Starting phenix.real_space_refine on Sun Mar 24 08:17:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d58_30577/03_2024/7d58_30577_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d58_30577/03_2024/7d58_30577.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d58_30577/03_2024/7d58_30577.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d58_30577/03_2024/7d58_30577.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d58_30577/03_2024/7d58_30577_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d58_30577/03_2024/7d58_30577_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 7 6.06 5 P 46 5.49 5 S 275 5.16 5 C 25509 2.51 5 N 7040 2.21 5 O 7687 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 8": "OE1" <-> "OE2" Residue "A PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 26": "OE1" <-> "OE2" Residue "A ARG 29": "NH1" <-> "NH2" Residue "A ARG 59": "NH1" <-> "NH2" Residue "A ASP 78": "OD1" <-> "OD2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 87": "OD1" <-> "OD2" Residue "A PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 99": "NH1" <-> "NH2" Residue "A ASP 127": "OD1" <-> "OD2" Residue "A TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A ARG 151": "NH1" <-> "NH2" Residue "A GLU 177": "OE1" <-> "OE2" Residue "A ASP 187": "OD1" <-> "OD2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A ARG 254": "NH1" <-> "NH2" Residue "A ASP 269": "OD1" <-> "OD2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "A PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 297": "NH1" <-> "NH2" Residue "A PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 376": "NH1" <-> "NH2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A ARG 430": "NH1" <-> "NH2" Residue "A ARG 437": "NH1" <-> "NH2" Residue "A GLU 438": "OE1" <-> "OE2" Residue "A GLU 443": "OE1" <-> "OE2" 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 GLU 504": "OE1" <-> "OE2" Residue "A ARG 533": "NH1" <-> "NH2" Residue "A GLU 536": "OE1" <-> "OE2" 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 ARG 669": "NH1" <-> "NH2" Residue "A ASP 670": "OD1" <-> "OD2" Residue "A GLU 675": "OE1" <-> "OE2" Residue "A ARG 682": "NH1" <-> "NH2" Residue "A ARG 685": "NH1" <-> "NH2" Residue "A ASP 725": "OD1" <-> "OD2" Residue "A GLU 749": "OE1" <-> "OE2" Residue "A ARG 769": "NH1" <-> "NH2" Residue "A GLU 770": "OE1" <-> "OE2" 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 ASP 860": "OD1" <-> "OD2" Residue "A GLU 913": "OE1" <-> "OE2" Residue "A PHE 932": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 944": "OE1" <-> "OE2" Residue "A ASP 963": "OD1" <-> "OD2" Residue "A PHE 965": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 984": "NH1" <-> "NH2" Residue "A ASP 985": "OD1" <-> "OD2" Residue "A TYR 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 991": "OD1" <-> "OD2" Residue "A TYR 1001": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1004": "OD1" <-> "OD2" Residue "A ARG 1024": "NH1" <-> "NH2" Residue "A GLU 1028": "OE1" <-> "OE2" Residue "A PHE 1053": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1072": "OE1" <-> "OE2" Residue "A ASP 1092": "OD1" <-> "OD2" Residue "A ASP 1094": "OD1" <-> "OD2" Residue "A ASP 1096": "OD1" <-> "OD2" Residue "A TYR 1097": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1104": "NH1" <-> "NH2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1124": "OD1" <-> "OD2" Residue "A PHE 1127": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 1179": "OE1" <-> "OE2" Residue "A ASP 1195": "OD1" <-> "OD2" Residue "A ARG 1264": "NH1" <-> "NH2" Residue "A ARG 1285": "NH1" <-> "NH2" Residue "A TYR 1296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1345": "OE1" <-> "OE2" Residue "A PHE 1360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 28": "NH1" <-> "NH2" Residue "B GLU 54": "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 GLU 182": "OE1" <-> "OE2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "B ARG 226": "NH1" <-> "NH2" Residue "B GLU 270": "OE1" <-> "OE2" Residue "B TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 310": "NH1" <-> "NH2" Residue "B PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 355": "OD1" <-> "OD2" Residue "B TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 363": "OE1" <-> "OE2" Residue "B ASP 375": "OD1" <-> "OD2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 407": "NH1" <-> "NH2" Residue "B ASP 432": "OD1" <-> "OD2" Residue "B ARG 463": "NH1" <-> "NH2" Residue "B ASP 505": "OD1" <-> "OD2" Residue "B ASP 508": "OD1" <-> "OD2" Residue "B PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 570": "OE1" <-> "OE2" Residue "B ARG 581": "NH1" <-> "NH2" Residue "B TYR 584": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 637": "OE1" <-> "OE2" Residue "B ASP 640": "OD1" <-> "OD2" Residue "B GLU 658": "OE1" <-> "OE2" Residue "B PHE 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 706": "OD1" <-> "OD2" Residue "B GLU 752": "OE1" <-> "OE2" Residue "B ARG 768": "NH1" <-> "NH2" Residue "B ARG 805": "NH1" <-> "NH2" Residue "B ASP 810": "OD1" <-> "OD2" Residue "B GLU 819": "OE1" <-> "OE2" Residue "B GLU 822": "OE1" <-> "OE2" Residue "B TYR 858": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 863": "OD1" <-> "OD2" Residue "B PHE 879": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 900": "NH1" <-> "NH2" Residue "B ARG 937": "NH1" <-> "NH2" Residue "B ASP 955": "OD1" <-> "OD2" Residue "B ARG 957": "NH1" <-> "NH2" Residue "B PHE 958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 971": "OD1" <-> "OD2" Residue "B TYR 981": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 988": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 1105": "NH1" <-> "NH2" Residue "B TYR 1108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1125": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C ARG 22": "NH1" <-> "NH2" Residue "C ASP 28": "OD1" <-> "OD2" Residue "C ASP 41": "OD1" <-> "OD2" Residue "C ASP 57": "OD1" <-> "OD2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "C ARG 120": "NH1" <-> "NH2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "C TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 243": "OE1" <-> "OE2" Residue "C GLU 246": "OE1" <-> "OE2" Residue "C ARG 274": "NH1" <-> "NH2" Residue "C ARG 279": "NH1" <-> "NH2" Residue "C ASP 281": "OD1" <-> "OD2" Residue "C ARG 285": "NH1" <-> "NH2" Residue "C ARG 303": "NH1" <-> "NH2" Residue "C TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 311": "OE1" <-> "OE2" Residue "C PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 338": "OD1" <-> "OD2" Residue "C ASP 341": "OD1" <-> "OD2" Residue "C ASP 346": "OD1" <-> "OD2" Residue "D ARG 90": "NH1" <-> "NH2" Residue "D GLU 102": "OE1" <-> "OE2" Residue "D GLU 111": "OE1" <-> "OE2" Residue "E GLU 5": "OE1" <-> "OE2" Residue "E TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 23": "OD1" <-> "OD2" Residue "E GLU 32": "OE1" <-> "OE2" Residue "E ASP 66": "OD1" <-> "OD2" Residue "E ASP 67": "OD1" <-> "OD2" Residue "E PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 96": "OE1" <-> "OE2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "E ASP 177": "OD1" <-> "OD2" 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 ASP 88": "OD1" <-> "OD2" Residue "F ARG 107": "NH1" <-> "NH2" Residue "F TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 116": "OE1" <-> "OE2" Residue "G GLU 6": "OE1" <-> "OE2" Residue "G PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 56": "OD1" <-> "OD2" Residue "G TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 63": "OD1" <-> "OD2" Residue "G ARG 73": "NH1" <-> "NH2" Residue "G GLU 124": "OE1" <-> "OE2" Residue "G ARG 149": "NH1" <-> "NH2" Residue "G PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 154": "OD1" <-> "OD2" Residue "H PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 11": "OD1" <-> "OD2" Residue "H ASP 14": "OD1" <-> "OD2" Residue "H ARG 24": "NH1" <-> "NH2" Residue "H ARG 27": "NH1" <-> "NH2" Residue "H PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 66": "OE1" <-> "OE2" Residue "H ASP 67": "OD1" <-> "OD2" Residue "H ASP 72": "OD1" <-> "OD2" Residue "H TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 103": "OE1" <-> "OE2" Residue "H ARG 111": "NH1" <-> "NH2" Residue "H TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 128": "OD1" <-> "OD2" 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 GLU 48": "OE1" <-> "OE2" Residue "I ASP 50": "OD1" <-> "OD2" Residue "I ASP 63": "OD1" <-> "OD2" 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 "J ARG 47": "NH1" <-> "NH2" Residue "J TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 66": "OE1" <-> "OE2" Residue "K PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 112": "OD1" <-> "OD2" Residue "K ASP 120": "OD1" <-> "OD2" Residue "K ASP 123": "OD1" <-> "OD2" Residue "L ASP 32": "OD1" <-> "OD2" Residue "L ARG 48": "NH1" <-> "NH2" Residue "L ASP 56": "OD1" <-> "OD2" Residue "L ARG 58": "NH1" <-> "NH2" Residue "M GLU 5": "OE1" <-> "OE2" Residue "M GLU 12": "OE1" <-> "OE2" Residue "M TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 33": "NH1" <-> "NH2" Residue "M GLU 75": "OE1" <-> "OE2" Residue "M ARG 113": "NH1" <-> "NH2" Residue "M TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 143": "OD1" <-> "OD2" Residue "M ARG 150": "NH1" <-> "NH2" Residue "M PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 219": "OE1" <-> "OE2" Residue "N ASP 248": "OD1" <-> "OD2" Residue "N GLU 253": "OE1" <-> "OE2" Residue "N ASP 273": "OD1" <-> "OD2" Residue "N ASP 320": "OD1" <-> "OD2" Residue "N GLU 323": "OE1" <-> "OE2" Residue "N PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 394": "OD1" <-> "OD2" Residue "O GLU 15": "OE1" <-> "OE2" Residue "O PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 127": "OD1" <-> "OD2" Residue "O GLU 131": "OE1" <-> "OE2" Residue "O ASP 140": "OD1" <-> "OD2" Residue "O TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 159": "NH1" <-> "NH2" Residue "O GLU 184": "OE1" <-> "OE2" Residue "O ASP 240": "OD1" <-> "OD2" Residue "O ARG 258": "NH1" <-> "NH2" Residue "O PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 318": "OD1" <-> "OD2" Residue "O TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 376": "OE1" <-> "OE2" Residue "O ASP 393": "OD1" <-> "OD2" Residue "O GLU 401": "OE1" <-> "OE2" Residue "O PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 517": "OD1" <-> "OD2" Residue "O GLU 518": "OE1" <-> "OE2" Residue "O GLU 528": "OE1" <-> "OE2" Residue "O ARG 533": "NH1" <-> "NH2" Residue "P GLU 175": "OE1" <-> "OE2" Residue "P PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 245": "OD1" <-> "OD2" Residue "P TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 295": "OD1" <-> "OD2" Residue "Q ASP 42": "OD1" <-> "OD2" Residue "Q TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 65": "NH1" <-> "NH2" Residue "Q ARG 70": "NH1" <-> "NH2" Residue "Q TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 40568 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 10886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1387, 10886 Classifications: {'peptide': 1387} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 65, 'TRANS': 1321} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 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: 1493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1493 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 12, 'TRANS': 174} 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: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 746 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 11, 'TRANS': 74} Chain: "R" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 346 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "S" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 493 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "T" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 106 Classifications: {'RNA': 5} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 3} Link IDs: {'rna3p': 4} 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 57.001 104.140 88.635 1.00115.93 S ATOM 883 SG CYS A 112 70.501 81.767 133.873 1.00113.13 S ATOM 19132 SG CYS B1080 62.140 112.388 104.186 1.00 95.80 S ATOM 19217 SG CYS B1092 60.293 108.758 104.656 1.00 92.65 S ATOM 19245 SG CYS B1095 59.781 109.673 108.550 1.00 89.96 S ATOM 28409 SG CYS I 5 119.774 39.307 116.688 1.00149.63 S ATOM 28426 SG CYS I 8 116.432 37.978 114.229 1.00148.59 S ATOM 28557 SG CYS I 25 116.433 39.191 118.960 1.00157.61 S ATOM 28578 SG CYS I 28 116.546 35.626 116.951 1.00155.81 S ATOM 29139 SG CYS I 98 139.994 109.604 98.025 1.00194.05 S ATOM 29167 SG CYS I 102 138.811 111.223 100.950 1.00189.84 S ATOM 29280 SG CYS J 7 113.284 107.138 41.015 1.00 62.64 S ATOM 29304 SG CYS J 10 114.613 110.503 39.098 1.00 65.29 S ATOM 30681 SG CYS L 19 78.870 79.992 39.103 1.00101.80 S ATOM 30817 SG CYS L 36 75.449 77.944 36.933 1.00116.57 S ATOM 30843 SG CYS L 39 78.381 76.193 38.192 1.00118.15 S ATOM 38652 SG CYS P 290 47.344 88.635 116.075 1.00109.42 S ATOM 38699 SG CYS P 296 50.310 93.866 117.666 1.00109.09 S ATOM 38776 SG CYS P 307 43.703 92.773 115.963 1.00114.75 S ATOM 38634 SG CYS P 287 46.424 91.361 122.216 1.00111.08 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="ZN ZN I 202 " occ=0.75 Time building chain proxies: 20.34, per 1000 atoms: 0.50 Number of scatterers: 40568 At special positions: 0 Unit cell: (172.7, 173.8, 181.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 7 29.99 Fe 4 26.01 S 275 16.00 P 46 15.00 O 7687 8.00 N 7040 7.00 C 25509 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: 15.80 Conformation dependent library (CDL) restraints added in 7.