Starting phenix.real_space_refine (version: dev) on Thu Dec 22 14:09:19 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t9i_10412/12_2022/6t9i_10412_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t9i_10412/12_2022/6t9i_10412.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t9i_10412/12_2022/6t9i_10412.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t9i_10412/12_2022/6t9i_10412.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t9i_10412/12_2022/6t9i_10412_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t9i_10412/12_2022/6t9i_10412_neut.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 143": "OE1" <-> "OE2" Residue "B GLU 177": "OE1" <-> "OE2" Residue "B PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 314": "OE1" <-> "OE2" Residue "B ASP 338": "OD1" <-> "OD2" Residue "B PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 482": "OE1" <-> "OE2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C GLU 27": "OE1" <-> "OE2" Residue "C ARG 54": "NH1" <-> "NH2" Residue "C ASP 63": "OD1" <-> "OD2" Residue "C PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 86": "OD1" <-> "OD2" Residue "C GLU 144": "OE1" <-> "OE2" Residue "C GLU 151": "OE1" <-> "OE2" Residue "C ARG 207": "NH1" <-> "NH2" Residue "C ASP 214": "OD1" <-> "OD2" Residue "C ASP 264": "OD1" <-> "OD2" Residue "C ARG 303": "NH1" <-> "NH2" Residue "C GLU 306": "OE1" <-> "OE2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "D TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 75": "NH1" <-> "NH2" Residue "D ARG 86": "NH1" <-> "NH2" Residue "D GLU 106": "OE1" <-> "OE2" Residue "D GLU 150": "OE1" <-> "OE2" Residue "D ARG 154": "NH1" <-> "NH2" Residue "D TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 202": "OD1" <-> "OD2" Residue "D PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 226": "OD1" <-> "OD2" Residue "D GLU 232": "OE1" <-> "OE2" Residue "D TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 442": "NH1" <-> "NH2" Residue "D TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 476": "OD1" <-> "OD2" Residue "D ASP 513": "OD1" <-> "OD2" Residue "D ASP 536": "OD1" <-> "OD2" Residue "D ASP 546": "OD1" <-> "OD2" Residue "D TYR 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 592": "NH1" <-> "NH2" Residue "D TYR 600": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 613": "OD1" <-> "OD2" Residue "D PHE 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 664": "NH1" <-> "NH2" Residue "D ARG 685": "NH1" <-> "NH2" Residue "D ARG 690": "NH1" <-> "NH2" Residue "D ASP 744": "OD1" <-> "OD2" Residue "E ASP 19": "OD1" <-> "OD2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E ASP 31": "OD1" <-> "OD2" Residue "E GLU 47": "OE1" <-> "OE2" Residue "E ASP 68": "OD1" <-> "OD2" Residue "E ARG 74": "NH1" <-> "NH2" Residue "E PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 112": "OE1" <-> "OE2" Residue "E GLU 114": "OE1" <-> "OE2" Residue "E ASP 175": "OD1" <-> "OD2" Residue "E ASP 193": "OD1" <-> "OD2" Residue "E GLU 291": "OE1" <-> "OE2" Residue "E ASP 330": "OD1" <-> "OD2" Residue "E GLU 335": "OE1" <-> "OE2" Residue "E TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 406": "NH1" <-> "NH2" Residue "E ARG 417": "NH1" <-> "NH2" Residue "E PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 62": "NH1" <-> "NH2" Residue "F ARG 94": "NH1" <-> "NH2" Residue "F GLU 120": "OE1" <-> "OE2" Residue "F ARG 121": "NH1" <-> "NH2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "G PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 106": "OD1" <-> "OD2" Residue "G ASP 187": "OD1" <-> "OD2" Residue "G GLU 194": "OE1" <-> "OE2" Residue "G PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 206": "NH1" <-> "NH2" Residue "H ASP 192": "OD1" <-> "OD2" Residue "H ARG 195": "NH1" <-> "NH2" Residue "H PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 217": "NH1" <-> "NH2" Residue "H ASP 268": "OD1" <-> "OD2" Residue "H GLU 282": "OE1" <-> "OE2" Residue "H ASP 290": "OD1" <-> "OD2" Residue "H ARG 292": "NH1" <-> "NH2" Residue "H GLU 295": "OE1" <-> "OE2" Residue "H ARG 317": "NH1" <-> "NH2" Residue "H ARG 319": "NH1" <-> "NH2" Residue "H ARG 320": "NH1" <-> "NH2" Residue "H TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 344": "OD1" <-> "OD2" Residue "H GLU 361": "OE1" <-> "OE2" Residue "H GLU 398": "OE1" <-> "OE2" Residue "H GLU 401": "OE1" <-> "OE2" Residue "I PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 366": "OE1" <-> "OE2" Residue "I ASP 410": "OD1" <-> "OD2" Residue "I ARG 418": "NH1" <-> "NH2" Residue "I ARG 421": "NH1" <-> "NH2" Residue "I PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 463": "NH1" <-> "NH2" Residue "I ARG 476": "NH1" <-> "NH2" Residue "I ARG 484": "NH1" <-> "NH2" Residue "I TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 156": "OD1" <-> "OD2" Residue "K GLU 158": "OE1" <-> "OE2" Residue "K PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 730": "OD1" <-> "OD2" Residue "K GLU 733": "OE1" <-> "OE2" Residue "K GLU 747": "OE1" <-> "OE2" Residue "K GLU 754": "OE1" <-> "OE2" Residue "K GLU 875": "OE1" <-> "OE2" Residue "K ASP 876": "OD1" <-> "OD2" Residue "K ASP 880": "OD1" <-> "OD2" Residue "K ARG 881": "NH1" <-> "NH2" Residue "K ARG 926": "NH1" <-> "NH2" Residue "K GLU 1027": "OE1" <-> "OE2" Residue "K ARG 1051": "NH1" <-> "NH2" Residue "Q GLU 355": "OE1" <-> "OE2" Residue "Q ARG 382": "NH1" <-> "NH2" Residue "Q PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 420": "OD1" <-> "OD2" Residue "Q ASP 422": "OD1" <-> "OD2" Residue "Q PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 430": "NH1" <-> "NH2" Residue "T GLU 8": "OE1" <-> "OE2" Residue "T TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 33": "OD1" <-> "OD2" Residue "T PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 67": "OD1" <-> "OD2" Residue "T ASP 81": "OD1" <-> "OD2" Residue "T PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 101": "OE1" <-> "OE2" Residue "T GLU 112": "OE1" <-> "OE2" Residue "T GLU 113": "OE1" <-> "OE2" Residue "T PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 320": "OD1" <-> "OD2" Residue "T ASP 327": "OD1" <-> "OD2" Residue "T ARG 352": "NH1" <-> "NH2" Residue "T TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 405": "OE1" <-> "OE2" Residue "T GLU 412": "OE1" <-> "OE2" Residue "T ARG 459": "NH1" <-> "NH2" Residue "T ARG 474": "NH1" <-> "NH2" Residue "T TYR 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 513": "OE1" <-> "OE2" Residue "T GLU 516": "OE1" <-> "OE2" Residue "T PHE 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 629": "OE1" <-> "OE2" Residue "T GLU 630": "OE1" <-> "OE2" Residue "T GLU 681": "OE1" <-> "OE2" Residue "T ASP 684": "OD1" <-> "OD2" Residue "T ARG 712": "NH1" <-> "NH2" Residue "T GLU 715": "OE1" <-> "OE2" Residue "T GLU 804": "OE1" <-> "OE2" Residue "T TYR 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 813": "NH1" <-> "NH2" Residue "T ARG 817": "NH1" <-> "NH2" Residue "T GLU 854": "OE1" <-> "OE2" Residue "T ARG 868": "NH1" <-> "NH2" Residue "T GLU 902": "OE1" <-> "OE2" Residue "T ASP 906": "OD1" <-> "OD2" Residue "T GLU 911": "OE1" <-> "OE2" Residue "T GLU 918": "OE1" <-> "OE2" Residue "T ASP 923": "OD1" <-> "OD2" Residue "T GLU 971": "OE1" <-> "OE2" Residue "T GLU 1058": "OE1" <-> "OE2" Residue "T ASP 1071": "OD1" <-> "OD2" Residue "T TYR 1088": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 1101": "OD1" <-> "OD2" Residue "T ARG 1123": "NH1" <-> "NH2" Residue "T GLU 1159": "OE1" <-> "OE2" Residue "T GLU 1162": "OE1" <-> "OE2" Residue "T ARG 1170": "NH1" <-> "NH2" Residue "T TYR 1179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 1204": "OE1" <-> "OE2" Residue "T ASP 1221": "OD1" <-> "OD2" Residue "T ASP 1247": "OD1" <-> "OD2" Residue "T GLU 1261": "OE1" <-> "OE2" Residue "T ASP 1266": "OD1" <-> "OD2" Residue "T ASP 1274": "OD1" <-> "OD2" Residue "T ASP 1291": "OD1" <-> "OD2" Residue "T GLU 1295": "OE1" <-> "OE2" Residue "T ARG 1304": "NH1" <-> "NH2" Residue "T GLU 1388": "OE1" <-> "OE2" Residue "T GLU 1427": "OE1" <-> "OE2" Residue "T ARG 1437": "NH1" <-> "NH2" Residue "T GLU 1469": "OE1" <-> "OE2" Residue "T GLU 1508": "OE1" <-> "OE2" Residue "T PHE 1514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 1520": "NH1" <-> "NH2" Residue "T PHE 1539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 1542": "OD1" <-> "OD2" Residue "T PHE 1559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 1567": "OD1" <-> "OD2" Residue "T PHE 1569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 1572": "OD1" <-> "OD2" Residue "T ARG 1585": "NH1" <-> "NH2" Residue "T PHE 1592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 1610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 1632": "OE1" <-> "OE2" Residue "T GLU 1638": "OE1" <-> "OE2" Residue "T GLU 1641": "OE1" <-> "OE2" Residue "T ASP 1671": "OD1" <-> "OD2" Residue "T GLU 1683": "OE1" <-> "OE2" Residue "T ASP 1697": "OD1" <-> "OD2" Residue "T GLU 1734": "OE1" <-> "OE2" Residue "T GLU 1777": "OE1" <-> "OE2" Residue "T ASP 1785": "OD1" <-> "OD2" Residue "T ASP 1793": "OD1" <-> "OD2" Residue "T GLU 1814": "OE1" <-> "OE2" Residue "T GLU 1827": "OE1" <-> "OE2" Residue "T TYR 1851": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 1861": "NH1" <-> "NH2" Residue "T ASP 1885": "OD1" <-> "OD2" Residue "T GLU 1897": "OE1" <-> "OE2" Residue "T GLU 1976": "OE1" <-> "OE2" Residue "T PHE 1988": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 2001": "OD1" <-> "OD2" Residue "T ASP 2030": "OD1" <-> "OD2" Residue "T ARG 2093": "NH1" <-> "NH2" Residue "T TYR 2169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 2182": "OE1" <-> "OE2" Residue "T GLU 2249": "OE1" <-> "OE2" Residue "T ASP 2288": "OD1" <-> "OD2" Residue "T ASP 2297": "OD1" <-> "OD2" Residue "T ASP 2327": "OD1" <-> "OD2" Residue "T ASP 2345": "OD1" <-> "OD2" Residue "T PHE 2361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 2387": "OE1" <-> "OE2" Residue "T GLU 2396": "OE1" <-> "OE2" Residue "T PHE 2402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 2407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 2432": "NH1" <-> "NH2" Residue "T ARG 2445": "NH1" <-> "NH2" Residue "T ASP 2446": "OD1" <-> "OD2" Residue "T ARG 2456": "NH1" <-> "NH2" Residue "T ASP 2465": "OD1" <-> "OD2" Residue "T ARG 2482": "NH1" <-> "NH2" Residue "T TYR 2492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 2503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 2516": "OD1" <-> "OD2" Residue "T ARG 2581": "NH1" <-> "NH2" Residue "T ASP 2650": "OD1" <-> "OD2" Residue "T ARG 2681": "NH1" <-> "NH2" Residue "T GLU 2708": "OE1" <-> "OE2" Residue "T ARG 2715": "NH1" <-> "NH2" Residue "T PHE 2803": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 2807": "NH1" <-> "NH2" Residue "T ASP 2810": "OD1" <-> "OD2" Residue "T ARG 2887": "NH1" <-> "NH2" Residue "T ARG 2969": "NH1" <-> "NH2" Residue "T TYR 2971": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 2980": "OE1" <-> "OE2" Residue "T GLU 2987": "OE1" <-> "OE2" Residue "T TYR 3013": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 3034": "NH1" <-> "NH2" Residue "T GLU 3037": "OE1" <-> "OE2" Residue "T ASP 3111": "OD1" <-> "OD2" Residue "T ASP 3112": "OD1" <-> "OD2" Residue "T ARG 