Starting phenix.real_space_refine (version: dev) on Wed Feb 22 07:46:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8o_24239/02_2023/7n8o_24239_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8o_24239/02_2023/7n8o_24239.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8o_24239/02_2023/7n8o_24239_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8o_24239/02_2023/7n8o_24239_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8o_24239/02_2023/7n8o_24239_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8o_24239/02_2023/7n8o_24239.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8o_24239/02_2023/7n8o_24239.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8o_24239/02_2023/7n8o_24239_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8o_24239/02_2023/7n8o_24239_neut_updated.pdb" } resolution = 1.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 Process input model Symmetric amino acids flipped Residue "A PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 61": "OD1" <-> "OD2" Residue "A TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 98": "OE1" <-> "OE2" Residue "A GLU 104": "OE1" <-> "OE2" Residue "A TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 136": "NH1" <-> "NH2" Residue "A TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 229": "OE1" <-> "OE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 242": "OE1" <-> "OE2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "A PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 312": "NH1" <-> "NH2" Residue "A ASP 319": "OD1" <-> "OD2" Residue "A PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 329": "OE1" <-> "OE2" Residue "B TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 15": "OD1" <-> "OD2" Residue "B TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 41": "OE1" <-> "OE2" Residue "B ASP 49": "OD1" <-> "OD2" Residue "B ASP 87": "OD1" <-> "OD2" Residue "B PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 125": "OD1" <-> "OD2" Residue "B PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 223": "OE1" <-> "OE2" Residue "B TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 266": "OE1" <-> "OE2" Residue "B PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 282": "OE1" <-> "OE2" Residue "B GLU 300": "OE1" <-> "OE2" Residue "B PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 339": "OE1" <-> "OE2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 352": "NH1" <-> "NH2" Residue "B GLU 355": "OE1" <-> "OE2" Residue "B PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 372": "OD1" <-> "OD2" Residue "B ASP 374": "OD1" <-> "OD2" Residue "B ARG 378": "NH1" <-> "NH2" Residue "B PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B ASP 431": "OD1" <-> "OD2" Residue "B GLU 435": "OE1" <-> "OE2" Residue "B ASP 440": "OD1" <-> "OD2" Residue "B PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 487": "OE1" <-> "OE2" Residue "B GLU 488": "OE1" <-> "OE2" Residue "B PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 500": "OD1" <-> "OD2" Residue "B ARG 504": "NH1" <-> "NH2" Residue "C ASP 14": "OD1" <-> "OD2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 70": "OE1" <-> "OE2" Residue "C PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 122": "NH1" <-> "NH2" Residue "C GLU 128": "OE1" <-> "OE2" Residue "C GLU 129": "OE1" <-> "OE2" Residue "C PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 137": "OD1" <-> "OD2" Residue "C TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 218": "OE1" <-> "OE2" Residue "C PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 249": "NH1" <-> "NH2" Residue "C PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 308": "OD1" <-> "OD2" Residue "C ARG 310": "NH1" <-> "NH2" Residue "C ASP 347": "OD1" <-> "OD2" Residue "C ARG 349": "NH1" <-> "NH2" Residue "C ASP 365": "OD1" <-> "OD2" Residue "C ARG 368": "NH1" <-> "NH2" Residue "C ASP 370": "OD1" <-> "OD2" Residue "C TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 400": "OD1" <-> "OD2" Residue "C PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 436": "NH1" <-> "NH2" Residue "C ARG 448": "NH1" <-> "NH2" Residue "C GLU 451": "OE1" <-> "OE2" Residue "D ARG 12": "NH1" <-> "NH2" Residue "D PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 16": "OD1" <-> "OD2" Residue "D ASP 20": "OD1" <-> "OD2" Residue "D ARG 24": "NH1" <-> "NH2" Residue "D ASP 25": "OD1" <-> "OD2" Residue "D PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "D PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 131": "OE1" <-> "OE2" Residue "D PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 228": "OD1" <-> "OD2" Residue "D PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 294": "NH1" <-> "NH2" Residue "D ASP 297": "OD1" <-> "OD2" Residue "D GLU 302": "OE1" <-> "OE2" Residue "D PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 312": "OE1" <-> "OE2" Residue "D PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 323": "OE1" <-> "OE2" Residue "D ASP 333": "OD1" <-> "OD2" Residue "D GLU 337": "OE1" <-> "OE2" Residue "D GLU 344": "OE1" <-> "OE2" Residue "D ARG 348": "NH1" <-> "NH2" Residue "E PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 12": "OD1" <-> "OD2" Residue "E TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 53": "OD1" <-> "OD2" Residue "E ARG 60": "NH1" <-> "NH2" Residue "E GLU 62": "OE1" <-> "OE2" Residue "E ASP 71": "OD1" <-> "OD2" Residue "E GLU 75": "OE1" <-> "OE2" Residue "F TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 4": "NH1" <-> "NH2" Residue "H ARG 6": "NH1" <-> "NH2" Residue "H ASP 9": "OD1" <-> "OD2" Residue "H PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 56": "OE1" <-> "OE2" Residue "H PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 27": "OD1" <-> "OD2" Residue "I ARG 30": "NH1" <-> "NH2" Residue "I ASP 36": "OD1" <-> "OD2" Residue "J PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 22": "OD1" <-> "OD2" Residue "K PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 2": "OD1" <-> "OD2" Residue "L ARG 3": "NH1" <-> "NH2" Residue "L ARG 9": "NH1" <-> "NH2" Residue "L ARG 16": "NH1" <-> "NH2" Residue "L PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 37": "OD1" <-> "OD2" Residue "O GLU 50": "OE1" <-> "OE2" Residue "O PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 60": "OE1" <-> "OE2" Residue "O PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 71": "OD1" <-> "OD2" Residue "O GLU 75": "OE1" <-> "OE2" Residue "O GLU 78": "OE1" <-> "OE2" Residue "O GLU 84": "OE1" <-> "OE2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O GLU 108": "OE1" <-> "OE2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "O ASP 119": "OD1" <-> "OD2" Residue "O ASP 128": "OD1" <-> "OD2" Residue "O GLU 143": "OE1" <-> "OE2" Residue "O PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 159": "OE1" <-> "OE2" Residue "O PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 174": "OD1" <-> "OD2" Residue "O TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 181": "NH1" <-> "NH2" Residue "O TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 198": "OD1" <-> "OD2" Residue "O GLU 237": "OE1" <-> "OE2" Residue "O GLU 243": "OE1" <-> "OE2" Residue "O GLU 245": "OE1" <-> "OE2" Residue "O ASP 251": "OD1" <-> "OD2" Residue "O GLU 256": "OE1" <-> "OE2" Residue "O ASP 259": "OD1" <-> "OD2" Residue "O ARG 263": "NH1" <-> "NH2" Residue "O PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 36": "OE1" <-> "OE2" Residue "Q GLU 56": "OE1" <-> "OE2" Residue "Q ASP 70": "OD1" <-> "OD2" Residue "Q TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 97": "OD1" <-> "OD2" Residue "Q GLU 113": "OE1" <-> "OE2" Residue "Q ASP 121": "OD1" <-> "OD2" Residue "Q TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 133": "OE1" <-> "OE2" Residue "R ASP 2": "OD1" <-> "OD2" Residue "R ARG 29": "NH1" <-> "NH2" Residue "T PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 54": "OD1" <-> "OD2" Residue "U ARG 61": "NH1" <-> "NH2" Residue "U ASP 62": "OD1" <-> "OD2" Residue "U PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 64": "NH1" <-> "NH2" Residue "U PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 76": "OE1" <-> "OE2" Residue "U ASP 84": "OD1" <-> "OD2" Residue "U GLU 87": "OE1" <-> "OE2" Residue "U GLU 97": "OE1" <-> "OE2" Residue "U ARG 102": "NH1" <-> "NH2" Residue "U GLU 104": "OE1" <-> "OE2" Residue "U PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 30": "OE1" <-> "OE2" Residue "V ARG 33": "NH1" <-> "NH2" Residue "V PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 83": "OD1" <-> "OD2" Residue "V GLU 88": "OE1" <-> "OE2" Residue "V ARG 90": "NH1" <-> "NH2" Residue "V GLU 110": "OE1" <-> "OE2" Residue "V ASP 111": "OD1" <-> "OD2" Residue "V ASP 112": "OD1" <-> "OD2" Residue "V TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 115": "OE1" <-> "OE2" Residue "V ARG 122": "NH1" <-> "NH2" Residue "V TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 128": "OE1" <-> "OE2" Residue "V ASP 136": "OD1" <-> "OD2" Residue "V ASP 139": "OD1" <-> "OD2" Residue "V ASP 151": "OD1" <-> "OD2" Residue "V ARG 153": "NH1" <-> "NH2" Residue "V TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 64": "OE1" <-> "OE2" Residue "Y PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 89": "NH1" <-> "NH2" Residue "Y ASP 92": "OD1" <-> "OD2" Residue "Z PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 34": "OD1" <-> "OD2" Residue "Z ARG 35": "NH1" <-> "NH2" Residue "Z TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 61": "OD1" <-> "OD2" Residue "a TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 98": "OE1" <-> "OE2" Residue "a GLU 104": "OE1" <-> "OE2" Residue "a TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 136": "NH1" <-> "NH2" Residue "a TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 229": "OE1" <-> "OE2" Residue "a GLU 231": "OE1" <-> "OE2" Residue "a TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 242": "OE1" <-> "OE2" Residue "a GLU 244": "OE1" <-> "OE2" Residue "a PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 312": "NH1" <-> "NH2" Residue "a ASP 319": "OD1" <-> "OD2" Residue "a PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 329": "OE1" <-> "OE2" Residue "b TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 15": "OD1" <-> "OD2" Residue "b TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 41": "OE1" <-> "OE2" Residue "b ASP 49": "OD1" <-> "OD2" Residue "b ASP 87": "OD1" <-> "OD2" Residue "b PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 125": "OD1" <-> "OD2" Residue "b PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 223": "OE1" <-> "OE2" Residue "b TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 266": "OE1" <-> "OE2" Residue "b PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 282": "OE1" <-> "OE2" Residue "b GLU 300": "OE1" <-> "OE2" Residue "b PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 339": "OE1" <-> "OE2" Residue "b PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 352": "NH1" <-> "NH2" Residue "b GLU 355": "OE1" <-> "OE2" Residue "b PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 372": "OD1" <-> "OD2" Residue "b ASP 374": "OD1" <-> "OD2" Residue "b ARG 