Starting phenix.real_space_refine on Tue Apr 16 16:40:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d59_30578/04_2024/7d59_30578_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d59_30578/04_2024/7d59_30578.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d59_30578/04_2024/7d59_30578.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d59_30578/04_2024/7d59_30578.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d59_30578/04_2024/7d59_30578_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d59_30578/04_2024/7d59_30578_updated.pdb" } resolution = 3.1 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= 0.001 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: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 7 6.06 5 S 275 5.16 5 C 25230 2.51 5 N 6906 2.21 5 O 7476 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 10": "OD1" <-> "OD2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A ARG 29": "NH1" <-> "NH2" Residue "A ARG 59": "NH1" <-> "NH2" Residue "A GLU 64": "OE1" <-> "OE2" Residue "A ASP 78": "OD1" <-> "OD2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 99": "NH1" <-> "NH2" Residue "A GLU 120": "OE1" <-> "OE2" Residue "A TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A ASP 148": "OD1" <-> "OD2" Residue "A ARG 151": "NH1" <-> "NH2" Residue "A GLU 177": "OE1" <-> "OE2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A ASP 234": "OD1" <-> "OD2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A ARG 254": "NH1" <-> "NH2" Residue "A PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 297": "NH1" <-> "NH2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 362": "OD1" <-> "OD2" Residue "A ARG 376": "NH1" <-> "NH2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A GLU 413": "OE1" <-> "OE2" Residue "A PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 430": "NH1" <-> "NH2" Residue "A ARG 437": "NH1" <-> "NH2" Residue "A GLU 438": "OE1" <-> "OE2" Residue "A ASP 456": "OD1" <-> "OD2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A ARG 484": "NH1" <-> "NH2" Residue "A ARG 487": "NH1" <-> "NH2" Residue "A TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 499": "OD1" <-> "OD2" Residue "A ARG 533": "NH1" <-> "NH2" Residue "A ASP 544": "OD1" <-> "OD2" Residue "A ASP 556": "OD1" <-> "OD2" Residue "A PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A ARG 614": "NH1" <-> "NH2" Residue "A ARG 618": "NH1" <-> "NH2" Residue "A GLU 629": "OE1" <-> "OE2" Residue "A ARG 669": "NH1" <-> "NH2" Residue "A ASP 670": "OD1" <-> "OD2" Residue "A ASP 678": "OD1" <-> "OD2" Residue "A ARG 682": "NH1" <-> "NH2" Residue "A ARG 685": "NH1" <-> "NH2" Residue "A GLU 726": "OE1" <-> "OE2" Residue "A GLU 729": "OE1" <-> "OE2" Residue "A ASP 761": "OD1" <-> "OD2" Residue "A ARG 769": "NH1" <-> "NH2" Residue "A PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 846": "OE1" <-> "OE2" Residue "A PHE 848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 874": "NH1" <-> "NH2" Residue "A GLU 880": "OE1" <-> "OE2" Residue "A ASP 905": "OD1" <-> "OD2" Residue "A ASP 916": "OD1" <-> "OD2" Residue "A GLU 917": "OE1" <-> "OE2" Residue "A GLU 920": "OE1" <-> "OE2" Residue "A ASP 926": "OD1" <-> "OD2" Residue "A PHE 932": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 957": "OE1" <-> "OE2" Residue "A PHE 965": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 978": "OE1" <-> "OE2" Residue "A ARG 984": "NH1" <-> "NH2" Residue "A ASP 985": "OD1" <-> "OD2" Residue "A TYR 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 996": "OE1" <-> "OE2" Residue "A TYR 1001": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1024": "NH1" <-> "NH2" Residue "A GLU 1043": "OE1" <-> "OE2" Residue "A GLU 1072": "OE1" <-> "OE2" Residue "A ASP 1092": "OD1" <-> "OD2" Residue "A ASP 1093": "OD1" <-> "OD2" Residue "A ASP 1096": "OD1" <-> "OD2" Residue "A TYR 1097": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1104": "NH1" <-> "NH2" Residue "A TYR 1116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1135": "OE1" <-> "OE2" Residue "A ARG 1136": "NH1" <-> "NH2" Residue "A ARG 1141": "NH1" <-> "NH2" Residue "A ARG 1150": "NH1" <-> "NH2" Residue "A ARG 1178": "NH1" <-> "NH2" Residue "A GLU 1194": "OE1" <-> "OE2" Residue "A GLU 1253": "OE1" <-> "OE2" Residue "A ARG 1264": "NH1" <-> "NH2" Residue "A ARG 1285": "NH1" <-> "NH2" Residue "A ASP 1326": "OD1" <-> "OD2" Residue "A ASP 1330": "OD1" <-> "OD2" Residue "A ASP 1338": "OD1" <-> "OD2" Residue "A PHE 1360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1375": "NH1" <-> "NH2" Residue "A PHE 1384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 28": "NH1" <-> "NH2" Residue "B ASP 70": "OD1" <-> "OD2" Residue "B GLU 88": "OE1" <-> "OE2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "B TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 135": "NH1" <-> "NH2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "B ARG 226": "NH1" <-> "NH2" Residue "B GLU 246": "OE1" <-> "OE2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "B GLU 258": "OE1" <-> "OE2" Residue "B TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 308": "OE1" <-> "OE2" Residue "B ARG 310": "NH1" <-> "NH2" Residue "B GLU 311": "OE1" <-> "OE2" Residue "B ASP 348": "OD1" <-> "OD2" Residue "B TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 363": "OE1" <-> "OE2" Residue "B GLU 374": "OE1" <-> "OE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 389": "OD1" <-> "OD2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 407": "NH1" <-> "NH2" Residue "B GLU 460": "OE1" <-> "OE2" Residue "B ARG 463": "NH1" <-> "NH2" Residue "B GLU 486": "OE1" <-> "OE2" Residue "B GLU 488": "OE1" <-> "OE2" Residue "B ASP 505": "OD1" <-> "OD2" Residue "B ASP 508": "OD1" <-> "OD2" Residue "B GLU 521": "OE1" <-> "OE2" Residue "B GLU 530": "OE1" <-> "OE2" Residue "B PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 580": "OD1" <-> "OD2" Residue "B ARG 581": "NH1" <-> "NH2" Residue "B TYR 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 588": "OD1" <-> "OD2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B ARG 619": "NH1" <-> "NH2" Residue "B PHE 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 623": "OD1" <-> "OD2" Residue "B TYR 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 640": "OD1" <-> "OD2" Residue "B GLU 647": "OE1" <-> "OE2" Residue "B ASP 653": "OD1" <-> "OD2" Residue "B PHE 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 706": "OD1" <-> "OD2" Residue "B ARG 768": "NH1" <-> "NH2" Residue "B ARG 805": "NH1" <-> "NH2" Residue "B GLU 807": "OE1" <-> "OE2" Residue "B ASP 812": "OD1" <-> "OD2" Residue "B GLU 822": "OE1" <-> "OE2" Residue "B TYR 858": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 876": "OE1" <-> "OE2" Residue "B PHE 879": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 900": "NH1" <-> "NH2" Residue "B GLU 914": "OE1" <-> "OE2" Residue "B ASP 920": "OD1" <-> "OD2" Residue "B ARG 937": "NH1" <-> "NH2" Residue "B ARG 957": "NH1" <-> "NH2" Residue "B PHE 958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 971": "OD1" <-> "OD2" Residue "B GLU 974": "OE1" <-> "OE2" Residue "B TYR 981": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 988": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1018": "OD1" <-> "OD2" Residue "B ARG 1033": "NH1" <-> "NH2" Residue "B ARG 1039": "NH1" <-> "NH2" Residue "B ARG 1041": "NH1" <-> "NH2" Residue "B ASP 1042": "OD1" <-> "OD2" Residue "B GLU 1076": "OE1" <-> "OE2" Residue "B ARG 1105": "NH1" <-> "NH2" Residue "B TYR 1108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1125": "NH1" <-> "NH2" Residue "B GLU 1133": "OE1" <-> "OE2" Residue "C GLU 9": "OE1" <-> "OE2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C ARG 22": "NH1" <-> "NH2" Residue "C ASP 28": "OD1" <-> "OD2" Residue "C ASP 57": "OD1" <-> "OD2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C ARG 120": "NH1" <-> "NH2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "C ASP 136": "OD1" <-> "OD2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C ASP 155": "OD1" <-> "OD2" Residue "C ASP 158": "OD1" <-> "OD2" Residue "C GLU 161": "OE1" <-> "OE2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "C ASP 196": "OD1" <-> "OD2" Residue "C TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 248": "OE1" <-> "OE2" Residue "C GLU 251": "OE1" <-> "OE2" Residue "C ARG 274": "NH1" <-> "NH2" Residue "C ARG 279": "NH1" <-> "NH2" Residue "C ARG 285": "NH1" <-> "NH2" Residue "C GLU 291": "OE1" <-> "OE2" Residue "C ARG 303": "NH1" <-> "NH2" Residue "C ASP 304": "OD1" <-> "OD2" Residue "C GLU 311": "OE1" <-> "OE2" Residue "C PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 341": "OD1" <-> "OD2" Residue "D ASP 5": "OD1" <-> "OD2" Residue "D ASP 22": "OD1" <-> "OD2" Residue "D GLU 25": "OE1" <-> "OE2" Residue "D ARG 90": "NH1" <-> "NH2" Residue "D GLU 102": "OE1" <-> "OE2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "D GLU 106": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D GLU 114": "OE1" <-> "OE2" Residue "E ASP 3": "OD1" <-> "OD2" Residue "E TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 34": "OD1" <-> "OD2" Residue "E GLU 39": "OE1" <-> "OE2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "E ASP 66": "OD1" <-> "OD2" Residue "E ASP 67": "OD1" <-> "OD2" Residue "E PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 78": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E GLU 134": "OE1" <-> "OE2" Residue "E GLU 154": "OE1" <-> "OE2" Residue "E GLU 158": "OE1" <-> "OE2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "E GLU 198": "OE1" <-> "OE2" Residue "F ARG 51": "NH1" <-> "NH2" Residue "F TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 64": "NH1" <-> "NH2" Residue "F GLU 84": "OE1" <-> "OE2" Residue "F ARG 107": "NH1" <-> "NH2" Residue "F TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 6": "OE1" <-> "OE2" Residue "G ASP 9": "OD1" <-> "OD2" Residue "G GLU 19": "OE1" <-> "OE2" Residue "G ASP 24": "OD1" <-> "OD2" Residue "G PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 55": "OE1" <-> "OE2" Residue "G ASP 56": "OD1" <-> "OD2" Residue "G ASP 63": "OD1" <-> "OD2" Residue "G ARG 73": "NH1" <-> "NH2" Residue "G PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 82": "OD1" <-> "OD2" Residue "G GLU 83": "OE1" <-> "OE2" Residue "G ASP 105": "OD1" <-> "OD2" Residue "G ASP 106": "OD1" <-> "OD2" Residue "G GLU 112": "OE1" <-> "OE2" Residue "G PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 121": "OD1" <-> "OD2" Residue "G GLU 132": "OE1" <-> "OE2" Residue "G GLU 134": "OE1" <-> "OE2" Residue "G TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 149": "NH1" <-> "NH2" Residue "G ASP 154": "OD1" <-> "OD2" Residue "G ASP 159": "OD1" <-> "OD2" Residue "G GLU 181": "OE1" <-> "OE2" Residue "H GLU 7": "OE1" <-> "OE2" Residue "H PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 18": "OE1" <-> "OE2" Residue "H ARG 24": "NH1" <-> "NH2" Residue "H ARG 27": "NH1" <-> "NH2" Residue "H PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 71": "OD1" <-> "OD2" Residue "H ASP 80": "OD1" <-> "OD2" Residue "H GLU 100": "OE1" <-> "OE2" Residue "H ASP 102": "OD1" <-> "OD2" Residue "H ARG 111": "NH1" <-> "NH2" Residue "H TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 22": "NH1" <-> "NH2" Residue "I ARG 36": "NH1" <-> "NH2" Residue "I ASP 51": "OD1" <-> "OD2" Residue "I GLU 73": "OE1" <-> "OE2" Residue "I ARG 76": "NH1" <-> "NH2" Residue "I TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 89": "OE1" <-> "OE2" Residue "I PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 108": "OD1" <-> "OD2" Residue "J GLU 19": "OE1" <-> "OE2" Residue "J ARG 47": "NH1" <-> "NH2" Residue "J TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 28": "OE1" <-> "OE2" Residue "K ASP 48": "OD1" <-> "OD2" Residue "K GLU 64": "OE1" <-> "OE2" Residue "K PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 94": "OE1" <-> "OE2" Residue "K ASP 112": "OD1" <-> "OD2" Residue "L GLU 25": "OE1" <-> "OE2" Residue "L ARG 48": "NH1" <-> "NH2" Residue "L ARG 58": "NH1" <-> "NH2" Residue "M GLU 4": "OE1" <-> "OE2" Residue "M GLU 23": "OE1" <-> "OE2" Residue "M ARG 33": "NH1" <-> "NH2" Residue "M ASP 40": "OD1" <-> "OD2" Residue "M ASP 41": "OD1" <-> "OD2" Residue "M TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 113": "NH1" <-> "NH2" Residue "M ASP 146": "OD1" <-> "OD2" Residue "M ARG 150": "NH1" <-> "NH2" Residue "M GLU 234": "OE1" <-> "OE2" Residue "N ARG 29": "NH1" <-> "NH2" Residue "N GLU 253": "OE1" <-> "OE2" Residue "N GLU 257": "OE1" <-> "OE2" Residue "N GLU 323": "OE1" <-> "OE2" Residue "N ASP 