3172": "NH1" <-> "NH2" Residue "T ASP 3235": "OD1" <-> "OD2" Residue "T PHE 3237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 3243": "OE1" <-> "OE2" Residue "T TYR 3291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 3296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 3302": "OD1" <-> "OD2" Residue "T ARG 3313": "NH1" <-> "NH2" Residue "T ARG 3320": "NH1" <-> "NH2" Residue "T PHE 3349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 3358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 3373": "NH1" <-> "NH2" Residue "T PHE 3374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 3382": "NH1" <-> "NH2" Residue "T TYR 3388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 3407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 3417": "OE1" <-> "OE2" Residue "T ARG 3424": "NH1" <-> "NH2" Residue "T GLU 3435": "OE1" <-> "OE2" Residue "T ARG 3438": "NH1" <-> "NH2" Residue "T GLU 3473": "OE1" <-> "OE2" Residue "T ASP 3491": "OD1" <-> "OD2" Residue "T ASP 3499": "OD1" <-> "OD2" Residue "T ARG 3545": "NH1" <-> "NH2" Residue "T PHE 3548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 3557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 3593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 3622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 3641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 3658": "OE1" <-> "OE2" Residue "T ARG 3689": "NH1" <-> "NH2" Residue "T ASP 3737": "OD1" <-> "OD2" Time to flip residues: 0.24s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 48821 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 1891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1891 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 8, 'TRANS': 215} Chain breaks: 4 Chain: "C" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1774 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 204} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 4474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4474 Classifications: {'peptide': 566} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 536} Chain breaks: 3 Chain: "E" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3441 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 19, 'TRANS': 413} Chain breaks: 3 Chain: "F" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 902 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 6, 'TRANS': 104} Chain breaks: 1 Chain: "G" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1108 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "H" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1803 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 7, 'TRANS': 219} Chain breaks: 2 Chain: "I" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1351 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 10, 'TRANS': 162} Chain: "K" Number of atoms: 2258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2258 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 6, 'TRANS': 272} Chain breaks: 3 Chain: "Q" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 675 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 7, 'TRANS': 76} Chain: "T" Number of atoms: 28729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3513, 28729 Classifications: {'peptide': 3513} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 149, 'TRANS': 3363} Chain breaks: 11 Chain: "U" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 415 Classifications: {'peptide': 83} Link IDs: {'TRANS': 82} Chain breaks: 2 Time building chain proxies: 26.88, per 1000 atoms: 0.55 Number of scatterers: 48821 At special positions: 0 Unit cell: (134.4, 199.5, 282.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 191 16.00 O 9066 8.00 N 8265 7.00 C 31299 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: 20.09 Conformation dependent library (CDL) restraints added in 7.7 seconds 11918 Ramachandran restraints generated. 5959 Oldfield, 0 Emsley, 5959 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11724 Finding SS restraints... Secondary structure from input PDB file: 284 helices and 17 sheets defined 59.7% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.69 Creating SS restraints... Processing helix chain 'B' and resid 123 through 130 Processing helix chain 'B' and resid 178 through 183 Processing helix chain 'B' and resid 184 through 186 No H-bonds generated for 'chain 'B' and resid 184 through 186' Processing helix chain 'B' and resid 195 through 203 Processing helix chain 'B' and resid 288 through 300 removed outlier: 3.550A pdb=" N THR B 292 " --> pdb=" O ASN B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 322 removed outlier: 3.809A pdb=" N TYR B 310 " --> pdb=" O SER B 306 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B 322 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 345 removed outlier: 3.678A pdb=" N ALA B 344 " --> pdb=" O GLU B 341 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N PHE B 345 " --> pdb=" O GLU B 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 341 through 345' Processing helix chain 'B' and resid 403 through 413 Processing helix chain 'B' and resid 475 through 488 Processing helix chain 'C' and resid 7 through 19 removed outlier: 3.782A pdb=" N VAL C 17 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER C 18 " --> pdb=" O MET C 14 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY C 19 " --> pdb=" O MET C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 55 removed outlier: 3.553A pdb=" N THR C 29 " --> pdb=" O PRO C 25 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU C 53 " --> pdb=" O LYS C 49 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG C 54 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 66 removed outlier: 4.010A pdb=" N VAL C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE C 65 " --> pdb=" O PRO C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 69 No H-bonds generated for 'chain 'C' and resid 67 through 69' Processing helix chain 'C' and resid 71 through 82 Processing helix chain 'C' and resid 192 through 202 removed outlier: 3.763A pdb=" N CYS C 199 " --> pdb=" O HIS C 195 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG C 200 " --> pdb=" O TRP C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 217 removed outlier: 3.936A pdb=" N ASP C 214 " --> pdb=" O LYS C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 222 removed outlier: 4.162A pdb=" N LEU C 221 " --> pdb=" O GLY C 217 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR C 222 " --> pdb=" O ILE C 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 217 through 222' Processing helix chain 'C' and resid 229 through 264 removed outlier: 4.001A pdb=" N THR C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP C 264 " --> pdb=" O GLN C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 313 Processing helix chain 'C' and resid 320 through 324 removed outlier: 3.828A pdb=" N ASN C 324 " --> pdb=" O ALA C 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 71 Processing helix chain 'D' and resid 74 through 87 removed outlier: 3.590A pdb=" N THR D 87 " --> pdb=" O GLU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 165 removed outlier: 3.590A pdb=" N ALA D 155 " --> pdb=" O ASN D 151 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU D 159 " --> pdb=" O ALA D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 190 removed outlier: 3.778A pdb=" N LEU D 174 " --> pdb=" O TYR D 170 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N TYR D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) Proline residue: D 180 - end of helix Processing helix chain 'D' and resid 193 through 204 removed outlier: 3.534A pdb=" N ASP D 202 " --> pdb=" O ARG D 198 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE D 204 " --> pdb=" O PHE D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 213 Processing helix chain 'D' and resid 214 through 219 Processing helix chain 'D' and resid 224 through 229 removed outlier: 3.522A pdb=" N ILE D 228 " --> pdb=" O SER D 224 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS D 229 " --> pdb=" O ILE D 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 224 through 229' Processing helix chain 'D' and resid 231 through 240 removed outlier: 3.945A pdb=" N GLN D 238 " --> pdb=" O ALA D 234 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER D 239 " --> pdb=" O SER D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 259 Processing helix chain 'D' and resid 265 through 276 removed outlier: 3.524A pdb=" N VAL D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'E' and resid 17 through 25 removed outlier: 3.778A pdb=" N SER E 23 " --> pdb=" O ASP E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 59 removed outlier: 3.853A pdb=" N GLN E 51 " --> pdb=" O GLU E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 70 removed outlier: 3.615A pdb=" N VAL E 69 " --> pdb=" O THR E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 76 removed outlier: 4.077A pdb=" N ARG E 74 " --> pdb=" O SER E 70 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL E 75 " --> pdb=" O LYS E 71 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU E 76 " --> pdb=" O ALA E 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 70 through 76' Processing helix chain 'E' and resid 117 through 122 removed outlier: 3.522A pdb=" N ASN E 122 " --> pdb=" O ASP E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 232 Processing helix chain 'E' and resid 244 through 258 Processing helix chain 'E' and resid 264 through 278 removed outlier: 3.575A pdb=" N ILE E 269 " --> pdb=" O VAL E 265 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE E 271 " --> pdb=" O TYR E 267 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLN E 275 " --> pdb=" O PHE E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 297 Processing helix chain 'E' and resid 305 through 309 removed outlier: 3.788A pdb=" N ILE E 308 " --> pdb=" O ASP E 305 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N HIS E 309 " --> pdb=" O PRO E 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 305 through 309' Processing helix chain 'E' and resid 311 through 320 removed outlier: 3.584A pdb=" N ILE E 315 " --> pdb=" O LEU E 311 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU E 320 " --> pdb=" O LEU E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 361 removed outlier: 4.018A pdb=" N LEU E 346 " --> pdb=" O ARG E 342 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG E 347 " --> pdb=" O THR E 343 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER E 352 " --> pdb=" O ASP E 348 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR E 356 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS E 359 " --> pdb=" O ASP E 355 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE E 361 " --> pdb=" O VAL E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 381 Processing helix chain 'E' and resid 386 through 399 removed outlier: 3.570A pdb=" N TYR E 390 " --> pdb=" O VAL E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 407 Processing helix chain 'E' and resid 408 through 411 removed outlier: 4.313A pdb=" N ASN E 411 " --> pdb=" O PHE E 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 408 through 