378": "NH1" <-> "NH2" Residue "b PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 385": "NH1" <-> "NH2" Residue "b ASP 431": "OD1" <-> "OD2" Residue "b GLU 435": "OE1" <-> "OE2" Residue "b ASP 440": "OD1" <-> "OD2" Residue "b PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 487": "OE1" <-> "OE2" Residue "b GLU 488": "OE1" <-> "OE2" Residue "b PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 500": "OD1" <-> "OD2" Residue "b ARG 504": "NH1" <-> "NH2" Residue "c ASP 14": "OD1" <-> "OD2" Residue "c GLU 58": "OE1" <-> "OE2" Residue "c TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 70": "OE1" <-> "OE2" Residue "c PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 122": "NH1" <-> "NH2" Residue "c GLU 128": "OE1" <-> "OE2" Residue "c GLU 129": "OE1" <-> "OE2" Residue "c PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 137": "OD1" <-> "OD2" Residue "c TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 218": "OE1" <-> "OE2" Residue "c PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 249": "NH1" <-> "NH2" Residue "c PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 308": "OD1" <-> "OD2" Residue "c ARG 310": "NH1" <-> "NH2" Residue "c ASP 347": "OD1" <-> "OD2" Residue "c ARG 349": "NH1" <-> "NH2" Residue "c ASP 365": "OD1" <-> "OD2" Residue "c ARG 368": "NH1" <-> "NH2" Residue "c ASP 370": "OD1" <-> "OD2" Residue "c TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 400": "OD1" <-> "OD2" Residue "c PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 436": "NH1" <-> "NH2" Residue "c ARG 448": "NH1" <-> "NH2" Residue "c GLU 451": "OE1" <-> "OE2" Residue "d ARG 12": "NH1" <-> "NH2" Residue "d PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 16": "OD1" <-> "OD2" Residue "d ASP 20": "OD1" <-> "OD2" Residue "d ARG 24": "NH1" <-> "NH2" Residue "d ASP 25": "OD1" <-> "OD2" Residue "d PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 69": "OE1" <-> "OE2" Residue "d PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 131": "OE1" <-> "OE2" Residue "d PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 228": "OD1" <-> "OD2" Residue "d PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 294": "NH1" <-> "NH2" Residue "d ASP 297": "OD1" <-> "OD2" Residue "d GLU 302": "OE1" <-> "OE2" Residue "d PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 312": "OE1" <-> "OE2" Residue "d PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 323": "OE1" <-> "OE2" Residue "d ASP 333": "OD1" <-> "OD2" Residue "d GLU 337": "OE1" <-> "OE2" Residue "d GLU 344": "OE1" <-> "OE2" Residue "d ARG 348": "NH1" <-> "NH2" Residue "e PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 12": "OD1" <-> "OD2" Residue "e TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 53": "OD1" <-> "OD2" Residue "e ARG 60": "NH1" <-> "NH2" Residue "e GLU 62": "OE1" <-> "OE2" Residue "e ASP 71": "OD1" <-> "OD2" Residue "e GLU 75": "OE1" <-> "OE2" Residue "f TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 4": "NH1" <-> "NH2" Residue "h ARG 6": "NH1" <-> "NH2" Residue "h ASP 9": "OD1" <-> "OD2" Residue "h PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 56": "OE1" <-> "OE2" Residue "h PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 27": "OD1" <-> "OD2" Residue "i ARG 30": "NH1" <-> "NH2" Residue "i ASP 36": "OD1" <-> "OD2" Residue "j PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 22": "OD1" <-> "OD2" Residue "k PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 2": "OD1" <-> "OD2" Residue "l ARG 3": "NH1" <-> "NH2" Residue "l ARG 9": "NH1" <-> "NH2" Residue "l ARG 16": "NH1" <-> "NH2" Residue "l PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 37": "OD1" <-> "OD2" Residue "o GLU 50": "OE1" <-> "OE2" Residue "o PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 60": "OE1" <-> "OE2" Residue "o PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 71": "OD1" <-> "OD2" Residue "o GLU 75": "OE1" <-> "OE2" Residue "o GLU 78": "OE1" <-> "OE2" Residue "o GLU 84": "OE1" <-> "OE2" Residue "o ARG 102": "NH1" <-> "NH2" Residue "o GLU 108": "OE1" <-> "OE2" Residue "o ARG 111": "NH1" <-> "NH2" Residue "o ASP 119": "OD1" <-> "OD2" Residue "o ASP 128": "OD1" <-> "OD2" Residue "o GLU 143": "OE1" <-> "OE2" Residue "o PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 159": "OE1" <-> "OE2" Residue "o PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 174": "OD1" <-> "OD2" Residue "o TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 181": "NH1" <-> "NH2" Residue "o TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 198": "OD1" <-> "OD2" Residue "o GLU 237": "OE1" <-> "OE2" Residue "o GLU 243": "OE1" <-> "OE2" Residue "o GLU 245": "OE1" <-> "OE2" Residue "o ASP 251": "OD1" <-> "OD2" Residue "o GLU 256": "OE1" <-> "OE2" Residue "o ASP 259": "OD1" <-> "OD2" Residue "o ARG 263": "NH1" <-> "NH2" Residue "o PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 36": "OE1" <-> "OE2" Residue "q GLU 56": "OE1" <-> "OE2" Residue "q ASP 70": "OD1" <-> "OD2" Residue "q TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 97": "OD1" <-> "OD2" Residue "q GLU 113": "OE1" <-> "OE2" Residue "q ASP 121": "OD1" <-> "OD2" Residue "q TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 133": "OE1" <-> "OE2" Residue "r ASP 2": "OD1" <-> "OD2" Residue "r ARG 29": "NH1" <-> "NH2" Residue "t PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ASP 54": "OD1" <-> "OD2" Residue "u ARG 61": "NH1" <-> "NH2" Residue "u ASP 62": "OD1" <-> "OD2" Residue "u PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 64": "NH1" <-> "NH2" Residue "u PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 76": "OE1" <-> "OE2" Residue "u ASP 84": "OD1" <-> "OD2" Residue "u GLU 87": "OE1" <-> "OE2" Residue "u GLU 97": "OE1" <-> "OE2" Residue "u ARG 102": "NH1" <-> "NH2" Residue "u GLU 104": "OE1" <-> "OE2" Residue "u PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 30": "OE1" <-> "OE2" Residue "v ARG 33": "NH1" <-> "NH2" Residue "v PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ASP 83": "OD1" <-> "OD2" Residue "v GLU 88": "OE1" <-> "OE2" Residue "v ARG 90": "NH1" <-> "NH2" Residue "v GLU 110": "OE1" <-> "OE2" Residue "v ASP 111": "OD1" <-> "OD2" Residue "v ASP 112": "OD1" <-> "OD2" Residue "v TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 115": "OE1" <-> "OE2" Residue "v ARG 122": "NH1" <-> "NH2" Residue "v TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 128": "OE1" <-> "OE2" Residue "v ASP 136": "OD1" <-> "OD2" Residue "v ASP 139": "OD1" <-> "OD2" Residue "v ASP 151": "OD1" <-> "OD2" Residue "v ARG 153": "NH1" <-> "NH2" Residue "v TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y GLU 64": "OE1" <-> "OE2" Residue "y PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 89": "NH1" <-> "NH2" Residue "y ASP 92": "OD1" <-> "OD2" Residue "z PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ASP 34": "OD1" <-> "OD2" Residue "z ARG 35": "NH1" <-> "NH2" Residue "z TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 54656 Number of models: 1 Model: "" Number of chains: 113 Chain: "A" Number of atoms: 2624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2624 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 14, 'TRANS': 319} Chain: "B" Number of atoms: 3935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3935 Classifications: {'peptide': 503} Link IDs: {'PTRANS': 27, 'TRANS': 475} Chain: "C" Number of atoms: 3493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3493 Classifications: {'peptide': 450} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 425} Chain: "D" Number of atoms: 2726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2726 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 324} Chain: "E" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 645 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "F" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 279 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 32} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 494 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "I" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 286 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 2, 'TRANS': 33} 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: "J" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 279 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1, 'FME:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 299 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 32} Chain: "L" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 316 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 36} Chain: "M" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 245 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} 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: "O" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1869 Classifications: {'peptide': 243} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 228} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Q" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 916 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 112} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "R" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 258 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "T" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 241 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 2, 'TRANS': 27} 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: "U" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 740 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 89} Chain: "V" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1065 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 127} Chain: "X" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 288 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain: "Y" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 242 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 29} Chain: "Z" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 460 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "a" Number of atoms: 2624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2624 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 14, 'TRANS': 319} Chain: "b" Number of atoms: 3935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3935 Classifications: {'peptide': 503} Link IDs: {'PTRANS': 27, 'TRANS': 475} Chain: "c" Number of atoms: 3493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3493 Classifications: {'peptide': 450} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 425} Chain: "d" Number of atoms: 2726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2726 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 324} Chain: "e" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 645 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "f" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 279 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 32} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "h" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 494 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "i" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 286 