347": "OD1" <-> "OD2" Residue "N ASP 367": "OD1" <-> "OD2" Residue "O PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 19": "OE1" <-> "OE2" Residue "O ARG 37": "NH1" <-> "NH2" Residue "O ASP 42": "OD1" <-> "OD2" Residue "O ASP 48": "OD1" <-> "OD2" Residue "O TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 101": "OD1" <-> "OD2" Residue "O GLU 108": "OE1" <-> "OE2" Residue "O ASP 127": "OD1" <-> "OD2" Residue "O GLU 131": "OE1" <-> "OE2" Residue "O TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 153": "OD1" <-> "OD2" Residue "O ARG 159": "NH1" <-> "NH2" Residue "O ASP 186": "OD1" <-> "OD2" Residue "O ARG 258": "NH1" <-> "NH2" Residue "O PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 292": "OE1" <-> "OE2" Residue "O ASP 309": "OD1" <-> "OD2" Residue "O ASP 318": "OD1" <-> "OD2" Residue "O GLU 351": "OE1" <-> "OE2" Residue "O GLU 356": "OE1" <-> "OE2" Residue "O PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 390": "OE1" <-> "OE2" Residue "O PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 448": "OE1" <-> "OE2" Residue "O GLU 480": "OE1" <-> "OE2" Residue "O GLU 488": "OE1" <-> "OE2" Residue "O GLU 489": "OE1" <-> "OE2" Residue "O ASP 517": "OD1" <-> "OD2" Residue "O GLU 518": "OE1" <-> "OE2" Residue "O GLU 524": "OE1" <-> "OE2" Residue "O GLU 528": "OE1" <-> "OE2" Residue "O ARG 533": "NH1" <-> "NH2" Residue "P ASP 169": "OD1" <-> "OD2" Residue "P PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 222": "OE1" <-> "OE2" Residue "P GLU 233": "OE1" <-> "OE2" Residue "P ASP 234": "OD1" <-> "OD2" Residue "P ASP 245": "OD1" <-> "OD2" Residue "P TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 298": "OE1" <-> "OE2" Residue "P GLU 315": "OE1" <-> "OE2" Residue "Q GLU 25": "OE1" <-> "OE2" Residue "Q PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 54": "OE1" <-> "OE2" Residue "Q TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 63": "OE1" <-> "OE2" Residue "Q ARG 65": "NH1" <-> "NH2" Residue "Q ARG 70": "NH1" <-> "NH2" Residue "Q TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 79": "OE1" <-> "OE2" Residue "Q ASP 83": "OD1" <-> "OD2" Residue "Q GLU 85": "OE1" <-> "OE2" Residue "Q TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 187": "OE1" <-> "OE2" Residue "Q TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 189": "OD1" <-> "OD2" Residue "Q GLU 190": "OE1" <-> "OE2" Residue "Q GLU 191": "OE1" <-> "OE2" Residue "Q GLU 195": "OE1" <-> "OE2" Residue "Q ASP 198": "OD1" <-> "OD2" Residue "Q TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 206": "OD1" <-> "OD2" Residue "Q ASP 208": "OD1" <-> "OD2" Residue "Q PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 220": "OE1" <-> "OE2" Residue "Q TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 39898 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 10881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1386, 10881 Classifications: {'peptide': 1386} Link IDs: {'PTRANS': 65, 'TRANS': 1320} Chain: "B" Number of atoms: 8668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8668 Classifications: {'peptide': 1095} Link IDs: {'PTRANS': 49, 'TRANS': 1045} Chain breaks: 2 Chain: "C" Number of atoms: 2752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2752 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 17, 'TRANS': 327} Chain: "D" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1013 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "E" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1723 Classifications: {'peptide': 210} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 198} Chain: "F" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 636 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "G" Number of atoms: 1470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1470 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 11, 'TRANS': 171} Chain breaks: 2 Chain: "H" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1197 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain: "I" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 857 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "L" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 397 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "M" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1797 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 13, 'TRANS': 208} Chain breaks: 3 Chain: "N" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1038 Classifications: {'peptide': 136} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 126} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3913 Classifications: {'peptide': 490} Link IDs: {'PTRANS': 16, 'TRANS': 473} Chain breaks: 2 Chain: "P" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1103 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 7, 'TRANS': 131} Chain breaks: 1 Chain: "Q" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1049 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 12, 'TRANS': 108} Chain breaks: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 550 SG CYS A 69 54.653 108.165 92.906 1.00155.88 S ATOM 620 SG CYS A 79 58.931 108.579 92.852 1.00133.57 S ATOM 883 SG CYS A 112 68.677 80.410 132.900 1.00158.01 S ATOM 19127 SG CYS B1080 62.971 113.987 110.709 1.00123.98 S ATOM 19146 SG CYS B1083 62.708 109.790 111.897 1.00126.17 S ATOM 19212 SG CYS B1092 60.235 110.521 108.514 1.00127.53 S ATOM 28381 SG CYS I 5 118.169 35.651 107.873 1.00162.49 S ATOM 28398 SG CYS I 8 114.768 36.865 107.068 1.00162.55 S ATOM 28529 SG CYS I 25 115.414 37.842 111.809 1.00167.43 S ATOM 28550 SG CYS I 28 115.075 34.333 109.593 1.00164.81 S ATOM 29111 SG CYS I 98 137.804 109.699 94.458 1.00231.72 S ATOM 29252 SG CYS J 7 106.870 111.937 39.723 1.00 76.18 S ATOM 29276 SG CYS J 10 108.124 115.266 37.879 1.00 80.33 S ATOM 30653 SG CYS L 19 71.825 84.885 38.622 1.00113.18 S ATOM 30672 SG CYS L 22 71.018 84.086 34.555 1.00119.05 S ATOM 30789 SG CYS L 36 67.977 83.884 36.821 1.00126.01 S ATOM 30815 SG CYS L 39 70.993 81.549 37.334 1.00130.06 S ATOM 38624 SG CYS P 290 44.561 89.676 119.081 1.00178.43 S ATOM 38671 SG CYS P 296 48.300 94.393 120.566 1.00160.77 S ATOM 38748 SG CYS P 307 41.782 94.335 120.100 1.00175.10 S ATOM 38606 SG CYS P 287 45.381 91.660 125.530 1.00183.21 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="ZN ZN I 202 " occ=0.75 Time building chain proxies: 19.53, per 1000 atoms: 0.49 Number of scatterers: 39898 At special positions: 0 Unit cell: (168.95, 173.31, 185.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 7 29.99 Fe 4 26.01 S 275 16.00 O 7476 8.00 N 6906 7.00 C 25230 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.75 Conformation dependent library (CDL) restraints added in 7.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 P 400 " pdb="FE2 SF4 P 400 " - pdb=" SG CYS P 296 " pdb="FE3 SF4 P 400 " - pdb=" SG CYS P 307 " pdb="FE4 SF4 P 400 " - pdb=" SG CYS P 287 " pdb="FE1 SF4 P 400 " - pdb=" SG CYS P 290 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 82 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 69 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 79 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 112 " pdb=" ZN B2001 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1080 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1083 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1092 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 5 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 8 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 28 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 25 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 98 " pdb=" ZN J 100 " pdb="ZN ZN J 100 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 100 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " Number of angles added : 12 9896 Ramachandran restraints generated. 4948 Oldfield, 0 Emsley, 4948 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9434 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 157 helices and 52 sheets defined 32.1% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.16 Creating SS restraints... Processing helix chain 'A' and resid 25 through 31 Processing helix chain 'A' and resid 98 through 107 removed outlier: 3.706A pdb=" N GLN A 106 " --> pdb=" O ILE A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 129 Processing helix chain 'A' and resid 136 through 152 removed outlier: 3.554A pdb=" N ARG A 140 " --> pdb=" O TYR A 136 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 142 " --> pdb=" O GLN A 138 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS A 143 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 202 removed outlier: 3.506A pdb=" N PHE A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR A 199 " --> pdb=" O GLN A 195 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ALA A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE A 201 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N GLU A 202 " --> pdb=" O GLU A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 228 removed outlier: 3.613A pdb=" N ASN A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'A' and resid 278 through 299 removed outlier: 3.534A pdb=" N PHE A 288 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 318 Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 401 through 410 removed outlier: 3.709A pdb=" N LYS A 406 " --> pdb=" O ASN A 402 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 407 " --> pdb=" O PHE A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 442 removed outlier: 3.885A pdb=" N GLN A 442 " --> pdb=" O GLU A 438 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 438 through 442' Processing helix chain 'A' and resid 470 through 472 No H-bonds generated for 'chain 'A' and resid 470 through 472' Processing helix chain 'A' and resid 490 through 496 removed outlier: 4.190A pdb=" N THR A 494 " --> pdb=" O CYS A 491 " (cutoff:3.500A) Proline residue: A 495 - end of helix Processing helix chain 'A' and resid 513 through 521 removed outlier: 3.705A pdb=" N ALA A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU A 518 " --> pdb=" O GLU A 514 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 520 " --> pdb=" O LYS A 516 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 552 Processing helix chain 'A' and resid 561 through 567 Processing helix chain 'A' and resid 597 through 605 removed outlier: 3.976A pdb=" N VAL A 603 " --> pdb=" O GLN A 599 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU A 605 " --> pdb=" O PHE A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 670 Processing helix chain 'A' and resid 683 through 694 Proline residue: A 688 - end of helix Processing helix chain 'A' and resid 707 through 733 removed outlier: 4.363A pdb=" N LYS A 711 " --> pdb=" O GLN A 707 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A 715 " --> pdb=" O LYS A 711 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A 716 " --> pdb=" O ALA A 712 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU A 726 " --> pdb=" O LYS A 722 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR A 727 " --> pdb=" O LYS A 723 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE A 728 " --> pdb=" O CYS A 724 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU A 729 " --> pdb=" O ASP A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 751 Processing helix chain 'A' and resid 753 through 770 removed outlier: 3.719A pdb=" N SER A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE A 759 " --> pdb=" O GLU A 755 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG A 760 " --> pdb=" O LEU A 756 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG A 769 " --> pdb=" O SER A 765 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 783 Processing helix chain 'A' and resid 789 through 796 Processing helix chain 'A' and resid 828 through 831 No H-bonds generated for 'chain 'A' and resid 828 through 831' Processing helix chain 'A' and resid 844 through 862 removed outlier: 3.600A pdb=" N ALA A 853 " --> pdb=" O PHE A 849 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU A 856 " --> pdb=" O MET A 852 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY A 857 " --> pdb=" O ALA A 853 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP A 860 " --> pdb=" O GLU A 856 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR A 861 " --> pdb=" O GLY A 857 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 862 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 876 Processing helix chain 'A' and resid 921 through 931 removed outlier: 3.929A pdb=" N ALA A 