Starting phenix.real_space_refine on Mon Mar 11 01:47:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rcv_24407/03_2024/7rcv_24407_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rcv_24407/03_2024/7rcv_24407.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rcv_24407/03_2024/7rcv_24407_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rcv_24407/03_2024/7rcv_24407_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rcv_24407/03_2024/7rcv_24407_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rcv_24407/03_2024/7rcv_24407.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rcv_24407/03_2024/7rcv_24407.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rcv_24407/03_2024/7rcv_24407_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rcv_24407/03_2024/7rcv_24407_neut_updated.pdb" } resolution = 2.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 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. 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 PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 61": "OD1" <-> "OD2" Residue "A GLU 65": "OE1" <-> "OE2" 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 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 "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 GLU 121": "OE1" <-> "OE2" Residue "B PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 294": "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 353": "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 PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 407": "OD1" <-> "OD2" Residue "B ASP 416": "OD1" <-> "OD2" 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 ASP 483": "OD1" <-> "OD2" Residue "B GLU 487": "OE1" <-> "OE2" Residue "B GLU 488": "OE1" <-> "OE2" Residue "B ASP 500": "OD1" <-> "OD2" Residue "B ARG 504": "NH1" <-> "NH2" Residue "C ASP 14": "OD1" <-> "OD2" Residue "C PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 70": "OE1" <-> "OE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C PHE 96": "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 ASP 182": "OD1" <-> "OD2" 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 ARG 368": "NH1" <-> "NH2" Residue "C ASP 370": "OD1" <-> "OD2" Residue "C TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 GLU 241": "OE1" <-> "OE2" Residue "D PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 257": "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 GLU 7": "OE1" <-> "OE2" Residue "E PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 54": "OE1" <-> "OE2" Residue "E ARG 60": "NH1" <-> "NH2" Residue "E GLU 62": "OE1" <-> "OE2" Residue "E GLU 75": "OE1" <-> "OE2" Residue "F PHE 15": "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 "H ASP 61": "OD1" <-> "OD2" Residue "I TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 27": "OD1" <-> "OD2" Residue "I ARG 30": "NH1" <-> "NH2" 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 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 31": "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 GLU 13": "OE1" <-> "OE2" Residue "L ARG 16": "NH1" <-> "NH2" Residue "L PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 60": "OE1" <-> "OE2" Residue "O GLU 62": "OE1" <-> "OE2" Residue "O PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 84": "OE1" <-> "OE2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "O ASP 119": "OD1" <-> "OD2" Residue "O PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 143": "OE1" <-> "OE2" Residue "O GLU 144": "OE1" <-> "OE2" Residue "O PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 170": "OD1" <-> "OD2" Residue "O PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 208": "OD1" <-> "OD2" Residue "O ASP 232": "OD1" <-> "OD2" Residue "O GLU 237": "OE1" <-> "OE2" Residue "O GLU 256": "OE1" <-> "OE2" 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 GLU 133": "OE1" <-> "OE2" Residue "R ARG 29": "NH1" <-> "NH2" Residue "T PHE 18": "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 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 "U ASP 124": "OD1" <-> "OD2" Residue "V GLU 30": "OE1" <-> "OE2" Residue "V ARG 33": "NH1" <-> "NH2" Residue "V PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 88": "OE1" <-> "OE2" Residue "V ARG 90": "NH1" <-> "NH2" Residue "V GLU 99": "OE1" <-> "OE2" Residue "V GLU 110": "OE1" <-> "OE2" Residue "V ASP 111": "OD1" <-> "OD2" Residue "V ASP 112": "OD1" <-> "OD2" Residue "V ARG 122": "NH1" <-> "NH2" Residue "V GLU 128": "OE1" <-> "OE2" Residue "V ASP 136": "OD1" <-> "OD2" Residue "V ASP 151": "OD1" <-> "OD2" Residue "V ARG 153": "NH1" <-> "NH2" Residue "Y GLU 64": "OE1" <-> "OE2" Residue "Y PHE 67": "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 PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 61": "OD1" <-> "OD2" Residue "a GLU 65": "OE1" <-> "OE2" 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 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 "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 GLU 121": "OE1" <-> "OE2" Residue "b PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 130": "OE1" <-> "OE2" Residue "b PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 294": "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 353": "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 PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 407": "OD1" <-> "OD2" Residue "b ASP 416": "OD1" <-> "OD2" 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 ASP 483": "OD1" <-> "OD2" Residue "b GLU 487": "OE1" <-> "OE2" Residue "b GLU 488": "OE1" <-> "OE2" Residue "b ASP 500": "OD1" <-> "OD2" Residue "b ARG 504": "NH1" <-> "NH2" Residue "c ASP 14": "OD1" <-> "OD2" Residue "c PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 58": "OE1" <-> "OE2" Residue "c TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 70": "OE1" <-> "OE2" Residue "c GLU 91": "OE1" <-> "OE2" Residue "c PHE 96": "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 ASP 182": "OD1" <-> "OD2" 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 ARG 368": "NH1" <-> "NH2" Residue "c ASP 370": "OD1" <-> "OD2" Residue "c TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 GLU 241": "OE1" <-> "OE2" Residue "d PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 257": "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 GLU 7": "OE1" <-> "OE2" Residue "e PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 54": "OE1" <-> "OE2" Residue "e ARG 60": "NH1" <-> "NH2" Residue "e GLU 62": "OE1" <-> "OE2" Residue "e GLU 75": "OE1" <-> "OE2" Residue "f PHE 15": "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 "h ASP 61": "OD1" <-> "OD2" Residue "i TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 27": "OD1" <-> "OD2" Residue "i ARG 30": "NH1" <-> "NH2" 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 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 31": "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 GLU 13": "OE1" <-> "OE2" Residue "l ARG 16": "NH1" <-> "NH2" Residue "l PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 60": "OE1" <-> "OE2" Residue "o GLU 62": "OE1" <-> "OE2" Residue "o PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 84": "OE1" <-> "OE2" Residue "o ARG 102": "NH1" <-> "NH2" Residue "o ARG 111": "NH1" <-> "NH2" Residue "o ASP 119": "OD1" <-> "OD2" Residue "o PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 143": "OE1" <-> "OE2" Residue "o GLU 144": "OE1" <-> "OE2" Residue "o PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 170": "OD1" <-> "OD2" Residue "o PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 208": "OD1" <-> "OD2" Residue "o ASP 232": "OD1" <-> "OD2" Residue "o GLU 237": "OE1" <-> "OE2" Residue "o GLU 256": "OE1" <-> "OE2" 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 GLU 133": "OE1" <-> "OE2" Residue "r ARG 29": "NH1" <-> "NH2" Residue "t PHE 18": "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 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 "u ASP 124": "OD1" <-> "OD2" Residue "v GLU 30": "OE1" <-> "OE2" Residue "v ARG 33": "NH1" <-> "NH2" Residue "v PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 88": "OE1" <-> "OE2" Residue "v ARG 90": "NH1" <-> "NH2" Residue "v GLU 99": "OE1" <-> "OE2" Residue "v GLU 110": "OE1" <-> "OE2" Residue "v ASP 111": "OD1" <-> "OD2" Residue "v ASP 112": "OD1" <-> "OD2" Residue "v ARG 122": "NH1" <-> "NH2" Residue "v GLU 128": "OE1" <-> "OE2" Residue "v ASP 136": "OD1" <-> "OD2" Residue "v ASP 151": "OD1" <-> "OD2" Residue "v ARG 153": "NH1" <-> "NH2" Residue "y GLU 64": "OE1" <-> "OE2" Residue "y PHE 67": "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: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 54656 Number of models: 1 Model: "" Number of chains: 114 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: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 714 Unusual residues: {' CL': 2, 'BCR': 1, 'BCT': 1, 'CLA': 3, 'FE2': 1, 'LHG': 1, 'LMG': 2, 'LMT': 2, 'OEX': 1, 'PHO': 1, 'PL9': 1, 'SQD': 3} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 1382 Unusual residues: {'BCR': 3, 'CLA': 16, 'LHG': 1, 'LMG': 1, 'LMT': 4, 'SQD': 1} Classifications: {'undetermined': 26} Link IDs: {None: 25} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 1297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 1297 Unusual residues: {'BCR': 2, 'CLA': 13, 'DGD': 3, 'LMG': 2, 'LMT': 4} Classifications: {'undetermined': 24} Link IDs: {None: 23} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 13 Chain: "D" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 587 Unusual residues: {'BCR': 1, 'CLA': 3, 'LHG': 2, 'LMG': 1, 'LMT': 3, 'PHO': 1, 'PL9': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 10 Chain: "E" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 97 Unusual residues: {'LHG': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 112 Unusual residues: {'HEM': 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: 30 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: 80 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 dihedrals: 26 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 121 Unusual residues: {' CA': 1, 'BCR': 1, 'LMT': 1, 'SQD': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Chain: "L" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 