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 P 400 " pdb="FE2 SF4 P 400 " - pdb=" SG CYS P 296 " pdb="FE1 SF4 P 400 " - pdb=" SG CYS P 290 " pdb="FE3 SF4 P 400 " - pdb=" SG CYS P 307 " pdb="FE4 SF4 P 400 " - pdb=" SG CYS P 287 " 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 A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 112 " pdb=" ZN B2001 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1095 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1092 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1080 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 8 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 5 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 25 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 28 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 102 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 98 " pdb=" ZN J 100 " pdb="ZN ZN J 100 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 100 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " Number of angles added : 6 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9376 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 156 helices and 51 sheets defined 31.8% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.20 Creating SS restraints... Processing helix chain 'A' and resid 25 through 31 Processing helix chain 'A' and resid 98 through 107 Processing helix chain 'A' and resid 119 through 129 removed outlier: 3.552A pdb=" N LYS A 123 " --> pdb=" O GLN A 119 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TYR A 128 " --> pdb=" O GLN A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 152 removed outlier: 3.536A pdb=" N LYS A 143 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 198 through 200 No H-bonds generated for 'chain 'A' and resid 198 through 200' Processing helix chain 'A' and resid 211 through 213 No H-bonds generated for 'chain 'A' and resid 211 through 213' Processing helix chain 'A' and resid 220 through 226 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 278 through 299 removed outlier: 3.683A pdb=" N ILE A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE A 298 " --> pdb=" O LYS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.717A pdb=" N ASP A 309 " --> pdb=" O MET A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 345 removed outlier: 3.581A pdb=" N LEU A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 341 through 345' Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.673A pdb=" N ILE A 389 " --> pdb=" O HIS A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 410 removed outlier: 3.666A pdb=" N LYS A 406 " --> pdb=" O ASN A 402 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 407 " --> pdb=" O PHE A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 442 removed outlier: 4.076A pdb=" N GLN A 442 " --> pdb=" O GLU A 438 " (cutoff:3.500A) 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: 4.189A 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 516 No H-bonds generated for 'chain 'A' and resid 513 through 516' Processing helix chain 'A' and resid 518 through 521 No H-bonds generated for 'chain 'A' and resid 518 through 521' Processing helix chain 'A' and resid 543 through 552 Processing helix chain 'A' and resid 561 through 567 removed outlier: 3.509A pdb=" N CYS A 565 " --> pdb=" O ARG A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 603 removed outlier: 3.717A pdb=" N PHE A 601 " --> pdb=" O GLY A 597 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER A 602 " --> pdb=" O LYS A 598 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL A 603 " --> pdb=" O GLN A 599 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 597 through 603' Processing helix chain 'A' and resid 663 through 670 Processing helix chain 'A' and resid 674 through 678 Processing helix chain 'A' and resid 680 through 694 removed outlier: 3.732A pdb=" N ALA A 684 " --> pdb=" O MET A 680 " (cutoff:3.500A) Proline residue: A 688 - end of helix Processing helix chain 'A' and resid 707 through 733 removed outlier: 4.002A pdb=" N LYS A 711 " --> pdb=" O GLN A 707 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA A 712 " --> pdb=" O GLY A 708 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU A 715 " --> pdb=" O LYS A 711 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 716 " --> pdb=" O ALA A 712 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU A 726 " --> pdb=" O LYS A 722 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TYR A 727 " --> pdb=" O LYS A 723 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ILE A 728 " --> pdb=" O CYS A 724 " (cutoff:3.500A) removed outlier: 4.641A 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 768 removed outlier: 3.625A pdb=" N SER A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 758 " --> pdb=" O LYS A 754 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE A 759 " --> pdb=" O GLU A 755 " (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 858 removed outlier: 3.822A pdb=" N ALA A 853 " --> pdb=" O PHE A 849 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 857 " --> pdb=" O ALA A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 876 removed outlier: 4.826A pdb=" N THR A 865 " --> pdb=" O THR A 861 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ALA A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU A 867 " --> pdb=" O VAL A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 931 removed outlier: 4.147A pdb=" N ALA A 930 " --> pdb=" O ASP A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 953 removed outlier: 3.781A pdb=" N LEU A 947 " --> pdb=" O ASN A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 987 removed outlier: 3.533A pdb=" N PHE A 972 " --> pdb=" O GLU A 968 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER A 977 " --> pdb=" O ILE A 973 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A 978 " --> pdb=" O LYS A 974 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS A 982 " --> pdb=" O GLU A 978 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A 983 " --> pdb=" O LYS A 979 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR A 987 " --> pdb=" O THR A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1001 No H-bonds generated for 'chain 'A' and resid 999 through 1001' Processing helix chain 'A' and resid 1008 through 1024 removed outlier: 3.816A pdb=" N GLU A1012 " --> pdb=" O PRO A1008 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1038 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: 3.504A pdb=" N ARG A1104 " --> pdb=" O LEU A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1138 No H-bonds generated for 'chain 'A' and resid 1135 through 1138' Processing helix chain 'A' and resid 1146 through 1155 Processing helix chain 'A' and resid 1185 through 1192 Processing helix chain 'A' and resid 1232 through 1236 Processing helix chain 'A' and resid 1251 through 1257 Processing helix chain 'A' and resid 1263 through 1276 removed outlier: 3.531A pdb=" N ILE A1267 " --> pdb=" O ALA A1263 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE A1268 " --> pdb=" O ARG A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1284 through 1293 Processing helix chain 'A' and resid 1305 through 1311 Processing helix chain 'A' and resid 1315 through 1320 Processing helix chain 'A' and resid 1324 through 1334 Processing helix chain 'A' and resid 1343 through 1349 Processing helix chain 'A' and resid 1357 through 1359 No H-bonds generated for 'chain 'A' and resid 1357 through 1359' Processing helix chain 'B' and resid 26 through 36 removed outlier: 3.576A pdb=" N LEU B 29 " --> pdb=" O LYS B 26 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU B 30 " --> pdb=" O TRP B 27 " (cutoff:3.500A) Proline residue: B 31 - end of helix removed outlier: 3.507A pdb=" N LYS B 35 " --> pdb=" O ALA B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 50 removed outlier: 3.775A 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 104 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 removed outlier: 3.744A pdb=" N ALA B 263 " --> pdb=" O GLU B 259 " (cutoff:3.500A) No H-bonds generated for '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 315 Processing helix chain 'B' and resid 329 through 345 Processing helix chain 'B' and resid 365 through 387 removed outlier: 3.699A pdb=" N LYS B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 420 Processing helix chain 'B' and resid 445 through 452 removed outlier: 3.536A pdb=" N LEU B 449 " --> pdb=" O TYR B 445 " (cutoff:3.500A) removed outlier: 3.715A 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 530 through 532 No H-bonds generated for 'chain 'B' and resid 530 through 532' Processing helix chain 'B' and resid 552 through 565 Processing helix chain 'B' and resid 608 through 616 removed outlier: 3.751A pdb=" N GLU B 613 " --> pdb=" O LYS B 609 " (cutoff:3.500A) removed outlier: 3.795A 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 662 through 664 No H-bonds generated for 'chain 'B' and resid 662 through 664' Processing helix chain 'B' and resid 669 through 671 No H-bonds generated for 'chain 'B' and resid 669 through 671' Processing helix chain 'B' and resid 680 through 689 Processing helix chain 'B' and resid 723 through 728 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: 3.573A pdb=" N ASP B 975 " --> pdb=" O ASP B 971 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL B 977 " --> pdb=" O CYS B 973 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG B 978 " --> pdb=" O GLU B 974 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N HIS B 979 " --> pdb=" O ASP B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 1049 through 1058 removed outlier: 3.530A 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: 3.966A pdb=" N SER B1119 " --> pdb=" O GLN B1115 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N MET B1120 " --> pdb=" O GLU B1116 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 12 removed outlier: 3.733A pdb=" N ARG C 11 " --> pdb=" O VAL C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 48 removed outlier: 3.644A pdb=" N LYS C 47 " --> pdb=" O ASP C 43 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 318 through 345 removed outlier: 3.706A pdb=" N VAL C 322 " --> pdb=" O PRO C 318 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS C 327 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS C 332 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N CYS C 333 " --> pdb=" O LEU C 329 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 337 " --> pdb=" O CYS C 333 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA C 342 " --> pdb=" O ASP C 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 25 removed outlier: 3.815A pdb=" N ASP D 22 " --> pdb=" O GLN D 18 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS D 24 " --> pdb=" O LEU D 20 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU D 25 " --> pdb=" O THR D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 30 No H-bonds generated for 'chain 'D' and resid 27 through 30' Processing helix chain 'D' and resid 36 through 55 removed outlier: 3.803A pdb=" N LEU D 42 " --> pdb=" O GLY D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 75 removed outlier: 4.163A pdb=" N SER D 75 " --> pdb=" O THR D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 88 removed outlier: 4.111A pdb=" N LEU D 84 " --> pdb=" O LYS D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.646A pdb=" N GLN D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 121 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: 3.923A pdb=" N GLN E 43 " --> pdb=" O GLU E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 94 removed outlier: 4.052A pdb=" N TYR E 90 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET E 94 " --> pdb=" O TYR E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 120 Processing helix chain 'E' and resid 153 through 163 removed outlier: 3.881A 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: 3.702A pdb=" N MET F 75 " --> pdb=" O LEU F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 98 removed outlier: 3.794A pdb=" N MET F 94 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS F 95 " --> pdb=" O LEU F 91 " (cutoff:3.500A) removed outlier: 3.516A 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 59 No H-bonds generated for 'chain 'J' and resid 56 through 59' Processing helix chain 'K' and resid 49 through 61 Processing helix chain 'K' and resid 92 through 129 removed outlier: 4.049A pdb=" N PHE K 96 " --> pdb=" O ALA K 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 6 No H-bonds generated for 'chain 'M' and resid 4 through 6' Processing helix chain 'M' and resid 71 through 82 Processing helix chain 'M' and resid 141 through 154 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: 3.962A 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 16 Processing helix chain 'O' and resid 19 through 30 removed outlier: 3.518A pdb=" N ILE O 29 " --> pdb=" O GLY O 25 " (cutoff:3.500A) removed outlier: 3.599A 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 85 removed outlier: 3.968A pdb=" N ARG O 84 " --> pdb=" O SER O 80 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N MET O 85 " --> pdb=" O ARG O 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 88 through 98 removed outlier: 3.803A pdb=" N LEU O 98 " --> pdb=" O THR O 94 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 110 removed outlier: 4.346A pdb=" N GLU O 109 " --> pdb=" O LEU O 105 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU O 110 " --> pdb=" O ILE O 106 " (cutoff:3.500A) Processing helix chain 'O' and resid 118 through 132 Processing helix chain 'O' and resid 141 through 153 Processing helix chain 'O' and resid 239 through 258 Processing helix chain 'O' and resid 262 through 272 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: 3.661A pdb=" N SER O 344 " --> pdb=" O LYS O 340 " (cutoff:3.500A) Processing helix chain 'O' and resid 360 through 371 Processing helix chain 'O' and resid 379 through 383 removed outlier: 3.978A pdb=" N PHE O 383 " --> pdb=" O GLN O 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 379 through 383' Processing helix chain 'O' and resid 388 through 401 removed outlier: 3.614A pdb=" N GLU O 401 " --> pdb=" O LYS O 397 " (cutoff:3.500A) Processing helix chain 'O' and resid 428 through 452 removed outlier: 3.579A pdb=" N TYR O 440 " --> pdb=" O LEU O 436 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS O 441 " --> pdb=" O HIS O 437 " (cutoff:3.500A) Processing helix chain 'O' and resid 458 through 477 removed outlier: 3.602A pdb=" N ALA O 469 " --> pdb=" O GLN O 465 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE O 470 " --> pdb=" O ARG O 466 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE O 471 " --> pdb=" O VAL O 467 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET O 474 " --> pdb=" O ILE O 470 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA O 476 " --> pdb=" O ALA O 472 " (cutoff:3.500A) removed outlier: 3.550A 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: 3.607A pdb=" N GLN O 498 " --> pdb=" O PRO O 494 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LEU O 499 " --> pdb=" O GLU O 495 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU O 500 " --> pdb=" O ARG O 496 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR O 501 " --> pdb=" O GLN O 497 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG O 504 " --> pdb=" O GLU O 500 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE O 514 " --> pdb=" O ASP O 510 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR O 519 " --> pdb=" O GLN O 515 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER O 525 " --> pdb=" O PHE O 521 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TYR O 526 " --> pdb=" O LEU O 522 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE O 527 " --> pdb=" O LEU O 523 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU O 528 " --> pdb=" O GLU O 524 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N CYS O 529 " --> pdb=" O SER O 525 " (cutoff:3.500A) removed outlier: 3.803A 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: 3.573A 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 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 Processing sheet with id= A, first strand: chain 'A' and resid 84 through 87 Processing sheet with id= B, first strand: chain 'A' and resid 165 through 168 removed outlier: 3.726A pdb=" N LYS A 167 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE A 174 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU A 216 " --> pdb=" O HIS A 176 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 266 through 268 removed outlier: 3.798A pdb=" N GLY A 273 " --> pdb=" O SER A 268 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 364 through 368 Processing sheet with id= E, first strand: chain 'A' and resid 369 through 371 removed outlier: 6.106A pdb=" N PHE A 486 " --> pdb=" O SER A 370 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 391 through 395 removed outlier: 3.619A pdb=" N ILE A 449 " --> pdb=" O GLN A 422 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE A 420 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N HIS A 453 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ALA A 418 " --> pdb=" O HIS A 453 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 616 through 620 Processing sheet with id= H, first strand: chain 'A' and resid 1209 through 1216 removed outlier: 3.898A pdb=" N ARG A1209 " --> pdb=" O GLU A1228 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N TYR A1223 " --> pdb=" O LEU A1089 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU A1089 " --> pdb=" O TYR A1223 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ARG A1245 " --> pdb=" O GLN A1088 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1165 through 1167 removed outlier: 3.992A pdb=" N TYR A1116 " --> pdb=" O LYS A1131 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 64 through 66 removed outlier: 3.828A pdb=" N VAL B 65 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N TYR B 74 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ASP B 116 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ILE B 80 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N THR B 114 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE B 117 " --> pdb=" O ARG B 128 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG B 128 " --> pdb=" O ILE B 117 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 86 through 88 removed outlier: 3.880A pdb=" N VAL B 87 " --> pdb=" O ARG B 95 " (cutoff:3.500A) removed outlier: 3.951A 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 169 through 171 Processing sheet with id= M, first strand: chain 'B' and resid 181 through 183 Processing sheet with id= N, first strand: chain 'B' and resid 188 through 193 removed outlier: 3.996A pdb=" N ARG B 188 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL B 203 " --> pdb=" O ARG B 188 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ALA B 198 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL B 218 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 423 through 426 Processing sheet with id= P, first strand: chain 'B' and resid 454 through 456 Processing sheet with id= Q, first strand: chain 'B' and resid 573 through 577 removed outlier: 6.239A pdb=" N LEU B 538 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE B 585 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE B 540 " --> pdb=" O ILE B 585 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY B 547 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU B 541 " --> pdb=" O ILE B 545 " (cutoff:3.500A) removed outlier: 5.539A 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: 3.860A pdb=" N ARG B 594 " --> pdb=" O LEU B 633 " (cutoff:3.500A) removed outlier: 3.607A 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: 3.936A pdb=" N LYS B 868 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ARG B 886 " --> pdb=" O ILE B 866 " (cutoff:3.500A) removed outlier: 5.248A 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: 4.020A pdb=" N TYR B1003 " --> pdb=" O VAL B 743 " (cutoff:3.500A) removed outlier: 6.767A 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 1075 through 1079 Processing sheet with id= X, first strand: chain 'B' and resid 110 through 115 removed outlier: 4.105A pdb=" N GLY B 134 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL B 115 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 825 through 828 removed outlier: 3.829A pdb=" N GLN B 825 " --> pdb=" O TYR B 858 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE B 856 " --> pdb=" O LEU B 827 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 13 through 16 removed outlier: 4.716A pdb=" N LEU C 299 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LEU C 236 " --> pdb=" O VAL C 302 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 50 through 56 removed outlier: 6.891A pdb=" N GLU C 62 " --> pdb=" O VAL C 54 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N MET C 56 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N SER C 60 " --> pdb=" O MET C 56 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER C 232 " --> pdb=" O SER C 309 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 138 through 145 removed outlier: 3.675A pdb=" N LYS C 91 " --> pdb=" O HIS C 213 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL C 215 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N VAL C 89 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLY C 217 " --> pdb=" O MET C 87 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N MET C 87 " --> pdb=" O GLY C 217 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 262 through 267 Processing sheet with id= AD, first strand: chain 'E' and resid 59 through 63 removed outlier: 6.818A pdb=" N ARG E 101 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N PHE E 75 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU E 103 " --> pdb=" O PHE E 75 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE E 126 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ILE E 104 " --> pdb=" O ILE E 126 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLU E 128 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL E 106 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 6.068A 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 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: 3.682A pdb=" N ASP G 9 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL G 70 " --> pdb=" O ASP G 9 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER G 66 " --> pdb=" O ILE G 13 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS G 47 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N PHE G 77 " --> pdb=" O CYS G 45 " (cutoff:3.500A) removed outlier: 6.223A 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: 6.967A pdb=" N ARG G 151 " --> pdb=" O ILE G 190 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE G 190 " --> pdb=" O ARG G 151 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL G 153 " --> pdb=" O GLY G 188 " (cutoff:3.500A) removed outlier: 5.203A 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: 5.972A pdb=" N SER G 100 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 5.194A 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: 3.568A pdb=" N ASP G 50 " --> pdb=" O ARG G 73 " (cutoff:3.500A) removed outlier: 7.142A 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 30 removed outlier: 3.799A pdb=" N SER H 26 " --> pdb=" O VAL H 43 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL H 43 " --> pdb=" O SER H 26 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU H 39 " --> pdb=" O CYS H 30 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP H 42 " --> pdb=" O LEU H 122 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU H 121 " --> pdb=" O TYR H 118 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR H 115 " --> pdb=" O TYR H 97 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 7.064A 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 64 through 66 removed outlier: 4.139A pdb=" N ALA I 77 " --> pdb=" O THR I 65 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N PHE I 94 " --> pdb=" O ASP I 108 " (cutoff:3.500A) removed outlier: 3.506A 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: 6.961A pdb=" N GLY M 131 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N GLN M 29 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LEU M 133 " --> pdb=" O GLN M 29 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE M 132 " --> pdb=" O THR M 107 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR M 107 " --> pdb=" O ILE M 132 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN M 134 " --> pdb=" O SER M 105 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N VAL M 56 " --> pdb=" O SER M 104 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU M 59 " --> pdb=" O SER M 46 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER M 46 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ALA M 61 " --> pdb=" O HIS M 44 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N HIS M 44 " --> pdb=" O ALA M 61 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'N' and resid 268 through 270 removed outlier: 4.451A pdb=" N VAL N 337 " --> pdb=" O VAL N 348 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'N' and resid 359 through 365 removed outlier: 6.327A pdb=" N SER N 362 " --> pdb=" O VAL N 375 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N VAL N 375 " --> pdb=" O SER N 362 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N GLY N 364 " --> pdb=" O MET N 373 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N MET N 373 " --> pdb=" O GLY N 364 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'O' and resid 63 through 68 Processing sheet with id= AV, first strand: chain 'O' and resid 157 through 159 Processing sheet with id= AW, first strand: chain 'O' and resid 323 through 327 Processing sheet with id= AX, first strand: chain 'O' and resid 405 through 410 Processing sheet with id= AY, first strand: chain 'P' and resid 248 through 253 1219 hydrogen bonds defined for protein. 3531 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: 14.79 Time building geometry restraints manager: 17.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.44: 17215 1.44 - 1.66: 23763 1.66 - 1.88: 427 1.88 - 2.10: 0 2.10 - 2.32: 12 Bond restraints: 41417 Sorted by residual: bond pdb=" C GLU A 996 " pdb=" N PRO A 997 " ideal model delta sigma weight residual 1.332 1.360 -0.028 1.12e-02 7.97e+03 6.43e+00 bond pdb=" N GLU B 752 " pdb=" CA GLU B 752 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.29e-02 6.01e+03 3.15e+00 bond pdb=" N LYS O 69 " pdb=" CA LYS O 69 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.17e-02 7.31e+03 2.85e+00 bond pdb=" N LEU D 78 " pdb=" CA LEU D 78 " ideal model delta sigma weight residual 1.457 1.478 -0.021 1.29e-02 6.01e+03 2.56e+00 bond pdb=" S1 SF4 P 400 " pdb="FE3 SF4 P 400 " ideal model delta sigma weight residual 2.280 2.325 -0.045 3.00e-02 1.11e+03 2.25e+00 ... (remaining 41412 not shown) Histogram of bond angle deviations from ideal: 70.15 - 82.96: 12 82.96 - 95.78: 0 95.78 - 108.59: 2577 108.59 - 121.41: 43183 121.41 - 134.23: 10336 Bond angle restraints: 56108 Sorted by residual: angle pdb=" N ASN A1180 " pdb=" CA ASN A1180 " pdb=" C ASN A1180 " ideal model delta sigma weight residual 108.52 116.23 -7.71 1.52e+00 4.33e-01 2.57e+01 angle pdb=" C GLY A 914 " pdb=" N LYS A 915 " pdb=" CA LYS A 915 " ideal model delta sigma weight residual 121.54 131.16 -9.62 1.91e+00 2.74e-01 2.54e+01 angle pdb=" N VAL A 37 " pdb=" CA VAL A 37 " pdb=" C VAL A 37 " ideal model delta sigma weight residual 113.71 109.03 4.68 9.50e-01 1.11e+00 2.43e+01 angle pdb=" N THR A 111 " pdb=" CA THR A 111 " pdb=" C THR A 111 " ideal model delta sigma weight residual 114.56 108.99 5.57 1.27e+00 6.20e-01 1.92e+01 angle pdb=" N ILE A1378 " pdb=" CA ILE A1378 " pdb=" C ILE A1378 " ideal model delta sigma weight residual 113.10 108.87 4.23 9.70e-01 1.06e+00 1.90e+01 ... (remaining 56103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 22834 17.35 - 34.71: 1910 34.71 - 52.06: 475 52.06 - 69.42: 98 69.42 - 86.77: 40 Dihedral angle restraints: 25357 sinusoidal: 10855 harmonic: 14502 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 -130.90 -49.10 0 5.00e+00 4.00e-02 9.64e+01 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 -136.74 -43.26 0 5.00e+00 4.00e-02 7.49e+01 dihedral pdb=" CA ILE B 751 " pdb=" C ILE B 751 " pdb=" N GLU B 752 " pdb=" CA GLU B 752 " ideal model delta harmonic sigma weight residual -180.00 -141.93 -38.07 0 5.00e+00 4.00e-02 5.80e+01 ... (remaining 25354 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.276: 6301 4.276 - 8.553: 0 8.553 - 12.829: 0 12.829 - 17.105: 0 17.105 - 21.381: 4 Chirality restraints: 6305 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 10.75 -21.31 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 6302 not shown) Planarity restraints: 7071 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS O 68 " -0.012 2.00e-02 2.50e+03 2.54e-02 6.45e+00 pdb=" C HIS O 68 " 0.044 2.00e-02 2.50e+03 pdb=" O HIS O 68 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS O 69 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 208 " 0.036 5.00e-02 4.00e+02 5.49e-02 4.82e+00 pdb=" N PRO A 209 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 209 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 209 " 0.031 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 2.95e+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 7068 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 816 2.69 - 3.24: 37713 3.24 - 3.80: 60522 3.80 - 4.35: 79819 4.35 - 4.90: 130356 Nonbonded interactions: 309226 Sorted by model distance: nonbonded pdb=" OG1 THR O 2 " pdb=" OE1 GLU O 5 " model vdw 2.139 2.440 nonbonded pdb=" OH TYR P 309 " pdb=" O PRO Q 39 " model vdw 2.140 2.440 nonbonded pdb=" O THR P 194 " pdb=" OG SER P 198 " model vdw 2.224 2.440 nonbonded pdb=" OG1 THR B 66 " pdb=" O TRP B 73 " model vdw 2.225 2.440 nonbonded pdb=" O LEU D 78 " pdb=" OG1 THR D 79 " model vdw 2.240 2.440 ... (remaining 309221 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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 9.110 Check model and map are aligned: 0.520 Set scattering table: 0.320 Process input model: 113.490 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.130 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: 0.010 Load rotamer database and sin/cos tables:13.