 through 183 removed outlier: 4.333A pdb=" N GLUce 181 " --> pdb=" O GLUce 177 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILEce 182 " --> pdb=" O LYSce 178 " (cutoff:3.500A) Processing helix chain 'ce' and resid 185 through 190 removed outlier: 4.290A pdb=" N HISce 189 " --> pdb=" O VALce 185 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLUce 190 " --> pdb=" O TYRce 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'ce' and resid 185 through 190' Processing helix chain 'ce' and resid 203 through 224 removed outlier: 3.720A pdb=" N VALce 207 " --> pdb=" O GLYce 203 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEUce 220 " --> pdb=" O SERce 216 " (cutoff:3.500A) Processing helix chain 'ce' and resid 230 through 242 removed outlier: 4.221A pdb=" N VALce 234 " --> pdb=" O ASPce 230 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THRce 242 " --> pdb=" O LEUce 238 " (cutoff:3.500A) Processing helix chain 'ce' and resid 244 through 249 removed outlier: 3.604A pdb=" N ASPce 248 " --> pdb=" O THRce 244 " (cutoff:3.500A) Processing helix chain 'ce' and resid 249 through 266 removed outlier: 3.503A pdb=" N SERce 255 " --> pdb=" O LEUce 251 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THRce 258 " --> pdb=" O ASNce 254 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLNce 259 " --> pdb=" O SERce 255 " (cutoff:3.500A) Processing helix chain 'ce' and resid 279 through 303 removed outlier: 3.626A pdb=" N ILEce 284 " --> pdb=" O PROce 280 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALAce 285 " --> pdb=" O VALce 281 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARGce 291 " --> pdb=" O VALce 287 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILEce 292 " --> pdb=" O THRce 288 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYRce 294 " --> pdb=" O GLYce 290 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEUce 302 " --> pdb=" O GLYce 298 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLNce 303 " --> pdb=" O CYSce 299 " (cutoff:3.500A) Processing helix chain 'ce' and resid 340 through 357 removed outlier: 3.664A pdb=" N LEUce 355 " --> pdb=" O LEUce 351 " (cutoff:3.500A) Processing helix chain 'ce' and resid 366 through 387 removed outlier: 3.953A pdb=" N ARGce 374 " --> pdb=" O LEUce 370 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILEce 379 " --> pdb=" O ARGce 375 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYRce 382 " --> pdb=" O ASPce 378 " (cutoff:3.500A) Processing helix chain 'ce' and resid 393 through 422 removed outlier: 3.630A pdb=" N ARGce 397 " --> pdb=" O SERce 393 " (cutoff:3.500A) Processing helix chain 'ce' and resid 426 through 448 removed outlier: 3.606A pdb=" N LYSce 430 " --> pdb=" O ASPce 426 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILEce 438 " --> pdb=" O TYRce 434 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASNce 445 " --> pdb=" O LEUce 441 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALAce 448 " --> pdb=" O ASNce 444 " (cutoff:3.500A) Processing helix chain 'ce' and resid 450 through 455 removed outlier: 3.890A pdb=" N ASNce 454 " --> pdb=" O GLUce 451 " (cutoff:3.500A) Processing helix chain 'ce' and resid 456 through 475 removed outlier: 4.307A pdb=" N METce 460 " --> pdb=" O HISce 456 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLNce 461 " --> pdb=" O PROce 457 " (cutoff:3.500A) Processing helix chain 'ce' and resid 479 through 495 removed outlier: 3.677A pdb=" N VALce 487 " --> pdb=" O LYSce 483 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASPce 488 " --> pdb=" O GLNce 484 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THRce 493 " --> pdb=" O LEUce 489 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALAce 494 " --> pdb=" O THRce 490 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASNce 495 " --> pdb=" O GLUce 491 " (cutoff:3.500A) Processing helix chain 'ce' and resid 497 through 500 removed outlier: 3.905A pdb=" N PHEce 500 " --> pdb=" O PROce 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'ce' and resid 497 through 500' Processing helix chain 'ce' and resid 501 through 516 removed outlier: 3.562A pdb=" N VALce 508 " --> pdb=" O LEUce 504 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYSce 516 " --> pdb=" O GLUce 512 " (cutoff:3.500A) Processing helix chain 'ce' and resid 516 through 524 removed outlier: 3.551A pdb=" N LEUce 520 " --> pdb=" O LYSce 516 " (cutoff:3.500A) Processing helix chain 'ce' and resid 535 through 553 removed outlier: 3.680A pdb=" N LYSce 539 " --> pdb=" O HISce 535 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILEce 540 " --> pdb=" O PROce 536 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILEce 545 " --> pdb=" O LEUce 541 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILEce 548 " --> pdb=" O ASPce 544 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYSce 551 " --> pdb=" O ILEce 547 " (cutoff:3.500A) Processing helix chain 'ce' and resid 554 through 562 removed outlier: 3.617A pdb=" N LEUce 558 " --> pdb=" O GLUce 554 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILEce 559 " --> pdb=" O METce 555 " (cutoff:3.500A) Processing helix chain 'ce' and resid 590 through 601 Processing helix chain 'L' and resid 48 through 52 removed outlier: 3.997A pdb=" N ASP L 51 " --> pdb=" O THR L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 93 through 96 Processing helix chain 'L' and resid 97 through 103 Processing helix chain 'L' and resid 103 through 108 removed outlier: 3.885A pdb=" N TYR L 107 " --> pdb=" O LEU L 103 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLY L 108 " --> pdb=" O LYS L 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 103 through 108' Processing helix chain 'L' and resid 117 through 129 removed outlier: 3.938A pdb=" N ILE L 122 " --> pdb=" O GLN L 118 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N LYS L 123 " --> pdb=" O LYS L 119 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ALA L 125 " --> pdb=" O MET L 121 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP L 126 " --> pdb=" O ILE L 122 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA L 127 " --> pdb=" O LYS L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 153 through 157 removed outlier: 3.805A pdb=" N LYS L 156 " --> pdb=" O THR L 153 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN L 157 " --> pdb=" O GLN L 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 153 through 157' Processing helix chain 'L' and resid 166 through 178 removed outlier: 3.657A pdb=" N GLY L 176 " --> pdb=" O GLY L 172 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 187 removed outlier: 3.638A pdb=" N ASP L 186 " --> pdb=" O HIS L 182 " (cutoff:3.500A) Processing helix chain 'L' and resid 188 through 196 Processing helix chain 'L' and resid 229 through 241 removed outlier: 4.143A pdb=" N LEU L 233 " --> pdb=" O ARG L 229 " (cutoff:3.500A) Processing helix chain 'SK' and resid 21 through 25 Processing helix chain 'SK' and resid 83 through 97 removed outlier: 3.813A pdb=" N LYSSK 89 " --> pdb=" O SERSK 85 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLUSK 95 " --> pdb=" O ILESK 91 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N HISSK 96 " --> pdb=" O GLUSK 92 " (cutoff:3.500A) Processing helix chain 'SK' and resid 108 through 114 Processing helix chain 'SK' and resid 117 through 125 removed outlier: 3.746A pdb=" N GLUSK 122 " --> pdb=" O SERSK 118 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHESK 123 " --> pdb=" O TRPSK 119 " (cutoff:3.500A) Processing helix chain 'SK' and resid 127 through 142 removed outlier: 3.748A pdb=" N TYRSK 132 " --> pdb=" O GLNSK 128 " (cutoff:3.500A) Processing helix chain 'SK' and resid 143 through 161 removed outlier: 3.701A pdb=" N VALSK 153 " --> pdb=" O ALASK 149 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VALSK 154 " --> pdb=" O GLYSK 150 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILESK 158 " --> pdb=" O VALSK 154 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARGSK 159 " --> pdb=" O ALASK 155 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARGSK 161 " --> pdb=" O METSK 157 " (cutoff:3.500A) Processing helix chain 'SK' and resid 162 through 170 removed outlier: 3.814A pdb=" N ILESK 166 " --> pdb=" O SERSK 162 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARGSK 167 " --> pdb=" O PROSK 163 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARGSK 168 " --> pdb=" O GLUSK 164 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHESK 170 " --> pdb=" O ILESK 166 " (cutoff:3.500A) Processing helix chain 'SK' and resid 177 through 192 removed outlier: 3.907A pdb=" N ARGSK 185 " --> pdb=" O GLUSK 181 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARGSK 186 " --> pdb=" O ALASK 182 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLUSK 187 " --> pdb=" O ALASK 183 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASNSK 188 " --> pdb=" O ILESK 184 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLUSK 189 " --> pdb=" O ARGSK 185 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TRPSK 190 " --> pdb=" O ARGSK 186 " (cutoff:3.500A) Processing helix chain 'CE' and resid 30 through 37 Processing helix chain 'CE' and resid 39 through 45 removed outlier: 3.828A pdb=" N SERCE 45 " --> pdb=" O GLUCE 41 " (cutoff:3.500A) Processing helix chain 'CE' and resid 56 through 73 removed outlier: 4.376A pdb=" N ASPCE 60 " --> pdb=" O GLUCE 56 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLNCE 66 " --> pdb=" O LEUCE 62 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASNCE 67 " --> pdb=" O LEUCE 63 " (cutoff:3.500A) Processing helix chain 'CE' and resid 96 through 106 removed outlier: 3.635A pdb=" N METCE 103 " --> pdb=" O CYSCE 99 " (cutoff:3.500A) Processing helix chain 'CE' and resid 107 through 118 removed outlier: 3.751A pdb=" N PHECE 112 " --> pdb=" O LYSCE 108 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLNCE 113 " --> pdb=" O ASPCE 109 " (cutoff:3.500A) Processing helix chain 'CE' and resid 133 through 149 removed outlier: 3.902A pdb=" N LEUCE 138 " --> pdb=" O SERCE 134 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLUCE 141 " --> pdb=" O TYRCE 137 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALACE 148 " --> pdb=" O TRPCE 144 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASPCE 149 " --> pdb=" O ASPCE 145 " (cutoff:3.500A) Processing helix chain 'CE' and resid 153 through 174 removed outlier: 3.523A pdb=" N TRPCE 159 " --> pdb=" O ASPCE 155 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TRPCE 164 " --> pdb=" O ASPCE 160 " (cutoff:3.500A) Processing helix chain 'CE' and resid 175 through 183 removed outlier: 3.557A pdb=" N ALACE 180 " --> pdb=" O VALCE 176 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLUCE 181 " --> pdb=" O GLUCE 177 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILECE 182 " --> pdb=" O LYSCE 178 " (cutoff:3.500A) Processing helix chain 'CE' and resid 185 through 193 removed outlier: 3.512A pdb=" N HISCE 189 " --> pdb=" O VALCE 185 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLUCE 190 " --> pdb=" O TYRCE 186 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N TYRCE 191 " --> pdb=" O PROCE 187 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEUCE 192 " --> pdb=" O LEUCE 188 " (cutoff:3.500A) Processing helix chain 'CE' and resid 203 through 224 removed outlier: 3.545A pdb=" N ASNCE 211 " --> pdb=" O VALCE 207 " (cutoff:3.500A) Processing helix chain 'CE' and resid 231 through 241 removed outlier: 3.513A pdb=" N ILECE 239 " --> pdb=" O GLNCE 235 " (cutoff:3.500A) Processing helix chain 'CE' and resid 244 through 249 Processing helix chain 'CE' and resid 249 through 265 Processing helix chain 'CE' and resid 279 through 303 removed outlier: 3.639A pdb=" N ARGCE 291 " --> pdb=" O VALCE 287 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILECE 292 " --> pdb=" O THRCE 288 " (cutoff:3.500A) Processing helix chain 'CE' and resid 340 through 361 removed outlier: 3.563A pdb=" N ILECE 349 " --> pdb=" O TYRCE 345 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASPCE 354 " --> pdb=" O SERCE 350 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEUCE 355 " --> pdb=" O LEUCE 351 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASPCE 356 " --> pdb=" O ASPCE 352 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TYRCE 358 " --> pdb=" O ASPCE 354 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEUCE 359 " --> pdb=" O LEUCE 355 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASNCE 360 " --> pdb=" O ASPCE 356 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYSCE 361 " --> pdb=" O GLNCE 357 " (cutoff:3.500A) Processing helix chain 'CE' and resid 366 through 371 Processing helix chain 'CE' and resid 371 through 383 removed outlier: 3.989A pdb=" N ARGCE 375 " --> pdb=" O ASPCE 371 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLUCE 376 " --> pdb=" O ALACE 372 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILECE 379 " --> pdb=" O ARGCE 375 " (cutoff:3.500A) Processing helix chain 'CE' and resid 393 through 423 removed outlier: 3.885A pdb=" N ARGCE 397 " --> pdb=" O SERCE 393 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILECE 407 " --> pdb=" O ALACE 403 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYSCE 413 " --> pdb=" O THRCE 409 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEUCE 419 " --> pdb=" O PHECE 415 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYRCE 421 " --> pdb=" O METCE 417 " (cutoff:3.500A) Processing helix chain 'CE' and resid 426 through 445 removed outlier: 3.549A pdb=" N LYSCE 430 " --> pdb=" O ASPCE 426 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILECE 438 " --> pdb=" O TYRCE 434 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILECE 442 " --> pdb=" O ILECE 438 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VALCE 443 " --> pdb=" O ILECE 439 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASNCE 445 " --> pdb=" O LEUCE 441 " (cutoff:3.500A) Processing helix chain 'CE' and resid 452 through 457 removed outlier: 3.692A pdb=" N HISCE 456 " --> pdb=" O PHECE 453 " (cutoff:3.500A) Proline residue: CE 457 - end of helix Processing helix chain 'CE' and resid 458 through 475 removed outlier: 3.827A pdb=" N ARGCE 465 " --> pdb=" O GLNCE 461 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILECE 475 " --> pdb=" O SERCE 471 " (cutoff:3.500A) Processing helix chain 'CE' and resid 479 through 495 removed outlier: 3.563A pdb=" N VALCE 487 " --> pdb=" O LYSCE 483 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASPCE 488 " --> pdb=" O GLNCE 484 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEUCE 489 " --> pdb=" O LEUCE 485 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLUCE 491 " --> pdb=" O VALCE 487 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALACE 494 " --> pdb=" O THRCE 490 " (cutoff:3.500A) Processing helix chain 'CE' and resid 501 through 524 removed outlier: 3.674A pdb=" N ASPCE 505 " --> pdb=" O GLYCE 501 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEUCE 507 " --> pdb=" O LYSCE 503 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VALCE 508 " --> pdb=" O LEUCE 504 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYRCE 509 " --> pdb=" O ASPCE 505 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYSCE 518 " --> pdb=" O LEUCE 514 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEUCE 519 " --> pdb=" O SERCE 515 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYSCE 523 " --> pdb=" O LEUCE 519 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VALCE 524 " --> pdb=" O LEUCE 520 " (cutoff:3.500A) Processing helix chain 'CE' and resid 535 through 552 removed outlier: 3.670A pdb=" N LYSCE 539 " --> pdb=" O HISCE 535 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYSCE 546 " --> pdb=" O GLNCE 542 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILECE 547 " --> pdb=" O ASNCE 543 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILECE 548 " --> pdb=" O ASPCE 544 " (cutoff:3.500A) Processing helix chain 'CE' and resid 554 through 563 removed outlier: 3.916A pdb=" N GLYCE 563 " --> pdb=" O ILECE 559 " (cutoff:3.500A) Processing helix chain 'CE' and resid 590 through 601 Processing helix chain 'CE' and resid 602 through 606 removed outlier: 3.501A pdb=" N ILECE 606 " --> pdb=" O ILECE 603 " (cutoff:3.500A) Processing helix chain 'P' and resid 99 through 112 Processing helix chain 'P' and resid 133 through 140 removed outlier: 3.602A pdb=" N THR P 140 " --> pdb=" O LYS P 136 " (cutoff:3.500A) Processing helix chain 'P' and resid 149 through 160 removed outlier: 3.559A pdb=" N HIS P 160 " --> pdb=" O TYR P 156 " (cutoff:3.500A) Processing helix chain 'P' and resid 224 through 234 removed outlier: 4.358A pdb=" N GLN P 230 " --> pdb=" O LEU P 226 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LEU P 231 " --> pdb=" O LYS P 227 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR P 234 " --> pdb=" O GLN P 230 " (cutoff:3.500A) Processing helix chain 'P' and resid 236 through 266 Processing helix chain 'P' and resid 333 through 349 Processing helix chain 'P' and resid 350 through 361 removed outlier: 3.561A pdb=" N LYS P 355 " --> pdb=" O LYS P 351 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N CYS P 361 " --> pdb=" O ILE P 357 " (cutoff:3.500A) Processing helix chain 'P' and resid 363 through 369 removed outlier: 3.918A pdb=" N TYR P 367 " --> pdb=" O PHE P 363 " (cutoff:3.500A) Processing helix chain 'Q' and resid 129 through 142 removed outlier: 4.511A pdb=" N VAL Q 133 " --> pdb=" O GLU Q 129 " (cutoff:3.500A) Processing helix chain 'Q' and resid 155 through 181 Processing helix chain 'Q' and resid 181 through 190 removed outlier: 3.639A pdb=" N HIS Q 190 " --> pdb=" O ASN Q 186 " (cutoff:3.500A) Processing helix chain 'Q' and resid 192 through 220 removed outlier: 3.585A pdb=" N VAL Q 196 " --> pdb=" O ASP Q 192 " (cutoff:3.500A) Processing helix chain 'Q' and resid 228 through 232 Processing helix chain 'Q' and resid 233 through 293 removed outlier: 4.179A pdb=" N ILE Q 237 " --> pdb=" O ASP Q 233 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER Q 239 " --> pdb=" O GLU Q 235 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG Q 264 " --> pdb=" O ALA Q 260 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE Q 292 " --> pdb=" O THR Q 288 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLN Q 293 " --> pdb=" O GLU Q 289 " (cutoff:3.500A) Processing helix chain 'Q' and resid 298 through 309 removed outlier: 4.384A pdb=" N LYS Q 302 " --> pdb=" O PRO Q 298 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA Q 303 " --> pdb=" O VAL Q 299 " (cutoff:3.500A) Processing helix chain 'Q' and resid 320 through 333 Processing helix chain 'Q' and resid 350 through 357 Processing helix chain 'Q' and resid 357 through 382 removed outlier: 4.014A pdb=" N LYS Q 361 " --> pdb=" O LEU Q 357 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLN Q 376 " --> pdb=" O GLU Q 372 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET Q 377 " --> pdb=" O THR Q 373 " (cutoff:3.500A) Processing helix chain 'Q' and resid 382 through 391 removed outlier: 3.622A pdb=" N ILE Q 386 " --> pdb=" O HIS Q 382 " (cutoff:3.500A) Processing helix chain 'OO' and resid 127 through 132 removed outlier: 3.786A pdb=" N LEUOO 131 " --> pdb=" O GLYOO 127 " (cutoff:3.500A) Processing helix chain 'OO' and resid 134 through 139 Processing helix chain 'OO' and resid 140 through 143 Processing helix chain 'OO' and resid 153 through 171 removed outlier: 3.699A pdb=" N ASPOO 162 " --> pdb=" O SEROO 158 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYROO 163 " --> pdb=" O GLUOO 159 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILEOO 164 " --> pdb=" O LEUOO 160 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VALOO 165 " --> pdb=" O GLUOO 161 " (cutoff:3.500A) Processing helix chain 'OO' and resid 245 through 253 removed outlier: 3.826A pdb=" N THROO 253 " --> pdb=" O ILEOO 249 " (cutoff:3.500A) Processing helix chain 'OO' and resid 260 through 291 removed outlier: 3.620A pdb=" N PHEOO 267 " --> pdb=" O ASPOO 263 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARGOO 282 " --> pdb=" O VALOO 278 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLNOO 283 " --> pdb=" O GLNOO 279 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILEOO 284 " --> pdb=" O LYSOO 280 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHEOO 285 " --> pdb=" O ARGOO 281 " (cutoff:3.500A) Processing helix chain 'OO' and resid 337 through 349 removed outlier: 3.535A pdb=" N LYSOO 343 " --> pdb=" O ASNOO 339 " (cutoff:3.500A) Processing helix chain 'OO' and resid 352 through 367 removed outlier: 4.430A pdb=" N GLUOO 356 " --> pdb=" O LEUOO 352 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LEUOO 357 " --> pdb=" O ASPOO 353 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASNOO 360 " --> pdb=" O GLUOO 356 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N HISOO 361 " --> pdb=" O LEUOO 357 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THROO 365 " --> pdb=" O HISOO 361 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILEOO 366 " --> pdb=" O SEROO 362 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHEOO 367 " --> pdb=" O PHEOO 363 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 27 removed outlier: 3.559A pdb=" N VAL N 20 " --> pdb=" O ASP N 16 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS N 26 " --> pdb=" O LYS N 22 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU N 27 " --> pdb=" O GLN N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 44 removed outlier: 3.502A pdb=" N LEU N 32 " --> pdb=" O PRO N 28 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP N 34 " --> pdb=" O THR N 30 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS N 42 " --> pdb=" O SER N 38 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 64 removed outlier: 3.521A pdb=" N ILE N 62 " --> pdb=" O LEU N 58 " (cutoff:3.500A) Processing helix chain 'N' and resid 67 through 78 removed outlier: 3.533A pdb=" N ILE N 71 " --> pdb=" O ARG N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 100 Processing helix chain 'N' and resid 126 through 138 removed outlier: 3.680A pdb=" N GLU N 130 " --> pdb=" O ALA N 126 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN N 131 " --> pdb=" O LYS N 127 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU N 132 " --> pdb=" O PHE N 128 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS N 138 " --> pdb=" O THR N 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 220 through 234 removed outlier: 3.732A pdb=" N GLN N 226 " --> pdb=" O ARG N 222 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU N 234 " --> pdb=" O ARG N 230 " (cutoff:3.500A) Processing helix chain 'N' and resid 250 through 259 removed outlier: 3.690A pdb=" N THR N 256 " --> pdb=" O HIS N 252 " (cutoff:3.500A) Processing helix chain 'N' and resid 267 through 269 No H-bonds generated for 'chain 'N' and resid 267 through 269' Processing helix chain 'N' and resid 270 through 275 removed outlier: 3.901A pdb=" N ALA N 274 " --> pdb=" O TRP N 270 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER N 275 " --> pdb=" O GLU N 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 270 through 275' Processing helix chain 'N' and resid 289 through 294 removed outlier: 4.059A pdb=" N THR N 293 " --> pdb=" O HIS N 289 " (cutoff:3.500A) Processing helix chain 'N' and resid 318 through 335 removed outlier: 3.668A pdb=" N ASN N 329 " --> pdb=" O ARG N 325 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET N 330 " --> pdb=" O LEU N 326 " (cutoff:3.500A) Processing helix chain 'N' and resid 408 through 419 Processing helix chain 'N' and resid 428 through 433 Processing helix chain 'T' and resid 274 through 289 Processing helix chain 'T' and resid 295 through 316 removed outlier: 3.739A pdb=" N SER T 299 " --> pdb=" O LYS T 295 " (cutoff:3.500A) Processing helix chain 'T' and resid 320 through 331 Processing helix chain 'T' and resid 336 through 348 Processing helix chain 'T' and resid 349 through 360 removed outlier: 3.705A pdb=" N GLN T 353 " --> pdb=" O PRO T 349 " (cutoff:3.500A) Processing helix chain 'U' and resid 134 through 149 Processing helix chain 'U' and resid 149 through 161 Processing helix chain 'U' and resid 164 through 232 removed outlier: 4.180A pdb=" N ASN U 196 " --> pdb=" O ILE U 192 " (cutoff:3.500A) Processing helix chain 'U' and resid 233 through 265 Processing helix chain 'U' and resid 286 through 299 removed outlier: 3.861A pdb=" N LEU U 290 " --> pdb=" O ASP U 286 " (cutoff:3.500A) Processing helix chain 'U' and resid 304 through 320 Processing helix chain 'PP' and resid 99 through 112 removed outlier: 3.563A pdb=" N ILEPP 108 " --> pdb=" O PHEPP 104 " (cutoff:3.500A) Processing helix chain 'PP' and resid 133 through 141 Processing helix chain 'PP' and resid 149 through 159 Processing helix chain 'PP' and resid 224 through 235 removed outlier: 3.970A pdb=" N GLNPP 230 " --> pdb=" O LEUPP 226 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEUPP 231 " --> pdb=" O LYSPP 227 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALAPP 233 " --> pdb=" O LYSPP 229 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THRPP 234 " --> pdb=" O GLNPP 230 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARGPP 235 " --> pdb=" O LEUPP 231 " (cutoff:3.500A) Processing helix chain 'PP' and resid 236 through 267 removed outlier: 3.973A pdb=" N CYSPP 240 " --> pdb=" O ASNPP 236 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ARGPP 267 " --> pdb=" O ASNPP 263 " (cutoff:3.500A) Processing helix chain 'PP' and resid 335 through 349 removed outlier: 3.898A pdb=" N GLUPP 339 " --> pdb=" O ILEPP 335 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILEPP 340 " --> pdb=" O ASPPP 336 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N CYSPP 341 " --> pdb=" O LEUPP 337 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEUPP 344 " --> pdb=" O ILEPP 340 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILEPP 345 " --> pdb=" O CYSPP 341 " (cutoff:3.500A) Processing helix chain 'PP' and resid 349 through 362 removed outlier: 3.534A pdb=" N LEUPP 354 " --> pdb=" O VALPP 350 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LYSPP 355 " --> pdb=" O LYSPP 351 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLUPP 356 " --> pdb=" O THRPP 352 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILEPP 357 " --> pdb=" O GLYPP 353 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N CYSPP 358 " --> pdb=" O LEUPP 354 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 15 Processing helix chain 'W' and resid 37 through 69 Processing helix chain 'W' and resid 74 through 89 removed outlier: 3.800A pdb=" N ILE W 78 " --> pdb=" O TYR W 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 125 through 130 Processing helix chain 'O' and resid 134 through 139 Processing helix chain 'O' and resid 139 through 148 removed outlier: 3.908A pdb=" N LYS O 148 " --> pdb=" O LYS O 144 " (cutoff:3.500A) Processing helix chain 'O' and resid 154 through 172 Processing helix chain 'O' and resid 182 through 184 No H-bonds generated for 'chain 'O' and resid 182 through 184' Processing helix chain 'O' and resid 245 through 253 Processing helix chain 'O' and resid 254 through 256 No H-bonds generated for 'chain 'O' and resid 254 through 256' Processing helix chain 'O' and resid 260 through 292 removed outlier: 3.905A pdb=" N GLN O 274 " --> pdb=" O ARG O 270 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU O 275 " --> pdb=" O VAL O 271 " (cutoff:3.500A) Processing helix chain 'O' and resid 337 through 349 removed outlier: 3.780A pdb=" N ALA O 347 " --> pdb=" O LYS O 343 " (cutoff:3.500A) Processing helix chain 'O' and resid 354 through 366 removed outlier: 3.848A pdb=" N THR O 365 " --> pdb=" O HIS O 361 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE O 366 " --> pdb=" O SER O 362 " (cutoff:3.500A) Processing helix chain 'Y' and resid 3 through 14 removed outlier: 4.231A pdb=" N SER Y 7 " --> pdb=" O ASP Y 3 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 32 removed outlier: 3.964A pdb=" N GLY Y 32 " --> pdb=" O ASP Y 28 " (cutoff:3.500A) Processing helix chain 'Y' and resid 36 through 43 removed outlier: 3.724A pdb=" N LYS Y 43 " --> pdb=" O CYS Y 39 " (cutoff:3.500A) Processing helix chain 'Y' and resid 46 through 51 Processing helix chain 'Y' and resid 55 through 83 Processing helix chain 'Y' and resid 89 through 93 removed outlier: 3.614A pdb=" N SER Y 92 " --> pdb=" O PRO Y 89 " (cutoff:3.500A) Processing helix chain 'Y' and resid 94 through 102 Processing helix chain 'Y' and resid 110 through 119 Processing helix chain 'Y' and resid 137 through 186 removed outlier: 3.997A pdb=" N GLU Y 186 " --> pdb=" O LYS Y 182 " (cutoff:3.500A) Processing helix chain 'Y' and resid 190 through 219 removed outlier: 4.904A pdb=" N ASN Y 198 " --> pdb=" O PHE Y 194 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLY Y 199 " --> pdb=" O ALA Y 195 " (cutoff:3.500A) Processing helix chain 'Y' and resid 221 through 238 Processing helix chain 'Z' and resid 4 through 14 Processing helix chain 'Z' and resid 21 through 30 Processing helix chain 'Z' and resid 35 through 84 removed outlier: 3.506A pdb=" N LEU Z 39 " --> pdb=" O ASP Z 35 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP Z 50 " --> pdb=" O LEU Z 46 " (cutoff:3.500A) Processing helix chain 'Z' and resid 86 through 127 removed outlier: 3.680A pdb=" N LEU Z 90 " --> pdb=" O SER Z 86 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N MET Z 125 " --> pdb=" O GLU Z 121 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL Z 126 " --> pdb=" O PHE Z 122 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ARG Z 127 " --> pdb=" O GLU Z 123 " (cutoff:3.500A) Processing helix chain 'Z' and resid 134 through 153 Processing helix chain 'UU' and resid 134 through 149 Processing helix chain 'UU' and resid 149 through 159 Processing helix chain 'UU' and resid 167 through 233 removed outlier: 4.499A pdb=" N TYRUU 171 " --> pdb=" O ARGUU 167 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYSUU 172 " --> pdb=" O LYSUU 168 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYSUU 190 " --> pdb=" O THRUU 186 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASPUU 191 " --> pdb=" O ARGUU 187 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VALUU 197 " --> pdb=" O LEUUU 193 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASNUU 200 " --> pdb=" O ASNUU 196 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLNUU 208 " --> pdb=" O TYRUU 204 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VALUU 209 " --> pdb=" O GLNUU 205 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASPUU 215 " --> pdb=" O ALAUU 211 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLNUU 218 " --> pdb=" O GLUUU 214 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLNUU 219 " --> pdb=" O ASPUU 215 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYSUU 231 " --> pdb=" O ILEUU 227 " (cutoff:3.500A) Processing helix chain 'UU' and resid 233 through 265 Processing helix chain 'UU' and resid 287 through 299 removed outlier: 3.830A pdb=" N ASPUU 291 " --> pdb=" O SERUU 287 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILEUU 292 " --> pdb=" O ASNUU 288 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HISUU 294 " --> pdb=" O LEUUU 290 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHEUU 295 " --> pdb=" O ASPUU 291 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASPUU 297 " --> pdb=" O ALAUU 293 " (cutoff:3.500A) Processing helix chain 'UU' and resid 305 through 321 removed outlier: 3.865A pdb=" N GLUUU 314 " --> pdb=" O ASNUU 310 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SERUU 317 " --> pdb=" O ASNUU 313 " (cutoff:3.500A) Processing helix chain 'YY' and resid 3 through 14 removed outlier: 4.231A pdb=" N SERYY 7 " --> pdb=" O ASPYY 3 " (cutoff:3.500A) Processing helix chain 'YY' and resid 16 through 32 removed outlier: 3.964A pdb=" N GLYYY 32 " --> pdb=" O ASPYY 28 " (cutoff:3.500A) Processing helix chain 'YY' and resid 36 through 43 removed outlier: 3.725A pdb=" N LYSYY 43 " --> pdb=" O CYSYY 39 " (cutoff:3.500A) Processing helix chain 'YY' and resid 46 through 51 Processing helix chain 'YY' and resid 55 through 83 Processing helix chain 'YY' and resid 89 through 93 removed outlier: 3.614A pdb=" N SERYY 92 " --> pdb=" O PROYY 89 " (cutoff:3.500A) Processing helix chain 'YY' and resid 94 through 102 Processing helix chain 'YY' and resid 110 through 119 Processing helix chain 'YY' and resid 137 through 186 removed outlier: 3.998A pdb=" N GLUYY 186 " --> pdb=" O LYSYY 182 " (cutoff:3.500A) Processing helix chain 'YY' and resid 190 through 219 removed outlier: 4.904A pdb=" N ASNYY 198 " --> pdb=" O PHEYY 194 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLYYY 199 " --> pdb=" O ALAYY 195 " (cutoff:3.500A) Processing helix chain 'YY' and resid 221 through 238 Processing helix chain 'ZZ' and resid 4 through 15 removed outlier: 3.695A pdb=" N TYRZZ 10 " --> pdb=" O LEUZZ 6 " (cutoff:3.500A) Processing helix chain 'ZZ' and resid 21 through 29 removed outlier: 3.967A pdb=" N GLNZZ 27 " --> pdb=" O GLNZZ 23 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLNZZ 28 " --> pdb=" O GLUZZ 24 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEUZZ 29 " --> pdb=" O PHEZZ 25 " (cutoff:3.500A) Processing helix chain 'ZZ' and resid 35 through 84 removed outlier: 3.699A pdb=" N ARGZZ 52 " --> pdb=" O ALAZZ 48 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALAZZ 59 " --> pdb=" O SERZZ 55 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILEZZ 61 " --> pdb=" O LEUZZ 57 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYSZZ 62 " --> pdb=" O GLUZZ 58 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLNZZ 63 " --> pdb=" O ALAZZ 59 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHEZZ 65 " --> pdb=" O ILEZZ 61 " (cutoff:3.500A) Processing helix chain 'ZZ' and resid 86 through 127 removed outlier: 3.690A pdb=" N LYSZZ 96 " --> pdb=" O ASPZZ 92 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLNZZ 103 " --> pdb=" O ASPZZ 99 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARGZZ 104 " --> pdb=" O LEUZZ 100 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALAZZ 120 " --> pdb=" O THRZZ 116 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLUZZ 121 " --> pdb=" O SERZZ 117 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHEZZ 122 " --> pdb=" O GLUZZ 118 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLUZZ 123 " --> pdb=" O LEUZZ 119 " (cutoff:3.500A) Processing helix chain 'ZZ' and resid 134 through 151 removed outlier: 3.527A pdb=" N SERZZ 145 " --> pdb=" O GLNZZ 141 " (cutoff:3.500A) Processing helix chain 'II' and resid 2 through 15 removed outlier: 3.605A pdb=" N ALAII 15 " --> pdb=" O SERII 11 " (cutoff:3.500A) Processing helix chain 'II' and resid 22 through 39 removed outlier: 3.651A pdb=" N GLUII 33 " --> pdb=" O SERII 29 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYSII 36 " --> pdb=" O TYRII 32 " (cutoff:3.500A) Processing helix chain 'II' and resid 41 through 55 removed outlier: 3.839A pdb=" N CYSII 53 " --> pdb=" O VALII 49 " (cutoff:3.500A) Processing helix chain 'II' and resid 59 through 70 Processing helix chain 'II' and resid 78 through 89 Processing helix chain 'II' and resid 103 through 117 removed outlier: 3.618A pdb=" N LEUII 114 " --> pdb=" O LEUII 110 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VALII 115 " --> pdb=" O CYSII 111 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HISII 116 " --> pdb=" O LYSII 112 " (cutoff:3.500A) Processing helix chain 'II' and resid 118 through 121 Processing helix chain 'II' and resid 128 through 140 Processing helix chain 'II' and resid 141 through 144 removed outlier: 6.338A pdb=" N PHEII 144 " --> pdb=" O GLNII 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'II' and resid 141 through 144' Processing helix chain 'II' and resid 145 through 157 Proline residue: II 151 - end of helix removed outlier: 3.728A pdb=" N TRPII 155 " --> pdb=" O PROII 151 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLNII 156 " --> pdb=" O LEUII 152 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALAII 157 " --> pdb=" O VALII 153 " (cutoff:3.500A) Processing helix chain 'II' and resid 164 through 177 Processing helix chain 'II' and resid 182 through 199 removed outlier: 3.968A pdb=" N LEUII 189 " --> pdb=" O GLYII 185 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEUII 197 " --> pdb=" O ARGII 193 " (cutoff:3.500A) Processing helix chain 'II' and resid 201 through 212 removed outlier: 3.609A pdb=" N GLUII 206 " --> pdb=" O SERII 202 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SERII 207 " --> pdb=" O GLNII 203 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THRII 210 " --> pdb=" O GLUII 206 " (cutoff:3.500A) Processing helix chain 'II' and resid 215 through 223 Processing helix chain 'II' and resid 227 through 242 Processing helix chain 'II' and resid 247 through 268 removed outlier: 3.624A pdb=" N ILEII 262 " --> pdb=" O TYRII 258 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLYII 266 " --> pdb=" O ILEII 262 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALAII 267 " --> pdb=" O HISII 263 " (cutoff:3.500A) Processing helix chain 'II' and resid 295 through 303 Processing helix chain 'II' and resid 336 through 348 removed outlier: 3.776A pdb=" N SERII 341 " --> pdb=" O LYSII 337 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEUII 345 " --> pdb=" O SERII 341 " (cutoff:3.500A) Processing helix chain 'II' and resid 354 through 369 removed outlier: 3.931A pdb=" N ILEII 361 " --> pdb=" O TYRII 357 " (cutoff:3.500A) Processing helix chain 'II' and resid 377 through 388 removed outlier: 4.262A pdb=" N ILEII 381 " --> pdb=" O GLUII 377 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N METII 388 " --> pdb=" O SERII 384 " (cutoff:3.500A) Processing helix chain 'II' and resid 389 through 401 removed outlier: 3.740A pdb=" N ARGII 395 " --> pdb=" O LYSII 391 " (cutoff:3.500A) Processing helix chain 'II' and resid 403 through 408 removed outlier: 3.806A pdb=" N LEUII 408 " --> pdb=" O LYSII 404 " (cutoff:3.500A) Processing helix chain 'II' and resid 409 through 421 removed outlier: 3.814A pdb=" N LEUII 413 " --> pdb=" O ASPII 409 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLYII 419 " --> pdb=" O LYSII 415 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILEII 420 " --> pdb=" O VALII 416 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEUII 421 " --> pdb=" O CYSII 417 " (cutoff:3.500A) Processing helix chain 'II' and resid 432 through 451 removed outlier: 3.841A pdb=" N LYSII 438 " --> pdb=" O GLUII 434 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILEII 443 " --> pdb=" O PHEII 439 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARGII 449 " --> pdb=" O METII 445 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASPII 450 " --> pdb=" O TRPII 446 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLYII 451 " --> pdb=" O SERII 447 " (cutoff:3.500A) Processing helix chain 'II' and resid 456 through 475 removed outlier: 3.714A pdb=" N GLUII 460 " --> pdb=" O CYSII 456 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYRII 464 " --> pdb=" O GLUII 460 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VALII 