94 Unusual residues: {'LMT': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 5 Chain: "T" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'LMT': 1, 'SQD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 26 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: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 122 Unusual residues: {'LMT': 3, 'RRX': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 55 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: 29 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: 13 Unresolved non-hydrogen chiralities: 1 Chain: "a" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 714 Unusual residues: {' CL': 2, 'BCR': 1, 'BCT': 1, 'CLA': 3, 'FE2': 1, 'LHG': 1, 'LMG': 2, 'LMT': 2, 'OEX': 1, 'PHO': 1, 'PL9': 1, 'SQD': 3} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 5 Chain: "b" Number of atoms: 1328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 1328 Unusual residues: {'BCR': 3, 'CLA': 16, 'LHG': 1, 'LMG': 1, 'LMT': 4} Classifications: {'undetermined': 25} Link IDs: {None: 24} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 5 Chain: "c" Number of atoms: 1297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 1297 Unusual residues: {'BCR': 2, 'CLA': 13, 'DGD': 3, 'LMG': 2, 'LMT': 4} Classifications: {'undetermined': 24} Link IDs: {None: 23} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 13 Chain: "d" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 587 Unusual residues: {'BCR': 1, 'CLA': 3, 'LHG': 2, 'LMG': 1, 'LMT': 3, 'PHO': 1, 'PL9': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 10 Chain: "e" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 97 Unusual residues: {'LHG': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 5 Chain: "f" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 112 Unusual residues: {'HEM': 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: 30 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: 80 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 dihedrals: 26 Unresolved non-hydrogen chiralities: 5 Chain: "k" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 121 Unusual residues: {' CA': 1, 'BCR': 1, 'LMT': 1, 'SQD': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Chain: "l" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 94 Unusual residues: {'LMT': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 26 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 dihedrals: 26 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: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 122 Unusual residues: {'LMT': 3, 'RRX': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 55 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: 29 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: 13 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 115 Classifications: {'water': 115} Link IDs: {None: 114} Chain: "B" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 119 Classifications: {'water': 119} Link IDs: {None: 118} Chain: "C" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} Chain: "D" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 119 Classifications: {'water': 119} Link IDs: {None: 118} Chain: "E" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "H" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "I" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} 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: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "M" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "T" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "U" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "V" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} 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: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 115 Classifications: {'water': 115} Link IDs: {None: 114} Chain: "b" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 116 Classifications: {'water': 116} Link IDs: {None: 115} Chain: "c" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} Chain: "d" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 119 Classifications: {'water': 119} Link IDs: {None: 118} Chain: "e" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "f" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "h" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "i" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "j" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} 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: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "m" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "o" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "t" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "u" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "v" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} 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: 22.33, 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=78, symmetry=0 Number of additional bonds: simple=78, symmetry=0 Coordination: Other bonds: Time building additional restraints: 20.13 Conformation dependent library (CDL) restraints added in 6.1 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 54.8% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.60 Creating SS restraints... Processing helix chain 'A' and resid 13 through 21 Processing helix chain 'A' and resid 31 through 54 removed outlier: 3.712A 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: 3.978A 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: 4.078A pdb=" N PHE A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 331 removed outlier: 3.775A pdb=" N MET A 331 " --> pdb=" O GLY A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 12 removed outlier: 3.606A pdb=" N VAL B 8 " --> pdb=" O TRP B 5 " (cutoff:3.500A) removed outlier: 5.607A 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: 3.854A 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 156 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 276 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 312 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: 3.884A pdb=" N LEU B 426 " --> pdb=" O ARG B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 474 removed outlier: 3.591A 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: 5.950A 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 71 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 199 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 340 through 345 Processing helix chain 'C' and resid 351 through 356 Proline residue: C 355 - end of helix No H-bonds generated for 'chain 'C' and resid 351 through 356' Processing helix chain 'C' and resid 364 through 369 Processing helix chain 'C' and resid 373 through 384 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: 4.067A pdb=" N LEU D 35 " --> pdb=" O GLY D 31 " (cutoff:3.500A) removed outlier: 4.163A 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 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: 4.303A 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 233 No H-bonds generated for 'chain 'D' and resid 231 through 233' 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: 3.812A 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 14 Processing helix chain 'E' and resid 17 through 39 removed outlier: 4.316A 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: 3.624A pdb=" N LEU F 25 " --> pdb=" O ALA F 21 " (cutoff:3.500A) Proline residue: F 28 - end of helix removed outlier: 4.128A 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 24 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: 3.783A 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: 4.404A 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: 3.711A pdb=" N PHE K 36 " --> pdb=" O LEU K 32 " (cutoff:3.500A) Processing helix chain 'L' and resid 16 through 38 removed outlier: 4.606A pdb=" N SER L 35 " --> pdb=" O ILE L 31 " (cutoff:3.500A) removed outlier: 4.690A 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: 3.870A pdb=" N ALA O 207 " --> pdb=" O PRO O 204 " (cutoff:3.500A) removed outlier: 6.152A 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: 3.685A pdb=" N ALA Q 39 " --> pdb=" O PRO Q 35 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL Q 43 " --> pdb=" O ALA Q 39 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N TYR Q 44 " --> pdb=" O GLN Q 40 " (cutoff:3.500A) Proline residue: Q 47 - end of helix removed outlier: 4.097A pdb=" N LEU Q 59 " --> pdb=" O MET Q 55 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLN Q 60 " --> pdb=" O GLU Q 56 " (cutoff:3.500A) removed outlier: 4.085A 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: 3.718A 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: 6.030A pdb=" N ALA R 25 " --> pdb=" O ILE R 21 " (cutoff:3.500A) removed outlier: 6.527A 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 80 Processing helix chain 'U' and resid 86 through 91 Processing helix chain 'U' and resid 97 through 105 Processing helix chain 'U' and resid 107 through 109 No H-bonds generated for 'chain 'U' and resid 107 through 109' Processing helix chain 'U' and resid 117 through 123 removed outlier: 7.057A pdb=" N GLY U 122 " --> pdb=" O GLU U 118 " (cutoff:3.500A) removed outlier: 6.521A 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: 8.611A pdb=" N GLN V 68 " --> pdb=" O GLN V 64 " (cutoff:3.500A) removed outlier: 7.014A 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: 4.767A pdb=" N VAL X 25 " --> pdb=" O ILE X 21 " (cutoff:3.500A) Processing helix chain 'Y' and resid 64 through 89 removed outlier: 3.944A 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: 4.484A pdb=" N ASP Z 34 " --> pdb=" O GLN Z 31 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ARG Z 35 " --> pdb=" O ASN Z 32 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER Z 36 " --> pdb=" O TRP Z 33 " (cutoff:3.500A) removed outlier: 4.479A 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: 3.712A 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: 3.979A 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: 4.079A pdb=" N PHE a 295 " --> pdb=" O SER a 291 " (cutoff:3.500A) Processing helix chain 'a' and resid 317 through 331 removed outlier: 