Starting phenix.real_space_refine on Sun Nov 19 12:00:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5l4k_4002/11_2023/5l4k_4002.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5l4k_4002/11_2023/5l4k_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_4002/11_2023/5l4k_4002.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5l4k_4002/11_2023/5l4k_4002.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5l4k_4002/11_2023/5l4k_4002.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5l4k_4002/11_2023/5l4k_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: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 26.09, per 1000 atoms: 0.33 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: 52.27 Conformation dependent library (CDL) restraints added in 5.9 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: 4.61 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: 30.63 Time building geometry restraints manager: 55.11 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: 29655 17.98 - 35.95: 1724 35.95 - 53.93: 414 53.93 - 71.90: 192 71.90 - 89.88: 100 Dihedral angle restraints: 32085 sinusoidal: 15365 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 32082 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: 5.060 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: 14.250 Check model and map are aligned: 0.870 Set scattering table: 0.550 Process input model: 201.540 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 227.040 ------------------------------------------------------------------------------- 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 *********************** 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 : 4.630 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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symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 166 outliers final: 52 residues processed: 1707 average time/residue: 1.1933 time to fit residues: 3153.9568 Evaluate side-chains 1065 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 1013 time to evaluate : 4.664 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 8 residues processed: 52 average time/residue: 0.9306 time to fit residues: 88.0082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 417 optimal weight: 6.9990 chunk 375 optimal weight: 5.9990 chunk 208 optimal weight: 8.9990 chunk 128 optimal weight: 10.0000 chunk 253 optimal weight: 9.9990 chunk 200 optimal weight: 9.9990 chunk 387 optimal weight: 6.9990 chunk 150 optimal weight: 0.9980 chunk 235 optimal weight: 0.5980 chunk 288 optimal weight: 5.9990 chunk 449 optimal weight: 1.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 29 GLN W 137 ASN V 232 GLN V 298 GLN ** T 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 127 ASN T 170 GLN T 195 ASN T 202 GLN T 228 HIS Z 51 GLN Z 53 GLN Z 81 GLN ** Z 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 139 GLN N 149 GLN ** N 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 355 ASN N 421 GLN ** N 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 500 ASN N 540 GLN S 168 GLN S 193 GLN ** S 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 329 HIS S 350 GLN ** P 440 ASN ** 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 225 GLN U 235 ASN O 12 GLN O 264 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 40342 Z= 0.265 Angle : 0.763 13.469 54493 Z= 0.412 Chirality : 0.040 0.316 6198 Planarity : 0.006 0.150 7021 Dihedral : 6.427 49.859 5401 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.87 % Allowed : 8.27 % Favored : 90.87 % Rotamer: Outliers : 2.83 % Allowed : 16.11 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 1.22 % Twisted General : 0.12 % 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: -4.54 (0.10), residues: 4970 helix: -2.73 (0.07), residues: 3096 sheet: -2.11 (0.39), residues: 160 loop : -3.35 (0.13), residues: 1714 *********************** 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 1166 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 1043 time to evaluate : 4.889 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 outliers start: 123 outliers final: 87 residues processed: 1122 average time/residue: 1.1418 time to fit residues: 1999.0142 Evaluate side-chains 1007 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 920 time to evaluate : 4.744 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 87 outliers final: 7 residues processed: 87 average time/residue: 0.8151 time to fit residues: 133.4699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 249 optimal weight: 9.9990 chunk 139 optimal weight: 0.0570 chunk 374 optimal weight: 0.3980 chunk 306 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 450 optimal weight: 5.9990 chunk 486 optimal weight: 5.9990 chunk 401 optimal weight: 0.7980 chunk 446 optimal weight: 4.9990 chunk 153 optimal weight: 5.9990 chunk 361 optimal weight: 4.9990 overall best weight: 2.2502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 137 ASN ** T 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 127 ASN ** Z 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 356 ASN Z 396 ASN Z 566 HIS N 149 GLN N 259 GLN N 398 ASN N 718 ASN ** S 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 283 ASN ** S 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 28 HIS R 48 ASN R 302 HIS ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 40342 Z= 0.217 Angle : 0.682 11.455 54493 Z= 0.363 Chirality : 0.038 0.212 6198 Planarity : 0.005 0.110 7021 Dihedral : 5.934 48.621 5401 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.72 % Allowed : 8.27 % Favored : 91.01 % Rotamer: Outliers : 1.54 % Allowed : 17.23 % Favored : 81.22 % 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: -3.53 (0.11), residues: 4970 helix: -1.84 (0.08), residues: 3121 sheet: -1.84 (0.39), residues: 174 loop : -3.14 (0.14), residues: 1675 *********************** 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 1031 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 964 time to evaluate : 4.774 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 outliers start: 67 outliers final: 47 residues processed: 994 average time/residue: 1.1087 time to fit residues: 1728.2210 Evaluate side-chains 946 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 899 time to evaluate : 4.661 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 9 residues processed: 47 average time/residue: 0.8578 time to fit residues: 76.2138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 444 optimal weight: 3.9990 chunk 338 optimal weight: 6.9990 chunk 233 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 214 optimal weight: 20.0000 chunk 302 optimal weight: 10.0000 chunk 451 optimal weight: 0.7980 chunk 478 optimal weight: 10.0000 chunk 236 optimal weight: 8.9990 chunk 428 optimal weight: 5.9990 chunk 128 optimal weight: 20.0000 overall best weight: 5.3588 ------------------------------------------------------------------------------- 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 105 HIS W 137 ASN ** W 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 127 ASN T 170 GLN ** T 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 209 HIS ** T 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 14 GLN ** Z 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 356 ASN ** Z 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 750 GLN ** N 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 338 HIS N 389 ASN ** S 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 487 HIS P 107 GLN Q 28 HIS R 14 ASN R 196 GLN R 302 HIS ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 124 ASN O 143 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.6169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 40342 Z= 0.364 Angle : 0.768 10.439 54493 Z= 0.415 Chirality : 0.040 0.204 6198 Planarity : 0.006 0.135 7021 Dihedral : 6.041 48.280 5401 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.76 % Allowed : 8.97 % Favored : 90.26 % Rotamer: Outliers : 3.04 % Allowed : 18.18 % Favored : 78.79 % 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: -3.29 (0.11), residues: 4970 helix: -1.59 (0.08), residues: 3131 sheet: -1.80 (0.40), residues: 173 loop : -3.18 (0.14), residues: 1666 *********************** 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 1053 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 921 time to evaluate : 4.678 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 outliers start: 132 outliers final: 88 residues processed: 991 average time/residue: 1.1384 time to fit residues: 1779.7100 Evaluate side-chains 937 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 849 time to evaluate : 4.854 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 8 residues processed: 88 average time/residue: 0.8791 time to fit residues: 141.5096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 398 optimal weight: 2.9990 chunk 271 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 356 optimal weight: 0.9980 chunk 197 optimal weight: 8.9990 chunk 408 optimal weight: 2.9990 chunk 330 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 244 optimal weight: 9.9990 chunk 429 optimal weight: 5.9990 chunk 120 optimal weight: 9.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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** ** V 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 206 ASN ** 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** Z 323 ASN ** Z 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 782 HIS N 111 GLN N 345 ASN ** N 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 177 ASN S 252 ASN ** S 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 28 HIS R 302 HIS ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 12 HIS U 32 GLN ** U 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.6675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 40342 Z= 0.263 Angle : 0.684 10.862 54493 Z= 0.366 Chirality : 0.038 0.206 6198 Planarity : 0.005 0.141 7021 Dihedral : 5.835 47.528 5401 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.66 % Allowed : 8.71 % Favored : 90.62 % Rotamer: Outliers : 1.73 % Allowed : 20.09 % Favored : 78.19 % 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: -2.90 (0.11), residues: 4970 helix: -1.28 (0.09), residues: 3137 sheet: -1.47 (0.40), residues: 170 loop : -3.06 (0.14), residues: 1663 *********************** 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 960 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 885 time to evaluate : 4.806 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 outliers start: 75 outliers final: 42 residues processed: 926 average time/residue: 1.1023 time to fit residues: 1603.3656 Evaluate side-chains 882 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 840 time to evaluate : 4.764 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 7 residues processed: 42 average time/residue: 0.8613 time to fit residues: 68.1291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 160 optimal weight: 20.0000 chunk 430 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 280 optimal weight: 0.8980 chunk 118 optimal weight: 9.9990 chunk 478 optimal weight: 6.9990 chunk 397 optimal weight: 9.9990 chunk 221 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 158 optimal weight: 6.9990 chunk 251 optimal weight: 20.