Starting phenix.real_space_refine on Sat Feb 24 07:31:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvy_32149/02_2024/7vvy_32149_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvy_32149/02_2024/7vvy_32149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvy_32149/02_2024/7vvy_32149.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvy_32149/02_2024/7vvy_32149.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvy_32149/02_2024/7vvy_32149_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvy_32149/02_2024/7vvy_32149_updated.pdb" } resolution = 3.1 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 174 5.16 5 C 27371 2.51 5 N 7131 2.21 5 O 7862 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 229": "OD1" <-> "OD2" Residue "E TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 332": "OE1" <-> "OE2" Residue "E PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 365": "OE1" <-> "OE2" Residue "E TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 550": "OD1" <-> "OD2" Residue "E GLU 551": "OE1" <-> "OE2" Residue "E TYR 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 572": "OE1" <-> "OE2" Residue "E ASP 593": "OD1" <-> "OD2" Residue "E PHE 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 609": "OE1" <-> "OE2" Residue "E PHE 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 655": "OD1" <-> "OD2" Residue "E GLU 657": "OE1" <-> "OE2" Residue "E TYR 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 689": "OE1" <-> "OE2" Residue "E PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 711": "OD1" <-> "OD2" Residue "E PHE 730": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 761": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 772": "OE1" <-> "OE2" Residue "F TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 13": "OE1" <-> "OE2" Residue "F ASP 34": "OD1" <-> "OD2" Residue "F PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 50": "OD1" <-> "OD2" Residue "F ASP 68": "OD1" <-> "OD2" Residue "F TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 126": "OE1" <-> "OE2" Residue "F PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 135": "OE1" <-> "OE2" Residue "F TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 163": "OD1" <-> "OD2" Residue "F ASP 172": "OD1" <-> "OD2" Residue "F PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 202": "OE1" <-> "OE2" Residue "F ASP 222": "OD1" <-> "OD2" Residue "F GLU 261": "OE1" <-> "OE2" Residue "F GLU 271": "OE1" <-> "OE2" Residue "F GLU 277": "OE1" <-> "OE2" Residue "F PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 387": "OD1" <-> "OD2" Residue "F GLU 447": "OE1" <-> "OE2" Residue "F TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 476": "OE1" <-> "OE2" Residue "F ASP 486": "OD1" <-> "OD2" Residue "G ASP 24": "OD1" <-> "OD2" Residue "G PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 56": "OD1" <-> "OD2" Residue "G GLU 57": "OE1" <-> "OE2" Residue "G TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 100": "OE1" <-> "OE2" Residue "G GLU 117": "OE1" <-> "OE2" Residue "G GLU 125": "OE1" <-> "OE2" Residue "G PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 187": "OD1" <-> "OD2" Residue "G GLU 195": "OE1" <-> "OE2" Residue "G PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 259": "OE1" <-> "OE2" Residue "G ASP 288": "OD1" <-> "OD2" Residue "G GLU 311": "OE1" <-> "OE2" Residue "K GLU 82": "OE1" <-> "OE2" Residue "K TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 180": "OD1" <-> "OD2" Residue "K PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 188": "OD1" <-> "OD2" Residue "K TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 233": "OE1" <-> "OE2" Residue "K GLU 260": "OE1" <-> "OE2" Residue "K GLU 265": "OE1" <-> "OE2" Residue "K TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 313": "NH1" <-> "NH2" Residue "H TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 531": "OD1" <-> "OD2" Residue "H PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 541": "OD1" <-> "OD2" Residue "H PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 605": "OD1" <-> "OD2" Residue "H GLU 618": "OE1" <-> "OE2" Residue "H TYR 620": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 621": "OD1" <-> "OD2" Residue "H GLU 625": "OE1" <-> "OE2" Residue "H TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 669": "OD1" <-> "OD2" Residue "H PHE 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 672": "OD1" <-> "OD2" Residue "H GLU 677": "OE1" <-> "OE2" Residue "H GLU 701": "OE1" <-> "OE2" Residue "H TYR 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 750": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 755": "OE1" <-> "OE2" Residue "L GLU 8": "OE1" <-> "OE2" Residue "L TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 33": "OD1" <-> "OD2" Residue "L PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 67": "OD1" <-> "OD2" Residue "L ASP 81": "OD1" <-> "OD2" Residue "L PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 101": "OE1" <-> "OE2" Residue "L GLU 112": "OE1" <-> "OE2" Residue "L GLU 113": "OE1" <-> "OE2" Residue "L PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 320": "OD1" <-> "OD2" Residue "L ASP 327": "OD1" <-> "OD2" Residue "L ARG 352": "NH1" <-> "NH2" Residue "L TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 405": "OE1" <-> "OE2" Residue "L GLU 412": "OE1" <-> "OE2" Residue "L ARG 459": "NH1" <-> "NH2" Residue "L ARG 474": "NH1" <-> "NH2" Residue "L TYR 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 513": "OE1" <-> "OE2" Residue "L GLU 516": "OE1" <-> "OE2" Residue "L PHE 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 629": "OE1" <-> "OE2" Residue "L GLU 630": "OE1" <-> "OE2" Residue "L GLU 681": "OE1" <-> "OE2" Residue "L ASP 684": "OD1" <-> "OD2" Residue "L ARG 712": "NH1" <-> "NH2" Residue "L GLU 715": "OE1" <-> "OE2" Residue "L GLU 804": "OE1" <-> "OE2" Residue "L TYR 808": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 813": "NH1" <-> "NH2" Residue "L ARG 817": "NH1" <-> "NH2" Residue "L GLU 854": "OE1" <-> "OE2" Residue "L ARG 868": "NH1" <-> "NH2" Residue "L GLU 902": "OE1" <-> "OE2" Residue "L ASP 906": "OD1" <-> "OD2" Residue "L GLU 911": "OE1" <-> "OE2" Residue "L GLU 918": "OE1" <-> "OE2" Residue "L ASP 923": "OD1" <-> "OD2" Residue "L GLU 971": "OE1" <-> "OE2" Residue "L GLU 1058": "OE1" <-> "OE2" Residue "L ASP 1071": "OD1" <-> "OD2" Residue "L TYR 1088": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 1101": "OD1" <-> "OD2" Residue "L ARG 1123": "NH1" <-> "NH2" Residue "L GLU 1159": "OE1" <-> "OE2" Residue "L GLU 1162": "OE1" <-> "OE2" Residue "L ARG 1170": "NH1" <-> "NH2" Residue "L GLU 1204": "OE1" <-> "OE2" Residue "L ASP 1221": "OD1" <-> "OD2" Residue "L ASP 1247": "OD1" <-> "OD2" Residue "L GLU 1261": "OE1" <-> "OE2" Residue "L ASP 1266": "OD1" <-> "OD2" Residue "L ASP 1274": "OD1" <-> "OD2" Residue "L ASP 1291": "OD1" <-> "OD2" Residue "L GLU 1295": "OE1" <-> "OE2" Residue "L ARG 1304": "NH1" <-> "NH2" Residue "L GLU 1388": "OE1" <-> "OE2" Residue "L GLU 1427": "OE1" <-> "OE2" Residue "L ARG 1437": "NH1" <-> "NH2" Residue "L GLU 1469": "OE1" <-> "OE2" Residue "L GLU 1508": "OE1" <-> "OE2" Residue "L PHE 1514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 1520": "NH1" <-> "NH2" Residue "L PHE 1539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 1542": "OD1" <-> "OD2" Residue "L PHE 1559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 1567": "OD1" <-> "OD2" Residue "L PHE 1569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 1572": "OD1" <-> "OD2" Residue "L ARG 1585": "NH1" <-> "NH2" Residue "L PHE 1592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 1610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 1632": "OE1" <-> "OE2" Residue "L GLU 1638": "OE1" <-> "OE2" Residue "L GLU 1641": "OE1" <-> "OE2" Residue "L ASP 1671": "OD1" <-> "OD2" Residue "L GLU 1683": "OE1" <-> "OE2" Residue "L ASP 1697": "OD1" <-> "OD2" Residue "L GLU 1734": "OE1" <-> "OE2" Residue "L GLU 1777": "OE1" <-> "OE2" Residue "L ASP 1785": "OD1" <-> "OD2" Residue "L ASP 1793": "OD1" <-> "OD2" Residue "L GLU 1814": "OE1" <-> "OE2" Residue "L GLU 1827": "OE1" <-> "OE2" Residue "L ARG 1861": "NH1" <-> "NH2" Residue "L ASP 1885": "OD1" <-> "OD2" Residue "L GLU 1897": "OE1" <-> "OE2" Residue "L GLU 1976": "OE1" <-> "OE2" Residue "L PHE 1988": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 2001": "OD1" <-> "OD2" Residue "L ASP 2030": "OD1" <-> "OD2" Residue "L ARG 2093": "NH1" <-> "NH2" Residue "L TYR 2169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 2182": "OE1" <-> "OE2" Residue "L GLU 2249": "OE1" <-> "OE2" Residue "L ASP 2288": "OD1" <-> "OD2" Residue "L ASP 2297": "OD1" <-> "OD2" Residue "L ASP 2327": "OD1" <-> "OD2" Residue "L ASP 2345": "OD1" <-> "OD2" Residue "L PHE 2361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 2387": "OE1" <-> "OE2" Residue "L GLU 2396": "OE1" <-> "OE2" Residue "L PHE 2402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 2407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 2432": "NH1" <-> "NH2" Residue "L ARG 2445": "NH1" <-> "NH2" Residue "L ASP 2446": "OD1" <-> "OD2" Residue "L ARG 2456": "NH1" <-> "NH2" Residue "L ASP 2465": "OD1" <-> "OD2" Residue "L ARG 2482": "NH1" <-> "NH2" Residue "L TYR 2492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 2503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 2516": "OD1" <-> "OD2" Residue "L ARG 2581": "NH1" <-> "NH2" Residue "L ASP 2650": "OD1" <-> "OD2" Residue "L ARG 2681": "NH1" <-> "NH2" Residue "L GLU 2708": "OE1" <-> "OE2" Residue "L ARG 2715": "NH1" <-> "NH2" Residue "L PHE 2803": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 2807": "NH1" <-> "NH2" Residue "L ASP 2810": "OD1" <-> "OD2" Residue "L ARG 2887": "NH1" <-> "NH2" Residue "L ARG 2969": "NH1" <-> "NH2" Residue "L TYR 2971": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 2980": "OE1" <-> "OE2" Residue "L GLU 2987": "OE1" <-> "OE2" Residue "L TYR 3013": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 3034": "NH1" <-> "NH2" Residue "L GLU 3037": "OE1" <-> "OE2" Residue "L ASP 3111": "OD1" <-> "OD2" Residue "L ASP 3112": "OD1" <-> "OD2" Residue "L ARG 3172": "NH1" <-> "NH2" Residue "L ASP 3235": "OD1" <-> "OD2" Residue "L PHE 3237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 3243": "OE1" <-> "OE2" Residue "L TYR 3260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 3274": "OE1" <-> "OE2" Residue "L TYR 3291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 3300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 3302": "OD1" <-> "OD2" Residue "L ARG 3313": "NH1" <-> "NH2" Residue "L ARG 3320": "NH1" <-> "NH2" Residue "L PHE 3349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 3358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 3373": "NH1" <-> "NH2" Residue "L PHE 3374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 3382": "NH1" <-> "NH2" Residue "L TYR 3388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 3407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 3417": "OE1" <-> "OE2" Residue "L ARG 3424": "NH1" <-> "NH2" Residue "L GLU 3435": "OE1" <-> "OE2" Residue "L ARG 3438": "NH1" <-> "NH2" Residue "L GLU 3473": "OE1" <-> "OE2" Residue "L ASP 3491": "OD1" <-> "OD2" Residue "L ARG 3545": "NH1" <-> "NH2" Residue "L PHE 3548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 3557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 3593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 3622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 3641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 3658": "OE1" <-> "OE2" Residue "L ARG 3689": "NH1" <-> "NH2" Residue "L ASP 3737": "OD1" <-> "OD2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 42546 Number of models: 1 Model: "" Number of chains: 8 Chain: "E" Number of atoms: 3448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3448 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 24, 'TRANS': 390} Chain breaks: 4 Chain: "F" Number of atoms: 3278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3278 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 20, 'TRANS': 393} Chain breaks: 1 Chain: "G" Number of atoms: 2788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2788 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 18, 'TRANS': 338} Chain breaks: 1 Chain: "K" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1989 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 11, 'TRANS': 225} Chain breaks: 3 Chain: "H" Number of atoms: 2250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2250 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 12, 'TRANS': 256} Chain breaks: 2 Chain: "L" Number of atoms: 28729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3513, 28729 Classifications: {'peptide': 3513} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 148, 'TRANS': 3363} Chain breaks: 11 Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 22.17, per 1000 atoms: 0.52 Number of scatterers: 42546 At special positions: 0 Unit cell: (229.49, 159.127, 210.005, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 174 16.00 P 6 15.00 Mg 2 11.99 O 7862 8.00 N 7131 7.00 C 27371 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.35 Conformation dependent library (CDL) restraints added in 7.8 seconds 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10096 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 247 helices and 16 sheets defined 54.9% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 18.80 Creating SS restraints... Processing helix chain 'E' and resid 242 through 247 Processing helix chain 'E' and resid 287 through 296 removed outlier: 4.229A pdb=" N THR E 296 " --> pdb=" O TYR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 304 removed outlier: 3.710A pdb=" N ILE E 303 " --> pdb=" O ILE E 300 " (cutoff:3.500A) Proline residue: E 304 - end of helix Processing helix chain 'E' and resid 313 through 336 Processing helix chain 'E' and resid 358 through 396 Processing helix chain 'E' and resid 549 through 551 No H-bonds generated for 'chain 'E' and resid 549 through 551' Processing helix chain 'E' and resid 554 through 562 Processing helix chain 'E' and resid 612 through 614 No H-bonds generated for 'chain 'E' and resid 612 through 614' Processing helix chain 'E' and resid 628 through 630 No H-bonds generated for 'chain 'E' and resid 628 through 630' Processing helix chain 'E' and resid 654 through 665 Processing helix chain 'E' and resid 671 through 676 Processing helix chain 'E' and resid 693 through 703 Processing helix chain 'E' and resid 717 through 734 Processing helix chain 'E' and resid 745 through 747 No H-bonds generated for 'chain 'E' and resid 