411' Processing helix chain 'E' and resid 412 through 420 Processing helix chain 'E' and resid 429 through 433 removed outlier: 4.037A pdb=" N HIS E 433 " --> pdb=" O ILE E 430 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 460 removed outlier: 3.766A pdb=" N ILE E 458 " --> pdb=" O VAL E 454 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA E 460 " --> pdb=" O THR E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 464 Processing helix chain 'F' and resid 31 through 43 Processing helix chain 'F' and resid 50 through 78 removed outlier: 4.353A pdb=" N LEU F 54 " --> pdb=" O ASP F 50 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG F 62 " --> pdb=" O ASP F 58 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA F 78 " --> pdb=" O TYR F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 99 Processing helix chain 'F' and resid 110 through 122 Processing helix chain 'F' and resid 139 through 143 Processing helix chain 'G' and resid 73 through 82 Processing helix chain 'G' and resid 89 through 101 removed outlier: 3.683A pdb=" N ILE G 93 " --> pdb=" O PRO G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 135 removed outlier: 3.643A pdb=" N LYS G 110 " --> pdb=" O ASP G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 145 removed outlier: 3.581A pdb=" N VAL G 140 " --> pdb=" O SER G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 155 removed outlier: 3.719A pdb=" N GLN G 152 " --> pdb=" O ALA G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 177 removed outlier: 3.765A pdb=" N GLN G 172 " --> pdb=" O GLN G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 194 removed outlier: 4.619A pdb=" N SER G 190 " --> pdb=" O ASN G 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 188 removed outlier: 3.576A pdb=" N LEU H 188 " --> pdb=" O ILE H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 199 Processing helix chain 'H' and resid 211 through 221 Processing helix chain 'H' and resid 229 through 239 removed outlier: 3.765A pdb=" N ASN H 239 " --> pdb=" O ARG H 235 " (cutoff:3.500A) Processing helix chain 'H' and resid 243 through 256 removed outlier: 3.860A pdb=" N TRP H 247 " --> pdb=" O THR H 243 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN H 249 " --> pdb=" O LEU H 245 " (cutoff:3.500A) Processing helix chain 'H' and resid 259 through 264 removed outlier: 3.781A pdb=" N SER H 263 " --> pdb=" O LEU H 259 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS H 264 " --> pdb=" O ALA H 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 259 through 264' Processing helix chain 'H' and resid 268 through 284 Processing helix chain 'H' and resid 292 through 317 removed outlier: 4.913A pdb=" N THR H 315 " --> pdb=" O PHE H 311 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL H 316 " --> pdb=" O THR H 312 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG H 317 " --> pdb=" O ILE H 313 " (cutoff:3.500A) Processing helix chain 'H' and resid 340 through 349 removed outlier: 4.073A pdb=" N ARG H 346 " --> pdb=" O ALA H 342 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP H 347 " --> pdb=" O ALA H 343 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA H 348 " --> pdb=" O ASP H 344 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS H 349 " --> pdb=" O LYS H 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 353 removed outlier: 3.844A pdb=" N LEU H 353 " --> pdb=" O ILE H 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 350 through 353' Processing helix chain 'H' and resid 356 through 365 Processing helix chain 'H' and resid 407 through 418 removed outlier: 3.687A pdb=" N ILE H 412 " --> pdb=" O THR H 408 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR H 413 " --> pdb=" O ASN H 409 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER H 417 " --> pdb=" O TYR H 413 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE H 418 " --> pdb=" O ASP H 414 " (cutoff:3.500A) Processing helix chain 'I' and resid 419 through 428 Processing helix chain 'I' and resid 439 through 468 removed outlier: 3.919A pdb=" N THR I 455 " --> pdb=" O ASP I 451 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE I 460 " --> pdb=" O ASN I 456 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG I 463 " --> pdb=" O ALA I 459 " (cutoff:3.500A) Processing helix chain 'I' and resid 474 through 485 removed outlier: 4.109A pdb=" N ILE I 478 " --> pdb=" O GLU I 474 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN I 485 " --> pdb=" O HIS I 481 " (cutoff:3.500A) Processing helix chain 'I' and resid 507 through 524 removed outlier: 3.542A pdb=" N ASN I 511 " --> pdb=" O SER I 507 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 163 Processing helix chain 'K' and resid 167 through 185 Processing helix chain 'K' and resid 731 through 741 removed outlier: 3.559A pdb=" N SER K 735 " --> pdb=" O ASP K 731 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP K 737 " --> pdb=" O GLU K 733 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR K 741 " --> pdb=" O TRP K 737 " (cutoff:3.500A) Processing helix chain 'K' and resid 743 through 753 removed outlier: 3.513A pdb=" N GLU K 747 " --> pdb=" O LYS K 743 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR K 753 " --> pdb=" O CYS K 749 " (cutoff:3.500A) Processing helix chain 'K' and resid 868 through 884 removed outlier: 3.598A pdb=" N ASP K 872 " --> pdb=" O THR K 868 " (cutoff:3.500A) Processing helix chain 'K' and resid 901 through 916 Processing helix chain 'K' and resid 917 through 929 Processing helix chain 'K' and resid 975 through 989 removed outlier: 3.679A pdb=" N ILE K 979 " --> pdb=" O ASN K 975 " (cutoff:3.500A) Processing helix chain 'K' and resid 1000 through 1027 removed outlier: 3.707A pdb=" N ILE K1004 " --> pdb=" O HIS K1000 " (cutoff:3.500A) Processing helix chain 'K' and resid 1035 through 1046 removed outlier: 3.763A pdb=" N LEU K1040 " --> pdb=" O ASN K1036 " (cutoff:3.500A) Processing helix chain 'K' and resid 1053 through 1064 Processing helix chain 'K' and resid 1065 through 1085 Processing helix chain 'Q' and resid 354 through 366 Processing helix chain 'Q' and resid 381 through 398 removed outlier: 3.918A pdb=" N PHE Q 398 " --> pdb=" O PHE Q 394 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 10 removed outlier: 3.733A pdb=" N GLN T 6 " --> pdb=" O LEU T 3 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU T 8 " --> pdb=" O GLU T 5 " (cutoff:3.500A) Processing helix chain 'T' and resid 27 through 31 removed outlier: 3.777A pdb=" N GLU T 30 " --> pdb=" O THR T 27 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LEU T 31 " --> pdb=" O LEU T 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 27 through 31' Processing helix chain 'T' and resid 44 through 61 removed outlier: 4.149A pdb=" N GLN T 49 " --> pdb=" O HIS T 45 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ALA T 50 " --> pdb=" O PHE T 46 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE T 52 " --> pdb=" O LEU T 48 " (cutoff:3.500A) Proline residue: T 53 - end of helix removed outlier: 4.287A pdb=" N GLU T 61 " --> pdb=" O ASN T 57 " (cutoff:3.500A) Processing helix chain 'T' and resid 72 through 86 removed outlier: 3.518A pdb=" N ASN T 84 " --> pdb=" O LEU T 80 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG T 85 " --> pdb=" O ASP T 81 " (cutoff:3.500A) Processing helix chain 'T' and resid 91 through 97 removed outlier: 3.998A pdb=" N TYR T 95 " --> pdb=" O THR T 91 " (cutoff:3.500A) Processing helix chain 'T' and resid 99 through 104 removed outlier: 3.941A pdb=" N LEU T 103 " --> pdb=" O VAL T 99 " (cutoff:3.500A) Processing helix chain 'T' and resid 117 through 132 removed outlier: 4.586A pdb=" N THR T 123 " --> pdb=" O MET T 119 " (cutoff:3.500A) Processing helix chain 'T' and resid 141 through 157 removed outlier: 3.887A pdb=" N ILE T 145 " --> pdb=" O ILE T 141 " (cutoff:3.500A) Proline residue: T 152 - end of helix Processing helix chain 'T' and resid 231 through 240 Processing helix chain 'T' and resid 250 through 254 removed outlier: 3.535A pdb=" N ILE T 253 " --> pdb=" O THR T 250 " (cutoff:3.500A) Processing helix chain 'T' and resid 293 through 309 Processing helix chain 'T' and resid 310 through 314 Processing helix chain 'T' and resid 324 through 335 removed outlier: 3.825A pdb=" N LEU T 328 " --> pdb=" O PHE T 324 " (cutoff:3.500A) Processing helix chain 'T' and resid 341 through 356 removed outlier: 4.072A pdb=" N LYS T 345 " --> pdb=" O SER T 341 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU T 346 " --> pdb=" O SER T 342 " (cutoff:3.500A) Processing helix chain 'T' and resid 363 through 369 Processing helix chain 'T' and resid 374 through 378 Processing helix chain 'T' and resid 387 through 403 Processing helix chain 'T' and resid 407 through 424 removed outlier: 3.627A pdb=" N ILE T 417 " --> pdb=" O LYS T 413 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLY T 420 " --> pdb=" O LYS T 416 " (cutoff:3.500A) Processing helix chain 'T' and resid 428 through 453 removed outlier: 3.695A pdb=" N GLN T 432 " --> pdb=" O ALA T 428 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU T 444 " --> pdb=" O LEU T 440 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ARG T 445 " --> pdb=" O ASN T 441 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN T 453 " --> pdb=" O LEU T 449 " (cutoff:3.500A) Processing helix chain 'T' and resid 456 through 480 removed outlier: 3.711A pdb=" N LEU T 463 " --> pdb=" O ARG T 459 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE T 468 " --> pdb=" O LEU T 464 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP T 469 " --> pdb=" O MET T 465 " (cutoff:3.500A) Processing helix chain 'T' and resid 481 through 498 removed outlier: 3.703A pdb=" N LYS T 496 " --> pdb=" O TYR T 492 " (cutoff:3.500A) Processing helix chain 'T' and resid 512 through 520 Processing helix chain 'T' and resid 561 through 567 removed outlier: 3.698A pdb=" N LYS T 564 " --> pdb=" O PHE T 561 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA T 567 " --> pdb=" O LYS T 564 " (cutoff:3.500A) Processing helix chain 'T' and resid 578 through 601 Processing helix chain 'T' and resid 602 through 605 removed outlier: 4.015A pdb=" N ASN T 605 " --> pdb=" O LYS T 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 602 through 605' Processing helix chain 'T' and resid 627 through 644 removed outlier: 4.060A pdb=" N VAL T 633 " --> pdb=" O GLU T 629 " (cutoff:3.500A) Processing helix chain 'T' and resid 645 through 647 No H-bonds generated for 'chain 'T' and resid 645 through 647' Processing helix chain 'T' and resid 676 through 690 removed outlier: 3.560A pdb=" N PHE T 690 " --> pdb=" O LEU T 686 " (cutoff:3.500A) Processing helix chain 'T' and resid 694 through 714 removed outlier: 4.089A pdb=" N GLU T 700 " --> pdb=" O ALA T 696 " (cutoff:3.500A) Proline residue: T 707 - end of helix Processing helix chain 'T' and resid 716 through 718 No H-bonds generated for 'chain 'T' and resid 716 through 718' Processing helix chain 'T' and resid 719 through 728 removed outlier: 3.681A pdb=" N ALA T 723 " --> pdb=" O LEU T 719 " (cutoff:3.500A) Processing helix chain 'T' and resid 732 through 748 removed outlier: 3.794A pdb=" N GLY T 746 " --> pdb=" O ARG T 