Starting phenix.real_space_refine on Sun Mar 17 13:38:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5l4k_4002/03_2024/5l4k_4002.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5l4k_4002/03_2024/5l4k_4002.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/5l4k_4002/03_2024/5l4k_4002.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5l4k_4002/03_2024/5l4k_4002.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5l4k_4002/03_2024/5l4k_4002.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5l4k_4002/03_2024/5l4k_4002.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 220 5.16 5 C 25123 2.51 5 N 6779 2.21 5 O 7537 1.98 5 H 39990 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "W GLU 14": "OE1" <-> "OE2" Residue "W TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W ASP 57": "OD1" <-> "OD2" Residue "W ASP 67": "OD1" <-> "OD2" Residue "W ASP 139": "OD1" <-> "OD2" Residue "W PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W GLU 146": "OE1" <-> "OE2" Residue "W PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W ASP 181": "OD1" <-> "OD2" Residue "V ASP 21": "OD1" <-> "OD2" Residue "V ASP 26": "OD1" <-> "OD2" Residue "V GLU 52": "OE1" <-> "OE2" Residue "V ASP 71": "OD1" <-> "OD2" Residue "V PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V GLU 106": "OE1" <-> "OE2" Residue "V PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V GLU 138": "OE1" <-> "OE2" Residue "V TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V GLU 211": "OE1" <-> "OE2" Residue "V GLU 227": "OE1" <-> "OE2" Residue "V GLU 247": "OE1" <-> "OE2" Residue "V GLU 261": "OE1" <-> "OE2" Residue "V ASP 263": "OD1" <-> "OD2" Residue "V ASP 279": "OD1" <-> "OD2" Residue "V GLU 285": "OE1" <-> "OE2" Residue "V ASP 289": "OD1" <-> "OD2" Residue "V PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T GLU 149": "OE1" <-> "OE2" Residue "T ASP 160": "OD1" <-> "OD2" Residue "T GLU 165": "OE1" <-> "OE2" Residue "T TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T ASP 177": "OD1" <-> "OD2" Residue "T GLU 184": "OE1" <-> "OE2" Residue "T TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T GLU 207": "OE1" <-> "OE2" Residue "T PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T GLU 211": "OE1" <-> "OE2" Residue "T TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T GLU 254": "OE1" <-> "OE2" Residue "T PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T GLU 270": "OE1" <-> "OE2" Residue "T GLU 280": "OE1" <-> "OE2" Residue "T PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T ASP 327": "OD1" <-> "OD2" Residue "T GLU 341": "OE1" <-> "OE2" Residue "T TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y ASP 16": "OD1" <-> "OD2" Residue "Y ASP 17": "OD1" <-> "OD2" Residue "Y GLU 18": "OE1" <-> "OE2" Residue "Y GLU 20": "OE1" <-> "OE2" Residue "Y PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y GLU 25": "OE1" <-> "OE2" Residue "Y ASP 26": "OD1" <-> "OD2" Residue "Y ASP 31": "OD1" <-> "OD2" Residue "Y ASP 33": "OD1" <-> "OD2" Residue "Y ASP 35": "OD1" <-> "OD2" Residue "Y ASP 44": "OD1" <-> "OD2" Residue "Y ASP 45": "OD1" <-> "OD2" Residue "Y GLU 49": "OE1" <-> "OE2" Residue "Y ASP 51": "OD1" <-> "OD2" Residue "Y TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z GLU 3": "OE1" <-> "OE2" Residue "Z GLU 32": "OE1" <-> "OE2" Residue "Z GLU 44": "OE1" <-> "OE2" Residue "Z GLU 47": "OE1" <-> "OE2" Residue "Z GLU 65": "OE1" <-> "OE2" Residue "Z TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z ASP 124": "OD1" <-> "OD2" Residue "Z GLU 138": "OE1" <-> "OE2" Residue "Z GLU 149": "OE1" <-> "OE2" Residue "Z GLU 150": "OE1" <-> "OE2" Residue "Z TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z GLU 165": "OE1" <-> "OE2" Residue "Z GLU 169": "OE1" <-> "OE2" Residue "Z GLU 177": "OE1" <-> "OE2" Residue "Z GLU 203": "OE1" <-> "OE2" Residue "Z GLU 212": "OE1" <-> "OE2" Residue "Z ASP 220": "OD1" <-> "OD2" Residue "Z ASP 222": "OD1" <-> "OD2" Residue "Z TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z ASP 274": "OD1" <-> "OD2" Residue "Z GLU 279": "OE1" <-> "OE2" Residue "Z ASP 280": "OD1" <-> "OD2" Residue "Z PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z ASP 287": "OD1" <-> "OD2" Residue "Z PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z GLU 306": "OE1" <-> "OE2" Residue "Z GLU 309": "OE1" <-> "OE2" Residue "Z TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z ASP 316": "OD1" <-> "OD2" Residue "Z ASP 338": "OD1" <-> "OD2" Residue "Z ASP 347": "OD1" <-> "OD2" Residue "Z TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z GLU 354": "OE1" <-> "OE2" Residue "Z PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z ASP 388": "OD1" <-> "OD2" Residue "Z ASP 393": "OD1" <-> "OD2" Residue "Z ASP 394": "OD1" <-> "OD2" Residue "Z ASP 423": "OD1" <-> "OD2" Residue "Z TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z GLU 458": "OE1" <-> "OE2" Residue "Z ASP 468": "OD1" <-> "OD2" Residue "Z TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z ASP 552": "OD1" <-> "OD2" Residue "Z TYR 554": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z GLU 571": "OE1" <-> "OE2" Residue "Z PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z TYR 600": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z GLU 618": "OE1" <-> "OE2" Residue "Z ASP 621": "OD1" <-> "OD2" Residue "Z GLU 624": "OE1" <-> "OE2" Residue "Z GLU 627": "OE1" <-> "OE2" Residue "Z ASP 628": "OD1" <-> "OD2" Residue "Z ASP 638": "OD1" <-> "OD2" Residue "Z GLU 641": "OE1" <-> "OE2" Residue "Z GLU 669": "OE1" <-> "OE2" Residue "Z PHE 675": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z GLU 683": "OE1" <-> "OE2" Residue "Z ASP 716": "OD1" <-> "OD2" Residue "Z TYR 723": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z ARG 740": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Z ASP 755": "OD1" <-> "OD2" Residue "Z ASP 784": "OD1" <-> "OD2" Residue "Z ASP 805": "OD1" <-> "OD2" Residue "Z ARG 807": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Z TYR 816": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z ASP 851": "OD1" <-> "OD2" Residue "Z GLU 878": "OE1" <-> "OE2" Residue "Z GLU 881": "OE1" <-> "OE2" Residue "Z GLU 886": "OE1" <-> "OE2" Residue "Z PHE 897": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 13": "OD1" <-> "OD2" Residue "N GLU 16": "OE1" <-> "OE2" Residue "N PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 33": "OD1" <-> "OD2" Residue "N PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 51": "OD1" <-> "OD2" Residue "N PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N GLU 76": "OE1" <-> "OE2" Residue "N TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 117": "OD1" <-> "OD2" Residue "N GLU 120": "OE1" <-> "OE2" Residue "N ASP 143": "OD1" <-> "OD2" Residue "N ASP 144": "OD1" <-> "OD2" Residue "N TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 172": "OD1" <-> "OD2" Residue "N TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N GLU 209": "OE1" <-> "OE2" Residue "N ASP 212": "OD1" <-> "OD2" Residue "N PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N GLU 234": "OE1" <-> "OE2" Residue "N GLU 239": "OE1" <-> "OE2" Residue "N GLU 332": "OE1" <-> "OE2" Residue "N ASP 349": "OD1" <-> "OD2" Residue "N ASP 358": "OD1" <-> "OD2" Residue "N ASP 383": "OD1" <-> "OD2" Residue "N PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 430": "OD1" <-> "OD2" Residue "N TYR 437": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 456": "OD1" <-> "OD2" Residue "N ASP 459": "OD1" <-> "OD2" Residue "N ASP 492": "OD1" <-> "OD2" Residue "N TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 531": "OD1" <-> "OD2" Residue "N GLU 538": "OE1" <-> "OE2" Residue "N GLU 561": "OE1" <-> "OE2" Residue "N GLU 568": "OE1" <-> "OE2" Residue "N ASP 575": "OD1" <-> "OD2" Residue "N ASP 612": "OD1" <-> "OD2" Residue "N GLU 620": "OE1" <-> "OE2" Residue "N TYR 644": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N GLU 667": "OE1" <-> "OE2" Residue "N ASP 678": "OD1" <-> "OD2" Residue "N TYR 682": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N GLU 700": "OE1" <-> "OE2" Residue "N PHE 709": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 722": "OD1" <-> "OD2" Residue "N ASP 723": "OD1" <-> "OD2" Residue "N PHE 728": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 738": "OD1" <-> "OD2" Residue "N PHE 769": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 771": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N GLU 826": "OE1" <-> "OE2" Residue "N GLU 872": "OE1" <-> "OE2" Residue "N ASP 879": "OD1" <-> "OD2" Residue "N PHE 903": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 916": "OD1" <-> "OD2" Residue "N GLU 919": "OE1" <-> "OE2" Residue "N ASP 920": "OD1" <-> "OD2" Residue "N GLU 937": "OE1" <-> "OE2" Residue "N GLU 938": "OE1" <-> "OE2" Residue "N GLU 939": "OE1" <-> "OE2" Residue "S ASP 52": "OD1" <-> "OD2" Residue "S GLU 61": "OE1" <-> "OE2" Residue "S GLU 66": "OE1" <-> "OE2" Residue "S ASP 74": "OD1" <-> "OD2" Residue "S GLU 77": "OE1" <-> "OE2" Residue "S GLU 83": "OE1" <-> "OE2" Residue "S TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S ASP 129": "OD1" <-> "OD2" Residue "S PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S GLU 137": "OE1" <-> "OE2" Residue "S GLU 162": "OE1" <-> "OE2" Residue "S TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S GLU 183": "OE1" <-> "OE2" Residue "S ASP 190": "OD1" <-> "OD2" Residue "S ASP 204": "OD1" <-> "OD2" Residue "S TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S GLU 219": "OE1" <-> "OE2" Residue "S PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S ASP 222": "OD1" <-> "OD2" Residue "S ASP 225": "OD1" <-> "OD2" Residue "S ASP 245": "OD1" <-> "OD2" Residue "S TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S ASP 265": "OD1" <-> "OD2" Residue "S PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S GLU 284": "OE1" <-> "OE2" Residue "S PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S ASP 421": "OD1" <-> "OD2" Residue "S ASP 429": "OD1" <-> "OD2" Residue "S ASP 433": "OD1" <-> "OD2" Residue "S ASP 444": "OD1" <-> "OD2" Residue "S GLU 462": "OE1" <-> "OE2" Residue "S ASP 465": "OD1" <-> "OD2" Residue "S TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S ASP 485": "OD1" <-> "OD2" Residue "S GLU 515": "OE1" <-> "OE2" Residue "S PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ASP 3": "OD1" <-> "OD2" Residue "P ASP 19": "OD1" <-> "OD2" Residue "P TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P GLU 30": "OE1" <-> "OE2" Residue "P GLU 42": "OE1" <-> "OE2" Residue "P GLU 51": "OE1" <-> "OE2" Residue "P ASP 59": "OD1" <-> "OD2" Residue "P TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P GLU 85": "OE1" <-> "OE2" Residue "P GLU 113": "OE1" <-> "OE2" Residue "P ASP 117": "OD1" <-> "OD2" Residue "P ASP 126": "OD1" <-> "OD2" Residue "P GLU 154": "OE1" <-> "OE2" Residue "P ASP 158": "OD1" <-> "OD2" Residue "P GLU 181": "OE1" <-> "OE2" Residue "P PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ASP 198": "OD1" <-> "OD2" Residue "P GLU 216": "OE1" <-> "OE2" Residue "P GLU 217": "OE1" <-> "OE2" Residue "P GLU 220": "OE1" <-> "OE2" Residue "P ASP 234": "OD1" <-> "OD2" Residue "P TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P GLU 259": "OE1" <-> "OE2" Residue "P GLU 261": "OE1" <-> "OE2" Residue "P PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ASP 280": "OD1" <-> "OD2" Residue "P ASP 293": "OD1" <-> "OD2" Residue "P GLU 297": "OE1" <-> "OE2" Residue "P TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ASP 304": "OD1" <-> "OD2" Residue "P PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P GLU 345": "OE1" <-> "OE2" Residue "P ASP 353": "OD1" <-> "OD2" Residue "P GLU 360": "OE1" <-> "OE2" Residue "P TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ASP 387": "OD1" <-> "OD2" Residue "P GLU 390": "OE1" <-> "OE2" Residue "P PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 415": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q GLU 8": "OE1" <-> "OE2" Residue "Q PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q GLU 21": "OE1" <-> "OE2" Residue "Q ASP 25": "OD1" <-> "OD2" Residue "Q ASP 34": "OD1" <-> "OD2" Residue "Q GLU 47": "OE1" <-> "OE2" Residue "Q GLU 65": "OE1" <-> "OE2" Residue "Q TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q ASP 98": "OD1" <-> "OD2" Residue "Q GLU 120": "OE1" <-> "OE2" Residue "Q PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q GLU 130": "OE1" <-> "OE2" Residue "Q ASP 162": "OD1" <-> "OD2" Residue "Q GLU 168": "OE1" <-> "OE2" Residue "Q GLU 173": "OE1" <-> "OE2" Residue "Q ASP 211": "OD1" <-> "OD2" Residue "Q TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q ASP 243": "OD1" <-> "OD2" Residue "Q ASP 266": "OD1" <-> "OD2" Residue "Q GLU 285": "OE1" <-> "OE2" Residue "Q ASP 308": "OD1" <-> "OD2" Residue "Q TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q ASP 315": "OD1" <-> "OD2" Residue "Q TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q GLU 382": "OE1" <-> "OE2" Residue "Q GLU 390": "OE1" <-> "OE2" Residue "Q GLU 398": "OE1" <-> "OE2" Residue "Q TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ASP 16": "OD1" <-> "OD2" Residue "R ARG 18": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ASP 34": "OD1" <-> "OD2" Residue "R ASP 39": "OD1" <-> "OD2" Residue "R GLU 40": "OE1" <-> "OE2" Residue "R TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R GLU 55": "OE1" <-> "OE2" Residue "R ASP 62": "OD1" <-> "OD2" Residue "R ASP 68": "OD1" <-> "OD2" Residue "R ASP 79": "OD1" <-> "OD2" Residue "R ASP 85": "OD1" <-> "OD2" Residue "R GLU 86": "OE1" <-> "OE2" Residue "R GLU 87": "OE1" <-> "OE2" Residue "R GLU 89": "OE1" <-> "OE2" Residue "R ASP 90": "OD1" <-> "OD2" Residue "R GLU 92": "OE1" <-> "OE2" Residue "R GLU 99": "OE1" <-> "OE2" Residue "R ASP 102": "OD1" <-> "OD2" Residue "R GLU 109": "OE1" <-> "OE2" Residue "R ASP 116": "OD1" <-> "OD2" Residue "R PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ASP 129": "OD1" <-> "OD2" Residue "R TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ASP 153": "OD1" <-> "OD2" Residue "R ASP 175": "OD1" <-> "OD2" Residue "R TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ASP 193": "OD1" <-> "OD2" Residue "R PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R GLU 199": "OE1" <-> "OE2" Residue "R PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ASP 215": "OD1" <-> "OD2" Residue "R GLU 232": "OE1" <-> "OE2" Residue "R ASP 235": "OD1" <-> "OD2" Residue "R GLU 238": "OE1" <-> "OE2" Residue "R TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R GLU 279": "OE1" <-> "OE2" Residue "R TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R GLU 321": "OE1" <-> "OE2" Residue "R PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R GLU 333": "OE1" <-> "OE2" Residue "R GLU 368": "OE1" <-> "OE2" Residue "U PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U ASP 59": "OD1" <-> "OD2" Residue "U GLU 60": "OE1" <-> "OE2" Residue "U ASP 61": "OD1" <-> "OD2" Residue "U ASP 71": "OD1" <-> "OD2" Residue "U TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U ASP 130": "OD1" <-> "OD2" Residue "U GLU 136": "OE1" <-> "OE2" Residue "U TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U GLU 142": "OE1" <-> "OE2" Residue "U GLU 143": "OE1" <-> "OE2" Residue "U ASP 146": "OD1" <-> "OD2" Residue "U ASP 181": "OD1" <-> "OD2" Residue "U ASP 239": "OD1" <-> "OD2" Residue "U PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U ASP 255": "OD1" <-> "OD2" Residue "U ASP 284": "OD1" <-> "OD2" Residue "O ASP 3": "OD1" <-> "OD2" Residue "O PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O GLU 26": "OE1" <-> "OE2" Residue "O PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O ASP 47": "OD1" <-> "OD2" Residue "O PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O ASP 54": "OD1" <-> "OD2" Residue "O GLU 102": "OE1" <-> "OE2" Residue "O GLU 109": "OE1" <-> "OE2" Residue "O GLU 136": "OE1" <-> "OE2" Residue "O ASP 137": "OD1" <-> "OD2" Residue "O TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O ASP 175": "OD1" <-> "OD2" Residue "O PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O ASP 184": "OD1" <-> "OD2" Residue "O PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O GLU 215": "OE1" <-> "OE2" Residue "O ASP 229": "OD1" <-> "OD2" Residue "O GLU 279": "OE1" <-> "OE2" Residue "O GLU 308": "OE1" <-> "OE2" Residue "O ASP 325": "OD1" <-> "OD2" Residue "O ASP 359": "OD1" <-> "OD2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 79649 Number of models: 1 Model: "" Number of chains: 12 Chain: "W" Number of atoms: 3019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 3019 Classifications: {'peptide': 196} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 186} Chain: "V" Number of atoms: 4612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4612 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 280} Chain: "T" Number of atoms: 4435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 4435 Classifications: {'peptide': 272} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 259} Chain: "Y" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 848 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "Z" Number of atoms: 13583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 881, 13583 Classifications: {'peptide': 881} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 32, 'TRANS': 848} Chain breaks: 1 Chain: "N" Number of atoms: 13720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 876, 13720 Classifications: {'peptide': 876} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 842} Chain breaks: 2 Chain: "S" Number of atoms: 7977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 7977 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 473} Chain: "P" Number of atoms: 7525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 7525 Classifications: {'peptide': 456} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 447} Chain: "Q" Number of atoms: 6770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 6770 Classifications: {'peptide': 422} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 10, 'TRANS': 411} Chain: "R" Number of atoms: 6406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 6406 Classifications: {'peptide': 389} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 379} Chain: "U" Number of atoms: 4693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 4693 Classifications: {'peptide': 292} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 281} Chain: "O" Number of atoms: 6061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 6061 Classifications: {'peptide': 376} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 363} Time building chain proxies: 25.53, per 1000 atoms: 0.32 Number of scatterers: 79649 At special positions: 0 Unit cell: (218.7, 225.45, 232.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 220 16.00 O 7537 8.00 N 6779 7.00 C 25123 6.00 H 39990 1.00 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: 48.91 Conformation dependent library (CDL) restraints added in 6.2 seconds 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9472 Finding SS restraints... Secondary structure from input PDB file: 271 helices and 16 sheets defined 64.6% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.56 Creating SS restraints... Processing helix chain 'W' and resid 13 through 17 Processing helix chain 'W' and resid 24 through 39 removed outlier: 3.616A pdb=" N HIS W 38 " --> pdb=" O ASN W 34 " (cutoff:3.500A) Processing helix chain 'W' and resid 67 through 76 removed outlier: 3.691A pdb=" N ILE W 71 " --> pdb=" O ASP W 67 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU W 75 " --> pdb=" O ILE W 71 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N HIS W 76 " --> pdb=" O LEU W 72 " (cutoff:3.500A) Processing helix chain 'W' and resid 86 through 99 removed outlier: 3.583A pdb=" N LEU W 95 " --> pdb=" O ARG W 91 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N HIS W 99 " --> pdb=" O LEU W 95 " (cutoff:3.500A) Processing helix chain 'W' and resid 120 through 135 removed outlier: 3.535A pdb=" N LEU W 124 " --> pdb=" O ASN W 120 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS W 129 " --> pdb=" O VAL W 125 " (cutoff:3.500A) Processing helix chain 'W' and resid 151 through 158 removed outlier: 4.471A pdb=" N ALA W 155 " --> pdb=" O GLU W 151 " (cutoff:3.500A) Processing helix chain 'V' and resid 35 through 47 removed outlier: 3.979A pdb=" N LEU V 39 " --> pdb=" O SER V 35 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS V 40 " --> pdb=" O LEU V 36 " (cutoff:3.500A) Processing helix chain 'V' and resid 88 through 101 removed outlier: 3.576A pdb=" N GLN V 92 " --> pdb=" O ASP V 88 " (cutoff:3.500A) Processing helix chain 'V' and resid 123 through 137 removed outlier: 3.594A pdb=" N SER V 132 " --> pdb=" O ASN V 128 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE V 133 " --> pdb=" O THR V 129 " (cutoff:3.500A) Processing helix chain 'V' and resid 164 through 170 Processing helix chain 'V' and resid 172 through 176 removed outlier: 3.941A pdb=" N GLN V 176 " --> pdb=" O GLU V 173 " (cutoff:3.500A) Processing helix chain 'V' and resid 188 through 193 Processing helix chain 'V' and resid 210 through 218 Processing helix chain 'V' and resid 237 through 264 removed outlier: 3.550A pdb=" N ASN V 241 " --> pdb=" O HIS V 237 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER V 243 " --> pdb=" O LYS V 239 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU V 249 " --> pdb=" O VAL V 245 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN V 254 " --> pdb=" O GLU V 250 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU V 261 " --> pdb=" O LYS V 257 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASP V 263 " --> pdb=" O VAL V 259 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS V 264 " --> pdb=" O GLU V 260 " (cutoff:3.500A) Processing helix chain 'V' and resid 266 through 272 removed outlier: 3.593A pdb=" N LEU V 270 " --> pdb=" O THR V 266 " (cutoff:3.500A) Processing helix chain 'V' and resid 280 through 309 removed outlier: 4.120A pdb=" N LEU V 284 " --> pdb=" O PRO V 280 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL V 290 " --> pdb=" O GLU V 286 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA V 302 " --> pdb=" O GLN V 298 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N MET V 303 " --> pdb=" O CYS V 299 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL V 307 " --> pdb=" O MET V 303 " (cutoff:3.500A) Processing helix chain 'T' and resid 80 through 96 removed outlier: 3.702A pdb=" N ALA T 90 " --> pdb=" O ALA T 86 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N MET T 94 " --> pdb=" O ALA T 90 " (cutoff:3.500A) Processing helix chain 'T' and resid 96 through 101 Processing helix chain 'T' and resid 110 through 115 Processing helix chain 'T' and resid 119 through 124 Processing helix chain 'T' and resid 125 through 127 No H-bonds generated for 'chain 'T' and resid 125 through 127' Processing helix chain 'T' and resid 134 through 140 Processing helix chain 'T' and resid 141 through 159 removed outlier: 3.872A pdb=" N ASP T 146 " --> pdb=" O ILE T 142 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE T 147 " --> pdb=" O LEU T 143 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU T 148 " --> pdb=" O ALA T 144 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY T 151 " --> pdb=" O ILE T 147 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TRP T 154 " --> pdb=" O ILE T 150 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU T 157 " --> pdb=" O GLN T 153 " (cutoff:3.500A) Processing helix chain 'T' and resid 160 through 174 removed outlier: 3.672A pdb=" N PHE T 164 " --> pdb=" O ASP T 160 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR T 167 " --> pdb=" O SER T 163 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET T 168 " --> pdb=" O PHE T 164 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA T 169 " --> pdb=" O GLU T 165 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLN T 170 " --> pdb=" O ARG T 166 " (cutoff:3.500A) Processing helix chain 'T' and resid 176 through 181 removed outlier: 3.815A pdb=" N GLN T 181 " --> pdb=" O ASP T 177 " (cutoff:3.500A) Processing helix chain 'T' and resid 190 through 202 removed outlier: 3.642A pdb=" N LEU T 194 " --> pdb=" O GLN T 190 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU T 199 " --> pdb=" O ASN T 195 " (cutoff:3.500A) Processing helix chain 'T' and resid 204 through 213 removed outlier: 3.540A pdb=" N PHE T 208 " --> pdb=" O ARG T 204 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS T 209 " --> pdb=" O VAL T 205 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR T 210 " --> pdb=" O ALA T 206 " (cutoff:3.500A) Processing helix chain 'T' and resid 216 through 220 Processing helix chain 'T' and resid 226 through 238 removed outlier: 3.507A pdb=" N GLU T 238 " --> pdb=" O GLN T 234 " (cutoff:3.500A) Processing helix chain 'T' and resid 244 through 248 removed outlier: 3.517A pdb=" N ALA T 247 " --> pdb=" O VAL T 244 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS T 248 " --> pdb=" O PHE T 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 244 through 248' Processing helix chain 'T' and resid 253 through 260 removed outlier: 3.897A pdb=" N THR T 257 " --> pdb=" O ALA T 253 " (cutoff:3.500A) Processing helix chain 'T' and resid 263 through 279 removed outlier: 3.723A pdb=" N ARG T 268 " --> pdb=" O LEU T 264 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP T 269 " --> pdb=" O ASP T 265 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LYS T 277 " --> pdb=" O GLY T 273 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR T 279 " --> pdb=" O ILE T 275 " (cutoff:3.500A) Processing helix chain 'T' and resid 284 through 291 Processing helix chain 'T' and resid 295 through 306 removed outlier: 4.238A pdb=" N MET T 299 " --> pdb=" O THR T 295 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG T 306 " --> pdb=" O TYR T 302 " (cutoff:3.500A) Processing helix chain 'T' and resid 332 through 348 Processing helix chain 'Y' and resid 51 through 63 removed outlier: 3.683A pdb=" N HIS Y 63 " --> pdb=" O GLU Y 59 " (cutoff:3.500A) Processing helix chain 'Z' and resid 11 through 16 Processing helix chain 'Z' and resid 19 through 25 removed outlier: 3.694A pdb=" N GLY Z 23 " --> pdb=" O ALA Z 19 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP Z 25 " --> pdb=" O PRO Z 21 " (cutoff:3.500A) Processing helix chain 'Z' and resid 44 through 50 removed outlier: 3.540A pdb=" N ASP Z 49 " --> pdb=" O LEU Z 45 " (cutoff:3.500A) Processing helix chain 'Z' and resid 51 through 56 Processing helix chain 'Z' and resid 60 through 65 removed outlier: 3.541A pdb=" N GLY Z 64 " --> pdb=" O VAL Z 60 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU Z 65 " --> pdb=" O GLU Z 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 60 through 65' Processing helix chain 'Z' and resid 67 through 72 Processing helix chain 'Z' and resid 72 through 81 removed outlier: 3.837A pdb=" N LEU Z 78 " --> pdb=" O ALA Z 74 " (cutoff:3.500A) Processing helix chain 'Z' and resid 94 through 99 Processing helix chain 'Z' and resid 106 through 111 removed outlier: 3.723A pdb=" N TYR Z 110 " --> pdb=" O LEU Z 106 " (cutoff:3.500A) Processing helix chain 'Z' and resid 120 through 128 removed outlier: 3.821A pdb=" N ILE Z 126 " --> pdb=" O ALA Z 122 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL Z 128 " --> pdb=" O ASP Z 124 " (cutoff:3.500A) Processing helix chain 'Z' and resid 132 through 143 removed outlier: 3.588A pdb=" N ARG Z 137 " --> pdb=" O MET Z 133 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N GLU Z 138 " --> pdb=" O SER Z 134 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS Z 141 " --> pdb=" O ARG Z 137 " (cutoff:3.500A) Processing helix chain 'Z' and resid 166 through 170 removed outlier: 3.608A pdb=" N GLU Z 169 " --> pdb=" O VAL Z 166 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TRP Z 170 " --> pdb=" O ALA Z 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 166 through 170' Processing helix chain 'Z' and resid 176 through 181 removed outlier: 3.616A pdb=" N GLN Z 180 " --> pdb=" O ALA Z 176 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG Z 181 " --> pdb=" O GLU Z 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 176 through 181' Processing helix chain 'Z' and resid 187 through 190 Processing helix chain 'Z' and resid 191 through 197 Processing helix chain 'Z' and resid 201 through 216 removed outlier: 3.866A pdb=" N ASP Z 206 " --> pdb=" O HIS Z 202 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU Z 207 " --> pdb=" O GLU Z 203 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU Z 208 " --> pdb=" O ALA Z 204 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU Z 212 " --> pdb=" O LEU Z 208 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL Z 214 " --> pdb=" O GLU Z 210 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET Z 216 " --> pdb=" O GLU Z 212 " (cutoff:3.500A) Processing helix chain 'Z' and resid 226 through 237 removed outlier: 3.752A pdb=" N CYS Z 230 " --> pdb=" O TYR Z 226 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU Z 231 " --> pdb=" O ALA Z 227 " (cutoff:3.500A) Processing helix chain 'Z' and resid 241 through 252 removed outlier: 4.596A pdb=" N ALA Z 247 " --> pdb=" O PRO Z 243 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG Z 250 " --> pdb=" O SER Z 246 " (cutoff:3.500A) Processing helix chain 'Z' and resid 253 through 259 removed outlier: 3.801A pdb=" N LYS Z 258 " --> pdb=" O GLY Z 254 " (cutoff:3.500A) Processing helix chain 'Z' and resid 262 through 273 removed outlier: 3.549A pdb=" N MET Z 271 " --> pdb=" O ARG Z 267 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU Z 272 " --> pdb=" O LEU Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 274 through 285 removed outlier: 4.103A pdb=" N ASP Z 280 " --> pdb=" O GLU Z 276 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE Z 281 " --> pdb=" O LEU Z 277 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE Z 282 " --> pdb=" O VAL Z 278 " (cutoff:3.500A) Processing helix chain 'Z' and resid 292 through 310 removed outlier: 3.736A pdb=" N MET Z 297 " --> pdb=" O GLN Z 293 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY Z 299 " --> pdb=" O ALA Z 295 " (cutoff:3.500A) Processing helix chain 'Z' and resid 316 through 329 removed outlier: 3.682A pdb=" N GLN Z 325 " --> pdb=" O MET Z 321 " (cutoff:3.500A) Processing helix chain 'Z' and resid 332 through 341 removed outlier: 3.673A pdb=" N GLU Z 336 " --> pdb=" O ALA Z 332 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ASP Z 338 " --> pdb=" O ALA Z 334 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ILE Z 339 " --> pdb=" O ARG Z 335 " (cutoff:3.500A) Processing helix chain 'Z' and resid 344 through 357 removed outlier: 3.841A pdb=" N LYS Z 350 " --> pdb=" O ASP Z 346 " (cutoff:3.500A) Processing helix chain 'Z' and resid 369 through 382 removed outlier: 3.661A pdb=" N GLY Z 379 " --> pdb=" O SER Z 375 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN Z 382 " --> pdb=" O ASN Z 378 " (cutoff:3.500A) Processing helix chain 'Z' and resid 389 through 394 Processing helix chain 'Z' and resid 395 through 400 Processing helix chain 'Z' and resid 403 through 406 Processing helix chain 'Z' and resid 407 through 418 removed outlier: 3.598A pdb=" N LEU Z 414 " --> pdb=" O ALA Z 410 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY Z 415 " --> pdb=" O ALA Z 411 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE Z 417 " --> pdb=" O SER Z 413 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU Z 418 " --> pdb=" O LEU Z 414 " (cutoff:3.500A) Processing helix chain 'Z' and resid 425 through 434 removed outlier: 3.929A pdb=" N LYS Z 431 " --> pdb=" O THR Z 427 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N TYR Z 432 " --> pdb=" O GLN Z 428 " (cutoff:3.500A) Processing helix chain 'Z' and resid 439 through 453 removed outlier: 4.121A pdb=" N LEU Z 446 " --> pdb=" O SER Z 442 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N CYS Z 448 " --> pdb=" O ALA Z 444 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY Z 449 " --> pdb=" O LEU Z 445 " (cutoff:3.500A) Processing helix chain 'Z' and resid 461 through 465 removed outlier: 3.657A pdb=" N LEU Z 465 " --> pdb=" O ALA Z 462 " (cutoff:3.500A) Processing helix chain 'Z' and resid 466 through 471 removed outlier: 3.557A pdb=" N LEU Z 471 " --> pdb=" O SER Z 467 " (cutoff:3.500A) Processing helix chain 'Z' and resid 476 through 489 removed outlier: 3.615A pdb=" N TYR Z 489 " --> pdb=" O LEU Z 485 " (cutoff:3.500A) Processing helix chain 'Z' and resid 494 through 499 Processing helix chain 'Z' and resid 501 through 508 removed outlier: 3.760A pdb=" N SER Z 508 " --> pdb=" O VAL Z 504 " (cutoff:3.500A) Processing helix chain 'Z' and resid 517 through 527 Processing helix chain 'Z' and resid 534 through 545 removed outlier: 4.002A pdb=" N ILE Z 538 " --> pdb=" O VAL Z 534 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR Z 541 " --> pdb=" O THR Z 537 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE Z 542 " --> pdb=" O ILE Z 538 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET Z 543 " --> pdb=" O LEU Z 539 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU Z 544 " --> pdb=" O GLN Z 540 " (cutoff:3.500A) Processing helix chain 'Z' and resid 551 through 566 removed outlier: 3.628A pdb=" N ALA Z 555 " --> pdb=" O LYS Z 551 " (cutoff:3.500A) Proline residue: Z 559 - end of helix Processing helix chain 'Z' and resid 575 through 580 Processing helix chain 'Z' and resid 587 through 598 removed outlier: 4.125A pdb=" N ALA Z 591 " --> pdb=" O PHE Z 587 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR Z 593 " --> pdb=" O SER Z 589 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU Z 594 " --> pdb=" O PHE Z 590 " (cutoff:3.500A) Processing helix chain 'Z' and resid 607 through 615 removed outlier: 3.715A pdb=" N GLN Z 611 " --> pdb=" O LEU Z 607 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU Z 612 " --> pdb=" O LYS Z 608 " (cutoff:3.500A) Processing helix chain 'Z' and resid 616 through 618 No H-bonds generated for 'chain 'Z' and resid 616 through 618' Processing helix chain 'Z' and resid 625 through 640 Processing helix chain 'Z' and resid 645 through 659 removed outlier: 3.561A pdb=" N GLY Z 651 " --> pdb=" O GLY Z 647 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL Z 652 " --> pdb=" O ALA Z 648 " (cutoff:3.500A) Processing helix chain 'Z' and resid 659 through 664 Processing helix chain 'Z' and resid 666 through 683 removed outlier: 4.510A pdb=" N LEU Z 672 " --> pdb=" O ALA Z 668 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ARG Z 673 " --> pdb=" O GLU Z 669 " (cutoff:3.500A) Processing helix chain 'Z' and resid 688 through 698 removed outlier: 4.444A pdb=" N LEU Z 692 " --> pdb=" O ARG Z 688 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE Z 697 " --> pdb=" O ALA Z 693 " (cutoff:3.500A) Processing helix chain 'Z' and resid 699 through 701 No H-bonds generated for 'chain 'Z' and resid 699 through 701' Processing helix chain 'Z' and resid 704 through 715 removed outlier: 4.225A pdb=" N ASP Z 708 " --> pdb=" O LEU Z 704 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR Z 709 " --> pdb=" O ASN Z 705 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE Z 713 " --> pdb=" O THR Z 709 " (cutoff:3.500A) Processing helix chain 'Z' and resid 721 through 736 removed outlier: 3.963A pdb=" N SER Z 725 " --> pdb=" O VAL Z 721 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE Z 726 " --> pdb=" O SER Z 722 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER Z 734 " --> pdb=" O GLY Z 730 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR Z 736 " --> pdb=" O VAL Z 732 " (cutoff:3.500A) Processing helix chain 'Z' and resid 742 through 754 removed outlier: 3.804A pdb=" N ARG Z 746 " --> pdb=" O ALA Z 742 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN Z 747 " --> pdb=" O ALA Z 743 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN Z 750 " --> pdb=" O ARG Z 746 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TYR Z 751 " --> pdb=" O GLN Z 747 " (cutoff:3.500A) Processing helix chain 'Z' and resid 755 through 759 removed outlier: 3.724A pdb=" N LEU Z 759 " --> pdb=" O PRO Z 756 " (cutoff:3.500A) Processing helix chain 'Z' and resid 774 through 786 removed outlier: 3.671A pdb=" N CYS Z 779 " --> pdb=" O THR Z 775 " (cutoff:3.500A) Proline residue: Z 780 - end of helix removed outlier: 3.956A pdb=" N GLN Z 786 " --> pdb=" O HIS Z 782 " (cutoff:3.500A) Processing helix chain 'Z' and resid 790 through 795 Processing helix chain 'N' and resid 5 through 10 Processing helix chain 'N' and resid 16 through 22 removed outlier: 3.601A pdb=" N GLU N 21 " --> pdb=" O PRO N 17 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE N 22 " --> pdb=" O GLN N 18 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 27 Processing helix chain 'N' and resid 34 through 39 removed outlier: 3.500A pdb=" N ILE N 38 " --> pdb=" O PHE N 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 42 through 51 removed outlier: 3.626A pdb=" N LEU N 48 " --> pdb=" O LYS N 44 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 71 removed outlier: 3.500A pdb=" N PHE N 68 " --> pdb=" O ALA N 64 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N HIS N 70 " --> pdb=" O LYS N 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 75 through 82 removed outlier: 3.651A pdb=" N ASN N 79 " --> pdb=" O GLU N 75 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 85 No H-bonds generated for 'chain 'N' and resid 83 through 85' Processing helix chain 'N' and resid 94 through 118 removed outlier: 3.863A pdb=" N ALA N 102 " --> pdb=" O GLU N 98 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN N 111 " --> pdb=" O HIS N 107 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU N 114 " --> pdb=" O LYS N 110 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU N 118 " --> pdb=" O GLU N 114 " (cutoff:3.500A) Processing helix chain 'N' and resid 127 through 144 removed outlier: 3.781A pdb=" N GLU N 131 " --> pdb=" O ASP N 127 " (cutoff:3.500A) Processing helix chain 'N' and resid 146 through 157 removed outlier: 4.842A pdb=" N GLY N 152 " --> pdb=" O LYS N 148 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU N 155 " --> pdb=" O ILE N 151 " (cutoff:3.500A) Processing helix chain 'N' and resid 159 through 169 removed outlier: 3.513A pdb=" N PHE N 163 " --> pdb=" O ARG N 159 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE N 167 " --> pdb=" O PHE N 163 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU N 168 " --> pdb=" O GLU N 164 " (cutoff:3.500A) Processing helix chain 'N' and resid 172 through 186 removed outlier: 3.626A pdb=" N MET N 176 " --> pdb=" O ASP N 172 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA N 178 " --> pdb=" O PRO N 174 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU N 181 " --> pdb=" O LEU N 177 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS N 182 " --> pdb=" O ALA N 178 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET N 185 " --> pdb=" O LEU N 181 " (cutoff:3.500A) Processing helix chain 'N' and resid 190 through 204 removed outlier: 3.793A pdb=" N VAL N 200 " --> pdb=" O LYS N 196 " (cutoff:3.500A) Processing helix chain 'N' and resid 212 through 224 removed outlier: 3.629A pdb=" N VAL N 216 " --> pdb=" O ASP N 212 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N CYS N 217 " --> pdb=" O PHE N 213 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN N 218 " --> pdb=" O ILE N 214 " (cutoff:3.500A) Processing helix chain 'N' and resid 225 through 234 removed outlier: 3.544A pdb=" N VAL N 229 " --> pdb=" O ASP N 225 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASP N 231 " --> pdb=" O GLN N 227 " (cutoff:3.500A) Processing helix chain 'N' and resid 241 through 256 removed outlier: 4.117A pdb=" N GLN N 247 " --> pdb=" O LEU N 243 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE N 248 " --> pdb=" O MET N 244 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS N 249 " --> pdb=" O ALA N 245 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP N 251 " --> pdb=" O GLN N 247 " (cutoff:3.500A) Processing helix chain 'N' and resid 257 through 273 removed outlier: 3.622A pdb=" N SER N 263 " --> pdb=" O GLN N 259 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE N 265 " --> pdb=" O LEU N 261 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN N 266 " --> pdb=" O SER N 262 " (cutoff:3.500A) Processing helix chain 'N' and resid 331 through 345 Processing helix chain 'N' and resid 351 through 360 removed outlier: 3.838A pdb=" N ASN N 355 " --> pdb=" O MET N 351 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL N 360 " --> pdb=" O THR N 356 " (cutoff:3.500A) Processing helix chain 'N' and resid 364 through 377 removed outlier: 4.206A pdb=" N SER N 374 " --> pdb=" O VAL N 370 " (cutoff:3.500A) Processing helix chain 'N' and resid 383 through 388 removed outlier: 3.670A pdb=" N ASP N 388 " --> pdb=" O GLN N 384 " (cutoff:3.500A) Processing helix chain 'N' and resid 390 through 396 removed outlier: 3.694A pdb=" N ALA N 394 " --> pdb=" O LEU N 390 " (cutoff:3.500A) Processing helix chain 'N' and resid 418 through 423 Processing helix chain 'N' and resid 424 through 426 No H-bonds generated for 'chain 'N' and resid 424 through 426' Processing helix chain 'N' and resid 435 through 450 removed outlier: 3.774A pdb=" N GLU N 439 " --> pdb=" O SER N 435 " (cutoff:3.500A) Processing helix chain 'N' and resid 455 through 467 removed outlier: 3.947A pdb=" N ASP N 459 " --> pdb=" O GLY N 455 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN N 467 " --> pdb=" O ASN N 463 " (cutoff:3.500A) Processing helix chain 'N' and resid 470 through 485 removed outlier: 3.747A pdb=" N LEU N 483 " --> pdb=" O LEU N 479 " (cutoff:3.500A) Processing helix chain 'N' and resid 490 through 502 removed outlier: 3.514A pdb=" N TYR N 494 " --> pdb=" O ARG N 490 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU N 501 " --> pdb=" O LEU N 497 " (cutoff:3.500A) Processing helix chain 'N' and resid 505 through 520 removed outlier: 3.814A pdb=" N GLU N 510 " --> pdb=" O ALA N 506 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA N 511 " --> pdb=" O VAL N 507 " (cutoff:3.500A) Processing helix chain 'N' and resid 525 through 539 removed outlier: 3.660A pdb=" N GLU N 530 " --> pdb=" O ALA N 526 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY N 534 " --> pdb=" O GLU N 530 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU N 538 " --> pdb=" O GLY N 534 " (cutoff:3.500A) Processing helix chain 'N' and resid 543 through 554 removed outlier: 3.616A pdb=" N GLY N 551 " --> pdb=" O GLY N 547 " (cutoff:3.500A) Processing helix chain 'N' and resid 566 through 571 Processing helix chain 'N' and resid 576 through 590 removed outlier: 3.586A pdb=" N GLY N 582 " --> pdb=" O LEU N 578 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N VAL N 586 " --> pdb=" O GLY N 582 " (cutoff:3.500A) Processing helix chain 'N' and resid 596 through 601 removed outlier: 3.534A pdb=" N ARG N 601 " --> pdb=" O LYS N 597 " (cutoff:3.500A) Processing helix chain 'N' and resid 614 through 621 removed outlier: 3.902A pdb=" N VAL N 619 " --> pdb=" O ARG N 615 " (cutoff:3.500A) Processing helix chain 'N' and resid 621 through 626 Processing helix chain 'N' and resid 632 through 636 Processing helix chain 'N' and resid 637 through 642 removed outlier: 3.758A pdb=" N GLU N 642 " --> pdb=" O SER N 638 " (cutoff:3.500A) Processing helix chain 'N' and resid 645 through 660 removed outlier: 3.522A pdb=" N ARG N 649 " --> pdb=" O ASN N 645 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE N 658 " --> pdb=" O MET N 654 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N CYS N 659 " --> pdb=" O ALA N 655 " (cutoff:3.500A) Processing helix chain 'N' and resid 665 through 677 removed outlier: 3.599A pdb=" N ILE N 669 " --> pdb=" O ASN N 665 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU N 671 " --> pdb=" O GLU N 667 " (cutoff:3.500A) Proline residue: N 674 - end of helix removed outlier: 3.504A pdb=" N ASN N 677 " --> pdb=" O GLU N 673 " (cutoff:3.500A) Processing helix chain 'N' and resid 680 through 695 removed outlier: 3.737A pdb=" N ARG N 684 " --> pdb=" O VAL N 680 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLN N 685 " --> pdb=" O ASN N 681 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY N 686 " --> pdb=" O TYR N 682 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE N 689 " --> pdb=" O GLN N 685 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA N 690 " --> pdb=" O GLY N 686 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER N 691 " --> pdb=" O ALA N 687 " (cutoff:3.500A) Processing helix chain 'N' and resid 705 through 716 removed outlier: 3.760A pdb=" N VAL N 716 " --> pdb=" O LEU N 712 " (cutoff:3.500A) Processing helix chain 'N' and resid 723 through 736 removed outlier: 4.515A pdb=" N GLY N 729 " --> pdb=" O MET N 725 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU N 732 " --> pdb=" O PHE N 728 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA N 733 " --> pdb=" O GLY N 729 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN N 734 " --> pdb=" O ALA N 730 " (cutoff:3.500A) Processing helix chain 'N' and resid 738 through 743 removed outlier: 3.567A pdb=" N HIS N 742 " --> pdb=" O ASP N 738 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN N 743 " --> pdb=" O ALA N 739 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 738 through 743' Processing helix chain 'N' and resid 756 through 768 removed outlier: 3.530A pdb=" N VAL N 760 " --> pdb=" O HIS N 756 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE N 766 " --> pdb=" O GLY N 762 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR N 767 " --> pdb=" O VAL N 763 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN N 768 " --> pdb=" O LEU N 764 " (cutoff:3.500A) Processing helix chain 'N' and resid 777 through 781 Processing helix chain 'N' and resid 807 through 812 removed outlier: 3.720A pdb=" N PHE N 811 " --> pdb=" O LYS N 807 " (cutoff:3.500A) Processing helix chain 'N' and resid 819 through 852 removed outlier: 3.758A pdb=" N SER N 834 " --> pdb=" O THR N 830 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE N 835 " --> pdb=" O ALA N 831 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU N 843 " --> pdb=" O ALA N 839 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS N 848 " --> pdb=" O LYS N 844 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLU N 850 " --> pdb=" O LYS N 846 " (cutoff:3.500A) Processing helix chain 'N' and resid 885 through 890 removed outlier: 4.021A pdb=" N LYS N 890 " --> pdb=" O PRO N 886 " (cutoff:3.500A) Processing helix chain 'N' and resid 934 through 940 removed outlier: 3.981A pdb=" N GLU N 938 " --> pdb=" O LYS N 934 " (cutoff:3.500A) Processing helix chain 'S' and resid 54 through 75 removed outlier: 3.569A pdb=" N ALA S 59 " --> pdb=" O THR S 55 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA S 60 " --> pdb=" O ALA S 56 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR S 69 " --> pdb=" O ARG S 65 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU S 73 " --> pdb=" O THR S 69 " (cutoff:3.500A) Processing helix chain 'S' and resid 77 through 85 removed outlier: 4.243A pdb=" N GLU S 83 " --> pdb=" O VAL S 79 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA S 85 " --> pdb=" O GLN S 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 89 through 94 removed outlier: 3.816A pdb=" N PHE S 93 " --> pdb=" O LYS S 89 " (cutoff:3.500A) Processing helix chain 'S' and resid 95 through 99 Processing helix chain 'S' and resid 102 through 107 removed outlier: 3.823A pdb=" N ARG S 106 " --> pdb=" O SER S 103 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG S 107 " --> pdb=" O THR S 104 " (cutoff:3.500A) Processing helix chain 'S' and resid 127 through 132 removed outlier: 3.560A pdb=" N LEU S 132 " --> pdb=" O ARG S 128 " (cutoff:3.500A) Processing helix chain 'S' and resid 159 through 178 removed outlier: 3.728A pdb=" N LEU S 170 " --> pdb=" O TYR S 166 " (cutoff:3.500A) Processing helix chain 'S' and resid 181 through 196 removed outlier: 3.782A pdb=" N SER S 188 " --> pdb=" O ALA S 184 " (cutoff:3.500A) Processing helix chain 'S' and resid 202 through 223 removed outlier: 3.984A pdb=" N VAL S 206 " --> pdb=" O ALA S 202 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS S 209 " --> pdb=" O LEU S 205 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE S 220 " --> pdb=" O ARG S 216 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LEU S 221 " --> pdb=" O VAL S 217 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASP S 222 " --> pdb=" O TYR S 218 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS S 223 " --> pdb=" O GLU S 219 " (cutoff:3.500A) Processing helix chain 'S' and resid 225 through 242 removed outlier: 4.091A pdb=" N SER S 229 " --> pdb=" O ASP S 225 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE S 230 " --> pdb=" O VAL S 226 " (cutoff:3.500A) Processing helix chain 'S' and resid 243 through 261 removed outlier: 3.664A pdb=" N TYR S 261 " --> pdb=" O ASN S 257 " (cutoff:3.500A) Processing helix chain 'S' and resid 263 through 274 removed outlier: 3.592A pdb=" N LEU S 270 " --> pdb=" O GLN S 266 " (cutoff:3.500A) Processing helix chain 'S' and resid 281 through 299 removed outlier: 3.661A pdb=" N GLY S 293 " --> pdb=" O LEU S 289 " (cutoff:3.500A) Processing helix chain 'S' and resid 301 through 314 removed outlier: 3.659A pdb=" N ALA S 305 " --> pdb=" O GLU S 301 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG S 307 " --> pdb=" O SER S 303 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR S 310 " --> pdb=" O ARG S 306 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN S 311 " --> pdb=" O ARG S 307 " (cutoff:3.500A) Processing helix chain 'S' and resid 321 through 340 removed outlier: 3.803A pdb=" N LYS S 330 " --> pdb=" O GLN S 326 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL S 334 " --> pdb=" O LYS S 330 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU S 337 " --> pdb=" O ILE S 333 " (cutoff:3.500A) Processing helix chain 'S' and resid 344 through 349 removed outlier: 3.517A pdb=" N GLN S 347 " --> pdb=" O ASP S 344 " (cutoff:3.500A) Processing helix chain 'S' and resid 351 through 355 removed outlier: 4.021A pdb=" N LYS S 354 " --> pdb=" O PRO S 351 " (cutoff:3.500A) Processing helix chain 'S' and resid 357 through 370 removed outlier: 3.786A pdb=" N LEU S 362 " --> pdb=" O MET S 358 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA S 366 " --> pdb=" O LEU S 362 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR S 369 " --> pdb=" O GLN S 365 " (cutoff:3.500A) Processing helix chain 'S' and resid 371 through 382 removed outlier: 3.859A pdb=" N PHE S 375 " --> pdb=" O ASN S 371 " (cutoff:3.500A) Processing helix chain 'S' and resid 382 through 387 Processing helix chain 'S' and resid 391 through 396 removed outlier: 3.628A pdb=" N ILE S 396 " --> pdb=" O TYR S 392 " (cutoff:3.500A) Processing helix chain 'S' and resid 398 through 413 removed outlier: 3.809A pdb=" N ILE S 403 " --> pdb=" O ARG S 399 " (cutoff:3.500A) Processing helix chain 'S' and resid 419 through 426 removed outlier: 3.661A pdb=" N GLN S 424 " --> pdb=" O ALA S 420 " (cutoff:3.500A) Processing helix chain 'S' and resid 430 through 444 removed outlier: 3.815A pdb=" N GLU S 435 " --> pdb=" O PRO S 431 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE S 436 " --> pdb=" O GLU S 432 " (cutoff:3.500A) Processing helix chain 'S' and resid 470 through 495 removed outlier: 3.719A pdb=" N SER S 481 " --> pdb=" O HIS S 477 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HIS S 487 " --> pdb=" O CYS S 483 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL S 491 " --> pdb=" O HIS S 487 " (cutoff:3.500A) Processing helix chain 'S' and resid 495 through 504 removed outlier: 3.516A pdb=" N LYS S 499 " --> pdb=" O ARG S 495 " (cutoff:3.500A) Processing helix chain 'S' and resid 509 through 532 removed outlier: 3.700A pdb=" N GLU S 513 " --> pdb=" O GLU S 509 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE S 521 " --> pdb=" O GLN S 517 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA S 522 " --> pdb=" O ASP S 518 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET S 525 " --> pdb=" O PHE S 521 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 11 Processing helix chain 'P' and resid 11 through 20 removed outlier: 4.644A pdb=" N LYS P 15 " --> pdb=" O GLY P 11 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET P 16 " --> pdb=" O ARG P 12 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU P 17 " --> pdb=" O ILE P 13 " (cutoff:3.500A) Processing helix chain 'P' and resid 20 through 35 removed outlier: 3.575A pdb=" N ASP P 25 " --> pdb=" O SER P 21 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLN P 26 " --> pdb=" O ALA P 22 " (cutoff:3.500A) Proline residue: P 29 - end of helix removed outlier: 3.616A pdb=" N ALA P 32 " --> pdb=" O LEU P 28 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS P 33 " --> pdb=" O PRO P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 51 removed outlier: 3.698A pdb=" N GLU P 45 " --> pdb=" O GLN P 41 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR P 46 " --> pdb=" O GLU P 42 " (cutoff:3.500A) Processing helix chain 'P' and resid 54 through 60 removed outlier: 4.221A pdb=" N ASP P 59 " --> pdb=" O ARG P 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 60 through 72 removed outlier: 3.715A pdb=" N SER P 64 " --> pdb=" O MET P 60 " (cutoff:3.500A) Processing helix chain 'P' and resid 76 through 81 Processing helix chain 'P' and resid 82 through 93 removed outlier: 3.531A pdb=" N ASN P 86 " --> pdb=" O LEU P 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 113 removed outlier: 3.674A pdb=" N VAL P 101 " --> pdb=" O LEU P 97 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR P 110 " --> pdb=" O GLN P 106 " (cutoff:3.500A) Processing helix chain 'P' and resid 117 through 120 Processing helix chain 'P' and resid 121 through 130 removed outlier: 3.788A pdb=" N THR P 127 " --> pdb=" O ARG P 123 " (cutoff:3.500A) Processing helix chain 'P' and resid 137 through 150 removed outlier: 3.562A pdb=" N GLU P 141 " --> pdb=" O TYR P 137 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ALA P 143 " --> pdb=" O GLU P 139 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ARG P 144 " --> pdb=" O ILE P 140 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR P 148 " --> pdb=" O ARG P 144 " (cutoff:3.500A) Processing helix chain 'P' and resid 161 through 166 Processing helix chain 'P' and resid 178 through 196 removed outlier: 3.518A pdb=" N ARG P 182 " --> pdb=" O GLU P 178 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL P 196 " --> pdb=" O LEU P 192 " (cutoff:3.500A) Processing helix chain 'P' and resid 198 through 206 removed outlier: 3.736A pdb=" N ILE P 204 " --> pdb=" O ILE P 200 " (cutoff:3.500A) Processing helix chain 'P' and resid 207 through 209 No H-bonds generated for 'chain 'P' and resid 207 through 209' Processing helix chain 'P' and resid 211 through 216 Processing helix chain 'P' and resid 219 through 238 removed outlier: 3.644A pdb=" N LYS P 225 " --> pdb=" O LYS P 221 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN P 232 " --> pdb=" O ASN P 228 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N HIS P 236 " --> pdb=" O GLN P 232 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU P 237 " --> pdb=" O LEU P 233 " (cutoff:3.500A) Processing helix chain 'P' and resid 239 through 251 removed outlier: 3.566A pdb=" N ILE P 243 " --> pdb=" O SER P 239 " (cutoff:3.500A) Processing helix chain 'P' and resid 253 through 258 removed outlier: 3.602A pdb=" N GLN P 257 " --> pdb=" O THR P 253 " (cutoff:3.500A) Processing helix chain 'P' and resid 259 through 277 removed outlier: 3.617A pdb=" N TRP P 263 " --> pdb=" O GLU P 259 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN P 264 " --> pdb=" O SER P 260 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLN P 265 " --> pdb=" O GLU P 261 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER P 269 " --> pdb=" O GLN P 265 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE P 275 " --> pdb=" O VAL P 271 " (cutoff:3.500A) Processing helix chain 'P' and resid 281 through 290 removed outlier: 3.514A pdb=" N HIS P 288 " --> pdb=" O SER P 284 " (cutoff:3.500A) Processing helix chain 'P' and resid 294 through 298 Processing helix chain 'P' and resid 299 through 311 removed outlier: 3.816A pdb=" N ASP P 304 " --> pdb=" O PRO P 300 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU P 305 " --> pdb=" O LYS P 301 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE P 309 " --> pdb=" O LEU P 305 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR P 311 " --> pdb=" O LYS P 307 " (cutoff:3.500A) Processing helix chain 'P' and resid 316 through 323 removed outlier: 3.590A pdb=" N ASP P 323 " --> pdb=" O THR P 319 " (cutoff:3.500A) Processing helix chain 'P' and resid 346 through 370 removed outlier: 3.984A pdb=" N TRP P 351 " --> pdb=" O GLY P 347 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS P 368 " --> pdb=" O ARG P 364 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR P 369 " --> pdb=" O ILE P 365 " (cutoff:3.500A) Processing helix chain 'P' and resid 375 through 381 Processing helix chain 'P' and resid 387 through 392 removed outlier: 3.851A pdb=" N ALA P 391 " --> pdb=" O ASP P 387 " (cutoff:3.500A) Processing helix chain 'P' and resid 420 through 454 removed outlier: 3.636A pdb=" N GLN P 430 " --> pdb=" O ASN P 426 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET P 451 " --> pdb=" O ALA P 447 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE P 452 " --> pdb=" O LYS P 448 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 10 Processing helix chain 'Q' and resid 13 through 19 removed outlier: 4.107A pdb=" N THR Q 18 " --> pdb=" O SER Q 14 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP Q 19 " --> pdb=" O LEU Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 23 through 31 removed outlier: 3.830A pdb=" N LEU Q 27 " --> pdb=" O SER Q 23 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HIS Q 28 " --> pdb=" O ILE Q 24 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER Q 29 " --> pdb=" O ASP Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 58 removed outlier: 3.809A pdb=" N LEU Q 53 " --> pdb=" O SER Q 49 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY Q 54 " --> pdb=" O ILE Q 50 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER Q 55 " --> pdb=" O LEU Q 51 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA Q 58 " --> pdb=" O GLY Q 54 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 68 Processing helix chain 'Q' and resid 69 through 74 removed outlier: 3.889A pdb=" N TYR Q 72 " --> pdb=" O LEU Q 69 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL Q 73 " --> pdb=" O LEU Q 70 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG Q 74 " --> pdb=" O LYS Q 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 69 through 74' Processing helix chain 'Q' and resid 83 through 98 removed outlier: 5.495A pdb=" N VAL Q 89 " --> pdb=" O ALA Q 85 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU Q 93 " --> pdb=" O VAL Q 89 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP Q 94 " --> pdb=" O ARG Q 90 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LEU Q 95 " --> pdb=" O SER Q 91 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N PHE Q 96 " --> pdb=" O LEU Q 92 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU Q 97 " --> pdb=" O LEU Q 93 " (cutoff:3.500A) Processing helix chain 'Q' and resid 105 through 117 removed outlier: 3.616A pdb=" N LEU Q 109 " --> pdb=" O GLN Q 105 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU Q 111 " --> pdb=" O VAL Q 107 " (cutoff:3.500A) Processing helix chain 'Q' and resid 123 through 137 removed outlier: 3.589A pdb=" N ALA Q 131 " --> pdb=" O GLN Q 127 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG Q 132 " --> pdb=" O ALA Q 128 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL Q 134 " --> pdb=" O GLU Q 130 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N SER Q 135 " --> pdb=" O ALA Q 131 " (cutoff:3.500A) Processing helix chain 'Q' and resid 142 through 150 removed outlier: 3.858A pdb=" N HIS Q 148 " --> pdb=" O GLN Q 144 " (cutoff:3.500A) Processing helix chain 'Q' and resid 161 through 165 removed outlier: 3.753A pdb=" N ALA Q 164 " --> pdb=" O ASP Q 161 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU Q 165 " --> pdb=" O ASP Q 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 161 through 165' Processing helix chain 'Q' and resid 167 through 180 