930 " --> pdb=" O ASP A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 953 removed outlier: 3.787A pdb=" N LEU A 947 " --> pdb=" O ASN A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 987 removed outlier: 3.542A pdb=" N SER A 977 " --> pdb=" O ILE A 973 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS A 979 " --> pdb=" O GLY A 975 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS A 982 " --> pdb=" O GLU A 978 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR A 987 " --> pdb=" O THR A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1002 No H-bonds generated for 'chain 'A' and resid 1000 through 1002' Processing helix chain 'A' and resid 1008 through 1024 removed outlier: 3.787A pdb=" N GLU A1012 " --> pdb=" O PRO A1008 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LYS A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE A1014 " --> pdb=" O GLN A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1040 Processing helix chain 'A' and resid 1042 through 1046 Processing helix chain 'A' and resid 1067 through 1075 Processing helix chain 'A' and resid 1095 through 1104 removed outlier: 3.533A pdb=" N GLY A1103 " --> pdb=" O ARG A1099 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG A1104 " --> pdb=" O LEU A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1110 through 1113 No H-bonds generated for 'chain 'A' and resid 1110 through 1113' Processing helix chain 'A' and resid 1134 through 1140 Processing helix chain 'A' and resid 1146 through 1154 Processing helix chain 'A' and resid 1185 through 1193 Processing helix chain 'A' and resid 1232 through 1236 Processing helix chain 'A' and resid 1251 through 1257 Processing helix chain 'A' and resid 1260 through 1275 removed outlier: 3.684A pdb=" N ARG A1264 " --> pdb=" O ILE A1260 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N THR A1265 " --> pdb=" O GLU A1261 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR A1266 " --> pdb=" O ALA A1262 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A1268 " --> pdb=" O ARG A1264 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A1271 " --> pdb=" O ILE A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1284 through 1293 removed outlier: 3.632A pdb=" N LEU A1290 " --> pdb=" O HIS A1286 " (cutoff:3.500A) Processing helix chain 'A' and resid 1305 through 1311 removed outlier: 3.652A pdb=" N ALA A1309 " --> pdb=" O ARG A1305 " (cutoff:3.500A) Processing helix chain 'A' and resid 1315 through 1321 removed outlier: 4.148A pdb=" N SER A1320 " --> pdb=" O LEU A1316 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE A1321 " --> pdb=" O MET A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1326 through 1334 removed outlier: 3.568A pdb=" N ALA A1332 " --> pdb=" O LEU A1328 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1349 Processing helix chain 'A' and resid 1382 through 1385 No H-bonds generated for 'chain 'A' and resid 1382 through 1385' Processing helix chain 'B' and resid 26 through 36 removed outlier: 3.927A pdb=" N LEU B 30 " --> pdb=" O TRP B 27 " (cutoff:3.500A) Proline residue: B 31 - end of helix removed outlier: 3.533A pdb=" N LYS B 35 " --> pdb=" O ALA B 32 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL B 36 " --> pdb=" O PHE B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 48 removed outlier: 3.732A pdb=" N PHE B 47 " --> pdb=" O HIS B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 61 Processing helix chain 'B' and resid 99 through 105 Processing helix chain 'B' and resid 152 through 155 No H-bonds generated for 'chain 'B' and resid 152 through 155' Processing helix chain 'B' and resid 236 through 243 Processing helix chain 'B' and resid 248 through 255 Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 266 through 274 Processing helix chain 'B' and resid 280 through 290 Processing helix chain 'B' and resid 305 through 314 Processing helix chain 'B' and resid 329 through 345 Processing helix chain 'B' and resid 365 through 387 removed outlier: 3.551A pdb=" N LYS B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 421 Processing helix chain 'B' and resid 445 through 452 removed outlier: 3.507A pdb=" N LEU B 449 " --> pdb=" O TYR B 445 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET B 452 " --> pdb=" O ALA B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 518 Processing helix chain 'B' and resid 552 through 565 Processing helix chain 'B' and resid 608 through 616 removed outlier: 3.678A pdb=" N GLU B 613 " --> pdb=" O LYS B 609 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU B 614 " --> pdb=" O HIS B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 626 Processing helix chain 'B' and resid 638 through 640 No H-bonds generated for 'chain 'B' and resid 638 through 640' Processing helix chain 'B' and resid 661 through 664 removed outlier: 3.761A pdb=" N LEU B 664 " --> pdb=" O PRO B 661 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 661 through 664' Processing helix chain 'B' and resid 668 through 671 removed outlier: 3.985A pdb=" N LEU B 671 " --> pdb=" O CYS B 668 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 668 through 671' Processing helix chain 'B' and resid 680 through 690 Processing helix chain 'B' and resid 723 through 728 Processing helix chain 'B' and resid 730 through 732 No H-bonds generated for 'chain 'B' and resid 730 through 732' Processing helix chain 'B' and resid 759 through 764 Processing helix chain 'B' and resid 934 through 937 No H-bonds generated for 'chain 'B' and resid 934 through 937' Processing helix chain 'B' and resid 941 through 955 Processing helix chain 'B' and resid 971 through 979 removed outlier: 3.604A pdb=" N ASP B 975 " --> pdb=" O ASP B 971 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL B 977 " --> pdb=" O CYS B 973 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG B 978 " --> pdb=" O GLU B 974 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N HIS B 979 " --> pdb=" O ASP B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 1049 through 1058 removed outlier: 4.099A pdb=" N CYS B1054 " --> pdb=" O MET B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1062 through 1066 Processing helix chain 'B' and resid 1108 through 1120 removed outlier: 3.782A pdb=" N GLN B1118 " --> pdb=" O PHE B1114 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N SER B1119 " --> pdb=" O GLN B1115 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N MET B1120 " --> pdb=" O GLU B1116 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 12 removed outlier: 3.691A pdb=" N ARG C 11 " --> pdb=" O VAL C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 48 Processing helix chain 'C' and resid 70 through 79 Processing helix chain 'C' and resid 103 through 111 Processing helix chain 'C' and resid 159 through 162 No H-bonds generated for 'chain 'C' and resid 159 through 162' Processing helix chain 'C' and resid 170 through 172 No H-bonds generated for 'chain 'C' and resid 170 through 172' Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'C' and resid 247 through 256 removed outlier: 3.763A pdb=" N ARG C 255 " --> pdb=" O GLU C 251 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N CYS C 256 " --> pdb=" O GLU C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 345 removed outlier: 3.511A pdb=" N VAL C 322 " --> pdb=" O PRO C 318 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE C 326 " --> pdb=" O VAL C 322 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS C 327 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS C 332 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N CYS C 333 " --> pdb=" O LEU C 329 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU C 337 " --> pdb=" O CYS C 333 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA C 342 " --> pdb=" O ASP C 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 21 Processing helix chain 'D' and resid 23 through 30 removed outlier: 4.067A pdb=" N GLU D 29 " --> pdb=" O GLU D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 55 removed outlier: 3.723A pdb=" N LEU D 42 " --> pdb=" O GLY D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 73 Processing helix chain 'D' and resid 80 through 87 removed outlier: 4.141A pdb=" N LEU D 84 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU D 87 " --> pdb=" O LYS D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.805A pdb=" N GLN D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU D 99 " --> pdb=" O VAL D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 121 removed outlier: 3.572A pdb=" N LEU D 116 " --> pdb=" O GLN D 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 24 Processing helix chain 'E' and resid 30 through 33 No H-bonds generated for 'chain 'E' and resid 30 through 33' Processing helix chain 'E' and resid 37 through 43 removed outlier: 3.678A pdb=" N GLN E 43 " --> pdb=" O GLU E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 94 removed outlier: 3.618A pdb=" N TYR E 90 " --> pdb=" O THR E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 120 Processing helix chain 'E' and resid 153 through 163 removed outlier: 3.822A pdb=" N GLU E 158 " --> pdb=" O GLU E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 183 Processing helix chain 'F' and resid 59 through 75 removed outlier: 3.682A pdb=" N MET F 75 " --> pdb=" O LEU F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 98 removed outlier: 3.691A pdb=" N MET F 94 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS F 95 " --> pdb=" O LEU F 91 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU F 97 " --> pdb=" O ALA F 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 33 Processing helix chain 'I' and resid 56 through 59 No H-bonds generated for 'chain 'I' and resid 56 through 59' Processing helix chain 'J' and resid 18 through 24 Processing helix chain 'J' and resid 31 through 38 Processing helix chain 'J' and resid 47 through 50 No H-bonds generated for 'chain 'J' and resid 47 through 50' Processing helix chain 'J' and resid 56 through 60 Processing helix chain 'K' and resid 49 through 61 removed outlier: 3.555A pdb=" N SER K 54 " --> pdb=" O THR K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 129 removed outlier: 4.042A pdb=" N PHE K 96 " --> pdb=" O ALA K 92 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN K 97 " --> pdb=" O VAL K 93 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 82 Processing helix chain 'M' and resid 141 through 154 removed outlier: 3.513A pdb=" N ALA M 145 " --> pdb=" O TYR M 141 " (cutoff:3.500A) Processing helix chain 'M' and resid 193 through 202 Processing helix chain 'M' and resid 216 through 226 Processing helix chain 'M' and resid 242 through 249 removed outlier: 3.708A pdb=" N MET M 247 " --> pdb=" O SER M 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 251 through 260 Processing helix chain 'N' and resid 389 through 397 Processing helix chain 'O' and resid 3 through 15 Processing helix chain 'O' and resid 19 through 30 removed outlier: 3.883A pdb=" N ARG O 30 " --> pdb=" O VAL O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 36 through 43 Processing helix chain 'O' and resid 47 through 59 Processing helix chain 'O' and resid 79 through 84 removed outlier: 4.600A pdb=" N ARG O 84 " --> pdb=" O SER O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 88 through 98 removed outlier: 4.428A pdb=" N LEU O 98 " --> pdb=" O THR O 94 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 108 Processing helix chain 'O' and resid 110 through 113 No H-bonds generated for 'chain 'O' and resid 110 through 113' Processing helix chain 'O' and resid 118 through 132 removed outlier: 3.618A pdb=" N LYS O 123 " --> pdb=" O SER O 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 141 through 153 removed outlier: 3.764A pdb=" N THR O 147 " --> pdb=" O GLU O 143 " (cutoff:3.500A) Processing helix chain 'O' and resid 239 through 258 Processing helix chain 'O' and resid 263 through 272 Processing helix chain 'O' and resid 274 through 277 No H-bonds generated for 'chain 'O' and resid 274 through 277' Processing helix chain 'O' and resid 290 through 295 Processing helix chain 'O' and resid 305 through 316 Processing helix chain 'O' and resid 339 through 357 removed outlier: 3.671A pdb=" N SER O 344 " --> pdb=" O LYS O 340 " (cutoff:3.500A) Processing helix chain 'O' and resid 360 through 371 removed outlier: 3.683A pdb=" N ILE O 365 " --> pdb=" O ARG O 361 " (cutoff:3.500A) Processing helix chain 'O' and resid 380 through 383 No H-bonds generated for 'chain 'O' and resid 380 through 383' Processing helix chain 'O' and resid 388 through 400 