3.775A pdb=" N MET a 331 " --> pdb=" O GLY a 327 " (cutoff:3.500A) Processing helix chain 'b' and resid 5 through 12 removed outlier: 3.606A pdb=" N VAL b 8 " --> pdb=" O TRP b 5 " (cutoff:3.500A) removed outlier: 5.607A 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: 3.854A 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 156 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 276 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 312 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: 3.884A pdb=" N LEU b 426 " --> pdb=" O ARG b 422 " (cutoff:3.500A) Processing helix chain 'b' and resid 447 through 474 removed outlier: 3.591A 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: 5.949A 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 71 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 199 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 340 through 345 Processing helix chain 'c' and resid 351 through 356 Proline residue: c 355 - end of helix No H-bonds generated for 'chain 'c' and resid 351 through 356' Processing helix chain 'c' and resid 364 through 369 Processing helix chain 'c' and resid 373 through 384 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: 4.067A pdb=" N LEU d 35 " --> pdb=" O GLY d 31 " (cutoff:3.500A) removed outlier: 4.163A 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 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: 4.302A 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 233 No H-bonds generated for 'chain 'd' and resid 231 through 233' 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: 3.811A 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 14 Processing helix chain 'e' and resid 17 through 39 removed outlier: 4.316A 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: 3.624A pdb=" N LEU f 25 " --> pdb=" O ALA f 21 " (cutoff:3.500A) Proline residue: f 28 - end of helix removed outlier: 4.129A 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 24 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: 3.783A 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: 4.404A 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: 3.712A pdb=" N PHE k 36 " --> pdb=" O LEU k 32 " (cutoff:3.500A) Processing helix chain 'l' and resid 16 through 38 removed outlier: 4.606A pdb=" N SER l 35 " --> pdb=" O ILE l 31 " (cutoff:3.500A) removed outlier: 4.690A 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: 3.871A pdb=" N ALA o 207 " --> pdb=" O PRO o 204 " (cutoff:3.500A) removed outlier: 6.152A 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: 3.685A pdb=" N ALA q 39 " --> pdb=" O PRO q 35 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL q 43 " --> pdb=" O ALA q 39 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N TYR q 44 " --> pdb=" O GLN q 40 " (cutoff:3.500A) Proline residue: q 47 - end of helix removed outlier: 4.097A pdb=" N LEU q 59 " --> pdb=" O MET q 55 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLN q 60 " --> pdb=" O GLU q 56 " (cutoff:3.500A) removed outlier: 4.085A 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: 3.719A 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: 6.030A pdb=" N ALA r 25 " --> pdb=" O ILE r 21 " (cutoff:3.500A) removed outlier: 6.527A 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 80 Processing helix chain 'u' and resid 86 through 91 Processing helix chain 'u' and resid 97 through 105 Processing helix chain 'u' and resid 107 through 109 No H-bonds generated for 'chain 'u' and resid 107 through 109' Processing helix chain 'u' and resid 117 through 123 removed outlier: 7.057A pdb=" N GLY u 122 " --> pdb=" O GLU u 118 " (cutoff:3.500A) removed outlier: 6.521A 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: 8.611A pdb=" N GLN v 68 " --> pdb=" O GLN v 64 " (cutoff:3.500A) removed outlier: 7.015A 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: 4.767A pdb=" N VAL x 25 " --> pdb=" O ILE x 21 " (cutoff:3.500A) Processing helix chain 'y' and resid 64 through 89 removed outlier: 3.943A 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: 4.484A pdb=" N ASP z 34 " --> pdb=" O GLN z 31 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ARG z 35 " --> pdb=" O ASN z 32 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER z 36 " --> pdb=" O TRP z 33 " (cutoff:3.500A) removed outlier: 4.479A 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: 6.421A 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: 6.390A pdb=" N SER O 113 " --> pdb=" O GLU O 126 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N GLU O 126 " --> pdb=" O SER O 113 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ALA O 115 " --> pdb=" O PHE O 124 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N PHE O 124 " --> pdb=" O ALA O 115 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LYS O 221 " --> pdb=" O PRO O 247 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ALA O 239 " --> pdb=" O THR O 229 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N VAL O 231 " --> pdb=" O GLU O 237 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N GLU O 237 " --> pdb=" O VAL O 231 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASP O 259 " --> pdb=" O LYS O 82 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE O 265 " --> pdb=" O PRO O 76 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N TYR O 267 " --> pdb=" O MET O 74 " (cutoff:3.500A) removed outlier: 5.303A 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: 6.421A 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: 6.390A pdb=" N SER o 113 " --> pdb=" O GLU o 126 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N GLU o 126 " --> pdb=" O SER o 113 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ALA o 115 " --> pdb=" O PHE o 124 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N PHE o 124 " --> pdb=" O ALA o 115 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LYS o 221 " --> pdb=" O PRO o 247 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ALA o 239 " --> pdb=" O THR o 229 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N VAL o 231 " --> pdb=" O GLU o 237 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N GLU o 237 " --> pdb=" O VAL o 231 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASP o 259 " --> pdb=" O LYS o 82 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE o 265 " --> pdb=" O PRO o 76 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N TYR o 267 " --> pdb=" O MET o 74 " (cutoff:3.500A) removed outlier: 5.302A 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 2078 hydrogen bonds defined for protein. 5940 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: 13.90 Time building geometry restraints manager: 21.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.73: 54692 1.73 - 2.28: 592 2.28 - 2.83: 14 2.83 - 3.38: 2 3.38 - 3.93: 8 Bond restraints: 55308 Sorted by residual: bond pdb=" C25 RRX x 102 " pdb=" C26 RRX x 102 " ideal model delta sigma weight residual 1.603 1.344 0.259 2.00e-02 2.50e+03 1.67e+02 bond pdb=" C25 RRX X 102 " pdb=" C26 RRX X 102 " ideal model delta sigma weight residual 1.603 1.345 0.258 2.00e-02 2.50e+03 1.66e+02 bond pdb=" C10 BCR Z 101 " pdb=" C11 BCR Z 101 " ideal model delta sigma weight residual 1.436 1.179 0.257 2.00e-02 2.50e+03 1.65e+02 bond pdb=" C10 BCR z 101 " pdb=" C11 BCR z 101 " ideal model delta sigma weight residual 1.436 1.179 0.257 2.00e-02 2.50e+03 1.65e+02 bond pdb=" C10 BCR C 514 " pdb=" C11 BCR C 514 " ideal model delta sigma weight residual 1.436 1.179 0.257 2.00e-02 2.50e+03 1.65e+02 ... (remaining 55303 not shown) Histogram of bond angle deviations from ideal: 67.33 - 89.50: 160 89.50 - 111.67: 27575 111.67 - 133.84: 47234 133.84 - 156.01: 491 156.01 - 178.19: 238 Bond angle restraints: 75698 Sorted by residual: angle pdb=" C10 BCR k 102 " pdb=" C11 BCR k 102 " pdb=" C12 BCR k 102 " ideal model delta sigma weight residual 122.66 178.19 -55.53 3.00e+00 1.11e-01 3.43e+02 angle pdb=" C10 BCR K 102 " pdb=" C11 BCR K 102 " pdb=" C12 BCR K 102 " ideal model delta sigma weight residual 122.66 178.18 -55.52 3.00e+00 1.11e-01 3.42e+02 angle pdb=" C10 BCR c 514 " pdb=" C11 BCR c 514 " pdb=" C12 BCR c 514 " ideal model delta sigma weight residual 122.66 177.91 -55.25 3.00e+00 1.11e-01 3.39e+02 angle pdb=" C10 BCR C 514 " pdb=" C11 BCR C 514 " pdb=" C12 BCR C 514 " ideal model delta sigma weight residual 122.66 177.90 -55.24 3.00e+00 1.11e-01 3.39e+02 angle pdb=" C10 BCR C 522 " pdb=" C11 BCR C 522 " pdb=" C12 BCR C 522 " ideal model delta sigma weight residual 122.66 177.47 -54.81 3.00e+00 1.11e-01 3.34e+02 ... (remaining 75693 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.52: 29442 31.52 - 63.05: 2509 63.05 - 94.57: 267 94.57 - 126.09: 126 126.09 - 157.61: 10 Dihedral angle restraints: 32354 sinusoidal: 16698 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 180.00 134.25 45.75 0 5.00e+00 4.00e-02 8.37e+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 180.00 134.28 45.72 0 5.00e+00 4.00e-02 8.36e+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 180.00 142.66 37.34 0 5.00e+00 4.00e-02 5.58e+01 ... (remaining 32351 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.898: 7706 0.898 - 1.796: 0 1.796 - 2.694: 0 2.694 - 3.591: 0 3.591 - 4.489: 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 2.10 -4.49 2.00e-01 2.50e+01 5.04e+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 2.10 -4.49 2.00e-01 2.50e+01 5.04e+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 -0.80 2.00e-01 2.50e+01 1.60e+01 ... (remaining 7705 not shown) Planarity restraints: 9172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 BCR K 102 " -0.278 2.00e-02 2.50e+03 1.59e-01 3.15e+02 pdb=" C11 BCR K 102 " 0.189 2.00e-02 2.50e+03 pdb=" C34 BCR K 102 " 0.065 2.00e-02 2.50e+03 pdb=" C8 BCR K 102 " 0.077 2.00e-02 2.50e+03 pdb=" C9 BCR K 102 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BCR k 102 " 0.278 2.00e-02 2.50e+03 1.59e-01 3.15e+02 pdb=" C11 BCR k 102 " -0.189 2.00e-02 2.50e+03 pdb=" C34 BCR k 102 " -0.065 2.00e-02 2.50e+03 pdb=" C8 BCR k 102 " -0.077 2.00e-02 2.50e+03 pdb=" C9 BCR k 102 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BCR c 522 " 0.268 2.00e-02 2.50e+03 1.54e-01 2.96e+02 pdb=" C11 BCR c 522 " -0.183 2.00e-02 2.50e+03 pdb=" C34 BCR c 