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 140.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2502 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 0.045 41417 Z= 0.161 Angle : 0.660 9.740 56108 Z= 0.405 Chirality : 0.536 21.381 6305 Planarity : 0.003 0.055 7071 Dihedral : 14.069 86.770 15981 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.77 % Favored : 94.19 % Rotamer: Outliers : 0.09 % Allowed : 4.09 % Favored : 95.82 % 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: -3.64 (0.10), residues: 4922 helix: -1.99 (0.10), residues: 1734 sheet: -1.40 (0.17), residues: 774 loop : -3.14 (0.10), residues: 2414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 27 HIS 0.008 0.001 HIS D 118 PHE 0.015 0.001 PHE G 104 TYR 0.016 0.001 TYR B1003 ARG 0.004 0.000 ARG B 226 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 977 residues out of total 4400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 973 time to evaluate : 4.100 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 322 ASN cc_start: 0.3266 (t0) cc_final: 0.3018 (m-40) REVERT: A 671 TRP cc_start: 0.1532 (m100) cc_final: 0.0931 (m-90) REVERT: A 751 LEU cc_start: 0.3395 (mt) cc_final: 0.3085 (mp) REVERT: B 97 VAL cc_start: 0.3052 (p) cc_final: 0.2744 (m) REVERT: B 279 THR cc_start: 0.5932 (p) cc_final: 0.4512 (p) REVERT: B 910 ILE cc_start: 0.6149 (mt) cc_final: 0.5851 (mt) REVERT: C 251 GLU cc_start: 0.7061 (mp0) cc_final: 0.6549 (tp30) REVERT: D 11 LEU cc_start: 0.3699 (pt) cc_final: 0.3401 (pt) REVERT: E 85 LYS cc_start: 0.8171 (tptt) cc_final: 0.7494 (mptt) REVERT: G 98 HIS cc_start: 0.6441 (m-70) cc_final: 0.6031 (m170) REVERT: G 142 MET cc_start: 0.0923 (mmt) cc_final: 0.0594 (mmt) REVERT: M 33 ARG cc_start: 0.0326 (tpt170) cc_final: -0.0024 (tpt-90) REVERT: M 80 ASN cc_start: 0.5966 (m-40) cc_final: 0.4578 (t0) REVERT: M 97 MET cc_start: 0.3616 (mpp) cc_final: 0.3184 (tmt) REVERT: M 244 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6728 (mm-30) REVERT: M 248 MET cc_start: 0.3502 (ttm) cc_final: 0.2994 (ppp) REVERT: N 339 LEU cc_start: 0.5170 (tt) cc_final: 0.4712 (mm) REVERT: O 28 LEU cc_start: 0.2974 (mt) cc_final: 0.2618 (mt) REVERT: O 298 PRO cc_start: 0.4668 (Cg_exo) cc_final: 0.3214 (Cg_endo) REVERT: P 179 VAL cc_start: 0.8529 (m) cc_final: 0.8254 (m) REVERT: Q 67 THR cc_start: 0.4601 (p) cc_final: 0.3620 (t) REVERT: Q 110 MET cc_start: 0.1801 (tmm) cc_final: 0.1289 (ttp) REVERT: Q 111 MET cc_start: -0.0252 (tpt) cc_final: -0.0761 (tmt) outliers start: 4 outliers final: 2 residues processed: 976 average time/residue: 1.5153 time to fit residues: 1789.4242 Evaluate side-chains 539 residues out of total 4400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 537 time to evaluate : 4.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain I residue 36 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 414 optimal weight: 7.9990 chunk 372 optimal weight: 0.7980 chunk 206 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 chunk 251 optimal weight: 4.9990 chunk 198 optimal weight: 0.0170 chunk 384 optimal weight: 8.9990 chunk 148 optimal weight: 0.6980 chunk 234 optimal weight: 4.9990 chunk 286 optimal weight: 10.0000 chunk 445 optimal weight: 0.7980 overall best weight: 1.4620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN A 47 GLN A 157 HIS A 195 GLN A 225 ASN ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 GLN ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 GLN A 673 GLN A 693 ASN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 ASN A 794 GLN ** A 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 885 GLN A1039 GLN A1180 ASN A1202 GLN ** A1231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1286 HIS A1385 HIS ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN B 280 GLN B 381 ASN B 399 GLN ** B 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 GLN B 569 ASN B 683 ASN ** B 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1021 HIS B1034 GLN C 32 ASN C 55 HIS C 172 HIS C 194 HIS D 76 HIS ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN E 35 GLN E 107 GLN ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN G 17 GLN H 76 ASN H 87 GLN H 126 GLN I 99 ASN K 45 HIS K 129 ASN L 23 HIS M 66 ASN M 106 GLN ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 197 GLN M 200 HIS M 235 ASN M 707 GLN O 16 HIS ** O 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 62 GLN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3282 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.324 41417 Z= 0.356 Angle : 1.069 51.526 56108 Z= 0.632 Chirality : 0.163 6.413 6305 Planarity : 0.005 0.064 7071 Dihedral : 9.648 72.869 5950 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.05 % Favored : 93.93 % Rotamer: Outliers : 3.43 % Allowed : 15.42 % Favored : 81.15 % 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: -2.72 (0.11), residues: 4922 helix: -1.09 (0.12), residues: 1745 sheet: -0.85 (0.17), residues: 785 loop : -2.74 (0.11), residues: 2392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 476 HIS 0.017 0.002 HIS B1093 PHE 0.027 0.003 PHE E 183 TYR 0.028 0.002 TYR H 90 ARG 0.020 0.001 ARG F 107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 4400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 630 time to evaluate : 4.819 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: A 116 MET cc_start: 0.3050 (mpt) cc_final: 0.2747 (mpp) REVERT: A 211 LEU cc_start: 0.3131 (OUTLIER) cc_final: 0.2755 (mt) REVERT: A 260 LEU cc_start: 0.4069 (OUTLIER) cc_final: 0.3327 (tp) REVERT: A 543 GLN cc_start: 0.2531 (OUTLIER) cc_final: 0.1811 (pp30) REVERT: A 1353 MET cc_start: 0.4328 (OUTLIER) cc_final: 0.3413 (mtp) REVERT: B 254 MET cc_start: 0.1983 (mtt) cc_final: -0.0070 (tpt) REVERT: B 349 ASN cc_start: 0.5901 (p0) cc_final: 0.5535 (m-40) REVERT: B 384 MET cc_start: 0.5062 (ppp) cc_final: 0.4489 (mmt) REVERT: B 415 MET cc_start: 0.3037 (ptp) cc_final: 0.2508 (tpt) REVERT: B 621 PHE cc_start: 0.2064 (t80) cc_final: 0.1064 (t80) REVERT: B 766 PHE cc_start: 0.4465 (t80) cc_final: 0.3860 (t80) REVERT: B 791 MET cc_start: 0.3765 (pmm) cc_final: 0.3503 (pmm) REVERT: B 987 ASP cc_start: 0.2181 (m-30) cc_final: 0.1946 (m-30) REVERT: B 1032 THR cc_start: 0.0702 (t) cc_final: -0.0834 (p) REVERT: C 96 ASN cc_start: 0.5097 (t0) cc_final: 0.4874 (p0) REVERT: C 192 PRO cc_start: 0.4346 (Cg_endo) cc_final: 0.4051 (Cg_exo) REVERT: C 251 GLU cc_start: 0.7117 (mp0) cc_final: 0.6555 (tp30) REVERT: C 324 GLU cc_start: 0.5761 (OUTLIER) cc_final: 0.4531 (tp30) REVERT: D 49 THR cc_start: 0.7018 (t) cc_final: 0.6815 (m) REVERT: E 84 ILE cc_start: 0.5828 (OUTLIER) cc_final: 0.5512 (pt) REVERT: E 85 LYS cc_start: 0.8186 (tptt) cc_final: 0.7734 (mmtt) REVERT: E 110 MET cc_start: 0.0055 (tpt) cc_final: -0.4123 (ptm) REVERT: G 48 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6662 (tm) REVERT: K 80 ILE cc_start: 0.4821 (mt) cc_final: 0.4418 (mt) REVERT: M 80 ASN cc_start: 0.6356 (m-40) cc_final: 0.4803 (t0) REVERT: M 97 MET cc_start: 0.3755 (mpp) cc_final: 0.3135 (tmt) REVERT: M 217 ARG cc_start: 0.1539 (OUTLIER) cc_final: 0.0250 (ppt170) REVERT: M 221 GLU cc_start: 0.6516 (mm-30) cc_final: 0.6057 (pt0) REVERT: M 248 MET cc_start: 0.3285 (ttm) cc_final: 0.2536 (ptm) REVERT: M 250 MET cc_start: 0.3435 (mmt) cc_final: 0.3076 (mmm) REVERT: P 301 GLU cc_start: 0.5559 (pt0) cc_final: 0.4517 (mt-10) REVERT: Q 57 MET cc_start: 0.6555 (mpp) cc_final: 0.6235 (mmm) REVERT: Q 110 MET cc_start: 0.1971 (tmm) cc_final: 0.1194 (ttp) outliers start: 151 outliers final: 44 residues processed: 727 average time/residue: 1.3782 time to fit residues: 1240.8559 Evaluate side-chains 537 residues out of total 4400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 485 time to evaluate : 3.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 543 GLN Chi-restraints excluded: chain A residue 921 PHE Chi-restraints excluded: chain A residue 1248 SER Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain A residue 1353 MET Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain B residue 453 THR Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 495 ASN Chi-restraints excluded: chain B residue 516 SER Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain I residue 32 HIS Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 4 GLU Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 217 ARG Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 137 LYS Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain O residue 157 VAL Chi-restraints excluded: chain O residue 313 THR Chi-restraints excluded: chain P residue 208 SER Chi-restraints excluded: chain P residue 311 THR Chi-restraints excluded: chain Q residue 49 LYS Chi-restraints excluded: chain Q residue 77 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 247 optimal weight: 0.4980 chunk 138 optimal weight: 0.0770 chunk 371 optimal weight: 0.9980 chunk 303 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 446 optimal weight: 20.0000 chunk 482 optimal weight: 7.9990 chunk 397 optimal weight: 0.0270 chunk 442 optimal weight: 7.9990 chunk 152 optimal weight: 2.9990 chunk 358 optimal weight: 0.8980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 163 ASN A 192 ASN ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 HIS A 397 ASN ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 GLN A 738 GLN ** A 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 GLN B 159 ASN B 215 ASN ** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 ASN B 475 GLN ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 HIS F 72 GLN M 106 GLN M 121 GLN O 27 HIS O 337 ASN ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3412 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.248 41417 Z= 0.292 Angle : 1.019 50.539 56108 Z= 0.608 Chirality : 0.164 6.341 6305 Planarity : 0.004 0.054 7071 Dihedral : 9.505 73.188 5944 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.22 % Favored : 94.72 % Rotamer: Outliers : 3.43 % Allowed : 19.62 % Favored : 76.94 % 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: -2.25 (0.11), residues: 4922 helix: -0.59 (0.12), residues: 1748 sheet: -0.69 (0.17), residues: 760 loop : -2.50 (0.11), residues: 2414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP Q 99 HIS 0.011 0.001 HIS B 901 PHE 0.025 0.001 PHE B 50 TYR 0.026 0.001 TYR H 90 ARG 0.009 0.001 ARG A 855 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 4400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 522 time to evaluate : 4.481 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 22 MET cc_start: 0.3891 (OUTLIER) cc_final: 0.3439 (mpp) REVERT: A 117 LEU cc_start: 0.5005 (OUTLIER) cc_final: 0.4169 (tp) REVERT: A 211 LEU cc_start: 0.3020 (OUTLIER) cc_final: 0.2657 (mt) REVERT: A 332 MET cc_start: 0.1127 (ttp) cc_final: 0.0467 (ttt) REVERT: A 438 GLU cc_start: 0.5191 (tp30) cc_final: 0.4662 (tp30) REVERT: A 543 GLN cc_start: 0.2474 (OUTLIER) cc_final: 0.2016 (pp30) REVERT: A 680 MET cc_start: 0.4285 (mpt) cc_final: 0.3227 (mpt) REVERT: A 852 MET cc_start: 0.2431 (ptp) cc_final: 0.0307 (tpt) REVERT: A 1353 MET cc_start: 0.4580 (OUTLIER) cc_final: 0.4130 (mpt) REVERT: B 59 MET cc_start: 0.4754 (OUTLIER) cc_final: 0.4519 (ptp) REVERT: B 254 MET cc_start: 0.1444 (mtt) cc_final: 0.0277 (ttp) REVERT: B 349 ASN cc_start: 0.5989 (p0) cc_final: 0.5608 (m-40) REVERT: B 415 MET cc_start: 0.2855 (ptp) cc_final: 0.2631 (tpt) REVERT: B 703 ASN cc_start: 0.4779 (OUTLIER) cc_final: 0.4503 (p0) REVERT: B 744 MET cc_start: 0.2487 (tmm) cc_final: 0.2094 (ttt) REVERT: B 1032 THR cc_start: 0.0549 (t) cc_final: -0.1000 (p) REVERT: C 251 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6648 (tp30) REVERT: C 345 MET cc_start: 0.5845 (OUTLIER) cc_final: 0.5613 (ppp) REVERT: D 49 THR cc_start: 0.6843 (t) cc_final: 0.6612 (m) REVERT: E 85 LYS cc_start: 0.8134 (tptt) cc_final: 0.7741 (mptt) REVERT: E 110 MET cc_start: -0.0427 (tpt) cc_final: -0.1200 (tpp) REVERT: E 151 MET cc_start: 0.0090 (pp-130) cc_final: -0.0751 (tpt) REVERT: G 89 ILE cc_start: 0.7163 (OUTLIER) cc_final: 0.6676 (tp) REVERT: G 98 HIS cc_start: 0.6889 (m-70) cc_final: 0.6546 (m90) REVERT: K 80 ILE cc_start: 0.4357 (mt) cc_final: 0.4050 (mt) REVERT: M 73 LYS cc_start: 0.6789 (tttt) cc_final: 0.6312 (pttt) REVERT: M 80 ASN cc_start: 0.6117 (m-40) cc_final: 0.4799 (t0) REVERT: M 97 MET cc_start: 0.3839 (mpp) cc_final: 0.3080 (tmt) REVERT: M 248 MET cc_start: 0.3671 (ttm) cc_final: 0.3072 (ppp) REVERT: M 250 MET cc_start: 0.3277 (mmt) cc_final: 0.2941 (mmm) REVERT: O 526 TYR cc_start: 0.3529 (t80) cc_final: 0.2726 (t80) REVERT: P 191 LYS cc_start: 0.1551 (pttm) cc_final: 0.1235 (ptpt) REVERT: P 301 GLU cc_start: 0.5451 (pt0) cc_final: 0.4472 (mt-10) REVERT: Q 110 MET cc_start: 0.1768 (tmm) cc_final: 0.1129 (ttp) outliers start: 151 outliers final: 46 residues processed: 617 average time/residue: 1.3142 time to fit residues: 1015.2026 Evaluate side-chains 501 residues out of total 4400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 445 time to evaluate : 4.