Processing helix chain 'Q' and resid 185 through 197 removed outlier: 3.692A pdb=" N THR Q 191 " --> pdb=" O ARG Q 187 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR Q 196 " --> pdb=" O SER Q 192 " (cutoff:3.500A) Processing helix chain 'Q' and resid 203 through 220 removed outlier: 3.722A pdb=" N ASP Q 211 " --> pdb=" O GLN Q 207 " (cutoff:3.500A) Processing helix chain 'Q' and resid 224 through 242 removed outlier: 3.525A pdb=" N TYR Q 229 " --> pdb=" O TRP Q 225 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N SER Q 230 " --> pdb=" O LYS Q 226 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR Q 231 " --> pdb=" O THR Q 227 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR Q 233 " --> pdb=" O TYR Q 229 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE Q 242 " --> pdb=" O GLY Q 238 " (cutoff:3.500A) Processing helix chain 'Q' and resid 245 through 260 removed outlier: 4.592A pdb=" N THR Q 249 " --> pdb=" O PRO Q 245 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR Q 253 " --> pdb=" O THR Q 249 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS Q 258 " --> pdb=" O MET Q 254 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE Q 259 " --> pdb=" O LEU Q 255 " (cutoff:3.500A) Processing helix chain 'Q' and resid 261 through 263 No H-bonds generated for 'chain 'Q' and resid 261 through 263' Processing helix chain 'Q' and resid 264 through 271 removed outlier: 3.876A pdb=" N GLN Q 268 " --> pdb=" O PRO Q 264 " (cutoff:3.500A) Processing helix chain 'Q' and resid 276 through 280 Processing helix chain 'Q' and resid 281 through 297 removed outlier: 3.566A pdb=" N GLU Q 285 " --> pdb=" O GLY Q 281 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU Q 287 " --> pdb=" O GLN Q 283 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N CYS Q 289 " --> pdb=" O GLU Q 285 " (cutoff:3.500A) Processing helix chain 'Q' and resid 298 through 309 removed outlier: 3.802A pdb=" N PHE Q 302 " --> pdb=" O SER Q 298 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU Q 303 " --> pdb=" O LEU Q 299 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP Q 308 " --> pdb=" O LYS Q 304 " (cutoff:3.500A) Processing helix chain 'Q' and resid 311 through 316 removed outlier: 3.808A pdb=" N ASP Q 315 " --> pdb=" O ALA Q 311 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ASP Q 316 " --> pdb=" O GLU Q 312 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 311 through 316' Processing helix chain 'Q' and resid 318 through 340 removed outlier: 3.943A pdb=" N HIS Q 322 " --> pdb=" O ILE Q 318 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ALA Q 324 " --> pdb=" O SER Q 320 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS Q 325 " --> pdb=" O THR Q 321 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASP Q 328 " --> pdb=" O ALA Q 324 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN Q 329 " --> pdb=" O LYS Q 325 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN Q 333 " --> pdb=" O ASN Q 329 " (cutoff:3.500A) Processing helix chain 'Q' and resid 347 through 355 removed outlier: 3.508A pdb=" N LEU Q 353 " --> pdb=" O HIS Q 349 " (cutoff:3.500A) Processing helix chain 'Q' and resid 357 through 371 removed outlier: 3.717A pdb=" N GLU Q 362 " --> pdb=" O LYS Q 358 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG Q 363 " --> pdb=" O ALA Q 359 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS Q 364 " --> pdb=" O ASP Q 360 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER Q 366 " --> pdb=" O GLU Q 362 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN Q 367 " --> pdb=" O ARG Q 363 " (cutoff:3.500A) Processing helix chain 'Q' and resid 394 through 422 removed outlier: 3.892A pdb=" N GLU Q 398 " --> pdb=" O ASP Q 394 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA Q 400 " --> pdb=" O THR Q 396 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS Q 409 " --> pdb=" O GLN Q 405 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS Q 420 " --> pdb=" O ASN Q 416 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU Q 421 " --> pdb=" O LYS Q 417 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR Q 422 " --> pdb=" O ALA Q 418 " (cutoff:3.500A) Processing helix chain 'R' and resid 18 through 26 removed outlier: 4.495A pdb=" N PHE R 24 " --> pdb=" O ALA R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 47 removed outlier: 3.938A pdb=" N VAL R 37 " --> pdb=" O GLY R 33 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG R 38 " --> pdb=" O ASP R 34 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU R 40 " --> pdb=" O ALA R 36 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA R 44 " --> pdb=" O GLU R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 92 removed outlier: 3.503A pdb=" N LEU R 70 " --> pdb=" O ASP R 66 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LYS R 72 " --> pdb=" O ASP R 68 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET R 73 " --> pdb=" O LEU R 69 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP R 85 " --> pdb=" O LEU R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 111 removed outlier: 3.537A pdb=" N ILE R 100 " --> pdb=" O GLY R 96 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ASP R 102 " --> pdb=" O SER R 98 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA R 103 " --> pdb=" O GLU R 99 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR R 110 " --> pdb=" O ALA R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 129 Processing helix chain 'R' and resid 133 through 151 removed outlier: 3.777A pdb=" N LEU R 144 " --> pdb=" O ILE R 140 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU R 149 " --> pdb=" O LEU R 145 " (cutoff:3.500A) Processing helix chain 'R' and resid 153 through 172 removed outlier: 3.965A pdb=" N ASN R 160 " --> pdb=" O LEU R 156 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER R 166 " --> pdb=" O GLU R 162 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU R 167 " --> pdb=" O LYS R 163 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 191 removed outlier: 3.557A pdb=" N ARG R 177 " --> pdb=" O ASP R 173 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG R 179 " --> pdb=" O ASP R 175 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE R 191 " --> pdb=" O TYR R 187 " (cutoff:3.500A) Processing helix chain 'R' and resid 194 through 204 removed outlier: 3.580A pdb=" N THR R 204 " --> pdb=" O LEU R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 231 removed outlier: 4.438A pdb=" N ILE R 229 " --> pdb=" O TYR R 225 " (cutoff:3.500A) Processing helix chain 'R' and resid 235 through 240 Processing helix chain 'R' and resid 244 through 251 Processing helix chain 'R' and resid 253 through 266 removed outlier: 5.020A pdb=" N TYR R 259 " --> pdb=" O ALA R 255 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER R 262 " --> pdb=" O GLN R 258 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU R 263 " --> pdb=" O TYR R 259 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR R 264 " --> pdb=" O LEU R 260 " (cutoff:3.500A) Processing helix chain 'R' and resid 267 through 283 removed outlier: 3.834A pdb=" N PHE R 272 " --> pdb=" O TYR R 268 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL R 277 " --> pdb=" O GLN R 273 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET R 282 " --> pdb=" O VAL R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 291 through 307 removed outlier: 3.915A pdb=" N VAL R 296 " --> pdb=" O TYR R 292 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE R 301 " --> pdb=" O ARG R 297 " (cutoff:3.500A) Processing helix chain 'R' and resid 315 through 323 removed outlier: 3.889A pdb=" N GLU R 321 " --> pdb=" O GLY R 317 " (cutoff:3.500A) Processing helix chain 'R' and resid 326 through 340 Processing helix chain 'R' and resid 360 through 364 Processing helix chain 'R' and resid 366 through 389 Processing helix chain 'U' and resid 12 through 26 removed outlier: 3.753A pdb=" N LEU U 16 " --> pdb=" O HIS U 12 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASN U 24 " --> pdb=" O VAL U 20 " (cutoff:3.500A) Processing helix chain 'U' and resid 71 through 84 removed outlier: 4.694A pdb=" N GLY U 80 " --> pdb=" O GLU U 76 " (cutoff:3.500A) Processing helix chain 'U' and resid 104 through 114 removed outlier: 3.559A pdb=" N LEU U 111 " --> pdb=" O ALA U 107 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG U 114 " --> pdb=" O GLU U 110 " (cutoff:3.500A) Processing helix chain 'U' and resid 165 through 176 Processing helix chain 'U' and resid 185 through 217 removed outlier: 3.832A pdb=" N LEU U 198 " --> pdb=" O GLN U 194 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER U 203 " --> pdb=" O LYS U 199 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR U 217 " --> pdb=" O GLU U 213 " (cutoff:3.500A) Processing helix chain 'U' and resid 223 through 237 removed outlier: 3.789A pdb=" N ILE U 227 " --> pdb=" O ASN U 223 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP U 232 " --> pdb=" O TYR U 228 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE U 234 " --> pdb=" O LEU U 230 " (cutoff:3.500A) Processing helix chain 'U' and resid 241 through 290 removed outlier: 3.585A pdb=" N PHE U 245 " --> pdb=" O SER U 241 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU U 251 " --> pdb=" O LYS U 247 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS U 288 " --> pdb=" O ASP U 284 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY U 290 " --> pdb=" O GLU U 286 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 9 removed outlier: 3.580A pdb=" N GLY O 6 " --> pdb=" O LYS O 2 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN O 9 " --> pdb=" O PRO O 5 " (cutoff:3.500A) Processing helix chain 'O' and resid 17 through 32 removed outlier: 4.043A pdb=" N GLU O 26 " --> pdb=" O TRP O 22 " (cutoff:3.500A) Processing helix chain 'O' and resid 33 through 45 removed outlier: 3.589A pdb=" N LEU O 39 " --> pdb=" O HIS O 35 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU O 42 " --> pdb=" O THR O 38 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP O 43 " --> pdb=" O LEU O 39 " (cutoff:3.500A) Processing helix chain 'O' and resid 57 through 62 Processing helix chain 'O' and resid 72 through 87 removed outlier: 3.529A pdb=" N VAL O 77 " --> pdb=" O PRO O 73 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU O 78 " --> pdb=" O LEU O 74 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL O 84 " --> pdb=" O ILE O 80 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG O 85 " --> pdb=" O LEU O 81 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN O 86 " --> pdb=" O HIS O 82 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N MET O 87 " --> pdb=" O VAL O 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 91 through 105 removed outlier: 3.580A pdb=" N THR O 95 " --> pdb=" O ASN O 91 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS O 103 " --> pdb=" O LYS O 99 " (cutoff:3.500A) Processing helix chain 'O' and resid 111 through 126 removed outlier: 3.534A pdb=" N ALA O 117 " --> pdb=" O LEU O 113 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN O 124 " --> pdb=" O ALA O 120 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY O 126 " --> pdb=" O LYS O 122 " (cutoff:3.500A) Processing helix chain 'O' and resid 127 through 144 removed outlier: 3.952A pdb=" N THR O 131 " --> pdb=" O ASP O 127 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN O 143 " --> pdb=" O GLU O 139 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN O 144 " --> pdb=" O GLU O 140 " (cutoff:3.500A) Processing helix chain 'O' and resid 151 through 167 Processing helix chain 'O' and resid 168 through 181 removed outlier: 3.697A pdb=" N LEU O 177 " --> pdb=" O TYR O 173 " (cutoff:3.500A) Processing helix chain 'O' and resid 189 through 207 removed outlier: 3.544A pdb=" N GLN O 193 " --> pdb=" O PRO O 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN O 194 " --> pdb=" O VAL O 190 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU O 195 " --> pdb=" O SER O 191 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE O 198 " --> pdb=" O GLN O 194 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU O 202 " --> pdb=" O PHE O 198 " (cutoff:3.500A) Processing helix chain 'O' and resid 212 through 217 removed outlier: 3.627A pdb=" N LEU O 216 " --> pdb=" O ASN O 212 " (cutoff:3.500A) Processing helix chain 'O' and resid 230 through 243 removed outlier: 3.826A pdb=" N ASP O 235 " --> pdb=" O GLN O 231 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA O 239 " --> pdb=" O ASP O 235 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER O 242 " --> pdb=" O TYR O 238 " (cutoff:3.500A) Processing helix chain 'O' and resid 244 through 250 Processing helix chain 'O' and resid 258 through 264 removed outlier: 3.565A pdb=" N ALA O 262 " --> pdb=" O GLN O 258 " (cutoff:3.500A) Processing helix chain 'O' and resid 269 through 284 removed outlier: 3.574A pdb=" N GLN O 273 " --> pdb=" O LEU O 269 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU O 275 " --> pdb=" O LYS O 271 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE O 282 " --> pdb=" O MET O 278 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR O 283 " --> pdb=" O GLU O 279 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ARG O 284 " --> pdb=" O MET O 280 " (cutoff:3.500A) Processing helix chain 'O' and resid 293 through 301 removed outlier: 4.252A pdb=" N LYS O 298 " --> pdb=" O GLU O 294 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER O 299 " --> pdb=" O GLU O 295 " (cutoff:3.500A) Processing helix chain 'O' and resid 306 through 318 removed outlier: 3.518A pdb=" N ALA O 314 " --> pdb=" O LEU O 310 " (cutoff:3.500A) Processing helix chain 'O' and resid 342 through 369 removed outlier: 3.603A pdb=" N LYS O 347 " --> pdb=" O LEU O 343 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY O 348 " --> pdb=" O GLN O 344 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP O 351 " --> pdb=" O LYS O 347 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TRP O 356 " --> pdb=" O ARG O 352 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP O 359 " --> pdb=" O PHE O 355 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS O 369 " --> pdb=" O MET O 365 " (cutoff:3.500A) Processing helix chain 'O' and resid 370 through 376 Processing sheet with id=AA1, first strand: chain 'W' and resid 60 through 65 removed outlier: 7.541A pdb=" N LEU W 61 " --> pdb=" O THR W 53 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N THR W 53 " --> pdb=" O LEU W 61 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N THR W 63 " --> pdb=" O LEU W 51 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LEU W 51 " --> pdb=" O THR W 63 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL W 8 " --> pdb=" O GLY W 50 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N SER W 5 " --> pdb=" O ARG W 108 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE W 110 " --> pdb=" O SER W 5 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N MET W 7 " --> pdb=" O ILE W 110 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N PHE W 112 " --> pdb=" O MET W 7 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N CYS W 9 " --> pdb=" O PHE W 112 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N MET W 107 " --> pdb=" O ASN W 137 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ASP W 139 " --> pdb=" O MET W 107 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE W 109 " --> pdb=" O ASP W 139 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ILE W 141 " --> pdb=" O ILE W 109 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ALA W 111 " --> pdb=" O ILE W 141 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE W 143 " --> pdb=" O ALA W 111 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N VAL W 113 " --> pdb=" O PHE W 143 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL W 173 " --> pdb=" O ASN W 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'V' and resid 200 through 202 removed outlier: 3.717A pdb=" N ARG V 161 " --> pdb=" O TYR V 201 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL V 141 " --> pdb=" O VAL V 109 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N MET V 107 " --> pdb=" O GLY V 59 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N MET V 57 " --> pdb=" O VAL V 109 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TRP V 111 " --> pdb=" O GLY V 55 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLY V 55 " --> pdb=" O TRP V 111 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLU V 60 " --> pdb=" O VAL V 69 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N VAL V 69 " --> pdb=" O GLU V 60 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL V 62 " --> pdb=" O VAL V 67 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N VAL V 67 " --> pdb=" O VAL V 62 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASP V 71 " --> pdb=" O SER V 34 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL V 31 " --> pdb=" O ASN V 206 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ARG V 208 " --> pdb=" O VAL V 31 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ILE V 33 " --> pdb=" O ARG V 208 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'T' and resid 281 through 283 removed outlier: 3.691A pdb=" N TYR T 315 " --> pdb=" O VAL T 309 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL T 309 " --> pdb=" O TYR T 315 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Z' and resid 810 through 811 removed outlier: 6.489A pdb=" N LEU Z 811 " --> pdb=" O THR Z 884 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N GLU Z 886 " --> pdb=" O LEU Z 811 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ALA Z 883 " --> pdb=" O VAL Z 872 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Z' and resid 845 through 846 Processing sheet with id=AA6, first strand: chain 'N' and resid 745 through 746 Processing sheet with id=AA7, first strand: chain 'N' and resid 749 through 750 removed outlier: 3.763A pdb=" N HIS N 754 " --> pdb=" O SER N 750 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 881 through 883 Processing sheet with id=AA9, first strand: chain 'N' and resid 803 through 804 removed outlier: 3.581A pdb=" N THR N 893 " --> pdb=" O LYS N 803 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 449 through 452 removed outlier: 6.881A pdb=" N SER S 415 " --> pdb=" O SER S 460 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'P' and resid 372 through 374 Processing sheet with id=AB3, first strand: chain 'Q' and resid 345 through 346 removed outlier: 3.583A pdb=" N VAL Q 345 " --> pdb=" O LEU Q 385 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'U' and resid 156 through 158 removed outlier: 4.176A pdb=" N ALA U 137 " --> pdb=" O VAL U 158 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL U 120 " --> pdb=" O VAL U 92 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL U 122 " --> pdb=" O TRP U 94 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS U 96 " --> pdb=" O VAL U 122 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE U 124 " --> pdb=" O HIS U 96 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ILE U 91 " --> pdb=" O GLY U 41 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLY U 41 " --> pdb=" O ILE U 91 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY U 93 " --> pdb=" O LEU U 39 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL U 38 " --> pdb=" O PHE U 54 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE U 54 " --> pdb=" O VAL U 38 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N SER U 42 " --> pdb=" O VAL U 50 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N VAL U 50 " --> pdb=" O SER U 42 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LYS U 8 " --> pdb=" O LEU U 48 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL U 50 " --> pdb=" O LYS U 8 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL U 10 " --> pdb=" O VAL U 50 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N ASN U 52 " --> pdb=" O VAL U 10 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N VAL U 9 " --> pdb=" O GLU U 161 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'U' and resid 58 through 60 Processing sheet with id=AB6, first strand: chain 'U' and resid 142 through 143 removed outlier: 3.628A pdb=" N GLU U 143 " --> pdb=" O SER U 152 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER U 152 " --> pdb=" O GLU U 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'O' and resid 290 through 292 removed outlier: 6.681A pdb=" N LYS O 321 " --> pdb=" O THR O 334 " (cutoff:3.500A) 1764 hydrogen bonds defined for protein. 5169 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: 28.32 Time building geometry restraints manager: 51.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 39855 1.06 - 1.27: 6979 1.27 - 1.49: 15755 1.49 - 1.71: 17368 1.71 - 1.93: 375 Bond restraints: 80332 Sorted by residual: bond pdb=" C LEU R 28 " pdb=" N PRO R 29 " ideal model delta sigma weight residual 1.334 1.928 -0.594 2.34e-02 1.83e+03 6.45e+02 bond pdb=" CA SER V 294 " pdb=" C SER V 294 " ideal model delta sigma weight residual 1.522 1.261 0.262 1.36e-02 5.41e+03 3.71e+02 bond pdb=" N ASN V 295 " pdb=" CA ASN V 295 " ideal model delta sigma weight residual 1.456 1.206 0.250 1.35e-02 5.49e+03 3.42e+02 bond pdb=" N GLN V 298 " pdb=" CA GLN V 298 " ideal model delta sigma weight residual 1.459 1.296 0.163 1.20e-02 6.94e+03 1.86e+02 bond pdb=" N SER V 294 " pdb=" CA SER V 294 " ideal model delta sigma weight residual 1.459 1.300 0.158 1.25e-02 6.40e+03 1.60e+02 ... (remaining 80327 not shown) Histogram of bond angle deviations from ideal: 54.18 - 72.86: 48 72.86 - 91.54: 21 91.54 - 110.23: 79628 110.23 - 128.91: 65673 128.91 - 147.59: 280 Bond angle restraints: 145650 Sorted by residual: angle pdb=" HZ2 LYS T 120 " pdb=" NZ LYS T 120 " pdb=" HZ3 LYS T 120 " ideal model delta sigma weight residual 109.00 54.18 54.82 3.00e+00 1.11e-01 3.34e+02 angle pdb=" HZ1 LYS R 283 " pdb=" NZ LYS R 283 " pdb=" HZ2 LYS R 283 " ideal model delta sigma weight residual 109.00 54.21 54.79 3.00e+00 1.11e-01 3.34e+02 angle pdb=" HZ1 LYS T 218 " pdb=" NZ LYS T 218 " pdb=" HZ2 LYS T 218 " ideal model delta sigma weight residual 109.00 54.22 54.78 3.00e+00 1.11e-01 3.33e+02 angle pdb=" HZ2 LYS O 313 " pdb=" NZ LYS O 313 " pdb=" HZ3 LYS O 313 " ideal model delta sigma weight residual 109.00 54.23 54.77 3.00e+00 1.11e-01 3.33e+02 angle pdb=" HZ1 LYS U 103 " pdb=" NZ LYS U 103 " pdb=" HZ2 LYS U 103 " ideal model delta sigma weight residual 109.00 54.27 54.73 3.00e+00 1.11e-01 3.33e+02 ... (remaining 145645 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 34349 17.98 - 35.95: 2034 35.95 - 53.93: 673 53.93 - 71.90: 273 71.90 - 89.88: 100 Dihedral angle restraints: 37429 sinusoidal: 20709 harmonic: 16720 Sorted by residual: dihedral pdb=" CA TYR T 241 " pdb=" C TYR T 241 " pdb=" N ASN T 242 " pdb=" CA ASN T 242 " ideal model delta harmonic sigma weight residual -180.00 -136.15 -43.85 0 5.00e+00 4.00e-02 7.69e+01 dihedral pdb=" CA PRO R 234 " pdb=" C PRO R 234 " pdb=" N ASP R 235 " pdb=" CA ASP R 235 " ideal model delta harmonic sigma weight residual 180.00 136.65 43.35 0 5.00e+00 4.00e-02 7.52e+01 dihedral pdb=" CA VAL P 398 " pdb=" C VAL P 398 " pdb=" N ASN P 399 " pdb=" CA ASN P 399 " ideal model delta harmonic sigma weight residual -180.00 -137.29 -42.71 0 5.00e+00 4.00e-02 7.30e+01 ... (remaining 37426 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 6169 0.147 - 0.294: 22 0.294 - 0.442: 4 0.442 - 0.589: 1 0.589 - 0.736: 2 Chirality restraints: 6198 Sorted by residual: chirality pdb=" CA SER V 294 " pdb=" N SER V 294 " pdb=" C SER V 294 " pdb=" CB SER V 294 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.74 2.00e-01 2.50e+01 1.35e+01 chirality pdb=" CA ASN V 295 " pdb=" N ASN V 295 " pdb=" C ASN V 295 " pdb=" CB ASN V 295 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.17e+01 chirality pdb=" CA VAL V 308 " pdb=" N VAL V 308 " pdb=" C VAL V 308 " pdb=" CB VAL V 308 " both_signs ideal model delta sigma weight residual False 2.44 1.98 0.46 2.00e-01 2.50e+01 5.28e+00 ... (remaining 6195 not shown) Planarity restraints: 11842 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL V 297 " -0.063 2.00e-02 2.50e+03 1.11e-01 1.24e+02 pdb=" C VAL V 297 " 0.193 2.00e-02 2.50e+03 pdb=" O VAL V 297 " -0.069 2.00e-02 2.50e+03 pdb=" N GLN V 298 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE V 309 " 0.011 2.00e-02 2.50e+03 4.82e-02 6.96e+01 pdb=" CG PHE V 309 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 PHE V 309 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE V 309 " -0.036 2.00e-02 2.50e+03 pdb=" CE1 PHE V 309 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 PHE V 309 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE V 309 " -0.034 2.00e-02 2.50e+03 pdb=" HD1 PHE V 309 " -0.004 2.00e-02 2.50e+03 pdb=" HD2 PHE V 309 " 0.099 2.00e-02 2.50e+03 pdb=" HE1 PHE V 309 " 0.032 2.00e-02 2.50e+03 pdb=" HE2 PHE V 309 " -0.077 2.00e-02 2.50e+03 pdb=" HZ PHE V 309 " 0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR V 293 " -0.034 2.00e-02 2.50e+03 5.88e-02 3.45e+01 pdb=" C THR V 293 " 0.102 2.00e-02 2.50e+03 pdb=" O THR V 293 " -0.040 2.00e-02 2.50e+03 pdb=" N SER V 294 " -0.028 2.00e-02 2.50e+03 ... (remaining 11839 not shown) Histogram of nonbonded interaction distances: 1.04 - 1.75: 73 1.75 - 2.46: 50444 2.46 - 3.18: 247469 3.18 - 3.89: 309921 3.89 - 4.60: 500032 Nonbonded interactions: 1107939 Sorted by model distance: nonbonded pdb=" O ILE V 296 " pdb=" HB2 CYS V 299 " model vdw 1.040 2.620 nonbonded pdb=" O ASP V 289 " pdb="HG23 THR V 293 " model vdw 1.314 2.620 nonbonded pdb=" NE2 HIS V 237 " pdb=" HG2 GLN V 298 " model vdw 1.380 2.770 nonbonded pdb=" O ASN O 227 " pdb=" HG1 THR O 228 " model vdw 1.454 1.850 nonbonded pdb=" O ASP S 465 " pdb=" H TYR S 467 " model vdw 1.462 1.850 ... (remaining 1107934 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.860 Extract box with map and model: 13.520 Check model and map are aligned: 0.870 Set scattering table: 0.550 Process input model: 189.820 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 212.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 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 0.594 40342 Z= 0.462 Angle : 0.846 21.955 54493 Z= 0.496 Chirality : 0.045 0.736 6198 Planarity : 0.006 0.111 7021 Dihedral : 16.121 89.878 15271 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 3.16 % Allowed : 11.81 % Favored : 85.03 % Rotamer: Outliers : 3.82 % Allowed : 7.34 % Favored : 88.84 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.15 (0.08), residues: 4970 helix: -4.14 (0.05), residues: 2988 sheet: -2.47 (0.35), residues: 175 loop : -3.82 (0.12), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP P 80 HIS 0.011 0.002 HIS N 931 PHE 0.024 0.002 PHE V 309 TYR 0.030 0.002 TYR N 813 ARG 0.009 0.001 ARG S 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 296 is missing expected H atoms. Skipping. Evaluate side-chains 1767 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 1601 time to evaluate : 4.