522 " -0.044 2.00e-02 2.50e+03 pdb=" C8 BCR c 522 " -0.092 2.00e-02 2.50e+03 pdb=" C9 BCR c 522 " 0.051 2.00e-02 2.50e+03 ... (remaining 9169 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 785 2.51 - 3.11: 40984 3.11 - 3.71: 95945 3.71 - 4.30: 148501 4.30 - 4.90: 231660 Nonbonded interactions: 517875 Sorted by model distance: nonbonded pdb=" OE1 GLN v 64 " pdb="CA CA v 202 " model vdw 1.915 2.510 nonbonded pdb=" OE1 GLN V 64 " pdb="CA CA V 202 " model vdw 1.916 2.510 nonbonded pdb=" OG SER a 309 " pdb=" OE1 GLU v 27 " model vdw 2.007 2.440 nonbonded pdb=" OG SER A 309 " pdb=" OE1 GLU V 27 " model vdw 2.007 2.440 nonbonded pdb=" OE1 GLU V 128 " pdb=" O HOH V 301 " model vdw 2.029 2.440 ... (remaining 517870 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' and (resid 2 through 504 or resid 601 through 619 or (resid 623 throu \ gh 625 and (name C1 or name C1' or name C10 or name C11 or name C12 or name C2 o \ r name C2' or name C3 or name C3' or name C4 or name C4' or name C5 or name C5' \ or name C6 or name C6' or name C7 or name C8 or name C9 or name O1' or name O1B \ or name O2' or name O3' or name O5' or name O6')))) selection = (chain 'b' and (resid 2 through 504 or resid 601 through 619 or (resid 623 throu \ gh 625 and (name C1 or name C1' or name C10 or name C11 or name C12 or name C2 o \ r name C2' or name C3 or name C3' or name C4 or name C4' or name C5 or name C5' \ or name C6 or name C6' or name C7 or name C8 or name C9 or name O1' or name O1B \ or name O2' or name O3' or name O5' or name O6')))) } 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' selection = chain 'l' } ncs_group { reference = chain 'M' 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' and resid 1 through 30) selection = (chain 't' and resid 1 through 30) } 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 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: 0.030 Extract box with map and model: 12.750 Check model and map are aligned: 0.650 Set scattering table: 0.390 Process input model: 112.030 Find NCS groups from input model: 2.480 Set up NCS constraints: 0.780 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 140.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 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 0.542 55308 Z= 1.333 Angle : 2.385 55.525 75698 Z= 0.849 Chirality : 0.107 4.489 7708 Planarity : 0.011 0.159 9172 Dihedral : 22.232 157.614 22362 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.59 % Favored : 97.40 % Rotamer: Outliers : 1.99 % Allowed : 15.40 % Favored : 82.61 % 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: 0.92 (0.11), residues: 5452 helix: 1.25 (0.09), residues: 2952 sheet: 0.54 (0.34), residues: 218 loop : -0.13 (0.13), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 131 HIS 0.013 0.003 HIS C 417 PHE 0.039 0.003 PHE b 390 TYR 0.046 0.002 TYR o 36 ARG 0.010 0.001 ARG d 233 *********************** 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 951 residues out of total 4532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 861 time to evaluate : 4.253 Fit side-chains REVERT: A 265 PHE cc_start: 0.7913 (m-80) cc_final: 0.7501 (m-80) REVERT: B 347 LYS cc_start: 0.7517 (OUTLIER) cc_final: 0.7205 (mmtm) REVERT: D 228 ASP cc_start: 0.7122 (m-30) cc_final: 0.6829 (m-30) REVERT: T 8 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7619 (tp) REVERT: a 172 MET cc_start: 0.8882 (ttp) cc_final: 0.8601 (ttp) REVERT: b 347 LYS cc_start: 0.7582 (OUTLIER) cc_final: 0.7288 (mmtm) REVERT: h 12 ARG cc_start: 0.7710 (tpm170) cc_final: 0.7485 (tpm170) REVERT: h 14 LEU cc_start: 0.8205 (mt) cc_final: 0.7963 (mt) REVERT: t 8 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7740 (tp) REVERT: u 38 LEU cc_start: 0.6999 (mt) cc_final: 0.6736 (mp) outliers start: 90 outliers final: 21 residues processed: 900 average time/residue: 1.2557 time to fit residues: 1459.6048 Evaluate side-chains 832 residues out of total 4532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 807 time to evaluate : 4.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 73 THR Chi-restraints excluded: chain R residue 7 VAL Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain U residue 116 SER Chi-restraints excluded: chain U residue 121 SER Chi-restraints excluded: chain V residue 43 THR Chi-restraints excluded: chain V residue 65 CYS Chi-restraints excluded: chain Z residue 14 LEU Chi-restraints excluded: chain a residue 53 ILE Chi-restraints excluded: chain b residue 347 LYS Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain h residue 37 LEU Chi-restraints excluded: chain q residue 50 VAL Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain r residue 7 VAL Chi-restraints excluded: chain t residue 8 LEU Chi-restraints excluded: chain u residue 116 SER Chi-restraints excluded: chain u residue 121 SER Chi-restraints excluded: chain v residue 43 THR Chi-restraints excluded: chain v residue 65 CYS Chi-restraints excluded: chain z residue 14 LEU 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: 5.9990 chunk 225 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 274 optimal weight: 1.9990 chunk 217 optimal weight: 0.9980 chunk 420 optimal weight: 1.9990 chunk 162 optimal weight: 0.9990 chunk 255 optimal weight: 1.9990 chunk 312 optimal weight: 5.9990 chunk 486 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN A 130 GLN A 234 ASN A 310 GLN A 338 ASN B 179 GLN B 260 ASN B 281 GLN B 425 GLN B 489 GLN C 375 GLN C 405 ASN D 129 GLN E 23 HIS H 3 GLN H 47 GLN H 50 ASN I 31 ASN L 4 ASN L 8 ASN L 10 GLN O 103 GLN O 109 GLN O 176 ASN O 199 ASN O 227 GLN O 246 GLN Q 67 ASN Q 76 HIS Q 143 ASN U 80 ASN U 106 ASN V 50 GLN V 53 ASN V 119 ASN X 7 ASN Y 68 GLN Z 32 ASN a 16 GLN a 19 GLN a 130 GLN a 234 ASN a 310 GLN a 338 ASN b 76 ASN b 179 GLN b 260 ASN b 281 GLN b 409 GLN b 489 GLN c 142 ASN c 375 GLN c 405 ASN d 129 GLN e 23 HIS h 3 GLN h 47 GLN h 50 ASN i 31 ASN l 4 ASN l 8 ASN l 10 GLN o 109 GLN o 176 ASN o 199 ASN o 227 GLN o 246 GLN q 67 ASN q 76 HIS q 130 GLN q 143 ASN u 80 ASN u 106 ASN v 50 GLN v 119 ASN x 7 ASN y 68 GLN z 32 ASN z 58 ASN Total number of N/Q/H flips: 79 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 55308 Z= 0.242 Angle : 0.827 28.922 75698 Z= 0.357 Chirality : 0.047 0.302 7708 Planarity : 0.006 0.061 9172 Dihedral : 19.934 137.872 12858 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.57 % Allowed : 14.27 % Favored : 83.16 % 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: 0.94 (0.11), residues: 5452 helix: 1.20 (0.09), residues: 2970 sheet: 0.60 (0.34), residues: 218 loop : -0.03 (0.13), residues: 2264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 131 HIS 0.011 0.003 HIS B 466 PHE 0.036 0.002 PHE c 304 TYR 0.020 0.002 TYR B 172 ARG 0.007 0.000 ARG o 269 *********************** 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 953 residues out of total 4532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 837 time to evaluate : 4.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 122 ARG cc_start: 0.6687 (OUTLIER) cc_final: 0.5851 (ttt90) REVERT: D 228 ASP cc_start: 0.7036 (m-30) cc_final: 0.6773 (m-30) REVERT: F 20 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7739 (tt) REVERT: T 2 GLU cc_start: 0.7492 (pm20) cc_final: 0.7258 (pm20) REVERT: T 8 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7569 (tp) REVERT: c 98 PHE cc_start: 0.7794 (m-80) cc_final: 0.7469 (m-80) REVERT: c 276 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.8148 (t80) REVERT: c 456 MET cc_start: 0.8262 (mtt) cc_final: 0.7630 (mtt) REVERT: d 228 ASP cc_start: 0.6985 (m-30) cc_final: 0.6738 (m-30) REVERT: t 8 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7658 (tp) outliers start: 116 outliers final: 47 residues processed: 905 average time/residue: 1.2310 time to fit residues: 1442.9224 Evaluate side-chains 854 residues out of total 4532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 802 time to evaluate : 4.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain O residue 121 THR Chi-restraints excluded: chain O residue 143 GLU Chi-restraints excluded: chain O residue 208 ASP Chi-restraints excluded: chain Q residue 73 THR Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 112 VAL Chi-restraints excluded: chain V residue 43 THR Chi-restraints excluded: chain V residue 116 LEU Chi-restraints excluded: chain V residue 121 SER Chi-restraints excluded: chain Z residue 14 LEU Chi-restraints excluded: chain b residue 236 THR Chi-restraints excluded: chain b residue 260 ASN Chi-restraints excluded: chain b residue 297 SER Chi-restraints excluded: chain b residue 362 PHE Chi-restraints excluded: chain b residue 374 ASP Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 227 ILE Chi-restraints excluded: chain c residue 229 LEU Chi-restraints excluded: chain c residue 276 PHE Chi-restraints excluded: chain c residue 294 MET Chi-restraints excluded: chain c residue 383 MET Chi-restraints excluded: chain d residue 345 VAL Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain h residue 30 VAL Chi-restraints excluded: chain h residue 37 LEU Chi-restraints excluded: chain k residue 24 LEU Chi-restraints excluded: chain o residue 143 GLU Chi-restraints excluded: chain o residue 208 ASP Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain t residue 8 LEU Chi-restraints excluded: chain u residue 89 VAL Chi-restraints excluded: chain u residue 112 VAL Chi-restraints excluded: chain v residue 28 LEU Chi-restraints excluded: chain v residue 94 VAL Chi-restraints excluded: chain v residue 116 LEU Chi-restraints excluded: chain v residue 121 SER Chi-restraints excluded: chain v residue 135 ASP Chi-restraints excluded: chain z residue 14 LEU Chi-restraints excluded: chain z residue 54 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 270 optimal weight: 6.9990 chunk 151 optimal weight: 1.9990 chunk 405 optimal weight: 6.9990 chunk 331 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 487 optimal weight: 1.9990 chunk 526 optimal weight: 0.9990 chunk 434 optimal weight: 5.9990 chunk 483 optimal weight: 6.9990 chunk 166 optimal weight: 7.9990 chunk 391 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN A 310 GLN B 179 GLN B 338 GLN B 409 GLN C 142 ASN H 3 GLN ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 ASN L 10 GLN O 176 ASN O 199 ASN O 227 GLN ** U 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 50 GLN V 53 ASN a 19 GLN a 310 GLN b 260 ASN b 338 GLN b 409 GLN b 425 GLN c 314 ASN h 3 GLN k 15 GLN l 10 GLN o 176 ASN o 199 ASN o 227 GLN q 130 GLN ** u 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 50 GLN v 53 ASN z 58 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 55308 Z= 0.332 Angle : 0.886 26.854 75698 Z= 0.393 Chirality : 0.051 0.361 7708 Planarity : 0.007 0.063 9172 Dihedral : 19.219 131.971 12835 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.81 % Favored : 97.16 % Rotamer: Outliers : 2.41 % Allowed : 14.49 % Favored : 83.10 % 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: 0.67 (0.11), residues: 5452 helix: 0.96 (0.09), residues: 2942 sheet: 0.53 (0.35), residues: 216 loop : -0.11 (0.13), residues: 2294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP a 131 HIS 0.011 0.003 HIS B 466 PHE 0.042 0.003 PHE c 304 TYR 0.025 0.003 TYR B 273 ARG 0.007 0.001 ARG b 272 *********************** 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 947 residues out of total 4532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 838 time to evaluate : 4.