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 543 GLN Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain A residue 1049 THR Chi-restraints excluded: chain A residue 1353 MET Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 769 CYS Chi-restraints excluded: chain B residue 973 CYS Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 78 HIS Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain I residue 32 HIS Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 75 GLU Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 363 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 157 VAL Chi-restraints excluded: chain P residue 178 GLU Chi-restraints excluded: chain Q residue 49 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 441 optimal weight: 2.9990 chunk 335 optimal weight: 10.0000 chunk 231 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 213 optimal weight: 0.0980 chunk 299 optimal weight: 5.9990 chunk 448 optimal weight: 9.9990 chunk 474 optimal weight: 8.9990 chunk 234 optimal weight: 3.9990 chunk 424 optimal weight: 10.0000 chunk 127 optimal weight: 7.9990 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 HIS A 163 ASN A 182 ASN ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 ASN A 397 ASN ** A 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN A 673 GLN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 GLN ** A 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1239 HIS A1249 ASN B 144 ASN B 159 ASN B 413 ASN B 557 ASN B 648 HIS ** B 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 823 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 959 HIS ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1082 GLN ** B1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 ASN D 88 ASN ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 HIS ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 GLN J 61 ASN ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 GLN M 44 HIS ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 358 GLN O 155 HIS ** O 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 244 GLN O 337 ASN O 374 HIS ** O 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 379 GLN ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 483 GLN O 498 GLN ** P 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5562 moved from start: 1.0772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.321 41417 Z= 0.663 Angle : 1.503 50.617 56108 Z= 0.840 Chirality : 0.175 6.660 6305 Planarity : 0.011 0.196 7071 Dihedral : 11.061 82.016 5944 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 31.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.28 % Favored : 90.53 % Rotamer: Outliers : 7.16 % Allowed : 19.60 % Favored : 73.24 % Cbeta Deviations : 0.06 % 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: -3.36 (0.10), residues: 4922 helix: -1.85 (0.11), residues: 1700 sheet: -1.12 (0.18), residues: 737 loop : -2.90 (0.11), residues: 2485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP A 310 HIS 0.034 0.004 HIS O 68 PHE 0.088 0.006 PHE C 225 TYR 0.207 0.006 TYR B 710 ARG 0.055 0.002 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1168 residues out of total 4400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 315 poor density : 853 time to evaluate : 4.440 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: A 389 ILE cc_start: 0.8414 (mm) cc_final: 0.8027 (mp) REVERT: A 553 THR cc_start: 0.4567 (OUTLIER) cc_final: 0.3038 (p) REVERT: A 579 ILE cc_start: 0.7184 (mm) cc_final: 0.6978 (mt) REVERT: A 660 LYS cc_start: 0.5295 (OUTLIER) cc_final: 0.4813 (tmtp) REVERT: A 770 GLU cc_start: 0.2007 (OUTLIER) cc_final: 0.1554 (tp30) REVERT: A 855 ARG cc_start: 0.5325 (mmt180) cc_final: 0.5110 (ttp80) REVERT: A 885 GLN cc_start: 0.5406 (mm-40) cc_final: 0.5173 (mm110) REVERT: A 927 ASN cc_start: 0.7755 (t0) cc_final: 0.7380 (t0) REVERT: A 954 LYS cc_start: 0.3511 (OUTLIER) cc_final: 0.3183 (ptmm) REVERT: A 1048 MET cc_start: 0.1315 (OUTLIER) cc_final: -0.0724 (mpt) REVERT: A 1254 VAL cc_start: 0.2415 (p) cc_final: 0.2151 (p) REVERT: A 1385 HIS cc_start: 0.5225 (OUTLIER) cc_final: 0.4823 (t70) REVERT: B 106 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.7525 (t0) REVERT: B 254 MET cc_start: 0.2161 (mtt) cc_final: 0.0961 (ttp) REVERT: B 338 MET cc_start: 0.7011 (tmt) cc_final: 0.5493 (mtm) REVERT: B 413 ASN cc_start: 0.8142 (t0) cc_final: 0.7570 (p0) REVERT: B 478 MET cc_start: 0.5099 (OUTLIER) cc_final: 0.3330 (pmm) REVERT: B 637 GLU cc_start: 0.5612 (tt0) cc_final: 0.5094 (tp30) REVERT: B 660 GLU cc_start: 0.5287 (mm-30) cc_final: 0.4599 (tp30) REVERT: B 703 ASN cc_start: 0.8229 (OUTLIER) cc_final: 0.7894 (m110) REVERT: B 719 MET cc_start: 0.5072 (pmm) cc_final: 0.4481 (mtp) REVERT: B 738 ASN cc_start: 0.8398 (OUTLIER) cc_final: 0.8171 (t0) REVERT: B 803 ILE cc_start: 0.4614 (mt) cc_final: 0.4296 (mp) REVERT: B 938 MET cc_start: 0.5381 (OUTLIER) cc_final: 0.5160 (tpp) REVERT: B 1002 ILE cc_start: 0.7606 (mm) cc_final: 0.7082 (mm) REVERT: B 1020 MET cc_start: 0.2744 (tpt) cc_final: 0.2222 (ppp) REVERT: B 1051 GLU cc_start: 0.7344 (mp0) cc_final: 0.7140 (mp0) REVERT: B 1089 SER cc_start: 0.7177 (m) cc_final: 0.6692 (p) REVERT: C 251 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7394 (tp30) REVERT: C 345 MET cc_start: 0.6191 (OUTLIER) cc_final: 0.5916 (ppp) REVERT: D 125 PRO cc_start: 0.5128 (Cg_endo) cc_final: 0.3030 (Cg_exo) REVERT: E 85 LYS cc_start: 0.8586 (tptt) cc_final: 0.7984 (mptt) REVERT: E 101 ARG cc_start: 0.4649 (OUTLIER) cc_final: 0.3404 (pmm150) REVERT: E 110 MET cc_start: 0.0905 (tpt) cc_final: 0.0604 (tpp) REVERT: F 90 LEU cc_start: 0.6427 (OUTLIER) cc_final: 0.6031 (pp) REVERT: F 101 LYS cc_start: 0.7827 (mttt) cc_final: 0.7488 (mmtm) REVERT: G 98 HIS cc_start: 0.6822 (m-70) cc_final: 0.6379 (m90) REVERT: G 151 ARG cc_start: 0.3839 (pmm-80) cc_final: 0.3329 (tpp-160) REVERT: G 190 ILE cc_start: 0.4676 (mt) cc_final: 0.4327 (mt) REVERT: H 92 MET cc_start: 0.5169 (OUTLIER) cc_final: 0.4908 (ptp) REVERT: H 126 GLN cc_start: 0.4219 (OUTLIER) cc_final: 0.3513 (mm110) REVERT: I 1 MET cc_start: 0.4566 (pmm) cc_final: 0.3698 (pp-130) REVERT: J 1 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.7425 (mtp) REVERT: J 41 LYS cc_start: 0.8839 (tmmt) cc_final: 0.8597 (tppp) REVERT: K 66 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.6495 (mm-30) REVERT: K 80 ILE cc_start: 0.5005 (mt) cc_final: 0.4719 (mt) REVERT: K 128 ARG cc_start: 0.6991 (OUTLIER) cc_final: 0.6347 (tpp-160) REVERT: M 73 LYS cc_start: 0.6542 (tttt) cc_final: 0.6153 (pttt) REVERT: M 129 LEU cc_start: 0.0315 (OUTLIER) cc_final: 0.0045 (mp) REVERT: M 248 MET cc_start: 0.4710 (ttm) cc_final: 0.4244 (ppp) REVERT: N 39 ARG cc_start: 0.5526 (OUTLIER) cc_final: 0.5206 (tmm-80) REVERT: O 7 LYS cc_start: 0.6760 (tptp) cc_final: 0.6460 (pttm) REVERT: O 118 MET cc_start: 0.1861 (ttt) cc_final: 0.0461 (pp-130) REVERT: O 133 MET cc_start: 0.2346 (mtm) cc_final: 0.1176 (ppp) REVERT: O 333 MET cc_start: 0.5408 (mpt) cc_final: 0.4936 (mmt) REVERT: O 513 GLU cc_start: 0.5820 (OUTLIER) cc_final: 0.5086 (tm-30) REVERT: O 531 MET cc_start: 0.6919 (tmm) cc_final: 0.6638 (ttp) REVERT: P 174 SER cc_start: 0.5792 (m) cc_final: 0.5273 (m) REVERT: P 175 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7407 (tm-30) REVERT: P 201 ASN cc_start: 0.6146 (t0) cc_final: 0.5925 (t0) REVERT: P 220 ILE cc_start: 0.8121 (mm) cc_final: 0.7855 (pp) REVERT: Q 46 VAL cc_start: 0.4187 (t) cc_final: 0.3881 (t) REVERT: Q 74 PHE cc_start: 0.6732 (t80) cc_final: 0.6405 (t80) REVERT: Q 110 MET cc_start: 0.3163 (tmm) cc_final: 0.2872 (tpp) outliers start: 315 outliers final: 82 residues processed: 1069 average time/residue: 1.2969 time to fit residues: 1736.7891 Evaluate side-chains 683 residues out of total 4400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 578 time to evaluate : 4.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 660 LYS Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 954 LYS Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1215 ASP Chi-restraints excluded: chain A residue 1311 MET Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1353 MET Chi-restraints excluded: chain A residue 1385 HIS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 495 ASN Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 738 ASN Chi-restraints excluded: chain B residue 752 GLU Chi-restraints excluded: chain B residue 814 ILE Chi-restraints excluded: chain B residue 892 GLU Chi-restraints excluded: chain B residue 938 MET Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 41 ASN Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 101 ARG Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 121 ASP Chi-restraints excluded: chain G residue 125 GLN Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 126 GLN Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 128 ARG Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 12 GLU Chi-restraints excluded: chain M residue 39 TYR Chi-restraints excluded: chain M residue 129 LEU Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 39 ARG Chi-restraints excluded: chain N residue 255 LEU Chi-restraints excluded: chain N residue 269 LEU Chi-restraints excluded: chain N residue 271 LEU Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 16 HIS Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 137 LYS Chi-restraints excluded: chain O residue 141 TYR Chi-restraints excluded: chain O residue 253 SER Chi-restraints excluded: chain O residue 304 SER Chi-restraints excluded: chain O residue 313 THR Chi-restraints excluded: chain O residue 328 ASP Chi-restraints excluded: chain O residue 513 GLU Chi-restraints excluded: chain P residue 208 SER Chi-restraints excluded: chain P residue 311 THR Chi-restraints excluded: chain Q residue 67 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 395 optimal weight: 2.9990 chunk 269 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 353 optimal weight: 0.3980 chunk 195 optimal weight: 0.6980 chunk 404 optimal weight: 0.9980 chunk 328 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 242 optimal weight: 0.7980 chunk 425 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 ASN A 508 HIS A 511 GLN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 885 GLN A 899 GLN A 962 GLN ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 GLN B 159 ASN ** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 472 GLN B 557 ASN B 825 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1082 GLN ** B1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 ASN ** C 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN ** E 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 138 HIS H 46 GLN I 32 HIS J 61 ASN K 97 GLN ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 377 GLN O 379 GLN O 437 HIS ** P 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 62 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5645 moved from start: 1.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.244 41417 Z= 0.321 Angle : 1.123 50.570 56108 Z= 0.650 Chirality : 0.165 6.283 6305 Planarity : 0.005 0.068 7071 Dihedral : 9.995 76.692 5944 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.77 % Favored : 94.19 % Rotamer: Outliers : 4.68 % Allowed : 27.10 % Favored : 68.21 % 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: -2.52 (0.11), residues: 4922 helix: -0.91 (0.12), residues: 1702 sheet: -0.83 (0.18), residues: 712 loop : -2.53 (0.11), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP Q 99 HIS 0.023 0.001 HIS O 16 PHE 0.050 0.002 PHE H 56 TYR 0.030 0.002 TYR H 97 ARG 0.014 0.001 ARG A 484 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 4400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 658 time to evaluate : 4.866 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: A 58 HIS cc_start: 0.4880 (OUTLIER) cc_final: 0.4508 (t70) REVERT: A 117 LEU cc_start: 0.5572 (pp) cc_final: 0.4964 (tp) REVERT: A 198 GLU cc_start: 0.7487 (mm-30) cc_final: 0.6846 (pp20) REVERT: A 428 MET cc_start: 0.7191 (ppp) cc_final: 0.6465 (ppp) REVERT: A 451 GLU cc_start: 0.6766 (mm-30) cc_final: 0.6475 (mm-30) REVERT: A 534 ASN cc_start: 0.5866 (t0) cc_final: 0.5648 (t0) REVERT: A 553 THR cc_start: 0.4083 (OUTLIER) cc_final: 0.2549 (p) REVERT: A 767 CYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7789 (p) REVERT: A 1048 MET cc_start: 0.1775 (OUTLIER) cc_final: 0.0131 (mpt) REVERT: A 1088 GLN cc_start: 0.6595 (OUTLIER) cc_final: 0.6315 (tm-30) REVERT: A 1106 GLU cc_start: 0.5215 (pm20) cc_final: 0.5006 (mm-30) REVERT: A 1385 HIS cc_start: 0.5311 (OUTLIER) cc_final: 0.4913 (t70) REVERT: B 222 ARG cc_start: 0.3516 (tpt90) cc_final: 0.2868 (mtm180) REVERT: B 254 MET cc_start: 0.2302 (mtt) cc_final: 0.1369 (ptm) REVERT: B 271 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6823 (mp0) REVERT: B 356 TYR cc_start: 0.4527 (m-80) cc_final: 0.3320 (m-80) REVERT: B 413 ASN cc_start: 0.8217 (t0) cc_final: 0.7796 (p0) REVERT: B 471 LEU cc_start: 0.6242 (tp) cc_final: 0.5954 (tp) REVERT: B 478 MET cc_start: 0.5064 (OUTLIER) cc_final: 0.4122 (pmm) REVERT: B 637 GLU cc_start: 0.5625 (tt0) cc_final: 0.5248 (tp30) REVERT: B 660 GLU cc_start: 0.4930 (mm-30) cc_final: 0.4252 (mp0) REVERT: B 803 ILE cc_start: 0.4657 (mt) cc_final: 0.4411 (mp) REVERT: B 808 ILE cc_start: 0.7791 (OUTLIER) cc_final: 0.7513 (mm) REVERT: B 979 HIS cc_start: 0.7219 (m90) cc_final: 0.6913 (m-70) REVERT: B 1020 MET cc_start: 0.2330 (tpt) cc_final: -0.0170 (ppp) REVERT: B 1051 GLU cc_start: 0.7221 (mp0) cc_final: 0.6928 (mp0) REVERT: B 1089 SER cc_start: 0.6443 (m) cc_final: 0.6176 (p) REVERT: B 1096 