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 2, 'TRANS': 33} 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: "j" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 279 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1, 'FME:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "k" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 299 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 32} Chain: "l" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 316 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 36} Chain: "m" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 245 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} 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: "o" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1869 Classifications: {'peptide': 243} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 228} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "q" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 916 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 112} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "r" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 258 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "t" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 241 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 2, 'TRANS': 27} 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: "u" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 740 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 89} Chain: "v" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1065 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 127} Chain: "x" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 288 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain: "y" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 242 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 29} Chain: "z" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 460 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 614 Unusual residues: {' CL': 2, 'BCR': 1, 'BCT': 1, 'CLA': 3, 'FE2': 1, 'LMG': 2, 'LMT': 2, 'OEX': 1, 'PHO': 1, 'PL9': 1, 'SQD': 2} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 1491 Unusual residues: {'BCR': 3, 'CLA': 16, 'LHG': 2, 'LMG': 1, 'LMT': 6, 'SQD': 1} Classifications: {'undetermined': 29} Link IDs: {None: 28} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 1311 Unusual residues: {'BCR': 1, 'CLA': 13, 'DGD': 3, 'LMG': 2, 'LMT': 4, 'SQD': 1} Classifications: {'undetermined': 24} Link IDs: {None: 23} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 13 Chain: "D" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 603 Unusual residues: {'CLA': 3, 'LHG': 3, 'LMG': 1, 'LMT': 3, 'PHO': 1, 'PL9': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 140 Unusual residues: {'HEM': 1, 'LHG': 1, 'LMT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 109 Unusual residues: {'BCR': 1, 'LMT': 1, 'SQD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "H" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 140 Unusual residues: {'DGD': 1, 'LMT': 1, 'SQD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 105 Unusual residues: {'LMT': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 15 Chain: "J" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 161 Unusual residues: {' CA': 1, 'BCR': 2, 'LMT': 1, 'SQD': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Chain: "L" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'LMT': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 5 Chain: "T" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {' CA': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 87 Unusual residues: {'LMT': 2, 'RRX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 10 Chain: "Y" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 76 Unusual residues: {'BCR': 1, 'LHG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "a" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 614 Unusual residues: {' CL': 2, 'BCR': 1, 'BCT': 1, 'CLA': 3, 'FE2': 1, 'LMG': 2, 'LMT': 2, 'OEX': 1, 'PHO': 1, 'PL9': 1, 'SQD': 2} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 5 Chain: "b" Number of atoms: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 1491 Unusual residues: {'BCR': 3, 'CLA': 16, 'LHG': 2, 'LMG': 1, 'LMT': 6, 'SQD': 1} Classifications: {'undetermined': 29} Link IDs: {None: 28} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 5 Chain: "c" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 1311 Unusual residues: {'BCR': 1, 'CLA': 13, 'DGD': 3, 'LMG': 2, 'LMT': 4, 'SQD': 1} Classifications: {'undetermined': 24} Link IDs: {None: 23} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 13 Chain: "d" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 603 Unusual residues: {'CLA': 3, 'LHG': 3, 'LMG': 1, 'LMT': 3, 'PHO': 1, 'PL9': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 5 Chain: "e" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 140 Unusual residues: {'HEM': 1, 'LHG': 1, 'LMT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 5 Chain: "f" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 109 Unusual residues: {'BCR': 1, 'LMT': 1, 'SQD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "h" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 140 Unusual residues: {'DGD': 1, 'LMT': 1, 'SQD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 5 Chain: "i" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 105 Unusual residues: {'LMT': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 15 Chain: "j" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 5 Chain: "k" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 161 Unusual residues: {' CA': 1, 'BCR': 2, 'LMT': 1, 'SQD': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Chain: "m" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 5 Chain: "t" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 5 Chain: "u" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "v" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {' CA': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "x" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 87 Unusual residues: {'LMT': 2, 'RRX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 10 Chain: "y" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 Chain: "z" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 76 Unusual residues: {'BCR': 1, 'LHG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 119 Classifications: {'water': 119} Link IDs: {None: 118} Chain: "B" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 114 Classifications: {'water': 114} Link IDs: {None: 113} Chain: "C" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 122 Classifications: {'water': 122} Link IDs: {None: 121} Chain: "D" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 120 Classifications: {'water': 120} Link IDs: {None: 119} Chain: "E" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "L" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "M" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "O" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "U" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "V" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "X" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "a" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 119 Classifications: {'water': 119} Link IDs: {None: 118} Chain: "b" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 114 Classifications: {'water': 114} Link IDs: {None: 113} Chain: "c" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 122 Classifications: {'water': 122} Link IDs: {None: 121} Chain: "d" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 120 Classifications: {'water': 120} Link IDs: {None: 119} Chain: "e" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "f" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "h" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "i" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "j" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "k" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "l" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "m" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "o" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "t" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "u" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "v" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "x" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Time building chain proxies: 22.57, per 1000 atoms: 0.41 Number of scatterers: 54656 At special positions: 0 Unit cell: (208.832, 147.264, 122.304, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 10 Type Number sf(0) Fe 6 26.01 Mn 8 24.99 Ca 8 19.99 Cl 4 17.00 S 160 16.00 P 14 15.00 Mg 70 11.99 O 10434 8.00 N 7446 7.00 C 36506 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=80, symmetry=0 Number of additional bonds: simple=80, symmetry=0 Coordination: Other bonds: Time building additional restraints: 19.53 Conformation dependent library (CDL) restraints added in 4.6 seconds 10904 Ramachandran restraints generated. 5452 Oldfield, 0 Emsley, 5452 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9992 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 244 helices and 18 sheets defined 54.9% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.62 Creating SS restraints... Processing helix chain 'A' and resid 13 through 21 Processing helix chain 'A' and resid 31 through 54 removed outlier: 3.756A pdb=" N LEU A 36 " --> pdb=" O TRP A 32 " (cutoff:3.500A) Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 102 through 107 Processing helix chain 'A' and resid 110 through 136 Processing helix chain 'A' and resid 143 through 158 removed outlier: 3.943A pdb=" N ALA A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) Proline residue: A 150 - end of helix Processing helix chain 'A' and resid 160 through 165 Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 176 through 190 Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 196 through 221 Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 248 through 258 Processing helix chain 'A' and resid 261 through 263 No H-bonds generated for 'chain 'A' and resid 261 through 263' Processing helix chain 'A' and resid 268 through 295 Proline residue: A 279 - end of helix removed outlier: 4.027A pdb=" N PHE A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 331 removed outlier: 3.689A pdb=" N MET A 331 " --> pdb=" O GLY A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 12 removed outlier: 5.632A pdb=" N HIS B 9 " --> pdb=" O TYR B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 44 Processing helix chain 'B' and resid 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' Processing helix chain 'B' and resid 63 through 69 removed outlier: 3.891A pdb=" N LEU B 69 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 116 Processing helix chain 'B' and resid 121 through 123 No H-bonds generated for 'chain 'B' and resid 121 through 123' Processing helix chain 'B' and resid 135 through 155 Processing helix chain 'B' and resid 187 through 190 Processing helix chain 'B' and resid 195 through 216 