742 " (cutoff:3.500A) Processing helix chain 'T' and resid 749 through 751 No H-bonds generated for 'chain 'T' and resid 749 through 751' Processing helix chain 'T' and resid 755 through 776 removed outlier: 3.914A pdb=" N VAL T 773 " --> pdb=" O SER T 769 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN T 774 " --> pdb=" O PHE T 770 " (cutoff:3.500A) Processing helix chain 'T' and resid 788 through 799 Processing helix chain 'T' and resid 805 through 819 removed outlier: 4.392A pdb=" N PHE T 809 " --> pdb=" O PRO T 805 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE T 819 " --> pdb=" O LEU T 815 " (cutoff:3.500A) Processing helix chain 'T' and resid 827 through 830 removed outlier: 4.007A pdb=" N SER T 830 " --> pdb=" O LEU T 827 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 827 through 830' Processing helix chain 'T' and resid 831 through 844 removed outlier: 3.574A pdb=" N LEU T 842 " --> pdb=" O LEU T 838 " (cutoff:3.500A) Processing helix chain 'T' and resid 853 through 863 removed outlier: 3.501A pdb=" N ILE T 863 " --> pdb=" O VAL T 859 " (cutoff:3.500A) Processing helix chain 'T' and resid 879 through 889 removed outlier: 3.572A pdb=" N VAL T 884 " --> pdb=" O MET T 880 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE T 885 " --> pdb=" O LYS T 881 " (cutoff:3.500A) Processing helix chain 'T' and resid 893 through 907 removed outlier: 3.822A pdb=" N ARG T 899 " --> pdb=" O SER T 895 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASN T 907 " --> pdb=" O LEU T 903 " (cutoff:3.500A) Processing helix chain 'T' and resid 917 through 919 No H-bonds generated for 'chain 'T' and resid 917 through 919' Processing helix chain 'T' and resid 920 through 929 Processing helix chain 'T' and resid 930 through 932 No H-bonds generated for 'chain 'T' and resid 930 through 932' Processing helix chain 'T' and resid 942 through 952 Processing helix chain 'T' and resid 996 through 1006 Processing helix chain 'T' and resid 1010 through 1031 removed outlier: 4.646A pdb=" N SER T1031 " --> pdb=" O LEU T1027 " (cutoff:3.500A) Processing helix chain 'T' and resid 1038 through 1049 Processing helix chain 'T' and resid 1068 through 1089 Processing helix chain 'T' and resid 1090 through 1092 No H-bonds generated for 'chain 'T' and resid 1090 through 1092' Processing helix chain 'T' and resid 1095 through 1121 removed outlier: 3.561A pdb=" N ALA T1099 " --> pdb=" O LEU T1095 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU T1112 " --> pdb=" O ASP T1108 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL T1115 " --> pdb=" O CYS T1111 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASN T1116 " --> pdb=" O LEU T1112 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N THR T1117 " --> pdb=" O LEU T1113 " (cutoff:3.500A) Processing helix chain 'T' and resid 1122 through 1124 No H-bonds generated for 'chain 'T' and resid 1122 through 1124' Processing helix chain 'T' and resid 1148 through 1154 removed outlier: 3.625A pdb=" N SER T1154 " --> pdb=" O PRO T1150 " (cutoff:3.500A) Processing helix chain 'T' and resid 1157 through 1180 removed outlier: 3.745A pdb=" N VAL T1163 " --> pdb=" O GLU T1159 " (cutoff:3.500A) Processing helix chain 'T' and resid 1180 through 1185 removed outlier: 4.083A pdb=" N LEU T1185 " --> pdb=" O GLU T1181 " (cutoff:3.500A) Processing helix chain 'T' and resid 1188 through 1201 removed outlier: 4.044A pdb=" N GLU T1192 " --> pdb=" O SER T1188 " (cutoff:3.500A) Processing helix chain 'T' and resid 1205 through 1223 removed outlier: 3.549A pdb=" N LYS T1209 " --> pdb=" O THR T1205 " (cutoff:3.500A) Processing helix chain 'T' and resid 1228 through 1233 Processing helix chain 'T' and resid 1233 through 1247 removed outlier: 3.687A pdb=" N LEU T1245 " --> pdb=" O LEU T1241 " (cutoff:3.500A) Processing helix chain 'T' and resid 1254 through 1272 Processing helix chain 'T' and resid 1283 through 1294 removed outlier: 3.591A pdb=" N ASN T1287 " --> pdb=" O LYS T1283 " (cutoff:3.500A) Processing helix chain 'T' and resid 1300 through 1313 removed outlier: 3.531A pdb=" N ARG T1304 " --> pdb=" O ASN T1300 " (cutoff:3.500A) Processing helix chain 'T' and resid 1321 through 1326 Processing helix chain 'T' and resid 1329 through 1340 removed outlier: 3.517A pdb=" N LEU T1333 " --> pdb=" O SER T1329 " (cutoff:3.500A) Proline residue: T1336 - end of helix removed outlier: 3.748A pdb=" N LYS T1340 " --> pdb=" O PRO T1336 " (cutoff:3.500A) Processing helix chain 'T' and resid 1346 through 1363 removed outlier: 3.572A pdb=" N LEU T1363 " --> pdb=" O PHE T1359 " (cutoff:3.500A) Processing helix chain 'T' and resid 1371 through 1383 removed outlier: 3.517A pdb=" N PHE T1375 " --> pdb=" O ASN T1371 " (cutoff:3.500A) Processing helix chain 'T' and resid 1404 through 1424 Processing helix chain 'T' and resid 1436 through 1447 removed outlier: 3.734A pdb=" N VAL T1443 " --> pdb=" O ARG T1439 " (cutoff:3.500A) Processing helix chain 'T' and resid 1452 through 1467 removed outlier: 3.514A pdb=" N ILE T1456 " --> pdb=" O SER T1452 " (cutoff:3.500A) Processing helix chain 'T' and resid 1468 through 1470 No H-bonds generated for 'chain 'T' and resid 1468 through 1470' Processing helix chain 'T' and resid 1477 through 1482 removed outlier: 3.936A pdb=" N LEU T1482 " --> pdb=" O LEU T1478 " (cutoff:3.500A) Processing helix chain 'T' and resid 1482 through 1489 Processing helix chain 'T' and resid 1496 through 1508 Processing helix chain 'T' and resid 1517 through 1528 Processing helix chain 'T' and resid 1532 through 1538 removed outlier: 3.570A pdb=" N THR T1537 " --> pdb=" O GLU T1533 " (cutoff:3.500A) Processing helix chain 'T' and resid 1546 through 1558 Processing helix chain 'T' and resid 1570 through 1584 Processing helix chain 'T' and resid 1593 through 1604 removed outlier: 3.882A pdb=" N ARG T1602 " --> pdb=" O ARG T1598 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE T1603 " --> pdb=" O TYR T1599 " (cutoff:3.500A) Processing helix chain 'T' and resid 1605 through 1613 removed outlier: 3.966A pdb=" N GLU T1609 " --> pdb=" O ASN T1605 " (cutoff:3.500A) Processing helix chain 'T' and resid 1617 through 1629 removed outlier: 4.031A pdb=" N GLN T1629 " --> pdb=" O CYS T1625 " (cutoff:3.500A) Processing helix chain 'T' and resid 1633 through 1642 removed outlier: 4.137A pdb=" N GLU T1638 " --> pdb=" O LYS T1634 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS T1642 " --> pdb=" O GLU T1638 " (cutoff:3.500A) Processing helix chain 'T' and resid 1643 through 1659 Proline residue: T1656 - end of helix Processing helix chain 'T' and resid 1661 through 1679 Processing helix chain 'T' and resid 1690 through 1709 Processing helix chain 'T' and resid 1715 through 1734 removed outlier: 3.763A pdb=" N ASN T1719 " --> pdb=" O HIS T1715 " (cutoff:3.500A) Processing helix chain 'T' and resid 1739 through 1750 removed outlier: 4.079A pdb=" N LEU T1743 " --> pdb=" O ASP T1739 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU T1744 " --> pdb=" O GLN T1740 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE T1750 " --> pdb=" O ASP T1746 " (cutoff:3.500A) Processing helix chain 'T' and resid 1762 through 1770 Processing helix chain 'T' and resid 1771 through 1775 removed outlier: 3.824A pdb=" N SER T1774 " --> pdb=" O ILE T1771 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASN T1775 " --> pdb=" O ALA T1772 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 1771 through 1775' Processing helix chain 'T' and resid 1777 through 1792 removed outlier: 3.507A pdb=" N ASN T1781 " --> pdb=" O GLU T1777 " (cutoff:3.500A) Processing helix chain 'T' and resid 1796 through 1817 removed outlier: 3.553A pdb=" N ILE T1800 " --> pdb=" O LEU T1796 " (cutoff:3.500A) Processing helix chain 'T' and resid 1833 through 1843 removed outlier: 3.744A pdb=" N LYS T1843 " --> pdb=" O ASN T1839 " (cutoff:3.500A) Processing helix chain 'T' and resid 1844 through 1845 No H-bonds generated for 'chain 'T' and resid 1844 through 1845' Processing helix chain 'T' and resid 1846 through 1850 Processing helix chain 'T' and resid 1858 through 1875 removed outlier: 3.546A pdb=" N PHE T1862 " --> pdb=" O ASP T1858 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP T1875 " --> pdb=" O PHE T1871 " (cutoff:3.500A) Processing helix chain 'T' and resid 1882 through 1893 removed outlier: 3.794A pdb=" N PHE T1893 " --> pdb=" O PHE T1889 " (cutoff:3.500A) Processing helix chain 'T' and resid 1899 through 1916 Processing helix chain 'T' and resid 1920 through 1931 removed outlier: 4.542A pdb=" N THR T1924 " --> pdb=" O ILE T1920 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN T1925 " --> pdb=" O LYS T1921 " (cutoff:3.500A) Processing helix chain 'T' and resid 1935 through 1937 No H-bonds generated for 'chain 'T' and resid 1935 through 1937' Processing helix chain 'T' and resid 1938 through 1958 removed outlier: 3.506A pdb=" N VAL T1942 " --> pdb=" O ALA T1938 " (cutoff:3.500A) Proline residue: T1951 - end of helix removed outlier: 3.667A pdb=" N GLU T1955 " --> pdb=" O PRO T1951 " (cutoff:3.500A) Processing helix chain 'T' and resid 1964 through 1977 removed outlier: 4.177A pdb=" N ASN T1968 " --> pdb=" O ASP T1964 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL T1970 " --> pdb=" O TRP T1966 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN T1977 " --> pdb=" O VAL T1973 " (cutoff:3.500A) Processing helix chain 'T' and resid 1982 through 1988 removed outlier: 4.359A pdb=" N TYR T1986 " --> pdb=" O ASN T1982 " (cutoff:3.500A) Processing helix chain 'T' and resid 2001 through 2015 removed outlier: 3.829A pdb=" N SER T2005 " --> pdb=" O ASP T2001 " (cutoff:3.500A) Processing helix chain 'T' and resid 2024 through 2043 removed outlier: 3.558A pdb=" N ALA T2028 " --> pdb=" O SER T2024 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP T2030 " --> pdb=" O THR T2026 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR T2037 " --> pdb=" O SER T2033 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU T2043 " --> pdb=" O GLU T2039 " (cutoff:3.500A) Processing helix chain 'T' and resid 2090 through 2107 removed outlier: 3.944A pdb=" N GLU T2094 " --> pdb=" O LEU T2090 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER T2107 " --> pdb=" O TYR T2103 " (cutoff:3.500A) Processing helix chain 'T' and resid 2116 through 2129 removed outlier: 4.205A pdb=" N SER T2129 " --> pdb=" O SER T2125 " (cutoff:3.500A) Processing helix chain 'T' and resid 2155 through 2173 removed outlier: 4.077A pdb=" N TYR T2169 " --> pdb=" O LEU T2165 " (cutoff:3.500A) Processing helix chain 'T' and resid 2183 through 2196 removed outlier: 4.646A pdb=" N LYS T2193 " --> pdb=" O ASN T2189 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N CYS T2194 " --> pdb=" O LEU T2190 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS T2196 " --> pdb=" O GLU T2192 " (cutoff:3.500A) Processing helix chain 'T' and resid 2203 through 2217 removed outlier: 5.164A pdb=" N GLN T2211 " --> pdb=" O GLN T2207 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N VAL T2212 " --> pdb=" O LYS T2208 " (cutoff:3.500A) Processing helix chain 'T' and resid 2228 through 2245 removed outlier: 4.048A pdb=" N GLY T2232 " --> pdb=" O GLU T2228 " (cutoff:3.500A) Processing helix chain 'T' and resid 2251 through 2267 removed outlier: 4.400A pdb=" N ALA T2255 " --> pdb=" O SER T2251 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY T2256 " --> pdb=" O SER T2252 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL T2257 " --> pdb=" O VAL T2253 " (cutoff:3.500A) Processing helix chain 'T' and resid 2275 through 2290 Processing helix chain 'T' and resid 2302 through 2321 removed outlier: 3.661A pdb=" N ILE T2306 " --> pdb=" O GLU T2302 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N THR T2308 " --> pdb=" O ALA T2304 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE T2317 " --> pdb=" O LYS T2313 " (cutoff:3.500A) Processing helix chain 'T' and resid 2328 through 2342 removed outlier: 3.709A pdb=" N PHE T2332 " --> pdb=" O SER T2328 " (cutoff:3.500A) Processing helix chain 'T' and resid 2345 through 2361 removed outlier: 3.539A pdb=" N LEU T2349 " --> pdb=" O ASP T2345 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LYS T2351 " --> pdb=" O ASN T2347 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE T2361 " --> pdb=" O ARG T2357 " (cutoff:3.500A) Processing helix chain 'T' and resid 2369 through 2378 removed outlier: 3.643A pdb=" N LYS T2378 " --> pdb=" O ALA T2374 " (cutoff:3.500A) Processing helix chain 'T' and resid 2381 through 2386 Processing helix chain 'T' and resid 2387 through 2402 removed outlier: 3.521A pdb=" N SER T2391 " --> pdb=" O GLU T2387 " (cutoff:3.500A) Processing helix chain 'T' and resid 2417 through 2424 removed outlier: 3.845A pdb=" N LEU T2421 " --> pdb=" O GLU T2417 " (cutoff:3.500A) Processing helix chain 'T' and resid 2428 through 2443 removed outlier: 3.778A pdb=" N LEU T2443 " --> pdb=" O LEU T2439 " (cutoff:3.500A) Processing helix chain 'T' and resid 2446 through 2456 Processing helix chain 'T' and resid 2468 through 2477 Processing helix chain 'T' and resid 2478 through 2480 No H-bonds generated for 'chain 'T' and resid 2478 through 2480' Processing helix chain 'T' and resid 2499 through 2503 removed outlier: 3.721A pdb=" N TYR T2503 " --> pdb=" O LEU T2500 " (cutoff:3.500A) Processing helix chain 'T' and resid 2518 through 2534 removed outlier: 3.565A pdb=" N LYS T2524 " --> pdb=" O SER T2520 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY T2532 " --> pdb=" O ALA T2528 " (cutoff:3.500A) Processing helix chain 'T' and resid 2537 through 2550 removed outlier: 4.430A pdb=" N PHE T2541 " --> pdb=" O ILE T2537 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU T2547 " --> pdb=" O ASP T2543 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE T2548 " --> pdb=" O SER T2544 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE T2549 " --> pdb=" O LEU T2545 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR T2550 " --> pdb=" O ILE T2546 " (cutoff:3.500A) Processing helix chain 'T' and resid 2553 through 2568 removed outlier: 3.681A pdb=" N HIS T2557 " --> pdb=" O PRO T2553 " (cutoff:3.500A) Proline residue: T2565 - end of helix Processing helix chain 'T' and resid 2569 through 2571 No H-bonds generated for 'chain 'T' and resid 2569 through 2571' Processing helix chain 'T' and resid 2575 through 2588 Processing helix chain 'T' and resid 2589 through 2596 removed outlier: 3.798A pdb=" N HIS T2592 " --> pdb=" O LYS T2589 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR T2593 " --> pdb=" O PRO T2590 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG T2594 " --> pdb=" O TYR T2591 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE T2596 " --> pdb=" O THR T2593 " (cutoff:3.500A) Processing helix chain 'T' and resid 2601 through 2611 removed outlier: 3.834A pdb=" N SER T2609 " --> pdb=" O MET T2605 " (cutoff:3.500A) Processing helix chain 'T' and resid 2622 through 2627 Processing helix chain 'T' and resid 2632 through 2645 removed outlier: 3.677A pdb=" N ILE T2639 " --> pdb=" O GLN T2635 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE T2643 " --> pdb=" O ILE T2639 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN T2644 " --> pdb=" O LEU T2640 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER T2645 " --> pdb=" O GLU T2641 " (cutoff:3.500A) Processing helix chain 'T' and resid 2654 through 2669 Processing helix chain 'T' and resid 2671 through 2683 Processing helix chain 'T' and resid 2685 through 2698 removed outlier: 3.851A pdb=" N ASN T2689 " --> pdb=" O TYR T2685 " (cutoff:3.500A) Processing helix chain 'T' and resid 2699 through 2716 removed outlier: 3.614A pdb=" N ALA T2714 " --> pdb=" O ALA T2710 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG T2715 " --> pdb=" O GLN T2711 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER T2716 " --> pdb=" O VAL T2712 " (cutoff:3.500A) Processing helix chain 'T' and resid 2724 through 2740 removed outlier: 3.550A pdb=" N LEU T2728 " --> pdb=" O SER T2724 " (cutoff:3.500A) Processing helix chain 'T' and resid 2742 through 2753 removed outlier: 3.507A pdb=" N LEU T2746 " --> pdb=" O HIS T2742 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU T2748 " --> pdb=" O ASP T2744 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU T2753 " --> pdb=" O LEU T2749 " (cutoff:3.500A) Processing helix chain 'T' and resid 2772 through 2784 removed outlier: 3.802A pdb=" N SER T2779 " --> pdb=" O ALA T2775 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL T2783 " --> pdb=" O SER T2779 " (cutoff:3.500A) Processing helix chain 'T' and resid 2788 through 2806 Processing helix chain 'T' and resid 2812 through 2831 removed outlier: 4.061A pdb=" N ASP T2818 " --> pdb=" O ARG T2814 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU T2831 " --> pdb=" O LYS T2827 " (cutoff:3.500A) Processing helix chain 'T' and resid 2838 through 2864 removed outlier: 3.932A pdb=" N LEU T2842 " --> pdb=" O ALA T2838 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR T2864 " --> pdb=" O ALA T2860 " (cutoff:3.500A) Processing helix chain 'T' and resid 2865 through 2868 Processing helix chain 'T' and resid 2873 through 2886 removed outlier: 3.700A pdb=" N ILE T2877 " --> pdb=" O LYS T2873 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP T2886 " --> pdb=" O GLN T2882 " (cutoff:3.500A) Processing helix chain 'T' and resid 2894 through 2916 removed outlier: 3.806A pdb=" N ILE T2912 " --> pdb=" O ALA T2908 " (cutoff:3.500A) Processing helix chain 'T' and resid 2920 through 2924 removed outlier: 3.519A pdb=" N LEU T2923 " --> pdb=" O ILE T2920 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN T2924 " --> pdb=" O PRO T2921 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 2920 through 2924' Processing helix chain 'T' and resid 2942 through 2957 removed outlier: 3.790A pdb=" N VAL T2946 " --> pdb=" O GLU T2942 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE T2950 " --> pdb=" O VAL T2946 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG T2955 " --> pdb=" O ALA T2951 " (cutoff:3.500A) Processing helix chain 'T' and resid 2959 through 2966 Processing helix chain 'T' and resid 2979 through 2992 removed outlier: 3.835A pdb=" N HIS T2992 " --> pdb=" O GLN T2988 " (cutoff:3.500A) Processing helix chain 'T' and resid 2998 through 3007 removed outlier: 4.052A pdb=" N VAL T3005 " --> pdb=" O THR T3001 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE T3006 " --> pdb=" O GLY T3002 " (cutoff:3.500A) Processing helix chain 'T' and resid 3017 through 3033 removed outlier: 3.935A pdb=" N LEU T3033 " --> pdb=" O PHE T3029 " (cutoff:3.500A) Processing helix chain 'T' and resid 3036 through 3048 removed outlier: 4.003A pdb=" N ASN T3040 " --> pdb=" O TYR T3036 " (cutoff:3.500A) Processing helix chain 'T' and resid 3053 through 3069 removed outlier: 3.791A pdb=" N TRP T3057 " --> pdb=" O LEU T3053 " (cutoff:3.500A) Processing helix chain 'T' and resid 3077 through 3091 removed outlier: 3.736A pdb=" N ALA T3081 " --> pdb=" O PHE T3077 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU T3091 " --> pdb=" O GLN T3087 " (cutoff:3.500A) Processing helix chain 'T' and resid 3097 through 3109 removed outlier: 3.973A pdb=" N SER T3109 " --> pdb=" O LEU T3105 " (cutoff:3.500A) Processing helix chain 'T' and resid 3115 through 3123 removed outlier: 3.614A pdb=" N ASN T3119 " --> pdb=" O GLY T3115 " (cutoff:3.500A) Processing helix chain 'T' and resid 3130 through 3135 removed outlier: 3.973A pdb=" N THR T3135 " --> pdb=" O TYR T3132 " (cutoff:3.500A) Processing helix chain 'T' and resid 3136 through 3142 Processing helix chain 'T' and resid 3151 through 3163 removed outlier: 3.942A pdb=" N ILE T3155 " --> pdb=" O MET T3151 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER T3162 " --> pdb=" O ARG T3158 " (cutoff:3.500A) Processing helix chain 'T' and resid 3163 through 3180 removed outlier: 4.247A pdb=" N LEU T3167 " --> pdb=" O TYR T3163 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N HIS T3168 " --> pdb=" O PRO T3164 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N PHE T3169 " --> pdb=" O GLN T3165 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N GLN T3170 " --> pdb=" O ALA T3166 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL T3180 " --> pdb=" O GLU T3176 " (cutoff:3.500A) Processing helix chain 'T' and resid 3203 through 3218 Processing helix chain 'T' and resid 3219 through 3237 removed outlier: 3.512A pdb=" N ALA T3223 " --> pdb=" O TYR T3219 " (cutoff:3.500A) Processing helix chain 'T' and resid 3240 through 3260 Processing helix chain 'T' and resid 3273 through 3286 removed outlier: 3.523A pdb=" N GLU T3277 " --> pdb=" O PRO T3273 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR T3285 " --> pdb=" O VAL T3281 " (cutoff:3.500A) Processing helix chain 'T' and resid 3292 through 3297 Processing helix chain 'T' and resid 3298 through 3300 No H-bonds generated for 'chain 'T' and resid 3298 through 3300' Processing helix chain 'T' and resid 3308 through 3327 Processing helix chain 'T' and resid 3333 through 3338 Processing helix chain 'T' and resid 3338 through 3343 removed outlier: 3.612A pdb=" N SER T3342 " --> pdb=" O CYS T3338 " (cutoff:3.500A) Processing helix chain 'T' and resid 3343 through 3348 removed outlier: 3.800A pdb=" N GLN T3347 " --> pdb=" O ASN T3343 " (cutoff:3.500A) Processing helix chain 'T' and resid 3412 through 3426 removed outlier: 3.511A pdb=" N GLU T3416 " --> pdb=" O HIS T3412 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE T3426 " --> pdb=" O LEU T3422 " (cutoff:3.500A) Processing helix chain 'T' and resid 3428 through 3433 removed outlier: 3.538A pdb=" N LYS T3432 " --> pdb=" O LYS T3428 " (cutoff:3.500A) Processing helix chain 'T' and resid 3433 through 3439 removed outlier: 3.634A pdb=" N ARG T3439 " --> pdb=" O GLU T3435 " (cutoff:3.500A) Processing helix chain 'T' and resid 3467 through 3478 removed outlier: 3.521A pdb=" N LYS T3478 " --> pdb=" O PHE T3474 " (cutoff:3.500A) Processing helix chain 'T' and resid 3482 through 3495 removed outlier: 4.113A pdb=" N GLN T3486 " --> pdb=" O PRO T3482 " (cutoff:3.500A) Processing helix chain 'T' and resid 3505 through 3521 removed outlier: 3.954A pdb=" N LEU T3509 " --> pdb=" O ASP T3505 " (cutoff:3.500A) Processing helix chain 'T' and resid 3525 through 3535 removed outlier: 3.685A pdb=" N PHE T3535 " --> pdb=" O PHE