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 6 THR cc_start: 0.9205 (m) cc_final: 0.8971 (p) REVERT: W 39 SER cc_start: 0.9307 (m) cc_final: 0.9063 (p) REVERT: W 70 ARG cc_start: 0.8884 (mtp180) cc_final: 0.8410 (tpp-160) REVERT: W 112 PHE cc_start: 0.5706 (m-80) cc_final: 0.5458 (m-10) REVERT: W 116 PRO cc_start: 0.7676 (Cg_exo) cc_final: 0.7424 (Cg_endo) REVERT: W 140 ILE cc_start: 0.7346 (mt) cc_final: 0.6961 (mt) REVERT: V 26 ASP cc_start: 0.6044 (OUTLIER) cc_final: 0.5582 (m-30) REVERT: V 32 TYR cc_start: 0.7560 (m-10) cc_final: 0.7268 (m-10) REVERT: V 145 VAL cc_start: 0.9382 (t) cc_final: 0.9174 (m) REVERT: V 152 LYS cc_start: 0.7872 (mmtt) cc_final: 0.7174 (tmtt) REVERT: V 167 MET cc_start: 0.8508 (mtp) cc_final: 0.8251 (mmm) REVERT: V 175 ARG cc_start: 0.8003 (tpp-160) cc_final: 0.7328 (ttm-80) REVERT: V 177 THR cc_start: 0.7559 (m) cc_final: 0.7285 (t) REVERT: V 190 GLN cc_start: 0.8449 (tm-30) cc_final: 0.8097 (tm-30) REVERT: V 262 GLU cc_start: 0.8437 (pt0) cc_final: 0.8172 (pp20) REVERT: T 220 ILE cc_start: 0.8336 (pt) cc_final: 0.8080 (tt) REVERT: T 258 PHE cc_start: 0.7904 (m-10) cc_final: 0.7639 (m-10) REVERT: T 265 ASP cc_start: 0.8809 (m-30) cc_final: 0.7931 (t0) REVERT: T 269 ASP cc_start: 0.8233 (m-30) cc_final: 0.7175 (m-30) REVERT: T 322 GLN cc_start: 0.7581 (tp40) cc_final: 0.6974 (pt0) REVERT: Y 21 GLU cc_start: 0.7839 (pt0) cc_final: 0.7560 (pm20) REVERT: Y 67 MET cc_start: 0.3832 (mpp) cc_final: 0.3561 (ptt) REVERT: Z 58 MET cc_start: 0.2707 (mmt) cc_final: 0.2380 (mmm) REVERT: Z 113 MET cc_start: 0.2636 (mmt) cc_final: 0.1811 (mtm) REVERT: Z 161 HIS cc_start: 0.7682 (OUTLIER) cc_final: 0.7296 (m90) REVERT: Z 216 MET cc_start: 0.2767 (ttp) cc_final: 0.2108 (tpt) REVERT: Z 281 ILE cc_start: 0.7490 (tp) cc_final: 0.6690 (tp) REVERT: Z 296 PHE cc_start: 0.6733 (t80) cc_final: 0.6501 (t80) REVERT: Z 301 HIS cc_start: 0.7030 (t70) cc_final: 0.6707 (t70) REVERT: Z 380 PHE cc_start: 0.6222 (m-10) cc_final: 0.6020 (m-10) REVERT: Z 389 LYS cc_start: 0.6496 (mttm) cc_final: 0.5842 (tmmt) REVERT: Z 472 HIS cc_start: 0.4499 (OUTLIER) cc_final: 0.3867 (p-80) REVERT: Z 498 LEU cc_start: 0.6801 (tp) cc_final: 0.6583 (mt) REVERT: Z 547 GLU cc_start: 0.6949 (pt0) cc_final: 0.6649 (pp20) REVERT: Z 551 LYS cc_start: 0.6641 (mtmm) cc_final: 0.6268 (mptt) REVERT: Z 569 LYS cc_start: 0.3425 (mttt) cc_final: 0.3105 (mttm) REVERT: Z 574 GLU cc_start: 0.6771 (OUTLIER) cc_final: 0.5607 (pm20) REVERT: Z 593 THR cc_start: 0.5324 (p) cc_final: 0.4818 (t) REVERT: Z 657 ILE cc_start: 0.7922 (mm) cc_final: 0.7468 (mm) REVERT: Z 662 MET cc_start: 0.3638 (mtp) cc_final: 0.3284 (ttt) REVERT: Z 699 VAL cc_start: 0.3853 (p) cc_final: 0.3545 (p) REVERT: Z 761 MET cc_start: 0.1170 (ttm) cc_final: 0.0967 (ttm) REVERT: Z 788 MET cc_start: 0.5065 (ptm) cc_final: 0.4745 (tpp) REVERT: N 48 LEU cc_start: 0.9298 (mt) cc_final: 0.8980 (tp) REVERT: N 70 HIS cc_start: 0.8363 (OUTLIER) cc_final: 0.8041 (m90) REVERT: N 95 GLU cc_start: 0.8621 (pm20) cc_final: 0.8146 (mp0) REVERT: N 184 CYS cc_start: 0.5957 (OUTLIER) cc_final: 0.5661 (m) REVERT: N 202 VAL cc_start: 0.8620 (t) cc_final: 0.8310 (t) REVERT: N 349 ASP cc_start: 0.7623 (t0) cc_final: 0.7418 (t70) REVERT: N 358 ASP cc_start: 0.7669 (m-30) cc_final: 0.7426 (t0) REVERT: N 397 THR cc_start: 0.8172 (p) cc_final: 0.7776 (p) REVERT: N 449 ILE cc_start: 0.5917 (mt) cc_final: 0.4840 (mt) REVERT: N 495 ASP cc_start: 0.7209 (m-30) cc_final: 0.6939 (p0) REVERT: N 538 GLU cc_start: 0.8481 (mt-10) cc_final: 0.7618 (tm-30) REVERT: N 539 THR cc_start: 0.6215 (p) cc_final: 0.5002 (p) REVERT: N 573 ASP cc_start: 0.7268 (m-30) cc_final: 0.6786 (m-30) REVERT: N 604 HIS cc_start: 0.6731 (p90) cc_final: 0.5462 (m-70) REVERT: N 609 ASP cc_start: 0.6887 (OUTLIER) cc_final: 0.6266 (t70) REVERT: N 725 MET cc_start: 0.7960 (mtm) cc_final: 0.7552 (mtm) REVERT: N 772 TRP cc_start: 0.7447 (t-100) cc_final: 0.6494 (t-100) REVERT: N 847 GLU cc_start: 0.6810 (mt-10) cc_final: 0.5913 (tp30) REVERT: N 879 ASP cc_start: 0.7888 (m-30) cc_final: 0.7365 (p0) REVERT: S 66 GLU cc_start: 0.9298 (tt0) cc_final: 0.8999 (tp30) REVERT: S 69 THR cc_start: 0.8797 (m) cc_final: 0.8542 (p) REVERT: S 76 LYS cc_start: 0.8780 (ttpp) cc_final: 0.8222 (mmmt) REVERT: S 77 GLU cc_start: 0.7205 (mm-30) cc_final: 0.5944 (tm-30) REVERT: S 114 TYR cc_start: 0.8500 (t80) cc_final: 0.8033 (t80) REVERT: S 166 TYR cc_start: 0.8435 (t80) cc_final: 0.7935 (t80) REVERT: S 171 VAL cc_start: 0.8793 (t) cc_final: 0.8572 (t) REVERT: S 224 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8462 (mp) REVERT: S 289 LEU cc_start: 0.8494 (mt) cc_final: 0.8264 (mt) REVERT: S 301 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7565 (tt0) REVERT: S 307 ARG cc_start: 0.8698 (ttp-110) cc_final: 0.8494 (ptt90) REVERT: S 315 LYS cc_start: 0.8683 (mttt) cc_final: 0.8464 (mmtt) REVERT: S 389 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7938 (p0) REVERT: S 393 THR cc_start: 0.8902 (m) cc_final: 0.8535 (p) REVERT: S 408 ARG cc_start: 0.9015 (ttp-110) cc_final: 0.8775 (ttp-110) REVERT: S 411 SER cc_start: 0.8512 (OUTLIER) cc_final: 0.8154 (p) REVERT: S 433 ASP cc_start: 0.8344 (t0) cc_final: 0.7672 (t0) REVERT: S 436 PHE cc_start: 0.8593 (m-10) cc_final: 0.8289 (m-10) REVERT: S 440 LYS cc_start: 0.9172 (tptt) cc_final: 0.8946 (tppt) REVERT: S 476 PHE cc_start: 0.8859 (m-80) cc_final: 0.8656 (m-10) REVERT: S 520 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8381 (tp30) REVERT: P 1 MET cc_start: 0.6618 (mmt) cc_final: 0.5896 (mmt) REVERT: P 44 ILE cc_start: 0.8888 (mm) cc_final: 0.8563 (pt) REVERT: P 60 MET cc_start: 0.8679 (tpp) cc_final: 0.8221 (tpp) REVERT: P 73 MET cc_start: 0.8749 (mtp) cc_final: 0.8504 (mtm) REVERT: P 88 MET cc_start: 0.9112 (ttp) cc_final: 0.8512 (mmm) REVERT: P 103 LYS cc_start: 0.8706 (mmtm) cc_final: 0.8353 (mmmm) REVERT: P 126 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.8092 (t70) REVERT: P 129 ARG cc_start: 0.8443 (ttm110) cc_final: 0.8120 (ttp-110) REVERT: P 230 MET cc_start: 0.9505 (mmm) cc_final: 0.9224 (mmm) REVERT: P 304 ASP cc_start: 0.8698 (m-30) cc_final: 0.8423 (p0) REVERT: P 326 MET cc_start: 0.8545 (ptt) cc_final: 0.8039 (ppp) REVERT: P 332 SER cc_start: 0.6542 (OUTLIER) cc_final: 0.6145 (t) REVERT: P 353 ASP cc_start: 0.9117 (t0) cc_final: 0.8885 (t0) REVERT: P 364 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7876 (ttm110) REVERT: P 365 ILE cc_start: 0.8348 (mt) cc_final: 0.7870 (mt) REVERT: P 387 ASP cc_start: 0.8795 (t70) cc_final: 0.8593 (m-30) REVERT: P 430 GLN cc_start: 0.8835 (mm-40) cc_final: 0.8593 (mm-40) REVERT: P 440 ASN cc_start: 0.9197 (m-40) cc_final: 0.8593 (m110) REVERT: Q 41 GLU cc_start: 0.3673 (OUTLIER) cc_final: 0.3142 (mp0) REVERT: Q 51 LEU cc_start: 0.8878 (tp) cc_final: 0.8645 (tp) REVERT: Q 72 TYR cc_start: 0.7872 (m-10) cc_final: 0.7631 (m-80) REVERT: Q 94 ASP cc_start: 0.7475 (m-30) cc_final: 0.7075 (p0) REVERT: Q 152 GLN cc_start: 0.7535 (mm-40) cc_final: 0.7225 (tm-30) REVERT: Q 174 SER cc_start: 0.8963 (t) cc_final: 0.8513 (p) REVERT: Q 249 THR cc_start: 0.8833 (p) cc_final: 0.8323 (p) REVERT: Q 254 MET cc_start: 0.9204 (ttp) cc_final: 0.8894 (ttp) REVERT: Q 257 CYS cc_start: 0.9121 (m) cc_final: 0.8864 (p) REVERT: Q 258 LYS cc_start: 0.9132 (mmmt) cc_final: 0.8869 (mmmm) REVERT: Q 260 MET cc_start: 0.9053 (mmm) cc_final: 0.8338 (mmm) REVERT: Q 275 LEU cc_start: 0.8686 (mt) cc_final: 0.8208 (mp) REVERT: Q 382 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8204 (mp0) REVERT: Q 390 GLU cc_start: 0.7057 (tt0) cc_final: 0.6729 (tt0) REVERT: Q 394 ASP cc_start: 0.9210 (t70) cc_final: 0.8231 (p0) REVERT: Q 395 LYS cc_start: 0.9047 (mmtt) cc_final: 0.8746 (mttm) REVERT: Q 412 ASP cc_start: 0.9385 (m-30) cc_final: 0.9095 (m-30) REVERT: R 16 ASP cc_start: 0.8706 (t0) cc_final: 0.8052 (p0) REVERT: R 42 MET cc_start: 0.9044 (mmm) cc_final: 0.8507 (tmm) REVERT: R 86 GLU cc_start: 0.9238 (tt0) cc_final: 0.8901 (tp30) REVERT: R 145 LEU cc_start: 0.9426 (tp) cc_final: 0.9155 (mt) REVERT: R 155 ASP cc_start: 0.9054 (m-30) cc_final: 0.8833 (m-30) REVERT: R 158 THR cc_start: 0.9390 (m) cc_final: 0.9099 (t) REVERT: R 162 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8620 (mm-30) REVERT: R 187 TYR cc_start: 0.8538 (t80) cc_final: 0.8302 (t80) REVERT: R 225 TYR cc_start: 0.9239 (m-10) cc_final: 0.9031 (m-10) REVERT: R 234 PRO cc_start: 0.8827 (OUTLIER) cc_final: 0.8551 (Cg_endo) REVERT: R 282 MET cc_start: 0.7107 (mtp) cc_final: 0.6586 (mtp) REVERT: R 283 LYS cc_start: 0.8703 (mmtt) cc_final: 0.8476 (mmtp) REVERT: R 286 TRP cc_start: 0.6367 (m100) cc_final: 0.6020 (m100) REVERT: R 302 HIS cc_start: 0.8648 (t-90) cc_final: 0.8377 (t-90) REVERT: R 355 GLU cc_start: 0.8381 (mt-10) cc_final: 0.7972 (pm20) REVERT: R 368 GLU cc_start: 0.9324 (tp30) cc_final: 0.9014 (tp30) REVERT: R 374 ASP cc_start: 0.9059 (m-30) cc_final: 0.8646 (p0) REVERT: R 379 ARG cc_start: 0.8407 (ttm170) cc_final: 0.8190 (mtp85) REVERT: U 9 VAL cc_start: 0.9138 (t) cc_final: 0.8912 (t) REVERT: U 44 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7731 (pm20) REVERT: U 49 ASP cc_start: 0.8905 (m-30) cc_final: 0.8619 (m-30) REVERT: U 56 VAL cc_start: 0.8205 (t) cc_final: 0.7746 (m) REVERT: U 65 ASP cc_start: 0.8013 (p0) cc_final: 0.6926 (t0) REVERT: U 104 ASN cc_start: 0.8517 (t0) cc_final: 0.7690 (m-40) REVERT: U 108 ILE cc_start: 0.8735 (mt) cc_final: 0.8481 (mt) REVERT: U 136 GLU cc_start: 0.8327 (mp0) cc_final: 0.8037 (mp0) REVERT: U 140 SER cc_start: 0.8556 (t) cc_final: 0.8313 (m) REVERT: U 157 HIS cc_start: 0.8423 (t70) cc_final: 0.7852 (t70) REVERT: U 161 GLU cc_start: 0.8076 (pt0) cc_final: 0.7511 (pm20) REVERT: U 169 GLU cc_start: 0.9345 (tp30) cc_final: 0.9046 (tm-30) REVERT: U 189 GLN cc_start: 0.9443 (tp40) cc_final: 0.9204 (tp-100) REVERT: U 193 ASN cc_start: 0.8942 (m-40) cc_final: 0.8302 (m110) REVERT: U 229 GLN cc_start: 0.9220 (tt0) cc_final: 0.8925 (tt0) REVERT: U 247 LYS cc_start: 0.8885 (tttt) cc_final: 0.8674 (tptt) REVERT: U 267 ARG cc_start: 0.8460 (ttt180) cc_final: 0.7935 (ttt180) REVERT: U 284 ASP cc_start: 0.8458 (m-30) cc_final: 0.7687 (t0) REVERT: O 39 LEU cc_start: 0.8562 (mt) cc_final: 0.8358 (pp) REVERT: O 74 LEU cc_start: 0.8312 (mt) cc_final: 0.8000 (tp) REVERT: O 121 LEU cc_start: 0.9238 (mt) cc_final: 0.9018 (tt) REVERT: O 157 ASP cc_start: 0.9487 (t70) cc_final: 0.9232 (t70) REVERT: O 174 LYS cc_start: 0.9019 (tttt) cc_final: 0.8686 (tppt) REVERT: O 216 LEU cc_start: 0.9011 (tp) cc_final: 0.8757 (tp) REVERT: O 339 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7444 (ptt180) outliers start: 166 outliers final: 52 residues processed: 1707 average time/residue: 1.1756 time to fit residues: 3118.5399 Evaluate side-chains 1124 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 1054 time to evaluate : 4.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 10 VAL Chi-restraints excluded: chain W residue 41 THR Chi-restraints excluded: chain W residue 47 ASN Chi-restraints excluded: chain W residue 67 ASP Chi-restraints excluded: chain W residue 189 LEU Chi-restraints excluded: chain V residue 26 ASP Chi-restraints excluded: chain V residue 120 CYS Chi-restraints excluded: chain V residue 238 CYS Chi-restraints excluded: chain T residue 178 TYR Chi-restraints excluded: chain T residue 231 SER Chi-restraints excluded: chain T residue 243 LYS Chi-restraints excluded: chain Y residue 35 ASP Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 452 ASN Chi-restraints excluded: chain Z residue 472 HIS Chi-restraints excluded: chain Z residue 574 GLU Chi-restraints excluded: chain Z residue 606 VAL Chi-restraints excluded: chain Z residue 608 LYS Chi-restraints excluded: chain Z residue 707 LEU Chi-restraints excluded: chain Z residue 741 LEU Chi-restraints excluded: chain Z residue 748 LEU Chi-restraints excluded: chain Z residue 759 LEU Chi-restraints excluded: chain Z residue 873 LEU Chi-restraints excluded: chain N residue 70 HIS Chi-restraints excluded: chain N residue 165 LYS Chi-restraints excluded: chain N residue 184 CYS Chi-restraints excluded: chain N residue 345 ASN Chi-restraints excluded: chain N residue 609 ASP Chi-restraints excluded: chain N residue 620 GLU Chi-restraints excluded: chain N residue 621 SER Chi-restraints excluded: chain N residue 672 LEU Chi-restraints excluded: chain N residue 838 LYS Chi-restraints excluded: chain N residue 892 LEU Chi-restraints excluded: chain S residue 111 TYR Chi-restraints excluded: chain S residue 125 ASN Chi-restraints excluded: chain S residue 224 LEU Chi-restraints excluded: chain S residue 257 ASN Chi-restraints excluded: chain S residue 302 TYR Chi-restraints excluded: chain S residue 353 LEU Chi-restraints excluded: chain S residue 354 LYS Chi-restraints excluded: chain S residue 389 ASP Chi-restraints excluded: chain S residue 411 SER Chi-restraints excluded: chain S residue 469 THR Chi-restraints excluded: chain P residue 126 ASP Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain P residue 332 SER Chi-restraints excluded: chain P residue 364 ARG Chi-restraints excluded: chain P residue 451 MET Chi-restraints excluded: chain Q residue 41 GLU Chi-restraints excluded: chain Q residue 328 ASP Chi-restraints excluded: chain Q residue 333 GLN Chi-restraints excluded: chain Q residue 382 GLU Chi-restraints excluded: chain Q residue 388 PHE Chi-restraints excluded: chain Q residue 415 TYR Chi-restraints excluded: chain R residue 63 TRP Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 209 THR Chi-restraints excluded: chain R residue 210 SER Chi-restraints excluded: chain R residue 234 PRO Chi-restraints excluded: chain R residue 235 ASP Chi-restraints excluded: chain R residue 346 LYS Chi-restraints excluded: chain R residue 382 LYS Chi-restraints excluded: chain U residue 44 GLN Chi-restraints excluded: chain U residue 100 LYS Chi-restraints excluded: chain U residue 250 TYR Chi-restraints excluded: chain U residue 253 THR Chi-restraints excluded: chain O residue 208 GLU Chi-restraints excluded: chain O residue 244 ASN Chi-restraints excluded: chain O residue 339 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 417 optimal weight: 5.9990 chunk 375 optimal weight: 6.9990 chunk 208 optimal weight: 9.9990 chunk 128 optimal weight: 9.9990 chunk 253 optimal weight: 9.9990 chunk 200 optimal weight: 9.9990 chunk 387 optimal weight: 6.9990 chunk 150 optimal weight: 8.9990 chunk 235 optimal weight: 0.9990 chunk 288 optimal weight: 5.9990 chunk 449 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 44 ASN W 56 ASN W 137 ASN V 206 ASN V 232 GLN V 298 GLN T 108 ASN T 127 ASN T 170 GLN T 202 GLN Z 51 GLN Z 53 GLN Z 81 GLN ** Z 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 149 GLN ** N 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 338 HIS N 355 ASN N 500 ASN N 540 GLN S 168 GLN S 193 GLN ** S 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 257 ASN ** S 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 28 HIS Q 36 GLN Q 405 GLN ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 225 GLN U 235 ASN O 12 GLN O 264 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 40342 Z= 0.321 Angle : 0.786 9.117 54493 Z= 0.427 Chirality : 0.041 0.260 6198 Planarity : 0.006 0.145 7021 Dihedral : 8.280 86.280 5556 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.89 % Allowed : 8.21 % Favored : 90.91 % Rotamer: Outliers : 3.98 % Allowed : 15.14 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.59 (0.10), residues: 4970 helix: -2.75 (0.07), residues: 3124 sheet: -2.20 (0.37), residues: 168 loop : -3.40 (0.13), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP P 80 HIS 0.015 0.002 HIS S 110 PHE 0.024 0.002 PHE O 282 TYR 0.029 0.002 TYR Z 781 ARG 0.012 0.001 ARG S 236 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 296 is missing expected H atoms. Skipping. Evaluate side-chains 1251 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 1078 time to evaluate : 4.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 1 MET cc_start: 0.3576 (mtp) cc_final: 0.3176 (mtp) REVERT: W 47 ASN cc_start: 0.6579 (OUTLIER) cc_final: 0.6050 (t0) REVERT: W 70 ARG cc_start: 0.9037 (mtp180) cc_final: 0.8600 (mmp80) REVERT: W 112 PHE cc_start: 0.5884 (m-80) cc_final: 0.5446 (m-10) REVERT: V 32 TYR cc_start: 0.7513 (m-10) cc_final: 0.6972 (m-10) REVERT: V 40 LYS cc_start: 0.8652 (mttm) cc_final: 0.8333 (tptt) REVERT: V 122 LEU cc_start: 0.9068 (mt) cc_final: 0.8847 (mp) REVERT: V 145 VAL cc_start: 0.9438 (t) cc_final: 0.9175 (m) REVERT: V 158 ASP cc_start: 0.8148 (m-30) cc_final: 0.7790 (m-30) REVERT: V 175 ARG cc_start: 0.8062 (tpp-160) cc_final: 0.7444 (ttm-80) REVERT: V 223 LYS cc_start: 0.8984 (mttt) cc_final: 0.8664 (mttt) REVERT: V 260 GLU cc_start: 0.8823 (tp30) cc_final: 0.8136 (mp0) REVERT: T 207 GLU cc_start: 0.9330 (mm-30) cc_final: 0.8790 (mp0) REVERT: T 212 LEU cc_start: 0.9213 (tp) cc_final: 0.8828 (mm) REVERT: T 219 ASP cc_start: 0.8846 (m-30) cc_final: 0.8317 (t0) REVERT: T 220 ILE cc_start: 0.8327 (pt) cc_final: 0.8036 (tt) REVERT: T 223 ASN cc_start: 0.6523 (OUTLIER) cc_final: 0.6010 (t0) REVERT: T 234 GLN cc_start: 0.8237 (tm-30) cc_final: 0.7786 (tm-30) REVERT: T 258 PHE cc_start: 0.7678 (m-10) cc_final: 0.7463 (m-10) REVERT: T 265 ASP cc_start: 0.8798 (m-30) cc_final: 0.8207 (t0) REVERT: T 269 ASP cc_start: 0.8342 (m-30) cc_final: 0.7853 (m-30) REVERT: T 322 GLN cc_start: 0.7781 (tp40) cc_final: 0.7124 (pt0) REVERT: Z 33 ARG cc_start: 0.3468 (mmt-90) cc_final: 0.3250 (mmt180) REVERT: Z 58 MET cc_start: 0.2902 (mmt) cc_final: 0.2631 (mmm) REVERT: Z 103 TYR cc_start: 0.2490 (OUTLIER) cc_final: 0.1699 (m-80) REVERT: Z 113 MET cc_start: 0.2376 (mmt) cc_final: 0.1465 (mtm) REVERT: Z 216 MET cc_start: 0.2427 (ttp) cc_final: 0.1836 (tpt) REVERT: Z 281 ILE cc_start: 0.6745 (tp) cc_final: 0.6544 (tp) REVERT: Z 296 PHE cc_start: 0.6625 (t80) cc_final: 0.5120 (t80) REVERT: Z 335 ARG cc_start: 0.7285 (mtt-85) cc_final: 0.7026 (ptm160) REVERT: Z 389 LYS cc_start: 0.6597 (mttm) cc_final: 0.6066 (pttp) REVERT: Z 432 TYR cc_start: 0.6272 (m-80) cc_final: 0.5339 (m-80) REVERT: Z 551 LYS cc_start: 0.6764 (mtmm) cc_final: 0.6484 (mmtt) REVERT: Z 593 THR cc_start: 0.6317 (p) cc_final: 0.5901 (t) REVERT: Z 662 MET cc_start: 0.3985 (mtp) cc_final: 0.3527 (ttt) REVERT: Z 699 VAL cc_start: 0.3768 (p) cc_final: 0.3255 (p) REVERT: Z 718 ASP cc_start: 0.2903 (OUTLIER) cc_final: 0.2610 (t70) REVERT: Z 744 MET cc_start: 0.5968 (ppp) cc_final: 0.5749 (ppp) REVERT: N 37 GLU cc_start: 0.9063 (tm-30) cc_final: 0.8698 (mp0) REVERT: N 46 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7045 (tm-30) REVERT: N 48 LEU cc_start: 0.9307 (mt) cc_final: 0.8993 (tp) REVERT: N 76 GLU cc_start: 0.8222 (mp0) cc_final: 0.8001 (mp0) REVERT: N 495 ASP cc_start: 0.6811 (m-30) cc_final: 0.6584 (m-30) REVERT: N 538 GLU cc_start: 0.8723 (mt-10) cc_final: 0.7806 (tm-30) REVERT: N 539 THR cc_start: 0.6953 (p) cc_final: 0.6479 (p) REVERT: N 580 ARG cc_start: 0.8959 (ttp-170) cc_final: 0.8642 (tmm-80) REVERT: N 601 ARG cc_start: 0.6382 (mtm180) cc_final: 0.6012 (mtt180) REVERT: N 604 HIS cc_start: 0.6994 (p90) cc_final: 0.5677 (m-70) REVERT: N 605 VAL cc_start: 0.8108 (t) cc_final: 0.7892 (t) REVERT: N 695 MET cc_start: 0.2454 (mmt) cc_final: 0.2183 (mmt) REVERT: N 725 MET cc_start: 0.8226 (mtm) cc_final: 0.7669 (mmt) REVERT: N 847 GLU cc_start: 0.6799 (mt-10) cc_final: 0.5663 (tp30) REVERT: N 879 ASP cc_start: 0.8130 (m-30) cc_final: 0.7682 (p0) REVERT: S 66 GLU cc_start: 0.9295 (tt0) cc_final: 0.9023 (tp30) REVERT: S 114 TYR cc_start: 0.8442 (t80) cc_final: 0.8117 (t80) REVERT: S 166 TYR cc_start: 0.8498 (t80) cc_final: 0.8151 (t80) REVERT: S 219 GLU cc_start: 0.8698 (tt0) cc_final: 0.8417 (tt0) REVERT: S 243 ASP cc_start: 0.8481 (p0) cc_final: 0.8254 (m-30) REVERT: S 263 LEU cc_start: 0.9166 (mt) cc_final: 0.8842 (mt) REVERT: S 281 ASN cc_start: 0.8313 (t0) cc_final: 0.8104 (t0) REVERT: S 283 ASN cc_start: 0.8458 (t0) cc_final: 0.8169 (t0) REVERT: S 315 LYS cc_start: 0.8883 (mttt) cc_final: 0.8625 (mmtt) REVERT: S 399 ARG cc_start: 0.8824 (mtp-110) cc_final: 0.8482 (mtm110) REVERT: S 408 ARG cc_start: 0.8954 (ttp-110) cc_final: 0.8689 (ttp-110) REVERT: P 1 MET cc_start: 0.6601 (mmt) cc_final: 0.5927 (mmt) REVERT: P 60 MET cc_start: 0.8460 (tpp) cc_final: 0.8214 (tpp) REVERT: P 126 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.7338 (t70) REVERT: P 154 GLU cc_start: 0.9113 (tt0) cc_final: 0.8599 (pp20) REVERT: P 275 ILE cc_start: 0.9287 (pt) cc_final: 0.8990 (mp) REVERT: P 303 LYS cc_start: 0.8640 (ttpp) cc_final: 0.8372 (tppt) REVERT: P 304 ASP cc_start: 0.8669 (m-30) cc_final: 0.8202 (p0) REVERT: P 326 MET cc_start: 0.8542 (ptt) cc_final: 0.8110 (pmm) REVERT: P 332 SER cc_start: 0.6845 (OUTLIER) cc_final: 0.6513 (t) REVERT: P 353 ASP cc_start: 0.8973 (t0) cc_final: 0.8633 (t0) REVERT: P 364 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7931 (ttm110) REVERT: P 387 ASP cc_start: 0.8893 (t70) cc_final: 0.8640 (m-30) REVERT: P 436 MET cc_start: 0.7717 (tpt) cc_final: 0.7267 (mmm) REVERT: Q 41 GLU cc_start: 0.3434 (OUTLIER) cc_final: 0.2801 (mp0) REVERT: Q 93 LEU cc_start: 0.6628 (tp) cc_final: 0.6424 (tp) REVERT: Q 94 ASP cc_start: 0.7611 (m-30) cc_final: 0.7230 (p0) REVERT: Q 187 ARG cc_start: 0.7963 (tpm170) cc_final: 0.7593 (tpm170) REVERT: Q 257 CYS cc_start: 0.9110 (m) cc_final: 0.8843 (p) REVERT: Q 260 MET cc_start: 0.9069 (mmm) cc_final: 0.8797 (mmm) REVERT: Q 289 CYS cc_start: 0.9054 (t) cc_final: 0.8592 (p) REVERT: Q 290 VAL cc_start: 0.9377 (t) cc_final: 0.9147 (m) REVERT: Q 312 GLU cc_start: 0.8651 (mp0) cc_final: 0.8362 (mp0) REVERT: R 16 ASP cc_start: 0.8575 (t0) cc_final: 0.8050 (p0) REVERT: R 42 MET cc_start: 0.9125 (mmm) cc_final: 0.8523 (tmm) REVERT: R 86 GLU cc_start: 0.9253 (tt0) cc_final: 0.9002 (tp30) REVERT: R 158 THR cc_start: 0.9322 (m) cc_final: 0.9048 (t) REVERT: R 162 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8595 (mm-30) REVERT: R 187 TYR cc_start: 0.8678 (t80) cc_final: 0.8435 (t80) REVERT: R 195 LYS cc_start: 0.8783 (ttpt) cc_final: 0.8471 (ttpt) REVERT: R 225 TYR cc_start: 0.9309 (m-10) cc_final: 0.8823 (m-10) REVERT: R 272 PHE cc_start: 0.7880 (OUTLIER) cc_final: 0.7195 (t80) REVERT: R 282 MET cc_start: 0.7258 (mtp) cc_final: 0.6862 (mtp) REVERT: R 286 TRP cc_start: 0.6449 (m100) cc_final: 0.6071 (m100) REVERT: R 302 HIS cc_start: 0.8713 (t-90) cc_final: 0.8439 (t70) REVERT: R 304 TYR cc_start: 0.7922 (m-10) cc_final: 0.7369 (m-10) REVERT: R 333 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6856 (tt0) REVERT: R 355 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8134 (pm20) REVERT: U 44 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7855 (pm20) REVERT: U 49 ASP cc_start: 0.8848 (m-30) cc_final: 0.8592 (m-30) REVERT: U 65 ASP cc_start: 0.8417 (p0) cc_final: 0.8137 (m-30) REVERT: U 79 TYR cc_start: 0.8499 (t80) cc_final: 0.8245 (t80) REVERT: U 86 ASN cc_start: 0.8846 (t0) cc_final: 0.8556 (t0) REVERT: U 100 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8121 (pttp) REVERT: U 136 GLU cc_start: 0.8219 (mp0) cc_final: 0.7872 (mp0) REVERT: U 169 GLU cc_start: 0.9259 (tp30) cc_final: 0.8816 (tm-30) REVERT: U 189 GLN cc_start: 0.9445 (tp40) cc_final: 0.9217 (tp40) REVERT: U 229 GLN cc_start: 0.9219 (tt0) cc_final: 0.8824 (tt0) REVERT: O 39 LEU cc_start: 0.8439 (mt) cc_final: 0.8235 (tp) REVERT: O 74 LEU cc_start: 0.8313 (mt) cc_final: 0.7950 (tp) REVERT: O 78 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7977 (mt-10) REVERT: O 121 LEU cc_start: 0.9348 (mt) cc_final: 0.9030 (tt) REVERT: O 154 ARG cc_start: 0.9177 (mmt90) cc_final: 0.8815 (mtp85) REVERT: O 339 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7850 (ptt-90) outliers start: 173 outliers final: 121 residues processed: 1196 average time/residue: 1.1381 time to fit residues: 2144.7062 Evaluate side-chains 1085 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 951 time to evaluate : 4.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 47 ASN Chi-restraints excluded: chain W residue 67 ASP Chi-restraints excluded: chain W residue 185 SER Chi-restraints excluded: chain W residue 186 SER Chi-restraints excluded: chain W residue 188 ILE Chi-restraints excluded: chain V residue 88 ASP Chi-restraints excluded: chain V residue 97 ASP Chi-restraints excluded: chain V residue 120 CYS Chi-restraints excluded: chain V residue 180 ASN Chi-restraints excluded: chain V residue 233 ASP Chi-restraints excluded: chain V residue 238 CYS Chi-restraints excluded: chain V residue 293 THR Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 178 TYR Chi-restraints excluded: chain T residue 198 PHE Chi-restraints excluded: chain T residue 223 ASN Chi-restraints excluded: chain T residue 231 SER Chi-restraints excluded: chain T residue 243 LYS Chi-restraints excluded: chain T residue 274 CYS Chi-restraints excluded: chain T residue 275 ILE Chi-restraints excluded: chain T residue 313 ASN Chi-restraints excluded: chain Y residue 50 ASP Chi-restraints excluded: chain Y residue 60 LEU Chi-restraints excluded: chain Z residue 55 GLU Chi-restraints excluded: chain Z residue 103 TYR Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 232 TYR Chi-restraints excluded: chain Z residue 356 ASN Chi-restraints excluded: chain Z residue 376 PHE Chi-restraints excluded: chain Z residue 535 THR Chi-restraints excluded: chain Z residue 574 GLU Chi-restraints excluded: chain Z residue 606 VAL Chi-restraints excluded: chain Z residue 608 LYS Chi-restraints excluded: chain Z residue 711 SER Chi-restraints excluded: chain Z residue 718 ASP Chi-restraints excluded: chain Z residue 741 LEU Chi-restraints excluded: chain Z residue 748 LEU Chi-restraints excluded: chain Z residue 759 LEU Chi-restraints excluded: chain Z residue 873 LEU Chi-restraints excluded: chain N residue 149 GLN Chi-restraints excluded: chain N residue 165 LYS Chi-restraints excluded: chain N residue 183 LEU Chi-restraints excluded: chain N residue 207 ASN Chi-restraints excluded: chain N residue 233 LEU Chi-restraints excluded: chain N residue 350 LEU Chi-restraints excluded: chain N residue 386 LEU Chi-restraints excluded: chain N residue 395 ARG Chi-restraints excluded: chain N residue 459 ASP Chi-restraints excluded: chain N residue 469 SER Chi-restraints excluded: chain N residue 486 MET Chi-restraints excluded: chain N residue 620 GLU Chi-restraints excluded: chain N residue 621 SER Chi-restraints excluded: chain N residue 638 SER Chi-restraints excluded: chain N residue 672 LEU Chi-restraints excluded: chain N residue 731 ILE Chi-restraints excluded: chain N residue 776 SER Chi-restraints excluded: chain N residue 838 LYS Chi-restraints excluded: chain N residue 892 LEU Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain S residue 125 ASN Chi-restraints excluded: chain S residue 210 CYS Chi-restraints excluded: chain S residue 221 LEU Chi-restraints excluded: chain S residue 260 HIS Chi-restraints excluded: chain S residue 302 TYR Chi-restraints excluded: chain S residue 353 LEU Chi-restraints excluded: chain S residue 354 LYS Chi-restraints excluded: chain S residue 356 SER Chi-restraints excluded: chain S residue 389 ASP Chi-restraints excluded: chain S residue 411 SER Chi-restraints excluded: chain S residue 437 ILE Chi-restraints excluded: chain S residue 469 THR Chi-restraints excluded: chain P residue 105 VAL Chi-restraints excluded: chain P residue 106 GLN Chi-restraints excluded: chain P residue 126 ASP Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain P residue 165 ILE Chi-restraints excluded: chain P residue 172 GLU Chi-restraints excluded: chain P residue 188 GLU Chi-restraints excluded: chain P residue 198 ASP Chi-restraints excluded: chain P residue 244 CYS Chi-restraints excluded: chain P residue 332 SER Chi-restraints excluded: chain P residue 364 ARG Chi-restraints excluded: chain P residue 413 ILE Chi-restraints excluded: chain P residue 449 GLU Chi-restraints excluded: chain Q residue 41 GLU Chi-restraints excluded: chain Q residue 182 ASN Chi-restraints excluded: chain Q residue 214 SER Chi-restraints excluded: chain Q residue 224 ASP Chi-restraints excluded: chain Q residue 227 THR Chi-restraints excluded: chain Q residue 234 GLU Chi-restraints excluded: chain Q residue 241 SER Chi-restraints excluded: chain Q residue 328 ASP Chi-restraints excluded: chain Q residue 372 LYS Chi-restraints excluded: chain Q residue 388 PHE Chi-restraints excluded: chain Q residue 415 TYR Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 48 ASN Chi-restraints excluded: chain R residue 63 TRP Chi-restraints excluded: chain R residue 94 ASN Chi-restraints excluded: chain R residue 154 ASN Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 209 THR Chi-restraints excluded: chain R residue 214 MET Chi-restraints excluded: chain R residue 235 ASP Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 250 LEU Chi-restraints excluded: chain R residue 272 PHE Chi-restraints excluded: chain R residue 333 GLU Chi-restraints excluded: chain R residue 346 LYS Chi-restraints excluded: chain R residue 377 LEU Chi-restraints excluded: chain U residue 14 LEU Chi-restraints excluded: chain U residue 15 VAL Chi-restraints excluded: chain U residue 44 GLN Chi-restraints excluded: chain U residue 48 LEU Chi-restraints excluded: chain U residue 71 ASP Chi-restraints excluded: chain U residue 73 ASP Chi-restraints excluded: chain U residue 77 ASN Chi-restraints excluded: chain U residue 96 HIS Chi-restraints excluded: chain U residue 100 LYS Chi-restraints excluded: chain U residue 168 GLU Chi-restraints excluded: chain U residue 192 THR Chi-restraints excluded: chain U residue 235 ASN Chi-restraints excluded: chain U residue 249 PHE Chi-restraints excluded: chain U residue 250 TYR Chi-restraints excluded: chain U residue 253 THR Chi-restraints excluded: chain O residue 144 ASN Chi-restraints excluded: chain O residue 145 LEU Chi-restraints excluded: chain O residue 150 SER Chi-restraints excluded: chain O residue 208 GLU Chi-restraints excluded: chain O residue 244 ASN Chi-restraints excluded: chain O residue 260 ASP Chi-restraints excluded: chain O residue 264 ASN Chi-restraints excluded: chain O residue 339 ARG Chi-restraints excluded: chain O residue 360 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 249 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 374 optimal weight: 1.9990 chunk 306 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 450 optimal weight: 5.9990 chunk 486 optimal weight: 6.9990 chunk 401 optimal weight: 2.9990 chunk 446 optimal weight: 1.9990 chunk 153 optimal weight: 6.9990 chunk 361 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 137 ASN T 127 ASN ** T 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 228 HIS Z 171 GLN Z 356 ASN ** Z 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 566 HIS N 111 GLN ** N 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 259 GLN N 421 GLN N 611 ASN ** N 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 318 GLN P 26 GLN ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.5023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 40342 Z= 0.228 Angle : 0.674 16.760 54493 Z= 0.362 Chirality : 0.038 0.243 6198 Planarity : 0.005 0.164 7021 Dihedral : 7.474 85.733 5510 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.72 % Allowed : 8.49 % Favored : 90.78 % Rotamer: Outliers : 3.64 % Allowed : 17.05 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.11), residues: 4970 helix: -1.89 (0.08), residues: 3128 sheet: -1.94 (0.38), residues: 174 loop : -3.17 (0.14), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP N 392 HIS 0.015 0.002 HIS U 157 PHE 0.017 0.002 PHE R 150 TYR 0.025 0.002 TYR Z 349 ARG 0.016 0.001 ARG Z 267 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 296 is missing expected H atoms. Skipping. Evaluate side-chains 1148 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 990 time to evaluate : 4.