Processing helix chain 'B' and resid 223 through 228 Processing helix chain 'B' and resid 234 through 258 Processing helix chain 'B' and resid 265 through 268 No H-bonds generated for 'chain 'B' and resid 265 through 268' Processing helix chain 'B' and resid 272 through 277 Processing helix chain 'B' and resid 279 through 294 Processing helix chain 'B' and resid 298 through 304 Processing helix chain 'B' and resid 307 through 313 Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 319 through 321 No H-bonds generated for 'chain 'B' and resid 319 through 321' Processing helix chain 'B' and resid 330 through 332 No H-bonds generated for 'chain 'B' and resid 330 through 332' Processing helix chain 'B' and resid 392 through 395 No H-bonds generated for 'chain 'B' and resid 392 through 395' Processing helix chain 'B' and resid 414 through 426 removed outlier: 3.901A pdb=" N LEU B 426 " --> pdb=" O ARG B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 474 removed outlier: 3.566A pdb=" N PHE B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'C' and resid 15 through 18 No H-bonds generated for 'chain 'C' and resid 15 through 18' Processing helix chain 'C' and resid 22 through 29 removed outlier: 5.865A pdb=" N ASN C 26 " --> pdb=" O TRP C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 60 Processing helix chain 'C' and resid 68 through 70 No H-bonds generated for 'chain 'C' and resid 68 through 70' Processing helix chain 'C' and resid 76 through 81 Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 96 through 121 Processing helix chain 'C' and resid 141 through 168 Processing helix chain 'C' and resid 193 through 201 removed outlier: 4.130A pdb=" N LEU C 200 " --> pdb=" O ILE C 196 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU C 201 " --> pdb=" O PHE C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 240 Processing helix chain 'C' and resid 245 through 250 Processing helix chain 'C' and resid 255 through 279 Processing helix chain 'C' and resid 286 through 289 No H-bonds generated for 'chain 'C' and resid 286 through 289' Processing helix chain 'C' and resid 293 through 311 Processing helix chain 'C' and resid 341 through 345 Processing helix chain 'C' and resid 354 through 356 No H-bonds generated for 'chain 'C' and resid 354 through 356' Processing helix chain 'C' and resid 364 through 369 Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 409 through 440 Processing helix chain 'C' and resid 452 through 455 Processing helix chain 'D' and resid 14 through 22 Processing helix chain 'D' and resid 31 through 54 removed outlier: 3.889A pdb=" N LEU D 35 " --> pdb=" O GLY D 31 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU D 36 " --> pdb=" O TRP D 32 " (cutoff:3.500A) Proline residue: D 39 - end of helix Processing helix chain 'D' and resid 67 through 69 No H-bonds generated for 'chain 'D' and resid 67 through 69' Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 101 through 106 Processing helix chain 'D' and resid 109 through 136 Processing helix chain 'D' and resid 141 through 157 removed outlier: 4.348A pdb=" N GLY D 148 " --> pdb=" O ILE D 144 " (cutoff:3.500A) Proline residue: D 149 - end of helix Processing helix chain 'D' and resid 159 through 163 Processing helix chain 'D' and resid 167 through 169 No H-bonds generated for 'chain 'D' and resid 167 through 169' Processing helix chain 'D' and resid 175 through 189 Processing helix chain 'D' and resid 191 through 193 No H-bonds generated for 'chain 'D' and resid 191 through 193' Processing helix chain 'D' and resid 195 through 220 Processing helix chain 'D' and resid 231 through 234 Processing helix chain 'D' and resid 246 through 257 Processing helix chain 'D' and resid 264 through 291 Proline residue: D 275 - end of helix removed outlier: 3.772A pdb=" N LEU D 291 " --> pdb=" O VAL D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 307 Processing helix chain 'D' and resid 314 through 333 Proline residue: D 331 - end of helix Processing helix chain 'D' and resid 335 through 337 No H-bonds generated for 'chain 'D' and resid 335 through 337' Processing helix chain 'D' and resid 343 through 345 No H-bonds generated for 'chain 'D' and resid 343 through 345' Processing helix chain 'E' and resid 10 through 15 Processing helix chain 'E' and resid 17 through 39 removed outlier: 4.336A pdb=" N ILE E 25 " --> pdb=" O VAL E 21 " (cutoff:3.500A) Proline residue: E 28 - end of helix Processing helix chain 'E' and resid 42 through 47 Processing helix chain 'E' and resid 72 through 79 Processing helix chain 'F' and resid 17 through 41 removed outlier: 3.670A pdb=" N LEU F 25 " --> pdb=" O ALA F 21 " (cutoff:3.500A) Proline residue: F 28 - end of helix removed outlier: 3.989A pdb=" N PHE F 41 " --> pdb=" O ALA F 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 15 Proline residue: H 13 - end of helix Processing helix chain 'H' and resid 28 through 49 Processing helix chain 'I' and resid 3 through 23 Processing helix chain 'I' and resid 27 through 29 No H-bonds generated for 'chain 'I' and resid 27 through 29' Processing helix chain 'J' and resid 9 through 32 removed outlier: 3.755A pdb=" N TYR J 32 " --> pdb=" O PHE J 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 14 No H-bonds generated for 'chain 'K' and resid 12 through 14' Processing helix chain 'K' and resid 18 through 41 removed outlier: 4.004A pdb=" N VAL K 23 " --> pdb=" O PRO K 19 " (cutoff:3.500A) Proline residue: K 25 - end of helix Proline residue: K 28 - end of helix removed outlier: 3.724A pdb=" N PHE K 36 " --> pdb=" O LEU K 32 " (cutoff:3.500A) Processing helix chain 'L' and resid 16 through 38 removed outlier: 4.607A pdb=" N SER L 35 " --> pdb=" O ILE L 31 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N TYR L 36 " --> pdb=" O LEU L 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 7 through 28 Proline residue: M 18 - end of helix Processing helix chain 'O' and resid 36 through 39 No H-bonds generated for 'chain 'O' and resid 36 through 39' Processing helix chain 'O' and resid 44 through 46 No H-bonds generated for 'chain 'O' and resid 44 through 46' Processing helix chain 'O' and resid 204 through 209 removed outlier: 3.714A pdb=" N ALA O 207 " --> pdb=" O PRO O 204 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASP O 208 " --> pdb=" O SER O 205 " (cutoff:3.500A) Processing helix chain 'O' and resid 211 through 213 No H-bonds generated for 'chain 'O' and resid 211 through 213' Processing helix chain 'Q' and resid 35 through 64 removed outlier: 3.783A pdb=" N ALA Q 39 " --> pdb=" O PRO Q 35 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN Q 40 " --> pdb=" O GLU Q 36 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL Q 43 " --> pdb=" O ALA Q 39 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N TYR Q 44 " --> pdb=" O GLN Q 40 " (cutoff:3.500A) Proline residue: Q 47 - end of helix removed outlier: 4.007A pdb=" N LEU Q 59 " --> pdb=" O MET Q 55 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLN Q 60 " --> pdb=" O GLU Q 56 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY Q 61 " --> pdb=" O LYS Q 57 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 76 Processing helix chain 'Q' and resid 82 through 91 Processing helix chain 'Q' and resid 97 through 120 Processing helix chain 'Q' and resid 124 through 144 removed outlier: 3.820A pdb=" N LEU Q 144 " --> pdb=" O SER Q 140 " (cutoff:3.500A) Processing helix chain 'R' and resid 3 through 33 Proline residue: R 11 - end of helix removed outlier: 5.953A pdb=" N ALA R 25 " --> pdb=" O ILE R 21 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA R 26 " --> pdb=" O ASN R 22 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 22 Processing helix chain 'U' and resid 41 through 46 Processing helix chain 'U' and resid 48 through 50 No H-bonds generated for 'chain 'U' and resid 48 through 50' Processing helix chain 'U' and resid 60 through 63 Processing helix chain 'U' and resid 72 through 79 Processing helix chain 'U' and resid 87 through 91 Processing helix chain 'U' and resid 97 through 109 removed outlier: 5.405A pdb=" N GLY U 108 " --> pdb=" O GLU U 104 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N SER U 109 " --> pdb=" O ALA U 105 " (cutoff:3.500A) Processing helix chain 'U' and resid 117 through 123 removed outlier: 6.778A pdb=" N GLY U 122 " --> pdb=" O GLU U 118 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASP U 123 " --> pdb=" O LEU U 119 " (cutoff:3.500A) Processing helix chain 'V' and resid 48 through 61 Processing helix chain 'V' and resid 63 through 69 removed outlier: 8.826A pdb=" N GLN V 68 " --> pdb=" O GLN V 64 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLY V 69 " --> pdb=" O CYS V 65 " (cutoff:3.500A) Processing helix chain 'V' and resid 81 through 86 Processing helix chain 'V' and resid 94 through 102 Processing helix chain 'V' and resid 127 through 129 No H-bonds generated for 'chain 'V' and resid 127 through 129' Processing helix chain 'V' and resid 134 through 150 Proline residue: V 148 - end of helix Processing helix chain 'X' and resid 3 through 18 Processing helix chain 'X' and resid 20 through 33 removed outlier: 4.564A pdb=" N VAL X 25 " --> pdb=" O ILE X 21 " (cutoff:3.500A) Processing helix chain 'Y' and resid 64 through 89 removed outlier: 3.796A pdb=" N GLY Y 79 " --> pdb=" O ILE Y 75 " (cutoff:3.500A) Proline residue: Y 80 - end of helix Processing helix chain 'Z' and resid 3 through 27 Proline residue: Z 24 - end of helix Processing helix chain 'Z' and resid 31 through 60 removed outlier: 4.475A pdb=" N ASP Z 34 " --> pdb=" O GLN Z 31 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ARG Z 35 " --> pdb=" O ASN Z 32 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER Z 36 " --> pdb=" O TRP Z 33 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LYS Z 37 " --> pdb=" O ASP Z 34 " (cutoff:3.500A) Proline residue: Z 38 - end of helix Processing helix chain 'a' and resid 13 through 21 Processing helix chain 'a' and resid 31 through 54 removed outlier: 3.756A pdb=" N LEU a 36 " --> pdb=" O TRP a 32 " (cutoff:3.500A) Proline residue: a 39 - end of helix Processing helix chain 'a' and resid 71 through 73 No H-bonds generated for 'chain 'a' and resid 71 through 73' Processing helix chain 'a' and resid 96 through 98 No H-bonds generated for 'chain 'a' and resid 96 through 98' Processing helix chain 'a' and resid 102 through 107 Processing helix chain 'a' and resid 110 through 136 Processing helix chain 'a' and resid 143 through 158 removed outlier: 3.943A pdb=" N ALA a 149 " --> pdb=" O VAL a 145 " (cutoff:3.500A) Proline residue: a 150 - end of helix Processing helix chain 'a' and resid 160 through 165 Processing helix chain 'a' and resid 168 through 170 No H-bonds generated for 'chain 'a' and resid 168 through 170' Processing helix chain 'a' and resid 176 through 190 Processing helix chain 'a' and resid 192 through 194 No H-bonds generated for 'chain 'a' and resid 192 through 194' Processing helix chain 'a' and resid 196 through 221 Processing helix chain 'a' and resid 233 through 236 Processing helix chain 'a' and resid 248 through 258 Processing helix chain 'a' and resid 261 through 263 