Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 13:01:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsh_12567/04_2023/7nsh_12567_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsh_12567/04_2023/7nsh_12567.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsh_12567/04_2023/7nsh_12567.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsh_12567/04_2023/7nsh_12567.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsh_12567/04_2023/7nsh_12567_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsh_12567/04_2023/7nsh_12567_neut_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.008 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: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 1616 5.49 5 Mg 221 5.21 5 S 296 5.16 5 C 64943 2.51 5 N 20462 2.21 5 O 24907 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B0 PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B0 TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B0 GLU 93": "OE1" <-> "OE2" Residue "B0 TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B0 PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B0 GLU 139": "OE1" <-> "OE2" Residue "BY GLU 66": "OE1" <-> "OE2" Residue "BY GLU 139": "OE1" <-> "OE2" Residue "BY GLU 142": "OE1" <-> "OE2" Residue "BY GLU 184": "OE1" <-> "OE2" Residue "BY GLU 206": "OE1" <-> "OE2" Residue "Ba GLU 42": "OE1" <-> "OE2" Residue "Ba TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ba ASP 101": "OD1" <-> "OD2" Residue "Ba GLU 115": "OE1" <-> "OE2" Residue "Ba ASP 141": "OD1" <-> "OD2" Residue "Ba GLU 148": "OE1" <-> "OE2" Residue "Ba GLU 152": "OE1" <-> "OE2" Residue "Ba TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ba GLU 246": "OE1" <-> "OE2" Residue "Ba PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ba PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ba ASP 307": "OD1" <-> "OD2" Residue "Ba ASP 332": "OD1" <-> "OD2" Residue "Ba GLU 337": "OE1" <-> "OE2" Residue "Ba GLU 368": "OE1" <-> "OE2" Residue "Ba ASP 377": "OD1" <-> "OD2" Residue "Ba PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B8 GLU 146": "OE1" <-> "OE2" Residue "B8 ASP 159": "OD1" <-> "OD2" Residue "Bb ASP 39": "OD1" <-> "OD2" Residue "Bb TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bb GLU 80": "OE1" <-> "OE2" Residue "Bb GLU 133": "OE1" <-> "OE2" Residue "Bb GLU 140": "OE1" <-> "OE2" Residue "Bb TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bb TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bb GLU 203": "OE1" <-> "OE2" Residue "Bb GLU 207": "OE1" <-> "OE2" Residue "Bb ASP 209": "OD1" <-> "OD2" Residue "Bb GLU 210": "OE1" <-> "OE2" Residue "Bb GLU 231": "OE1" <-> "OE2" Residue "Bb GLU 250": "OE1" <-> "OE2" Residue "Bb PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bb PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bb ASP 284": "OD1" <-> "OD2" Residue "Bb GLU 343": "OE1" <-> "OE2" Residue "Bc GLU 39": "OE1" <-> "OE2" Residue "Bc GLU 48": "OE1" <-> "OE2" Residue "Bc GLU 63": "OE1" <-> "OE2" Residue "Bc GLU 94": "OE1" <-> "OE2" Residue "Bc TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bc GLU 152": "OE1" <-> "OE2" Residue "Bc ASP 179": "OD1" <-> "OD2" Residue "Bc GLU 194": "OE1" <-> "OE2" Residue "Bc GLU 219": "OE1" <-> "OE2" Residue "Bc GLU 239": "OE1" <-> "OE2" Residue "Bc ASP 256": "OD1" <-> "OD2" Residue "Bc GLU 276": "OE1" <-> "OE2" Residue "Bc GLU 322": "OE1" <-> "OE2" Residue "Bd PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bd GLU 61": "OE1" <-> "OE2" Residue "Bd GLU 66": "OE1" <-> "OE2" Residue "Bd GLU 84": "OE1" <-> "OE2" Residue "Bd GLU 88": "OE1" <-> "OE2" Residue "Bd GLU 97": "OE1" <-> "OE2" Residue "Bd GLU 100": "OE1" <-> "OE2" Residue "Be ASP 16": "OD1" <-> "OD2" Residue "Be GLU 53": "OE1" <-> "OE2" Residue "Be TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bf GLU 110": "OE1" <-> "OE2" Residue "Bg TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bg GLU 86": "OE1" <-> "OE2" Residue "Bg GLU 87": "OE1" <-> "OE2" Residue "Bg GLU 95": "OE1" <-> "OE2" Residue "Bg ASP 106": "OD1" <-> "OD2" Residue "Bg PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bh GLU 44": "OE1" <-> "OE2" Residue "Bh GLU 46": "OE1" <-> "OE2" Residue "Bh GLU 62": "OE1" <-> "OE2" Residue "Bh GLU 113": "OE1" <-> "OE2" Residue "Bh GLU 124": "OE1" <-> "OE2" Residue "Bh GLU 127": "OE1" <-> "OE2" Residue "Bh GLU 151": "OE1" <-> "OE2" Residue "Bh GLU 176": "OE1" <-> "OE2" Residue "Bh GLU 183": "OE1" <-> "OE2" Residue "Bh GLU 227": "OE1" <-> "OE2" Residue "Bh GLU 230": "OE1" <-> "OE2" Residue "Bh GLU 243": "OE1" <-> "OE2" Residue "Bh TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bh GLU 295": "OE1" <-> "OE2" Residue "Bh PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bh ASP 315": "OD1" <-> "OD2" Residue "Bi ASP 86": "OD1" <-> "OD2" Residue "Bi GLU 127": "OE1" <-> "OE2" Residue "Bi GLU 147": "OE1" <-> "OE2" Residue "Bi GLU 166": "OE1" <-> "OE2" Residue "Bi TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bi TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bi GLU 244": "OE1" <-> "OE2" Residue "Bi GLU 249": "OE1" <-> "OE2" Residue "Bi GLU 291": "OE1" <-> "OE2" Residue "Bi GLU 292": "OE1" <-> "OE2" Residue "Bj GLU 80": "OE1" <-> "OE2" Residue "Bj GLU 182": "OE1" <-> "OE2" Residue "Bj GLU 197": "OE1" <-> "OE2" Residue "Bj GLU 201": "OE1" <-> "OE2" Residue "Bk TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bk TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bk GLU 104": "OE1" <-> "OE2" Residue "Bk GLU 122": "OE1" <-> "OE2" Residue "Bk GLU 133": "OE1" <-> "OE2" Residue "Bk GLU 192": "OE1" <-> "OE2" Residue "Bk GLU 205": "OE1" <-> "OE2" Residue "Bl TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bl GLU 44": "OE1" <-> "OE2" Residue "Bl GLU 49": "OE1" <-> "OE2" Residue "Bl TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bm GLU 72": "OE1" <-> "OE2" Residue "Bm GLU 93": "OE1" <-> "OE2" Residue "Bm PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bn ASP 45": "OD1" <-> "OD2" Residue "Bo GLU 103": "OE1" <-> "OE2" Residue "Bp GLU 85": "OE1" <-> "OE2" Residue "Bq PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bq GLU 109": "OE1" <-> "OE2" Residue "Bq ASP 111": "OD1" <-> "OD2" Residue "Bt ARG 11": "NH1" <-> "NH2" Residue "Bt GLU 57": "OE1" <-> "OE2" Residue "Bu GLU 51": "OE1" <-> "OE2" Residue "Bu GLU 112": "OE1" <-> "OE2" Residue "Bu GLU 180": "OE1" <-> "OE2" Residue "Bv PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bv GLU 80": "OE1" <-> "OE2" Residue "Bv GLU 86": "OE1" <-> "OE2" Residue "Bv GLU 88": "OE1" <-> "OE2" Residue "Bv GLU 89": "OE1" <-> "OE2" Residue "Bv GLU 101": "OE1" <-> "OE2" Residue "Bv ARG 104": "NH1" <-> "NH2" Residue "Bv GLU 110": "OE1" <-> "OE2" Residue "Bv GLU 111": "OE1" <-> "OE2" Residue "Bv GLU 122": "OE1" <-> "OE2" Residue "Bv GLU 123": "OE1" <-> "OE2" Residue "Bv ARG 136": "NH1" <-> "NH2" Residue "Bv GLU 141": "OE1" <-> "OE2" Residue "Bw GLU 64": "OE1" <-> "OE2" Residue "Bw GLU 78": "OE1" <-> "OE2" Residue "Bw TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bw GLU 138": "OE1" <-> "OE2" Residue "Bw GLU 147": "OE1" <-> "OE2" Residue "Bw GLU 209": "OE1" <-> "OE2" Residue "Bw GLU 243": "OE1" <-> "OE2" Residue "Bw GLU 273": "OE1" <-> "OE2" Residue "Bw ASP 298": "OD1" <-> "OD2" Residue "Bw GLU 315": "OE1" <-> "OE2" Residue "Bw GLU 342": "OE1" <-> "OE2" Residue "Bw TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bw GLU 397": "OE1" <-> "OE2" Residue "Bx GLU 40": "OE1" <-> "OE2" Residue "Bx GLU 84": "OE1" <-> "OE2" Residue "Bx GLU 111": "OE1" <-> "OE2" Residue "Bx GLU 137": "OE1" <-> "OE2" Residue "Bx TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B1 GLU 33": "OE1" <-> "OE2" Residue "B1 GLU 60": "OE1" <-> "OE2" Residue "B1 GLU 113": "OE1" <-> "OE2" Residue "B1 TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B1 ASP 120": "OD1" <-> "OD2" Residue "B1 ASP 136": "OD1" <-> "OD2" Residue "B1 ASP 173": "OD1" <-> "OD2" Residue "EL GLU 78": "OE1" <-> "OE2" Residue "B9 PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B9 TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "GL GLU 78": "OE1" <-> "OE2" Residue "B2 ASP 72": "OD1" <-> "OD2" Residue "B2 GLU 98": "OE1" <-> "OE2" Residue "B2 GLU 120": "OE1" <-> "OE2" Residue "B2 GLU 132": "OE1" <-> "OE2" Residue "B2 GLU 135": "OE1" <-> "OE2" Residue "B2 GLU 152": "OE1" <-> "OE2" Residue "B2 GLU 163": "OE1" <-> "OE2" Residue "B3 GLU 82": "OE1" <-> "OE2" Residue "B3 GLU 92": "OE1" <-> "OE2" Residue "B4 TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B4 GLU 71": "OE1" <-> "OE2" Residue "B5 GLU 133": "OE1" <-> "OE2" Residue "B5 GLU 136": "OE1" <-> "OE2" Residue "BC ASP 147": "OD1" <-> "OD2" Residue "BC GLU 153": "OE1" <-> "OE2" Residue "BC ARG 190": "NH1" <-> "NH2" Residue "BC GLU 228": "OE1" <-> "OE2" Residue "BC ASP 237": "OD1" <-> "OD2" Residue "BC ASP 288": "OD1" <-> "OD2" Residue "BC PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC ARG 355": "NH1" <-> "NH2" Residue "BC TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC GLU 408": "OE1" <-> "OE2" Residue "BC ARG 409": "NH1" <-> "NH2" Residue "BC ARG 412": "NH1" <-> "NH2" Residue "BC ASP 445": "OD1" <-> "OD2" Residue "BC GLU 487": "OE1" <-> "OE2" Residue "BC GLU 506": "OE1" <-> "OE2" Residue "BC ARG 546": "NH1" <-> "NH2" Residue "BC GLU 550": "OE1" <-> "OE2" Residue "BC ARG 565": "NH1" <-> "NH2" Residue "BC GLU 599": "OE1" <-> "OE2" Residue "BC GLU 613": "OE1" <-> "OE2" Residue "BC GLU 617": "OE1" <-> "OE2" Residue "BC GLU 628": "OE1" <-> "OE2" Residue "BC ARG 712": "NH1" <-> "NH2" Residue "BC GLU 735": "OE1" <-> "OE2" Residue "BC ARG 744": "NH1" <-> "NH2" Residue "BD ASP 108": "OD1" <-> "OD2" Residue "BD GLU 125": "OE1" <-> "OE2" Residue "BD GLU 156": "OE1" <-> "OE2" Residue "BD ASP 162": "OD1" <-> "OD2" Residue "BD GLU 198": "OE1" <-> "OE2" Residue "BD GLU 239": "OE1" <-> "OE2" Residue "BD TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BG ARG 71": "NH1" <-> "NH2" Residue "BG GLU 153": "OE1" <-> "OE2" Residue "BQ GLU 46": "OE1" <-> "OE2" Residue "BQ PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BQ GLU 54": "OE1" <-> "OE2" Residue "BQ GLU 65": "OE1" <-> "OE2" Residue "BQ GLU 103": "OE1" <-> "OE2" Residue "BQ PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BQ GLU 196": "OE1" <-> "OE2" Residue "BQ GLU 203": "OE1" <-> "OE2" Residue "BQ GLU 204": "OE1" <-> "OE2" Residue "LL GLU 136": "OE1" <-> "OE2" Residue "LL GLU 148": "OE1" <-> "OE2" Residue "LL GLU 180": "OE1" <-> "OE2" Residue "BE GLU 51": "OE1" <-> "OE2" Residue "BE GLU 83": "OE1" <-> "OE2" Residue "BE ASP 113": "OD1" <-> "OD2" Residue "BE GLU 136": "OE1" <-> "OE2" Residue "BE TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BE GLU 167": "OE1" <-> "OE2" Residue "BE ASP 247": "OD1" <-> "OD2" Residue "BE ASP 265": "OD1" <-> "OD2" Residue "BE TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BE GLU 326": "OE1" <-> "OE2" Residue "BE ASP 331": "OD1" <-> "OD2" Residue "BE ASP 334": "OD1" <-> "OD2" Residue "BE PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BF TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BF TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BF TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BF TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BI GLU 143": "OE1" <-> "OE2" Residue "BI GLU 149": "OE1" <-> "OE2" Residue "BJ GLU 75": "OE1" <-> "OE2" Residue "BJ GLU 85": "OE1" <-> "OE2" Residue "BJ GLU 137": "OE1" <-> "OE2" Residue "BJ PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BJ TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BJ ARG 227": "NH1" <-> "NH2" Residue "BK PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BK GLU 55": "OE1" <-> "OE2" Residue "BK GLU 62": "OE1" <-> "OE2" Residue "BK GLU 98": "OE1" <-> "OE2" Residue "BK GLU 162": "OE1" <-> "OE2" Residue "BK GLU 180": "OE1" <-> "OE2" Residue "BN TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BN PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BN TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BN GLU 143": "OE1" <-> "OE2" Residue "BN TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BN PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BN GLU 174": "OE1" <-> "OE2" Residue "BO TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BO GLU 109": "OE1" <-> "OE2" Residue "BO PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BP GLU 68": "OE1" <-> "OE2" Residue "BP TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BP GLU 142": "OE1" <-> "OE2" Residue "BP GLU 168": "OE1" <-> "OE2" Residue "BP GLU 185": "OE1" <-> "OE2" Residue "BP GLU 208": "OE1" <-> "OE2" Residue "BP TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BP TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BP TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BP GLU 251": "OE1" <-> "OE2" Residue "BR GLU 23": "OE1" <-> "OE2" Residue "BR ASP 61": "OD1" <-> "OD2" Residue "BR TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BR GLU 82": "OE1" <-> "OE2" Residue "BR ASP 84": "OD1" <-> "OD2" Residue "BR GLU 125": "OE1" <-> "OE2" Residue "BS GLU 40": "OE1" <-> "OE2" Residue "BS PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BS GLU 57": "OE1" <-> "OE2" Residue "BS GLU 65": "OE1" <-> "OE2" Residue "BS GLU 95": "OE1" <-> "OE2" Residue "BS GLU 126": "OE1" <-> "OE2" Residue "BS GLU 134": "OE1" <-> "OE2" Residue "BS GLU 152": "OE1" <-> "OE2" Residue "BS GLU 174": "OE1" <-> "OE2" Residue "BT GLU 101": "OE1" <-> "OE2" Residue "BT GLU 156": "OE1" <-> "OE2" Residue "BT GLU 161": "OE1" <-> "OE2" Residue "BT GLU 214": "OE1" <-> "OE2" Residue "BT GLU 234": "OE1" <-> "OE2" Residue "BT GLU 256": "OE1" <-> "OE2" Residue "BT TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BT GLU 279": "OE1" <-> "OE2" Residue "BT GLU 285": "OE1" <-> "OE2" Residue "BT GLU 287": "OE1" <-> "OE2" Residue "BU GLU 78": "OE1" <-> "OE2" Residue "BU GLU 96": "OE1" <-> "OE2" Residue "BU GLU 109": "OE1" <-> "OE2" Residue "BV PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BW GLU 50": "OE1" <-> "OE2" Residue "BW GLU 70": "OE1" <-> "OE2" Residue "BW GLU 117": "OE1" <-> "OE2" Residue "BW GLU 121": "OE1" <-> "OE2" Residue "BW TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BW GLU 178": "OE1" <-> "OE2" Residue "BW GLU 196": "OE1" <-> "OE2" Residue "BX GLU 47": "OE1" <-> "OE2" Residue "BX TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BX GLU 113": "OE1" <-> "OE2" Residue "BX PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 112448 Number of models: 1 Model: "" Number of chains: 79 Chain: "B0" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "BY" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1678 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 17, 'TRANS': 188} Chain: "Ba" Number of atoms: 3173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3173 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 35, 'TRANS': 357} Chain: "B8" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 833 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 1, 'TRANS': 93} Chain: "Bb" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2952 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 32, 'TRANS': 321} Chain: "Bc" Number of atoms: 2408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2408 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 15, 'TRANS': 279} Chain: "Bd" Number of atoms: 1177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1177 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 13, 'TRANS': 126} Chain: "Be" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 972 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 11, 'TRANS': 110} Chain: "Bf" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 827 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 12, 'TRANS': 95} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 4, 'HIS:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "Bg" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1167 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 10, 'TRANS': 137} Chain: "Bh" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2319 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 18, 'TRANS': 270} Chain: "Bi" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2138 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 23, 'TRANS': 236} Chain: "Bj" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1775 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 2 Chain: "Bk" Number of atoms: 1246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1246 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 5, 'TRANS': 