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 70 ARG cc_start: 0.9069 (mtp180) cc_final: 0.8517 (tpp-160) REVERT: W 112 PHE cc_start: 0.5864 (m-80) cc_final: 0.5463 (m-10) REVERT: V 40 LYS cc_start: 0.8664 (mttm) cc_final: 0.8327 (tptt) REVERT: V 75 MET cc_start: 0.9026 (mtp) cc_final: 0.8776 (mtm) REVERT: V 122 LEU cc_start: 0.9072 (mt) cc_final: 0.8837 (mp) REVERT: V 158 ASP cc_start: 0.8347 (m-30) cc_final: 0.7963 (m-30) REVERT: V 175 ARG cc_start: 0.8010 (tpp-160) cc_final: 0.7533 (ttm-80) REVERT: V 260 GLU cc_start: 0.8871 (tp30) cc_final: 0.8113 (mp0) REVERT: T 166 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8455 (tmm-80) REVERT: T 212 LEU cc_start: 0.9221 (tp) cc_final: 0.8886 (mm) REVERT: T 219 ASP cc_start: 0.8961 (m-30) cc_final: 0.8448 (t0) REVERT: T 220 ILE cc_start: 0.8336 (pt) cc_final: 0.8030 (tt) REVERT: T 223 ASN cc_start: 0.6704 (OUTLIER) cc_final: 0.6144 (t0) REVERT: T 234 GLN cc_start: 0.8161 (tm-30) cc_final: 0.7688 (tm-30) REVERT: T 258 PHE cc_start: 0.7748 (m-10) cc_final: 0.7504 (m-10) REVERT: T 265 ASP cc_start: 0.8766 (m-30) cc_final: 0.7839 (t0) REVERT: T 269 ASP cc_start: 0.8444 (m-30) cc_final: 0.7429 (m-30) REVERT: T 322 GLN cc_start: 0.7891 (tp40) cc_final: 0.7404 (pm20) REVERT: Z 33 ARG cc_start: 0.3767 (mmt-90) cc_final: 0.3334 (mmt180) REVERT: Z 103 TYR cc_start: 0.2495 (OUTLIER) cc_final: 0.1956 (m-80) REVERT: Z 113 MET cc_start: 0.2459 (mmt) cc_final: 0.1573 (mtm) REVERT: Z 216 MET cc_start: 0.2380 (ttp) cc_final: 0.1817 (tpt) REVERT: Z 261 ARG cc_start: 0.7794 (ttt180) cc_final: 0.7559 (ttm170) REVERT: Z 296 PHE cc_start: 0.6589 (t80) cc_final: 0.5153 (t80) REVERT: Z 335 ARG cc_start: 0.7271 (mtt-85) cc_final: 0.7039 (ptm160) REVERT: Z 389 LYS cc_start: 0.6666 (mttm) cc_final: 0.6096 (pttp) REVERT: Z 551 LYS cc_start: 0.6787 (mtmm) cc_final: 0.6521 (mmtt) REVERT: Z 593 THR cc_start: 0.6367 (p) cc_final: 0.6054 (t) REVERT: Z 662 MET cc_start: 0.4079 (mtp) cc_final: 0.3714 (ttt) REVERT: Z 718 ASP cc_start: 0.2884 (OUTLIER) cc_final: 0.2542 (t70) REVERT: N 46 GLU cc_start: 0.7751 (mt-10) cc_final: 0.6934 (tm-30) REVERT: N 48 LEU cc_start: 0.9159 (mt) cc_final: 0.8814 (tp) REVERT: N 76 GLU cc_start: 0.8182 (mp0) cc_final: 0.7940 (mp0) REVERT: N 349 ASP cc_start: 0.7265 (t70) cc_final: 0.6923 (p0) REVERT: N 521 LEU cc_start: 0.8485 (tt) cc_final: 0.8083 (tp) REVERT: N 538 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8017 (tm-30) REVERT: N 539 THR cc_start: 0.7187 (p) cc_final: 0.6757 (p) REVERT: N 580 ARG cc_start: 0.8953 (ttp-170) cc_final: 0.8598 (tmm-80) REVERT: N 601 ARG cc_start: 0.6302 (mtm180) cc_final: 0.6001 (mtt180) REVERT: N 604 HIS cc_start: 0.6952 (p90) cc_final: 0.5528 (m-70) REVERT: N 605 VAL cc_start: 0.8164 (t) cc_final: 0.7922 (t) REVERT: N 719 ASP cc_start: 0.7051 (m-30) cc_final: 0.6354 (t0) REVERT: N 725 MET cc_start: 0.8285 (mtm) cc_final: 0.7645 (mmt) REVERT: N 757 MET cc_start: 0.7728 (mmt) cc_final: 0.7286 (tpp) REVERT: N 772 TRP cc_start: 0.7239 (t-100) cc_final: 0.6989 (t-100) REVERT: N 847 GLU cc_start: 0.6914 (mt-10) cc_final: 0.5734 (tp30) REVERT: N 879 ASP cc_start: 0.8466 (m-30) cc_final: 0.7962 (p0) REVERT: S 66 GLU cc_start: 0.9300 (tt0) cc_final: 0.9025 (tp30) REVERT: S 96 ARG cc_start: 0.7836 (ttt-90) cc_final: 0.7531 (tmm-80) REVERT: S 166 TYR cc_start: 0.8495 (t80) cc_final: 0.8251 (t80) REVERT: S 168 GLN cc_start: 0.8898 (tt0) cc_final: 0.8620 (tp-100) REVERT: S 219 GLU cc_start: 0.8684 (tt0) cc_final: 0.8445 (tt0) REVERT: S 300 LEU cc_start: 0.8134 (tp) cc_final: 0.7843 (mm) REVERT: S 315 LYS cc_start: 0.8880 (mttt) cc_final: 0.8590 (mmtt) REVERT: S 399 ARG cc_start: 0.8832 (mtp-110) cc_final: 0.8526 (mtm110) REVERT: S 408 ARG cc_start: 0.8964 (ttp-110) cc_final: 0.8664 (ttp-110) REVERT: P 1 MET cc_start: 0.6561 (mmt) cc_final: 0.5895 (mmt) REVERT: P 16 MET cc_start: 0.6684 (mtp) cc_final: 0.6404 (mtp) REVERT: P 60 MET cc_start: 0.8553 (tpp) cc_final: 0.8199 (tpp) REVERT: P 154 GLU cc_start: 0.9071 (tt0) cc_final: 0.8694 (pt0) REVERT: P 230 MET cc_start: 0.8994 (mmm) cc_final: 0.8686 (mmm) REVERT: P 303 LYS cc_start: 0.8610 (ttpp) cc_final: 0.8350 (tppt) REVERT: P 304 ASP cc_start: 0.8681 (m-30) cc_final: 0.8240 (p0) REVERT: P 326 MET cc_start: 0.8518 (ptt) cc_final: 0.8244 (pmm) REVERT: P 332 SER cc_start: 0.6725 (OUTLIER) cc_final: 0.6409 (t) REVERT: P 353 ASP cc_start: 0.8945 (t0) cc_final: 0.8593 (t0) REVERT: P 449 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8338 (tm-30) REVERT: Q 41 GLU cc_start: 0.3705 (OUTLIER) cc_final: 0.2719 (mp0) REVERT: Q 48 GLN cc_start: 0.8730 (mm-40) cc_final: 0.8512 (mm-40) REVERT: Q 72 TYR cc_start: 0.7862 (m-80) cc_final: 0.7591 (m-80) REVERT: Q 94 ASP cc_start: 0.7629 (m-30) cc_final: 0.7296 (p0) REVERT: Q 138 PHE cc_start: 0.7672 (t80) cc_final: 0.7157 (t80) REVERT: Q 289 CYS cc_start: 0.9006 (t) cc_final: 0.8591 (p) REVERT: Q 312 GLU cc_start: 0.8646 (mp0) cc_final: 0.8306 (mp0) REVERT: Q 416 ASN cc_start: 0.8790 (OUTLIER) cc_final: 0.8498 (t0) REVERT: R 42 MET cc_start: 0.9099 (mmm) cc_final: 0.8525 (tmm) REVERT: R 86 GLU cc_start: 0.9275 (tt0) cc_final: 0.9003 (tp30) REVERT: R 99 GLU cc_start: 0.8384 (tt0) cc_final: 0.8033 (tt0) REVERT: R 158 THR cc_start: 0.9311 (m) cc_final: 0.8927 (t) REVERT: R 170 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7314 (mt-10) REVERT: R 210 SER cc_start: 0.8287 (OUTLIER) cc_final: 0.7891 (p) REVERT: R 225 TYR cc_start: 0.9369 (m-10) cc_final: 0.9096 (m-10) REVERT: R 272 PHE cc_start: 0.7776 (OUTLIER) cc_final: 0.7254 (t80) REVERT: R 282 MET cc_start: 0.7223 (mtp) cc_final: 0.6925 (mtp) REVERT: R 302 HIS cc_start: 0.8796 (t-90) cc_final: 0.8526 (t70) REVERT: R 333 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7036 (tt0) REVERT: R 354 VAL cc_start: 0.8563 (t) cc_final: 0.8091 (t) REVERT: R 355 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8130 (pm20) REVERT: U 1 MET cc_start: 0.3930 (mtm) cc_final: 0.3647 (mtm) REVERT: U 44 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7954 (pm20) REVERT: U 49 ASP cc_start: 0.8819 (m-30) cc_final: 0.8527 (m-30) REVERT: U 86 ASN cc_start: 0.9009 (t0) cc_final: 0.8536 (t0) REVERT: U 100 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.8041 (pttp) REVERT: U 136 GLU cc_start: 0.8221 (mp0) cc_final: 0.7891 (mp0) REVERT: U 169 GLU cc_start: 0.9205 (tp30) cc_final: 0.8786 (tm-30) REVERT: U 189 GLN cc_start: 0.9392 (tp40) cc_final: 0.9123 (tp40) REVERT: U 229 GLN cc_start: 0.9107 (tt0) cc_final: 0.8708 (tt0) REVERT: U 262 LEU cc_start: 0.9105 (tp) cc_final: 0.8740 (tt) REVERT: O 39 LEU cc_start: 0.8409 (mt) cc_final: 0.8197 (tp) REVERT: O 40 GLN cc_start: 0.8234 (tp40) cc_final: 0.8033 (tp40) REVERT: O 74 LEU cc_start: 0.8192 (mt) cc_final: 0.7844 (tp) REVERT: O 78 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7821 (mt-10) REVERT: O 121 LEU cc_start: 0.9343 (mt) cc_final: 0.9070 (tt) REVERT: O 154 ARG cc_start: 0.9131 (mmt90) cc_final: 0.8839 (mtp85) REVERT: O 174 LYS cc_start: 0.9330 (mtpp) cc_final: 0.8999 (ptpp) REVERT: O 267 GLN cc_start: 0.9106 (tt0) cc_final: 0.8863 (tt0) REVERT: O 278 MET cc_start: 0.8701 (ttt) cc_final: 0.8431 (tmm) outliers start: 158 outliers final: 120 residues processed: 1093 average time/residue: 1.0749 time to fit residues: 1852.2823 Evaluate side-chains 1059 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 925 time to evaluate : 4.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 47 ASN Chi-restraints excluded: chain W residue 67 ASP Chi-restraints excluded: chain W residue 97 LEU Chi-restraints excluded: chain W residue 185 SER Chi-restraints excluded: chain W residue 186 SER Chi-restraints excluded: chain V residue 41 MET Chi-restraints excluded: chain V residue 88 ASP Chi-restraints excluded: chain V residue 180 ASN Chi-restraints excluded: chain V residue 233 ASP Chi-restraints excluded: chain V residue 238 CYS Chi-restraints excluded: chain V residue 293 THR Chi-restraints excluded: chain T residue 166 ARG Chi-restraints excluded: chain T residue 178 TYR Chi-restraints excluded: chain T residue 191 LEU Chi-restraints excluded: chain T residue 223 ASN Chi-restraints excluded: chain T residue 231 SER Chi-restraints excluded: chain T residue 243 LYS Chi-restraints excluded: chain T residue 274 CYS Chi-restraints excluded: chain T residue 275 ILE Chi-restraints excluded: chain T residue 313 ASN Chi-restraints excluded: chain Y residue 60 LEU Chi-restraints excluded: chain Z residue 29 SER Chi-restraints excluded: chain Z residue 55 GLU Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain Z residue 103 TYR Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 232 TYR Chi-restraints excluded: chain Z residue 356 ASN Chi-restraints excluded: chain Z residue 574 GLU Chi-restraints excluded: chain Z residue 608 LYS Chi-restraints excluded: chain Z residue 711 SER Chi-restraints excluded: chain Z residue 718 ASP Chi-restraints excluded: chain Z residue 731 MET Chi-restraints excluded: chain Z residue 748 LEU Chi-restraints excluded: chain Z residue 759 LEU Chi-restraints excluded: chain Z residue 873 LEU Chi-restraints excluded: chain N residue 8 ILE Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 163 PHE Chi-restraints excluded: chain N residue 165 LYS Chi-restraints excluded: chain N residue 183 LEU Chi-restraints excluded: chain N residue 207 ASN Chi-restraints excluded: chain N residue 233 LEU Chi-restraints excluded: chain N residue 386 LEU Chi-restraints excluded: chain N residue 459 ASP Chi-restraints excluded: chain N residue 461 LEU Chi-restraints excluded: chain N residue 486 MET Chi-restraints excluded: chain N residue 510 GLU Chi-restraints excluded: chain N residue 611 ASN Chi-restraints excluded: chain N residue 620 GLU Chi-restraints excluded: chain N residue 633 CYS Chi-restraints excluded: chain N residue 638 SER Chi-restraints excluded: chain N residue 672 LEU Chi-restraints excluded: chain N residue 731 ILE Chi-restraints excluded: chain N residue 742 HIS Chi-restraints excluded: chain N residue 838 LYS Chi-restraints excluded: chain N residue 892 LEU Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain S residue 125 ASN Chi-restraints excluded: chain S residue 170 LEU Chi-restraints excluded: chain S residue 249 THR Chi-restraints excluded: chain S residue 302 TYR Chi-restraints excluded: chain S residue 346 LEU Chi-restraints excluded: chain S residue 353 LEU Chi-restraints excluded: chain S residue 354 LYS Chi-restraints excluded: chain S residue 356 SER Chi-restraints excluded: chain S residue 389 ASP Chi-restraints excluded: chain S residue 411 SER Chi-restraints excluded: chain S residue 469 THR Chi-restraints excluded: chain P residue 105 VAL Chi-restraints excluded: chain P residue 126 ASP Chi-restraints excluded: chain P residue 139 GLU Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain P residue 165 ILE Chi-restraints excluded: chain P residue 172 GLU Chi-restraints excluded: chain P residue 244 CYS Chi-restraints excluded: chain P residue 332 SER Chi-restraints excluded: chain P residue 364 ARG Chi-restraints excluded: chain P residue 449 GLU Chi-restraints excluded: chain Q residue 41 GLU Chi-restraints excluded: chain Q residue 160 MET Chi-restraints excluded: chain Q residue 182 ASN Chi-restraints excluded: chain Q residue 227 THR Chi-restraints excluded: chain Q residue 234 GLU Chi-restraints excluded: chain Q residue 241 SER Chi-restraints excluded: chain Q residue 328 ASP Chi-restraints excluded: chain Q residue 415 TYR Chi-restraints excluded: chain Q residue 416 ASN Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 48 ASN Chi-restraints excluded: chain R residue 63 TRP Chi-restraints excluded: chain R residue 94 ASN Chi-restraints excluded: chain R residue 109 GLU Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 154 ASN Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 173 ASP Chi-restraints excluded: chain R residue 175 ASP Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 196 GLN Chi-restraints excluded: chain R residue 209 THR Chi-restraints excluded: chain R residue 210 SER Chi-restraints excluded: chain R residue 214 MET Chi-restraints excluded: chain R residue 235 ASP Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 272 PHE Chi-restraints excluded: chain R residue 278 VAL Chi-restraints excluded: chain R residue 301 ILE Chi-restraints excluded: chain R residue 333 GLU Chi-restraints excluded: chain R residue 377 LEU Chi-restraints excluded: chain U residue 14 LEU Chi-restraints excluded: chain U residue 15 VAL Chi-restraints excluded: chain U residue 44 GLN Chi-restraints excluded: chain U residue 48 LEU Chi-restraints excluded: chain U residue 71 ASP Chi-restraints excluded: chain U residue 73 ASP Chi-restraints excluded: chain U residue 96 HIS Chi-restraints excluded: chain U residue 100 LYS Chi-restraints excluded: chain U residue 188 SER Chi-restraints excluded: chain U residue 192 THR Chi-restraints excluded: chain U residue 228 TYR Chi-restraints excluded: chain U residue 249 PHE Chi-restraints excluded: chain U residue 250 TYR Chi-restraints excluded: chain U residue 253 THR Chi-restraints excluded: chain O residue 145 LEU Chi-restraints excluded: chain O residue 149 THR Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain O residue 208 GLU Chi-restraints excluded: chain O residue 240 PHE Chi-restraints excluded: chain O residue 244 ASN Chi-restraints excluded: chain O residue 260 ASP Chi-restraints excluded: chain O residue 275 LEU Chi-restraints excluded: chain O residue 339 ARG Chi-restraints excluded: chain O residue 360 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 444 optimal weight: 7.9990 chunk 338 optimal weight: 6.9990 chunk 233 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 214 optimal weight: 9.9990 chunk 302 optimal weight: 9.9990 chunk 451 optimal weight: 0.0770 chunk 478 optimal weight: 10.0000 chunk 236 optimal weight: 5.9990 chunk 428 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 overall best weight: 5.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 105 HIS W 137 ASN ** W 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 108 ASN ** T 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 209 HIS Y 47 ASN Z 14 GLN Z 323 ASN ** Z 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 750 GLN N 389 ASN N 611 ASN ** N 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 177 ASN ** S 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 107 GLN R 14 ASN R 178 ASN ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 12 HIS ** U 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 124 ASN O 143 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.5863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 40342 Z= 0.347 Angle : 0.735 9.915 54493 Z= 0.400 Chirality : 0.039 0.209 6198 Planarity : 0.006 0.129 7021 Dihedral : 7.342 87.691 5499 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.74 % Allowed : 9.28 % Favored : 89.98 % Rotamer: Outliers : 4.99 % Allowed : 17.53 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.06 % 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: -3.37 (0.11), residues: 4970 helix: -1.67 (0.08), residues: 3129 sheet: -1.84 (0.40), residues: 172 loop : -3.17 (0.14), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP N 35 HIS 0.018 0.002 HIS U 157 PHE 0.021 0.002 PHE O 240 TYR 0.031 0.002 TYR Z 349 ARG 0.007 0.001 ARG R 297 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 296 is missing expected H atoms. Skipping. Evaluate side-chains 1161 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 944 time to evaluate : 4.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 70 ARG cc_start: 0.9165 (mtp180) cc_final: 0.8542 (mmp80) REVERT: W 112 PHE cc_start: 0.6199 (m-80) cc_final: 0.5851 (m-10) REVERT: V 40 LYS cc_start: 0.8637 (mttm) cc_final: 0.8321 (tptt) REVERT: V 75 MET cc_start: 0.9030 (mtp) cc_final: 0.8830 (mtm) REVERT: V 158 ASP cc_start: 0.8801 (m-30) cc_final: 0.8337 (m-30) REVERT: V 175 ARG cc_start: 0.8042 (tpp-160) cc_final: 0.7575 (ttm-80) REVERT: V 238 CYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8115 (t) REVERT: T 166 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.8261 (tmm-80) REVERT: T 207 GLU cc_start: 0.9302 (mm-30) cc_final: 0.9035 (mp0) REVERT: T 212 LEU cc_start: 0.9229 (tp) cc_final: 0.8865 (mm) REVERT: T 214 ARG cc_start: 0.6649 (mmt-90) cc_final: 0.6386 (mpt180) REVERT: T 219 ASP cc_start: 0.8959 (m-30) cc_final: 0.8480 (t0) REVERT: T 220 ILE cc_start: 0.8327 (pt) cc_final: 0.8063 (tt) REVERT: T 223 ASN cc_start: 0.6955 (OUTLIER) cc_final: 0.6309 (t0) REVERT: T 234 GLN cc_start: 0.8257 (tm-30) cc_final: 0.8041 (tm-30) REVERT: T 258 PHE cc_start: 0.7838 (m-10) cc_final: 0.7590 (m-10) REVERT: T 265 ASP cc_start: 0.8761 (m-30) cc_final: 0.7821 (t0) REVERT: T 269 ASP cc_start: 0.8450 (m-30) cc_final: 0.7414 (m-30) REVERT: T 322 GLN cc_start: 0.7933 (tp40) cc_final: 0.7432 (pm20) REVERT: Z 33 ARG cc_start: 0.3807 (mmt-90) cc_final: 0.3526 (mmt180) REVERT: Z 103 TYR cc_start: 0.2829 (OUTLIER) cc_final: 0.1954 (m-80) REVERT: Z 113 MET cc_start: 0.2235 (mmt) cc_final: 0.1303 (mtm) REVERT: Z 216 MET cc_start: 0.2081 (ttp) cc_final: 0.1433 (tpt) REVERT: Z 296 PHE cc_start: 0.6616 (t80) cc_final: 0.5541 (t80) REVERT: Z 335 ARG cc_start: 0.7349 (mtt-85) cc_final: 0.7077 (ptm160) REVERT: Z 389 LYS cc_start: 0.6574 (mttm) cc_final: 0.5994 (pttp) REVERT: Z 466 LEU cc_start: 0.6174 (mt) cc_final: 0.5959 (mt) REVERT: Z 481 SER cc_start: 0.3274 (OUTLIER) cc_final: 0.2843 (t) REVERT: Z 489 TYR cc_start: 0.3938 (m-10) cc_final: 0.3711 (m-80) REVERT: Z 551 LYS cc_start: 0.6785 (mtmm) cc_final: 0.6517 (mptt) REVERT: Z 593 THR cc_start: 0.6522 (p) cc_final: 0.6130 (t) REVERT: Z 662 MET cc_start: 0.4267 (mtp) cc_final: 0.3852 (ttt) REVERT: Z 788 MET cc_start: 0.4926 (ptm) cc_final: 0.4640 (tpp) REVERT: N 1 MET cc_start: 0.7662 (tpp) cc_final: 0.7416 (ttm) REVERT: N 40 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8194 (mt-10) REVERT: N 48 LEU cc_start: 0.9081 (mt) cc_final: 0.8712 (tp) REVERT: N 218 GLN cc_start: 0.8758 (mt0) cc_final: 0.8352 (tm-30) REVERT: N 222 PHE cc_start: 0.5866 (m-80) cc_final: 0.5574 (m-80) REVERT: N 351 MET cc_start: 0.5695 (tmm) cc_final: 0.4904 (tmm) REVERT: N 521 LEU cc_start: 0.8503 (tt) cc_final: 0.7953 (tt) REVERT: N 538 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8058 (tm-30) REVERT: N 539 THR cc_start: 0.7305 (p) cc_final: 0.6902 (p) REVERT: N 566 LEU cc_start: 0.7939 (mt) cc_final: 0.7679 (tp) REVERT: N 580 ARG cc_start: 0.8979 (ttp-170) cc_final: 0.8640 (tmm-80) REVERT: N 601 ARG cc_start: 0.6396 (mtm180) cc_final: 0.6095 (mtt90) REVERT: N 609 ASP cc_start: 0.7467 (OUTLIER) cc_final: 0.7073 (t70) REVERT: N 725 MET cc_start: 0.8030 (mtm) cc_final: 0.7507 (mmt) REVERT: N 757 MET cc_start: 0.7675 (mmt) cc_final: 0.7192 (ttm) REVERT: N 772 TRP cc_start: 0.7366 (t-100) cc_final: 0.7158 (t-100) REVERT: N 847 GLU cc_start: 0.6858 (mt-10) cc_final: 0.5665 (tp30) REVERT: N 879 ASP cc_start: 0.8483 (m-30) cc_final: 0.7958 (p0) REVERT: N 898 CYS cc_start: 0.6107 (m) cc_final: 0.5526 (m) REVERT: S 66 GLU cc_start: 0.9321 (tt0) cc_final: 0.9030 (tp30) REVERT: S 77 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7664 (mp0) REVERT: S 96 ARG cc_start: 0.7863 (ttt-90) cc_final: 0.7605 (tmm-80) REVERT: S 219 GLU cc_start: 0.8737 (tt0) cc_final: 0.8534 (tt0) REVERT: S 300 LEU cc_start: 0.8161 (tp) cc_final: 0.7873 (mm) REVERT: S 315 LYS cc_start: 0.8940 (mttt) cc_final: 0.8643 (mmtt) REVERT: S 325 LYS cc_start: 0.8608 (mttp) cc_final: 0.8129 (mmmm) REVERT: S 477 HIS cc_start: 0.8523 (OUTLIER) cc_final: 0.7773 (t70) REVERT: P 1 MET cc_start: 0.6907 (mmt) cc_final: 0.6244 (mmt) REVERT: P 42 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8275 (mm-30) REVERT: P 60 MET cc_start: 0.8599 (tpp) cc_final: 0.8279 (tpp) REVERT: P 73 MET cc_start: 0.8522 (mtp) cc_final: 0.8105 (mtm) REVERT: P 154 GLU cc_start: 0.9088 (tt0) cc_final: 0.8787 (pt0) REVERT: P 230 MET cc_start: 0.9016 (mmm) cc_final: 0.8759 (mmm) REVERT: P 239 SER cc_start: 0.9249 (m) cc_final: 0.8918 (t) REVERT: P 296 LEU cc_start: 0.9589 (tp) cc_final: 0.9361 (tp) REVERT: P 303 LYS cc_start: 0.8624 (ttpp) cc_final: 0.8282 (tppt) REVERT: P 304 ASP cc_start: 0.8657 (m-30) cc_final: 0.8211 (p0) REVERT: P 353 ASP cc_start: 0.8976 (t0) cc_final: 0.8649 (t0) REVERT: P 364 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.8158 (mtp-110) REVERT: P 449 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8316 (tm-30) REVERT: Q 94 ASP cc_start: 0.7918 (m-30) cc_final: 0.7687 (p0) REVERT: Q 96 PHE cc_start: 0.6255 (p90) cc_final: 0.5829 (p90) REVERT: Q 236 PHE cc_start: 0.8447 (t80) cc_final: 0.7882 (t80) REVERT: Q 289 CYS cc_start: 0.9042 (t) cc_final: 0.8675 (p) REVERT: Q 312 GLU cc_start: 0.8467 (mp0) cc_final: 0.8119 (mp0) REVERT: Q 372 LYS cc_start: 0.8483 (mttp) cc_final: 0.8198 (mmtm) REVERT: R 16 ASP cc_start: 0.8689 (t0) cc_final: 0.8063 (p0) REVERT: R 42 MET cc_start: 0.9125 (mmm) cc_final: 0.8584 (tmm) REVERT: R 116 ASP cc_start: 0.8677 (t0) cc_final: 0.8385 (t0) REVERT: R 170 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7352 (mt-10) REVERT: R 210 SER cc_start: 0.8279 (OUTLIER) cc_final: 0.7934 (p) REVERT: R 225 TYR cc_start: 0.9401 (m-10) cc_final: 0.9136 (m-10) REVERT: R 272 PHE cc_start: 0.7895 (OUTLIER) cc_final: 0.7554 (t80) REVERT: R 302 HIS cc_start: 0.9048 (t-90) cc_final: 0.8805 (t70) REVERT: R 305 SER cc_start: 0.9097 (t) cc_final: 0.8584 (p) REVERT: R 354 VAL cc_start: 0.8585 (t) cc_final: 0.8335 (t) REVERT: R 355 GLU cc_start: 0.8588 (mt-10) cc_final: 0.7936 (pm20) REVERT: U 9 VAL cc_start: 0.9035 (t) cc_final: 0.8724 (p) REVERT: U 100 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7995 (pttp) REVERT: U 136 GLU cc_start: 0.8187 (mp0) cc_final: 0.7892 (mp0) REVERT: U 169 GLU cc_start: 0.9207 (tp30) cc_final: 0.8722 (tm-30) REVERT: U 189 GLN cc_start: 0.9506 (tp40) cc_final: 0.9184 (tp-100) REVERT: U 193 ASN cc_start: 0.9056 (m-40) cc_final: 0.8507 (m110) REVERT: U 204 LYS cc_start: 0.9284 (mmtp) cc_final: 0.9032 (ttmt) REVERT: U 262 LEU cc_start: 0.9101 (tp) cc_final: 0.8834 (tt) REVERT: O 39 LEU cc_start: 0.8404 (mt) cc_final: 0.7955 (tp) REVERT: O 43 ASP cc_start: 0.8904 (t0) cc_final: 0.8627 (m-30) REVERT: O 74 LEU cc_start: 0.8199 (mt) cc_final: 0.7895 (tp) REVERT: O 78 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7700 (mt-10) REVERT: O 121 LEU cc_start: 0.9373 (mt) cc_final: 0.9092 (tt) REVERT: O 205 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8650 (mm) REVERT: O 278 MET cc_start: 0.8603 (ttt) cc_final: 0.8395 (tmm) REVERT: O 339 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7780 (ptp90) outliers start: 217 outliers final: 165 residues processed: 1089 average time/residue: 1.1445 time to fit residues: 1984.4031 Evaluate side-chains 1072 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 892 time to evaluate : 4.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 97 LEU Chi-restraints excluded: chain W residue 115 SER Chi-restraints excluded: chain W residue 140 ILE Chi-restraints excluded: chain W residue 151 GLU Chi-restraints excluded: chain W residue 185 SER Chi-restraints excluded: chain W residue 186 SER Chi-restraints excluded: chain V residue 88 ASP Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 97 ASP Chi-restraints excluded: chain V residue 120 CYS Chi-restraints excluded: chain V residue 180 ASN Chi-restraints excluded: chain V residue 233 ASP Chi-restraints excluded: chain V residue 238 CYS Chi-restraints excluded: chain V residue 293 THR Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 166 ARG Chi-restraints excluded: chain T residue 178 TYR Chi-restraints excluded: chain T residue 223 ASN Chi-restraints excluded: chain T residue 231 SER Chi-restraints excluded: chain T residue 243 LYS Chi-restraints excluded: chain T residue 274 CYS Chi-restraints excluded: chain T residue 275 ILE Chi-restraints excluded: chain T residue 313 ASN Chi-restraints excluded: chain Y residue 35 ASP Chi-restraints excluded: chain Y residue 50 ASP Chi-restraints excluded: chain Y residue 60 LEU Chi-restraints excluded: chain Z residue 1 MET Chi-restraints excluded: chain Z residue 29 SER Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain Z residue 103 TYR Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 232 TYR Chi-restraints excluded: chain Z residue 419 LEU Chi-restraints excluded: chain Z residue 445 LEU Chi-restraints excluded: chain Z residue 481 SER Chi-restraints excluded: chain Z residue 535 THR Chi-restraints excluded: chain Z residue 574 GLU Chi-restraints excluded: chain Z residue 608 LYS Chi-restraints excluded: chain Z residue 711 SER Chi-restraints excluded: chain Z residue 731 MET Chi-restraints excluded: chain Z residue 741 LEU Chi-restraints excluded: chain Z residue 748 LEU Chi-restraints excluded: chain Z residue 759 LEU Chi-restraints excluded: chain Z residue 873 LEU Chi-restraints excluded: chain N residue 8 ILE Chi-restraints excluded: chain N residue 22 PHE Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 149 GLN Chi-restraints excluded: chain N residue 165 LYS Chi-restraints excluded: chain N residue 176 MET Chi-restraints excluded: chain N residue 183 LEU Chi-restraints excluded: chain N residue 207 ASN Chi-restraints excluded: chain N residue 233 LEU Chi-restraints excluded: chain N residue 349 ASP Chi-restraints excluded: chain N residue 386 LEU Chi-restraints excluded: chain N residue 395 ARG Chi-restraints excluded: chain N residue 397 THR Chi-restraints excluded: chain N residue 448 LEU Chi-restraints excluded: chain N residue 459 ASP Chi-restraints excluded: chain N residue 461 LEU Chi-restraints excluded: chain N residue 486 MET Chi-restraints excluded: chain N residue 510 GLU Chi-restraints excluded: chain N residue 609 ASP Chi-restraints excluded: chain N residue 611 ASN Chi-restraints excluded: chain N residue 620 GLU Chi-restraints excluded: chain N residue 633 CYS Chi-restraints excluded: chain N residue 638 SER Chi-restraints excluded: chain N residue 672 LEU Chi-restraints excluded: chain N residue 731 ILE Chi-restraints excluded: chain N residue 742 HIS Chi-restraints excluded: chain N residue 776 SER Chi-restraints excluded: chain N residue 794 ASP Chi-restraints excluded: chain N residue 838 LYS Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain S residue 113 LEU Chi-restraints excluded: chain S residue 125 ASN Chi-restraints excluded: chain S residue 170 LEU Chi-restraints excluded: chain S residue 189 ASP Chi-restraints excluded: chain S residue 210 CYS Chi-restraints excluded: chain S residue 235 LEU Chi-restraints excluded: chain S residue 249 THR Chi-restraints excluded: chain S residue 260 HIS Chi-restraints excluded: chain S residue 281 ASN Chi-restraints excluded: chain S residue 302 TYR Chi-restraints excluded: chain S residue 346 LEU Chi-restraints excluded: chain S residue 353 LEU Chi-restraints excluded: chain S residue 354 LYS Chi-restraints excluded: chain S residue 356 SER Chi-restraints excluded: chain S residue 389 ASP Chi-restraints excluded: chain S residue 411 SER Chi-restraints excluded: chain S residue 412 LEU Chi-restraints excluded: chain S residue 444 ASP Chi-restraints excluded: chain S residue 447 ILE Chi-restraints excluded: chain S residue 469 THR Chi-restraints excluded: chain S residue 477 HIS Chi-restraints excluded: chain S residue 485 ASP Chi-restraints excluded: chain P residue 105 VAL Chi-restraints excluded: chain P residue 107 GLN Chi-restraints excluded: chain P residue 139 GLU Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain P residue 165 ILE Chi-restraints excluded: chain P residue 172 GLU Chi-restraints excluded: chain P residue 188 GLU Chi-restraints excluded: chain P residue 244 CYS Chi-restraints excluded: chain P residue 315 MET Chi-restraints excluded: chain P residue 322 GLU Chi-restraints excluded: chain P residue 332 SER Chi-restraints excluded: chain P residue 343 SER Chi-restraints excluded: chain P residue 364 ARG Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain P residue 387 ASP Chi-restraints excluded: chain P residue 449 GLU Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 119 SER Chi-restraints excluded: chain Q residue 160 MET Chi-restraints excluded: chain Q residue 174 SER Chi-restraints excluded: chain Q residue 182 ASN Chi-restraints excluded: chain Q residue 224 ASP Chi-restraints excluded: chain Q residue 227 THR Chi-restraints excluded: chain Q residue 234 GLU Chi-restraints excluded: chain Q residue 241 SER Chi-restraints excluded: chain Q residue 242 ILE Chi-restraints excluded: chain Q residue 296 ASN Chi-restraints excluded: chain Q residue 328 ASP Chi-restraints excluded: chain Q residue 415 TYR Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 48 ASN Chi-restraints excluded: chain R residue 63 TRP Chi-restraints excluded: chain R residue 68 ASP Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 94 ASN Chi-restraints excluded: chain R residue 109 GLU Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 154 ASN Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 173 ASP Chi-restraints excluded: chain R residue 175 ASP Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 196 GLN Chi-restraints excluded: chain R residue 209 THR Chi-restraints excluded: chain R residue 210 SER Chi-restraints excluded: chain R residue 214 MET Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 235 ASP Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 272 PHE Chi-restraints excluded: chain R residue 278 VAL Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain R residue 377 LEU Chi-restraints excluded: chain R residue 389 MET Chi-restraints excluded: chain U residue 14 LEU Chi-restraints excluded: chain U residue 15 VAL Chi-restraints excluded: chain U residue 44 GLN Chi-restraints excluded: chain U residue 48 LEU Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain U residue 69 PHE Chi-restraints excluded: chain U residue 71 ASP Chi-restraints excluded: chain U residue 73 ASP Chi-restraints excluded: chain U residue 96 HIS Chi-restraints excluded: chain U residue 100 LYS Chi-restraints excluded: chain U residue 192 THR Chi-restraints excluded: chain U residue 249 PHE Chi-restraints excluded: chain U residue 250 TYR Chi-restraints excluded: chain U residue 278 ASN Chi-restraints excluded: chain O residue 144 ASN Chi-restraints excluded: chain O residue 145 LEU Chi-restraints excluded: chain O residue 149 THR Chi-restraints excluded: chain O residue 150 SER Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain O residue 205 LEU Chi-restraints excluded: chain O residue 208 GLU Chi-restraints excluded: chain O residue 227 ASN Chi-restraints excluded: chain O residue 240 PHE Chi-restraints excluded: chain O residue 244 ASN Chi-restraints excluded: chain O residue 260 ASP Chi-restraints excluded: chain O residue 275 LEU Chi-restraints excluded: chain O residue 312 MET Chi-restraints excluded: chain O residue 339 ARG Chi-restraints excluded: chain O residue 360 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 398 optimal weight: 3.9990 chunk 271 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 356 optimal weight: 10.0000 chunk 197 optimal weight: 0.8980 chunk 408 optimal weight: 0.7980 chunk 330 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 244 optimal weight: 20.0000 chunk 429 optimal weight: 4.9990 chunk 120 optimal weight: 7.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 137 ASN ** W 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 32 GLN ** U 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.6224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 40342 Z= 0.221 Angle : 0.647 9.743 54493 Z= 0.346 Chirality : 0.037 0.224 6198 Planarity : 0.005 0.135 7021 Dihedral : 6.980 85.324 5487 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.68 % Allowed : 8.51 % Favored : 90.80 % Rotamer: Outliers : 4.30 % Allowed : 18.91 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.04 % 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: -2.80 (0.11), residues: 4970 helix: -1.22 (0.09), residues: 3134 sheet: -1.50 (0.40), residues: 169 loop : -2.97 (0.14), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP N 392 HIS 0.013 0.001 HIS S 110 PHE 0.015 0.002 PHE N 213 TYR 0.031 0.002 TYR Z 349 ARG 0.006 0.001 ARG P 123 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 296 is missing expected H atoms. Skipping. Evaluate side-chains 1128 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 941 time to evaluate : 4.