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8370 (mmtp) REVERT: C 95 TYR cc_start: 0.7052 (m-10) cc_final: 0.6667 (m-10) REVERT: C 124 TYR cc_start: 0.8278 (OUTLIER) cc_final: 0.7509 (t80) REVERT: C 251 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7440 (tp30) REVERT: E 110 MET cc_start: 0.0710 (tpt) cc_final: 0.0467 (tpp) REVERT: E 151 MET cc_start: 0.1216 (OUTLIER) cc_final: 0.0705 (ttp) REVERT: G 89 ILE cc_start: 0.7790 (tp) cc_final: 0.7315 (tp) REVERT: G 98 HIS cc_start: 0.6734 (m-70) cc_final: 0.6369 (m90) REVERT: H 92 MET cc_start: 0.5309 (OUTLIER) cc_final: 0.5006 (ptp) REVERT: I 1 MET cc_start: 0.4801 (pmm) cc_final: 0.4059 (pp-130) REVERT: I 101 GLN cc_start: 0.4558 (pp30) cc_final: 0.3616 (mm-40) REVERT: J 41 LYS cc_start: 0.8784 (tmmt) cc_final: 0.8568 (tppp) REVERT: L 15 MET cc_start: 0.5050 (OUTLIER) cc_final: 0.4798 (ttp) REVERT: L 16 ILE cc_start: 0.7084 (pp) cc_final: 0.6424 (pp) REVERT: M 73 LYS cc_start: 0.6597 (tttt) cc_final: 0.6183 (pttt) REVERT: M 97 MET cc_start: 0.3732 (mmt) cc_final: 0.2431 (tmt) REVERT: M 113 ARG cc_start: 0.6408 (pmm-80) cc_final: 0.5496 (ptm160) REVERT: M 221 GLU cc_start: 0.6323 (mm-30) cc_final: 0.5915 (pt0) REVERT: M 248 MET cc_start: 0.4637 (ttm) cc_final: 0.4164 (ppp) REVERT: O 7 LYS cc_start: 0.6961 (tptp) cc_final: 0.6647 (pttm) REVERT: O 15 GLU cc_start: 0.5377 (OUTLIER) cc_final: 0.4863 (mm-30) REVERT: O 118 MET cc_start: 0.2026 (ttt) cc_final: 0.0804 (pp-130) REVERT: O 301 TYR cc_start: 0.5604 (m-80) cc_final: 0.5187 (m-80) REVERT: O 333 MET cc_start: 0.5596 (mpt) cc_final: 0.5221 (mmt) REVERT: O 455 LYS cc_start: 0.7067 (OUTLIER) cc_final: 0.6844 (mmmm) REVERT: P 175 GLU cc_start: 0.7102 (tm-30) cc_final: 0.6895 (tm-30) REVERT: P 191 LYS cc_start: 0.1748 (OUTLIER) cc_final: 0.1471 (ptpt) REVERT: P 201 ASN cc_start: 0.6078 (t0) cc_final: 0.5834 (t0) REVERT: Q 71 MET cc_start: 0.4217 (tpt) cc_final: 0.3969 (tpt) REVERT: Q 86 ARG cc_start: 0.4052 (mmt180) cc_final: 0.3790 (mmt-90) REVERT: Q 110 MET cc_start: 0.3725 (tmm) cc_final: 0.3301 (tpp) outliers start: 206 outliers final: 63 residues processed: 796 average time/residue: 1.2959 time to fit residues: 1296.5411 Evaluate side-chains 626 residues out of total 4400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 545 time to evaluate : 4.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 58 HIS Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 543 GLN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1031 SER Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1049 THR Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1088 GLN Chi-restraints excluded: chain A residue 1215 ASP Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1385 HIS Chi-restraints excluded: chain B residue 49 TYR Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 155 PHE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 346 GLN Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 648 HIS Chi-restraints excluded: chain B residue 784 ASN Chi-restraints excluded: chain B residue 808 ILE Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 1096 LYS Chi-restraints excluded: chain C residue 124 TYR Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 56 PHE Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain I residue 32 HIS Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain L residue 15 MET Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain M residue 39 TYR Chi-restraints excluded: chain M residue 75 GLU Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 271 LEU Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain N residue 385 CYS Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 141 TYR Chi-restraints excluded: chain O residue 328 ASP Chi-restraints excluded: chain O residue 377 GLN Chi-restraints excluded: chain O residue 403 PHE Chi-restraints excluded: chain O residue 455 LYS Chi-restraints excluded: chain P residue 191 LYS Chi-restraints excluded: chain Q residue 58 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 159 optimal weight: 0.0770 chunk 427 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 278 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 chunk 475 optimal weight: 5.9990 chunk 394 optimal weight: 0.9990 chunk 219 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 249 optimal weight: 4.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 HIS ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 ASN B 703 ASN B 738 ASN ** B1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 HIS D 89 HIS E 108 GLN ** G 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 138 HIS ** M 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 191 GLN ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 16 HIS ** O 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 437 HIS O 483 GLN ** P 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 62 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5865 moved from start: 1.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.242 41417 Z= 0.328 Angle : 1.107 50.546 56108 Z= 0.643 Chirality : 0.164 6.297 6305 Planarity : 0.005 0.062 7071 Dihedral : 9.752 75.148 5944 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.42 % Favored : 93.54 % Rotamer: Outliers : 4.37 % Allowed : 29.42 % Favored : 66.21 % 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: -2.20 (0.11), residues: 4922 helix: -0.62 (0.12), residues: 1699 sheet: -0.78 (0.18), residues: 745 loop : -2.33 (0.11), residues: 2478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 118 HIS 0.043 0.002 HIS I 32 PHE 0.037 0.002 PHE B 730 TYR 0.052 0.002 TYR Q 43 ARG 0.019 0.001 ARG A 430 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 4400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 634 time to evaluate : 4.479 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: A 117 LEU cc_start: 0.5561 (OUTLIER) cc_final: 0.5138 (tp) REVERT: A 198 GLU cc_start: 0.7505 (mm-30) cc_final: 0.6949 (pp20) REVERT: A 443 GLU cc_start: 0.6561 (mp0) cc_final: 0.6359 (mp0) REVERT: A 451 GLU cc_start: 0.6887 (mt-10) cc_final: 0.6498 (mm-30) REVERT: A 767 CYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8006 (p) REVERT: A 912 MET cc_start: 0.4834 (mmp) cc_final: 0.3342 (mpt) REVERT: A 1215 ASP cc_start: 0.4532 (OUTLIER) cc_final: 0.3740 (m-30) REVERT: A 1236 MET cc_start: 0.3265 (pmm) cc_final: 0.2857 (pmm) REVERT: A 1385 HIS cc_start: 0.5337 (OUTLIER) cc_final: 0.4912 (t70) REVERT: B 254 MET cc_start: 0.2377 (mtt) cc_final: 0.1422 (ptm) REVERT: B 271 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6983 (mp0) REVERT: B 384 MET cc_start: 0.4392 (OUTLIER) cc_final: 0.2940 (ppp) REVERT: B 406 MET cc_start: 0.3537 (tpt) cc_final: 0.2920 (mmm) REVERT: B 413 ASN cc_start: 0.8180 (t0) cc_final: 0.7707 (p0) REVERT: B 478 MET cc_start: 0.5782 (OUTLIER) cc_final: 0.4457 (pmm) REVERT: B 660 GLU cc_start: 0.5124 (mm-30) cc_final: 0.4538 (mp0) REVERT: B 729 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6885 (tm-30) REVERT: B 791 MET cc_start: 0.7001 (pmm) cc_final: 0.6767 (pmm) REVERT: B 803 ILE cc_start: 0.4572 (mt) cc_final: 0.4317 (mp) REVERT: B 1020 MET cc_start: 0.3995 (tpt) cc_final: 0.0149 (ppp) REVERT: B 1050 MET cc_start: 0.7696 (mmm) cc_final: 0.7349 (mtm) REVERT: B 1051 GLU cc_start: 0.7144 (mp0) cc_final: 0.6789 (mp0) REVERT: B 1089 SER cc_start: 0.6558 (m) cc_final: 0.6290 (p) REVERT: B 1096 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8494 (mmtp) REVERT: C 251 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7405 (tp30) REVERT: C 307 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7365 (mm) REVERT: D 73 LEU cc_start: 0.7592 (mt) cc_final: 0.7302 (mp) REVERT: D 78 LEU cc_start: 0.6400 (mp) cc_final: 0.6060 (mm) REVERT: E 1 MET cc_start: 0.4030 (OUTLIER) cc_final: 0.3659 (mmm) REVERT: E 110 MET cc_start: 0.1329 (tpt) cc_final: 0.0979 (tpp) REVERT: G 89 ILE cc_start: 0.7887 (tp) cc_final: 0.7499 (tp) REVERT: G 98 HIS cc_start: 0.6780 (m-70) cc_final: 0.6466 (m90) REVERT: G 143 ASP cc_start: 0.1948 (OUTLIER) cc_final: 0.1557 (t0) REVERT: G 151 ARG cc_start: 0.3803 (pmm-80) cc_final: 0.3003 (mpt-90) REVERT: G 190 ILE cc_start: 0.4970 (mt) cc_final: 0.4519 (mp) REVERT: H 47 ILE cc_start: 0.7288 (OUTLIER) cc_final: 0.6969 (pt) REVERT: I 1 MET cc_start: 0.4734 (pmm) cc_final: 0.4112 (pp-130) REVERT: I 101 GLN cc_start: 0.4607 (pp30) cc_final: 0.4399 (mm-40) REVERT: J 29 TYR cc_start: 0.8127 (OUTLIER) cc_final: 0.7821 (t80) REVERT: K 46 GLU cc_start: 0.7212 (pt0) cc_final: 0.6901 (pp20) REVERT: K 79 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8186 (tmmm) REVERT: K 80 ILE cc_start: 0.5892 (mt) cc_final: 0.5482 (mt) REVERT: M 73 LYS cc_start: 0.6569 (tttt) cc_final: 0.6116 (pttt) REVERT: M 113 ARG cc_start: 0.6558 (pmm-80) cc_final: 0.5855 (ptm160) REVERT: M 221 GLU cc_start: 0.6299 (mm-30) cc_final: 0.5933 (pt0) REVERT: M 248 MET cc_start: 0.4698 (ttm) cc_final: 0.3962 (ppp) REVERT: N 350 MET cc_start: 0.6224 (pmm) cc_final: 0.5927 (pmm) REVERT: O 7 LYS cc_start: 0.7018 (tptp) cc_final: 0.6713 (pttm) REVERT: O 15 GLU cc_start: 0.5086 (OUTLIER) cc_final: 0.4830 (mm-30) REVERT: O 118 MET cc_start: 0.2444 (ttt) cc_final: 0.1103 (pp-130) REVERT: O 133 MET cc_start: 0.2487 (mtm) cc_final: 0.0651 (tmm) REVERT: O 139 MET cc_start: 0.1606 (pmm) cc_final: 0.1246 (pmm) REVERT: O 187 MET cc_start: 0.3538 (mpp) cc_final: 0.3309 (mpp) REVERT: O 333 MET cc_start: 0.5587 (mpt) cc_final: 0.5247 (mmt) REVERT: O 424 TYR cc_start: 0.4730 (m-80) cc_final: 0.4412 (m-80) REVERT: O 455 LYS cc_start: 0.7052 (OUTLIER) cc_final: 0.6810 (mmmm) REVERT: O 531 MET cc_start: 0.7214 (tmm) cc_final: 0.6688 (ttp) REVERT: P 191 LYS cc_start: 0.1867 (OUTLIER) cc_final: 0.1554 (ptpt) REVERT: P 220 ILE cc_start: 0.7765 (mm) cc_final: 0.7386 (pp) REVERT: P 301 GLU cc_start: 0.5888 (pt0) cc_final: 0.5478 (mt-10) REVERT: Q 62 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7407 (mp10) REVERT: Q 74 PHE cc_start: 0.7129 (t80) cc_final: 0.6768 (t80) REVERT: Q 110 MET cc_start: 0.3791 (tmm) cc_final: 0.3374 (tpp) outliers start: 192 outliers final: 66 residues processed: 769 average time/residue: 1.2635 time to fit residues: 1226.1646 Evaluate side-chains 641 residues out of total 4400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 555 time to evaluate : 4.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1031 SER Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1215 ASP Chi-restraints excluded: chain A residue 1248 SER Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1385 HIS Chi-restraints excluded: chain B residue 49 TYR Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 155 PHE Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 346 GLN Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 648 HIS Chi-restraints excluded: chain B residue 729 GLU Chi-restraints excluded: chain B residue 856 ILE Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 1096 LYS Chi-restraints excluded: chain B residue 1106 ILE Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 141 TYR Chi-restraints excluded: chain G residue 143 ASP Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 56 PHE Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain J residue 29 TYR Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain M residue 39 TYR Chi-restraints excluded: chain M residue 75 GLU Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 385 CYS Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 328 ASP Chi-restraints excluded: chain O residue 403 PHE Chi-restraints excluded: chain O residue 455 LYS Chi-restraints excluded: chain P residue 191 LYS Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain Q residue 62 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 458 optimal weight: 0.7980 chunk 53 optimal weight: 0.0020 chunk 270 optimal weight: 0.9990 chunk 346 optimal weight: 3.9990 chunk 268 optimal weight: 3.9990 chunk 399 optimal weight: 2.9990 chunk 265 optimal weight: 0.0870 chunk 473 optimal weight: 20.0000 chunk 296 optimal weight: 0.9990 chunk 288 optimal weight: 9.9990 chunk 218 optimal weight: 3.9990 overall best weight: 0.5770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 ASN ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 ASN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN A1039 GLN B 220 GLN ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 887 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1021 HIS ** B1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 HIS D 89 HIS E 108 GLN G 138 HIS I 32 HIS ** M 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 437 HIS ** P 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5941 moved from start: 1.