Processing helix chain 'O' and resid 428 through 454 removed outlier: 3.691A pdb=" N HIS O 437 " --> pdb=" O ARG O 433 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N TYR O 440 " --> pdb=" O LEU O 436 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS O 441 " --> pdb=" O HIS O 437 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU O 453 " --> pdb=" O ARG O 449 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR O 454 " --> pdb=" O ARG O 450 " (cutoff:3.500A) Processing helix chain 'O' and resid 458 through 477 removed outlier: 3.564A pdb=" N VAL O 467 " --> pdb=" O LYS O 463 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU O 468 " --> pdb=" O SER O 464 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE O 470 " --> pdb=" O ARG O 466 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE O 471 " --> pdb=" O VAL O 467 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET O 474 " --> pdb=" O ILE O 470 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA O 476 " --> pdb=" O ALA O 472 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR O 477 " --> pdb=" O SER O 473 " (cutoff:3.500A) Processing helix chain 'O' and resid 481 through 490 Processing helix chain 'O' and resid 493 through 530 removed outlier: 3.602A pdb=" N GLN O 498 " --> pdb=" O PRO O 494 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LEU O 499 " --> pdb=" O GLU O 495 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU O 500 " --> pdb=" O ARG O 496 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG O 504 " --> pdb=" O GLU O 500 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE O 514 " --> pdb=" O ASP O 510 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN O 515 " --> pdb=" O ALA O 511 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR O 519 " --> pdb=" O GLN O 515 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE O 520 " --> pdb=" O VAL O 516 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N TYR O 526 " --> pdb=" O LEU O 522 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE O 527 " --> pdb=" O LEU O 523 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU O 528 " --> pdb=" O GLU O 524 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N CYS O 529 " --> pdb=" O SER O 525 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR O 530 " --> pdb=" O TYR O 526 " (cutoff:3.500A) Processing helix chain 'P' and resid 174 through 198 Processing helix chain 'P' and resid 204 through 207 No H-bonds generated for 'chain 'P' and resid 204 through 207' Processing helix chain 'P' and resid 213 through 223 removed outlier: 3.578A pdb=" N LYS P 218 " --> pdb=" O HIS P 214 " (cutoff:3.500A) Processing helix chain 'P' and resid 231 through 245 Processing helix chain 'P' and resid 281 through 284 No H-bonds generated for 'chain 'P' and resid 281 through 284' Processing helix chain 'P' and resid 286 through 289 No H-bonds generated for 'chain 'P' and resid 286 through 289' Processing helix chain 'P' and resid 308 through 315 Processing helix chain 'Q' and resid 52 through 69 removed outlier: 3.549A pdb=" N ALA Q 59 " --> pdb=" O GLU Q 55 " (cutoff:3.500A) Processing helix chain 'Q' and resid 89 through 92 No H-bonds generated for 'chain 'Q' and resid 89 through 92' Processing helix chain 'Q' and resid 190 through 193 No H-bonds generated for 'chain 'Q' and resid 190 through 193' Processing sheet with id= A, first strand: chain 'A' and resid 17 through 19 Processing sheet with id= B, first strand: chain 'A' and resid 84 through 87 Processing sheet with id= C, first strand: chain 'A' and resid 165 through 169 removed outlier: 4.135A pdb=" N ILE A 174 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU A 216 " --> pdb=" O HIS A 176 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 266 through 268 Processing sheet with id= E, first strand: chain 'A' and resid 364 through 368 Processing sheet with id= F, first strand: chain 'A' and resid 369 through 371 removed outlier: 6.129A pdb=" N PHE A 486 " --> pdb=" O SER A 370 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 391 through 395 removed outlier: 3.992A pdb=" N PHE A 420 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N HIS A 453 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ALA A 418 " --> pdb=" O HIS A 453 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 616 through 620 Processing sheet with id= I, first strand: chain 'A' and resid 1209 through 1216 removed outlier: 4.171A pdb=" N ARG A1209 " --> pdb=" O GLU A1228 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N TYR A1223 " --> pdb=" O LEU A1089 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU A1089 " --> pdb=" O TYR A1223 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ARG A1245 " --> pdb=" O GLN A1088 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1165 through 1167 removed outlier: 3.712A pdb=" N PHE A1127 " --> pdb=" O VAL A1120 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR A1116 " --> pdb=" O LYS A1131 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 86 through 88 removed outlier: 3.842A pdb=" N VAL B 87 " --> pdb=" O ARG B 95 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG B 95 " --> pdb=" O VAL B 87 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'B' and resid 124 through 128 removed outlier: 3.541A pdb=" N GLN B 124 " --> pdb=" O ARG B 121 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE B 117 " --> pdb=" O ARG B 128 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN B 79 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLU B 118 " --> pdb=" O TYR B 77 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N TYR B 77 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N THR B 120 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N LEU B 75 " --> pdb=" O THR B 120 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 176 through 178 Processing sheet with id= N, first strand: chain 'B' and resid 361 through 363 removed outlier: 3.921A pdb=" N ILE B 180 " --> pdb=" O ARG B 454 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 188 through 193 removed outlier: 4.038A pdb=" N ARG B 188 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL B 203 " --> pdb=" O ARG B 188 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ALA B 198 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL B 218 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 424 through 426 Processing sheet with id= Q, first strand: chain 'B' and resid 573 through 577 removed outlier: 6.489A pdb=" N LEU B 538 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE B 585 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N PHE B 540 " --> pdb=" O ILE B 585 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY B 547 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU B 541 " --> pdb=" O ILE B 545 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE B 545 " --> pdb=" O LEU B 541 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 594 through 597 removed outlier: 3.746A pdb=" N ARG B 594 " --> pdb=" O LEU B 633 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU B 633 " --> pdb=" O ARG B 594 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 708 through 712 removed outlier: 4.026A pdb=" N LYS B 868 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ARG B 886 " --> pdb=" O ILE B 866 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE B 866 " --> pdb=" O ARG B 886 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 1003 through 1009 removed outlier: 3.932A pdb=" N TYR B1003 " --> pdb=" O VAL B 743 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE B 927 " --> pdb=" O ALA B 742 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 831 through 833 Processing sheet with id= V, first strand: chain 'B' and resid 896 through 898 Processing sheet with id= W, first strand: chain 'B' and resid 1076 through 1079 Processing sheet with id= X, first strand: chain 'B' and resid 110 through 115 removed outlier: 4.433A pdb=" N GLY B 134 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL B 115 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 13 through 16 removed outlier: 4.779A pdb=" N LEU C 299 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU C 236 " --> pdb=" O VAL C 302 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 50 through 56 removed outlier: 6.976A pdb=" N GLU C 62 " --> pdb=" O VAL C 54 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N MET C 56 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N SER C 60 " --> pdb=" O MET C 56 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER C 232 " --> pdb=" O SER C 309 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.808A pdb=" N ASN C 96 " --> pdb=" O ASP C 209 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP C 209 " --> pdb=" O ASN C 96 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU C 207 " --> pdb=" O THR C 98 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 262 through 267 removed outlier: 3.503A pdb=" N LYS C 270 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 86 through 94 removed outlier: 6.481A pdb=" N HIS C 213 " --> pdb=" O GLU C 90 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL C 92 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU C 211 " --> pdb=" O VAL C 92 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 59 through 63 removed outlier: 6.473A pdb=" N ARG E 101 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N PHE E 75 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU E 103 " --> pdb=" O PHE E 75 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE E 126 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ILE E 104 " --> pdb=" O ILE E 126 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLU E 128 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VAL E 106 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE E 130 " --> pdb=" O VAL E 106 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'E' and resid 147 through 150 removed outlier: 4.411A pdb=" N GLN E 189 " --> pdb=" O VAL E 209 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 105 through 109 Processing sheet with id= AG, first strand: chain 'G' and resid 3 through 13 removed outlier: 3.630A pdb=" N VAL G 3 " --> pdb=" O VAL G 76 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP G 9 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL G 70 " --> pdb=" O ASP G 9 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER G 66 " --> pdb=" O ILE G 13 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N CYS G 47 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N PHE G 77 " --> pdb=" O CYS G 45 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N CYS G 45 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'G' and resid 84 through 87 removed outlier: 6.681A pdb=" N ARG G 151 " --> pdb=" O ILE G 190 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE G 190 " --> pdb=" O ARG G 151 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL G 153 " --> pdb=" O GLY G 188 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLY G 188 " --> pdb=" O VAL G 153 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'G' and resid 107 through 109 removed outlier: 6.372A pdb=" N SER G 100 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ILE G 89 " --> pdb=" O SER G 100 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'G' and resid 117 through 119 Processing sheet with id= AK, first strand: chain 'G' and resid 50 through 54 removed outlier: 7.148A pdb=" N HIS G 71 " --> pdb=" O THR G 52 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'H' and resid 25 through 31 removed outlier: 3.943A pdb=" N SER H 26 " --> pdb=" O VAL H 43 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL H 43 " --> pdb=" O SER H 26 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASP H 38 " --> pdb=" O GLN H 126 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP H 42 " --> pdb=" O LEU H 122 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU H 121 " --> pdb=" O TYR H 118 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR H 115 " --> pdb=" O TYR H 97 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'I' and resid 13 through 16 Processing sheet with id= AN, first strand: chain 'I' and resid 77 through 85 removed outlier: 4.058A pdb=" N PHE I 94 " --> pdb=" O ASP I 108 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP I 108 " --> pdb=" O PHE I 94 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'K' and resid 27 through 31 Processing sheet with id= AP, first strand: chain 'L' and resid 17 through 19 Processing sheet with id= AQ, first strand: chain 'M' and