745 through 747' Processing helix chain 'E' and resid 750 through 752 No H-bonds generated for 'chain 'E' and resid 750 through 752' Processing helix chain 'E' and resid 756 through 771 Processing helix chain 'E' and resid 797 through 806 Processing helix chain 'F' and resid 83 through 96 Processing helix chain 'F' and resid 118 through 129 Processing helix chain 'F' and resid 142 through 150 Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 187 through 197 Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 227 through 236 Processing helix chain 'F' and resid 238 through 246 Processing helix chain 'F' and resid 258 through 263 Processing helix chain 'F' and resid 282 through 292 removed outlier: 4.824A pdb=" N ALA F 289 " --> pdb=" O ARG F 285 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LEU F 292 " --> pdb=" O PHE F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 394 Processing helix chain 'F' and resid 398 through 407 removed outlier: 3.640A pdb=" N ARG F 401 " --> pdb=" O VAL F 398 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ALA F 402 " --> pdb=" O ASP F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 416 No H-bonds generated for 'chain 'F' and resid 414 through 416' Processing helix chain 'F' and resid 420 through 431 Processing helix chain 'F' and resid 445 through 449 Processing helix chain 'F' and resid 451 through 461 Processing helix chain 'F' and resid 466 through 468 No H-bonds generated for 'chain 'F' and resid 466 through 468' Processing helix chain 'F' and resid 472 through 478 Processing helix chain 'G' and resid 55 through 60 removed outlier: 3.874A pdb=" N SER G 60 " --> pdb=" O GLU G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 91 Processing helix chain 'G' and resid 98 through 100 No H-bonds generated for 'chain 'G' and resid 98 through 100' Processing helix chain 'G' and resid 113 through 126 Processing helix chain 'G' and resid 137 through 144 Processing helix chain 'G' and resid 172 through 174 No H-bonds generated for 'chain 'G' and resid 172 through 174' Processing helix chain 'G' and resid 182 through 196 removed outlier: 3.783A pdb=" N SER G 194 " --> pdb=" O MET G 190 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLU G 195 " --> pdb=" O LYS G 191 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ARG G 196 " --> pdb=" O ILE G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 216 Processing helix chain 'G' and resid 223 through 232 Processing helix chain 'G' and resid 256 through 261 removed outlier: 4.725A pdb=" N LEU G 261 " --> pdb=" O ALA G 257 " (cutoff:3.500A) Processing helix chain 'G' and resid 274 through 284 Processing helix chain 'G' and resid 290 through 294 Processing helix chain 'G' and resid 302 through 304 No H-bonds generated for 'chain 'G' and resid 302 through 304' Processing helix chain 'G' and resid 309 through 320 Processing helix chain 'G' and resid 335 through 347 removed outlier: 5.536A pdb=" N VAL G 339 " --> pdb=" O LYS G 336 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 354 removed outlier: 3.797A pdb=" N GLN G 354 " --> pdb=" O THR G 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 351 through 354' Processing helix chain 'G' and resid 359 through 365 Processing helix chain 'G' and resid 367 through 373 removed outlier: 3.616A pdb=" N LYS G 373 " --> pdb=" O VAL G 370 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 49 Processing helix chain 'K' and resid 110 through 114 Processing helix chain 'K' and resid 125 through 131 Processing helix chain 'K' and resid 166 through 179 Processing helix chain 'K' and resid 183 through 189 Processing helix chain 'K' and resid 199 through 215 Processing helix chain 'K' and resid 221 through 224 Processing helix chain 'K' and resid 230 through 244 Processing helix chain 'K' and resid 248 through 282 removed outlier: 3.783A pdb=" N ALA K 267 " --> pdb=" O LYS K 263 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA K 268 " --> pdb=" O PHE K 264 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LYS K 269 " --> pdb=" O GLU K 265 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG K 270 " --> pdb=" O MET K 266 " (cutoff:3.500A) Processing helix chain 'K' and resid 291 through 295 Processing helix chain 'K' and resid 297 through 308 Processing helix chain 'K' and resid 325 through 328 No H-bonds generated for 'chain 'K' and resid 325 through 328' Processing helix chain 'H' and resid 505 through 531 removed outlier: 3.566A pdb=" N ASP H 531 " --> pdb=" O ARG H 527 " (cutoff:3.500A) Processing helix chain 'H' and resid 560 through 562 No H-bonds generated for 'chain 'H' and resid 560 through 562' Processing helix chain 'H' and resid 564 through 569 removed outlier: 4.040A pdb=" N LYS H 569 " --> pdb=" O ILE H 565 " (cutoff:3.500A) Processing helix chain 'H' and resid 581 through 586 Processing helix chain 'H' and resid 610 through 615 Processing helix chain 'H' and resid 667 through 670 removed outlier: 3.642A pdb=" N PHE H 670 " --> pdb=" O LEU H 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 667 through 670' Processing helix chain 'H' and resid 673 through 680 Processing helix chain 'H' and resid 694 through 696 No H-bonds generated for 'chain 'H' and resid 694 through 696' Processing helix chain 'H' and resid 698 through 710 removed outlier: 4.043A pdb=" N TRP H 709 " --> pdb=" O LEU H 705 " (cutoff:3.500A) Processing helix chain 'H' and resid 714 through 716 No H-bonds generated for 'chain 'H' and resid 714 through 716' Processing helix chain 'H' and resid 725 through 730 Processing helix chain 'H' and resid 735 through 765 Processing helix chain 'L' and resid 4 through 9 removed outlier: 3.798A pdb=" N GLU L 8 " --> pdb=" O GLU L 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 28 through 30 No H-bonds generated for 'chain 'L' and resid 28 through 30' Processing helix chain 'L' and resid 44 through 60 removed outlier: 3.848A pdb=" N LEU L 48 " --> pdb=" O HIS L 45 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLN L 49 " --> pdb=" O PHE L 46 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL L 51 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE L 52 " --> pdb=" O GLN L 49 " (cutoff:3.500A) Proline residue: L 53 - end of helix removed outlier: 3.567A pdb=" N LYS L 60 " --> pdb=" O ASN L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 85 Processing helix chain 'L' and resid 92 through 98 removed outlier: 4.386A pdb=" N GLU L 98 " --> pdb=" O PRO L 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 100 through 103 No H-bonds generated for 'chain 'L' and resid 100 through 103' Processing helix chain 'L' and resid 118 through 131 removed outlier: 4.430A pdb=" N THR L 123 " --> pdb=" O MET L 119 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 156 removed outlier: 3.763A pdb=" N ILE L 145 " --> pdb=" O ILE L 141 " (cutoff:3.500A) Proline residue: L 152 - end of helix Processing helix chain 'L' and resid 232 through 242 removed outlier: 4.662A pdb=" N LEU L 241 " --> pdb=" O SER L 237 " (cutoff:3.500A) Processing helix chain 'L' and resid 294 through 315 removed outlier: 4.547A pdb=" N ILE L 310 " --> pdb=" O ALA L 306 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ARG L 311 " --> pdb=" O TYR L 307 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLY L 312 " --> pdb=" O VAL L 308 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR L 313 " --> pdb=" O PHE L 309 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA L 314 " --> pdb=" O ILE L 310 " (cutoff:3.500A) Proline residue: L 315 - end of helix Processing helix chain 'L' and resid 325 through 334 Processing helix chain 'L' and resid 342 through 355 removed outlier: 3.925A pdb=" N GLU L 346 " --> pdb=" O SER L 342 " (cutoff:3.500A) Processing helix chain 'L' and resid 360 through 367 removed outlier: 3.855A pdb=" N LEU L 364 " --> pdb=" O LYS L 360 " (cutoff:3.500A) Proline residue: L 365 - end of helix No H-bonds generated for 'chain 'L' and resid 360 through 367' Processing helix chain 'L' and resid 375 through 377 No H-bonds generated for 'chain 'L' and resid 375 through 377' Processing helix chain 'L' and resid 388 through 402 Processing helix chain 'L' and resid 408 through 423 removed outlier: 3.594A pdb=" N ILE L 417 " --> pdb=" O LYS L 413 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLY L 420 " --> pdb=" O LYS L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 429 through 452 removed outlier: 4.347A pdb=" N GLU L 444 " --> pdb=" O LEU L 440 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG L 445 " --> pdb=" O ASN L 441 " (cutoff:3.500A) Processing helix chain 'L' and resid 454 through 500 Proline residue: L 458 - end of helix removed outlier: 3.948A pdb=" N LYS L 462 " --> pdb=" O ARG L 459 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE L 467 " --> pdb=" O LEU L 464 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE L 468 " --> pdb=" O MET L 465 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE L 475 " --> pdb=" O MET L 472 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARG L 480 " --> pdb=" O THR L 477 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ASP L 483 " --> pdb=" O ARG L 480 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N HIS L 495 " --> pdb=" O TYR L 492 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLU L 498 " --> pdb=" O HIS L 495 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA L 500 " --> pdb=" O LYS L 497 " (cutoff:3.500A) Processing helix chain 'L' and resid 513 through 519 Processing helix chain 'L' and resid 562 through 566 Processing helix chain 'L' and resid 579 through 604 removed outlier: 4.562A pdb=" N LYS L 602 " --> pdb=" O ILE L 598 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N VAL L 603 " --> pdb=" O HIS L 599 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N PHE L 604 " --> pdb=" O ASP L 600 " (cutoff:3.500A) Processing helix chain 'L' and resid 628 through 646 removed outlier: 3.732A pdb=" N VAL L 633 " --> pdb=" O GLU L 629 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU L 645 " --> pdb=" O CYS L 641 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LYS L 646 " --> pdb=" O ILE L 642 " (cutoff:3.500A) Processing helix chain 'L' and resid 677 through 689 Processing helix chain 'L' and resid 695 through 713 removed outlier: 3.976A pdb=" N GLU L 700 " --> pdb=" O ALA L 696 " (cutoff:3.500A) Proline residue: L 707 - end of helix Processing helix chain 'L' and resid 717 through 727 removed outlier: 3.587A pdb=" N LEU L 720 " --> pdb=" O SER L 717 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN L 724 " --> pdb=" O HIS L 721 " (cutoff:3.500A) Processing helix chain 'L' and resid 733 through 750 removed outlier: 3.779A pdb=" N GLY L 746 " --> pdb=" O ARG L 742 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LYS L 749 " --> pdb=" O LYS L 745 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ASP L 750 " --> pdb=" O GLY L 746 " (cutoff:3.500A) Processing helix chain 'L' and resid 756 through 775 removed outlier: 3.823A pdb=" N VAL L 773 " --> pdb=" O SER L 769 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN L 774 " --> pdb=" O PHE L 770 " (cutoff:3.500A) Processing helix chain 'L' and resid 782 through 785 No H-bonds generated for 'chain 'L' and resid 782 through 785' Processing helix chain 'L' and resid 789 through 798 Processing helix chain 'L' and resid 807 through 818 Processing helix chain 'L' and resid 828 through 830 No H-bonds generated for 'chain 'L' and resid 828 through 830' Processing helix chain 'L' and resid 832 through 843 Processing helix chain 'L' and resid 854 through 862 Processing helix chain 'L' and resid 877 through 889 removed outlier: 3.770A pdb=" N MET L 880 " --> pdb=" O PRO L 877 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LYS L 881 " --> pdb=" O PHE L 878 " (cutoff:3.500A) Proline residue: L 882 - end of helix removed outlier: 4.417A pdb=" N GLN L 889 " --> pdb=" O ALA L 886 " (cutoff:3.500A) Processing helix chain 'L' and resid 894 through 906 Processing helix chain 'L' and resid 914 through 931 Proline residue: L 919 - end of helix removed outlier: 5.224A pdb=" N ASP L 922 " --> pdb=" O GLU L 918 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ASP L 923 " --> pdb=" O PRO L 919 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN L 930 " --> pdb=" O LYS L 926 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU L 931 " --> pdb=" O ALA L 927 " (cutoff:3.500A) Processing helix chain 'L' and resid 943 through 951 Processing helix chain 'L' and resid 997 through 1005 Processing helix chain 'L' and resid 1012 through 1032 removed outlier: 4.743A pdb=" N SER L1031 " --> pdb=" O LEU L1027 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N SER L1032 " --> pdb=" O MET L1028 " (cutoff:3.500A) Processing helix chain 'L' and resid 1039 through 1048 Processing helix chain 'L' and resid 1069 through 1091 removed outlier: 3.780A pdb=" N THR L1090 " --> pdb=" O VAL L1086 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N SER L1091 " --> pdb=" O PHE L1087 " (cutoff:3.500A) Processing helix chain 'L' and resid 1096 through 1123 removed outlier: 3.820A pdb=" N LEU L1112 " --> pdb=" O ASP L1108 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL L1115 " --> pdb=" O CYS L1111 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ASN L1116 " --> pdb=" O LEU L1112 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR L1117 " --> pdb=" O LEU L1113 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS L1122 " --> pdb=" O THR L1118 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ARG L1123 " --> pdb=" O LEU L1119 " (cutoff:3.500A) Processing helix chain 'L' and resid 1149 through 1153 Processing helix chain 'L' and resid 1158 through 1179 removed outlier: 3.798A pdb=" N VAL L1163 " --> pdb=" O GLU L1159 " (cutoff:3.500A) Processing helix chain 'L' and resid 1181 through 1187 removed outlier: 4.090A pdb=" N LEU L1185 " --> pdb=" O GLU L1181 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N SER L1186 " --> pdb=" O GLU L1182 " (cutoff:3.500A) Processing helix chain 'L' and resid 1189 through 1202 removed outlier: 3.942A pdb=" N TYR L1202 " --> pdb=" O ILE L1198 " (cutoff:3.500A) Processing helix chain 'L' and resid 1206 through 1222 Processing helix chain 'L' and resid 1229 through 1232 No H-bonds generated for 'chain 'L' and resid 1229 through 1232' Processing helix chain 'L' and resid 1234 through 1246 removed outlier: 3.597A pdb=" N LEU L1245 " --> pdb=" O LEU L1241 " (cutoff:3.500A) Processing helix chain 'L' and resid 1254 through 1271 Processing helix chain 'L' and resid 1284 through 1293 Processing helix chain 'L' and resid 1301 through 1315 Processing helix chain 'L' and