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.243 41417 Z= 0.301 Angle : 1.091 50.488 56108 Z= 0.634 Chirality : 0.165 6.305 6305 Planarity : 0.005 0.141 7071 Dihedral : 9.602 75.724 5944 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.69 % Favored : 94.27 % Rotamer: Outliers : 3.87 % Allowed : 30.88 % Favored : 65.26 % 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: -1.88 (0.11), residues: 4922 helix: -0.28 (0.12), residues: 1690 sheet: -0.56 (0.18), residues: 719 loop : -2.20 (0.11), residues: 2513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 118 HIS 0.012 0.001 HIS I 32 PHE 0.031 0.002 PHE A 462 TYR 0.041 0.001 TYR Q 43 ARG 0.014 0.001 ARG B1067 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 4400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 596 time to evaluate : 4.297 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: A 305 MET cc_start: 0.4892 (ppp) cc_final: 0.4632 (ppp) REVERT: A 389 ILE cc_start: 0.8764 (mp) cc_final: 0.8536 (mp) REVERT: A 523 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7353 (mmm) REVERT: A 554 LEU cc_start: 0.6092 (OUTLIER) cc_final: 0.5819 (tm) REVERT: A 770 GLU cc_start: 0.2759 (OUTLIER) cc_final: 0.2300 (tt0) REVERT: A 1215 ASP cc_start: 0.4642 (OUTLIER) cc_final: 0.4189 (m-30) REVERT: A 1385 HIS cc_start: 0.5433 (OUTLIER) cc_final: 0.5126 (t70) REVERT: B 254 MET cc_start: 0.2546 (mtt) cc_final: 0.1620 (ptm) REVERT: B 271 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7097 (mp0) REVERT: B 384 MET cc_start: 0.4027 (OUTLIER) cc_final: 0.2900 (ppp) REVERT: B 406 MET cc_start: 0.2790 (tpt) cc_final: 0.2208 (mmm) REVERT: B 413 ASN cc_start: 0.8414 (t0) cc_final: 0.8012 (p0) REVERT: B 476 TRP cc_start: 0.7346 (OUTLIER) cc_final: 0.6675 (m100) REVERT: B 478 MET cc_start: 0.5737 (OUTLIER) cc_final: 0.4544 (pmm) REVERT: B 660 GLU cc_start: 0.5316 (mm-30) cc_final: 0.4714 (tp30) REVERT: B 1051 GLU cc_start: 0.7247 (mp0) cc_final: 0.6874 (mp0) REVERT: B 1089 SER cc_start: 0.6592 (m) cc_final: 0.6391 (p) REVERT: D 78 LEU cc_start: 0.5995 (mp) cc_final: 0.5357 (mm) REVERT: E 1 MET cc_start: 0.4018 (tpt) cc_final: 0.3587 (mmm) REVERT: E 26 TYR cc_start: 0.3949 (m-80) cc_final: 0.3671 (t80) REVERT: E 151 MET cc_start: 0.3377 (mmm) cc_final: 0.2077 (ttp) REVERT: E 165 LEU cc_start: 0.0998 (pt) cc_final: 0.0754 (pt) REVERT: G 89 ILE cc_start: 0.7867 (tp) cc_final: 0.7486 (tp) REVERT: G 98 HIS cc_start: 0.6661 (m-70) cc_final: 0.6421 (m90) REVERT: G 143 ASP cc_start: 0.1620 (OUTLIER) cc_final: 0.1329 (t0) REVERT: G 151 ARG cc_start: 0.3548 (pmm-80) cc_final: 0.2857 (mpt-90) REVERT: H 37 MET cc_start: 0.5590 (tmt) cc_final: 0.4500 (mtt) REVERT: H 38 ASP cc_start: 0.5574 (t70) cc_final: 0.4829 (m-30) REVERT: H 41 LEU cc_start: 0.4381 (pt) cc_final: 0.4141 (pt) REVERT: H 47 ILE cc_start: 0.7600 (OUTLIER) cc_final: 0.7357 (pt) REVERT: H 65 TYR cc_start: 0.6811 (m-80) cc_final: 0.6584 (m-80) REVERT: I 1 MET cc_start: 0.4937 (pmm) cc_final: 0.4357 (pp-130) REVERT: I 91 MET cc_start: 0.5596 (mmp) cc_final: 0.4574 (mtt) REVERT: J 19 GLU cc_start: 0.7677 (pm20) cc_final: 0.7456 (OUTLIER) REVERT: J 29 TYR cc_start: 0.8108 (OUTLIER) cc_final: 0.7707 (t80) REVERT: K 46 GLU cc_start: 0.7253 (pt0) cc_final: 0.6949 (pp20) REVERT: K 80 ILE cc_start: 0.5861 (mt) cc_final: 0.5346 (mt) REVERT: M 73 LYS cc_start: 0.6812 (tttt) cc_final: 0.6344 (pttt) REVERT: M 113 ARG cc_start: 0.6743 (pmm-80) cc_final: 0.6208 (ptm160) REVERT: M 221 GLU cc_start: 0.6183 (mm-30) cc_final: 0.5787 (pt0) REVERT: M 248 MET cc_start: 0.4439 (ttm) cc_final: 0.3931 (ppp) REVERT: N 262 LYS cc_start: 0.5392 (OUTLIER) cc_final: 0.5051 (pptt) REVERT: N 350 MET cc_start: 0.6342 (pmm) cc_final: 0.6111 (pmm) REVERT: O 7 LYS cc_start: 0.7151 (tptp) cc_final: 0.6787 (pttm) REVERT: O 85 MET cc_start: 0.6761 (mmp) cc_final: 0.6255 (mpt) REVERT: O 118 MET cc_start: 0.2458 (ttt) cc_final: 0.1421 (pp-130) REVERT: O 133 MET cc_start: 0.2438 (mtm) cc_final: 0.0585 (tmm) REVERT: O 301 TYR cc_start: 0.5684 (m-80) cc_final: 0.5339 (m-80) REVERT: O 424 TYR cc_start: 0.4796 (m-80) cc_final: 0.4207 (m-80) REVERT: O 455 LYS cc_start: 0.7027 (OUTLIER) cc_final: 0.6816 (mmmm) REVERT: P 220 ILE cc_start: 0.7964 (mm) cc_final: 0.7697 (pp) REVERT: Q 74 PHE cc_start: 0.7013 (t80) cc_final: 0.6652 (t80) REVERT: Q 99 TRP cc_start: 0.2720 (OUTLIER) cc_final: -0.0118 (p90) REVERT: Q 110 MET cc_start: 0.3498 (tmm) cc_final: 0.2568 (ttp) outliers start: 170 outliers final: 71 residues processed: 718 average time/residue: 1.3423 time to fit residues: 1208.8345 Evaluate side-chains 619 residues out of total 4400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 534 time to evaluate : 4.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1031 SER Chi-restraints excluded: chain A residue 1049 THR Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1215 ASP Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1248 SER Chi-restraints excluded: chain A residue 1385 HIS Chi-restraints excluded: chain B residue 49 TYR Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 155 PHE Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 495 ASN Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 648 HIS Chi-restraints excluded: chain B residue 856 ILE Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 141 TYR Chi-restraints excluded: chain G residue 143 ASP Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 56 PHE Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 29 TYR Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 39 TYR Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 262 LYS Chi-restraints excluded: chain N residue 385 CYS Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 288 LEU Chi-restraints excluded: chain O residue 328 ASP Chi-restraints excluded: chain O residue 403 PHE Chi-restraints excluded: chain O residue 455 LYS Chi-restraints excluded: chain P residue 208 SER Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain Q residue 99 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 292 optimal weight: 7.9990 chunk 188 optimal weight: 0.0470 chunk 282 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 300 optimal weight: 6.9990 chunk 322 optimal weight: 1.9990 chunk 233 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 371 optimal weight: 0.9980 overall best weight: 0.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 ASN A 422 GLN ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 662 ASN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1039 GLN B 220 GLN B 701 GLN B 703 ASN B 716 GLN ** B 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1014 HIS ** B1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 HIS D 89 HIS E 107 GLN G 67 HIS ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 138 HIS ** M 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 437 HIS ** P 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6111 moved from start: 1.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.242 41417 Z= 0.313 Angle : 1.101 50.518 56108 Z= 0.640 Chirality : 0.165 6.311 6305 Planarity : 0.005 0.117 7071 Dihedral : 9.536 75.138 5944 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.38 % Favored : 93.56 % Rotamer: Outliers : 3.25 % Allowed : 31.72 % Favored : 65.03 % 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: -1.80 (0.11), residues: 4922 helix: -0.22 (0.13), residues: 1696 sheet: -0.36 (0.18), residues: 717 loop : -2.19 (0.11), residues: 2509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 118 HIS 0.024 0.001 HIS D 60 PHE 0.031 0.002 PHE A 462 TYR 0.026 0.001 TYR Q 43 ARG 0.015 0.001 ARG G 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 4400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 606 time to evaluate : 5.032 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: A 307 MET cc_start: 0.4581 (tpp) cc_final: 0.4124 (tpt) REVERT: A 310 TRP cc_start: 0.6584 (t60) cc_final: 0.5828 (t60) REVERT: A 451 GLU cc_start: 0.7270 (mm-30) cc_final: 0.6980 (mm-30) REVERT: A 523 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7461 (mtm) REVERT: A 937 GLU cc_start: 0.4513 (tt0) cc_final: 0.3273 (tm-30) REVERT: A 1214 ILE cc_start: 0.2280 (OUTLIER) cc_final: 0.1859 (tp) REVERT: A 1215 ASP cc_start: 0.4868 (OUTLIER) cc_final: 0.4066 (m-30) REVERT: A 1374 LYS cc_start: 0.4524 (mmtt) cc_final: 0.4205 (mmtp) REVERT: B 75 LEU cc_start: 0.6213 (pt) cc_final: 0.5908 (pt) REVERT: B 254 MET cc_start: 0.2608 (mtt) cc_final: 0.1669 (ptm) REVERT: B 271 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7217 (mp0) REVERT: B 384 MET cc_start: 0.4136 (OUTLIER) cc_final: 0.3031 (ppp) REVERT: B 406 MET cc_start: 0.3340 (tpt) cc_final: 0.1944 (mmm) REVERT: B 413 ASN cc_start: 0.8275 (t0) cc_final: 0.7966 (p0) REVERT: B 476 TRP cc_start: 0.7482 (OUTLIER) cc_final: 0.6813 (m100) REVERT: B 478 MET cc_start: 0.5926 (OUTLIER) cc_final: 0.4879 (pmm) REVERT: B 637 GLU cc_start: 0.7488 (tp30) cc_final: 0.6990 (tt0) REVERT: B 660 GLU cc_start: 0.5178 (mm-30) cc_final: 0.4534 (tp30) REVERT: B 794 MET cc_start: 0.5834 (ptp) cc_final: 0.5628 (ptm) REVERT: B 1051 GLU cc_start: 0.7309 (mp0) cc_final: 0.6899 (mp0) REVERT: B 1069 MET cc_start: 0.5069 (pmm) cc_final: 0.4518 (ppp) REVERT: C 307 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.8117 (mp) REVERT: D 1 MET cc_start: 0.0550 (mmt) cc_final: -0.1700 (mmm) REVERT: D 78 LEU cc_start: 0.6451 (mp) cc_final: 0.5565 (mt) REVERT: E 1 MET cc_start: 0.4329 (OUTLIER) cc_final: 0.4057 (mmm) REVERT: E 110 MET cc_start: 0.0615 (tpp) cc_final: 0.0347 (tpp) REVERT: E 151 MET cc_start: 0.4012 (mmm) cc_final: 0.2504 (ttp) REVERT: E 173 ILE cc_start: -0.2121 (OUTLIER) cc_final: -0.2472 (mm) REVERT: F 83 LEU cc_start: 0.7591 (pt) cc_final: 0.7150 (pp) REVERT: G 89 ILE cc_start: 0.8093 (tp) cc_final: 0.7751 (tp) REVERT: G 143 ASP cc_start: 0.1864 (OUTLIER) cc_final: 0.1531 (t0) REVERT: G 151 ARG cc_start: 0.3529 (pmm-80) cc_final: 0.2880 (mpt-90) REVERT: I 1 MET cc_start: 0.4780 (pmm) cc_final: 0.4067 (pp-130) REVERT: J 29 TYR cc_start: 0.8091 (OUTLIER) cc_final: 0.7710 (t80) REVERT: K 46 GLU cc_start: 0.7416 (pt0) cc_final: 0.7082 (pp20) REVERT: L 13 GLN cc_start: 0.5577 (pp30) cc_final: 0.4556 (pm20) REVERT: M 73 LYS cc_start: 0.6923 (tttt) cc_final: 0.6478 (pttt) REVERT: M 113 ARG cc_start: 0.6700 (pmm-80) cc_final: 0.6112 (ptm160) REVERT: M 211 TYR cc_start: 0.7281 (t80) cc_final: 0.6677 (t80) REVERT: M 248 MET cc_start: 0.4512 (ttm) cc_final: 0.3949 (ppp) REVERT: N 262 LYS cc_start: 0.5681 (OUTLIER) cc_final: 0.5328 (pptt) REVERT: N 350 MET cc_start: 0.6356 (pmm) cc_final: 0.6069 (pmm) REVERT: O 7 LYS cc_start: 0.7256 (tptp) cc_final: 0.6977 (pttm) REVERT: O 118 MET cc_start: 0.2645 (ttt) cc_final: 0.1868 (ppp) REVERT: O 133 MET cc_start: 0.2564 (mtm) cc_final: 0.0774 (tmm) REVERT: O 139 MET cc_start: 0.2580 (pmm) cc_final: 0.1874 (pmm) REVERT: O 270 MET cc_start: 0.7798 (tpt) cc_final: 0.7555 (tpp) REVERT: O 355 GLN cc_start: 0.6790 (OUTLIER) cc_final: 0.6446 (pm20) REVERT: O 385 MET cc_start: 0.0800 (tpt) cc_final: -0.0340 (tpt) REVERT: O 424 TYR cc_start: 0.4829 (m-80) cc_final: 0.4162 (m-80) REVERT: O 455 LYS cc_start: 0.7140 (OUTLIER) cc_final: 0.6929 (mmmm) REVERT: P 220 ILE cc_start: 0.7812 (mm) cc_final: 0.7542 (pp) REVERT: Q 62 GLN cc_start: 0.7820 (mt0) cc_final: 0.7577 (mp10) REVERT: Q 74 PHE cc_start: 0.6852 (t80) cc_final: 0.6426 (t80) outliers start: 143 outliers final: 65 residues processed: 702 average time/residue: 1.3071 time to fit residues: 1156.5958 Evaluate side-chains 636 residues out of total 4400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 556 time to evaluate : 4.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1031 SER Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1214 ILE Chi-restraints excluded: chain A residue 1215 ASP Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain B residue 155 PHE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 856 ILE Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 883 MET Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 143 ASP Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain J residue 29 TYR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 39 TYR Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 262 LYS Chi-restraints excluded: chain N residue 385 CYS Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 328 ASP Chi-restraints excluded: chain O residue 355 GLN Chi-restraints excluded: chain O residue 403 PHE Chi-restraints excluded: chain O residue 455 LYS Chi-restraints excluded: chain P residue 208 SER Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 311 THR Chi-restraints excluded: chain Q residue 58 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 430 optimal weight: 1.9990 chunk 453 optimal weight: 10.0000 chunk 413 optimal weight: 6.9990 chunk 441 optimal weight: 1.9990 chunk 265 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 chunk 346 optimal weight: 3.9990 chunk 135 optimal weight: 0.0970 chunk 398 optimal weight: 9.9990 chunk 417 optimal weight: 1.9990 chunk 439 optimal weight: 0.6980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 HIS A 304 GLN A 422 GLN A 662 ASN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN A 899 GLN A 962 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1039 GLN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 ASN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN ** B 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1100 HIS B1132 ASN D 89 HIS G 67 HIS ** M 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 379 GLN O 437 HIS ** O 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 240 ASN ** Q 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 moved from start: 1.4769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.242 41417 Z= 0.373 Angle : 1.178 50.517 56108 Z= 0.673 Chirality : 0.166 6.324 6305 Planarity : 0.006 0.104 7071 Dihedral : 9.664 76.067 5944 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.66 % Favored : 93.30 % Rotamer: Outliers : 3.16 % Allowed : 32.88 % Favored : 63.96 % 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: -1.86 (0.11), residues: 4922 helix: -0.34 (0.12), residues: 1704 sheet: -0.47 (0.18), residues: 700 loop : -2.15 (0.11), residues: 2518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 424 HIS 0.037 0.002 HIS D 60 PHE 0.077 0.003 PHE A 849 TYR 0.027 0.002 TYR B 81 ARG 0.013 0.001 ARG O 272 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 4400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 671 time to evaluate : 4.907 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 89 GLU cc_start: 0.5732 (mp0) cc_final: 0.4576 (mt-10) REVERT: A 305 MET cc_start: 0.5230 (ppp) cc_final: 0.4933 (ppp) REVERT: A 307 MET cc_start: 0.4605 (tpp) cc_final: 0.4108 (tpt) REVERT: A 310 TRP cc_start: 0.6569 (t60) cc_final: 0.6120 (t60) REVERT: A 394 GLU cc_start: 0.6915 (pt0) cc_final: 0.6706 (pt0) REVERT: A 474 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7935 (mtt) REVERT: A 709 LEU cc_start: 0.5431 (OUTLIER) cc_final: 0.5097 (tp) REVERT: A 801 GLN cc_start: 0.6148 (pm20) cc_final: 0.5563 (tt0) REVERT: A 937 GLU cc_start: 0.5674 (tt0) cc_final: 0.4276 (tm-30) REVERT: A 954 LYS cc_start: 0.6361 (OUTLIER) cc_final: 0.6113 (ptpp) REVERT: A 1028 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7556 (mm-30) REVERT: A 1161 LYS cc_start: 0.8129 (tttm) cc_final: 0.7807 (ptmm) REVERT: A 1305 ARG cc_start: 0.5948 (ptp-170) cc_final: 0.5441 (ptp-170) REVERT: A 1337 LYS cc_start: 0.7221 (OUTLIER) cc_final: 0.6844 (ptmm) REVERT: A 1374 LYS cc_start: 0.5325 (mmtt) cc_final: 0.5035 (mmtp) REVERT: B 63 GLU cc_start: 0.3806 (mm-30) cc_final: 0.3517 (mm-30) REVERT: B 220 GLN cc_start: 0.6628 (pp30) cc_final: 0.5206 (pp30) REVERT: B 254 MET cc_start: 0.2433 (mtt) cc_final: 0.1646 (ptm) REVERT: B 384 MET cc_start: 0.4776 (OUTLIER) cc_final: 0.3917 (ppp) REVERT: B 406 MET cc_start: 0.3216 (tpt) cc_final: 0.1902 (mmm) REVERT: B 478 MET cc_start: 0.6822 (OUTLIER) cc_final: 0.5737 (ptp) REVERT: B 562 MET cc_start: 0.2767 (tpt) cc_final: 0.2233 (tpt) REVERT: B 660 GLU cc_start: 0.5300 (mm-30) cc_final: 0.4703 (tp30) REVERT: B 1015 MET cc_start: 0.9143 (mtm) cc_final: 0.8926 (mpp) REVERT: B 1051 GLU cc_start: 0.7741 (mp0) cc_final: 0.7243 (mp0) REVERT: B 1069 MET cc_start: 0.5735 (pmm) cc_final: 0.5114 (ppp) REVERT: C 307 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8503 (mp) REVERT: D 1 MET cc_start: 0.0367 (mmt) cc_final: -0.1762 (mmm) REVERT: E 1 MET cc_start: 0.4362 (tpt) cc_final: 0.4124 (mmm) REVERT: E 144 LEU cc_start: 0.6892 (OUTLIER) cc_final: 0.6579 (pp) REVERT: E 151 MET cc_start: 0.5481 (mmm) cc_final: 0.4378 (ttp) REVERT: E 165 LEU cc_start: 0.1545 (pt) cc_final: 0.1323 (pp) REVERT: E 173 ILE cc_start: -0.1596 (OUTLIER) cc_final: -0.2007 (mm) REVERT: F 83 LEU cc_start: 0.7823 (pt) cc_final: 0.7340 (pp) REVERT: G 89 ILE cc_start: 0.8335 (tp) cc_final: 0.7979 (tp) REVERT: G 143 ASP cc_start: 0.2144 (OUTLIER) cc_final: 0.1623 (t0) REVERT: G 151 ARG cc_start: 0.3606 (pmm-80) cc_final: 0.2886 (mpt-90) REVERT: H 100 GLU cc_start: 0.4240 (pt0) cc_final: 0.3884 (pm20) REVERT: I 1 MET cc_start: 0.4543 (pmm) cc_final: 0.3618 (pp-130) REVERT: I 91 MET cc_start: 0.5318 (mmp) cc_final: 0.4920 (mtt) REVERT: J 29 TYR cc_start: 0.8246 (OUTLIER) cc_final: 0.7949 (t80) REVERT: K 46 GLU cc_start: 0.7604 (pt0) cc_final: 0.7297 (pp20) REVERT: M 73 LYS cc_start: 0.7123 (tttt) cc_final: 0.6747 (pttt) REVERT: M 136 ARG cc_start: 0.4811 (ptp90) cc_final: 0.4416 (mpt180) REVERT: M 211 TYR cc_start: 0.8061 (t80) cc_final: 0.7230 (t80) REVERT: M 248 MET cc_start: 0.4595 (ttm) cc_final: 0.4008 (ppp) REVERT: N 262 LYS cc_start: 0.6024 (OUTLIER) cc_final: 0.5713 (pptt) REVERT: N 372 GLU cc_start: 0.6424 (tp30) cc_final: 0.5996 (tp30) REVERT: O 60 HIS cc_start: 0.8123 (m90) cc_final: 0.7769 (m90) REVERT: O 85 MET cc_start: 0.6717 (mmp) cc_final: 0.6364 (mpt) REVERT: O 91 TYR cc_start: 0.6115 (t80) cc_final: 0.5754 (t80) REVERT: O 107 VAL cc_start: 0.6181 (OUTLIER) cc_final: 0.5975 (p) REVERT: O 133 MET cc_start: 0.2589 (mtm) cc_final: 0.1038 (tmm) REVERT: O 140 ASP cc_start: 0.5628 (t70) cc_final: 0.5159 (t70) REVERT: O 274 SER cc_start: 0.8032 (m) cc_final: 0.7591 (p) REVERT: O 376 GLU cc_start: 0.6384 (mm-30) cc_final: 0.6167 (mm-30) REVERT: O 455 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.7262 (mmmm) REVERT: O 527 ILE cc_start: 0.6483 (mp) cc_final: 0.6166 (mm) REVERT: O 531 MET cc_start: 0.7377 (tmm) cc_final: 0.7030 (ttp) REVERT: P 220 ILE cc_start: 0.7823 (mm) cc_final: 0.7524 (pp) REVERT: Q 57 MET cc_start: 0.6608 (tpp) cc_final: 0.6279 (tpt) REVERT: Q 74 PHE cc_start: 0.6761 (t80) cc_final: 0.6424 (t80) REVERT: Q 110 MET cc_start: 0.5820 (ppp) cc_final: 0.5550 (ppp) outliers start: 139 outliers final: 63 residues processed: 762 average time/residue: 1.3930 time to fit residues: 1321.7596 Evaluate side-chains 627 residues out of total 4400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 550 time to evaluate : 4.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 402 ASN Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 898 ILE Chi-restraints excluded: chain A residue 954 LYS Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1031 SER Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1215 ASP Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1337 LYS Chi-restraints excluded: chain B residue 155 PHE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 495 ASN Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 883 MET Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 143 ASP Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 29 TYR Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain M residue 39 TYR Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 262 LYS Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 328 ASP Chi-restraints excluded: chain O residue 355 GLN Chi-restraints excluded: chain O residue 439 CYS Chi-restraints excluded: chain O residue 455 LYS Chi-restraints excluded: chain P residue 208 SER Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 311 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 289 optimal weight: 7.9990 chunk 466 optimal weight: 7.9990 chunk 284 optimal weight: 7.9990 chunk 221 optimal weight: 5.9990 chunk 324 optimal weight: 3.9990 chunk 489 optimal weight: 9.9990 chunk 450 optimal weight: 5.9990 chunk 389 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 300 optimal weight: 7.9990 chunk 238 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 GLN ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 ASN ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 511 GLN A 662 ASN A 673 GLN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1039 GLN A1213 HIS A1286 HIS ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 ASN B 399 GLN B 535 ASN B 642 ASN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 737 GLN ** B1014 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN D 89 HIS E 108 GLN F 72 GLN ** G 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 138 HIS I 10 ASN ** I 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 109 HIS ** M 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 377 GLN ** O 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 1.7468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.236 41417 Z= 0.507 Angle : 1.336 50.525 56108 Z= 0.751 Chirality : 0.168 6.347 6305 Planarity : 0.008 0.283 7071 Dihedral : 10.215 76.438 5944 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 21.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.62 % Favored : 92.28 % Rotamer: Outliers : 3.02 % Allowed : 34.86 % Favored : 62.12 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.42 (0.11), residues: 4922 helix: -1.00 (0.12), residues: 1686 sheet: -0.67 (0.19), residues: 664 loop : -2.32 (0.11), residues: 2572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP A 595 HIS 0.018 0.002 HIS B 501 PHE 0.063 0.004 PHE B 328 TYR 0.034 0.003 TYR A 42 ARG 0.033 0.001 ARG B 704 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 4400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 736 time to evaluate : 4.530 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: A 58 HIS cc_start: 0.7777 (OUTLIER) cc_final: 0.7411 (t70) REVERT: A 62 THR cc_start: 0.9204 (p) cc_final: 0.8832 (t) REVERT: A 307 MET cc_start: 0.5701 (tpp) cc_final: 0.5364 (tpt) REVERT: A 528 ASN cc_start: 0.8243 (m-40) cc_final: 0.7894 (m110) REVERT: A 709 LEU cc_start: 0.6951 (OUTLIER) cc_final: 0.6408 (tt) REVERT: A 1071 LYS cc_start: 0.8305 (tttt) cc_final: 0.7867 (ttmm) REVERT: A 1075 ASN cc_start: 0.7974 (m-40) cc_final: 0.7710 (m-40) REVERT: A 1290 LEU cc_start: 0.9518 (tm) cc_final: 0.9300 (tp) REVERT: B 106 ASP cc_start: 0.8051 (t0) cc_final: 0.7803 (t0) REVERT: B 243 MET cc_start: 0.2881 (OUTLIER) cc_final: 0.2303 (mmt) REVERT: B 254 MET cc_start: 0.2643 (mtt) cc_final: 0.2227 (ptm) REVERT: B 289 ASN cc_start: 0.6483 (OUTLIER) cc_final: 0.6199 (t0) REVERT: B 329 ARG cc_start: 0.5798 (mmt180) cc_final: 0.5266 (mmt180) REVERT: B 381 ASN cc_start: 0.7125 (m110) cc_final: 0.6786 (p0) REVERT: B 384 MET cc_start: 0.5729 (OUTLIER) cc_final: 0.4901 (ppp) REVERT: B 406 MET cc_start: 0.3752 (tpt) cc_final: 0.2816 (tpt) REVERT: B 506 MET cc_start: 0.5244 (pmm) cc_final: 0.5018 (pmm) REVERT: B 551 ASP cc_start: 0.4478 (t0) cc_final: 0.4139 (t0) REVERT: B 562 MET cc_start: 0.3751 (tpt) cc_final: 0.3090 (tpt) REVERT: B 581 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.7221 (mtt180) REVERT: B 660 GLU cc_start: 0.5638 (mm-30) cc_final: 0.5063 (tp30) REVERT: B 791 MET cc_start: 0.7196 (OUTLIER) cc_final: 0.6477 (mmp) REVERT: B 1015 MET cc_start: 0.9257 (mtm) cc_final: 0.8817 (mpp) REVERT: B 1066 GLU cc_start: 0.8220 (pp20) cc_final: 0.8019 (pp20) REVERT: C 5 GLN cc_start: 0.8020 (mp10) cc_final: 0.7784 (mp10) REVERT: C 294 LYS cc_start: 0.7077 (mmtt) cc_final: 0.6221 (mtpm) REVERT: C 307 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8884 (mp) REVERT: E 108 GLN cc_start: 0.6279 (mp10) cc_final: 0.5932 (mp10) REVERT: E 151 MET cc_start: 0.6166 (mmm) cc_final: 0.5586 (mtp) REVERT: E 173 ILE cc_start: 0.0250 (OUTLIER) cc_final: -0.0183 (mp) REVERT: E 207 ARG cc_start: 0.7315 (tmm160) cc_final: 0.6952 (mtt-85) REVERT: F 83 LEU cc_start: 0.8272 (pt) cc_final: 0.7846 (pp) REVERT: F 91 LEU cc_start: 0.9058 (tm) cc_final: 0.8858 (tm) REVERT: F 117 ASP cc_start: 0.8277 (p0) cc_final: 0.7948 (p0) REVERT: G 74 CYS cc_start: 0.7434 (p) cc_final: 0.7014 (t) REVERT: G 89 ILE cc_start: 0.8303 (tp) cc_final: 0.7951 (tp) REVERT: G 143 ASP cc_start: 0.1919 (OUTLIER) cc_final: 0.1508 (t0) REVERT: G 151 ARG cc_start: 0.3706 (pmm-80) cc_final: 0.3005 (mpt-90) REVERT: H 124 ARG cc_start: 0.7904 (ttt180) cc_final: 0.7415 (tpt-90) REVERT: I 1 MET cc_start: 0.4128 (pmm) cc_final: 0.2815 (pp-130) REVERT: I 3 LEU cc_start: 0.4929 (mt) cc_final: 0.4557 (tp) REVERT: I 91 MET cc_start: 0.5859 (mmp) cc_final: 0.4982 (mtt) REVERT: J 29 TYR cc_start: 0.8355 (OUTLIER) cc_final: 0.7967 (t80) REVERT: K 36 ASP cc_start: 0.6608 (p0) cc_final: 0.6282 (p0) REVERT: K 47 GLU cc_start: 0.6632 (mm-30) cc_final: 0.6055 (mm-30) REVERT: K 125 LYS cc_start: 0.8146 (tppt) cc_final: 0.7822 (ttpt) REVERT: L 13 GLN cc_start: 0.6377 (pp30) cc_final: 0.5562 (pm20) REVERT: M 136 ARG cc_start: 0.5052 (ptp90) cc_final: 0.4641 (mpt180) REVERT: M 211 TYR cc_start: 0.8516 (t80) cc_final: 0.7632 (t80) REVERT: N 262 LYS cc_start: 0.6293 (OUTLIER) cc_final: 0.6009 (pmmt) REVERT: N 347 ASP cc_start: 0.7655 (t0) cc_final: 0.7337 (t0) REVERT: O 7 LYS cc_start: 0.8491 (tppt) cc_final: 0.8264 (tppt) REVERT: O 11 LEU cc_start: 0.8161 (mt) cc_final: 0.7881 (mm) REVERT: O 90 ARG cc_start: 0.5737 (mtm180) cc_final: 0.5164 (mtm180) REVERT: O 93 TYR cc_start: 0.5540 (t80) cc_final: 0.4874 (t80) REVERT: O 322 PHE cc_start: 0.7134 (t80) cc_final: 0.6710 (m-80) REVERT: O 490 MET cc_start: 0.1112 (pmt) cc_final: 0.0879 (pmt) REVERT: P 184 CYS cc_start: 0.7318 (p) cc_final: 0.6914 (p) REVERT: P 250 MET cc_start: 0.4976 (tpt) cc_final: 0.3413 (ppp) REVERT: Q 62 GLN cc_start: 0.8560 (mt0) cc_final: 0.8337 (mp10) outliers start: 133 outliers final: 59 residues processed: 826 average time/residue: 1.4442 time to fit residues: 1475.9330 Evaluate side-chains 650 residues out of total 4400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 579 time to evaluate : 4.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 58 HIS Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 402 ASN Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 954 LYS Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1231 ASN Chi-restraints excluded: chain A residue 1248 SER Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 155 PHE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 581 ARG Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 648 HIS Chi-restraints excluded: chain B residue 791 MET Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 143 ASP Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain J residue 29 TYR Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain M residue 39 TYR Chi-restraints excluded: chain M residue 706 VAL Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 262 LYS Chi-restraints excluded: chain N residue 330 LEU Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 328 ASP Chi-restraints excluded: chain O residue 355 GLN Chi-restraints excluded: chain O residue 375 ILE Chi-restraints excluded: chain O residue 439 CYS Chi-restraints excluded: chain P residue 208 SER Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 306 ASN Chi-restraints excluded: chain P residue 311 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 491 random chunks: chunk 309 optimal weight: 5.9990 chunk 414 optimal weight: 7.9990 chunk 119 optimal weight: 9.9990 chunk 359 optimal weight: 20.0000 chunk 57 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 390 optimal weight: 9.9990 chunk 163 optimal weight: 0.7980 chunk 400 optimal weight: 3.9990 chunk 49 optimal weight: 0.4980 chunk 71 optimal weight: 3.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 ASN ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 HIS A 497 ASN A 662 ASN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1039 GLN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 932 HIS ** B1014 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 ASN C 265 GLN C 305 HIS ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 HIS D 89 HIS D 98 GLN ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 GLN H 131 ASN ** I 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 GLN ** M 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 113 ASN O 374 HIS ** O 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 379 GLN ** O 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.141618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.106233 restraints weight = 96758.179| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 3.95 r_work: 0.3544 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3544 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3544 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 1.8040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.243 41417 Z= 0.397 Angle : 1.224 50.794 56108 Z= 0.690 Chirality : 0.166 6.403 6305 Planarity : 0.006 0.092 7071 Dihedral : 9.999 76.418 5944 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.38 % Favored : 93.60 % Rotamer: Outliers : 2.46 % Allowed : 37.79 % Favored : 59.75 % 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: -2.21 (0.11), residues: 4922 helix: -0.71 (0.12), residues: 1680 sheet: -0.62 (0.19), residues: 682 loop : -2.29 (0.11), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 595 HIS 0.013 0.002 HIS B 501 PHE 0.040 0.003 PHE A1334 TYR 0.072 0.002 TYR M 193 ARG 0.015 0.001 ARG O 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19210.70 seconds wall clock time: 338 minutes 43.31 seconds (20323.31 seconds total)