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 122 ARG cc_start: 0.6864 (OUTLIER) cc_final: 0.6010 (ttt90) REVERT: C 276 PHE cc_start: 0.8869 (OUTLIER) cc_final: 0.7996 (t80) REVERT: D 228 ASP cc_start: 0.7005 (m-30) cc_final: 0.6777 (m-30) REVERT: F 20 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7769 (tt) REVERT: T 8 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7709 (tp) REVERT: T 25 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6924 (tp30) REVERT: c 192 ASN cc_start: 0.7570 (t0) cc_final: 0.7293 (t0) REVERT: c 276 PHE cc_start: 0.8857 (OUTLIER) cc_final: 0.8008 (t80) REVERT: c 456 MET cc_start: 0.8324 (mtt) cc_final: 0.7590 (mtt) REVERT: d 24 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.7060 (mtt180) REVERT: d 228 ASP cc_start: 0.7004 (m-30) cc_final: 0.6702 (m-30) REVERT: t 8 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7695 (tp) REVERT: t 25 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6830 (tp30) outliers start: 109 outliers final: 65 residues processed: 899 average time/residue: 1.2563 time to fit residues: 1460.2311 Evaluate side-chains 894 residues out of total 4532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 820 time to evaluate : 4.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 276 PHE Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 233 ARG Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain I residue 16 ILE Chi-restraints excluded: chain J residue 7 ILE Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain L residue 2 ASP Chi-restraints excluded: chain O residue 38 ASP Chi-restraints excluded: chain O residue 87 ASN Chi-restraints excluded: chain O residue 121 THR Chi-restraints excluded: chain O residue 143 GLU Chi-restraints excluded: chain O residue 157 THR Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 193 LEU Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 73 THR Chi-restraints excluded: chain Q residue 93 LEU Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain V residue 94 VAL Chi-restraints excluded: chain V residue 116 LEU Chi-restraints excluded: chain V residue 135 ASP Chi-restraints excluded: chain Z residue 14 LEU Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain b residue 236 THR Chi-restraints excluded: chain b residue 300 GLU Chi-restraints excluded: chain b residue 362 PHE Chi-restraints excluded: chain b residue 374 ASP Chi-restraints excluded: chain c residue 76 LEU Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 227 ILE Chi-restraints excluded: chain c residue 276 PHE Chi-restraints excluded: chain c residue 294 MET Chi-restraints excluded: chain c residue 383 MET Chi-restraints excluded: chain d residue 24 ARG Chi-restraints excluded: chain d residue 233 ARG Chi-restraints excluded: chain f residue 11 THR Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain h residue 30 VAL Chi-restraints excluded: chain h residue 37 LEU Chi-restraints excluded: chain j residue 23 VAL Chi-restraints excluded: chain k residue 24 LEU Chi-restraints excluded: chain o residue 121 THR Chi-restraints excluded: chain o residue 143 GLU Chi-restraints excluded: chain q residue 50 VAL Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain q residue 93 LEU Chi-restraints excluded: chain t residue 8 LEU Chi-restraints excluded: chain t residue 25 GLU Chi-restraints excluded: chain u residue 89 VAL Chi-restraints excluded: chain u residue 112 VAL Chi-restraints excluded: chain v residue 28 LEU Chi-restraints excluded: chain v residue 43 THR Chi-restraints excluded: chain v residue 94 VAL Chi-restraints excluded: chain v residue 116 LEU Chi-restraints excluded: chain v residue 135 ASP Chi-restraints excluded: chain v residue 153 ARG Chi-restraints excluded: chain z residue 14 LEU Chi-restraints excluded: chain z residue 54 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 481 optimal weight: 6.9990 chunk 366 optimal weight: 10.0000 chunk 253 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 232 optimal weight: 0.6980 chunk 327 optimal weight: 3.9990 chunk 489 optimal weight: 10.0000 chunk 518 optimal weight: 0.7980 chunk 255 optimal weight: 3.9990 chunk 463 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN A 310 GLN B 179 GLN C 314 ASN H 3 GLN L 4 ASN L 10 GLN O 176 ASN O 199 ASN O 227 GLN ** U 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 50 GLN V 53 ASN a 19 GLN a 310 GLN b 409 GLN c 314 ASN h 3 GLN l 4 ASN l 10 GLN o 199 ASN o 227 GLN q 130 GLN ** u 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 50 GLN v 53 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 55308 Z= 0.273 Angle : 0.811 26.093 75698 Z= 0.359 Chirality : 0.048 0.370 7708 Planarity : 0.006 0.062 9172 Dihedral : 18.331 128.897 12834 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.68 % Allowed : 14.31 % Favored : 83.01 % 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: 0.74 (0.11), residues: 5452 helix: 1.03 (0.09), residues: 2954 sheet: 0.45 (0.35), residues: 218 loop : -0.09 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP a 131 HIS 0.008 0.003 HIS B 216 PHE 0.037 0.002 PHE c 304 TYR 0.023 0.002 TYR B 273 ARG 0.006 0.001 ARG l 9 *********************** 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 955 residues out of total 4532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 834 time to evaluate : 4.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 276 PHE cc_start: 0.8877 (OUTLIER) cc_final: 0.7983 (t80) REVERT: D 24 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.7030 (mtt180) REVERT: D 228 ASP cc_start: 0.6997 (m-30) cc_final: 0.6765 (m-30) REVERT: E 17 ILE cc_start: 0.7385 (OUTLIER) cc_final: 0.7176 (mp) REVERT: L 9 ARG cc_start: 0.6851 (mtm-85) cc_final: 0.6382 (mtp180) REVERT: Q 94 LEU cc_start: 0.0957 (OUTLIER) cc_final: 0.0458 (tm) REVERT: T 8 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7618 (tp) REVERT: T 25 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6822 (tp30) REVERT: c 201 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7340 (mp) REVERT: c 276 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.8004 (t80) REVERT: c 456 MET cc_start: 0.8366 (mtt) cc_final: 0.7579 (mtt) REVERT: d 228 ASP cc_start: 0.6943 (m-30) cc_final: 0.6620 (m-30) REVERT: k 30 PHE cc_start: 0.7209 (m-10) cc_final: 0.6995 (m-10) REVERT: t 8 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7642 (tp) REVERT: t 25 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6835 (tp30) outliers start: 121 outliers final: 70 residues processed: 906 average time/residue: 1.2571 time to fit residues: 1471.3675 Evaluate side-chains 893 residues out of total 4532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 813 time to evaluate : 4.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 276 PHE Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 233 ARG Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain I residue 16 ILE Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain L residue 2 ASP Chi-restraints excluded: chain O residue 38 ASP Chi-restraints excluded: chain O residue 87 ASN Chi-restraints excluded: chain O residue 143 GLU Chi-restraints excluded: chain O residue 193 LEU Chi-restraints excluded: chain O residue 255 LYS Chi-restraints excluded: chain Q residue 73 THR Chi-restraints excluded: chain Q residue 93 LEU Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain U residue 47 THR Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 90 LEU Chi-restraints excluded: chain U residue 112 VAL Chi-restraints excluded: chain V residue 28 LEU Chi-restraints excluded: chain V residue 43 THR Chi-restraints excluded: chain V residue 94 VAL Chi-restraints excluded: chain V residue 116 LEU Chi-restraints excluded: chain V residue 135 ASP Chi-restraints excluded: chain b residue 236 THR Chi-restraints excluded: chain b residue 362 PHE Chi-restraints excluded: chain b residue 374 ASP Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain c residue 229 LEU Chi-restraints excluded: chain c residue 276 PHE Chi-restraints excluded: chain c residue 294 MET Chi-restraints excluded: chain c residue 317 SER Chi-restraints excluded: chain c residue 383 MET Chi-restraints excluded: chain d residue 264 LYS Chi-restraints excluded: chain f residue 11 THR Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain h residue 30 VAL Chi-restraints excluded: chain h residue 37 LEU Chi-restraints excluded: chain k residue 24 LEU Chi-restraints excluded: chain o residue 87 ASN Chi-restraints excluded: chain o residue 143 GLU Chi-restraints excluded: chain o residue 163 THR Chi-restraints excluded: chain o residue 193 LEU Chi-restraints excluded: chain o residue 255 LYS Chi-restraints excluded: chain q residue 50 VAL Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain q residue 93 LEU Chi-restraints excluded: chain t residue 8 LEU Chi-restraints excluded: chain t residue 25 GLU Chi-restraints excluded: chain u residue 47 THR Chi-restraints excluded: chain u residue 89 VAL Chi-restraints excluded: chain u residue 90 LEU Chi-restraints excluded: chain u residue 112 VAL Chi-restraints excluded: chain v residue 28 LEU Chi-restraints excluded: chain v residue 43 THR Chi-restraints excluded: chain v residue 94 VAL Chi-restraints excluded: chain v residue 116 LEU Chi-restraints excluded: chain v residue 135 ASP Chi-restraints excluded: chain v residue 153 ARG Chi-restraints excluded: chain z residue 3 ILE Chi-restraints excluded: chain z residue 14 LEU Chi-restraints excluded: chain z residue 54 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 431 optimal weight: 6.9990 chunk 294 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 385 optimal weight: 2.9990 chunk 213 optimal weight: 0.8980 chunk 442 optimal weight: 0.0370 chunk 358 optimal weight: 0.0980 chunk 0 optimal weight: 7.9990 chunk 264 optimal weight: 0.2980 chunk 465 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN A 19 GLN A 310 GLN B 179 GLN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 ASN D 98 GLN H 3 GLN L 10 GLN O 176 ASN O 199 ASN O 227 GLN ** U 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 50 GLN V 53 ASN a 19 GLN a 310 GLN b 76 ASN b 425 GLN ** d 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 3 GLN l 4 ASN l 10 GLN o 199 ASN o 227 GLN ** u 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 50 GLN v 53 ASN x 32 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 55308 Z= 0.157 Angle : 0.672 24.129 75698 Z= 0.292 Chirality : 0.042 0.401 7708 Planarity : 0.005 0.058 9172 Dihedral : 16.702 124.899 12832 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.71 % Allowed : 15.64 % Favored : 82.65 % 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: 1.14 (0.11), residues: 5452 helix: 1.49 (0.09), residues: 2956 sheet: 0.18 (0.33), residues: 236 loop : -0.07 (0.13), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 131 HIS 0.006 0.001 HIS b 201 PHE 0.027 0.001 PHE B 246 TYR 0.017 0.001 TYR b 279 ARG 0.009 0.000 ARG o 269 *********************** 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 918 residues out of total 4532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 841 time to evaluate : 4.395 Fit side-chains revert: symmetry clash REVERT: C 276 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.7916 (t80) REVERT: D 228 ASP cc_start: 0.6859 (m-30) cc_final: 0.6622 (m-30) REVERT: L 9 ARG cc_start: 0.6794 (mtm-85) cc_final: 0.6427 (mtp180) REVERT: Q 86 MET cc_start: 0.3978 (mtm) cc_final: 0.3630 (ptp) REVERT: R 4 ARG cc_start: 0.7189 (mtm180) cc_final: 0.6928 (mtm180) REVERT: V 33 ARG cc_start: 0.7619 (mtm110) cc_final: 0.7330 (mtm110) REVERT: b 385 ARG cc_start: 0.7965 (mpp-170) cc_final: 0.7732 (mpp-170) REVERT: c 276 PHE cc_start: 0.8781 (OUTLIER) cc_final: 0.7882 (t80) REVERT: k 30 PHE cc_start: 0.7194 (m-10) cc_final: 0.6971 (m-10) REVERT: l 9 ARG cc_start: 0.6629 (mtm-85) cc_final: 0.6279 (mtp180) REVERT: q 94 LEU cc_start: 0.0806 (OUTLIER) cc_final: 0.0389 (tp) REVERT: q 115 LEU cc_start: 0.6634 (tp) cc_final: 0.6422 (tp) outliers start: 77 outliers final: 33 residues processed: 886 average time/residue: 1.2930 time to fit residues: 1484.6144 Evaluate side-chains 847 residues out of total 4532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 811 time to evaluate : 4.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 276 PHE Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain L residue 2 ASP Chi-restraints excluded: chain O residue 38 ASP Chi-restraints excluded: chain O residue 87 ASN Chi-restraints excluded: chain O residue 143 GLU Chi-restraints excluded: chain O residue 157 THR Chi-restraints excluded: chain Q residue 73 THR Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 112 VAL Chi-restraints excluded: chain V residue 43 THR Chi-restraints excluded: chain b residue 362 PHE Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 276 PHE Chi-restraints excluded: chain c residue 294 MET Chi-restraints excluded: chain d residue 233 ARG Chi-restraints excluded: chain d residue 345 VAL Chi-restraints excluded: chain f residue 11 THR Chi-restraints excluded: chain h residue 30 VAL Chi-restraints excluded: chain l residue 2 ASP Chi-restraints excluded: chain o residue 87 ASN Chi-restraints excluded: chain o residue 157 THR Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain u residue 89 VAL Chi-restraints excluded: chain u residue 112 VAL Chi-restraints excluded: chain v residue 28 LEU Chi-restraints excluded: chain v residue 43 THR Chi-restraints excluded: chain v residue 94 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 174 optimal weight: 2.9990 chunk 466 optimal weight: 8.9990 chunk 102 optimal weight: 9.9990 chunk 304 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 518 optimal weight: 2.9990 chunk 430 optimal weight: 0.3980 chunk 240 optimal weight: 0.2980 chunk 43 optimal weight: 10.0000 chunk 171 optimal weight: 7.9990 chunk 272 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN A 19 GLN A 310 GLN B 76 ASN H 3 GLN L 4 ASN L 10 GLN O 176 ASN O 199 ASN ** O 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 230 GLN R 22 ASN ** U 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 50 GLN V 53 ASN X 32 GLN a 16 GLN a 19 GLN a 310 GLN b 76 ASN b 179 GLN b 409 GLN b 425 GLN h 3 GLN h 47 GLN l 10 GLN o 153 ASN o 176 ASN o 199 ASN o 227 GLN ** u 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 50 GLN v 53 ASN v 103 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 55308 Z= 0.193 Angle : 0.703 24.160 75698 Z= 0.310 Chirality : 0.043 0.414 7708 Planarity : 0.005 0.059 9172 Dihedral : 16.383 126.497 12824 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.84 % Allowed : 16.02 % Favored : 82.14 % 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: 1.17 (0.11), residues: 5452 helix: 1.44 (0.09), residues: 2960 sheet: 0.22 (0.33), residues: 230 loop : 0.05 (0.13), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP a 131 HIS 0.007 0.002 HIS B 466 PHE 0.029 0.002 PHE B 246 TYR 0.018 0.002 TYR b 273 ARG 0.007 0.000 ARG o 269 *********************** 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 908 residues out of total 4532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 825 time to evaluate : 4.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 347 LYS cc_start: 0.7188 (mtpp) cc_final: 0.6507 (mttp) REVERT: C 276 PHE cc_start: 0.8851 (OUTLIER) cc_final: 0.7893 (t80) REVERT: D 24 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.7013 (mtt180) REVERT: L 9 ARG cc_start: 0.6817 (mtm-85) cc_final: 0.6468 (mtp180) REVERT: Q 94 LEU cc_start: 0.0907 (OUTLIER) cc_final: 0.0405 (tm) REVERT: T 25 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6855 (tp30) REVERT: V 94 VAL cc_start: 0.7688 (t) cc_final: 0.7401 (p) REVERT: b 385 ARG cc_start: 0.7967 (mpp-170) cc_final: 0.7748 (mpp-170) REVERT: c 201 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7324 (mp) REVERT: c 276 PHE cc_start: 0.8789 (OUTLIER) cc_final: 0.7871 (t80) REVERT: k 30 PHE cc_start: 0.7208 (m-10) cc_final: 0.6946 (m-10) REVERT: l 9 ARG cc_start: 0.6695 (mtm-85) cc_final: 0.6364 (mtp180) REVERT: q 94 LEU cc_start: 0.0783 (OUTLIER) cc_final: 0.0475 (tm) REVERT: q 130 GLN cc_start: 0.5268 (OUTLIER) cc_final: 0.4720 (mp10) outliers start: 83 outliers final: 45 residues processed: 876 average time/residue: 1.3077 time to fit residues: 1475.3558 Evaluate side-chains 853 residues out of total 4532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 800 time to evaluate : 4.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 276 PHE Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain O residue 38 ASP Chi-restraints excluded: chain O residue 87 ASN Chi-restraints excluded: chain O residue 143 GLU Chi-restraints excluded: chain O residue 157 THR Chi-restraints excluded: chain O residue 166 ASN Chi-restraints excluded: chain O residue 208 ASP Chi-restraints excluded: chain O residue 212 THR Chi-restraints excluded: chain Q residue 73 THR Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 112 VAL Chi-restraints excluded: chain U residue 121 SER Chi-restraints excluded: chain V residue 28 LEU Chi-restraints excluded: chain V residue 43 THR Chi-restraints excluded: chain V residue 116 LEU Chi-restraints excluded: chain b residue 362 PHE Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain c residue 229 LEU Chi-restraints excluded: chain c residue 276 PHE Chi-restraints excluded: chain c residue 294 MET Chi-restraints excluded: chain d residue 233 ARG Chi-restraints excluded: chain d residue 345 VAL Chi-restraints excluded: chain d residue 352 LEU Chi-restraints excluded: chain f residue 11 THR Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain h residue 30 VAL Chi-restraints excluded: chain i residue 16 ILE Chi-restraints excluded: chain o residue 87 ASN Chi-restraints excluded: chain o residue 143 GLU Chi-restraints excluded: chain o residue 208 ASP Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain q residue 130 GLN Chi-restraints excluded: chain u residue 89 VAL Chi-restraints excluded: chain u residue 112 VAL Chi-restraints excluded: chain v residue 28 LEU Chi-restraints excluded: chain v residue 94 VAL Chi-restraints excluded: chain v residue 116 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 499 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 295 optimal weight: 6.9990 chunk 378 optimal weight: 6.9990 chunk 293 optimal weight: 9.9990 chunk 436 optimal weight: 9.9990 chunk 289 optimal weight: 7.9990 chunk 516 optimal weight: 0.9980 chunk 323 optimal weight: 2.9990 chunk 314 optimal weight: 1.9990 chunk 238 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN A 19 GLN A 310 GLN B 76 ASN B 438 ASN C 314 ASN H 3 GLN K 15 GLN L 10 GLN ** O 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 199 ASN O 227 GLN ** O 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 50 GLN V 53 ASN a 16 GLN a 19 GLN a 310 GLN b 179 GLN b 409 GLN h 3 GLN l 4 ASN l 10 GLN o 153 ASN o 176 ASN o 199 ASN o 227 GLN ** o 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 22 ASN ** u 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 50 GLN v 53 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 55308 Z= 0.300 Angle : 0.820 25.052 75698 Z= 0.367 Chirality : 0.049 0.440 7708 Planarity : 0.007 0.062 9172 Dihedral : 16.890 131.957 12824 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.37 % Allowed : 15.44 % Favored : 82.19 % 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: 1.15 (0.09), residues: 2942 sheet: 0.05 (0.32), residues: 244 loop : -0.02 (0.13), residues: 2266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP a 131 HIS 0.010 0.003 HIS F 23 PHE 0.041 0.003 PHE H 41 TYR 0.024 0.003 TYR b 273 ARG 0.006 0.001 ARG v 122 *********************** 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 937 residues out of total 4532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 830 time to evaluate : 4.