No H-bonds generated for 'chain 'a' and resid 261 through 263' Processing helix chain 'a' and resid 268 through 295 Proline residue: a 279 - end of helix removed outlier: 4.026A pdb=" N PHE a 295 " --> pdb=" O SER a 291 " (cutoff:3.500A) Processing helix chain 'a' and resid 317 through 331 removed outlier: 3.689A pdb=" N MET a 331 " --> pdb=" O GLY a 327 " (cutoff:3.500A) Processing helix chain 'b' and resid 5 through 12 removed outlier: 5.632A pdb=" N HIS b 9 " --> pdb=" O TYR b 6 " (cutoff:3.500A) Processing helix chain 'b' and resid 16 through 44 Processing helix chain 'b' and resid 55 through 57 No H-bonds generated for 'chain 'b' and resid 55 through 57' Processing helix chain 'b' and resid 63 through 69 removed outlier: 3.891A pdb=" N LEU b 69 " --> pdb=" O PHE b 65 " (cutoff:3.500A) Processing helix chain 'b' and resid 93 through 116 Processing helix chain 'b' and resid 121 through 123 No H-bonds generated for 'chain 'b' and resid 121 through 123' Processing helix chain 'b' and resid 135 through 155 Processing helix chain 'b' and resid 187 through 190 Processing helix chain 'b' and resid 195 through 216 Processing helix chain 'b' and resid 223 through 228 Processing helix chain 'b' and resid 234 through 258 Processing helix chain 'b' and resid 265 through 268 No H-bonds generated for 'chain 'b' and resid 265 through 268' Processing helix chain 'b' and resid 272 through 277 Processing helix chain 'b' and resid 279 through 294 Processing helix chain 'b' and resid 298 through 304 Processing helix chain 'b' and resid 307 through 313 Processing helix chain 'b' and resid 315 through 317 No H-bonds generated for 'chain 'b' and resid 315 through 317' Processing helix chain 'b' and resid 319 through 321 No H-bonds generated for 'chain 'b' and resid 319 through 321' Processing helix chain 'b' and resid 330 through 332 No H-bonds generated for 'chain 'b' and resid 330 through 332' Processing helix chain 'b' and resid 392 through 395 No H-bonds generated for 'chain 'b' and resid 392 through 395' Processing helix chain 'b' and resid 414 through 426 removed outlier: 3.901A pdb=" N LEU b 426 " --> pdb=" O ARG b 422 " (cutoff:3.500A) Processing helix chain 'b' and resid 447 through 474 removed outlier: 3.567A pdb=" N PHE b 464 " --> pdb=" O LEU b 460 " (cutoff:3.500A) Processing helix chain 'b' and resid 476 through 478 No H-bonds generated for 'chain 'b' and resid 476 through 478' Processing helix chain 'c' and resid 15 through 18 No H-bonds generated for 'chain 'c' and resid 15 through 18' Processing helix chain 'c' and resid 22 through 29 removed outlier: 5.866A pdb=" N ASN c 26 " --> pdb=" O TRP c 23 " (cutoff:3.500A) Processing helix chain 'c' and resid 33 through 60 Processing helix chain 'c' and resid 68 through 70 No H-bonds generated for 'chain 'c' and resid 68 through 70' Processing helix chain 'c' and resid 76 through 81 Processing helix chain 'c' and resid 88 through 90 No H-bonds generated for 'chain 'c' and resid 88 through 90' Processing helix chain 'c' and resid 96 through 121 Processing helix chain 'c' and resid 141 through 168 Processing helix chain 'c' and resid 193 through 201 removed outlier: 4.131A pdb=" N LEU c 200 " --> pdb=" O ILE c 196 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU c 201 " --> pdb=" O PHE c 197 " (cutoff:3.500A) Processing helix chain 'c' and resid 217 through 240 Processing helix chain 'c' and resid 245 through 250 Processing helix chain 'c' and resid 255 through 279 Processing helix chain 'c' and resid 286 through 289 No H-bonds generated for 'chain 'c' and resid 286 through 289' Processing helix chain 'c' and resid 293 through 311 Processing helix chain 'c' and resid 341 through 345 Processing helix chain 'c' and resid 354 through 356 No H-bonds generated for 'chain 'c' and resid 354 through 356' Processing helix chain 'c' and resid 364 through 369 Processing helix chain 'c' and resid 373 through 385 Processing helix chain 'c' and resid 409 through 440 Processing helix chain 'c' and resid 452 through 455 Processing helix chain 'd' and resid 14 through 22 Processing helix chain 'd' and resid 31 through 54 removed outlier: 3.889A pdb=" N LEU d 35 " --> pdb=" O GLY d 31 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU d 36 " --> pdb=" O TRP d 32 " (cutoff:3.500A) Proline residue: d 39 - end of helix Processing helix chain 'd' and resid 67 through 69 No H-bonds generated for 'chain 'd' and resid 67 through 69' Processing helix chain 'd' and resid 83 through 85 No H-bonds generated for 'chain 'd' and resid 83 through 85' Processing helix chain 'd' and resid 101 through 106 Processing helix chain 'd' and resid 109 through 136 Processing helix chain 'd' and resid 141 through 157 removed outlier: 4.348A pdb=" N GLY d 148 " --> pdb=" O ILE d 144 " (cutoff:3.500A) Proline residue: d 149 - end of helix Processing helix chain 'd' and resid 159 through 163 Processing helix chain 'd' and resid 167 through 169 No H-bonds generated for 'chain 'd' and resid 167 through 169' Processing helix chain 'd' and resid 175 through 189 Processing helix chain 'd' and resid 191 through 193 No H-bonds generated for 'chain 'd' and resid 191 through 193' Processing helix chain 'd' and resid 195 through 220 Processing helix chain 'd' and resid 231 through 234 Processing helix chain 'd' and resid 246 through 257 Processing helix chain 'd' and resid 264 through 291 Proline residue: d 275 - end of helix removed outlier: 3.773A pdb=" N LEU d 291 " --> pdb=" O VAL d 287 " (cutoff:3.500A) Processing helix chain 'd' and resid 299 through 307 Processing helix chain 'd' and resid 314 through 333 Proline residue: d 331 - end of helix Processing helix chain 'd' and resid 335 through 337 No H-bonds generated for 'chain 'd' and resid 335 through 337' Processing helix chain 'd' and resid 343 through 345 No H-bonds generated for 'chain 'd' and resid 343 through 345' Processing helix chain 'e' and resid 10 through 15 Processing helix chain 'e' and resid 17 through 39 removed outlier: 4.337A pdb=" N ILE e 25 " --> pdb=" O VAL e 21 " (cutoff:3.500A) Proline residue: e 28 - end of helix Processing helix chain 'e' and resid 42 through 47 Processing helix chain 'e' and resid 72 through 79 Processing helix chain 'f' and resid 17 through 41 removed outlier: 3.671A pdb=" N LEU f 25 " --> pdb=" O ALA f 21 " (cutoff:3.500A) Proline residue: f 28 - end of helix removed outlier: 3.990A pdb=" N PHE f 41 " --> pdb=" O ALA f 37 " (cutoff:3.500A) Processing helix chain 'h' and resid 6 through 15 Proline residue: h 13 - end of helix Processing helix chain 'h' and resid 28 through 49 Processing helix chain 'i' and resid 3 through 23 Processing helix chain 'i' and resid 27 through 29 No H-bonds generated for 'chain 'i' and resid 27 through 29' Processing helix chain 'j' and resid 9 through 32 removed outlier: 3.755A pdb=" N TYR j 32 " --> pdb=" O PHE j 28 " (cutoff:3.500A) Processing helix chain 'k' and resid 12 through 14 No H-bonds generated for 'chain 'k' and resid 12 through 14' Processing helix chain 'k' and resid 18 through 41 removed outlier: 4.004A pdb=" N VAL k 23 " --> pdb=" O PRO k 19 " (cutoff:3.500A) Proline residue: k 25 - end of helix Proline residue: k 28 - end of helix removed outlier: 3.724A pdb=" N PHE k 36 " --> pdb=" O LEU k 32 " (cutoff:3.500A) Processing helix chain 'l' and resid 16 through 38 removed outlier: 4.607A pdb=" N SER l 35 " --> pdb=" O ILE l 31 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N TYR l 36 " --> pdb=" O LEU l 32 " (cutoff:3.500A) Processing helix chain 'm' and resid 7 through 28 Proline residue: m 18 - end of helix Processing helix chain 'o' and resid 36 through 39 No H-bonds generated for 'chain 'o' and resid 36 through 39' Processing helix chain 'o' and resid 44 through 46 No H-bonds generated for 'chain 'o' and resid 44 through 46' Processing helix chain 'o' and resid 204 through 209 removed outlier: 3.714A pdb=" N ALA o 207 " --> pdb=" O PRO o 204 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASP o 208 " --> pdb=" O SER o 205 " (cutoff:3.500A) Processing helix chain 'o' and resid 211 through 213 No H-bonds generated for 'chain 'o' and resid 211 through 213' Processing helix chain 'q' and resid 35 through 64 removed outlier: 3.784A pdb=" N ALA q 39 " --> pdb=" O PRO q 35 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN q 40 " --> pdb=" O GLU q 36 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL q 43 " --> pdb=" O ALA q 39 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N TYR q 44 " --> pdb=" O GLN q 40 " (cutoff:3.500A) Proline residue: q 47 - end of helix removed outlier: 4.008A pdb=" N LEU q 59 " --> pdb=" O MET q 55 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLN q 60 " --> pdb=" O GLU q 56 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY q 61 " --> pdb=" O LYS q 57 " (cutoff:3.500A) Processing helix chain 'q' and resid 68 through 76 Processing helix chain 'q' and resid 82 through 91 Processing helix chain 'q' and resid 97 through 120 Processing helix chain 'q' and resid 124 through 144 removed outlier: 3.820A pdb=" N LEU q 144 " --> pdb=" O SER q 140 " (cutoff:3.500A) Processing helix chain 'r' and resid 3 through 33 Proline residue: r 11 - end of helix removed outlier: 5.953A pdb=" N ALA r 25 " --> pdb=" O ILE r 21 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA r 26 " --> pdb=" O ASN r 22 " (cutoff:3.500A) Processing helix chain 't' and resid 3 through 22 Processing helix chain 'u' and resid 41 through 46 Processing helix chain 'u' and resid 48 through 50 No H-bonds generated for 'chain 'u' and resid 48 through 50' Processing helix chain 'u' and resid 60 through 63 Processing helix chain 'u' and resid 72 through 79 Processing helix chain 'u' and resid 87 through 91 Processing helix chain 'u' and resid 97 through 109 removed outlier: 5.405A pdb=" N GLY u 108 " --> pdb=" O GLU u 104 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N SER u 109 " --> pdb=" O ALA u 105 " (cutoff:3.500A) Processing helix chain 'u' and resid 117 through 123 removed outlier: 6.779A pdb=" N GLY u 122 " --> pdb=" O GLU u 118 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASP u 123 " --> pdb=" O LEU u 119 " (cutoff:3.500A) Processing helix chain 'v' and resid 48 through 61 Processing helix chain 'v' and resid 63 through 69 removed outlier: 8.826A pdb=" N GLN v 68 " --> pdb=" O GLN v 64 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLY v 69 " --> pdb=" O CYS v 65 " (cutoff:3.500A) Processing helix chain 'v' and resid 81 through 86 Processing helix chain 'v' and resid 94 through 102 Processing helix chain 'v' and resid 127 through 129 No H-bonds generated for 'chain 'v' and resid 127 through 129' Processing helix chain 'v' and resid 134 through 150 Proline residue: v 148 - end of helix Processing helix chain 'x' and resid 3 through 18 Processing helix chain 'x' and resid 20 through 33 removed outlier: 4.564A pdb=" N VAL x 25 " --> pdb=" O ILE x 21 " (cutoff:3.500A) Processing helix chain 'y' and resid 64 through 89 removed outlier: 3.796A pdb=" N GLY y 79 " --> pdb=" O ILE y 75 " (cutoff:3.500A) Proline residue: y 80 - end of helix Processing helix chain 'z' and resid 3 through 27 Proline residue: z 24 - end of helix Processing helix chain 'z' and resid 31 through 60 removed outlier: 4.475A pdb=" N ASP z 34 " --> pdb=" O GLN z 31 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ARG z 35 " --> pdb=" O ASN z 32 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER z 36 " --> pdb=" O TRP z 33 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LYS z 37 " --> pdb=" O ASP z 34 " (cutoff:3.500A) Proline residue: z 38 - end of helix Processing sheet with id= A, first strand: chain 'B' and resid 166 through 168 Processing sheet with id= B, first strand: chain 'B' and resid 343 through 347 Processing sheet with id= C, first strand: chain 'B' and resid 336 through 340 removed outlier: 6.621A pdb=" N ASP B 431 " --> pdb=" O GLN B 338 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 369 through 371 Processing sheet with id= E, first strand: chain 'C' and resid 172 through 174 Processing sheet with id= F, first strand: chain 'C' and resid 328 through 330 Processing sheet with id= G, first strand: chain 'O' and resid 66 through 69 removed outlier: 6.355A pdb=" N SER O 113 " --> pdb=" O GLU O 126 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N GLU O 126 " --> pdb=" O SER O 113 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ALA O 115 " --> pdb=" O PHE O 124 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N PHE O 124 " --> pdb=" O ALA O 115 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LYS O 221 " --> pdb=" O PRO O 247 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA O 239 " --> pdb=" O THR O 229 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL O 231 " --> pdb=" O GLU O 237 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLU O 237 " --> pdb=" O VAL O 231 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ASP O 259 " --> pdb=" O LYS O 82 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE O 265 " --> pdb=" O PRO O 76 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N TYR O 267 " --> pdb=" O MET O 74 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N MET O 74 " --> pdb=" O TYR O 267 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'O' and resid 132 through 138 Processing sheet with id= I, first strand: chain 'V' and resid 34 through 36 Processing sheet with id= J, first strand: chain 'b' and resid 166 through 168 Processing sheet with id= K, first strand: chain 'b' and resid 343 through 347 Processing sheet with id= L, first strand: chain 'b' and resid 336 through 340 removed outlier: 6.621A pdb=" N ASP b 431 " --> pdb=" O GLN b 338 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'b' and resid 369 through 371 Processing sheet with id= N, first strand: chain 'c' and resid 172 through 174 Processing sheet with id= O, first strand: chain 'c' and resid 328 through 330 Processing sheet with id= P, first strand: chain 'o' and resid 66 through 69 removed outlier: 6.355A pdb=" N SER o 113 " --> pdb=" O GLU o 126 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N GLU o 126 " --> pdb=" O SER o 113 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ALA o 115 " --> pdb=" O PHE o 124 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N PHE o 124 " --> pdb=" O ALA o 115 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N LYS o 221 " --> pdb=" O PRO o 247 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA o 239 " --> pdb=" O THR o 229 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL o 231 " --> pdb=" O GLU o 237 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLU o 237 " --> pdb=" O VAL o 231 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ASP o 259 " --> pdb=" O LYS o 82 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE o 265 " --> pdb=" O PRO o 76 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N TYR o 267 " --> pdb=" O MET o 74 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N MET o 74 " --> pdb=" O TYR o 267 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'o' and resid 132 through 138 Processing sheet with id= R, first strand: chain 'v' and resid 34 through 36 2080 hydrogen bonds defined for protein. 5952 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.72 Time building geometry restraints manager: 20.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.71: 54692 1.71 - 2.25: 594 2.25 - 2.79: 12 2.79 - 3.33: 2 3.33 - 3.86: 8 Bond restraints: 55308 Sorted by residual: bond pdb=" O1 OEX a 401 " pdb="MN2 OEX a 401 " ideal model delta sigma weight residual 2.000 2.687 -0.687 5.00e-02 4.00e+02 1.89e+02 bond pdb=" O1 OEX A 401 " pdb="MN2 OEX A 401 " ideal model delta sigma weight residual 2.000 2.687 -0.687 5.00e-02 4.00e+02 1.89e+02 bond pdb=" C10 BCR c 515 " pdb=" C11 BCR c 515 " ideal model delta sigma weight residual 1.436 1.173 0.263 2.00e-02 2.50e+03 1.73e+02 bond pdb=" C10 BCR C 515 " pdb=" C11 BCR C 515 " ideal model delta sigma weight residual 1.436 1.173 0.263 2.00e-02 2.50e+03 1.73e+02 bond pdb=" O5 OEX a 401 " pdb="CA1 OEX a 401 " ideal model delta sigma weight residual 2.800 2.145 0.655 5.00e-02 4.00e+02 1.72e+02 ... (remaining 55303 not shown) Histogram of bond angle deviations from ideal: 64.25 - 87.06: 88 87.06 - 109.87: 10745 109.87 - 132.68: 64115 132.68 - 155.49: 508 155.49 - 178.30: 242 Bond angle restraints: 75698 Sorted by residual: angle pdb=" C10 BCR k 103 " pdb=" C11 BCR k 103 " pdb=" C12 BCR k 103 " ideal model delta sigma weight residual 122.66 177.56 -54.90 3.00e+00 1.11e-01 3.35e+02 angle pdb=" C10 BCR K 103 " pdb=" C11 BCR K 103 " pdb=" C12 BCR K 103 " ideal model delta sigma weight residual 122.66 177.50 -54.84 3.00e+00 1.11e-01 3.34e+02 angle pdb=" C10 BCR c 515 " pdb=" C11 BCR c 515 " pdb=" C12 BCR c 515 " ideal model delta sigma weight residual 122.66 177.01 -54.35 3.00e+00 1.11e-01 3.28e+02 angle pdb=" C10 BCR z 101 " pdb=" C11 BCR z 101 " pdb=" C12 BCR z 101 " ideal model delta sigma weight residual 122.66 176.99 -54.33 3.00e+00 1.11e-01 3.28e+02 angle pdb=" C10 BCR Z 101 " pdb=" C11 BCR Z 101 " pdb=" C12 BCR Z 101 " ideal model delta sigma weight residual 122.66 176.99 -54.33 3.00e+00 1.11e-01 3.28e+02 ... (remaining 75693 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.47: 27020 32.47 - 64.94: 1932 64.94 - 97.42: 152 97.42 - 129.89: 22 129.89 - 162.36: 2 Dihedral angle restraints: 29128 sinusoidal: 13472 harmonic: 15656 Sorted by residual: dihedral pdb=" CA ILE x 21 " pdb=" C ILE x 21 " pdb=" N PRO x 22 " pdb=" CA PRO x 22 " ideal model delta harmonic sigma weight residual 180.00 135.64 44.36 0 5.00e+00 4.00e-02 7.87e+01 dihedral pdb=" CA ILE X 21 " pdb=" C ILE X 21 " pdb=" N PRO X 22 " pdb=" CA PRO X 22 " ideal model delta harmonic sigma weight residual 180.00 135.67 44.33 0 5.00e+00 4.00e-02 7.86e+01 dihedral pdb=" CA LYS O 88 " pdb=" C LYS O 88 " pdb=" N ARG O 89 " pdb=" CA ARG O 89 " ideal model delta harmonic sigma weight residual 180.00 143.25 36.75 0 5.00e+00 4.00e-02 5.40e+01 ... (remaining 29125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.902: 7706 0.902 - 1.804: 0 1.804 - 2.705: 0 2.705 - 3.607: 0 3.607 - 4.509: 2 Chirality restraints: 7708 Sorted by residual: chirality pdb=" C1 SQD K 101 " pdb=" C2 SQD K 101 " pdb=" O5 SQD K 101 " pdb=" O6 SQD K 101 " both_signs ideal model delta sigma weight residual False -2.39 2.12 -4.51 2.00e-01 2.50e+01 5.08e+02 chirality pdb=" C1 SQD k 101 " pdb=" C2 SQD k 101 " pdb=" O5 SQD k 101 " pdb=" O6 SQD k 101 " both_signs ideal model delta sigma weight residual False -2.39 2.12 -4.51 2.00e-01 2.50e+01 5.08e+02 chirality pdb=" C3A CLA b 604 " pdb=" C2A CLA b 604 " pdb=" C4A CLA b 604 " pdb=" CMA CLA b 604 " both_signs ideal model delta sigma weight residual False -2.76 -1.96 -0.81 2.00e-01 2.50e+01 1.62e+01 ... (remaining 7705 not shown) Planarity restraints: 9156 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C20 RRX X 102 " -0.266 2.00e-02 2.50e+03 2.20e-01 6.06e+02 pdb=" C21 RRX X 102 " 0.374 2.00e-02 2.50e+03 pdb=" C22 RRX X 102 " 0.066 2.00e-02 2.50e+03 pdb=" C23 RRX X 102 " -0.164 2.00e-02 2.50e+03 pdb=" C37 RRX X 102 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C20 RRX x 102 " 0.266 2.00e-02 2.50e+03 2.20e-01 6.06e+02 pdb=" C21 RRX x 102 " -0.374 2.00e-02 2.50e+03 pdb=" C22 RRX x 102 " -0.066 2.00e-02 2.50e+03 pdb=" C23 RRX x 102 " 0.164 2.00e-02 2.50e+03 pdb=" C37 RRX x 102 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 RRX X 102 " -0.181 2.00e-02 2.50e+03 1.83e-01 3.33e+02 pdb=" C19 RRX X 102 " 0.183 2.00e-02 2.50e+03 pdb=" C20 RRX X 102 " 0.182 2.00e-02 2.50e+03 pdb=" C21 RRX X 102 " -0.184 2.00e-02 2.50e+03 ... (remaining 9153 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.20: 104 2.20 - 2.87: 21027 2.87 - 3.55: 83854 3.55 - 4.22: 156573 4.22 - 4.90: 257273 Nonbonded interactions: 518831 Sorted by model distance: nonbonded pdb=" OE2 GLU e 7 " pdb=" O HOH e 201 " model vdw 1.522 2.440 nonbonded pdb=" OE2 GLU E 7 " pdb=" O HOH E 201 " model vdw 1.522 2.440 nonbonded pdb=" OD2 ASP O 249 " pdb=" O HOH O 301 " model vdw 1.784 2.440 nonbonded pdb=" OD2 ASP o 249 " pdb=" O HOH o 301 " model vdw 1.784 2.440 nonbonded pdb=" OE2 GLU a 242 " pdb=" O HOH a 501 " model vdw 1.818 2.440 ... (remaining 518826 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 'A' selection = chain 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = chain 'C' selection = chain 'c' } ncs_group { reference = chain 'D' selection = chain 'd' } ncs_group { reference = chain 'E' selection = chain 'e' } ncs_group { reference = chain 'F' selection = chain 'f' } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'I' selection = chain 'i' } ncs_group { reference = chain 'J' selection = chain 'j' } ncs_group { reference = chain 'K' selection = chain 'k' } ncs_group { reference = (chain 'L' and resid 1 through 39) selection = chain 'l' } ncs_group { reference = (chain 'M' and (resid 1 through 31 or (resid 101 and (name C1 or name C1' or nam \ e C10 or name C11 or name C12 or name C2 or name C2' or name C3 or name C3' or n \ ame C4 or name C4' or name C5 or name C5' or name C6 or name C6' or name C7 or n \ ame C8 or name C9 or name O1' or name O1B or name O2' or name O3' or name O5' or \ name O6')))) selection = chain 'm' } ncs_group { reference = chain 'O' selection = chain 'o' } ncs_group { reference = chain 'Q' selection = chain 'q' } ncs_group { reference = chain 'R' selection = chain 'r' } ncs_group { reference = chain 'T' selection = chain 't' } ncs_group { reference = chain 'U' selection = chain 'u' } ncs_group { reference = chain 'V' selection = chain 'v' } ncs_group { reference = chain 'X' selection = chain 'x' } ncs_group { reference = chain 'Y' selection = chain 'y' } ncs_group { reference = chain 'Z' selection = chain 'z' } 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: 10 Type Number sf(0) Gaussians Ca 8 9.91 5 Mn 8 7.51 5 Fe 6 7.16 5 P 14 5.49 5 Mg 70 5.21 5 S 160 5.16 5 Cl 4 4.86 5 C 36506 2.51 5 N 7446 2.21 5 O 10434 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: 3.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 14.320 Check model and map are aligned: 0.600 Process input model: 100.820 Find NCS groups from input model: 2.640 Set up NCS constraints: 0.680 Set refine NCS operators: 0.000 Set scattering table: 0.360 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 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 : 0.024 0.687 55308 Z= 1.315 Angle : 2.359 54.896 75698 Z= 0.865 Chirality : 0.105 4.509 7708 Planarity : 0.013 0.220 9156 Dihedral : 20.288 162.360 19136 Min Nonbonded Distance : 1.522 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.01 % Favored : 96.92 % Rotamer Outliers : 1.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.70 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.11), residues: 5452 helix: 1.11 (0.09), residues: 2946 sheet: 0.31 (0.33), residues: 244 loop : -0.18 (0.13), residues: 2262 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10904 Ramachandran restraints generated. 5452 Oldfield, 0 Emsley, 5452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10904 Ramachandran restraints generated. 5452 Oldfield, 0 Emsley, 5452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 936 residues out of total 4532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 850 time to evaluate : 3.951 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 86 outliers final: 27 residues processed: 899 average time/residue: 1.2567 time to fit residues: 1464.6388 Evaluate side-chains 821 residues out of total 4532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 794 time to evaluate : 3.885 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 24 residues processed: 3 average time/residue: 1.1463 time to fit residues: 9.6278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 452 optimal weight: 4.9990 chunk 406 optimal weight: 2.9990 chunk 225 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 274 optimal weight: 0.8980 chunk 217 optimal weight: 0.1980 chunk 420 optimal weight: 0.6980 chunk 162 optimal weight: 0.7980 chunk 255 optimal weight: 0.6980 chunk 312 optimal weight: 0.7980 chunk 486 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 25 ASN A 130 GLN A 234 ASN A 310 GLN A 338 ASN B 260 ASN B 409 GLN B 489 GLN C 142 ASN C 309 GLN C 375 GLN C 405 ASN D 129 GLN E 23 HIS E 73 ASN H 50 ASN I 31 ASN L 8 ASN L 10 GLN O 109 GLN O 166 ASN O 199 ASN O 230 GLN O 246 GLN Q 67 ASN Q 76 HIS Q 143 ASN U 106 ASN V 50 GLN V 93 ASN V 119 ASN X 7 ASN Z 32 ASN a 19 GLN a 25 ASN a 130 GLN a 234 ASN a 310 GLN a 338 ASN b 260 ASN b 409 GLN b 489 GLN c 142 ASN ** c 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 375 GLN c 405 ASN d 129 GLN e 23 HIS e 73 ASN h 50 ASN i 31 ASN l 10 GLN o 109 GLN o 166 ASN o 199 ASN o 230 GLN o 246 GLN q 67 ASN q 76 HIS q 143 ASN u 106 ASN v 50 GLN v 93 ASN v 119 ASN x 7 ASN y 68 GLN z 32 ASN z 58 ASN Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 55308 Z= 0.194 Angle : 0.743 25.559 75698 Z= 0.324 Chirality : 0.044 0.284 7708 Planarity : 0.006 0.059 9156 Dihedral : 18.643 157.040 9594 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.38 % Favored : 97.58 % Rotamer Outliers : 2.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.70 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.11), residues: 5452 helix: 1.28 (0.09), residues: 2976 sheet: 0.54 (0.34), residues: 226 loop : 0.02 (0.13), residues: 2250 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10904 Ramachandran restraints generated. 5452 Oldfield, 0 Emsley, 5452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10904 Ramachandran restraints generated. 5452 Oldfield, 0 Emsley, 5452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 949 residues out of total 4532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 853 time to evaluate : 3.901 Fit side-chains revert: symmetry clash outliers start: 96 outliers final: 39 residues processed: 916 average time/residue: 1.2654 time to fit residues: 1507.8925 Evaluate side-chains 850 residues out of total 4532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 811 time to evaluate : 3.926 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 30 residues processed: 9 average time/residue: 0.6222 time to fit residues: 14.0059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 270 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 405 optimal weight: 2.9990 chunk 331 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 487 optimal weight: 10.0000 chunk 526 optimal weight: 4.9990 chunk 434 optimal weight: 3.9990 chunk 483 optimal weight: 8.9990 chunk 166 optimal weight: 5.9990 chunk 391 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 310 GLN A 338 ASN B 409 GLN B 489 GLN E 73 ASN L 8 ASN L 10 GLN O 199 ASN O 230 GLN ** R 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 106 ASN V 55 GLN V 93 ASN X 7 ASN Y 68 GLN Z 58 ASN a 338 ASN b 409 GLN b 489 GLN c 309 GLN e 73 ASN e 77 GLN l 10 GLN o 199 ASN o 230 GLN u 106 ASN v 55 GLN v 93 ASN x 7 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.111 55308 Z= 0.321 Angle : 0.839 23.154 75698 Z= 0.383 Chirality : 0.049 0.292 7708 Planarity : 0.007 0.064 9156 Dihedral : 18.707 158.803 9594 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.88 % Favored : 97.08 % Rotamer Outliers : 2.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.70 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.11), residues: 5452 helix: 1.01 (0.09), residues: 2958 sheet: 0.48 (0.34), residues: 232 loop : 0.01 (0.13), residues: 2262 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10904 Ramachandran restraints generated. 5452 Oldfield, 0 Emsley, 5452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10904 Ramachandran restraints generated. 5452 Oldfield, 0 Emsley, 5452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 956 residues out of total 4532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 849 time to evaluate : 3.947 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 107 outliers final: 54 residues processed: 916 average time/residue: 1.2601 time to fit residues: 1506.7084 Evaluate side-chains 880 residues out of total 4532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 826 time to evaluate : 3.927 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 38 residues processed: 17 average time/residue: 0.6224 time to fit residues: 22.1822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 481 optimal weight: 8.9990 chunk 366 optimal weight: 0.8980 chunk 253 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 232 optimal weight: 0.9990 chunk 327 optimal weight: 0.4980 chunk 489 optimal weight: 10.0000 chunk 518 optimal weight: 1.9990 chunk 255 optimal weight: 7.9990 chunk 463 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 ASN B 409 GLN B 489 GLN C 309 GLN E 73 ASN L 10 GLN O 199 ASN O 230 GLN ** R 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 106 ASN a 19 GLN a 310 GLN a 338 ASN b 409 GLN b 489 GLN c 309 GLN e 73 ASN o 199 ASN o 230 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.082 55308 Z= 0.230 Angle : 0.737 22.504 75698 Z= 0.333 Chirality : 0.045 0.271 7708 Planarity : 0.006 0.061 9156 Dihedral : 18.152 158.377 9594 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.57 % Favored : 97.40 % Rotamer Outliers : 2.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.70 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.11), residues: 5452 helix: 1.19 (0.09), residues: 2962 sheet: 0.48 (0.35), residues: 224 loop : 0.08 (0.13), residues: 2266 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10904 Ramachandran restraints generated. 5452 Oldfield, 0 Emsley, 5452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10904 Ramachandran restraints generated. 5452 Oldfield, 0 Emsley, 5452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 972 residues out of total 4532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 862 time to evaluate : 4.042 Fit side-chains revert: symmetry clash outliers start: 110 outliers final: 55 residues processed: 922 average time/residue: 1.2568 time to fit residues: 1518.7170 Evaluate side-chains 917 residues out of total 4532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 862 time to evaluate : 3.927 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 40 residues processed: 16 average time/residue: 0.5405 time to fit residues: 19.7733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 431 optimal weight: 0.7980 chunk 294 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 385 optimal weight: 0.8980 chunk 213 optimal weight: 8.9990 chunk 442 optimal weight: 4.9990 chunk 358 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 264 optimal weight: 0.0270 chunk 465 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 338 ASN B 409 GLN B 489 GLN C 309 GLN E 73 ASN L 8 ASN L 10 GLN O 199 ASN ** R 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 106 ASN V 93 ASN a 310 GLN a 338 ASN b 409 GLN b 489 GLN c 309 GLN e 73 ASN o 199 ASN r 22 ASN v 93 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 55308 Z= 0.170 Angle : 0.665 21.989 75698 Z= 0.297 Chirality : 0.042 0.274 7708 Planarity : 0.005 0.057 9156 Dihedral : 17.356 157.966 9594 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer Outliers : 2.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.70 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.11), residues: 5452 helix: 1.48 (0.09), residues: 2958 sheet: 0.56 (0.35), residues: 224 loop : 0.17 (0.14), residues: 2270 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10904 Ramachandran restraints generated. 5452 Oldfield, 0 Emsley, 5452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10904 Ramachandran restraints generated. 5452 Oldfield, 0 Emsley, 5452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 970 residues out of total 4532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 865 time to evaluate : 3.983 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 105 outliers final: 48 residues processed: 936 average time/residue: 1.2713 time to fit residues: 1554.4440 Evaluate side-chains 890 residues out of total 4532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 842 time to evaluate : 3.918 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 36 residues processed: 12 average time/residue: 0.5749 time to fit residues: 16.4842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 174 optimal weight: 0.9990 chunk 466 optimal weight: 0.3980 chunk 102 optimal weight: 5.9990 chunk 304 optimal weight: 3.9990 chunk 127 optimal weight: 0.5980 chunk 518 optimal weight: 0.9990 chunk 430 optimal weight: 0.9980 chunk 240 optimal weight: 0.7980 chunk 43 optimal weight: 9.9990 chunk 171 optimal weight: 4.9990 chunk 272 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 338 ASN B 285 GLN B 409 GLN B 489 GLN C 309 GLN E 73 ASN O 199 ASN ** R 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 106 ASN V 93 ASN X 32 GLN a 19 GLN a 338 ASN b 409 GLN b 489 GLN c 309 GLN c 372 GLN e 73 ASN l 10 GLN o 199 ASN r 22 ASN ** r 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 93 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 55308 Z= 0.178 Angle : 0.670 22.000 75698 Z= 0.299 Chirality : 0.042 0.271 7708 Planarity : 0.005 0.056 9156 Dihedral : 16.932 158.271 9594 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 2.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.70 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.11), residues: 5452 helix: 1.50 (0.09), residues: 2950 sheet: 0.75 (0.35), residues: 220 loop : 0.22 (0.14), residues: 2282 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10904 Ramachandran restraints generated. 5452 Oldfield, 0 Emsley, 5452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10904 Ramachandran restraints generated. 5452 Oldfield, 0 Emsley, 5452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 950 residues out of total 4532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 856 time to evaluate : 3.968 Fit side-chains revert: symmetry clash outliers start: 94 outliers final: 53 residues processed: 919 average time/residue: 1.2568 time to fit residues: 1511.8724 Evaluate side-chains 887 residues out of total 4532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 834 time to evaluate : 3.932 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 41 residues processed: 12 average time/residue: 0.5742 time to fit residues: 16.4488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 499 optimal weight: 8.9990 chunk 58 optimal weight: 0.9990 chunk 295 optimal weight: 0.6980 chunk 378 optimal weight: 5.9990 chunk 293 optimal weight: 7.9990 chunk 436 optimal weight: 5.9990 chunk 289 optimal weight: 4.9990 chunk 516 optimal weight: 5.9990 chunk 323 optimal weight: 0.0170 chunk 314 optimal weight: 0.7980 chunk 238 optimal weight: 5.9990 overall best weight: 1.5022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 ASN B 285 GLN B 409 GLN B 489 GLN C 309 GLN C 372 GLN E 73 ASN L 8 ASN O 199 ASN ** R 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 106 ASN V 93 ASN X 32 GLN a 19 GLN a 338 ASN b 409 GLN b 489 GLN c 309 GLN c 372 GLN e 73 ASN l 10 GLN o 199 ASN o 230 GLN r 22 ASN ** r 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 93 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.084 55308 Z= 0.232 Angle : 0.727 22.566 75698 Z= 0.329 Chirality : 0.045 0.265 7708 Planarity : 0.006 0.059 9156 Dihedral : 17.000 158.878 9594 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 2.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.70 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.11), residues: 5452 helix: 1.32 (0.09), residues: 2960 sheet: 0.55 (0.34), residues: 234 loop : 0.19 (0.14), residues: 2258 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10904 Ramachandran restraints generated. 5452 Oldfield, 0 Emsley, 5452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10904 Ramachandran restraints generated. 5452 Oldfield, 0 Emsley, 5452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 959 residues out of total 4532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 862 time to evaluate : 4.071 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 53 residues processed: 924 average time/residue: 1.2594 time to fit residues: 1527.1124 Evaluate side-chains 907 residues out of total 4532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 854 time to evaluate : 3.972 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 40 residues processed: 13 average time/residue: 0.6493 time to fit residues: 18.5877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 319 optimal weight: 0.4980 chunk 206 optimal weight: 6.9990 chunk 308 optimal weight: 8.9990 chunk 155 optimal weight: 7.9990 chunk 101 optimal weight: 0.0570 chunk 100 optimal weight: 6.9990 chunk 328 optimal weight: 0.6980 chunk 351 optimal weight: 4.9990 chunk 255 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 406 optimal weight: 2.9990 overall best weight: 1.0502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 ASN B 409 GLN C 309 GLN C 372 GLN E 73 ASN L 8 ASN O 199 ASN R 22 ASN ** R 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 106 ASN V 93 ASN X 32 GLN ** a 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 338 ASN b 409 GLN b 489 GLN c 309 GLN e 73 ASN o 199 ASN o 227 GLN o 230 GLN r 22 ASN ** r 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 93 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 55308 Z= 0.199 Angle : 0.690 22.414 75698 Z= 0.311 Chirality : 0.043 0.268 7708 Planarity : 0.005 0.058 9156 Dihedral : 16.715 158.336 9594 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.70 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.11), residues: 5452 helix: 1.43 (0.09), residues: 2944 sheet: 0.79 (0.35), residues: 220 loop : 0.19 (0.14), residues: 2288 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10904 Ramachandran restraints generated. 5452 Oldfield, 0 Emsley, 5452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10904 Ramachandran restraints generated. 5452 Oldfield, 0 Emsley, 5452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 915 residues out of total 4532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 837 time to evaluate : 4.083 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 50 residues processed: 895 average time/residue: 1.3133 time to fit residues: 1543.1585 Evaluate side-chains 872 residues out of total 4532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 822 time to evaluate : 3.918 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 42 residues processed: 8 average time/residue: 0.4814 time to fit residues: 12.2025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 469 optimal weight: 10.0000 chunk 494 optimal weight: 30.0000 chunk 451 optimal weight: 4.9990 chunk 481 optimal weight: 0.6980 chunk 289 optimal weight: 1.9990 chunk 209 optimal weight: 10.0000 chunk 378 optimal weight: 5.9990 chunk 147 optimal weight: 10.0000 chunk 435 optimal weight: 0.9980 chunk 455 optimal weight: 6.9990 chunk 479 optimal weight: 0.9980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 ASN B 409 GLN C 309 GLN E 73 ASN L 8 ASN ** R 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 106 ASN V 93 ASN X 32 GLN ** a 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 338 ASN b 409 GLN b 489 GLN c 309 GLN e 73 ASN l 8 ASN o 199 ASN r 22 ASN ** r 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 93 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.095 55308 Z= 0.268 Angle : 0.770 22.724 75698 Z= 0.351 Chirality : 0.047 0.278 7708 Planarity : 0.006 0.063 9156 Dihedral : 17.037 158.918 9594 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.88 % Favored : 97.08 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.70 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.11), residues: 5452 helix: 1.22 (0.09), residues: 2952 sheet: 0.32 (0.33), residues: 252 loop : 0.16 (0.14), residues: 2248 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10904 Ramachandran restraints generated. 5452 Oldfield, 0 Emsley, 5452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10904 Ramachandran restraints generated. 5452 Oldfield, 0 Emsley, 5452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 915 residues out of total 4532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 842 time to evaluate : 3.948 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 49 residues processed: 899 average time/residue: 1.2783 time to fit residues: 1512.7321 Evaluate side-chains 869 residues out of total 4532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 820 time to evaluate : 3.939 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 43 residues processed: 6 average time/residue: 0.4484 time to fit residues: 10.1605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 316 optimal weight: 3.9990 chunk 509 optimal weight: 0.0980 chunk 310 optimal weight: 0.8980 chunk 241 optimal weight: 5.9990 chunk 353 optimal weight: 1.9990 chunk 533 optimal weight: 5.9990 chunk 491 optimal weight: 6.9990 chunk 425 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 328 optimal weight: 2.9990 chunk 260 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 ASN B 409 GLN B 489 GLN C 309 GLN E 73 ASN L 8 ASN O 199 ASN ** R 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 93 ASN X 32 GLN ** a 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 338 ASN b 409 GLN b 489 GLN c 309 GLN e 73 ASN o 199 ASN o 227 GLN r 22 ASN ** r 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 93 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 55308 Z= 0.220 Angle : 0.715 22.392 75698 Z= 0.324 Chirality : 0.045 0.266 7708 Planarity : 0.006 0.061 9156 Dihedral : 16.836 158.446 9594 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer Outliers : 1.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.70 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.11), residues: 5452 helix: 1.32 (0.09), residues: 2950 sheet: 0.50 (0.34), residues: 234 loop : 0.19 (0.14), residues: 2268 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10904 Ramachandran restraints generated. 5452 Oldfield, 0 Emsley, 5452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10904 Ramachandran restraints generated. 5452 Oldfield, 0 Emsley, 5452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 891 residues out of total 4532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 823 time to evaluate : 3.994 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 50 residues processed: 879 average time/residue: 1.3447 time to fit residues: 1573.0846 Evaluate side-chains 861 residues out of total 4532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 811 time to evaluate : 4.035 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 42 residues processed: 8 average time/residue: 0.7796 time to fit residues: 15.3926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 337 optimal weight: 4.9990 chunk 452 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 392 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 425 optimal weight: 0.8980 chunk 178 optimal weight: 6.9990 chunk 437 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 78 optimal weight: 0.6980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 ASN B 409 GLN B 489 GLN C 309 GLN E 73 ASN L 8 ASN ** Q 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 93 ASN X 32 GLN ** a 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 338 ASN b 409 GLN b 489 GLN c 309 GLN e 73 ASN l 8 ASN l 10 GLN o 199 ASN ** q 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 22 ASN ** r 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 93 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.189430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.170674 restraints weight = 36821.135| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 0.43 r_work: 0.3726 rms_B_bonded: 1.05 restraints_weight: 0.5000 r_work: 0.3661 rms_B_bonded: 1.64 restraints_weight: 0.2500 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.106 55308 Z= 0.312 Angle : 0.819 22.595 75698 Z= 0.376 Chirality : 0.049 0.294 7708 Planarity : 0.007 0.062 9156 Dihedral : 17.295 158.885 9594 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.95 % Favored : 97.01 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.70 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.11), residues: 5452 helix: 1.05 (0.09), residues: 2954 sheet: 0.23 (0.32), residues: 252 loop : 0.11 (0.14), residues: 2246 =============================================================================== Job complete usr+sys time: 20493.23 seconds wall clock time: 356 minutes 22.34 seconds (21382.34 seconds total)