T3531 " (cutoff:3.500A) Processing helix chain 'T' and resid 3537 through 3561 removed outlier: 3.846A pdb=" N SER T3550 " --> pdb=" O LYS T3546 " (cutoff:3.500A) Processing helix chain 'T' and resid 3562 through 3564 No H-bonds generated for 'chain 'T' and resid 3562 through 3564' Processing helix chain 'T' and resid 3625 through 3633 Processing helix chain 'T' and resid 3634 through 3640 Processing helix chain 'T' and resid 3640 through 3654 removed outlier: 3.880A pdb=" N SER T3649 " --> pdb=" O LEU T3645 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE T3653 " --> pdb=" O SER T3649 " (cutoff:3.500A) Processing helix chain 'T' and resid 3658 through 3678 removed outlier: 4.269A pdb=" N LEU T3665 " --> pdb=" O THR T3661 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU T3670 " --> pdb=" O PHE T3666 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU T3678 " --> pdb=" O TRP T3674 " (cutoff:3.500A) Processing helix chain 'T' and resid 3685 through 3707 removed outlier: 3.680A pdb=" N ARG T3689 " --> pdb=" O ASN T3685 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU T3706 " --> pdb=" O LYS T3702 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY T3707 " --> pdb=" O VAL T3703 " (cutoff:3.500A) Processing helix chain 'T' and resid 3718 through 3727 Processing helix chain 'T' and resid 3729 through 3734 Processing helix chain 'U' and resid 17 through 29 removed outlier: 3.656A pdb=" N ALA U 21 " --> pdb=" O ALA U 17 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA U 29 " --> pdb=" O ALA U 25 " (cutoff:3.500A) Processing helix chain 'U' and resid 107 through 113 Processing helix chain 'U' and resid 125 through 137 removed outlier: 3.760A pdb=" N ALA U 137 " --> pdb=" O ALA U 133 " (cutoff:3.500A) Processing helix chain 'U' and resid 141 through 152 removed outlier: 3.851A pdb=" N ALA U 145 " --> pdb=" O ALA U 141 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 172 through 173 removed outlier: 3.816A pdb=" N LEU B 211 " --> pdb=" O LEU B 285 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 349 through 350 removed outlier: 3.691A pdb=" N HIS B 349 " --> pdb=" O SER B 356 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 242 through 245 removed outlier: 6.428A pdb=" N TYR D 242 " --> pdb=" O ASP D 278 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ASN D 280 " --> pdb=" O TYR D 242 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE D 244 " --> pdb=" O ASN D 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 781 through 784 removed outlier: 5.937A pdb=" N SER D 456 " --> pdb=" O ALA D 790 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA D 792 " --> pdb=" O SER D 456 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N CYS D 458 " --> pdb=" O ALA D 792 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N GLY D 794 " --> pdb=" O CYS D 458 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N TYR D 460 " --> pdb=" O GLY D 794 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 469 through 474 removed outlier: 4.835A pdb=" N GLY D 484 " --> pdb=" O SER D 470 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU D 472 " --> pdb=" O ALA D 482 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA D 482 " --> pdb=" O LEU D 472 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N PHE D 474 " --> pdb=" O ILE D 480 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ILE D 480 " --> pdb=" O PHE D 474 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 528 through 533 removed outlier: 6.455A pdb=" N VAL D 549 " --> pdb=" O SER D 562 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N SER D 562 " --> pdb=" O VAL D 549 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU D 551 " --> pdb=" O LEU D 560 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 570 through 574 removed outlier: 6.450A pdb=" N ALA D 585 " --> pdb=" O TRP D 571 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL D 573 " --> pdb=" O ALA D 583 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ALA D 583 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER D 586 " --> pdb=" O THR D 590 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N THR D 590 " --> pdb=" O SER D 586 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N SER D 595 " --> pdb=" O PRO D 601 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 612 through 617 removed outlier: 3.832A pdb=" N THR D 632 " --> pdb=" O SER D 628 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N CYS D 633 " --> pdb=" O LEU D 646 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU D 646 " --> pdb=" O CYS D 633 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N MET D 635 " --> pdb=" O VAL D 644 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 654 through 659 removed outlier: 3.626A pdb=" N LYS D 687 " --> pdb=" O VAL D 677 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASP D 679 " --> pdb=" O ARG D 685 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ARG D 685 " --> pdb=" O ASP D 679 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 701 through 702 removed outlier: 3.925A pdb=" N ALA D 770 " --> pdb=" O VAL D 720 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ASP D 722 " --> pdb=" O LEU D 768 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N LEU D 768 " --> pdb=" O ASP D 722 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 100 through 101 Processing sheet with id=AB3, first strand: chain 'E' and resid 115 through 116 Processing sheet with id=AB4, first strand: chain 'H' and resid 335 through 337 removed outlier: 6.561A pdb=" N TYR H 335 " --> pdb=" O VAL I 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'T' and resid 977 through 980 Processing sheet with id=AB6, first strand: chain 'T' and resid 3331 through 3332 Processing sheet with id=AB7, first strand: chain 'T' and resid 3331 through 3332 removed outlier: 4.143A pdb=" N ARG T3389 " --> pdb=" O VAL T3405 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'T' and resid 3464 through 3466 2301 hydrogen bonds defined for protein. 6798 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: 25.46 Time building geometry restraints manager: 21.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 12669 1.33 - 1.46: 10815 1.46 - 1.58: 26013 1.58 - 1.70: 2 1.70 - 1.83: 322 Bond restraints: 49821 Sorted by residual: bond pdb=" C ARG T 288 " pdb=" N PRO T 289 " ideal model delta sigma weight residual 1.334 1.406 -0.072 2.34e-02 1.83e+03 9.39e+00 bond pdb=" C PRO E 162 " pdb=" N PRO E 163 " ideal model delta sigma weight residual 1.334 1.359 -0.025 8.40e-03 1.42e+04 9.17e+00 bond pdb=" C ASN D 123 " pdb=" N PRO D 124 " ideal model delta sigma weight residual 1.326 1.362 -0.036 1.44e-02 4.82e+03 6.32e+00 bond pdb=" CA VAL T 62 " pdb=" CB VAL T 62 " ideal model delta sigma weight residual 1.537 1.568 -0.031 1.29e-02 6.01e+03 5.63e+00 bond pdb=" C GLU T3654 " pdb=" N PRO T3655 " ideal model delta sigma weight residual 1.334 1.388 -0.054 2.34e-02 1.83e+03 5.27e+00 ... (remaining 49816 not shown) Histogram of bond angle deviations from ideal: 98.21 - 105.79: 1049 105.79 - 113.37: 27469 113.37 - 120.96: 25171 120.96 - 128.54: 13385 128.54 - 136.12: 400 Bond angle restraints: 67474 Sorted by residual: angle pdb=" N VAL T 871 " pdb=" CA VAL T 871 " pdb=" C VAL T 871 " ideal model delta sigma weight residual 108.36 99.34 9.02 1.43e+00 4.89e-01 3.98e+01 angle pdb=" CA VAL T 62 " pdb=" CB VAL T 62 " pdb=" CG1 VAL T 62 " ideal model delta sigma weight residual 110.40 120.34 -9.94 1.70e+00 3.46e-01 3.42e+01 angle pdb=" C ASN H 239 " pdb=" N ASN H 240 " pdb=" CA ASN H 240 " ideal model delta sigma weight residual 122.61 131.70 -9.09 1.56e+00 4.11e-01 3.39e+01 angle pdb=" CA LYS D 775 " pdb=" CB LYS D 775 " pdb=" CG LYS D 775 " ideal model delta sigma weight residual 114.10 125.12 -11.02 2.00e+00 2.50e-01 3.04e+01 angle pdb=" C ASP D 476 " pdb=" N ASP D 477 " pdb=" CA ASP D 477 " ideal model delta sigma weight residual 125.66 135.21 -9.55 1.85e+00 2.92e-01 2.66e+01 ... (remaining 67469 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 26837 17.98 - 35.96: 2874 35.96 - 53.95: 479 53.95 - 71.93: 118 71.93 - 89.91: 41 Dihedral angle restraints: 30349 sinusoidal: 12401 harmonic: 17948 Sorted by residual: dihedral pdb=" CA ASP D 476 " pdb=" C ASP D 476 " pdb=" N ASP D 477 " pdb=" CA ASP D 477 " ideal model delta harmonic sigma weight residual 180.00 -148.34 -31.66 0 5.00e+00 4.00e-02 4.01e+01 dihedral pdb=" CA HIS T2621 " pdb=" C HIS T2621 " pdb=" N LEU T2622 " pdb=" CA LEU T2622 " ideal model delta harmonic sigma weight residual 180.00 150.36 29.64 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA THR T2756 " pdb=" C THR T2756 " pdb=" N ASP T2757 " pdb=" CA ASP T2757 " ideal model delta harmonic sigma weight residual 180.00 151.01 28.99 0 5.00e+00 4.00e-02 3.36e+01 ... (remaining 30346 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 7291 0.116 - 0.233: 392 0.233 - 0.349: 22 0.349 - 0.465: 1 0.465 - 0.582: 3 Chirality restraints: 7709 Sorted by residual: chirality pdb=" CB ILE T2628 " pdb=" CA ILE T2628 " pdb=" CG1 ILE T2628 " pdb=" CG2 ILE T2628 " both_signs ideal model delta sigma weight residual False 2.64 2.06 0.58 2.00e-01 2.50e+01 8.46e+00 chirality pdb=" CB ILE T1848 " pdb=" CA ILE T1848 " pdb=" CG1 ILE T1848 " pdb=" CG2 ILE T1848 " both_signs ideal model delta sigma weight residual False 2.64 2.12 0.53 2.00e-01 2.50e+01 6.89e+00 chirality pdb=" CG LEU T1021 " pdb=" CB LEU T1021 " pdb=" CD1 LEU T1021 " pdb=" CD2 LEU T1021 " both_signs ideal model delta sigma weight residual False -2.59 -2.08 -0.51 2.00e-01 2.50e+01 6.39e+00 ... (remaining 7706 not shown) Planarity restraints: 8589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR T1348 " 0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C THR T1348 " -0.063 2.00e-02 2.50e+03 pdb=" O THR T1348 " 0.023 2.00e-02 2.50e+03 pdb=" N MET T1349 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO T2619 " -0.057 5.00e-02 4.00e+02 8.68e-02 1.21e+01 pdb=" N PRO T2620 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO T2620 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO T2620 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE T2755 " -0.011 2.00e-02 2.50e+03 2.58e-02 1.16e+01 pdb=" CG PHE T2755 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE T2755 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 PHE T2755 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE T2755 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 PHE T2755 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE T2755 " -0.002 2.00e-02 2.50e+03 ... (remaining 8586 not shown) Histogram of nonbonded interaction distances: 1.05 - 1.82: 2 1.82 - 2.59: 481 2.59 - 3.36: 62131 3.36 - 4.13: 115182 4.13 - 4.90: 215906 Nonbonded interactions: 393702 Sorted by model distance: nonbonded pdb=" NH1 ARG I 418 " pdb=" OE2 GLU I 422 " model vdw 1.047 2.520 nonbonded pdb=" CB ARG T 850 " pdb=" OE1 GLU T 854 " model vdw 1.805 3.440 nonbonded pdb=" CZ ARG I 418 " pdb=" OE2 GLU I 422 " model vdw 1.913 3.270 nonbonded pdb=" CD ARG I 418 " pdb=" NH2 ARG I 421 " model vdw 1.978 3.520 nonbonded pdb=" CG ARG I 418 " pdb=" NE ARG I 421 " model vdw 1.999 3.520 ... (remaining 393697 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 191 5.16 5 C 31299 2.51 5 N 8265 2.21 5 O 9066 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.200 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: 0.060 Extract box with map and model: 16.990 Check model and map are aligned: 0.720 Convert atoms to be neutral: 0.420 Process input model: 131.960 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 156.