465 " --> pdb=" O THRII 461 " (cutoff:3.500A) Processing helix chain 'II' and resid 478 through 494 removed outlier: 3.528A pdb=" N ASPII 488 " --> pdb=" O THRII 484 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N METII 489 " --> pdb=" O LEUII 485 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SERII 491 " --> pdb=" O HISII 487 " (cutoff:3.500A) Processing helix chain 'II' and resid 505 through 525 removed outlier: 3.779A pdb=" N THRII 509 " --> pdb=" O ASNII 505 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SERII 514 " --> pdb=" O METII 510 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SERII 515 " --> pdb=" O ALAII 511 " (cutoff:3.500A) Processing helix chain 'II' and resid 531 through 536 removed outlier: 3.673A pdb=" N LEUII 535 " --> pdb=" O ALAII 531 " (cutoff:3.500A) Processing helix chain 'II' and resid 541 through 548 removed outlier: 3.815A pdb=" N VALII 545 " --> pdb=" O ILEII 541 " (cutoff:3.500A) Processing helix chain 'II' and resid 550 through 567 removed outlier: 3.803A pdb=" N LYSII 567 " --> pdb=" O ALAII 563 " (cutoff:3.500A) Processing helix chain 'II' and resid 575 through 593 Processing helix chain 'II' and resid 607 through 618 removed outlier: 4.067A pdb=" N PHEII 611 " --> pdb=" O SERII 607 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILEII 614 " --> pdb=" O PHEII 610 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLUII 616 " --> pdb=" O LYSII 612 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASNII 617 " --> pdb=" O GLNII 613 " (cutoff:3.500A) Processing helix chain 'II' and resid 625 through 631 removed outlier: 3.607A pdb=" N LYSII 629 " --> pdb=" O PHEII 625 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N PHEII 630 " --> pdb=" O LYSII 626 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N PHEII 631 " --> pdb=" O ASNII 627 " (cutoff:3.500A) No H-bonds generated for 'chain 'II' and resid 625 through 631' Processing helix chain 'II' and resid 636 through 639 Processing helix chain 'II' and resid 640 through 655 removed outlier: 3.518A pdb=" N ILEII 644 " --> pdb=" O SERII 640 " (cutoff:3.500A) Processing helix chain 'II' and resid 666 through 677 Processing helix chain 'II' and resid 677 through 682 removed outlier: 3.676A pdb=" N GLYII 682 " --> pdb=" O HISII 678 " (cutoff:3.500A) Processing helix chain 'II' and resid 692 through 707 removed outlier: 3.813A pdb=" N VALII 698 " --> pdb=" O HISII 694 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEUII 701 " --> pdb=" O ARGII 697 " (cutoff:3.500A) Processing helix chain 'II' and resid 711 through 722 removed outlier: 3.781A pdb=" N THRII 720 " --> pdb=" O ALAII 716 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYRII 721 " --> pdb=" O PHEII 717 " (cutoff:3.500A) Processing helix chain 'II' and resid 724 through 728 removed outlier: 3.561A pdb=" N LYSII 727 " --> pdb=" O SERII 724 " (cutoff:3.500A) Processing helix chain 'KK' and resid 6 through 40 removed outlier: 3.755A pdb=" N GLUKK 16 " --> pdb=" O ILEKK 12 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLNKK 18 " --> pdb=" O ASNKK 14 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASPKK 34 " --> pdb=" O GLNKK 30 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILEKK 36 " --> pdb=" O ALAKK 32 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THRKK 37 " --> pdb=" O ILEKK 33 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYSKK 38 " --> pdb=" O ASPKK 34 " (cutoff:3.500A) Processing helix chain 'KK' and resid 49 through 59 Processing helix chain 'KK' and resid 69 through 128 removed outlier: 3.656A pdb=" N SERKK 73 " --> pdb=" O PROKK 69 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THRKK 75 " --> pdb=" O GLYKK 71 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SERKK 87 " --> pdb=" O ALAKK 83 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLNKK 100 " --> pdb=" O GLNKK 96 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALAKK 102 " --> pdb=" O VALKK 98 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N METKK 103 " --> pdb=" O ASPKK 99 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEUKK 118 " --> pdb=" O LEUKK 114 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILEKK 127 " --> pdb=" O HISKK 123 " (cutoff:3.500A) Processing helix chain 'KK' and resid 129 through 136 removed outlier: 3.665A pdb=" N ASPKK 134 " --> pdb=" O SERKK 130 " (cutoff:3.500A) Processing helix chain 'KK' and resid 141 through 159 Processing helix chain 'KK' and resid 159 through 165 removed outlier: 3.579A pdb=" N ASPKK 165 " --> pdb=" O VALKK 161 " (cutoff:3.500A) Processing helix chain 'KK' and resid 172 through 188 Processing helix chain 'KK' and resid 198 through 200 No H-bonds generated for 'chain 'KK' and resid 198 through 200' Processing helix chain 'KK' and resid 201 through 212 removed outlier: 3.593A pdb=" N TYRKK 205 " --> pdb=" O THRKK 201 " (cutoff:3.500A) Processing helix chain 'HH' and resid 6 through 18 removed outlier: 3.570A pdb=" N GLUHH 10 " --> pdb=" O GLUHH 6 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLNHH 14 " --> pdb=" O GLUHH 10 " (cutoff:3.500A) Processing helix chain 'HH' and resid 20 through 39 removed outlier: 3.508A pdb=" N LEUHH 33 " --> pdb=" O THRHH 29 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYRHH 34 " --> pdb=" O LEUHH 30 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYSHH 38 " --> pdb=" O TYRHH 34 " (cutoff:3.500A) Processing helix chain 'HH' and resid 46 through 72 removed outlier: 3.504A pdb=" N ARGHH 56 " --> pdb=" O LEUHH 52 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEUHH 68 " --> pdb=" O GLUHH 64 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEUHH 72 " --> pdb=" O LEUHH 68 " (cutoff:3.500A) Processing helix chain 'HH' and resid 80 through 135 removed outlier: 3.704A pdb=" N GLNHH 87 " --> pdb=" O PHEHH 83 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASNHH 88 " --> pdb=" O THRHH 84 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEUHH 89 " --> pdb=" O LYSHH 85 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEUHH 90 " --> pdb=" O LEUHH 86 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLUHH 91 " --> pdb=" O GLNHH 87 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLUHH 92 " --> pdb=" O ASNHH 88 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SERHH 93 " --> pdb=" O LEUHH 89 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEUHH 96 " --> pdb=" O GLUHH 92 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASPHH 97 " --> pdb=" O SERHH 93 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TYRHH 98 " --> pdb=" O ASNHH 94 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLUHH 99 " --> pdb=" O SERHH 95 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEUHH 101 " --> pdb=" O ASPHH 97 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLNHH 102 " --> pdb=" O TYRHH 98 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLUHH 123 " --> pdb=" O ALAHH 119 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEUHH 128 " --> pdb=" O LEUHH 124 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILEHH 129 " --> pdb=" O METHH 125 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLUHH 130 " --> pdb=" O SERHH 126 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEUHH 131 " --> pdb=" O LYSHH 127 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SERHH 133 " --> pdb=" O ILEHH 129 " (cutoff:3.500A) Processing helix chain 'HH' and resid 147 through 172 removed outlier: 3.840A pdb=" N GLUHH 153 " --> pdb=" O GLYHH 149 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILEHH 166 " --> pdb=" O GLNHH 162 " (cutoff:3.500A) Processing helix chain 'QQ' and resid 129 through 138 Processing helix chain 'QQ' and resid 157 through 181 removed outlier: 3.651A pdb=" N VALQQ 177 " --> pdb=" O ALAQQ 173 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N PHEQQ 178 " --> pdb=" O LEUQQ 174 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLUQQ 179 " --> pdb=" O ASPQQ 175 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYSQQ 180 " --> pdb=" O SERQQ 176 " (cutoff:3.500A) Processing helix chain 'QQ' and resid 184 through 189 removed outlier: 3.654A pdb=" N METQQ 188 " --> pdb=" O GLUQQ 184 " (cutoff:3.500A) Processing helix chain 'QQ' and resid 192 through 220 removed outlier: 4.062A pdb=" N LEUQQ 207 " --> pdb=" O LYSQQ 203 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILEQQ 209 " --> pdb=" O ARGQQ 205 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILEQQ 210 " --> pdb=" O LEUQQ 206 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLNQQ 220 " --> pdb=" O LYSQQ 216 " (cutoff:3.500A) Processing helix chain 'QQ' and resid 228 through 233 Processing helix chain 'QQ' and resid 233 through 288 removed outlier: 3.606A pdb=" N ILEQQ 237 " --> pdb=" O ASPQQ 233 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLUQQ 251 " --> pdb=" O ARGQQ 247 " (cutoff:3.500A) Processing helix chain 'QQ' and resid 297 through 308 removed outlier: 3.764A pdb=" N LYSQQ 302 " --> pdb=" O PROQQ 298 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALAQQ 303 " --> pdb=" O VALQQ 299 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYRQQ 306 " --> pdb=" O LYSQQ 302 " (cutoff:3.500A) Processing helix chain 'QQ' and resid 321 through 332 removed outlier: 3.527A pdb=" N PHEQQ 325 " --> pdb=" O GLYQQ 321 " (cutoff:3.500A) Processing helix chain 'QQ' and resid 352 through 357 removed outlier: 3.697A pdb=" N LEUQQ 356 " --> pdb=" O GLUQQ 352 " (cutoff:3.500A) Processing helix chain 'QQ' and resid 358 through 382 removed outlier: 3.869A pdb=" N GLUQQ 362 " --> pdb=" O PROQQ 358 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLNQQ 376 " --> pdb=" O GLUQQ 372 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N METQQ 377 " --> pdb=" O THRQQ 373 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILEQQ 378 " --> pdb=" O METQQ 374 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SERQQ 379 " --> pdb=" O GLYQQ 375 " (cutoff:3.500A) Processing helix chain 'QQ' and resid 382 through 391 removed outlier: 3.795A pdb=" N ILEQQ 386 " --> pdb=" O HISQQ 382 " (cutoff:3.500A) Processing helix chain 'b' and resid 31 through 43 Processing helix chain 'b' and resid 50 through 77 removed outlier: 3.940A pdb=" N GLU b 54 " --> pdb=" O LEU b 50 " (cutoff:3.500A) Processing helix chain 'b' and resid 83 through 95 Processing helix chain 'd' and resid 41 through 53 Processing helix chain 'd' and resid 59 through 88 Processing helix chain 'd' and resid 94 through 106 Processing helix chain 'd' and resid 107 through 128 removed outlier: 4.132A pdb=" N HIS d 113 " --> pdb=" O GLU d 109 " (cutoff:3.500A) Processing helix chain 'e' and resid 134 through 147 Processing helix chain 'e' and resid 154 through 169 Processing helix chain 'e' and resid 179 through 208 Processing helix chain 'e' and resid 214 through 226 Processing helix chain 'f' and resid 31 through 43 removed outlier: 3.674A pdb=" N ILE f 35 " --> pdb=" O THR f 31 " (cutoff:3.500A) Processing helix chain 'f' and resid 50 through 77 removed outlier: 3.910A pdb=" N ASP f 69 " --> pdb=" O SER f 65 " (cutoff:3.500A) Processing helix chain 'f' and resid 83 through 95 Processing helix chain 'g' and resid 18 through 23 Processing helix chain 'g' and resid 29 through 39 Processing helix chain 'g' and resid 48 through 76 Processing helix chain 'g' and resid 81 through 92 Processing helix chain 'g' and resid 92 through 99 removed outlier: 3.967A pdb=" N LEU g 98 " --> pdb=" O GLU g 94 " (cutoff:3.500A) Processing helix chain 'h' and resid 42 through 53 Processing helix chain 'h' and resid 59 through 88 Processing helix chain 'h' and resid 94 through 106 Processing helix chain 'h' and resid 107 through 131 removed outlier: 3.867A pdb=" N HIS h 113 " --> pdb=" O GLU h 109 " (cutoff:3.500A) Processing helix chain 'c' and resid 18 through 24 Processing helix chain 'c' and resid 29 through 39 Processing helix chain 'c' and resid 47 through 75 removed outlier: 4.410A pdb=" N VAL c 51 " --> pdb=" O SER c 47 " (cutoff:3.500A) Processing helix chain 'c' and resid 81 through 92 Processing helix chain 'c' and resid 92 through 99 Processing helix chain 'a' and resid 134 through 147 Processing helix chain 'a' and resid 154 through 169 Processing helix chain 'a' and resid 179 through 208 Processing helix chain 'a' and resid 214 through 226 Processing helix chain 'TT' and resid 274 through 289 removed outlier: 4.918A pdb=" N GLNTT 284 " --> pdb=" O HISTT 280 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N PHETT 285 " --> pdb=" O LEUTT 281 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLUTT 288 " --> pdb=" O GLNTT 284 " (cutoff:3.500A) Processing helix chain 'TT' and resid 294 through 316 removed outlier: 3.501A pdb=" N THRTT 300 " --> pdb=" O GLNTT 296 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASNTT 307 " --> pdb=" O GLUTT 303 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYSTT 313 " --> pdb=" O METTT 309 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLNTT 314 " --> pdb=" O ASPTT 310 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILETT 316 " --> pdb=" O LEUTT 312 " (cutoff:3.500A) Processing helix chain 'TT' and resid 320 through 331 removed outlier: 3.749A pdb=" N VALTT 325 " --> pdb=" O LYSTT 321 " (cutoff:3.500A) Processing helix chain 'TT' and resid 338 through 348 Processing helix chain 'TT' and resid 349 through 360 removed outlier: 3.617A pdb=" N SERTT 354 " --> pdb=" O LEUTT 350 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ARGTT 355 " --> pdb=" O GLUTT 351 " (cutoff:3.500A) Processing helix chain 'WW' and resid 2 through 15 removed outlier: 3.512A pdb=" N ARGWW 12 " --> pdb=" O ASNWW 8 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLNWW 13 " --> pdb=" O TYRWW 9 " (cutoff:3.500A) Processing helix chain 'WW' and resid 37 through 68 removed outlier: 3.541A pdb=" N ASNWW 41 " --> pdb=" O SERWW 37 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYSWW 42 " --> pdb=" O GLNWW 38 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALAWW 47 " --> pdb=" O LYSWW 43 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLUWW 68 " --> pdb=" O ARGWW 64 " (cutoff:3.500A) Processing helix chain 'WW' and resid 75 through 89 removed outlier: 3.830A pdb=" N GLUWW 79 " --> pdb=" O PROWW 75 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALAWW 80 " --> pdb=" O TYRWW 76 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'LL' and resid 35 through 36 removed outlier: 3.621A pdb=" N METLL 58 " --> pdb=" O PHELL 73 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LYSLL 72 " --> pdb=" O CYSLL 90 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N CYSLL 90 " --> pdb=" O LYSLL 72 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEULL 76 " --> pdb=" O PHELL 86 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILELL 221 " --> pdb=" O TRPLL 5 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SERLL 207 " --> pdb=" O TYRLL 148 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLNLL 160 " --> pdb=" O ASNNN 405 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N GLYNN 386 " --> pdb=" O GLYNN 440 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILENN 442 " --> pdb=" O GLYNN 386 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N THRNN 388 " --> pdb=" O ILENN 442 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'LL' and resid 130 through 132 Processing sheet with id=AA3, first strand: chain 'NN' and resid 107 through 113 removed outlier: 3.608A pdb=" N ARGNN 113 " --> pdb=" O LYSNN 117 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'NN' and resid 117 through 118 current: chain 'NN' and resid 155 through 163 WARNING: can't find start of bonding for strands! previous: chain 'NN' and resid 195 through 196 current: chain 'NN' and resid 210 through 213 Processing sheet with id=AA4, first strand: chain 'NN' and resid 295 through 298 Processing sheet with id=AA5, first strand: chain 'CT' and resid 138 through 142 removed outlier: 4.099A pdb=" N VALCT 140 " --> pdb=" O TYRCT 131 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLUCT 119 " --> pdb=" O ALACT 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'CT' and resid 198 through 201 removed outlier: 3.547A pdb=" N VALCT 199 " --> pdb=" O LYSCT 275 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THRCT 277 " --> pdb=" O VALCT 199 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SERCT 315 " --> pdb=" O VALCT 278 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VALCT 342 " --> pdb=" O ARGCT 316 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ASNCT 318 " --> pdb=" O VALCT 342 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEUCT 337 " --> pdb=" O THRCT 360 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N LYSCT 362 " --> pdb=" O LEUCT 337 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEUCT 339 " --> pdb=" O LYSCT 362 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'CT' and resid 326 through 327 removed outlier: 6.646A pdb=" N ALACT 326 " --> pdb=" O VALCT 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'CT' and resid 410 through 413 removed outlier: 6.091A pdb=" N ARGCT 410 " --> pdb=" O VALCT 476 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VALCT 478 " --> pdb=" O ARGCT 410 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LYSCT 412 " --> pdb=" O VALCT 478 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N VALCT 455 " --> pdb=" O ILECT 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'ce' and resid 527 through 528 removed outlier: 4.036A pdb=" N LEUce 527 " --> pdb=" O TYRce 534 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYRce 534 " --> pdb=" O LEUce 527 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'L' and resid 35 through 36 removed outlier: 3.622A pdb=" N MET L 58 " --> pdb=" O PHE L 73 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LYS L 72 " --> pdb=" O CYS L 90 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N CYS L 90 " --> pdb=" O LYS L 72 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU L 76 " --> pdb=" O PHE L 86 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE L 221 " --> pdb=" O TRP L 5 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER L 207 " --> pdb=" O TYR L 148 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN L 160 " --> pdb=" O ASN N 405 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL N 385 " --> pdb=" O PHE N 404 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ILE N 442 " --> pdb=" O GLY N 386 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR N 388 " --> pdb=" O ILE N 442 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 130 through 132 Processing sheet with id=AB3, first strand: chain 'SK' and resid 7 through 9 Processing sheet with id=AB4, first strand: chain 'CE' and resid 527 through 528 Processing sheet with id=AB5, first strand: chain 'P' and resid 125 through 128 removed outlier: 3.522A pdb=" N VAL N 297 " --> pdb=" O GLU P 126 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE P 128 " --> pdb=" O LYS N 295 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS N 295 " --> pdb=" O ILE P 128 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'P' and resid 165 through 175 removed outlier: 6.828A pdb=" N VAL P 184 " --> pdb=" O GLN P 170 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ARG P 172 " --> pdb=" O VAL P 182 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL P 182 " --> pdb=" O ARG P 172 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ARG P 174 " --> pdb=" O ILE P 180 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE P 180 " --> pdb=" O ARG P 174 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N GLU P 198 " --> pdb=" O ILE P 220 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ILE P 220 " --> pdb=" O GLU P 198 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLN P 200 " --> pdb=" O LEU P 218 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LYS P 206 " --> pdb=" O LEU P 212 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU P 212 " --> pdb=" O LYS P 206 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 270 through 274 removed outlier: 3.585A pdb=" N MET P 274 " --> pdb=" O SER P 279 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN P 299 " --> pdb=" O SER P 322 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER P 322 " --> pdb=" O ASN P 299 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU P 330 " --> pdb=" O LYS P 327 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'OO' and resid 175 through 180 removed outlier: 3.929A pdb=" N LEUOO 180 " --> pdb=" O METOO 201 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N METOO 201 " --> pdb=" O LEUOO 180 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYSOO 237 " --> pdb=" O LEUOO 223 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LYSOO 225 " --> pdb=" O LEUOO 235 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LEUOO 235 " --> pdb=" O LYSOO 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'OO' and resid 186 through 188 Processing sheet with id=AC1, first strand: chain 'OO' and resid 305 through 309 removed outlier: 3.820A pdb=" N VALOO 306 " --> pdb=" O LEUOO 317 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N LYSOO 320 " --> pdb=" O ILEOO 324 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILEOO 324 " --> pdb=" O LYSOO 320 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 105 through 113 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 117 through 118 current: chain 'N' and resid 155 through 163 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 195 through 196 current: chain 'N' and resid 210 through 213 Processing sheet with id=AC3, first strand: chain 'PP' and resid 165 through 175 removed outlier: 7.470A pdb=" N VALPP 184 " --> pdb=" O GLNPP 170 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ARGPP 172 " --> pdb=" O VALPP 182 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VALPP 182 " --> pdb=" O ARGPP 172 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ARGPP 174 " --> pdb=" O ILEPP 180 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILEPP 180 " --> pdb=" O ARGPP 174 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLUPP 198 " --> pdb=" O ILEPP 220 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ILEPP 220 " --> pdb=" O GLUPP 198 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N GLNPP 200 " --> pdb=" O LEUPP 218 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LYSPP 214 " --> pdb=" O PHEPP 204 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'PP' and resid 271 through 273 removed outlier: 3.793A pdb=" N LEUPP 280 " --> pdb=" O ILEPP 298 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARGPP 284 " --> pdb=" O ILEPP 294 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYSPP 295 " --> pdb=" O TRPPP 326 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'O' and resid 175 through 179 removed outlier: 3.534A pdb=" N LYS O 237 " --> pdb=" O LEU O 223 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LYS O 225 " --> pdb=" O LEU O 235 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LEU O 235 " --> pdb=" O LYS O 225 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'O' and resid 186 through 188 removed outlier: 3.502A pdb=" N LYS O 187 " --> pdb=" O PHE O 196 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'O' and resid 209 through 210 removed outlier: 3.623A pdb=" N SER O 210 " --> pdb=" O GLN O 215 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN O 215 " --> pdb=" O SER O 210 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'O' and resid 305 through 309 removed outlier: 3.519A pdb=" N VAL O 306 " --> pdb=" O LEU O 317 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LYS O 314 " --> pdb=" O ILE O 329 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ILE O 329 " --> pdb=" O LYS O 314 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLU O 316 " --> pdb=" O CYS O 327 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N CYS O 327 " --> pdb=" O GLU O 316 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N PHE O 318 " --> pdb=" O VAL O 325 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'II' and resid 288 through 289 removed outlier: 5.808A pdb=" N VALII 288 " --> pdb=" O HISII 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'KK' and resid 214 through 217 Processing sheet with id=AD2, first strand: chain 'b' and resid 46 through 47 removed outlier: 7.525A pdb=" N ARG b 46 " --> pdb=" O ILE a 213 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'e' and resid 212 through 213 removed outlier: 3.957A pdb=" N ILE e 213 " --> pdb=" O ARG f 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'g' and resid 44 through 45 removed outlier: 7.244A pdb=" N ARG g 44 " --> pdb=" O ILE h 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'g' and resid 79 through 80 4088 hydrogen bonds defined for protein. 12120 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 318 hydrogen bonds 636 hydrogen bond angles 0 basepair planarities 132 basepair parallelities 264 stacking parallelities Total time for adding SS restraints: 33.26 Time building geometry restraints manager: 31.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 12368 1.26 - 1.40: 19566 1.40 - 1.54: 46868 1.54 - 1.68: 1414 1.68 - 1.82: 487 Bond restraints: 80703 Sorted by residual: bond pdb=" CG PROTT 272 " pdb=" CD PROTT 272 " ideal model delta sigma weight residual 1.503 1.117 0.386 3.40e-02 8.65e+02 1.29e+02 bond pdb=" C HIS Q 297 " pdb=" N PRO Q 298 " ideal model delta sigma weight residual 1.333 1.407 -0.074 1.44e-02 4.82e+03 2.63e+01 bond pdb=" C1' DG E 75 " pdb=" N9 DG E 75 " ideal model delta sigma weight residual 1.460 1.390 0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C1' DG E 76 " pdb=" N9 DG E 76 " ideal model delta sigma weight residual 1.460 1.390 0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" N PROTT 272 " pdb=" CD PROTT 272 " ideal model delta sigma weight residual 1.473 1.521 -0.048 1.40e-02 5.10e+03 1.17e+01 ... (remaining 80698 not shown) Histogram of bond angle deviations from ideal: 81.63 - 92.25: 2 92.25 - 102.87: 690 102.87 - 113.50: 47313 113.50 - 124.12: 59833 124.12 - 134.74: 2432 Bond angle restraints: 110270 Sorted by residual: angle pdb=" N PROTT 272 " pdb=" CD PROTT 272 " pdb=" CG PROTT 272 " ideal model delta sigma weight residual 103.20 81.63 21.57 1.50e+00 4.44e-01 2.07e+02 angle pdb=" CA PROTT 272 " pdb=" N PROTT 272 " pdb=" CD PROTT 272 " ideal model delta sigma weight residual 112.00 98.62 13.38 1.40e+00 5.10e-01 9.14e+01 angle pdb=" CA GLU Y 115 " pdb=" CB GLU Y 115 " pdb=" CG GLU Y 115 " ideal model delta sigma weight residual 114.10 133.09 -18.99 2.00e+00 2.50e-01 9.01e+01 angle pdb=" CA GLUYY 115 " pdb=" CB GLUYY 115 " pdb=" CG GLUYY 115 " ideal model delta sigma weight residual 114.10 133.08 -18.98 2.00e+00 2.50e-01 9.01e+01 angle pdb=" CA PROTT 272 " pdb=" CB PROTT 272 " pdb=" CG PROTT 272 " ideal model delta sigma weight residual 104.50 88.21 16.29 1.90e+00 2.77e-01 7.35e+01 ... (remaining 110265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.73: 45842 33.73 - 67.46: 2612 67.46 - 101.19: 132 101.19 - 134.93: 0 134.93 - 168.66: 1 Dihedral angle restraints: 48587 sinusoidal: 22157 harmonic: 26430 Sorted by residual: dihedral pdb=" CA TYR I 534 " pdb=" C TYR I 534 " pdb=" N LEU I 535 " pdb=" CA LEU I 535 " ideal model delta harmonic sigma weight residual -180.00 -131.09 -48.91 0 5.00e+00 4.00e-02 9.57e+01 dihedral pdb=" CA ASPKK 68 " pdb=" C ASPKK 68 " pdb=" N PROKK 69 " pdb=" CA PROKK 69 " ideal model delta harmonic sigma weight residual 180.00 138.44 41.56 0 5.00e+00 4.00e-02 6.91e+01 dihedral pdb=" CA ASPCT 116 " pdb=" C ASPCT 116 " pdb=" N ALACT 117 " pdb=" CA ALACT 117 " ideal model delta harmonic sigma weight residual 180.00 141.09 38.91 0 5.00e+00 4.00e-02 6.06e+01 ... (remaining 48584 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 11112 0.059 - 0.117: 1374 0.117 - 0.176: 106 0.176 - 0.235: 8 0.235 - 0.293: 4 Chirality restraints: 12604 Sorted by residual: chirality pdb=" CG LEUPP 362 " pdb=" CB LEUPP 362 " pdb=" CD1 LEUPP 362 " pdb=" CD2 LEUPP 362 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CB ILE Y 12 " pdb=" CA ILE Y 12 " pdb=" CG1 ILE Y 12 " pdb=" CG2 ILE Y 12 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CB ILEYY 12 " pdb=" CA ILEYY 12 " pdb=" CG1 ILEYY 12 " pdb=" CG2 ILEYY 12 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 12601 not shown) Planarity restraints: 12874 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS I 425 " -0.031 2.00e-02 2.50e+03 6.06e-02 3.68e+01 pdb=" C LYS I 425 " 0.105 2.00e-02 2.50e+03 pdb=" O LYS I 425 " -0.039 2.00e-02 2.50e+03 pdb=" N PRO I 426 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS Q 297 " -0.031 2.00e-02 2.50e+03 6.01e-02 3.61e+01 pdb=" C HIS Q 297 " 0.104 2.00e-02 2.50e+03 pdb=" O HIS Q 297 " -0.040 2.00e-02 2.50e+03 pdb=" N PRO Q 298 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VALQQ 391 " 0.027 2.00e-02 2.50e+03 5.29e-02 2.80e+01 pdb=" C VALQQ 391 " -0.091 2.00e-02 2.50e+03 pdb=" O VALQQ 391 " 0.034 2.00e-02 2.50e+03 pdb=" N PROQQ 392 " 0.030 2.00e-02 2.50e+03 ... (remaining 12871 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 219 2.42 - 3.04: 47097 3.04 - 3.66: 124784 3.66 - 4.28: 177784 4.28 - 4.90: 281532 Nonbonded interactions: 631416 Sorted by model distance: nonbonded pdb=" N1 DG D 82 " pdb=" N1 DG E 75 " model vdw 1.800 3.200 nonbonded pdb=" N3 DG D 82 " pdb=" N2 DG E 75 " model vdw 1.894 2.600 nonbonded pdb=" C2 DG D 82 " pdb=" N2 DG E 75 " model vdw 1.962 3.340 nonbonded pdb=" O ASPYY 68 " pdb=" OG SERYY 71 " model vdw 2.087 2.440 nonbonded pdb=" O ASP Y 68 " pdb=" OG SER Y 71 " model vdw 2.087 2.440 ... (remaining 631411 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 221 through 330) } ncs_group { reference = (chain 'CE' and (resid 54 through 567 or resid 589 through 608)) selection = (chain 'ce' and (resid 54 through 313 or resid 339 through 567 or resid 589 thro \ ugh 608)) } ncs_group { reference = (chain 'H' and (resid 5 through 180 or (resid 181 and (name N or name CA or name \ C or name O or name CB or name CG1 or name CG2 or name CD1)))) selection = (chain 'HH' and (resid 5 through 139 or resid 147 through 181)) } ncs_group { reference = (chain 'I' and (resid 25 through 451 or resid 454 through 729)) selection = (chain 'II' and (resid 25 through 117 or resid 130 through 268 or resid 286 thro \ ugh 676 or resid 685 through 729)) } ncs_group { reference = (chain 'K' and (resid 5 through 130 or resid 140 through 218 or resid 222 throug \ h 237)) selection = (chain 'KK' and (resid 5 through 60 or resid 69 through 130 or resid 140 through \ 237)) } ncs_group { reference = chain 'L' selection = chain 'LL' } ncs_group { reference = (chain 'N' and (resid 3 through 60 or (resid 61 and (name N or name CA or name C \ or name O or name CB )) or resid 62 through 309 or resid 317 through 451)) selection = (chain 'NN' and (resid 3 through 165 or (resid 192 and (name N or name CA or nam \ e C or name O or name CB )) or resid 193 through 451)) } ncs_group { reference = (chain 'O' and (resid 126 through 147 or resid 153 through 368)) selection = (chain 'OO' and (resid 126 through 147 or resid 153 through 368)) } ncs_group { reference = (chain 'P' and (resid 98 through 306 or resid 314 through 368)) selection = (chain 'PP' and (resid 98 through 306 or resid 314 through 368)) } ncs_group { reference = (chain 'Q' and (resid 127 through 141 or resid 156 through 310 or (resid 311 thr \ ough 319 and (name N or name CA or name C or name O or name CB )) or resid 320 t \ hrough 394)) selection = chain 'QQ' } ncs_group { reference = chain 'T' selection = chain 'TT' } ncs_group { reference = (chain 'U' and (resid 133 through 266 or resid 277 through 321)) selection = chain 'UU' } ncs_group { reference = (chain 'W' and (resid 1 through 88 or (resid 89 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name OE1 or name NE2)))) selection = chain 'WW' } ncs_group { reference = chain 'Y' selection = chain 'YY' } ncs_group { reference = chain 'Z' selection = chain 'ZZ' } ncs_group { reference = chain 'a' selection = chain 'e' } ncs_group { reference = chain 'b' selection = (chain 'f' and (resid 25 through 54 or (resid 55 and (name N or name CA or name \ C or name O or name CB )) or resid 56 through 103)) } ncs_group { reference = chain 'c' selection = (chain 'g' and (resid 17 through 112 or (resid 113 and (name N or name CA or nam \ e C or name O or name CB )))) } ncs_group { reference = (chain 'd' and ((resid 35 through 38 and (name N or name CA or name C or name O \ or name CB )) or resid 39 through 128)) selection = (chain 'h' and ((resid 35 through 38 and (name N or name CA or name C or name O \ or name CB )) or resid 39 through 128)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 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: 3.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 11.730 Check model and map are aligned: 0.860 Set scattering table: 0.540 Process input model: 179.020 Find NCS groups from input model: 3.730 Set up NCS constraints: 0.680 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 202.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5099 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 : 0.003 0.386 80703 Z= 0.208 Angle : 0.648 21.575 110270 Z= 0.360 Chirality : 0.039 0.293 12604 Planarity : 0.004 0.090 12874 Dihedral : 18.384 168.656 31317 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.02 % Favored : 96.96 % Rotamer: Outliers : 1.37 % Allowed : 0.62 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.03 % Twisted Proline : 0.37 % Twisted General : 0.10 % 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: 0.32 (0.09), residues: 8762 helix: 0.79 (0.07), residues: 5264 sheet: 0.82 (0.23), residues: 547 loop : -0.84 (0.11), residues: 2951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.001 TRPNN 39 HIS 0.013 0.001 HIS H 41 PHE 0.054 0.001 PHEUU 295 TYR 0.026 0.001 TYRce 601 ARG 0.028 0.001 ARG Y 74 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17524 Ramachandran restraints generated. 8762 Oldfield, 0 Emsley, 8762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17524 Ramachandran restraints generated. 8762 Oldfield, 0 Emsley, 8762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1171 residues out of total 8239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 1060 time to evaluate : 6.617 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: 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: 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: 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: I 315 MET cc_start: 0.6731 (mtt) cc_final: 0.6087 (mtm) REVERT: CT 267 MET cc_start: 0.6605 (mpp) cc_final: 0.6258 (mmp) REVERT: CT 479 ILE cc_start: 0.5158 (mt) cc_final: 0.4925 (mt) REVERT: ce 78 TYR cc_start: 0.5877 (m-80) cc_final: 0.5549 (m-10) REVERT: ce 346 TRP cc_start: 0.7654 (t-100) cc_final: 0.7023 (t60) REVERT: ce 414 LEU cc_start: 0.7691 (tp) cc_final: 0.7461 (tp) REVERT: P 318 MET cc_start: 0.3191 (mtp) cc_final: 0.1550 (ttp) REVERT: N 341 MET cc_start: 0.6544 (ppp) cc_final: 0.6226 (tpt) REVERT: PP 318 MET cc_start: -0.0352 (mmm) cc_final: -0.0677 (tpp) REVERT: Y 173 SER cc_start: 0.3660 (OUTLIER) cc_final: 0.3228 (p) REVERT: Y 188 ASP cc_start: 0.6457 (m-30) cc_final: 0.6257 (m-30) REVERT: YY 54 MET cc_start: 0.2548 (mmt) cc_final: 0.1975 (mmp) REVERT: YY 173 SER cc_start: 0.2446 (OUTLIER) cc_final: 0.2054 (p) REVERT: II 1 MET cc_start: 0.1263 (ttt) cc_final: 0.0867 (tpt) REVERT: QQ 188 MET cc_start: -0.6608 (ptt) cc_final: -0.6867 (ptt) REVERT: c 41 TYR cc_start: 0.4898 (m-80) cc_final: 0.4242 (m-80) REVERT: TT 331 MET cc_start: -0.6104 (mtt) cc_final: -0.6955 (ttt) REVERT: WW 1 MET cc_start: -0.0403 (mtt) cc_final: -0.1216 (mpp) outliers start: 111 outliers final: 21 residues processed: 1149 average time/residue: 0.7924 time to fit residues: 1555.1354 Evaluate side-chains 561 residues out of total 8239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 538 time to evaluate : 6.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LL residue 52 GLU Chi-restraints excluded: chain LL residue 59 ARG Chi-restraints excluded: chain LL residue 104 LYS Chi-restraints excluded: chain LL residue 130 VAL Chi-restraints excluded: chain L residue 6 LYS Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain L residue 80 LYS Chi-restraints excluded: chain Y residue 14 ASN Chi-restraints excluded: chain Y residue 65 GLU Chi-restraints excluded: chain Y residue 74 ARG Chi-restraints excluded: chain Y residue 112 ARG Chi-restraints excluded: chain Y residue 173 SER Chi-restraints excluded: chain YY residue 14 ASN Chi-restraints excluded: chain YY residue 65 GLU Chi-restraints excluded: chain YY residue 74 ARG Chi-restraints excluded: chain YY residue 112 ARG Chi-restraints excluded: chain YY residue 115 GLU Chi-restraints excluded: chain YY residue 138 LYS Chi-restraints excluded: chain YY residue 173 SER Chi-restraints excluded: chain e residue 156 ILE Chi-restraints excluded: chain e residue 191 GLU Chi-restraints excluded: chain e residue 209 LYS Chi-restraints excluded: chain a residue 191 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 763 optimal weight: 30.0000 chunk 685 optimal weight: 7.9990 chunk 380 optimal weight: 0.8980 chunk 234 optimal weight: 4.9990 chunk 462 optimal weight: 5.9990 chunk 366 optimal weight: 0.5980 chunk 708 optimal weight: 6.9990 chunk 274 optimal weight: 4.9990 chunk 430 optimal weight: 10.0000 chunk 527 optimal weight: 20.0000 chunk 820 optimal weight: 10.0000 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 HIS ** I 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 617 ASN ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** NN 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NN 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ce 254 ASN ** ce 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SK 31 ASN SK 128 GLN CE 82 GLN CE 211 ASN CE 259 GLN CE 262 HIS ** CE 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 164 HIS ** OO 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 143 HIS ** N 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 435 ASN ** T 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** PP 177 ASN ** Y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 8 HIS Z 41 HIS Z 102 GLN Z 103 GLN ** UU 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** UU 237 HIS ** YY 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** II 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** II 307 HIS II 371 GLN II 581 GLN ** II 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** KK 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** KK 77 ASN KK 163 ASN HH 50 GLN ** HH 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** QQ 135 GLN ** QQ 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** QQ 394 HIS d 60 GLN e 200 HIS ** e 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 17 GLN g 91 ASN ** h 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5388 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 80703 Z= 0.220 Angle : 0.670 11.304 110270 Z= 0.351 Chirality : 0.041 0.307 12604 Planarity : 0.004 0.093 12874 Dihedral : 18.103 174.293 13141 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.22 % Favored : 96.77 % Rotamer: Outliers : 1.71 % Allowed : 9.75 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.03 % Twisted Proline : 0.37 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.09), residues: 8762 helix: 0.98 (0.07), residues: 5457 sheet: 0.54 (0.22), residues: 561 loop : -0.89 (0.12), residues: 2744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRPCE 200 HIS 0.010 0.001 HIS H 41 PHE 0.032 0.002 PHEUU 178 TYR 0.025 0.002 TYR a 193 ARG 0.008 0.001 ARG a 147 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17524 Ramachandran restraints generated. 