Starting phenix.real_space_refine (version: dev) on Wed Apr 13 17:55:10 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gaw_4368/04_2022/6gaw_4368_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gaw_4368/04_2022/6gaw_4368.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/6gaw_4368/04_2022/6gaw_4368.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gaw_4368/04_2022/6gaw_4368.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gaw_4368/04_2022/6gaw_4368_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gaw_4368/04_2022/6gaw_4368_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= 0.002 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "CL GLU 42": "OE1" <-> "OE2" Residue "DL GLU 78": "OE1" <-> "OE2" Residue "FL GLU 78": "OE1" <-> "OE2" Residue "HL GLU 78": "OE1" <-> "OE2" Residue "B0 TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B0 TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B0 GLU 102": "OE1" <-> "OE2" Residue "B0 PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B1 TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B1 ASP 142": "OD1" <-> "OD2" Residue "B1 PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B1 PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B1 PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B2 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B2 PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B2 TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B2 ASP 153": "OD1" <-> "OD2" Residue "B2 TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B2 TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B3 PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B5 TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B6 PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B6 PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B6 ASP 47": "OD1" <-> "OD2" Residue "B8 TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B8 PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B8 ASP 182": "OD1" <-> "OD2" Residue "B9 ASP 75": "OD1" <-> "OD2" Residue "B9 PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B9 TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC GLU 429": "OE1" <-> "OE2" Residue "BC TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC PHE 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC PHE 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BD TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BD GLU 125": "OE1" <-> "OE2" Residue "BD TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BD GLU 179": "OE1" <-> "OE2" Residue "BD TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BE PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BE PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BE TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BE PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BE PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BE ASP 265": "OD1" <-> "OD2" Residue "BE PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BE TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BE ASP 334": "OD1" <-> "OD2" Residue "BE PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BF PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BF GLU 270": "OE1" <-> "OE2" Residue "BF TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BJ PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BJ PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BJ PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BJ TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BJ ARG 227": "NH1" <-> "NH2" Residue "BK PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BK PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BL GLU 166": "OE1" <-> "OE2" Residue "BL GLU 182": "OE1" <-> "OE2" Residue "BN TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BN PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BN TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BO ASP 42": "OD1" <-> "OD2" Residue "BP TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BP TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BP ASP 261": "OD1" <-> "OD2" Residue "BP TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BP TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BQ PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BS PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BS TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BT PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BT TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BU TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BU PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BV PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BV PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BW TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BW TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BW PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BW PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BX PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BX PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BX TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BY ASP 31": "OD1" <-> "OD2" Residue "BY PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BY TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ba PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ba PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ba TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ba PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ba PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ba TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ba ASP 363": "OD1" <-> "OD2" Residue "Ba TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ba PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bb PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bb TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bb PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bb TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bb ASP 209": "OD1" <-> "OD2" Residue "Bb ASP 222": "OD1" <-> "OD2" Residue "Bb TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bb PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bb PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bb PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bb TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bb PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bb ASP 324": "OD1" <-> "OD2" Residue "Bb PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bb TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bc PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bc TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bc TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bc PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Be PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bf TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bf GLU 101": "OE1" <-> "OE2" Residue "Bg PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bg GLU 96": "OE1" <-> "OE2" Residue "Bh PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bh PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bh PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bh TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bh GLU 293": "OE1" <-> "OE2" Residue "Bh TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bi PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bi TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bi ASP 175": "OD1" <-> "OD2" Residue "Bi TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bi TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bi TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bj ASP 145": "OD1" <-> "OD2" Residue "Bj PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bk TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bk TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bl TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bl TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bl GLU 163": "OE1" <-> "OE2" Residue "Bm TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bn TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bo TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bp PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bq TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bq PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bq PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bt ARG 11": "NH1" <-> "NH2" Residue "Bt GLU 40": "OE1" <-> "OE2" Residue "Bu PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bv TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bv GLU 101": "OE1" <-> "OE2" Residue "Bv ARG 104": "NH1" <-> "NH2" Residue "Bv ARG 136": "NH1" <-> "NH2" Residue "Bw TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bw TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bw TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bw TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bw PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bw ASP 284": "OD1" <-> "OD2" Residue "Bw PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bw GLU 315": "OE1" <-> "OE2" Residue "Bw PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bw TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bw PHE 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bw TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bw PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bw ASP 410": "OD1" <-> "OD2" Residue "Bx TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bx TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AB PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AB TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AB PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AB PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AB TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AB TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AB PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AB TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AB TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AC GLU 88": "OE1" <-> "OE2" Residue "AC ASP 89": "OD1" <-> "OD2" Residue "AC PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AC PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AE PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AE GLU 224": "OE1" <-> "OE2" Residue "AE PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AE PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AE TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AE GLU 398": "OE1" <-> "OE2" Residue "AF TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AF PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AF TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AG PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AG GLU 87": "OE1" <-> "OE2" Residue "AG TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AG PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AG PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AG GLU 231": "OE1" <-> "OE2" Residue "AI PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AI PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AI TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AI PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AI TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AI PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AI GLU 361": "OE1" <-> "OE2" Residue "AJ TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AK TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AL PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AN TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AN ASP 37": "OD1" <-> "OD2" Residue "AO PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AP TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AP ASP 71": "OD1" <-> "OD2" Residue "AQ PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AQ PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AR TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AR PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AR ASP 127": "OD1" <-> "OD2" Residue "AU PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AU TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AU PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Aa PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Aa PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Aa TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Aa PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Aa PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Aa GLU 258": "OE1" <-> "OE2" Residue "Aa PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Aa TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ab PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ab TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ab PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ab PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ac TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ac PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ac PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ac TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ac TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ad PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ae GLU 102": "OE1" <-> "OE2" Residue "Ae ARG 122": "NH1" <-> "NH2" Residue "Ae TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ae TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ae PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ae ASP 180": "OD1" <-> "OD2" Residue "Ae PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ae TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ae TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ae ARG 242": "NH1" <-> "NH2" Residue "Ae TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ae GLU 362": "OE1" <-> "OE2" Residue "Ae TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ae TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Af PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Af TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ag PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ag PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ag TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ah PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ah PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ai TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ai TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Aj TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Aj TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Aj PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Aj TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Aj PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Aj TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ak TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ak ASP 186": "OD1" <-> "OD2" Residue "Ak TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ak GLU 247": "OE1" <-> "OE2" Residue "Am ARG 17": "NH1" <-> "NH2" Residue "Am GLU 42": "OE1" <-> "OE2" Residue "An PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "An TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ao TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ao TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ao TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ao PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ao PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ao PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ao TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ao PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ao GLU 362": "OE1" <-> "OE2" Residue "Ao TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ao PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ao PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ao TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ao PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ao PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ao ASP 504": "OD1" <-> "OD2" Residue "Ao TYR 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ao PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ao PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ao PHE 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ap TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ap TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ap PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ap TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ap TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.25s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 178372 Number of models: 1 Model: "" Number of chains: 121 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: "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: "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: "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: "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: "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: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 381 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 3, 'TRANS': 41} 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: "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: "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: "BA" Number of atoms: 32950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1549, 32950 Classifications: {'RNA': 1549} Modifications used: {'rna3p_pyr': 583, 'rna2p_pur': 172, 'rna3p_pur': 685, 'rna2p_pyr': 109} Link IDs: {'rna3p': 1268, 'rna2p': 280} Chain breaks: 1 Chain: "BB" Number of atoms: 1427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1427 Classifications: {'RNA': 67} Modifications used: {'rna2p_pyr': 3, 'rna3p_pyr': 27, 'p5*END': 1, 'rna3p_pur': 35, 'rna2p_pur': 2} Link IDs: {'rna3p': 61, 'rna2p': 5} Chain breaks: 2 Chain: "BC" Number of atoms: 4364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4364 Classifications: {'peptide': 571} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 21, 'TRANS': 549} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 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: "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: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1303 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 166, 'PCIS': 1} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "BL" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 537 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 66, 'PCIS': 1} 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: "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: "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: {'PTRANS': 5, 'TRANS': 136, 'PCIS': 1} Chain: "BT" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1954 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 19, 'TRANS': 219, 'PCIS': 1} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 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: {'PTRANS': 9, 'TRANS': 144, 'PCIS': 1} 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: "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: "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: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 832 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 11, 'TRANS': 87} 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: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1087 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} 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: {'PTRANS': 15, 'TRANS': 116, 'PCIS': 1} 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: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 542 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 62} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 26 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: {'PTRANS': 25, 'TRANS': 360, 'PCIS': 1} 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: "Bz" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 410 Classifications: {'peptide': 82} Link IDs: {'TRANS': 81} Chain breaks: 5 Chain: "AA" Number of atoms: 20411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 960, 20411 Classifications: {'RNA': 960} Modifications used: {'rna3p_pyr': 373, 'rna2p_pur': 82, 'rna3p_pur': 440, 'rna2p_pyr': 65} Link IDs: {'rna3p': 812, 'rna2p': 147} Chain: "AB" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1762 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 12, 'TRANS': 207} Chain: "AC" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1075 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 7, 'TRANS': 124} Chain: "AE" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2732 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "AF" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 981 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "AG" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1721 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 12, 'TRANS': 195} Chain: "AI" Number of atoms: 2650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2650 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 14, 'TRANS': 313} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "AJ" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1155 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 8, 'TRANS': 131} Chain: "AK" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1007 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 9, 'TRANS': 127} Chain: "AL" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 10, 'TRANS': 98} Chain: "AN" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 858 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "AO" Number of atoms: 1448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1448 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain: "AP" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 932 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "AQ" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 875 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "AR" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 784 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 8, 'TRANS': 88} Chain: "AU" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 734 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain: "AV" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1498 Classifications: {'RNA': 71} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna3p_pur': 29, 'rna2p_pyr': 2, 'rna3p_pyr': 35} Link IDs: {'rna3p': 64, 'rna2p': 6} Chain: "AX" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 354 Classifications: {'RNA': 17} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 7, 'rna2p_pyr': 2, 'rna3p_pyr': 7} Link IDs: {'rna3p': 13, 'rna2p': 3} Chain: "AZ" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 90 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "Aa" Number of atoms: 2378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2378 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 13, 'TRANS': 278} Chain: "Ab" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1101 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain: "Ac" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1367 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 11, 'TRANS': 157} Chain: "Ad" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1467 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 7, 'TRANS': 169} Chain: "Ae" Number of atoms: 3109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3109 Classifications: {'peptide': 388} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 12, 'TRANS': 375} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "Af" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 778 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "Ag" Number of atoms: 2875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2875 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 17, 'TRANS': 335} Chain: "Ah" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1015 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 114, 'PCIS': 1} Chain: "Ai" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 824 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "Aj" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1788 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 16, 'TRANS': 196} Chain: "Ak" Number of atoms: 2222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2222 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 17, 'TRANS': 257} Chain: "Am" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 930 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 9, 'TRANS': 106} Chain: "An" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 639 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "Ao" Number of atoms: 4526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4526 Classifications: {'peptide': 572} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 28, 'TRANS': 543} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 78 Chain: "Ap" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1564 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 21, 'TRANS': 168} 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: "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: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 264 Unusual residues: {' MG': 202, 'SPM': 1} Classifications: {'undetermined': 203, 'RNA': 2} Modifications used: {'rna2p': 2} Link IDs: {None: 203, 'rna2p': 1} 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 198 not shown) Chain breaks: 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: "BC" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' NA': 1, 'GSP': 1, ' MG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: "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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'SPM': 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 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: "AA" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 119 Unusual residues: {' MG': 105, 'SPM': 1} Classifications: {'undetermined': 106} Link IDs: {None: 105} Chain: "AB" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "AR" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "AV" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AX" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Ac" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Ag" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'GTP': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "An" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Ap" 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Ag" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7436 SG CYSB5 110 275.439 135.828 140.064 1.00 33.27 S ATOM 7458 SG CYSB5 113 277.125 137.888 137.391 1.00 26.94 S ATOM 7539 SG CYSB5 123 273.476 137.003 137.061 1.00 26.61 S ATOM 7561 SG CYSB5 126 276.107 134.330 136.665 1.00 32.03 S ATOM 9810 SG CYSB9 73 172.244 162.960 181.362 1.00 39.33 S ATOM 9835 SG CYSB9 76 175.504 164.498 180.255 1.00 36.18 S ATOM 9959 SG CYSB9 89 175.393 160.881 181.281 1.00 43.37 S ATOM 56188 SG CYSBJ 64 192.590 193.195 198.997 1.00 55.72 S ATOM A0642 SG CYSBx 70 190.802 191.222 201.677 1.00 76.91 S ATOM A064N SG CYSBx 73 194.553 191.192 201.486 1.00 64.86 S ATOM A06CW SG CYSBx 108 192.521 189.415 198.865 1.00 36.32 S ATOM A0RXF SG CYSAF 105 144.827 122.765 34.128 1.00 73.92 S ATOM A1110 SG CYSAR 66 143.123 126.097 33.331 1.00 71.22 S ATOM A111M SG CYSAR 69 141.638 122.870 32.281 1.00 74.93 S ATOM A118R SG CYSAR 101 141.729 123.859 35.931 1.00 75.94 S ATOM A0ZLU SG CYSAP 26 142.755 70.370 125.930 1.00 86.53 S ATOM A174Z SG CYSAc 139 141.784 69.987 122.294 1.00 74.47 S ATOM A175D SG CYSAc 141 140.060 67.866 124.946 1.00 85.46 S ATOM A176Z SG CYSAc 149 139.380 71.618 124.802 1.00 80.98 S ATOM A1N6P SG CYSAp 94 113.843 87.334 123.505 1.00 71.50 S ATOM A1N8U SG CYSAp 105 114.606 87.219 119.794 1.00 71.36 S ATOM A1N9F SG CYSAp 108 112.871 84.342 121.469 1.00 98.86 S ATOM A1NHC SG CYSAp 143 116.534 85.011 122.142 1.00 65.92 S Time building chain proxies: 63.12, per 1000 atoms: 0.35 Number of scatterers: 178372 At special positions: 0 Unit cell: (343.33, 305.8, 303.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 6 29.99 S 497 16.00 P 2670 15.00 Mg 326 11.99 Na 1 11.00 O 39848 8.00 N 32449 7.00 C 102575 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYSAm 45 " - pdb=" SG CYSAm 76 " distance=2.04 Simple disulfide: pdb=" SG CYSAm 55 " - pdb=" SG CYSAm 66 " distance=2.04 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 50.28 Conformation dependent library (CDL) restraints added in 11.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZNAR 500 " pdb="ZN ZNAR 500 " - pdb=" SG CYSAR 69 " pdb="ZN ZNAR 500 " - pdb=" SG CYSAR 101 " pdb="ZN ZNAR 500 " - pdb=" SG CYSAR 66 " pdb="ZN ZNAR 500 " - pdb=" SG CYSAF 105 " pdb=" ZNAc 500 " pdb="ZN ZNAc 500 " - pdb=" SG CYSAP 26 " pdb="ZN ZNAc 500 " - pdb=" SG CYSAc 149 " pdb="ZN ZNAc 500 " - pdb=" SG CYSAc 139 " pdb="ZN ZNAc 500 " - pdb=" SG CYSAc 141 " pdb=" ZNAp 500 " pdb="ZN ZNAp 500 " - pdb=" SG CYSAp 105 " pdb="ZN ZNAp 500 " - pdb=" SG CYSAp 108 " pdb="ZN ZNAp 500 " - pdb=" SG CYSAp 143 " pdb="ZN ZNAp 500 " - pdb=" SG CYSAp 94 " pdb=" ZNB5 500 " pdb="ZN ZNB5 500 " - pdb=" SG CYSB5 113 " pdb="ZN ZNB5 500 " - pdb=" SG CYSB5 126 " pdb="ZN ZNB5 500 " - pdb=" SG CYSB5 123 " pdb="ZN ZNB5 500 " - pdb=" SG CYSB5 110 " pdb=" ZNB9 500 " pdb="ZN ZNB9 500 " - pdb=" ND1 HISB9 95 " pdb="ZN ZNB9 500 " - pdb=" SG CYSB9 76 " pdb="ZN ZNB9 500 " - pdb=" SG CYSB9 73 " pdb="ZN ZNB9 500 " - pdb=" SG CYSB9 89 " pdb=" ZNBx 500 " pdb="ZN ZNBx 500 " - pdb=" SG CYSBx 73 " pdb="ZN ZNBx 500 " - pdb=" SG CYSBx 70 " pdb="ZN ZNBx 500 " - pdb=" SG CYSBJ 64 " pdb="ZN ZNBx 500 " - pdb=" SG CYSBx 108 " Number of angles added : 33 29678 Ramachandran restraints generated. 14839 Oldfield, 0 Emsley, 14839 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 28430 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: 532 helices and 117 sheets defined 47.3% alpha, 11.7% beta 714 base pairs and 1408 stacking pairs defined. Time for finding SS restraints: 69.35 Creating SS restraints... Processing helix chain 'CL' and resid 25 through 38 removed outlier: 3.798A pdb=" N GLNCL 29 " --> pdb=" O PROCL 25 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEUCL 38 " --> pdb=" O ASPCL 34 " (cutoff:3.500A) Processing helix chain 'CL' and resid 39 through 54 removed outlier: 3.712A pdb=" N THRCL 53 " --> pdb=" O LEUCL 49 " (cutoff:3.500A) Processing helix chain 'DL' and resid 64 through 74 removed outlier: 3.743A pdb=" N LEUDL 74 " --> pdb=" O ASPDL 70 " (cutoff:3.500A) Processing helix chain 'DL' and resid 75 through 90 removed outlier: 3.819A pdb=" N LEUDL 90 " --> pdb=" O LEUDL 86 " (cutoff:3.500A) Processing helix chain 'FL' and resid 64 through 74 removed outlier: 3.860A 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: 3.516A pdb=" N VALGL 68 " --> pdb=" O ILEGL 64 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEUGL 74 " --> pdb=" O ASPGL 70 " (cutoff:3.500A) Processing helix chain 'GL' and resid 75 through 90 removed outlier: 3.719A pdb=" N LEUGL 90 " --> pdb=" O LEUGL 86 " (cutoff:3.500A) Processing helix chain 'EL' and resid 64 through 75 removed outlier: 3.505A pdb=" N SEREL 73 " --> pdb=" O GLNEL 69 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEUEL 74 " --> pdb=" O ASPEL 70 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N THREL 75 " --> pdb=" O ILEEL 71 " (cutoff:3.500A) Processing helix chain 'EL' and resid 76 through 90 Processing helix chain 'HL' and resid 64 through 75 removed outlier: 3.855A pdb=" N LEUHL 74 " --> pdb=" O ASPHL 70 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N THRHL 75 " --> pdb=" O ILEHL 71 " (cutoff:3.500A) Processing helix chain 'HL' and resid 76 through 89 removed outlier: 3.644A pdb=" N LYSHL 88 " --> pdb=" O GLUHL 84 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THRHL 89 " --> pdb=" O LEUHL 85 " (cutoff:3.500A) Processing helix chain 'B0' and resid 110 through 120 removed outlier: 3.948A pdb=" N LEUB0 120 " --> pdb=" O LEUB0 116 " (cutoff:3.500A) Processing helix chain 'B1' and resid 7 through 19 removed outlier: 3.773A pdb=" N TRPB1 11 " --> pdb=" O PROB1 7 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LYSB1 12 " --> pdb=" O VALB1 8 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N GLNB1 13 " --> pdb=" O GLYB1 9 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEUB1 16 " --> pdb=" O LYSB1 12 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRPB1 17 " --> pdb=" O GLNB1 13 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLUB1 18 " --> pdb=" O LEUB1 14 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N GLYB1 19 " --> pdb=" O ARGB1 15 " (cutoff:3.500A) Processing helix chain 'B1' and resid 25 through 35 removed outlier: 3.911A pdb=" N GLUB1 34 " --> pdb=" O ARGB1 30 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ALAB1 35 " --> pdb=" O SERB1 31 " (cutoff:3.500A) Processing helix chain 'B1' and resid 72 through 79 removed outlier: 4.090A pdb=" N GLNB1 76 " --> pdb=" O PROB1 72 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEUB1 77 " --> pdb=" O PROB1 73 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLYB1 78 " --> pdb=" O GLUB1 74 " (cutoff:3.500A) removed outlier: 4.622A 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 removed outlier: 3.538A pdb=" N THRB1 148 " --> pdb=" O TYRB1 144 " (cutoff:3.500A) 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: 3.810A pdb=" N ARGB1 190 " --> pdb=" O ALAB1 186 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYRB1 191 " --> pdb=" O ILEB1 187 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYSB1 192 " --> pdb=" O TYRB1 188 " (cutoff:3.500A) Processing helix chain 'B1' and resid 197 through 205 removed outlier: 3.510A pdb=" N GLUB1 202 " --> pdb=" O GLUB1 198 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TRPB1 203 " --> pdb=" O ALAB1 199 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VALB1 204 " --> pdb=" O GLUB1 200 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N GLYB1 205 " --> pdb=" O ALAB1 201 " (cutoff:3.500A) Processing helix chain 'B1' and resid 207 through 220 Processing helix chain 'B1' and resid 225 through 245 removed outlier: 3.732A pdb=" N ILEB1 229 " --> pdb=" O PROB1 225 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SERB1 244 " --> pdb=" O GLNB1 240 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLUB1 245 " --> pdb=" O GLNB1 241 " (cutoff:3.500A) Processing helix chain 'B2' and resid 66 through 71 removed outlier: 4.932A pdb=" N PHEB2 70 " --> pdb=" O LEUB2 66 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ASPB2 71 " --> pdb=" O GLUB2 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'B2' and resid 66 through 71' Processing helix chain 'B2' and resid 72 through 77 removed outlier: 3.947A pdb=" N TRPB2 76 " --> pdb=" O ASPB2 72 " (cutoff:3.500A) removed outlier: 5.336A 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: 3.524A pdb=" N LEUB2 92 " --> pdb=" O THRB2 88 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASNB2 94 " --> pdb=" O GLNB2 90 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYSB2 95 " --> pdb=" O GLNB2 91 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N SERB2 96 " --> pdb=" O LEUB2 92 " (cutoff:3.500A) Processing helix chain 'B2' and resid 97 through 125 removed outlier: 3.861A pdb=" N TYRB2 105 " --> pdb=" O HISB2 101 " (cutoff:3.500A) Processing helix chain 'B2' and resid 131 through 160 removed outlier: 3.923A pdb=" N GLUB2 135 " --> pdb=" O PROB2 131 " (cutoff:3.500A) Processing helix chain 'B2' and resid 189 through 194 removed outlier: 3.743A pdb=" N ASNB2 193 " --> pdb=" O PROB2 189 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LYSB2 194 " --> pdb=" O TRPB2 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'B2' and resid 189 through 194' Processing helix chain 'B2' and resid 204 through 241 removed outlier: 4.150A pdb=" N GLUB2 208 " --> pdb=" O METB2 204 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ARGB2 209 " --> pdb=" O PROB2 205 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHEB2 210 " --> pdb=" O TYRB2 206 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEUB2 228 " --> pdb=" O ARGB2 224 " (cutoff:3.500A) Proline residue: B2 241 - end of helix Processing helix chain 'B3' and resid 42 through 48 removed outlier: 4.503A pdb=" N PHEB3 46 " --> pdb=" O PROB3 42 " (cutoff:3.500A) Proline residue: B3 48 - end of helix Processing helix chain 'B3' and resid 49 through 57 removed outlier: 4.053A pdb=" N HISB3 53 " --> pdb=" O SERB3 49 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLUB3 54 " --> pdb=" O PROB3 50 " (cutoff:3.500A) Processing helix chain 'B3' and resid 79 through 90 removed outlier: 3.667A pdb=" N GLYB3 90 " --> pdb=" O ILEB3 86 " (cutoff:3.500A) Processing helix chain 'B3' and resid 103 through 114 removed outlier: 4.124A pdb=" N LYSB3 109 " --> pdb=" O SERB3 105 " (cutoff:3.500A) Processing helix chain 'B3' and resid 130 through 135 removed outlier: 3.763A pdb=" N METB3 134 " --> pdb=" O THRB3 130 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ALAB3 135 " --> pdb=" O GLUB3 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'B3' and resid 130 through 135' Processing helix chain 'B4' and resid 35 through 41 removed outlier: 5.333A pdb=" N ALAB4 39 " --> pdb=" O ASPB4 35 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LEUB4 40 " --> pdb=" O CYSB4 36 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEUB4 41 " --> pdb=" O ASNB4 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'B4' and resid 35 through 41' Processing helix chain 'B5' and resid 86 through 95 Processing helix chain 'B5' and resid 96 through 101 removed outlier: 5.688A pdb=" N ILEB5 101 " --> pdb=" O PROB5 97 " (cutoff:3.500A) Processing helix chain 'B5' and resid 124 through 146 removed outlier: 3.581A pdb=" N GLNB5 144 " --> pdb=" O GLNB5 140 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLUB5 145 " --> pdb=" O METB5 141 " (cutoff:3.500A) removed outlier: 4.866A 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 75 removed outlier: 4.370A pdb=" N THRB7 75 " --> pdb=" O ARGB7 71 " (cutoff:3.500A) Processing helix chain 'B7' and resid 76 through 89 Processing helix chain 'B8' and resid 107 through 114 removed outlier: 3.786A pdb=" N ILEB8 111 " --> pdb=" O VALB8 107 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARGB8 113 " --> pdb=" O ALAB8 109 " (cutoff:3.500A) Processing helix chain 'B8' and resid 132 through 137 removed outlier: 4.220A pdb=" N LYSB8 136 " --> pdb=" O LYSB8 132 " (cutoff:3.500A) removed outlier: 5.546A 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 146 removed outlier: 3.531A pdb=" N GLUB8 146 " --> pdb=" O ARGB8 142 " (cutoff:3.500A) Processing helix chain 'B8' and resid 151 through 163 removed outlier: 4.901A pdb=" N THRB8 163 " --> pdb=" O ASPB8 159 " (cutoff:3.500A) Processing helix chain 'B8' and resid 177 through 182 removed outlier: 3.681A pdb=" N GLNB8 181 " --> pdb=" O TYRB8 177 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ASPB8 182 " --> pdb=" O GLNB8 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'B8' and resid 177 through 182' Processing helix chain 'BC' and resid 192 through 202 Processing helix chain 'BC' and resid 204 through 209 removed outlier: 4.343A pdb=" N VALBC 208 " --> pdb=" O GLNBC 204 " (cutoff:3.500A) Processing helix chain 'BC' and resid 241 through 252 removed outlier: 3.612A pdb=" N ARGBC 247 " --> pdb=" O ALABC 243 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THRBC 252 " --> pdb=" O GLYBC 248 " (cutoff:3.500A) Processing helix chain 'BC' and resid 266 through 280 Processing helix chain 'BC' and resid 296 through 308 removed outlier: 3.641A pdb=" N VALBC 300 " --> pdb=" O ASPBC 296 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYRBC 307 " --> pdb=" O GLUBC 303 " (cutoff:3.500A) Processing helix chain 'BC' and resid 330 through 346 removed outlier: 3.534A pdb=" N GLUBC 346 " --> pdb=" O ALABC 342 " (cutoff:3.500A) Processing helix chain 'BC' and resid 436 through 482 removed outlier: 4.315A pdb=" N TYRBC 481 " --> pdb=" O ALABC 477 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLYBC 482 " --> pdb=" O ARGBC 478 " (cutoff:3.500A) Processing helix chain 'BC' and resid 485 through 497 removed outlier: 4.193A pdb=" N PHEBC 494 " --> pdb=" O SERBC 490 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N LEUBC 495 " --> pdb=" O ILEBC 491 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLUBC 496 " --> pdb=" O LEUBC 492 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ARGBC 497 " --> pdb=" O ARGBC 493 " (cutoff:3.500A) Processing helix chain 'BC' and resid 507 through 512 removed outlier: 4.904A pdb=" N ARGBC 511 " --> pdb=" O GLUBC 507 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ASPBC 512 " --> pdb=" O LYSBC 508 " (cutoff:3.500A) No H-bonds generated for 'chain 'BC' and resid 507 through 512' Processing helix chain 'BC' and resid 524 through 538 removed outlier: 4.001A pdb=" N TYRBC 538 " --> pdb=" O ILEBC 534 " (cutoff:3.500A) Processing helix chain 'BC' and resid 557 through 568 Processing helix chain 'BC' and resid 579 through 590 Processing helix chain 'BC' and resid 598 through 614 Processing helix chain 'BD' and resid 184 through 189 removed outlier: 3.868A 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: 3.749A pdb=" N ASNBD 264 " --> pdb=" O LYSBD 260 " (cutoff:3.500A) Processing helix chain 'BD' and resid 250 through 255 removed outlier: 4.150A pdb=" N ASNBD 254 " --> pdb=" O VALBD 251 " (cutoff:3.500A) Processing helix chain 'BE' and resid 54 through 83 Proline residue: BE 59 - end of helix removed outlier: 3.593A pdb=" N LEUBE 77 " --> pdb=" O LEUBE 73 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N CYSBE 78 " --> pdb=" O ALABE 74 " (cutoff:3.500A) Proline residue: BE 79 - end of helix removed outlier: 4.013A pdb=" N ASPBE 82 " --> pdb=" O CYSBE 78 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLUBE 83 " --> pdb=" O PROBE 79 " (cutoff:3.500A) Processing helix chain 'BE' and resid 134 through 139 removed outlier: 3.566A pdb=" N HISBE 138 " --> pdb=" O PROBE 134 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASNBE 139 " --> pdb=" O LYSBE 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'BE' and resid 134 through 139' Processing helix chain 'BE' and resid 158 through 169 Processing helix chain 'BE' and resid 217 through 222 Processing helix chain 'BE' and resid 310 through 315 removed outlier: 4.839A 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: 4.087A pdb=" N ASPBE 324 " --> pdb=" O PHEBE 320 " (cutoff:3.500A) removed outlier: 4.625A 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 'BE' and resid 194 through 199 removed outlier: 4.313A pdb=" N ARGBE 199 " --> pdb=" O ALABE 196 " (cutoff:3.500A) Processing helix chain 'BF' and resid 92 through 109 removed outlier: 4.710A pdb=" N LYSBF 107 " --> pdb=" O GLNBF 103 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ARGBF 108 " --> pdb=" O LYSBF 104 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ILEBF 109 " --> pdb=" O ASNBF 105 " (cutoff:3.500A) Processing helix chain 'BF' and resid 166 through 185 removed outlier: 3.603A pdb=" N ASPBF 185 " --> pdb=" O LYSBF 181 " (cutoff:3.500A) Processing helix chain 'BF' and resid 199 through 211 removed outlier: 3.922A pdb=" N LEUBF 203 " --> pdb=" O ASPBF 199 " (cutoff:3.500A) Processing helix chain 'BF' and resid 227 through 238 removed outlier: 3.865A pdb=" N GLYBF 236 " --> pdb=" O ALABF 232 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEUBF 237 " --> pdb=" O ALABF 233 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LYSBF 238 " --> pdb=" O THRBF 234 " (cutoff:3.500A) Processing helix chain 'BF' and resid 249 through 257 removed outlier: 5.306A pdb=" N GLNBF 257 " --> pdb=" O METBF 253 " (cutoff:3.500A) Processing helix chain 'BF' and resid 262 through 279 removed outlier: 3.609A pdb=" N GLUBF 271 " --> pdb=" O ALABF 267 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N HISBF 276 " --> pdb=" O LYSBF 272 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ASNBF 277 " --> pdb=" O LEUBF 273 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N SERBF 278 " --> pdb=" O LEUBF 274 " (cutoff:3.500A) removed outlier: 3.656A 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: 4.375A pdb=" N ARGBI 78 " --> pdb=" O HISBI 74 " (cutoff:3.500A) removed outlier: 4.425A 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: 3.710A 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: 4.049A pdb=" N LEUBI 139 " --> pdb=" O GLUBI 135 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHEBI 140 " --> pdb=" O ASNBI 136 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLNBI 148 " --> pdb=" O LYSBI 144 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLUBI 149 " --> pdb=" O LEUBI 145 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLYBI 150 " --> pdb=" O LEUBI 146 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 41 through 52 removed outlier: 3.630A pdb=" N GLUBJ 52 " --> pdb=" O METBJ 48 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 61 through 66 Proline residue: BJ 66 - end of helix Processing helix chain 'BJ' and resid 76 through 93 removed outlier: 3.595A pdb=" N ASNBJ 93 " --> pdb=" O VALBJ 89 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 105 through 120 removed outlier: 3.879A pdb=" N HISBJ 119 " --> pdb=" O GLNBJ 115 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 127 through 138 Proline residue: BJ 133 - end of helix Processing helix chain 'BJ' and resid 140 through 148 removed outlier: 4.648A pdb=" N LEUBJ 144 " --> pdb=" O TYRBJ 140 " (cutoff:3.500A) Proline residue: BJ 145 - end of helix removed outlier: 4.206A pdb=" N VALBJ 148 " --> pdb=" O LEUBJ 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'BJ' and resid 140 through 148' Processing helix chain 'BJ' and resid 160 through 172 removed outlier: 3.840A pdb=" N METBJ 164 " --> pdb=" O LYSBJ 160 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILEBJ 167 " --> pdb=" O GLUBJ 163 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLYBJ 170 " --> pdb=" O ARGBJ 166 " (cutoff:3.500A) removed outlier: 3.827A 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 223 removed outlier: 4.107A pdb=" N VALBJ 208 " --> pdb=" O GLNBJ 204 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLYBJ 209 " --> pdb=" O GLYBJ 205 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N LEUBJ 214 " --> pdb=" O GLYBJ 210 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N THRBJ 215 " --> pdb=" O LEUBJ 211 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 224 through 239 removed outlier: 3.996A pdb=" N LEUBJ 229 " --> pdb=" O GLNBJ 225 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THRBJ 230 " --> pdb=" O PROBJ 226 " (cutoff:3.500A) Processing helix chain 'BK' and resid 33 through 43 Proline residue: BK 37 - end of helix removed outlier: 3.544A pdb=" N GLNBK 41 " --> pdb=" O PROBK 37 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARGBK 42 " --> pdb=" O ILEBK 38 " (cutoff:3.500A) Processing helix chain 'BK' and resid 45 through 58 removed outlier: 3.772A 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 128 removed outlier: 3.644A pdb=" N VALBK 117 " --> pdb=" O THRBK 113 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLNBK 126 " --> pdb=" O ARGBK 122 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ASPBK 127 " --> pdb=" O VALBK 123 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ASPBK 128 " --> pdb=" O LYSBK 124 " (cutoff:3.500A) Processing helix chain 'BK' and resid 129 through 134 removed outlier: 4.080A pdb=" N GLNBK 133 " --> pdb=" O ALABK 129 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ASPBK 134 " --> pdb=" O PHEBK 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'BK' and resid 129 through 134' Processing helix chain 'BK' and resid 136 through 152 removed outlier: 3.675A pdb=" N VALBK 140 " --> pdb=" O PROBK 136 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SERBK 150 " --> pdb=" O GLYBK 146 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEUBK 151 " --> pdb=" O SERBK 147 " (cutoff:3.500A) Processing helix chain 'BK' and resid 164 through 192 removed outlier: 4.234A pdb=" N ALABK 172 " --> pdb=" O GLNBK 168 " (cutoff:3.500A) Processing helix chain 'BL' and resid 141 through 154 removed outlier: 3.878A pdb=" N GLNBL 154 " --> pdb=" O LYSBL 150 " (cutoff:3.500A) Processing helix chain 'BL' and resid 157 through 168 removed outlier: 3.940A pdb=" N LEUBL 168 " --> pdb=" O LEUBL 164 " (cutoff:3.500A) Processing helix chain 'BL' and resid 177 through 192 removed outlier: 3.601A pdb=" N GLYBL 192 " --> pdb=" O LEUBL 188 " (cutoff:3.500A) Processing helix chain 'BN' and resid 5 through 15 Processing helix chain 'BN' and resid 27 through 41 removed outlier: 3.662A 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: 4.628A pdb=" N ARGBN 119 " --> pdb=" O ASNBN 115 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THRBN 120 " --> pdb=" O LEUBN 116 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLNBN 123 " --> pdb=" O ARGBN 119 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARGBN 124 " --> pdb=" O THRBN 120 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEUBN 125 " --> pdb=" O METBN 121 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N HISBN 126 " --> pdb=" O METBN 122 " (cutoff:3.500A) Processing helix chain 'BN' and resid 134 through 141 removed outlier: 3.785A pdb=" N ASNBN 140 " --> pdb=" O ASPBN 136 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEUBN 141 " --> pdb=" O ILEBN 137 " (cutoff:3.500A) Processing helix chain 'BN' and resid 159 through 167 Proline residue: BN 167 - end of helix Processing helix chain 'BO' and resid 124 through 131 removed outlier: 4.823A pdb=" N ARGBO 128 " --> pdb=" O PROBO 124 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLNBO 129 " --> pdb=" O SERBO 125 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ARGBO 130 " --> pdb=" O SERBO 126 " (cutoff:3.500A) removed outlier: 4.902A 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: 4.058A pdb=" N ILEBO 140 " --> pdb=" O LYSBO 136 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALABO 141 " --> pdb=" O VALBO 137 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N GLNBO 142 " --> pdb=" O LEUBO 138 " (cutoff:3.500A) Processing helix chain 'BP' and resid 10 through 20 removed outlier: 4.256A pdb=" N ASPBP 14 " --> pdb=" O PROBP 10 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEUBP 15 " --> pdb=" O ARGBP 11 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARGBP 17 " --> pdb=" O LEUBP 13 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALABP 18 " --> pdb=" O ASPBP 14 " (cutoff:3.500A) Proline residue: BP 20 - end of helix Processing helix chain 'BP' and resid 55 through 60 removed outlier: 4.053A pdb=" N ARGBP 59 " --> pdb=" O GLYBP 55 " (cutoff:3.500A) Processing helix chain 'BP' and resid 73 through 78 removed outlier: 3.651A pdb=" N ILEBP 78 " --> pdb=" O PHEBP 74 " (cutoff:3.500A) Processing helix chain 'BP' and resid 86 through 91 removed outlier: 3.606A pdb=" N ARGBP 90 " --> pdb=" O GLYBP 86 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N HISBP 91 " --> pdb=" O HISBP 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'BP' and resid 86 through 91' 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 removed outlier: 4.170A pdb=" N ASNBP 170 " --> pdb=" O ALABP 166 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLYBP 171 " --> pdb=" O ILEBP 167 " (cutoff:3.500A) 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: 3.829A pdb=" N ARGBP 196 " --> pdb=" O PROBP 192 " (cutoff:3.500A) removed outlier: 4.184A 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: 3.992A pdb=" N ASPBP 216 " --> pdb=" O PROBP 212 " (cutoff:3.500A) Processing helix chain 'BP' and resid 225 through 241 removed outlier: 3.735A pdb=" N PHEBP 229 " --> pdb=" O ASPBP 225 " (cutoff:3.500A) Proline residue: BP 230 - end of helix removed outlier: 3.671A pdb=" N ALABP 237 " --> pdb=" O ARGBP 233 " (cutoff:3.500A) Processing helix chain 'BP' and resid 252 through 258 removed outlier: 3.966A pdb=" N THRBP 258 " --> pdb=" O LYSBP 254 " (cutoff:3.500A) Processing helix chain 'BP' and resid 287 through 296 Processing helix chain 'BQ' and resid 68 through 74 removed outlier: 5.132A pdb=" N ILEBQ 72 " --> pdb=" O ASNBQ 68 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARGBQ 73 " --> pdb=" O LEUBQ 69 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N GLYBQ 74 " --> pdb=" O SERBQ 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'BQ' and resid 68 through 74' Processing helix chain 'BQ' and resid 98 through 113 Processing helix chain 'BQ' and resid 170 through 184 removed outlier: 4.201A pdb=" N LEUBQ 178 " --> pdb=" O GLYBQ 174 " (cutoff:3.500A) removed outlier: 3.761A 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 removed outlier: 3.664A pdb=" N ALABQ 221 " --> pdb=" O ARGBQ 217 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 225 through 231 removed outlier: 4.672A pdb=" N VALBQ 229 " --> pdb=" O GLYBQ 225 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N SERBQ 231 " --> pdb=" O ARGBQ 227 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 232 through 238 removed outlier: 4.375A pdb=" N THRBQ 236 " --> pdb=" O PROBQ 232 " (cutoff:3.500A) Processing helix chain 'BR' and resid 21 through 40 Processing helix chain 'BR' and resid 46 through 66 removed outlier: 4.308A pdb=" N GLYBR 54 " --> pdb=" O ASPBR 50 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N TYRBR 55 " --> pdb=" O GLUBR 51 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILEBR 60 " --> pdb=" O ALABR 56 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASPBR 61 " --> pdb=" O GLUBR 57 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLYBR 66 " --> pdb=" O TYRBR 62 " (cutoff:3.500A) Processing helix chain 'BR' and resid 69 through 80 Processing helix chain 'BR' and resid 82 through 98 removed outlier: 4.443A pdb=" N ILEBR 86 " --> pdb=" O GLUBR 82 " (cutoff:3.500A) Proline residue: BR 87 - end of helix removed outlier: 3.732A pdb=" N LEUBR 93 " --> pdb=" O LEUBR 89 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ALABR 94 " --> pdb=" O PHEBR 90 " (cutoff:3.500A) Proline residue: BR 95 - end of helix removed outlier: 4.698A pdb=" N GLNBR 98 " --> pdb=" O ALABR 94 " (cutoff:3.500A) Processing helix chain 'BR' and resid 144 through 161 removed outlier: 3.505A pdb=" N LEUBR 153 " --> pdb=" O LEUBR 149 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SERBR 161 " --> pdb=" O GLNBR 157 " (cutoff:3.500A) Processing helix chain 'BS' and resid 54 through 60 Processing helix chain 'BS' and resid 109 through 116 removed outlier: 4.105A pdb=" N HISBS 115 " --> pdb=" O ALABS 111 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEUBS 116 " --> pdb=" O ILEBS 112 " (cutoff:3.500A) Processing helix chain 'BS' and resid 121 through 140 Processing helix chain 'BS' and resid 149 through 156 removed outlier: 3.628A pdb=" N ALABS 154 " --> pdb=" O PROBS 150 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SERBS 155 " --> pdb=" O TRPBS 151 " (cutoff:3.500A) removed outlier: 5.863A 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 64 through 69 Proline residue: BT 68 - end of helix No H-bonds generated for 'chain 'BT' and resid 64 through 69' Processing helix chain 'BT' and resid 88 through 106 removed outlier: 4.131A pdb=" N PHEBT 92 " --> pdb=" O ASNBT 88 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYSBT 104 " --> pdb=" O LEUBT 100 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILEBT 105 " --> pdb=" O GLUBT 101 " (cutoff:3.500A) Processing helix chain 'BT' and resid 188 through 194 removed outlier: 4.794A pdb=" N ASPBT 192 " --> pdb=" O LEUBT 188 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEUBT 194 " --> pdb=" O LEUBT 190 " (cutoff:3.500A) Processing helix chain 'BT' and resid 195 through 200 removed outlier: 5.390A pdb=" N PHEBT 200 " --> pdb=" O GLUBT 196 " (cutoff:3.500A) Processing helix chain 'BT' and resid 244 through 249 removed outlier: 4.076A pdb=" N CYSBT 248 " --> pdb=" O ARGBT 244 " (cutoff:3.500A) Processing helix chain 'BT' and resid 250 through 268 removed outlier: 3.540A pdb=" N GLNBT 258 " --> pdb=" O METBT 254 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYSBT 259 " --> pdb=" O ARGBT 255 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N TRPBT 260 " --> pdb=" O GLUBT 256 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N SERBT 261 " --> pdb=" O ALABT 257 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N GLNBT 262 " --> pdb=" O GLNBT 258 " (cutoff:3.500A) Proline residue: BT 263 - end of helix removed outlier: 4.711A pdb=" N GLUBT 266 " --> pdb=" O GLNBT 262 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N PHEBT 267 " --> pdb=" O PROBT 263 " (cutoff:3.500A) Processing helix chain 'BT' and resid 275 through 292 removed outlier: 3.849A pdb=" N SERBT 292 " --> pdb=" O ALABT 288 " (cutoff:3.500A) Processing helix chain 'BT' and resid 77 through 82 Proline residue: BT 82 - end of helix Processing helix chain 'BU' and resid 16 through 29 removed outlier: 3.564A pdb=" N ARGBU 20 " --> pdb=" O ASPBU 16 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VALBU 24 " --> pdb=" O ARGBU 20 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N HISBU 27 " --> pdb=" O GLUBU 23 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALABU 28 " --> pdb=" O VALBU 24 " (cutoff:3.500A) Processing helix chain 'BU' and resid 33 through 38 removed outlier: 4.956A pdb=" N ARGBU 37 " --> pdb=" O GLYBU 33 " (cutoff:3.500A) Processing helix chain 'BU' and resid 46 through 79 removed outlier: 4.257A pdb=" N LYSBU 61 " --> pdb=" O ARGBU 57 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ARGBU 62 " --> pdb=" O ARGBU 58 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N HISBU 79 " --> pdb=" O ALABU 75 " (cutoff:3.500A) Processing helix chain 'BU' and resid 82 through 94 removed outlier: 3.548A pdb=" N CYSBU 93 " --> pdb=" O ASNBU 89 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLNBU 94 " --> pdb=" O LEUBU 90 " (cutoff:3.500A) Processing helix chain 'BU' and resid 98 through 109 Processing helix chain 'BU' and resid 110 through 134 removed outlier: 3.623A pdb=" N ASPBU 134 " --> pdb=" O ALABU 130 " (cutoff:3.500A) Processing helix chain 'BV' and resid 72 through 94 Processing helix chain 'BV' and resid 154 through 159 removed outlier: 3.613A pdb=" N VALBV 158 " --> pdb=" O GLYBV 154 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ARGBV 159 " --> pdb=" O LYSBV 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'BV' and resid 154 through 159' Processing helix chain 'BW' and resid 47 through 55 removed outlier: 5.189A pdb=" N LYSBW 51 " --> pdb=" O ARGBW 47 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASNBW 53 " --> pdb=" O TRPBW 49 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LYSBW 54 " --> pdb=" O GLUBW 50 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILEBW 55 " --> pdb=" O LYSBW 51 " (cutoff:3.500A) Processing helix chain 'BW' and resid 81 through 93 removed outlier: 3.825A pdb=" N LEUBW 88 " --> pdb=" O LYSBW 84 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILEBW 92 " --> pdb=" O LEUBW 88 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARGBW 93 " --> pdb=" O ALABW 89 " (cutoff:3.500A) Processing helix chain 'BW' and resid 96 through 108 removed outlier: 3.797A pdb=" N PHEBW 106 " --> pdb=" O ALABW 102 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SERBW 107 " --> pdb=" O GLNBW 103 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ASPBW 108 " --> pdb=" O LEUBW 104 " (cutoff:3.500A) Processing helix chain 'BW' and resid 109 through 129 removed outlier: 4.279A pdb=" N GLNBW 113 " --> pdb=" O LYSBW 109 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILEBW 114 " --> pdb=" O LYSBW 110 " (cutoff:3.500A) Processing helix chain 'BW' and resid 189 through 204 removed outlier: 3.637A pdb=" N ARGBW 204 " --> pdb=" O GLUBW 200 " (cutoff:3.500A) Processing helix chain 'BX' and resid 49 through 60 Processing helix chain 'BX' and resid 114 through 136 Processing helix chain 'BY' and resid 28 through 36 Proline residue: BY 36 - end of helix Processing helix chain 'BY' and resid 50 through 55 removed outlier: 3.562A pdb=" N TRPBY 54 " --> pdb=" O SERBY 50 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N HISBY 55 " --> pdb=" O ASPBY 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'BY' and resid 50 through 55' Processing helix chain 'BY' and resid 116 through 121 removed outlier: 3.891A pdb=" N VALBY 120 " --> pdb=" O LEUBY 116 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LYSBY 121 " --> pdb=" O HISBY 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'BY' and resid 116 through 121' Processing helix chain 'BY' and resid 178 through 184 Processing helix chain 'BY' and resid 193 through 203 Processing helix chain 'Ba' and resid 35 through 40 removed outlier: 5.688A pdb=" N LYSBa 40 " --> pdb=" O ARGBa 36 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 47 through 52 removed outlier: 4.287A pdb=" N GLUBa 51 " --> pdb=" O ASPBa 47 " (cutoff:3.500A) removed outlier: 4.134A 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 removed outlier: 3.567A pdb=" N ASPBa 142 " --> pdb=" O ARGBa 138 " (cutoff:3.500A) 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: 4.439A pdb=" N GLNBa 191 " --> pdb=" O LEUBa 187 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILEBa 192 " --> pdb=" O CYSBa 188 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LEUBa 193 " --> pdb=" O LYSBa 189 " (cutoff:3.500A) removed outlier: 5.382A 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: 3.690A pdb=" N LYSBa 249 " --> pdb=" O VALBa 245 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASNBa 250 " --> pdb=" O GLUBa 246 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N HISBa 251 " --> pdb=" O ALABa 247 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N VALBa 252 " --> pdb=" O THRBa 248 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 299 through 304 removed outlier: 3.627A pdb=" N ARGBa 303 " --> pdb=" O LEUBa 299 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N PHEBa 304 " --> pdb=" O ARGBa 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ba' and resid 299 through 304' Processing helix chain 'Ba' and resid 305 through 329 removed outlier: 3.599A pdb=" N GLNBa 324 " --> pdb=" O SERBa 320 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYRBa 329 " --> pdb=" O ALABa 325 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 407 through 420 removed outlier: 3.984A pdb=" N PHEBa 411 " --> pdb=" O GLNBa 407 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 44 through 49 removed outlier: 4.162A pdb=" N LEUBb 48 " --> pdb=" O ASPBb 44 " (cutoff:3.500A) removed outlier: 5.560A 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: 3.573A pdb=" N TYRBb 57 " --> pdb=" O SERBb 53 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARGBb 66 " --> pdb=" O GLUBb 62 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYSBb 67 " --> pdb=" O GLNBb 63 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 73 through 79 removed outlier: 3.571A pdb=" N HISBb 77 " --> pdb=" O THRBb 73 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 98 through 116 removed outlier: 3.729A pdb=" N ASNBb 116 " --> pdb=" O GLUBb 112 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 117 through 126 removed outlier: 3.687A pdb=" N GLNBb 126 " --> pdb=" O ALABb 122 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 131 through 142 Processing helix chain 'Bb' and resid 143 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 281 through 286 removed outlier: 3.672A pdb=" N THRBb 285 " --> pdb=" O PHEBb 281 " (cutoff:3.500A) removed outlier: 5.919A 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: 4.018A pdb=" N THRBb 297 " --> pdb=" O LEUBb 293 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 299 through 308 removed outlier: 3.681A pdb=" N HISBb 307 " --> pdb=" O PHEBb 303 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 324 through 333 removed outlier: 4.268A pdb=" N THRBb 328 " --> pdb=" O ASPBb 324 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ARGBb 329 " --> pdb=" O ASPBb 325 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VALBb 330 " --> pdb=" O SERBb 326 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHEBb 331 " --> pdb=" O VALBb 327 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HISBb 332 " --> pdb=" O THRBb 328 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 362 through 370 removed outlier: 4.819A pdb=" N LEUBb 366 " --> pdb=" O PROBb 362 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ASPBb 367 " --> pdb=" O LEUBb 363 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARGBb 368 " --> pdb=" O ARGBb 364 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N TYRBb 369 " --> pdb=" O TYRBb 365 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARGBb 370 " --> pdb=" O LEUBb 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bb' and resid 362 through 370' Processing helix chain 'Bc' and resid 33 through 57 removed outlier: 3.590A pdb=" N ILEBc 38 " --> pdb=" O PROBc 34 " (cutoff:3.500A) removed outlier: 3.794A 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 removed outlier: 4.010A pdb=" N HISBc 91 " --> pdb=" O SERBc 87 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEUBc 92 " --> pdb=" O CYSBc 88 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 94 through 100 Processing helix chain 'Bc' and resid 132 through 155 removed outlier: 3.981A pdb=" N PHEBc 155 " --> pdb=" O ILEBc 151 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 183 through 188 removed outlier: 3.738A pdb=" N ASPBc 187 " --> pdb=" O ASPBc 183 " (cutoff:3.500A) removed outlier: 5.373A 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: 3.648A pdb=" N LYSBc 209 " --> pdb=" O ALABc 205 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ASPBc 210 " --> pdb=" O LEUBc 206 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 219 through 228 removed outlier: 3.837A pdb=" N GLUBc 225 " --> pdb=" O LYSBc 221 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILEBc 226 " --> pdb=" O VALBc 222 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHEBc 227 " --> pdb=" O ALABc 223 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 230 through 245 removed outlier: 4.006A 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: 3.632A pdb=" N ARGBc 317 " --> pdb=" O LEUBc 313 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYSBc 318 " --> pdb=" O GLUBc 314 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 268 through 273 removed outlier: 3.934A pdb=" N ILEBc 271 " --> pdb=" O ARGBc 268 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N PHEBc 273 " --> pdb=" O SERBc 270 " (cutoff:3.500A) Processing helix chain 'Bd' and resid 107 through 154 removed outlier: 3.540A pdb=" N SERBd 111 " --> pdb=" O PROBd 107 " (cutoff:3.500A) Processing helix chain 'Bd' and resid 155 through 162 removed outlier: 3.893A pdb=" N THRBd 162 " --> pdb=" O HISBd 158 " (cutoff:3.500A) Processing helix chain 'Bd' and resid 95 through 101 removed outlier: 4.038A pdb=" N GLUBd 98 " --> pdb=" O LEUBd 95 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ARGBd 99 " --> pdb=" O ASNBd 96 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLNBd 100 " --> pdb=" O LYSBd 97 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARGBd 101 " --> pdb=" O GLUBd 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bd' and resid 95 through 101' Processing helix chain 'Be' and resid 51 through 56 removed outlier: 3.639A 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 removed outlier: 3.533A pdb=" N THRBe 93 " --> pdb=" O LEUBe 89 " (cutoff:3.500A) Processing helix chain 'Be' and resid 95 through 105 Processing helix chain 'Bf' and resid 68 through 73 removed outlier: 4.031A pdb=" N THRBf 72 " --> pdb=" O PROBf 68 " (cutoff:3.500A) removed outlier: 5.538A 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: 3.658A pdb=" N LEUBf 96 " --> pdb=" O LEUBf 92 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLUBf 97 " --> pdb=" O LYSBf 93 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLUBf 98 " --> pdb=" O THRBf 94 " (cutoff:3.500A) removed outlier: 5.001A 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 127 through 134 removed outlier: 3.791A pdb=" N ARGBf 133 " --> pdb=" O TYRBf 129 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARGBf 134 " --> pdb=" O HISBf 130 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 16 through 21 removed outlier: 4.510A pdb=" N GLYBg 20 " --> pdb=" O HISBg 16 " (cutoff:3.500A) removed outlier: 6.578A 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: 3.964A pdb=" N ARGBg 41 " --> pdb=" O ALABg 37 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N GLYBg 42 " --> pdb=" O PROBg 38 " (cutoff:3.500A) removed outlier: 5.533A 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 removed outlier: 3.592A pdb=" N ILEBg 97 " --> pdb=" O SERBg 93 " (cutoff:3.500A) Processing helix chain 'Bh' and resid 34 through 54 removed outlier: 4.780A pdb=" N ALABh 38 " --> pdb=" O GLYBh 34 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLUBh 44 " --> pdb=" O ARGBh 40 " (cutoff:3.500A) Proline residue: Bh 54 - end of helix Processing helix chain 'Bh' and resid 59 through 64 removed outlier: 3.674A pdb=" N LYSBh 63 " --> pdb=" O ARGBh 59 " (cutoff:3.500A) Proline residue: Bh 64 - end of helix No H-bonds generated for 'chain 'Bh' and resid 59 through 64' Processing helix chain 'Bh' and resid 67 through 80 removed outlier: 3.709A pdb=" N LEUBh 79 " --> pdb=" O PHEBh 75 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLNBh 80 " --> pdb=" O GLYBh 76 " (cutoff:3.500A) Processing helix chain 'Bh' and resid 84 through 94 removed outlier: 3.972A pdb=" N VALBh 93 " --> pdb=" O LYSBh 89 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ASNBh 94 " --> pdb=" O THRBh 90 " (cutoff:3.500A) Processing helix chain 'Bh' and resid 95 through 109 removed outlier: 3.527A pdb=" N LEUBh 108 " --> pdb=" O LYSBh 104 " (cutoff:3.500A) Processing helix chain 'Bh' and resid 113 through 119 removed outlier: 4.227A pdb=" N LEUBh 119 " --> pdb=" O ALABh 115 " (cutoff:3.500A) Processing helix chain 'Bh' and resid 122 through 146 Proline residue: Bh 146 - end of helix 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: 3.932A pdb=" N ILEBh 220 " --> pdb=" O ARGBh 216 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THRBh 221 " --> pdb=" O ASPBh 217 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N GLNBh 222 " --> pdb=" O PHEBh 218 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N METBh 223 " --> pdb=" O LEUBh 219 " (cutoff:3.500A) Processing helix chain 'Bh' and resid 227 through 233 removed outlier: 4.537A pdb=" N METBh 231 " --> pdb=" O GLUBh 227 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THRBh 233 " --> pdb=" O PHEBh 229 " (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: 4.295A pdb=" N SERBi 52 " --> pdb=" O PROBi 48 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYSBi 54 " --> pdb=" O TYRBi 50 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 65 through 72 removed outlier: 3.762A pdb=" N HISBi 69 " --> pdb=" O LEUBi 65 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEUBi 72 " --> pdb=" O PROBi 68 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 93 through 101 removed outlier: 3.748A pdb=" N SERBi 98 " --> pdb=" O ASPBi 94 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SERBi 99 " --> pdb=" O ALABi 95 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LEUBi 100 " --> pdb=" O ARGBi 96 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N SERBi 101 " --> pdb=" O ILEBi 97 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 102 through 115 removed outlier: 3.850A pdb=" N ALABi 106 " --> pdb=" O LYSBi 102 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASNBi 115 " --> pdb=" O ARGBi 111 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 116 through 129 Processing helix chain 'Bi' and resid 133 through 155 removed outlier: 3.753A pdb=" N PHEBi 137 " --> pdb=" O LYSBi 133 " (cutoff:3.500A) Proline residue: Bi 138 - end of helix removed outlier: 3.662A pdb=" N ASNBi 154 " --> pdb=" O LEUBi 150 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 156 through 164 removed outlier: 3.612A pdb=" N LEUBi 160 " --> pdb=" O ASPBi 156 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THRBi 162 " --> pdb=" O ASPBi 158 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 165 through 173 Proline residue: Bi 170 - end of helix Processing helix chain 'Bj' and resid 64 through 82 Processing helix chain 'Bj' and resid 85 through 104 removed outlier: 3.768A pdb=" N GLUBj 94 " --> pdb=" O ARGBj 90 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALABj 99 " --> pdb=" O ALABj 95 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SERBj 103 " --> pdb=" O ALABj 99 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASPBj 104 " --> pdb=" O LYSBj 100 " (cutoff:3.500A) Processing helix chain 'Bj' and resid 116 through 132 removed outlier: 3.812A pdb=" N LEUBj 120 " --> pdb=" O LEUBj 116 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHEBj 131 " --> pdb=" O LYSBj 127 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N LYSBj 132 " --> pdb=" O PHEBj 128 " (cutoff:3.500A) Processing helix chain 'Bj' and resid 137 through 143 removed outlier: 4.673A pdb=" N ASPBj 141 " --> pdb=" O LEUBj 137 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LYSBj 142 " --> pdb=" O THRBj 138 " (cutoff:3.500A) Processing helix chain 'Bj' and resid 183 through 197 removed outlier: 3.648A pdb=" N SERBj 196 " --> pdb=" O LEUBj 192 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLUBj 197 " --> pdb=" O ALABj 193 " (cutoff:3.500A) Processing helix chain 'Bj' and resid 256 through 264 removed outlier: 3.836A pdb=" N LEUBj 264 " --> pdb=" O LEUBj 260 " (cutoff:3.500A) Processing helix chain 'Bj' and resid 266 through 277 removed outlier: 3.782A pdb=" N GLNBj 271 " --> pdb=" O LYSBj 267 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VALBj 272 " --> pdb=" O TYRBj 268 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ARGBj 273 " --> pdb=" O LEUBj 269 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ARGBj 274 " --> pdb=" O ALABj 270 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHEBj 275 " --> pdb=" O GLNBj 271 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N LEUBj 277 " --> pdb=" O ARGBj 273 " (cutoff:3.500A) Processing helix chain 'Bk' and resid 59 through 64 removed outlier: 4.111A pdb=" N VALBk 63 " --> pdb=" O TYRBk 59 " (cutoff:3.500A) removed outlier: 4.695A 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 'Bl' and resid 44 through 52 removed outlier: 3.889A pdb=" N VALBl 48 " --> pdb=" O GLUBl 44 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARGBl 50 " --> pdb=" O HISBl 46 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LEUBl 51 " --> pdb=" O PHEBl 47 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEUBl 52 " --> pdb=" O VALBl 48 " (cutoff:3.500A) Processing helix chain 'Bl' and resid 116 through 132 removed outlier: 3.708A pdb=" N LEUBl 120 " --> pdb=" O ASPBl 116 " (cutoff:3.500A) 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 122 removed outlier: 4.749A pdb=" N HISBm 119 " --> pdb=" O ASNBm 115 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLNBm 120 " --> pdb=" O SERBm 116 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N CYSBm 122 " --> pdb=" O LEUBm 118 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 123 through 133 removed outlier: 4.253A pdb=" N VALBm 127 " --> pdb=" O ARGBm 123 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VALBm 133 " --> pdb=" O ASPBm 129 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 139 through 148 removed outlier: 3.635A pdb=" N ALABm 146 " --> pdb=" O ASPBm 142 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SERBm 147 " --> pdb=" O GLUBm 143 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ASNBm 148 " --> pdb=" O LEUBm 144 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 48 through 54 removed outlier: 3.586A pdb=" N PHEBn 54 " --> pdb=" O LYSBn 50 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 59 through 64 Processing helix chain 'Bn' and resid 69 through 74 removed outlier: 4.577A pdb=" N LEUBn 73 " --> pdb=" O HISBn 69 " (cutoff:3.500A) removed outlier: 4.127A 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 removed outlier: 3.608A pdb=" N ARGBo 28 " --> pdb=" O GLYBo 24 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLYBo 32 " --> pdb=" O ARGBo 28 " (cutoff:3.500A) Processing helix chain 'Bo' and resid 41 through 46 Processing helix chain 'Bo' and resid 60 through 108 removed outlier: 3.646A pdb=" N GLUBo 103 " --> pdb=" O LEUBo 99 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLNBo 106 " --> pdb=" O GLUBo 102 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASNBo 108 " --> pdb=" O GLYBo 104 " (cutoff:3.500A) Processing helix chain 'Bo' and resid 114 through 119 removed outlier: 4.559A pdb=" N GLNBo 118 " --> pdb=" O GLYBo 114 " (cutoff:3.500A) removed outlier: 4.381A 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: 3.625A pdb=" N ALABp 6 " --> pdb=" O ALABp 2 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEUBp 8 " --> pdb=" O ALABp 4 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLYBp 9 " --> pdb=" O LEUBp 5 " (cutoff:3.500A) Processing helix chain 'Bp' and resid 27 through 39 removed outlier: 3.718A pdb=" N SERBp 39 " --> pdb=" O GLNBp 35 " (cutoff:3.500A) Processing helix chain 'Bp' and resid 40 through 47 removed outlier: 4.310A pdb=" N ASNBp 46 " --> pdb=" O VALBp 42 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N LEUBp 47 " --> pdb=" O ARGBp 43 " (cutoff:3.500A) Processing helix chain 'Bp' and resid 82 through 98 removed outlier: 3.654A pdb=" N ALABp 96 " --> pdb=" O SERBp 92 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARGBp 97 " --> pdb=" O HISBp 93 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLYBp 98 " --> pdb=" O ILEBp 94 " (cutoff:3.500A) Processing helix chain 'Bq' and resid 76 through 84 removed outlier: 4.003A pdb=" N GLYBq 81 " --> pdb=" O ILEBq 77 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VALBq 84 " --> pdb=" O GLUBq 80 " (cutoff:3.500A) Processing helix chain 'Bq' and resid 93 through 99 removed outlier: 4.400A pdb=" N PHEBq 97 " --> pdb=" O PROBq 93 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLUBq 98 " --> pdb=" O GLUBq 94 " (cutoff:3.500A) Processing helix chain 'Bq' and resid 106 through 111 removed outlier: 3.746A pdb=" N LEUBq 110 " --> pdb=" O LYSBq 106 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ASPBq 111 " --> pdb=" O LEUBq 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bq' and resid 106 through 111' Processing helix chain 'Bq' and resid 114 through 135 removed outlier: 3.805A pdb=" N TRPBq 118 " --> pdb=" O THRBq 114 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYSBq 134 " --> pdb=" O ASNBq 130 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ASNBq 135 " --> pdb=" O ARGBq 131 " (cutoff:3.500A) Processing helix chain 'Bt' and resid 28 through 51 removed outlier: 3.908A pdb=" N SERBt 50 " --> pdb=" O GLNBt 46 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ARGBt 51 " --> pdb=" O TYRBt 47 " (cutoff:3.500A) Processing helix chain 'Bt' and resid 55 through 60 removed outlier: 3.508A pdb=" N GLUBt 59 " --> pdb=" O THRBt 55 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARGBt 60 " --> pdb=" O ALABt 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bt' and resid 55 through 60' Processing helix chain 'Bt' and resid 63 through 81 removed outlier: 4.510A pdb=" N ARGBt 67 " --> pdb=" O ALABt 63 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ARGBt 81 " --> pdb=" O ALABt 77 " (cutoff:3.500A) Processing helix chain 'Bt' and resid 87 through 97 removed outlier: 3.922A pdb=" N GLNBt 91 " --> pdb=" O ARGBt 87 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LEUBt 95 " --> pdb=" O GLNBt 91 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEUBt 96 " --> pdb=" O LEUBt 92 " (cutoff:3.500A) removed outlier: 4.662A 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: 3.734A pdb=" N LYSBu 66 " --> pdb=" O PROBu 62 " (cutoff:3.500A) removed outlier: 3.990A 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: 4.202A pdb=" N LEUBu 76 " --> pdb=" O PROBu 72 " (cutoff:3.500A) removed outlier: 5.493A 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 removed outlier: 3.716A pdb=" N ALABu 119 " --> pdb=" O ARGBu 115 " (cutoff:3.500A) Processing helix chain 'Bu' and resid 141 through 163 Proline residue: Bu 163 - end of helix Processing helix chain 'Bu' and resid 170 through 189 removed outlier: 4.047A pdb=" N LEUBu 174 " --> pdb=" O GLUBu 170 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ARGBu 176 " --> pdb=" O ALABu 172 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N SERBu 177 " --> pdb=" O GLUBu 173 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEUBu 187 " --> pdb=" O ASNBu 183 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYSBu 189 " --> pdb=" O GLUBu 185 " (cutoff:3.500A) Processing helix chain 'Bv' and resid 48 through 53 removed outlier: 3.851A pdb=" N LEUBv 52 " --> pdb=" O PROBv 48 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SERBv 53 " --> pdb=" O ARGBv 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bv' and resid 48 through 53' Processing helix chain 'Bv' and resid 54 through 64 Processing helix chain 'Bv' and resid 71 through 76 removed outlier: 4.370A pdb=" N LEUBv 75 " --> pdb=" O ALABv 71 " (cutoff:3.500A) removed outlier: 4.660A 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: 3.509A pdb=" N LYSBv 127 " --> pdb=" O GLUBv 123 " (cutoff:3.500A) Proline residue: Bv 129 - end of helix removed outlier: 3.580A pdb=" N LEUBv 156 " --> pdb=" O ARGBv 152 " (cutoff:3.500A) 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: 3.929A pdb=" N TRPBw 105 " --> pdb=" O ASNBw 101 " (cutoff:3.500A) Processing helix chain 'Bw' and resid 132 through 149 removed outlier: 3.599A pdb=" N LEUBw 136 " --> pdb=" O ASPBw 132 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYSBw 143 " --> pdb=" O ALABw 139 " (cutoff:3.500A) Processing helix chain 'Bw' and resid 164 through 184 Proline residue: Bw 169 - end of helix removed outlier: 4.004A pdb=" N VALBw 184 " --> pdb=" O GLYBw 180 " (cutoff:3.500A) Processing helix chain 'Bw' and resid 186 through 193 removed outlier: 4.475A pdb=" N ALABw 190 " --> pdb=" O ASNBw 186 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALABw 191 " --> pdb=" O PROBw 187 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ALABw 193 " --> pdb=" O LEUBw 189 " (cutoff:3.500A) Processing helix chain 'Bw' and resid 261 through 266 removed outlier: 4.738A 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: 3.643A pdb=" N VALBw 316 " --> pdb=" O ASPBw 312 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHEBw 318 " --> pdb=" O ILEBw 314 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHEBw 327 " --> pdb=" O ILEBw 323 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLYBw 338 " --> pdb=" O ALABw 334 " (cutoff:3.500A) Processing helix chain 'Bw' and resid 374 through 379 removed outlier: 4.020A pdb=" N GLNBw 379 " --> pdb=" O ALABw 375 " (cutoff:3.500A) Processing helix chain 'Bw' and resid 408 through 421 removed outlier: 3.752A pdb=" N LEUBw 412 " --> pdb=" O ASNBw 408 " (cutoff:3.500A) Processing helix chain 'Bx' and resid 70 through 76 removed outlier: 3.775A pdb=" N TRPBx 75 " --> pdb=" O PROBx 71 " (cutoff:3.500A) Processing helix chain 'Bx' and resid 85 through 94 removed outlier: 4.401A pdb=" N GLNBx 91 " --> pdb=" O LEUBx 87 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N PHEBx 92 " --> pdb=" O LEUBx 88 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILEBx 93 " --> pdb=" O LEUBx 89 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ARGBx 94 " --> pdb=" O SERBx 90 " (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: 3.807A pdb=" N PHEBx 139 " --> pdb=" O LEUBx 135 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N VALBx 140 " --> pdb=" O PROBx 136 " (cutoff:3.500A) Proline residue: Bx 141 - end of helix No H-bonds generated for 'chain 'Bx' and resid 135 through 142' Processing helix chain 'Bx' and resid 178 through 183 removed outlier: 4.100A pdb=" N LYSBx 182 " --> pdb=" O SERBx 178 " (cutoff:3.500A) removed outlier: 5.238A 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 'Bz' and resid 301 through 315 removed outlier: 3.606A pdb=" N ALABz 315 " --> pdb=" O ALABz 311 " (cutoff:3.500A) Processing helix chain 'Bz' and resid 399 through 415 removed outlier: 3.552A pdb=" N ALABz 403 " --> pdb=" O ALABz 399 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALABz 415 " --> pdb=" O ALABz 411 " (cutoff:3.500A) Processing helix chain 'Bz' and resid 601 through 615 removed outlier: 3.617A pdb=" N ALABz 615 " --> pdb=" O ALABz 611 " (cutoff:3.500A) Processing helix chain 'Bz' and resid 700 through 710 Processing helix chain 'Bz' and resid 1001 through 1016 removed outlier: 3.504A pdb=" N ALABz1005 " --> pdb=" O ALABz1001 " (cutoff:3.500A) Processing helix chain 'AB' and resid 55 through 69 Proline residue: AB 65 - end of helix removed outlier: 4.481A pdb=" N HISAB 68 " --> pdb=" O GLUAB 64 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ALAAB 69 " --> pdb=" O PROAB 65 " (cutoff:3.500A) Processing helix chain 'AB' and resid 79 through 87 Processing helix chain 'AB' and resid 101 through 106 removed outlier: 5.592A pdb=" N PHEAB 106 " --> pdb=" O GLUAB 102 " (cutoff:3.500A) Processing helix chain 'AB' and resid 116 through 138 removed outlier: 3.727A pdb=" N LEUAB 126 " --> pdb=" O ALAAB 122 " (cutoff:3.500A) Processing helix chain 'AB' and resid 150 through 162 Processing helix chain 'AB' and resid 177 through 182 removed outlier: 3.874A pdb=" N LEUAB 181 " --> pdb=" O ASNAB 177 " (cutoff:3.500A) Processing helix chain 'AB' and resid 205 through 215 removed outlier: 4.085A pdb=" N ARGAB 209 " --> pdb=" O HISAB 205 " (cutoff:3.500A) Processing helix chain 'AB' and resid 241 through 274 removed outlier: 4.117A pdb=" N GLYAB 274 " --> pdb=" O TYRAB 270 " (cutoff:3.500A) Processing helix chain 'AC' and resid 52 through 57 removed outlier: 4.008A pdb=" N HISAC 57 " --> pdb=" O TYRAC 53 " (cutoff:3.500A) Processing helix chain 'AC' and resid 81 through 101 Proline residue: AC 101 - end of helix Processing helix chain 'AC' and resid 128 through 148 Processing helix chain 'AE' and resid 94 through 104 removed outlier: 3.690A pdb=" N ALAAE 104 " --> pdb=" O LYSAE 100 " (cutoff:3.500A) Processing helix chain 'AE' and resid 107 through 113 removed outlier: 4.179A pdb=" N ARGAE 111 " --> pdb=" O GLYAE 107 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYSAE 112 " --> pdb=" O ALAAE 108 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLYAE 113 " --> pdb=" O GLYAE 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'AE' and resid 107 through 113' Processing helix chain 'AE' and resid 161 through 185 removed outlier: 4.006A pdb=" N METAE 185 " --> pdb=" O ARGAE 181 " (cutoff:3.500A) Processing helix chain 'AE' and resid 263 through 279 removed outlier: 4.162A pdb=" N HISAE 277 " --> pdb=" O ASNAE 273 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYRAE 278 " --> pdb=" O ARGAE 274 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LEUAE 279 " --> pdb=" O ALAAE 275 " (cutoff:3.500A) Processing helix chain 'AE' and resid 317 through 328 Processing helix chain 'AE' and resid 341 through 356 removed outlier: 3.825A pdb=" N GLNAE 356 " --> pdb=" O GLYAE 352 " (cutoff:3.500A) Processing helix chain 'AE' and resid 358 through 367 Processing helix chain 'AE' and resid 407 through 416 Processing helix chain 'AE' and resid 420 through 425 removed outlier: 4.171A pdb=" N GLYAE 424 " --> pdb=" O SERAE 420 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LEUAE 425 " --> pdb=" O VALAE 421 " (cutoff:3.500A) No H-bonds generated for 'chain 'AE' and resid 420 through 425' Processing helix chain 'AE' and resid 141 through 146 Processing helix chain 'AF' and resid 14 through 33 removed outlier: 3.507A pdb=" N ARGAF 32 " --> pdb=" O ALAAF 28 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLYAF 33 " --> pdb=" O LEUAF 29 " (cutoff:3.500A) Processing helix chain 'AF' and resid 74 through 86 removed outlier: 5.829A pdb=" N ILEAF 86 " --> pdb=" O LEUAF 82 " (cutoff:3.500A) Processing helix chain 'AF' and resid 96 through 101 removed outlier: 4.009A pdb=" N GLNAF 100 " --> pdb=" O HISAF 96 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N GLUAF 101 " --> pdb=" O PROAF 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'AF' and resid 96 through 101' Processing helix chain 'AG' and resid 47 through 54 removed outlier: 4.128A pdb=" N TYRAG 51 " --> pdb=" O ASPAG 47 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYSAG 53 " --> pdb=" O GLUAG 49 " (cutoff:3.500A) Proline residue: AG 54 - end of helix Processing helix chain 'AG' and resid 57 through 70 Processing helix chain 'AG' and resid 88 through 100 removed outlier: 5.648A pdb=" N LYSAG 100 " --> pdb=" O ASNAG 96 " (cutoff:3.500A) Processing helix chain 'AG' and resid 103 through 129 removed outlier: 3.881A pdb=" N ALAAG 107 " --> pdb=" O ASNAG 103 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALAAG 128 " --> pdb=" O ALAAG 124 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALAAG 129 " --> pdb=" O LYSAG 125 " (cutoff:3.500A) Processing helix chain 'AG' and resid 130 through 137 Processing helix chain 'AG' and resid 140 through 153 Processing helix chain 'AG' and resid 175 through 194 Processing helix chain 'AG' and resid 200 through 215 Processing helix chain 'AG' and resid 217 through 238 removed outlier: 3.639A pdb=" N ASNAG 233 " --> pdb=" O METAG 229 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARGAG 234 " --> pdb=" O ALAAG 230 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ALAAG 235 " --> pdb=" O GLUAG 231 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEUAG 236 " --> pdb=" O ALAAG 232 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALAAG 237 " --> pdb=" O ASNAG 233 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N HISAG 238 " --> pdb=" O ARGAG 234 " (cutoff:3.500A) Processing helix chain 'AI' and resid 70 through 93 Processing helix chain 'AI' and resid 100 through 112 Processing helix chain 'AI' and resid 127 through 132 Processing helix chain 'AI' and resid 155 through 183 removed outlier: 3.890A pdb=" N TYRAI 159 " --> pdb=" O LYSAI 155 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASPAI 183 " --> pdb=" O LEUAI 179 " (cutoff:3.500A) Processing helix chain 'AI' and resid 202 through 211 Processing helix chain 'AI' and resid 215 through 233 removed outlier: 3.965A pdb=" N LEUAI 232 " --> pdb=" O ARGAI 228 " (cutoff:3.500A) Proline residue: AI 233 - end of helix Processing helix chain 'AI' and resid 235 through 247 removed outlier: 3.624A pdb=" N ARGAI 244 " --> pdb=" O ASPAI 240 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N PHEAI 245 " --> pdb=" O PHEAI 241 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARGAI 246 " --> pdb=" O VALAI 242 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ARGAI 247 " --> pdb=" O ASNAI 243 " (cutoff:3.500A) Processing helix chain 'AI' and resid 300 through 306 Proline residue: AI 306 - end of helix Processing helix chain 'AI' and resid 307 through 322 removed outlier: 3.571A pdb=" N ARGAI 311 " --> pdb=" O VALAI 307 " (cutoff:3.500A) Proline residue: AI 317 - end of helix Processing helix chain 'AI' and resid 337 through 357 removed outlier: 3.754A pdb=" N CYSAI 354 " --> pdb=" O ALAAI 350 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N SERAI 355 " --> pdb=" O ARGAI 351 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N PHEAI 356 " --> pdb=" O ALAAI 352 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VALAI 357 " --> pdb=" O LEUAI 353 " (cutoff:3.500A) Processing helix chain 'AI' and resid 358 through 369 removed outlier: 3.765A pdb=" N GLUAI 363 " --> pdb=" O GLUAI 359 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 84 through 103 removed outlier: 3.897A pdb=" N LEUAJ 88 " --> pdb=" O ASPAJ 84 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEUAJ 102 " --> pdb=" O ALAAJ 98 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 149 through 164 Processing helix chain 'AJ' and resid 182 through 187 removed outlier: 5.430A pdb=" N LYSAJ 186 " --> pdb=" O GLUAJ 182 " (cutoff:3.500A) Proline residue: AJ 187 - end of helix No H-bonds generated for 'chain 'AJ' and resid 182 through 187' Processing helix chain 'AK' and resid 113 through 118 removed outlier: 3.902A pdb=" N GLYAK 118 " --> pdb=" O CYSAK 114 " (cutoff:3.500A) Processing helix chain 'AK' and resid 121 through 126 removed outlier: 4.291A pdb=" N GLYAK 125 " --> pdb=" O ASNAK 121 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THRAK 126 " --> pdb=" O ALAAK 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'AK' and resid 121 through 126' Processing helix chain 'AK' and resid 127 through 145 removed outlier: 3.570A pdb=" N LYSAK 144 " --> pdb=" O LYSAK 140 " (cutoff:3.500A) Processing helix chain 'AK' and resid 159 through 171 removed outlier: 3.845A pdb=" N GLYAK 171 " --> pdb=" O LEUAK 167 " (cutoff:3.500A) Processing helix chain 'AL' and resid 32 through 40 Processing helix chain 'AN' and resid 31 through 48 Processing helix chain 'AN' and resid 49 through 59 removed outlier: 3.678A pdb=" N LEUAN 57 " --> pdb=" O ARGAN 53 " (cutoff:3.500A) Processing helix chain 'AN' and resid 64 through 79 removed outlier: 3.808A pdb=" N VALAN 70 " --> pdb=" O ASPAN 66 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEUAN 78 " --> pdb=" O GLUAN 74 " (cutoff:3.500A) Proline residue: AN 79 - end of helix Processing helix chain 'AN' and resid 107 through 118 removed outlier: 3.520A pdb=" N HISAN 117 " --> pdb=" O HISAN 113 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLYAN 118 " --> pdb=" O LEUAN 114 " (cutoff:3.500A) Processing helix chain 'AO' and resid 74 through 79 removed outlier: 3.554A pdb=" N GLNAO 78 " --> pdb=" O LEUAO 74 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ASNAO 79 " --> pdb=" O LEUAO 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'AO' and resid 74 through 79' Processing helix chain 'AO' and resid 87 through 95 Processing helix chain 'AO' and resid 100 through 117 removed outlier: 3.995A pdb=" N LYSAO 104 " --> pdb=" O ASNAO 100 " (cutoff:3.500A) Processing helix chain 'AO' and resid 125 through 148 removed outlier: 3.875A pdb=" N ARGAO 148 " --> pdb=" O METAO 144 " (cutoff:3.500A) Processing helix chain 'AO' and resid 150 through 175 removed outlier: 3.623A pdb=" N LYSAO 154 " --> pdb=" O ASPAO 150 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLUAO 173 " --> pdb=" O LYSAO 169 " (cutoff:3.500A) Processing helix chain 'AO' and resid 176 through 187 Processing helix chain 'AO' and resid 201 through 239 removed outlier: 3.789A pdb=" N GLYAO 239 " --> pdb=" O ALAAO 235 " (cutoff:3.500A) Processing helix chain 'AP' and resid 69 through 80 Processing helix chain 'AP' and resid 84 through 95 Processing helix chain 'AP' and resid 100 through 126 removed outlier: 3.519A pdb=" N ILEAP 104 " --> pdb=" O HISAP 100 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASPAP 126 " --> pdb=" O SERAP 122 " (cutoff:3.500A) Processing helix chain 'AR' and resid 77 through 86 removed outlier: 3.816A pdb=" N LEUAR 81 " --> pdb=" O ASNAR 77 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHEAR 84 " --> pdb=" O LEUAR 80 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILEAR 85 " --> pdb=" O LEUAR 81 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N SERAR 86 " --> pdb=" O SERAR 82 " (cutoff:3.500A) Processing helix chain 'AR' and resid 94 through 99 Processing helix chain 'AR' and resid 101 through 119 Processing helix chain 'AR' and resid 127 through 132 removed outlier: 3.759A pdb=" N LEUAR 131 " --> pdb=" O ASPAR 127 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LYSAR 132 " --> pdb=" O PROAR 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'AR' and resid 127 through 132' Processing helix chain 'AU' and resid 18 through 34 removed outlier: 3.868A pdb=" N ALAAU 22 " --> pdb=" O ASNAU 18 " (cutoff:3.500A) Processing helix chain 'AU' and resid 35 through 45 removed outlier: 3.714A pdb=" N ARGAU 43 " --> pdb=" O ILEAU 39 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N TYRAU 44 " --> pdb=" O LYSAU 40 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N TYRAU 45 " --> pdb=" O ARGAU 41 " (cutoff:3.500A) Processing helix chain 'AU' and resid 47 through 80 removed outlier: 4.825A pdb=" N ARGAU 77 " --> pdb=" O ASNAU 73 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N LYSAU 78 " --> pdb=" O PHEAU 74 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASNAU 79 " --> pdb=" O LEUAU 75 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ARGAU 80 " --> pdb=" O METAU 76 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 698 through 707 removed outlier: 4.050A pdb=" N ALAAZ 702 " --> pdb=" O ALAAZ 698 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 94 through 106 removed outlier: 3.524A pdb=" N GLYAa 106 " --> pdb=" O ILEAa 102 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 108 through 114 removed outlier: 3.986A pdb=" N LYSAa 114 " --> pdb=" O GLNAa 110 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 129 through 149 Processing helix chain 'Aa' and resid 167 through 172 removed outlier: 4.299A pdb=" N GLUAa 171 " --> pdb=" O ASPAa 167 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N GLYAa 172 " --> pdb=" O LYSAa 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'Aa' and resid 167 through 172' Processing helix chain 'Aa' and resid 207 through 219 Processing helix chain 'Aa' and resid 233 through 244 Processing helix chain 'Aa' and resid 245 through 257 Processing helix chain 'Aa' and resid 261 through 279 removed outlier: 3.767A pdb=" N ILEAa 265 " --> pdb=" O SERAa 261 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 280 through 286 removed outlier: 4.630A pdb=" N LEUAa 284 " --> pdb=" O LYSAa 280 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARGAa 285 " --> pdb=" O TYRAa 281 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N SERAa 286 " --> pdb=" O ASPAa 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'Aa' and resid 280 through 286' Processing helix chain 'Aa' and resid 289 through 301 removed outlier: 3.921A pdb=" N METAa 293 " --> pdb=" O HISAa 289 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 303 through 314 removed outlier: 3.629A pdb=" N ASPAa 314 " --> pdb=" O GLNAa 310 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 315 through 331 removed outlier: 3.801A pdb=" N ALAAa 319 " --> pdb=" O LEUAa 315 " (cutoff:3.500A) Proline residue: Aa 331 - end of helix Processing helix chain 'Aa' and resid 333 through 343 Processing helix chain 'Aa' and resid 345 through 357 Processing helix chain 'Aa' and resid 360 through 379 removed outlier: 4.077A pdb=" N ILEAa 364 " --> pdb=" O LYSAa 360 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 11 through 23 Processing helix chain 'Ab' and resid 29 through 39 removed outlier: 3.911A pdb=" N ASPAb 33 " --> pdb=" O PROAb 29 " (cutoff:3.500A) Proline residue: Ab 39 - end of helix Processing helix chain 'Ab' and resid 65 through 78 removed outlier: 3.629A pdb=" N ARGAb 69 " --> pdb=" O TYRAb 65 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYSAb 73 " --> pdb=" O ARGAb 69 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 94 through 110 removed outlier: 3.664A pdb=" N LEUAb 109 " --> pdb=" O GLUAb 105 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLYAb 110 " --> pdb=" O LEUAb 106 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 113 through 129 removed outlier: 3.891A pdb=" N GLUAb 128 " --> pdb=" O ALAAb 124 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 7 through 12 removed outlier: 4.595A pdb=" N ARGAc 11 " --> pdb=" O PHEAc 7 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THRAc 12 " --> pdb=" O PROAc 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ac' and resid 7 through 12' Processing helix chain 'Ac' and resid 13 through 19 Processing helix chain 'Ac' and resid 38 through 60 removed outlier: 4.213A pdb=" N GLUAc 42 " --> pdb=" O GLYAc 38 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N GLYAc 43 " --> pdb=" O GLUAc 39 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ALAAc 44 " --> pdb=" O LEUAc 40 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILEAc 52 " --> pdb=" O VALAc 48 " (cutoff:3.500A) Proline residue: Ac 53 - end of helix Proline residue: Ac 60 - end of helix Processing helix chain 'Ac' and resid 94 through 106 Processing helix chain 'Ac' and resid 109 through 124 removed outlier: 3.874A pdb=" N LEUAc 123 " --> pdb=" O GLUAc 119 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N SERAc 124 " --> pdb=" O LYSAc 120 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 139 through 144 removed outlier: 5.123A pdb=" N VALAc 143 " --> pdb=" O CYSAc 139 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N GLUAc 144 " --> pdb=" O METAc 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ac' and resid 139 through 144' Processing helix chain 'Ac' and resid 149 through 154 Proline residue: Ac 154 - end of helix Processing helix chain 'Ac' and resid 156 through 161 removed outlier: 3.785A pdb=" N THRAc 160 " --> pdb=" O PROAc 156 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N GLYAc 161 " --> pdb=" O LYSAc 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ac' and resid 156 through 161' Processing helix chain 'Ac' and resid 162 through 170 removed outlier: 3.650A pdb=" N THRAc 170 " --> pdb=" O ALAAc 166 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 35 through 42 removed outlier: 4.789A pdb=" N GLYAd 40 " --> pdb=" O LYSAd 36 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ARGAd 41 " --> pdb=" O SERAd 37 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N VALAd 42 " --> pdb=" O LYSAd 38 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 50 through 150 removed outlier: 7.803A pdb=" N VALAd 89 " --> pdb=" O ALAAd 85 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N GLNAd 90 " --> pdb=" O ARGAd 86 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ALAAd 91 " --> pdb=" O ALAAd 87 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 152 through 161 Processing helix chain 'Ad' and resid 169 through 184 removed outlier: 5.261A pdb=" N GLUAd 174 " --> pdb=" O ARGAd 170 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ALAAd 175 " --> pdb=" O GLUAd 171 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASPAd 182 " --> pdb=" O GLUAd 178 " (cutoff:3.500A) Proline residue: Ad 184 - end of helix Processing helix chain 'Ae' and resid 68 through 75 removed outlier: 3.649A pdb=" N ALAAe 72 " --> pdb=" O CYSAe 68 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VALAe 75 " --> pdb=" O SERAe 71 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 76 through 84 removed outlier: 4.152A pdb=" N ASPAe 84 " --> pdb=" O TRPAe 80 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 89 through 104 removed outlier: 3.542A pdb=" N LEUAe 93 " --> pdb=" O HISAe 89 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 108 through 119 removed outlier: 3.860A pdb=" N ILEAe 112 " --> pdb=" O SERAe 108 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILEAe 119 " --> pdb=" O PHEAe 115 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 121 through 139 removed outlier: 3.760A pdb=" N SERAe 138 " --> pdb=" O LYSAe 134 " (cutoff:3.500A) Proline residue: Ae 139 - end of helix Processing helix chain 'Ae' and resid 145 through 160 removed outlier: 3.625A pdb=" N ILEAe 149 " --> pdb=" O ARGAe 145 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 161 through 172 removed outlier: 4.842A pdb=" N ALAAe 165 " --> pdb=" O ALAAe 161 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N LEUAe 166 " --> pdb=" O GLNAe 162 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 181 through 195 removed outlier: 4.475A pdb=" N ASNAe 185 " --> pdb=" O ASNAe 181 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYSAe 194 " --> pdb=" O TYRAe 190 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 196 through 211 removed outlier: 3.797A pdb=" N ALAAe 200 " --> pdb=" O ASNAe 196 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLUAe 211 " --> pdb=" O ILEAe 207 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 216 through 233 removed outlier: 3.514A pdb=" N LEUAe 220 " --> pdb=" O PROAe 216 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LYSAe 233 " --> pdb=" O CYSAe 229 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 237 through 251 Proline residue: Ae 251 - end of helix Processing helix chain 'Ae' and resid 257 through 278 removed outlier: 3.977A pdb=" N LEUAe 261 " --> pdb=" O ASNAe 257 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 279 through 285 removed outlier: 3.977A pdb=" N VALAe 283 " --> pdb=" O GLYAe 279 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYRAe 284 " --> pdb=" O LEUAe 280 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 294 through 307 removed outlier: 4.950A pdb=" N ARGAe 298 " --> pdb=" O GLYAe 294 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VALAe 306 " --> pdb=" O VALAe 302 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ALAAe 307 " --> pdb=" O METAe 303 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 313 through 335 removed outlier: 6.004A pdb=" N GLYAe 317 " --> pdb=" O GLYAe 313 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALAAe 332 " --> pdb=" O LYSAe 328 " (cutoff:3.500A) Proline residue: Ae 333 - end of helix Processing helix chain 'Ae' and resid 345 through 353 Processing helix chain 'Ae' and resid 363 through 385 removed outlier: 3.918A pdb=" N LYSAe 367 " --> pdb=" O THRAe 363 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEUAe 368 " --> pdb=" O GLUAe 364 " (cutoff:3.500A) Proline residue: Ae 369 - end of helix removed outlier: 3.666A pdb=" N GLUAe 373 " --> pdb=" O PROAe 369 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLNAe 383 " --> pdb=" O ARGAe 379 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALAAe 384 " --> pdb=" O SERAe 380 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 392 through 411 removed outlier: 3.511A pdb=" N LEUAe 396 " --> pdb=" O SERAe 392 " (cutoff:3.500A) Proline residue: Ae 406 - end of helix Processing helix chain 'Ae' and resid 412 through 452 removed outlier: 3.634A pdb=" N GLNAe 418 " --> pdb=" O ALAAe 414 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N HISAe 424 " --> pdb=" O LEUAe 420 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALAAe 451 " --> pdb=" O ALAAe 447 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYSAe 452 " --> pdb=" O ARGAe 448 " (cutoff:3.500A) Processing helix chain 'Af' and resid 80 through 88 removed outlier: 3.567A pdb=" N HISAf 87 " --> pdb=" O SERAf 83 " (cutoff:3.500A) Processing helix chain 'Af' and resid 89 through 94 removed outlier: 3.838A pdb=" N GLYAf 94 " --> pdb=" O LEUAf 90 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 70 through 78 Processing helix chain 'Ag' and resid 83 through 94 Processing helix chain 'Ag' and resid 101 through 114 removed outlier: 3.891A pdb=" N ASNAg 113 " --> pdb=" O HISAg 109 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THRAg 114 " --> pdb=" O TYRAg 110 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 132 through 148 removed outlier: 3.916A pdb=" N ILEAg 140 " --> pdb=" O SERAg 136 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASNAg 148 " --> pdb=" O CYSAg 144 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 156 through 162 removed outlier: 4.595A pdb=" N TRPAg 160 " --> pdb=" O ASPAg 156 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VALAg 161 " --> pdb=" O ALAAg 157 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 179 through 195 removed outlier: 3.903A pdb=" N THRAg 192 " --> pdb=" O LYSAg 188 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASNAg 194 " --> pdb=" O PHEAg 190 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLUAg 195 " --> pdb=" O LYSAg 191 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 196 through 201 removed outlier: 3.806A pdb=" N GLNAg 200 " --> pdb=" O HISAg 196 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 220 through 232 removed outlier: 3.956A pdb=" N VALAg 224 " --> pdb=" O PROAg 220 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARGAg 231 " --> pdb=" O GLNAg 227 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VALAg 232 " --> pdb=" O GLYAg 228 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 233 through 250 removed outlier: 6.043A pdb=" N ASPAg 237 " --> pdb=" O ARGAg 233 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 263 through 269 removed outlier: 4.759A pdb=" N LEUAg 267 " --> pdb=" O GLYAg 263 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TRPAg 268 " --> pdb=" O VALAg 264 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 282 through 287 removed outlier: 3.995A pdb=" N LEUAg 286 " --> pdb=" O ALAAg 282 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ALAAg 287 " --> pdb=" O PROAg 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ag' and resid 282 through 287' Processing helix chain 'Ag' and resid 288 through 298 removed outlier: 3.738A pdb=" N LYSAg 294 " --> pdb=" O HISAg 290 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N METAg 295 " --> pdb=" O ASNAg 291 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VALAg 296 " --> pdb=" O LEUAg 292 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYSAg 297 " --> pdb=" O ARGAg 293 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ASNAg 298 " --> pdb=" O LYSAg 294 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 323 through 329 Processing helix chain 'Ag' and resid 330 through 337 removed outlier: 3.881A pdb=" N ASPAg 337 " --> pdb=" O PHEAg 333 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 348 through 363 Processing helix chain 'Ag' and resid 372 through 384 removed outlier: 3.880A pdb=" N LYSAg 376 " --> pdb=" O THRAg 372 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 386 through 397 removed outlier: 4.067A pdb=" N TYRAg 396 " --> pdb=" O ARGAg 392 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEUAg 397 " --> pdb=" O LEUAg 393 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 268 through 283 removed outlier: 3.677A pdb=" N ILEAh 272 " --> pdb=" O SERAh 268 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VALAh 281 " --> pdb=" O GLNAh 277 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 288 through 300 Processing helix chain 'Ah' and resid 319 through 325 removed outlier: 3.626A pdb=" N HISAh 323 " --> pdb=" O GLUAh 319 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 326 through 331 removed outlier: 3.723A pdb=" N LEUAh 330 " --> pdb=" O LEUAh 326 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLNAh 331 " --> pdb=" O ASPAh 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ah' and resid 326 through 331' Processing helix chain 'Ah' and resid 337 through 354 removed outlier: 3.716A pdb=" N HISAh 341 " --> pdb=" O GLYAh 337 " (cutoff:3.500A) Proline residue: Ah 354 - end of helix Processing helix chain 'Ah' and resid 357 through 376 removed outlier: 3.510A pdb=" N LYSAh 361 " --> pdb=" O SERAh 357 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ARGAh 376 " --> pdb=" O PHEAh 372 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 377 through 383 removed outlier: 4.300A pdb=" N GLYAh 383 " --> pdb=" O LEUAh 379 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 5 through 20 removed outlier: 3.510A pdb=" N VALAi 9 " --> pdb=" O SERAi 5 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 27 through 40 removed outlier: 3.539A pdb=" N METAi 31 " --> pdb=" O ASPAi 27 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYSAi 32 " --> pdb=" O SERAi 28 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N VALAi 33 " --> pdb=" O LYSAi 29 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VALAi 34 " --> pdb=" O SERAi 30 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N GLNAi 40 " --> pdb=" O LEUAi 36 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 45 through 50 Processing helix chain 'Ai' and resid 54 through 69 removed outlier: 3.546A pdb=" N TYRAi 58 " --> pdb=" O ASNAi 54 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 73 through 90 Processing helix chain 'Aj' and resid 9 through 27 removed outlier: 4.836A pdb=" N GLUAj 13 " --> pdb=" O ARGAj 9 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 29 through 35 removed outlier: 3.663A pdb=" N ALAAj 35 " --> pdb=" O SERAj 31 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 51 through 61 removed outlier: 3.617A pdb=" N TRPAj 55 " --> pdb=" O PROAj 51 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ALAAj 56 " --> pdb=" O METAj 52 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ASPAj 57 " --> pdb=" O ARGAj 53 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLUAj 61 " --> pdb=" O ASPAj 57 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 63 through 72 removed outlier: 3.522A pdb=" N LEUAj 67 " --> pdb=" O ARGAj 63 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASNAj 69 " --> pdb=" O LEUAj 65 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ARGAj 70 " --> pdb=" O GLNAj 66 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEUAj 71 " --> pdb=" O LEUAj 67 " (cutoff:3.500A) Proline residue: Aj 72 - end of helix Processing helix chain 'Aj' and resid 82 through 89 Processing helix chain 'Aj' and resid 144 through 151 removed outlier: 4.617A pdb=" N GLUAj 148 " --> pdb=" O LYSAj 144 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ALAAj 149 " --> pdb=" O HISAj 145 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 167 through 182 removed outlier: 3.622A pdb=" N TYRAj 181 " --> pdb=" O GLNAj 177 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLYAj 182 " --> pdb=" O ARGAj 178 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 57 through 62 removed outlier: 4.485A pdb=" N LYSAk 61 " --> pdb=" O PROAk 57 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 67 through 73 removed outlier: 4.290A pdb=" N VALAk 71 " --> pdb=" O ASPAk 67 " (cutoff:3.500A) Proline residue: Ak 73 - end of helix Processing helix chain 'Ak' and resid 79 through 84 removed outlier: 3.675A pdb=" N VALAk 83 " --> pdb=" O LYSAk 79 " (cutoff:3.500A) Proline residue: Ak 84 - end of helix No H-bonds generated for 'chain 'Ak' and resid 79 through 84' Processing helix chain 'Ak' and resid 104 through 111 removed outlier: 3.734A pdb=" N LEUAk 108 " --> pdb=" O ASNAk 104 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILEAk 110 " --> pdb=" O GLUAk 106 " (cutoff:3.500A) Proline residue: Ak 111 - end of helix Processing helix chain 'Ak' and resid 117 through 130 removed outlier: 5.158A pdb=" N ASPAk 130 " --> pdb=" O GLUAk 126 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 141 through 149 Processing helix chain 'Ak' and resid 178 through 183 removed outlier: 4.288A pdb=" N LEUAk 182 " --> pdb=" O LYSAk 178 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ASNAk 183 " --> pdb=" O LEUAk 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ak' and resid 178 through 183' Processing helix chain 'Ak' and resid 185 through 197 Processing helix chain 'Ak' and resid 216 through 238 removed outlier: 3.713A pdb=" N TRPAk 236 " --> pdb=" O TYRAk 232 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LYSAk 237 " --> pdb=" O HISAk 233 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N THRAk 238 " --> pdb=" O GLUAk 234 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 239 through 245 removed outlier: 4.202A pdb=" N LYSAk 243 " --> pdb=" O GLUAk 239 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYSAk 244 " --> pdb=" O GLUAk 240 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYSAk 245 " --> pdb=" O TRPAk 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ak' and resid 239 through 245' Processing helix chain 'Ak' and resid 258 through 276 removed outlier: 3.825A pdb=" N LYSAk 262 " --> pdb=" O SERAk 258 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYSAk 276 " --> pdb=" O LYSAk 272 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 281 through 288 removed outlier: 3.764A pdb=" N THRAk 288 " --> pdb=" O GLUAk 284 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 289 through 304 Processing helix chain 'Ak' and resid 307 through 323 Processing helix chain 'Ak' and resid 167 through 172 removed outlier: 3.860A pdb=" N ARGAk 171 " --> pdb=" O PROAk 168 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VALAk 172 " --> pdb=" O LYSAk 169 " (cutoff:3.500A) Processing helix chain 'Am' and resid 45 through 60 Processing helix chain 'Am' and resid 62 through 94 removed outlier: 4.238A pdb=" N CYSAm 66 " --> pdb=" O ARGAm 62 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ARGAm 67 " --> pdb=" O ASPAm 63 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LYSAm 68 " --> pdb=" O GLUAm 64 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N GLUAm 69 " --> pdb=" O ALAAm 65 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ILEAm 70 " --> pdb=" O CYSAm 66 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SERAm 88 " --> pdb=" O ARGAm 84 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ILEAm 89 " --> pdb=" O LYSAm 85 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLNAm 90 " --> pdb=" O METAm 86 " (cutoff:3.500A) Processing helix chain 'Am' and resid 100 through 112 Proline residue: Am 112 - end of helix Processing helix chain 'An' and resid 128 through 151 removed outlier: 5.115A pdb=" N LYSAn 132 " --> pdb=" O LYSAn 128 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILEAn 133 " --> pdb=" O ASNAn 129 " (cutoff:3.500A) Processing helix chain 'An' and resid 152 through 181 removed outlier: 3.666A pdb=" N GLYAn 181 " --> pdb=" O TRPAn 177 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 68 through 79 removed outlier: 4.116A pdb=" N THRAo 77 " --> pdb=" O ALAAo 73 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VALAo 78 " --> pdb=" O LEUAo 74 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N HISAo 79 " --> pdb=" O ALAAo 75 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 99 through 125 Proline residue: Ao 125 - end of helix Processing helix chain 'Ao' and resid 152 through 163 removed outlier: 4.552A pdb=" N GLNAo 158 " --> pdb=" O GLUAo 154 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 201 through 215 removed outlier: 3.836A pdb=" N GLNAo 214 " --> pdb=" O GLNAo 210 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SERAo 215 " --> pdb=" O GLNAo 211 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 219 through 234 removed outlier: 3.933A pdb=" N GLUAo 223 " --> pdb=" O GLUAo 219 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALAAo 224 " --> pdb=" O GLUAo 220 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 240 through 252 removed outlier: 3.686A pdb=" N LYSAo 244 " --> pdb=" O THRAo 240 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 257 through 273 removed outlier: 3.705A pdb=" N SERAo 261 " --> pdb=" O LYSAo 257 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N CYSAo 263 " --> pdb=" O ALAAo 259 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VALAo 270 " --> pdb=" O ILEAo 266 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYSAo 271 " --> pdb=" O ARGAo 267 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 274 through 289 removed outlier: 4.380A pdb=" N ALAAo 278 " --> pdb=" O ALAAo 274 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASNAo 288 " --> pdb=" O VALAo 284 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARGAo 289 " --> pdb=" O LEUAo 285 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 293 through 308 removed outlier: 5.092A pdb=" N VALAo 308 " --> pdb=" O THRAo 304 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 311 through 330 removed outlier: 4.299A pdb=" N LYSAo 315 " --> pdb=" O LYSAo 311 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASNAo 318 " --> pdb=" O GLUAo 314 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASNAo 330 " --> pdb=" O METAo 326 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 334 through 349 removed outlier: 3.628A pdb=" N PHEAo 338 " --> pdb=" O ASNAo 334 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARGAo 347 " --> pdb=" O LYSAo 343 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N PHEAo 348 " --> pdb=" O CYSAo 344 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TYRAo 349 " --> pdb=" O LEUAo 345 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 352 through 367 removed outlier: 3.688A pdb=" N ALAAo 356 " --> pdb=" O GLYAo 352 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYSAo 364 " --> pdb=" O LEUAo 360 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILEAo 366 " --> pdb=" O GLUAo 362 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLYAo 367 " --> pdb=" O METAo 363 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 371 through 387 Processing helix chain 'Ao' and resid 389 through 405 removed outlier: 4.423A pdb=" N SERAo 393 " --> pdb=" O SERAo 389 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEUAo 394 " --> pdb=" O LYSAo 390 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLYAo 405 " --> pdb=" O ASNAo 401 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 415 through 430 removed outlier: 4.241A pdb=" N PHEAo 419 " --> pdb=" O ASPAo 415 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLNAo 420 " --> pdb=" O ASPAo 416 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N METAo 423 " --> pdb=" O PHEAo 419 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VALAo 425 " --> pdb=" O SERAo 421 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N CYSAo 426 " --> pdb=" O ALAAo 422 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SERAo 427 " --> pdb=" O METAo 423 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SERAo 428 " --> pdb=" O ARGAo 424 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 431 through 446 removed outlier: 3.869A pdb=" N ALAAo 435 " --> pdb=" O ASPAo 431 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THRAo 444 " --> pdb=" O GLYAo 440 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLYAo 445 " --> pdb=" O LEUAo 441 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASPAo 446 " --> pdb=" O LEUAo 442 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 453 through 471 removed outlier: 3.799A pdb=" N TYRAo 460 " --> pdb=" O ARGAo 456 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYRAo 461 " --> pdb=" O ARGAo 457 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHEAo 470 " --> pdb=" O ASNAo 466 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 473 through 485 removed outlier: 3.750A pdb=" N LYSAo 479 " --> pdb=" O ASPAo 475 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYSAo 482 " --> pdb=" O LEUAo 478 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASPAo 483 " --> pdb=" O LYSAo 479 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 492 through 507 removed outlier: 3.579A pdb=" N ASPAo 498 " --> pdb=" O GLNAo 494 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEUAo 499 " --> pdb=" O THRAo 495 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEUAo 500 " --> pdb=" O METAo 496 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VALAo 505 " --> pdb=" O GLNAo 501 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALAAo 506 " --> pdb=" O ALAAo 502 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASNAo 507 " --> pdb=" O LEUAo 503 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 511 through 523 removed outlier: 3.574A pdb=" N GLUAo 521 " --> pdb=" O LYSAo 517 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 526 through 541 removed outlier: 4.496A pdb=" N GLUAo 532 " --> pdb=" O ASNAo 528 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLUAo 533 " --> pdb=" O GLUAo 529 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N METAo 536 " --> pdb=" O GLUAo 532 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEUAo 537 " --> pdb=" O GLUAo 533 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N METAo 538 " --> pdb=" O ILEAo 534 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALAAo 539 " --> pdb=" O LEUAo 535 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARGAo 540 " --> pdb=" O METAo 536 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ASPAo 541 " --> pdb=" O LEUAo 537 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 547 through 565 removed outlier: 3.620A pdb=" N ILEAo 558 " --> pdb=" O CYSAo 554 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SERAo 564 " --> pdb=" O SERAo 560 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLNAo 565 " --> pdb=" O THRAo 561 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 575 through 590 removed outlier: 4.070A pdb=" N LEUAo 579 " --> pdb=" O PROAo 575 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 591 through 606 removed outlier: 4.370A pdb=" N ALAAo 595 " --> pdb=" O ARGAo 591 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HISAo 605 " --> pdb=" O LEUAo 601 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASNAo 606 " --> pdb=" O PHEAo 602 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 610 through 625 removed outlier: 3.858A pdb=" N LEUAo 614 " --> pdb=" O ARGAo 610 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SERAo 624 " --> pdb=" O SERAo 620 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SERAo 625 " --> pdb=" O ALAAo 621 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 626 through 641 removed outlier: 3.585A pdb=" N ALAAo 630 " --> pdb=" O SERAo 626 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHEAo 640 " --> pdb=" O LEUAo 636 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 644 through 660 Processing helix chain 'Ao' and resid 661 through 674 removed outlier: 3.505A pdb=" N ALAAo 665 " --> pdb=" O GLUAo 661 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SERAo 674 " --> pdb=" O THRAo 670 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 54 through 61 removed outlier: 4.611A pdb=" N TYRAp 58 " --> pdb=" O GLUAp 54 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEUAp 59 " --> pdb=" O PROAp 55 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 62 through 68 Processing helix chain 'Ap' and resid 105 through 111 removed outlier: 4.161A pdb=" N ASPAp 110 " --> pdb=" O PROAp 106 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLNAp 111 " --> pdb=" O ILEAp 107 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 119 through 128 removed outlier: 3.536A pdb=" N LEUAp 123 " --> pdb=" O ASNAp 119 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLNAp 125 " --> pdb=" O LYSAp 121 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHEAp 126 " --> pdb=" O LEUAp 122 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VALAp 127 " --> pdb=" O LEUAp 123 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N CYSAp 128 " --> pdb=" O GLUAp 124 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 136 through 141 removed outlier: 3.625A pdb=" N THRAp 140 " --> pdb=" O HISAp 136 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 143 through 161 Processing helix chain 'Ap' and resid 190 through 196 removed outlier: 3.836A pdb=" N SERAp 195 " --> pdb=" O PROAp 191 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 209 through 221 Processing sheet with id= 1, first strand: chain 'B0' and resid 81 through 84 removed outlier: 4.221A pdb=" N CYSB0 88 " --> pdb=" O GLYB0 84 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'B1' and resid 49 through 53 removed outlier: 5.141A pdb=" N LYSB1 49 " --> pdb=" O VALB1 62 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLNB1 58 " --> pdb=" O ASNB1 53 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'B1' and resid 85 through 91 Processing sheet with id= 4, first strand: chain 'B2' and resid 167 through 172 Processing sheet with id= 5, first strand: chain 'B3' and resid 97 through 101 removed outlier: 5.203A pdb=" N LEUB3 66 " --> pdb=" O LEUB3 122 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N LEUB3 116 " --> pdb=" O ILEB3 72 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B3' and resid 137 through 140 Processing sheet with id= 7, first strand: chain 'B4' and resid 64 through 68 Processing sheet with id= 8, first strand: chain 'B5' and resid 107 through 110 removed outlier: 4.411A pdb=" N HISB5 115 " --> pdb=" O CYSB5 110 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'B5' and resid 155 through 161 Processing sheet with id= 10, first strand: chain 'B6' and resid 28 through 33 removed outlier: 5.979A pdb=" N PHEB6 28 " --> pdb=" O SERB6 22 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEUB6 17 " --> pdb=" O ILEB6 62 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'B6' and resid 41 through 46 removed outlier: 6.514A pdb=" N LEUB6 41 " --> pdb=" O GLUB6 58 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'B8' and resid 122 through 125 No H-bonds generated for sheet with id= 12 Processing sheet with id= 13, first strand: chain 'B9' and resid 63 through 67 removed outlier: 6.104A pdb=" N HISB9 95 " --> pdb=" O CYSB9 89 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N CYSB9 89 " --> pdb=" O HISB9 95 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N TRPB9 85 " --> pdb=" O GLNB9 99 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'BC' and resid 217 through 224 removed outlier: 3.580A pdb=" N GLYBC 218 " --> pdb=" O ASPBC 234 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLUBC 228 " --> pdb=" O LEUBC 224 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THRBC 235 " --> pdb=" O ILEBC 185 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N GLYBC 187 " --> pdb=" O THRBC 235 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLNBC 319 " --> pdb=" O ILEBC 283 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'BC' and resid 355 through 360 removed outlier: 5.533A pdb=" N VALBC 355 " --> pdb=" O GLUBC 433 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLUBC 429 " --> pdb=" O VALBC 359 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VALBC 386 " --> pdb=" O VALBC 434 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N SERBC 385 " --> pdb=" O VALBC 396 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'BC' and resid 361 through 365 removed outlier: 3.565A pdb=" N GLUBC 361 " --> pdb=" O THRBC 373 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'BC' and resid 544 through 549 removed outlier: 7.709A pdb=" N ILEBC 520 " --> pdb=" O VALBC 549 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N HISBC 550 " --> pdb=" O VALBC 518 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'BC' and resid 592 through 596 Processing sheet with id= 19, first strand: chain 'BC' and resid 616 through 623 removed outlier: 6.672A pdb=" N GLUBC 625 " --> pdb=" O GLNBC 649 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLYBC 645 " --> pdb=" O LEUBC 629 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'BC' and resid 651 through 654 removed outlier: 7.873A pdb=" N GLYBC 651 " --> pdb=" O THRBC 688 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THRBC 688 " --> pdb=" O GLYBC 651 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'BC' and resid 668 through 672 removed outlier: 3.885A pdb=" N TRPBC 669 " --> pdb=" O LEUBC 661 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'BC' and resid 674 through 678 Processing sheet with id= 23, first strand: chain 'BC' and resid 517 through 522 Processing sheet with id= 24, first strand: chain 'BC' and resid 643 through 649 removed outlier: 4.415A pdb=" N METBC 690 " --> pdb=" O VALBC 648 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'BC' and resid 657 through 663 Processing sheet with id= 26, first strand: chain 'BD' and resid 122 through 127 removed outlier: 5.979A pdb=" N GLYBD 180 " --> pdb=" O THRBD 163 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N LEUBD 165 " --> pdb=" O GLYBD 180 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'BD' and resid 129 through 132 removed outlier: 3.628A pdb=" N ALABD 129 " --> pdb=" O LEUBD 142 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ASPBD 139 " --> pdb=" O ALABD 154 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'BD' and resid 192 through 195 removed outlier: 4.428A pdb=" N THRBD 192 " --> pdb=" O LEUBD 217 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILEBD 226 " --> pdb=" O LEUBD 218 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARGBD 233 " --> pdb=" O LEUBD 229 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEUBD 238 " --> pdb=" O TYRBD 296 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'BE' and resid 98 through 101 Processing sheet with id= 30, first strand: chain 'BE' and resid 105 through 111 removed outlier: 4.013A pdb=" N GLYBE 105 " --> pdb=" O LEUBE 121 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLNBE 115 " --> pdb=" O THRBE 111 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ASNBE 281 " --> pdb=" O VALBE 124 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'BE' and resid 126 through 130 removed outlier: 6.482A pdb=" N ASPBE 126 " --> pdb=" O LYSBE 150 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYSBE 150 " --> pdb=" O ASPBE 126 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HISBE 128 " --> pdb=" O GLYBE 148 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N THRBE 146 " --> pdb=" O LEUBE 130 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LYSBE 175 " --> pdb=" O GLYBE 149 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'BF' and resid 47 through 50 removed outlier: 3.762A pdb=" N VALBF 47 " --> pdb=" O VALBF 77 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'BF' and resid 186 through 189 Processing sheet with id= 34, first strand: chain 'BI' and resid 55 through 58 removed outlier: 6.830A pdb=" N ILEBI 55 " --> pdb=" O VALBI 83 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'BI' and resid 94 through 98 removed outlier: 3.923A pdb=" N ASPBI 110 " --> pdb=" O LEUBI 98 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'BJ' and resid 95 through 101 removed outlier: 3.967A pdb=" N HISBJ 101 " --> pdb=" O HISBJ 150 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N HISBJ 150 " --> pdb=" O HISBJ 101 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'BK' and resid 17 through 24 Processing sheet with id= 38, first strand: chain 'BL' and resid 169 through 172 removed outlier: 6.832A pdb=" N VALBL 132 " --> pdb=" O ILEBL 172 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N THRBL 194 " --> pdb=" O THRBL 135 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'BN' and resid 55 through 60 removed outlier: 3.640A pdb=" N GLUBN 143 " --> pdb=" O TRPBN 18 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ASPBN 22 " --> pdb=" O LEUBN 145 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'BN' and resid 77 through 81 removed outlier: 7.412A pdb=" N GLYBN 86 " --> pdb=" O THRBN 81 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'BO' and resid 35 through 38 removed outlier: 4.141A pdb=" N THRBO 36 " --> pdb=" O CYSBO 57 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'BO' and resid 71 through 76 removed outlier: 4.142A pdb=" N ASPBO 71 " --> pdb=" O ILEBO 86 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N SERBO 102 " --> pdb=" O ARGBO 90 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARGBO 90 " --> pdb=" O SERBO 102 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLYBO 88 " --> pdb=" O ASNBO 104 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'BP' and resid 93 through 96 Processing sheet with id= 44, first strand: chain 'BP' and resid 273 through 277 Processing sheet with id= 45, first strand: chain 'BQ' and resid 93 through 97 removed outlier: 6.808A pdb=" N GLYBQ 93 " --> pdb=" O ALABQ 156 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'BQ' and resid 118 through 123 removed outlier: 5.853A pdb=" N ILEBQ 160 " --> pdb=" O ARGBQ 123 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VALBQ 161 " --> pdb=" O ILEBQ 89 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'BR' and resid 41 through 44 removed outlier: 4.398A pdb=" N METBR 121 " --> pdb=" O ILEBR 110 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'BS' and resid 79 through 85 removed outlier: 6.546A pdb=" N ILEBS 90 " --> pdb=" O THRBS 107 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VALBS 103 " --> pdb=" O VALBS 94 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'BT' and resid 129 through 135 removed outlier: 4.675A pdb=" N LYSBT 129 " --> pdb=" O ASPBT 123 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILEBT 116 " --> pdb=" O VALBT 177 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLUBT 173 " --> pdb=" O THRBT 120 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'BT' and resid 139 through 142 removed outlier: 4.212A pdb=" N GLNBT 139 " --> pdb=" O ILEBT 150 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'BV' and resid 109 through 113 removed outlier: 7.282A pdb=" N LEUBV 138 " --> pdb=" O GLYBV 149 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'BV' and resid 116 through 121 removed outlier: 3.563A pdb=" N ASPBV 116 " --> pdb=" O ILEBV 199 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VALBV 196 " --> pdb=" O ILEBV 165 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLUBV 161 " --> pdb=" O ASNBV 200 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VALBV 160 " --> pdb=" O LEUBV 134 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLUBV 130 " --> pdb=" O VALBV 164 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'BV' and resid 166 through 169 Processing sheet with id= 54, first strand: chain 'BV' and resid 172 through 179 removed outlier: 4.233A pdb=" N TYRBV 184 " --> pdb=" O GLNBV 179 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'BW' and resid 69 through 76 removed outlier: 4.743A pdb=" N ALABW 69 " --> pdb=" O GLUBW 178 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LYSBW 175 " --> pdb=" O ALABW 141 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'BW' and resid 150 through 157 No H-bonds generated for sheet with id= 56 Processing sheet with id= 57, first strand: chain 'BX' and resid 26 through 29 removed outlier: 4.496A pdb=" N GLNBX 41 " --> pdb=" O VALBX 29 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASPBX 38 " --> pdb=" O LEUBX 99 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYSBX 93 " --> pdb=" O ILEBX 44 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLYBX 75 " --> pdb=" O PROBX 90 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'BY' and resid 92 through 97 removed outlier: 5.271A pdb=" N ASNBY 92 " --> pdb=" O ALABY 113 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'BY' and resid 132 through 135 removed outlier: 7.179A pdb=" N ASPBY 132 " --> pdb=" O THRBY 148 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARGBY 145 " --> pdb=" O ILEBY 154 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARGBY 152 " --> pdb=" O SERBY 147 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'Ba' and resid 126 through 130 Processing sheet with id= 61, first strand: chain 'Ba' and resid 200 through 205 removed outlier: 9.065A pdb=" N ARGBa 200 " --> pdb=" O LYSBa 233 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEUBa 230 " --> pdb=" O HISBa 289 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'Ba' and resid 208 through 214 removed outlier: 4.881A pdb=" N LEUBa 219 " --> pdb=" O ALABa 103 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'Ba' and resid 350 through 353 removed outlier: 8.410A pdb=" N ARGBa 350 " --> pdb=" O LEUBa 382 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'Bb' and resid 183 through 187 removed outlier: 6.254A pdb=" N ASPBb 183 " --> pdb=" O VALBb 179 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VALBb 175 " --> pdb=" O VALBb 187 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'Bb' and resid 190 through 193 removed outlier: 3.861A pdb=" N ASNBb 191 " --> pdb=" O PHEBb 318 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ARGBb 322 " --> pdb=" O VALBb 193 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ARGBb 267 " --> pdb=" O LEUBb 221 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEUBb 213 " --> pdb=" O GLNBb 275 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEUBb 218 " --> pdb=" O HISBb 234 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'Bb' and resid 215 through 218 Processing sheet with id= 67, first strand: chain 'Bb' and resid 272 through 275 removed outlier: 6.069A pdb=" N LEUBb 272 " --> pdb=" O ALABb 314 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'Bc' and resid 74 through 79 removed outlier: 4.751A pdb=" N THRBc 74 " --> pdb=" O HISBc 66 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N CYSBc 120 " --> pdb=" O GLUBc 63 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N PHEBc 124 " --> pdb=" O VALBc 67 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'Bc' and resid 161 through 164 removed outlier: 6.865A pdb=" N GLNBc 294 " --> pdb=" O SERBc 278 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'Bc' and resid 214 through 218 Processing sheet with id= 71, first strand: chain 'Bc' and resid 279 through 284 Processing sheet with id= 72, first strand: chain 'Be' and resid 40 through 43 removed outlier: 4.856A pdb=" N LYSBe 47 " --> pdb=" O GLYBe 43 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'Bg' and resid 61 through 68 removed outlier: 3.874A pdb=" N ALABg 83 " --> pdb=" O TYRBg 79 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'Bh' and resid 254 through 258 removed outlier: 6.555A pdb=" N PHEBh 271 " --> pdb=" O THRBh 258 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALABh 282 " --> pdb=" O LEUBh 274 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'Bi' and resid 192 through 195 removed outlier: 6.868A pdb=" N THRBi 213 " --> pdb=" O VALBi 195 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYRBi 245 " --> pdb=" O LYSBi 264 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LYSBi 264 " --> pdb=" O TYRBi 245 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VALBi 247 " --> pdb=" O HISBi 262 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'Bi' and resid 199 through 203 removed outlier: 3.708A pdb=" N SERBi 200 " --> pdb=" O TYRBi 209 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYRBi 209 " --> pdb=" O SERBi 200 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'Bj' and resid 158 through 162 removed outlier: 4.700A pdb=" N HISBj 251 " --> pdb=" O ARGBj 162 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'Bj' and resid 174 through 177 Processing sheet with id= 79, first strand: chain 'Bj' and resid 211 through 217 removed outlier: 3.856A pdb=" N PHEBj 217 " --> pdb=" O LEUBj 227 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEUBj 227 " --> pdb=" O PHEBj 217 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'Bk' and resid 123 through 127 removed outlier: 4.058A pdb=" N GLUBk 123 " --> pdb=" O GLNBk 158 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLUBk 154 " --> pdb=" O METBk 127 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'Bl' and resid 95 through 101 removed outlier: 5.291A pdb=" N VALBl 137 " --> pdb=" O LYSBl 150 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'Bp' and resid 49 through 56 removed outlier: 3.630A pdb=" N SERBp 50 " --> pdb=" O LYSBp 14 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLYBp 78 " --> pdb=" O PROBp 62 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'Bu' and resid 78 through 85 removed outlier: 3.759A pdb=" N GLYBu 85 " --> pdb=" O LYSBu 93 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYSBu 93 " --> pdb=" O GLYBu 85 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'Bw' and resid 90 through 93 No H-bonds generated for sheet with id= 84 Processing sheet with id= 85, first strand: chain 'Bw' and resid 112 through 116 removed outlier: 7.051A pdb=" N ASNBw 385 " --> pdb=" O ASNBw 369 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASNBw 369 " --> pdb=" O ASNBw 385 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N CYSBw 387 " --> pdb=" O GLNBw 367 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N GLNBw 367 " --> pdb=" O CYSBw 387 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N GLYBw 389 " --> pdb=" O CYSBw 365 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N CYSBw 365 " --> pdb=" O GLYBw 389 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLNBw 391 " --> pdb=" O PHEBw 363 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N PHEBw 363 " --> pdb=" O GLNBw 391 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N LYSBw 359 " --> pdb=" O LEUBw 395 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'Bx' and resid 35 through 42 removed outlier: 4.539A pdb=" N PHEBx 35 " --> pdb=" O THRBx 54 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'AB' and resid 89 through 92 removed outlier: 5.173A pdb=" N HISAB 89 " --> pdb=" O ILEAB 115 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ASPAB 113 " --> pdb=" O GLYAB 91 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'AB' and resid 163 through 167 Processing sheet with id= 89, first strand: chain 'AC' and resid 69 through 72 removed outlier: 5.547A pdb=" N LEUAC 69 " --> pdb=" O LEUAC 108 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'AE' and resid 201 through 204 removed outlier: 4.244A pdb=" N VALAE 201 " --> pdb=" O ILEAE 222 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N THRAE 220 " --> pdb=" O LEUAE 203 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEUAE 244 " --> pdb=" O LEUAE 223 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 'AE' and resid 292 through 297 removed outlier: 7.567A pdb=" N HISAE 292 " --> pdb=" O LYSAE 307 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N LYSAE 307 " --> pdb=" O HISAE 292 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLNAE 308 " --> pdb=" O ASPAE 331 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ASPAE 331 " --> pdb=" O GLNAE 308 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N LEUAE 332 " --> pdb=" O GLYAE 313 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'AE' and resid 370 through 373 removed outlier: 6.707A pdb=" N VALAE 370 " --> pdb=" O VALAE 384 " (cutoff:3.500A) Processing sheet with id= 93, first strand: chain 'AE' and resid 241 through 248 Processing sheet with id= 94, first strand: chain 'AF' and resid 42 through 46 removed outlier: 3.876A pdb=" N GLYAF 43 " --> pdb=" O TYRAF 63 " (cutoff:3.500A) Processing sheet with id= 95, first strand: chain 'AG' and resid 156 through 162 Processing sheet with id= 96, first strand: chain 'AI' and resid 269 through 276 removed outlier: 7.805A pdb=" N ALAAI 269 " --> pdb=" O GLYAI 288 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N HISAI 327 " --> pdb=" O SERAI 291 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARGAI 293 " --> pdb=" O HISAI 327 " (cutoff:3.500A) Processing sheet with id= 97, first strand: chain 'AJ' and resid 106 through 111 Processing sheet with id= 98, first strand: chain 'AK' and resid 109 through 112 removed outlier: 4.237A pdb=" N SERAK 176 " --> pdb=" O VALAK 149 " (cutoff:3.500A) Processing sheet with id= 99, first strand: chain 'AL' and resid 57 through 61 removed outlier: 5.095A pdb=" N LEUAL 109 " --> pdb=" O VALAL 126 " (cutoff:3.500A) Processing sheet with id=100, first strand: chain 'AL' and resid 64 through 69 removed outlier: 3.586A pdb=" N ARGAL 64 " --> pdb=" O ARGAL 82 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N LYSAL 79 " --> pdb=" O ILEAL 95 " (cutoff:3.500A) Processing sheet with id=101, first strand: chain 'AP' and resid 19 through 25 removed outlier: 3.570A pdb=" N LEUAP 65 " --> pdb=" O ASPAP 55 " (cutoff:3.500A) Processing sheet with id=102, first strand: chain 'AQ' and resid 12 through 16 Processing sheet with id=103, first strand: chain 'AQ' and resid 24 through 37 removed outlier: 4.671A pdb=" N LYSAQ 24 " --> pdb=" O ASPAQ 53 " (cutoff:3.500A) Processing sheet with id=104, first strand: chain 'AQ' and resid 91 through 94 removed outlier: 4.042A pdb=" N VALAQ 91 " --> pdb=" O CYSAQ 100 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYSAQ 98 " --> pdb=" O ASPAQ 93 " (cutoff:3.500A) Processing sheet with id=105, first strand: chain 'Aa' and resid 177 through 182 removed outlier: 5.112A pdb=" N PHEAa 193 " --> pdb=" O ASPAa 182 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N THRAa 202 " --> pdb=" O GLUAa 198 " (cutoff:3.500A) Processing sheet with id=106, first strand: chain 'Ac' and resid 62 through 68 removed outlier: 4.537A pdb=" N GLUAc 84 " --> pdb=" O LEUAc 80 " (cutoff:3.500A) Processing sheet with id=107, first strand: chain 'Ad' and resid 189 through 192 removed outlier: 3.710A pdb=" N LEUAd 196 " --> pdb=" O THRAd 192 " (cutoff:3.500A) Processing sheet with id=108, first strand: chain 'Af' and resid 100 through 105 removed outlier: 4.268A pdb=" N THRAf 139 " --> pdb=" O ILEAf 105 " (cutoff:3.500A) Processing sheet with id=109, first strand: chain 'Af' and resid 112 through 116 Processing sheet with id=110, first strand: chain 'Af' and resid 150 through 153 removed outlier: 7.123A pdb=" N LEUAf 150 " --> pdb=" O ILEAf 163 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SERAf 152 " --> pdb=" O THRAf 161 " (cutoff:3.500A) Processing sheet with id=111, first strand: chain 'Ag' and resid 65 through 69 removed outlier: 4.407A pdb=" N GLNAg 65 " --> pdb=" O VALAg 100 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALAAg 96 " --> pdb=" O ILEAg 69 " (cutoff:3.500A) Processing sheet with id=112, first strand: chain 'Ag' and resid 149 through 155 removed outlier: 3.706A pdb=" N LEUAg 257 " --> pdb=" O GLYAg 302 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VALAg 121 " --> pdb=" O GLYAg 303 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N GLYAg 127 " --> pdb=" O VALAg 309 " (cutoff:3.500A) Processing sheet with id=113, first strand: chain 'Aj' and resid 41 through 44 removed outlier: 7.577A pdb=" N METAj 41 " --> pdb=" O LEUAj 50 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASNAj 48 " --> pdb=" O ARGAj 43 " (cutoff:3.500A) Processing sheet with id=114, first strand: chain 'Aj' and resid 78 through 81 removed outlier: 4.630A pdb=" N ARGAj 78 " --> pdb=" O LEUAj 97 " (cutoff:3.500A) Processing sheet with id=115, first strand: chain 'Aj' and resid 99 through 103 removed outlier: 3.991A pdb=" N ARGAj 99 " --> pdb=" O TRPAj 115 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N HISAj 111 " --> pdb=" O ASPAj 103 " (cutoff:3.500A) Processing sheet with id=116, first strand: chain 'Aj' and resid 162 through 165 removed outlier: 7.296A pdb=" N LEUAj 162 " --> pdb=" O LEUAj 193 " (cutoff:3.500A) Processing sheet with id=117, first strand: chain 'Ak' and resid 151 through 155 removed outlier: 3.554A pdb=" N VALAk 206 " --> pdb=" O CYSAk 201 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ARGAk 199 " --> pdb=" O THRAk 208 " (cutoff:3.500A) 5058 hydrogen bonds defined for protein. 15042 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1724 hydrogen bonds 2998 hydrogen bond angles 0 basepair planarities 714 basepair parallelities 1408 stacking parallelities Total time for adding SS restraints: 118.75 Time building geometry restraints manager: 55.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 49422 1.34 - 1.48: 63432 1.48 - 1.63: 73919 1.63 - 1.77: 9 1.77 - 1.91: 781 Bond restraints: 187563 Sorted by residual: bond pdb=" CA PROAj 167 " pdb=" C PROAj 167 " ideal model delta sigma weight residual 1.514 1.543 -0.029 5.50e-03 3.31e+04 2.74e+01 bond pdb=" CA ILEAc 52 " pdb=" CB ILEAc 52 " ideal model delta sigma weight residual 1.537 1.563 -0.026 5.00e-03 4.00e+04 2.73e+01 bond pdb=" CA PROBT 56 " pdb=" C PROBT 56 " ideal model delta sigma weight residual 1.514 1.539 -0.025 5.50e-03 3.31e+04 2.05e+01 bond pdb=" CA ILEAa 183 " pdb=" CB ILEAa 183 " ideal model delta sigma weight residual 1.535 1.588 -0.053 1.29e-02 6.01e+03 1.66e+01 bond pdb=" CA PROAB 242 " pdb=" C PROAB 242 " ideal model delta sigma weight residual 1.517 1.553 -0.036 9.30e-03 1.16e+04 1.50e+01 ... (remaining 187558 not shown) Histogram of bond angle deviations from ideal: 96.50 - 104.59: 13853 104.59 - 112.68: 103428 112.68 - 120.76: 86844 120.76 - 128.85: 58294 128.85 - 136.94: 3972 Bond angle restraints: 266391 Sorted by residual: angle pdb=" C GLYBh 284 " pdb=" N PROBh 285 " pdb=" CA PROBh 285 " ideal model delta sigma weight residual 120.31 132.92 -12.61 9.80e-01 1.04e+00 1.66e+02 angle pdb=" C ARGBt 23 " pdb=" N PROBt 24 " pdb=" CA PROBt 24 " ideal model delta sigma weight residual 119.82 131.15 -11.33 9.80e-01 1.04e+00 1.34e+02 angle pdb=" N PROBT 68 " pdb=" CA PROBT 68 " pdb=" CB PROBT 68 " ideal model delta sigma weight residual 103.25 113.70 -10.45 1.05e+00 9.07e-01 9.90e+01 angle pdb=" C TYRBe 129 " pdb=" N PROBe 130 " pdb=" CA PROBe 130 " ideal model delta sigma weight residual 119.87 110.12 9.75 1.04e+00 9.25e-01 8.79e+01 angle pdb=" C ARGBt 25 " pdb=" N PROBt 26 " pdb=" CA PROBt 26 " ideal model delta sigma weight residual 120.31 129.24 -8.93 9.80e-01 1.04e+00 8.31e+01 ... (remaining 266386 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 103232 35.97 - 71.94: 4536 71.94 - 107.90: 276 107.90 - 143.87: 20 143.87 - 179.84: 43 Dihedral angle restraints: 108107 sinusoidal: 64259 harmonic: 43848 Sorted by residual: dihedral pdb=" CA PHEBE 316 " pdb=" C PHEBE 316 " pdb=" N PROBE 317 " pdb=" CA PROBE 317 " ideal model delta harmonic sigma weight residual 180.00 95.34 84.66 0 5.00e+00 4.00e-02 2.87e+02 dihedral pdb=" O4' CBA 890 " pdb=" C1' CBA 890 " pdb=" N1 CBA 890 " pdb=" C2 CBA 890 " ideal model delta sinusoidal sigma weight residual 200.00 24.50 175.50 1 1.50e+01 4.44e-03 8.52e+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 200.00 25.00 175.00 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 108104 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 28686 0.080 - 0.159: 2549 0.159 - 0.239: 160 0.239 - 0.318: 13 0.318 - 0.398: 3 Chirality restraints: 31411 Sorted by residual: chirality pdb=" C3' UBA 48 " pdb=" C4' UBA 48 " pdb=" O3' UBA 48 " pdb=" C2' UBA 48 " both_signs ideal model delta sigma weight residual False -2.74 -2.35 -0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" CA PROBT 68 " pdb=" N PROBT 68 " pdb=" C PROBT 68 " pdb=" CB PROBT 68 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" CA ASNBx 164 " pdb=" N ASNBx 164 " pdb=" C ASNBx 164 " pdb=" CB ASNBx 164 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.08e+00 ... (remaining 31408 not shown) Planarity restraints: 24357 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' UBA 693 " -0.046 2.00e-02 2.50e+03 2.47e-02 1.37e+01 pdb=" N1 UBA 693 " 0.055 2.00e-02 2.50e+03 pdb=" C2 UBA 693 " 0.004 2.00e-02 2.50e+03 pdb=" O2 UBA 693 " 0.003 2.00e-02 2.50e+03 pdb=" N3 UBA 693 " -0.004 2.00e-02 2.50e+03 pdb=" C4 UBA 693 " -0.010 2.00e-02 2.50e+03 pdb=" O4 UBA 693 " -0.009 2.00e-02 2.50e+03 pdb=" C5 UBA 693 " -0.001 2.00e-02 2.50e+03 pdb=" C6 UBA 693 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARGBg 144 " 0.048 5.00e-02 4.00e+02 7.24e-02 8.40e+00 pdb=" N PROBg 145 " -0.125 5.00e-02 4.00e+02 pdb=" CA PROBg 145 " 0.037 5.00e-02 4.00e+02 pdb=" CD PROBg 145 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHEBE 316 " 0.047 5.00e-02 4.00e+02 7.15e-02 8.19e+00 pdb=" N PROBE 317 " -0.124 5.00e-02 4.00e+02 pdb=" CA PROBE 317 " 0.037 5.00e-02 4.00e+02 pdb=" CD PROBE 317 " 0.040 5.00e-02 4.00e+02 ... (remaining 24354 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 461 2.41 - 3.03: 97215 3.03 - 3.65: 282224 3.65 - 4.28: 457763 4.28 - 4.90: 682119 Nonbonded interactions: 1519782 Sorted by model distance: nonbonded pdb=" OP2 AAA 925 " pdb="MG MGAA3011 " model vdw 1.785 2.170 nonbonded pdb=" OP1 UBA 373 " pdb="MG MGBA3065 " model vdw 1.863 2.170 nonbonded pdb=" OP2 GBA1325 " pdb="MG MGBA3071 " model vdw 1.910 2.170 nonbonded pdb=" OP1 ABA 762 " pdb="MG MGBA3069 " model vdw 1.918 2.170 nonbonded pdb=" OP2 ABA1518 " pdb="MG MGBA3095 " model vdw 1.921 2.170 ... (remaining 1519777 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 Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 6 6.06 5 P 2670 5.49 5 Mg 326 5.21 5 S 497 5.16 5 Na 1 4.78 5 C 102575 2.51 5 N 32449 2.21 5 O 39848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.290 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: 0.090 Extract box with map and model: 15.930 Check model and map are aligned: 1.700 Convert atoms to be neutral: 1.000 Process input model: 443.140 Find NCS groups from input model: 6.060 Set up NCS constraints: 0.470 Set refine NCS operators: 0.000 Set scattering table: 0.040 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:2.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 471.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.104 187563 Z= 0.470 Angle : 1.089 15.939 266391 Z= 0.717 Chirality : 0.046 0.398 31411 Planarity : 0.005 0.072 24357 Dihedral : 17.077 179.841 79671 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.75 % Favored : 96.08 % Rotamer Outliers : 9.18 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.11 % 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: -2.74 (0.06), residues: 14839 helix: -2.53 (0.05), residues: 5766 sheet: -0.82 (0.10), residues: 1710 loop : -1.33 (0.06), residues: 7363 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29678 Ramachandran restraints generated. 14839 Oldfield, 0 Emsley, 14839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29678 Ramachandran restraints generated. 14839 Oldfield, 0 Emsley, 14839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5199 residues out of total 13087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1187 poor density : 4012 time to evaluate : 10.831 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 1187 outliers final: 270 residues processed: 4765 average time/residue: 1.6051 time to fit residues: 13031.9302 Evaluate side-chains 2648 residues out of total 13087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 270 poor density : 2378 time to evaluate : 10.661 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 270 outliers final: 2 residues processed: 270 average time/residue: 1.2869 time to fit residues: 662.4142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1725 random chunks: chunk 1456 optimal weight: 2.9990 chunk 1307 optimal weight: 5.9990 chunk 725 optimal weight: 5.9990 chunk 446 optimal weight: 5.9990 chunk 881 optimal weight: 6.9990 chunk 698 optimal weight: 5.9990 chunk 1352 optimal weight: 30.0000 chunk 523 optimal weight: 1.9990 chunk 822 optimal weight: 0.9990 chunk 1006 optimal weight: 2.9990 chunk 1566 optimal weight: 20.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B0 41 ASN B0 59 HIS ** B1 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1 42 HIS B1 175 GLN B2 90 GLN B2 94 ASN ** B2 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 67 HIS B5 83 ASN B5 118 GLN B5 170 GLN B6 59 GLN B7 65 HIS B8 118 HIS ** BC 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BC 215 GLN BC 238 HIS BC 514 ASN BC 575 ASN BC 580 ASN BC 649 GLN BD 183 HIS BE 72 GLN BE 115 GLN BE 128 HIS ** BE 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BE 166 GLN BE 197 HIS BE 227 GLN BE 281 ASN BE 292 HIS ** BF 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BF 97 HIS BF 103 GLN BF 105 ASN BF 184 GLN BF 257 GLN BI 88 HIS BI 93 ASN BI 136 ASN BJ 41 HIS BJ 73 GLN BJ 115 GLN BJ 119 HIS BJ 217 GLN BK 103 HIS BL 152 HIS BN 40 GLN BN 48 HIS BN 74 GLN BN 80 HIS BN 123 GLN ** BN 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BO 43 ASN BO 89 HIS ** BO 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BP 53 HIS BP 84 ASN BP 87 HIS BP 94 GLN BP 170 ASN BQ 68 ASN ** BQ 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 110 ASN BQ 173 GLN BQ 202 GLN BQ 209 ASN BR 112 ASN BR 142 ASN BR 148 GLN ** BS 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BS 79 HIS ** BS 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BS 147 HIS BT 153 ASN BT 262 GLN BU 94 GLN BV 109 GLN BV 122 ASN BV 175 ASN BW 60 GLN BW 149 GLN BW 157 HIS BW 171 HIS BW 199 GLN BW 203 ASN BW 208 HIS BX 77 ASN BX 103 GLN BY 84 ASN Ba 65 HIS Ba 108 HIS Ba 119 GLN Ba 156 ASN ** Ba 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 223 HIS Ba 266 GLN Ba 289 HIS Ba 343 GLN Ba 358 GLN Ba 360 ASN Ba 420 HIS Bb 220 ASN Bb 224 HIS Bb 243 ASN Bb 266 HIS ** Bb 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 308 GLN Bc 46 ASN Bc 79 ASN Bc 81 ASN Bc 197 HIS Bc 243 GLN Bc 252 HIS Bc 274 GLN ** Bc 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bc 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bd 129 HIS Bd 143 GLN Bd 174 GLN Bf 44 ASN Bf 62 HIS Bf 121 HIS Bf 130 HIS Bg 17 ASN Bg 107 GLN Bg 127 GLN Bg 131 HIS Bg 135 ASN Bh 118 ASN Bh 172 ASN Bh 310 ASN Bi 47 GLN Bi 115 ASN Bi 153 ASN Bi 154 ASN Bi 235 GLN Bj 54 GLN Bj 87 HIS Bj 175 GLN Bj 271 GLN Bk 54 HIS Bk 111 HIS Bk 115 ASN ** Bl 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bn 33 HIS ** Bn 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bn 122 ASN Bo 63 GLN Bt 34 ASN Bt 85 HIS ** Bu 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bv 107 GLN Bv 130 GLN ** Bw 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bw 201 HIS ** Bw 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bw 385 ASN ** Bw 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bw 414 GLN Bw 421 ASN Bx 69 GLN Bx 164 ASN Bx 184 ASN Bx 196 HIS AB 68 HIS AB 133 HIS AB 253 GLN AC 72 HIS AE 145 ASN AE 196 ASN AE 292 HIS AE 317 HIS AE 356 GLN ** AE 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AF 41 ASN ** AG 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 122 GLN AG 196 HIS AG 227 HIS AG 233 ASN AG 238 HIS AI 101 GLN ** AI 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AI 178 GLN AI 262 GLN AI 367 GLN AJ 109 HIS AK 73 ASN AK 98 GLN AK 111 HIS AK 121 ASN AL 35 GLN AL 37 HIS ** AL 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 77 ASN AL 100 HIS ** AL 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AO 153 HIS AO 163 GLN AO 170 ASN AP 28 ASN AQ 23 GLN AQ 76 HIS AQ 79 HIS ** AR 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AR 83 GLN AR 116 GLN ** AU 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 246 HIS Aa 299 ASN ** Aa 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 359 GLN Aa 372 GLN Ab 61 GLN Ac 59 ASN Ac 63 GLN ** Ac 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 125 HIS Ad 102 HIS Ad 117 HIS Ad 142 GLN ** Ae 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 185 ASN ** Ae 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 314 GLN Ae 370 GLN Ae 424 HIS ** Ae 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 142 HIS Ag 153 HIS Ag 173 ASN ** Ag 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 301 GLN Ag 386 ASN Ah 288 ASN Ah 295 GLN Ah 308 ASN Ah 321 HIS Ah 323 HIS ** Ah 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 82 GLN Aj 111 HIS Aj 133 GLN Ak 112 ASN Ak 323 ASN Ao 104 HIS Ao 129 GLN Ao 246 ASN Ao 258 ASN ** Ao 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 385 HIS ** Ao 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 103 ASN ** Ap 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 147 HIS Ap 181 HIS Total number of N/Q/H flips: 221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.098 187563 Z= 0.272 Angle : 0.692 15.496 266391 Z= 0.360 Chirality : 0.041 0.334 31411 Planarity : 0.006 0.110 24357 Dihedral : 15.584 179.540 48656 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.90 % Favored : 97.03 % Rotamer Outliers : 3.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.11 % 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: -0.87 (0.06), residues: 14839 helix: -0.27 (0.06), residues: 5888 sheet: -0.41 (0.11), residues: 1805 loop : -0.77 (0.07), residues: 7146 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29678 Ramachandran restraints generated. 14839 Oldfield, 0 Emsley, 14839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29678 Ramachandran restraints generated. 14839 Oldfield, 0 Emsley, 14839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3071 residues out of total 13087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 466 poor density : 2605 time to evaluate : 10.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 466 outliers final: 235 residues processed: 2916 average time/residue: 1.5205 time to fit residues: 7649.9387 Evaluate side-chains 2429 residues out of total 13087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 2194 time to evaluate : 11.976 Switching outliers to nearest non-outliers outliers start: 235 outliers final: 0 residues processed: 235 average time/residue: 1.1748 time to fit residues: 538.7586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1725 random chunks: chunk 870 optimal weight: 0.0050 chunk 486 optimal weight: 9.9990 chunk 1303 optimal weight: 6.9990 chunk 1066 optimal weight: 10.0000 chunk 432 optimal weight: 0.8980 chunk 1569 optimal weight: 8.9990 chunk 1695 optimal weight: 7.9990 chunk 1397 optimal weight: 30.0000 chunk 1556 optimal weight: 40.0000 chunk 535 optimal weight: 8.9990 chunk 1258 optimal weight: 6.9990 overall best weight: 4.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B0 76 HIS B2 75 ASN B2 112 ASN ** B2 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 61 GLN B5 144 GLN ** BC 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 514 ASN BC 580 ASN BD 196 ASN ** BE 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BF 103 GLN BF 138 HIS BF 184 GLN BF 257 GLN BJ 61 ASN BJ 128 ASN BJ 150 HIS BJ 224 HIS ** BN 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BO 43 ASN BP 219 ASN BQ 98 HIS BQ 202 GLN BR 116 GLN BR 142 ASN ** BS 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BV 108 HIS BW 77 GLN BW 131 ASN BX 103 GLN ** Ba 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bb 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 354 GLN Bc 274 GLN Bc 305 HIS Bg 27 GLN Bh 310 ASN Bi 154 ASN ** Bi 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bj 54 GLN Bk 108 GLN Bk 111 HIS Bk 177 ASN ** Bn 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bo 95 GLN Bo 108 ASN Bp 84 GLN Bu 145 ASN Bv 106 GLN ** Bw 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bx 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 253 GLN AC 81 HIS ** AC 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AE 211 ASN AE 277 HIS ** AE 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 238 HIS AI 87 HIS AI 101 GLN ** AI 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AK 89 HIS AK 98 GLN ** AL 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AR 72 HIS Aa 251 ASN Aa 342 GLN Ac 54 GLN Ac 59 ASN Ac 95 ASN Ac 101 HIS ** Ac 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 117 HIS ** Ae 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 370 GLN ** Ag 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 234 ASN ** Ag 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 295 GLN ** Ah 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 270 GLN ** Am 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 104 HIS Ao 122 ASN ** Ao 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 543 HIS Ao 615 ASN Ap 111 GLN Ap 130 HIS Ap 169 GLN Total number of N/Q/H flips: 69 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.129 187563 Z= 0.341 Angle : 0.681 19.343 266391 Z= 0.349 Chirality : 0.042 0.392 31411 Planarity : 0.006 0.102 24357 Dihedral : 15.409 179.581 48656 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.38 % Favored : 96.56 % Rotamer Outliers : 3.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.11 % 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: -0.20 (0.07), residues: 14839 helix: 0.60 (0.07), residues: 5898 sheet: -0.22 (0.11), residues: 1816 loop : -0.66 (0.07), residues: 7125 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29678 Ramachandran restraints generated. 14839 Oldfield, 0 Emsley, 14839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29678 Ramachandran restraints generated. 14839 Oldfield, 0 Emsley, 14839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2771 residues out of total 13087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 423 poor density : 2348 time to evaluate : 11.002 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 outliers start: 423 outliers final: 215 residues processed: 2638 average time/residue: 1.4299 time to fit residues: 6588.2737 Evaluate side-chains 2346 residues out of total 13087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 2131 time to evaluate : 10.731 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 215 outliers final: 1 residues processed: 215 average time/residue: 1.1281 time to fit residues: 472.0443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1725 random chunks: chunk 1550 optimal weight: 0.9990 chunk 1179 optimal weight: 3.9990 chunk 814 optimal weight: 10.0000 chunk 173 optimal weight: 7.9990 chunk 748 optimal weight: 3.9990 chunk 1053 optimal weight: 0.8980 chunk 1574 optimal weight: 5.9990 chunk 1667 optimal weight: 5.9990 chunk 822 optimal weight: 0.7980 chunk 1492 optimal weight: 1.9990 chunk 449 optimal weight: 20.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2 75 ASN B5 140 GLN B6 31 ASN ** BC 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 275 HIS BE 154 HIS ** BF 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BF 103 GLN BF 257 GLN BI 136 ASN BJ 224 HIS ** BN 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BO 43 ASN ** BO 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BR 116 GLN BR 142 ASN BS 89 HIS BS 100 GLN BT 212 ASN BX 103 GLN ** Ba 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 149 GLN ** Bb 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 354 GLN Bg 107 GLN Bg 127 GLN Bh 172 ASN Bi 115 ASN Bi 154 ASN ** Bi 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bj 67 GLN Bk 177 ASN Bl 93 ASN ** Bn 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bp 35 GLN Bt 33 GLN Bu 145 ASN Bv 106 GLN Bw 96 GLN ** Bw 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bw 381 ASN ** Bw 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bx 69 GLN AB 73 ASN AB 253 GLN ** AC 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AE 155 GLN AE 388 GLN ** AE 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 238 HIS ** AI 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AK 98 GLN ** AL 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AO 170 ASN AR 116 GLN Aa 139 GLN ** Ac 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 109 ASN Ad 117 HIS Ad 142 GLN ** Ae 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 219 GLN ** Ae 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 58 HIS ** Ag 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 295 GLN ** Ah 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 219 GLN Ak 270 GLN Ak 307 ASN Ak 323 ASN ** Am 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 104 HIS Ap 111 GLN ** Ap 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.129 187563 Z= 0.192 Angle : 0.601 16.311 266391 Z= 0.307 Chirality : 0.038 0.287 31411 Planarity : 0.005 0.118 24357 Dihedral : 15.281 179.812 48656 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.24 % Favored : 96.69 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.11 % Twisted General : 0.01 % 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: 0.27 (0.07), residues: 14839 helix: 1.12 (0.07), residues: 5891 sheet: -0.06 (0.11), residues: 1815 loop : -0.50 (0.07), residues: 7133 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29678 Ramachandran restraints generated. 14839 Oldfield, 0 Emsley, 14839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29678 Ramachandran restraints generated. 14839 Oldfield, 0 Emsley, 14839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2590 residues out of total 13087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 2335 time to evaluate : 10.948 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 outliers start: 255 outliers final: 114 residues processed: 2487 average time/residue: 1.3995 time to fit residues: 5971.4838 Evaluate side-chains 2238 residues out of total 13087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 2124 time to evaluate : 10.649 Switching outliers to nearest non-outliers outliers start: 114 outliers final: 0 residues processed: 114 average time/residue: 1.1085 time to fit residues: 252.3319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1725 random chunks: chunk 1388 optimal weight: 9.9990 chunk 946 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 1241 optimal weight: 20.0000 chunk 687 optimal weight: 2.9990 chunk 1422 optimal weight: 3.9990 chunk 1152 optimal weight: 50.0000 chunk 1 optimal weight: 6.9990 chunk 851 optimal weight: 20.0000 chunk 1496 optimal weight: 10.0000 chunk 420 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1 46 HIS B2 75 ASN B5 144 GLN ** BC 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BF 103 GLN BF 257 GLN BI 136 ASN BJ 224 HIS BN 140 ASN BO 43 ASN ** BQ 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BS 88 HIS BS 100 GLN BS 121 ASN BT 219 GLN BX 103 GLN BY 18 ASN ** Ba 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 191 ASN Bb 220 ASN ** Bb 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 354 GLN Bc 274 GLN ** Bd 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 107 GLN Bg 127 GLN Bh 310 ASN Bi 154 ASN Bj 67 GLN ** Bj 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bk 175 HIS Bk 177 ASN ** Bn 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bo 108 ASN Bp 35 GLN Bu 145 ASN Bv 106 GLN Bw 96 GLN ** Bw 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bw 290 HIS ** Bw 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bx 69 GLN Bx 131 HIS AB 253 GLN ** AC 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AE 155 GLN AE 388 GLN ** AE 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 96 ASN AG 207 GLN AG 238 HIS ** AI 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 125 HIS AK 98 GLN ** AK 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 180 ASN ** AL 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AO 139 ASN AR 83 GLN Ac 59 ASN ** Ac 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 219 GLN ** Ag 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 295 GLN Ah 364 HIS Ak 270 GLN Ak 307 ASN Ak 323 ASN ** Am 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 115 ASN ** Ap 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.132 187563 Z= 0.238 Angle : 0.603 16.586 266391 Z= 0.307 Chirality : 0.038 0.336 31411 Planarity : 0.005 0.122 24357 Dihedral : 15.132 179.674 48656 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.48 % Favored : 96.45 % Rotamer Outliers : 1.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.11 % Twisted General : 0.01 % 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: 0.44 (0.07), residues: 14839 helix: 1.33 (0.07), residues: 5898 sheet: 0.01 (0.11), residues: 1813 loop : -0.47 (0.07), residues: 7128 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29678 Ramachandran restraints generated. 14839 Oldfield, 0 Emsley, 14839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29678 Ramachandran restraints generated. 14839 Oldfield, 0 Emsley, 14839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2460 residues out of total 13087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 2221 time to evaluate : 10.805 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 outliers start: 239 outliers final: 129 residues processed: 2352 average time/residue: 1.3816 time to fit residues: 5596.8352 Evaluate side-chains 2215 residues out of total 13087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 2086 time to evaluate : 10.723 Switching outliers to nearest non-outliers outliers start: 129 outliers final: 0 residues processed: 129 average time/residue: 1.1010 time to fit residues: 283.2537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1725 random chunks: chunk 560 optimal weight: 2.9990 chunk 1501 optimal weight: 40.0000 chunk 329 optimal weight: 0.9990 chunk 978 optimal weight: 20.0000 chunk 411 optimal weight: 5.9990 chunk 1669 optimal weight: 5.9990 chunk 1385 optimal weight: 0.8980 chunk 772 optimal weight: 7.9990 chunk 138 optimal weight: 7.9990 chunk 552 optimal weight: 2.9990 chunk 876 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2 75 ASN B5 144 GLN ** BC 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BF 103 GLN BF 257 GLN BN 140 ASN BO 43 ASN ** BP 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 181 HIS BQ 202 GLN ** BQ 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BS 100 GLN BX 103 GLN ** BY 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 191 ASN ** Bb 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bc 46 ASN Bd 129 HIS ** Bd 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Be 73 ASN Bg 107 GLN Bg 127 GLN Bh 310 ASN Bi 119 GLN Bi 154 ASN Bi 217 HIS ** Bj 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bk 177 ASN ** Bn 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bo 108 ASN Bp 35 GLN Bu 145 ASN Bu 183 ASN ** Bw 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bw 414 GLN Bx 69 GLN AB 253 GLN ** AC 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AE 155 GLN AE 415 GLN ** AF 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 96 ASN AG 238 HIS ** AI 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AI 156 GLN AI 221 GLN AJ 125 HIS AK 98 GLN ** AL 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 117 HIS Ae 196 ASN ** Ae 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 301 GLN Ae 357 GLN Af 136 GLN ** Ag 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 194 ASN Ag 256 HIS ** Ag 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 295 GLN ** Aj 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 270 GLN Ak 307 ASN ** Am 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.256 187563 Z= 0.240 Angle : 0.604 21.268 266391 Z= 0.307 Chirality : 0.038 0.408 31411 Planarity : 0.005 0.106 24357 Dihedral : 15.059 179.833 48656 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.53 % Favored : 96.38 % Rotamer Outliers : 1.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.11 % Twisted General : 0.01 % 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: 0.54 (0.07), residues: 14839 helix: 1.44 (0.07), residues: 5921 sheet: 0.09 (0.11), residues: 1794 loop : -0.45 (0.07), residues: 7124 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29678 Ramachandran restraints generated. 14839 Oldfield, 0 Emsley, 14839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29678 Ramachandran restraints generated. 14839 Oldfield, 0 Emsley, 14839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2408 residues out of total 13087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 2202 time to evaluate : 11.073 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 outliers start: 206 outliers final: 116 residues processed: 2316 average time/residue: 1.4062 time to fit residues: 5589.4881 Evaluate side-chains 2189 residues out of total 13087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 2073 time to evaluate : 10.727 Switching outliers to nearest non-outliers outliers start: 116 outliers final: 0 residues processed: 116 average time/residue: 1.1549 time to fit residues: 267.7076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1725 random chunks: chunk 1609 optimal weight: 5.9990 chunk 188 optimal weight: 10.0000 chunk 950 optimal weight: 8.9990 chunk 1218 optimal weight: 10.0000 chunk 944 optimal weight: 0.0000 chunk 1404 optimal weight: 50.0000 chunk 931 optimal weight: 3.9990 chunk 1662 optimal weight: 50.0000 chunk 1040 optimal weight: 9.9990 chunk 1013 optimal weight: 10.0000 chunk 767 optimal weight: 10.0000 overall best weight: 5.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2 75 ASN B2 193 ASN ** B2 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 187 GLN ** BC 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BF 103 GLN BJ 228 GLN BN 140 ASN BO 43 ASN ** BP 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 208 ASN ** BR 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BS 100 GLN ** BT 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BX 103 GLN ** Ba 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 149 GLN Bb 191 ASN ** Bb 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Be 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 24 GLN Bg 58 ASN Bg 107 GLN Bg 127 GLN Bh 77 HIS Bi 47 GLN Bi 119 GLN Bi 154 ASN ** Bi 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bj 67 GLN ** Bj 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bk 177 ASN ** Bn 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bn 120 HIS ** Bu 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bu 183 ASN ** Bw 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bx 69 GLN AB 253 GLN ** AC 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 96 ASN AG 238 HIS AI 87 HIS ** AI 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AK 98 GLN ** AK 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AP 75 HIS AQ 23 GLN AR 77 ASN Aa 132 GLN Ac 59 ASN ** Ac 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 90 GLN ** Ae 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 87 HIS Af 98 ASN ** Af 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 325 GLN Ah 295 GLN ** Ai 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 270 GLN Ak 307 ASN ** Am 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 129 GLN Ao 473 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.354 187563 Z= 0.415 Angle : 0.707 22.624 266391 Z= 0.359 Chirality : 0.043 0.351 31411 Planarity : 0.006 0.123 24357 Dihedral : 15.153 179.429 48656 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.02 % Favored : 95.89 % Rotamer Outliers : 1.85 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.22 % Twisted General : 0.01 % 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: 0.31 (0.07), residues: 14839 helix: 1.26 (0.07), residues: 5956 sheet: -0.02 (0.12), residues: 1807 loop : -0.61 (0.07), residues: 7076 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29678 Ramachandran restraints generated. 14839 Oldfield, 0 Emsley, 14839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29678 Ramachandran restraints generated. 14839 Oldfield, 0 Emsley, 14839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2402 residues out of total 13087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 2163 time to evaluate : 10.776 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 outliers start: 239 outliers final: 136 residues processed: 2301 average time/residue: 1.4418 time to fit residues: 5697.5395 Evaluate side-chains 2157 residues out of total 13087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 2021 time to evaluate : 10.824 Switching outliers to nearest non-outliers outliers start: 136 outliers final: 0 residues processed: 136 average time/residue: 1.1350 time to fit residues: 304.7720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1725 random chunks: chunk 1028 optimal weight: 3.9990 chunk 663 optimal weight: 0.8980 chunk 992 optimal weight: 4.9990 chunk 500 optimal weight: 0.9980 chunk 326 optimal weight: 10.0000 chunk 322 optimal weight: 4.9990 chunk 1057 optimal weight: 50.0000 chunk 1132 optimal weight: 20.0000 chunk 822 optimal weight: 0.9980 chunk 154 optimal weight: 8.9990 chunk 1306 optimal weight: 20.0000 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2 75 ASN B2 193 ASN ** B2 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 61 GLN ** BC 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BF 103 GLN BJ 224 HIS BJ 228 GLN BK 28 GLN BO 43 ASN ** BO 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BP 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BR 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BS 100 GLN ** BT 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BX 103 GLN ** Ba 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 101 GLN Bb 149 GLN ** Bb 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 332 HIS Bg 127 GLN Bi 154 ASN ** Bi 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bj 67 GLN ** Bj 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bk 153 HIS Bk 177 ASN ** Bn 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bt 33 GLN ** Bu 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bu 183 ASN ** Bw 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bw 274 ASN ** Bx 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 253 GLN ** AC 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 96 ASN AG 238 HIS ** AI 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AK 98 GLN ** AK 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 59 ASN ** Ac 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 325 GLN ** Ah 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 270 GLN ** Am 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 31 ASN ** Ao 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.802 187563 Z= 0.460 Angle : 0.799 106.082 266391 Z= 0.398 Chirality : 0.042 0.545 31411 Planarity : 0.006 0.143 24357 Dihedral : 15.154 179.463 48656 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.03 % Favored : 95.85 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.11 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.07), residues: 14839 helix: 1.26 (0.07), residues: 5956 sheet: -0.03 (0.12), residues: 1807 loop : -0.63 (0.07), residues: 7076 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29678 Ramachandran restraints generated. 14839 Oldfield, 0 Emsley, 14839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29678 Ramachandran restraints generated. 14839 Oldfield, 0 Emsley, 14839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2120 residues out of total 13087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 2041 time to evaluate : 10.973 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 outliers start: 79 outliers final: 60 residues processed: 2082 average time/residue: 1.5240 time to fit residues: 5461.3318 Evaluate side-chains 2080 residues out of total 13087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 2020 time to evaluate : 10.904 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 0 residues processed: 60 average time/residue: 1.2200 time to fit residues: 151.3382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1725 random chunks: chunk 1512 optimal weight: 10.0000 chunk 1592 optimal weight: 9.9990 chunk 1453 optimal weight: 20.0000 chunk 1549 optimal weight: 20.0000 chunk 932 optimal weight: 0.9990 chunk 674 optimal weight: 0.6980 chunk 1216 optimal weight: 10.0000 chunk 475 optimal weight: 8.9990 chunk 1400 optimal weight: 40.0000 chunk 1465 optimal weight: 6.9990 chunk 1543 optimal weight: 0.0020 overall best weight: 3.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2 75 ASN B2 193 ASN ** B2 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BF 103 GLN BJ 224 HIS BO 43 ASN ** BO 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BP 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BR 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BS 100 GLN ** BT 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 101 GLN Bb 149 GLN ** Bb 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Be 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 127 GLN Bh 310 ASN ** Bi 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bj 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bk 177 ASN ** Bn 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bt 33 GLN ** Bu 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bu 183 ASN ** Bw 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bx 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 253 GLN ** AC 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 96 ASN AG 238 HIS ** AI 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AK 98 GLN ** AK 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AR 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 59 ASN ** Ac 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 325 GLN ** Ah 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 270 GLN ** Am 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 31 ASN ** Ao 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 1.576 187563 Z= 0.528 Angle : 0.819 106.100 266391 Z= 0.414 Chirality : 0.042 0.543 31411 Planarity : 0.006 0.148 24357 Dihedral : 15.154 179.462 48656 Min Nonbonded Distance : 1.638 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.03 % Favored : 95.85 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.11 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.07), residues: 14839 helix: 1.26 (0.07), residues: 5956 sheet: -0.03 (0.12), residues: 1807 loop : -0.63 (0.07), residues: 7076 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29678 Ramachandran restraints generated. 14839 Oldfield, 0 Emsley, 14839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29678 Ramachandran restraints generated. 14839 Oldfield, 0 Emsley, 14839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2036 residues out of total 13087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 2033 time to evaluate : 10.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 2035 average time/residue: 1.4814 time to fit residues: 5178.1743 Evaluate side-chains 2021 residues out of total 13087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2021 time to evaluate : 10.818 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 13.8961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1725 random chunks: chunk 1017 optimal weight: 5.9990 chunk 1638 optimal weight: 7.9990 chunk 999 optimal weight: 6.9990 chunk 777 optimal weight: 20.0000 chunk 1138 optimal weight: 40.0000 chunk 1718 optimal weight: 0.8980 chunk 1581 optimal weight: 20.0000 chunk 1368 optimal weight: 6.9990 chunk 142 optimal weight: 6.9990 chunk 1057 optimal weight: 50.0000 chunk 839 optimal weight: 2.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2 75 ASN B2 193 ASN ** B2 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BF 103 GLN BJ 228 GLN BO 43 ASN ** BO 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BP 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BR 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BS 100 GLN ** BT 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 101 GLN Bb 149 GLN ** Bb 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Be 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 127 GLN ** Bi 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bj 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bk 177 ASN ** Bn 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bt 33 GLN ** Bu 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bu 183 ASN ** Bw 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bx 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 253 GLN ** AC 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 96 ASN AG 238 HIS ** AI 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AK 98 GLN ** AK 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AR 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 59 ASN ** Ac 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 325 GLN ** Ah 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 270 GLN ** Am 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 31 ASN ** Ao 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 1.576 187563 Z= 0.528 Angle : 0.819 106.100 266391 Z= 0.414 Chirality : 0.042 0.543 31411 Planarity : 0.006 0.148 24357 Dihedral : 15.154 179.462 48656 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.03 % Favored : 95.85 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.11 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.07), residues: 14839 helix: 1.26 (0.07), residues: 5956 sheet: -0.03 (0.12), residues: 1807 loop : -0.63 (0.07), residues: 7076 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29678 Ramachandran restraints generated. 14839 Oldfield, 0 Emsley, 14839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29678 Ramachandran restraints generated. 14839 Oldfield, 0 Emsley, 14839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2025 residues out of total 13087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 2022 time to evaluate : 12.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 2024 average time/residue: 1.4908 time to fit residues: 5174.2345 Evaluate side-chains 2020 residues out of total 13087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2020 time to evaluate : 10.941 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 13.9650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1725 random chunks: chunk 1087 optimal weight: 10.0000 chunk 1457 optimal weight: 7.9990 chunk 419 optimal weight: 3.9990 chunk 1261 optimal weight: 6.9990 chunk 202 optimal weight: 10.0000 chunk 380 optimal weight: 0.5980 chunk 1370 optimal weight: 8.9990 chunk 573 optimal weight: 0.0070 chunk 1407 optimal weight: 0.2980 chunk 173 optimal weight: 7.9990 chunk 252 optimal weight: 8.9990 overall best weight: 2.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2 75 ASN B2 193 ASN ** B2 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BF 103 GLN BJ 224 HIS BJ 228 GLN BO 43 ASN ** BO 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BP 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BR 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BS 100 GLN ** BT 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 101 GLN Bb 149 GLN ** Bb 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Be 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 127 GLN ** Bi 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bj 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bk 177 ASN ** Bn 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bt 33 GLN ** Bu 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bu 183 ASN ** Bw 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bx 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 253 GLN ** AC 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 96 ASN AG 238 HIS ** AI 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AK 98 GLN ** AK 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AR 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 59 ASN ** Ac 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 325 GLN ** Ah 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 270 GLN ** Am 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 31 ASN ** Ao 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.169603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.143533 restraints weight = 225403.238| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.69 r_work: 0.3487 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 1.92 restraints_weight: 0.2500 r_work: 0.3408 rms_B_bonded: 2.41 restraints_weight: 0.1250 r_work: 0.3352 rms_B_bonded: 3.16 restraints_weight: 0.0625 r_work: 0.3270 rms_B_bonded: 4.31 restraints_weight: 0.0312 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 1.576 187563 Z= 0.528 Angle : 0.818 106.100 266391 Z= 0.414 Chirality : 0.042 0.543 31411 Planarity : 0.006 0.148 24357 Dihedral : 15.154 179.462 48656 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.03 % Favored : 95.85 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.11 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.07), residues: 14839 helix: 1.26 (0.07), residues: 5956 sheet: -0.03 (0.12), residues: 1807 loop : -0.63 (0.07), residues: 7076 =============================================================================== Job complete usr+sys time: 77477.73 seconds wall clock time: 1330 minutes 0.27 seconds (79800.27 seconds total)