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- 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 190 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** Z 325 GLN Z 356 ASN Z 737 ASN N 611 ASN ** N 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 399 ASN Q 28 HIS ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 48 ASN R 64 GLN R 77 ASN R 302 HIS ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 231 GLN ** O 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.7225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 40342 Z= 0.328 Angle : 0.727 13.131 54493 Z= 0.391 Chirality : 0.039 0.227 6198 Planarity : 0.005 0.148 7021 Dihedral : 5.901 50.219 5401 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.60 % Allowed : 10.18 % Favored : 89.22 % Rotamer: Outliers : 2.28 % Allowed : 20.96 % Favored : 76.76 % 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: -2.89 (0.11), residues: 4970 helix: -1.27 (0.09), residues: 3124 sheet: -1.52 (0.40), residues: 170 loop : -3.06 (0.14), residues: 1676 *********************** 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 963 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 864 time to evaluate : 4.694 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 outliers start: 99 outliers final: 65 residues processed: 915 average time/residue: 1.1014 time to fit residues: 1586.6823 Evaluate side-chains 892 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 827 time to evaluate : 4.841 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 8 residues processed: 65 average time/residue: 0.7725 time to fit residues: 96.7590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 461 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 272 optimal weight: 5.9990 chunk 349 optimal weight: 8.9990 chunk 270 optimal weight: 10.0000 chunk 403 optimal weight: 0.8980 chunk 267 optimal weight: 6.9990 chunk 477 optimal weight: 5.9990 chunk 298 optimal weight: 4.9990 chunk 290 optimal weight: 0.8980 chunk 220 optimal weight: 7.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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** ** V 190 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 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 647 HIS ** S 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 28 HIS R 302 HIS ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.7363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 40342 Z= 0.193 Angle : 0.646 14.329 54493 Z= 0.340 Chirality : 0.037 0.191 6198 Planarity : 0.005 0.153 7021 Dihedral : 5.623 48.294 5401 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.54 % Allowed : 8.51 % Favored : 90.95 % Rotamer: Outliers : 1.08 % Allowed : 21.93 % Favored : 76.99 % 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: -2.35 (0.11), residues: 4970 helix: -0.85 (0.09), residues: 3131 sheet: -1.53 (0.39), residues: 174 loop : -2.81 (0.14), residues: 1665 *********************** 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 916 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 869 time to evaluate : 4.695 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 outliers start: 47 outliers final: 32 residues processed: 897 average time/residue: 1.1084 time to fit residues: 1566.9602 Evaluate side-chains 858 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 826 time to evaluate : 4.793 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 8 residues processed: 32 average time/residue: 0.9805 time to fit residues: 57.7756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 295 optimal weight: 10.0000 chunk 190 optimal weight: 9.9990 chunk 284 optimal weight: 1.9990 chunk 143 optimal weight: 8.9990 chunk 93 optimal weight: 20.0000 chunk 92 optimal weight: 1.9990 chunk 303 optimal weight: 6.9990 chunk 325 optimal weight: 2.9990 chunk 235 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 375 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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** ** V 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 89 GLN ** T 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 209 HIS ** 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 356 ASN N 685 GLN ** S 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 302 HIS ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.7644 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= 0.256 Angle : 0.677 15.289 54493 Z= 0.359 Chirality : 0.038 0.201 6198 Planarity : 0.005 0.158 7021 Dihedral : 5.640 49.354 5401 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.54 % Allowed : 9.64 % Favored : 89.82 % Rotamer: Outliers : 1.01 % Allowed : 22.92 % Favored : 76.07 % 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: -2.31 (0.11), residues: 4970 helix: -0.79 (0.09), residues: 3124 sheet: -1.43 (0.39), residues: 173 loop : -2.86 (0.14), residues: 1673 *********************** 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 892 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 848 time to evaluate : 4.811 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 outliers start: 44 outliers final: 36 residues processed: 863 average time/residue: 1.1316 time to fit residues: 1543.9378 Evaluate side-chains 853 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 817 time to evaluate : 4.712 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 7 residues processed: 36 average time/residue: 0.8037 time to fit residues: 57.5902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 434 optimal weight: 1.9990 chunk 457 optimal weight: 0.6980 chunk 417 optimal weight: 5.9990 chunk 444 optimal weight: 0.9980 chunk 456 optimal weight: 0.8980 chunk 267 optimal weight: 4.9990 chunk 193 optimal weight: 20.0000 chunk 349 optimal weight: 9.9990 chunk 136 optimal weight: 10.0000 chunk 401 optimal weight: 5.9990 chunk 420 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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** ** T 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 302 HIS ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.7739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 40342 Z= 0.181 Angle : 0.636 15.228 54493 Z= 0.331 Chirality : 0.037 0.209 6198 Planarity : 0.005 0.158 7021 Dihedral : 5.417 47.569 5401 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.99 % Favored : 91.53 % Rotamer: Outliers : 0.55 % Allowed : 23.10 % Favored : 76.35 % 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: -1.79 (0.12), residues: 4970 helix: -0.37 (0.09), residues: 3103 sheet: -1.35 (0.40), residues: 172 loop : -2.65 (0.15), residues: 1695 *********************** 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 878 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 854 time to evaluate : 4.893 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 outliers start: 24 outliers final: 17 residues processed: 866 average time/residue: 1.1356 time to fit residues: 1554.7861 Evaluate side-chains 840 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 823 time to evaluate : 4.718 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 6 residues processed: 17 average time/residue: 0.9364 time to fit residues: 32.6350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 470 optimal weight: 9.9990 chunk 286 optimal weight: 4.9990 chunk 223 optimal weight: 8.9990 chunk 326 optimal weight: 5.9990 chunk 493 optimal weight: 6.9990 chunk 453 optimal weight: 5.9990 chunk 392 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 303 optimal weight: 6.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 48 ASN ** W 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 209 HIS ** 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 428 GLN ** N 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 193 GLN ** S 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 502 ASN ** P 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 302 HIS ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.7986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 40342 Z= 0.273 Angle : 0.688 15.624 54493 Z= 0.365 Chirality : 0.038 0.190 6198 Planarity : 0.005 0.161 7021 Dihedral : 5.538 50.390 5401 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 19.60 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.74 % Favored : 89.78 % Rotamer: Outliers : 0.51 % Allowed : 23.72 % Favored : 75.77 % 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: -2.00 (0.12), residues: 4970 helix: -0.51 (0.09), residues: 3127 sheet: -1.43 (0.39), residues: 168 loop : -2.81 (0.14), residues: 1675 ********************** 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 846 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 824 time to evaluate : 4.777 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 outliers start: 22 outliers final: 18 residues processed: 833 average time/residue: 1.1413 time to fit residues: 1502.7755 Evaluate side-chains 825 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 807 time to evaluate : 4.695 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 7 residues processed: 18 average time/residue: 0.9226 time to fit residues: 34.1894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 240 optimal weight: 7.9990 chunk 311 optimal weight: 6.9990 chunk 418 optimal weight: 5.9990 chunk 120 optimal weight: 8.9990 chunk 362 optimal weight: 0.2980 chunk 57 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 chunk 393 optimal weight: 4.9990 chunk 164 optimal weight: 0.2980 chunk 403 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 170 GLN ** T 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 209 HIS ** 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 N 139 GLN ** N 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 901 GLN ** S 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 177 ASN ** S 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 302 HIS ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.154665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.125357 restraints weight = 415082.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.128597 restraints weight = 192251.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.130146 restraints weight = 111454.866| |-----------------------------------------------------------------------------| r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.8157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 40342 Z= 0.237 Angle : 0.673 14.387 54493 Z= 0.354 Chirality : 0.038 0.207 6198 Planarity : 0.005 0.156 7021 Dihedral : 5.544 50.519 5401 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 18.51 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.15 % Favored : 90.36 % Rotamer: Outliers : 0.58 % Allowed : 23.65 % Favored : 75.77 % 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: -1.87 (0.12), residues: 4970 helix: -0.38 (0.09), residues: 3109 sheet: -1.38 (0.39), residues: 170 loop : -2.79 (0.14), residues: 1691 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24535.28 seconds wall clock time: 422 minutes 28.90 seconds (25348.90 seconds total)