8762 Oldfield, 0 Emsley, 8762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17524 Ramachandran restraints generated. 8762 Oldfield, 0 Emsley, 8762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 8239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 576 time to evaluate : 6.613 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: 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: 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: I 315 MET cc_start: 0.7144 (mtt) cc_final: 0.6581 (mtm) REVERT: I 569 MET cc_start: 0.7784 (mpp) cc_final: 0.7340 (pmm) REVERT: K 125 MET cc_start: -0.0873 (mtt) cc_final: -0.2055 (mmt) REVERT: CT 334 LEU cc_start: 0.7485 (tp) cc_final: 0.7206 (tt) REVERT: CT 361 MET cc_start: 0.4153 (ptp) cc_final: 0.3826 (mtm) REVERT: L 111 MET cc_start: 0.4129 (OUTLIER) cc_final: 0.3474 (mmp) REVERT: CE 43 MET cc_start: -0.1969 (OUTLIER) cc_final: -0.2300 (tmm) REVERT: N 25 MET cc_start: 0.7984 (mtm) cc_final: 0.7753 (tmm) REVERT: PP 318 MET cc_start: -0.0641 (mmm) cc_final: -0.1314 (mtt) REVERT: Y 65 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8243 (pt0) REVERT: YY 82 MET cc_start: 0.4200 (mmt) cc_final: 0.3256 (mmt) REVERT: II 1 MET cc_start: 0.1389 (ttt) cc_final: 0.0991 (tpt) REVERT: II 315 MET cc_start: 0.4033 (OUTLIER) cc_final: 0.3398 (tmm) REVERT: II 388 MET cc_start: 0.5793 (OUTLIER) cc_final: 0.5453 (mmm) REVERT: HH 125 MET cc_start: 0.3905 (ptt) cc_final: 0.3225 (ptt) REVERT: a 181 MET cc_start: 0.7509 (pmm) cc_final: 0.7105 (pmm) REVERT: TT 331 MET cc_start: -0.5860 (mtt) cc_final: -0.6923 (ttt) outliers start: 138 outliers final: 58 residues processed: 666 average time/residue: 0.7403 time to fit residues: 854.2759 Evaluate side-chains 526 residues out of total 8239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 463 time to evaluate : 6.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain LL residue 130 VAL Chi-restraints excluded: chain NN residue 244 GLN Chi-restraints excluded: chain NN residue 341 MET Chi-restraints excluded: chain NN residue 416 LEU Chi-restraints excluded: chain CT residue 314 LEU Chi-restraints excluded: chain CT residue 350 ILE Chi-restraints excluded: chain ce residue 154 VAL Chi-restraints excluded: chain ce residue 257 LEU Chi-restraints excluded: chain ce residue 279 ASP Chi-restraints excluded: chain ce residue 352 ASP Chi-restraints excluded: chain ce residue 500 PHE Chi-restraints excluded: chain ce residue 558 LEU Chi-restraints excluded: chain L residue 111 MET Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 159 ARG Chi-restraints excluded: chain CE residue 43 MET Chi-restraints excluded: chain CE residue 88 THR Chi-restraints excluded: chain CE residue 202 ASP Chi-restraints excluded: chain CE residue 234 VAL Chi-restraints excluded: chain CE residue 442 ILE Chi-restraints excluded: chain CE residue 544 ASP Chi-restraints excluded: chain CE residue 548 ILE Chi-restraints excluded: chain CE residue 559 ILE Chi-restraints excluded: chain CE residue 592 THR Chi-restraints excluded: chain P residue 156 TYR Chi-restraints excluded: chain P residue 197 PHE Chi-restraints excluded: chain P residue 274 MET Chi-restraints excluded: chain P residue 304 MET Chi-restraints excluded: chain N residue 87 PHE Chi-restraints excluded: chain N residue 243 VAL Chi-restraints excluded: chain N residue 308 ASN Chi-restraints excluded: chain N residue 331 ILE Chi-restraints excluded: chain N residue 393 ILE Chi-restraints excluded: chain N residue 427 VAL Chi-restraints excluded: chain O residue 275 LEU Chi-restraints excluded: chain Y residue 14 ASN Chi-restraints excluded: chain Y residue 65 GLU Chi-restraints excluded: chain Z residue 41 HIS Chi-restraints excluded: chain YY residue 14 ASN Chi-restraints excluded: chain YY residue 65 GLU Chi-restraints excluded: chain II residue 315 MET Chi-restraints excluded: chain II residue 388 MET Chi-restraints excluded: chain II residue 536 ILE Chi-restraints excluded: chain II residue 599 SER Chi-restraints excluded: chain II residue 625 PHE Chi-restraints excluded: chain II residue 696 LEU Chi-restraints excluded: chain II residue 698 VAL Chi-restraints excluded: chain II residue 726 SER Chi-restraints excluded: chain HH residue 22 VAL Chi-restraints excluded: chain HH residue 26 LEU Chi-restraints excluded: chain b residue 66 VAL Chi-restraints excluded: chain b residue 69 ASP Chi-restraints excluded: chain d residue 60 GLN Chi-restraints excluded: chain d residue 105 ILE Chi-restraints excluded: chain d residue 110 LEU Chi-restraints excluded: chain e residue 147 ARG Chi-restraints excluded: chain e residue 209 LYS Chi-restraints excluded: chain g residue 76 LYS Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain a residue 147 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 456 optimal weight: 6.9990 chunk 254 optimal weight: 5.9990 chunk 683 optimal weight: 20.0000 chunk 559 optimal weight: 3.9990 chunk 226 optimal weight: 9.9990 chunk 822 optimal weight: 9.9990 chunk 888 optimal weight: 9.9990 chunk 732 optimal weight: 20.0000 chunk 815 optimal weight: 10.0000 chunk 280 optimal weight: 0.7980 chunk 659 optimal weight: 50.0000 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 338 HIS ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** NN 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CT 440 HIS ** ce 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ce 211 ASN ** ce 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ce 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ce 542 GLN ** ce 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SK 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CE 399 GLN ** CE 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CE 484 GLN P 275 ASN Q 169 ASN OO 220 HIS ** OO 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 143 HIS ** N 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 405 ASN ** N 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 218 GLN Y 79 GLN Z 41 HIS ** UU 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** YY 79 GLN ** II 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** II 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** II 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** KK 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** KK 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** KK 107 GLN ** HH 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HH 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HH 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** QQ 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 51 GLN ** c 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 174 GLN a 200 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5560 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 80703 Z= 0.254 Angle : 0.650 16.937 110270 Z= 0.342 Chirality : 0.040 0.258 12604 Planarity : 0.004 0.079 12874 Dihedral : 18.156 175.584 13086 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.14 % Favored : 96.85 % Rotamer: Outliers : 1.92 % Allowed : 12.92 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.03 % Twisted Proline : 0.37 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.09), residues: 8762 helix: 1.15 (0.07), residues: 5470 sheet: 0.32 (0.21), residues: 559 loop : -0.92 (0.12), residues: 2733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP e 178 HIS 0.024 0.001 HIS Z 41 PHE 0.029 0.002 PHE f 62 TYR 0.047 0.002 TYR O 163 ARG 0.010 0.001 ARGCE 295 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17524 Ramachandran restraints generated. 8762 Oldfield, 0 Emsley, 8762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17524 Ramachandran restraints generated. 8762 Oldfield, 0 Emsley, 8762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 8239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 465 time to evaluate : 6.624 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 MET cc_start: 0.6299 (mpp) cc_final: 0.5848 (mpp) REVERT: I 315 MET cc_start: 0.6778 (mtt) cc_final: 0.6372 (mtm) REVERT: I 476 ASP cc_start: 0.7506 (OUTLIER) cc_final: 0.7242 (p0) REVERT: K 125 MET cc_start: -0.0573 (mtt) cc_final: -0.1630 (mmt) REVERT: CT 361 MET cc_start: 0.4444 (OUTLIER) cc_final: 0.3917 (mtm) REVERT: ce 127 PHE cc_start: 0.6783 (OUTLIER) cc_final: 0.6370 (t80) REVERT: L 111 MET cc_start: 0.4643 (mmp) cc_final: 0.4092 (mmp) REVERT: CE 458 MET cc_start: 0.7028 (ppp) cc_final: 0.6457 (ppp) REVERT: CE 485 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9186 (mm) REVERT: N 25 MET cc_start: 0.8151 (mtm) cc_final: 0.7890 (tmm) REVERT: PP 318 MET cc_start: -0.0657 (mmm) cc_final: -0.1255 (mtt) REVERT: Z 41 HIS cc_start: 0.7101 (OUTLIER) cc_final: 0.6617 (p-80) REVERT: YY 82 MET cc_start: 0.3889 (mmt) cc_final: 0.2881 (mmt) REVERT: HH 125 MET cc_start: 0.4048 (ptt) cc_final: 0.3601 (ppp) REVERT: TT 331 MET cc_start: -0.5904 (mtt) cc_final: -0.6813 (ttt) outliers start: 155 outliers final: 79 residues processed: 586 average time/residue: 0.7204 time to fit residues: 744.1874 Evaluate side-chains 512 residues out of total 8239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 428 time to evaluate : 6.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain I residue 476 ASP Chi-restraints excluded: chain I residue 545 VAL Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain LL residue 130 VAL Chi-restraints excluded: chain LL residue 219 GLU Chi-restraints excluded: chain NN residue 244 GLN Chi-restraints excluded: chain NN residue 341 MET Chi-restraints excluded: chain NN residue 416 LEU Chi-restraints excluded: chain CT residue 293 PHE Chi-restraints excluded: chain CT residue 318 ASN Chi-restraints excluded: chain CT residue 350 ILE Chi-restraints excluded: chain CT residue 361 MET Chi-restraints excluded: chain ce residue 127 PHE Chi-restraints excluded: chain ce residue 154 VAL Chi-restraints excluded: chain ce residue 257 LEU Chi-restraints excluded: chain ce residue 279 ASP Chi-restraints excluded: chain ce residue 352 ASP Chi-restraints excluded: chain ce residue 378 ASP Chi-restraints excluded: chain ce residue 458 MET Chi-restraints excluded: chain ce residue 500 PHE Chi-restraints excluded: chain ce residue 558 LEU Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain L residue 159 ARG Chi-restraints excluded: chain L residue 185 ASN Chi-restraints excluded: chain SK residue 146 LEU Chi-restraints excluded: chain CE residue 85 LEU Chi-restraints excluded: chain CE residue 167 PHE Chi-restraints excluded: chain CE residue 168 THR Chi-restraints excluded: chain CE residue 202 ASP Chi-restraints excluded: chain CE residue 234 VAL Chi-restraints excluded: chain CE residue 352 ASP Chi-restraints excluded: chain CE residue 385 ASP Chi-restraints excluded: chain CE residue 438 ILE Chi-restraints excluded: chain CE residue 442 ILE Chi-restraints excluded: chain CE residue 485 LEU Chi-restraints excluded: chain CE residue 544 ASP Chi-restraints excluded: chain CE residue 559 ILE Chi-restraints excluded: chain CE residue 564 SER Chi-restraints excluded: chain CE residue 592 THR Chi-restraints excluded: chain P residue 183 LEU Chi-restraints excluded: chain P residue 187 TYR Chi-restraints excluded: chain P residue 197 PHE Chi-restraints excluded: chain P residue 250 ILE Chi-restraints excluded: chain P residue 304 MET Chi-restraints excluded: chain Q residue 167 GLU Chi-restraints excluded: chain Q residue 353 VAL Chi-restraints excluded: chain OO residue 306 VAL Chi-restraints excluded: chain N residue 87 PHE Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 243 VAL Chi-restraints excluded: chain N residue 301 GLU Chi-restraints excluded: chain N residue 308 ASN Chi-restraints excluded: chain N residue 389 LEU Chi-restraints excluded: chain N residue 393 ILE Chi-restraints excluded: chain N residue 427 VAL Chi-restraints excluded: chain Y residue 14 ASN Chi-restraints excluded: chain Z residue 41 HIS Chi-restraints excluded: chain Z residue 90 LEU Chi-restraints excluded: chain YY residue 14 ASN Chi-restraints excluded: chain YY residue 19 LEU Chi-restraints excluded: chain YY residue 54 MET Chi-restraints excluded: chain II residue 331 MET Chi-restraints excluded: chain II residue 435 PHE Chi-restraints excluded: chain II residue 536 ILE Chi-restraints excluded: chain II residue 625 PHE Chi-restraints excluded: chain II residue 630 PHE Chi-restraints excluded: chain II residue 686 TRP Chi-restraints excluded: chain II residue 696 LEU Chi-restraints excluded: chain II residue 698 VAL Chi-restraints excluded: chain HH residue 25 GLU Chi-restraints excluded: chain HH residue 26 LEU Chi-restraints excluded: chain HH residue 31 ASP Chi-restraints excluded: chain b residue 66 VAL Chi-restraints excluded: chain b residue 69 ASP Chi-restraints excluded: chain d residue 105 ILE Chi-restraints excluded: chain e residue 147 ARG Chi-restraints excluded: chain e residue 209 LYS Chi-restraints excluded: chain g residue 76 LYS Chi-restraints excluded: chain a residue 147 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 812 optimal weight: 10.0000 chunk 618 optimal weight: 50.0000 chunk 426 optimal weight: 5.9990 chunk 91 optimal weight: 50.0000 chunk 392 optimal weight: 7.9990 chunk 552 optimal weight: 0.0970 chunk 825 optimal weight: 0.9990 chunk 873 optimal weight: 20.0000 chunk 431 optimal weight: 4.9990 chunk 782 optimal weight: 30.0000 chunk 235 optimal weight: 0.0470 overall best weight: 2.4282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NN 95 HIS ** NN 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ce 74 ASN ** ce 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ce 381 GLN ** ce 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CE 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CE 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OO 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 143 HIS N 160 GLN ** N 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 41 HIS ** UU 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** YY 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ZZ 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** II 124 HIS ** II 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** II 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** KK 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HH 50 GLN HH 62 ASN HH 113 GLN ** QQ 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 187 GLN ** e 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 227 GLN ** c 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5518 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 80703 Z= 0.171 Angle : 0.594 14.010 110270 Z= 0.307 Chirality : 0.039 0.350 12604 Planarity : 0.004 0.067 12874 Dihedral : 18.121 176.540 13080 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.14 % Favored : 96.85 % Rotamer: Outliers : 1.71 % Allowed : 14.45 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.03 % Twisted Proline : 0.37 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.09), residues: 8762 helix: 1.35 (0.07), residues: 5478 sheet: 0.50 (0.22), residues: 528 loop : -0.92 (0.11), residues: 2756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP e 178 HIS 0.008 0.001 HIS H 41 PHE 0.030 0.001 PHE a 228 TYR 0.022 0.001 TYRCE 137 ARG 0.009 0.000 ARG N 74 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17524 Ramachandran restraints generated. 8762 Oldfield, 0 Emsley, 8762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17524 Ramachandran restraints generated. 8762 Oldfield, 0 Emsley, 8762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 8239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 474 time to evaluate : 6.566 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 MET cc_start: 0.6444 (mpp) cc_final: 0.6057 (mpp) REVERT: I 294 THR cc_start: 0.1179 (OUTLIER) cc_final: 0.0678 (m) REVERT: I 315 MET cc_start: 0.6685 (mtt) cc_final: 0.6287 (mtm) REVERT: K 125 MET cc_start: -0.0616 (mtt) cc_final: -0.1457 (mmt) REVERT: K 179 MET cc_start: 0.4335 (mmm) cc_final: 0.3932 (mmp) REVERT: ce 127 PHE cc_start: 0.6685 (OUTLIER) cc_final: 0.6366 (t80) REVERT: L 111 MET cc_start: 0.4495 (mmp) cc_final: 0.3998 (mmp) REVERT: CE 458 MET cc_start: 0.6943 (ppp) cc_final: 0.6497 (ppp) REVERT: N 33 TYR cc_start: 0.6972 (t80) cc_final: 0.6633 (t80) REVERT: N 341 MET cc_start: 0.7771 (pmm) cc_final: 0.6818 (ptp) REVERT: PP 318 MET cc_start: -0.0687 (mmm) cc_final: -0.1258 (mtt) REVERT: W 1 MET cc_start: 0.4509 (tmm) cc_final: 0.3999 (tmm) REVERT: YY 82 MET cc_start: 0.4126 (mmt) cc_final: 0.3188 (mmt) REVERT: II 445 MET cc_start: 0.8377 (ptp) cc_final: 0.8132 (ptp) REVERT: II 586 MET cc_start: 0.6085 (ppp) cc_final: 0.5704 (ppp) REVERT: HH 125 MET cc_start: 0.3966 (ptt) cc_final: 0.3165 (ptt) REVERT: QQ 335 MET cc_start: 0.2210 (pmm) cc_final: 0.1924 (pmm) REVERT: TT 331 MET cc_start: -0.5924 (mtt) cc_final: -0.6837 (ttt) outliers start: 138 outliers final: 75 residues processed: 581 average time/residue: 0.6748 time to fit residues: 689.5399 Evaluate side-chains 508 residues out of total 8239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 431 time to evaluate : 6.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain I residue 294 THR Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain LL residue 85 MET Chi-restraints excluded: chain LL residue 99 VAL Chi-restraints excluded: chain LL residue 130 VAL Chi-restraints excluded: chain LL residue 142 TRP Chi-restraints excluded: chain LL residue 217 MET Chi-restraints excluded: chain LL residue 219 GLU Chi-restraints excluded: chain NN residue 146 MET Chi-restraints excluded: chain NN residue 215 VAL Chi-restraints excluded: chain NN residue 244 GLN Chi-restraints excluded: chain NN residue 341 MET Chi-restraints excluded: chain CT residue 256 THR Chi-restraints excluded: chain CT residue 350 ILE Chi-restraints excluded: chain ce residue 74 ASN Chi-restraints excluded: chain ce residue 127 PHE Chi-restraints excluded: chain ce residue 154 VAL Chi-restraints excluded: chain ce residue 176 VAL Chi-restraints excluded: chain ce residue 257 LEU Chi-restraints excluded: chain ce residue 279 ASP Chi-restraints excluded: chain ce residue 334 VAL Chi-restraints excluded: chain ce residue 458 MET Chi-restraints excluded: chain ce residue 558 LEU Chi-restraints excluded: chain L residue 58 MET Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain CE residue 86 THR Chi-restraints excluded: chain CE residue 168 THR Chi-restraints excluded: chain CE residue 169 MET Chi-restraints excluded: chain CE residue 234 VAL Chi-restraints excluded: chain CE residue 377 LEU Chi-restraints excluded: chain CE residue 438 ILE Chi-restraints excluded: chain CE residue 442 ILE Chi-restraints excluded: chain CE residue 482 VAL Chi-restraints excluded: chain CE residue 485 LEU Chi-restraints excluded: chain CE residue 488 ASP Chi-restraints excluded: chain CE residue 544 ASP Chi-restraints excluded: chain CE residue 592 THR Chi-restraints excluded: chain P residue 183 LEU Chi-restraints excluded: chain P residue 197 PHE Chi-restraints excluded: chain P residue 304 MET Chi-restraints excluded: chain Q residue 167 GLU Chi-restraints excluded: chain OO residue 306 VAL Chi-restraints excluded: chain N residue 87 PHE Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain N residue 219 ILE Chi-restraints excluded: chain N residue 220 TYR Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 243 VAL Chi-restraints excluded: chain N residue 301 GLU Chi-restraints excluded: chain N residue 308 ASN Chi-restraints excluded: chain N residue 389 LEU Chi-restraints excluded: chain N residue 427 VAL Chi-restraints excluded: chain U residue 314 GLU Chi-restraints excluded: chain Z residue 41 HIS Chi-restraints excluded: chain UU residue 208 GLN Chi-restraints excluded: chain YY residue 54 MET Chi-restraints excluded: chain II residue 536 ILE Chi-restraints excluded: chain II residue 625 PHE Chi-restraints excluded: chain II residue 630 PHE Chi-restraints excluded: chain II residue 686 TRP Chi-restraints excluded: chain II residue 698 VAL Chi-restraints excluded: chain HH residue 25 GLU Chi-restraints excluded: chain HH residue 26 LEU Chi-restraints excluded: chain b residue 86 ASP Chi-restraints excluded: chain e residue 147 ARG Chi-restraints excluded: chain e residue 209 LYS Chi-restraints excluded: chain f residue 98 LEU Chi-restraints excluded: chain g residue 43 GLN Chi-restraints excluded: chain g residue 64 ILE Chi-restraints excluded: chain g residue 76 LYS Chi-restraints excluded: chain h residue 55 ASP Chi-restraints excluded: chain a residue 147 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 727 optimal weight: 5.9990 chunk 496 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 650 optimal weight: 5.9990 chunk 360 optimal weight: 9.9990 chunk 745 optimal weight: 9.9990 chunk 604 optimal weight: 40.0000 chunk 1 optimal weight: 0.8980 chunk 446 optimal weight: 0.8980 chunk 784 optimal weight: 1.9990 chunk 220 optimal weight: 5.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** NN 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NN 95 HIS ** NN 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ce 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ce 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CE 406 GLN ** CE 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CE 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 170 GLN ** OO 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 143 HIS ** N 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** PP 166 GLN Z 41 HIS ** UU 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** UU 217 ASN ** YY 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ZZ 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** II 471 ASN ** II 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** II 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** KK 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HH 8 GLN HH 13 GLN ** QQ 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 99 GLN e 187 GLN e 207 HIS ** c 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5562 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 80703 Z= 0.181 Angle : 0.592 13.910 110270 Z= 0.308 Chirality : 0.039 0.359 12604 Planarity : 0.004 0.063 12874 Dihedral : 18.085 175.599 13076 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.21 % Favored : 96.78 % Rotamer: Outliers : 1.85 % Allowed : 15.45 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.03 % Twisted Proline : 0.37 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.09), residues: 8762 helix: 1.46 (0.07), residues: 5475 sheet: 0.38 (0.22), residues: 539 loop : -0.88 (0.12), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP e 178 HIS 0.012 0.001 HIS T 280 PHE 0.030 0.001 PHE T 341 TYR 0.019 0.001 TYR c 41 ARG 0.012 0.000 ARGce 392 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17524 Ramachandran restraints generated. 8762 Oldfield, 0 Emsley, 8762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17524 Ramachandran restraints generated. 8762 Oldfield, 0 Emsley, 8762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 8239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 447 time to evaluate : 6.583 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: 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: A 330 MET cc_start: 0.6736 (mpp) cc_final: 0.6332 (mpp) REVERT: I 315 MET cc_start: 0.6673 (mtt) cc_final: 0.6256 (mtm) REVERT: K 125 MET cc_start: -0.0654 (mtt) cc_final: -0.1357 (mmt) REVERT: K 179 MET cc_start: 0.4401 (mmm) cc_final: 0.4092 (mmp) REVERT: ce 127 PHE cc_start: 0.6921 (OUTLIER) cc_final: 0.6569 (t80) REVERT: ce 277 ASN cc_start: 0.7030 (OUTLIER) cc_final: 0.6659 (p0) REVERT: L 111 MET cc_start: 0.4269 (mmp) cc_final: 0.3815 (mmp) REVERT: CE 458 MET cc_start: 0.6791 (ppp) cc_final: 0.6281 (ppp) REVERT: Q 188 MET cc_start: -0.1510 (ptt) cc_final: -0.1738 (ptt) REVERT: N 341 MET cc_start: 0.7733 (pmm) cc_final: 0.6962 (ptp) REVERT: T 340 MET cc_start: -0.3238 (OUTLIER) cc_final: -0.3439 (ppp) REVERT: PP 318 MET cc_start: -0.0597 (mmm) cc_final: -0.1230 (mtt) REVERT: W 1 MET cc_start: 0.5325 (tmm) cc_final: 0.5048 (tmm) REVERT: Y 82 MET cc_start: 0.6008 (mmt) cc_final: 0.5571 (mmt) REVERT: Z 41 HIS cc_start: 0.6956 (OUTLIER) cc_final: 0.6378 (p-80) REVERT: YY 82 MET cc_start: 0.5077 (mmt) cc_final: 0.3955 (mmt) REVERT: II 156 GLN cc_start: 0.0680 (OUTLIER) cc_final: 0.0440 (mm-40) REVERT: II 468 MET cc_start: 0.7567 (tmm) cc_final: 0.7148 (tmm) REVERT: HH 125 MET cc_start: 0.4028 (ptt) cc_final: 0.3451 (ppp) REVERT: f 64 GLU cc_start: 0.5574 (pt0) cc_final: 0.5335 (pt0) REVERT: c 54 THR cc_start: 0.7163 (p) cc_final: 0.6760 (p) REVERT: TT 331 MET cc_start: -0.5987 (mtt) cc_final: -0.6860 (ttt) outliers start: 150 outliers final: 89 residues processed: 567 average time/residue: 0.6779 time to fit residues: 677.8118 Evaluate side-chains 513 residues out of total 8239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 419 time to evaluate : 7.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain I residue 545 VAL Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain LL residue 85 MET Chi-restraints excluded: chain LL residue 130 VAL Chi-restraints excluded: chain LL residue 142 TRP Chi-restraints excluded: chain LL residue 149 PHE Chi-restraints excluded: chain LL residue 219 GLU Chi-restraints excluded: chain NN residue 215 VAL Chi-restraints excluded: chain NN residue 244 GLN Chi-restraints excluded: chain NN residue 341 MET Chi-restraints excluded: chain NN residue 416 LEU Chi-restraints excluded: chain CT residue 256 THR Chi-restraints excluded: chain CT residue 325 LEU Chi-restraints excluded: chain CT residue 334 LEU Chi-restraints excluded: chain CT residue 350 ILE Chi-restraints excluded: chain ce residue 74 ASN Chi-restraints excluded: chain ce residue 127 PHE Chi-restraints excluded: chain ce residue 154 VAL Chi-restraints excluded: chain ce residue 176 VAL Chi-restraints excluded: chain ce residue 257 LEU Chi-restraints excluded: chain ce residue 277 ASN Chi-restraints excluded: chain ce residue 279 ASP Chi-restraints excluded: chain ce residue 334 VAL Chi-restraints excluded: chain ce residue 458 MET Chi-restraints excluded: chain ce residue 500 PHE Chi-restraints excluded: chain ce residue 558 LEU Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 58 MET Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain SK residue 33 LEU Chi-restraints excluded: chain SK residue 146 LEU Chi-restraints excluded: chain CE residue 85 LEU Chi-restraints excluded: chain CE residue 86 THR Chi-restraints excluded: chain CE residue 88 THR Chi-restraints excluded: chain CE residue 168 THR Chi-restraints excluded: chain CE residue 169 MET Chi-restraints excluded: chain CE residue 186 TYR Chi-restraints excluded: chain CE residue 234 VAL Chi-restraints excluded: chain CE residue 352 ASP Chi-restraints excluded: chain CE residue 377 LEU Chi-restraints excluded: chain CE residue 385 ASP Chi-restraints excluded: chain CE residue 438 ILE Chi-restraints excluded: chain CE residue 442 ILE Chi-restraints excluded: chain CE residue 482 VAL Chi-restraints excluded: chain CE residue 485 LEU Chi-restraints excluded: chain CE residue 488 ASP Chi-restraints excluded: chain CE residue 544 ASP Chi-restraints excluded: chain CE residue 592 THR Chi-restraints excluded: chain P residue 197 PHE Chi-restraints excluded: chain P residue 304 MET Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain Q residue 167 GLU Chi-restraints excluded: chain Q residue 185 MET Chi-restraints excluded: chain OO residue 306 VAL Chi-restraints excluded: chain N residue 87 PHE Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain N residue 219 ILE Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 243 VAL Chi-restraints excluded: chain N residue 301 GLU Chi-restraints excluded: chain N residue 308 ASN Chi-restraints excluded: chain N residue 389 LEU Chi-restraints excluded: chain N residue 417 CYS Chi-restraints excluded: chain N residue 427 VAL Chi-restraints excluded: chain T residue 340 MET Chi-restraints excluded: chain W residue 46 LEU Chi-restraints excluded: chain Y residue 14 ASN Chi-restraints excluded: chain Z residue 41 HIS Chi-restraints excluded: chain UU residue 208 GLN Chi-restraints excluded: chain YY residue 19 LEU Chi-restraints excluded: chain II residue 156 GLN Chi-restraints excluded: chain II residue 478 LEU Chi-restraints excluded: chain II residue 525 GLN Chi-restraints excluded: chain II residue 536 ILE Chi-restraints excluded: chain II residue 625 PHE Chi-restraints excluded: chain II residue 630 PHE Chi-restraints excluded: chain II residue 686 TRP Chi-restraints excluded: chain II residue 698 VAL Chi-restraints excluded: chain HH residue 22 VAL Chi-restraints excluded: chain HH residue 26 LEU Chi-restraints excluded: chain b residue 86 ASP Chi-restraints excluded: chain b residue 98 LEU Chi-restraints excluded: chain e residue 147 ARG Chi-restraints excluded: chain e residue 209 LYS Chi-restraints excluded: chain f residue 98 LEU Chi-restraints excluded: chain g residue 64 ILE Chi-restraints excluded: chain g residue 76 LYS Chi-restraints excluded: chain h residue 55 ASP Chi-restraints excluded: chain a residue 147 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 293 optimal weight: 7.9990 chunk 786 optimal weight: 7.9990 chunk 172 optimal weight: 30.0000 chunk 513 optimal weight: 20.0000 chunk 215 optimal weight: 3.9990 chunk 874 optimal weight: 3.9990 chunk 726 optimal weight: 6.9990 chunk 404 optimal weight: 40.0000 chunk 72 optimal weight: 0.7980 chunk 289 optimal weight: 9.9990 chunk 459 optimal weight: 1.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 590 ASN ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LL 160 GLN ** NN 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NN 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ce 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ce 74 ASN ** ce 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CE 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CE 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OO 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 143 HIS ** N 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 41 HIS UU 148 ASN ** UU 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** YY 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ZZ 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** II 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** II 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** KK 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** QQ 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5598 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 80703 Z= 0.187 Angle : 0.604 15.365 110270 Z= 0.312 Chirality : 0.039 0.341 12604 Planarity : 0.004 0.064 12874 Dihedral : 18.113 175.643 13076 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.09 % Favored : 96.90 % Rotamer: Outliers : 1.88 % Allowed : 16.21 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.03 % Twisted Proline : 0.37 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.09), residues: 8762 helix: 1.50 (0.07), residues: 5478 sheet: 0.34 (0.22), residues: 549 loop : -0.91 (0.11), residues: 2735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP e 178 HIS 0.011 0.001 HIS Z 41 PHE 0.028 0.001 PHE T 341 TYR 0.021 0.001 TYR A 315 ARG 0.008 0.000 ARG B 318 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17524 Ramachandran restraints generated. 8762 Oldfield, 0 Emsley, 8762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17524 Ramachandran restraints generated. 8762 Oldfield, 0 Emsley, 8762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 8239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 430 time to evaluate : 6.659 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: 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: I 315 MET cc_start: 0.6671 (mtt) cc_final: 0.6252 (mtm) REVERT: I 476 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.7281 (p0) REVERT: I 586 MET cc_start: 0.9222 (mmt) cc_final: 0.8869 (ppp) REVERT: K 125 MET cc_start: -0.0734 (mtt) cc_final: -0.1238 (mmt) REVERT: ce 127 PHE cc_start: 0.6992 (OUTLIER) cc_final: 0.6695 (t80) REVERT: ce 277 ASN cc_start: 0.7003 (OUTLIER) cc_final: 0.6622 (p0) REVERT: L 111 MET cc_start: 0.4632 (OUTLIER) cc_final: 0.4188 (mmp) REVERT: CE 458 MET cc_start: 0.6755 (ppp) cc_final: 0.6357 (ppp) REVERT: N 341 MET cc_start: 0.7551 (pmm) cc_final: 0.6692 (ptp) REVERT: PP 318 MET cc_start: -0.0557 (mmm) cc_final: -0.1074 (mtt) REVERT: W 1 MET cc_start: 0.5464 (tmm) cc_final: 0.5169 (tmm) REVERT: Z 41 HIS cc_start: 0.7030 (OUTLIER) cc_final: 0.6439 (p-80) REVERT: YY 82 MET cc_start: 0.4883 (mmt) cc_final: 0.3894 (mmt) REVERT: II 1 MET cc_start: 0.0823 (tpt) cc_final: -0.0068 (tpt) REVERT: HH 125 MET cc_start: 0.4056 (ptt) cc_final: 0.3339 (ppp) REVERT: QQ 220 GLN cc_start: 0.5645 (OUTLIER) cc_final: 0.5382 (pp30) REVERT: QQ 335 MET cc_start: 0.1673 (pmm) cc_final: 0.1470 (pmm) REVERT: f 64 GLU cc_start: 0.5334 (pt0) cc_final: 0.4934 (pt0) REVERT: TT 331 MET cc_start: -0.5870 (mtt) cc_final: -0.6777 (ttt) outliers start: 152 outliers final: 109 residues processed: 551 average time/residue: 0.6686 time to fit residues: 652.0083 Evaluate side-chains 529 residues out of total 8239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 414 time to evaluate : 6.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain I residue 476 ASP Chi-restraints excluded: chain I residue 545 VAL Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain LL residue 99 VAL Chi-restraints excluded: chain LL residue 142 TRP Chi-restraints excluded: chain LL residue 149 PHE Chi-restraints excluded: chain NN residue 146 MET Chi-restraints excluded: chain NN residue 156 ILE Chi-restraints excluded: chain NN residue 215 VAL Chi-restraints excluded: chain NN residue 244 GLN Chi-restraints excluded: chain NN residue 416 LEU Chi-restraints excluded: chain CT residue 256 THR Chi-restraints excluded: chain CT residue 293 PHE Chi-restraints excluded: chain CT residue 334 LEU Chi-restraints excluded: chain CT residue 350 ILE Chi-restraints excluded: chain CT residue 365 SER Chi-restraints excluded: chain ce residue 74 ASN Chi-restraints excluded: chain ce residue 127 PHE Chi-restraints excluded: chain ce residue 154 VAL Chi-restraints excluded: chain ce residue 176 VAL Chi-restraints excluded: chain ce residue 257 LEU Chi-restraints excluded: chain ce residue 277 ASN Chi-restraints excluded: chain ce residue 279 ASP Chi-restraints excluded: chain ce residue 334 VAL Chi-restraints excluded: chain ce residue 458 MET Chi-restraints excluded: chain ce residue 487 VAL Chi-restraints excluded: chain ce residue 500 PHE Chi-restraints excluded: chain ce residue 558 LEU Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 58 MET Chi-restraints excluded: chain L residue 111 MET Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain SK residue 9 VAL Chi-restraints excluded: chain SK residue 33 LEU Chi-restraints excluded: chain SK residue 146 LEU Chi-restraints excluded: chain CE residue 85 LEU Chi-restraints excluded: chain CE residue 86 THR Chi-restraints excluded: chain CE residue 88 THR Chi-restraints excluded: chain CE residue 168 THR Chi-restraints excluded: chain CE residue 169 MET Chi-restraints excluded: chain CE residue 186 TYR Chi-restraints excluded: chain CE residue 234 VAL Chi-restraints excluded: chain CE residue 243 THR Chi-restraints excluded: chain CE residue 352 ASP Chi-restraints excluded: chain CE residue 377 LEU Chi-restraints excluded: chain CE residue 385 ASP Chi-restraints excluded: chain CE residue 438 ILE Chi-restraints excluded: chain CE residue 442 ILE Chi-restraints excluded: chain CE residue 482 VAL Chi-restraints excluded: chain CE residue 488 ASP Chi-restraints excluded: chain CE residue 493 THR Chi-restraints excluded: chain CE residue 544 ASP Chi-restraints excluded: chain CE residue 592 THR Chi-restraints excluded: chain P residue 197 PHE Chi-restraints excluded: chain P residue 304 MET Chi-restraints excluded: chain P residue 316 LEU Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain Q residue 167 GLU Chi-restraints excluded: chain OO residue 306 VAL Chi-restraints excluded: chain N residue 87 PHE Chi-restraints excluded: chain N residue 115 ASP Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain N residue 219 ILE Chi-restraints excluded: chain N residue 220 TYR Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 243 VAL Chi-restraints excluded: chain N residue 301 GLU Chi-restraints excluded: chain N residue 308 ASN Chi-restraints excluded: chain N residue 389 LEU Chi-restraints excluded: chain N residue 417 CYS Chi-restraints excluded: chain N residue 427 VAL Chi-restraints excluded: chain N residue 441 THR Chi-restraints excluded: chain T residue 340 MET Chi-restraints excluded: chain U residue 219 GLN Chi-restraints excluded: chain U residue 255 ARG Chi-restraints excluded: chain PP residue 184 VAL Chi-restraints excluded: chain W residue 46 LEU Chi-restraints excluded: chain Y residue 14 ASN Chi-restraints excluded: chain Z residue 27 GLN Chi-restraints excluded: chain Z residue 41 HIS Chi-restraints excluded: chain YY residue 19 LEU Chi-restraints excluded: chain YY residue 161 GLU Chi-restraints excluded: chain II residue 374 THR Chi-restraints excluded: chain II residue 478 LEU Chi-restraints excluded: chain II residue 525 GLN Chi-restraints excluded: chain II residue 536 ILE Chi-restraints excluded: chain II residue 625 PHE Chi-restraints excluded: chain II residue 630 PHE Chi-restraints excluded: chain II residue 686 TRP Chi-restraints excluded: chain II residue 691 ASN Chi-restraints excluded: chain II residue 698 VAL Chi-restraints excluded: chain KK residue 104 LEU Chi-restraints excluded: chain HH residue 22 VAL Chi-restraints excluded: chain HH residue 26 LEU Chi-restraints excluded: chain QQ residue 220 GLN Chi-restraints excluded: chain b residue 69 ASP Chi-restraints excluded: chain b residue 86 ASP Chi-restraints excluded: chain b residue 96 ARG Chi-restraints excluded: chain b residue 98 LEU Chi-restraints excluded: chain d residue 110 LEU Chi-restraints excluded: chain e residue 147 ARG Chi-restraints excluded: chain e residue 209 LYS Chi-restraints excluded: chain e residue 214 MET Chi-restraints excluded: chain f residue 82 VAL Chi-restraints excluded: chain f residue 98 LEU Chi-restraints excluded: chain g residue 64 ILE Chi-restraints excluded: chain g residue 76 LYS Chi-restraints excluded: chain h residue 55 ASP Chi-restraints excluded: chain a residue 147 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 843 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 498 optimal weight: 10.0000 chunk 638 optimal weight: 1.9990 chunk 494 optimal weight: 3.9990 chunk 736 optimal weight: 6.9990 chunk 488 optimal weight: 30.0000 chunk 871 optimal weight: 20.0000 chunk 545 optimal weight: 0.7980 chunk 531 optimal weight: 0.9980 chunk 402 optimal weight: 10.