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 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 : 0.007 0.095 49821 Z= 0.431 Angle : 1.003 14.273 67474 Z= 0.537 Chirality : 0.060 0.582 7709 Planarity : 0.008 0.087 8589 Dihedral : 15.348 89.908 18625 Min Nonbonded Distance : 1.047 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.45 % Favored : 92.48 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.38 (0.08), residues: 5959 helix: -2.60 (0.06), residues: 3381 sheet: -1.38 (0.31), residues: 240 loop : -3.39 (0.11), residues: 2338 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11918 Ramachandran restraints generated. 5959 Oldfield, 0 Emsley, 5959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11918 Ramachandran restraints generated. 5959 Oldfield, 0 Emsley, 5959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 5449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 759 time to evaluate : 6.089 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 outliers start: 53 outliers final: 12 residues processed: 806 average time/residue: 0.6593 time to fit residues: 866.0984 Evaluate side-chains 498 residues out of total 5449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 486 time to evaluate : 6.012 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.4619 time to fit residues: 18.5340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 506 optimal weight: 0.8980 chunk 454 optimal weight: 5.9990 chunk 252 optimal weight: 7.9990 chunk 155 optimal weight: 0.2980 chunk 306 optimal weight: 3.9990 chunk 242 optimal weight: 0.0570 chunk 470 optimal weight: 0.6980 chunk 181 optimal weight: 8.9990 chunk 285 optimal weight: 0.8980 chunk 350 optimal weight: 6.9990 chunk 544 optimal weight: 2.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN B 336 HIS C 227 HIS D 274 ASN D 275 GLN ** D 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 486 GLN D 504 ASN ** D 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 568 HIS D 618 HIS ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 GLN G 118 GLN G 155 GLN G 173 ASN H 240 ASN H 303 GLN H 307 ASN H 352 GLN H 371 ASN H 373 ASN I 412 GLN I 456 ASN I 472 ASN ** I 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 505 ASN ** K 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 914 GLN K1050 ASN T 6 GLN T 77 ASN ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 114 ASN ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 150 ASN T 153 ASN T 400 HIS T 441 ASN T 473 ASN T 565 ASN T 794 ASN T 843 ASN T 853 HIS T 938 ASN T1105 ASN ** T1109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T1234 GLN T1298 ASN T1479 GLN T1560 HIS T1587 GLN T1619 GLN T1626 ASN T1629 GLN T1654 ASN T1659 GLN T1856 HIS T1857 HIS T1892 ASN T1903 GLN T1958 ASN T1968 ASN T2266 ASN T2289 HIS T2354 ASN T2441 ASN T2521 ASN T2557 HIS ** T2601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T2668 ASN T2770 ASN T2802 ASN T2822 GLN T2844 HIS T2863 HIS T2906 GLN T2910 GLN T2992 HIS T3040 ASN T3041 GLN T3064 ASN T3154 HIS T3259 ASN T3261 ASN T3340 HIS T3357 GLN T3433 ASN T3442 GLN ** T3472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T3486 GLN T3497 HIS T3537 GLN T3570 HIS ** T3657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 85 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 49821 Z= 0.182 Angle : 0.659 15.367 67474 Z= 0.334 Chirality : 0.042 0.251 7709 Planarity : 0.005 0.143 8589 Dihedral : 5.610 48.885 6523 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.29 % Favored : 93.66 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.10), residues: 5959 helix: -0.82 (0.08), residues: 3410 sheet: -0.94 (0.33), residues: 234 loop : -3.08 (0.11), residues: 2315 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11918 Ramachandran restraints generated. 5959 Oldfield, 0 Emsley, 5959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11918 Ramachandran restraints generated. 5959 Oldfield, 0 Emsley, 5959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 5449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 531 time to evaluate : 5.730 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 outliers start: 95 outliers final: 44 residues processed: 596 average time/residue: 0.6271 time to fit residues: 628.9849 Evaluate side-chains 495 residues out of total 5449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 451 time to evaluate : 5.801 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.4901 time to fit residues: 48.1568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 302 optimal weight: 0.6980 chunk 169 optimal weight: 2.9990 chunk 453 optimal weight: 0.0980 chunk 371 optimal weight: 9.9990 chunk 150 optimal weight: 2.9990 chunk 545 optimal weight: 0.6980 chunk 589 optimal weight: 3.9990 chunk 486 optimal weight: 2.9990 chunk 541 optimal weight: 0.3980 chunk 186 optimal weight: 9.9990 chunk 437 optimal weight: 9.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 ASN ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 ASN D 276 HIS ** D 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 502 ASN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 219 ASN H 371 ASN I 381 ASN ** I 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 163 GLN Q 413 HIS ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T1234 GLN T1287 ASN T1298 ASN T1560 HIS T1719 ASN ** T2010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T3154 HIS T3261 ASN ** T3472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T3497 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.087 49821 Z= 0.196 Angle : 0.624 14.240 67474 Z= 0.315 Chirality : 0.042 0.231 7709 Planarity : 0.004 0.060 8589 Dihedral : 5.143 44.429 6523 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.78 % Favored : 93.20 % Rotamer Outliers : 1.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.54 (0.11), residues: 5959 helix: 0.07 (0.09), residues: 3416 sheet: -0.77 (0.35), residues: 220 loop : -2.77 (0.12), residues: 2323 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11918 Ramachandran restraints generated. 5959 Oldfield, 0 Emsley, 5959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11918 Ramachandran restraints generated. 5959 Oldfield, 0 Emsley, 5959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 5449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 505 time to evaluate : 6.460 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 outliers start: 102 outliers final: 56 residues processed: 575 average time/residue: 0.6075 time to fit residues: 590.9987 Evaluate side-chains 504 residues out of total 5449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 448 time to evaluate : 5.844 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 0.4812 time to fit residues: 58.5522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 539 optimal weight: 0.4980 chunk 410 optimal weight: 8.9990 chunk 283 optimal weight: 20.0000 chunk 60 optimal weight: 0.9980 chunk 260 optimal weight: 1.9990 chunk 366 optimal weight: 20.0000 chunk 547 optimal weight: 3.9990 chunk 579 optimal weight: 4.9990 chunk 286 optimal weight: 4.9990 chunk 519 optimal weight: 50.0000 chunk 156 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 312 GLN ** D 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 270 GLN G 142 ASN H 371 ASN ** I 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 163 GLN ** K 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 379 ASN ** T 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T1298 ASN T1546 GLN T1560 HIS T1654 ASN T1779 GLN ** T2010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T2531 GLN ** T2621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T2913 ASN ** T3468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.100 49821 Z= 0.334 Angle : 0.676 13.193 67474 Z= 0.343 Chirality : 0.045 0.236 7709 Planarity : 0.004 0.066 8589 Dihedral : 5.165 41.780 6523 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.85 % Favored : 92.11 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.18 (0.11), residues: 5959 helix: 0.43 (0.09), residues: 3397 sheet: -0.87 (0.34), residues: 220 loop : -2.66 (0.12), residues: 2342 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11918 Ramachandran restraints generated. 5959 Oldfield, 0 Emsley, 5959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11918 Ramachandran restraints generated. 5959 Oldfield, 0 Emsley, 5959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 5449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 470 time to evaluate : 7.896 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 outliers start: 94 outliers final: 51 residues processed: 531 average time/residue: 0.6530 time to fit residues: 581.1944 Evaluate side-chains 477 residues out of total 5449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 426 time to evaluate : 5.771 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.4978 time to fit residues: 54.8090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 483 optimal weight: 0.5980 chunk 329 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 431 optimal weight: 9.9990 chunk 239 optimal weight: 6.9990 chunk 494 optimal weight: 0.6980 chunk 400 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 296 optimal weight: 0.8980 chunk 520 optimal weight: 50.0000 chunk 146 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 312 GLN D 451 GLN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 914 GLN K1036 ASN T 93 GLN T 134 GLN ** T1109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T1298 ASN ** T2010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T2638 ASN T2907 HIS ** T3261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.108 49821 Z= 0.173 Angle : 0.611 13.286 67474 Z= 0.304 Chirality : 0.042 0.213 7709 Planarity : 0.004 0.054 8589 Dihedral : 4.904 37.725 6523 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.58 % Favored : 93.40 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.83 (0.11), residues: 5959 helix: 0.73 (0.09), residues: 3393 sheet: -0.77 (0.35), residues: 208 loop : -2.52 (0.12), residues: 2358 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11918 Ramachandran restraints generated. 5959 Oldfield, 0 Emsley, 5959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11918 Ramachandran restraints generated. 