149} Chain breaks: 1 Chain: "Bl" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1097 Classifications: {'peptide': 133} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 116} Chain: "Bm" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 893 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "Bn" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 837 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "Bo" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 772 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 6, 'TRANS': 90} Chain: "Bp" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 742 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "Bq" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 672 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 73} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Bt" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 780 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "Bu" Number of atoms: 1198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1198 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "Bv" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1131 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 12, 'TRANS': 122} Chain: "Bw" Number of atoms: 3126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3126 Classifications: {'peptide': 387} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 360} Chain: "Bx" Number of atoms: 1325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1325 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 18, 'TRANS': 143} Chain: "CL" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 317 Classifications: {'peptide': 45} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 4, 'TRANS': 40} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B1" Number of atoms: 2036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 2036 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 18, 'TRANS': 225} Chain: "DL" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 213 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "EL" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 222 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "FL" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 213 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "B9" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 335 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "GL" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 213 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "HL" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 205 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "BA" Number of atoms: 32844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1544, 32844 Classifications: {'RNA': 1544} Modifications used: {'rna2p_pur': 172, 'rna2p_pyr': 110, 'rna3p_pur': 682, 'rna3p_pyr': 580} Link IDs: {'rna2p': 281, 'rna3p': 1262} Chain breaks: 1 Chain: "B2" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1548 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain: "B3" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 968 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 11, 'TRANS': 106} Chain: "B4" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 474 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 57} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "B5" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 902 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "B6" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 425 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 1, 'TRANS': 50} Chain: "B7" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 387 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "BB" Number of atoms: 1427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1427 Classifications: {'RNA': 67} Modifications used: {'p5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 35, 'rna3p_pyr': 27} Link IDs: {'rna2p': 5, 'rna3p': 61} Chain breaks: 2 Chain: "BC" Number of atoms: 5434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5434 Classifications: {'peptide': 700} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 34, 'TRANS': 665} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "BD" Number of atoms: 1860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1860 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 14, 'TRANS': 225} Chain: "BG" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1520 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 6, 'TRANS': 189} Chain: "BQ" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1803 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 17, 'TRANS': 204} Chain: "LL" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 537 Classifications: {'peptide': 70} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 66} Chain: "BE" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2420 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 25, 'TRANS': 281} Chain: "BF" Number of atoms: 2011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2011 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 20, 'TRANS': 229} Chain: "BI" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 805 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "BJ" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1705 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 18, 'TRANS': 193} Chain: "BK" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1339 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 166} Chain: "BN" Number of atoms: 1444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1444 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 15, 'TRANS': 161} Chain: "BO" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 896 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 9, 'TRANS': 105} Chain: "BP" Number of atoms: 2312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2312 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 27, 'TRANS': 260} Chain: "BR" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1240 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 8, 'TRANS': 144} Chain: "BS" Number of atoms: 1168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1168 Classifications: {'peptide': 143} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 136} Chain: "BT" Number of atoms: 1851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1851 Classifications: {'peptide': 223} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 207} Chain: "BU" Number of atoms: 1159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1159 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "BV" Number of atoms: 1231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1231 Classifications: {'peptide': 155} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 144} Chain: "BW" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1374 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 10, 'TRANS': 155} Chain: "BX" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1181 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 12, 'TRANS': 136} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 38 Chain: "B0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Bb" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Be" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Bl" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Bt" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Bx" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B9" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "BA" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 281 Unusual residues: {' MG': 205, 'SPM': 2} Classifications: {'RNA': 2, 'undetermined': 207} Modifications used: {'rna2p': 2} Link IDs: {'rna2p': 1, None: 207} Not linked: pdbres=" MGBA3001 " pdbres=" MGBA3002 " Not linked: pdbres=" MGBA3002 " pdbres=" MGBA3003 " Not linked: pdbres=" MGBA3003 " pdbres=" MGBA3004 " Not linked: pdbres=" MGBA3004 " pdbres=" MGBA3005 " Not linked: pdbres=" MGBA3005 " pdbres=" MGBA3006 " ... (remaining 202 not shown) Chain breaks: 1 Chain: "B3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "BC" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "BD" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "BQ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "BE" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "BJ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "BP" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "BR" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "BC" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 35047 SG CYSBx 70 105.772 107.857 190.595 1.00 32.26 S ATOM 35068 SG CYSBx 73 107.795 110.689 189.143 1.00 28.71 S ATOM 35365 SG CYSBx 108 105.529 108.644 186.919 1.00 21.28 S ATOM 95510 SG CYSBJ 64 104.052 111.020 189.456 1.00 42.70 S ATOM 39186 SG CYSB9 73 90.267 81.840 167.784 1.00 23.73 S ATOM 39211 SG CYSB9 76 93.587 83.384 166.881 1.00 16.38 S ATOM 39335 SG CYSB9 89 93.373 79.703 167.673 1.00 13.42 S ATOM 75946 SG CYSB5 110 197.969 65.734 133.612 1.00 27.68 S ATOM 75968 SG CYSB5 113 199.732 67.673 130.899 1.00 27.19 S ATOM 76049 SG CYSB5 123 196.021 67.048 130.662 1.00 14.48 S ATOM 76071 SG CYSB5 126 198.447 64.197 130.200 1.00 19.10 S Time building chain proxies: 41.40, per 1000 atoms: 0.37 Number of scatterers: 112448 At special positions: 0 Unit cell: (261.967, 227.183, 280.446, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 S 296 16.00 P 1616 15.00 Mg 221 11.99 O 24907 8.00 N 20462 7.00 C 64943 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 37.01 Conformation dependent library (CDL) restraints added in 8.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNB5 500 " pdb="ZN ZNB5 500 " - pdb=" SG CYSB5 123 " pdb="ZN ZNB5 500 " - pdb=" SG CYSB5 113 " pdb="ZN ZNB5 500 " - pdb=" SG CYSB5 126 " pdb="ZN ZNB5 500 " - pdb=" SG CYSB5 110 " pdb=" ZNB9 500 " pdb="ZN ZNB9 500 " - pdb=" SG CYSB9 76 " pdb="ZN ZNB9 500 " - pdb=" ND1 HISB9 95 " pdb="ZN ZNB9 500 " - pdb=" SG CYSB9 89 " pdb="ZN ZNB9 500 " - pdb=" SG CYSB9 73 " pdb=" ZNBx 500 " pdb="ZN ZNBx 500 " - pdb=" SG CYSBx 70 " pdb="ZN ZNBx 500 " - pdb=" SG CYSBx 73 " pdb="ZN ZNBx 500 " - pdb=" SG CYSBx 108 " pdb="ZN ZNBx 500 " - pdb=" SG CYSBJ 64 " Number of angles added : 15 19030 Ramachandran restraints generated. 9515 Oldfield, 0 Emsley, 9515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18218 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 324 helices and 92 sheets defined 42.7% alpha, 14.6% beta 423 base pairs and 771 stacking pairs defined. Time for finding SS restraints: 44.56 Creating SS restraints... Processing helix chain 'B0' and resid 110 through 120 Processing helix chain 'BY' and resid 28 through 36 Proline residue: BY 36 - end of helix Processing helix chain 'BY' and resid 116 through 121 removed outlier: 4.623A pdb=" N LYSBY 121 " --> pdb=" O HISBY 117 " (cutoff:3.500A) Processing helix chain 'BY' and resid 178 through 184 Processing helix chain 'BY' and resid 193 through 203 Processing helix chain 'Ba' and resid 47 through 52 removed outlier: 4.218A pdb=" N GLUBa 51 " --> pdb=" O ASPBa 47 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILEBa 52 " --> pdb=" O ARGBa 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ba' and resid 47 through 52' Processing helix chain 'Ba' and resid 116 through 125 Processing helix chain 'Ba' and resid 133 through 142 Processing helix chain 'Ba' and resid 149 through 163 Processing helix chain 'Ba' and resid 172 through 196 Proline residue: Ba 178 - end of helix removed outlier: 4.231A pdb=" N GLNBa 191 " --> pdb=" O LEUBa 187 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ILEBa 192 " --> pdb=" O CYSBa 188 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LEUBa 193 " --> pdb=" O LYSBa 189 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LYSBa 194 " --> pdb=" O SERBa 190 " (cutoff:3.500A) Proline residue: Ba 196 - end of helix Processing helix chain 'Ba' and resid 241 through 252 removed outlier: 3.758A pdb=" N LYSBa 249 " --> pdb=" O VALBa 245 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASNBa 250 " --> pdb=" O GLUBa 246 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N HISBa 251 " --> pdb=" O ALABa 247 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N VALBa 252 " --> pdb=" O THRBa 248 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 299 through 304 removed outlier: 5.005A pdb=" N PHEBa 304 " --> pdb=" O ARGBa 300 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 305 through 329 Processing helix chain 'Ba' and resid 407 through 420 removed outlier: 4.270A pdb=" N PHEBa 411 " --> pdb=" O GLNBa 407 " (cutoff:3.500A) Processing helix chain 'B8' and resid 107 through 114 removed outlier: 4.087A pdb=" N ILEB8 111 " --> pdb=" O VALB8 107 " (cutoff:3.500A) Processing helix chain 'B8' and resid 132 through 137 removed outlier: 3.865A pdb=" N LYSB8 136 " --> pdb=" O LYSB8 132 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N THRB8 137 " --> pdb=" O LEUB8 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'B8' and resid 132 through 137' Processing helix chain 'B8' and resid 138 through 147 removed outlier: 5.669A pdb=" N PHEB8 147 " --> pdb=" O ARGB8 143 " (cutoff:3.500A) Processing helix chain 'B8' and resid 151 through 163 removed outlier: 4.899A pdb=" N THRB8 163 " --> pdb=" O ASPB8 159 " (cutoff:3.500A) Processing helix chain 'B8' and resid 177 through 182 removed outlier: 4.670A pdb=" N ASPB8 182 " --> pdb=" O GLNB8 178 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 44 through 49 removed outlier: 3.736A pdb=" N LEUBb 48 " --> pdb=" O ASPBb 44 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N LYSBb 49 " --> pdb=" O LEUBb 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bb' and resid 44 through 49' Processing helix chain 'Bb' and resid 53 through 67 removed outlier: 3.642A pdb=" N ARGBb 66 " --> pdb=" O GLUBb 62 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYSBb 67 " --> pdb=" O GLNBb 63 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 73 through 79 removed outlier: 3.609A pdb=" N HISBb 77 " --> pdb=" O THRBb 73 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 98 through 116 removed outlier: 3.990A pdb=" N ASNBb 116 " --> pdb=" O GLUBb 112 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 117 through 126 Processing helix chain 'Bb' and resid 131 through 143 Processing helix chain 'Bb' and resid 144 through 156 Processing helix chain 'Bb' and resid 157 through 162 Processing helix chain 'Bb' and resid 194 through 199 Processing helix chain 'Bb' and resid 244 through 249 removed outlier: 3.600A pdb=" N GLYBb 248 " --> pdb=" O ARGBb 244 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N GLNBb 249 " --> pdb=" O VALBb 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bb' and resid 244 through 249' Processing helix chain 'Bb' and resid 281 through 286 removed outlier: 5.281A pdb=" N THRBb 285 " --> pdb=" O PHEBb 281 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ARGBb 286 " --> pdb=" O SERBb 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bb' and resid 281 through 286' Processing helix chain 'Bb' and resid 292 through 297 removed outlier: 3.710A pdb=" N THRBb 297 " --> pdb=" O LEUBb 293 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 299 through 308 Processing helix chain 'Bb' and resid 324 through 333 removed outlier: 4.344A pdb=" N THRBb 328 " --> pdb=" O ASPBb 324 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ARGBb 329 " --> pdb=" O ASPBb 325 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 364 through 370 removed outlier: 3.613A pdb=" N ARGBb 368 " --> pdb=" O ARGBb 364 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N TYRBb 369 " --> pdb=" O TYRBb 365 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARGBb 370 " --> pdb=" O LEUBb 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bb' and resid 364 through 370' Processing helix chain 'Bc' and resid 33 through 57 removed outlier: 4.096A pdb=" N THRBc 56 " --> pdb=" O GLNBc 52 " (cutoff:3.500A) Proline residue: Bc 57 - end of helix Processing helix chain 'Bc' and resid 84 through 93 Processing helix chain 'Bc' and resid 94 through 100 Processing helix chain 'Bc' and resid 132 through 155 removed outlier: 3.988A pdb=" N PHEBc 155 " --> pdb=" O ILEBc 151 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 183 through 188 removed outlier: 3.891A pdb=" N ASPBc 187 " --> pdb=" O ASPBc 183 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLUBc 188 " --> pdb=" O LYSBc 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bc' and resid 183 through 188' Processing helix chain 'Bc' and resid 192 through 210 removed outlier: 3.566A pdb=" N LYSBc 209 " --> pdb=" O ALABc 205 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ASPBc 210 " --> pdb=" O LEUBc 206 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 219 through 228 removed outlier: 3.893A pdb=" N GLUBc 225 " --> pdb=" O LYSBc 221 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 230 through 245 removed outlier: 3.875A pdb=" N GLNBc 243 " --> pdb=" O GLUBc 239 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASNBc 244 " --> pdb=" O LYSBc 240 " (cutoff:3.500A) Proline residue: Bc 245 - end of helix Processing helix chain 'Bc' and resid 305 through 318 removed outlier: 4.040A pdb=" N LYSBc 318 " --> pdb=" O GLUBc 314 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 268 through 273 removed outlier: 3.627A pdb=" N ILEBc 271 " --> pdb=" O ARGBc 268 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N PHEBc 273 " --> pdb=" O SERBc 270 " (cutoff:3.500A) Processing helix chain 'Bd' and resid 17 through 35 removed outlier: 5.401A pdb=" N SERBd 35 " --> pdb=" O LEUBd 31 " (cutoff:3.500A) Processing helix chain 'Bd' and resid 41 through 46 removed outlier: 3.875A pdb=" N ILEBd 45 " --> pdb=" O ILEBd 41 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N THRBd 46 " --> pdb=" O GLUBd 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bd' and resid 41 through 46' Processing helix chain 'Bd' and resid 47 through 52 removed outlier: 4.521A pdb=" N LEUBd 51 " --> pdb=" O PROBd 47 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ASNBd 52 " --> pdb=" O VALBd 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bd' and resid 47 through 52' Processing helix chain 'Bd' and resid 63 through 110 Processing helix chain 'Bd' and resid 111 through 119 removed outlier: 4.375A pdb=" N LYSBd 119 " --> pdb=" O ALABd 115 " (cutoff:3.500A) Processing helix chain 'Bd' and resid 121 through 126 removed outlier: 3.759A pdb=" N LEUBd 124 " --> pdb=" O ASPBd 121 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N PHEBd 125 " --> pdb=" O PROBd 122 " (cutoff:3.500A) Proline residue: Bd 126 - end of helix No H-bonds generated for 'chain 'Bd' and resid 121 through 126' Processing helix chain 'Be' and resid 22 through 27 removed outlier: 4.387A pdb=" N GLYBe 26 " --> pdb=" O THRBe 22 " (cutoff:3.500A) Proline residue: Be 27 - end of helix No H-bonds generated for 'chain 'Be' and resid 22 through 27' Processing helix chain 'Be' and resid 51 through 56 removed outlier: 3.577A pdb=" N ILEBe 55 " --> pdb=" O ILEBe 51 " (cutoff:3.500A) Proline residue: Be 56 - end of helix No H-bonds generated for 'chain 'Be' and resid 51 through 56' Processing helix chain 'Be' and resid 85 through 94 Processing helix chain 'Be' and resid 95 through 105 Processing helix chain 'Bf' and resid 68 through 73 removed outlier: 4.036A pdb=" N THRBf 72 " --> pdb=" O PROBf 68 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LYSBf 73 " --> pdb=" O TYRBf 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bf' and resid 68 through 73' Processing helix chain 'Bf' and resid 88 through 99 removed outlier: 4.473A pdb=" N LYSBf 99 " --> pdb=" O ARGBf 95 " (cutoff:3.500A) Processing helix chain 'Bf' and resid 104 through 117 Processing helix chain 'Bf' and resid 119 through 124 removed outlier: 4.715A pdb=" N TRPBf 123 " --> pdb=" O THRBf 119 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N TYRBf 124 " --> pdb=" O LYSBf 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bf' and resid 119 through 124' Processing helix chain 'Bf' and resid 127 through 134 removed outlier: 3.831A pdb=" N ARGBf 133 " --> pdb=" O TYRBf 129 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARGBf 134 " --> pdb=" O HISBf 130 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 16 through 21 removed outlier: 4.668A pdb=" N GLYBg 20 " --> pdb=" O HISBg 16 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ARGBg 21 " --> pdb=" O ASNBg 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bg' and resid 16 through 21' Processing helix chain 'Bg' and resid 37 through 50 removed outlier: 3.935A pdb=" N ARGBg 41 " --> pdb=" O ALABg 37 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N GLYBg 42 " --> pdb=" O PROBg 38 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ALABg 43 " --> pdb=" O SERBg 39 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 51 through 59 Proline residue: Bg 59 - end of helix Processing helix chain 'Bg' and resid 93 through 107 Processing helix chain 'Bg' and resid 131 through 137 removed outlier: 4.615A pdb=" N ASNBg 135 " --> pdb=" O HISBg 131 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LYSBg 136 " --> pdb=" O PROBg 132 " (cutoff:3.500A) Proline residue: Bg 137 - end of helix No H-bonds generated for 'chain 'Bg' and resid 131 through 137' Processing helix chain 'Bh' and resid 34 through 54 removed outlier: 4.862A pdb=" N ALABh 38 " --> pdb=" O GLYBh 34 " (cutoff:3.500A) Proline residue: Bh 54 - end of helix Processing helix chain 'Bh' and resid 59 through 64 Proline residue: Bh 64 - end of helix Processing helix chain 'Bh' and resid 67 through 80 removed outlier: 3.840A pdb=" N LEUBh 79 " --> pdb=" O PHEBh 75 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLNBh 80 " --> pdb=" O GLYBh 76 " (cutoff:3.500A) Processing helix chain 'Bh' and resid 84 through 94 removed outlier: 3.716A pdb=" N VALBh 93 " --> pdb=" O LYSBh 89 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ASNBh 94 " --> pdb=" O THRBh 90 " (cutoff:3.500A) Processing helix chain 'Bh' and resid 95 through 109 Processing helix chain 'Bh' and resid 114 through 119 removed outlier: 5.300A pdb=" N ASNBh 118 " --> pdb=" O ALABh 114 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEUBh 119 " --> pdb=" O ALABh 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bh' and resid 114 through 119' Processing helix chain 'Bh' and resid 122 through 145 Processing helix chain 'Bh' and resid 149 through 162 Processing helix chain 'Bh' and resid 163 through 174 Processing helix chain 'Bh' and resid 187 through 206 Processing helix chain 'Bh' and resid 207 through 223 removed outlier: 3.649A pdb=" N ILEBh 220 " --> pdb=" O ARGBh 216 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N THRBh 221 " --> pdb=" O ASPBh 217 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N GLNBh 222 " --> pdb=" O PHEBh 218 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N METBh 223 " --> pdb=" O LEUBh 219 " (cutoff:3.500A) Processing helix chain 'Bh' and resid 227 through 233 removed outlier: 4.097A pdb=" N METBh 231 " --> pdb=" O GLUBh 227 " (cutoff:3.500A) Processing helix chain 'Bh' and resid 236 through 249 Processing helix chain 'Bh' and resid 288 through 306 Processing helix chain 'Bi' and resid 48 through 54 removed outlier: 4.641A pdb=" N SERBi 52 " --> pdb=" O PROBi 48 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLUBi 53 " --> pdb=" O LYSBi 49 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LYSBi 54 " --> pdb=" O TYRBi 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bi' and resid 48 through 54' Processing helix chain 'Bi' and resid 65 through 72 removed outlier: 4.364A pdb=" N LEUBi 72 " --> pdb=" O PROBi 68 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 93 through 101 removed outlier: 5.008A pdb=" N ILEBi 97 " --> pdb=" O GLYBi 93 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SERBi 99 " --> pdb=" O ALABi 95 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N LEUBi 100 " --> pdb=" O ARGBi 96 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N SERBi 101 " --> pdb=" O ILEBi 97 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 102 through 115 removed outlier: 4.381A pdb=" N GLNBi 107 " --> pdb=" O GLUBi 103 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASNBi 115 " --> pdb=" O ARGBi 111 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 116 through 130 Proline residue: Bi 130 - end of helix Processing helix chain 'Bi' and resid 133 through 155 removed outlier: 3.564A pdb=" N PHEBi 137 " --> pdb=" O LYSBi 133 " (cutoff:3.500A) Proline residue: Bi 138 - end of helix Processing helix chain 'Bi' and resid 156 through 164 Processing helix chain 'Bi' and resid 165 through 177 Proline residue: Bi 170 - end of helix removed outlier: 5.644A pdb=" N ASPBi 175 " --> pdb=" O ASPBi 171 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ILEBi 176 " --> pdb=" O METBi 172 " (cutoff:3.500A) Processing helix chain 'Bj' and resid 64 through 82 Processing helix chain 'Bj' and resid 85 through 104 removed outlier: 3.726A pdb=" N SERBj 103 " --> pdb=" O ALABj 99 " (cutoff:3.500A) Processing helix chain 'Bj' and resid 116 through 132 removed outlier: 5.162A pdb=" N LYSBj 132 " --> pdb=" O PHEBj 128 " (cutoff:3.500A) Processing helix chain 'Bj' and resid 137 through 143 removed outlier: 5.757A pdb=" N ASPBj 141 " --> pdb=" O LEUBj 137 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LYSBj 142 " --> pdb=" O THRBj 138 " (cutoff:3.500A) Processing helix chain 'Bj' and resid 183 through 195 Processing helix chain 'Bj' and resid 256 through 264 Processing helix chain 'Bj' and resid 266 through 277 removed outlier: 3.634A pdb=" N GLNBj 271 " --> pdb=" O LYSBj 267 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VALBj 272 " --> pdb=" O TYRBj 268 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ARGBj 273 " --> pdb=" O LEUBj 269 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ARGBj 274 " --> pdb=" O ALABj 270 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHEBj 275 " --> pdb=" O GLNBj 271 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LEUBj 277 " --> pdb=" O ARGBj 273 " (cutoff:3.500A) Processing helix chain 'Bk' and resid 59 through 64 removed outlier: 3.647A pdb=" N VALBk 63 " --> pdb=" O TYRBk 59 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LYSBk 64 " --> pdb=" O LYSBk 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bk' and resid 59 through 64' Processing helix chain 'Bk' and resid 99 through 118 Processing helix chain 'Bk' and resid 163 through 178 Processing helix chain 'Bk' and resid 190 through 199 removed outlier: 4.049A pdb=" N ARGBk 197 " --> pdb=" O ASPBk 193 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N PHEBk 198 " --> pdb=" O PHEBk 194 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N LYSBk 199 " --> pdb=" O LYSBk 195 " (cutoff:3.500A) Processing helix chain 'Bk' and resid 201 through 212 Processing helix chain 'Bl' and resid 44 through 52 removed outlier: 4.454A pdb=" N VALBl 48 " --> pdb=" O GLUBl 44 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLUBl 49 " --> pdb=" O TYRBl 45 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ARGBl 50 " --> pdb=" O HISBl 46 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEUBl 51 " --> pdb=" O PHEBl 47 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEUBl 52 " --> pdb=" O VALBl 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bl' and resid 44 through 52' Processing helix chain 'Bl' and resid 116 through 132 Proline residue: Bl 130 - end of helix Processing helix chain 'Bl' and resid 153 through 165 Processing helix chain 'Bm' and resid 66 through 80 Processing helix chain 'Bm' and resid 94 through 110 Processing helix chain 'Bm' and resid 114 through 121 removed outlier: 4.921A pdb=" N HISBm 119 " --> pdb=" O ASNBm 115 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLNBm 120 " --> pdb=" O SERBm 116 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 123 through 133 removed outlier: 3.969A pdb=" N VALBm 133 " --> pdb=" O ASPBm 129 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 139 through 148 removed outlier: 4.572A pdb=" N ASNBm 148 " --> pdb=" O LEUBm 144 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 48 through 54 Processing helix chain 'Bn' and resid 59 through 64 Processing helix chain 'Bn' and resid 69 through 74 removed outlier: 4.409A pdb=" N LEUBn 73 " --> pdb=" O HISBn 69 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILEBn 74 " --> pdb=" O PROBn 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bn' and resid 69 through 74' Processing helix chain 'Bn' and resid 86 through 98 Processing helix chain 'Bn' and resid 103 through 123 Processing helix chain 'Bo' and resid 24 through 32 Processing helix chain 'Bo' and resid 41 through 46 removed outlier: 3.588A pdb=" N LEUBo 46 " --> pdb=" O PROBo 42 " (cutoff:3.500A) Processing helix chain 'Bo' and resid 60 through 108 removed outlier: 3.590A pdb=" N GLNBo 106 " --> pdb=" O GLUBo 102 " (cutoff:3.500A) Processing helix chain 'Bo' and resid 114 through 119 removed outlier: 4.966A pdb=" N GLNBo 118 " --> pdb=" O GLYBo 114 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASNBo 119 " --> pdb=" O ALABo 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bo' and resid 114 through 119' Processing helix chain 'Bp' and resid 2 through 9 removed outlier: 3.588A pdb=" N LEUBp 8 " --> pdb=" O ALABp 4 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLYBp 9 " --> pdb=" O LEUBp 5 " (cutoff:3.500A) Processing helix chain 'Bp' and resid 27 through 39 removed outlier: 3.651A pdb=" N SERBp 39 " --> pdb=" O GLNBp 35 " (cutoff:3.500A) Processing helix chain 'Bp' and resid 40 through 47 removed outlier: 3.680A pdb=" N ASNBp 46 " --> pdb=" O VALBp 42 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEUBp 47 " --> pdb=" O ARGBp 43 " (cutoff:3.500A) Processing helix chain 'Bp' and resid 82 through 98 removed outlier: 4.198A pdb=" N GLYBp 98 " --> pdb=" O ILEBp 94 " (cutoff:3.500A) Processing helix chain 'Bq' and resid 66 through 71 Processing helix chain 'Bq' and resid 88 through 93 Proline residue: Bq 93 - end of helix Processing helix chain 'Bq' and resid 94 through 99 removed outlier: 4.114A pdb=" N GLUBq 98 " --> pdb=" O GLUBq 94 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N METBq 99 " --> pdb=" O TRPBq 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bq' and resid 94 through 99' Processing helix chain 'Bq' and resid 106 through 111 removed outlier: 5.420A pdb=" N ASPBq 111 " --> pdb=" O LEUBq 107 " (cutoff:3.500A) Processing helix chain 'Bq' and resid 114 through 134 removed outlier: 3.655A pdb=" N TRPBq 118 " --> pdb=" O THRBq 114 " (cutoff:3.500A) Processing helix chain 'Bt' and resid 28 through 51 removed outlier: 3.801A pdb=" N SERBt 50 " --> pdb=" O GLNBt 46 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ARGBt 51 " --> pdb=" O TYRBt 47 " (cutoff:3.500A) Processing helix chain 'Bt' and resid 55 through 60 removed outlier: 3.551A pdb=" N ARGBt 60 " --> pdb=" O ALABt 56 " (cutoff:3.500A) Processing helix chain 'Bt' and resid 63 through 81 removed outlier: 4.547A pdb=" N ARGBt 67 " --> pdb=" O ALABt 63 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ARGBt 81 " --> pdb=" O ALABt 77 " (cutoff:3.500A) Processing helix chain 'Bt' and resid 87 through 97 removed outlier: 3.648A pdb=" N GLNBt 91 " --> pdb=" O ARGBt 87 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N HISBt 94 " --> pdb=" O GLUBt 90 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LEUBt 95 " --> pdb=" O GLNBt 91 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEUBt 96 " --> pdb=" O LEUBt 92 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N VALBt 97 " --> pdb=" O GLYBt 93 " (cutoff:3.500A) Processing helix chain 'Bu' and resid 44 through 50 Proline residue: Bu 50 - end of helix Processing helix chain 'Bu' and resid 62 through 67 removed outlier: 3.816A pdb=" N LYSBu 66 " --> pdb=" O PROBu 62 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLNBu 67 " --> pdb=" O ASPBu 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bu' and resid 62 through 67' Processing helix chain 'Bu' and resid 72 through 77 removed outlier: 3.710A pdb=" N LEUBu 76 " --> pdb=" O PROBu 72 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N THRBu 77 " --> pdb=" O VALBu 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bu' and resid 72 through 77' Processing helix chain 'Bu' and resid 111 through 122 Processing helix chain 'Bu' and resid 141 through 163 Proline residue: Bu 163 - end of helix Processing helix chain 'Bu' and resid 173 through 189 removed outlier: 4.387A pdb=" N SERBu 177 " --> pdb=" O GLUBu 173 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEUBu 187 " --> pdb=" O ASNBu 183 " (cutoff:3.500A) Processing helix chain 'Bv' and resid 48 through 53 removed outlier: 3.751A pdb=" N LEUBv 52 " --> pdb=" O PROBv 48 " (cutoff:3.500A) Processing helix chain 'Bv' and resid 54 through 64 Processing helix chain 'Bv' and resid 71 through 76 removed outlier: 4.558A pdb=" N LEUBv 75 " --> pdb=" O ALABv 71 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N TRPBv 76 " --> pdb=" O ALABv 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bv' and resid 71 through 76' Processing helix chain 'Bv' and resid 78 through 93 Processing helix chain 'Bv' and resid 95 through 159 removed outlier: 3.792A pdb=" N LYSBv 127 " --> pdb=" O GLUBv 123 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N METBv 128 " --> pdb=" O CYSBv 124 " (cutoff:3.500A) Proline residue: Bv 129 - end of helix Processing helix chain 'Bw' and resid 55 through 73 Processing helix chain 'Bw' and resid 75 through 85 Processing helix chain 'Bw' and resid 101 through 111 removed outlier: 4.232A pdb=" N TRPBw 105 " --> pdb=" O ASNBw 101 " (cutoff:3.500A) Processing helix chain 'Bw' and resid 132 through 149 Processing helix chain 'Bw' and resid 164 through 187 Proline residue: Bw 169 - end of helix removed outlier: 4.603A pdb=" N VALBw 184 " --> pdb=" O GLYBw 180 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N HISBw 185 " --> pdb=" O LEUBw 181 " (cutoff:3.500A) Proline residue: Bw 187 - end of helix Processing helix chain 'Bw' and resid 261 through 266 removed outlier: 4.545A pdb=" N LEUBw 265 " --> pdb=" O LYSBw 261 " (cutoff:3.500A) Proline residue: Bw 266 - end of helix No H-bonds generated for 'chain 'Bw' and resid 261 through 266' Processing helix chain 'Bw' and resid 301 through 309 Processing helix chain 'Bw' and resid 312 through 338 removed outlier: 3.867A pdb=" N VALBw 316 " --> pdb=" O ASPBw 312 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N PHEBw 318 " --> pdb=" O ILEBw 314 " (cutoff:3.500A) Processing helix chain 'Bw' and resid 374 through 379 removed outlier: 3.790A pdb=" N GLNBw 379 " --> pdb=" O ALABw 375 " (cutoff:3.500A) Processing helix chain 'Bw' and resid 408 through 421 removed outlier: 4.007A pdb=" N LEUBw 412 " --> pdb=" O ASNBw 408 " (cutoff:3.500A) Processing helix chain 'Bx' and resid 70 through 76 Processing helix chain 'Bx' and resid 85 through 93 removed outlier: 4.365A pdb=" N GLNBx 91 " --> pdb=" O LEUBx 87 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHEBx 92 " --> pdb=" O LEUBx 88 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILEBx 93 " --> pdb=" O LEUBx 89 " (cutoff:3.500A) Processing helix chain 'Bx' and resid 101 through 106 Processing helix chain 'Bx' and resid 108 through 126 Processing helix chain 'Bx' and resid 135 through 142 removed outlier: 3.803A pdb=" N VALBx 140 " --> pdb=" O PROBx 136 " (cutoff:3.500A) Proline residue: Bx 141 - end of helix Processing helix chain 'Bx' and resid 178 through 183 removed outlier: 4.206A pdb=" N LYSBx 182 " --> pdb=" O SERBx 178 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ASPBx 183 " --> pdb=" O PROBx 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bx' and resid 178 through 183' Processing helix chain 'CL' and resid 61 through 74 removed outlier: 4.168A pdb=" N GLNCL 65 " --> pdb=" O PROCL 61 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEUCL 74 " --> pdb=" O ASPCL 70 " (cutoff:3.500A) Processing helix chain 'CL' and resid 75 through 90 Processing helix chain 'B1' and resid 7 through 19 removed outlier: 3.693A pdb=" N TRPB1 11 " --> pdb=" O PROB1 7 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LYSB1 12 " --> pdb=" O VALB1 8 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N GLNB1 13 " --> pdb=" O GLYB1 9 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLYB1 19 " --> pdb=" O ARGB1 15 " (cutoff:3.500A) Processing helix chain 'B1' and resid 25 through 35 removed outlier: 5.647A pdb=" N ALAB1 35 " --> pdb=" O SERB1 31 " (cutoff:3.500A) Processing helix chain 'B1' and resid 72 through 79 removed outlier: 4.237A pdb=" N GLNB1 76 " --> pdb=" O PROB1 72 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEUB1 77 " --> pdb=" O PROB1 73 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLYB1 78 " --> pdb=" O GLUB1 74 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LEUB1 79 " --> pdb=" O SERB1 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'B1' and resid 72 through 79' Processing helix chain 'B1' and resid 128 through 139 Processing helix chain 'B1' and resid 140 through 148 Processing helix chain 'B1' and resid 149 through 154 Processing helix chain 'B1' and resid 155 through 172 Processing helix chain 'B1' and resid 180 through 192 removed outlier: 3.556A pdb=" N ARGB1 190 " --> pdb=" O ALAB1 186 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYRB1 191 " --> pdb=" O ILEB1 187 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYSB1 192 " --> pdb=" O TYRB1 188 " (cutoff:3.500A) Processing helix chain 'B1' and resid 197 through 202 removed outlier: 3.882A pdb=" N GLUB1 202 " --> pdb=" O GLUB1 198 " (cutoff:3.500A) Processing helix chain 'B1' and resid 207 through 220 Processing helix chain 'B1' and resid 225 through 245 removed outlier: 3.750A pdb=" N ILEB1 229 " --> pdb=" O PROB1 225 " (cutoff:3.500A) Processing helix chain 'DL' and resid 64 through 74 removed outlier: 3.881A pdb=" N VALDL 68 " --> pdb=" O ILEDL 64 " (cutoff:3.500A) Processing helix chain 'DL' and resid 75 through 90 removed outlier: 3.531A pdb=" N ILEDL 79 " --> pdb=" O THRDL 75 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYSDL 88 " --> pdb=" O GLUDL 84 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THRDL 89 " --> pdb=" O LEUDL 85 " (cutoff:3.500A) Processing helix chain 'FL' and resid 64 through 74 removed outlier: 3.919A pdb=" N VALFL 68 " --> pdb=" O ILEFL 64 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILEFL 71 " --> pdb=" O LEUFL 67 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SERFL 73 " --> pdb=" O GLNFL 69 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LEUFL 74 " --> pdb=" O ASPFL 70 " (cutoff:3.500A) Processing helix chain 'FL' and resid 75 through 90 Processing helix chain 'GL' and resid 64 through 74 removed outlier: 3.752A pdb=" N VALGL 68 " --> pdb=" O ILEGL 64 " (cutoff:3.500A) Processing helix chain 'GL' and resid 75 through 90 Processing helix chain 'EL' and resid 64 through 75 removed outlier: 3.552A pdb=" N LEUEL 74 " --> pdb=" O ASPEL 70 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N THREL 75 " --> pdb=" O ILEEL 71 " (cutoff:3.500A) Processing helix chain 'EL' and resid 76 through 91 Processing helix chain 'HL' and resid 64 through 75 removed outlier: 4.336A pdb=" N VALHL 68 " --> pdb=" O ILEHL 64 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N THRHL 75 " --> pdb=" O ILEHL 71 " (cutoff:3.500A) Processing helix chain 'HL' and resid 76 through 89 removed outlier: 3.620A pdb=" N LYSHL 88 " --> pdb=" O GLUHL 84 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THRHL 89 " --> pdb=" O LEUHL 85 " (cutoff:3.500A) Processing helix chain 'B2' and resid 72 through 77 removed outlier: 3.668A pdb=" N TRPB2 76 " --> pdb=" O ASPB2 72 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N GLYB2 77 " --> pdb=" O PROB2 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'B2' and resid 72 through 77' Processing helix chain 'B2' and resid 88 through 96 removed outlier: 3.569A pdb=" N LYSB2 95 " --> pdb=" O GLNB2 91 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N SERB2 96 " --> pdb=" O LEUB2 92 " (cutoff:3.500A) Processing helix chain 'B2' and resid 97 through 125 removed outlier: 3.700A pdb=" N TYRB2 105 " --> pdb=" O HISB2 101 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLUB2 110 " --> pdb=" O VALB2 106 " (cutoff:3.500A) Processing helix chain 'B2' and resid 131 through 160 removed outlier: 3.979A pdb=" N GLUB2 135 " --> pdb=" O PROB2 131 " (cutoff:3.500A) Processing helix chain 'B2' and resid 193 through 200 removed outlier: 3.844A pdb=" N ARGB2 198 " --> pdb=" O LYSB2 194 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYSB2 199 " --> pdb=" O LYSB2 195 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ARGB2 200 " --> pdb=" O TYRB2 196 " (cutoff:3.500A) Processing helix chain 'B2' and resid 204 through 241 removed outlier: 4.372A pdb=" N GLUB2 208 " --> pdb=" O METB2 204 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ARGB2 209 " --> pdb=" O PROB2 205 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N PHEB2 210 " --> pdb=" O TYRB2 206 " (cutoff:3.500A) Proline residue: B2 241 - end of helix Processing helix chain 'B2' and resid 65 through 70 removed outlier: 3.507A pdb=" N GLUB2 68 " --> pdb=" O GLYB2 65 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHEB2 69 " --> pdb=" O LEUB2 66 " (cutoff:3.500A) Processing helix chain 'B3' and resid 42 through 48 removed outlier: 4.349A pdb=" N PHEB3 46 " --> pdb=" O PROB3 42 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLNB3 47 " --> pdb=" O ASPB3 43 " (cutoff:3.500A) Proline residue: B3 48 - end of helix No H-bonds generated for 'chain 'B3' and resid 42 through 48' Processing helix chain 'B3' and resid 49 through 57 removed outlier: 3.729A pdb=" N HISB3 53 " --> pdb=" O SERB3 49 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLUB3 54 " --> pdb=" O PROB3 50 " (cutoff:3.500A) Processing helix chain 'B3' and resid 79 through 90 removed outlier: 3.505A pdb=" N GLYB3 90 " --> pdb=" O ILEB3 86 " (cutoff:3.500A) Processing helix chain 'B3' and resid 103 through 114 removed outlier: 4.197A pdb=" N LYSB3 109 " --> pdb=" O SERB3 105 " (cutoff:3.500A) Processing helix chain 'B4' and resid 85 through 96 Processing helix chain 'B5' and resid 86 through 96 removed outlier: 4.007A pdb=" N ASNB5 96 " --> pdb=" O CYSB5 92 " (cutoff:3.500A) Processing helix chain 'B5' and resid 123 through 146 removed outlier: 3.775A pdb=" N GLUB5 145 " --> pdb=" O METB5 141 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N GLYB5 146 " --> pdb=" O GLYB5 142 " (cutoff:3.500A) Processing helix chain 'B7' and resid 59 through 67 Processing helix chain 'B7' and resid 68 through 76 removed outlier: 4.193A pdb=" N THRB7 75 " --> pdb=" O ARGB7 71 " (cutoff:3.500A) Proline residue: B7 76 - end of helix Processing helix chain 'B7' and resid 77 through 89 Processing helix chain 'BC' and resid 82 through 95 Processing helix chain 'BC' and resid 113 through 120 Processing helix chain 'BC' and resid 148 through 159 removed outlier: 3.982A pdb=" N LEUBC 159 " --> pdb=" O CYSBC 155 " (cutoff:3.500A) Processing helix chain 'BC' and resid 173 through 187 removed outlier: 3.522A pdb=" N LEUBC 177 " --> pdb=" O GLUBC 173 " (cutoff:3.500A) Processing helix chain 'BC' and resid 203 through 214 Processing helix chain 'BC' and resid 259 through 265 removed outlier: 4.792A pdb=" N GLUBC 263 " --> pdb=" O LYSBC 259 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N METBC 264 " --> pdb=" O PROBC 260 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASNBC 265 " --> pdb=" O LEUBC 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'BC' and resid 259 through 265' Processing helix chain 'BC' and resid 266 through 288 Processing helix chain 'BC' and resid 289 through 298 Processing helix chain 'BC' and resid 309 through 322 removed outlier: 3.890A pdb=" N GLNBC 322 " --> pdb=" O VALBC 318 " (cutoff:3.500A) Processing helix chain 'BC' and resid 337 through 348 Processing helix chain 'BC' and resid 357 through 363 Processing helix chain 'BC' and resid 498 through 517 Proline residue: BC 503 - end of helix Proline residue: BC 517 - end of helix Processing helix chain 'BC' and resid 536 through 550 Processing helix chain 'BC' and resid 600 through 605 Proline residue: BC 605 - end of helix Processing helix chain 'BC' and resid 621 through 638 removed outlier: 3.983A pdb=" N GLNBC 637 " --> pdb=" O SERBC 633 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N GLYBC 638 " --> pdb=" O ALABC 634 " (cutoff:3.500A) Processing helix chain 'BC' and resid 662 through 682 removed outlier: 3.542A pdb=" N ALABC 681 " --> pdb=" O ALABC 677 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ASPBC 682 " --> pdb=" O LEUBC 678 " (cutoff:3.500A) Processing helix chain 'BC' and resid 697 through 712 removed outlier: 3.728A pdb=" N LEUBC 701 " --> pdb=" O ALABC 697 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N SERBC 702 " --> pdb=" O ARGBC 698 " (cutoff:3.500A) Proline residue: BC 703 - end of helix Processing helix chain 'BC' and resid 732 through 737 removed outlier: 3.777A pdb=" N ILEBC 736 " --> pdb=" O PROBC 732 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N METBC 737 " --> pdb=" O LEUBC 733 " (cutoff:3.500A) No H-bonds generated for 'chain 'BC' and resid 732 through 737' Processing helix chain 'BC' and resid 738 through 748 removed outlier: 3.677A pdb=" N VALBC 742 " --> pdb=" O GLYBC 738 " (cutoff:3.500A) Processing helix chain 'BC' and resid 764 through 777 Processing helix chain 'BD' and resid 184 through 189 removed outlier: 3.872A pdb=" N LEUBD 188 " --> pdb=" O PROBD 184 " (cutoff:3.500A) Proline residue: BD 189 - end of helix No H-bonds generated for 'chain 'BD' and resid 184 through 189' Processing helix chain 'BD' and resid 260 through 268 removed outlier: 4.096A pdb=" N ASNBD 264 " --> pdb=" O LYSBD 260 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARGBD 265 " --> pdb=" O ALABD 261 " (cutoff:3.500A) Processing helix chain 'BG' and resid 75 through 80 removed outlier: 6.573A pdb=" N VALBG 79 " --> pdb=" O ASNBG 75 " (cutoff:3.500A) Processing helix chain 'BG' and resid 84 through 106 Processing helix chain 'BG' and resid 112 through 118 removed outlier: 3.557A pdb=" N LEUBG 116 " --> pdb=" O SERBG 112 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASPBG 117 " --> pdb=" O PROBG 113 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LYSBG 118 " --> pdb=" O GLYBG 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'BG' and resid 112 through 118' Processing helix chain 'BG' and resid 129 through 134 Processing helix chain 'BG' and resid 154 through 165 Processing helix chain 'BG' and resid 186 through 224 removed outlier: 5.020A pdb=" N ASPBG 224 " --> pdb=" O LYSBG 220 " (cutoff:3.500A) Processing helix chain 'BG' and resid 227 through 261 Processing helix chain 'BQ' and resid 69 through 74 removed outlier: 5.305A pdb=" N GLYBQ 74 " --> pdb=" O SERBQ 70 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 98 through 113 Processing helix chain 'BQ' and resid 170 through 184 removed outlier: 4.353A pdb=" N LEUBQ 178 " --> pdb=" O GLYBQ 174 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VALBQ 179 " --> pdb=" O PHEBQ 175 " (cutoff:3.500A) Proline residue: BQ 184 - end of helix Processing helix chain 'BQ' and resid 191 through 209 Processing helix chain 'BQ' and resid 214 through 222 Processing helix chain 'BQ' and resid 225 through 231 removed outlier: 4.687A pdb=" N VALBQ 229 " --> pdb=" O GLYBQ 225 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N SERBQ 231 " --> pdb=" O ARGBQ 227 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 232 through 238 removed outlier: 4.748A pdb=" N THRBQ 236 " --> pdb=" O PROBQ 232 " (cutoff:3.500A) Processing helix chain 'LL' and resid 141 through 154 removed outlier: 3.839A pdb=" N ILELL 146 " --> pdb=" O LYSLL 142 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYSLL 147 " --> pdb=" O VALLL 143 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLULL 148 " --> pdb=" O LYSLL 144 " (cutoff:3.500A) Processing helix chain 'LL' and resid 157 through 168 removed outlier: 3.951A pdb=" N LEULL 168 " --> pdb=" O LEULL 164 " (cutoff:3.500A) Processing helix chain 'LL' and resid 177 through 192 removed outlier: 3.727A pdb=" N VALLL 191 " --> pdb=" O ALALL 187 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLYLL 192 " --> pdb=" O LEULL 188 " (cutoff:3.500A) Processing helix chain 'BE' and resid 48 through 54 removed outlier: 4.790A pdb=" N HISBE 52 " --> pdb=" O TRPBE 48 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LEUBE 53 " --> pdb=" O TRPBE 49 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N SERBE 54 " --> pdb=" O ASPBE 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'BE' and resid 48 through 54' Processing helix chain 'BE' and resid 55 through 83 Proline residue: BE 59 - end of helix removed outlier: 3.736A pdb=" N LYSBE 76 " --> pdb=" O GLNBE 72 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEUBE 77 " --> pdb=" O LEUBE 73 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N CYSBE 78 " --> pdb=" O ALABE 74 " (cutoff:3.500A) Proline residue: BE 79 - end of helix removed outlier: 4.199A pdb=" N ASPBE 82 " --> pdb=" O CYSBE 78 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLUBE 83 " --> pdb=" O PROBE 79 " (cutoff:3.500A) Processing helix chain 