resid 1322 through 1325 No H-bonds generated for 'chain 'L' and resid 1322 through 1325' Processing helix chain 'L' and resid 1330 through 1339 Proline residue: L1336 - end of helix Processing helix chain 'L' and resid 1347 through 1362 Processing helix chain 'L' and resid 1372 through 1382 Processing helix chain 'L' and resid 1405 through 1423 Processing helix chain 'L' and resid 1437 through 1446 removed outlier: 3.742A pdb=" N VAL L1443 " --> pdb=" O ARG L1439 " (cutoff:3.500A) Processing helix chain 'L' and resid 1453 through 1469 removed outlier: 4.625A pdb=" N ALA L1468 " --> pdb=" O LYS L1464 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N GLU L1469 " --> pdb=" O GLY L1465 " (cutoff:3.500A) Processing helix chain 'L' and resid 1477 through 1481 removed outlier: 4.255A pdb=" N GLY L1481 " --> pdb=" O LEU L1478 " (cutoff:3.500A) Processing helix chain 'L' and resid 1483 through 1488 Processing helix chain 'L' and resid 1497 through 1507 Processing helix chain 'L' and resid 1518 through 1529 Processing helix chain 'L' and resid 1533 through 1537 Processing helix chain 'L' and resid 1547 through 1559 removed outlier: 3.550A pdb=" N PHE L1559 " --> pdb=" O ILE L1555 " (cutoff:3.500A) Processing helix chain 'L' and resid 1571 through 1583 Processing helix chain 'L' and resid 1594 through 1603 removed outlier: 3.952A pdb=" N ARG L1602 " --> pdb=" O ARG L1598 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N PHE L1603 " --> pdb=" O TYR L1599 " (cutoff:3.500A) Processing helix chain 'L' and resid 1606 through 1612 Processing helix chain 'L' and resid 1618 through 1628 Processing helix chain 'L' and resid 1634 through 1640 removed outlier: 4.376A pdb=" N GLU L1638 " --> pdb=" O LYS L1634 " (cutoff:3.500A) Processing helix chain 'L' and resid 1644 through 1658 Proline residue: L1656 - end of helix Processing helix chain 'L' and resid 1662 through 1678 Processing helix chain 'L' and resid 1691 through 1708 Processing helix chain 'L' and resid 1716 through 1735 removed outlier: 3.571A pdb=" N LEU L1735 " --> pdb=" O ARG L1731 " (cutoff:3.500A) Processing helix chain 'L' and resid 1740 through 1749 removed outlier: 3.797A pdb=" N LEU L1744 " --> pdb=" O GLN L1740 " (cutoff:3.500A) Processing helix chain 'L' and resid 1763 through 1769 Processing helix chain 'L' and resid 1772 through 1774 No H-bonds generated for 'chain 'L' and resid 1772 through 1774' Processing helix chain 'L' and resid 1778 through 1791 Processing helix chain 'L' and resid 1797 through 1816 Processing helix chain 'L' and resid 1834 through 1844 removed outlier: 3.773A pdb=" N ASN L1844 " --> pdb=" O LYS L1840 " (cutoff:3.500A) Processing helix chain 'L' and resid 1847 through 1849 No H-bonds generated for 'chain 'L' and resid 1847 through 1849' Processing helix chain 'L' and resid 1859 through 1874 Processing helix chain 'L' and resid 1883 through 1892 Processing helix chain 'L' and resid 1900 through 1915 Processing helix chain 'L' and resid 1921 through 1930 removed outlier: 3.689A pdb=" N GLN L1925 " --> pdb=" O LYS L1921 " (cutoff:3.500A) Processing helix chain 'L' and resid 1936 through 1957 removed outlier: 3.777A pdb=" N ARG L1939 " --> pdb=" O VAL L1936 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N TYR L1940 " --> pdb=" O GLU L1937 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU L1941 " --> pdb=" O ALA L1938 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N THR L1950 " --> pdb=" O ASP L1947 " (cutoff:3.500A) Proline residue: L1951 - end of helix removed outlier: 4.243A pdb=" N HIS L1954 " --> pdb=" O PRO L1951 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N MET L1957 " --> pdb=" O HIS L1954 " (cutoff:3.500A) Processing helix chain 'L' and resid 1965 through 1974 removed outlier: 4.277A pdb=" N VAL L1970 " --> pdb=" O TRP L1966 " (cutoff:3.500A) Processing helix chain 'L' and resid 1981 through 1987 removed outlier: 3.633A pdb=" N LEU L1985 " --> pdb=" O ASN L1982 " (cutoff:3.500A) Processing helix chain 'L' and resid 1989 through 1992 No H-bonds generated for 'chain 'L' and resid 1989 through 1992' Processing helix chain 'L' and resid 2002 through 2014 Processing helix chain 'L' and resid 2024 through 2042 removed outlier: 3.634A pdb=" N ILE L2029 " --> pdb=" O THR L2026 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER L2033 " --> pdb=" O ASP L2030 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU L2036 " --> pdb=" O SER L2033 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASN L2040 " --> pdb=" O TYR L2037 " (cutoff:3.500A) Processing helix chain 'L' and resid 2091 through 2106 Processing helix chain 'L' and resid 2117 through 2128 Processing helix chain 'L' and resid 2156 through 2172 removed outlier: 4.088A pdb=" N TYR L2169 " --> pdb=" O LEU L2165 " (cutoff:3.500A) Processing helix chain 'L' and resid 2184 through 2195 removed outlier: 4.813A pdb=" N LYS L2193 " --> pdb=" O ASN L2189 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N CYS L2194 " --> pdb=" O LEU L2190 " (cutoff:3.500A) Processing helix chain 'L' and resid 2204 through 2216 removed outlier: 4.855A pdb=" N GLN L2211 " --> pdb=" O GLN L2207 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL L2212 " --> pdb=" O LYS L2208 " (cutoff:3.500A) Processing helix chain 'L' and resid 2229 through 2244 Processing helix chain 'L' and resid 2252 through 2266 removed outlier: 4.020A pdb=" N GLY L2256 " --> pdb=" O SER L2252 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL L2257 " --> pdb=" O VAL L2253 " (cutoff:3.500A) Processing helix chain 'L' and resid 2276 through 2289 Processing helix chain 'L' and resid 2303 through 2320 removed outlier: 4.777A pdb=" N THR L2308 " --> pdb=" O ALA L2304 " (cutoff:3.500A) Processing helix chain 'L' and resid 2328 through 2341 Processing helix chain 'L' and resid 2346 through 2360 removed outlier: 4.217A pdb=" N LYS L2351 " --> pdb=" O ASN L2347 " (cutoff:3.500A) Processing helix chain 'L' and resid 2370 through 2385 removed outlier: 4.233A pdb=" N MET L2379 " --> pdb=" O ILE L2375 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LEU L2380 " --> pdb=" O LEU L2376 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ALA L2381 " --> pdb=" O THR L2377 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N PHE L2382 " --> pdb=" O LYS L2378 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N GLU L2383 " --> pdb=" O MET L2379 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE L2384 " --> pdb=" O LEU L2380 " (cutoff:3.500A) Processing helix chain 'L' and resid 2388 through 2403 Processing helix chain 'L' and resid 2413 through 2425 removed outlier: 3.541A pdb=" N GLU L2417 " --> pdb=" O THR L2413 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLN L2418 " --> pdb=" O VAL L2414 " (cutoff:3.500A) Proline residue: L2419 - end of helix removed outlier: 3.693A pdb=" N VAL L2422 " --> pdb=" O GLN L2418 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG L2425 " --> pdb=" O LEU L2421 " (cutoff:3.500A) Processing helix chain 'L' and resid 2429 through 2442 Processing helix chain 'L' and resid 2447 through 2455 Processing helix chain 'L' and resid 2469 through 2479 removed outlier: 3.639A pdb=" N GLY L2478 " --> pdb=" O GLN L2474 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER L2479 " --> pdb=" O LEU L2475 " (cutoff:3.500A) Processing helix chain 'L' and resid 2500 through 2502 No H-bonds generated for 'chain 'L' and resid 2500 through 2502' Processing helix chain 'L' and resid 2519 through 2533 removed outlier: 3.619A pdb=" N GLY L2532 " --> pdb=" O ALA L2528 " (cutoff:3.500A) Processing helix chain 'L' and resid 2538 through 2549 removed outlier: 4.010A pdb=" N GLU L2547 " --> pdb=" O ASP L2543 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE L2548 " --> pdb=" O SER L2544 " (cutoff:3.500A) Processing helix chain 'L' and resid 2553 through 2570 removed outlier: 3.631A pdb=" N HIS L2557 " --> pdb=" O PRO L2553 " (cutoff:3.500A) Proline residue: L2565 - end of helix removed outlier: 4.308A pdb=" N LYS L2569 " --> pdb=" O PRO L2565 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N SER L2570 " --> pdb=" O GLN L2566 " (cutoff:3.500A) Processing helix chain 'L' and resid 2576 through 2587 Processing helix chain 'L' and resid 2590 through 2595 Processing helix chain 'L' and resid 2602 through 2612 removed outlier: 3.671A pdb=" N SER L2609 " --> pdb=" O MET L2605 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS L2612 " --> pdb=" O ASP L2608 " (cutoff:3.500A) Processing helix chain 'L' and resid 2624 through 2626 No H-bonds generated for 'chain 'L' and resid 2624 through 2626' Processing helix chain 'L' and resid 2633 through 2641 Processing helix chain 'L' and resid 2655 through 2668 Processing helix chain 'L' and resid 2672 through 2682 Processing helix chain 'L' and resid 2686 through 2697 Processing helix chain 'L' and resid 2700 through 2715 Processing helix chain 'L' and resid 2721 through 2723 No H-bonds generated for 'chain 'L' and resid 2721 through 2723' Processing helix chain 'L' and resid 2725 through 2739 Processing helix chain 'L' and resid 2743 through 2751 removed outlier: 3.855A pdb=" N GLU L2748 " --> pdb=" O ASP L2744 " (cutoff:3.500A) Processing helix chain 'L' and resid 2758 through 2760 No H-bonds generated for 'chain 'L' and resid 2758 through 2760' Processing helix chain 'L' and resid 2773 through 2783 removed outlier: 3.773A pdb=" N SER L2779 " --> pdb=" O ALA L2775 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL L2783 " --> pdb=" O SER L2779 " (cutoff:3.500A) Processing helix chain 'L' and resid 2789 through 2805 Processing helix chain 'L' and resid 2813 through 2830 removed outlier: 3.773A pdb=" N ASP L2818 " --> pdb=" O ARG L2814 " (cutoff:3.500A) Processing helix chain 'L' and resid 2837 through 2863 removed outlier: 3.605A pdb=" N TRP L2841 " --> pdb=" O ALA L2838 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS L2863 " --> pdb=" O ALA L2860 " (cutoff:3.500A) Processing helix chain 'L' and resid 2865 through 2867 No H-bonds generated for 'chain 'L' and resid 2865 through 2867' Processing helix chain 'L' and resid 2874 through 2885 Processing helix chain 'L' and resid 2895 through 2915 removed outlier: 3.719A pdb=" N ILE L2912 " --> pdb=" O ALA L2908 " (cutoff:3.500A) Processing helix chain 'L' and resid 2921 through 2923 No H-bonds generated for 'chain 'L' and resid 2921 through 2923' Processing helix chain 'L' and resid 2942 through 2956 removed outlier: 4.628A pdb=" N ARG L2949 " --> pdb=" O VAL L2946 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA L2954 " --> pdb=" O ALA L2951 " (cutoff:3.500A) Processing helix chain 'L' and resid 2960 through 2966 Processing helix chain 'L' and resid 2980 through 2993 removed outlier: 3.748A pdb=" N HIS L2992 " --> pdb=" O GLN L2988 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR L2993 " --> pdb=" O ALA L2989 " (cutoff:3.500A) Processing helix chain 'L' and resid 2996 through 3006 removed outlier: 3.825A pdb=" N LEU L2999 " --> pdb=" O MET L2996 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N THR L3000 " --> pdb=" O ASN L2997 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ASP L3004 " --> pdb=" O THR L3001 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL L3005 " --> pdb=" O GLY L3002 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE L3006 " --> pdb=" O LEU L3003 " (cutoff:3.500A) Processing helix chain 'L' and resid 3017 through 3032 Processing helix chain 'L' and resid 3037 through 3047 Processing helix chain 'L' and resid 3054 through 3070 removed outlier: 3.990A pdb=" N GLU L3070 " --> pdb=" O ARG L3066 " (cutoff:3.500A) Processing helix chain 'L' and resid 3076 through 3090 removed outlier: 3.520A pdb=" N GLN L3087 " --> pdb=" O CYS L3084 " (cutoff:3.500A) Processing helix chain 'L' and resid 3098 through 3108 Processing helix chain 'L' and resid 3116 through 3122 Processing helix chain 'L' and resid 3130 through 3141 removed outlier: 4.015A pdb=" N THR L3135 " --> pdb=" O TYR L3132 " (cutoff:3.500A) Proline residue: L3138 - end of helix Processing helix chain 'L' and resid 3152 through 3162 removed outlier: 3.553A pdb=" N SER L3162 " --> pdb=" O ARG L3158 " (cutoff:3.500A) Processing helix chain 'L' and resid 3164 through 3179 removed outlier: 5.201A pdb=" N PHE L3169 " --> pdb=" O GLN L3165 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N GLN L3170 " --> pdb=" O ALA L3166 " (cutoff:3.500A) Processing helix chain 'L' and resid 3203 through 3217 Processing helix chain 'L' and resid 3220 through 3236 Processing helix chain 'L' and resid 3241 through 3262 Processing helix chain 'L' and resid 3274 through 3286 removed outlier: 3.858A pdb=" N THR L3285 " --> pdb=" O VAL L3281 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR L3286 " --> pdb=" O LYS L3282 " (cutoff:3.500A) Processing helix chain 'L' and resid 3292 through 3301 removed outlier: 3.562A pdb=" N ASP L3299 " --> pdb=" O LYS L3295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE L3300 " --> pdb=" O PHE L3296 " (cutoff:3.500A) Processing helix chain 'L' and resid 3309 through 3326 Processing helix chain 'L' and resid 3334 through 3337 No H-bonds generated for 'chain 'L' and resid 3334 through 3337' Processing helix chain 'L' and resid 3339 through 3342 No H-bonds generated for 'chain 'L' and resid 3339 through 3342' Processing helix chain 'L' and resid 3344 through 3347 No H-bonds generated for 'chain 'L' and resid 3344 through 3347' Processing helix chain 'L' and resid 3413 through 3427 removed outlier: 3.733A pdb=" N PHE L3426 " --> pdb=" O LEU L3422 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN L3427 " --> pdb=" O TYR L3423 " (cutoff:3.500A) Processing helix chain 'L' and resid 3429 through 3432 No H-bonds generated for 'chain 'L' and resid 3429 through 3432' Processing helix chain 'L' and resid 3434 through 3438 Processing helix chain 'L' and resid 3467 through 3477 Processing helix chain 'L' and resid 3484 through 3497 removed outlier: 3.631A pdb=" N ALA L3496 " --> pdb=" O LYS L3492 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N HIS L3497 " --> pdb=" O LEU L3493 " (cutoff:3.500A) Processing helix chain 'L' and resid 3506 through 3520 Processing helix chain 'L' and resid 3526 through 3534 Processing helix chain 'L' and resid 3538 through 3563 removed outlier: 3.905A pdb=" N SER L3550 " --> pdb=" O LYS L3546 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N MET L3562 " --> pdb=" O MET L3558 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET L3563 " --> pdb=" O SER L3559 " (cutoff:3.500A) Processing helix chain 'L' and resid 3626 through 3632 Processing helix chain 'L' and resid 3635 through 3639 Processing helix chain 'L' and resid 3641 through 