5959 Oldfield, 0 Emsley, 5959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 5449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 476 time to evaluate : 6.289 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 outliers start: 62 outliers final: 23 residues processed: 520 average time/residue: 0.6276 time to fit residues: 553.2959 Evaluate side-chains 461 residues out of total 5449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 438 time to evaluate : 6.533 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.5114 time to fit residues: 30.3060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 195 optimal weight: 0.8980 chunk 522 optimal weight: 4.9990 chunk 114 optimal weight: 0.0270 chunk 340 optimal weight: 6.9990 chunk 143 optimal weight: 0.8980 chunk 580 optimal weight: 1.9990 chunk 481 optimal weight: 1.9990 chunk 268 optimal weight: 1.9990 chunk 48 optimal weight: 0.0000 chunk 192 optimal weight: 3.9990 chunk 304 optimal weight: 3.9990 overall best weight: 0.7644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 312 GLN C 152 HIS ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 ASN G 142 ASN ** H 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 400 HIS ** K 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 639 HIS T 789 ASN ** T1109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T1298 ASN T1560 HIS ** T2010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T3041 GLN ** T3261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T3497 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.102 49821 Z= 0.175 Angle : 0.613 12.271 67474 Z= 0.305 Chirality : 0.042 0.247 7709 Planarity : 0.004 0.050 8589 Dihedral : 4.754 35.737 6523 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.70 % Favored : 93.29 % Rotamer Outliers : 1.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.60 (0.11), residues: 5959 helix: 0.92 (0.09), residues: 3404 sheet: -0.59 (0.36), residues: 199 loop : -2.45 (0.12), residues: 2356 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11918 Ramachandran restraints generated. 5959 Oldfield, 0 Emsley, 5959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11918 Ramachandran restraints generated. 5959 Oldfield, 0 Emsley, 5959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 5449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 466 time to evaluate : 5.912 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 outliers start: 65 outliers final: 21 residues processed: 510 average time/residue: 0.6523 time to fit residues: 561.4054 Evaluate side-chains 462 residues out of total 5449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 441 time to evaluate : 5.943 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.4655 time to fit residues: 26.6238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 559 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 330 optimal weight: 0.9990 chunk 423 optimal weight: 8.9990 chunk 328 optimal weight: 1.9990 chunk 488 optimal weight: 0.5980 chunk 324 optimal weight: 0.0470 chunk 578 optimal weight: 5.9990 chunk 361 optimal weight: 5.9990 chunk 352 optimal weight: 0.9980 chunk 266 optimal weight: 4.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 312 GLN D 608 HIS ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 ASN G 142 ASN ** H 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 692 GLN T1298 ASN T1560 HIS ** T2010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.105 49821 Z= 0.170 Angle : 0.618 17.398 67474 Z= 0.305 Chirality : 0.042 0.206 7709 Planarity : 0.004 0.051 8589 Dihedral : 4.656 35.004 6523 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.63 % Favored : 93.35 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.11), residues: 5959 helix: 1.04 (0.09), residues: 3409 sheet: -0.55 (0.36), residues: 198 loop : -2.40 (0.12), residues: 2352 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11918 Ramachandran restraints generated. 5959 Oldfield, 0 Emsley, 5959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11918 Ramachandran restraints generated. 5959 Oldfield, 0 Emsley, 5959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 5449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 472 time to evaluate : 5.960 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 outliers start: 41 outliers final: 20 residues processed: 498 average time/residue: 0.6487 time to fit residues: 544.8921 Evaluate side-chains 458 residues out of total 5449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 438 time to evaluate : 6.123 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.5276 time to fit residues: 27.2151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 357 optimal weight: 0.2980 chunk 230 optimal weight: 6.9990 chunk 345 optimal weight: 0.6980 chunk 174 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 367 optimal weight: 10.0000 chunk 393 optimal weight: 0.9980 chunk 285 optimal weight: 20.0000 chunk 53 optimal weight: 0.7980 chunk 454 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 312 GLN ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 ASN ** H 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 373 ASN ** K 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1298 ASN T1407 GLN T1560 HIS ** T1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.112 49821 Z= 0.208 Angle : 0.633 14.745 67474 Z= 0.312 Chirality : 0.043 0.259 7709 Planarity : 0.004 0.053 8589 Dihedral : 4.637 33.958 6523 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.91 % Favored : 93.07 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.41 (0.11), residues: 5959 helix: 1.08 (0.09), residues: 3406 sheet: -0.49 (0.37), residues: 198 loop : -2.38 (0.12), residues: 2355 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11918 Ramachandran restraints generated. 5959 Oldfield, 0 Emsley, 5959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11918 Ramachandran restraints generated. 5959 Oldfield, 0 Emsley, 5959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 5449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 446 time to evaluate : 6.587 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 outliers start: 32 outliers final: 19 residues processed: 466 average time/residue: 0.6436 time to fit residues: 511.2134 Evaluate side-chains 457 residues out of total 5449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 438 time to evaluate : 5.634 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.4856 time to fit residues: 25.4016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 526 optimal weight: 10.0000 chunk 554 optimal weight: 3.9990 chunk 505 optimal weight: 0.5980 chunk 538 optimal weight: 5.9990 chunk 553 optimal weight: 0.8980 chunk 324 optimal weight: 0.0470 chunk 234 optimal weight: 0.5980 chunk 423 optimal weight: 0.3980 chunk 165 optimal weight: 0.9980 chunk 486 optimal weight: 0.6980 chunk 509 optimal weight: 1.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 312 GLN ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 ASN ** H 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 917 HIS K1036 ASN Q 413 HIS ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 840 GLN T 888 GLN ** T1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T3275 ASN ** T3486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 49821 Z= 0.154 Angle : 0.625 13.917 67474 Z= 0.306 Chirality : 0.041 0.234 7709 Planarity : 0.004 0.055 8589 Dihedral : 4.549 33.800 6523 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.33 % Favored : 93.66 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.29 (0.11), residues: 5959 helix: 1.19 (0.09), residues: 3398 sheet: -0.59 (0.36), residues: 203 loop : -2.33 (0.12), residues: 2358 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11918 Ramachandran restraints generated. 5959 Oldfield, 0 Emsley, 5959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11918 Ramachandran restraints generated. 5959 Oldfield, 0 Emsley, 5959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 5449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 471 time to evaluate : 5.802 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 outliers start: 19 outliers final: 9 residues processed: 484 average time/residue: 0.6455 time to fit residues: 535.2149 Evaluate side-chains 456 residues out of total 5449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 447 time to evaluate : 5.675 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.4506 time to fit residues: 15.4389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 537 optimal weight: 7.9990 chunk 353 optimal weight: 0.8980 chunk 569 optimal weight: 2.9990 chunk 347 optimal weight: 0.8980 chunk 270 optimal weight: 7.9990 chunk 396 optimal weight: 0.0770 chunk 597 optimal weight: 20.0000 chunk 550 optimal weight: 3.9990 chunk 475 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 367 optimal weight: 30.0000 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 888 GLN ** T1109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T1560 HIS ** T1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T2203 GLN ** T2266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 49821 Z= 0.209 Angle : 0.649 13.618 67474 Z= 0.319 Chirality : 0.043 0.242 7709 Planarity : 0.004 0.059 8589 Dihedral : 4.575 32.848 6523 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.93 % Favored : 93.04 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.29 (0.11), residues: 5959 helix: 1.17 (0.09), residues: 3408 sheet: -0.51 (0.37), residues: 198 loop : -2.31 (0.12), residues: 2353 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11918 Ramachandran restraints generated. 5959 Oldfield, 0 Emsley, 5959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11918 Ramachandran restraints generated. 5959 Oldfield, 0 Emsley, 5959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 5449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 442 time to evaluate : 5.954 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 outliers start: 13 outliers final: 6 residues processed: 448 average time/residue: 0.6446 time to fit residues: 494.1562 Evaluate side-chains 442 residues out of total 5449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 436 time to evaluate : 5.942 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.5349 time to fit residues: 14.4055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 291 optimal weight: 5.9990 chunk 378 optimal weight: 0.0000 chunk 507 optimal weight: 7.9990 chunk 145 optimal weight: 0.5980 chunk 438 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 476 optimal weight: 0.6980 chunk 199 optimal weight: 1.9990 chunk 489 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 134 GLN T 888 GLN ** T1109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.124199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.094245 restraints weight = 115816.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.092278 restraints weight = 107881.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.093427 restraints weight = 118285.053| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.085 49821 Z= 0.183 Angle : 0.641 13.356 67474 Z= 0.313 Chirality : 0.042 0.359 7709 Planarity : 0.004 0.057 8589 Dihedral : 4.534 32.970 6523 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.61 % Favored : 93.37 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.11), residues: 5959 helix: 1.22 (0.09), residues: 3410 sheet: -0.49 (0.37), residues: 198 loop : -2.29 (0.12), residues: 2351 =============================================================================== Job complete usr+sys time: 10680.56 seconds wall clock time: 193 minutes 48.21 seconds (11628.21 seconds total)