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 35 ILE cc_start: 0.9413 (tp) cc_final: 0.9120 (pt) REVERT: W 70 ARG cc_start: 0.9147 (mtp180) cc_final: 0.8645 (mmp80) REVERT: W 112 PHE cc_start: 0.6329 (m-80) cc_final: 0.6005 (m-10) REVERT: V 40 LYS cc_start: 0.8700 (mttm) cc_final: 0.8405 (tptt) REVERT: V 68 ARG cc_start: 0.9026 (mtp180) cc_final: 0.8496 (mmm-85) REVERT: V 75 MET cc_start: 0.9093 (mtp) cc_final: 0.8842 (mtm) REVERT: V 158 ASP cc_start: 0.8777 (m-30) cc_final: 0.8294 (m-30) REVERT: V 175 ARG cc_start: 0.7900 (tpp-160) cc_final: 0.7451 (ttm-80) REVERT: V 208 ARG cc_start: 0.7774 (mtm180) cc_final: 0.7481 (mtm180) REVERT: V 260 GLU cc_start: 0.8797 (tp30) cc_final: 0.8066 (mp0) REVERT: T 166 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8532 (tmm-80) REVERT: T 212 LEU cc_start: 0.9220 (tp) cc_final: 0.8857 (mm) REVERT: T 214 ARG cc_start: 0.6654 (mmt-90) cc_final: 0.6405 (mpt180) REVERT: T 219 ASP cc_start: 0.9012 (m-30) cc_final: 0.8572 (t0) REVERT: T 220 ILE cc_start: 0.8324 (pt) cc_final: 0.8022 (tt) REVERT: T 223 ASN cc_start: 0.6987 (OUTLIER) cc_final: 0.6422 (t0) REVERT: T 234 GLN cc_start: 0.8512 (tm-30) cc_final: 0.7952 (tm-30) REVERT: T 258 PHE cc_start: 0.7774 (m-10) cc_final: 0.7523 (m-10) REVERT: T 265 ASP cc_start: 0.8738 (m-30) cc_final: 0.7760 (t0) REVERT: T 269 ASP cc_start: 0.8420 (m-30) cc_final: 0.7344 (m-30) REVERT: T 322 GLN cc_start: 0.7907 (tp40) cc_final: 0.7400 (pm20) REVERT: Z 33 ARG cc_start: 0.3900 (mmt-90) cc_final: 0.3499 (mmt180) REVERT: Z 103 TYR cc_start: 0.3025 (OUTLIER) cc_final: 0.2286 (m-80) REVERT: Z 113 MET cc_start: 0.2241 (OUTLIER) cc_final: 0.1325 (mtm) REVERT: Z 216 MET cc_start: 0.2050 (ttp) cc_final: 0.1428 (tpt) REVERT: Z 466 LEU cc_start: 0.6244 (mt) cc_final: 0.6035 (mt) REVERT: Z 481 SER cc_start: 0.3217 (OUTLIER) cc_final: 0.2767 (t) REVERT: Z 489 TYR cc_start: 0.3797 (m-10) cc_final: 0.3559 (m-80) REVERT: Z 551 LYS cc_start: 0.6934 (mtmm) cc_final: 0.6656 (mmtt) REVERT: Z 593 THR cc_start: 0.6505 (p) cc_final: 0.6171 (t) REVERT: Z 662 MET cc_start: 0.3989 (mtp) cc_final: 0.3605 (ttt) REVERT: N 40 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8009 (mt-10) REVERT: N 46 GLU cc_start: 0.7737 (mt-10) cc_final: 0.6936 (tm-30) REVERT: N 48 LEU cc_start: 0.9072 (mt) cc_final: 0.8732 (tp) REVERT: N 218 GLN cc_start: 0.8716 (mt0) cc_final: 0.8296 (tm-30) REVERT: N 222 PHE cc_start: 0.5801 (m-80) cc_final: 0.5523 (m-80) REVERT: N 349 ASP cc_start: 0.7230 (OUTLIER) cc_final: 0.6281 (p0) REVERT: N 351 MET cc_start: 0.5662 (tmm) cc_final: 0.4755 (tmm) REVERT: N 459 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7630 (t0) REVERT: N 492 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.8002 (p0) REVERT: N 521 LEU cc_start: 0.8446 (tt) cc_final: 0.7940 (tt) REVERT: N 532 MET cc_start: 0.5103 (ttp) cc_final: 0.4797 (ttp) REVERT: N 538 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8327 (tm-30) REVERT: N 539 THR cc_start: 0.7302 (p) cc_final: 0.6978 (p) REVERT: N 566 LEU cc_start: 0.7945 (mt) cc_final: 0.7673 (tp) REVERT: N 580 ARG cc_start: 0.8966 (ttp-170) cc_final: 0.8623 (tmm-80) REVERT: N 601 ARG cc_start: 0.6354 (mtm180) cc_final: 0.6111 (mtt90) REVERT: N 695 MET cc_start: 0.2272 (mmt) cc_final: 0.1775 (mmt) REVERT: N 725 MET cc_start: 0.7843 (mtm) cc_final: 0.7276 (mmt) REVERT: N 757 MET cc_start: 0.7656 (mmt) cc_final: 0.7198 (ttm) REVERT: N 847 GLU cc_start: 0.6709 (mt-10) cc_final: 0.5526 (tp30) REVERT: N 879 ASP cc_start: 0.8454 (m-30) cc_final: 0.7949 (p0) REVERT: S 66 GLU cc_start: 0.9255 (tt0) cc_final: 0.8977 (tp30) REVERT: S 77 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7665 (mp0) REVERT: S 96 ARG cc_start: 0.7881 (ttt-90) cc_final: 0.7545 (tmm-80) REVERT: S 315 LYS cc_start: 0.8948 (mttt) cc_final: 0.8656 (mmtt) REVERT: S 399 ARG cc_start: 0.8771 (mtp-110) cc_final: 0.8546 (mtm110) REVERT: P 42 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8249 (mm-30) REVERT: P 60 MET cc_start: 0.8524 (tpp) cc_final: 0.8195 (tpp) REVERT: P 73 MET cc_start: 0.8510 (mtp) cc_final: 0.8066 (mtm) REVERT: P 93 ARG cc_start: 0.7626 (ttm-80) cc_final: 0.7049 (ttt180) REVERT: P 126 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.7765 (t70) REVERT: P 230 MET cc_start: 0.9025 (mmm) cc_final: 0.8772 (mmm) REVERT: P 239 SER cc_start: 0.9206 (m) cc_final: 0.8886 (t) REVERT: P 296 LEU cc_start: 0.9561 (tp) cc_final: 0.9334 (tp) REVERT: P 303 LYS cc_start: 0.8590 (ttpp) cc_final: 0.8310 (tppt) REVERT: P 304 ASP cc_start: 0.8635 (m-30) cc_final: 0.8197 (p0) REVERT: P 326 MET cc_start: 0.7702 (pmm) cc_final: 0.7499 (pmm) REVERT: P 353 ASP cc_start: 0.8950 (t0) cc_final: 0.8615 (t0) REVERT: P 364 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8161 (mtp85) REVERT: P 441 LYS cc_start: 0.9213 (mttt) cc_final: 0.8958 (mttt) REVERT: P 449 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8240 (tm-30) REVERT: Q 94 ASP cc_start: 0.7900 (m-30) cc_final: 0.7698 (p0) REVERT: Q 96 PHE cc_start: 0.6416 (p90) cc_final: 0.6041 (p90) REVERT: Q 159 LYS cc_start: 0.5938 (OUTLIER) cc_final: 0.5529 (ptpt) REVERT: Q 221 GLU cc_start: 0.7884 (tt0) cc_final: 0.7458 (mp0) REVERT: Q 225 TRP cc_start: 0.8182 (m-10) cc_final: 0.7884 (m100) REVERT: Q 236 PHE cc_start: 0.8399 (t80) cc_final: 0.7777 (t80) REVERT: Q 289 CYS cc_start: 0.9053 (t) cc_final: 0.8673 (p) REVERT: Q 312 GLU cc_start: 0.8411 (mp0) cc_final: 0.8075 (mp0) REVERT: R 42 MET cc_start: 0.9119 (mmm) cc_final: 0.8569 (tmm) REVERT: R 63 TRP cc_start: 0.6364 (OUTLIER) cc_final: 0.5035 (m-90) REVERT: R 116 ASP cc_start: 0.8554 (t0) cc_final: 0.8303 (t0) REVERT: R 225 TYR cc_start: 0.9403 (m-10) cc_final: 0.9093 (m-10) REVERT: R 272 PHE cc_start: 0.7941 (OUTLIER) cc_final: 0.7511 (t80) REVERT: R 302 HIS cc_start: 0.9031 (t-90) cc_final: 0.8787 (t70) REVERT: R 305 SER cc_start: 0.9098 (t) cc_final: 0.8580 (p) REVERT: R 354 VAL cc_start: 0.8593 (t) cc_final: 0.8355 (t) REVERT: R 355 GLU cc_start: 0.8541 (mt-10) cc_final: 0.7927 (pm20) REVERT: U 9 VAL cc_start: 0.8939 (t) cc_final: 0.8639 (p) REVERT: U 76 GLU cc_start: 0.9609 (mm-30) cc_final: 0.9406 (mm-30) REVERT: U 100 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7956 (pttp) REVERT: U 136 GLU cc_start: 0.8284 (mp0) cc_final: 0.7826 (mp0) REVERT: U 169 GLU cc_start: 0.9219 (tp30) cc_final: 0.8694 (tm-30) REVERT: U 189 GLN cc_start: 0.9481 (tp40) cc_final: 0.9274 (tp40) REVERT: U 262 LEU cc_start: 0.9064 (tp) cc_final: 0.8843 (tt) REVERT: O 39 LEU cc_start: 0.8398 (mt) cc_final: 0.7952 (tp) REVERT: O 43 ASP cc_start: 0.8948 (t0) cc_final: 0.8723 (m-30) REVERT: O 74 LEU cc_start: 0.8164 (mt) cc_final: 0.7858 (tp) REVERT: O 121 LEU cc_start: 0.9389 (mt) cc_final: 0.9100 (tt) REVERT: O 154 ARG cc_start: 0.9048 (mmt90) cc_final: 0.8770 (mtp85) REVERT: O 174 LYS cc_start: 0.9392 (mtpp) cc_final: 0.9069 (ptpp) REVERT: O 339 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7383 (ptt-90) outliers start: 187 outliers final: 145 residues processed: 1064 average time/residue: 1.1006 time to fit residues: 1843.9276 Evaluate side-chains 1056 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 895 time to evaluate : 4.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain W residue 97 LEU Chi-restraints excluded: chain W residue 115 SER Chi-restraints excluded: chain W residue 126 LYS Chi-restraints excluded: chain W residue 140 ILE Chi-restraints excluded: chain W residue 185 SER Chi-restraints excluded: chain W residue 186 SER Chi-restraints excluded: chain V residue 88 ASP Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 120 CYS Chi-restraints excluded: chain V residue 180 ASN Chi-restraints excluded: chain V residue 186 LYS Chi-restraints excluded: chain V residue 233 ASP Chi-restraints excluded: chain V residue 293 THR Chi-restraints excluded: chain T residue 166 ARG Chi-restraints excluded: chain T residue 178 TYR Chi-restraints excluded: chain T residue 223 ASN Chi-restraints excluded: chain T residue 231 SER Chi-restraints excluded: chain T residue 243 LYS Chi-restraints excluded: chain T residue 274 CYS Chi-restraints excluded: chain T residue 275 ILE Chi-restraints excluded: chain T residue 313 ASN Chi-restraints excluded: chain Y residue 19 PHE Chi-restraints excluded: chain Y residue 35 ASP Chi-restraints excluded: chain Y residue 50 ASP Chi-restraints excluded: chain Y residue 60 LEU Chi-restraints excluded: chain Z residue 1 MET Chi-restraints excluded: chain Z residue 55 GLU Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain Z residue 103 TYR Chi-restraints excluded: chain Z residue 113 MET Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 232 TYR Chi-restraints excluded: chain Z residue 422 VAL Chi-restraints excluded: chain Z residue 445 LEU Chi-restraints excluded: chain Z residue 468 ASP Chi-restraints excluded: chain Z residue 481 SER Chi-restraints excluded: chain Z residue 574 GLU Chi-restraints excluded: chain Z residue 596 ASP Chi-restraints excluded: chain Z residue 711 SER Chi-restraints excluded: chain Z residue 731 MET Chi-restraints excluded: chain Z residue 741 LEU Chi-restraints excluded: chain Z residue 748 LEU Chi-restraints excluded: chain Z residue 759 LEU Chi-restraints excluded: chain Z residue 873 LEU Chi-restraints excluded: chain N residue 22 PHE Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 163 PHE Chi-restraints excluded: chain N residue 165 LYS Chi-restraints excluded: chain N residue 176 MET Chi-restraints excluded: chain N residue 183 LEU Chi-restraints excluded: chain N residue 207 ASN Chi-restraints excluded: chain N residue 233 LEU Chi-restraints excluded: chain N residue 349 ASP Chi-restraints excluded: chain N residue 386 LEU Chi-restraints excluded: chain N residue 388 ASP Chi-restraints excluded: chain N residue 395 ARG Chi-restraints excluded: chain N residue 397 THR Chi-restraints excluded: chain N residue 448 LEU Chi-restraints excluded: chain N residue 459 ASP Chi-restraints excluded: chain N residue 461 LEU Chi-restraints excluded: chain N residue 486 MET Chi-restraints excluded: chain N residue 492 ASP Chi-restraints excluded: chain N residue 510 GLU Chi-restraints excluded: chain N residue 629 THR Chi-restraints excluded: chain N residue 638 SER Chi-restraints excluded: chain N residue 672 LEU Chi-restraints excluded: chain N residue 731 ILE Chi-restraints excluded: chain N residue 742 HIS Chi-restraints excluded: chain N residue 794 ASP Chi-restraints excluded: chain N residue 838 LYS Chi-restraints excluded: chain N residue 892 LEU Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain S residue 113 LEU Chi-restraints excluded: chain S residue 125 ASN Chi-restraints excluded: chain S residue 131 LEU Chi-restraints excluded: chain S residue 235 LEU Chi-restraints excluded: chain S residue 236 ARG Chi-restraints excluded: chain S residue 240 LEU Chi-restraints excluded: chain S residue 249 THR Chi-restraints excluded: chain S residue 260 HIS Chi-restraints excluded: chain S residue 281 ASN Chi-restraints excluded: chain S residue 302 TYR Chi-restraints excluded: chain S residue 346 LEU Chi-restraints excluded: chain S residue 353 LEU Chi-restraints excluded: chain S residue 354 LYS Chi-restraints excluded: chain S residue 356 SER Chi-restraints excluded: chain S residue 412 LEU Chi-restraints excluded: chain S residue 447 ILE Chi-restraints excluded: chain S residue 469 THR Chi-restraints excluded: chain S residue 485 ASP Chi-restraints excluded: chain P residue 105 VAL Chi-restraints excluded: chain P residue 106 GLN Chi-restraints excluded: chain P residue 126 ASP Chi-restraints excluded: chain P residue 139 GLU Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain P residue 172 GLU Chi-restraints excluded: chain P residue 244 CYS Chi-restraints excluded: chain P residue 332 SER Chi-restraints excluded: chain P residue 364 ARG Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain P residue 449 GLU Chi-restraints excluded: chain P residue 453 HIS Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 119 SER Chi-restraints excluded: chain Q residue 159 LYS Chi-restraints excluded: chain Q residue 160 MET Chi-restraints excluded: chain Q residue 174 SER Chi-restraints excluded: chain Q residue 182 ASN Chi-restraints excluded: chain Q residue 218 HIS Chi-restraints excluded: chain Q residue 224 ASP Chi-restraints excluded: chain Q residue 227 THR Chi-restraints excluded: chain Q residue 234 GLU Chi-restraints excluded: chain Q residue 241 SER Chi-restraints excluded: chain Q residue 242 ILE Chi-restraints excluded: chain Q residue 328 ASP Chi-restraints excluded: chain Q residue 415 TYR Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 63 TRP Chi-restraints excluded: chain R residue 94 ASN Chi-restraints excluded: chain R residue 109 GLU Chi-restraints excluded: chain R residue 154 ASN Chi-restraints excluded: chain R residue 173 ASP Chi-restraints excluded: chain R residue 175 ASP Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 196 GLN Chi-restraints excluded: chain R residue 214 MET Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 235 ASP Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 248 GLU Chi-restraints excluded: chain R residue 272 PHE Chi-restraints excluded: chain R residue 278 VAL Chi-restraints excluded: chain R residue 389 MET Chi-restraints excluded: chain U residue 14 LEU Chi-restraints excluded: chain U residue 24 ASN Chi-restraints excluded: chain U residue 48 LEU Chi-restraints excluded: chain U residue 49 ASP Chi-restraints excluded: chain U residue 71 ASP Chi-restraints excluded: chain U residue 73 ASP Chi-restraints excluded: chain U residue 96 HIS Chi-restraints excluded: chain U residue 100 LYS Chi-restraints excluded: chain U residue 140 SER Chi-restraints excluded: chain U residue 192 THR Chi-restraints excluded: chain U residue 250 TYR Chi-restraints excluded: chain U residue 270 VAL Chi-restraints excluded: chain U residue 278 ASN Chi-restraints excluded: chain O residue 145 LEU Chi-restraints excluded: chain O residue 149 THR Chi-restraints excluded: chain O residue 202 LEU Chi-restraints excluded: chain O residue 208 GLU Chi-restraints excluded: chain O residue 227 ASN Chi-restraints excluded: chain O residue 240 PHE Chi-restraints excluded: chain O residue 244 ASN Chi-restraints excluded: chain O residue 255 TRP Chi-restraints excluded: chain O residue 260 ASP Chi-restraints excluded: chain O residue 275 LEU Chi-restraints excluded: chain O residue 339 ARG Chi-restraints excluded: chain O residue 360 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 160 optimal weight: 9.9990 chunk 430 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 280 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 478 optimal weight: 10.0000 chunk 397 optimal weight: 5.9990 chunk 221 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 158 optimal weight: 9.9990 chunk 251 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 325 GLN Z 371 ASN ** Z 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 340 GLN ** N 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 452 ASN ** P 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 77 ASN ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 231 GLN O 35 HIS ** O 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.6984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 40342 Z= 0.410 Angle : 0.782 14.618 54493 Z= 0.425 Chirality : 0.040 0.163 6198 Planarity : 0.006 0.154 7021 Dihedral : 7.063 58.909 5472 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 22.95 Ramachandran Plot: Outliers : 0.66 % Allowed : 11.05 % Favored : 88.29 % Rotamer: Outliers : 5.66 % Allowed : 18.96 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.04 % 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: -3.20 (0.11), residues: 4970 helix: -1.52 (0.08), residues: 3105 sheet: -1.67 (0.39), residues: 172 loop : -3.14 (0.14), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 174 HIS 0.020 0.002 HIS U 157 PHE 0.024 0.002 PHE Y 22 TYR 0.027 0.002 TYR Z 349 ARG 0.013 0.001 ARG Q 314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 296 is missing expected H atoms. Skipping. Evaluate side-chains 1142 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 896 time to evaluate : 4.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 70 ARG cc_start: 0.9211 (mtp180) cc_final: 0.8776 (mmp80) REVERT: W 112 PHE cc_start: 0.6492 (m-80) cc_final: 0.6199 (m-80) REVERT: V 32 TYR cc_start: 0.7793 (m-10) cc_final: 0.7450 (m-10) REVERT: V 40 LYS cc_start: 0.8690 (mttm) cc_final: 0.8486 (tptt) REVERT: V 175 ARG cc_start: 0.7902 (tpp-160) cc_final: 0.7444 (ttm-80) REVERT: T 166 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.8631 (tmm-80) REVERT: T 212 LEU cc_start: 0.9259 (tp) cc_final: 0.8890 (mm) REVERT: T 219 ASP cc_start: 0.8936 (OUTLIER) cc_final: 0.8482 (t0) REVERT: T 220 ILE cc_start: 0.8354 (pt) cc_final: 0.8047 (tt) REVERT: T 223 ASN cc_start: 0.7239 (OUTLIER) cc_final: 0.6548 (m-40) REVERT: T 234 GLN cc_start: 0.8499 (tm-30) cc_final: 0.8009 (tm-30) REVERT: T 265 ASP cc_start: 0.8823 (OUTLIER) cc_final: 0.8425 (t0) REVERT: T 299 MET cc_start: 0.7372 (mmm) cc_final: 0.7170 (mmm) REVERT: T 322 GLN cc_start: 0.7901 (tp40) cc_final: 0.7405 (pm20) REVERT: Z 103 TYR cc_start: 0.3915 (OUTLIER) cc_final: 0.3158 (m-80) REVERT: Z 113 MET cc_start: 0.2028 (OUTLIER) cc_final: 0.1146 (mtm) REVERT: Z 216 MET cc_start: 0.1953 (ttp) cc_final: 0.1330 (tpt) REVERT: Z 481 SER cc_start: 0.3138 (OUTLIER) cc_final: 0.2714 (t) REVERT: Z 495 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7094 (tm-30) REVERT: Z 551 LYS cc_start: 0.7025 (mtmm) cc_final: 0.6659 (mmtt) REVERT: Z 596 ASP cc_start: 0.7243 (OUTLIER) cc_final: 0.6428 (m-30) REVERT: Z 662 MET cc_start: 0.4091 (mtp) cc_final: 0.3682 (ttt) REVERT: Z 729 MET cc_start: 0.7410 (mtp) cc_final: 0.7204 (mtp) REVERT: Z 845 ARG cc_start: -0.1877 (OUTLIER) cc_final: -0.2466 (ptt180) REVERT: N 48 LEU cc_start: 0.9096 (mt) cc_final: 0.8719 (tp) REVERT: N 218 GLN cc_start: 0.8538 (mt0) cc_final: 0.8270 (tm-30) REVERT: N 351 MET cc_start: 0.5522 (tmm) cc_final: 0.4799 (tmm) REVERT: N 459 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7429 (t0) REVERT: N 492 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7635 (p0) REVERT: N 538 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8786 (mt-10) REVERT: N 580 ARG cc_start: 0.8994 (ttp-170) cc_final: 0.8713 (tmm-80) REVERT: N 601 ARG cc_start: 0.6377 (mtm180) cc_final: 0.6169 (mtt90) REVERT: N 625 ILE cc_start: 0.6231 (pt) cc_final: 0.5938 (pt) REVERT: N 695 MET cc_start: 0.2498 (mmt) cc_final: 0.2060 (mmt) REVERT: N 725 MET cc_start: 0.7582 (mtm) cc_final: 0.7080 (mmt) REVERT: S 66 GLU cc_start: 0.9204 (tt0) cc_final: 0.8956 (tp30) REVERT: S 315 LYS cc_start: 0.9025 (mttt) cc_final: 0.8680 (mmtt) REVERT: S 325 LYS cc_start: 0.8654 (mttp) cc_final: 0.8354 (mmmm) REVERT: S 399 ARG cc_start: 0.8799 (mtp-110) cc_final: 0.8599 (mtm110) REVERT: S 436 PHE cc_start: 0.8462 (m-10) cc_final: 0.8141 (m-10) REVERT: S 459 GLN cc_start: 0.9094 (tt0) cc_final: 0.8768 (pp30) REVERT: S 477 HIS cc_start: 0.8561 (OUTLIER) cc_final: 0.7931 (t70) REVERT: P 1 MET cc_start: 0.7081 (mmt) cc_final: 0.6806 (mmt) REVERT: P 42 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8413 (mm-30) REVERT: P 60 MET cc_start: 0.8563 (tpp) cc_final: 0.8238 (tpp) REVERT: P 126 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.7804 (t70) REVERT: P 230 MET cc_start: 0.9038 (mmm) cc_final: 0.8832 (mmm) REVERT: P 239 SER cc_start: 0.9128 (m) cc_final: 0.8804 (t) REVERT: P 326 MET cc_start: 0.7987 (pmm) cc_final: 0.7717 (pmm) REVERT: P 353 ASP cc_start: 0.9110 (t0) cc_final: 0.8838 (t0) REVERT: P 403 PHE cc_start: 0.8022 (m-80) cc_final: 0.7471 (t80) REVERT: P 449 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8169 (tm-30) REVERT: Q 76 PHE cc_start: 0.7128 (m-80) cc_final: 0.6861 (m-10) REVERT: Q 94 ASP cc_start: 0.8258 (m-30) cc_final: 0.7930 (p0) REVERT: Q 221 GLU cc_start: 0.8027 (tt0) cc_final: 0.7404 (mp0) REVERT: Q 225 TRP cc_start: 0.8101 (m-90) cc_final: 0.7720 (m-90) REVERT: Q 233 TYR cc_start: 0.8946 (t80) cc_final: 0.8740 (t80) REVERT: Q 372 LYS cc_start: 0.8481 (mttp) cc_final: 0.8183 (mmtm) REVERT: R 42 MET cc_start: 0.9119 (mmm) cc_final: 0.8643 (tmm) REVERT: R 63 TRP cc_start: 0.6364 (OUTLIER) cc_final: 0.5178 (m-90) REVERT: R 73 MET cc_start: 0.8781 (mmp) cc_final: 0.8456 (mtp) REVERT: R 116 ASP cc_start: 0.8579 (t0) cc_final: 0.8282 (t0) REVERT: R 170 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7735 (mt-10) REVERT: R 210 SER cc_start: 0.8412 (OUTLIER) cc_final: 0.8164 (p) REVERT: R 225 TYR cc_start: 0.9376 (m-10) cc_final: 0.9027 (m-10) REVERT: R 272 PHE cc_start: 0.7927 (OUTLIER) cc_final: 0.7535 (t80) REVERT: R 355 GLU cc_start: 0.8570 (mt-10) cc_final: 0.7905 (pm20) REVERT: U 9 VAL cc_start: 0.8855 (t) cc_final: 0.8539 (p) REVERT: U 100 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7918 (pttp) REVERT: U 136 GLU cc_start: 0.7974 (mp0) cc_final: 0.7547 (mp0) REVERT: U 169 GLU cc_start: 0.9170 (tp30) cc_final: 0.8324 (tm-30) REVERT: U 189 GLN cc_start: 0.9542 (tp40) cc_final: 0.9217 (tp40) REVERT: U 213 GLU cc_start: 0.9435 (OUTLIER) cc_final: 0.8810 (tm-30) REVERT: U 262 LEU cc_start: 0.9138 (tp) cc_final: 0.8880 (tt) REVERT: O 39 LEU cc_start: 0.8522 (mt) cc_final: 0.8033 (tp) REVERT: O 43 ASP cc_start: 0.9023 (t0) cc_final: 0.8732 (m-30) REVERT: O 74 LEU cc_start: 0.8148 (mt) cc_final: 0.7916 (tp) REVERT: O 339 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7686 (ptp90) outliers start: 246 outliers final: 183 residues processed: 1061 average time/residue: 1.0862 time to fit residues: 1806.5199 Evaluate side-chains 1060 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 855 time to evaluate : 4.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain W residue 97 LEU Chi-restraints excluded: chain W residue 123 ASP Chi-restraints excluded: chain W residue 126 LYS Chi-restraints excluded: chain W residue 140 ILE Chi-restraints excluded: chain W residue 151 GLU Chi-restraints excluded: chain W residue 185 SER Chi-restraints excluded: chain W residue 186 SER Chi-restraints excluded: chain V residue 60 GLU Chi-restraints excluded: chain V residue 88 ASP Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 97 ASP Chi-restraints excluded: chain V residue 107 MET Chi-restraints excluded: chain V residue 120 CYS Chi-restraints excluded: chain V residue 148 ILE Chi-restraints excluded: chain V residue 180 ASN Chi-restraints excluded: chain V residue 186 LYS Chi-restraints excluded: chain V residue 194 HIS Chi-restraints excluded: chain V residue 233 ASP Chi-restraints excluded: chain V residue 293 THR Chi-restraints excluded: chain V residue 307 VAL Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 166 ARG Chi-restraints excluded: chain T residue 178 TYR Chi-restraints excluded: chain T residue 187 TYR Chi-restraints excluded: chain T residue 219 ASP Chi-restraints excluded: chain T residue 223 ASN Chi-restraints excluded: chain T residue 231 SER Chi-restraints excluded: chain T residue 243 LYS Chi-restraints excluded: chain T residue 265 ASP Chi-restraints excluded: chain T residue 274 CYS Chi-restraints excluded: chain T residue 275 ILE Chi-restraints excluded: chain T residue 313 ASN Chi-restraints excluded: chain T residue 339 VAL Chi-restraints excluded: chain Y residue 19 PHE Chi-restraints excluded: chain Y residue 35 ASP Chi-restraints excluded: chain Y residue 50 ASP Chi-restraints excluded: chain Y residue 67 MET Chi-restraints excluded: chain Z residue 1 MET Chi-restraints excluded: chain Z residue 55 GLU Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain Z residue 103 TYR Chi-restraints excluded: chain Z residue 113 MET Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 301 HIS Chi-restraints excluded: chain Z residue 310 ASP Chi-restraints excluded: chain Z residue 422 VAL Chi-restraints excluded: chain Z residue 445 LEU Chi-restraints excluded: chain Z residue 468 ASP Chi-restraints excluded: chain Z residue 481 SER Chi-restraints excluded: chain Z residue 495 GLU Chi-restraints excluded: chain Z residue 574 GLU Chi-restraints excluded: chain Z residue 596 ASP Chi-restraints excluded: chain Z residue 711 SER Chi-restraints excluded: chain Z residue 731 MET Chi-restraints excluded: chain Z residue 741 LEU Chi-restraints excluded: chain Z residue 748 LEU Chi-restraints excluded: chain Z residue 845 ARG Chi-restraints excluded: chain Z residue 873 LEU Chi-restraints excluded: chain N residue 22 PHE Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 76 GLU Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain N residue 143 ASP Chi-restraints excluded: chain N residue 165 LYS Chi-restraints excluded: chain N residue 172 ASP Chi-restraints excluded: chain N residue 176 MET Chi-restraints excluded: chain N residue 183 LEU Chi-restraints excluded: chain N residue 207 ASN Chi-restraints excluded: chain N residue 233 LEU Chi-restraints excluded: chain N residue 337 LEU Chi-restraints excluded: chain N residue 349 ASP Chi-restraints excluded: chain N residue 358 ASP Chi-restraints excluded: chain N residue 383 ASP Chi-restraints excluded: chain N residue 386 LEU Chi-restraints excluded: chain N residue 388 ASP Chi-restraints excluded: chain N residue 395 ARG Chi-restraints excluded: chain N residue 397 THR Chi-restraints excluded: chain N residue 448 LEU Chi-restraints excluded: chain N residue 459 ASP Chi-restraints excluded: chain N residue 461 LEU Chi-restraints excluded: chain N residue 465 LEU Chi-restraints excluded: chain N residue 469 SER Chi-restraints excluded: chain N residue 486 MET Chi-restraints excluded: chain N residue 492 ASP Chi-restraints excluded: chain N residue 510 GLU Chi-restraints excluded: chain N residue 629 THR Chi-restraints excluded: chain N residue 633 CYS Chi-restraints excluded: chain N residue 638 SER Chi-restraints excluded: chain N residue 672 LEU Chi-restraints excluded: chain N residue 731 ILE Chi-restraints excluded: chain N residue 742 HIS Chi-restraints excluded: chain N residue 794 ASP Chi-restraints excluded: chain N residue 838 LYS Chi-restraints excluded: chain N residue 892 LEU Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain S residue 113 LEU Chi-restraints excluded: chain S residue 131 LEU Chi-restraints excluded: chain S residue 189 ASP Chi-restraints excluded: chain S residue 210 CYS Chi-restraints excluded: chain S residue 235 LEU Chi-restraints excluded: chain S residue 236 ARG Chi-restraints excluded: chain S residue 240 LEU Chi-restraints excluded: chain S residue 249 THR Chi-restraints excluded: chain S residue 260 HIS Chi-restraints excluded: chain S residue 263 LEU Chi-restraints excluded: chain S residue 281 ASN Chi-restraints excluded: chain S residue 346 LEU Chi-restraints excluded: chain S residue 353 LEU Chi-restraints excluded: chain S residue 354 LYS Chi-restraints excluded: chain S residue 356 SER Chi-restraints excluded: chain S residue 444 ASP Chi-restraints excluded: chain S residue 447 ILE Chi-restraints excluded: chain S residue 451 ILE Chi-restraints excluded: chain S residue 469 THR Chi-restraints excluded: chain S residue 477 HIS Chi-restraints excluded: chain S residue 485 ASP Chi-restraints excluded: chain P residue 105 VAL Chi-restraints excluded: chain P residue 126 ASP Chi-restraints excluded: chain P residue 139 GLU Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain P residue 172 GLU Chi-restraints excluded: chain P residue 188 GLU Chi-restraints excluded: chain P residue 198 ASP Chi-restraints excluded: chain P residue 244 CYS Chi-restraints excluded: chain P residue 322 GLU Chi-restraints excluded: chain P residue 343 SER Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain P residue 387 ASP Chi-restraints excluded: chain P residue 449 GLU Chi-restraints excluded: chain P residue 453 HIS Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 119 SER Chi-restraints excluded: chain Q residue 160 MET Chi-restraints excluded: chain Q residue 174 SER Chi-restraints excluded: chain Q residue 182 ASN Chi-restraints excluded: chain Q residue 218 HIS Chi-restraints excluded: chain Q residue 224 ASP Chi-restraints excluded: chain Q residue 234 GLU Chi-restraints excluded: chain Q residue 243 ASP Chi-restraints excluded: chain Q residue 328 ASP Chi-restraints excluded: chain Q residue 362 GLU Chi-restraints excluded: chain Q residue 408 SER Chi-restraints excluded: chain Q residue 415 TYR Chi-restraints excluded: chain Q residue 416 ASN Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 48 ASN Chi-restraints excluded: chain R residue 63 TRP Chi-restraints excluded: chain R residue 68 ASP Chi-restraints excluded: chain R residue 94 ASN Chi-restraints excluded: chain R residue 109 GLU Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 154 ASN Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 173 ASP Chi-restraints excluded: chain R residue 175 ASP Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 188 CYS Chi-restraints excluded: chain R residue 196 GLN Chi-restraints excluded: chain R residue 210 SER Chi-restraints excluded: chain R residue 214 MET Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 235 ASP Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 272 PHE Chi-restraints excluded: chain R residue 278 VAL Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain R residue 301 ILE Chi-restraints excluded: chain R residue 357 ASN Chi-restraints excluded: chain U residue 14 LEU Chi-restraints excluded: chain U residue 48 LEU Chi-restraints excluded: chain U residue 49 ASP Chi-restraints excluded: chain U residue 53 SER Chi-restraints excluded: chain U residue 71 ASP Chi-restraints excluded: chain U residue 73 ASP Chi-restraints excluded: chain U residue 85 VAL Chi-restraints excluded: chain U residue 96 HIS Chi-restraints excluded: chain U residue 100 LYS Chi-restraints excluded: chain U residue 122 VAL Chi-restraints excluded: chain U residue 159 THR Chi-restraints excluded: chain U residue 192 THR Chi-restraints excluded: chain U residue 213 GLU Chi-restraints excluded: chain U residue 249 PHE Chi-restraints excluded: chain U residue 250 TYR Chi-restraints excluded: chain U residue 254 ASN Chi-restraints excluded: chain U residue 267 ARG Chi-restraints excluded: chain U residue 270 VAL Chi-restraints excluded: chain U residue 278 ASN Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain O residue 60 TYR Chi-restraints excluded: chain O residue 145 LEU Chi-restraints excluded: chain O residue 149 THR Chi-restraints excluded: chain O residue 158 LEU Chi-restraints excluded: chain O residue 166 ILE Chi-restraints excluded: chain O residue 202 LEU Chi-restraints excluded: chain O residue 227 ASN Chi-restraints excluded: chain O residue 240 PHE Chi-restraints excluded: chain O residue 244 ASN Chi-restraints excluded: chain O residue 255 TRP Chi-restraints excluded: chain O residue 260 ASP Chi-restraints excluded: chain O residue 275 LEU Chi-restraints excluded: chain O residue 312 MET Chi-restraints excluded: chain O residue 339 ARG Chi-restraints excluded: chain O residue 360 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 461 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 272 optimal weight: 6.9990 chunk 349 optimal weight: 8.9990 chunk 270 optimal weight: 9.9990 chunk 403 optimal weight: 0.9980 chunk 267 optimal weight: 2.9990 chunk 477 optimal weight: 3.9990 chunk 298 optimal weight: 3.9990 chunk 290 optimal weight: 10.0000 chunk 220 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 619 HIS Z 737 ASN Z 782 HIS ** N 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 340 GLN ** N 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 193 GLN ** S 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 350 GLN ** S 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 502 ASN ** P 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 296 ASN ** U 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.7223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 40342 Z= 0.239 Angle : 0.674 19.662 54493 Z= 0.356 Chirality : 0.038 0.230 6198 Planarity : 0.005 0.174 7021 Dihedral : 6.641 59.994 5458 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.56 % Allowed : 8.81 % Favored : 90.62 % Rotamer: Outliers : 4.58 % Allowed : 20.94 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 1.22 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.11), residues: 4970 helix: -1.13 (0.09), residues: 3122 sheet: -1.51 (0.39), residues: 171 loop : -2.96 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP N 392 HIS 0.015 0.002 HIS U 157 PHE 0.017 0.002 PHE O 155 TYR 0.036 0.002 TYR N 557 ARG 0.008 0.001 ARG S 228 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 296 is missing expected H atoms. Skipping. Evaluate side-chains 1083 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 884 time to evaluate : 4.