resid 14 through 17 Processing sheet with id= AR, first strand: chain 'M' and resid 26 through 29 removed outlier: 6.785A pdb=" N GLY M 131 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N GLN M 29 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU M 133 " --> pdb=" O GLN M 29 " (cutoff:3.500A) No H-bonds generated for sheet with id= AR Processing sheet with id= AS, first strand: chain 'M' and resid 206 through 208 removed outlier: 3.639A pdb=" N ALA M 47 " --> pdb=" O LEU M 208 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLU M 59 " --> pdb=" O LEU M 45 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ALA M 47 " --> pdb=" O GLU M 57 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLU M 57 " --> pdb=" O ALA M 47 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILE M 49 " --> pdb=" O LYS M 55 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LYS M 55 " --> pdb=" O ILE M 49 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'N' and resid 268 through 270 removed outlier: 4.674A pdb=" N VAL N 337 " --> pdb=" O VAL N 348 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'N' and resid 359 through 365 removed outlier: 3.504A pdb=" N GLY N 377 " --> pdb=" O LEU N 360 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N SER N 362 " --> pdb=" O VAL N 375 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N VAL N 375 " --> pdb=" O SER N 362 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY N 364 " --> pdb=" O MET N 373 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N MET N 373 " --> pdb=" O GLY N 364 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'O' and resid 63 through 68 Processing sheet with id= AW, first strand: chain 'O' and resid 157 through 159 Processing sheet with id= AX, first strand: chain 'O' and resid 323 through 327 Processing sheet with id= AY, first strand: chain 'O' and resid 405 through 409 Processing sheet with id= AZ, first strand: chain 'P' and resid 248 through 253 1208 hydrogen bonds defined for protein. 3507 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: 15.85 Time building geometry restraints manager: 15.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.45: 16809 1.45 - 1.67: 23391 1.67 - 1.89: 427 1.89 - 2.11: 0 2.11 - 2.33: 12 Bond restraints: 40639 Sorted by residual: bond pdb=" C ARG N 30 " pdb=" N PRO N 31 " ideal model delta sigma weight residual 1.333 1.357 -0.023 1.01e-02 9.80e+03 5.31e+00 bond pdb=" N GLU B 752 " pdb=" CA GLU B 752 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.23e-02 6.61e+03 5.01e+00 bond pdb=" C GLU A 996 " pdb=" N PRO A 997 " ideal model delta sigma weight residual 1.333 1.354 -0.020 1.01e-02 9.80e+03 4.09e+00 bond pdb=" CA GLU G 95 " pdb=" CB GLU G 95 " ideal model delta sigma weight residual 1.527 1.572 -0.045 2.48e-02 1.63e+03 3.30e+00 bond pdb=" C ILE B 392 " pdb=" N PRO B 393 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.30e-02 5.92e+03 3.16e+00 ... (remaining 40634 not shown) Histogram of bond angle deviations from ideal: 70.14 - 82.92: 12 82.92 - 95.71: 0 95.71 - 108.49: 1995 108.49 - 121.28: 42346 121.28 - 134.06: 10502 Bond angle restraints: 54855 Sorted by residual: angle pdb=" C GLY A 914 " pdb=" N LYS A 915 " pdb=" CA LYS A 915 " ideal model delta sigma weight residual 121.54 130.83 -9.29 1.91e+00 2.74e-01 2.37e+01 angle pdb=" N ASN A1180 " pdb=" CA ASN A1180 " pdb=" C ASN A1180 " ideal model delta sigma weight residual 108.52 115.32 -6.80 1.52e+00 4.33e-01 2.00e+01 angle pdb=" N VAL B 391 " pdb=" CA VAL B 391 " pdb=" C VAL B 391 " ideal model delta sigma weight residual 113.53 109.23 4.30 9.80e-01 1.04e+00 1.93e+01 angle pdb=" N VAL A 37 " pdb=" CA VAL A 37 " pdb=" C VAL A 37 " ideal model delta sigma weight residual 113.71 109.60 4.11 9.50e-01 1.11e+00 1.88e+01 angle pdb=" N LEU A 529 " pdb=" CA LEU A 529 " pdb=" C LEU A 529 " ideal model delta sigma weight residual 114.56 109.30 5.26 1.27e+00 6.20e-01 1.72e+01 ... (remaining 54850 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 22515 17.95 - 35.89: 2001 35.89 - 53.84: 354 53.84 - 71.78: 81 71.78 - 89.73: 45 Dihedral angle restraints: 24996 sinusoidal: 10404 harmonic: 14592 Sorted by residual: dihedral pdb=" CA LYS D 77 " pdb=" C LYS D 77 " pdb=" N LEU D 78 " pdb=" CA LEU D 78 " ideal model delta harmonic sigma weight residual -180.00 -128.52 -51.48 0 5.00e+00 4.00e-02 1.06e+02 dihedral pdb=" CA HIS O 68 " pdb=" C HIS O 68 " pdb=" N LYS O 69 " pdb=" CA LYS O 69 " ideal model delta harmonic sigma weight residual -180.00 -135.43 -44.57 0 5.00e+00 4.00e-02 7.94e+01 dihedral pdb=" CA LYS A 915 " pdb=" C LYS A 915 " pdb=" N ASP A 916 " pdb=" CA ASP A 916 " ideal model delta harmonic sigma weight residual 180.00 153.09 26.91 0 5.00e+00 4.00e-02 2.90e+01 ... (remaining 24993 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.276: 6143 4.276 - 8.552: 0 8.552 - 12.828: 0 12.828 - 17.105: 0 17.105 - 21.381: 4 Chirality restraints: 6147 Sorted by residual: chirality pdb="FE4 SF4 P 400 " pdb=" S1 SF4 P 400 " pdb=" S2 SF4 P 400 " pdb=" S3 SF4 P 400 " both_signs ideal model delta sigma weight residual False 10.55 -10.83 21.38 2.00e-01 2.50e+01 1.14e+04 chirality pdb="FE3 SF4 P 400 " pdb=" S1 SF4 P 400 " pdb=" S2 SF4 P 400 " pdb=" S4 SF4 P 400 " both_signs ideal model delta sigma weight residual False -10.55 10.76 -21.32 2.00e-01 2.50e+01 1.14e+04 chirality pdb="FE2 SF4 P 400 " pdb=" S1 SF4 P 400 " pdb=" S3 SF4 P 400 " pdb=" S4 SF4 P 400 " both_signs ideal model delta sigma weight residual False 10.55 -10.72 21.28 2.00e-01 2.50e+01 1.13e+04 ... (remaining 6144 not shown) Planarity restraints: 7080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS O 68 " 0.013 2.00e-02 2.50e+03 2.74e-02 7.52e+00 pdb=" C HIS O 68 " -0.047 2.00e-02 2.50e+03 pdb=" O HIS O 68 " 0.018 2.00e-02 2.50e+03 pdb=" N LYS O 69 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU Q 27 " 0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO Q 28 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO Q 28 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO Q 28 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO G 110 " -0.028 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO G 111 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO G 111 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 111 " -0.024 5.00e-02 4.00e+02 ... (remaining 7077 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2473 2.74 - 3.28: 38552 3.28 - 3.82: 62464 3.82 - 4.36: 71955 4.36 - 4.90: 124472 Nonbonded interactions: 299916 Sorted by model distance: nonbonded pdb=" OG SER I 86 " pdb=" O GLU I 89 " model vdw 2.196 2.440 nonbonded pdb=" OG SER O 289 " pdb=" OD1 ASN O 291 " model vdw 2.216 2.440 nonbonded pdb=" O ALA D 72 " pdb=" OG SER D 75 " model vdw 2.223 2.440 nonbonded pdb=" OE1 GLU E 78 " pdb=" OH TYR E 90 " model vdw 2.273 2.440 nonbonded pdb=" NH2 ARG O 241 " pdb=" OE1 GLU O 275 " model vdw 2.285 2.520 ... (remaining 299911 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.75 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: 2.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 10.190 Check model and map are aligned: 0.580 Set scattering table: 0.330 Process input model: 112.010 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.140 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 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 : 0.002 0.046 40639 Z= 0.147 Angle : 0.609 9.289 54855 Z= 0.372 Chirality : 0.543 21.381 6147 Planarity : 0.003 0.045 7080 Dihedral : 14.302 89.729 15562 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.51 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.52 (0.10), residues: 4948 helix: -1.83 (0.11), residues: 1724 sheet: -1.05 (0.18), residues: 721 loop : -3.19 (0.09), residues: 2503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 40 HIS 0.004 0.000 HIS E 142 PHE 0.010 0.001 PHE M 139 TYR 0.014 0.001 TYR B 983 ARG 0.005 0.000 ARG C 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9896 Ramachandran restraints generated. 4948 Oldfield, 0 Emsley, 4948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9896 Ramachandran restraints generated. 4948 Oldfield, 0 Emsley, 4948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 951 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 951 time to evaluate : 5.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ARG cc_start: 0.6727 (ttp80) cc_final: 0.6243 (ttp80) REVERT: A 107 MET cc_start: 0.8064 (mmp) cc_final: 0.6858 (mtt) REVERT: A 228 LYS cc_start: 0.9070 (mttt) cc_final: 0.8759 (mtmm) REVERT: A 324 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7263 (mm-30) REVERT: A 353 ARG cc_start: 0.6494 (ptt90) cc_final: 0.6107 (ptt90) REVERT: A 440 MET cc_start: 0.8345 (mmp) cc_final: 0.7821 (mtt) REVERT: A 635 ASP cc_start: 0.7733 (t70) cc_final: 0.7388 (t0) REVERT: A 646 MET cc_start: 0.8038 (mmm) cc_final: 0.7714 (mmm) REVERT: A 678 ASP cc_start: 0.7945 (t0) cc_final: 0.7612 (t0) REVERT: A 759 ILE cc_start: 0.7974 (pt) cc_final: 0.7716 (pt) REVERT: A 963 ASP cc_start: 0.7927 (t0) cc_final: 0.7686 (t0) REVERT: A 968 GLU cc_start: 0.8431 (tm-30) cc_final: 0.8118 (tm-30) REVERT: A 1118 GLU cc_start: 0.7498 (pt0) cc_final: 0.6305 (pt0) REVERT: A 1191 PHE cc_start: 0.8504 (t80) cc_final: 0.8227 (t80) REVERT: A 1193 LYS cc_start: 0.9482 (pptt) cc_final: 0.9135 (pttt) REVERT: A 1250 ASN cc_start: 0.8221 (t0) cc_final: 0.6758 (t0) REVERT: A 1252 TYR cc_start: 0.7675 (t80) cc_final: 0.7256 (t80) REVERT: A 1255 GLU cc_start: 0.8753 (pp20) cc_final: 0.8535 (pp20) REVERT: A 1318 LEU cc_start: 0.8980 (mt) cc_final: 0.8615 (tt) REVERT: A 1330 ASP cc_start: 0.8075 (m-30) cc_final: 0.7819 (m-30) REVERT: B 54 GLU cc_start: 0.8310 (tp30) cc_final: 0.7793 (mp0) REVERT: B 106 ASP cc_start: 0.7150 (m-30) cc_final: 0.6850 (m-30) REVERT: B 192 GLU cc_start: 0.7348 (mm-30) cc_final: 0.5529 (mm-30) REVERT: B 239 ILE cc_start: 0.9244 (mm) cc_final: 0.8962 (mm) REVERT: B 354 ARG cc_start: 0.7769 (mtt90) cc_final: 0.7548 (mpt-90) REVERT: B 1121 ASN cc_start: 0.6967 (t0) cc_final: 0.6576 (t0) REVERT: C 180 ASN cc_start: 0.8436 (t0) cc_final: 0.8223 (p0) REVERT: D 100 MET cc_start: 0.6205 (mmt) cc_final: 0.5905 (mmm) REVERT: E 73 PHE cc_start: 0.8465 (t80) cc_final: 0.7709 (t80) REVERT: F 88 ASP cc_start: 0.7491 (t70) cc_final: 0.7151 (t70) REVERT: F 91 LEU cc_start: 0.9090 (tp) cc_final: 0.8883 (tp) REVERT: G 82 ASP cc_start: 0.7273 (p0) cc_final: 0.6915 (p0) REVERT: G 108 LEU cc_start: 0.9034 (pp) cc_final: 0.8828 (tt) REVERT: G 185 THR cc_start: 0.9030 (m) cc_final: 0.8771 (p) REVERT: I 13 ILE cc_start: 0.8260 (pt) cc_final: 0.7876 (pt) REVERT: I 15 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7167 (mm-30) REVERT: K 28 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7502 (mp0) REVERT: K 60 MET cc_start: 0.9149 (mmt) cc_final: 0.8906 (mmt) REVERT: K 64 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7655 (tp30) REVERT: M 60 MET cc_start: 0.8293 (ptm) cc_final: 0.7989 (ppp) REVERT: M 220 HIS cc_start: 0.8835 (m-70) cc_final: 0.8589 (m90) REVERT: N 382 LYS cc_start: 0.9292 (ttpt) cc_final: 0.8792 (tttm) REVERT: O 513 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8610 (mt-10) REVERT: P 185 PHE cc_start: 0.9235 (t80) cc_final: 0.8995 (t80) REVERT: P 245 ASP cc_start: 0.8558 (t70) cc_final: 0.8157 (t70) REVERT: P 247 LYS cc_start: 0.8343 (mtmm) cc_final: 0.7665 (pttm) REVERT: P 250 MET cc_start: 0.7776 (ttt) cc_final: 0.7311 (tpt) REVERT: P 295 ASP cc_start: 0.8353 (t70) cc_final: 0.7515 (t0) REVERT: Q 43 TYR cc_start: 0.6231 (m-80) cc_final: 0.5782 (m-80) REVERT: Q 61 LYS cc_start: 0.9003 (ttpt) cc_final: 0.8628 (ptmt) outliers start: 0 outliers final: 0 residues processed: 951 average time/residue: 0.7034 time to fit residues: 1030.6162 Evaluate side-chains 583 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 583 time to evaluate : 4.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 415 optimal weight: 4.9990 chunk 372 optimal weight: 4.9990 chunk 206 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 251 optimal weight: 3.9990 chunk 199 optimal weight: 6.9990 chunk 385 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 chunk 234 optimal weight: 0.8980 chunk 287 optimal weight: 0.0980 chunk 446 optimal weight: 3.