'BE' and resid 134 through 139 Processing helix chain 'BE' and resid 158 through 169 Processing helix chain 'BE' and resid 194 through 199 removed outlier: 4.917A pdb=" N PHEBE 198 " --> pdb=" O TYRBE 194 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ARGBE 199 " --> pdb=" O ALABE 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'BE' and resid 194 through 199' Processing helix chain 'BE' and resid 217 through 222 Processing helix chain 'BE' and resid 310 through 315 removed outlier: 4.115A pdb=" N LEUBE 314 " --> pdb=" O PHEBE 310 " (cutoff:3.500A) Proline residue: BE 315 - end of helix No H-bonds generated for 'chain 'BE' and resid 310 through 315' Processing helix chain 'BE' and resid 320 through 325 removed outlier: 3.953A pdb=" N ASPBE 324 " --> pdb=" O PHEBE 320 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLUBE 325 " --> pdb=" O PROBE 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'BE' and resid 320 through 325' Processing helix chain 'BF' and resid 92 through 109 removed outlier: 4.818A pdb=" N LYSBF 107 " --> pdb=" O GLNBF 103 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ARGBF 108 " --> pdb=" O LYSBF 104 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ILEBF 109 " --> pdb=" O ASNBF 105 " (cutoff:3.500A) Processing helix chain 'BF' and resid 166 through 185 removed outlier: 3.684A pdb=" N ASPBF 185 " --> pdb=" O LYSBF 181 " (cutoff:3.500A) Processing helix chain 'BF' and resid 199 through 211 removed outlier: 3.608A pdb=" N LEUBF 203 " --> pdb=" O ASPBF 199 " (cutoff:3.500A) Processing helix chain 'BF' and resid 227 through 238 removed outlier: 3.951A pdb=" N GLYBF 236 " --> pdb=" O ALABF 232 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEUBF 237 " --> pdb=" O ALABF 233 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LYSBF 238 " --> pdb=" O THRBF 234 " (cutoff:3.500A) Processing helix chain 'BF' and resid 249 through 257 removed outlier: 5.070A pdb=" N GLNBF 257 " --> pdb=" O METBF 253 " (cutoff:3.500A) Processing helix chain 'BF' and resid 262 through 279 removed outlier: 3.553A pdb=" N TRPBF 275 " --> pdb=" O GLUBF 271 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N HISBF 276 " --> pdb=" O LYSBF 272 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ASNBF 277 " --> pdb=" O LEUBF 273 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N SERBF 278 " --> pdb=" O LEUBF 274 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARGBF 279 " --> pdb=" O TRPBF 275 " (cutoff:3.500A) Processing helix chain 'BF' and resid 84 through 89 Processing helix chain 'BI' and resid 74 through 79 removed outlier: 4.082A pdb=" N ARGBI 78 " --> pdb=" O HISBI 74 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VALBI 79 " --> pdb=" O ARGBI 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'BI' and resid 74 through 79' Processing helix chain 'BI' and resid 85 through 90 removed outlier: 4.020A pdb=" N ARGBI 89 " --> pdb=" O ASPBI 85 " (cutoff:3.500A) Proline residue: BI 90 - end of helix No H-bonds generated for 'chain 'BI' and resid 85 through 90' Processing helix chain 'BI' and resid 115 through 122 Processing helix chain 'BI' and resid 133 through 150 removed outlier: 3.647A pdb=" N LEUBI 139 " --> pdb=" O GLUBI 135 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 41 through 52 Processing helix chain 'BJ' and resid 76 through 92 Processing helix chain 'BJ' and resid 105 through 120 removed outlier: 3.662A pdb=" N HISBJ 119 " --> pdb=" O GLNBJ 115 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 127 through 139 Proline residue: BJ 133 - end of helix removed outlier: 4.662A pdb=" N LYSBJ 139 " --> pdb=" O LEUBJ 135 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 143 through 148 removed outlier: 3.728A pdb=" N PHEBJ 147 " --> pdb=" O LEUBJ 143 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VALBJ 148 " --> pdb=" O LEUBJ 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'BJ' and resid 143 through 148' Processing helix chain 'BJ' and resid 160 through 172 removed outlier: 3.668A pdb=" N METBJ 164 " --> pdb=" O LYSBJ 160 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLYBJ 170 " --> pdb=" O ARGBJ 166 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ILEBJ 171 " --> pdb=" O ILEBJ 167 " (cutoff:3.500A) Proline residue: BJ 172 - end of helix Processing helix chain 'BJ' and resid 187 through 198 Proline residue: BJ 198 - end of helix Processing helix chain 'BJ' and resid 199 through 225 removed outlier: 3.596A pdb=" N VALBJ 208 " --> pdb=" O GLNBJ 204 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEUBJ 214 " --> pdb=" O GLYBJ 210 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N THRBJ 215 " --> pdb=" O LEUBJ 211 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLNBJ 225 " --> pdb=" O METBJ 221 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 226 through 240 removed outlier: 3.649A pdb=" N GLNBJ 240 " --> pdb=" O TYRBJ 236 " (cutoff:3.500A) Processing helix chain 'BK' and resid 33 through 43 Proline residue: BK 37 - end of helix Processing helix chain 'BK' and resid 45 through 58 removed outlier: 3.789A pdb=" N PHEBK 49 " --> pdb=" O SERBK 45 " (cutoff:3.500A) Processing helix chain 'BK' and resid 86 through 96 Processing helix chain 'BK' and resid 113 through 125 Processing helix chain 'BK' and resid 127 through 134 removed outlier: 4.156A pdb=" N ASPBK 134 " --> pdb=" O PHEBK 130 " (cutoff:3.500A) Processing helix chain 'BK' and resid 136 through 152 removed outlier: 3.852A pdb=" N VALBK 140 " --> pdb=" O PROBK 136 " (cutoff:3.500A) Processing helix chain 'BK' and resid 162 through 192 removed outlier: 3.506A pdb=" N GLUBK 170 " --> pdb=" O ALABK 166 " (cutoff:3.500A) Processing helix chain 'BN' and resid 5 through 15 Processing helix chain 'BN' and resid 27 through 41 removed outlier: 3.770A pdb=" N METBN 34 " --> pdb=" O LYSBN 30 " (cutoff:3.500A) Processing helix chain 'BN' and resid 70 through 75 Processing helix chain 'BN' and resid 91 through 99 Processing helix chain 'BN' and resid 101 through 113 Proline residue: BN 113 - end of helix Processing helix chain 'BN' and resid 115 through 126 removed outlier: 4.935A pdb=" N ARGBN 119 " --> pdb=" O ASNBN 115 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THRBN 120 " --> pdb=" O LEUBN 116 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARGBN 124 " --> pdb=" O THRBN 120 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEUBN 125 " --> pdb=" O METBN 121 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N HISBN 126 " --> pdb=" O METBN 122 " (cutoff:3.500A) Processing helix chain 'BN' and resid 134 through 141 removed outlier: 3.790A pdb=" N ASNBN 140 " --> pdb=" O ASPBN 136 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEUBN 141 " --> pdb=" O ILEBN 137 " (cutoff:3.500A) Processing helix chain 'BN' and resid 154 through 159 removed outlier: 5.682A pdb=" N THRBN 159 " --> pdb=" O LEUBN 155 " (cutoff:3.500A) Processing helix chain 'BN' and resid 160 through 167 Proline residue: BN 167 - end of helix Processing helix chain 'BO' and resid 44 through 49 Processing helix chain 'BO' and resid 124 through 131 removed outlier: 4.752A pdb=" N ARGBO 128 " --> pdb=" O PROBO 124 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLNBO 129 " --> pdb=" O SERBO 125 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ARGBO 130 " --> pdb=" O SERBO 126 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLUBO 131 " --> pdb=" O LEUBO 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'BO' and resid 124 through 131' Processing helix chain 'BO' and resid 134 through 142 removed outlier: 3.611A pdb=" N ILEBO 140 " --> pdb=" O LYSBO 136 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALABO 141 " --> pdb=" O VALBO 137 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLNBO 142 " --> pdb=" O LEUBO 138 " (cutoff:3.500A) Processing helix chain 'BP' and resid 10 through 20 removed outlier: 4.007A pdb=" N ASPBP 14 " --> pdb=" O PROBP 10 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARGBP 17 " --> pdb=" O LEUBP 13 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALABP 18 " --> pdb=" O ASPBP 14 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEUBP 19 " --> pdb=" O LEUBP 15 " (cutoff:3.500A) Proline residue: BP 20 - end of helix Processing helix chain 'BP' and resid 55 through 60 removed outlier: 4.069A pdb=" N ARGBP 59 " --> pdb=" O GLYBP 55 " (cutoff:3.500A) Processing helix chain 'BP' and resid 73 through 78 removed outlier: 3.741A pdb=" N ILEBP 78 " --> pdb=" O PHEBP 74 " (cutoff:3.500A) Processing helix chain 'BP' and resid 97 through 108 Processing helix chain 'BP' and resid 117 through 125 Processing helix chain 'BP' and resid 160 through 171 Processing helix chain 'BP' and resid 180 through 190 Proline residue: BP 190 - end of helix Processing helix chain 'BP' and resid 191 through 197 removed outlier: 3.720A pdb=" N GLYBP 197 " --> pdb=" O PHEBP 193 " (cutoff:3.500A) Processing helix chain 'BP' and resid 207 through 216 Proline residue: BP 212 - end of helix removed outlier: 3.500A pdb=" N ASPBP 216 " --> pdb=" O PROBP 212 " (cutoff:3.500A) Processing helix chain 'BP' and resid 225 through 241 removed outlier: 3.855A pdb=" N PHEBP 229 " --> pdb=" O ASPBP 225 " (cutoff:3.500A) Proline residue: BP 230 - end of helix Processing helix chain 'BP' and resid 246 through 251 removed outlier: 3.905A pdb=" N ASPBP 250 " --> pdb=" O ASPBP 246 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N GLUBP 251 " --> pdb=" O ILEBP 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'BP' and resid 246 through 251' Processing helix chain 'BP' and resid 252 through 258 Processing helix chain 'BP' and resid 287 through 296 Processing helix chain 'BR' and resid 21 through 40 Processing helix chain 'BR' and resid 46 through 66 removed outlier: 4.310A pdb=" N GLYBR 54 " --> pdb=" O ASPBR 50 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N TYRBR 55 " --> pdb=" O GLUBR 51 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLYBR 66 " --> pdb=" O TYRBR 62 " (cutoff:3.500A) Processing helix chain 'BR' and resid 69 through 81 removed outlier: 5.040A pdb=" N THRBR 81 " --> pdb=" O ASPBR 77 " (cutoff:3.500A) Processing helix chain 'BR' and resid 82 through 98 removed outlier: 4.491A pdb=" N ILEBR 86 " --> pdb=" O GLUBR 82 " (cutoff:3.500A) Proline residue: BR 87 - end of helix removed outlier: 3.785A pdb=" N LEUBR 93 " --> pdb=" O LEUBR 89 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ALABR 94 " --> pdb=" O PHEBR 90 " (cutoff:3.500A) Proline residue: BR 95 - end of helix removed outlier: 4.040A pdb=" N GLNBR 98 " --> pdb=" O ALABR 94 " (cutoff:3.500A) Processing helix chain 'BR' and resid 144 through 161 Processing helix chain 'BS' and resid 54 through 60 Processing helix chain 'BS' and resid 109 through 116 removed outlier: 3.828A pdb=" N HISBS 115 " --> pdb=" O ALABS 111 " (cutoff:3.500A) Processing helix chain 'BS' and resid 121 through 140 Processing helix chain 'BS' and resid 149 through 156 removed outlier: 3.660A pdb=" N ALABS 154 " --> pdb=" O PROBS 150 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SERBS 155 " --> pdb=" O TRPBS 151 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ASPBS 156 " --> pdb=" O GLUBS 152 " (cutoff:3.500A) Processing helix chain 'BS' and resid 157 through 169 Processing helix chain 'BT' and resid 88 through 107 removed outlier: 3.932A pdb=" N PHEBT 92 " --> pdb=" O ASNBT 88 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILEBT 105 " --> pdb=" O GLUBT 101 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N HISBT 107 " --> pdb=" O ARGBT 103 " (cutoff:3.500A) Processing helix chain 'BT' and resid 189 through 194 removed outlier: 5.271A pdb=" N LEUBT 194 " --> pdb=" O LEUBT 190 " (cutoff:3.500A) Processing helix chain 'BT' and resid 244 through 249 removed outlier: 4.047A pdb=" N CYSBT 248 " --> pdb=" O ARGBT 244 " (cutoff:3.500A) Processing helix chain 'BT' and resid 250 through 261 removed outlier: 3.835A pdb=" N LYSBT 259 " --> pdb=" O ARGBT 255 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TRPBT 260 " --> pdb=" O GLUBT 256 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N SERBT 261 " --> pdb=" O ALABT 257 " (cutoff:3.500A) Processing helix chain 'BT' and resid 262 through 268 removed outlier: 4.397A pdb=" N GLUBT 266 " --> pdb=" O GLNBT 262 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHEBT 267 " --> pdb=" O PROBT 263 " (cutoff:3.500A) Processing helix chain 'BT' and resid 275 through 292 Processing helix chain 'BU' and resid 16 through 29 removed outlier: 3.858A pdb=" N VALBU 24 " --> pdb=" O ARGBU 20 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N HISBU 27 " --> pdb=" O GLUBU 23 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALABU 28 " --> pdb=" O VALBU 24 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARGBU 29 " --> pdb=" O LEUBU 25 " (cutoff:3.500A) Processing helix chain 'BU' and resid 46 through 79 removed outlier: 4.348A pdb=" N LYSBU 61 " --> pdb=" O ARGBU 57 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ARGBU 62 " --> pdb=" O ARGBU 58 " (cutoff:3.500A) Processing helix chain 'BU' and resid 82 through 94 removed outlier: 3.583A pdb=" N GLNBU 94 " --> pdb=" O LEUBU 90 " (cutoff:3.500A) Processing helix chain 'BU' and resid 98 through 108 Processing helix chain 'BU' and resid 109 through 134 Processing helix chain 'BV' and resid 72 through 94 Processing helix chain 'BV' and resid 154 through 159 removed outlier: 4.619A pdb=" N ARGBV 159 " --> pdb=" O LYSBV 155 " (cutoff:3.500A) Processing helix chain 'BW' and resid 47 through 55 removed outlier: 4.762A pdb=" N LYSBW 51 " --> pdb=" O ARGBW 47 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ASNBW 53 " --> pdb=" O TRPBW 49 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LYSBW 54 " --> pdb=" O GLUBW 50 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILEBW 55 " --> pdb=" O LYSBW 51 " (cutoff:3.500A) Processing helix chain 'BW' and resid 81 through 93 removed outlier: 3.693A pdb=" N LEUBW 88 " --> pdb=" O LYSBW 84 " (cutoff:3.500A) Processing helix chain 'BW' and resid 96 through 107 removed outlier: 3.702A pdb=" N PHEBW 106 " --> pdb=" O ALABW 102 " (cutoff:3.500A) Processing helix chain 'BW' and resid 109 through 129 removed outlier: 4.451A pdb=" N GLNBW 113 " --> pdb=" O LYSBW 109 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILEBW 114 " --> pdb=" O LYSBW 110 " (cutoff:3.500A) Processing helix chain 'BW' and resid 189 through 204 removed outlier: 3.758A pdb=" N ARGBW 204 " --> pdb=" O GLUBW 200 " (cutoff:3.500A) Processing helix chain 'BX' and resid 49 through 59 Processing helix chain 'BX' and resid 114 through 136 Processing sheet with id= 1, first strand: chain 'B0' and resid 81 through 84 removed outlier: 4.505A pdb=" N CYSB0 88 " --> pdb=" O GLYB0 84 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'B0' and resid 97 through 102 Processing sheet with id= 3, first strand: chain 'BY' and resid 78 through 81 removed outlier: 3.568A pdb=" N GLNBY 78 " --> pdb=" O VALBY 87 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'BY' and resid 92 through 97 removed outlier: 5.689A pdb=" N ASNBY 92 " --> pdb=" O ALABY 113 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'Ba' and resid 126 through 130 removed outlier: 5.394A pdb=" N LEUBa 351 " --> pdb=" O ASPBa 348 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THRBa 290 " --> pdb=" O LEUBa 230 " (cutoff:3.500A) removed outlier: 9.059A pdb=" N ARGBa 200 " --> pdb=" O LYSBa 233 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'Ba' and resid 208 through 214 removed outlier: 4.748A pdb=" N LEUBa 219 " --> pdb=" O ALABa 103 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'Ba' and resid 230 through 233 removed outlier: 6.679A pdb=" N LEUBa 230 " --> pdb=" O HISBa 289 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'Bb' and resid 183 through 187 removed outlier: 6.028A pdb=" N ASPBb 183 " --> pdb=" O VALBb 179 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VALBb 175 " --> pdb=" O VALBb 187 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'Bb' and resid 190 through 193 removed outlier: 3.751A pdb=" N ASNBb 191 " --> pdb=" O PHEBb 318 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ARGBb 322 " --> pdb=" O VALBb 193 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ARGBb 267 " --> pdb=" O LEUBb 221 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEUBb 213 " --> pdb=" O GLNBb 275 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEUBb 218 " --> pdb=" O HISBb 234 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'Bb' and resid 215 through 218 removed outlier: 3.661A pdb=" N TRPBb 235 " --> pdb=" O LEUBb 218 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'Bb' and resid 272 through 275 removed outlier: 6.544A pdb=" N LEUBb 272 " --> pdb=" O ALABb 314 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'Bc' and resid 74 through 79 removed outlier: 4.291A pdb=" N THRBc 74 " --> pdb=" O HISBc 66 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N CYSBc 120 " --> pdb=" O GLUBc 63 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N PHEBc 124 " --> pdb=" O VALBc 67 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLNBc 108 " --> pdb=" O VALBc 105 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'Bc' and resid 161 through 164 removed outlier: 6.779A pdb=" N GLNBc 294 " --> pdb=" O SERBc 278 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'Bc' and resid 214 through 218 Processing sheet with id= 15, first strand: chain 'Bc' and resid 279 through 284 Processing sheet with id= 16, first strand: chain 'Be' and resid 40 through 43 removed outlier: 5.570A pdb=" N LYSBe 47 " --> pdb=" O GLYBe 43 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'Bf' and resid 44 through 52 removed outlier: 4.857A pdb=" N ASNBf 44 " --> pdb=" O VALBf 65 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N THRBf 57 " --> pdb=" O THRBf 52 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'Bg' and resid 61 through 68 removed outlier: 4.137A pdb=" N ALABg 83 " --> pdb=" O TYRBg 79 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'Bh' and resid 254 through 258 removed outlier: 6.785A pdb=" N PHEBh 271 " --> pdb=" O THRBh 258 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALABh 282 " --> pdb=" O LEUBh 274 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'Bi' and resid 192 through 195 removed outlier: 6.956A pdb=" N THRBi 213 " --> pdb=" O VALBi 195 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLNBi 196 " --> pdb=" O THRBi 213 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'Bi' and resid 262 through 266 Processing sheet with id= 22, first strand: chain 'Bi' and resid 209 through 218 Processing sheet with id= 23, first strand: chain 'Bj' and resid 174 through 177 removed outlier: 10.998A pdb=" N LEUBj 51 " --> pdb=" O VALBj 161 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N VALBj 161 " --> pdb=" O LEUBj 51 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEUBj 53 " --> pdb=" O LEUBj 159 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ARGBj 155 " --> pdb=" O PROBj 57 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N HISBj 251 " --> pdb=" O ARGBj 162 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'Bj' and resid 211 through 217 removed outlier: 5.621A pdb=" N LEUBj 227 " --> pdb=" O PHEBj 217 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASNBj 199 " --> pdb=" O ASPBj 242 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASPBj 242 " --> pdb=" O ASNBj 199 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'Bj' and resid 44 through 55 Processing sheet with id= 26, first strand: chain 'Bk' and resid 78 through 81 removed outlier: 7.606A pdb=" N ARGBk 78 " --> pdb=" O GLYBk 89 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLYBk 89 " --> pdb=" O ARGBk 78 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALABk 148 " --> pdb=" O VALBk 134 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N GLUBk 154 " --> pdb=" O PROBk 128 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VALBk 156 " --> pdb=" O ALABk 126 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ALABk 126 " --> pdb=" O VALBk 156 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'Bk' and resid 91 through 97 Processing sheet with id= 28, first strand: chain 'Bl' and resid 95 through 101 removed outlier: 5.371A pdb=" N VALBl 137 " --> pdb=" O LYSBl 150 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'Bp' and resid 49 through 56 Processing sheet with id= 30, first strand: chain 'Bu' and resid 78 through 85 removed outlier: 3.931A pdb=" N GLYBu 85 " --> pdb=" O LYSBu 93 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'Bw' and resid 90 through 93 removed outlier: 4.191A pdb=" N ASNBw 228 " --> pdb=" O VALBw 93 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'Bw' and resid 112 through 116 Processing sheet with id= 33, first strand: chain 'Bw' and resid 192 through 196 Processing sheet with id= 34, first strand: chain 'Bw' and resid 291 through 296 removed outlier: 4.426A pdb=" N TYRBw 360 " --> pdb=" O ASPBw 357 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'Bx' and resid 35 through 42 Processing sheet with id= 36, first strand: chain 'B1' and resid 49 through 53 removed outlier: 4.989A pdb=" N LYSB1 49 " --> pdb=" O VALB1 62 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLNB1 58 " --> pdb=" O ASNB1 53 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'B1' and resid 85 through 90 Processing sheet with id= 38, first strand: chain 'B9' and resid 63 through 67 removed outlier: 5.994A pdb=" N HISB9 95 " --> pdb=" O CYSB9 89 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N CYSB9 89 " --> pdb=" O HISB9 95 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TRPB9 85 " --> pdb=" O GLNB9 99 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'B2' and resid 167 through 172 Processing sheet with id= 40, first strand: chain 'B3' and resid 97 through 101 removed outlier: 5.111A pdb=" N LEUB3 66 " --> pdb=" O LEUB3 122 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N LEUB3 116 " --> pdb=" O ILEB3 72 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'B4' and resid 64 through 67 Processing sheet with id= 42, first strand: chain 'B5' and resid 107 through 111 removed outlier: 4.256A pdb=" N HISB5 115 " --> pdb=" O CYSB5 110 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'B5' and resid 155 through 160 Processing sheet with id= 44, first strand: chain 'B6' and resid 28 through 33 removed outlier: 5.650A pdb=" N PHEB6 28 " --> pdb=" O SERB6 22 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEUB6 17 " --> pdb=" O ILEB6 62 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'B6' and resid 41 through 46 removed outlier: 6.118A pdb=" N LEUB6 41 " --> pdb=" O GLUB6 58 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'BC' and resid 124 through 131 removed outlier: 7.293A pdb=" N GLNBC 124 " --> pdb=" O PROBC 143 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ALABC 77 " --> pdb=" O THRBC 142 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLYBC 161 " --> pdb=" O ASNBC 72 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N ALABC 324 " --> pdb=" O ILEBC 188 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ARGBC 190 " --> pdb=" O ALABC 324 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VALBC 325 " --> pdb=" O LYSBC 218 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N CYSBC 329 " --> pdb=" O LEUBC 222 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'BC' and resid 223 through 226 removed outlier: 6.967A pdb=" N GLYBC 234 " --> pdb=" O ILEBC 226 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLUBC 242 " --> pdb=" O ASPBC 237 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'BC' and resid 373 through 377 removed outlier: 3.636A pdb=" N ASPBC 377 " --> pdb=" O GLYBC 381 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N PHEBC 385 " --> pdb=" O PHEBC 372 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LEUBC 367 " --> pdb=" O SERBC 449 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N SERBC 449 " --> pdb=" O LEUBC 367 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THRBC 446 " --> pdb=" O ILEBC 402 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEUBC 397 " --> pdb=" O ILEBC 410 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILEBC 410 " --> pdb=" O LEUBC 397 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N CYSBC 406 " --> pdb=" O ASNBC 401 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'BC' and resid 412 through 415 removed outlier: 3.551A pdb=" N ARGBC 412 " --> pdb=" O VALBC 436 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'BC' and resid 519 through 524 removed outlier: 13.966A pdb=" N GLYBC 528 " --> pdb=" O PROBC 496 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N THRBC 530 " --> pdb=" O ILEBC 494 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'BC' and resid 571 through 579 removed outlier: 6.388A pdb=" N GLUBC 592 " --> pdb=" O HISBC 653 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VALBC 648 " --> pdb=" O GLUBC 608 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'BC' and resid 717 through 721 Processing sheet with id= 53, first strand: chain 'BC' and resid 383 through 388 removed outlier: 3.689A pdb=" N ASNBC 431 " --> pdb=" O ILEBC 388 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'BC' and resid 564 through 568 Processing sheet with id= 55, first strand: chain 'BC' and resid 588 through 592 removed outlier: 5.157A pdb=" N LEUBC 588 " --> pdb=" O HISBC 658 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'BC' and resid 686 through 689 No H-bonds generated for sheet with id= 56 Processing sheet with id= 57, first strand: chain 'BD' and resid 122 through 127 removed outlier: 3.981A pdb=" N ASPBD 162 " --> pdb=" O VALBD 127 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'BD' and resid 129 through 132 removed outlier: 3.881A pdb=" N ALABD 129 " --> pdb=" O LEUBD 142 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ASPBD 139 " --> pdb=" O ALABD 154 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'BD' and resid 215 through 218 removed outlier: 6.982A pdb=" N ILEBD 226 " --> pdb=" O LEUBD 218 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARGBD 233 " --> pdb=" O LEUBD 229 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'BG' and resid 135 through 138 removed outlier: 7.208A pdb=" N GLNBG 142 " --> pdb=" O ILEBG 182 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'BQ' and resid 93 through 96 No H-bonds generated for sheet with id= 61 Processing sheet with id= 62, first strand: chain 'BQ' and resid 119 through 123 removed outlier: 6.051A pdb=" N ILEBQ 160 " --> pdb=" O ARGBQ 123 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VALBQ 161 " --> pdb=" O ILEBQ 89 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'BQ' and resid 131 through 134 removed outlier: 6.776A pdb=" N ILEBQ 131 " --> pdb=" O ASPBQ 148 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'LL' and resid 131 through 135 removed outlier: 7.160A pdb=" N THRLL 194 " --> pdb=" O THRLL 135 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'BE' and resid 98 through 101 Processing sheet with id= 66, first strand: chain 'BE' and resid 105 through 111 removed outlier: 3.985A pdb=" N GLYBE 105 " --> pdb=" O LEUBE 121 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLNBE 115 " --> pdb=" O THRBE 111 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ASNBE 281 " --> pdb=" O VALBE 124 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARGBE 275 " --> pdb=" O TYRBE 284 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N GLUBE 330 " --> pdb=" O THRBE 278 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'BE' and resid 175 through 182 removed outlier: 5.648A pdb=" N LYSBE 175 " --> pdb=" O GLYBE 149 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THRBE 146 " --> pdb=" O LEUBE 130 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYSBE 150 " --> pdb=" O ASPBE 126 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASPBE 126 " --> pdb=" O LYSBE 150 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N CYSBE 127 " --> pdb=" O LEUBE 193 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THRBE 191 " --> pdb=" O VALBE 129 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'BE' and resid 265 through 269 removed outlier: 4.095A pdb=" N GLNBE 202 " --> pdb=" O VALBE 273 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'BF' and resid 47 through 50 removed outlier: 3.688A pdb=" N VALBF 47 " --> pdb=" O VALBF 77 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'BF' and resid 186 through 189 Processing sheet with id= 71, first strand: chain 'BI' and resid 55 through 58 removed outlier: 7.180A pdb=" N ILEBI 55 " --> pdb=" O VALBI 83 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'BI' and resid 94 through 98 removed outlier: 4.310A pdb=" N ASPBI 110 " --> pdb=" O LEUBI 98 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'BJ' and resid 95 through 101 removed outlier: 5.345A pdb=" N HISBJ 150 " --> pdb=" O HISBJ 101 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'BK' and resid 17 through 24 removed outlier: 4.347A pdb=" N GLYBK 18 " --> pdb=" O VALBK 72 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VALBK 72 " --> pdb=" O GLYBK 18 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'BN' and resid 55 through 60 removed outlier: 3.738A pdb=" N GLUBN 143 " --> pdb=" O TRPBN 18 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ASPBN 22 " --> pdb=" O LEUBN 145 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'BN' and resid 77 through 81 removed outlier: 7.393A pdb=" N GLYBN 86 " --> pdb=" O THRBN 81 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'BO' and resid 38 through 41 Processing sheet with id= 78, first strand: chain 'BO' and resid 72 through 76 Processing sheet with id= 79, first strand: chain 'BP' and resid 93 through 96 Processing sheet with id= 80, first strand: chain 'BP' and resid 273 through 277 Processing sheet with id= 81, first strand: chain 'BR' and resid 41 through 45 removed outlier: 4.206A pdb=" N METBR 121 " --> pdb=" O ILEBR 110 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N TYRBR 104 " --> pdb=" O LYSBR 127 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'BS' and resid 80 through 85 removed outlier: 6.358A pdb=" N ILEBS 90 " --> pdb=" O THRBS 107 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VALBS 103 " --> pdb=" O VALBS 94 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'BT' and resid 129 through 135 removed outlier: 4.808A pdb=" N LYSBT 129 " --> pdb=" O ASPBT 123 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILEBT 116 " --> pdb=" O VALBT 177 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLUBT 173 " --> pdb=" O THRBT 120 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'BT' and resid 139 through 142 removed outlier: 3.957A pdb=" N GLNBT 139 " --> pdb=" O ILEBT 150 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ALABT 147 " --> pdb=" O LEUBT 166 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'BV' and resid 109 through 113 removed outlier: 7.376A pdb=" N LEUBV 138 " --> pdb=" O GLYBV 149 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHEBV 145 " --> pdb=" O ALABV 142 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'BV' and resid 116 through 121 removed outlier: 6.593A pdb=" N VALBV 196 " --> pdb=" O ILEBV 165 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLUBV 161 " --> pdb=" O ASNBV 200 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VALBV 160 " --> pdb=" O LEUBV 134 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLUBV 130 " --> pdb=" O VALBV 164 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'BV' and resid 166 through 169 removed outlier: 3.824A pdb=" N GLUBV 166 " --> pdb=" O VALBV 196 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'BV' and resid 172 through 179 removed outlier: 4.303A pdb=" N TYRBV 184 " --> pdb=" O GLNBV 179 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'BW' and resid 69 through 76 removed outlier: 4.907A pdb=" N ALABW 69 " --> pdb=" O GLUBW 178 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LYSBW 175 " --> pdb=" O ALABW 141 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'BW' and resid 142 through 148 removed outlier: 5.913A pdb=" N PHEBW 169 " --> pdb=" O GLYBW 148 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 'BW' and resid 150 through 157 No H-bonds generated for sheet with id= 91 Processing sheet with id= 92, first strand: chain 'BX' and resid 26 through 29 removed outlier: 4.367A pdb=" N GLNBX 41 " --> pdb=" O VALBX 29 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ASPBX 38 " --> pdb=" O LEUBX 99 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYSBX 93 " --> pdb=" O ILEBX 44 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N LYSBX 88 " --> pdb=" O ASNBX 77 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ASNBX 77 " --> pdb=" O LYSBX 88 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLYBX 75 " --> pdb=" O PROBX 90 " (cutoff:3.500A) 3152 hydrogen bonds defined for protein. 9333 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1017 hydrogen bonds 1738 hydrogen bond angles 0 basepair planarities 423 basepair parallelities 771 stacking parallelities Total time for adding SS restraints: 63.31 Time building geometry restraints manager: 40.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 31064 1.34 - 1.46: 35562 1.46 - 1.59: 47796 1.59 - 1.71: 3223 1.71 - 1.84: 469 Bond restraints: 118114 Sorted by residual: bond pdb=" CB THRFL 89 " pdb=" OG1 THRFL 89 " ideal model delta sigma weight residual 1.433 1.522 -0.089 1.60e-02 3.91e+03 3.13e+01 bond pdb=" CG PROBC 659 " pdb=" CD PROBC 659 " ideal model delta sigma weight residual 1.503 1.316 0.187 3.40e-02 8.65e+02 3.04e+01 bond pdb=" N3B GNPBC1000 " pdb=" PG GNPBC1000 " ideal model delta sigma weight residual 1.801 1.708 0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" O5' GNPBC1000 " pdb=" PA GNPBC1000 " ideal model delta sigma weight residual 1.660 1.573 0.087 2.00e-02 2.50e+03 1.87e+01 bond pdb=" CG PROBD 289 " pdb=" CD PROBD 289 " ideal model delta sigma weight residual 1.503 1.382 0.121 3.40e-02 8.65e+02 1.28e+01 ... (remaining 118109 not shown) Histogram of bond angle deviations from ideal: 89.93 - 98.81: 3 98.81 - 107.68: 14475 107.68 - 116.56: 78614 116.56 - 125.44: 67035 125.44 - 134.32: 7408 Bond angle restraints: 167535 Sorted by residual: angle pdb=" N PROBC 659 " pdb=" CD PROBC 659 " pdb=" CG PROBC 659 " ideal model delta sigma weight residual 103.20 89.93 13.27 1.50e+00 4.44e-01 7.83e+01 angle pdb=" N PROBC 65 " pdb=" CA PROBC 65 " pdb=" CB PROBC 65 " ideal model delta sigma weight residual 103.08 111.02 -7.94 9.70e-01 1.06e+00 6.70e+01 angle pdb=" N PROBf 80 " pdb=" CA PROBf 80 " pdb=" CB PROBf 80 " ideal model delta sigma weight residual 103.25 111.23 -7.98 1.05e+00 9.07e-01 5.78e+01 angle pdb=" N PROBu 167 " pdb=" CA PROBu 167 " pdb=" CB PROBu 167 " ideal model delta sigma weight residual 103.25 111.15 -7.90 1.05e+00 9.07e-01 5.66e+01 angle pdb=" N PROBf 78 " pdb=" CA PROBf 78 " pdb=" CB PROBf 78 " ideal model delta sigma weight residual 103.25 111.14 -7.89 1.05e+00 9.07e-01 5.64e+01 ... (remaining 167530 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 66064 35.97 - 71.93: 1999 71.93 - 107.90: 179 107.90 - 143.87: 14 143.87 - 179.84: 26 Dihedral angle restraints: 68282 sinusoidal: 40199 harmonic: 28083 Sorted by residual: dihedral pdb=" O4' UBA1536 " pdb=" C1' UBA1536 " pdb=" N1 UBA1536 " pdb=" C2 UBA1536 " ideal model delta sinusoidal sigma weight residual 200.00 22.20 177.80 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' CBA 238 " pdb=" C1' CBA 238 " pdb=" N1 CBA 238 " pdb=" C2 CBA 238 " ideal model delta sinusoidal sigma weight residual -160.00 9.13 -169.13 1 1.50e+01 4.44e-03 8.46e+01 dihedral pdb=" O4' CBA 825 " pdb=" C1' CBA 825 " pdb=" N1 CBA 825 " pdb=" C2 CBA 825 " ideal model delta sinusoidal sigma weight residual -160.00 7.58 -167.58 1 1.50e+01 4.44e-03 8.43e+01 ... (remaining 68279 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.017: 19746 1.017 - 2.034: 0 2.034 - 3.052: 0 3.052 - 4.069: 0 4.069 - 5.086: 1 Chirality restraints: 19747 Sorted by residual: chirality pdb=" CB THRFL 89 " pdb=" CA THRFL 89 " pdb=" OG1 THRFL 89 " pdb=" CG2 THRFL 89 " both_signs ideal model delta sigma weight residual False 2.55 -2.53 5.09 2.00e-01 2.50e+01 6.47e+02 chirality pdb=" CA PROBu 167 " pdb=" N PROBu 167 " pdb=" C PROBu 167 " pdb=" CB PROBu 167 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA PROBq 59 " pdb=" N PROBq 59 " pdb=" C PROBq 59 " pdb=" CB PROBq 59 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 19744 not shown) Planarity restraints: 15568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEUBC 349 " 0.072 5.00e-02 4.00e+02 1.09e-01 1.89e+01 pdb=" N PROBC 350 " -0.188 5.00e-02 4.00e+02 pdb=" CA PROBC 350 " 0.058 5.00e-02 4.00e+02 pdb=" CD PROBC 350 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VALBb 171 " -0.070 5.00e-02 4.00e+02 1.06e-01 1.79e+01 pdb=" N PROBb 172 " 0.183 5.00e-02 4.00e+02 pdb=" CA PROBb 172 " -0.056 5.00e-02 4.00e+02 pdb=" CD PROBb 172 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRPBw 329 " 0.029 2.00e-02 2.50e+03 2.06e-02 1.06e+01 pdb=" CG TRPBw 329 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TRPBw 329 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRPBw 329 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRPBw 329 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRPBw 329 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRPBw 329 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRPBw 329 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRPBw 329 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRPBw 329 " 0.002 2.00e-02 2.50e+03 ... (remaining 15565 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.93: 4 1.93 - 2.67: 3947 2.67 - 3.41: 144403 3.41 - 4.16: 308803 4.16 - 4.90: 502705 Nonbonded interactions: 959862 Sorted by model distance: nonbonded pdb="MG MGBA3022 " pdb="MG MGBA3026 " model vdw 1.187 1.300 nonbonded pdb="MG MGBA3023 " pdb="MG MGBA3097 " model vdw 1.221 1.300 nonbonded pdb="MG MGBA3161 " pdb="MG MGB3 201 " model vdw 1.284 1.300 nonbonded pdb="MG MGBA3086 " pdb="MG MGBA3182 " model vdw 1.290 1.300 nonbonded pdb=" OP1 CBA 435 " pdb="MG MGBA3034 " model vdw 1.968 2.170 ... (remaining 959857 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'DL' and resid 64 through 89) selection = (chain 'EL' and resid 64 through 89) selection = (chain 'FL' and resid 64 through 89) selection = (chain 'GL' and resid 64 through 89) selection = chain 'HL' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.720 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: 0.070 Extract box with map and model: 28.780 Check model and map are aligned: 1.200 Set scattering table: 0.710 Process input model: 282.150 Find NCS groups from input model: 3.530 Set up NCS constraints: 0.350 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: 0.030 Load rotamer database and sin/cos tables:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 323.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.187 118114 Z= 0.166 Angle : 0.534 13.272 167535 Z= 0.296 Chirality : 0.050 5.086 19747 Planarity : 0.004 0.109 15568 Dihedral : 15.689 179.836 50064 Min Nonbonded Distance : 1.187 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.17 % Favored : 95.75 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.09), residues: 9515 helix: 2.03 (0.09), residues: 3395 sheet: 0.07 (0.14), residues: 1360 loop : -0.54 (0.09), residues: 4760 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19030 Ramachandran restraints generated. 9515 Oldfield, 0 Emsley, 9515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19030 Ramachandran restraints generated. 9515 Oldfield, 0 Emsley, 9515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2211 residues out of total 8481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 2209 time to evaluate : 7.758 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 outliers start: 2 outliers final: 0 residues processed: 2209 average time/residue: 1.0420 time to fit residues: 3841.5970 Evaluate side-chains 1576 residues out of total 8481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1576 time to evaluate : 8.971 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 10.1371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1097 random chunks: chunk 926 optimal weight: 4.9990 chunk 831 optimal weight: 4.9990 chunk 461 optimal weight: 20.0000 chunk 284 optimal weight: 4.9990 chunk 560 optimal weight: 6.9990 chunk 444 optimal weight: 4.9990 chunk 859 optimal weight: 7.9990 chunk 332 optimal weight: 0.4980 chunk 522 optimal weight: 10.0000 chunk 639 optimal weight: 2.9990 chunk 996 optimal weight: 6.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B0 107 ASN BY 84 ASN Ba 65 HIS Ba 289 HIS Ba 343 GLN Bb 191 ASN Bb 243 ASN Bb 354 GLN Bc 50 ASN Bc 282 ASN Bd 82 GLN Bg 27 GLN Bg 127 GLN Bh 177 GLN Bi 59 HIS ** Bj 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bj 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bk 158 GLN Bk 175 HIS Bl 93 ASN Bl 155 GLN Bl 156 GLN Bm 88 GLN ** Bp 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bq 71 HIS Bv 130 GLN ** Bw 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 124 GLN B2 159 GLN B2 185 GLN B2 197 ASN B3 126 GLN B3 136 ASN ** B4 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 66 HIS BC 182 GLN ** BC 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 624 GLN BQ 98 HIS LL 152 HIS ** BE 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 184 GLN ** BJ 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BN 140 ASN BP 84 ASN BP 94 GLN ** BS 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BS 121 ASN BT 291 ASN BU 22 GLN BU 94 GLN BV 122 ASN BX 11 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.099 118114 Z= 0.424 Angle : 0.637 10.138 167535 Z= 0.321 Chirality : 0.041 0.249 19747 Planarity : 0.005 0.076 15568 Dihedral : 14.446 179.321 30024 Min Nonbonded Distance : 0.964 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.87 % Favored : 95.08 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.09), residues: 9515 helix: 1.87 (0.09), residues: 3378 sheet: -0.01 (0.14), residues: 1385 loop : -0.60 (0.09), residues: 4752 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19030 Ramachandran restraints generated. 9515 Oldfield, 0 Emsley, 9515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19030 Ramachandran restraints generated. 9515 Oldfield, 0 Emsley, 9515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1741 residues out of total 8481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1582 time to evaluate : 7.796 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 outliers start: 159 outliers final: 110 residues processed: 1659 average time/residue: 1.0160 time to fit residues: 2881.9082 Evaluate side-chains 1565 residues out of total 8481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 1455 time to evaluate : 9.098 Switching outliers to nearest non-outliers outliers start: 110 outliers final: 0 residues processed: 110 average time/residue: 0.7262 time to fit residues: 162.1636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1097 random chunks: chunk 553 optimal weight: 3.9990 chunk 309 optimal weight: 6.9990 chunk 829 optimal weight: 0.9990 chunk 678 optimal weight: 1.9990 chunk 274 optimal weight: 10.0000 chunk 997 optimal weight: 3.9990 chunk 1078 optimal weight: 1.9990 chunk 888 optimal weight: 10.0000 chunk 989 optimal weight: 1.9990 chunk 340 optimal weight: 9.9990 chunk 800 optimal weight: 20.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BY 35 ASN BY 84 ASN Bc 50 ASN Bd 82 GLN Be 50 GLN Be 88 GLN Bg 127 GLN Bh 65 ASN ** Bi 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bj 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bj 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bj 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bl 65 HIS Bl 155 GLN Bm 68 GLN Bm 107 ASN Bn 65 ASN ** Bp 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bq 135 ASN Bt 10 ASN Bt 72 GLN ** Bu 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bx 69 GLN B2 90 GLN B2 197 ASN B3 136 ASN ** B4 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 66 HIS ** BC 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 376 HIS ** BC 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BF 74 GLN ** BF 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 241 ASN ** BJ 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BP 123 ASN BP 170 ASN BP 219 ASN ** BS 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BT 239 ASN BT 291 ASN BU 22 GLN BV 122 ASN BW 149 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 118114 Z= 0.269 Angle : 0.552 11.014 167535 Z= 0.279 Chirality : 0.038 0.269 19747 Planarity : 0.004 0.064 15568 Dihedral : 14.496 179.567 30024 Min Nonbonded Distance : 0.992 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.29 % Favored : 95.66 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.09), residues: 9515 helix: 1.95 (0.09), residues: 3403 sheet: -0.06 (0.14), residues: 1389 loop : -0.57 (0.09), residues: 4723 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19030 Ramachandran restraints generated. 9515 Oldfield, 0 Emsley, 9515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19030 Ramachandran restraints generated. 9515 Oldfield, 0 Emsley, 9515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1633 residues out of total 8481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 1527 time to evaluate : 8.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 106 outliers final: 63 residues processed: 1572 average time/residue: 1.0361 time to fit residues: 2761.8572 Evaluate side-chains 1518 residues out of total 8481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 1455 time to evaluate : 7.806 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 0 residues processed: 63 average time/residue: 0.8668 time to fit residues: 110.0613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1097 random chunks: chunk 986 optimal weight: 5.9990 chunk 750 optimal weight: 0.1980 chunk 517 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 476 optimal weight: 7.9990 chunk 670 optimal weight: 6.9990 chunk 1001 optimal weight: 6.9990 chunk 1060 optimal weight: 0.8980 chunk 523 optimal weight: 10.0000 chunk 949 optimal weight: 4.9990 chunk 285 optimal weight: 4.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BY 35 ASN Bb 191 ASN ** Bb 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 243 ASN Bc 50 ASN Bc 274 GLN Be 50 GLN Bg 25 GLN Bg 58 ASN Bg 129 GLN Bh 65 ASN Bh 69 HIS Bh 172 ASN ** Bj 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bj 118 GLN ** Bj 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bj 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bl 65 HIS Bl 155 GLN Bm 68 GLN Bm 107 ASN Bm 115 ASN Bm 120 GLN ** Bp 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bu 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bw 352 GLN ** Bw 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 136 ASN B4 66 HIS ** BC 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BD 92 GLN BD 157 ASN ** BE 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BF 153 HIS BF 184 GLN BN 140 ASN BP 123 ASN ** BS 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BT 291 ASN BU 22 GLN BV 122 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.080 118114 Z= 0.376 Angle : 0.596 10.393 167535 Z= 0.301 Chirality : 0.040 0.261 19747 Planarity : 0.005 0.058 15568 Dihedral : 14.533 179.770 30024 Min Nonbonded Distance : 0.943 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.82 % Favored : 95.13 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.09), residues: 9515 helix: 1.87 (0.09), residues: 3391 sheet: 0.01 (0.14), residues: 1352 loop : -0.61 (0.09), residues: 4772 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19030 Ramachandran restraints generated. 9515 Oldfield, 0 Emsley, 9515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19030 Ramachandran restraints generated. 9515 Oldfield, 0 Emsley, 9515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1655 residues out of total 8481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 1510 time to evaluate : 7.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 145 outliers final: 96 residues processed: 1568 average time/residue: 1.0167 time to fit residues: 2725.2020 Evaluate side-chains 1546 residues out of total 8481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 1450 time to evaluate : 7.897 Switching outliers to nearest non-outliers outliers start: 96 outliers final: 0 residues processed: 96 average time/residue: 0.7837 time to fit residues: 153.4039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1097 random chunks: chunk 883 optimal weight: 0.7980 chunk 601 optimal weight: 5.9990 chunk 15 optimal weight: 0.4980 chunk 789 optimal weight: 0.4980 chunk 437 optimal weight: 9.9990 chunk 904 optimal weight: 0.0470 chunk 732 optimal weight: 9.9990 chunk 1 optimal weight: 0.6980 chunk 541 optimal weight: 6.9990 chunk 951 optimal weight: 0.9990 chunk 267 optimal weight: 8.