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 3 LEU cc_start: 0.8460 (mt) cc_final: 0.8186 (pp) REVERT: W 35 ILE cc_start: 0.9374 (tp) cc_final: 0.9050 (pt) REVERT: W 70 ARG cc_start: 0.9174 (mtp180) cc_final: 0.8691 (mmp80) REVERT: W 112 PHE cc_start: 0.6484 (m-80) cc_final: 0.6204 (m-80) REVERT: V 32 TYR cc_start: 0.7978 (m-10) cc_final: 0.7432 (m-10) REVERT: V 40 LYS cc_start: 0.8712 (mttm) cc_final: 0.8480 (tptt) REVERT: T 166 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8638 (tmm-80) REVERT: T 212 LEU cc_start: 0.9264 (tp) cc_final: 0.8879 (mm) REVERT: T 219 ASP cc_start: 0.9087 (m-30) cc_final: 0.8688 (t0) REVERT: T 220 ILE cc_start: 0.8329 (pt) cc_final: 0.8032 (tt) REVERT: T 223 ASN cc_start: 0.7194 (OUTLIER) cc_final: 0.6531 (m-40) REVERT: T 234 GLN cc_start: 0.8542 (tm-30) cc_final: 0.8028 (tm-30) REVERT: T 265 ASP cc_start: 0.8861 (m-30) cc_final: 0.8447 (t0) REVERT: T 299 MET cc_start: 0.7439 (mmm) cc_final: 0.7200 (mmm) REVERT: T 322 GLN cc_start: 0.7854 (tp40) cc_final: 0.7329 (pm20) REVERT: Z 103 TYR cc_start: 0.3285 (OUTLIER) cc_final: 0.3047 (m-80) REVERT: Z 113 MET cc_start: 0.1810 (OUTLIER) cc_final: 0.0930 (mtm) REVERT: Z 216 MET cc_start: 0.1981 (ttp) cc_final: 0.1370 (tpt) REVERT: Z 481 SER cc_start: 0.3248 (OUTLIER) cc_final: 0.2927 (t) REVERT: Z 551 LYS cc_start: 0.6919 (mtmm) cc_final: 0.6531 (mmtt) REVERT: Z 571 GLU cc_start: 0.6610 (tp30) cc_final: 0.6246 (pm20) REVERT: Z 574 GLU cc_start: 0.6473 (OUTLIER) cc_final: 0.5916 (mp0) REVERT: Z 596 ASP cc_start: 0.7263 (OUTLIER) cc_final: 0.6494 (m-30) REVERT: Z 662 MET cc_start: 0.3813 (mtp) cc_final: 0.3442 (ttt) REVERT: Z 729 MET cc_start: 0.7418 (mtp) cc_final: 0.7212 (mtp) REVERT: Z 845 ARG cc_start: -0.1636 (OUTLIER) cc_final: -0.2353 (ptt180) REVERT: N 48 LEU cc_start: 0.9075 (mt) cc_final: 0.8685 (tp) REVERT: N 218 GLN cc_start: 0.8475 (mt0) cc_final: 0.8194 (tm-30) REVERT: N 351 MET cc_start: 0.5265 (tmm) cc_final: 0.4507 (tmm) REVERT: N 459 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7110 (t0) REVERT: N 492 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7845 (p0) REVERT: N 538 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8865 (mt-10) REVERT: N 580 ARG cc_start: 0.9006 (ttp-170) cc_final: 0.8709 (tmm-80) REVERT: N 601 ARG cc_start: 0.6476 (mtm180) cc_final: 0.6028 (mtt90) REVERT: N 604 HIS cc_start: 0.6341 (p90) cc_final: 0.4960 (t-90) REVERT: N 625 ILE cc_start: 0.6137 (pt) cc_final: 0.5854 (pt) REVERT: N 654 MET cc_start: 0.6615 (mmm) cc_final: 0.6318 (mmm) REVERT: N 695 MET cc_start: 0.2392 (mmt) cc_final: 0.1840 (mmt) REVERT: N 725 MET cc_start: 0.7558 (mtm) cc_final: 0.7253 (mmt) REVERT: N 772 TRP cc_start: 0.7371 (t-100) cc_final: 0.7146 (t-100) REVERT: N 847 GLU cc_start: 0.6939 (mt-10) cc_final: 0.5889 (tp30) REVERT: S 66 GLU cc_start: 0.9189 (tt0) cc_final: 0.8937 (tp30) REVERT: S 76 LYS cc_start: 0.7895 (mmmt) cc_final: 0.7658 (mmmt) REVERT: S 77 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7955 (mp0) REVERT: S 315 LYS cc_start: 0.8992 (mttt) cc_final: 0.8666 (mmtt) REVERT: S 325 LYS cc_start: 0.8363 (mttp) cc_final: 0.8055 (mmmm) REVERT: P 1 MET cc_start: 0.6883 (mmt) cc_final: 0.6626 (mmt) REVERT: P 42 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8291 (mm-30) REVERT: P 60 MET cc_start: 0.8405 (tpp) cc_final: 0.8098 (tpp) REVERT: P 230 MET cc_start: 0.9023 (mmm) cc_final: 0.8820 (mmm) REVERT: P 239 SER cc_start: 0.9116 (m) cc_final: 0.8797 (t) REVERT: P 326 MET cc_start: 0.7832 (pmm) cc_final: 0.7614 (pmm) REVERT: P 353 ASP cc_start: 0.8994 (t0) cc_final: 0.8631 (t0) REVERT: P 403 PHE cc_start: 0.7995 (m-80) cc_final: 0.7468 (t80) REVERT: P 449 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8322 (tm-30) REVERT: Q 76 PHE cc_start: 0.7071 (m-80) cc_final: 0.6779 (m-10) REVERT: Q 94 ASP cc_start: 0.8129 (m-30) cc_final: 0.7821 (p0) REVERT: Q 159 LYS cc_start: 0.5846 (OUTLIER) cc_final: 0.5524 (ptpt) REVERT: Q 221 GLU cc_start: 0.7895 (tt0) cc_final: 0.7222 (mp0) REVERT: Q 289 CYS cc_start: 0.9075 (t) cc_final: 0.8830 (t) REVERT: Q 372 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8184 (mmtm) REVERT: R 42 MET cc_start: 0.9110 (mmm) cc_final: 0.8625 (tmm) REVERT: R 63 TRP cc_start: 0.6420 (OUTLIER) cc_final: 0.5253 (m-90) REVERT: R 73 MET cc_start: 0.8858 (mmp) cc_final: 0.8441 (mtp) REVERT: R 116 ASP cc_start: 0.8498 (t0) cc_final: 0.8280 (t0) REVERT: R 170 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7707 (mt-10) REVERT: R 210 SER cc_start: 0.8460 (OUTLIER) cc_final: 0.8236 (p) REVERT: R 225 TYR cc_start: 0.9349 (m-10) cc_final: 0.9091 (m-10) REVERT: R 272 PHE cc_start: 0.7898 (OUTLIER) cc_final: 0.7505 (t80) REVERT: R 355 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8015 (pm20) REVERT: R 372 LYS cc_start: 0.8784 (mmmm) cc_final: 0.8368 (mmtm) REVERT: U 9 VAL cc_start: 0.8935 (t) cc_final: 0.8637 (p) REVERT: U 100 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7909 (pttp) REVERT: U 136 GLU cc_start: 0.8138 (mp0) cc_final: 0.7595 (mp0) REVERT: U 169 GLU cc_start: 0.9167 (tp30) cc_final: 0.8316 (tm-30) REVERT: U 189 GLN cc_start: 0.9514 (tp40) cc_final: 0.9274 (tp-100) REVERT: U 193 ASN cc_start: 0.8927 (m-40) cc_final: 0.8439 (m110) REVERT: U 262 LEU cc_start: 0.9034 (tp) cc_final: 0.8760 (tt) REVERT: O 39 LEU cc_start: 0.8513 (mt) cc_final: 0.8030 (tp) REVERT: O 43 ASP cc_start: 0.9085 (t0) cc_final: 0.8866 (m-30) REVERT: O 74 LEU cc_start: 0.7996 (mt) cc_final: 0.7772 (tp) REVERT: O 112 ILE cc_start: 0.8788 (mm) cc_final: 0.8273 (mm) REVERT: O 121 LEU cc_start: 0.9422 (mt) cc_final: 0.9184 (tt) REVERT: O 174 LYS cc_start: 0.9388 (mtpp) cc_final: 0.9068 (ptpp) REVERT: O 339 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7427 (ptp90) outliers start: 199 outliers final: 155 residues processed: 1013 average time/residue: 1.1059 time to fit residues: 1757.7885 Evaluate side-chains 1030 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 856 time to evaluate : 4.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain W residue 97 LEU Chi-restraints excluded: chain W residue 126 LYS Chi-restraints excluded: chain W residue 140 ILE Chi-restraints excluded: chain W residue 185 SER Chi-restraints excluded: chain W residue 186 SER Chi-restraints excluded: chain V residue 41 MET Chi-restraints excluded: chain V residue 88 ASP Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 120 CYS Chi-restraints excluded: chain V residue 173 GLU Chi-restraints excluded: chain V residue 186 LYS Chi-restraints excluded: chain V residue 233 ASP Chi-restraints excluded: chain V residue 293 THR Chi-restraints excluded: chain V residue 307 VAL Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 166 ARG Chi-restraints excluded: chain T residue 178 TYR Chi-restraints excluded: chain T residue 223 ASN Chi-restraints excluded: chain T residue 231 SER Chi-restraints excluded: chain T residue 243 LYS Chi-restraints excluded: chain T residue 274 CYS Chi-restraints excluded: chain T residue 275 ILE Chi-restraints excluded: chain T residue 313 ASN Chi-restraints excluded: chain Y residue 19 PHE Chi-restraints excluded: chain Y residue 35 ASP Chi-restraints excluded: chain Y residue 50 ASP Chi-restraints excluded: chain Y residue 67 MET Chi-restraints excluded: chain Z residue 1 MET Chi-restraints excluded: chain Z residue 55 GLU Chi-restraints excluded: chain Z residue 103 TYR Chi-restraints excluded: chain Z residue 113 MET Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 232 TYR Chi-restraints excluded: chain Z residue 301 HIS Chi-restraints excluded: chain Z residue 422 VAL Chi-restraints excluded: chain Z residue 468 ASP Chi-restraints excluded: chain Z residue 481 SER Chi-restraints excluded: chain Z residue 574 GLU Chi-restraints excluded: chain Z residue 596 ASP Chi-restraints excluded: chain Z residue 711 SER Chi-restraints excluded: chain Z residue 731 MET Chi-restraints excluded: chain Z residue 741 LEU Chi-restraints excluded: chain Z residue 748 LEU Chi-restraints excluded: chain Z residue 845 ARG Chi-restraints excluded: chain Z residue 873 LEU Chi-restraints excluded: chain N residue 22 PHE Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 165 LYS Chi-restraints excluded: chain N residue 176 MET Chi-restraints excluded: chain N residue 183 LEU Chi-restraints excluded: chain N residue 207 ASN Chi-restraints excluded: chain N residue 233 LEU Chi-restraints excluded: chain N residue 337 LEU Chi-restraints excluded: chain N residue 349 ASP Chi-restraints excluded: chain N residue 386 LEU Chi-restraints excluded: chain N residue 388 ASP Chi-restraints excluded: chain N residue 395 ARG Chi-restraints excluded: chain N residue 397 THR Chi-restraints excluded: chain N residue 448 LEU Chi-restraints excluded: chain N residue 459 ASP Chi-restraints excluded: chain N residue 465 LEU Chi-restraints excluded: chain N residue 469 SER Chi-restraints excluded: chain N residue 486 MET Chi-restraints excluded: chain N residue 492 ASP Chi-restraints excluded: chain N residue 510 GLU Chi-restraints excluded: chain N residue 629 THR Chi-restraints excluded: chain N residue 638 SER Chi-restraints excluded: chain N residue 672 LEU Chi-restraints excluded: chain N residue 731 ILE Chi-restraints excluded: chain N residue 742 HIS Chi-restraints excluded: chain N residue 757 MET Chi-restraints excluded: chain N residue 838 LYS Chi-restraints excluded: chain N residue 880 ASN Chi-restraints excluded: chain N residue 892 LEU Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain S residue 113 LEU Chi-restraints excluded: chain S residue 124 ASN Chi-restraints excluded: chain S residue 153 LYS Chi-restraints excluded: chain S residue 176 MET Chi-restraints excluded: chain S residue 210 CYS Chi-restraints excluded: chain S residue 235 LEU Chi-restraints excluded: chain S residue 236 ARG Chi-restraints excluded: chain S residue 240 LEU Chi-restraints excluded: chain S residue 249 THR Chi-restraints excluded: chain S residue 263 LEU Chi-restraints excluded: chain S residue 281 ASN Chi-restraints excluded: chain S residue 346 LEU Chi-restraints excluded: chain S residue 353 LEU Chi-restraints excluded: chain S residue 354 LYS Chi-restraints excluded: chain S residue 356 SER Chi-restraints excluded: chain S residue 447 ILE Chi-restraints excluded: chain S residue 451 ILE Chi-restraints excluded: chain S residue 469 THR Chi-restraints excluded: chain S residue 485 ASP Chi-restraints excluded: chain P residue 105 VAL Chi-restraints excluded: chain P residue 139 GLU Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain P residue 172 GLU Chi-restraints excluded: chain P residue 244 CYS Chi-restraints excluded: chain P residue 322 GLU Chi-restraints excluded: chain P residue 343 SER Chi-restraints excluded: chain P residue 362 ASN Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain P residue 387 ASP Chi-restraints excluded: chain P residue 449 GLU Chi-restraints excluded: chain P residue 453 HIS Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 119 SER Chi-restraints excluded: chain Q residue 159 LYS Chi-restraints excluded: chain Q residue 174 SER Chi-restraints excluded: chain Q residue 182 ASN Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 218 HIS Chi-restraints excluded: chain Q residue 224 ASP Chi-restraints excluded: chain Q residue 234 GLU Chi-restraints excluded: chain Q residue 243 ASP Chi-restraints excluded: chain Q residue 328 ASP Chi-restraints excluded: chain Q residue 372 LYS Chi-restraints excluded: chain Q residue 404 ILE Chi-restraints excluded: chain Q residue 408 SER Chi-restraints excluded: chain Q residue 415 TYR Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 48 ASN Chi-restraints excluded: chain R residue 63 TRP Chi-restraints excluded: chain R residue 94 ASN Chi-restraints excluded: chain R residue 109 GLU Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 154 ASN Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 173 ASP Chi-restraints excluded: chain R residue 175 ASP Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 196 GLN Chi-restraints excluded: chain R residue 210 SER Chi-restraints excluded: chain R residue 214 MET Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 235 ASP Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 272 PHE Chi-restraints excluded: chain R residue 278 VAL Chi-restraints excluded: chain R residue 389 MET Chi-restraints excluded: chain U residue 14 LEU Chi-restraints excluded: chain U residue 48 LEU Chi-restraints excluded: chain U residue 49 ASP Chi-restraints excluded: chain U residue 53 SER Chi-restraints excluded: chain U residue 71 ASP Chi-restraints excluded: chain U residue 73 ASP Chi-restraints excluded: chain U residue 85 VAL Chi-restraints excluded: chain U residue 96 HIS Chi-restraints excluded: chain U residue 100 LYS Chi-restraints excluded: chain U residue 192 THR Chi-restraints excluded: chain U residue 239 ASP Chi-restraints excluded: chain U residue 250 TYR Chi-restraints excluded: chain U residue 267 ARG Chi-restraints excluded: chain U residue 270 VAL Chi-restraints excluded: chain U residue 278 ASN Chi-restraints excluded: chain O residue 3 ASP Chi-restraints excluded: chain O residue 60 TYR Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 145 LEU Chi-restraints excluded: chain O residue 149 THR Chi-restraints excluded: chain O residue 158 LEU Chi-restraints excluded: chain O residue 227 ASN Chi-restraints excluded: chain O residue 240 PHE Chi-restraints excluded: chain O residue 244 ASN Chi-restraints excluded: chain O residue 255 TRP Chi-restraints excluded: chain O residue 260 ASP Chi-restraints excluded: chain O residue 275 LEU Chi-restraints excluded: chain O residue 339 ARG Chi-restraints excluded: chain O residue 360 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 295 optimal weight: 9.9990 chunk 190 optimal weight: 10.0000 chunk 284 optimal weight: 4.9990 chunk 143 optimal weight: 9.9990 chunk 93 optimal weight: 20.0000 chunk 92 optimal weight: 1.9990 chunk 303 optimal weight: 9.9990 chunk 325 optimal weight: 2.9990 chunk 235 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 375 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 302 HIS ** U 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 370 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.7479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 40342 Z= 0.248 Angle : 0.665 15.004 54493 Z= 0.354 Chirality : 0.037 0.211 6198 Planarity : 0.005 0.157 7021 Dihedral : 6.510 59.730 5458 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.88 % Favored : 89.56 % Rotamer: Outliers : 4.49 % Allowed : 21.10 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 1.22 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.11), residues: 4970 helix: -0.89 (0.09), residues: 3116 sheet: -1.51 (0.38), residues: 173 loop : -2.88 (0.14), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP Q 225 HIS 0.012 0.001 HIS Z 352 PHE 0.021 0.002 PHE N 222 TYR 0.030 0.002 TYR Q 229 ARG 0.011 0.001 ARG S 368 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 296 is missing expected H atoms. Skipping. Evaluate side-chains 1083 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 888 time to evaluate : 4.912 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 3 LEU cc_start: 0.8464 (mt) cc_final: 0.8157 (pp) REVERT: W 35 ILE cc_start: 0.9371 (tp) cc_final: 0.9050 (pt) REVERT: W 70 ARG cc_start: 0.9190 (mtp180) cc_final: 0.8701 (mmp80) REVERT: W 112 PHE cc_start: 0.6421 (m-80) cc_final: 0.6217 (m-80) REVERT: V 32 TYR cc_start: 0.8020 (m-10) cc_final: 0.7527 (m-80) REVERT: V 40 LYS cc_start: 0.8698 (mttm) cc_final: 0.8480 (tptt) REVERT: V 175 ARG cc_start: 0.7675 (tpp-160) cc_final: 0.6946 (ttm-80) REVERT: T 212 LEU cc_start: 0.9257 (tp) cc_final: 0.8880 (mm) REVERT: T 219 ASP cc_start: 0.9073 (m-30) cc_final: 0.8746 (t0) REVERT: T 220 ILE cc_start: 0.8355 (pt) cc_final: 0.8059 (tt) REVERT: T 223 ASN cc_start: 0.7185 (OUTLIER) cc_final: 0.6753 (t0) REVERT: T 265 ASP cc_start: 0.8877 (m-30) cc_final: 0.8475 (t0) REVERT: T 299 MET cc_start: 0.7772 (mmm) cc_final: 0.7546 (mmm) REVERT: T 322 GLN cc_start: 0.7711 (tp40) cc_final: 0.7216 (pm20) REVERT: Z 103 TYR cc_start: 0.3390 (OUTLIER) cc_final: 0.3141 (m-80) REVERT: Z 113 MET cc_start: 0.1812 (OUTLIER) cc_final: 0.0896 (mtm) REVERT: Z 216 MET cc_start: 0.2254 (ttp) cc_final: 0.1676 (tpt) REVERT: Z 481 SER cc_start: 0.3228 (OUTLIER) cc_final: 0.2864 (t) REVERT: Z 551 LYS cc_start: 0.6944 (mtmm) cc_final: 0.6550 (mmtt) REVERT: Z 571 GLU cc_start: 0.6636 (tp30) cc_final: 0.6351 (pm20) REVERT: Z 574 GLU cc_start: 0.6391 (OUTLIER) cc_final: 0.5881 (mp0) REVERT: Z 596 ASP cc_start: 0.7178 (OUTLIER) cc_final: 0.6520 (m-30) REVERT: Z 662 MET cc_start: 0.3685 (mtp) cc_final: 0.3354 (ttt) REVERT: Z 729 MET cc_start: 0.7455 (mtp) cc_final: 0.7242 (mtp) REVERT: Z 845 ARG cc_start: -0.1982 (OUTLIER) cc_final: -0.2868 (ptt180) REVERT: N 46 GLU cc_start: 0.7598 (mt-10) cc_final: 0.6845 (tm-30) REVERT: N 48 LEU cc_start: 0.9076 (mt) cc_final: 0.8720 (tp) REVERT: N 218 GLN cc_start: 0.8640 (mt0) cc_final: 0.8352 (tm-30) REVERT: N 351 MET cc_start: 0.5299 (tmm) cc_final: 0.4565 (tmm) REVERT: N 459 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7324 (t0) REVERT: N 492 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7850 (p0) REVERT: N 538 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8847 (mt-10) REVERT: N 580 ARG cc_start: 0.9032 (ttp-170) cc_final: 0.8754 (tmm-80) REVERT: N 601 ARG cc_start: 0.6502 (mtm180) cc_final: 0.5986 (mtt90) REVERT: N 604 HIS cc_start: 0.6384 (p90) cc_final: 0.5030 (t-90) REVERT: N 625 ILE cc_start: 0.5959 (pt) cc_final: 0.5686 (pt) REVERT: N 654 MET cc_start: 0.6955 (mmm) cc_final: 0.6699 (mmm) REVERT: N 695 MET cc_start: 0.2813 (mmt) cc_final: 0.2265 (mmt) REVERT: N 772 TRP cc_start: 0.7409 (t-100) cc_final: 0.7148 (t-100) REVERT: N 847 GLU cc_start: 0.6951 (mt-10) cc_final: 0.5894 (tp30) REVERT: S 77 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7914 (mp0) REVERT: S 315 LYS cc_start: 0.9158 (mttt) cc_final: 0.8873 (mmtm) REVERT: S 345 ARG cc_start: 0.7331 (tpt90) cc_final: 0.7074 (tpt90) REVERT: P 42 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8277 (mm-30) REVERT: P 60 MET cc_start: 0.8415 (tpp) cc_final: 0.8111 (tpp) REVERT: P 230 MET cc_start: 0.9019 (mmm) cc_final: 0.8813 (mmm) REVERT: P 239 SER cc_start: 0.9109 (m) cc_final: 0.8789 (t) REVERT: P 326 MET cc_start: 0.7978 (pmm) cc_final: 0.7755 (pmm) REVERT: P 353 ASP cc_start: 0.8973 (t0) cc_final: 0.8585 (t0) REVERT: P 403 PHE cc_start: 0.7994 (m-80) cc_final: 0.7529 (t80) REVERT: P 444 HIS cc_start: 0.8531 (m-70) cc_final: 0.8079 (m90) REVERT: P 449 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8247 (tm-30) REVERT: Q 76 PHE cc_start: 0.7304 (m-80) cc_final: 0.6951 (m-10) REVERT: Q 221 GLU cc_start: 0.7999 (tt0) cc_final: 0.7486 (mp0) REVERT: Q 266 ASP cc_start: 0.8794 (t70) cc_final: 0.8468 (t0) REVERT: Q 289 CYS cc_start: 0.9171 (t) cc_final: 0.8787 (p) REVERT: Q 372 LYS cc_start: 0.8501 (mttp) cc_final: 0.8206 (mmtm) REVERT: R 42 MET cc_start: 0.9098 (mmm) cc_final: 0.8623 (tmm) REVERT: R 63 TRP cc_start: 0.6410 (OUTLIER) cc_final: 0.5373 (m-90) REVERT: R 73 MET cc_start: 0.8863 (mmp) cc_final: 0.8444 (mtp) REVERT: R 170 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7712 (mt-10) REVERT: R 225 TYR cc_start: 0.9274 (m-10) cc_final: 0.8971 (m-10) REVERT: R 264 TYR cc_start: 0.8533 (t80) cc_final: 0.8098 (t80) REVERT: R 272 PHE cc_start: 0.7848 (OUTLIER) cc_final: 0.7501 (t80) REVERT: R 372 LYS cc_start: 0.8824 (mmmm) cc_final: 0.8411 (mmtm) REVERT: U 9 VAL cc_start: 0.8950 (t) cc_final: 0.8603 (p) REVERT: U 100 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7760 (pttp) REVERT: U 136 GLU cc_start: 0.7957 (mp0) cc_final: 0.7503 (mp0) REVERT: U 157 HIS cc_start: 0.7794 (t70) cc_final: 0.7331 (t70) REVERT: U 169 GLU cc_start: 0.9166 (tp30) cc_final: 0.8492 (tm-30) REVERT: U 189 GLN cc_start: 0.9507 (tp40) cc_final: 0.9188 (tp-100) REVERT: U 193 ASN cc_start: 0.8880 (m-40) cc_final: 0.8348 (m110) REVERT: U 213 GLU cc_start: 0.9442 (OUTLIER) cc_final: 0.8835 (tm-30) REVERT: U 262 LEU cc_start: 0.9000 (tp) cc_final: 0.8751 (tt) REVERT: O 39 LEU cc_start: 0.8518 (mt) cc_final: 0.7938 (tp) REVERT: O 43 ASP cc_start: 0.9127 (t0) cc_final: 0.8927 (m-30) REVERT: O 74 LEU cc_start: 0.8109 (mt) cc_final: 0.7878 (tp) REVERT: O 112 ILE cc_start: 0.8606 (mm) cc_final: 0.8210 (mm) REVERT: O 121 LEU cc_start: 0.9415 (mt) cc_final: 0.9186 (tt) REVERT: O 154 ARG cc_start: 0.7981 (ttm110) cc_final: 0.7774 (ttp-110) REVERT: O 174 LYS cc_start: 0.9375 (mtpp) cc_final: 0.9044 (ptpp) REVERT: O 339 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7402 (ptp90) outliers start: 195 outliers final: 160 residues processed: 1015 average time/residue: 1.1332 time to fit residues: 1822.3501 Evaluate side-chains 1028 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 852 time to evaluate : 4.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 115 SER Chi-restraints excluded: chain W residue 126 LYS Chi-restraints excluded: chain W residue 140 ILE Chi-restraints excluded: chain W residue 185 SER Chi-restraints excluded: chain W residue 186 SER Chi-restraints excluded: chain V residue 41 MET Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain V residue 88 ASP Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 97 ASP Chi-restraints excluded: chain V residue 107 MET Chi-restraints excluded: chain V residue 120 CYS Chi-restraints excluded: chain V residue 173 GLU Chi-restraints excluded: chain V residue 186 LYS Chi-restraints excluded: chain V residue 233 ASP Chi-restraints excluded: chain V residue 293 THR Chi-restraints excluded: chain V residue 307 VAL Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 178 TYR Chi-restraints excluded: chain T residue 223 ASN Chi-restraints excluded: chain T residue 243 LYS Chi-restraints excluded: chain T residue 275 ILE Chi-restraints excluded: chain T residue 295 THR Chi-restraints excluded: chain T residue 313 ASN Chi-restraints excluded: chain T residue 329 THR Chi-restraints excluded: chain Y residue 19 PHE Chi-restraints excluded: chain Y residue 35 ASP Chi-restraints excluded: chain Y residue 50 ASP Chi-restraints excluded: chain Y residue 67 MET Chi-restraints excluded: chain Z residue 1 MET Chi-restraints excluded: chain Z residue 55 GLU Chi-restraints excluded: chain Z residue 103 TYR Chi-restraints excluded: chain Z residue 113 MET Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 301 HIS Chi-restraints excluded: chain Z residue 422 VAL Chi-restraints excluded: chain Z residue 468 ASP Chi-restraints excluded: chain Z residue 481 SER Chi-restraints excluded: chain Z residue 574 GLU Chi-restraints excluded: chain Z residue 596 ASP Chi-restraints excluded: chain Z residue 618 GLU Chi-restraints excluded: chain Z residue 711 SER Chi-restraints excluded: chain Z residue 731 MET Chi-restraints excluded: chain Z residue 741 LEU Chi-restraints excluded: chain Z residue 746 ARG Chi-restraints excluded: chain Z residue 748 LEU Chi-restraints excluded: chain Z residue 845 ARG Chi-restraints excluded: chain Z residue 873 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 22 PHE Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain N residue 165 LYS Chi-restraints excluded: chain N residue 176 MET Chi-restraints excluded: chain N residue 183 LEU Chi-restraints excluded: chain N residue 207 ASN Chi-restraints excluded: chain N residue 233 LEU Chi-restraints excluded: chain N residue 337 LEU Chi-restraints excluded: chain N residue 386 LEU Chi-restraints excluded: chain N residue 388 ASP Chi-restraints excluded: chain N residue 395 ARG Chi-restraints excluded: chain N residue 397 THR Chi-restraints excluded: chain N residue 448 LEU Chi-restraints excluded: chain N residue 459 ASP Chi-restraints excluded: chain N residue 465 LEU Chi-restraints excluded: chain N residue 469 SER Chi-restraints excluded: chain N residue 486 MET Chi-restraints excluded: chain N residue 492 ASP Chi-restraints excluded: chain N residue 510 GLU Chi-restraints excluded: chain N residue 629 THR Chi-restraints excluded: chain N residue 638 SER Chi-restraints excluded: chain N residue 672 LEU Chi-restraints excluded: chain N residue 731 ILE Chi-restraints excluded: chain N residue 742 HIS Chi-restraints excluded: chain N residue 757 MET Chi-restraints excluded: chain N residue 794 ASP Chi-restraints excluded: chain N residue 838 LYS Chi-restraints excluded: chain N residue 880 ASN Chi-restraints excluded: chain N residue 892 LEU Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain S residue 113 LEU Chi-restraints excluded: chain S residue 124 ASN Chi-restraints excluded: chain S residue 131 LEU Chi-restraints excluded: chain S residue 176 MET Chi-restraints excluded: chain S residue 189 ASP Chi-restraints excluded: chain S residue 210 CYS Chi-restraints excluded: chain S residue 235 LEU Chi-restraints excluded: chain S residue 236 ARG Chi-restraints excluded: chain S residue 240 LEU Chi-restraints excluded: chain S residue 249 THR Chi-restraints excluded: chain S residue 263 LEU Chi-restraints excluded: chain S residue 281 ASN Chi-restraints excluded: chain S residue 346 LEU Chi-restraints excluded: chain S residue 353 LEU Chi-restraints excluded: chain S residue 354 LYS Chi-restraints excluded: chain S residue 447 ILE Chi-restraints excluded: chain S residue 451 ILE Chi-restraints excluded: chain S residue 483 CYS Chi-restraints excluded: chain S residue 485 ASP Chi-restraints excluded: chain P residue 139 GLU Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain P residue 172 GLU Chi-restraints excluded: chain P residue 188 GLU Chi-restraints excluded: chain P residue 244 CYS Chi-restraints excluded: chain P residue 322 GLU Chi-restraints excluded: chain P residue 343 SER Chi-restraints excluded: chain P residue 362 ASN Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain P residue 387 ASP Chi-restraints excluded: chain P residue 449 GLU Chi-restraints excluded: chain P residue 453 HIS Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 119 SER Chi-restraints excluded: chain Q residue 159 LYS Chi-restraints excluded: chain Q residue 174 SER Chi-restraints excluded: chain Q residue 182 ASN Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 224 ASP Chi-restraints excluded: chain Q residue 234 GLU Chi-restraints excluded: chain Q residue 243 ASP Chi-restraints excluded: chain Q residue 318 ILE Chi-restraints excluded: chain Q residue 328 ASP Chi-restraints excluded: chain Q residue 362 GLU Chi-restraints excluded: chain Q residue 404 ILE Chi-restraints excluded: chain Q residue 408 SER Chi-restraints excluded: chain Q residue 415 TYR Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 48 ASN Chi-restraints excluded: chain R residue 63 TRP Chi-restraints excluded: chain R residue 109 GLU Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 154 ASN Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 173 ASP Chi-restraints excluded: chain R residue 175 ASP Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 196 GLN Chi-restraints excluded: chain R residue 214 MET Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 235 ASP Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 248 GLU Chi-restraints excluded: chain R residue 272 PHE Chi-restraints excluded: chain R residue 278 VAL Chi-restraints excluded: chain R residue 357 ASN Chi-restraints excluded: chain R residue 389 MET Chi-restraints excluded: chain U residue 14 LEU Chi-restraints excluded: chain U residue 48 LEU Chi-restraints excluded: chain U residue 49 ASP Chi-restraints excluded: chain U residue 53 SER Chi-restraints excluded: chain U residue 71 ASP Chi-restraints excluded: chain U residue 73 ASP Chi-restraints excluded: chain U residue 85 VAL Chi-restraints excluded: chain U residue 96 HIS Chi-restraints excluded: chain U residue 100 LYS Chi-restraints excluded: chain U residue 192 THR Chi-restraints excluded: chain U residue 213 GLU Chi-restraints excluded: chain U residue 239 ASP Chi-restraints excluded: chain U residue 250 TYR Chi-restraints excluded: chain U residue 270 VAL Chi-restraints excluded: chain U residue 278 ASN Chi-restraints excluded: chain O residue 60 TYR Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 145 LEU Chi-restraints excluded: chain O residue 158 LEU Chi-restraints excluded: chain O residue 227 ASN Chi-restraints excluded: chain O residue 240 PHE Chi-restraints excluded: chain O residue 244 ASN Chi-restraints excluded: chain O residue 255 TRP Chi-restraints excluded: chain O residue 260 ASP Chi-restraints excluded: chain O residue 319 LEU Chi-restraints excluded: chain O residue 339 ARG Chi-restraints excluded: chain O residue 360 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 434 optimal weight: 3.9990 chunk 457 optimal weight: 4.9990 chunk 417 optimal weight: 5.9990 chunk 444 optimal weight: 6.9990 chunk 456 optimal weight: 2.9990 chunk 267 optimal weight: 7.9990 chunk 193 optimal weight: 20.0000 chunk 349 optimal weight: 8.9990 chunk 136 optimal weight: 20.0000 chunk 401 optimal weight: 6.9990 chunk 420 optimal weight: 0.8980 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 238 ASN Z 428 GLN ** N 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.7716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 40342 Z= 0.259 Angle : 0.674 15.136 54493 Z= 0.359 Chirality : 0.038 0.182 6198 Planarity : 0.005 0.158 7021 Dihedral : 6.458 59.583 5456 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.50 % Allowed : 9.90 % Favored : 89.60 % Rotamer: Outliers : 4.58 % Allowed : 21.72 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 1.22 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.11), residues: 4970 helix: -0.79 (0.09), residues: 3117 sheet: -1.56 (0.37), residues: 179 loop : -2.89 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP N 392 HIS 0.015 0.002 HIS U 157 PHE 0.020 0.002 PHE N 34 TYR 0.026 0.002 TYR Z 239 ARG 0.011 0.001 ARG S 368 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 296 is missing expected H atoms. Skipping. Evaluate side-chains 1067 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 868 time to evaluate : 4.