3653 removed outlier: 3.776A pdb=" N SER L3649 " --> pdb=" O LEU L3645 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE L3653 " --> pdb=" O SER L3649 " (cutoff:3.500A) Processing helix chain 'L' and resid 3659 through 3677 removed outlier: 4.081A pdb=" N LEU L3665 " --> pdb=" O THR L3661 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU L3670 " --> pdb=" O PHE L3666 " (cutoff:3.500A) Processing helix chain 'L' and resid 3686 through 3704 Processing helix chain 'L' and resid 3719 through 3726 Processing helix chain 'L' and resid 3730 through 3733 No H-bonds generated for 'chain 'L' and resid 3730 through 3733' Processing sheet with id= A, first strand: chain 'E' and resid 268 through 273 Processing sheet with id= B, first strand: chain 'F' and resid 38 through 41 removed outlier: 7.696A pdb=" N ILE F 19 " --> pdb=" O PRO F 107 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU F 109 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ALA F 136 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LEU F 110 " --> pdb=" O ALA F 136 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N TYR F 138 " --> pdb=" O LEU F 110 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N GLU F 112 " --> pdb=" O TYR F 138 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ALA F 140 " --> pdb=" O GLU F 112 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'F' and resid 408 through 411 removed outlier: 6.274A pdb=" N LEU F 156 " --> pdb=" O VAL F 409 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N THR F 411 " --> pdb=" O LEU F 156 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL F 158 " --> pdb=" O THR F 411 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'F' and resid 268 through 271 removed outlier: 4.079A pdb=" N ARG F 268 " --> pdb=" O PHE F 280 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'G' and resid 8 through 12 Processing sheet with id= F, first strand: chain 'G' and resid 34 through 36 Processing sheet with id= G, first strand: chain 'G' and resid 103 through 107 Processing sheet with id= H, first strand: chain 'G' and resid 297 through 300 removed outlier: 6.174A pdb=" N ILE G 151 " --> pdb=" O VAL G 298 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N SER G 300 " --> pdb=" O ILE G 151 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N LEU G 153 " --> pdb=" O SER G 300 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 238 through 241 Processing sheet with id= J, first strand: chain 'K' and resid 78 through 84 Processing sheet with id= K, first strand: chain 'H' and resid 636 through 642 Processing sheet with id= L, first strand: chain 'H' and resid 546 through 549 removed outlier: 3.530A pdb=" N ARG H 574 " --> pdb=" O ASP H 548 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'L' and resid 977 through 980 Processing sheet with id= N, first strand: chain 'L' and resid 3379 through 3382 removed outlier: 4.285A pdb=" N ARG L3389 " --> pdb=" O VAL L3405 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'L' and resid 3464 through 3466 Processing sheet with id= P, first strand: chain 'L' and resid 3371 through 3374 removed outlier: 6.855A pdb=" N ARG L3394 " --> pdb=" O ALA L3372 " (cutoff:3.500A) 1799 hydrogen bonds defined for protein. 4869 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 20.37 Time building geometry restraints manager: 18.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 7037 1.31 - 1.43: 11471 1.43 - 1.56: 24669 1.56 - 1.69: 12 1.69 - 1.82: 295 Bond restraints: 43484 Sorted by residual: bond pdb=" CB GLN L3629 " pdb=" CG GLN L3629 " ideal model delta sigma weight residual 1.520 1.400 0.120 3.00e-02 1.11e+03 1.61e+01 bond pdb=" CB PHE L2755 " pdb=" CG PHE L2755 " ideal model delta sigma weight residual 1.502 1.412 0.090 2.30e-02 1.89e+03 1.52e+01 bond pdb=" CB GLU L3512 " pdb=" CG GLU L3512 " ideal model delta sigma weight residual 1.520 1.419 0.101 3.00e-02 1.11e+03 1.12e+01 bond pdb=" CB VAL L3728 " pdb=" CG2 VAL L3728 " ideal model delta sigma weight residual 1.521 1.413 0.108 3.30e-02 9.18e+02 1.07e+01 bond pdb=" CB ASN L2658 " pdb=" CG ASN L2658 " ideal model delta sigma weight residual 1.516 1.438 0.078 2.50e-02 1.60e+03 9.81e+00 ... (remaining 43479 not shown) Histogram of bond angle deviations from ideal: 97.26 - 104.69: 791 104.69 - 112.11: 20977 112.11 - 119.53: 16706 119.53 - 126.96: 19878 126.96 - 134.38: 537 Bond angle restraints: 58889 Sorted by residual: angle pdb=" PB ATP G 502 " pdb=" O3B ATP G 502 " pdb=" PG ATP G 502 " ideal model delta sigma weight residual 139.87 130.72 9.15 1.00e+00 1.00e+00 8.37e+01 angle pdb=" PB ATP F1002 " pdb=" O3B ATP F1002 " pdb=" PG ATP F1002 " ideal model delta sigma weight residual 139.87 132.12 7.75 1.00e+00 1.00e+00 6.01e+01 angle pdb=" PA ATP G 502 " pdb=" O3A ATP G 502 " pdb=" PB ATP G 502 " ideal model delta sigma weight residual 136.83 130.96 5.87 1.00e+00 1.00e+00 3.45e+01 angle pdb=" N PRO L 852 " pdb=" CA PRO L 852 " pdb=" C PRO L 852 " ideal model delta sigma weight residual 112.47 100.72 11.75 2.06e+00 2.36e-01 3.25e+01 angle pdb=" N LEU E 310 " pdb=" CA LEU E 310 " pdb=" C LEU E 310 " ideal model delta sigma weight residual 112.45 119.74 -7.29 1.39e+00 5.18e-01 2.75e+01 ... (remaining 58884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 23793 17.89 - 35.78: 2162 35.78 - 53.66: 366 53.66 - 71.55: 112 71.55 - 89.44: 42 Dihedral angle restraints: 26475 sinusoidal: 10999 harmonic: 15476 Sorted by residual: dihedral pdb=" CA HIS L2621 " pdb=" C HIS L2621 " pdb=" N LEU L2622 " pdb=" CA LEU L2622 " ideal model delta harmonic sigma weight residual 180.00 149.53 30.47 0 5.00e+00 4.00e-02 3.71e+01 dihedral pdb=" CA THR L2756 " pdb=" C THR L2756 " pdb=" N ASP L2757 " pdb=" CA ASP L2757 " ideal model delta harmonic sigma weight residual 180.00 152.47 27.53 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA ARG L2425 " pdb=" C ARG L2425 " pdb=" N VAL L2426 " pdb=" CA VAL L2426 " ideal model delta harmonic sigma weight residual -180.00 -153.53 -26.47 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 26472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 6377 0.127 - 0.254: 245 0.254 - 0.381: 5 0.381 - 0.508: 0 0.508 - 0.635: 1 Chirality restraints: 6628 Sorted by residual: chirality pdb=" CB VAL L3728 " pdb=" CA VAL L3728 " pdb=" CG1 VAL L3728 " pdb=" CG2 VAL L3728 " both_signs ideal model delta sigma weight residual False -2.63 -1.99 -0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" CB VAL L2414 " pdb=" CA VAL L2414 " pdb=" CG1 VAL L2414 " pdb=" CG2 VAL L2414 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" CA ASN H 544 " pdb=" N ASN H 544 " pdb=" C ASN H 544 " pdb=" CB ASN H 544 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 6625 not shown) Planarity restraints: 7476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN L2418 " 0.091 5.00e-02 4.00e+02 1.36e-01 2.96e+01 pdb=" N PRO L2419 " -0.235 5.00e-02 4.00e+02 pdb=" CA PRO L2419 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO L2419 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE L2755 " 0.048 2.00e-02 2.50e+03 3.26e-02 1.86e+01 pdb=" CG PHE L2755 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE L2755 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE L2755 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE L2755 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE L2755 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE L2755 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L2492 " -0.042 2.00e-02 2.50e+03 2.91e-02 1.69e+01 pdb=" CG TYR L2492 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 TYR L2492 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR L2492 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR L2492 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR L2492 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR L2492 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR L2492 " -0.007 2.00e-02 2.50e+03 ... (remaining 7473 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 276 2.49 - 3.09: 32503 3.09 - 3.69: 65706 3.69 - 4.30: 95125 4.30 - 4.90: 157004 Nonbonded interactions: 350614 Sorted by model distance: nonbonded pdb=" OG1 THR E 312 " pdb=" O VAL L3728 " model vdw 1.885 2.440 nonbonded pdb=" NH2 ARG E 640 " pdb=" OE1 GLU E 726 " model vdw 1.981 2.520 nonbonded pdb=" OD1 ASN L 944 " pdb=" NH2 ARG L 947 " model vdw 2.010 2.520 nonbonded pdb=" OD2 ASP E 350 " pdb=" OH TYR K 206 " model vdw 2.105 2.440 nonbonded pdb=" O PRO F 433 " pdb=" OG SER F 434 " model vdw 2.108 2.440 ... (remaining 350609 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 13.220 Check model and map are aligned: 0.610 Set scattering table: 0.360 Process input model: 115.490 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 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 : 0.013 0.120 43484 Z= 0.822 Angle : 0.975 12.707 58889 Z= 0.549 Chirality : 0.059 0.635 6628 Planarity : 0.007 0.136 7476 Dihedral : 14.647 89.441 16379 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.90 % Favored : 92.00 % Rotamer: Outliers : 0.48 % Allowed : 7.26 % Favored : 92.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.65 (0.11), residues: 5149 helix: -1.25 (0.09), residues: 2969 sheet: -0.14 (0.38), residues: 210 loop : -2.65 (0.13), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP E 340 HIS 0.012 0.002 HIS L1012 PHE 0.068 0.003 PHE L2755 TYR 0.068 0.004 TYR L2492 ARG 0.019 0.001 ARG L3313 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 4766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 695 time to evaluate : 4.964 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: L 472 MET cc_start: 0.9346 (tmm) cc_final: 0.9018 (tmm) REVERT: L 588 ARG cc_start: 0.8764 (ttp-170) cc_final: 0.8460 (ttp80) REVERT: L 628 TYR cc_start: 0.8515 (t80) cc_final: 0.8067 (t80) REVERT: L 688 PHE cc_start: 0.8864 (t80) cc_final: 0.8618 (t80) REVERT: L 693 MET cc_start: 0.8631 (mtp) cc_final: 0.8370 (ttm) REVERT: L 711 GLU cc_start: 0.9112 (pt0) cc_final: 0.8905 (tm-30) REVERT: L 824 PHE cc_start: 0.8219 (p90) cc_final: 0.7935 (p90) REVERT: L 832 LYS cc_start: 0.8448 (mttt) cc_final: 0.7929 (mttt) REVERT: L 918 GLU cc_start: 0.7561 (tp30) cc_final: 0.7349 (tp30) REVERT: L 922 ASP cc_start: 0.7846 (p0) cc_final: 0.7593 (p0) REVERT: L 1294 CYS cc_start: 0.8851 (t) cc_final: 0.8468 (p) REVERT: L 1295 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7561 (mm-30) REVERT: L 1302 LYS cc_start: 0.8630 (mttm) cc_final: 0.8415 (mmtt) REVERT: L 1329 SER cc_start: 0.8577 (p) cc_final: 0.8366 (t) REVERT: L 1347 PHE cc_start: 0.8269 (m-10) cc_final: 0.7771 (m-10) REVERT: L 1407 GLN cc_start: 0.8618 (mt0) cc_final: 0.8212 (pt0) REVERT: L 1410 GLN cc_start: 0.8134 (mm-40) cc_final: 0.7911 (tm-30) REVERT: L 1501 ASP cc_start: 0.8399 (t0) cc_final: 0.8165 (t0) REVERT: L 1556 ILE cc_start: 0.8921 (mt) cc_final: 0.8702 (tt) REVERT: L 1589 ASP cc_start: 0.7582 (m-30) cc_final: 0.7068 (m-30) REVERT: L 1594 THR cc_start: 0.8882 (m) cc_final: 0.8650 (m) REVERT: L 1624 MET cc_start: 0.9289 (mmm) cc_final: 0.8946 (mmp) REVERT: L 1631 PRO cc_start: 0.8715 (Cg_exo) cc_final: 0.8243 (Cg_endo) REVERT: L 1648 TYR cc_start: 0.6176 (m-80) cc_final: 0.5883 (m-80) REVERT: L 1699 LEU cc_start: 0.9282 (tp) cc_final: 0.9001 (tp) REVERT: L 1974 MET cc_start: 0.8150 (ttt) cc_final: 0.7793 (tpp) REVERT: L 2103 TYR cc_start: 0.7677 (t80) cc_final: 0.7435 (t80) REVERT: L 2387 GLU cc_start: 0.7464 (mp0) cc_final: 0.7256 (mp0) REVERT: L 2490 ASN cc_start: 0.7028 (t0) cc_final: 0.6778 (t0) REVERT: L 2621 HIS cc_start: 0.7881 (p-80) cc_final: 0.7648 (p-80) outliers start: 23 outliers final: 9 residues processed: 714 average time/residue: 0.5988 time to fit residues: 684.9085 Evaluate side-chains 409 residues out of total 4766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 400 time to evaluate : 5.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain H residue 560 VAL Chi-restraints excluded: chain L residue 250 THR Chi-restraints excluded: chain L residue 1853 VAL Chi-restraints excluded: chain L residue 2415 ARG Chi-restraints excluded: chain L residue 3307 TYR Chi-restraints excluded: chain L residue 3347 GLN Chi-restraints excluded: chain L residue 3493 LEU Chi-restraints excluded: chain L residue 3498 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 436 optimal weight: 0.9990 chunk 391 optimal weight: 0.6980 chunk 217 optimal weight: 5.9990 chunk 133 optimal weight: 0.8980 chunk 264 optimal weight: 0.8980 chunk 209 optimal weight: 20.0000 chunk 405 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 246 optimal weight: 1.9990 chunk 301 optimal weight: 20.0000 chunk 469 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 222 ASN ** E 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 ASN G 78 ASN H 626 ASN L 6 GLN ** L 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 843 ASN L 889 GLN L 998 GLN L1328 HIS ** L1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1379 GLN L1629 GLN L1658 ASN ** L1754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1992 HIS L1998 ASN ** L2010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L2207 GLN L2592 HIS L2651 ASN L2741 GLN L2811 GLN L2907 HIS L2948 ASN L2992 HIS ** L3347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 43484 Z= 0.205 Angle : 0.671 14.959 58889 Z= 0.338 Chirality : 0.043 0.281 6628 Planarity : 0.005 0.099 7476 Dihedral : 6.726 86.732 5723 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.30 % Favored : 92.62 % Rotamer: Outliers : 1.72 % Allowed : 12.00 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.11), residues: 5149 helix: -0.24 (0.09), residues: 2953 sheet: -0.11 (0.39), residues: 199 loop : -2.44 (0.13), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP K 164 HIS 0.010 0.001 HIS L1328 PHE 0.049 0.002 PHE L1747 TYR 0.024 0.001 TYR L2492 ARG 0.016 0.001 ARG E 632 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 4766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 459 time to evaluate : 5.079 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: E 248 MET cc_start: 0.6846 (OUTLIER) cc_final: 0.6186 (mmm) REVERT: E 312 THR cc_start: 0.8240 (OUTLIER) cc_final: 0.7767 (m) REVERT: E 651 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8820 (tp) REVERT: F 206 LEU cc_start: 0.7533 (tp) cc_final: 0.7040 (tt) REVERT: F 444 HIS cc_start: 0.6870 (t-170) cc_final: 0.6111 (t-170) REVERT: G 227 MET cc_start: 0.5406 (tpt) cc_final: 0.5054 (tpp) REVERT: K 289 GLN cc_start: 0.7198 (mp10) cc_final: 0.6388 (mt0) REVERT: L 79 MET cc_start: 0.4907 (ptp) cc_final: 0.4169 (ptt) REVERT: L 383 MET cc_start: 0.4620 (pmm) cc_final: 0.4415 (pmm) REVERT: L 472 MET cc_start: 0.9393 (tmm) cc_final: 0.9175 (tmm) REVERT: L 588 ARG cc_start: 0.8720 (ttp-170) cc_final: 0.8447 (ttp80) REVERT: L 591 MET cc_start: 0.9358 (mtp) cc_final: 0.8857 (mmm) REVERT: L 628 TYR cc_start: 0.8448 (t80) cc_final: 0.8238 (t80) REVERT: L 771 MET cc_start: 0.8292 (ppp) cc_final: 0.8091 (ppp) REVERT: L 804 GLU cc_start: 0.8622 (tp30) cc_final: 0.8374 (tp30) REVERT: L 824 PHE cc_start: 0.8195 (p90) cc_final: 0.7954 (p90) REVERT: L 922 ASP cc_start: 0.7664 (p0) cc_final: 0.7447 (p0) REVERT: L 1294 CYS cc_start: 0.8919 (t) cc_final: 0.8458 (m) REVERT: L 1298 ASN cc_start: 0.8017 (t0) cc_final: 0.7724 (t0) REVERT: L 1302 LYS cc_start: 0.8710 (mttm) cc_final: 0.8405 (mmtt) REVERT: L 1329 SER cc_start: 0.8513 (p) cc_final: 0.8159 (t) REVERT: L 1355 ASP cc_start: 0.8464 (t0) cc_final: 0.7612 (m-30) REVERT: L 1501 ASP cc_start: 0.8215 (t0) cc_final: 0.7991 (t0) REVERT: L 1568 MET cc_start: 0.8054 (pmm) cc_final: 0.7491 (pmm) REVERT: L 1589 ASP cc_start: 0.7763 (m-30) cc_final: 0.6947 (m-30) REVERT: L 1691 MET cc_start: 0.6465 (mtt) cc_final: 0.6092 (mtt) REVERT: L 1957 MET cc_start: 0.5981 (tpt) cc_final: 0.5419 (tpp) REVERT: L 1974 MET cc_start: 0.8206 (ttt) cc_final: 0.7742 (tpt) REVERT: L 1986 TYR cc_start: 0.7700 (m-80) cc_final: 0.7367 (m-80) REVERT: L 2103 TYR cc_start: 0.7694 (t80) cc_final: 0.7468 (t80) REVERT: L 2490 ASN cc_start: 0.6833 (t0) cc_final: 0.6502 (t0) REVERT: L 2656 GLU cc_start: 0.6588 (pt0) cc_final: 0.6338 (tt0) REVERT: L 2723 GLN cc_start: 0.7796 (tm-30) cc_final: 0.7581 (tm-30) REVERT: L 3307 TYR cc_start: 0.8198 (OUTLIER) cc_final: 0.7157 (t80) outliers start: 82 outliers final: 34 residues processed: 521 average time/residue: 0.5636 time to fit residues: 491.4399 Evaluate side-chains 395 residues out of total 4766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 357 time to evaluate : 5.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 718 HIS Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 78 ASN Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain H residue 553 LYS Chi-restraints excluded: chain H residue 560 VAL Chi-restraints excluded: chain H residue 724 ASP Chi-restraints excluded: chain L residue 355 LEU Chi-restraints excluded: chain L residue 716 ASP Chi-restraints excluded: chain L residue 732 THR Chi-restraints excluded: chain L residue 917 ILE Chi-restraints excluded: chain L residue 998 GLN Chi-restraints excluded: chain L residue 1395 ASN Chi-restraints excluded: chain L residue 1588 LEU Chi-restraints excluded: chain L residue 1684 TRP Chi-restraints excluded: chain L residue 1992 HIS Chi-restraints excluded: chain L residue 1995 LEU Chi-restraints excluded: chain L residue 2143 PHE Chi-restraints excluded: chain L residue 2588 SER Chi-restraints excluded: chain L residue 2866 THR Chi-restraints excluded: chain L residue 3119 ASN Chi-restraints excluded: chain L residue 3152 VAL Chi-restraints excluded: chain L residue 3171 LEU Chi-restraints excluded: chain L residue 3307 TYR Chi-restraints excluded: chain L residue 3347 GLN Chi-restraints excluded: chain L residue 3371 ILE Chi-restraints excluded: chain L residue 3400 VAL Chi-restraints excluded: chain L residue 3449 ILE Chi-restraints excluded: chain L residue 3498 ASP Chi-restraints excluded: chain L residue 3685 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 260 optimal weight: 3.9990 chunk 145 optimal weight: 8.9990 chunk 390 optimal weight: 4.9990 chunk 319 optimal weight: 0.9980 chunk 129 optimal weight: 10.0000 chunk 470 optimal weight: 1.9990 chunk 508 optimal weight: 0.7980 chunk 418 optimal weight: 2.9990 chunk 466 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 chunk 377 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 78 ASN K 302 GLN H 559 ASN ** L 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 889 GLN L1234 GLN ** L1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1740 GLN L2592 HIS L2741 GLN L3261 ASN ** L3347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L3486 GLN L3657 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 43484 Z= 0.199 Angle : 0.633 15.968 58889 Z= 0.316 Chirality : 0.043 0.267 6628 Planarity : 0.004 0.060 7476 Dihedral : 6.343 78.405 5715 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.36 % Favored : 92.58 % Rotamer: Outliers : 2.04 % Allowed : 13.55 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.12), residues: 5149 helix: 0.23 (0.10), residues: 2946 sheet: 0.13 (0.39), residues: 191 loop : -2.31 (0.13), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP L2904 HIS 0.009 0.001 HIS L2621 PHE 0.054 0.001 PHE L1747 TYR 0.025 0.001 TYR L2316 ARG 0.010 0.000 ARG E 632 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 4766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 399 time to evaluate : 4.913 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: F 206 LEU cc_start: 0.7442 (tp) cc_final: 0.6984 (tt) REVERT: K 289 GLN cc_start: 0.7237 (mp10) cc_final: 0.6399 (mt0) REVERT: L 119 MET cc_start: 0.5825 (ptp) cc_final: 0.5601 (ptp) REVERT: L 304 PHE cc_start: 0.8564 (m-10) cc_final: 0.8153 (m-80) REVERT: L 465 MET cc_start: 0.9003 (mmt) cc_final: 0.8668 (mmt) REVERT: L 472 MET cc_start: 0.9400 (tmm) cc_final: 0.9195 (tmm) REVERT: L 588 ARG cc_start: 0.8719 (ttp-170) cc_final: 0.8467 (ttp80) REVERT: L 591 MET cc_start: 0.9375 (mtp) cc_final: 0.9091 (mmm) REVERT: L 700 GLU cc_start: 0.8691 (pt0) cc_final: 0.8266 (pt0) REVERT: L 844 GLN cc_start: 0.8260 (pp30) cc_final: 0.7590 (pp30) REVERT: L 922 ASP cc_start: 0.7557 (p0) cc_final: 0.7308 (p0) REVERT: L 1294 CYS cc_start: 0.8922 (t) cc_final: 0.8368 (m) REVERT: L 1295 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7663 (mm-30) REVERT: L 1298 ASN cc_start: 0.8129 (t0) cc_final: 0.7724 (t0) REVERT: L 1302 LYS cc_start: 0.8715 (mttm) cc_final: 0.8380 (mmtt) REVERT: L 1329 SER cc_start: 0.8512 (p) cc_final: 0.8178 (t) REVERT: L 1355 ASP cc_start: 0.8474 (t0) cc_final: 0.7635 (m-30) REVERT: L 1501 ASP cc_start: 0.8161 (t0) cc_final: 0.7960 (t0) REVERT: L 1588 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7660 (mm) REVERT: L 1589 ASP cc_start: 0.7748 (m-30) cc_final: 0.7286 (t0) REVERT: L 1954 HIS cc_start: 0.7224 (t70) cc_final: 0.6947 (t-170) REVERT: L 1957 MET cc_start: 0.5531 (tpt) cc_final: 0.5073 (tpp) REVERT: L 1974 MET cc_start: 0.8179 (ttt) cc_final: 0.7737 (tpt) REVERT: L 1986 TYR cc_start: 0.7694 (m-80) cc_final: 0.7411 (m-80) REVERT: L 2214 MET cc_start: 0.8542 (ppp) cc_final: 0.8144 (ppp) REVERT: L 2490 ASN cc_start: 0.6845 (t0) cc_final: 0.6412 (t0) REVERT: L 2723 GLN cc_start: 0.7845 (tm-30) cc_final: 0.7559 (tm-30) REVERT: L 3076 SER cc_start: 0.7619 (p) cc_final: 0.5732 (m) REVERT: L 3092 TYR cc_start: 0.6755 (t80) cc_final: 0.5871 (t80) REVERT: L 3307 TYR cc_start: 0.8161 (OUTLIER) cc_final: 0.7180 (t80) outliers start: 97 outliers final: 44 residues processed: 471 average time/residue: 0.5515 time to fit residues: 443.2095 Evaluate side-chains 401 residues out of total 4766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 355 time to evaluate : 5.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 681 THR Chi-restraints excluded: chain E residue 712 LEU Chi-restraints excluded: chain E residue 718 HIS Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain H residue 724 ASP Chi-restraints excluded: chain L residue 218 MET Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 612 THR Chi-restraints excluded: chain L residue 702 ILE Chi-restraints excluded: chain L residue 716 ASP Chi-restraints excluded: chain L residue 732 THR Chi-restraints excluded: chain L residue 828 TYR Chi-restraints excluded: chain L residue 917 ILE Chi-restraints excluded: chain L residue 960 LEU Chi-restraints excluded: chain L residue 1376 ARG Chi-restraints excluded: chain L residue 1395 ASN Chi-restraints excluded: chain L residue 1588 LEU Chi-restraints excluded: chain L residue 1684 TRP Chi-restraints excluded: chain L residue 1992 HIS Chi-restraints excluded: chain L residue 1995 LEU Chi-restraints excluded: chain L residue 2143 PHE Chi-restraints excluded: chain L residue 2537 ILE Chi-restraints excluded: chain L residue 2574 ASN Chi-restraints excluded: chain L residue 2601 ASN Chi-restraints excluded: chain L residue 2618 LEU Chi-restraints excluded: chain L residue 2679 TRP Chi-restraints excluded: chain L residue 2752 HIS Chi-restraints excluded: chain L residue 2758 LEU Chi-restraints excluded: chain L residue 2805 GLU Chi-restraints excluded: chain L residue 2866 THR Chi-restraints excluded: chain L residue 2888 LEU Chi-restraints excluded: chain L residue 3049 ILE Chi-restraints excluded: chain L residue 3111 ASP Chi-restraints excluded: chain L residue 3119 ASN Chi-restraints excluded: chain L residue 3152 VAL Chi-restraints excluded: chain L residue 3211 LEU Chi-restraints excluded: chain L residue 3307 TYR Chi-restraints excluded: chain L residue 3347 GLN Chi-restraints excluded: chain L residue 3371 ILE Chi-restraints excluded: chain L residue 3400 VAL Chi-restraints excluded: chain L residue 3498 ASP Chi-restraints excluded: chain L residue 3657 ASN Chi-restraints excluded: chain L residue 3709 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 464 optimal weight: 0.8980 chunk 353 optimal weight: 0.8980 chunk 244 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 224 optimal weight: 3.9990 chunk 315 optimal weight: 5.9990 chunk 472 optimal weight: 5.9990 chunk 499 optimal weight: 2.9990 chunk 246 optimal weight: 1.9990 chunk 447 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 744 ASN K 302 GLN L 6 GLN ** L 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 473 ASN L 998 GLN L1234 GLN ** L1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1629 GLN L1658 ASN L2188 GLN L2592 HIS ** L3261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L3657 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 43484 Z= 0.209 Angle : 0.625 16.699 58889 Z= 0.311 Chirality : 0.043 0.429 6628 Planarity : 0.004 0.048 7476 Dihedral : 6.055 76.812 5713 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.44 % Favored : 92.50 % Rotamer: Outliers : 2.06 % Allowed : 14.71 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.12), residues: 5149 helix: 0.53 (0.10), residues: 2942 sheet: 0.10 (0.38), residues: 195 loop : -2.21 (0.13), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L1684 HIS 0.010 0.001 HIS L2621 PHE 0.050 0.001 PHE L1747 TYR 0.034 0.001 TYR L2316 ARG 0.007 0.000 ARG L1731 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 4766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 374 time to evaluate : 4.972 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: E 248 MET cc_start: 0.6979 (OUTLIER) cc_final: 0.6140 (mmm) REVERT: E 651 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8765 (tp) REVERT: E 799 MET cc_start: 0.8308 (mmm) cc_final: 0.8087 (mmm) REVERT: F 206 LEU cc_start: 0.7499 (tp) cc_final: 0.7049 (tt) REVERT: K 289 GLN cc_start: 0.7191 (mp10) cc_final: 0.6352 (mt0) REVERT: L 472 MET cc_start: 0.9409 (tmm) cc_final: 0.9199 (tmm) REVERT: L 588 ARG cc_start: 0.8756 (ttp-170) cc_final: 0.8519 (ttp80) REVERT: L 591 MET cc_start: 0.9335 (mtp) cc_final: 0.8969 (mmm) REVERT: L 700 GLU cc_start: 0.8739 (pt0) cc_final: 0.8332 (pt0) REVERT: L 922 ASP cc_start: 0.7548 (p0) cc_final: 0.7279 (p0) REVERT: L 1295 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7673 (mm-30) REVERT: L 1298 ASN cc_start: 0.8171 (t0) cc_final: 0.7767 (t0) REVERT: L 1302 LYS cc_start: 0.8743 (mttm) cc_final: 0.8401 (mmtt) REVERT: L 1355 ASP cc_start: 0.8462 (t0) cc_final: 0.7634 (m-30) REVERT: L 1362 SER cc_start: 0.8253 (t) cc_final: 0.7931 (p) REVERT: L 1501 ASP cc_start: 0.8168 (t0) cc_final: 0.7966 (t0) REVERT: L 1588 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7501 (mm) REVERT: L 1589 ASP cc_start: 0.7768 (m-30) cc_final: 0.7260 (t0) REVERT: L 1615 MET cc_start: 0.6337 (mtm) cc_final: 0.6075 (mtm) REVERT: L 1974 MET cc_start: 0.8135 (ttt) cc_final: 0.7875 (tpt) REVERT: L 2214 MET cc_start: 0.8363 (ppp) cc_final: 0.7948 (ppp) REVERT: L 2490 ASN cc_start: 0.6819 (t0) cc_final: 0.6297 (t0) REVERT: L 2723 GLN cc_start: 0.7848 (tm-30) cc_final: 0.7638 (tm-30) REVERT: L 3092 TYR cc_start: 0.6824 (t80) cc_final: 0.6122 (t80) REVERT: L 3307 TYR cc_start: 0.8171 (OUTLIER) cc_final: 0.7247 (t80) REVERT: L 3685 ASN cc_start: 0.8504 (OUTLIER) cc_final: 0.8262 (p0) outliers start: 98 outliers final: 60 residues processed: 448 average time/residue: 0.5299 time to fit residues: 405.7726 Evaluate side-chains 405 residues out of total 4766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 340 time to evaluate : 5.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 662 ILE Chi-restraints excluded: chain E residue 681 THR Chi-restraints excluded: chain E residue 712 LEU Chi-restraints excluded: chain E residue 718 HIS Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 358 SER Chi-restraints excluded: chain K residue 292 THR Chi-restraints excluded: chain H residue 724 ASP Chi-restraints excluded: chain L residue 218 MET Chi-restraints excluded: chain L residue 233 THR Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 612 THR Chi-restraints excluded: chain L residue 732 THR Chi-restraints excluded: chain L residue 828 TYR Chi-restraints excluded: chain L residue 892 ASP Chi-restraints excluded: chain L residue 917 ILE Chi-restraints excluded: chain L residue 960 LEU Chi-restraints excluded: chain L residue 998 GLN Chi-restraints excluded: chain L residue 1098 ASP Chi-restraints excluded: chain L residue 1251 GLU Chi-restraints excluded: chain L residue 1376 ARG Chi-restraints excluded: chain L residue 1395 ASN Chi-restraints excluded: chain L residue 1588 LEU Chi-restraints excluded: chain L residue 1620 LEU Chi-restraints excluded: chain L residue 1824 TYR Chi-restraints excluded: chain L residue 1899 THR Chi-restraints excluded: chain L residue 1950 THR Chi-restraints excluded: chain L residue 1992 HIS Chi-restraints excluded: chain L residue 1995 LEU Chi-restraints excluded: chain L residue 2027 LEU Chi-restraints excluded: chain L residue 2094 GLU Chi-restraints excluded: chain L residue 2143 PHE Chi-restraints excluded: chain L residue 2379 MET Chi-restraints excluded: chain L residue 2465 ASP Chi-restraints excluded: chain L residue 2504 LEU Chi-restraints excluded: chain L residue 2537 ILE Chi-restraints excluded: chain L residue 2574 ASN Chi-restraints excluded: chain L residue 2601 ASN Chi-restraints excluded: chain L residue 2618 LEU Chi-restraints excluded: chain L residue 2679 TRP Chi-restraints excluded: chain L residue 2752 HIS Chi-restraints excluded: chain L residue 2805 GLU Chi-restraints excluded: chain L residue 2866 THR Chi-restraints excluded: chain L residue 2888 LEU Chi-restraints excluded: chain L residue 3049 ILE Chi-restraints excluded: chain L residue 3111 ASP Chi-restraints excluded: chain L residue 3119 ASN Chi-restraints excluded: chain L residue 3152 VAL Chi-restraints excluded: chain L residue 3211 LEU Chi-restraints excluded: chain L residue 3286 THR Chi-restraints excluded: chain L residue 3307 TYR Chi-restraints excluded: chain L residue 3347 GLN Chi-restraints excluded: chain L residue 3371 ILE Chi-restraints excluded: chain L residue 3400 VAL Chi-restraints excluded: chain L residue 3449 ILE Chi-restraints excluded: chain L residue 3498 ASP Chi-restraints excluded: chain L residue 3657 ASN Chi-restraints excluded: chain L residue 3685 ASN Chi-restraints excluded: chain L residue 3709 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 416 optimal weight: 0.6980 chunk 283 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 372 optimal weight: 7.9990 chunk 206 optimal weight: 0.5980 chunk 426 optimal weight: 6.9990 chunk 345 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 255 optimal weight: 0.9990 chunk 448 optimal weight: 0.0770 chunk 126 optimal weight: 7.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 302 GLN ** L 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 888 GLN L 889 GLN L 896 GLN L 998 GLN ** L1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1629 GLN ** L1958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L2592 HIS ** L3073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L3657 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 43484 Z= 0.157 Angle : 0.603 16.812 58889 Z= 0.296 Chirality : 0.042 0.367 6628 Planarity : 0.004 0.046 7476 Dihedral : 5.849 75.000 5713 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.42 % Favored : 92.52 % Rotamer: Outliers : 1.95 % Allowed : 15.36 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.12), residues: 5149 helix: 0.72 (0.10), residues: 2927 sheet: 0.31 (0.40), residues: 182 loop : -2.10 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L1684 HIS 0.007 0.001 HIS L2621 PHE 0.039 0.001 PHE L1747 TYR 0.035 0.001 TYR L2316 ARG 0.010 0.000 ARG H 517 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 4766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 375 time to evaluate : 5.263 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: E 248 MET cc_start: 0.6918 (mpp) cc_final: 0.6060 (ptp) REVERT: E 799 MET cc_start: 0.8375 (mmm) cc_final: 0.8163 (mmm) REVERT: F 206 LEU cc_start: 0.7455 (tp) cc_final: 0.7025 (tt) REVERT: K 289 GLN cc_start: 0.7122 (mp10) cc_final: 0.6313 (mt0) REVERT: L 465 MET cc_start: 0.8997 (mmt) cc_final: 0.8562 (mmt) REVERT: L 588 ARG cc_start: 0.8725 (ttp-170) cc_final: 0.8494 (ttp80) REVERT: L 591 MET cc_start: 0.9289 (mtp) cc_final: 0.8734 (mmm) REVERT: L 689 MET cc_start: 0.8922 (ttm) cc_final: 0.8410 (mtm) REVERT: L 700 GLU cc_start: 0.8721 (pt0) cc_final: 0.8353 (pt0) REVERT: L 804 GLU cc_start: 0.8656 (tp30) cc_final: 0.8065 (tm-30) REVERT: L 922 ASP cc_start: 0.7487 (p0) cc_final: 0.7220 (p0) REVERT: L 1295 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7657 (mm-30) REVERT: L 1298 ASN cc_start: 0.8158 (t0) cc_final: 0.7771 (t0) REVERT: L 1302 LYS cc_start: 0.8738 (mttm) cc_final: 0.8391 (mmtt) REVERT: L 1326 MET cc_start: 0.8662 (ptp) cc_final: 0.8398 (mpp) REVERT: L 1355 ASP cc_start: 0.8483 (t0) cc_final: 0.7620 (m-30) REVERT: L 1362 SER cc_start: 0.8196 (t) cc_final: 0.7884 (p) REVERT: L 1501 ASP cc_start: 0.8163 (t0) cc_final: 0.7952 (t0) REVERT: L 1558 ILE cc_start: 0.8835 (mm) cc_final: 0.8598 (mm) REVERT: L 1588 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7454 (mm) REVERT: L 1589 ASP cc_start: 0.7648 (m-30) cc_final: 0.7204 (t0) REVERT: L 1691 MET cc_start: 0.6623 (mtt) cc_final: 0.6227 (mtt) REVERT: L 1731 ARG cc_start: 0.8364 (ttp-110) cc_final: 0.8097 (mtm110) REVERT: L 1974 MET cc_start: 0.8103 (ttt) cc_final: 0.7797 (tpp) REVERT: L 2214 MET cc_start: 0.8370 (ppp) cc_final: 0.7999 (ppp) REVERT: L 2316 TYR cc_start: 0.7394 (m-80) cc_final: 0.7189 (m-80) REVERT: L 2791 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7136 (mtm180) REVERT: L 3092 TYR cc_start: 0.7122 (t80) cc_final: 0.6272 (t80) REVERT: L 3307 TYR cc_start: 0.8099 (OUTLIER) cc_final: 0.7252 (t80) REVERT: L 3685 ASN cc_start: 0.8406 (OUTLIER) cc_final: 0.8183 (p0) outliers start: 93 outliers final: 53 residues processed: 446 average time/residue: 0.5610 time to fit residues: 427.4440 Evaluate side-chains 398 residues out of total 4766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 341 time to evaluate : 5.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain E residue 712 LEU Chi-restraints excluded: chain E residue 718 HIS Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 358 SER Chi-restraints excluded: chain K residue 292 THR Chi-restraints excluded: chain L residue 218 MET Chi-restraints excluded: chain L residue 233 THR Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 612 THR Chi-restraints excluded: chain L residue 732 THR Chi-restraints excluded: chain L residue 828 TYR Chi-restraints excluded: chain L residue 917 ILE Chi-restraints excluded: chain L residue 960 LEU Chi-restraints excluded: chain L residue 998 GLN Chi-restraints excluded: chain L residue 1098 ASP Chi-restraints excluded: chain L residue 1251 GLU Chi-restraints excluded: chain L residue 1376 ARG Chi-restraints excluded: chain L residue 1588 LEU Chi-restraints excluded: chain L residue 1950 THR Chi-restraints excluded: chain L residue 1995 LEU Chi-restraints excluded: chain L residue 2027 LEU Chi-restraints excluded: chain L residue 2094 GLU Chi-restraints excluded: chain L residue 2143 PHE Chi-restraints excluded: chain L residue 2363 THR Chi-restraints excluded: chain L residue 2379 MET Chi-restraints excluded: chain L residue 2465 ASP Chi-restraints excluded: chain L residue 2504 LEU Chi-restraints excluded: chain L residue 2537 ILE Chi-restraints excluded: chain L residue 2574 ASN Chi-restraints excluded: chain L residue 2588 SER Chi-restraints excluded: chain L residue 2601 ASN Chi-restraints excluded: chain L residue 2618 LEU Chi-restraints excluded: chain L residue 2679 TRP Chi-restraints excluded: chain L residue 2752 HIS Chi-restraints excluded: chain L residue 2758 LEU Chi-restraints excluded: chain L residue 2791 ARG Chi-restraints excluded: chain L residue 2805 GLU Chi-restraints excluded: chain L residue 2866 THR Chi-restraints excluded: chain L residue 2888 LEU Chi-restraints excluded: chain L residue 3049 ILE Chi-restraints excluded: chain L residue 3119 ASN Chi-restraints excluded: chain L residue 3307 TYR Chi-restraints excluded: chain L residue 3360 LEU Chi-restraints excluded: chain L residue 3371 ILE Chi-restraints excluded: chain L residue 3400 VAL Chi-restraints excluded: chain L residue 3498 ASP Chi-restraints excluded: chain L residue 3596 VAL Chi-restraints excluded: chain L residue 3657 ASN Chi-restraints excluded: chain L residue 3685 ASN Chi-restraints excluded: chain L residue 3709 LEU Chi-restraints excluded: chain L residue 3711 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 168 optimal weight: 4.9990 chunk 450 optimal weight: 0.9980 chunk 98 optimal weight: 10.0000 chunk 293 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 500 optimal weight: 3.9990 chunk 415 optimal weight: 0.5980 chunk 231 optimal weight: 0.4980 chunk 41 optimal weight: 9.9990 chunk 165 optimal weight: 0.9990 chunk 262 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 134 GLN ** L 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 998 GLN ** L1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1629 GLN L2592 HIS L2857 GLN L3074 ASN ** L3261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L3657 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 43484 Z= 0.164 Angle : 0.602 16.724 58889 Z= 0.295 Chirality : 0.042 0.244 6628 Planarity : 0.004 0.049 7476 Dihedral : 5.700 74.333 5710 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.05 % Favored : 92.89 % Rotamer: Outliers : 2.04 % Allowed : 15.95 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.12), residues: 5149 helix: 0.81 (0.10), residues: 2932 sheet: 0.27 (0.40), residues: 181 loop : -2.07 (0.13), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP L2904 HIS 0.009 0.001 HIS F 444 PHE 0.033 0.001 PHE L1747 TYR 0.029 0.001 TYR L2316 ARG 0.011 0.000 ARG H 517 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 4766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 369 time to evaluate : 5.053 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: E 248 MET cc_start: 0.6943 (mpp) cc_final: 0.6154 (mmm) REVERT: E 651 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8578 (tp) REVERT: E 799 MET cc_start: 0.8341 (mmm) cc_final: 0.8109 (mmm) REVERT: F 206 LEU cc_start: 0.7470 (tp) cc_final: 0.7041 (tt) REVERT: K 289 GLN cc_start: 0.7155 (mp10) cc_final: 0.6313 (mt0) REVERT: L 359 TYR cc_start: 0.7873 (p90) cc_final: 0.7530 (p90) REVERT: L 465 MET cc_start: 0.9003 (mmt) cc_final: 0.8557 (mmt) REVERT: L 588 ARG cc_start: 0.8724 (ttp-170) cc_final: 0.8499 (ttp80) REVERT: L 591 MET cc_start: 0.9293 (mtp) cc_final: 0.8652 (mmm) REVERT: L 689 MET cc_start: 0.8934 (ttm) cc_final: 0.8490 (mtp) REVERT: L 691 MET cc_start: 0.8371 (mtp) cc_final: 0.7951 (mpp) REVERT: L 700 GLU cc_start: 0.8719 (pt0) cc_final: 0.8328 (pt0) REVERT: L 844 GLN cc_start: 0.8109 (pp30) cc_final: 0.7502 (pp30) REVERT: L 922 ASP cc_start: 0.7454 (p0) cc_final: 0.7202 (p0) REVERT: L 1295 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7659 (mm-30) REVERT: L 1298 ASN cc_start: 0.8153 (t0) cc_final: 0.7776 (t0) REVERT: L 1302 LYS cc_start: 0.8747 (mttm) cc_final: 0.8403 (mmtt) REVERT: L 1355 ASP cc_start: 0.8442 (t0) cc_final: 0.7632 (m-30) REVERT: L 1362 SER cc_start: 0.8109 (t) cc_final: 0.7792 (p) REVERT: L 1588 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7530 (mm) REVERT: L 1589 ASP cc_start: 0.7631 (m-30) cc_final: 0.7180 (t0) REVERT: L 1648 TYR cc_start: 0.5926 (m-80) cc_final: 0.5308 (m-80) REVERT: L 1767 PHE cc_start: 0.8576 (t80) cc_final: 0.8150 (t80) REVERT: L 1974 MET cc_start: 0.8095 (ttt) cc_final: 0.7857 (tpt) REVERT: L 2214 MET cc_start: 0.8385 (ppp) cc_final: 0.8050 (ppp) REVERT: L 2791 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7194 (mtm180) REVERT: L 3307 TYR cc_start: 0.8049 (OUTLIER) cc_final: 0.7417 (t80) REVERT: L 3613 ILE cc_start: 0.8379 (tp) cc_final: 0.8023 (tp) REVERT: L 3685 ASN cc_start: 0.8408 (OUTLIER) cc_final: 0.7181 (p0) outliers start: 97 outliers final: 70 residues processed: 442 average time/residue: 0.5568 time to fit residues: 420.2239 Evaluate side-chains 420 residues out of total 4766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 345 time to evaluate : 4.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 662 ILE Chi-restraints excluded: chain E residue 681 THR Chi-restraints excluded: chain E residue 712 LEU Chi-restraints excluded: chain E residue 718 HIS Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 358 SER Chi-restraints excluded: chain K residue 292 THR Chi-restraints excluded: chain H residue 724 ASP Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 218 MET Chi-restraints excluded: chain L residue 233 THR Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 612 THR Chi-restraints excluded: chain L residue 732 THR Chi-restraints excluded: chain L residue 828 TYR Chi-restraints excluded: chain L residue 892 ASP Chi-restraints excluded: chain L residue 917 ILE Chi-restraints excluded: chain L residue 960 LEU Chi-restraints excluded: chain L residue 998 GLN Chi-restraints excluded: chain L residue 1098 ASP Chi-restraints excluded: chain L residue 1251 GLU Chi-restraints excluded: chain L residue 1376 ARG Chi-restraints excluded: chain L residue 1395 ASN Chi-restraints excluded: chain L residue 1588 LEU Chi-restraints excluded: chain L residue 1620 LEU Chi-restraints excluded: chain L residue 1765 PHE Chi-restraints excluded: chain L residue 1824 TYR Chi-restraints excluded: chain L residue 1950 THR Chi-restraints excluded: chain L residue 1995 LEU Chi-restraints excluded: chain L residue 2027 LEU Chi-restraints excluded: chain L residue 2094 GLU Chi-restraints excluded: chain L residue 2143 PHE Chi-restraints excluded: chain L residue 2244 THR Chi-restraints excluded: chain L residue 2272 VAL Chi-restraints excluded: chain L residue 2363 THR Chi-restraints excluded: chain L residue 2379 MET Chi-restraints excluded: chain L residue 2465 ASP Chi-restraints excluded: chain L residue 2504 LEU Chi-restraints excluded: chain L residue 2537 ILE Chi-restraints excluded: chain L residue 2574 ASN Chi-restraints excluded: chain L residue 2588 SER Chi-restraints excluded: chain L residue 2600 THR Chi-restraints excluded: chain L residue 2601 ASN Chi-restraints excluded: chain L residue 2618 LEU Chi-restraints excluded: chain L residue 2679 TRP Chi-restraints excluded: chain L residue 2752 HIS Chi-restraints excluded: chain L residue 2758 LEU Chi-restraints excluded: chain L residue 2791 ARG Chi-restraints excluded: chain L residue 2805 GLU Chi-restraints excluded: chain L residue 2866 THR Chi-restraints excluded: chain L residue 2888 LEU Chi-restraints excluded: chain L residue 3049 ILE Chi-restraints excluded: chain L residue 3111 ASP Chi-restraints excluded: chain L residue 3152 VAL Chi-restraints excluded: chain L residue 3171 LEU Chi-restraints excluded: chain L residue 3211 LEU Chi-restraints excluded: chain L residue 3307 TYR Chi-restraints excluded: chain L residue 3347 GLN Chi-restraints excluded: chain L residue 3360 LEU Chi-restraints excluded: chain L residue 3371 ILE Chi-restraints excluded: chain L residue 3400 VAL Chi-restraints excluded: chain L residue 3449 ILE Chi-restraints excluded: chain L residue 3498 ASP Chi-restraints excluded: chain L residue 3596 VAL Chi-restraints excluded: chain L residue 3657 ASN Chi-restraints excluded: chain L residue 3685 ASN Chi-restraints excluded: chain L residue 3709 LEU Chi-restraints excluded: chain L residue 3711 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 482 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 285 optimal weight: 2.9990 chunk 365 optimal weight: 4.9990 chunk 283 optimal weight: 0.9980 chunk 421 optimal weight: 0.3980 chunk 279 optimal weight: 0.6980 chunk 498 optimal weight: 3.9990 chunk 311 optimal weight: 7.9990 chunk 303 optimal weight: 30.0000 chunk 230 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 302 GLN ** L 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 998 GLN ** L1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1866 GLN L1958 ASN L2857 GLN ** L3048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L3657 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 43484 Z= 0.194 Angle : 0.607 16.720 58889 Z= 0.299 Chirality : 0.042 0.251 6628 Planarity : 0.004 0.053 7476 Dihedral : 5.654 74.083 5710 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.40 % Favored : 92.56 % Rotamer: Outliers : 2.06 % Allowed : 16.34 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.12), residues: 5149 helix: 0.90 (0.10), residues: 2936 sheet: 0.24 (0.40), residues: 183 loop : -2.00 (0.14), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP L2904 HIS 0.011 0.001 HIS F 444 PHE 0.048 0.001 PHE L1747 TYR 0.032 0.001 TYR L1648 ARG 0.012 0.000 ARG H 517 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 4766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 357 time to evaluate : 4.960 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: E 248 MET cc_start: 0.6891 (mpp) cc_final: 0.6118 (ptp) REVERT: E 651 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8576 (tp) REVERT: E 799 MET cc_start: 0.8306 (mmm) cc_final: 0.8065 (mmm) REVERT: F 206 LEU cc_start: 0.7475 (tp) cc_final: 0.7062 (tt) REVERT: G 12 ASN cc_start: 0.7130 (m110) cc_final: 0.6922 (m110) REVERT: K 289 GLN cc_start: 0.7285 (OUTLIER) cc_final: 0.6405 (mt0) REVERT: L 218 MET cc_start: 0.3596 (OUTLIER) cc_final: 0.3063 (tpp) REVERT: L 359 TYR cc_start: 0.7888 (p90) cc_final: 0.7544 (p90) REVERT: L 465 MET cc_start: 0.8996 (mmt) cc_final: 0.8539 (mmt) REVERT: L 588 ARG cc_start: 0.8729 (ttp-170) cc_final: 0.8507 (ttp80) REVERT: L 591 MET cc_start: 0.9311 (mtp) cc_final: 0.8669 (mmm) REVERT: L 628 TYR cc_start: 0.8902 (t80) cc_final: 0.8624 (t80) REVERT: L 689 MET cc_start: 0.8969 (ttm) cc_final: 0.8495 (mtp) REVERT: L 700 GLU cc_start: 0.8703 (pt0) cc_final: 0.8329 (pt0) REVERT: L 1295 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7829 (mm-30) REVERT: L 1298 ASN cc_start: 0.8133 (t0) cc_final: 0.7743 (t0) REVERT: L 1302 LYS cc_start: 0.8759 (mttm) cc_final: 0.8413 (mmtt) REVERT: L 1355 ASP cc_start: 0.8482 (t0) cc_final: 0.7630 (m-30) REVERT: L 1362 SER cc_start: 0.8115 (t) cc_final: 0.7794 (p) REVERT: L 1588 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7775 (mm) REVERT: L 1648 TYR cc_start: 0.5855 (m-80) cc_final: 0.4595 (m-80) REVERT: L 1767 PHE cc_start: 0.8613 (t80) cc_final: 0.7634 (t80) REVERT: L 1974 MET cc_start: 0.8090 (ttt) cc_final: 0.7783 (tpt) REVERT: L 2214 MET cc_start: 0.8421 (ppp) cc_final: 0.8065 (ppp) REVERT: L 2791 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7203 (mtm180) REVERT: L 3307 TYR cc_start: 0.8086 (OUTLIER) cc_final: 0.7435 (t80) outliers start: 98 outliers final: 71 residues processed: 433 average time/residue: 0.5321 time to fit residues: 393.5359 Evaluate side-chains 419 residues out of total 4766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 342 time to evaluate : 4.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 662 ILE Chi-restraints excluded: chain E residue 681 THR Chi-restraints excluded: chain E residue 712 LEU Chi-restraints excluded: chain E residue 718 HIS Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 358 SER Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 289 GLN Chi-restraints excluded: chain K residue 292 THR Chi-restraints excluded: chain H residue 724 ASP Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 218 MET Chi-restraints excluded: chain L residue 233 THR Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 612 THR Chi-restraints excluded: chain L residue 732 THR Chi-restraints excluded: chain L residue 828 TYR Chi-restraints excluded: chain L residue 851 LEU Chi-restraints excluded: chain L residue 892 ASP Chi-restraints excluded: chain L residue 917 ILE Chi-restraints excluded: chain L residue 960 LEU Chi-restraints excluded: chain L residue 998 GLN Chi-restraints excluded: chain L residue 1098 ASP Chi-restraints excluded: chain L residue 1251 GLU Chi-restraints excluded: chain L residue 1376 ARG Chi-restraints excluded: chain L residue 1395 ASN Chi-restraints excluded: chain L residue 1463 LEU Chi-restraints excluded: chain L residue 1588 LEU Chi-restraints excluded: chain L residue 1620 LEU Chi-restraints excluded: chain L residue 1824 TYR Chi-restraints excluded: chain L residue 1899 THR Chi-restraints excluded: chain L residue 1950 THR Chi-restraints excluded: chain L residue 1995 LEU Chi-restraints excluded: chain L residue 2094 GLU Chi-restraints excluded: chain L residue 2143 PHE Chi-restraints excluded: chain L residue 2244 THR Chi-restraints excluded: chain L residue 2272 VAL Chi-restraints excluded: chain L residue 2363 THR Chi-restraints excluded: chain L residue 2465 ASP Chi-restraints excluded: chain L residue 2491 ILE Chi-restraints excluded: chain L residue 2504 LEU Chi-restraints excluded: chain L residue 2537 ILE Chi-restraints excluded: chain L residue 2574 ASN Chi-restraints excluded: chain L residue 2588 SER Chi-restraints excluded: chain L residue 2600 THR Chi-restraints excluded: chain L residue 2601 ASN Chi-restraints excluded: chain L residue 2618 LEU Chi-restraints excluded: chain L residue 2679 TRP Chi-restraints excluded: chain L residue 2758 LEU Chi-restraints excluded: chain L residue 2791 ARG Chi-restraints excluded: chain L residue 2805 GLU Chi-restraints excluded: chain L residue 2866 THR Chi-restraints excluded: chain L residue 2888 LEU Chi-restraints excluded: chain L residue 3049 ILE Chi-restraints excluded: chain L residue 3111 ASP Chi-restraints excluded: chain L residue 3152 VAL Chi-restraints excluded: chain L residue 3171 LEU Chi-restraints excluded: chain L residue 3211 LEU Chi-restraints excluded: chain L residue 3307 TYR Chi-restraints excluded: chain L residue 3347 GLN Chi-restraints excluded: chain L residue 3360 LEU Chi-restraints excluded: chain L residue 3371 ILE Chi-restraints excluded: chain L residue 3400 VAL Chi-restraints excluded: chain L residue 3449 ILE Chi-restraints excluded: chain L residue 3498 ASP Chi-restraints excluded: chain L residue 3596 VAL Chi-restraints excluded: chain L residue 3657 ASN Chi-restraints excluded: chain L residue 3709 LEU Chi-restraints excluded: chain L residue 3711 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 308 optimal weight: 1.9990 chunk 198 optimal weight: 4.9990 chunk 297 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 96 optimal weight: 20.0000 chunk 316 optimal weight: 0.9980 chunk 339 optimal weight: 5.9990 chunk 246 optimal weight: 0.6980 chunk 46 optimal weight: 6.9990 chunk 391 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 302 GLN L 998 GLN L1305 ASN ** L1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L2857 GLN ** L3119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L3657 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 43484 Z= 0.203 Angle : 0.623 16.850 58889 Z= 0.305 Chirality : 0.043 0.246 6628 Planarity : 0.004 0.056 7476 Dihedral : 5.623 73.542 5710 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.44 % Favored : 92.52 % Rotamer: Outliers : 2.04 % Allowed : 16.95 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.12), residues: 5149 helix: 0.93 (0.10), residues: 2938 sheet: 0.20 (0.39), residues: 185 loop : -1.96 (0.14), residues: 2026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP L2904 HIS 0.013 0.001 HIS F 444 PHE 0.045 0.001 PHE L1747 TYR 0.040 0.001 TYR L1648 ARG 0.013 0.000 ARG H 517 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 4766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 357 time to evaluate : 4.856 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: E 248 MET cc_start: 0.6939 (mpp) cc_final: 0.6206 (ptp) REVERT: E 651 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8574 (tp) REVERT: E 799 MET cc_start: 0.8332 (mmm) cc_final: 0.8127 (mmm) REVERT: F 206 LEU cc_start: 0.7385 (tp) cc_final: 0.7009 (tt) REVERT: G 12 ASN cc_start: 0.7036 (m110) cc_final: 0.6639 (m-40) REVERT: K 289 GLN cc_start: 0.7258 (OUTLIER) cc_final: 0.6423 (mt0) REVERT: H 518 LYS cc_start: 0.7282 (mmmm) cc_final: 0.7065 (mmmm) REVERT: L 242 THR cc_start: 0.5874 (OUTLIER) cc_final: 0.5598 (p) REVERT: L 359 TYR cc_start: 0.7894 (p90) cc_final: 0.7528 (p90) REVERT: L 465 MET cc_start: 0.9002 (mmt) cc_final: 0.8532 (mmt) REVERT: L 588 ARG cc_start: 0.8739 (ttp-170) cc_final: 0.8523 (ttp80) REVERT: L 591 MET cc_start: 0.9311 (mtp) cc_final: 0.8829 (mmm) REVERT: L 628 TYR cc_start: 0.8878 (t80) cc_final: 0.8597 (t80) REVERT: L 689 MET cc_start: 0.8955 (ttm) cc_final: 0.8532 (mtm) REVERT: L 691 MET cc_start: 0.8371 (mtp) cc_final: 0.7966 (mpp) REVERT: L 700 GLU cc_start: 0.8704 (pt0) cc_final: 0.8345 (pt0) REVERT: L 1295 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7827 (mm-30) REVERT: L 1298 ASN cc_start: 0.8148 (t0) cc_final: 0.7752 (t0) REVERT: L 1302 LYS cc_start: 0.8765 (mttm) cc_final: 0.8423 (mmtt) REVERT: L 1355 ASP cc_start: 0.8486 (t0) cc_final: 0.7633 (m-30) REVERT: L 1362 SER cc_start: 0.8074 (t) cc_final: 0.7742 (p) REVERT: L 1415 CYS cc_start: 0.8686 (m) cc_final: 0.8321 (t) REVERT: L 1588 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7834 (mm) REVERT: L 1974 MET cc_start: 0.8102 (ttt) cc_final: 0.7795 (tpt) REVERT: L 2214 MET cc_start: 0.8423 (ppp) cc_final: 0.8068 (ppp) REVERT: L 2735 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7714 (mp10) REVERT: L 2791 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7170 (mtm180) REVERT: L 3307 TYR cc_start: 0.8151 (OUTLIER) cc_final: 0.7302 (t80) outliers start: 97 outliers final: 79 residues processed: 429 average time/residue: 0.5811 time to fit residues: 427.1817 Evaluate side-chains 422 residues out of total 4766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 336 time to evaluate : 4.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 681 THR Chi-restraints excluded: chain E residue 712 LEU Chi-restraints excluded: chain E residue 718 HIS Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 358 SER Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 289 GLN Chi-restraints excluded: chain K residue 292 THR Chi-restraints excluded: chain H residue 724 ASP Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 218 MET Chi-restraints excluded: chain L residue 233 THR Chi-restraints excluded: chain L residue 242 THR Chi-restraints excluded: chain L residue 244 THR Chi-restraints excluded: chain L residue 257 LEU Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 440 LEU Chi-restraints excluded: chain L residue 612 THR Chi-restraints excluded: chain L residue 633 VAL Chi-restraints excluded: chain L residue 727 LEU Chi-restraints excluded: chain L residue 732 THR Chi-restraints excluded: chain L residue 828 TYR Chi-restraints excluded: chain L residue 851 LEU Chi-restraints excluded: chain L residue 892 ASP Chi-restraints excluded: chain L residue 917 ILE Chi-restraints excluded: chain L residue 998 GLN Chi-restraints excluded: chain L residue 1098 ASP Chi-restraints excluded: chain L residue 1251 GLU Chi-restraints excluded: chain L residue 1376 ARG Chi-restraints excluded: chain L residue 1395 ASN Chi-restraints excluded: chain L residue 1463 LEU Chi-restraints excluded: chain L residue 1588 LEU Chi-restraints excluded: chain L residue 1620 LEU Chi-restraints excluded: chain L residue 1824 TYR Chi-restraints excluded: chain L residue 1899 THR Chi-restraints excluded: chain L residue 1950 THR Chi-restraints excluded: chain L residue 1995 LEU Chi-restraints excluded: chain L residue 2094 GLU Chi-restraints excluded: chain L residue 2143 PHE Chi-restraints excluded: chain L residue 2244 THR Chi-restraints excluded: chain L residue 2272 VAL Chi-restraints excluded: chain L residue 2363 THR Chi-restraints excluded: chain L residue 2465 ASP Chi-restraints excluded: chain L residue 2491 ILE Chi-restraints excluded: chain L residue 2504 LEU Chi-restraints excluded: chain L residue 2537 ILE Chi-restraints excluded: chain L residue 2574 ASN Chi-restraints excluded: chain L residue 2588 SER Chi-restraints excluded: chain L residue 2600 THR Chi-restraints excluded: chain L residue 2601 ASN Chi-restraints excluded: chain L residue 2616 LEU Chi-restraints excluded: chain L residue 2618 LEU Chi-restraints excluded: chain L residue 2679 TRP Chi-restraints excluded: chain L residue 2735 GLN Chi-restraints excluded: chain L residue 2752 HIS Chi-restraints excluded: chain L residue 2758 LEU Chi-restraints excluded: chain L residue 2791 ARG Chi-restraints excluded: chain L residue 2805 GLU Chi-restraints excluded: chain L residue 2866 THR Chi-restraints excluded: chain L residue 2888 LEU Chi-restraints excluded: chain L residue 3049 ILE Chi-restraints excluded: chain L residue 3111 ASP Chi-restraints excluded: chain L residue 3152 VAL Chi-restraints excluded: chain L residue 3211 LEU Chi-restraints excluded: chain L residue 3286 THR Chi-restraints excluded: chain L residue 3307 TYR Chi-restraints excluded: chain L residue 3347 GLN Chi-restraints excluded: chain L residue 3360 LEU Chi-restraints excluded: chain L residue 3361 ASN Chi-restraints excluded: chain L residue 3371 ILE Chi-restraints excluded: chain L residue 3400 VAL Chi-restraints excluded: chain L residue 3449 ILE Chi-restraints excluded: chain L residue 3498 ASP Chi-restraints excluded: chain L residue 3596 VAL Chi-restraints excluded: chain L residue 3657 ASN Chi-restraints excluded: chain L residue 3709 LEU Chi-restraints excluded: chain L residue 3711 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 453 optimal weight: 3.9990 chunk 477 optimal weight: 0.2980 chunk 435 optimal weight: 0.9980 chunk 464 optimal weight: 0.9980 chunk 279 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 364 optimal weight: 6.9990 chunk 142 optimal weight: 6.9990 chunk 419 optimal weight: 0.6980 chunk 439 optimal weight: 2.9990 chunk 462 optimal weight: 7.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 302 GLN L 998 GLN ** L1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L2574 ASN L2857 GLN ** L3048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L3657 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 43484 Z= 0.178 Angle : 0.619 17.005 58889 Z= 0.302 Chirality : 0.042 0.303 6628 Planarity : 0.004 0.061 7476 Dihedral : 5.551 72.642 5710 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.48 % Favored : 92.50 % Rotamer: Outliers : 2.04 % Allowed : 17.12 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.12), residues: 5149 helix: 0.97 (0.10), residues: 2933 sheet: 0.23 (0.39), residues: 195 loop : -1.92 (0.14), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP L2904 HIS 0.009 0.001 HIS F 444 PHE 0.044 0.001 PHE L1747 TYR 0.043 0.001 TYR L2316 ARG 0.017 0.000 ARG L 850 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 4766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 358 time to evaluate : 4.931 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: E 248 MET cc_start: 0.6842 (mpp) cc_final: 0.6118 (ptp) REVERT: E 651 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8541 (tp) REVERT: G 12 ASN cc_start: 0.7080 (m110) cc_final: 0.6714 (m-40) REVERT: K 289 GLN cc_start: 0.7231 (OUTLIER) cc_final: 0.6423 (mt0) REVERT: L 242 THR cc_start: 0.5791 (OUTLIER) cc_final: 0.5507 (p) REVERT: L 359 TYR cc_start: 0.7890 (p90) cc_final: 0.7666 (p90) REVERT: L 465 MET cc_start: 0.8994 (mmt) cc_final: 0.8503 (mmt) REVERT: L 560 MET cc_start: 0.5760 (tpp) cc_final: 0.5301 (mmt) REVERT: L 588 ARG cc_start: 0.8720 (ttp-170) cc_final: 0.8501 (ttp80) REVERT: L 591 MET cc_start: 0.9311 (mtp) cc_final: 0.8827 (mmm) REVERT: L 628 TYR cc_start: 0.8870 (t80) cc_final: 0.8590 (t80) REVERT: L 689 MET cc_start: 0.8962 (ttm) cc_final: 0.8525 (mtm) REVERT: L 700 GLU cc_start: 0.8699 (pt0) cc_final: 0.8328 (pt0) REVERT: L 1295 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7812 (mm-30) REVERT: L 1298 ASN cc_start: 0.8155 (t0) cc_final: 0.7761 (t0) REVERT: L 1302 LYS cc_start: 0.8774 (mttm) cc_final: 0.8427 (mmtt) REVERT: L 1355 ASP cc_start: 0.8476 (t0) cc_final: 0.7623 (m-30) REVERT: L 1362 SER cc_start: 0.8078 (t) cc_final: 0.7757 (p) REVERT: L 1415 CYS cc_start: 0.8655 (m) cc_final: 0.8298 (t) REVERT: L 1588 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7780 (mm) REVERT: L 1665 PHE cc_start: 0.7711 (m-10) cc_final: 0.7303 (m-80) REVERT: L 1767 PHE cc_start: 0.8447 (t80) cc_final: 0.8171 (t80) REVERT: L 1974 MET cc_start: 0.8090 (ttt) cc_final: 0.7791 (tpt) REVERT: L 2127 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7883 (mt) REVERT: L 2214 MET cc_start: 0.8418 (ppp) cc_final: 0.8063 (ppp) REVERT: L 2735 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7710 (mp10) REVERT: L 2791 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7203 (mtm180) REVERT: L 3307 TYR cc_start: 0.8128 (OUTLIER) cc_final: 0.7291 (t80) outliers start: 97 outliers final: 77 residues processed: 434 average time/residue: 0.5470 time to fit residues: 402.0204 Evaluate side-chains 425 residues out of total 4766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 340 time to evaluate : 5.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 681 THR Chi-restraints excluded: chain E residue 712 LEU Chi-restraints excluded: chain E residue 718 HIS Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 358 SER Chi-restraints excluded: chain K residue 289 GLN Chi-restraints excluded: chain K residue 292 THR Chi-restraints excluded: chain H residue 724 ASP Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 218 MET Chi-restraints excluded: chain L residue 233 THR Chi-restraints excluded: chain L residue 242 THR Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 612 THR Chi-restraints excluded: chain L residue 633 VAL Chi-restraints excluded: chain L residue 727 LEU Chi-restraints excluded: chain L residue 732 THR Chi-restraints excluded: chain L residue 828 TYR Chi-restraints excluded: chain L residue 851 LEU Chi-restraints excluded: chain L residue 892 ASP Chi-restraints excluded: chain L residue 917 ILE Chi-restraints excluded: chain L residue 998 GLN Chi-restraints excluded: chain L residue 1098 ASP Chi-restraints excluded: chain L residue 1251 GLU Chi-restraints excluded: chain L residue 1395 ASN Chi-restraints excluded: chain L residue 1463 LEU Chi-restraints excluded: chain L residue 1588 LEU Chi-restraints excluded: chain L residue 1620 LEU Chi-restraints excluded: chain L residue 1824 TYR Chi-restraints excluded: chain L residue 1899 THR Chi-restraints excluded: chain L residue 1936 VAL Chi-restraints excluded: chain L residue 1950 THR Chi-restraints excluded: chain L residue 1995 LEU Chi-restraints excluded: chain L residue 2027 LEU Chi-restraints excluded: chain L residue 2094 GLU Chi-restraints excluded: chain L residue 2127 LEU Chi-restraints excluded: chain L residue 2143 PHE Chi-restraints excluded: chain L residue 2244 THR Chi-restraints excluded: chain L residue 2272 VAL Chi-restraints excluded: chain L residue 2276 THR Chi-restraints excluded: chain L residue 2363 THR Chi-restraints excluded: chain L residue 2465 ASP Chi-restraints excluded: chain L residue 2491 ILE Chi-restraints excluded: chain L residue 2504 LEU Chi-restraints excluded: chain L residue 2537 ILE Chi-restraints excluded: chain L residue 2574 ASN Chi-restraints excluded: chain L residue 2588 SER Chi-restraints excluded: chain L residue 2600 THR Chi-restraints excluded: chain L residue 2601 ASN Chi-restraints excluded: chain L residue 2616 LEU Chi-restraints excluded: chain L residue 2618 LEU Chi-restraints excluded: chain L residue 2679 TRP Chi-restraints excluded: chain L residue 2735 GLN Chi-restraints excluded: chain L residue 2752 HIS Chi-restraints excluded: chain L residue 2758 LEU Chi-restraints excluded: chain L residue 2791 ARG Chi-restraints excluded: chain L residue 2805 GLU Chi-restraints excluded: chain L residue 2866 THR Chi-restraints excluded: chain L residue 2888 LEU Chi-restraints excluded: chain L residue 3049 ILE Chi-restraints excluded: chain L residue 3111 ASP Chi-restraints excluded: chain L residue 3152 VAL Chi-restraints excluded: chain L residue 3171 LEU Chi-restraints excluded: chain L residue 3211 LEU Chi-restraints excluded: chain L residue 3286 THR Chi-restraints excluded: chain L residue 3307 TYR Chi-restraints excluded: chain L residue 3347 GLN Chi-restraints excluded: chain L residue 3360 LEU Chi-restraints excluded: chain L residue 3361 ASN Chi-restraints excluded: chain L residue 3371 ILE Chi-restraints excluded: chain L residue 3400 VAL Chi-restraints excluded: chain L residue 3449 ILE Chi-restraints excluded: chain L residue 3498 ASP Chi-restraints excluded: chain L residue 3596 VAL Chi-restraints excluded: chain L residue 3657 ASN Chi-restraints excluded: chain L residue 3709 LEU Chi-restraints excluded: chain L residue 3711 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 304 optimal weight: 2.9990 chunk 491 optimal weight: 2.9990 chunk 299 optimal weight: 8.9990 chunk 232 optimal weight: 0.9990 chunk 341 optimal weight: 9.9990 chunk 515 optimal weight: 0.7980 chunk 474 optimal weight: 5.9990 chunk 410 optimal weight: 1.9990 chunk 42 optimal weight: 0.2980 chunk 316 optimal weight: 0.6980 chunk 251 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 302 GLN L 753 ASN L 998 GLN ** L1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L2507 ASN L2857 GLN ** L3119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L3657 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 43484 Z= 0.177 Angle : 0.626 16.860 58889 Z= 0.305 Chirality : 0.042 0.262 6628 Planarity : 0.004 0.070 7476 Dihedral : 5.478 72.067 5710 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.55 % Favored : 92.43 % Rotamer: Outliers : 1.85 % Allowed : 17.44 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.12), residues: 5149 helix: 1.02 (0.10), residues: 2928 sheet: 0.23 (0.38), residues: 207 loop : -1.91 (0.14), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP L2904 HIS 0.011 0.001 HIS F 444 PHE 0.042 0.001 PHE L1747 TYR 0.041 0.001 TYR L2316 ARG 0.023 0.000 ARG L 850 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 4766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 350 time to evaluate : 4.952 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: E 248 MET cc_start: 0.6866 (mpp) cc_final: 0.6126 (ptp) REVERT: E 651 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8582 (tp) REVERT: G 12 ASN cc_start: 0.7089 (m110) cc_final: 0.6782 (m-40) REVERT: K 289 GLN cc_start: 0.7231 (OUTLIER) cc_final: 0.6440 (mt0) REVERT: L 242 THR cc_start: 0.5899 (OUTLIER) cc_final: 0.5608 (p) REVERT: L 352 ARG cc_start: 0.8734 (ptt90) cc_final: 0.8200 (ptt-90) REVERT: L 465 MET cc_start: 0.8966 (mmt) cc_final: 0.8479 (mmt) REVERT: L 560 MET cc_start: 0.5865 (tpp) cc_final: 0.5089 (mmt) REVERT: L 588 ARG cc_start: 0.8683 (ttp-170) cc_final: 0.8465 (ttp80) REVERT: L 591 MET cc_start: 0.9313 (mtp) cc_final: 0.8846 (mmm) REVERT: L 628 TYR cc_start: 0.8853 (t80) cc_final: 0.8562 (t80) REVERT: L 689 MET cc_start: 0.8964 (ttm) cc_final: 0.8514 (mtm) REVERT: L 691 MET cc_start: 0.8361 (mtp) cc_final: 0.7954 (mpp) REVERT: L 700 GLU cc_start: 0.8670 (pt0) cc_final: 0.8251 (pt0) REVERT: L 1295 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7809 (mm-30) REVERT: L 1298 ASN cc_start: 0.8158 (t0) cc_final: 0.7767 (t0) REVERT: L 1302 LYS cc_start: 0.8744 (mttm) cc_final: 0.8387 (mmtt) REVERT: L 1355 ASP cc_start: 0.8472 (t0) cc_final: 0.7621 (m-30) REVERT: L 1362 SER cc_start: 0.8076 (t) cc_final: 0.7760 (p) REVERT: L 1415 CYS cc_start: 0.8678 (m) cc_final: 0.8304 (t) REVERT: L 1448 MET cc_start: 0.6699 (mmm) cc_final: 0.6464 (mmm) REVERT: L 1588 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7760 (mm) REVERT: L 1767 PHE cc_start: 0.8519 (t80) cc_final: 0.8294 (t80) REVERT: L 1974 MET cc_start: 0.8091 (ttt) cc_final: 0.7794 (tpt) REVERT: L 2214 MET cc_start: 0.8409 (ppp) cc_final: 0.8053 (ppp) REVERT: L 2735 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7714 (mp10) REVERT: L 2791 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7168 (mtm180) REVERT: L 2904 TRP cc_start: 0.5951 (m100) cc_final: 0.4655 (m100) REVERT: L 3307 TYR cc_start: 0.8136 (OUTLIER) cc_final: 0.7315 (t80) outliers start: 88 outliers final: 72 residues processed: 418 average time/residue: 0.5625 time to fit residues: 399.6844 Evaluate side-chains 414 residues out of total 4766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 335 time to evaluate : 5.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 681 THR Chi-restraints excluded: chain E residue 712 LEU Chi-restraints excluded: chain E residue 718 HIS Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain K residue 289 GLN Chi-restraints excluded: chain K residue 292 THR Chi-restraints excluded: chain H residue 724 ASP Chi-restraints excluded: chain L residue 218 MET Chi-restraints excluded: chain L residue 233 THR Chi-restraints excluded: chain L residue 242 THR Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 612 THR Chi-restraints excluded: chain L residue 633 VAL Chi-restraints excluded: chain L residue 727 LEU Chi-restraints excluded: chain L residue 732 THR Chi-restraints excluded: chain L residue 828 TYR Chi-restraints excluded: chain L residue 892 ASP Chi-restraints excluded: chain L residue 917 ILE Chi-restraints excluded: chain L residue 998 GLN Chi-restraints excluded: chain L residue 1098 ASP Chi-restraints excluded: chain L residue 1251 GLU Chi-restraints excluded: chain L residue 1395 ASN Chi-restraints excluded: chain L residue 1463 LEU Chi-restraints excluded: chain L residue 1588 LEU Chi-restraints excluded: chain L residue 1620 LEU Chi-restraints excluded: chain L residue 1824 TYR Chi-restraints excluded: chain L residue 1899 THR Chi-restraints excluded: chain L residue 1936 VAL Chi-restraints excluded: chain L residue 1950 THR Chi-restraints excluded: chain L residue 1995 LEU Chi-restraints excluded: chain L residue 2027 LEU Chi-restraints excluded: chain L residue 2094 GLU Chi-restraints excluded: chain L residue 2143 PHE Chi-restraints excluded: chain L residue 2244 THR Chi-restraints excluded: chain L residue 2272 VAL Chi-restraints excluded: chain L residue 2276 THR Chi-restraints excluded: chain L residue 2363 THR Chi-restraints excluded: chain L residue 2410 THR Chi-restraints excluded: chain L residue 2465 ASP Chi-restraints excluded: chain L residue 2491 ILE Chi-restraints excluded: chain L residue 2504 LEU Chi-restraints excluded: chain L residue 2537 ILE Chi-restraints excluded: chain L residue 2588 SER Chi-restraints excluded: chain L residue 2600 THR Chi-restraints excluded: chain L residue 2601 ASN Chi-restraints excluded: chain L residue 2616 LEU Chi-restraints excluded: chain L residue 2618 LEU Chi-restraints excluded: chain L residue 2679 TRP Chi-restraints excluded: chain L residue 2701 ASP Chi-restraints excluded: chain L residue 2735 GLN Chi-restraints excluded: chain L residue 2752 HIS Chi-restraints excluded: chain L residue 2758 LEU Chi-restraints excluded: chain L residue 2791 ARG Chi-restraints excluded: chain L residue 2805 GLU Chi-restraints excluded: chain L residue 2866 THR Chi-restraints excluded: chain L residue 2888 LEU Chi-restraints excluded: chain L residue 3049 ILE Chi-restraints excluded: chain L residue 3152 VAL Chi-restraints excluded: chain L residue 3211 LEU Chi-restraints excluded: chain L residue 3286 THR Chi-restraints excluded: chain L residue 3307 TYR Chi-restraints excluded: chain L residue 3347 GLN Chi-restraints excluded: chain L residue 3360 LEU Chi-restraints excluded: chain L residue 3371 ILE Chi-restraints excluded: chain L residue 3400 VAL Chi-restraints excluded: chain L residue 3449 ILE Chi-restraints excluded: chain L residue 3498 ASP Chi-restraints excluded: chain L residue 3596 VAL Chi-restraints excluded: chain L residue 3657 ASN Chi-restraints excluded: chain L residue 3709 LEU Chi-restraints excluded: chain L residue 3711 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 325 optimal weight: 7.9990 chunk 436 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 378 optimal weight: 10.0000 chunk 60 optimal weight: 0.0370 chunk 113 optimal weight: 0.0370 chunk 410 optimal weight: 0.9990 chunk 171 optimal weight: 0.2980 chunk 421 optimal weight: 0.4980 chunk 52 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 302 GLN L 998 GLN L1075 GLN ** L1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1629 GLN L2732 ASN L2857 GLN L3119 ASN ** L3261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L3657 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.108064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.075526 restraints weight = 150912.449| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 3.35 r_work: 0.3254 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 43484 Z= 0.145 Angle : 0.620 16.909 58889 Z= 0.299 Chirality : 0.042 0.282 6628 Planarity : 0.004 0.062 7476 Dihedral : 5.359 71.071 5710 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.09 % Favored : 92.89 % Rotamer: Outliers : 1.57 % Allowed : 17.96 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.12), residues: 5149 helix: 1.04 (0.10), residues: 2928 sheet: 0.35 (0.39), residues: 197 loop : -1.90 (0.14), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP L2904 HIS 0.009 0.001 HIS F 444 PHE 0.041 0.001 PHE L1747 TYR 0.047 0.001 TYR L2316 ARG 0.020 0.000 ARG L 850 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10800.94 seconds wall clock time: 196 minutes 47.82 seconds (11807.82 seconds total)