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BY 35 ASN Bb 163 HIS Bc 50 ASN Be 50 GLN Bg 90 HIS Bh 65 ASN Bi 161 HIS ** Bj 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bj 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bl 155 GLN Bm 107 ASN Bm 115 ASN Bp 35 GLN ** Bu 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bw 402 ASN B3 136 ASN ** B4 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 66 HIS BC 356 ASN ** BQ 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 153 HIS ** BI 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 193 ASN BP 123 ASN ** BS 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BS 121 ASN BT 291 ASN BU 22 GLN BU 79 HIS ** BU 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 122 ASN BW 131 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.047 118114 Z= 0.137 Angle : 0.521 12.801 167535 Z= 0.262 Chirality : 0.035 0.206 19747 Planarity : 0.004 0.067 15568 Dihedral : 14.549 179.859 30024 Min Nonbonded Distance : 1.166 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.87 % Favored : 96.11 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.09), residues: 9515 helix: 2.06 (0.09), residues: 3383 sheet: 0.03 (0.14), residues: 1357 loop : -0.49 (0.09), residues: 4775 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19030 Ramachandran restraints generated. 9515 Oldfield, 0 Emsley, 9515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19030 Ramachandran restraints generated. 9515 Oldfield, 0 Emsley, 9515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1647 residues out of total 8481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 1565 time to evaluate : 7.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 41 residues processed: 1611 average time/residue: 1.0397 time to fit residues: 2868.3713 Evaluate side-chains 1509 residues out of total 8481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 1468 time to evaluate : 7.829 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.8226 time to fit residues: 74.1377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1097 random chunks: chunk 356 optimal weight: 7.9990 chunk 954 optimal weight: 10.0000 chunk 209 optimal weight: 3.9990 chunk 622 optimal weight: 6.9990 chunk 261 optimal weight: 30.0000 chunk 1061 optimal weight: 2.9990 chunk 881 optimal weight: 0.6980 chunk 491 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 chunk 351 optimal weight: 10.0000 chunk 557 optimal weight: 5.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B0 122 GLN BY 35 ASN Ba 84 HIS Ba 343 GLN ** Bb 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 243 ASN Bb 333 GLN Bc 50 ASN Bc 252 HIS Bc 282 ASN Be 50 GLN ** Bj 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bj 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bj 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bj 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bl 155 GLN Bm 115 ASN Bu 142 GLN B1 76 GLN ** B4 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 66 HIS B5 118 GLN BC 356 ASN ** BC 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BC 632 HIS ** BC 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 92 GLN ** BE 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BF 74 GLN ** BF 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 153 HIS BF 184 GLN BJ 193 ASN BN 140 ASN BP 123 ASN BP 170 ASN ** BS 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BT 291 ASN BU 22 GLN BV 122 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.087 118114 Z= 0.450 Angle : 0.633 14.998 167535 Z= 0.319 Chirality : 0.042 0.274 19747 Planarity : 0.005 0.056 15568 Dihedral : 14.544 179.246 30024 Min Nonbonded Distance : 0.985 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.01 % Favored : 94.94 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.09), residues: 9515 helix: 1.87 (0.09), residues: 3378 sheet: -0.03 (0.14), residues: 1359 loop : -0.60 (0.09), residues: 4778 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19030 Ramachandran restraints generated. 9515 Oldfield, 0 Emsley, 9515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19030 Ramachandran restraints generated. 9515 Oldfield, 0 Emsley, 9515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1619 residues out of total 8481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1484 time to evaluate : 8.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 135 outliers final: 90 residues processed: 1542 average time/residue: 1.0360 time to fit residues: 2734.2987 Evaluate side-chains 1511 residues out of total 8481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 1421 time to evaluate : 7.876 Switching outliers to nearest non-outliers outliers start: 90 outliers final: 0 residues processed: 90 average time/residue: 0.7565 time to fit residues: 139.8396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1097 random chunks: chunk 1023 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 604 optimal weight: 4.9990 chunk 775 optimal weight: 0.7980 chunk 600 optimal weight: 5.9990 chunk 893 optimal weight: 0.9990 chunk 592 optimal weight: 10.0000 chunk 1057 optimal weight: 0.6980 chunk 661 optimal weight: 2.9990 chunk 644 optimal weight: 0.8980 chunk 488 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BY 35 ASN ** Bb 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bc 50 ASN Bc 252 HIS Bd 82 GLN Be 50 GLN Bi 161 HIS ** Bj 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bj 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bj 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bk 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bl 155 GLN Bm 115 ASN Bn 65 ASN Bp 15 GLN Bt 72 GLN Bu 142 GLN B1 76 GLN HL 83 ASN ** B4 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 66 HIS BC 302 ASN BC 356 ASN ** BC 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 92 GLN ** BQ 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 153 HIS ** BO 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BS 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BT 291 ASN BU 22 GLN BV 122 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 118114 Z= 0.168 Angle : 0.534 13.581 167535 Z= 0.270 Chirality : 0.036 0.218 19747 Planarity : 0.004 0.062 15568 Dihedral : 14.569 179.859 30024 Min Nonbonded Distance : 1.066 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.19 % Favored : 95.78 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.09), residues: 9515 helix: 2.03 (0.09), residues: 3376 sheet: -0.05 (0.14), residues: 1357 loop : -0.51 (0.09), residues: 4782 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19030 Ramachandran restraints generated. 9515 Oldfield, 0 Emsley, 9515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19030 Ramachandran restraints generated. 9515 Oldfield, 0 Emsley, 9515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1570 residues out of total 8481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 1503 time to evaluate : 7.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 35 residues processed: 1536 average time/residue: 1.0193 time to fit residues: 2685.3458 Evaluate side-chains 1482 residues out of total 8481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 1447 time to evaluate : 7.842 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.8092 time to fit residues: 63.7480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1097 random chunks: chunk 654 optimal weight: 0.3980 chunk 422 optimal weight: 0.6980 chunk 631 optimal weight: 6.9990 chunk 318 optimal weight: 0.0470 chunk 207 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 chunk 672 optimal weight: 4.9990 chunk 720 optimal weight: 6.9990 chunk 522 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 831 optimal weight: 3.9990 overall best weight: 2.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BY 35 ASN Bb 163 HIS ** Bb 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 243 ASN Bc 252 HIS Bg 25 GLN ** Bj 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bj 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bj 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bk 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bl 155 GLN Bm 115 ASN Bp 15 GLN Bu 142 GLN Bw 379 GLN ** B4 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 66 HIS B5 118 GLN BC 356 ASN BC 376 HIS ** BC 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 92 GLN ** BQ 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 153 HIS BF 184 GLN BN 140 ASN ** BO 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BP 123 ASN ** BS 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BS 121 ASN BT 291 ASN BU 22 GLN BV 122 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 118114 Z= 0.259 Angle : 0.556 13.542 167535 Z= 0.280 Chirality : 0.038 0.233 19747 Planarity : 0.004 0.056 15568 Dihedral : 14.506 179.865 30024 Min Nonbonded Distance : 0.999 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.52 % Favored : 95.44 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.09), residues: 9515 helix: 2.01 (0.09), residues: 3378 sheet: -0.04 (0.14), residues: 1334 loop : -0.52 (0.09), residues: 4803 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19030 Ramachandran restraints generated. 9515 Oldfield, 0 Emsley, 9515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19030 Ramachandran restraints generated. 9515 Oldfield, 0 Emsley, 9515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1513 residues out of total 8481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 1451 time to evaluate : 8.039 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 outliers start: 62 outliers final: 42 residues processed: 1474 average time/residue: 1.0534 time to fit residues: 2659.9742 Evaluate side-chains 1464 residues out of total 8481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 1422 time to evaluate : 7.830 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.8251 time to fit residues: 75.0860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1097 random chunks: chunk 961 optimal weight: 8.9990 chunk 1012 optimal weight: 0.8980 chunk 924 optimal weight: 0.9990 chunk 985 optimal weight: 0.8980 chunk 593 optimal weight: 6.9990 chunk 429 optimal weight: 0.6980 chunk 773 optimal weight: 9.9990 chunk 302 optimal weight: 2.9990 chunk 890 optimal weight: 10.0000 chunk 931 optimal weight: 5.9990 chunk 981 optimal weight: 8.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BY 35 ASN ** Bb 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bc 50 ASN Bg 25 GLN ** Bh 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bi 161 HIS ** Bj 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bj 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bk 94 HIS Bl 155 GLN Bm 115 ASN Bn 65 ASN Bu 142 GLN Bw 337 GLN ** B4 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 66 HIS BC 356 ASN BC 376 HIS BC 400 HIS ** BC 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 92 GLN ** BQ 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BF 83 HIS ** BF 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 184 GLN ** BO 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BS 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BT 239 ASN BT 291 ASN BU 22 GLN BV 122 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 118114 Z= 0.189 Angle : 0.538 16.359 167535 Z= 0.271 Chirality : 0.036 0.213 19747 Planarity : 0.004 0.054 15568 Dihedral : 14.511 179.991 30024 Min Nonbonded Distance : 1.042 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.27 % Favored : 95.70 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.09), residues: 9515 helix: 2.04 (0.09), residues: 3389 sheet: -0.01 (0.14), residues: 1334 loop : -0.50 (0.09), residues: 4792 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19030 Ramachandran restraints generated. 9515 Oldfield, 0 Emsley, 9515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19030 Ramachandran restraints generated. 9515 Oldfield, 0 Emsley, 9515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1525 residues out of total 8481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 1488 time to evaluate : 7.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 21 residues processed: 1502 average time/residue: 1.0263 time to fit residues: 2639.9641 Evaluate side-chains 1469 residues out of total 8481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 1448 time to evaluate : 7.879 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.8773 time to fit residues: 43.7099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1097 random chunks: chunk 647 optimal weight: 4.9990 chunk 1041 optimal weight: 2.9990 chunk 635 optimal weight: 7.9990 chunk 494 optimal weight: 6.9990 chunk 724 optimal weight: 20.0000 chunk 1092 optimal weight: 2.9990 chunk 1005 optimal weight: 5.9990 chunk 870 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 672 optimal weight: 2.9990 chunk 533 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Bb 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 243 ASN ** Bc 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 25 GLN ** Bh 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bj 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bj 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bk 189 HIS Bl 141 ASN Bl 155 GLN Bm 115 ASN Bq 135 ASN Bu 142 GLN Bw 379 GLN ** B4 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 66 HIS BC 356 ASN BC 376 HIS BC 629 ASN ** BC 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 184 GLN BN 140 ASN BO 113 ASN BP 123 ASN ** BS 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BT 291 ASN BU 22 GLN BV 122 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 118114 Z= 0.267 Angle : 0.562 14.266 167535 Z= 0.284 Chirality : 0.038 0.228 19747 Planarity : 0.004 0.054 15568 Dihedral : 14.489 179.584 30024 Min Nonbonded Distance : 0.982 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.57 % Favored : 95.40 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.09), residues: 9515 helix: 2.01 (0.09), residues: 3385 sheet: -0.06 (0.14), residues: 1336 loop : -0.51 (0.09), residues: 4794 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19030 Ramachandran restraints generated. 9515 Oldfield, 0 Emsley, 9515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19030 Ramachandran restraints generated. 9515 Oldfield, 0 Emsley, 9515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1495 residues out of total 8481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 1460 time to evaluate : 7.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 25 residues processed: 1470 average time/residue: 1.0413 time to fit residues: 2615.3043 Evaluate side-chains 1451 residues out of total 8481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 1426 time to evaluate : 7.793 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.8284 time to fit residues: 49.6876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1097 random chunks: chunk 691 optimal weight: 0.3980 chunk 927 optimal weight: 9.9990 chunk 266 optimal weight: 40.0000 chunk 802 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 chunk 241 optimal weight: 0.0980 chunk 871 optimal weight: 0.9990 chunk 364 optimal weight: 6.9990 chunk 895 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BY 35 ASN ** Bb 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bc 41 GLN Bc 50 ASN Bg 25 GLN ** Bh 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bi 161 HIS Bi 211 GLN ** Bj 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bj 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bl 141 ASN Bl 155 GLN Bm 115 ASN Bp 15 GLN Bq 135 ASN B1 46 HIS ** B4 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 356 ASN BC 376 HIS BC 768 GLN ** BQ 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 184 GLN ** BO 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BS 121 ASN BT 291 ASN BU 22 GLN BV 122 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.125530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.082748 restraints weight = 182980.508| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 1.83 r_work: 0.2739 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.067 118114 Z= 0.147 Angle : 0.528 14.259 167535 Z= 0.266 Chirality : 0.035 0.206 19747 Planarity : 0.004 0.053 15568 Dihedral : 14.492 179.903 30024 Min Nonbonded Distance : 1.115 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.93 % Favored : 96.06 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.09), residues: 9515 helix: 2.13 (0.09), residues: 3381 sheet: 0.01 (0.14), residues: 1337 loop : -0.45 (0.09), residues: 4797 =============================================================================== Job complete usr+sys time: 38911.97 seconds wall clock time: 673 minutes 54.39 seconds (40434.39 seconds total)