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 3 LEU cc_start: 0.8443 (mt) cc_final: 0.8172 (pp) REVERT: W 35 ILE cc_start: 0.9372 (tp) cc_final: 0.9057 (pt) REVERT: W 70 ARG cc_start: 0.9196 (mtp180) cc_final: 0.8710 (mmp80) REVERT: V 40 LYS cc_start: 0.8680 (mttm) cc_final: 0.8472 (tptt) REVERT: V 175 ARG cc_start: 0.7480 (tpp-160) cc_final: 0.6783 (ttm-80) REVERT: T 212 LEU cc_start: 0.9259 (tp) cc_final: 0.8867 (mm) REVERT: T 219 ASP cc_start: 0.9053 (OUTLIER) cc_final: 0.8716 (t0) REVERT: T 220 ILE cc_start: 0.8363 (pt) cc_final: 0.7770 (mp) REVERT: T 223 ASN cc_start: 0.6992 (OUTLIER) cc_final: 0.6605 (t0) REVERT: T 265 ASP cc_start: 0.8920 (OUTLIER) cc_final: 0.8572 (t0) REVERT: T 322 GLN cc_start: 0.7664 (tp40) cc_final: 0.7210 (pm20) REVERT: Z 103 TYR cc_start: 0.3541 (OUTLIER) cc_final: 0.3332 (m-80) REVERT: Z 216 MET cc_start: 0.2289 (ttp) cc_final: 0.1712 (tpt) REVERT: Z 481 SER cc_start: 0.3408 (OUTLIER) cc_final: 0.3018 (t) REVERT: Z 551 LYS cc_start: 0.6785 (mtmm) cc_final: 0.6356 (mmtt) REVERT: Z 571 GLU cc_start: 0.6425 (tp30) cc_final: 0.6130 (pm20) REVERT: Z 574 GLU cc_start: 0.6384 (OUTLIER) cc_final: 0.5923 (mp0) REVERT: Z 596 ASP cc_start: 0.7168 (OUTLIER) cc_final: 0.6522 (m-30) REVERT: Z 620 PHE cc_start: 0.4249 (t80) cc_final: 0.3127 (m-10) REVERT: Z 662 MET cc_start: 0.3705 (mtp) cc_final: 0.3369 (ttt) REVERT: Z 729 MET cc_start: 0.7255 (OUTLIER) cc_final: 0.7032 (mtp) REVERT: Z 788 MET cc_start: 0.3719 (tpp) cc_final: 0.3501 (tpp) REVERT: Z 845 ARG cc_start: -0.2408 (OUTLIER) cc_final: -0.3355 (ptt180) REVERT: N 48 LEU cc_start: 0.9091 (mt) cc_final: 0.8709 (tp) REVERT: N 218 GLN cc_start: 0.8635 (mt0) cc_final: 0.8072 (mm-40) REVERT: N 351 MET cc_start: 0.5286 (tmm) cc_final: 0.4544 (tmm) REVERT: N 395 ARG cc_start: 0.6148 (OUTLIER) cc_final: 0.5836 (ptm-80) REVERT: N 459 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7297 (t0) REVERT: N 492 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7762 (p0) REVERT: N 538 GLU cc_start: 0.9071 (mt-10) cc_final: 0.8855 (mt-10) REVERT: N 580 ARG cc_start: 0.9036 (ttp-170) cc_final: 0.8756 (tmm-80) REVERT: N 601 ARG cc_start: 0.6494 (mtm180) cc_final: 0.5968 (mtt90) REVERT: N 604 HIS cc_start: 0.6362 (p90) cc_final: 0.5020 (t-90) REVERT: N 625 ILE cc_start: 0.5866 (pt) cc_final: 0.5588 (pt) REVERT: N 654 MET cc_start: 0.6996 (mmm) cc_final: 0.6728 (mmm) REVERT: N 695 MET cc_start: 0.2826 (mmt) cc_final: 0.2165 (mmt) REVERT: N 847 GLU cc_start: 0.6960 (mt-10) cc_final: 0.5905 (tp30) REVERT: S 77 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7997 (mp0) REVERT: S 315 LYS cc_start: 0.9159 (mttt) cc_final: 0.8869 (mmtm) REVERT: S 345 ARG cc_start: 0.7435 (tpt90) cc_final: 0.7128 (tpt90) REVERT: P 42 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8335 (mm-30) REVERT: P 60 MET cc_start: 0.8398 (tpp) cc_final: 0.8103 (tpp) REVERT: P 230 MET cc_start: 0.9021 (mmm) cc_final: 0.8821 (mmm) REVERT: P 239 SER cc_start: 0.9078 (m) cc_final: 0.8766 (t) REVERT: P 353 ASP cc_start: 0.8951 (t0) cc_final: 0.8554 (t0) REVERT: P 403 PHE cc_start: 0.7994 (m-80) cc_final: 0.7528 (t80) REVERT: P 449 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8248 (tm-30) REVERT: Q 76 PHE cc_start: 0.7331 (m-80) cc_final: 0.7028 (m-10) REVERT: Q 132 ARG cc_start: 0.8344 (mmp80) cc_final: 0.7947 (mmp80) REVERT: Q 159 LYS cc_start: 0.6588 (OUTLIER) cc_final: 0.6284 (ptpt) REVERT: Q 183 LEU cc_start: 0.7118 (OUTLIER) cc_final: 0.6918 (mp) REVERT: Q 221 GLU cc_start: 0.7942 (tt0) cc_final: 0.7462 (mp0) REVERT: Q 266 ASP cc_start: 0.8842 (t70) cc_final: 0.8506 (t0) REVERT: Q 289 CYS cc_start: 0.9159 (t) cc_final: 0.8755 (p) REVERT: Q 372 LYS cc_start: 0.8504 (mttp) cc_final: 0.8185 (mmtm) REVERT: R 42 MET cc_start: 0.9089 (mmm) cc_final: 0.8624 (tmm) REVERT: R 50 MET cc_start: 0.7269 (tpt) cc_final: 0.6663 (tpt) REVERT: R 63 TRP cc_start: 0.6616 (OUTLIER) cc_final: 0.5396 (m-90) REVERT: R 170 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7843 (mt-10) REVERT: R 225 TYR cc_start: 0.9267 (m-10) cc_final: 0.8969 (m-10) REVERT: R 272 PHE cc_start: 0.7825 (OUTLIER) cc_final: 0.7522 (t80) REVERT: R 372 LYS cc_start: 0.8821 (mmmm) cc_final: 0.8489 (mmtm) REVERT: U 9 VAL cc_start: 0.8957 (t) cc_final: 0.8616 (p) REVERT: U 100 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7837 (pttp) REVERT: U 169 GLU cc_start: 0.9158 (tp30) cc_final: 0.8387 (tm-30) REVERT: U 189 GLN cc_start: 0.9453 (tp40) cc_final: 0.9082 (tp-100) REVERT: U 193 ASN cc_start: 0.8852 (m-40) cc_final: 0.8305 (m110) REVERT: U 213 GLU cc_start: 0.9444 (OUTLIER) cc_final: 0.8839 (tm-30) REVERT: U 262 LEU cc_start: 0.8982 (tp) cc_final: 0.8744 (tt) REVERT: O 39 LEU cc_start: 0.8512 (mt) cc_final: 0.7912 (tp) REVERT: O 43 ASP cc_start: 0.9127 (t0) cc_final: 0.8914 (m-30) REVERT: O 74 LEU cc_start: 0.8034 (mt) cc_final: 0.7793 (tp) REVERT: O 112 ILE cc_start: 0.8615 (mm) cc_final: 0.8360 (mm) REVERT: O 121 LEU cc_start: 0.9414 (mt) cc_final: 0.9186 (tt) REVERT: O 139 GLU cc_start: 0.9497 (tp30) cc_final: 0.9098 (mt-10) REVERT: O 174 LYS cc_start: 0.9399 (mtpp) cc_final: 0.9094 (ptpp) REVERT: O 205 LEU cc_start: 0.8976 (mm) cc_final: 0.8707 (mm) REVERT: O 215 GLU cc_start: 0.9445 (tm-30) cc_final: 0.9151 (tp30) outliers start: 199 outliers final: 157 residues processed: 992 average time/residue: 1.1244 time to fit residues: 1771.2787 Evaluate side-chains 1028 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 851 time to evaluate : 4.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 115 SER Chi-restraints excluded: chain W residue 126 LYS Chi-restraints excluded: chain W residue 140 ILE Chi-restraints excluded: chain W residue 185 SER Chi-restraints excluded: chain W residue 186 SER Chi-restraints excluded: chain V residue 41 MET Chi-restraints excluded: chain V residue 88 ASP Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 107 MET Chi-restraints excluded: chain V residue 120 CYS Chi-restraints excluded: chain V residue 173 GLU Chi-restraints excluded: chain V residue 186 LYS Chi-restraints excluded: chain V residue 233 ASP Chi-restraints excluded: chain V residue 293 THR Chi-restraints excluded: chain V residue 307 VAL Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 178 TYR Chi-restraints excluded: chain T residue 219 ASP Chi-restraints excluded: chain T residue 223 ASN Chi-restraints excluded: chain T residue 243 LYS Chi-restraints excluded: chain T residue 265 ASP Chi-restraints excluded: chain T residue 270 GLU Chi-restraints excluded: chain T residue 275 ILE Chi-restraints excluded: chain T residue 295 THR Chi-restraints excluded: chain T residue 313 ASN Chi-restraints excluded: chain T residue 329 THR Chi-restraints excluded: chain Y residue 50 ASP Chi-restraints excluded: chain Z residue 1 MET Chi-restraints excluded: chain Z residue 103 TYR Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 301 HIS Chi-restraints excluded: chain Z residue 422 VAL Chi-restraints excluded: chain Z residue 468 ASP Chi-restraints excluded: chain Z residue 481 SER Chi-restraints excluded: chain Z residue 574 GLU Chi-restraints excluded: chain Z residue 596 ASP Chi-restraints excluded: chain Z residue 701 ASN Chi-restraints excluded: chain Z residue 711 SER Chi-restraints excluded: chain Z residue 723 TYR Chi-restraints excluded: chain Z residue 729 MET Chi-restraints excluded: chain Z residue 731 MET Chi-restraints excluded: chain Z residue 748 LEU Chi-restraints excluded: chain Z residue 768 LEU Chi-restraints excluded: chain Z residue 845 ARG Chi-restraints excluded: chain Z residue 873 LEU Chi-restraints excluded: chain N residue 22 PHE Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain N residue 138 PHE Chi-restraints excluded: chain N residue 163 PHE Chi-restraints excluded: chain N residue 165 LYS Chi-restraints excluded: chain N residue 176 MET Chi-restraints excluded: chain N residue 183 LEU Chi-restraints excluded: chain N residue 207 ASN Chi-restraints excluded: chain N residue 233 LEU Chi-restraints excluded: chain N residue 337 LEU Chi-restraints excluded: chain N residue 386 LEU Chi-restraints excluded: chain N residue 388 ASP Chi-restraints excluded: chain N residue 395 ARG Chi-restraints excluded: chain N residue 397 THR Chi-restraints excluded: chain N residue 448 LEU Chi-restraints excluded: chain N residue 459 ASP Chi-restraints excluded: chain N residue 465 LEU Chi-restraints excluded: chain N residue 469 SER Chi-restraints excluded: chain N residue 486 MET Chi-restraints excluded: chain N residue 492 ASP Chi-restraints excluded: chain N residue 510 GLU Chi-restraints excluded: chain N residue 629 THR Chi-restraints excluded: chain N residue 638 SER Chi-restraints excluded: chain N residue 672 LEU Chi-restraints excluded: chain N residue 731 ILE Chi-restraints excluded: chain N residue 742 HIS Chi-restraints excluded: chain N residue 757 MET Chi-restraints excluded: chain N residue 838 LYS Chi-restraints excluded: chain N residue 880 ASN Chi-restraints excluded: chain N residue 885 MET Chi-restraints excluded: chain N residue 892 LEU Chi-restraints excluded: chain S residue 96 ARG Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain S residue 113 LEU Chi-restraints excluded: chain S residue 124 ASN Chi-restraints excluded: chain S residue 131 LEU Chi-restraints excluded: chain S residue 210 CYS Chi-restraints excluded: chain S residue 235 LEU Chi-restraints excluded: chain S residue 236 ARG Chi-restraints excluded: chain S residue 240 LEU Chi-restraints excluded: chain S residue 249 THR Chi-restraints excluded: chain S residue 263 LEU Chi-restraints excluded: chain S residue 281 ASN Chi-restraints excluded: chain S residue 346 LEU Chi-restraints excluded: chain S residue 353 LEU Chi-restraints excluded: chain S residue 354 LYS Chi-restraints excluded: chain S residue 447 ILE Chi-restraints excluded: chain S residue 451 ILE Chi-restraints excluded: chain S residue 483 CYS Chi-restraints excluded: chain S residue 485 ASP Chi-restraints excluded: chain S residue 490 SER Chi-restraints excluded: chain P residue 139 GLU Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain P residue 172 GLU Chi-restraints excluded: chain P residue 188 GLU Chi-restraints excluded: chain P residue 244 CYS Chi-restraints excluded: chain P residue 322 GLU Chi-restraints excluded: chain P residue 343 SER Chi-restraints excluded: chain P residue 362 ASN Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain P residue 387 ASP Chi-restraints excluded: chain P residue 449 GLU Chi-restraints excluded: chain P residue 453 HIS Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 119 SER Chi-restraints excluded: chain Q residue 159 LYS Chi-restraints excluded: chain Q residue 174 SER Chi-restraints excluded: chain Q residue 182 ASN Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 224 ASP Chi-restraints excluded: chain Q residue 234 GLU Chi-restraints excluded: chain Q residue 243 ASP Chi-restraints excluded: chain Q residue 257 CYS Chi-restraints excluded: chain Q residue 328 ASP Chi-restraints excluded: chain Q residue 362 GLU Chi-restraints excluded: chain Q residue 408 SER Chi-restraints excluded: chain Q residue 415 TYR Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 48 ASN Chi-restraints excluded: chain R residue 63 TRP Chi-restraints excluded: chain R residue 68 ASP Chi-restraints excluded: chain R residue 109 GLU Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 154 ASN Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 173 ASP Chi-restraints excluded: chain R residue 175 ASP Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 196 GLN Chi-restraints excluded: chain R residue 214 MET Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 235 ASP Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 248 GLU Chi-restraints excluded: chain R residue 272 PHE Chi-restraints excluded: chain R residue 278 VAL Chi-restraints excluded: chain R residue 357 ASN Chi-restraints excluded: chain R residue 377 LEU Chi-restraints excluded: chain U residue 14 LEU Chi-restraints excluded: chain U residue 21 ASP Chi-restraints excluded: chain U residue 48 LEU Chi-restraints excluded: chain U residue 49 ASP Chi-restraints excluded: chain U residue 53 SER Chi-restraints excluded: chain U residue 71 ASP Chi-restraints excluded: chain U residue 73 ASP Chi-restraints excluded: chain U residue 85 VAL Chi-restraints excluded: chain U residue 96 HIS Chi-restraints excluded: chain U residue 100 LYS Chi-restraints excluded: chain U residue 192 THR Chi-restraints excluded: chain U residue 213 GLU Chi-restraints excluded: chain U residue 239 ASP Chi-restraints excluded: chain U residue 250 TYR Chi-restraints excluded: chain U residue 254 ASN Chi-restraints excluded: chain U residue 270 VAL Chi-restraints excluded: chain U residue 278 ASN Chi-restraints excluded: chain O residue 3 ASP Chi-restraints excluded: chain O residue 60 TYR Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 113 LEU Chi-restraints excluded: chain O residue 145 LEU Chi-restraints excluded: chain O residue 158 LEU Chi-restraints excluded: chain O residue 227 ASN Chi-restraints excluded: chain O residue 240 PHE Chi-restraints excluded: chain O residue 244 ASN Chi-restraints excluded: chain O residue 255 TRP Chi-restraints excluded: chain O residue 260 ASP Chi-restraints excluded: chain O residue 319 LEU Chi-restraints excluded: chain O residue 360 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 443 optimal weight: 6.9990 chunk 291 optimal weight: 0.4980 chunk 470 optimal weight: 5.9990 chunk 286 optimal weight: 4.9990 chunk 223 optimal weight: 1.9990 chunk 326 optimal weight: 3.9990 chunk 493 optimal weight: 3.9990 chunk 453 optimal weight: 3.9990 chunk 392 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 303 optimal weight: 2.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 901 GLN ** S 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 177 ASN ** S 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 399 ASN ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.7810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 40342 Z= 0.189 Angle : 0.641 13.583 54493 Z= 0.334 Chirality : 0.037 0.221 6198 Planarity : 0.005 0.152 7021 Dihedral : 6.195 59.374 5452 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.61 % Favored : 90.97 % Rotamer: Outliers : 3.45 % Allowed : 22.73 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 1.22 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.12), residues: 4970 helix: -0.44 (0.09), residues: 3126 sheet: -1.37 (0.38), residues: 172 loop : -2.75 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP N 392 HIS 0.012 0.001 HIS S 110 PHE 0.019 0.001 PHE S 174 TYR 0.026 0.002 TYR Z 349 ARG 0.011 0.001 ARG P 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9940 Ramachandran restraints generated. 4970 Oldfield, 0 Emsley, 4970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 296 is missing expected H atoms. Skipping. Evaluate side-chains 1061 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 911 time to evaluate : 4.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 3 LEU cc_start: 0.8531 (mt) cc_final: 0.8279 (pp) REVERT: W 35 ILE cc_start: 0.9363 (tp) cc_final: 0.9055 (pt) REVERT: W 70 ARG cc_start: 0.9187 (mtp180) cc_final: 0.8701 (mmp80) REVERT: V 40 LYS cc_start: 0.8653 (mttm) cc_final: 0.8430 (tptt) REVERT: V 175 ARG cc_start: 0.7375 (tpp-160) cc_final: 0.6684 (ttm-80) REVERT: T 178 TYR cc_start: 0.5256 (OUTLIER) cc_final: 0.4688 (t80) REVERT: T 212 LEU cc_start: 0.9260 (tp) cc_final: 0.8852 (mm) REVERT: T 219 ASP cc_start: 0.9009 (m-30) cc_final: 0.8683 (t0) REVERT: T 220 ILE cc_start: 0.8390 (pt) cc_final: 0.7785 (mp) REVERT: T 223 ASN cc_start: 0.6861 (OUTLIER) cc_final: 0.6656 (t0) REVERT: T 265 ASP cc_start: 0.8932 (OUTLIER) cc_final: 0.8542 (t0) REVERT: T 322 GLN cc_start: 0.7621 (tp40) cc_final: 0.7232 (pm20) REVERT: Z 216 MET cc_start: 0.2333 (ttp) cc_final: 0.1697 (tpt) REVERT: Z 551 LYS cc_start: 0.6699 (mtmm) cc_final: 0.6222 (mmtt) REVERT: Z 571 GLU cc_start: 0.6725 (tp30) cc_final: 0.6376 (pm20) REVERT: Z 574 GLU cc_start: 0.6423 (OUTLIER) cc_final: 0.5955 (mp0) REVERT: Z 596 ASP cc_start: 0.7107 (OUTLIER) cc_final: 0.6494 (m-30) REVERT: Z 620 PHE cc_start: 0.3804 (t80) cc_final: 0.2779 (m-10) REVERT: Z 662 MET cc_start: 0.3685 (mtp) cc_final: 0.3364 (ttt) REVERT: Z 729 MET cc_start: 0.7017 (OUTLIER) cc_final: 0.6799 (mtp) REVERT: Z 845 ARG cc_start: -0.1722 (OUTLIER) cc_final: -0.2469 (ptt180) REVERT: N 46 GLU cc_start: 0.7528 (mt-10) cc_final: 0.6769 (tm-30) REVERT: N 48 LEU cc_start: 0.9094 (mt) cc_final: 0.8730 (tp) REVERT: N 218 GLN cc_start: 0.8631 (mt0) cc_final: 0.8178 (tp-100) REVERT: N 222 PHE cc_start: 0.5919 (m-10) cc_final: 0.5437 (m-10) REVERT: N 333 MET cc_start: 0.8054 (ptp) cc_final: 0.7437 (pmm) REVERT: N 351 MET cc_start: 0.5413 (tmm) cc_final: 0.4710 (tmm) REVERT: N 395 ARG cc_start: 0.6173 (OUTLIER) cc_final: 0.5906 (ptm-80) REVERT: N 459 ASP cc_start: 0.7974 (OUTLIER) cc_final: 0.7443 (t0) REVERT: N 492 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7985 (p0) REVERT: N 538 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8828 (mt-10) REVERT: N 580 ARG cc_start: 0.9015 (ttp-170) cc_final: 0.8715 (tmm-80) REVERT: N 601 ARG cc_start: 0.6379 (mtm180) cc_final: 0.5847 (mtt90) REVERT: N 604 HIS cc_start: 0.6357 (p90) cc_final: 0.4932 (t-90) REVERT: N 625 ILE cc_start: 0.5795 (pt) cc_final: 0.5513 (pt) REVERT: N 654 MET cc_start: 0.6979 (mmm) cc_final: 0.6670 (mmm) REVERT: N 695 MET cc_start: 0.2720 (mmt) cc_final: 0.2076 (mmt) REVERT: N 847 GLU cc_start: 0.6891 (mt-10) cc_final: 0.5915 (tp30) REVERT: N 879 ASP cc_start: 0.8389 (m-30) cc_final: 0.7967 (p0) REVERT: S 77 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7986 (mp0) REVERT: S 96 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7702 (tmm160) REVERT: S 139 MET cc_start: 0.7592 (mpp) cc_final: 0.4397 (tmm) REVERT: S 315 LYS cc_start: 0.9147 (mttt) cc_final: 0.8843 (mmtt) REVERT: S 345 ARG cc_start: 0.7406 (tpt90) cc_final: 0.7094 (tpt90) REVERT: P 42 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8223 (mm-30) REVERT: P 60 MET cc_start: 0.8345 (tpp) cc_final: 0.7989 (tpp) REVERT: P 230 MET cc_start: 0.9017 (mmm) cc_final: 0.8808 (mmm) REVERT: P 239 SER cc_start: 0.9012 (m) cc_final: 0.8705 (t) REVERT: P 303 LYS cc_start: 0.8444 (ttpp) cc_final: 0.8237 (tppt) REVERT: P 353 ASP cc_start: 0.8920 (t0) cc_final: 0.8528 (t0) REVERT: P 403 PHE cc_start: 0.7945 (m-80) cc_final: 0.7512 (t80) REVERT: P 449 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8205 (tm-30) REVERT: Q 76 PHE cc_start: 0.7290 (m-80) cc_final: 0.6942 (m-10) REVERT: Q 221 GLU cc_start: 0.7986 (tt0) cc_final: 0.7498 (mp0) REVERT: Q 289 CYS cc_start: 0.9164 (t) cc_final: 0.8698 (p) REVERT: Q 372 LYS cc_start: 0.8526 (mttp) cc_final: 0.8209 (mmtm) REVERT: Q 405 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8613 (tm-30) REVERT: R 42 MET cc_start: 0.9082 (mmm) cc_final: 0.8563 (tmm) REVERT: R 50 MET cc_start: 0.7129 (tpt) cc_final: 0.6737 (tpt) REVERT: R 63 TRP cc_start: 0.6513 (OUTLIER) cc_final: 0.5408 (m-90) REVERT: R 73 MET cc_start: 0.8905 (mmp) cc_final: 0.8517 (mtp) REVERT: R 170 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7737 (mt-10) REVERT: R 225 TYR cc_start: 0.9269 (m-10) cc_final: 0.9026 (m-10) REVERT: R 272 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.7670 (t80) REVERT: R 305 SER cc_start: 0.9132 (t) cc_final: 0.8617 (p) REVERT: R 372 LYS cc_start: 0.8828 (mmmm) cc_final: 0.8522 (mmtm) REVERT: U 100 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7901 (pttp) REVERT: U 169 GLU cc_start: 0.9143 (tp30) cc_final: 0.8490 (tm-30) REVERT: U 189 GLN cc_start: 0.9425 (tp40) cc_final: 0.8923 (mt0) REVERT: O 39 LEU cc_start: 0.8488 (mt) cc_final: 0.7919 (tp) REVERT: O 43 ASP cc_start: 0.9130 (t0) cc_final: 0.8781 (m-30) REVERT: O 112 ILE cc_start: 0.8569 (mm) cc_final: 0.8248 (mm) REVERT: O 121 LEU cc_start: 0.9408 (mt) cc_final: 0.9183 (tt) REVERT: O 174 LYS cc_start: 0.9358 (mtpp) cc_final: 0.9029 (ptpp) REVERT: O 205 LEU cc_start: 0.8966 (mm) cc_final: 0.8694 (mm) REVERT: O 215 GLU cc_start: 0.9429 (tm-30) cc_final: 0.9138 (tp30) outliers start: 150 outliers final: 122 residues processed: 1004 average time/residue: 1.1253 time to fit residues: 1781.0202 Evaluate side-chains 1021 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 883 time to evaluate : 4.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 115 SER Chi-restraints excluded: chain W residue 140 ILE Chi-restraints excluded: chain W residue 186 SER Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 107 MET Chi-restraints excluded: chain V residue 120 CYS Chi-restraints excluded: chain V residue 186 LYS Chi-restraints excluded: chain V residue 233 ASP Chi-restraints excluded: chain V residue 293 THR Chi-restraints excluded: chain V residue 307 VAL Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 178 TYR Chi-restraints excluded: chain T residue 223 ASN Chi-restraints excluded: chain T residue 243 LYS Chi-restraints excluded: chain T residue 265 ASP Chi-restraints excluded: chain T residue 275 ILE Chi-restraints excluded: chain T residue 295 THR Chi-restraints excluded: chain T residue 313 ASN Chi-restraints excluded: chain Y residue 50 ASP Chi-restraints excluded: chain Z residue 1 MET Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain Z residue 103 TYR Chi-restraints excluded: chain Z residue 301 HIS Chi-restraints excluded: chain Z residue 422 VAL Chi-restraints excluded: chain Z residue 574 GLU Chi-restraints excluded: chain Z residue 596 ASP Chi-restraints excluded: chain Z residue 711 SER Chi-restraints excluded: chain Z residue 723 TYR Chi-restraints excluded: chain Z residue 729 MET Chi-restraints excluded: chain Z residue 731 MET Chi-restraints excluded: chain Z residue 746 ARG Chi-restraints excluded: chain Z residue 748 LEU Chi-restraints excluded: chain Z residue 768 LEU Chi-restraints excluded: chain Z residue 845 ARG Chi-restraints excluded: chain Z residue 873 LEU Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 163 PHE Chi-restraints excluded: chain N residue 165 LYS Chi-restraints excluded: chain N residue 176 MET Chi-restraints excluded: chain N residue 183 LEU Chi-restraints excluded: chain N residue 207 ASN Chi-restraints excluded: chain N residue 233 LEU Chi-restraints excluded: chain N residue 337 LEU Chi-restraints excluded: chain N residue 388 ASP Chi-restraints excluded: chain N residue 395 ARG Chi-restraints excluded: chain N residue 397 THR Chi-restraints excluded: chain N residue 448 LEU Chi-restraints excluded: chain N residue 459 ASP Chi-restraints excluded: chain N residue 465 LEU Chi-restraints excluded: chain N residue 469 SER Chi-restraints excluded: chain N residue 486 MET Chi-restraints excluded: chain N residue 492 ASP Chi-restraints excluded: chain N residue 510 GLU Chi-restraints excluded: chain N residue 629 THR Chi-restraints excluded: chain N residue 638 SER Chi-restraints excluded: chain N residue 672 LEU Chi-restraints excluded: chain N residue 731 ILE Chi-restraints excluded: chain N residue 742 HIS Chi-restraints excluded: chain N residue 838 LYS Chi-restraints excluded: chain N residue 880 ASN Chi-restraints excluded: chain N residue 892 LEU Chi-restraints excluded: chain S residue 96 ARG Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain S residue 113 LEU Chi-restraints excluded: chain S residue 124 ASN Chi-restraints excluded: chain S residue 131 LEU Chi-restraints excluded: chain S residue 210 CYS Chi-restraints excluded: chain S residue 235 LEU Chi-restraints excluded: chain S residue 236 ARG Chi-restraints excluded: chain S residue 240 LEU Chi-restraints excluded: chain S residue 249 THR Chi-restraints excluded: chain S residue 263 LEU Chi-restraints excluded: chain S residue 281 ASN Chi-restraints excluded: chain S residue 346 LEU Chi-restraints excluded: chain S residue 353 LEU Chi-restraints excluded: chain S residue 354 LYS Chi-restraints excluded: chain S residue 447 ILE Chi-restraints excluded: chain S residue 483 CYS Chi-restraints excluded: chain P residue 139 GLU Chi-restraints excluded: chain P residue 140 ILE Chi-restraints excluded: chain P residue 172 GLU Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 315 MET Chi-restraints excluded: chain P residue 360 GLU Chi-restraints excluded: chain P residue 362 ASN Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain P residue 449 GLU Chi-restraints excluded: chain P residue 453 HIS Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 119 SER Chi-restraints excluded: chain Q residue 224 ASP Chi-restraints excluded: chain Q residue 328 ASP Chi-restraints excluded: chain Q residue 362 GLU Chi-restraints excluded: chain Q residue 415 TYR Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 48 ASN Chi-restraints excluded: chain R residue 63 TRP Chi-restraints excluded: chain R residue 109 GLU Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 196 GLN Chi-restraints excluded: chain R residue 214 MET Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 235 ASP Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 248 GLU Chi-restraints excluded: chain R residue 272 PHE Chi-restraints excluded: chain R residue 278 VAL Chi-restraints excluded: chain R residue 357 ASN Chi-restraints excluded: chain R residue 377 LEU Chi-restraints excluded: chain U residue 21 ASP Chi-restraints excluded: chain U residue 48 LEU Chi-restraints excluded: chain U residue 49 ASP Chi-restraints excluded: chain U residue 53 SER Chi-restraints excluded: chain U residue 71 ASP Chi-restraints excluded: chain U residue 73 ASP Chi-restraints excluded: chain U residue 85 VAL Chi-restraints excluded: chain U residue 96 HIS Chi-restraints excluded: chain U residue 100 LYS Chi-restraints excluded: chain U residue 192 THR Chi-restraints excluded: chain U residue 250 TYR Chi-restraints excluded: chain U residue 254 ASN Chi-restraints excluded: chain U residue 270 VAL Chi-restraints excluded: chain U residue 278 ASN Chi-restraints excluded: chain O residue 60 TYR Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 145 LEU Chi-restraints excluded: chain O residue 158 LEU Chi-restraints excluded: chain O residue 227 ASN Chi-restraints excluded: chain O residue 240 PHE Chi-restraints excluded: chain O residue 244 ASN Chi-restraints excluded: chain O residue 255 TRP Chi-restraints excluded: chain O residue 319 LEU Chi-restraints excluded: chain O residue 360 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 240 optimal weight: 5.9990 chunk 311 optimal weight: 5.9990 chunk 418 optimal weight: 0.9980 chunk 120 optimal weight: 10.0000 chunk 362 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 393 optimal weight: 0.0040 chunk 164 optimal weight: 10.0000 chunk 403 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 overall best weight: 3.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 193 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.153732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.124323 restraints weight = 414349.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.127250 restraints weight = 192523.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.129232 restraints weight = 112103.579| |-----------------------------------------------------------------------------| r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.7981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 40342 Z= 0.242 Angle : 0.661 13.330 54493 Z= 0.350 Chirality : 0.038 0.209 6198 Planarity : 0.005 0.153 7021 Dihedral : 6.196 59.452 5450 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.82 % Favored : 89.78 % Rotamer: Outliers : 3.80 % Allowed : 22.57 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 1.22 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.12), residues: 4970 helix: -0.45 (0.09), residues: 3113 sheet: -1.48 (0.37), residues: 179 loop : -2.79 (0.14), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP N 772 HIS 0.012 0.001 HIS U 157 PHE 0.022 0.002 PHE N 34 TYR 0.026 0.002 TYR Z 349 ARG 0.011 0.001 ARG P 123 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26151.75 seconds wall clock time: 450 minutes 18.07 seconds (27018.07 seconds total)