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 276 PHE cc_start: 0.8869 (OUTLIER) cc_final: 0.7977 (t80) REVERT: D 24 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.7034 (mtt180) REVERT: L 9 ARG cc_start: 0.6856 (mtm-85) cc_final: 0.6475 (mtp180) REVERT: Q 86 MET cc_start: 0.4078 (mtm) cc_final: 0.3672 (ptp) REVERT: Q 94 LEU cc_start: 0.0873 (OUTLIER) cc_final: 0.0559 (tm) REVERT: T 25 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6832 (tp30) REVERT: b 260 ASN cc_start: 0.8176 (OUTLIER) cc_final: 0.7721 (p0) REVERT: c 201 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7335 (mp) REVERT: c 276 PHE cc_start: 0.8851 (OUTLIER) cc_final: 0.7935 (t80) REVERT: c 456 MET cc_start: 0.8352 (mtt) cc_final: 0.7552 (mtt) REVERT: q 94 LEU cc_start: 0.0810 (OUTLIER) cc_final: 0.0465 (tm) REVERT: t 25 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6890 (tp30) outliers start: 107 outliers final: 62 residues processed: 892 average time/residue: 1.2787 time to fit residues: 1474.8379 Evaluate side-chains 881 residues out of total 4532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 810 time to evaluate : 4.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 276 PHE Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain O residue 38 ASP Chi-restraints excluded: chain O residue 87 ASN Chi-restraints excluded: chain O residue 143 GLU Chi-restraints excluded: chain O residue 157 THR Chi-restraints excluded: chain O residue 166 ASN Chi-restraints excluded: chain O residue 212 THR Chi-restraints excluded: chain O residue 255 LYS Chi-restraints excluded: chain Q residue 73 THR Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 90 LEU Chi-restraints excluded: chain U residue 112 VAL Chi-restraints excluded: chain U residue 121 SER Chi-restraints excluded: chain V residue 28 LEU Chi-restraints excluded: chain V residue 43 THR Chi-restraints excluded: chain V residue 116 LEU Chi-restraints excluded: chain Z residue 14 LEU Chi-restraints excluded: chain b residue 260 ASN Chi-restraints excluded: chain b residue 300 GLU Chi-restraints excluded: chain b residue 362 PHE Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain c residue 276 PHE Chi-restraints excluded: chain c residue 294 MET Chi-restraints excluded: chain c residue 317 SER Chi-restraints excluded: chain d residue 233 ARG Chi-restraints excluded: chain d residue 352 LEU Chi-restraints excluded: chain e residue 72 ILE Chi-restraints excluded: chain f residue 11 THR Chi-restraints excluded: chain f residue 20 LEU Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain h residue 30 VAL Chi-restraints excluded: chain h residue 39 LEU Chi-restraints excluded: chain i residue 16 ILE Chi-restraints excluded: chain j residue 7 ILE Chi-restraints excluded: chain j residue 38 SER Chi-restraints excluded: chain o residue 87 ASN Chi-restraints excluded: chain o residue 143 GLU Chi-restraints excluded: chain o residue 157 THR Chi-restraints excluded: chain o residue 212 THR Chi-restraints excluded: chain o residue 255 LYS Chi-restraints excluded: chain q residue 50 VAL Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain q residue 103 THR Chi-restraints excluded: chain t residue 25 GLU Chi-restraints excluded: chain u residue 89 VAL Chi-restraints excluded: chain u residue 90 LEU Chi-restraints excluded: chain u residue 112 VAL Chi-restraints excluded: chain v residue 28 LEU Chi-restraints excluded: chain v residue 94 VAL Chi-restraints excluded: chain v residue 116 LEU Chi-restraints excluded: chain v residue 135 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 319 optimal weight: 1.9990 chunk 206 optimal weight: 4.9990 chunk 308 optimal weight: 0.6980 chunk 155 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 328 optimal weight: 4.9990 chunk 351 optimal weight: 2.9990 chunk 255 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 406 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN A 19 GLN A 310 GLN B 76 ASN H 3 GLN L 4 ASN L 10 GLN O 153 ASN O 176 ASN O 199 ASN O 227 GLN O 230 GLN R 22 ASN ** U 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 50 GLN V 53 ASN a 16 GLN a 19 GLN a 310 GLN b 76 ASN b 179 GLN b 409 GLN h 3 GLN h 47 GLN l 4 ASN l 10 GLN o 153 ASN o 176 ASN o 199 ASN o 227 GLN ** o 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 50 GLN v 53 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 55308 Z= 0.217 Angle : 0.732 24.481 75698 Z= 0.326 Chirality : 0.045 0.399 7708 Planarity : 0.006 0.061 9172 Dihedral : 16.390 132.135 12824 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.91 % Allowed : 16.02 % Favored : 82.08 % 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: 0.98 (0.11), residues: 5452 helix: 1.24 (0.09), residues: 2974 sheet: 0.39 (0.33), residues: 222 loop : -0.00 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP a 131 HIS 0.007 0.002 HIS B 100 PHE 0.033 0.002 PHE C 304 TYR 0.019 0.002 TYR b 273 ARG 0.013 0.000 ARG o 269 *********************** 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 904 residues out of total 4532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 818 time to evaluate : 4.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 291 GLN cc_start: 0.6995 (mm-40) cc_final: 0.6791 (mm-40) REVERT: C 276 PHE cc_start: 0.8863 (OUTLIER) cc_final: 0.7963 (t80) REVERT: D 24 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.7021 (mtt180) REVERT: L 9 ARG cc_start: 0.6826 (mtm-85) cc_final: 0.6474 (mtp180) REVERT: Q 86 MET cc_start: 0.4026 (mtm) cc_final: 0.3598 (ptp) REVERT: Q 94 LEU cc_start: 0.0900 (OUTLIER) cc_final: 0.0577 (tm) REVERT: T 25 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6819 (tp30) REVERT: c 201 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7335 (mp) REVERT: c 276 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.7915 (t80) REVERT: l 9 ARG cc_start: 0.6553 (mtm110) cc_final: 0.6241 (mtp180) REVERT: q 94 LEU cc_start: 0.0862 (OUTLIER) cc_final: 0.0427 (tp) outliers start: 86 outliers final: 53 residues processed: 873 average time/residue: 1.2879 time to fit residues: 1453.0835 Evaluate side-chains 866 residues out of total 4532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 806 time to evaluate : 4.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 276 PHE Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 233 ARG Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain O residue 38 ASP Chi-restraints excluded: chain O residue 87 ASN Chi-restraints excluded: chain O residue 143 GLU Chi-restraints excluded: chain O residue 153 ASN Chi-restraints excluded: chain O residue 157 THR Chi-restraints excluded: chain O residue 166 ASN Chi-restraints excluded: chain O residue 212 THR Chi-restraints excluded: chain Q residue 73 THR Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 112 VAL Chi-restraints excluded: chain U residue 121 SER Chi-restraints excluded: chain V residue 28 LEU Chi-restraints excluded: chain V residue 43 THR Chi-restraints excluded: chain V residue 116 LEU Chi-restraints excluded: chain Z residue 14 LEU Chi-restraints excluded: chain b residue 362 PHE Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain c residue 229 LEU Chi-restraints excluded: chain c residue 276 PHE Chi-restraints excluded: chain c residue 294 MET Chi-restraints excluded: chain d residue 233 ARG Chi-restraints excluded: chain d residue 352 LEU Chi-restraints excluded: chain f residue 11 THR Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain h residue 30 VAL Chi-restraints excluded: chain i residue 16 ILE Chi-restraints excluded: chain k residue 24 LEU Chi-restraints excluded: chain o residue 87 ASN Chi-restraints excluded: chain o residue 143 GLU Chi-restraints excluded: chain o residue 157 THR Chi-restraints excluded: chain o residue 212 THR Chi-restraints excluded: chain q residue 50 VAL Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain u residue 89 VAL Chi-restraints excluded: chain u residue 112 VAL Chi-restraints excluded: chain v residue 28 LEU Chi-restraints excluded: chain v residue 94 VAL Chi-restraints excluded: chain v residue 116 LEU Chi-restraints excluded: chain v residue 135 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 469 optimal weight: 9.9990 chunk 494 optimal weight: 0.6980 chunk 451 optimal weight: 3.9990 chunk 481 optimal weight: 5.9990 chunk 289 optimal weight: 7.9990 chunk 209 optimal weight: 10.0000 chunk 378 optimal weight: 6.9990 chunk 147 optimal weight: 7.9990 chunk 435 optimal weight: 1.9990 chunk 455 optimal weight: 9.9990 chunk 479 optimal weight: 8.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN A 19 GLN A 310 GLN B 76 ASN C 314 ASN H 3 GLN L 10 GLN O 153 ASN O 176 ASN O 199 ASN O 227 GLN ** O 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 50 GLN V 53 ASN a 16 GLN a 19 GLN a 310 GLN b 179 GLN b 409 GLN c 314 ASN h 3 GLN l 10 GLN o 153 ASN o 176 ASN o 199 ASN ** o 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 50 GLN v 53 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 55308 Z= 0.401 Angle : 0.934 26.473 75698 Z= 0.421 Chirality : 0.053 0.388 7708 Planarity : 0.008 0.077 9172 Dihedral : 17.278 143.748 12824 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.93 % Favored : 97.03 % Rotamer: Outliers : 2.15 % Allowed : 15.99 % Favored : 81.86 % 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: 0.49 (0.11), residues: 5452 helix: 0.79 (0.09), residues: 2954 sheet: -0.04 (0.33), residues: 240 loop : -0.11 (0.13), residues: 2258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP a 131 HIS 0.013 0.003 HIS F 23 PHE 0.045 0.003 PHE H 41 TYR 0.026 0.003 TYR b 273 ARG 0.010 0.001 ARG o 269 *********************** 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 916 residues out of total 4532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 819 time to evaluate : 4.