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 490 GLN ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** NN 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NN 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ce 74 ASN ** ce 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SK 128 GLN ** CE 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CE 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OO 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 143 HIS ** N 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 257 ASN Z 41 HIS ** UU 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** YY 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ZZ 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** II 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** II 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** KK 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** QQ 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5562 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 80703 Z= 0.153 Angle : 0.598 14.146 110270 Z= 0.304 Chirality : 0.039 0.346 12604 Planarity : 0.003 0.061 12874 Dihedral : 18.064 175.103 13075 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.96 % Favored : 97.03 % Rotamer: Outliers : 1.67 % Allowed : 16.91 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.03 % Twisted Proline : 0.37 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.09), residues: 8762 helix: 1.58 (0.07), residues: 5496 sheet: 0.43 (0.22), residues: 544 loop : -0.91 (0.12), residues: 2722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP e 178 HIS 0.007 0.001 HIS Q 382 PHE 0.027 0.001 PHE T 341 TYR 0.018 0.001 TYRCE 473 ARG 0.006 0.000 ARG N 74 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17524 Ramachandran restraints generated. 8762 Oldfield, 0 Emsley, 8762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17524 Ramachandran restraints generated. 8762 Oldfield, 0 Emsley, 8762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 8239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 451 time to evaluate : 6.675 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: 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: I 176 MET cc_start: 0.7850 (mmm) cc_final: 0.7594 (mmt) REVERT: I 315 MET cc_start: 0.6625 (mtt) cc_final: 0.6196 (mtm) REVERT: I 445 MET cc_start: 0.7322 (ppp) cc_final: 0.6778 (pmm) REVERT: I 586 MET cc_start: 0.9268 (mmt) cc_final: 0.8813 (ppp) REVERT: K 125 MET cc_start: -0.1466 (mtt) cc_final: -0.1821 (mmt) REVERT: ce 84 ASP cc_start: 0.3868 (OUTLIER) cc_final: 0.2773 (m-30) REVERT: ce 127 PHE cc_start: 0.6903 (OUTLIER) cc_final: 0.6609 (t80) REVERT: ce 277 ASN cc_start: 0.6921 (OUTLIER) cc_final: 0.6522 (p0) REVERT: L 85 MET cc_start: 0.5343 (tpp) cc_final: 0.4209 (tpp) REVERT: CE 458 MET cc_start: 0.6701 (ppp) cc_final: 0.6276 (ppp) REVERT: N 341 MET cc_start: 0.7551 (pmm) cc_final: 0.6744 (ptp) REVERT: PP 318 MET cc_start: -0.0536 (mmm) cc_final: -0.0777 (mtt) REVERT: W 1 MET cc_start: 0.5417 (tmm) cc_final: 0.5112 (tmm) REVERT: II 1 MET cc_start: 0.0741 (tpt) cc_final: -0.0093 (tpt) REVERT: KK 179 MET cc_start: -0.3514 (mmt) cc_final: -0.3788 (mmt) REVERT: HH 125 MET cc_start: 0.4054 (ptt) cc_final: 0.3291 (ppp) REVERT: QQ 220 GLN cc_start: 0.5628 (OUTLIER) cc_final: 0.5347 (pp30) REVERT: QQ 335 MET cc_start: 0.1642 (pmm) cc_final: 0.1356 (pmm) REVERT: h 66 LEU cc_start: 0.5677 (pp) cc_final: 0.5399 (mt) REVERT: c 54 THR cc_start: 0.7238 (p) cc_final: 0.6822 (p) REVERT: TT 331 MET cc_start: -0.5946 (mtt) cc_final: -0.6839 (ttt) outliers start: 135 outliers final: 86 residues processed: 557 average time/residue: 0.6721 time to fit residues: 665.2083 Evaluate side-chains 512 residues out of total 8239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 422 time to evaluate : 6.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain I residue 545 VAL Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain LL residue 132 VAL Chi-restraints excluded: chain LL residue 219 GLU Chi-restraints excluded: chain NN residue 146 MET Chi-restraints excluded: chain NN residue 156 ILE Chi-restraints excluded: chain NN residue 215 VAL Chi-restraints excluded: chain NN residue 244 GLN Chi-restraints excluded: chain NN residue 416 LEU Chi-restraints excluded: chain CT residue 256 THR Chi-restraints excluded: chain CT residue 334 LEU Chi-restraints excluded: chain CT residue 350 ILE Chi-restraints excluded: chain ce residue 84 ASP Chi-restraints excluded: chain ce residue 127 PHE Chi-restraints excluded: chain ce residue 154 VAL Chi-restraints excluded: chain ce residue 176 VAL Chi-restraints excluded: chain ce residue 257 LEU Chi-restraints excluded: chain ce residue 277 ASN Chi-restraints excluded: chain ce residue 279 ASP Chi-restraints excluded: chain ce residue 334 VAL Chi-restraints excluded: chain ce residue 458 MET Chi-restraints excluded: chain ce residue 500 PHE Chi-restraints excluded: chain ce residue 558 LEU Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 58 MET Chi-restraints excluded: chain L residue 59 ARG Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain SK residue 9 VAL Chi-restraints excluded: chain SK residue 146 LEU Chi-restraints excluded: chain CE residue 86 THR Chi-restraints excluded: chain CE residue 88 THR Chi-restraints excluded: chain CE residue 169 MET Chi-restraints excluded: chain CE residue 186 TYR Chi-restraints excluded: chain CE residue 234 VAL Chi-restraints excluded: chain CE residue 296 LEU Chi-restraints excluded: chain CE residue 377 LEU Chi-restraints excluded: chain CE residue 384 VAL Chi-restraints excluded: chain CE residue 385 ASP Chi-restraints excluded: chain CE residue 438 ILE Chi-restraints excluded: chain CE residue 442 ILE Chi-restraints excluded: chain CE residue 488 ASP Chi-restraints excluded: chain CE residue 544 ASP Chi-restraints excluded: chain CE residue 592 THR Chi-restraints excluded: chain P residue 197 PHE Chi-restraints excluded: chain P residue 316 LEU Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain OO residue 306 VAL Chi-restraints excluded: chain N residue 87 PHE Chi-restraints excluded: chain N residue 115 ASP Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain N residue 220 TYR Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 243 VAL Chi-restraints excluded: chain N residue 301 GLU Chi-restraints excluded: chain N residue 308 ASN Chi-restraints excluded: chain N residue 389 LEU Chi-restraints excluded: chain N residue 417 CYS Chi-restraints excluded: chain N residue 427 VAL Chi-restraints excluded: chain N residue 431 LEU Chi-restraints excluded: chain T residue 340 MET Chi-restraints excluded: chain U residue 219 GLN Chi-restraints excluded: chain W residue 46 LEU Chi-restraints excluded: chain Y residue 14 ASN Chi-restraints excluded: chain Z residue 27 GLN Chi-restraints excluded: chain Z residue 41 HIS Chi-restraints excluded: chain YY residue 161 GLU Chi-restraints excluded: chain II residue 374 THR Chi-restraints excluded: chain II residue 478 LEU Chi-restraints excluded: chain II residue 525 GLN Chi-restraints excluded: chain II residue 536 ILE Chi-restraints excluded: chain II residue 625 PHE Chi-restraints excluded: chain II residue 630 PHE Chi-restraints excluded: chain II residue 686 TRP Chi-restraints excluded: chain KK residue 104 LEU Chi-restraints excluded: chain HH residue 22 VAL Chi-restraints excluded: chain HH residue 26 LEU Chi-restraints excluded: chain QQ residue 220 GLN Chi-restraints excluded: chain b residue 98 LEU Chi-restraints excluded: chain d residue 110 LEU Chi-restraints excluded: chain e residue 147 ARG Chi-restraints excluded: chain f residue 82 VAL Chi-restraints excluded: chain f residue 98 LEU Chi-restraints excluded: chain g residue 64 ILE Chi-restraints excluded: chain g residue 76 LYS Chi-restraints excluded: chain a residue 156 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 539 optimal weight: 20.0000 chunk 347 optimal weight: 6.9990 chunk 520 optimal weight: 0.0370 chunk 262 optimal weight: 7.9990 chunk 171 optimal weight: 6.9990 chunk 168 optimal weight: 9.9990 chunk 553 optimal weight: 0.8980 chunk 593 optimal weight: 20.0000 chunk 430 optimal weight: 30.0000 chunk 81 optimal weight: 3.9990 chunk 684 optimal weight: 40.0000 overall best weight: 3.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 ASN ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** NN 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NN 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CT 452 ASN CT 475 GLN ce 66 GLN ** ce 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CE 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CE 484 GLN ** OO 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 143 HIS ** N 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** PP 133 ASN PP 260 ASN Z 41 HIS ** UU 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** YY 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ZZ 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** II 305 GLN ** II 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** II 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** KK 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** QQ 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5626 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 80703 Z= 0.192 Angle : 0.621 13.946 110270 Z= 0.317 Chirality : 0.039 0.336 12604 Planarity : 0.004 0.066 12874 Dihedral : 18.076 174.536 13071 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.26 % Favored : 96.72 % Rotamer: Outliers : 1.71 % Allowed : 17.54 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.03 % Twisted Proline : 0.37 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.09), residues: 8762 helix: 1.56 (0.07), residues: 5499 sheet: 0.37 (0.23), residues: 553 loop : -0.90 (0.12), residues: 2710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP a 178 HIS 0.008 0.001 HIS Q 382 PHE 0.028 0.001 PHE P 204 TYR 0.027 0.001 TYR a 193 ARG 0.007 0.000 ARG b 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17524 Ramachandran restraints generated. 8762 Oldfield, 0 Emsley, 8762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17524 Ramachandran restraints generated. 8762 Oldfield, 0 Emsley, 8762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 8239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 425 time to evaluate : 6.718 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: 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: I 176 MET cc_start: 0.7839 (mmm) cc_final: 0.7593 (mmt) REVERT: I 315 MET cc_start: 0.6685 (mtt) cc_final: 0.6248 (mtm) REVERT: I 476 ASP cc_start: 0.7412 (OUTLIER) cc_final: 0.7151 (p0) REVERT: I 586 MET cc_start: 0.9309 (mmt) cc_final: 0.8845 (ppp) REVERT: K 125 MET cc_start: -0.1551 (mtt) cc_final: -0.1820 (mmt) REVERT: ce 84 ASP cc_start: 0.3812 (OUTLIER) cc_final: 0.2871 (m-30) REVERT: ce 127 PHE cc_start: 0.7003 (OUTLIER) cc_final: 0.6689 (t80) REVERT: ce 277 ASN cc_start: 0.7092 (OUTLIER) cc_final: 0.6680 (p0) REVERT: L 85 MET cc_start: 0.5379 (tpp) cc_final: 0.4398 (tpp) REVERT: CE 458 MET cc_start: 0.6817 (ppp) cc_final: 0.6407 (ppp) REVERT: PP 318 MET cc_start: -0.0588 (mmm) cc_final: -0.0824 (mtt) REVERT: W 1 MET cc_start: 0.5490 (tmm) cc_final: 0.5180 (tmm) REVERT: II 1 MET cc_start: 0.0682 (tpt) cc_final: -0.0064 (tpt) REVERT: II 580 MET cc_start: 0.7401 (mpp) cc_final: 0.7127 (mpp) REVERT: KK 179 MET cc_start: -0.3534 (mmt) cc_final: -0.3802 (mmt) REVERT: HH 125 MET cc_start: 0.4177 (ptt) cc_final: 0.3389 (ppp) REVERT: QQ 220 GLN cc_start: 0.5638 (OUTLIER) cc_final: 0.5368 (pp30) REVERT: QQ 335 MET cc_start: 0.1810 (pmm) cc_final: 0.1533 (pmm) REVERT: TT 331 MET cc_start: -0.5957 (mtt) cc_final: -0.6849 (ttt) outliers start: 138 outliers final: 103 residues processed: 538 average time/residue: 0.6670 time to fit residues: 638.5721 Evaluate side-chains 520 residues out of total 8239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 412 time to evaluate : 6.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain I residue 476 ASP Chi-restraints excluded: chain I residue 545 VAL Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain LL residue 99 VAL Chi-restraints excluded: chain LL residue 132 VAL Chi-restraints excluded: chain LL residue 219 GLU Chi-restraints excluded: chain NN residue 146 MET Chi-restraints excluded: chain NN residue 156 ILE Chi-restraints excluded: chain NN residue 215 VAL Chi-restraints excluded: chain NN residue 244 GLN Chi-restraints excluded: chain NN residue 416 LEU Chi-restraints excluded: chain CT residue 256 THR Chi-restraints excluded: chain CT residue 293 PHE Chi-restraints excluded: chain CT residue 334 LEU Chi-restraints excluded: chain CT residue 350 ILE Chi-restraints excluded: chain CT residue 365 SER Chi-restraints excluded: chain ce residue 84 ASP Chi-restraints excluded: chain ce residue 127 PHE Chi-restraints excluded: chain ce residue 154 VAL Chi-restraints excluded: chain ce residue 176 VAL Chi-restraints excluded: chain ce residue 257 LEU Chi-restraints excluded: chain ce residue 277 ASN Chi-restraints excluded: chain ce residue 279 ASP Chi-restraints excluded: chain ce residue 458 MET Chi-restraints excluded: chain ce residue 487 VAL Chi-restraints excluded: chain ce residue 500 PHE Chi-restraints excluded: chain ce residue 558 LEU Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 58 MET Chi-restraints excluded: chain L residue 59 ARG Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain SK residue 9 VAL Chi-restraints excluded: chain SK residue 146 LEU Chi-restraints excluded: chain CE residue 86 THR Chi-restraints excluded: chain CE residue 88 THR Chi-restraints excluded: chain CE residue 103 MET Chi-restraints excluded: chain CE residue 168 THR Chi-restraints excluded: chain CE residue 169 MET Chi-restraints excluded: chain CE residue 176 VAL Chi-restraints excluded: chain CE residue 186 TYR Chi-restraints excluded: chain CE residue 234 VAL Chi-restraints excluded: chain CE residue 243 THR Chi-restraints excluded: chain CE residue 244 THR Chi-restraints excluded: chain CE residue 352 ASP Chi-restraints excluded: chain CE residue 384 VAL Chi-restraints excluded: chain CE residue 385 ASP Chi-restraints excluded: chain CE residue 438 ILE Chi-restraints excluded: chain CE residue 442 ILE Chi-restraints excluded: chain CE residue 482 VAL Chi-restraints excluded: chain CE residue 488 ASP Chi-restraints excluded: chain CE residue 493 THR Chi-restraints excluded: chain CE residue 544 ASP Chi-restraints excluded: chain CE residue 592 THR Chi-restraints excluded: chain P residue 161 THR Chi-restraints excluded: chain P residue 197 PHE Chi-restraints excluded: chain P residue 316 LEU Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain OO residue 306 VAL Chi-restraints excluded: chain N residue 87 PHE Chi-restraints excluded: chain N residue 115 ASP Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain N residue 220 TYR Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 243 VAL Chi-restraints excluded: chain N residue 301 GLU Chi-restraints excluded: chain N residue 308 ASN Chi-restraints excluded: chain N residue 389 LEU Chi-restraints excluded: chain N residue 417 CYS Chi-restraints excluded: chain N residue 427 VAL Chi-restraints excluded: chain N residue 431 LEU Chi-restraints excluded: chain N residue 441 THR Chi-restraints excluded: chain T residue 340 MET Chi-restraints excluded: chain U residue 219 GLN Chi-restraints excluded: chain PP residue 184 VAL Chi-restraints excluded: chain W residue 46 LEU Chi-restraints excluded: chain Y residue 14 ASN Chi-restraints excluded: chain Y residue 212 LEU Chi-restraints excluded: chain Z residue 27 GLN Chi-restraints excluded: chain Z residue 41 HIS Chi-restraints excluded: chain YY residue 19 LEU Chi-restraints excluded: chain YY residue 79 GLN Chi-restraints excluded: chain YY residue 161 GLU Chi-restraints excluded: chain II residue 374 THR Chi-restraints excluded: chain II residue 478 LEU Chi-restraints excluded: chain II residue 525 GLN Chi-restraints excluded: chain II residue 536 ILE Chi-restraints excluded: chain II residue 625 PHE Chi-restraints excluded: chain II residue 630 PHE Chi-restraints excluded: chain II residue 658 ILE Chi-restraints excluded: chain II residue 686 TRP Chi-restraints excluded: chain II residue 691 ASN Chi-restraints excluded: chain KK residue 104 LEU Chi-restraints excluded: chain HH residue 22 VAL Chi-restraints excluded: chain QQ residue 220 GLN Chi-restraints excluded: chain b residue 86 ASP Chi-restraints excluded: chain b residue 96 ARG Chi-restraints excluded: chain b residue 98 LEU Chi-restraints excluded: chain e residue 147 ARG Chi-restraints excluded: chain f residue 82 VAL Chi-restraints excluded: chain f residue 98 LEU Chi-restraints excluded: chain g residue 64 ILE Chi-restraints excluded: chain g residue 76 LYS Chi-restraints excluded: chain a residue 156 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 792 optimal weight: 10.0000 chunk 834 optimal weight: 0.9980 chunk 761 optimal weight: 4.9990 chunk 811 optimal weight: 10.0000 chunk 488 optimal weight: 50.0000 chunk 353 optimal weight: 10.0000 chunk 637 optimal weight: 5.9990 chunk 249 optimal weight: 2.9990 chunk 733 optimal weight: 7.9990 chunk 767 optimal weight: 30.0000 chunk 809 optimal weight: 10.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 ASN ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** NN 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ce 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SK 128 GLN ** CE 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CE 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CE 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CE 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 297 GLN ** OO 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 143 HIS ** T 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 41 HIS ** UU 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** YY 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ZZ 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** II 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** II 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** KK 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** QQ 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 187 GLN ** c 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5682 moved from start: 0.4789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 80703 Z= 0.213 Angle : 0.638 13.569 110270 Z= 0.328 Chirality : 0.040 0.393 12604 Planarity : 0.004 0.069 12874 Dihedral : 18.197 175.277 13071 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.44 % Favored : 96.55 % Rotamer: Outliers : 1.61 % Allowed : 17.87 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.03 % Twisted Proline : 0.37 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.09), residues: 8762 helix: 1.52 (0.07), residues: 5491 sheet: 0.28 (0.23), residues: 537 loop : -0.91 (0.12), residues: 2734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP a 178 HIS 0.015 0.001 HIS Z 41 PHE 0.027 0.001 PHE f 62 TYR 0.033 0.001 TYR a 140 ARG 0.028 0.001 ARG Z 74 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17524 Ramachandran restraints generated. 8762 Oldfield, 0 Emsley, 8762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17524 Ramachandran restraints generated. 