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 33 HIS A 44 GLN A 157 HIS ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 GLN ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 ASN A 534 ASN A 599 GLN A 616 ASN A 737 GLN A 775 ASN A 794 GLN ** A 815 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1039 GLN ** A1213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1231 ASN A1239 HIS A1286 HIS B 92 ASN ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN B 208 HIS B 280 GLN B 349 ASN B 410 GLN B 413 ASN B 501 HIS B 602 GLN B 683 ASN B 692 GLN B 758 ASN B 823 ASN B 850 GLN B 932 HIS B1034 GLN B1082 GLN B1121 ASN B1132 ASN C 25 HIS C 32 ASN C 127 GLN C 172 HIS C 344 GLN D 33 ASN ** E 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN E 168 ASN G 17 GLN ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 GLN I 32 HIS ** I 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 GLN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 707 GLN N 338 GLN N 358 GLN N 378 HIS ** N 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 397 HIS O 59 GLN O 60 HIS ** O 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 415 HIS O 515 GLN O 534 GLN P 181 ASN Q 185 GLN Q 197 ASN Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.296 40639 Z= 0.441 Angle : 1.030 51.629 54855 Z= 0.622 Chirality : 0.160 6.198 6147 Planarity : 0.005 0.096 7080 Dihedral : 3.949 46.727 5451 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.54 % Favored : 94.42 % Rotamer: Outliers : 2.33 % Allowed : 14.14 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.39 (0.11), residues: 4948 helix: -0.61 (0.12), residues: 1723 sheet: -0.44 (0.18), residues: 756 loop : -2.76 (0.10), residues: 2469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP M 700 HIS 0.015 0.001 HIS A 82 PHE 0.023 0.002 PHE B 223 TYR 0.033 0.002 TYR B1009 ARG 0.019 0.001 ARG B 222 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9896 Ramachandran restraints generated. 4948 Oldfield, 0 Emsley, 4948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9896 Ramachandran restraints generated. 4948 Oldfield, 0 Emsley, 4948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 594 time to evaluate : 5.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8612 (ttpt) REVERT: A 168 LYS cc_start: 0.8924 (pttt) cc_final: 0.8656 (tttm) REVERT: A 228 LYS cc_start: 0.9217 (mttt) cc_final: 0.8922 (mtmm) REVERT: A 353 ARG cc_start: 0.6658 (ptt90) cc_final: 0.6451 (ptt90) REVERT: A 440 MET cc_start: 0.8389 (mmp) cc_final: 0.7828 (mtt) REVERT: A 474 MET cc_start: 0.8352 (mtt) cc_final: 0.8152 (mtt) REVERT: A 572 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8909 (pp) REVERT: A 646 MET cc_start: 0.8525 (mmm) cc_final: 0.8296 (mmm) REVERT: A 968 GLU cc_start: 0.8337 (tm-30) cc_final: 0.8131 (tm-30) REVERT: A 1004 ASP cc_start: 0.6590 (p0) cc_final: 0.6281 (p0) REVERT: A 1061 MET cc_start: 0.7449 (mpp) cc_final: 0.7238 (mpp) REVERT: A 1096 ASP cc_start: 0.8381 (OUTLIER) cc_final: 0.8088 (t0) REVERT: A 1168 HIS cc_start: 0.8680 (m-70) cc_final: 0.8447 (m-70) REVERT: A 1193 LYS cc_start: 0.9586 (pptt) cc_final: 0.9259 (pttm) REVERT: B 405 HIS cc_start: 0.8566 (m90) cc_final: 0.8176 (m-70) REVERT: B 791 MET cc_start: 0.7786 (mmp) cc_final: 0.7551 (mmp) REVERT: B 1037 GLU cc_start: 0.7993 (tp30) cc_final: 0.7712 (tp30) REVERT: B 1094 TYR cc_start: 0.8762 (t80) cc_final: 0.8381 (t80) REVERT: C 124 TYR cc_start: 0.8013 (OUTLIER) cc_final: 0.7425 (t80) REVERT: E 72 MET cc_start: 0.8318 (tpt) cc_final: 0.7846 (tpt) REVERT: E 73 PHE cc_start: 0.8621 (t80) cc_final: 0.7889 (t80) REVERT: F 88 ASP cc_start: 0.7468 (t70) cc_final: 0.7040 (t0) REVERT: F 91 LEU cc_start: 0.9236 (tp) cc_final: 0.8892 (mt) REVERT: G 82 ASP cc_start: 0.7418 (p0) cc_final: 0.7179 (p0) REVERT: G 90 LYS cc_start: 0.8869 (mmmt) cc_final: 0.8623 (mtmm) REVERT: G 142 MET cc_start: 0.4844 (pmm) cc_final: 0.3688 (mmt) REVERT: G 185 THR cc_start: 0.9152 (m) cc_final: 0.8864 (p) REVERT: H 13 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8146 (mppt) REVERT: I 24 SER cc_start: 0.8719 (t) cc_final: 0.8218 (p) REVERT: K 28 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7476 (mp0) REVERT: K 64 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7876 (tp30) REVERT: K 112 ASP cc_start: 0.8062 (m-30) cc_final: 0.7840 (m-30) REVERT: M 60 MET cc_start: 0.8308 (ptm) cc_final: 0.8030 (ppp) REVERT: M 707 GLN cc_start: 0.4444 (OUTLIER) cc_final: 0.3533 (tp-100) REVERT: N 358 GLN cc_start: 0.8692 (mt0) cc_final: 0.8432 (mm110) REVERT: O 85 MET cc_start: 0.9010 (mtp) cc_final: 0.8625 (ttm) REVERT: O 284 PHE cc_start: 0.8747 (m-80) cc_final: 0.8363 (p90) REVERT: O 490 MET cc_start: 0.3699 (tmm) cc_final: 0.3459 (ppp) REVERT: O 507 ASN cc_start: 0.8953 (m-40) cc_final: 0.8750 (m-40) REVERT: P 180 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7994 (pp) REVERT: P 185 PHE cc_start: 0.9278 (t80) cc_final: 0.9002 (t80) REVERT: P 203 MET cc_start: 0.8605 (pmm) cc_final: 0.8401 (tpp) REVERT: P 230 LEU cc_start: 0.7231 (mm) cc_final: 0.6938 (tp) REVERT: P 245 ASP cc_start: 0.8639 (t70) cc_final: 0.8247 (t70) REVERT: P 250 MET cc_start: 0.7713 (ttt) cc_final: 0.7360 (tpt) REVERT: P 295 ASP cc_start: 0.8323 (t70) cc_final: 0.7986 (t0) REVERT: Q 61 LYS cc_start: 0.9093 (ttpt) cc_final: 0.8817 (ttpt) REVERT: Q 74 PHE cc_start: 0.7998 (t80) cc_final: 0.7765 (t80) REVERT: Q 203 TYR cc_start: 0.8567 (m-80) cc_final: 0.8245 (m-80) outliers start: 103 outliers final: 52 residues processed: 663 average time/residue: 0.6223 time to fit residues: 665.1470 Evaluate side-chains 575 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 516 time to evaluate : 4.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 711 LYS Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 1096 ASP Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1195 ASP Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 43 HIS Chi-restraints excluded: chain B residue 81 TYR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 1065 LEU Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 124 TYR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain D residue 13 ASN Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 76 HIS Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 116 GLN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain K residue 110 VAL Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 127 THR Chi-restraints excluded: chain M residue 139 PHE Chi-restraints excluded: chain M residue 707 GLN Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 343 LYS Chi-restraints excluded: chain N residue 355 SER Chi-restraints excluded: chain N residue 394 ASP Chi-restraints excluded: chain O residue 135 ASP Chi-restraints excluded: chain O residue 362 CYS Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 187 PHE Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 268 LYS Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 297 HIS Chi-restraints excluded: chain Q residue 40 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 248 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 371 optimal weight: 6.9990 chunk 304 optimal weight: 9.9990 chunk 123 optimal weight: 10.0000 chunk 447 optimal weight: 20.0000 chunk 483 optimal weight: 3.9990 chunk 398 optimal weight: 5.9990 chunk 443 optimal weight: 8.9990 chunk 152 optimal weight: 4.9990 chunk 359 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN A1168 HIS A1190 GLN ** A1213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN B 79 ASN B 159 ASN B 346 GLN B 524 ASN ** B 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 829 ASN C 213 HIS C 305 HIS D 41 ASN D 76 HIS ** E 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 HIS G 36 ASN H 126 GLN I 32 HIS ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 104 HIS K 85 GLN ** L 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 707 GLN ** N 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 113 ASN ** O 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 377 GLN O 465 GLN O 505 ASN ** P 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 207 ASN Q 197 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.235 40639 Z= 0.592 Angle : 1.087 50.541 54855 Z= 0.649 Chirality : 0.168 6.341 6147 Planarity : 0.005 0.070 7080 Dihedral : 4.537 43.057 5451 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.31 % Favored : 93.61 % Rotamer: Outliers : 4.13 % Allowed : 17.73 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.11), residues: 4948 helix: -0.16 (0.12), residues: 1741 sheet: -0.56 (0.18), residues: 796 loop : -2.58 (0.11), residues: 2411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 424 HIS 0.010 0.002 HIS B 676 PHE 0.023 0.002 PHE K 67 TYR 0.029 0.002 TYR B1009 ARG 0.011 0.001 ARG Q 70 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9896 Ramachandran restraints generated. 4948 Oldfield, 0 Emsley, 4948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9896 Ramachandran restraints generated. 4948 Oldfield, 0 Emsley, 4948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 533 time to evaluate : 4.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8117 (ptpt) cc_final: 0.7914 (pttp) REVERT: A 56 LEU cc_start: 0.9345 (tt) cc_final: 0.8788 (mp) REVERT: A 228 LYS cc_start: 0.9315 (mttt) cc_final: 0.9046 (mtmm) REVERT: A 440 MET cc_start: 0.8385 (mmp) cc_final: 0.8003 (mtt) REVERT: A 572 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.8956 (pp) REVERT: A 968 GLU cc_start: 0.8287 (tm-30) cc_final: 0.8037 (tm-30) REVERT: A 1004 ASP cc_start: 0.6708 (p0) cc_final: 0.6425 (p0) REVERT: A 1048 MET cc_start: 0.8142 (mtt) cc_final: 0.7929 (mtp) REVERT: A 1088 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7922 (mp10) REVERT: A 1096 ASP cc_start: 0.8534 (OUTLIER) cc_final: 0.8238 (t0) REVERT: A 1168 HIS cc_start: 0.8488 (m170) cc_final: 0.8249 (m-70) REVERT: A 1193 LYS cc_start: 0.9593 (pptt) cc_final: 0.9347 (pttt) REVERT: A 1349 MET cc_start: 0.8652 (mmm) cc_final: 0.8452 (mmm) REVERT: B 43 HIS cc_start: 0.8795 (OUTLIER) cc_final: 0.7819 (t70) REVERT: B 415 MET cc_start: 0.9032 (mmm) cc_final: 0.8815 (mmt) REVERT: B 794 MET cc_start: 0.8259 (tpp) cc_final: 0.7836 (tpp) REVERT: B 829 ASN cc_start: 0.8445 (OUTLIER) cc_final: 0.7984 (m110) REVERT: C 138 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8534 (mp) REVERT: D 47 TYR cc_start: 0.8477 (t80) cc_final: 0.8261 (t80) REVERT: D 100 MET cc_start: 0.6451 (mmt) cc_final: 0.5705 (mmm) REVERT: E 72 MET cc_start: 0.7772 (tpt) cc_final: 0.7495 (tpt) REVERT: E 73 PHE cc_start: 0.8581 (t80) cc_final: 0.7968 (t80) REVERT: E 110 MET cc_start: 0.6985 (tpp) cc_final: 0.6348 (tpt) REVERT: E 144 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7800 (pp) REVERT: E 165 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8907 (pp) REVERT: F 88 ASP cc_start: 0.7917 (t70) cc_final: 0.7538 (t0) REVERT: F 91 LEU cc_start: 0.9368 (tp) cc_final: 0.9128 (mt) REVERT: G 151 ARG cc_start: 0.8720 (mtp180) cc_final: 0.8304 (mtp85) REVERT: H 13 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8174 (mppt) REVERT: I 91 MET cc_start: 0.2446 (tpp) cc_final: 0.1920 (tmm) REVERT: I 104 HIS cc_start: 0.8003 (OUTLIER) cc_final: 0.7311 (m90) REVERT: J 31 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7244 (mm-30) REVERT: K 24 LYS cc_start: 0.6715 (tmtt) cc_final: 0.6364 (tmtt) REVERT: K 47 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8803 (mm-30) REVERT: K 112 ASP cc_start: 0.8071 (m-30) cc_final: 0.7863 (m-30) REVERT: K 128 ARG cc_start: 0.7246 (ttp80) cc_final: 0.7041 (ttp80) REVERT: M 37 MET cc_start: 0.8859 (ptp) cc_final: 0.8606 (ptp) REVERT: M 60 MET cc_start: 0.8377 (ptm) cc_final: 0.8120 (ppp) REVERT: M 220 HIS cc_start: 0.8665 (m-70) cc_final: 0.8444 (m-70) REVERT: M 248 MET cc_start: 0.8691 (ptp) cc_final: 0.8312 (ptp) REVERT: M 699 MET cc_start: 0.6289 (ppp) cc_final: 0.5450 (ppp) REVERT: M 707 GLN cc_start: 0.3877 (OUTLIER) cc_final: 0.3496 (tp40) REVERT: N 358 GLN cc_start: 0.8606 (mt0) cc_final: 0.8385 (mt0) REVERT: O 259 MET cc_start: 0.8383 (pmm) cc_final: 0.7905 (ppp) REVERT: O 385 MET cc_start: 0.8010 (ttm) cc_final: 0.7788 (ttm) REVERT: O 404 MET cc_start: 0.8460 (pmm) cc_final: 0.8206 (pmm) REVERT: O 419 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.8063 (ppt90) REVERT: O 490 MET cc_start: 0.3811 (tmm) cc_final: 0.3465 (ppp) REVERT: P 180 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8105 (pp) REVERT: P 185 PHE cc_start: 0.9302 (t80) cc_final: 0.9017 (t80) REVERT: P 210 PHE cc_start: 0.7391 (p90) cc_final: 0.7159 (p90) REVERT: P 219 TYR cc_start: 0.8894 (t80) cc_final: 0.8463 (m-10) REVERT: P 230 LEU cc_start: 0.7386 (mm) cc_final: 0.7080 (tp) REVERT: P 245 ASP cc_start: 0.8683 (t70) cc_final: 0.8244 (t70) REVERT: P 247 LYS cc_start: 0.8452 (mtmm) cc_final: 0.7965 (mtmm) REVERT: P 250 MET cc_start: 0.7817 (ttt) cc_final: 0.7458 (tpt) REVERT: P 295 ASP cc_start: 0.8474 (t70) cc_final: 0.8128 (t0) REVERT: Q 74 PHE cc_start: 0.8671 (t80) cc_final: 0.8467 (t80) outliers start: 183 outliers final: 99 residues processed: 667 average time/residue: 0.5585 time to fit residues: 601.0880 Evaluate side-chains 588 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 476 time to evaluate : 4.