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 276 PHE cc_start: 0.8880 (OUTLIER) cc_final: 0.8649 (t80) REVERT: D 24 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.7132 (mtt180) REVERT: D 228 ASP cc_start: 0.6870 (m-30) cc_final: 0.6646 (m-30) REVERT: L 9 ARG cc_start: 0.6876 (mtm-85) cc_final: 0.6490 (mtp180) REVERT: T 8 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7727 (tp) REVERT: T 25 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6850 (tp30) REVERT: c 201 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7339 (mp) REVERT: c 276 PHE cc_start: 0.8865 (OUTLIER) cc_final: 0.7973 (t80) REVERT: c 456 MET cc_start: 0.8339 (mtt) cc_final: 0.7477 (mtt) REVERT: t 8 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7745 (tp) REVERT: t 25 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6787 (tp30) outliers start: 97 outliers final: 68 residues processed: 874 average time/residue: 1.2751 time to fit residues: 1439.9414 Evaluate side-chains 890 residues out of total 4532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 814 time to evaluate : 4.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 276 PHE Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain I residue 16 ILE Chi-restraints excluded: chain J residue 7 ILE Chi-restraints excluded: chain J residue 38 SER Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain O residue 38 ASP Chi-restraints excluded: chain O residue 87 ASN Chi-restraints excluded: chain O residue 143 GLU Chi-restraints excluded: chain O residue 166 ASN Chi-restraints excluded: chain O residue 212 THR Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 73 THR Chi-restraints excluded: chain Q residue 144 LEU Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 90 LEU Chi-restraints excluded: chain U residue 121 SER Chi-restraints excluded: chain V residue 28 LEU Chi-restraints excluded: chain V residue 43 THR Chi-restraints excluded: chain V residue 116 LEU Chi-restraints excluded: chain V residue 135 ASP Chi-restraints excluded: chain Z residue 14 LEU Chi-restraints excluded: chain b residue 300 GLU Chi-restraints excluded: chain b residue 362 PHE Chi-restraints excluded: chain b residue 376 VAL Chi-restraints excluded: chain c residue 76 LEU Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain c residue 229 LEU Chi-restraints excluded: chain c residue 276 PHE Chi-restraints excluded: chain c residue 294 MET Chi-restraints excluded: chain c residue 317 SER Chi-restraints excluded: chain c residue 383 MET Chi-restraints excluded: chain d residue 233 ARG Chi-restraints excluded: chain d residue 352 LEU Chi-restraints excluded: chain f residue 11 THR Chi-restraints excluded: chain f residue 20 LEU Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 29 SER Chi-restraints excluded: chain h residue 30 VAL Chi-restraints excluded: chain i residue 16 ILE Chi-restraints excluded: chain j residue 23 VAL Chi-restraints excluded: chain j residue 38 SER Chi-restraints excluded: chain k residue 24 LEU Chi-restraints excluded: chain o residue 87 ASN Chi-restraints excluded: chain o residue 143 GLU Chi-restraints excluded: chain o residue 212 THR Chi-restraints excluded: chain q residue 50 VAL Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain q residue 103 THR Chi-restraints excluded: chain t residue 8 LEU Chi-restraints excluded: chain t residue 25 GLU Chi-restraints excluded: chain u residue 89 VAL Chi-restraints excluded: chain u residue 90 LEU Chi-restraints excluded: chain v residue 28 LEU Chi-restraints excluded: chain v residue 94 VAL Chi-restraints excluded: chain v residue 116 LEU Chi-restraints excluded: chain v residue 135 ASP Chi-restraints excluded: chain v residue 149 LYS 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: 1.9990 chunk 310 optimal weight: 6.9990 chunk 241 optimal weight: 8.9990 chunk 353 optimal weight: 6.9990 chunk 533 optimal weight: 0.7980 chunk 491 optimal weight: 0.8980 chunk 425 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 328 optimal weight: 2.9990 chunk 260 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN A 19 GLN A 310 GLN B 76 ASN E 67 GLN H 3 GLN L 4 ASN L 10 GLN O 176 ASN O 199 ASN O 227 GLN O 230 GLN R 22 ASN ** U 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 50 GLN V 53 ASN a 16 GLN a 19 GLN a 310 GLN b 76 ASN b 179 GLN b 260 ASN b 409 GLN e 67 GLN h 3 GLN l 10 GLN o 153 ASN o 176 ASN o 199 ASN o 227 GLN ** o 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 50 GLN v 53 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2245 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= 0.212 Angle : 0.736 24.770 75698 Z= 0.328 Chirality : 0.044 0.325 7708 Planarity : 0.006 0.059 9172 Dihedral : 16.436 144.275 12824 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.62 % Allowed : 16.55 % Favored : 81.83 % 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: 0.87 (0.11), residues: 5452 helix: 1.19 (0.09), residues: 2960 sheet: -0.08 (0.32), residues: 242 loop : -0.06 (0.13), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 131 HIS 0.007 0.002 HIS B 100 PHE 0.032 0.002 PHE c 304 TYR 0.020 0.002 TYR b 273 ARG 0.012 0.000 ARG o 269 ********************** 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 893 residues out of total 4532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 820 time to evaluate : 4.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 276 PHE cc_start: 0.8878 (OUTLIER) cc_final: 0.7991 (t80) REVERT: D 24 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.7021 (mtt180) REVERT: L 9 ARG cc_start: 0.6824 (mtm-85) cc_final: 0.6465 (mtp180) REVERT: O 267 TYR cc_start: 0.7814 (t80) cc_final: 0.7585 (t80) REVERT: T 8 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7571 (tp) REVERT: T 25 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6829 (tp30) REVERT: c 201 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7306 (mp) REVERT: c 276 PHE cc_start: 0.8855 (OUTLIER) cc_final: 0.7936 (t80) REVERT: l 9 ARG cc_start: 0.6594 (mtm110) cc_final: 0.6311 (mtp180) REVERT: t 8 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7597 (tp) REVERT: t 25 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6824 (tp30) outliers start: 73 outliers final: 51 residues processed: 865 average time/residue: 1.2909 time to fit residues: 1440.8588 Evaluate side-chains 857 residues out of total 4532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 798 time to evaluate : 4.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 276 PHE Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain O residue 38 ASP Chi-restraints excluded: chain O residue 87 ASN Chi-restraints excluded: chain O residue 143 GLU Chi-restraints excluded: chain O residue 166 ASN Chi-restraints excluded: chain O residue 212 THR Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 73 THR Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 121 SER Chi-restraints excluded: chain V residue 28 LEU Chi-restraints excluded: chain V residue 30 GLU Chi-restraints excluded: chain V residue 43 THR Chi-restraints excluded: chain V residue 116 LEU Chi-restraints excluded: chain Z residue 14 LEU Chi-restraints excluded: chain b residue 362 PHE Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain c residue 229 LEU Chi-restraints excluded: chain c residue 276 PHE Chi-restraints excluded: chain c residue 294 MET Chi-restraints excluded: chain c residue 317 SER Chi-restraints excluded: chain c residue 383 MET Chi-restraints excluded: chain d residue 233 ARG Chi-restraints excluded: chain d residue 352 LEU Chi-restraints excluded: chain f residue 11 THR Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 29 SER Chi-restraints excluded: chain h residue 30 VAL Chi-restraints excluded: chain k residue 24 LEU Chi-restraints excluded: chain o residue 87 ASN Chi-restraints excluded: chain o residue 143 GLU Chi-restraints excluded: chain o residue 212 THR Chi-restraints excluded: chain q residue 50 VAL Chi-restraints excluded: chain q residue 73 THR Chi-restraints excluded: chain q residue 103 THR Chi-restraints excluded: chain t residue 8 LEU Chi-restraints excluded: chain t residue 25 GLU Chi-restraints excluded: chain u residue 89 VAL Chi-restraints excluded: chain v residue 28 LEU Chi-restraints excluded: chain v residue 94 VAL Chi-restraints excluded: chain v residue 116 LEU Chi-restraints excluded: chain v residue 135 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 337 optimal weight: 5.9990 chunk 452 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 392 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 425 optimal weight: 0.4980 chunk 178 optimal weight: 6.9990 chunk 437 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN A 19 GLN A 310 GLN C 314 ASN H 3 GLN L 10 GLN O 176 ASN O 199 ASN O 227 GLN ** O 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 50 GLN a 16 GLN a 19 GLN a 310 GLN b 179 GLN b 409 GLN c 314 ASN h 3 GLN l 4 ASN l 10 GLN o 153 ASN o 176 ASN o 199 ASN ** o 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 50 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.162572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.133464 restraints weight = 42191.895| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 0.63 r_work: 0.3209 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work: 0.2973 rms_B_bonded: 3.92 restraints_weight: 0.1250 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 55308 Z= 0.321 Angle : 0.846 26.001 75698 Z= 0.381 Chirality : 0.050 0.308 7708 Planarity : 0.007 0.065 9172 Dihedral : 16.869 156.673 12824 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.86 % Favored : 97.10 % Rotamer: Outliers : 1.77 % Allowed : 16.44 % Favored : 81.79 % 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: 0.64 (0.11), residues: 5452 helix: 0.94 (0.09), residues: 2958 sheet: -0.10 (0.32), residues: 244 loop : -0.08 (0.13), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 131 HIS 0.010 0.003 HIS F 23 PHE 0.041 0.003 PHE H 41 TYR 0.025 0.003 TYR B 273 ARG 0.010 0.001 ARG o 269 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21288.28 seconds wall clock time: 370 minutes 17.32 seconds (22217.32 seconds total)