8762 Oldfield, 0 Emsley, 8762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 8239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 411 time to evaluate : 6.699 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: 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: A 330 MET cc_start: 0.6652 (mpp) cc_final: 0.6069 (mpp) REVERT: I 315 MET cc_start: 0.6707 (mtt) cc_final: 0.6264 (mtm) REVERT: I 586 MET cc_start: 0.9324 (mmt) cc_final: 0.8846 (ppp) REVERT: K 125 MET cc_start: -0.1499 (mtt) cc_final: -0.1881 (mmt) REVERT: ce 84 ASP cc_start: 0.3944 (OUTLIER) cc_final: 0.2996 (m-30) REVERT: ce 127 PHE cc_start: 0.7093 (OUTLIER) cc_final: 0.6789 (t80) REVERT: ce 277 ASN cc_start: 0.7060 (OUTLIER) cc_final: 0.6586 (p0) REVERT: L 85 MET cc_start: 0.5577 (tpp) cc_final: 0.4685 (tpp) REVERT: CE 458 MET cc_start: 0.6890 (ppp) cc_final: 0.6441 (ppp) REVERT: N 132 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6804 (tp) REVERT: PP 318 MET cc_start: -0.0432 (mmm) cc_final: -0.0811 (mtt) REVERT: W 1 MET cc_start: 0.4871 (tmm) cc_final: 0.4626 (tmm) REVERT: Y 82 MET cc_start: 0.6563 (mmt) cc_final: 0.6148 (mmt) REVERT: Z 41 HIS cc_start: 0.7012 (OUTLIER) cc_final: 0.6560 (p-80) REVERT: YY 82 MET cc_start: 0.5325 (mmt) cc_final: 0.4049 (mmt) REVERT: YY 138 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8451 (pttp) REVERT: II 1 MET cc_start: 0.0805 (tpt) cc_final: 0.0039 (tpt) REVERT: II 580 MET cc_start: 0.7349 (mpp) cc_final: 0.7094 (mpp) REVERT: KK 179 MET cc_start: -0.3647 (mmt) cc_final: -0.3880 (mmt) REVERT: HH 125 MET cc_start: 0.4286 (ptt) cc_final: 0.3403 (ptt) REVERT: QQ 185 MET cc_start: -0.4359 (mmp) cc_final: -0.4894 (mmt) REVERT: QQ 335 MET cc_start: 0.2071 (pmm) cc_final: 0.1278 (pmm) REVERT: TT 331 MET cc_start: -0.6023 (mtt) cc_final: -0.6766 (ttt) outliers start: 130 outliers final: 105 residues processed: 516 average time/residue: 0.6685 time to fit residues: 613.7122 Evaluate side-chains 506 residues out of total 8239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 395 time to evaluate : 6.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain I residue 545 VAL Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain LL residue 99 VAL Chi-restraints excluded: chain LL residue 132 VAL Chi-restraints excluded: chain LL residue 219 GLU Chi-restraints excluded: chain NN residue 146 MET Chi-restraints excluded: chain NN residue 156 ILE Chi-restraints excluded: chain NN residue 215 VAL Chi-restraints excluded: chain NN residue 244 GLN Chi-restraints excluded: chain NN residue 416 LEU Chi-restraints excluded: chain CT residue 256 THR Chi-restraints excluded: chain CT residue 293 PHE Chi-restraints excluded: chain CT residue 334 LEU Chi-restraints excluded: chain CT residue 350 ILE Chi-restraints excluded: chain CT residue 365 SER Chi-restraints excluded: chain ce residue 84 ASP Chi-restraints excluded: chain ce residue 127 PHE Chi-restraints excluded: chain ce residue 176 VAL Chi-restraints excluded: chain ce residue 228 HIS Chi-restraints excluded: chain ce residue 257 LEU Chi-restraints excluded: chain ce residue 277 ASN Chi-restraints excluded: chain ce residue 279 ASP Chi-restraints excluded: chain ce residue 458 MET Chi-restraints excluded: chain ce residue 487 VAL Chi-restraints excluded: chain ce residue 500 PHE Chi-restraints excluded: chain ce residue 558 LEU Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 58 MET Chi-restraints excluded: chain L residue 59 ARG Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain SK residue 9 VAL Chi-restraints excluded: chain SK residue 146 LEU Chi-restraints excluded: chain CE residue 82 GLN Chi-restraints excluded: chain CE residue 86 THR Chi-restraints excluded: chain CE residue 88 THR Chi-restraints excluded: chain CE residue 103 MET Chi-restraints excluded: chain CE residue 168 THR Chi-restraints excluded: chain CE residue 169 MET Chi-restraints excluded: chain CE residue 176 VAL Chi-restraints excluded: chain CE residue 186 TYR Chi-restraints excluded: chain CE residue 234 VAL Chi-restraints excluded: chain CE residue 243 THR Chi-restraints excluded: chain CE residue 244 THR Chi-restraints excluded: chain CE residue 296 LEU Chi-restraints excluded: chain CE residue 352 ASP Chi-restraints excluded: chain CE residue 384 VAL Chi-restraints excluded: chain CE residue 385 ASP Chi-restraints excluded: chain CE residue 438 ILE Chi-restraints excluded: chain CE residue 442 ILE Chi-restraints excluded: chain CE residue 482 VAL Chi-restraints excluded: chain CE residue 488 ASP Chi-restraints excluded: chain CE residue 493 THR Chi-restraints excluded: chain CE residue 544 ASP Chi-restraints excluded: chain CE residue 592 THR Chi-restraints excluded: chain P residue 197 PHE Chi-restraints excluded: chain P residue 304 MET Chi-restraints excluded: chain P residue 316 LEU Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain OO residue 145 ARG Chi-restraints excluded: chain OO residue 306 VAL Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 301 GLU Chi-restraints excluded: chain N residue 308 ASN Chi-restraints excluded: chain N residue 331 ILE Chi-restraints excluded: chain N residue 389 LEU Chi-restraints excluded: chain N residue 417 CYS Chi-restraints excluded: chain N residue 427 VAL Chi-restraints excluded: chain N residue 431 LEU Chi-restraints excluded: chain N residue 441 THR Chi-restraints excluded: chain T residue 340 MET Chi-restraints excluded: chain U residue 219 GLN Chi-restraints excluded: chain PP residue 184 VAL Chi-restraints excluded: chain W residue 46 LEU Chi-restraints excluded: chain Y residue 14 ASN Chi-restraints excluded: chain Y residue 212 LEU Chi-restraints excluded: chain Z residue 27 GLN Chi-restraints excluded: chain Z residue 41 HIS Chi-restraints excluded: chain Z residue 90 LEU Chi-restraints excluded: chain YY residue 19 LEU Chi-restraints excluded: chain YY residue 79 GLN Chi-restraints excluded: chain YY residue 138 LYS Chi-restraints excluded: chain YY residue 161 GLU Chi-restraints excluded: chain II residue 374 THR Chi-restraints excluded: chain II residue 478 LEU Chi-restraints excluded: chain II residue 525 GLN Chi-restraints excluded: chain II residue 536 ILE Chi-restraints excluded: chain II residue 625 PHE Chi-restraints excluded: chain II residue 630 PHE Chi-restraints excluded: chain II residue 686 TRP Chi-restraints excluded: chain II residue 691 ASN Chi-restraints excluded: chain KK residue 104 LEU Chi-restraints excluded: chain KK residue 182 MET Chi-restraints excluded: chain HH residue 22 VAL Chi-restraints excluded: chain b residue 86 ASP Chi-restraints excluded: chain b residue 98 LEU Chi-restraints excluded: chain e residue 147 ARG Chi-restraints excluded: chain f residue 82 VAL Chi-restraints excluded: chain f residue 98 LEU Chi-restraints excluded: chain g residue 64 ILE Chi-restraints excluded: chain g residue 76 LYS Chi-restraints excluded: chain a residue 156 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 533 optimal weight: 2.9990 chunk 858 optimal weight: 30.0000 chunk 524 optimal weight: 50.0000 chunk 407 optimal weight: 6.9990 chunk 596 optimal weight: 5.9990 chunk 900 optimal weight: 40.0000 chunk 828 optimal weight: 3.9990 chunk 717 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 chunk 553 optimal weight: 4.9990 chunk 439 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN ** I 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 ASN H 88 ASN ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** NN 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ce 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SK 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CE 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CE 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CE 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CE 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CE 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OO 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 414 HIS ** N 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** PP 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 13 GLN Z 41 HIS ** UU 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** UU 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** YY 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ZZ 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** II 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** II 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** KK 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** QQ 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5720 moved from start: 0.5118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 80703 Z= 0.224 Angle : 0.661 14.529 110270 Z= 0.338 Chirality : 0.040 0.404 12604 Planarity : 0.004 0.109 12874 Dihedral : 18.306 176.081 13071 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.42 % Favored : 96.56 % Rotamer: Outliers : 1.56 % Allowed : 18.18 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.03 % Twisted Proline : 0.37 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.09), residues: 8762 helix: 1.46 (0.07), residues: 5492 sheet: 0.22 (0.23), residues: 533 loop : -0.94 (0.12), residues: 2737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRPCT 370 HIS 0.029 0.001 HIS Z 41 PHE 0.027 0.002 PHE f 62 TYR 0.029 0.001 TYR a 140 ARG 0.011 0.000 ARGce 336 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17524 Ramachandran restraints generated. 8762 Oldfield, 0 Emsley, 8762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17524 Ramachandran restraints generated. 8762 Oldfield, 0 Emsley, 8762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 8239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 406 time to evaluate : 6.803 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: 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: A 330 MET cc_start: 0.6801 (mpp) cc_final: 0.6194 (mpp) REVERT: I 315 MET cc_start: 0.6736 (mtt) cc_final: 0.6293 (mtm) REVERT: I 586 MET cc_start: 0.9312 (mmt) cc_final: 0.8834 (ppp) REVERT: K 125 MET cc_start: -0.1408 (mtt) cc_final: -0.1822 (mmt) REVERT: ce 127 PHE cc_start: 0.7137 (OUTLIER) cc_final: 0.6835 (t80) REVERT: ce 277 ASN cc_start: 0.7025 (OUTLIER) cc_final: 0.6613 (p0) REVERT: L 85 MET cc_start: 0.5616 (tpp) cc_final: 0.4703 (tpp) REVERT: CE 458 MET cc_start: 0.6904 (ppp) cc_final: 0.6431 (ppp) REVERT: N 132 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.6777 (tp) REVERT: U 185 MET cc_start: -0.6257 (mtt) cc_final: -0.6908 (ttm) REVERT: PP 318 MET cc_start: -0.0360 (mmm) cc_final: -0.0668 (mtt) REVERT: W 1 MET cc_start: 0.5048 (tmm) cc_final: 0.4800 (tmm) REVERT: Y 82 MET cc_start: 0.6444 (mmt) cc_final: 0.6120 (mmt) REVERT: Z 41 HIS cc_start: 0.7174 (OUTLIER) cc_final: 0.6598 (p-80) REVERT: YY 82 MET cc_start: 0.5293 (mmt) cc_final: 0.4049 (mmt) REVERT: YY 138 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8478 (pttp) REVERT: II 1 MET cc_start: 0.0620 (tpt) cc_final: -0.0105 (tpt) REVERT: II 580 MET cc_start: 0.7313 (mpp) cc_final: 0.7072 (mpp) REVERT: KK 179 MET cc_start: -0.3536 (mmt) cc_final: -0.3808 (mmt) REVERT: HH 125 MET cc_start: 0.4088 (ptt) cc_final: 0.3146 (ptt) REVERT: QQ 185 MET cc_start: -0.4506 (mmp) cc_final: -0.5025 (mmt) REVERT: QQ 335 MET cc_start: 0.1929 (pmm) cc_final: 0.1268 (pmm) REVERT: TT 331 MET cc_start: -0.6012 (mtt) cc_final: -0.6770 (ttt) outliers start: 126 outliers final: 109 residues processed: 508 average time/residue: 0.6748 time to fit residues: 614.1189 Evaluate side-chains 507 residues out of total 8239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 393 time to evaluate : 6.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain I residue 545 VAL Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain H residue 34 TYR Chi-restraints excluded: chain LL residue 26 LEU Chi-restraints excluded: chain LL residue 99 VAL Chi-restraints excluded: chain LL residue 132 VAL Chi-restraints excluded: chain LL residue 219 GLU Chi-restraints excluded: chain NN residue 146 MET Chi-restraints excluded: chain NN residue 156 ILE Chi-restraints excluded: chain NN residue 215 VAL Chi-restraints excluded: chain NN residue 244 GLN Chi-restraints excluded: chain NN residue 416 LEU Chi-restraints excluded: chain CT residue 256 THR Chi-restraints excluded: chain CT residue 293 PHE Chi-restraints excluded: chain CT residue 318 ASN Chi-restraints excluded: chain CT residue 334 LEU Chi-restraints excluded: chain CT residue 350 ILE Chi-restraints excluded: chain CT residue 365 SER Chi-restraints excluded: chain ce residue 84 ASP Chi-restraints excluded: chain ce residue 127 PHE Chi-restraints excluded: chain ce residue 176 VAL Chi-restraints excluded: chain ce residue 228 HIS Chi-restraints excluded: chain ce residue 257 LEU Chi-restraints excluded: chain ce residue 277 ASN Chi-restraints excluded: chain ce residue 279 ASP Chi-restraints excluded: chain ce residue 378 ASP Chi-restraints excluded: chain ce residue 458 MET Chi-restraints excluded: chain ce residue 487 VAL Chi-restraints excluded: chain ce residue 500 PHE Chi-restraints excluded: chain ce residue 558 LEU Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 58 MET Chi-restraints excluded: chain L residue 59 ARG Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain SK residue 9 VAL Chi-restraints excluded: chain CE residue 82 GLN Chi-restraints excluded: chain CE residue 85 LEU Chi-restraints excluded: chain CE residue 86 THR Chi-restraints excluded: chain CE residue 88 THR Chi-restraints excluded: chain CE residue 103 MET Chi-restraints excluded: chain CE residue 168 THR Chi-restraints excluded: chain CE residue 169 MET Chi-restraints excluded: chain CE residue 176 VAL Chi-restraints excluded: chain CE residue 186 TYR Chi-restraints excluded: chain CE residue 234 VAL Chi-restraints excluded: chain CE residue 243 THR Chi-restraints excluded: chain CE residue 244 THR Chi-restraints excluded: chain CE residue 296 LEU Chi-restraints excluded: chain CE residue 352 ASP Chi-restraints excluded: chain CE residue 384 VAL Chi-restraints excluded: chain CE residue 385 ASP Chi-restraints excluded: chain CE residue 438 ILE Chi-restraints excluded: chain CE residue 442 ILE Chi-restraints excluded: chain CE residue 488 ASP Chi-restraints excluded: chain CE residue 493 THR Chi-restraints excluded: chain CE residue 544 ASP Chi-restraints excluded: chain CE residue 564 SER Chi-restraints excluded: chain CE residue 592 THR Chi-restraints excluded: chain P residue 197 PHE Chi-restraints excluded: chain P residue 304 MET Chi-restraints excluded: chain P residue 316 LEU Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain OO residue 145 ARG Chi-restraints excluded: chain OO residue 306 VAL Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain N residue 219 ILE Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 301 GLU Chi-restraints excluded: chain N residue 308 ASN Chi-restraints excluded: chain N residue 331 ILE Chi-restraints excluded: chain N residue 389 LEU Chi-restraints excluded: chain N residue 417 CYS Chi-restraints excluded: chain N residue 427 VAL Chi-restraints excluded: chain N residue 431 LEU Chi-restraints excluded: chain N residue 441 THR Chi-restraints excluded: chain T residue 340 MET Chi-restraints excluded: chain U residue 219 GLN Chi-restraints excluded: chain PP residue 184 VAL Chi-restraints excluded: chain W residue 46 LEU Chi-restraints excluded: chain Y residue 14 ASN Chi-restraints excluded: chain Z residue 27 GLN Chi-restraints excluded: chain Z residue 41 HIS Chi-restraints excluded: chain Z residue 90 LEU Chi-restraints excluded: chain YY residue 19 LEU Chi-restraints excluded: chain YY residue 79 GLN Chi-restraints excluded: chain YY residue 138 LYS Chi-restraints excluded: chain YY residue 161 GLU Chi-restraints excluded: chain II residue 374 THR Chi-restraints excluded: chain II residue 478 LEU Chi-restraints excluded: chain II residue 525 GLN Chi-restraints excluded: chain II residue 536 ILE Chi-restraints excluded: chain II residue 625 PHE Chi-restraints excluded: chain II residue 630 PHE Chi-restraints excluded: chain II residue 686 TRP Chi-restraints excluded: chain II residue 691 ASN Chi-restraints excluded: chain KK residue 104 LEU Chi-restraints excluded: chain KK residue 182 MET Chi-restraints excluded: chain HH residue 22 VAL Chi-restraints excluded: chain b residue 69 ASP Chi-restraints excluded: chain b residue 86 ASP Chi-restraints excluded: chain b residue 98 LEU Chi-restraints excluded: chain e residue 147 ARG Chi-restraints excluded: chain f residue 82 VAL Chi-restraints excluded: chain f residue 98 LEU Chi-restraints excluded: chain g residue 64 ILE Chi-restraints excluded: chain g residue 76 LYS Chi-restraints excluded: chain a residue 156 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 569 optimal weight: 20.0000 chunk 763 optimal weight: 20.0000 chunk 219 optimal weight: 6.9990 chunk 661 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 199 optimal weight: 9.9990 chunk 718 optimal weight: 4.9990 chunk 300 optimal weight: 6.9990 chunk 737 optimal weight: 7.9990 chunk 90 optimal weight: 20.0000 chunk 132 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 ASN ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NN 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NN 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ce 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SK 128 GLN ** CE 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CE 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CE 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CE 461 GLN ** CE 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OO 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** PP 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 215 GLN Y 198 ASN Z 41 HIS ** UU 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** UU 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** YY 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ZZ 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** II 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** II 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** KK 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HH 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** QQ 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 60 GLN ** c 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 187 GLN ** a 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.078227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.055072 restraints weight = 820573.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.054899 restraints weight = 540309.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.054089 restraints weight = 418538.827| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.5703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 80703 Z= 0.289 Angle : 0.710 13.946 110270 Z= 0.368 Chirality : 0.041 0.412 12604 Planarity : 0.005 0.065 12874 Dihedral : 18.592 177.502 13071 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 22.26 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.93 % Favored : 96.06 % Rotamer: Outliers : 1.58 % Allowed : 18.50 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.03 % Twisted Proline : 0.37 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.09), residues: 8762 helix: 1.19 (0.07), residues: 5503 sheet: -0.03 (0.23), residues: 541 loop : -1.06 (0.12), residues: 2718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRPNN 270 HIS 0.012 0.001 HIS Z 41 PHE 0.034 0.002 PHE f 62 TYR 0.028 0.002 TYR a 140 ARG 0.008 0.001 ARGce 336 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16380.82 seconds wall clock time: 290 minutes 44.09 seconds (17444.09 seconds total)