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 1084 ILE Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1088 GLN Chi-restraints excluded: chain A residue 1096 ASP Chi-restraints excluded: chain A residue 1108 THR Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1195 ASP Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1235 VAL Chi-restraints excluded: chain A residue 1241 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 43 HIS Chi-restraints excluded: chain B residue 81 TYR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 125 ARG Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 408 GLN Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 829 ASN Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 973 CYS Chi-restraints excluded: chain B residue 1032 THR Chi-restraints excluded: chain B residue 1065 LEU Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 116 GLN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 26 ASN Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 104 HIS Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 110 VAL Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 127 THR Chi-restraints excluded: chain M residue 139 PHE Chi-restraints excluded: chain M residue 707 GLN Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 343 LYS Chi-restraints excluded: chain N residue 394 ASP Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 135 ASP Chi-restraints excluded: chain O residue 248 ASP Chi-restraints excluded: chain O residue 362 CYS Chi-restraints excluded: chain O residue 419 ARG Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 187 PHE Chi-restraints excluded: chain P residue 188 LEU Chi-restraints excluded: chain P residue 268 LYS Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain Q residue 40 ASP Chi-restraints excluded: chain Q residue 43 TYR Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 197 ASN Chi-restraints excluded: chain Q residue 198 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 442 optimal weight: 3.9990 chunk 336 optimal weight: 8.9990 chunk 232 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 213 optimal weight: 3.9990 chunk 300 optimal weight: 0.9990 chunk 449 optimal weight: 10.0000 chunk 475 optimal weight: 30.0000 chunk 234 optimal weight: 0.7980 chunk 425 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1213 HIS B 43 HIS ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 ASN B 602 GLN B 806 HIS ** B 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 HIS ** E 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 104 HIS K 85 GLN K 109 HIS ** M 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 278 GLN ** O 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.242 40639 Z= 0.317 Angle : 0.978 50.530 54855 Z= 0.596 Chirality : 0.166 6.306 6147 Planarity : 0.004 0.073 7080 Dihedral : 4.169 43.139 5451 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.99 % Favored : 94.95 % Rotamer: Outliers : 2.62 % Allowed : 20.33 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.11), residues: 4948 helix: 0.30 (0.13), residues: 1727 sheet: -0.33 (0.18), residues: 781 loop : -2.38 (0.11), residues: 2440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP Q 103 HIS 0.014 0.001 HIS I 104 PHE 0.024 0.001 PHE A 193 TYR 0.027 0.001 TYR Q 43 ARG 0.009 0.000 ARG N 369 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9896 Ramachandran restraints generated. 4948 Oldfield, 0 Emsley, 4948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9896 Ramachandran restraints generated. 4948 Oldfield, 0 Emsley, 4948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 510 time to evaluate : 4.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.7945 (ptpt) cc_final: 0.7715 (pttp) REVERT: A 56 LEU cc_start: 0.9309 (tt) cc_final: 0.8779 (mp) REVERT: A 107 MET cc_start: 0.8299 (mmp) cc_final: 0.7291 (mtt) REVERT: A 197 PHE cc_start: 0.8170 (OUTLIER) cc_final: 0.7317 (m-80) REVERT: A 228 LYS cc_start: 0.9222 (mttt) cc_final: 0.8983 (mtmm) REVERT: A 440 MET cc_start: 0.8321 (mmp) cc_final: 0.8048 (mtt) REVERT: A 572 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.8936 (pp) REVERT: A 968 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7930 (tm-30) REVERT: A 1168 HIS cc_start: 0.8408 (m170) cc_final: 0.8101 (m-70) REVERT: A 1193 LYS cc_start: 0.9619 (pptt) cc_final: 0.9334 (pttm) REVERT: A 1318 LEU cc_start: 0.9107 (mt) cc_final: 0.8902 (mt) REVERT: B 43 HIS cc_start: 0.8518 (OUTLIER) cc_final: 0.7194 (t-90) REVERT: B 292 ARG cc_start: 0.8774 (ptt90) cc_final: 0.8206 (pmt-80) REVERT: B 787 PHE cc_start: 0.6934 (m-80) cc_final: 0.6641 (m-10) REVERT: B 794 MET cc_start: 0.8351 (tpp) cc_final: 0.8043 (tpp) REVERT: E 18 MET cc_start: 0.8368 (ttm) cc_final: 0.8123 (ttm) REVERT: E 72 MET cc_start: 0.8002 (tpt) cc_final: 0.7704 (tpt) REVERT: E 73 PHE cc_start: 0.8649 (t80) cc_final: 0.8019 (t80) REVERT: E 110 MET cc_start: 0.7260 (tpp) cc_final: 0.6415 (tpt) REVERT: E 165 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8704 (pp) REVERT: F 88 ASP cc_start: 0.7729 (t70) cc_final: 0.7396 (t70) REVERT: F 91 LEU cc_start: 0.9335 (tp) cc_final: 0.9131 (tp) REVERT: G 1 MET cc_start: 0.8780 (pmm) cc_final: 0.8361 (pmm) REVERT: G 151 ARG cc_start: 0.8673 (mtp180) cc_final: 0.8170 (ttm-80) REVERT: G 185 THR cc_start: 0.9231 (OUTLIER) cc_final: 0.8995 (p) REVERT: H 13 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8159 (mppt) REVERT: I 37 LYS cc_start: 0.6488 (tppt) cc_final: 0.6174 (tppt) REVERT: I 104 HIS cc_start: 0.7880 (OUTLIER) cc_final: 0.7350 (m170) REVERT: M 37 MET cc_start: 0.8751 (ptp) cc_final: 0.8151 (ptp) REVERT: M 60 MET cc_start: 0.8308 (ptm) cc_final: 0.8065 (ppp) REVERT: M 220 HIS cc_start: 0.8697 (m-70) cc_final: 0.8393 (m-70) REVERT: M 248 MET cc_start: 0.8619 (ptp) cc_final: 0.8230 (ptp) REVERT: M 699 MET cc_start: 0.6519 (ppp) cc_final: 0.6032 (ppp) REVERT: N 39 ARG cc_start: 0.6618 (OUTLIER) cc_final: 0.6364 (ttt-90) REVERT: N 390 GLU cc_start: 0.8831 (pm20) cc_final: 0.8530 (pm20) REVERT: N 396 LYS cc_start: 0.8771 (ttmm) cc_final: 0.8305 (ttmm) REVERT: O 385 MET cc_start: 0.8019 (ttm) cc_final: 0.7776 (ttm) REVERT: O 404 MET cc_start: 0.8492 (pmm) cc_final: 0.8210 (pmm) REVERT: P 185 PHE cc_start: 0.9298 (t80) cc_final: 0.9067 (t80) REVERT: P 230 LEU cc_start: 0.7226 (mm) cc_final: 0.6875 (tp) REVERT: P 245 ASP cc_start: 0.8605 (t70) cc_final: 0.8202 (t70) REVERT: P 250 MET cc_start: 0.7753 (ttt) cc_final: 0.7534 (ttt) REVERT: P 267 MET cc_start: 0.7327 (tpp) cc_final: 0.6794 (tpp) REVERT: P 295 ASP cc_start: 0.8475 (t70) cc_final: 0.8102 (t0) REVERT: Q 74 PHE cc_start: 0.8664 (t80) cc_final: 0.8364 (t80) REVERT: Q 92 MET cc_start: 0.4110 (mpp) cc_final: 0.3905 (mpp) REVERT: Q 104 ARG cc_start: 0.8735 (mpp-170) cc_final: 0.8322 (mmp80) outliers start: 116 outliers final: 72 residues processed: 586 average time/residue: 0.5592 time to fit residues: 534.5670 Evaluate side-chains 543 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 463 time to evaluate : 4.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1155 THR Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1195 ASP Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1235 VAL Chi-restraints excluded: chain A residue 1241 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 43 HIS Chi-restraints excluded: chain B residue 81 TYR Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 357 TYR Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 658 GLU Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 1032 THR Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain D residue 76 HIS Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 142 HIS Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 26 ASN Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 104 HIS Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain M residue 225 LEU Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 39 ARG Chi-restraints excluded: chain N residue 343 LYS Chi-restraints excluded: chain N residue 360 LEU Chi-restraints excluded: chain O residue 135 ASP Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 362 CYS Chi-restraints excluded: chain O residue 419 ARG Chi-restraints excluded: chain P residue 173 GLU Chi-restraints excluded: chain P residue 187 PHE Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 268 LYS Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain Q residue 40 ASP Chi-restraints excluded: chain Q residue 43 TYR Chi-restraints excluded: chain Q residue 197 ASN Chi-restraints excluded: chain Q residue 198 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 396 optimal weight: 10.0000 chunk 269 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 354 optimal weight: 7.9990 chunk 196 optimal weight: 4.9990 chunk 405 optimal weight: 8.9990 chunk 328 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 242 optimal weight: 8.9990 chunk 426 optimal weight: 8.9990 chunk 120 optimal weight: 6.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 GLN B 423 ASN ** B 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN C 213 HIS ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 GLN E 129 GLN ** G 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 108 GLN ** M 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 358 GLN ** N 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 197 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.5091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.232 40639 Z= 0.595 Angle : 1.074 50.589 54855 Z= 0.639 Chirality : 0.167 6.299 6147 Planarity : 0.005 0.070 7080 Dihedral : 4.556 42.820 5451 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.05 % Favored : 92.89 % Rotamer: Outliers : 4.63 % Allowed : 20.01 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.11), residues: 4948 helix: 0.23 (0.12), residues: 1738 sheet: -0.46 (0.18), residues: 811 loop : -2.39 (0.11), residues: 2399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP Q 103 HIS 0.026 0.002 HIS B 43 PHE 0.029 0.002 PHE M 195 TYR 0.026 0.002 TYR A 179 ARG 0.014 0.001 ARG N 29 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9896 Ramachandran restraints generated. 4948 Oldfield, 0 Emsley, 4948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9896 Ramachandran restraints generated. 4948 Oldfield, 0 Emsley, 4948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 479 time to evaluate : 5.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.9370 (tt) cc_final: 0.8873 (mp) REVERT: A 107 MET cc_start: 0.8382 (mmp) cc_final: 0.7519 (mtt) REVERT: A 197 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.7498 (m-80) REVERT: A 228 LYS cc_start: 0.9382 (mttt) cc_final: 0.9112 (mtmm) REVERT: A 572 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.8937 (pp) REVERT: A 912 MET cc_start: 0.8150 (mtp) cc_final: 0.7794 (mtp) REVERT: A 1004 ASP cc_start: 0.6679 (p0) cc_final: 0.6388 (p0) REVERT: A 1088 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7961 (mp10) REVERT: A 1168 HIS cc_start: 0.8497 (m170) cc_final: 0.8047 (m-70) REVERT: A 1193 LYS cc_start: 0.9596 (pptt) cc_final: 0.9365 (pttt) REVERT: A 1318 LEU cc_start: 0.9166 (mt) cc_final: 0.8900 (mt) REVERT: A 1363 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8036 (mp) REVERT: B 43 HIS cc_start: 0.8662 (OUTLIER) cc_final: 0.7736 (t70) REVERT: B 787 PHE cc_start: 0.7202 (m-80) cc_final: 0.6829 (m-10) REVERT: B 1042 ASP cc_start: 0.8710 (t0) cc_final: 0.8133 (t0) REVERT: C 138 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8524 (mp) REVERT: C 270 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7723 (mmmt) REVERT: D 100 MET cc_start: 0.6567 (mmt) cc_final: 0.5783 (mmm) REVERT: E 72 MET cc_start: 0.7635 (tpt) cc_final: 0.7397 (tpt) REVERT: E 73 PHE cc_start: 0.8638 (t80) cc_final: 0.7971 (t80) REVERT: E 110 MET cc_start: 0.7395 (tpp) cc_final: 0.6576 (tpt) REVERT: E 144 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8062 (pp) REVERT: E 165 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8823 (pp) REVERT: F 88 ASP cc_start: 0.8068 (t70) cc_final: 0.7705 (t70) REVERT: G 142 MET cc_start: 0.5047 (pmm) cc_final: 0.4800 (pmm) REVERT: G 151 ARG cc_start: 0.8722 (mtp180) cc_final: 0.8201 (ttm-80) REVERT: H 13 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8207 (mppt) REVERT: H 15 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8847 (mt) REVERT: I 74 HIS cc_start: 0.7792 (m-70) cc_final: 0.7513 (t-170) REVERT: I 91 MET cc_start: 0.3445 (tmm) cc_final: 0.2872 (tmm) REVERT: I 104 HIS cc_start: 0.8221 (OUTLIER) cc_final: 0.7768 (m-70) REVERT: J 31 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7298 (mm-30) REVERT: J 58 LYS cc_start: 0.9082 (mmmt) cc_final: 0.8840 (mmmm) REVERT: K 64 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7747 (tp30) REVERT: K 85 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8152 (mt0) REVERT: K 124 GLN cc_start: 0.8432 (tm-30) cc_final: 0.8182 (tm-30) REVERT: M 37 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8114 (ptp) REVERT: M 60 MET cc_start: 0.8326 (ptm) cc_final: 0.8023 (ppp) REVERT: M 220 HIS cc_start: 0.8681 (m-70) cc_final: 0.8378 (m-70) REVERT: M 248 MET cc_start: 0.8637 (ptp) cc_final: 0.8250 (ptp) REVERT: M 699 MET cc_start: 0.6630 (ppp) cc_final: 0.6309 (ppp) REVERT: N 30 ARG cc_start: 0.8522 (mmp80) cc_final: 0.8300 (mmp80) REVERT: N 39 ARG cc_start: 0.6793 (OUTLIER) cc_final: 0.6428 (ttt-90) REVERT: N 247 LYS cc_start: 0.8694 (tppt) cc_final: 0.8277 (tptp) REVERT: N 358 GLN cc_start: 0.8780 (mt0) cc_final: 0.8542 (mm110) REVERT: N 396 LYS cc_start: 0.8810 (ttmm) cc_final: 0.8379 (ttmm) REVERT: O 385 MET cc_start: 0.8155 (ttm) cc_final: 0.7904 (ttm) REVERT: O 398 MET cc_start: 0.9156 (mmt) cc_final: 0.8836 (mmt) REVERT: O 404 MET cc_start: 0.8475 (pmm) cc_final: 0.8178 (pmm) REVERT: O 419 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7557 (ppt90) REVERT: O 490 MET cc_start: 0.3603 (ppp) cc_final: 0.3152 (ppp) REVERT: P 185 PHE cc_start: 0.9283 (t80) cc_final: 0.9049 (t80) REVERT: P 203 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.7404 (ppp) REVERT: P 210 PHE cc_start: 0.7440 (p90) cc_final: 0.7207 (p90) REVERT: P 230 LEU cc_start: 0.7323 (mm) cc_final: 0.6972 (tp) REVERT: P 245 ASP cc_start: 0.8663 (t70) cc_final: 0.8218 (t70) REVERT: P 247 LYS cc_start: 0.8422 (mtmm) cc_final: 0.7974 (mtmm) REVERT: P 295 ASP cc_start: 0.8531 (t70) cc_final: 0.8143 (t0) REVERT: Q 71 MET cc_start: 0.7316 (tpp) cc_final: 0.6777 (mmm) REVERT: Q 74 PHE cc_start: 0.8837 (t80) cc_final: 0.8603 (t80) REVERT: Q 102 ASP cc_start: 0.9010 (t70) cc_final: 0.8400 (t0) REVERT: Q 104 ARG cc_start: 0.8894 (mpp-170) cc_final: 0.8468 (mmp80) REVERT: Q 204 PHE cc_start: 0.8570 (t80) cc_final: 0.8264 (t80) outliers start: 205 outliers final: 130 residues processed: 629 average time/residue: 0.5435 time to fit residues: 557.9479 Evaluate side-chains 596 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 449 time to evaluate : 4.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 320 TYR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1061 MET Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1088 GLN Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1108 THR Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1195 ASP Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1235 VAL Chi-restraints excluded: chain A residue 1241 VAL Chi-restraints excluded: chain A residue 1363 LEU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 43 HIS Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 81 TYR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 357 TYR Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 618 TYR Chi-restraints excluded: chain B residue 658 GLU Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 877 ASP Chi-restraints excluded: chain B residue 973 CYS Chi-restraints excluded: chain B residue 1032 THR Chi-restraints excluded: chain B residue 1065 LEU Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 76 HIS Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 116 GLN Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 26 ASN Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 104 HIS Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 85 GLN Chi-restraints excluded: chain K residue 127 SER Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 127 THR Chi-restraints excluded: chain M residue 139 PHE Chi-restraints excluded: chain M residue 250 MET Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 39 ARG Chi-restraints excluded: chain N residue 261 THR Chi-restraints excluded: chain N residue 343 LYS Chi-restraints excluded: chain N residue 360 LEU Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 135 ASP Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 362 CYS Chi-restraints excluded: chain O residue 419 ARG Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain O residue 529 CYS Chi-restraints excluded: chain P residue 173 GLU Chi-restraints excluded: chain P residue 187 PHE Chi-restraints excluded: chain P residue 188 LEU Chi-restraints excluded: chain P residue 203 MET Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 268 LYS Chi-restraints excluded: chain P residue 287 CYS Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 32 LEU Chi-restraints excluded: chain Q residue 40 ASP Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 77 THR Chi-restraints excluded: chain Q residue 197 ASN Chi-restraints excluded: chain Q residue 198 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 160 optimal weight: 2.9990 chunk 428 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 279 optimal weight: 0.6980 chunk 117 optimal weight: 9.9990 chunk 476 optimal weight: 0.4980 chunk 395 optimal weight: 5.9990 chunk 220 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 249 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 HIS ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN C 213 HIS ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 104 HIS K 38 HIS ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 108 GLN ** M 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.5071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.241 40639 Z= 0.330 Angle : 0.990 50.543 54855 Z= 0.600 Chirality : 0.166 6.301 6147 Planarity : 0.004 0.068 7080 Dihedral : 4.267 41.707 5451 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.25 % Favored : 94.66 % Rotamer: Outliers : 3.28 % Allowed : 21.84 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.11), residues: 4948 helix: 0.54 (0.13), residues: 1729 sheet: -0.28 (0.18), residues: 784 loop : -2.21 (0.11), residues: 2435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP P 217 HIS 0.005 0.001 HIS B 43 PHE 0.028 0.001 PHE P 176 TYR 0.022 0.001 TYR M 224 ARG 0.008 0.000 ARG M 189 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9896 Ramachandran restraints generated. 4948 Oldfield, 0 Emsley, 4948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9896 Ramachandran restraints generated. 4948 Oldfield, 0 Emsley, 4948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 486 time to evaluate : 4.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.9307 (tt) cc_final: 0.8847 (mp) REVERT: A 78 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.7692 (p0) REVERT: A 107 MET cc_start: 0.8308 (mmp) cc_final: 0.7433 (mtt) REVERT: A 197 PHE cc_start: 0.8360 (OUTLIER) cc_final: 0.7418 (m-80) REVERT: A 228 LYS cc_start: 0.9318 (mttt) cc_final: 0.9101 (mtmm) REVERT: A 572 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.8949 (pp) REVERT: A 1168 HIS cc_start: 0.8485 (m170) cc_final: 0.7997 (m-70) REVERT: A 1193 LYS cc_start: 0.9608 (pptt) cc_final: 0.9211 (pttt) REVERT: B 43 HIS cc_start: 0.8489 (OUTLIER) cc_final: 0.7244 (t-90) REVERT: B 562 MET cc_start: 0.8924 (mmm) cc_final: 0.8596 (tmm) REVERT: B 1042 ASP cc_start: 0.8682 (t0) cc_final: 0.8088 (t0) REVERT: C 270 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7944 (mmmt) REVERT: D 100 MET cc_start: 0.6535 (mmt) cc_final: 0.6077 (mmt) REVERT: E 72 MET cc_start: 0.7795 (tpt) cc_final: 0.7452 (tpt) REVERT: E 73 PHE cc_start: 0.8638 (t80) cc_final: 0.8006 (t80) REVERT: E 110 MET cc_start: 0.7285 (tpp) cc_final: 0.6541 (tpt) REVERT: E 144 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7920 (pp) REVERT: F 88 ASP cc_start: 0.7916 (t70) cc_final: 0.7591 (t70) REVERT: G 7 MET cc_start: 0.7989 (mmm) cc_final: 0.7462 (mmm) REVERT: G 151 ARG cc_start: 0.8686 (mtp180) cc_final: 0.8169 (ttm-80) REVERT: I 74 HIS cc_start: 0.7847 (m-70) cc_final: 0.7538 (t-170) REVERT: I 91 MET cc_start: 0.3593 (tmm) cc_final: 0.3012 (tmm) REVERT: I 104 HIS cc_start: 0.7701 (OUTLIER) cc_final: 0.7147 (m170) REVERT: K 64 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7703 (tp30) REVERT: K 124 GLN cc_start: 0.8389 (tm-30) cc_final: 0.8108 (tm-30) REVERT: M 37 MET cc_start: 0.8683 (ptp) cc_final: 0.8030 (ptp) REVERT: M 60 MET cc_start: 0.8258 (ptm) cc_final: 0.7901 (ppp) REVERT: M 220 HIS cc_start: 0.8722 (m-70) cc_final: 0.8399 (m-70) REVERT: M 699 MET cc_start: 0.6377 (ppp) cc_final: 0.6169 (ppp) REVERT: N 30 ARG cc_start: 0.8494 (mmp80) cc_final: 0.8280 (mmp80) REVERT: N 396 LYS cc_start: 0.8741 (ttmm) cc_final: 0.8296 (ttmm) REVERT: O 1 MET cc_start: 0.7820 (mtm) cc_final: 0.7268 (mmt) REVERT: O 133 MET cc_start: 0.6487 (ptt) cc_final: 0.5073 (ppp) REVERT: O 404 MET cc_start: 0.8569 (pmm) cc_final: 0.8317 (pmm) REVERT: O 490 MET cc_start: 0.3399 (ppp) cc_final: 0.3001 (ppp) REVERT: P 185 PHE cc_start: 0.9284 (t80) cc_final: 0.8992 (t80) REVERT: P 203 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.7736 (ppp) REVERT: P 206 ARG cc_start: 0.5708 (tpp80) cc_final: 0.5363 (tpp80) REVERT: P 210 PHE cc_start: 0.7279 (p90) cc_final: 0.7073 (p90) REVERT: P 217 TRP cc_start: 0.8887 (t60) cc_final: 0.8683 (t-100) REVERT: P 219 TYR cc_start: 0.8921 (t80) cc_final: 0.8493 (m-80) REVERT: P 232 MET cc_start: 0.4732 (mmp) cc_final: 0.3542 (tmm) REVERT: P 245 ASP cc_start: 0.8615 (t70) cc_final: 0.8181 (t70) REVERT: P 247 LYS cc_start: 0.8385 (mtmm) cc_final: 0.7857 (mtmm) REVERT: P 250 MET cc_start: 0.8002 (ttt) cc_final: 0.7593 (tpt) REVERT: P 295 ASP cc_start: 0.8495 (t70) cc_final: 0.8083 (t0) REVERT: Q 74 PHE cc_start: 0.8878 (t80) cc_final: 0.8644 (t80) REVERT: Q 102 ASP cc_start: 0.8866 (t70) cc_final: 0.8246 (t0) REVERT: Q 104 ARG cc_start: 0.8790 (mpp-170) cc_final: 0.8391 (mmp80) outliers start: 145 outliers final: 102 residues processed: 593 average time/residue: 0.5212 time to fit residues: 505.0139 Evaluate side-chains 565 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 455 time to evaluate : 4.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 1084 ILE Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1155 THR Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1188 VAL Chi-restraints excluded: chain A residue 1195 ASP Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1235 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 43 HIS Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 81 TYR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 658 GLU Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 921 SER Chi-restraints excluded: chain B residue 938 MET Chi-restraints excluded: chain B residue 1032 THR Chi-restraints excluded: chain B residue 1065 LEU Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 76 HIS Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 142 HIS Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 104 HIS Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain M residue 250 MET Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 39 ARG Chi-restraints excluded: chain N residue 249 VAL Chi-restraints excluded: chain N residue 261 THR Chi-restraints excluded: chain N residue 343 LYS Chi-restraints excluded: chain N residue 360 LEU Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 135 ASP Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 362 CYS Chi-restraints excluded: chain O residue 419 ARG Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain O residue 529 CYS Chi-restraints excluded: chain P residue 173 GLU Chi-restraints excluded: chain P residue 187 PHE Chi-restraints excluded: chain P residue 203 MET Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 268 LYS Chi-restraints excluded: chain P residue 287 CYS Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 296 CYS Chi-restraints excluded: chain Q residue 40 ASP Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 77 THR Chi-restraints excluded: chain Q residue 198 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 458 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 271 optimal weight: 10.0000 chunk 347 optimal weight: 4.9990 chunk 269 optimal weight: 5.9990 chunk 400 optimal weight: 20.0000 chunk 265 optimal weight: 6.9990 chunk 474 optimal weight: 4.9990 chunk 296 optimal weight: 3.9990 chunk 289 optimal weight: 10.0000 chunk 218 optimal weight: 0.2980 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: