Starting phenix.real_space_refine on Mon Mar 25 14:55:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tcz_10462/03_2024/6tcz_10462_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tcz_10462/03_2024/6tcz_10462.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tcz_10462/03_2024/6tcz_10462_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tcz_10462/03_2024/6tcz_10462_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tcz_10462/03_2024/6tcz_10462_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tcz_10462/03_2024/6tcz_10462.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tcz_10462/03_2024/6tcz_10462.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tcz_10462/03_2024/6tcz_10462_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tcz_10462/03_2024/6tcz_10462_updated.pdb" } resolution = 3.4 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= 0.005 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: 5 Type Number sf(0) Gaussians S 326 5.16 5 C 30952 2.51 5 N 8496 2.21 5 O 9472 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 23": "OE1" <-> "OE2" Residue "A ASP 43": "OD1" <-> "OD2" Residue "A ASP 55": "OD1" <-> "OD2" Residue "A ARG 56": "NH1" <-> "NH2" Residue "A ASP 61": "OD1" <-> "OD2" Residue "A ARG 80": "NH1" <-> "NH2" Residue "A TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "A PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 141": "OD1" <-> "OD2" Residue "A PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 220": "OE1" <-> "OE2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "B PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 40": "OD1" <-> "OD2" Residue "B ASP 67": "OD1" <-> "OD2" Residue "B GLU 68": "OE1" <-> "OE2" Residue "B TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 167": "OD1" <-> "OD2" Residue "B PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 175": "NH1" <-> "NH2" Residue "B ASP 198": "OD1" <-> "OD2" Residue "B GLU 204": "OE1" <-> "OE2" Residue "B GLU 217": "OE1" <-> "OE2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ASP 226": "OD1" <-> "OD2" Residue "B TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C GLU 15": "OE1" <-> "OE2" Residue "C GLU 59": "OE1" <-> "OE2" Residue "C ASP 63": "OD1" <-> "OD2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "C TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 109": "OE1" <-> "OE2" Residue "C ASP 115": "OD1" <-> "OD2" Residue "C TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 147": "NH1" <-> "NH2" Residue "C TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 174": "OD1" <-> "OD2" Residue "C ASP 184": "OD1" <-> "OD2" Residue "C ARG 222": "NH1" <-> "NH2" Residue "C ASP 230": "OD1" <-> "OD2" Residue "C ASP 234": "OD1" <-> "OD2" Residue "C PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 245": "NH1" <-> "NH2" Residue "C ARG 251": "NH1" <-> "NH2" Residue "C ARG 265": "NH1" <-> "NH2" Residue "D ASP 39": "OD1" <-> "OD2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D ARG 60": "NH1" <-> "NH2" Residue "D ASP 66": "OD1" <-> "OD2" Residue "D PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 79": "OD1" <-> "OD2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "D PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 99": "OE1" <-> "OE2" Residue "D ASP 100": "OD1" <-> "OD2" Residue "D ASP 105": "OD1" <-> "OD2" Residue "D ARG 109": "NH1" <-> "NH2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 138": "OE1" <-> "OE2" Residue "D ARG 157": "NH1" <-> "NH2" Residue "D ASP 183": "OD1" <-> "OD2" Residue "D GLU 184": "OE1" <-> "OE2" Residue "D GLU 198": "OE1" <-> "OE2" Residue "D GLU 228": "OE1" <-> "OE2" Residue "D GLU 236": "OE1" <-> "OE2" Residue "E TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 118": "OE1" <-> "OE2" Residue "E GLU 144": "OE1" <-> "OE2" Residue "E ARG 153": "NH1" <-> "NH2" Residue "E GLU 169": "OE1" <-> "OE2" Residue "E ASP 184": "OD1" <-> "OD2" Residue "E PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 248": "OE1" <-> "OE2" Residue "E GLU 275": "OE1" <-> "OE2" Residue "E GLU 313": "OE1" <-> "OE2" Residue "E ASP 323": "OD1" <-> "OD2" Residue "E ASP 324": "OD1" <-> "OD2" Residue "E GLU 334": "OE1" <-> "OE2" Residue "F ARG 215": "NH1" <-> "NH2" Residue "F GLU 220": "OE1" <-> "OE2" Residue "F GLU 226": "OE1" <-> "OE2" Residue "F ASP 232": "OD1" <-> "OD2" Residue "F TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 338": "OE1" <-> "OE2" Residue "F GLU 369": "OE1" <-> "OE2" Residue "F GLU 390": "OE1" <-> "OE2" Residue "F ASP 399": "OD1" <-> "OD2" Residue "F ARG 404": "NH1" <-> "NH2" Residue "G ASP 13": "OD1" <-> "OD2" Residue "G ASP 32": "OD1" <-> "OD2" Residue "G ASP 71": "OD1" <-> "OD2" Residue "G ARG 72": "NH1" <-> "NH2" Residue "G GLU 95": "OE1" <-> "OE2" Residue "G ASP 101": "OD1" <-> "OD2" Residue "G ARG 115": "NH1" <-> "NH2" Residue "G GLU 118": "OE1" <-> "OE2" Residue "G PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 143": "OD1" <-> "OD2" Residue "G ASP 187": "OD1" <-> "OD2" Residue "G GLU 199": "OE1" <-> "OE2" Residue "G GLU 210": "OE1" <-> "OE2" Residue "G GLU 212": "OE1" <-> "OE2" Residue "G ARG 222": "NH1" <-> "NH2" Residue "G PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 230": "OD1" <-> "OD2" Residue "H ARG 73": "NH1" <-> "NH2" Residue "H ARG 112": "NH1" <-> "NH2" Residue "H TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 205": "OE1" <-> "OE2" Residue "H TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 236": "OD1" <-> "OD2" Residue "I ASP 46": "OD1" <-> "OD2" Residue "I GLU 51": "OE1" <-> "OE2" Residue "I ARG 61": "NH1" <-> "NH2" Residue "I GLU 82": "OE1" <-> "OE2" Residue "I GLU 98": "OE1" <-> "OE2" Residue "I ASP 133": "OD1" <-> "OD2" Residue "I PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 179": "OE1" <-> "OE2" Residue "I GLU 182": "OE1" <-> "OE2" Residue "I TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 223": "OE1" <-> "OE2" Residue "I ARG 224": "NH1" <-> "NH2" Residue "I ARG 228": "NH1" <-> "NH2" Residue "I GLU 243": "OE1" <-> "OE2" Residue "I GLU 244": "OE1" <-> "OE2" Residue "I ARG 246": "NH1" <-> "NH2" Residue "J TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 25": "OD1" <-> "OD2" Residue "J GLU 30": "OE1" <-> "OE2" Residue "J GLU 78": "OE1" <-> "OE2" Residue "J GLU 79": "OE1" <-> "OE2" Residue "J GLU 118": "OE1" <-> "OE2" Residue "J ASP 125": "OD1" <-> "OD2" Residue "J GLU 134": "OE1" <-> "OE2" Residue "J TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 144": "OE1" <-> "OE2" Residue "J ASP 176": "OD1" <-> "OD2" Residue "J TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 12": "OD1" <-> "OD2" Residue "K TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 50": "OE1" <-> "OE2" Residue "K ARG 71": "NH1" <-> "NH2" Residue "K ARG 75": "NH1" <-> "NH2" Residue "K GLU 80": "OE1" <-> "OE2" Residue "K ARG 97": "NH1" <-> "NH2" Residue "K GLU 116": "OE1" <-> "OE2" Residue "K ASP 118": "OD1" <-> "OD2" Residue "K ASP 119": "OD1" <-> "OD2" Residue "K PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 155": "OD1" <-> "OD2" Residue "K ARG 159": "NH1" <-> "NH2" Residue "K GLU 200": "OE1" <-> "OE2" Residue "L PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 116": "OD1" <-> "OD2" Residue "L TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 161": "OE1" <-> "OE2" Residue "L GLU 166": "OE1" <-> "OE2" Residue "L ARG 168": "NH1" <-> "NH2" Residue "L PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 214": "OD1" <-> "OD2" Residue "L ASP 223": "OD1" <-> "OD2" Residue "L ARG 243": "NH1" <-> "NH2" Residue "L ASP 290": "OD1" <-> "OD2" Residue "M ASP 131": "OD1" <-> "OD2" Residue "M ASP 143": "OD1" <-> "OD2" Residue "M PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 225": "NH1" <-> "NH2" Residue "M TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 291": "OE1" <-> "OE2" Residue "M GLU 310": "OE1" <-> "OE2" Residue "M ASP 317": "OD1" <-> "OD2" Residue "N TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 64": "OE1" <-> "OE2" Residue "N GLU 68": "OE1" <-> "OE2" Residue "N GLU 115": "OE1" <-> "OE2" Residue "N ASP 122": "OD1" <-> "OD2" Residue "N ARG 127": "NH1" <-> "NH2" Residue "N GLU 129": "OE1" <-> "OE2" Residue "N ASP 131": "OD1" <-> "OD2" Residue "N TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 151": "OE1" <-> "OE2" Residue "N GLU 161": "OE1" <-> "OE2" Residue "N GLU 177": "OE1" <-> "OE2" Residue "N GLU 198": "OE1" <-> "OE2" Residue "N ASP 201": "OD1" <-> "OD2" Residue "N GLU 203": "OE1" <-> "OE2" Residue "a GLU 23": "OE1" <-> "OE2" Residue "a ASP 43": "OD1" <-> "OD2" Residue "a ASP 55": "OD1" <-> "OD2" Residue "a ARG 56": "NH1" <-> "NH2" Residue "a ASP 61": "OD1" <-> "OD2" Residue "a ARG 80": "NH1" <-> "NH2" Residue "a TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 105": "OE1" <-> "OE2" Residue "a PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 141": "OD1" <-> "OD2" Residue "a PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 220": "OE1" <-> "OE2" Residue "a GLU 238": "OE1" <-> "OE2" Residue "b PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 40": "OD1" <-> "OD2" Residue "b ASP 67": "OD1" <-> "OD2" Residue "b GLU 68": "OE1" <-> "OE2" Residue "b TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 167": "OD1" <-> "OD2" Residue "b PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 175": "NH1" <-> "NH2" Residue "b ASP 198": "OD1" <-> "OD2" Residue "b GLU 204": "OE1" <-> "OE2" Residue "b GLU 217": "OE1" <-> "OE2" Residue "b ARG 225": "NH1" <-> "NH2" Residue "b ASP 226": "OD1" <-> "OD2" Residue "b TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 8": "NH1" <-> "NH2" Residue "c GLU 15": "OE1" <-> "OE2" Residue "c GLU 59": "OE1" <-> "OE2" Residue "c ASP 63": "OD1" <-> "OD2" Residue "c GLU 69": "OE1" <-> "OE2" Residue "c TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 109": "OE1" <-> "OE2" Residue "c ASP 115": "OD1" <-> "OD2" Residue "c TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 147": "NH1" <-> "NH2" Residue "c TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 174": "OD1" <-> "OD2" Residue "c ASP 184": "OD1" <-> "OD2" Residue "c ARG 222": "NH1" <-> "NH2" Residue "c ASP 230": "OD1" <-> "OD2" Residue "c ASP 234": "OD1" <-> "OD2" Residue "c PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 245": "NH1" <-> "NH2" Residue "c ARG 251": "NH1" <-> "NH2" Residue "c ARG 265": "NH1" <-> "NH2" Residue "d ASP 39": "OD1" <-> "OD2" Residue "d ARG 57": "NH1" <-> "NH2" Residue "d ARG 60": "NH1" <-> "NH2" Residue "d ASP 66": "OD1" <-> "OD2" Residue "d PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 79": "OD1" <-> "OD2" Residue "d GLU 90": "OE1" <-> "OE2" Residue "d PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 99": "OE1" <-> "OE2" Residue "d ASP 100": "OD1" <-> "OD2" Residue "d ASP 105": "OD1" <-> "OD2" Residue "d ARG 109": "NH1" <-> "NH2" Residue "d PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 138": "OE1" <-> "OE2" Residue "d ARG 157": "NH1" <-> "NH2" Residue "d ASP 183": "OD1" <-> "OD2" Residue "d GLU 184": "OE1" <-> "OE2" Residue "d GLU 198": "OE1" <-> "OE2" Residue "d GLU 228": "OE1" <-> "OE2" Residue "d GLU 236": "OE1" <-> "OE2" Residue "e TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 118": "OE1" <-> "OE2" Residue "e GLU 144": "OE1" <-> "OE2" Residue "e ARG 153": "NH1" <-> "NH2" Residue "e GLU 169": "OE1" <-> "OE2" Residue "e ASP 184": "OD1" <-> "OD2" Residue "e PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 248": "OE1" <-> "OE2" Residue "e GLU 275": "OE1" <-> "OE2" Residue "e GLU 313": "OE1" <-> "OE2" Residue "e ASP 323": "OD1" <-> "OD2" Residue "e ASP 324": "OD1" <-> "OD2" Residue "e GLU 334": "OE1" <-> "OE2" Residue "f ARG 215": "NH1" <-> "NH2" Residue "f GLU 220": "OE1" <-> "OE2" Residue "f GLU 226": "OE1" <-> "OE2" Residue "f ASP 232": "OD1" <-> "OD2" Residue "f TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 338": "OE1" <-> "OE2" Residue "f GLU 369": "OE1" <-> "OE2" Residue "f GLU 390": "OE1" <-> "OE2" Residue "f ASP 399": "OD1" <-> "OD2" Residue "f ARG 404": "NH1" <-> "NH2" Residue "g ASP 13": "OD1" <-> "OD2" Residue "g ASP 32": "OD1" <-> "OD2" Residue "g ASP 71": "OD1" <-> "OD2" Residue "g ARG 72": "NH1" <-> "NH2" Residue "g GLU 95": "OE1" <-> "OE2" Residue "g ASP 101": "OD1" <-> "OD2" Residue "g ARG 115": "NH1" <-> "NH2" Residue "g GLU 118": "OE1" <-> "OE2" Residue "g PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 143": "OD1" <-> "OD2" Residue "g ASP 187": "OD1" <-> "OD2" Residue "g GLU 199": "OE1" <-> "OE2" Residue "g GLU 210": "OE1" <-> "OE2" Residue "g GLU 212": "OE1" <-> "OE2" Residue "g ARG 222": "NH1" <-> "NH2" Residue "g PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 230": "OD1" <-> "OD2" Residue "h ARG 73": "NH1" <-> "NH2" Residue "h ARG 112": "NH1" <-> "NH2" Residue "h TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 205": "OE1" <-> "OE2" Residue "h TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 236": "OD1" <-> "OD2" Residue "i ASP 46": "OD1" <-> "OD2" Residue "i GLU 51": "OE1" <-> "OE2" Residue "i ARG 61": "NH1" <-> "NH2" Residue "i GLU 82": "OE1" <-> "OE2" Residue "i GLU 98": "OE1" <-> "OE2" Residue "i ASP 133": "OD1" <-> "OD2" Residue "i PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 179": "OE1" <-> "OE2" Residue "i GLU 182": "OE1" <-> "OE2" Residue "i TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 223": "OE1" <-> "OE2" Residue "i ARG 224": "NH1" <-> "NH2" Residue "i ARG 228": "NH1" <-> "NH2" Residue "i GLU 243": "OE1" <-> "OE2" Residue "i GLU 244": "OE1" <-> "OE2" Residue "i ARG 246": "NH1" <-> "NH2" Residue "j TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 25": "OD1" <-> "OD2" Residue "j GLU 30": "OE1" <-> "OE2" Residue "j GLU 78": "OE1" <-> "OE2" Residue "j GLU 79": "OE1" <-> "OE2" Residue "j GLU 118": "OE1" <-> "OE2" Residue "j ASP 125": "OD1" <-> "OD2" Residue "j GLU 134": "OE1" <-> "OE2" Residue "j TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 144": "OE1" <-> "OE2" Residue "j ASP 176": "OD1" <-> "OD2" Residue "j TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 12": "OD1" <-> "OD2" Residue "k TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 50": "OE1" <-> "OE2" Residue "k ARG 71": "NH1" <-> "NH2" Residue "k ARG 75": "NH1" <-> "NH2" Residue "k GLU 80": "OE1" <-> "OE2" Residue "k ARG 97": "NH1" <-> "NH2" Residue "k GLU 116": "OE1" <-> "OE2" Residue "k ASP 118": "OD1" <-> "OD2" Residue "k ASP 119": "OD1" <-> "OD2" Residue "k PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 155": "OD1" <-> "OD2" Residue "k ARG 159": "NH1" <-> "NH2" Residue "k GLU 200": "OE1" <-> "OE2" Residue "l PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 116": "OD1" <-> "OD2" Residue "l TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 166": "OE1" <-> "OE2" Residue "l ARG 168": "NH1" <-> "NH2" Residue "l PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 214": "OD1" <-> "OD2" Residue "l ASP 223": "OD1" <-> "OD2" Residue "l ASP 239": "OD1" <-> "OD2" Residue "l ARG 243": "NH1" <-> "NH2" Residue "l GLU 280": "OE1" <-> "OE2" Residue "m ASP 131": "OD1" <-> "OD2" Residue "m ASP 143": "OD1" <-> "OD2" Residue "m PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 225": "NH1" <-> "NH2" Residue "m TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 291": "OE1" <-> "OE2" Residue "m GLU 310": "OE1" <-> "OE2" Residue "m ASP 317": "OD1" <-> "OD2" Residue "n TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 64": "OE1" <-> "OE2" Residue "n GLU 68": "OE1" <-> "OE2" Residue "n GLU 115": "OE1" <-> "OE2" Residue "n ASP 122": "OD1" <-> "OD2" Residue "n ARG 127": "NH1" <-> "NH2" Residue "n GLU 129": "OE1" <-> "OE2" Residue "n ASP 131": "OD1" <-> "OD2" Residue "n TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 151": "OE1" <-> "OE2" Residue "n GLU 161": "OE1" <-> "OE2" Residue "n GLU 177": "OE1" <-> "OE2" Residue "n GLU 198": "OE1" <-> "OE2" Residue "n ASP 201": "OD1" <-> "OD2" Residue "n GLU 203": "OE1" <-> "OE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 49248 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1861 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 12, 'TRANS': 232} Chain: "B" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1753 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "C" Number of atoms: 2155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2155 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 11, 'TRANS': 260} Chain: "D" Number of atoms: 1882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1882 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 4, 'TRANS': 235} Chain: "E" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1802 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 10, 'TRANS': 224} Chain: "F" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 8, 'TRANS': 229} Chain: "G" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1741 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 7, 'TRANS': 222} Chain: "H" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1709 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "I" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1659 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 10, 'TRANS': 208} Chain: "J" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1557 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 196} Chain: "K" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1612 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain: "L" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1577 Classifications: {'peptide': 202} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 199} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1702 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 205} Chain: "N" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1712 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "a" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1861 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 12, 'TRANS': 232} Chain: "b" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1753 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "c" Number of atoms: 2155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2155 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 11, 'TRANS': 260} Chain: "d" Number of atoms: 1882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1882 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 4, 'TRANS': 235} Chain: "e" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1802 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 10, 'TRANS': 224} Chain: "f" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 8, 'TRANS': 229} Chain: "g" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1741 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 7, 'TRANS': 222} Chain: "h" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1709 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "i" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1659 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 10, 'TRANS': 208} Chain: "j" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1557 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 196} Chain: "k" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1612 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain: "l" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1577 Classifications: {'peptide': 202} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 199} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "m" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1702 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 205} Chain: "n" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1712 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'N2E': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'N2E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 24.61, per 1000 atoms: 0.50 Number of scatterers: 49248 At special positions: 0 Unit cell: (138.876, 188.292, 133.764, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 326 16.00 F 2 9.00 O 9472 8.00 N 8496 7.00 C 30952 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: 17.33 Conformation dependent library (CDL) restraints added in 8.3 seconds 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11716 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 164 helices and 72 sheets defined 33.8% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.86 Creating SS restraints... Processing helix chain 'A' and resid 20 through 29 removed outlier: 3.865A pdb=" N PHE A 26 " --> pdb=" O VAL A 22 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LYS A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 102 removed outlier: 3.561A pdb=" N ARG A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 122 removed outlier: 3.789A pdb=" N ARG A 122 " --> pdb=" O LYS A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 185 Processing helix chain 'A' and resid 190 through 192 No H-bonds generated for 'chain 'A' and resid 190 through 192' Processing helix chain 'A' and resid 195 through 210 Processing helix chain 'A' and resid 216 through 218 No H-bonds generated for 'chain 'A' and resid 216 through 218' Processing helix chain 'A' and resid 236 through 246 removed outlier: 4.093A pdb=" N GLU A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 28 removed outlier: 3.572A pdb=" N GLY B 28 " --> pdb=" O THR B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 99 removed outlier: 3.965A pdb=" N VAL B 83 " --> pdb=" O PRO B 79 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS B 90 " --> pdb=" O ASP B 86 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS B 96 " --> pdb=" O CYS B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 119 removed outlier: 3.838A pdb=" N ILE B 115 " --> pdb=" O LYS B 111 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR B 116 " --> pdb=" O ILE B 112 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 175 removed outlier: 3.617A pdb=" N ALA B 170 " --> pdb=" O PRO B 166 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.667A pdb=" N GLY B 196 " --> pdb=" O THR B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 230 removed outlier: 3.658A pdb=" N TYR B 227 " --> pdb=" O GLN B 223 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLN B 230 " --> pdb=" O ASP B 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 30 removed outlier: 4.199A pdb=" N GLN C 30 " --> pdb=" O GLU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 107 removed outlier: 3.719A pdb=" N TYR C 90 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ALA C 91 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU C 92 " --> pdb=" O ASP C 88 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLN C 104 " --> pdb=" O ALA C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 119 Processing helix chain 'C' and resid 121 through 128 removed outlier: 3.640A pdb=" N TYR C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N THR C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 181 Processing helix chain 'C' and resid 191 through 206 Processing helix chain 'C' and resid 231 through 233 No H-bonds generated for 'chain 'C' and resid 231 through 233' Processing helix chain 'C' and resid 251 through 272 removed outlier: 3.516A pdb=" N LYS C 255 " --> pdb=" O ARG C 251 " (cutoff:3.500A) Proline residue: C 256 - end of helix removed outlier: 3.701A pdb=" N ARG C 260 " --> pdb=" O PRO C 256 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA C 271 " --> pdb=" O ALA C 267 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLU C 272 " --> pdb=" O GLU C 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 27 removed outlier: 3.615A pdb=" N LYS D 27 " --> pdb=" O GLN D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 97 removed outlier: 3.502A pdb=" N LYS D 86 " --> pdb=" O VAL D 82 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU D 96 " --> pdb=" O GLN D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 120 removed outlier: 3.688A pdb=" N THR D 119 " --> pdb=" O GLN D 115 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN D 120 " --> pdb=" O GLN D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 172 Processing helix chain 'D' and resid 182 through 195 removed outlier: 3.848A pdb=" N VAL D 186 " --> pdb=" O ARG D 182 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS D 187 " --> pdb=" O ASP D 183 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 240 removed outlier: 3.598A pdb=" N PHE D 225 " --> pdb=" O GLU D 221 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU D 228 " --> pdb=" O LYS D 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 133 removed outlier: 3.552A pdb=" N GLU E 129 " --> pdb=" O GLU E 125 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS E 132 " --> pdb=" O VAL E 128 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU E 133 " --> pdb=" O GLU E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'E' and resid 182 through 203 removed outlier: 3.880A pdb=" N ARG E 186 " --> pdb=" O VAL E 182 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE E 187 " --> pdb=" O ALA E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 220 removed outlier: 3.734A pdb=" N LEU E 219 " --> pdb=" O ALA E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 282 removed outlier: 4.281A pdb=" N GLU E 275 " --> pdb=" O GLY E 272 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA E 276 " --> pdb=" O GLY E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 304 Processing helix chain 'E' and resid 332 through 339 Processing helix chain 'F' and resid 184 through 195 removed outlier: 3.857A pdb=" N GLU F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL F 193 " --> pdb=" O ALA F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 263 removed outlier: 4.456A pdb=" N VAL F 248 " --> pdb=" O ALA F 244 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR F 252 " --> pdb=" O VAL F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 284 removed outlier: 4.075A pdb=" N ASP F 275 " --> pdb=" O ASN F 271 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N HIS F 284 " --> pdb=" O LYS F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 340 removed outlier: 4.381A pdb=" N ARG F 339 " --> pdb=" O THR F 335 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N HIS F 340 " --> pdb=" O TYR F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 362 removed outlier: 3.522A pdb=" N SER F 362 " --> pdb=" O LYS F 358 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 374 No H-bonds generated for 'chain 'F' and resid 372 through 374' Processing helix chain 'F' and resid 391 through 398 removed outlier: 4.161A pdb=" N ARG F 395 " --> pdb=" O GLU F 391 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LYS F 396 " --> pdb=" O GLU F 392 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N TYR F 397 " --> pdb=" O SER F 393 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 31 Processing helix chain 'G' and resid 82 through 101 removed outlier: 3.517A pdb=" N ASN G 98 " --> pdb=" O GLN G 94 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER G 99 " --> pdb=" O GLU G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 121 Processing helix chain 'G' and resid 170 through 174 Processing helix chain 'G' and resid 186 through 200 removed outlier: 4.644A pdb=" N GLY G 191 " --> pdb=" O ASP G 187 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA G 194 " --> pdb=" O VAL G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 218 through 220 No H-bonds generated for 'chain 'G' and resid 218 through 220' Processing helix chain 'G' and resid 229 through 231 No H-bonds generated for 'chain 'G' and resid 229 through 231' Processing helix chain 'H' and resid 103 through 124 removed outlier: 3.581A pdb=" N SER H 119 " --> pdb=" O ASN H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 143 Processing helix chain 'H' and resid 190 through 196 removed outlier: 4.185A pdb=" N ALA H 195 " --> pdb=" O SER H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 220 removed outlier: 4.209A pdb=" N ARG H 220 " --> pdb=" O HIS H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 245 through 247 No H-bonds generated for 'chain 'H' and resid 245 through 247' Processing helix chain 'H' and resid 256 through 258 No H-bonds generated for 'chain 'H' and resid 256 through 258' Processing helix chain 'I' and resid 78 through 99 removed outlier: 3.514A pdb=" N THR I 85 " --> pdb=" O THR I 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 119 removed outlier: 3.756A pdb=" N TYR I 119 " --> pdb=" O HIS I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 158 through 170 removed outlier: 4.364A pdb=" N ILE I 161 " --> pdb=" O SER I 158 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA I 162 " --> pdb=" O GLY I 159 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA I 163 " --> pdb=" O SER I 160 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N MET I 164 " --> pdb=" O ILE I 161 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA I 165 " --> pdb=" O ALA I 162 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU I 168 " --> pdb=" O ALA I 165 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 194 removed outlier: 3.956A pdb=" N GLY I 191 " --> pdb=" O ALA I 187 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE I 193 " --> pdb=" O ARG I 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 77 Processing helix chain 'J' and resid 84 through 97 Processing helix chain 'J' and resid 143 through 153 removed outlier: 3.576A pdb=" N ALA J 152 " --> pdb=" O GLY J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 160 through 176 removed outlier: 4.129A pdb=" N GLU J 165 " --> pdb=" O GLU J 161 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 72 Processing helix chain 'K' and resid 79 through 95 removed outlier: 3.988A pdb=" N ILE K 94 " --> pdb=" O LEU K 90 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ARG K 95 " --> pdb=" O ALA K 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 157 Processing helix chain 'K' and resid 164 through 181 Processing helix chain 'L' and resid 148 through 169 removed outlier: 3.503A pdb=" N ARG L 163 " --> pdb=" O GLY L 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 175 through 188 removed outlier: 3.939A pdb=" N LEU L 182 " --> pdb=" O ALA L 178 " (cutoff:3.500A) Processing helix chain 'L' and resid 231 through 239 removed outlier: 4.261A pdb=" N GLY L 236 " --> pdb=" O ILE L 232 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL L 237 " --> pdb=" O TYR L 233 " (cutoff:3.500A) Processing helix chain 'L' and resid 248 through 265 removed outlier: 3.599A pdb=" N HIS L 261 " --> pdb=" O ARG L 257 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG L 265 " --> pdb=" O HIS L 261 " (cutoff:3.500A) Processing helix chain 'L' and resid 291 through 298 removed outlier: 3.596A pdb=" N TYR L 295 " --> pdb=" O GLN L 291 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG L 297 " --> pdb=" O LYS L 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 203 removed outlier: 3.782A pdb=" N GLN M 191 " --> pdb=" O LEU M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 211 through 224 Processing helix chain 'M' and resid 268 through 278 Proline residue: M 273 - end of helix Processing helix chain 'M' and resid 294 through 308 Processing helix chain 'N' and resid 53 through 73 removed outlier: 3.567A pdb=" N ASN N 66 " --> pdb=" O GLN N 62 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE N 67 " --> pdb=" O VAL N 63 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU N 68 " --> pdb=" O GLU N 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 97 Processing helix chain 'N' and resid 136 through 139 removed outlier: 3.726A pdb=" N ALA N 139 " --> pdb=" O GLY N 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 136 through 139' Processing helix chain 'N' and resid 142 through 153 removed outlier: 4.318A pdb=" N ASN N 153 " --> pdb=" O ALA N 149 " (cutoff:3.500A) Processing helix chain 'N' and resid 159 through 176 removed outlier: 3.904A pdb=" N ILE N 165 " --> pdb=" O GLU N 161 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL N 172 " --> pdb=" O ASP N 168 " (cutoff:3.500A) Processing helix chain 'N' and resid 209 through 211 No H-bonds generated for 'chain 'N' and resid 209 through 211' Processing helix chain 'a' and resid 20 through 29 removed outlier: 3.865A pdb=" N PHE a 26 " --> pdb=" O VAL a 22 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LYS a 27 " --> pdb=" O GLU a 23 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL a 29 " --> pdb=" O ALA a 25 " (cutoff:3.500A) Processing helix chain 'a' and resid 81 through 102 removed outlier: 3.561A pdb=" N ARG a 85 " --> pdb=" O ALA a 81 " (cutoff:3.500A) Processing helix chain 'a' and resid 108 through 122 removed outlier: 3.789A pdb=" N ARG a 122 " --> pdb=" O LYS a 118 " (cutoff:3.500A) Processing helix chain 'a' and resid 174 through 185 Processing helix chain 'a' and resid 190 through 192 No H-bonds generated for 'chain 'a' and resid 190 through 192' Processing helix chain 'a' and resid 195 through 210 Processing helix chain 'a' and resid 216 through 218 No H-bonds generated for 'chain 'a' and resid 216 through 218' Processing helix chain 'a' and resid 236 through 246 removed outlier: 4.093A pdb=" N GLU a 241 " --> pdb=" O SER a 237 " (cutoff:3.500A) Processing helix chain 'b' and resid 18 through 28 removed outlier: 3.571A pdb=" N GLY b 28 " --> pdb=" O THR b 24 " (cutoff:3.500A) Processing helix chain 'b' and resid 78 through 99 removed outlier: 3.966A pdb=" N VAL b 83 " --> pdb=" O PRO b 79 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU b 84 " --> pdb=" O ASP b 80 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS b 90 " --> pdb=" O ASP b 86 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS b 96 " --> pdb=" O CYS b 92 " (cutoff:3.500A) Processing helix chain 'b' and resid 105 through 119 removed outlier: 3.839A pdb=" N ILE b 115 " --> pdb=" O LYS b 111 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR b 116 " --> pdb=" O ILE b 112 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN b 117 " --> pdb=" O SER b 113 " (cutoff:3.500A) Processing helix chain 'b' and resid 165 through 175 removed outlier: 3.617A pdb=" N ALA b 170 " --> pdb=" O PRO b 166 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS b 174 " --> pdb=" O ALA b 170 " (cutoff:3.500A) Processing helix chain 'b' and resid 182 through 196 removed outlier: 3.666A pdb=" N GLY b 196 " --> pdb=" O THR b 192 " (cutoff:3.500A) Processing helix chain 'b' and resid 221 through 230 removed outlier: 3.659A pdb=" N TYR b 227 " --> pdb=" O GLN b 223 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLN b 230 " --> pdb=" O ASP b 226 " (cutoff:3.500A) Processing helix chain 'c' and resid 19 through 30 removed outlier: 4.199A pdb=" N GLN c 30 " --> pdb=" O GLU c 26 " (cutoff:3.500A) Processing helix chain 'c' and resid 86 through 107 removed outlier: 3.720A pdb=" N TYR c 90 " --> pdb=" O THR c 86 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ALA c 91 " --> pdb=" O SER c 87 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU c 92 " --> pdb=" O ASP c 88 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLN c 104 " --> pdb=" O ALA c 100 " (cutoff:3.500A) Processing helix chain 'c' and resid 113 through 119 Processing helix chain 'c' and resid 121 through 128 removed outlier: 3.641A pdb=" N TYR c 127 " --> pdb=" O GLU c 123 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N THR c 128 " --> pdb=" O LYS c 124 " (cutoff:3.500A) Processing helix chain 'c' and resid 174 through 181 Processing helix chain 'c' and resid 191 through 206 Processing helix chain 'c' and resid 231 through 233 No H-bonds generated for 'chain 'c' and resid 231 through 233' Processing helix chain 'c' and resid 251 through 272 removed outlier: 3.516A pdb=" N LYS c 255 " --> pdb=" O ARG c 251 " (cutoff:3.500A) Proline residue: c 256 - end of helix removed outlier: 3.700A pdb=" N ARG c 260 " --> pdb=" O PRO c 256 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA c 271 " --> pdb=" O ALA c 267 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLU c 272 " --> pdb=" O GLU c 268 " (cutoff:3.500A) Processing helix chain 'd' and resid 17 through 27 removed outlier: 3.615A pdb=" N LYS d 27 " --> pdb=" O GLN d 23 " (cutoff:3.500A) Processing helix chain 'd' and resid 77 through 97 removed outlier: 3.502A pdb=" N LYS d 86 " --> pdb=" O VAL d 82 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU d 96 " --> pdb=" O GLN d 92 " (cutoff:3.500A) Processing helix chain 'd' and resid 104 through 120 removed outlier: 3.687A pdb=" N THR d 119 " --> pdb=" O GLN d 115 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN d 120 " --> pdb=" O GLN d 116 " (cutoff:3.500A) Processing helix chain 'd' and resid 165 through 172 Processing helix chain 'd' and resid 182 through 195 removed outlier: 3.848A pdb=" N VAL d 186 " --> pdb=" O ARG d 182 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS d 187 " --> pdb=" O ASP d 183 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU d 195 " --> pdb=" O LYS d 191 " (cutoff:3.500A) Processing helix chain 'd' and resid 219 through 240 removed outlier: 3.598A pdb=" N PHE d 225 " --> pdb=" O GLU d 221 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU d 228 " --> pdb=" O LYS d 224 " (cutoff:3.500A) Processing helix chain 'e' and resid 122 through 133 removed outlier: 3.553A pdb=" N GLU e 129 " --> pdb=" O GLU e 125 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE e 131 " --> pdb=" O ALA e 127 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS e 132 " --> pdb=" O VAL e 128 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU e 133 " --> pdb=" O GLU e 129 " (cutoff:3.500A) Processing helix chain 'e' and resid 161 through 163 No H-bonds generated for 'chain 'e' and resid 161 through 163' Processing helix chain 'e' and resid 182 through 203 removed outlier: 3.881A pdb=" N ARG e 186 " --> pdb=" O VAL e 182 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE e 187 " --> pdb=" O ALA e 183 " (cutoff:3.500A) Processing helix chain 'e' and resid 209 through 220 removed outlier: 3.734A pdb=" N LEU e 219 " --> pdb=" O ALA e 215 " (cutoff:3.500A) Processing helix chain 'e' and resid 272 through 282 removed outlier: 4.281A pdb=" N GLU e 275 " --> pdb=" O GLY e 272 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ALA e 276 " --> pdb=" O GLY e 273 " (cutoff:3.500A) Processing helix chain 'e' and resid 291 through 304 Processing helix chain 'e' and resid 332 through 339 Processing helix chain 'f' and resid 184 through 195 removed outlier: 3.858A pdb=" N GLU f 191 " --> pdb=" O GLU f 187 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL f 193 " --> pdb=" O ALA f 189 " (cutoff:3.500A) Processing helix chain 'f' and resid 243 through 263 removed outlier: 4.456A pdb=" N VAL f 248 " --> pdb=" O ALA f 244 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR f 252 " --> pdb=" O VAL f 248 " (cutoff:3.500A) Processing helix chain 'f' and resid 270 through 284 removed outlier: 4.075A pdb=" N ASP f 275 " --> pdb=" O ASN f 271 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N HIS f 284 " --> pdb=" O LYS f 280 " (cutoff:3.500A) Processing helix chain 'f' and resid 331 through 340 removed outlier: 4.381A pdb=" N ARG f 339 " --> pdb=" O THR f 335 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N HIS f 340 " --> pdb=" O TYR f 336 " (cutoff:3.500A) Processing helix chain 'f' and resid 349 through 362 removed outlier: 3.523A pdb=" N SER f 362 " --> pdb=" O LYS f 358 " (cutoff:3.500A) Processing helix chain 'f' and resid 372 through 374 No H-bonds generated for 'chain 'f' and resid 372 through 374' Processing helix chain 'f' and resid 391 through 398 removed outlier: 4.161A pdb=" N ARG f 395 " --> pdb=" O GLU f 391 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LYS f 396 " --> pdb=" O GLU f 392 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N TYR f 397 " --> pdb=" O SER f 393 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 31 Processing helix chain 'g' and resid 82 through 101 removed outlier: 3.518A pdb=" N ASN g 98 " --> pdb=" O GLN g 94 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER g 99 " --> pdb=" O GLU g 95 " (cutoff:3.500A) Processing helix chain 'g' and resid 109 through 121 Processing helix chain 'g' and resid 170 through 174 Processing helix chain 'g' and resid 186 through 200 removed outlier: 4.644A pdb=" N GLY g 191 " --> pdb=" O ASP g 187 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA g 194 " --> pdb=" O VAL g 190 " (cutoff:3.500A) Processing helix chain 'g' and resid 218 through 220 No H-bonds generated for 'chain 'g' and resid 218 through 220' Processing helix chain 'g' and resid 229 through 231 No H-bonds generated for 'chain 'g' and resid 229 through 231' Processing helix chain 'h' and resid 103 through 124 removed outlier: 3.581A pdb=" N SER h 119 " --> pdb=" O ASN h 115 " (cutoff:3.500A) Processing helix chain 'h' and resid 130 through 143 Processing helix chain 'h' and resid 190 through 196 removed outlier: 4.186A pdb=" N ALA h 195 " --> pdb=" O SER h 191 " (cutoff:3.500A) Processing helix chain 'h' and resid 203 through 220 removed outlier: 4.210A pdb=" N ARG h 220 " --> pdb=" O HIS h 216 " (cutoff:3.500A) Processing helix chain 'h' and resid 245 through 247 No H-bonds generated for 'chain 'h' and resid 245 through 247' Processing helix chain 'h' and resid 256 through 258 No H-bonds generated for 'chain 'h' and resid 256 through 258' Processing helix chain 'i' and resid 78 through 99 removed outlier: 3.514A pdb=" N THR i 85 " --> pdb=" O THR i 81 " (cutoff:3.500A) Processing helix chain 'i' and resid 105 through 119 removed outlier: 3.756A pdb=" N TYR i 119 " --> pdb=" O HIS i 115 " (cutoff:3.500A) Processing helix chain 'i' and resid 158 through 170 removed outlier: 4.365A pdb=" N ILE i 161 " --> pdb=" O SER i 158 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA i 162 " --> pdb=" O GLY i 159 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA i 163 " --> pdb=" O SER i 160 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N MET i 164 " --> pdb=" O ILE i 161 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA i 165 " --> pdb=" O ALA i 162 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU i 168 " --> pdb=" O ALA i 165 " (cutoff:3.500A) Processing helix chain 'i' and resid 177 through 194 removed outlier: 3.956A pdb=" N GLY i 191 " --> pdb=" O ALA i 187 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE i 193 " --> pdb=" O ARG i 189 " (cutoff:3.500A) Processing helix chain 'j' and resid 57 through 77 Processing helix chain 'j' and resid 84 through 97 Processing helix chain 'j' and resid 143 through 153 removed outlier: 3.575A pdb=" N ALA j 152 " --> pdb=" O GLY j 148 " (cutoff:3.500A) Processing helix chain 'j' and resid 160 through 176 removed outlier: 4.129A pdb=" N GLU j 165 " --> pdb=" O GLU j 161 " (cutoff:3.500A) Processing helix chain 'k' and resid 51 through 72 Processing helix chain 'k' and resid 79 through 95 removed outlier: 3.989A pdb=" N ILE k 94 " --> pdb=" O LEU k 90 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ARG k 95 " --> pdb=" O ALA k 91 " (cutoff:3.500A) Processing helix chain 'k' and resid 147 through 157 Processing helix chain 'k' and resid 164 through 181 Processing helix chain 'l' and resid 148 through 169 removed outlier: 3.515A pdb=" N ARG l 163 " --> pdb=" O GLY l 159 " (cutoff:3.500A) Processing helix chain 'l' and resid 175 through 188 removed outlier: 3.503A pdb=" N LYS l 180 " --> pdb=" O ALA l 176 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU l 182 " --> pdb=" O ALA l 178 " (cutoff:3.500A) Processing helix chain 'l' and resid 231 through 239 removed outlier: 4.237A pdb=" N GLY l 236 " --> pdb=" O ILE l 232 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL l 237 " --> pdb=" O TYR l 233 " (cutoff:3.500A) Processing helix chain 'l' and resid 248 through 265 removed outlier: 3.606A pdb=" N HIS l 261 " --> pdb=" O ARG l 257 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA l 262 " --> pdb=" O SER l 258 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG l 265 " --> pdb=" O HIS l 261 " (cutoff:3.500A) Processing helix chain 'l' and resid 291 through 298 removed outlier: 3.563A pdb=" N TYR l 295 " --> pdb=" O GLN l 291 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG l 297 " --> pdb=" O LYS l 293 " (cutoff:3.500A) Processing helix chain 'm' and resid 183 through 203 removed outlier: 3.782A pdb=" N GLN m 191 " --> pdb=" O LEU m 187 " (cutoff:3.500A) Processing helix chain 'm' and resid 211 through 224 Processing helix chain 'm' and resid 268 through 278 Proline residue: m 273 - end of helix Processing helix chain 'm' and resid 294 through 308 Processing helix chain 'n' and resid 53 through 73 removed outlier: 3.567A pdb=" N ASN n 66 " --> pdb=" O GLN n 62 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE n 67 " --> pdb=" O VAL n 63 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU n 68 " --> pdb=" O GLU n 64 " (cutoff:3.500A) Processing helix chain 'n' and resid 81 through 97 Processing helix chain 'n' and resid 136 through 139 removed outlier: 3.726A pdb=" N ALA n 139 " --> pdb=" O GLY n 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 136 through 139' Processing helix chain 'n' and resid 142 through 153 removed outlier: 4.319A pdb=" N ASN n 153 " --> pdb=" O ALA n 149 " (cutoff:3.500A) Processing helix chain 'n' and resid 159 through 176 removed outlier: 3.905A pdb=" N ILE n 165 " --> pdb=" O GLU n 161 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL n 172 " --> pdb=" O ASP n 168 " (cutoff:3.500A) Processing helix chain 'n' and resid 209 through 211 No H-bonds generated for 'chain 'n' and resid 209 through 211' Processing sheet with id= A, first strand: chain 'A' and resid 167 through 171 removed outlier: 5.569A pdb=" N LEU A 35 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N VAL A 221 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 149 through 156 removed outlier: 6.677A pdb=" N CYS A 75 " --> pdb=" O GLU A 68 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N GLU A 68 " --> pdb=" O CYS A 75 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N MET A 77 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU A 66 " --> pdb=" O MET A 77 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 158 through 161 removed outlier: 3.518A pdb=" N VAL B 42 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN B 207 " --> pdb=" O ALA B 46 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 74 through 76 removed outlier: 3.866A pdb=" N SER B 131 " --> pdb=" O SER B 75 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 134 through 138 removed outlier: 3.543A pdb=" N TRP B 154 " --> pdb=" O GLN B 146 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 63 through 67 removed outlier: 6.283A pdb=" N VAL B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 167 through 170 removed outlier: 3.587A pdb=" N ARG C 222 " --> pdb=" O ARG C 245 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 162 through 164 removed outlier: 3.711A pdb=" N THR C 156 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE C 140 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N CYS C 80 " --> pdb=" O LYS C 73 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LYS C 73 " --> pdb=" O CYS C 80 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N VAL C 82 " --> pdb=" O MET C 71 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N MET C 71 " --> pdb=" O VAL C 82 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 158 through 161 Processing sheet with id= J, first strand: chain 'D' and resid 63 through 66 removed outlier: 6.385A pdb=" N ILE D 69 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN D 137 " --> pdb=" O LYS D 141 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N LYS D 141 " --> pdb=" O ASN D 137 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 137 through 140 Processing sheet with id= L, first strand: chain 'E' and resid 145 through 151 Processing sheet with id= M, first strand: chain 'E' and resid 262 through 265 removed outlier: 4.598A pdb=" N LEU E 253 " --> pdb=" O TYR E 265 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP E 247 " --> pdb=" O GLY E 250 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA E 176 " --> pdb=" O GLU E 169 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N GLU E 169 " --> pdb=" O ALA E 176 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 323 through 326 Processing sheet with id= O, first strand: chain 'F' and resid 237 through 241 Processing sheet with id= P, first strand: chain 'F' and resid 300 through 303 removed outlier: 3.684A pdb=" N ASP F 303 " --> pdb=" O GLY F 306 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU F 309 " --> pdb=" O TYR F 321 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 162 through 165 Processing sheet with id= R, first strand: chain 'G' and resid 67 through 69 removed outlier: 3.871A pdb=" N ALA G 142 " --> pdb=" O GLY G 145 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'H' and resid 179 through 182 Processing sheet with id= T, first strand: chain 'H' and resid 88 through 90 removed outlier: 4.242A pdb=" N VAL H 165 " --> pdb=" O LEU H 177 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 153 through 157 removed outlier: 4.071A pdb=" N GLY I 40 " --> pdb=" O TYR I 37 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'I' and resid 148 through 150 removed outlier: 6.262A pdb=" N CYS I 72 " --> pdb=" O TYR I 65 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N TYR I 65 " --> pdb=" O CYS I 72 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N GLY I 74 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE I 63 " --> pdb=" O GLY I 74 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'J' and resid 136 through 140 Processing sheet with id= X, first strand: chain 'J' and resid 119 through 123 removed outlier: 3.886A pdb=" N ASN J 46 " --> pdb=" O ILE J 49 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N TYR J 51 " --> pdb=" O VAL J 44 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N VAL J 44 " --> pdb=" O TYR J 51 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'J' and resid 28 through 30 removed outlier: 6.275A pdb=" N GLU J 30 " --> pdb=" O THR J 34 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N THR J 34 " --> pdb=" O GLU J 30 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'K' and resid 140 through 143 removed outlier: 4.323A pdb=" N VAL K 191 " --> pdb=" O ILE K 202 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'K' and resid 36 through 38 Processing sheet with id= AB, first strand: chain 'K' and resid 22 through 24 removed outlier: 6.326A pdb=" N PHE K 24 " --> pdb=" O LYS K 28 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N LYS K 28 " --> pdb=" O PHE K 24 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'L' and resid 224 through 228 removed outlier: 6.528A pdb=" N HIS L 277 " --> pdb=" O LYS L 285 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N LYS L 285 " --> pdb=" O HIS L 277 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N HIS L 279 " --> pdb=" O TRP L 283 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N TRP L 283 " --> pdb=" O HIS L 279 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'L' and resid 133 through 135 removed outlier: 4.084A pdb=" N MET L 199 " --> pdb=" O THR L 143 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP L 204 " --> pdb=" O GLY L 207 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'L' and resid 119 through 121 removed outlier: 3.688A pdb=" N SER L 127 " --> pdb=" O ALA L 119 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N THR L 121 " --> pdb=" O ILE L 125 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ILE L 125 " --> pdb=" O THR L 121 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'M' and resid 261 through 265 removed outlier: 4.993A pdb=" N THR M 135 " --> pdb=" O ASP M 150 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'M' and resid 257 through 259 removed outlier: 3.513A pdb=" N VAL M 236 " --> pdb=" O TYR M 248 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N MET M 177 " --> pdb=" O GLN M 170 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N GLN M 170 " --> pdb=" O MET M 177 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N SER M 179 " --> pdb=" O ILE M 168 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ILE M 168 " --> pdb=" O SER M 179 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'N' and resid 132 through 134 Processing sheet with id= AI, first strand: chain 'N' and resid 38 through 41 removed outlier: 3.682A pdb=" N ARG N 112 " --> pdb=" O GLU N 115 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'N' and resid 24 through 26 removed outlier: 6.491A pdb=" N TYR N 26 " --> pdb=" O ALA N 30 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ALA N 30 " --> pdb=" O TYR N 26 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'a' and resid 167 through 171 removed outlier: 5.568A pdb=" N LEU a 35 " --> pdb=" O GLN a 50 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N VAL a 221 " --> pdb=" O VAL a 234 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'a' and resid 149 through 156 removed outlier: 6.677A pdb=" N CYS a 75 " --> pdb=" O GLU a 68 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N GLU a 68 " --> pdb=" O CYS a 75 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N MET a 77 " --> pdb=" O LEU a 66 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU a 66 " --> pdb=" O MET a 77 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'b' and resid 158 through 161 removed outlier: 3.518A pdb=" N VAL b 42 " --> pdb=" O VAL b 211 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN b 207 " --> pdb=" O ALA b 46 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'b' and resid 74 through 76 removed outlier: 3.866A pdb=" N SER b 131 " --> pdb=" O SER b 75 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'b' and resid 134 through 138 removed outlier: 3.543A pdb=" N TRP b 154 " --> pdb=" O GLN b 146 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'b' and resid 63 through 67 removed outlier: 6.283A pdb=" N VAL b 70 " --> pdb=" O LEU b 66 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'c' and resid 167 through 170 removed outlier: 3.586A pdb=" N ARG c 222 " --> pdb=" O ARG c 245 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'c' and resid 162 through 164 removed outlier: 3.711A pdb=" N THR c 156 " --> pdb=" O PHE c 140 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE c 140 " --> pdb=" O THR c 156 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N CYS c 80 " --> pdb=" O LYS c 73 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LYS c 73 " --> pdb=" O CYS c 80 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL c 82 " --> pdb=" O MET c 71 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N MET c 71 " --> pdb=" O VAL c 82 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'd' and resid 158 through 161 Processing sheet with id= AT, first strand: chain 'd' and resid 63 through 66 removed outlier: 6.385A pdb=" N ILE d 69 " --> pdb=" O VAL d 65 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN d 137 " --> pdb=" O LYS d 141 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N LYS d 141 " --> pdb=" O ASN d 137 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'e' and resid 137 through 140 Processing sheet with id= AV, first strand: chain 'e' and resid 145 through 151 Processing sheet with id= AW, first strand: chain 'e' and resid 262 through 265 removed outlier: 4.599A pdb=" N LEU e 253 " --> pdb=" O TYR e 265 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP e 247 " --> pdb=" O GLY e 250 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA e 176 " --> pdb=" O GLU e 169 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N GLU e 169 " --> pdb=" O ALA e 176 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'f' and resid 323 through 326 Processing sheet with id= AY, first strand: chain 'f' and resid 237 through 241 Processing sheet with id= AZ, first strand: chain 'f' and resid 300 through 303 removed outlier: 3.683A pdb=" N ASP f 303 " --> pdb=" O GLY f 306 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU f 309 " --> pdb=" O TYR f 321 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'g' and resid 162 through 165 Processing sheet with id= BB, first strand: chain 'g' and resid 67 through 69 removed outlier: 3.871A pdb=" N ALA g 142 " --> pdb=" O GLY g 145 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'h' and resid 179 through 182 Processing sheet with id= BD, first strand: chain 'h' and resid 88 through 90 removed outlier: 4.243A pdb=" N VAL h 165 " --> pdb=" O LEU h 177 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'i' and resid 153 through 157 removed outlier: 4.072A pdb=" N GLY i 40 " --> pdb=" O TYR i 37 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'i' and resid 148 through 150 removed outlier: 6.262A pdb=" N CYS i 72 " --> pdb=" O TYR i 65 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N TYR i 65 " --> pdb=" O CYS i 72 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N GLY i 74 " --> pdb=" O ILE i 63 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE i 63 " --> pdb=" O GLY i 74 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'j' and resid 136 through 140 Processing sheet with id= BH, first strand: chain 'j' and resid 119 through 123 removed outlier: 3.885A pdb=" N ASN j 46 " --> pdb=" O ILE j 49 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N TYR j 51 " --> pdb=" O VAL j 44 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N VAL j 44 " --> pdb=" O TYR j 51 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'j' and resid 28 through 30 removed outlier: 6.275A pdb=" N GLU j 30 " --> pdb=" O THR j 34 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N THR j 34 " --> pdb=" O GLU j 30 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'k' and resid 140 through 143 removed outlier: 4.323A pdb=" N VAL k 191 " --> pdb=" O ILE k 202 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'k' and resid 36 through 38 Processing sheet with id= BL, first strand: chain 'k' and resid 22 through 24 removed outlier: 6.325A pdb=" N PHE k 24 " --> pdb=" O LYS k 28 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N LYS k 28 " --> pdb=" O PHE k 24 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'l' and resid 224 through 228 removed outlier: 6.509A pdb=" N HIS l 277 " --> pdb=" O LYS l 285 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LYS l 285 " --> pdb=" O HIS l 277 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N HIS l 279 " --> pdb=" O TRP l 283 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N TRP l 283 " --> pdb=" O HIS l 279 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'l' and resid 140 through 142 removed outlier: 3.501A pdb=" N ASP l 204 " --> pdb=" O GLY l 207 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'l' and resid 119 through 121 removed outlier: 3.698A pdb=" N SER l 127 " --> pdb=" O ALA l 119 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N THR l 121 " --> pdb=" O ILE l 125 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE l 125 " --> pdb=" O THR l 121 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'm' and resid 261 through 265 removed outlier: 4.994A pdb=" N THR m 135 " --> pdb=" O ASP m 150 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'm' and resid 257 through 259 removed outlier: 3.513A pdb=" N VAL m 236 " --> pdb=" O TYR m 248 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N MET m 177 " --> pdb=" O GLN m 170 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N GLN m 170 " --> pdb=" O MET m 177 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N SER m 179 " --> pdb=" O ILE m 168 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ILE m 168 " --> pdb=" O SER m 179 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'n' and resid 132 through 134 Processing sheet with id= BS, first strand: chain 'n' and resid 38 through 41 removed outlier: 3.684A pdb=" N ARG n 112 " --> pdb=" O GLU n 115 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'n' and resid 24 through 26 removed outlier: 6.491A pdb=" N TYR n 26 " --> pdb=" O ALA n 30 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ALA n 30 " --> pdb=" O TYR n 26 " (cutoff:3.500A) 2217 hydrogen bonds defined for protein. 6279 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: 20.79 Time building geometry restraints manager: 18.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 14490 1.33 - 1.45: 7834 1.45 - 1.57: 27352 1.57 - 1.69: 0 1.69 - 1.81: 512 Bond restraints: 50188 Sorted by residual: bond pdb=" C1 N2E l 401 " pdb=" C9 N2E l 401 " ideal model delta sigma weight residual 1.355 1.475 -0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" C1 N2E L 401 " pdb=" C9 N2E L 401 " ideal model delta sigma weight residual 1.355 1.474 -0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" C7 N2E l 401 " pdb=" N6 N2E l 401 " ideal model delta sigma weight residual 1.353 1.244 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C7 N2E L 401 " pdb=" N6 N2E L 401 " ideal model delta sigma weight residual 1.353 1.244 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C18 N2E l 401 " pdb=" N17 N2E l 401 " ideal model delta sigma weight residual 1.453 1.351 0.102 2.00e-02 2.50e+03 2.61e+01 ... (remaining 50183 not shown) Histogram of bond angle deviations from ideal: 96.65 - 104.43: 718 104.43 - 112.20: 24862 112.20 - 119.97: 19947 119.97 - 127.74: 21983 127.74 - 135.52: 388 Bond angle restraints: 67898 Sorted by residual: angle pdb=" C11 N2E l 401 " pdb=" C10 N2E l 401 " pdb=" C5 N2E l 401 " ideal model delta sigma weight residual 134.57 118.95 15.62 3.00e+00 1.11e-01 2.71e+01 angle pdb=" C11 N2E L 401 " pdb=" C10 N2E L 401 " pdb=" C5 N2E L 401 " ideal model delta sigma weight residual 134.57 118.98 15.59 3.00e+00 1.11e-01 2.70e+01 angle pdb=" C15 N2E L 401 " pdb=" C10 N2E L 401 " pdb=" C5 N2E L 401 " ideal model delta sigma weight residual 105.43 120.80 -15.37 3.00e+00 1.11e-01 2.63e+01 angle pdb=" C15 N2E l 401 " pdb=" C10 N2E l 401 " pdb=" C5 N2E l 401 " ideal model delta sigma weight residual 105.43 120.79 -15.36 3.00e+00 1.11e-01 2.62e+01 angle pdb=" CA GLY f 236 " pdb=" C GLY f 236 " pdb=" N MET f 237 " ideal model delta sigma weight residual 114.58 118.53 -3.95 8.60e-01 1.35e+00 2.11e+01 ... (remaining 67893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 27067 17.88 - 35.77: 2404 35.77 - 53.65: 421 53.65 - 71.54: 146 71.54 - 89.42: 70 Dihedral angle restraints: 30108 sinusoidal: 11760 harmonic: 18348 Sorted by residual: dihedral pdb=" CA TYR k 25 " pdb=" C TYR k 25 " pdb=" N TYR k 26 " pdb=" CA TYR k 26 " ideal model delta harmonic sigma weight residual 180.00 154.10 25.90 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA TYR K 25 " pdb=" C TYR K 25 " pdb=" N TYR K 26 " pdb=" CA TYR K 26 " ideal model delta harmonic sigma weight residual 180.00 154.11 25.89 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA GLY J 101 " pdb=" C GLY J 101 " pdb=" N PRO J 102 " pdb=" CA PRO J 102 " ideal model delta harmonic sigma weight residual -180.00 -154.34 -25.66 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 30105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 4903 0.041 - 0.083: 2005 0.083 - 0.124: 564 0.124 - 0.166: 66 0.166 - 0.207: 10 Chirality restraints: 7548 Sorted by residual: chirality pdb=" CB ILE j 189 " pdb=" CA ILE j 189 " pdb=" CG1 ILE j 189 " pdb=" CG2 ILE j 189 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CB ILE J 189 " pdb=" CA ILE J 189 " pdb=" CG1 ILE J 189 " pdb=" CG2 ILE J 189 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ASP N 113 " pdb=" N ASP N 113 " pdb=" C ASP N 113 " pdb=" CB ASP N 113 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.98e-01 ... (remaining 7545 not shown) Planarity restraints: 8804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO l 300 " 0.019 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C PRO l 300 " -0.064 2.00e-02 2.50e+03 pdb=" O PRO l 300 " 0.024 2.00e-02 2.50e+03 pdb=" N SER l 301 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER d 11 " 0.041 5.00e-02 4.00e+02 6.13e-02 6.02e+00 pdb=" N PRO d 12 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO d 12 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO d 12 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 11 " 0.040 5.00e-02 4.00e+02 6.08e-02 5.92e+00 pdb=" N PRO D 12 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO D 12 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 12 " 0.033 5.00e-02 4.00e+02 ... (remaining 8801 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 575 2.62 - 3.19: 43992 3.19 - 3.76: 72985 3.76 - 4.33: 105870 4.33 - 4.90: 180934 Nonbonded interactions: 404356 Sorted by model distance: nonbonded pdb=" OG SER H 191 " pdb=" O PHE h 188 " model vdw 2.048 2.440 nonbonded pdb=" OH TYR J 136 " pdb=" OE1 GLU J 151 " model vdw 2.068 2.440 nonbonded pdb=" OH TYR j 136 " pdb=" OE1 GLU j 151 " model vdw 2.069 2.440 nonbonded pdb=" OH TYR L 124 " pdb=" OE1 GLU M 272 " model vdw 2.069 2.440 nonbonded pdb=" OH TYR l 124 " pdb=" OE1 GLU m 272 " model vdw 2.078 2.440 ... (remaining 404351 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = chain 'C' selection = chain 'c' } ncs_group { reference = chain 'D' selection = chain 'd' } ncs_group { reference = chain 'E' selection = chain 'e' } ncs_group { reference = chain 'F' selection = chain 'f' } ncs_group { reference = chain 'G' selection = chain 'g' } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'I' selection = chain 'i' } ncs_group { reference = chain 'J' selection = chain 'j' } ncs_group { reference = chain 'K' selection = chain 'k' } ncs_group { reference = chain 'L' selection = chain 'l' } ncs_group { reference = chain 'M' selection = chain 'm' } ncs_group { reference = chain 'N' selection = chain 'n' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 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: 8.690 Check model and map are aligned: 0.740 Set scattering table: 0.480 Process input model: 123.000 Find NCS groups from input model: 4.670 Set up NCS constraints: 0.530 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 142.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.120 50188 Z= 0.489 Angle : 0.800 15.616 67898 Z= 0.472 Chirality : 0.047 0.207 7548 Planarity : 0.004 0.061 8804 Dihedral : 15.068 89.423 18392 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.85 % Favored : 94.12 % Rotamer: Outliers : 0.84 % Allowed : 7.39 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.18 (0.09), residues: 6306 helix: -1.65 (0.09), residues: 2196 sheet: -1.81 (0.12), residues: 1484 loop : -2.57 (0.10), residues: 2626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 215 HIS 0.007 0.001 HIS m 224 PHE 0.020 0.002 PHE g 22 TYR 0.017 0.002 TYR h 218 ARG 0.012 0.001 ARG I 224 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1461 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 1417 time to evaluate : 5.361 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: A 27 LYS cc_start: 0.8610 (mttt) cc_final: 0.8398 (mttm) REVERT: A 77 MET cc_start: 0.8318 (mmt) cc_final: 0.7754 (mmt) REVERT: A 94 GLU cc_start: 0.7642 (tp30) cc_final: 0.7387 (tp30) REVERT: A 98 TYR cc_start: 0.8910 (t80) cc_final: 0.8556 (t80) REVERT: B 37 LYS cc_start: 0.8510 (mtpt) cc_final: 0.8271 (mtpp) REVERT: B 56 ASP cc_start: 0.8349 (t0) cc_final: 0.7866 (t0) REVERT: B 100 ASN cc_start: 0.8813 (t0) cc_final: 0.8399 (t0) REVERT: B 107 GLN cc_start: 0.8603 (mm110) cc_final: 0.8226 (mm-40) REVERT: B 210 ARG cc_start: 0.8027 (ptt90) cc_final: 0.7613 (ptt90) REVERT: B 226 ASP cc_start: 0.6886 (t0) cc_final: 0.6425 (t0) REVERT: C 26 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7620 (mm-30) REVERT: C 129 GLN cc_start: 0.8614 (tt0) cc_final: 0.8413 (tt0) REVERT: C 165 TRP cc_start: 0.8693 (m100) cc_final: 0.8333 (m100) REVERT: C 237 LYS cc_start: 0.8300 (tptm) cc_final: 0.8019 (tptm) REVERT: C 238 HIS cc_start: 0.6689 (t-90) cc_final: 0.6267 (t70) REVERT: C 260 ARG cc_start: 0.7122 (ttp-110) cc_final: 0.6793 (ptm160) REVERT: D 4 ASP cc_start: 0.7628 (p0) cc_final: 0.7153 (p0) REVERT: D 109 ARG cc_start: 0.7810 (mtm-85) cc_final: 0.7500 (mtm110) REVERT: D 117 LYS cc_start: 0.8838 (tttt) cc_final: 0.8615 (ttpt) REVERT: D 136 PHE cc_start: 0.8868 (m-80) cc_final: 0.8566 (m-80) REVERT: E 113 ASN cc_start: 0.8594 (m-40) cc_final: 0.8313 (m-40) REVERT: E 118 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7425 (mp0) REVERT: E 141 ARG cc_start: 0.8110 (ttp80) cc_final: 0.7867 (ttt90) REVERT: E 231 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7390 (ptmm) REVERT: E 251 PRO cc_start: 0.9052 (Cg_exo) cc_final: 0.8777 (Cg_endo) REVERT: E 283 GLU cc_start: 0.7230 (pp20) cc_final: 0.6681 (pp20) REVERT: F 220 GLU cc_start: 0.6965 (mp0) cc_final: 0.6198 (mt-10) REVERT: F 373 LYS cc_start: 0.8493 (mmmt) cc_final: 0.8184 (mtmt) REVERT: F 401 PHE cc_start: 0.6152 (t80) cc_final: 0.5839 (t80) REVERT: G 14 VAL cc_start: 0.9004 (t) cc_final: 0.8778 (m) REVERT: I 58 LYS cc_start: 0.8500 (mtmm) cc_final: 0.8276 (mttp) REVERT: I 101 LYS cc_start: 0.8794 (mmtp) cc_final: 0.8037 (mmtm) REVERT: J 201 LYS cc_start: 0.8628 (mmtp) cc_final: 0.8420 (mtpt) REVERT: K 1 MET cc_start: 0.5875 (mmm) cc_final: 0.4929 (mmm) REVERT: L 138 ASP cc_start: 0.7137 (t0) cc_final: 0.6841 (t0) REVERT: L 166 GLU cc_start: 0.8379 (tm-30) cc_final: 0.8162 (tm-30) REVERT: M 164 ASP cc_start: 0.8031 (t70) cc_final: 0.7768 (t0) REVERT: N 26 TYR cc_start: 0.8256 (t80) cc_final: 0.7932 (t80) REVERT: N 83 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7973 (mp0) REVERT: N 94 GLN cc_start: 0.8449 (tp40) cc_final: 0.8150 (tp40) REVERT: N 95 LYS cc_start: 0.8939 (mtpt) cc_final: 0.8691 (mtmm) REVERT: N 163 MET cc_start: 0.7486 (tpp) cc_final: 0.7176 (tpp) REVERT: a 77 MET cc_start: 0.8311 (mmt) cc_final: 0.7843 (mmt) REVERT: a 98 TYR cc_start: 0.9035 (t80) cc_final: 0.8773 (t80) REVERT: a 141 ASP cc_start: 0.8350 (p0) cc_final: 0.8137 (p0) REVERT: b 107 GLN cc_start: 0.8497 (mm110) cc_final: 0.8112 (mm-40) REVERT: b 210 ARG cc_start: 0.7999 (ptt90) cc_final: 0.7567 (ptt90) REVERT: b 215 ARG cc_start: 0.7317 (ptt-90) cc_final: 0.6627 (ptp90) REVERT: b 226 ASP cc_start: 0.6672 (t0) cc_final: 0.6198 (t0) REVERT: c 26 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7590 (mm-30) REVERT: c 234 ASP cc_start: 0.7684 (t0) cc_final: 0.7469 (t0) REVERT: c 238 HIS cc_start: 0.6560 (t-90) cc_final: 0.5898 (t70) REVERT: d 106 MET cc_start: 0.7810 (mtm) cc_final: 0.7520 (mtp) REVERT: d 117 LYS cc_start: 0.8846 (tttt) cc_final: 0.8640 (ttpt) REVERT: d 136 PHE cc_start: 0.8854 (m-80) cc_final: 0.8512 (m-80) REVERT: d 138 GLU cc_start: 0.7385 (mm-30) cc_final: 0.7130 (mm-30) REVERT: d 215 ARG cc_start: 0.8460 (ttp-110) cc_final: 0.8061 (ttp80) REVERT: e 113 ASN cc_start: 0.8556 (m-40) cc_final: 0.8199 (m-40) REVERT: e 118 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7434 (mp0) REVERT: e 231 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7466 (ptmm) REVERT: e 283 GLU cc_start: 0.7376 (pp20) cc_final: 0.7136 (pp20) REVERT: f 220 GLU cc_start: 0.6803 (mp0) cc_final: 0.6191 (mp0) REVERT: f 271 ASN cc_start: 0.8645 (m110) cc_final: 0.8380 (m110) REVERT: f 302 TYR cc_start: 0.8144 (t80) cc_final: 0.7892 (t80) REVERT: f 305 GLN cc_start: 0.8438 (mt0) cc_final: 0.8128 (mp10) REVERT: f 373 LYS cc_start: 0.8480 (mmmt) cc_final: 0.8122 (mtmt) REVERT: f 401 PHE cc_start: 0.6272 (t80) cc_final: 0.5853 (t80) REVERT: h 120 TYR cc_start: 0.9130 (t80) cc_final: 0.8908 (t80) REVERT: h 198 LYS cc_start: 0.8089 (mppt) cc_final: 0.7884 (mmtt) REVERT: i 58 LYS cc_start: 0.8449 (mtmm) cc_final: 0.8180 (mttp) REVERT: i 101 LYS cc_start: 0.8687 (mmtp) cc_final: 0.8092 (mmpt) REVERT: i 172 LYS cc_start: 0.7806 (pttm) cc_final: 0.7597 (mttp) REVERT: i 195 ASP cc_start: 0.8061 (t70) cc_final: 0.7850 (t70) REVERT: j 3 ILE cc_start: 0.8720 (mp) cc_final: 0.8435 (mm) REVERT: j 91 ILE cc_start: 0.8696 (pt) cc_final: 0.8400 (mt) REVERT: j 201 LYS cc_start: 0.8563 (mmtp) cc_final: 0.8256 (mtpt) REVERT: k 1 MET cc_start: 0.5929 (mmm) cc_final: 0.4918 (mmm) REVERT: k 180 ARG cc_start: 0.7976 (ttp-110) cc_final: 0.7766 (tpt90) REVERT: l 166 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8124 (tm-30) REVERT: m 152 ARG cc_start: 0.8501 (ttt180) cc_final: 0.7921 (ttt180) REVERT: m 164 ASP cc_start: 0.8039 (t70) cc_final: 0.7744 (t0) REVERT: n 83 GLU cc_start: 0.8227 (mt-10) cc_final: 0.8002 (mt-10) REVERT: n 94 GLN cc_start: 0.8415 (tp40) cc_final: 0.8141 (tp40) REVERT: n 95 LYS cc_start: 0.8769 (mtpt) cc_final: 0.8543 (mtmm) REVERT: n 163 MET cc_start: 0.7509 (tpp) cc_final: 0.7283 (tpp) REVERT: n 168 ASP cc_start: 0.7487 (m-30) cc_final: 0.7276 (m-30) REVERT: n 215 LYS cc_start: 0.8659 (mttm) cc_final: 0.8429 (mttt) outliers start: 44 outliers final: 11 residues processed: 1448 average time/residue: 0.6817 time to fit residues: 1557.6258 Evaluate side-chains 1076 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1061 time to evaluate : 5.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain a residue 97 ASP Chi-restraints excluded: chain a residue 156 VAL Chi-restraints excluded: chain b residue 14 SER Chi-restraints excluded: chain d residue 58 THR Chi-restraints excluded: chain e residue 118 GLU Chi-restraints excluded: chain e residue 231 LYS Chi-restraints excluded: chain f residue 245 ASP Chi-restraints excluded: chain i residue 54 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 525 optimal weight: 0.8980 chunk 471 optimal weight: 0.0770 chunk 261 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 chunk 318 optimal weight: 5.9990 chunk 251 optimal weight: 3.9990 chunk 487 optimal weight: 2.9990 chunk 188 optimal weight: 0.9990 chunk 296 optimal weight: 3.9990 chunk 362 optimal weight: 9.9990 chunk 564 optimal weight: 4.9990 overall best weight: 1.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN A 207 GLN A 228 ASN B 143 HIS B 207 GLN ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 GLN C 257 HIS D 18 GLN E 252 GLN F 190 ASN F 194 ASN F 195 ASN F 225 GLN F 259 ASN F 271 ASN F 343 HIS G 64 ASN H 63 ASN H 107 GLN H 264 GLN I 64 HIS I 201 GLN J 68 GLN J 169 GLN K 38 GLN K 64 ASN K 72 GLN K 73 HIS K 125 GLN K 136 GLN L 279 HIS M 165 GLN M 180 ASN M 244 HIS M 280 ASN M 282 GLN N 66 ASN a 21 GLN ** a 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 165 HIS a 195 GLN a 207 GLN a 228 ASN b 143 HIS b 207 GLN c 175 GLN d 18 GLN e 252 GLN f 190 ASN f 194 ASN f 195 ASN f 225 GLN f 259 ASN f 305 GLN g 64 ASN h 63 ASN h 107 GLN ** h 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 144 ASN h 264 GLN i 64 HIS i 174 ASN i 194 ASN k 38 GLN k 72 GLN k 136 GLN l 279 HIS m 165 GLN ** m 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 244 HIS m 280 ASN m 282 GLN n 66 ASN Total number of N/Q/H flips: 71 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 50188 Z= 0.208 Angle : 0.544 7.235 67898 Z= 0.290 Chirality : 0.043 0.160 7548 Planarity : 0.004 0.057 8804 Dihedral : 4.971 60.075 7018 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.40 % Allowed : 14.48 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.71 (0.10), residues: 6306 helix: 0.07 (0.11), residues: 2226 sheet: -1.28 (0.13), residues: 1496 loop : -2.06 (0.11), residues: 2584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP g 215 HIS 0.009 0.001 HIS F 343 PHE 0.013 0.001 PHE k 8 TYR 0.023 0.001 TYR H 218 ARG 0.007 0.000 ARG a 85 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1297 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1171 time to evaluate : 5.510 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: A 77 MET cc_start: 0.8342 (mmt) cc_final: 0.7724 (mmt) REVERT: A 94 GLU cc_start: 0.7777 (tp30) cc_final: 0.7550 (tp30) REVERT: A 98 TYR cc_start: 0.8984 (t80) cc_final: 0.8512 (t80) REVERT: A 99 GLN cc_start: 0.8325 (tp40) cc_final: 0.8070 (tp40) REVERT: A 141 ASP cc_start: 0.8102 (p0) cc_final: 0.7863 (p0) REVERT: B 98 MET cc_start: 0.7466 (ttm) cc_final: 0.7203 (ttt) REVERT: B 100 ASN cc_start: 0.8764 (t0) cc_final: 0.8393 (t0) REVERT: B 107 GLN cc_start: 0.8455 (mm110) cc_final: 0.8136 (mm-40) REVERT: B 154 TRP cc_start: 0.7419 (m-90) cc_final: 0.7052 (m100) REVERT: B 210 ARG cc_start: 0.7863 (ptt90) cc_final: 0.7492 (ptt90) REVERT: B 226 ASP cc_start: 0.6628 (t0) cc_final: 0.6237 (t0) REVERT: C 26 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7497 (mm-30) REVERT: C 165 TRP cc_start: 0.8613 (m100) cc_final: 0.8165 (m100) REVERT: C 221 MET cc_start: 0.7906 (tpt) cc_final: 0.7427 (tpt) REVERT: C 238 HIS cc_start: 0.6658 (t-90) cc_final: 0.6232 (t70) REVERT: D 4 ASP cc_start: 0.7445 (p0) cc_final: 0.7014 (p0) REVERT: D 109 ARG cc_start: 0.7768 (mtm-85) cc_final: 0.7556 (mtm110) REVERT: D 117 LYS cc_start: 0.8835 (tttt) cc_final: 0.8578 (ttpt) REVERT: E 113 ASN cc_start: 0.8533 (m-40) cc_final: 0.8155 (m-40) REVERT: E 189 VAL cc_start: 0.8723 (t) cc_final: 0.8441 (m) REVERT: E 283 GLU cc_start: 0.7261 (pp20) cc_final: 0.6984 (pp20) REVERT: E 338 ILE cc_start: 0.8566 (mm) cc_final: 0.8156 (mm) REVERT: F 220 GLU cc_start: 0.6974 (mp0) cc_final: 0.6311 (mt-10) REVERT: F 373 LYS cc_start: 0.8563 (mmmt) cc_final: 0.8214 (mtmt) REVERT: F 401 PHE cc_start: 0.6100 (t80) cc_final: 0.5834 (t80) REVERT: I 101 LYS cc_start: 0.8658 (mmtp) cc_final: 0.8118 (mmtt) REVERT: K 1 MET cc_start: 0.5711 (mmm) cc_final: 0.4837 (mmm) REVERT: K 28 LYS cc_start: 0.8743 (mtpp) cc_final: 0.8491 (ttpp) REVERT: K 177 GLU cc_start: 0.8289 (tp30) cc_final: 0.8089 (tp30) REVERT: K 180 ARG cc_start: 0.8167 (ttp80) cc_final: 0.7050 (tpt90) REVERT: L 138 ASP cc_start: 0.7176 (t0) cc_final: 0.6905 (t0) REVERT: N 26 TYR cc_start: 0.8208 (t80) cc_final: 0.7843 (t80) REVERT: N 68 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7235 (mp0) REVERT: N 94 GLN cc_start: 0.8351 (tp40) cc_final: 0.7877 (tp40) REVERT: N 95 LYS cc_start: 0.8808 (mtpt) cc_final: 0.8604 (mtmm) REVERT: a 77 MET cc_start: 0.8324 (mmt) cc_final: 0.7838 (mmt) REVERT: a 98 TYR cc_start: 0.9099 (t80) cc_final: 0.8737 (t80) REVERT: a 99 GLN cc_start: 0.8314 (tp40) cc_final: 0.8013 (tp40) REVERT: a 141 ASP cc_start: 0.8169 (p0) cc_final: 0.7849 (p0) REVERT: a 178 MET cc_start: 0.8550 (tpp) cc_final: 0.8335 (mmt) REVERT: b 67 ASP cc_start: 0.8352 (m-30) cc_final: 0.8078 (m-30) REVERT: b 98 MET cc_start: 0.7535 (ttm) cc_final: 0.7312 (ttt) REVERT: b 100 ASN cc_start: 0.8850 (t0) cc_final: 0.8478 (t0) REVERT: b 154 TRP cc_start: 0.7358 (m-90) cc_final: 0.7045 (m100) REVERT: b 183 GLU cc_start: 0.6834 (mp0) cc_final: 0.6246 (tt0) REVERT: b 210 ARG cc_start: 0.7862 (ptt90) cc_final: 0.7500 (ptt90) REVERT: b 226 ASP cc_start: 0.6645 (t0) cc_final: 0.6192 (t0) REVERT: c 26 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7608 (mm-30) REVERT: c 69 GLU cc_start: 0.7153 (tt0) cc_final: 0.6948 (mt-10) REVERT: c 165 TRP cc_start: 0.8569 (m100) cc_final: 0.8146 (m100) REVERT: c 221 MET cc_start: 0.7856 (tpt) cc_final: 0.7389 (tpt) REVERT: c 234 ASP cc_start: 0.7429 (t0) cc_final: 0.7226 (t0) REVERT: c 238 HIS cc_start: 0.6540 (t-90) cc_final: 0.6054 (t70) REVERT: d 4 ASP cc_start: 0.7165 (p0) cc_final: 0.6874 (p0) REVERT: d 117 LYS cc_start: 0.8867 (tttt) cc_final: 0.8628 (ttpt) REVERT: d 120 GLN cc_start: 0.8043 (tt0) cc_final: 0.7714 (tt0) REVERT: d 138 GLU cc_start: 0.7334 (mm-30) cc_final: 0.7108 (tp30) REVERT: e 113 ASN cc_start: 0.8447 (m-40) cc_final: 0.8096 (m-40) REVERT: e 189 VAL cc_start: 0.8694 (t) cc_final: 0.8414 (m) REVERT: f 220 GLU cc_start: 0.6782 (mp0) cc_final: 0.6073 (mt-10) REVERT: f 247 ARG cc_start: 0.7389 (mtp-110) cc_final: 0.7101 (ptm160) REVERT: f 302 TYR cc_start: 0.8045 (t80) cc_final: 0.7815 (t80) REVERT: f 373 LYS cc_start: 0.8474 (mmmt) cc_final: 0.8154 (mtmt) REVERT: f 401 PHE cc_start: 0.6073 (t80) cc_final: 0.5728 (t80) REVERT: h 120 TYR cc_start: 0.9150 (t80) cc_final: 0.8785 (t80) REVERT: j 201 LYS cc_start: 0.8576 (mmtp) cc_final: 0.8274 (mtpt) REVERT: k 1 MET cc_start: 0.5768 (mmm) cc_final: 0.4856 (mmm) REVERT: k 69 ARG cc_start: 0.7872 (ttp-110) cc_final: 0.7490 (mtm-85) REVERT: k 177 GLU cc_start: 0.8333 (tp30) cc_final: 0.8011 (tp30) REVERT: k 180 ARG cc_start: 0.8019 (ttp-110) cc_final: 0.7714 (tpt90) REVERT: l 138 ASP cc_start: 0.7168 (t0) cc_final: 0.6807 (t0) REVERT: l 239 ASP cc_start: 0.7864 (m-30) cc_final: 0.7160 (t0) REVERT: m 152 ARG cc_start: 0.8531 (ttt180) cc_final: 0.8112 (ttm170) REVERT: m 164 ASP cc_start: 0.8046 (t70) cc_final: 0.7784 (t0) REVERT: m 212 LYS cc_start: 0.7739 (ttpp) cc_final: 0.7514 (mtmm) REVERT: n 83 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7818 (mp0) REVERT: n 94 GLN cc_start: 0.8424 (tp40) cc_final: 0.8144 (tp40) REVERT: n 95 LYS cc_start: 0.8818 (mtpt) cc_final: 0.8610 (mtmm) outliers start: 126 outliers final: 88 residues processed: 1235 average time/residue: 0.6505 time to fit residues: 1322.2483 Evaluate side-chains 1128 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1040 time to evaluate : 4.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 271 ASN Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain H residue 243 ILE Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain I residue 209 LYS Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 81 ASP Chi-restraints excluded: chain J residue 111 SER Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain L residue 286 ILE Chi-restraints excluded: chain M residue 198 LYS Chi-restraints excluded: chain M residue 256 THR Chi-restraints excluded: chain M residue 259 PHE Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 300 MET Chi-restraints excluded: chain N residue 66 ASN Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 212 CYS Chi-restraints excluded: chain a residue 58 MET Chi-restraints excluded: chain a residue 156 VAL Chi-restraints excluded: chain a residue 208 SER Chi-restraints excluded: chain b residue 14 SER Chi-restraints excluded: chain b residue 184 ASP Chi-restraints excluded: chain b residue 211 VAL Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 50 MET Chi-restraints excluded: chain c residue 115 ASP Chi-restraints excluded: chain c residue 141 LEU Chi-restraints excluded: chain d residue 58 THR Chi-restraints excluded: chain d residue 119 THR Chi-restraints excluded: chain d residue 183 ASP Chi-restraints excluded: chain e residue 147 VAL Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain f residue 239 ILE Chi-restraints excluded: chain f residue 245 ASP Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 42 CYS Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 216 VAL Chi-restraints excluded: chain g residue 227 VAL Chi-restraints excluded: chain h residue 56 THR Chi-restraints excluded: chain h residue 129 ASN Chi-restraints excluded: chain h residue 242 THR Chi-restraints excluded: chain h residue 243 ILE Chi-restraints excluded: chain h residue 263 THR Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain i residue 148 THR Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 81 ASP Chi-restraints excluded: chain j residue 111 SER Chi-restraints excluded: chain j residue 134 GLU Chi-restraints excluded: chain j residue 189 ILE Chi-restraints excluded: chain l residue 286 ILE Chi-restraints excluded: chain m residue 256 THR Chi-restraints excluded: chain m residue 259 PHE Chi-restraints excluded: chain m residue 263 THR Chi-restraints excluded: chain m residue 300 MET Chi-restraints excluded: chain n residue 66 ASN Chi-restraints excluded: chain n residue 77 ASP Chi-restraints excluded: chain n residue 116 THR Chi-restraints excluded: chain n residue 212 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 313 optimal weight: 1.9990 chunk 175 optimal weight: 10.0000 chunk 470 optimal weight: 9.9990 chunk 384 optimal weight: 0.3980 chunk 155 optimal weight: 2.9990 chunk 565 optimal weight: 5.9990 chunk 611 optimal weight: 9.9990 chunk 503 optimal weight: 10.0000 chunk 561 optimal weight: 7.9990 chunk 192 optimal weight: 8.9990 chunk 453 optimal weight: 9.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 HIS F 194 ASN F 195 ASN F 225 GLN F 282 GLN ** F 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 115 HIS I 201 GLN J 26 ASN M 165 GLN M 280 ASN N 66 ASN ** a 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 228 ASN b 207 GLN ** e 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 194 ASN f 195 ASN f 282 GLN f 311 GLN h 144 ASN i 115 HIS j 26 ASN m 165 GLN ** m 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 280 ASN n 66 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 50188 Z= 0.357 Angle : 0.591 7.871 67898 Z= 0.314 Chirality : 0.045 0.164 7548 Planarity : 0.004 0.050 8804 Dihedral : 4.838 47.221 7002 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.70 % Allowed : 17.00 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.31 (0.10), residues: 6306 helix: 0.49 (0.11), residues: 2214 sheet: -1.07 (0.13), residues: 1500 loop : -1.90 (0.11), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP g 215 HIS 0.010 0.001 HIS E 262 PHE 0.020 0.002 PHE k 8 TYR 0.033 0.002 TYR H 218 ARG 0.007 0.000 ARG k 97 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1248 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 1054 time to evaluate : 5.400 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 77 MET cc_start: 0.8296 (mmt) cc_final: 0.7666 (mmt) REVERT: A 94 GLU cc_start: 0.7769 (tp30) cc_final: 0.7533 (tp30) REVERT: A 98 TYR cc_start: 0.9038 (t80) cc_final: 0.8738 (t80) REVERT: A 141 ASP cc_start: 0.8023 (p0) cc_final: 0.7564 (p0) REVERT: A 155 THR cc_start: 0.8475 (m) cc_final: 0.8230 (m) REVERT: B 98 MET cc_start: 0.7542 (ttm) cc_final: 0.7272 (ttt) REVERT: B 100 ASN cc_start: 0.8826 (t0) cc_final: 0.8479 (t0) REVERT: B 154 TRP cc_start: 0.7420 (m-90) cc_final: 0.7103 (m100) REVERT: B 210 ARG cc_start: 0.7888 (ptt90) cc_final: 0.7405 (ptt90) REVERT: C 26 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7602 (mm-30) REVERT: C 238 HIS cc_start: 0.6627 (t-90) cc_final: 0.6261 (t70) REVERT: D 4 ASP cc_start: 0.7295 (p0) cc_final: 0.6857 (p0) REVERT: D 109 ARG cc_start: 0.7849 (mtm-85) cc_final: 0.7605 (mtm110) REVERT: D 117 LYS cc_start: 0.8851 (tttt) cc_final: 0.8565 (ttpt) REVERT: D 120 GLN cc_start: 0.8111 (tt0) cc_final: 0.7859 (tt0) REVERT: E 113 ASN cc_start: 0.8518 (m-40) cc_final: 0.8159 (m-40) REVERT: F 220 GLU cc_start: 0.7069 (mp0) cc_final: 0.6352 (mt-10) REVERT: F 305 GLN cc_start: 0.8643 (mp10) cc_final: 0.8137 (mp10) REVERT: F 373 LYS cc_start: 0.8623 (mmmt) cc_final: 0.8098 (mtmt) REVERT: F 401 PHE cc_start: 0.5917 (t80) cc_final: 0.5611 (t80) REVERT: G 231 MET cc_start: 0.6451 (tpt) cc_final: 0.6170 (tpp) REVERT: H 145 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7849 (ptt90) REVERT: I 101 LYS cc_start: 0.8693 (mmtp) cc_final: 0.8182 (mmpt) REVERT: J 126 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8418 (pt) REVERT: K 1 MET cc_start: 0.5720 (mmm) cc_final: 0.4728 (mmm) REVERT: K 177 GLU cc_start: 0.8326 (tp30) cc_final: 0.7994 (tp30) REVERT: L 138 ASP cc_start: 0.7211 (t0) cc_final: 0.6967 (t0) REVERT: M 164 ASP cc_start: 0.8079 (t70) cc_final: 0.7857 (t0) REVERT: N 26 TYR cc_start: 0.8360 (t80) cc_final: 0.8018 (t80) REVERT: N 94 GLN cc_start: 0.8281 (tp40) cc_final: 0.7910 (tp40) REVERT: a 77 MET cc_start: 0.8366 (mmt) cc_final: 0.7755 (mmt) REVERT: a 98 TYR cc_start: 0.9174 (t80) cc_final: 0.8909 (t80) REVERT: a 141 ASP cc_start: 0.8170 (p0) cc_final: 0.7639 (p0) REVERT: a 166 ILE cc_start: 0.9020 (mt) cc_final: 0.8802 (mm) REVERT: b 67 ASP cc_start: 0.8447 (m-30) cc_final: 0.8245 (m-30) REVERT: b 98 MET cc_start: 0.7552 (ttm) cc_final: 0.7306 (ttt) REVERT: b 100 ASN cc_start: 0.8914 (t0) cc_final: 0.8564 (t0) REVERT: b 107 GLN cc_start: 0.8506 (mm110) cc_final: 0.8168 (mm-40) REVERT: b 210 ARG cc_start: 0.7869 (ptt90) cc_final: 0.7444 (ptt90) REVERT: b 226 ASP cc_start: 0.6620 (t0) cc_final: 0.6153 (t0) REVERT: c 26 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7736 (mm-30) REVERT: c 221 MET cc_start: 0.7953 (tpt) cc_final: 0.7454 (tpt) REVERT: c 238 HIS cc_start: 0.6749 (t-90) cc_final: 0.6236 (t70) REVERT: d 4 ASP cc_start: 0.7134 (p0) cc_final: 0.6724 (p0) REVERT: d 17 PHE cc_start: 0.8320 (OUTLIER) cc_final: 0.8014 (m-10) REVERT: d 103 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8347 (p0) REVERT: d 117 LYS cc_start: 0.8853 (tttt) cc_final: 0.8632 (ttpt) REVERT: d 120 GLN cc_start: 0.8113 (tt0) cc_final: 0.7819 (tt0) REVERT: e 113 ASN cc_start: 0.8488 (m-40) cc_final: 0.8123 (m-40) REVERT: f 220 GLU cc_start: 0.6886 (mp0) cc_final: 0.6199 (mt-10) REVERT: f 247 ARG cc_start: 0.7424 (mtp-110) cc_final: 0.7150 (ptm160) REVERT: f 302 TYR cc_start: 0.8076 (t80) cc_final: 0.7830 (t80) REVERT: f 373 LYS cc_start: 0.8530 (mmmt) cc_final: 0.8136 (mtmt) REVERT: f 401 PHE cc_start: 0.6126 (t80) cc_final: 0.5709 (t80) REVERT: i 47 THR cc_start: 0.8248 (p) cc_final: 0.8026 (p) REVERT: i 101 LYS cc_start: 0.8692 (mmtp) cc_final: 0.8087 (mmtt) REVERT: j 126 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8416 (pt) REVERT: k 1 MET cc_start: 0.5772 (mmm) cc_final: 0.4796 (mmm) REVERT: k 62 LYS cc_start: 0.8800 (mtpp) cc_final: 0.8551 (mtpp) REVERT: k 125 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.7286 (mp-120) REVERT: k 180 ARG cc_start: 0.8045 (ttp-170) cc_final: 0.7837 (tpt90) REVERT: l 243 ARG cc_start: 0.7764 (ptt180) cc_final: 0.7533 (ptt-90) REVERT: m 152 ARG cc_start: 0.8496 (ttt180) cc_final: 0.7859 (ttt180) REVERT: m 164 ASP cc_start: 0.8096 (t70) cc_final: 0.7872 (t0) REVERT: n 26 TYR cc_start: 0.8240 (t80) cc_final: 0.7938 (t80) REVERT: n 59 MET cc_start: 0.7905 (tpp) cc_final: 0.7586 (tpp) REVERT: n 94 GLN cc_start: 0.8369 (tp40) cc_final: 0.8080 (tp40) outliers start: 194 outliers final: 146 residues processed: 1167 average time/residue: 0.5979 time to fit residues: 1150.1710 Evaluate side-chains 1148 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 996 time to evaluate : 5.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 129 ASN Chi-restraints excluded: chain H residue 145 ARG Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain H residue 243 ILE Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 209 LYS Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 81 ASP Chi-restraints excluded: chain J residue 111 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 92 SER Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 160 MET Chi-restraints excluded: chain L residue 232 ILE Chi-restraints excluded: chain L residue 286 ILE Chi-restraints excluded: chain M residue 154 ASN Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 256 THR Chi-restraints excluded: chain M residue 259 PHE Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 293 THR Chi-restraints excluded: chain M residue 295 GLU Chi-restraints excluded: chain M residue 300 MET Chi-restraints excluded: chain M residue 317 ASP Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 66 ASN Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 98 ASP Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 129 GLU Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 212 CYS Chi-restraints excluded: chain a residue 27 LYS Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain a residue 58 MET Chi-restraints excluded: chain a residue 156 VAL Chi-restraints excluded: chain a residue 208 SER Chi-restraints excluded: chain b residue 14 SER Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 184 ASP Chi-restraints excluded: chain b residue 211 VAL Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 50 MET Chi-restraints excluded: chain c residue 56 PHE Chi-restraints excluded: chain c residue 111 MET Chi-restraints excluded: chain c residue 115 ASP Chi-restraints excluded: chain c residue 119 ILE Chi-restraints excluded: chain c residue 141 LEU Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain d residue 17 PHE Chi-restraints excluded: chain d residue 103 ASP Chi-restraints excluded: chain d residue 119 THR Chi-restraints excluded: chain d residue 147 THR Chi-restraints excluded: chain d residue 183 ASP Chi-restraints excluded: chain d residue 211 TYR Chi-restraints excluded: chain e residue 147 VAL Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 205 GLU Chi-restraints excluded: chain e residue 289 MET Chi-restraints excluded: chain f residue 221 LEU Chi-restraints excluded: chain f residue 239 ILE Chi-restraints excluded: chain f residue 245 ASP Chi-restraints excluded: chain f residue 355 HIS Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 42 CYS Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 163 VAL Chi-restraints excluded: chain g residue 216 VAL Chi-restraints excluded: chain g residue 227 VAL Chi-restraints excluded: chain h residue 56 THR Chi-restraints excluded: chain h residue 129 ASN Chi-restraints excluded: chain h residue 231 ILE Chi-restraints excluded: chain h residue 242 THR Chi-restraints excluded: chain h residue 243 ILE Chi-restraints excluded: chain h residue 263 THR Chi-restraints excluded: chain i residue 32 ILE Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain i residue 148 THR Chi-restraints excluded: chain i residue 212 THR Chi-restraints excluded: chain j residue 39 VAL Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 81 ASP Chi-restraints excluded: chain j residue 111 SER Chi-restraints excluded: chain j residue 126 LEU Chi-restraints excluded: chain j residue 166 ILE Chi-restraints excluded: chain j residue 189 ILE Chi-restraints excluded: chain k residue 4 THR Chi-restraints excluded: chain k residue 44 LEU Chi-restraints excluded: chain k residue 92 SER Chi-restraints excluded: chain k residue 121 VAL Chi-restraints excluded: chain k residue 125 GLN Chi-restraints excluded: chain l residue 199 MET Chi-restraints excluded: chain l residue 227 VAL Chi-restraints excluded: chain l residue 232 ILE Chi-restraints excluded: chain l residue 286 ILE Chi-restraints excluded: chain m residue 198 LYS Chi-restraints excluded: chain m residue 237 VAL Chi-restraints excluded: chain m residue 256 THR Chi-restraints excluded: chain m residue 259 PHE Chi-restraints excluded: chain m residue 263 THR Chi-restraints excluded: chain m residue 295 GLU Chi-restraints excluded: chain m residue 300 MET Chi-restraints excluded: chain n residue 50 THR Chi-restraints excluded: chain n residue 66 ASN Chi-restraints excluded: chain n residue 77 ASP Chi-restraints excluded: chain n residue 116 THR Chi-restraints excluded: chain n residue 212 CYS Chi-restraints excluded: chain n residue 218 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 559 optimal weight: 2.9990 chunk 425 optimal weight: 3.9990 chunk 293 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 270 optimal weight: 1.9990 chunk 379 optimal weight: 0.0870 chunk 567 optimal weight: 0.5980 chunk 601 optimal weight: 6.9990 chunk 296 optimal weight: 7.9990 chunk 538 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 228 ASN B 117 GLN B 121 GLN B 207 GLN ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 GLN ** E 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 194 ASN ** F 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 ASN H 144 ASN J 60 GLN L 137 ASN M 280 ASN M 303 ASN N 66 ASN a 50 GLN ** a 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 228 ASN b 207 GLN d 54 GLN ** e 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 194 ASN j 60 GLN k 64 ASN m 165 GLN ** m 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 280 ASN m 303 ASN n 66 ASN n 148 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 50188 Z= 0.165 Angle : 0.504 8.149 67898 Z= 0.268 Chirality : 0.042 0.148 7548 Planarity : 0.004 0.052 8804 Dihedral : 4.367 29.640 6996 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.30 % Allowed : 18.95 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.10), residues: 6306 helix: 0.95 (0.11), residues: 2228 sheet: -0.85 (0.13), residues: 1508 loop : -1.68 (0.11), residues: 2570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP l 165 HIS 0.004 0.001 HIS D 164 PHE 0.017 0.001 PHE l 299 TYR 0.023 0.001 TYR d 110 ARG 0.012 0.000 ARG b 175 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1271 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 1098 time to evaluate : 6.018 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: A 77 MET cc_start: 0.8327 (mmt) cc_final: 0.7587 (mmt) REVERT: A 87 LEU cc_start: 0.8893 (tp) cc_final: 0.8632 (tp) REVERT: A 98 TYR cc_start: 0.8967 (t80) cc_final: 0.8653 (t80) REVERT: A 141 ASP cc_start: 0.7979 (p0) cc_final: 0.7739 (p0) REVERT: B 18 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8161 (pt) REVERT: B 98 MET cc_start: 0.7458 (ttm) cc_final: 0.7229 (ttt) REVERT: B 100 ASN cc_start: 0.8703 (t0) cc_final: 0.8369 (t0) REVERT: B 107 GLN cc_start: 0.8460 (mm110) cc_final: 0.8082 (mm-40) REVERT: B 210 ARG cc_start: 0.7830 (ptt90) cc_final: 0.7373 (ptt90) REVERT: B 215 ARG cc_start: 0.6812 (ptt-90) cc_final: 0.6118 (ptp-170) REVERT: B 226 ASP cc_start: 0.6680 (t0) cc_final: 0.6244 (t0) REVERT: C 26 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7657 (mm-30) REVERT: C 165 TRP cc_start: 0.8624 (m100) cc_final: 0.8365 (m100) REVERT: C 215 ARG cc_start: 0.6788 (ttp-170) cc_final: 0.6022 (tpt170) REVERT: C 221 MET cc_start: 0.7912 (tpt) cc_final: 0.7434 (tpt) REVERT: C 238 HIS cc_start: 0.6746 (t-90) cc_final: 0.6493 (t70) REVERT: C 254 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7357 (tt) REVERT: D 4 ASP cc_start: 0.7256 (p0) cc_final: 0.6744 (p0) REVERT: D 109 ARG cc_start: 0.7803 (mtm-85) cc_final: 0.7597 (mtm110) REVERT: D 117 LYS cc_start: 0.8830 (tttt) cc_final: 0.8566 (ttpt) REVERT: E 195 GLU cc_start: 0.7792 (mp0) cc_final: 0.7426 (mm-30) REVERT: E 249 LYS cc_start: 0.7973 (mttm) cc_final: 0.6694 (tptp) REVERT: F 220 GLU cc_start: 0.7011 (mp0) cc_final: 0.6327 (mt-10) REVERT: F 305 GLN cc_start: 0.8552 (mp10) cc_final: 0.8057 (mp10) REVERT: F 373 LYS cc_start: 0.8608 (mmmt) cc_final: 0.8192 (mtmt) REVERT: F 401 PHE cc_start: 0.5940 (t80) cc_final: 0.5639 (t80) REVERT: G 175 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7898 (mm-30) REVERT: G 231 MET cc_start: 0.6447 (tpt) cc_final: 0.6214 (tpp) REVERT: I 213 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6895 (tt0) REVERT: J 114 LYS cc_start: 0.7816 (mmmm) cc_final: 0.7608 (mmtp) REVERT: J 126 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8526 (pt) REVERT: K 1 MET cc_start: 0.5551 (mmm) cc_final: 0.4661 (mmm) REVERT: K 28 LYS cc_start: 0.8695 (mtpp) cc_final: 0.8404 (ttpp) REVERT: K 177 GLU cc_start: 0.8273 (tp30) cc_final: 0.7944 (tp30) REVERT: L 138 ASP cc_start: 0.7207 (t0) cc_final: 0.6927 (t0) REVERT: M 164 ASP cc_start: 0.8093 (t70) cc_final: 0.7842 (t0) REVERT: M 281 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7358 (mmt180) REVERT: N 26 TYR cc_start: 0.8249 (t80) cc_final: 0.7899 (t80) REVERT: N 94 GLN cc_start: 0.8309 (tp40) cc_final: 0.7953 (tp40) REVERT: N 205 HIS cc_start: 0.6647 (m90) cc_final: 0.6108 (m-70) REVERT: a 55 ASP cc_start: 0.4149 (t70) cc_final: 0.3947 (t0) REVERT: a 77 MET cc_start: 0.8371 (mmt) cc_final: 0.7652 (mmt) REVERT: a 87 LEU cc_start: 0.8862 (tp) cc_final: 0.8598 (tp) REVERT: a 98 TYR cc_start: 0.9086 (t80) cc_final: 0.8779 (t80) REVERT: a 141 ASP cc_start: 0.8030 (p0) cc_final: 0.7518 (p0) REVERT: a 210 ILE cc_start: 0.7798 (pt) cc_final: 0.7519 (mt) REVERT: b 100 ASN cc_start: 0.8836 (t0) cc_final: 0.8464 (t0) REVERT: b 107 GLN cc_start: 0.8471 (mm110) cc_final: 0.8123 (mm-40) REVERT: b 187 HIS cc_start: 0.7277 (t70) cc_final: 0.6671 (t70) REVERT: b 210 ARG cc_start: 0.7818 (ptt90) cc_final: 0.7342 (ptt90) REVERT: b 215 ARG cc_start: 0.6769 (ptt-90) cc_final: 0.6036 (ptp-170) REVERT: b 226 ASP cc_start: 0.6654 (t0) cc_final: 0.6248 (t0) REVERT: c 26 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7749 (mm-30) REVERT: c 165 TRP cc_start: 0.8651 (m100) cc_final: 0.8361 (m100) REVERT: c 221 MET cc_start: 0.7881 (tpt) cc_final: 0.7388 (tpt) REVERT: c 238 HIS cc_start: 0.6590 (t-90) cc_final: 0.6280 (t70) REVERT: c 254 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7318 (tt) REVERT: d 4 ASP cc_start: 0.7068 (p0) cc_final: 0.6628 (p0) REVERT: d 17 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.8011 (m-10) REVERT: d 117 LYS cc_start: 0.8847 (tttt) cc_final: 0.8612 (ttpt) REVERT: d 120 GLN cc_start: 0.7975 (tt0) cc_final: 0.7689 (tt0) REVERT: e 195 GLU cc_start: 0.7774 (mp0) cc_final: 0.7374 (mm-30) REVERT: e 263 THR cc_start: 0.8892 (m) cc_final: 0.8615 (p) REVERT: f 220 GLU cc_start: 0.6807 (mp0) cc_final: 0.6009 (mt-10) REVERT: f 247 ARG cc_start: 0.7282 (mtp-110) cc_final: 0.7080 (ptm160) REVERT: f 373 LYS cc_start: 0.8513 (mmmt) cc_final: 0.8134 (mtmt) REVERT: f 401 PHE cc_start: 0.6126 (t80) cc_final: 0.5779 (t80) REVERT: i 101 LYS cc_start: 0.8656 (mmtp) cc_final: 0.8100 (mmtt) REVERT: j 3 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8374 (mm) REVERT: j 126 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8413 (pt) REVERT: k 1 MET cc_start: 0.5596 (mmm) cc_final: 0.4705 (mmm) REVERT: k 62 LYS cc_start: 0.8728 (mtpp) cc_final: 0.8507 (mtpp) REVERT: k 70 MET cc_start: 0.7632 (mmp) cc_final: 0.7180 (mtt) REVERT: k 177 GLU cc_start: 0.8332 (tp30) cc_final: 0.7933 (tp30) REVERT: k 180 ARG cc_start: 0.8001 (ttp-170) cc_final: 0.7719 (tpt90) REVERT: m 152 ARG cc_start: 0.8454 (ttt180) cc_final: 0.7881 (ttt180) REVERT: m 164 ASP cc_start: 0.8071 (t70) cc_final: 0.7777 (t0) REVERT: n 26 TYR cc_start: 0.8153 (t80) cc_final: 0.7864 (t80) outliers start: 173 outliers final: 115 residues processed: 1195 average time/residue: 0.5819 time to fit residues: 1155.9413 Evaluate side-chains 1134 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 1010 time to evaluate : 5.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 343 HIS Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain H residue 243 ILE Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 135 GLU Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 213 GLU Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 81 ASP Chi-restraints excluded: chain J residue 111 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 195 VAL Chi-restraints excluded: chain K residue 92 SER Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain K residue 188 TYR Chi-restraints excluded: chain L residue 232 ILE Chi-restraints excluded: chain L residue 286 ILE Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 256 THR Chi-restraints excluded: chain M residue 259 PHE Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 281 ARG Chi-restraints excluded: chain M residue 295 GLU Chi-restraints excluded: chain M residue 300 MET Chi-restraints excluded: chain M residue 317 ASP Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 66 ASN Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 209 GLU Chi-restraints excluded: chain N residue 212 CYS Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain a residue 58 MET Chi-restraints excluded: chain a residue 156 VAL Chi-restraints excluded: chain a residue 208 SER Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 184 ASP Chi-restraints excluded: chain b residue 211 VAL Chi-restraints excluded: chain c residue 50 MET Chi-restraints excluded: chain c residue 56 PHE Chi-restraints excluded: chain c residue 115 ASP Chi-restraints excluded: chain c residue 119 ILE Chi-restraints excluded: chain c residue 254 LEU Chi-restraints excluded: chain d residue 11 SER Chi-restraints excluded: chain d residue 17 PHE Chi-restraints excluded: chain d residue 211 TYR Chi-restraints excluded: chain e residue 147 VAL Chi-restraints excluded: chain e residue 289 MET Chi-restraints excluded: chain f residue 171 ASP Chi-restraints excluded: chain f residue 245 ASP Chi-restraints excluded: chain f residue 324 THR Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 42 CYS Chi-restraints excluded: chain g residue 216 VAL Chi-restraints excluded: chain g residue 227 VAL Chi-restraints excluded: chain h residue 56 THR Chi-restraints excluded: chain h residue 129 ASN Chi-restraints excluded: chain h residue 201 MET Chi-restraints excluded: chain h residue 230 THR Chi-restraints excluded: chain h residue 242 THR Chi-restraints excluded: chain h residue 243 ILE Chi-restraints excluded: chain h residue 263 THR Chi-restraints excluded: chain h residue 266 GLN Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain i residue 148 THR Chi-restraints excluded: chain i residue 212 THR Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 39 VAL Chi-restraints excluded: chain j residue 81 ASP Chi-restraints excluded: chain j residue 111 SER Chi-restraints excluded: chain j residue 126 LEU Chi-restraints excluded: chain j residue 134 GLU Chi-restraints excluded: chain j residue 166 ILE Chi-restraints excluded: chain j residue 189 ILE Chi-restraints excluded: chain j residue 199 LEU Chi-restraints excluded: chain k residue 44 LEU Chi-restraints excluded: chain k residue 92 SER Chi-restraints excluded: chain k residue 96 SER Chi-restraints excluded: chain k residue 121 VAL Chi-restraints excluded: chain k residue 188 TYR Chi-restraints excluded: chain l residue 199 MET Chi-restraints excluded: chain l residue 232 ILE Chi-restraints excluded: chain l residue 286 ILE Chi-restraints excluded: chain m residue 237 VAL Chi-restraints excluded: chain m residue 256 THR Chi-restraints excluded: chain m residue 259 PHE Chi-restraints excluded: chain m residue 263 THR Chi-restraints excluded: chain m residue 295 GLU Chi-restraints excluded: chain m residue 300 MET Chi-restraints excluded: chain n residue 50 THR Chi-restraints excluded: chain n residue 66 ASN Chi-restraints excluded: chain n residue 77 ASP Chi-restraints excluded: chain n residue 212 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 500 optimal weight: 7.9990 chunk 341 optimal weight: 0.9990 chunk 8 optimal weight: 9.9990 chunk 447 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 chunk 513 optimal weight: 4.9990 chunk 415 optimal weight: 0.0030 chunk 0 optimal weight: 10.0000 chunk 307 optimal weight: 8.9990 chunk 539 optimal weight: 10.0000 chunk 151 optimal weight: 0.9990 overall best weight: 2.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN B 207 GLN D 15 HIS D 120 GLN ** E 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 194 ASN F 195 ASN ** F 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 ASN M 165 GLN M 280 ASN N 66 ASN ** a 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 207 GLN ** e 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 194 ASN f 195 ASN i 201 GLN l 137 ASN m 165 GLN ** m 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 280 ASN n 66 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 50188 Z= 0.270 Angle : 0.539 8.050 67898 Z= 0.286 Chirality : 0.043 0.154 7548 Planarity : 0.004 0.050 8804 Dihedral : 4.430 31.883 6994 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.56 % Allowed : 19.39 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.10), residues: 6306 helix: 1.01 (0.11), residues: 2230 sheet: -0.83 (0.13), residues: 1516 loop : -1.62 (0.11), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP l 165 HIS 0.005 0.001 HIS N 89 PHE 0.017 0.001 PHE K 8 TYR 0.027 0.001 TYR H 218 ARG 0.006 0.000 ARG i 104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1258 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 1019 time to evaluate : 5.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8339 (mmt) cc_final: 0.7590 (mmt) REVERT: A 87 LEU cc_start: 0.8967 (tp) cc_final: 0.8696 (tp) REVERT: A 98 TYR cc_start: 0.8998 (t80) cc_final: 0.8697 (t80) REVERT: A 141 ASP cc_start: 0.7934 (p0) cc_final: 0.7720 (p0) REVERT: A 155 THR cc_start: 0.8344 (m) cc_final: 0.8082 (m) REVERT: A 210 ILE cc_start: 0.7799 (pt) cc_final: 0.7569 (mt) REVERT: B 18 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8181 (pt) REVERT: B 98 MET cc_start: 0.7480 (ttm) cc_final: 0.7222 (ttt) REVERT: B 100 ASN cc_start: 0.8728 (t0) cc_final: 0.8387 (t0) REVERT: B 210 ARG cc_start: 0.7852 (ptt90) cc_final: 0.7354 (ptt90) REVERT: B 215 ARG cc_start: 0.6792 (ptt-90) cc_final: 0.6028 (ptp-170) REVERT: C 26 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7719 (mm-30) REVERT: C 165 TRP cc_start: 0.8674 (m100) cc_final: 0.8341 (m100) REVERT: C 215 ARG cc_start: 0.6791 (ttp-170) cc_final: 0.6050 (tpt170) REVERT: C 221 MET cc_start: 0.7965 (tpt) cc_final: 0.7449 (tpt) REVERT: C 234 ASP cc_start: 0.7346 (t0) cc_final: 0.7051 (m-30) REVERT: C 238 HIS cc_start: 0.6791 (t-90) cc_final: 0.6544 (t70) REVERT: C 254 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7362 (tt) REVERT: D 4 ASP cc_start: 0.7323 (p0) cc_final: 0.6755 (p0) REVERT: D 117 LYS cc_start: 0.8850 (tttt) cc_final: 0.8577 (ttpt) REVERT: D 120 GLN cc_start: 0.8117 (tt0) cc_final: 0.7838 (tt0) REVERT: F 220 GLU cc_start: 0.7099 (mp0) cc_final: 0.6396 (mt-10) REVERT: F 321 TYR cc_start: 0.8065 (m-80) cc_final: 0.7860 (m-80) REVERT: F 373 LYS cc_start: 0.8644 (mmmt) cc_final: 0.8179 (mtmt) REVERT: F 401 PHE cc_start: 0.5977 (t80) cc_final: 0.5647 (t80) REVERT: G 175 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7927 (mm-30) REVERT: G 231 MET cc_start: 0.6433 (tpt) cc_final: 0.6157 (tpp) REVERT: H 145 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7671 (ptt90) REVERT: I 213 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6894 (tt0) REVERT: J 126 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8531 (pt) REVERT: L 138 ASP cc_start: 0.7282 (t0) cc_final: 0.6995 (t0) REVERT: M 164 ASP cc_start: 0.8086 (t70) cc_final: 0.7868 (t0) REVERT: M 183 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.7482 (tm-30) REVERT: N 26 TYR cc_start: 0.8320 (t80) cc_final: 0.7992 (t80) REVERT: N 94 GLN cc_start: 0.8254 (tp40) cc_final: 0.7958 (tp40) REVERT: a 55 ASP cc_start: 0.4189 (t70) cc_final: 0.3955 (t0) REVERT: a 77 MET cc_start: 0.8405 (mmt) cc_final: 0.7657 (mmt) REVERT: a 87 LEU cc_start: 0.8925 (tp) cc_final: 0.8649 (tp) REVERT: a 98 TYR cc_start: 0.9103 (t80) cc_final: 0.8849 (t80) REVERT: a 141 ASP cc_start: 0.8076 (p0) cc_final: 0.7534 (p0) REVERT: a 210 ILE cc_start: 0.7845 (pt) cc_final: 0.7562 (mt) REVERT: b 100 ASN cc_start: 0.8827 (t0) cc_final: 0.8482 (t0) REVERT: b 107 GLN cc_start: 0.8454 (mm110) cc_final: 0.8137 (mm-40) REVERT: b 210 ARG cc_start: 0.7896 (ptt90) cc_final: 0.7450 (ptt90) REVERT: b 215 ARG cc_start: 0.6831 (ptt-90) cc_final: 0.6080 (ptp-170) REVERT: b 226 ASP cc_start: 0.6653 (t0) cc_final: 0.6241 (t0) REVERT: c 26 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7767 (mm-30) REVERT: c 29 GLN cc_start: 0.7895 (mm110) cc_final: 0.7687 (mt0) REVERT: c 165 TRP cc_start: 0.8695 (m100) cc_final: 0.8363 (m100) REVERT: c 221 MET cc_start: 0.7956 (tpt) cc_final: 0.7448 (tpt) REVERT: c 234 ASP cc_start: 0.7349 (t0) cc_final: 0.7147 (t0) REVERT: c 238 HIS cc_start: 0.6620 (t-90) cc_final: 0.6419 (t70) REVERT: c 254 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7393 (tt) REVERT: d 4 ASP cc_start: 0.7176 (p0) cc_final: 0.6754 (p0) REVERT: d 17 PHE cc_start: 0.8378 (OUTLIER) cc_final: 0.8131 (m-10) REVERT: d 117 LYS cc_start: 0.8847 (tttt) cc_final: 0.8614 (ttpt) REVERT: d 120 GLN cc_start: 0.8085 (tt0) cc_final: 0.7784 (tt0) REVERT: d 230 GLU cc_start: 0.6723 (pp20) cc_final: 0.6260 (tm-30) REVERT: e 195 GLU cc_start: 0.7856 (mp0) cc_final: 0.7548 (mm-30) REVERT: f 220 GLU cc_start: 0.6894 (mp0) cc_final: 0.5496 (mp0) REVERT: f 247 ARG cc_start: 0.7295 (mtp-110) cc_final: 0.7083 (ptm160) REVERT: f 373 LYS cc_start: 0.8539 (mmmt) cc_final: 0.8120 (mtmt) REVERT: f 401 PHE cc_start: 0.6193 (t80) cc_final: 0.5680 (t80) REVERT: i 101 LYS cc_start: 0.8660 (mmtp) cc_final: 0.8084 (mmtt) REVERT: j 3 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8394 (mm) REVERT: j 126 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8516 (pt) REVERT: k 62 LYS cc_start: 0.8751 (mtpp) cc_final: 0.8531 (mtpp) REVERT: k 70 MET cc_start: 0.7699 (mmp) cc_final: 0.7237 (mtt) REVERT: l 138 ASP cc_start: 0.7213 (t0) cc_final: 0.6892 (t0) REVERT: m 152 ARG cc_start: 0.8467 (ttt180) cc_final: 0.7845 (ttt180) REVERT: m 164 ASP cc_start: 0.8086 (t70) cc_final: 0.7813 (t0) REVERT: m 183 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.7430 (tm-30) REVERT: n 26 TYR cc_start: 0.8207 (t80) cc_final: 0.7919 (t80) REVERT: n 94 GLN cc_start: 0.8500 (tp40) cc_final: 0.8252 (tp40) outliers start: 239 outliers final: 172 residues processed: 1171 average time/residue: 0.5891 time to fit residues: 1148.3790 Evaluate side-chains 1176 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 993 time to evaluate : 5.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 343 HIS Chi-restraints excluded: chain F residue 355 HIS Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 145 ARG Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain H residue 243 ILE Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 135 GLU Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 213 GLU Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 81 ASP Chi-restraints excluded: chain J residue 111 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 132 GLU Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 195 VAL Chi-restraints excluded: chain K residue 3 GLU Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 92 SER Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain K residue 188 TYR Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 232 ILE Chi-restraints excluded: chain L residue 286 ILE Chi-restraints excluded: chain M residue 154 ASN Chi-restraints excluded: chain M residue 183 GLN Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 256 THR Chi-restraints excluded: chain M residue 259 PHE Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 295 GLU Chi-restraints excluded: chain M residue 317 ASP Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 66 ASN Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 209 GLU Chi-restraints excluded: chain N residue 212 CYS Chi-restraints excluded: chain a residue 10 ILE Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain a residue 58 MET Chi-restraints excluded: chain a residue 156 VAL Chi-restraints excluded: chain a residue 208 SER Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 32 THR Chi-restraints excluded: chain b residue 60 ILE Chi-restraints excluded: chain b residue 147 VAL Chi-restraints excluded: chain b residue 184 ASP Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 50 MET Chi-restraints excluded: chain c residue 56 PHE Chi-restraints excluded: chain c residue 111 MET Chi-restraints excluded: chain c residue 115 ASP Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain c residue 253 GLU Chi-restraints excluded: chain c residue 254 LEU Chi-restraints excluded: chain d residue 11 SER Chi-restraints excluded: chain d residue 17 PHE Chi-restraints excluded: chain d residue 42 VAL Chi-restraints excluded: chain d residue 183 ASP Chi-restraints excluded: chain d residue 211 TYR Chi-restraints excluded: chain e residue 147 VAL Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 282 THR Chi-restraints excluded: chain e residue 289 MET Chi-restraints excluded: chain f residue 171 ASP Chi-restraints excluded: chain f residue 199 THR Chi-restraints excluded: chain f residue 221 LEU Chi-restraints excluded: chain f residue 239 ILE Chi-restraints excluded: chain f residue 245 ASP Chi-restraints excluded: chain f residue 324 THR Chi-restraints excluded: chain f residue 355 HIS Chi-restraints excluded: chain g residue 9 ASP Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 42 CYS Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 163 VAL Chi-restraints excluded: chain g residue 171 VAL Chi-restraints excluded: chain g residue 216 VAL Chi-restraints excluded: chain g residue 227 VAL Chi-restraints excluded: chain h residue 56 THR Chi-restraints excluded: chain h residue 129 ASN Chi-restraints excluded: chain h residue 201 MET Chi-restraints excluded: chain h residue 230 THR Chi-restraints excluded: chain h residue 231 ILE Chi-restraints excluded: chain h residue 242 THR Chi-restraints excluded: chain h residue 243 ILE Chi-restraints excluded: chain h residue 263 THR Chi-restraints excluded: chain h residue 266 GLN Chi-restraints excluded: chain i residue 32 ILE Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain i residue 148 THR Chi-restraints excluded: chain i residue 212 THR Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 37 THR Chi-restraints excluded: chain j residue 39 VAL Chi-restraints excluded: chain j residue 81 ASP Chi-restraints excluded: chain j residue 111 SER Chi-restraints excluded: chain j residue 126 LEU Chi-restraints excluded: chain j residue 166 ILE Chi-restraints excluded: chain j residue 189 ILE Chi-restraints excluded: chain j residue 199 LEU Chi-restraints excluded: chain k residue 3 GLU Chi-restraints excluded: chain k residue 4 THR Chi-restraints excluded: chain k residue 44 LEU Chi-restraints excluded: chain k residue 92 SER Chi-restraints excluded: chain k residue 96 SER Chi-restraints excluded: chain k residue 121 VAL Chi-restraints excluded: chain l residue 199 MET Chi-restraints excluded: chain l residue 232 ILE Chi-restraints excluded: chain l residue 286 ILE Chi-restraints excluded: chain m residue 183 GLN Chi-restraints excluded: chain m residue 198 LYS Chi-restraints excluded: chain m residue 237 VAL Chi-restraints excluded: chain m residue 256 THR Chi-restraints excluded: chain m residue 259 PHE Chi-restraints excluded: chain m residue 263 THR Chi-restraints excluded: chain m residue 277 CYS Chi-restraints excluded: chain m residue 295 GLU Chi-restraints excluded: chain m residue 300 MET Chi-restraints excluded: chain n residue 50 THR Chi-restraints excluded: chain n residue 66 ASN Chi-restraints excluded: chain n residue 77 ASP Chi-restraints excluded: chain n residue 116 THR Chi-restraints excluded: chain n residue 212 CYS Chi-restraints excluded: chain n residue 218 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 202 optimal weight: 9.9990 chunk 541 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 352 optimal weight: 10.0000 chunk 148 optimal weight: 9.9990 chunk 601 optimal weight: 1.9990 chunk 499 optimal weight: 8.9990 chunk 278 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 199 optimal weight: 10.0000 chunk 315 optimal weight: 8.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN ** E 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 194 ASN ** F 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 201 GLN L 137 ASN M 280 ASN N 66 ASN ** a 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 207 GLN ** e 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 194 ASN i 201 GLN l 137 ASN m 165 GLN ** m 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 280 ASN m 303 ASN n 66 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 50188 Z= 0.248 Angle : 0.535 9.080 67898 Z= 0.283 Chirality : 0.043 0.152 7548 Planarity : 0.004 0.050 8804 Dihedral : 4.416 33.156 6994 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.69 % Allowed : 20.65 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.10), residues: 6306 helix: 1.11 (0.11), residues: 2222 sheet: -0.74 (0.13), residues: 1504 loop : -1.57 (0.11), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP l 165 HIS 0.004 0.001 HIS n 89 PHE 0.016 0.001 PHE K 8 TYR 0.024 0.001 TYR H 218 ARG 0.006 0.000 ARG M 225 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1253 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 1007 time to evaluate : 5.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8344 (mmt) cc_final: 0.7600 (mmt) REVERT: A 87 LEU cc_start: 0.8962 (tp) cc_final: 0.8691 (tp) REVERT: A 98 TYR cc_start: 0.9000 (t80) cc_final: 0.8649 (t80) REVERT: A 141 ASP cc_start: 0.7956 (p0) cc_final: 0.7728 (p0) REVERT: A 155 THR cc_start: 0.8359 (m) cc_final: 0.8086 (m) REVERT: A 184 ARG cc_start: 0.8165 (tpt90) cc_final: 0.7903 (tpp-160) REVERT: B 18 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8172 (pt) REVERT: B 98 MET cc_start: 0.7501 (ttm) cc_final: 0.7250 (ttt) REVERT: B 100 ASN cc_start: 0.8724 (t0) cc_final: 0.8377 (t0) REVERT: B 107 GLN cc_start: 0.8405 (mm110) cc_final: 0.8074 (mm-40) REVERT: B 210 ARG cc_start: 0.7819 (ptt90) cc_final: 0.7314 (ptt90) REVERT: B 215 ARG cc_start: 0.6754 (ptt-90) cc_final: 0.5998 (ptp-170) REVERT: B 226 ASP cc_start: 0.6682 (t0) cc_final: 0.6228 (t0) REVERT: C 26 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7725 (mm-30) REVERT: C 165 TRP cc_start: 0.8692 (m100) cc_final: 0.8344 (m100) REVERT: C 215 ARG cc_start: 0.6749 (ttp-170) cc_final: 0.6184 (tpt170) REVERT: C 221 MET cc_start: 0.7979 (tpt) cc_final: 0.7469 (tpt) REVERT: C 238 HIS cc_start: 0.6787 (t-90) cc_final: 0.6508 (t70) REVERT: C 254 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7430 (tt) REVERT: D 4 ASP cc_start: 0.7335 (p0) cc_final: 0.6770 (p0) REVERT: D 117 LYS cc_start: 0.8858 (tttt) cc_final: 0.8594 (ttpt) REVERT: D 120 GLN cc_start: 0.8094 (tt0) cc_final: 0.7797 (tt0) REVERT: F 220 GLU cc_start: 0.7089 (mp0) cc_final: 0.6410 (mt-10) REVERT: F 373 LYS cc_start: 0.8654 (mmmt) cc_final: 0.8082 (mtmt) REVERT: G 175 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7954 (mm-30) REVERT: G 231 MET cc_start: 0.6319 (tpt) cc_final: 0.6038 (tpp) REVERT: H 145 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7636 (ptt90) REVERT: I 47 THR cc_start: 0.8090 (p) cc_final: 0.7829 (p) REVERT: I 213 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6904 (tt0) REVERT: J 126 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8533 (pt) REVERT: K 1 MET cc_start: 0.5440 (mmm) cc_final: 0.4514 (mmm) REVERT: K 177 GLU cc_start: 0.8292 (tp30) cc_final: 0.7986 (tp30) REVERT: L 138 ASP cc_start: 0.7230 (t0) cc_final: 0.6917 (t0) REVERT: M 164 ASP cc_start: 0.8100 (t70) cc_final: 0.7884 (t0) REVERT: M 183 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.7473 (tm-30) REVERT: N 26 TYR cc_start: 0.8310 (t80) cc_final: 0.7997 (t80) REVERT: N 94 GLN cc_start: 0.8307 (tp40) cc_final: 0.7993 (tp40) REVERT: a 55 ASP cc_start: 0.4128 (t70) cc_final: 0.3920 (t0) REVERT: a 77 MET cc_start: 0.8420 (mmt) cc_final: 0.7580 (mmt) REVERT: a 87 LEU cc_start: 0.8924 (tp) cc_final: 0.8646 (tp) REVERT: a 98 TYR cc_start: 0.9075 (t80) cc_final: 0.8760 (t80) REVERT: a 141 ASP cc_start: 0.8019 (p0) cc_final: 0.7488 (p0) REVERT: b 100 ASN cc_start: 0.8801 (t0) cc_final: 0.8484 (t0) REVERT: b 107 GLN cc_start: 0.8412 (mm110) cc_final: 0.8111 (mm-40) REVERT: b 210 ARG cc_start: 0.7874 (ptt90) cc_final: 0.7391 (ptt90) REVERT: b 215 ARG cc_start: 0.6735 (ptt-90) cc_final: 0.6001 (ptp-170) REVERT: c 26 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7755 (mm-30) REVERT: c 165 TRP cc_start: 0.8703 (m100) cc_final: 0.8345 (m100) REVERT: c 215 ARG cc_start: 0.6646 (ttp-170) cc_final: 0.6012 (tpt170) REVERT: c 221 MET cc_start: 0.7962 (tpt) cc_final: 0.7458 (tpt) REVERT: c 238 HIS cc_start: 0.6700 (t-90) cc_final: 0.6387 (t70) REVERT: c 254 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7456 (tt) REVERT: d 17 PHE cc_start: 0.8382 (OUTLIER) cc_final: 0.8136 (m-10) REVERT: d 117 LYS cc_start: 0.8847 (tttt) cc_final: 0.8611 (ttpt) REVERT: d 120 GLN cc_start: 0.8026 (tt0) cc_final: 0.7736 (tt0) REVERT: d 230 GLU cc_start: 0.6828 (pp20) cc_final: 0.6323 (tm-30) REVERT: e 263 THR cc_start: 0.8896 (m) cc_final: 0.8588 (p) REVERT: e 334 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.6493 (mp0) REVERT: f 220 GLU cc_start: 0.6952 (mp0) cc_final: 0.5556 (mp0) REVERT: f 247 ARG cc_start: 0.7296 (mtp-110) cc_final: 0.7081 (ptm160) REVERT: f 373 LYS cc_start: 0.8581 (mmmt) cc_final: 0.8120 (mtmt) REVERT: i 101 LYS cc_start: 0.8645 (mmtp) cc_final: 0.8069 (mmtt) REVERT: j 3 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8406 (mm) REVERT: j 126 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8546 (pt) REVERT: k 1 MET cc_start: 0.5518 (mmm) cc_final: 0.4590 (mmm) REVERT: k 62 LYS cc_start: 0.8749 (mtpp) cc_final: 0.8532 (mtpp) REVERT: k 70 MET cc_start: 0.7695 (mmp) cc_final: 0.7298 (mtt) REVERT: k 125 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.7326 (mp-120) REVERT: l 138 ASP cc_start: 0.7134 (t0) cc_final: 0.6833 (t0) REVERT: m 152 ARG cc_start: 0.8464 (ttt180) cc_final: 0.7856 (ttt180) REVERT: m 183 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.7434 (tm-30) REVERT: n 26 TYR cc_start: 0.8209 (t80) cc_final: 0.7870 (t80) outliers start: 246 outliers final: 187 residues processed: 1164 average time/residue: 0.5924 time to fit residues: 1154.0714 Evaluate side-chains 1176 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 976 time to evaluate : 5.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 169 GLU Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain F residue 180 THR Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 343 HIS Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 129 ASN Chi-restraints excluded: chain H residue 145 ARG Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 239 GLU Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain H residue 243 ILE Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 135 GLU Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 213 GLU Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 81 ASP Chi-restraints excluded: chain J residue 111 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 132 GLU Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 195 VAL Chi-restraints excluded: chain K residue 3 GLU Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 92 SER Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain K residue 188 TYR Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 160 MET Chi-restraints excluded: chain L residue 232 ILE Chi-restraints excluded: chain L residue 286 ILE Chi-restraints excluded: chain M residue 154 ASN Chi-restraints excluded: chain M residue 183 GLN Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 256 THR Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 259 PHE Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 295 GLU Chi-restraints excluded: chain M residue 317 ASP Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 66 ASN Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 98 ASP Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 209 GLU Chi-restraints excluded: chain N residue 212 CYS Chi-restraints excluded: chain a residue 10 ILE Chi-restraints excluded: chain a residue 27 LYS Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain a residue 58 MET Chi-restraints excluded: chain a residue 156 VAL Chi-restraints excluded: chain a residue 168 CYS Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain a residue 208 SER Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 32 THR Chi-restraints excluded: chain b residue 60 ILE Chi-restraints excluded: chain b residue 118 GLU Chi-restraints excluded: chain b residue 184 ASP Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 50 MET Chi-restraints excluded: chain c residue 56 PHE Chi-restraints excluded: chain c residue 111 MET Chi-restraints excluded: chain c residue 115 ASP Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain c residue 253 GLU Chi-restraints excluded: chain c residue 254 LEU Chi-restraints excluded: chain d residue 11 SER Chi-restraints excluded: chain d residue 17 PHE Chi-restraints excluded: chain d residue 42 VAL Chi-restraints excluded: chain d residue 119 THR Chi-restraints excluded: chain d residue 183 ASP Chi-restraints excluded: chain d residue 211 TYR Chi-restraints excluded: chain e residue 147 VAL Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 169 GLU Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 282 THR Chi-restraints excluded: chain e residue 289 MET Chi-restraints excluded: chain e residue 331 THR Chi-restraints excluded: chain e residue 334 GLU Chi-restraints excluded: chain f residue 171 ASP Chi-restraints excluded: chain f residue 180 THR Chi-restraints excluded: chain f residue 199 THR Chi-restraints excluded: chain f residue 221 LEU Chi-restraints excluded: chain f residue 239 ILE Chi-restraints excluded: chain f residue 245 ASP Chi-restraints excluded: chain f residue 324 THR Chi-restraints excluded: chain f residue 355 HIS Chi-restraints excluded: chain g residue 9 ASP Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 42 CYS Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 163 VAL Chi-restraints excluded: chain g residue 171 VAL Chi-restraints excluded: chain g residue 216 VAL Chi-restraints excluded: chain g residue 227 VAL Chi-restraints excluded: chain h residue 56 THR Chi-restraints excluded: chain h residue 129 ASN Chi-restraints excluded: chain h residue 201 MET Chi-restraints excluded: chain h residue 230 THR Chi-restraints excluded: chain h residue 231 ILE Chi-restraints excluded: chain h residue 242 THR Chi-restraints excluded: chain h residue 243 ILE Chi-restraints excluded: chain h residue 263 THR Chi-restraints excluded: chain i residue 32 ILE Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain i residue 148 THR Chi-restraints excluded: chain i residue 212 THR Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 37 THR Chi-restraints excluded: chain j residue 39 VAL Chi-restraints excluded: chain j residue 81 ASP Chi-restraints excluded: chain j residue 111 SER Chi-restraints excluded: chain j residue 126 LEU Chi-restraints excluded: chain j residue 166 ILE Chi-restraints excluded: chain j residue 189 ILE Chi-restraints excluded: chain j residue 190 VAL Chi-restraints excluded: chain j residue 199 LEU Chi-restraints excluded: chain k residue 3 GLU Chi-restraints excluded: chain k residue 4 THR Chi-restraints excluded: chain k residue 44 LEU Chi-restraints excluded: chain k residue 92 SER Chi-restraints excluded: chain k residue 96 SER Chi-restraints excluded: chain k residue 121 VAL Chi-restraints excluded: chain k residue 125 GLN Chi-restraints excluded: chain l residue 199 MET Chi-restraints excluded: chain l residue 232 ILE Chi-restraints excluded: chain l residue 286 ILE Chi-restraints excluded: chain m residue 183 GLN Chi-restraints excluded: chain m residue 237 VAL Chi-restraints excluded: chain m residue 256 THR Chi-restraints excluded: chain m residue 257 GLU Chi-restraints excluded: chain m residue 259 PHE Chi-restraints excluded: chain m residue 263 THR Chi-restraints excluded: chain m residue 277 CYS Chi-restraints excluded: chain m residue 295 GLU Chi-restraints excluded: chain m residue 300 MET Chi-restraints excluded: chain n residue 50 THR Chi-restraints excluded: chain n residue 66 ASN Chi-restraints excluded: chain n residue 77 ASP Chi-restraints excluded: chain n residue 116 THR Chi-restraints excluded: chain n residue 212 CYS Chi-restraints excluded: chain n residue 218 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 580 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 342 optimal weight: 8.9990 chunk 439 optimal weight: 7.9990 chunk 340 optimal weight: 8.9990 chunk 506 optimal weight: 10.0000 chunk 336 optimal weight: 7.9990 chunk 599 optimal weight: 0.8980 chunk 375 optimal weight: 10.0000 chunk 365 optimal weight: 10.0000 chunk 276 optimal weight: 5.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN ** E 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 ASN F 194 ASN ** F 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 ASN L 137 ASN M 280 ASN N 66 ASN ** a 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 207 GLN ** e 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 262 HIS ** e 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 194 ASN i 201 GLN j 60 GLN l 137 ASN l 222 GLN m 165 GLN m 280 ASN n 66 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 50188 Z= 0.502 Angle : 0.670 9.131 67898 Z= 0.354 Chirality : 0.048 0.168 7548 Planarity : 0.005 0.051 8804 Dihedral : 4.953 39.709 6994 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 5.04 % Allowed : 21.34 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.10), residues: 6306 helix: 0.80 (0.11), residues: 2192 sheet: -0.80 (0.13), residues: 1518 loop : -1.75 (0.11), residues: 2596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP g 215 HIS 0.011 0.001 HIS e 262 PHE 0.024 0.002 PHE k 8 TYR 0.038 0.002 TYR H 218 ARG 0.006 0.001 ARG i 104 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1259 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 995 time to evaluate : 5.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8381 (mmt) cc_final: 0.7646 (mmt) REVERT: A 87 LEU cc_start: 0.9004 (tp) cc_final: 0.8745 (tp) REVERT: A 98 TYR cc_start: 0.9117 (t80) cc_final: 0.8843 (t80) REVERT: A 141 ASP cc_start: 0.8027 (p0) cc_final: 0.7668 (p0) REVERT: A 155 THR cc_start: 0.8431 (m) cc_final: 0.8134 (m) REVERT: B 100 ASN cc_start: 0.8867 (t0) cc_final: 0.8498 (t0) REVERT: B 107 GLN cc_start: 0.8322 (mm110) cc_final: 0.8072 (mm-40) REVERT: B 210 ARG cc_start: 0.8023 (ptt90) cc_final: 0.7539 (ptt90) REVERT: B 215 ARG cc_start: 0.7003 (ptt-90) cc_final: 0.6170 (ptp-170) REVERT: C 26 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7793 (mm-30) REVERT: C 215 ARG cc_start: 0.6778 (ttp-170) cc_final: 0.6051 (tpt170) REVERT: C 234 ASP cc_start: 0.7350 (t0) cc_final: 0.7123 (m-30) REVERT: C 238 HIS cc_start: 0.6812 (t-90) cc_final: 0.6431 (t70) REVERT: C 254 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7401 (tt) REVERT: D 4 ASP cc_start: 0.7364 (p0) cc_final: 0.7055 (p0) REVERT: D 17 PHE cc_start: 0.8491 (OUTLIER) cc_final: 0.8248 (m-10) REVERT: D 117 LYS cc_start: 0.8861 (tttt) cc_final: 0.8582 (ttpt) REVERT: D 120 GLN cc_start: 0.8175 (tt0) cc_final: 0.7903 (tt0) REVERT: D 234 GLU cc_start: 0.3913 (OUTLIER) cc_final: 0.3421 (pt0) REVERT: F 220 GLU cc_start: 0.7236 (mp0) cc_final: 0.6520 (mt-10) REVERT: F 319 TYR cc_start: 0.7936 (m-80) cc_final: 0.7618 (m-10) REVERT: G 175 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7977 (mm-30) REVERT: H 145 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7725 (ptt90) REVERT: I 213 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6954 (tt0) REVERT: J 126 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8512 (pt) REVERT: K 125 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.7441 (mp-120) REVERT: K 176 ASP cc_start: 0.7960 (t70) cc_final: 0.7742 (t0) REVERT: L 138 ASP cc_start: 0.7266 (t0) cc_final: 0.6918 (t0) REVERT: M 164 ASP cc_start: 0.8151 (t70) cc_final: 0.7907 (t0) REVERT: M 183 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.7685 (tm-30) REVERT: N 94 GLN cc_start: 0.8227 (tp40) cc_final: 0.7946 (tp40) REVERT: a 77 MET cc_start: 0.8404 (mmt) cc_final: 0.7529 (mmt) REVERT: a 87 LEU cc_start: 0.8972 (tp) cc_final: 0.8674 (tp) REVERT: a 98 TYR cc_start: 0.9197 (t80) cc_final: 0.8972 (t80) REVERT: a 141 ASP cc_start: 0.8136 (p0) cc_final: 0.7610 (p0) REVERT: b 100 ASN cc_start: 0.8889 (t0) cc_final: 0.8546 (t0) REVERT: b 107 GLN cc_start: 0.8357 (mm110) cc_final: 0.8111 (mm-40) REVERT: b 215 ARG cc_start: 0.7077 (ptt-90) cc_final: 0.6140 (ptp-170) REVERT: c 215 ARG cc_start: 0.6689 (ttp-170) cc_final: 0.5933 (tpt170) REVERT: c 238 HIS cc_start: 0.6795 (t-90) cc_final: 0.6413 (t70) REVERT: c 254 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7450 (tt) REVERT: d 17 PHE cc_start: 0.8413 (OUTLIER) cc_final: 0.8010 (m-10) REVERT: d 117 LYS cc_start: 0.8854 (tttt) cc_final: 0.8581 (ttpt) REVERT: d 120 GLN cc_start: 0.8145 (tt0) cc_final: 0.7870 (tt0) REVERT: e 334 GLU cc_start: 0.6729 (OUTLIER) cc_final: 0.6458 (mp0) REVERT: f 220 GLU cc_start: 0.7114 (mp0) cc_final: 0.5617 (mp0) REVERT: f 373 LYS cc_start: 0.8639 (mmmt) cc_final: 0.8119 (mtmt) REVERT: h 145 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.7698 (ptt90) REVERT: i 101 LYS cc_start: 0.8716 (mmtp) cc_final: 0.8076 (mmtt) REVERT: j 126 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8501 (pt) REVERT: k 70 MET cc_start: 0.7814 (mmp) cc_final: 0.7404 (mtt) REVERT: k 125 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.7462 (mp-120) REVERT: l 138 ASP cc_start: 0.7181 (t0) cc_final: 0.6839 (t0) REVERT: l 243 ARG cc_start: 0.7882 (ptt180) cc_final: 0.7647 (ptt-90) REVERT: m 152 ARG cc_start: 0.8535 (ttt180) cc_final: 0.7895 (ttt180) REVERT: m 164 ASP cc_start: 0.8013 (t0) cc_final: 0.7793 (t0) REVERT: m 183 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.7696 (tm-30) REVERT: n 26 TYR cc_start: 0.8412 (t80) cc_final: 0.8089 (t80) outliers start: 264 outliers final: 201 residues processed: 1171 average time/residue: 0.5915 time to fit residues: 1152.9647 Evaluate side-chains 1169 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 953 time to evaluate : 5.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 169 GLU Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 314 ASN Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain F residue 180 THR Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 343 HIS Chi-restraints excluded: chain F residue 355 HIS Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 145 ARG Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 239 GLU Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain H residue 243 ILE Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 135 GLU Chi-restraints excluded: chain I residue 209 LYS Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 213 GLU Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 111 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 132 GLU Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 195 VAL Chi-restraints excluded: chain K residue 3 GLU Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 92 SER Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 160 MET Chi-restraints excluded: chain L residue 227 VAL Chi-restraints excluded: chain L residue 232 ILE Chi-restraints excluded: chain L residue 286 ILE Chi-restraints excluded: chain M residue 154 ASN Chi-restraints excluded: chain M residue 183 GLN Chi-restraints excluded: chain M residue 193 LEU Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 256 THR Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 259 PHE Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 295 GLU Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 45 SER Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 66 ASN Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 98 ASP Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 212 CYS Chi-restraints excluded: chain a residue 10 ILE Chi-restraints excluded: chain a residue 27 LYS Chi-restraints excluded: chain a residue 30 THR Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain a residue 58 MET Chi-restraints excluded: chain a residue 156 VAL Chi-restraints excluded: chain a residue 168 CYS Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain a residue 208 SER Chi-restraints excluded: chain a residue 214 VAL Chi-restraints excluded: chain b residue 18 ILE Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 32 THR Chi-restraints excluded: chain b residue 60 ILE Chi-restraints excluded: chain b residue 184 ASP Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 50 MET Chi-restraints excluded: chain c residue 56 PHE Chi-restraints excluded: chain c residue 111 MET Chi-restraints excluded: chain c residue 115 ASP Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain c residue 253 GLU Chi-restraints excluded: chain c residue 254 LEU Chi-restraints excluded: chain d residue 11 SER Chi-restraints excluded: chain d residue 17 PHE Chi-restraints excluded: chain d residue 40 SER Chi-restraints excluded: chain d residue 42 VAL Chi-restraints excluded: chain d residue 119 THR Chi-restraints excluded: chain d residue 147 THR Chi-restraints excluded: chain d residue 169 ILE Chi-restraints excluded: chain d residue 183 ASP Chi-restraints excluded: chain d residue 211 TYR Chi-restraints excluded: chain e residue 147 VAL Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 162 SER Chi-restraints excluded: chain e residue 169 GLU Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 262 HIS Chi-restraints excluded: chain e residue 282 THR Chi-restraints excluded: chain e residue 289 MET Chi-restraints excluded: chain e residue 331 THR Chi-restraints excluded: chain e residue 334 GLU Chi-restraints excluded: chain f residue 180 THR Chi-restraints excluded: chain f residue 199 THR Chi-restraints excluded: chain f residue 239 ILE Chi-restraints excluded: chain f residue 245 ASP Chi-restraints excluded: chain f residue 324 THR Chi-restraints excluded: chain f residue 355 HIS Chi-restraints excluded: chain g residue 9 ASP Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 42 CYS Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 163 VAL Chi-restraints excluded: chain g residue 171 VAL Chi-restraints excluded: chain g residue 204 GLN Chi-restraints excluded: chain g residue 208 LEU Chi-restraints excluded: chain g residue 216 VAL Chi-restraints excluded: chain g residue 227 VAL Chi-restraints excluded: chain h residue 56 THR Chi-restraints excluded: chain h residue 145 ARG Chi-restraints excluded: chain h residue 201 MET Chi-restraints excluded: chain h residue 218 TYR Chi-restraints excluded: chain h residue 230 THR Chi-restraints excluded: chain h residue 231 ILE Chi-restraints excluded: chain h residue 242 THR Chi-restraints excluded: chain h residue 243 ILE Chi-restraints excluded: chain h residue 263 THR Chi-restraints excluded: chain i residue 32 ILE Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain i residue 148 THR Chi-restraints excluded: chain i residue 212 THR Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 37 THR Chi-restraints excluded: chain j residue 39 VAL Chi-restraints excluded: chain j residue 58 THR Chi-restraints excluded: chain j residue 111 SER Chi-restraints excluded: chain j residue 126 LEU Chi-restraints excluded: chain j residue 166 ILE Chi-restraints excluded: chain j residue 189 ILE Chi-restraints excluded: chain k residue 3 GLU Chi-restraints excluded: chain k residue 4 THR Chi-restraints excluded: chain k residue 44 LEU Chi-restraints excluded: chain k residue 92 SER Chi-restraints excluded: chain k residue 121 VAL Chi-restraints excluded: chain k residue 125 GLN Chi-restraints excluded: chain l residue 143 THR Chi-restraints excluded: chain l residue 199 MET Chi-restraints excluded: chain l residue 227 VAL Chi-restraints excluded: chain l residue 232 ILE Chi-restraints excluded: chain l residue 286 ILE Chi-restraints excluded: chain m residue 183 GLN Chi-restraints excluded: chain m residue 193 LEU Chi-restraints excluded: chain m residue 198 LYS Chi-restraints excluded: chain m residue 237 VAL Chi-restraints excluded: chain m residue 256 THR Chi-restraints excluded: chain m residue 257 GLU Chi-restraints excluded: chain m residue 259 PHE Chi-restraints excluded: chain m residue 263 THR Chi-restraints excluded: chain m residue 277 CYS Chi-restraints excluded: chain m residue 295 GLU Chi-restraints excluded: chain m residue 300 MET Chi-restraints excluded: chain n residue 7 VAL Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain n residue 50 THR Chi-restraints excluded: chain n residue 66 ASN Chi-restraints excluded: chain n residue 77 ASP Chi-restraints excluded: chain n residue 116 THR Chi-restraints excluded: chain n residue 212 CYS Chi-restraints excluded: chain n residue 218 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 370 optimal weight: 0.9980 chunk 239 optimal weight: 1.9990 chunk 358 optimal weight: 0.1980 chunk 180 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 381 optimal weight: 7.9990 chunk 408 optimal weight: 1.9990 chunk 296 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 471 optimal weight: 10.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 142 GLN B 187 HIS B 207 GLN ** E 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 194 ASN F 271 ASN ** F 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 GLN L 137 ASN ** M 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 280 ASN N 66 ASN ** a 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 187 HIS b 207 GLN ** e 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 262 HIS f 194 ASN g 23 GLN j 60 GLN l 137 ASN m 165 GLN ** m 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 280 ASN n 66 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 50188 Z= 0.168 Angle : 0.523 8.310 67898 Z= 0.277 Chirality : 0.042 0.189 7548 Planarity : 0.004 0.050 8804 Dihedral : 4.388 32.860 6994 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.65 % Allowed : 23.11 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.11), residues: 6306 helix: 1.24 (0.11), residues: 2200 sheet: -0.57 (0.13), residues: 1490 loop : -1.54 (0.11), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP c 165 HIS 0.020 0.001 HIS e 262 PHE 0.033 0.001 PHE F 401 TYR 0.021 0.001 TYR l 264 ARG 0.007 0.000 ARG I 104 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1251 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 1060 time to evaluate : 5.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8356 (mmt) cc_final: 0.7511 (mmt) REVERT: A 87 LEU cc_start: 0.8939 (tp) cc_final: 0.8675 (tp) REVERT: A 98 TYR cc_start: 0.8961 (t80) cc_final: 0.8662 (t80) REVERT: A 141 ASP cc_start: 0.7910 (p0) cc_final: 0.7670 (p0) REVERT: B 18 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8184 (pt) REVERT: B 100 ASN cc_start: 0.8745 (t0) cc_final: 0.8419 (t0) REVERT: B 107 GLN cc_start: 0.8267 (mm110) cc_final: 0.7970 (mm-40) REVERT: B 174 LYS cc_start: 0.7137 (pptt) cc_final: 0.6347 (pttp) REVERT: B 210 ARG cc_start: 0.7840 (ptt90) cc_final: 0.7315 (ptt90) REVERT: B 215 ARG cc_start: 0.6710 (ptt-90) cc_final: 0.6032 (ptp-170) REVERT: B 226 ASP cc_start: 0.6691 (t0) cc_final: 0.6261 (t0) REVERT: C 8 ARG cc_start: 0.7831 (mtm-85) cc_final: 0.7274 (mtp180) REVERT: C 26 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7718 (mm-30) REVERT: C 165 TRP cc_start: 0.8695 (m100) cc_final: 0.8430 (m100) REVERT: C 215 ARG cc_start: 0.6721 (ttp-170) cc_final: 0.6008 (tpt170) REVERT: C 221 MET cc_start: 0.7938 (tpt) cc_final: 0.7451 (tpt) REVERT: C 238 HIS cc_start: 0.6669 (t-90) cc_final: 0.6396 (t70) REVERT: C 254 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7367 (tt) REVERT: D 4 ASP cc_start: 0.7385 (p0) cc_final: 0.7171 (p0) REVERT: D 17 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.8186 (m-10) REVERT: D 117 LYS cc_start: 0.8839 (tttt) cc_final: 0.8563 (ttpt) REVERT: D 120 GLN cc_start: 0.8081 (tt0) cc_final: 0.7774 (tt0) REVERT: E 156 SER cc_start: 0.8682 (t) cc_final: 0.8409 (p) REVERT: E 207 MET cc_start: 0.8433 (ttt) cc_final: 0.8219 (ttt) REVERT: E 263 THR cc_start: 0.8870 (m) cc_final: 0.8605 (p) REVERT: F 373 LYS cc_start: 0.8787 (mmmm) cc_final: 0.8309 (mmtm) REVERT: G 175 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7637 (mm-30) REVERT: I 47 THR cc_start: 0.8072 (p) cc_final: 0.7800 (p) REVERT: J 99 ARG cc_start: 0.8657 (ttt-90) cc_final: 0.8199 (ttt-90) REVERT: J 126 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8539 (pt) REVERT: J 127 ILE cc_start: 0.8746 (pt) cc_final: 0.8396 (mt) REVERT: K 177 GLU cc_start: 0.8263 (tp30) cc_final: 0.8024 (tp30) REVERT: L 138 ASP cc_start: 0.7236 (t0) cc_final: 0.6915 (t0) REVERT: M 164 ASP cc_start: 0.8136 (t70) cc_final: 0.7901 (t0) REVERT: M 183 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.7308 (tm-30) REVERT: N 26 TYR cc_start: 0.8241 (t80) cc_final: 0.7891 (t80) REVERT: N 94 GLN cc_start: 0.8298 (tp40) cc_final: 0.7917 (tp40) REVERT: N 148 GLN cc_start: 0.7707 (tt0) cc_final: 0.7466 (tt0) REVERT: a 77 MET cc_start: 0.8378 (mmt) cc_final: 0.7445 (mmt) REVERT: a 87 LEU cc_start: 0.8874 (tp) cc_final: 0.8602 (tp) REVERT: a 98 TYR cc_start: 0.9051 (t80) cc_final: 0.8746 (t80) REVERT: a 141 ASP cc_start: 0.7960 (p0) cc_final: 0.7587 (p0) REVERT: b 100 ASN cc_start: 0.8706 (t0) cc_final: 0.8402 (t0) REVERT: b 107 GLN cc_start: 0.8314 (mm110) cc_final: 0.8041 (mm-40) REVERT: b 210 ARG cc_start: 0.7695 (ptm-80) cc_final: 0.7351 (ptt90) REVERT: b 215 ARG cc_start: 0.6723 (ptt-90) cc_final: 0.6014 (ptp-170) REVERT: c 165 TRP cc_start: 0.8748 (m100) cc_final: 0.8518 (m100) REVERT: c 215 ARG cc_start: 0.6647 (ttp-170) cc_final: 0.6070 (tpt170) REVERT: c 221 MET cc_start: 0.7870 (tpt) cc_final: 0.7357 (tpt) REVERT: c 238 HIS cc_start: 0.6745 (t-90) cc_final: 0.6392 (t70) REVERT: c 254 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7533 (tt) REVERT: d 17 PHE cc_start: 0.8318 (OUTLIER) cc_final: 0.7997 (m-10) REVERT: d 117 LYS cc_start: 0.8849 (tttt) cc_final: 0.8604 (ttpt) REVERT: d 120 GLN cc_start: 0.8023 (tt0) cc_final: 0.7738 (tt0) REVERT: d 234 GLU cc_start: 0.3870 (OUTLIER) cc_final: 0.3366 (pt0) REVERT: e 195 GLU cc_start: 0.7826 (mp0) cc_final: 0.7503 (mm-30) REVERT: e 249 LYS cc_start: 0.7917 (mttm) cc_final: 0.6657 (tptp) REVERT: e 284 ARG cc_start: 0.7538 (ttm-80) cc_final: 0.7301 (mtp85) REVERT: e 331 THR cc_start: 0.7915 (OUTLIER) cc_final: 0.7277 (t) REVERT: e 334 GLU cc_start: 0.6692 (OUTLIER) cc_final: 0.6358 (mp0) REVERT: f 247 ARG cc_start: 0.7287 (mtp-110) cc_final: 0.7086 (ptm160) REVERT: f 373 LYS cc_start: 0.8592 (mmmt) cc_final: 0.8114 (mtmt) REVERT: i 101 LYS cc_start: 0.8625 (mmtp) cc_final: 0.8066 (mmtt) REVERT: j 3 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8441 (mm) REVERT: j 126 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8511 (pt) REVERT: k 62 LYS cc_start: 0.8752 (mtpp) cc_final: 0.8526 (mtpp) REVERT: k 70 MET cc_start: 0.7559 (mmp) cc_final: 0.7206 (mtt) REVERT: k 125 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.7237 (mp-120) REVERT: l 138 ASP cc_start: 0.7160 (t0) cc_final: 0.6848 (t0) REVERT: l 243 ARG cc_start: 0.7843 (ptt180) cc_final: 0.7631 (ptt-90) REVERT: m 152 ARG cc_start: 0.8471 (ttt180) cc_final: 0.7859 (ttt180) REVERT: m 183 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.7332 (tm-30) REVERT: m 317 ASP cc_start: 0.7058 (OUTLIER) cc_final: 0.6742 (m-30) REVERT: n 26 TYR cc_start: 0.8154 (t80) cc_final: 0.7788 (t80) outliers start: 191 outliers final: 130 residues processed: 1183 average time/residue: 0.5837 time to fit residues: 1144.1447 Evaluate side-chains 1159 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 1014 time to evaluate : 5.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 314 ASN Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 271 ASN Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 239 GLU Chi-restraints excluded: chain H residue 243 ILE Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain I residue 90 SER Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 111 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain K residue 3 GLU Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain L residue 232 ILE Chi-restraints excluded: chain L residue 286 ILE Chi-restraints excluded: chain M residue 183 GLN Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 256 THR Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 259 PHE Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 295 GLU Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 66 ASN Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 209 GLU Chi-restraints excluded: chain a residue 10 ILE Chi-restraints excluded: chain a residue 27 LYS Chi-restraints excluded: chain a residue 30 THR Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain a residue 156 VAL Chi-restraints excluded: chain a residue 168 CYS Chi-restraints excluded: chain a residue 208 SER Chi-restraints excluded: chain b residue 118 GLU Chi-restraints excluded: chain b residue 147 VAL Chi-restraints excluded: chain b residue 184 ASP Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 50 MET Chi-restraints excluded: chain c residue 56 PHE Chi-restraints excluded: chain c residue 115 ASP Chi-restraints excluded: chain c residue 253 GLU Chi-restraints excluded: chain c residue 254 LEU Chi-restraints excluded: chain d residue 11 SER Chi-restraints excluded: chain d residue 17 PHE Chi-restraints excluded: chain d residue 40 SER Chi-restraints excluded: chain d residue 42 VAL Chi-restraints excluded: chain d residue 147 THR Chi-restraints excluded: chain d residue 183 ASP Chi-restraints excluded: chain d residue 197 VAL Chi-restraints excluded: chain d residue 234 GLU Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 282 THR Chi-restraints excluded: chain e residue 289 MET Chi-restraints excluded: chain e residue 331 THR Chi-restraints excluded: chain e residue 334 GLU Chi-restraints excluded: chain f residue 199 THR Chi-restraints excluded: chain f residue 221 LEU Chi-restraints excluded: chain f residue 245 ASP Chi-restraints excluded: chain f residue 324 THR Chi-restraints excluded: chain f residue 380 VAL Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 42 CYS Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 171 VAL Chi-restraints excluded: chain h residue 56 THR Chi-restraints excluded: chain h residue 129 ASN Chi-restraints excluded: chain h residue 201 MET Chi-restraints excluded: chain h residue 243 ILE Chi-restraints excluded: chain h residue 263 THR Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain i residue 148 THR Chi-restraints excluded: chain i residue 212 THR Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 37 THR Chi-restraints excluded: chain j residue 39 VAL Chi-restraints excluded: chain j residue 111 SER Chi-restraints excluded: chain j residue 126 LEU Chi-restraints excluded: chain j residue 166 ILE Chi-restraints excluded: chain j residue 189 ILE Chi-restraints excluded: chain k residue 3 GLU Chi-restraints excluded: chain k residue 4 THR Chi-restraints excluded: chain k residue 14 VAL Chi-restraints excluded: chain k residue 44 LEU Chi-restraints excluded: chain k residue 121 VAL Chi-restraints excluded: chain k residue 125 GLN Chi-restraints excluded: chain k residue 188 TYR Chi-restraints excluded: chain l residue 232 ILE Chi-restraints excluded: chain l residue 286 ILE Chi-restraints excluded: chain m residue 183 GLN Chi-restraints excluded: chain m residue 237 VAL Chi-restraints excluded: chain m residue 256 THR Chi-restraints excluded: chain m residue 257 GLU Chi-restraints excluded: chain m residue 259 PHE Chi-restraints excluded: chain m residue 263 THR Chi-restraints excluded: chain m residue 295 GLU Chi-restraints excluded: chain m residue 300 MET Chi-restraints excluded: chain m residue 317 ASP Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain n residue 50 THR Chi-restraints excluded: chain n residue 66 ASN Chi-restraints excluded: chain n residue 77 ASP Chi-restraints excluded: chain n residue 116 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 545 optimal weight: 8.9990 chunk 574 optimal weight: 10.0000 chunk 524 optimal weight: 0.7980 chunk 558 optimal weight: 4.9990 chunk 336 optimal weight: 0.3980 chunk 243 optimal weight: 4.9990 chunk 438 optimal weight: 9.9990 chunk 171 optimal weight: 1.9990 chunk 504 optimal weight: 7.9990 chunk 528 optimal weight: 1.9990 chunk 556 optimal weight: 6.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 142 GLN B 187 HIS B 207 GLN ** E 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 HIS F 194 ASN F 271 ASN ** F 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 ASN L 137 ASN ** M 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 66 ASN ** a 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 207 GLN ** e 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 262 HIS f 194 ASN ** f 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 137 ASN m 165 GLN ** m 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 280 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 50188 Z= 0.218 Angle : 0.544 10.933 67898 Z= 0.286 Chirality : 0.043 0.189 7548 Planarity : 0.004 0.052 8804 Dihedral : 4.370 32.873 6994 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.78 % Allowed : 23.47 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.11), residues: 6306 helix: 1.32 (0.11), residues: 2200 sheet: -0.56 (0.13), residues: 1502 loop : -1.49 (0.11), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP c 165 HIS 0.014 0.001 HIS E 262 PHE 0.021 0.001 PHE F 401 TYR 0.028 0.001 TYR D 21 ARG 0.007 0.000 ARG i 104 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1221 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 1023 time to evaluate : 5.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8357 (mmt) cc_final: 0.7565 (mmt) REVERT: A 87 LEU cc_start: 0.8963 (tp) cc_final: 0.8694 (tp) REVERT: A 98 TYR cc_start: 0.8971 (t80) cc_final: 0.8651 (t80) REVERT: A 141 ASP cc_start: 0.7914 (p0) cc_final: 0.7635 (p0) REVERT: A 155 THR cc_start: 0.8348 (m) cc_final: 0.8066 (m) REVERT: A 178 MET cc_start: 0.8140 (mmt) cc_final: 0.7348 (mmt) REVERT: B 18 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8189 (pt) REVERT: B 107 GLN cc_start: 0.8267 (mm110) cc_final: 0.7995 (mm-40) REVERT: B 174 LYS cc_start: 0.7171 (pptt) cc_final: 0.6327 (pttp) REVERT: B 210 ARG cc_start: 0.7868 (ptt90) cc_final: 0.7316 (ptt90) REVERT: B 215 ARG cc_start: 0.6776 (ptt-90) cc_final: 0.6003 (ptp-170) REVERT: B 226 ASP cc_start: 0.6739 (t0) cc_final: 0.6343 (t0) REVERT: C 8 ARG cc_start: 0.7797 (mtm-85) cc_final: 0.7586 (mtm-85) REVERT: C 26 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7694 (mm-30) REVERT: C 165 TRP cc_start: 0.8697 (m100) cc_final: 0.8390 (m100) REVERT: C 215 ARG cc_start: 0.6718 (ttp-170) cc_final: 0.6042 (tpt170) REVERT: C 221 MET cc_start: 0.7959 (tpt) cc_final: 0.7435 (tpt) REVERT: C 238 HIS cc_start: 0.6613 (t-90) cc_final: 0.6402 (t70) REVERT: C 254 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7373 (tt) REVERT: D 4 ASP cc_start: 0.7349 (p0) cc_final: 0.7088 (p0) REVERT: D 117 LYS cc_start: 0.8854 (tttt) cc_final: 0.8585 (ttpt) REVERT: D 120 GLN cc_start: 0.8082 (tt0) cc_final: 0.7784 (tt0) REVERT: D 212 LYS cc_start: 0.7979 (mmtt) cc_final: 0.7608 (mmtm) REVERT: E 191 HIS cc_start: 0.8409 (t70) cc_final: 0.7800 (t-170) REVERT: E 249 LYS cc_start: 0.7924 (mttm) cc_final: 0.6723 (tptp) REVERT: E 263 THR cc_start: 0.8845 (m) cc_final: 0.8523 (p) REVERT: E 334 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6775 (mp0) REVERT: F 373 LYS cc_start: 0.8829 (mmmm) cc_final: 0.8410 (mmtm) REVERT: G 175 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7688 (mm-30) REVERT: J 99 ARG cc_start: 0.8660 (ttt-90) cc_final: 0.8193 (ttt-90) REVERT: J 126 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8576 (pt) REVERT: J 127 ILE cc_start: 0.8764 (pt) cc_final: 0.8453 (mt) REVERT: K 177 GLU cc_start: 0.8302 (tp30) cc_final: 0.8028 (tp30) REVERT: L 138 ASP cc_start: 0.7247 (t0) cc_final: 0.6929 (t0) REVERT: M 183 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.7369 (tm-30) REVERT: N 26 TYR cc_start: 0.8321 (t80) cc_final: 0.7980 (t80) REVERT: N 94 GLN cc_start: 0.8281 (tp40) cc_final: 0.7976 (tp40) REVERT: N 148 GLN cc_start: 0.7695 (tt0) cc_final: 0.7486 (tt0) REVERT: N 159 ARG cc_start: 0.8552 (tpt-90) cc_final: 0.8240 (ttt-90) REVERT: a 77 MET cc_start: 0.8371 (mmt) cc_final: 0.7439 (mmt) REVERT: a 87 LEU cc_start: 0.8932 (tp) cc_final: 0.8634 (tp) REVERT: a 98 TYR cc_start: 0.9055 (t80) cc_final: 0.8777 (t80) REVERT: a 141 ASP cc_start: 0.7947 (p0) cc_final: 0.7670 (p0) REVERT: b 100 ASN cc_start: 0.8713 (t0) cc_final: 0.8413 (t0) REVERT: b 107 GLN cc_start: 0.8287 (mm110) cc_final: 0.8026 (mm-40) REVERT: b 210 ARG cc_start: 0.7652 (ptm-80) cc_final: 0.7304 (ptt90) REVERT: b 215 ARG cc_start: 0.6784 (ptt-90) cc_final: 0.5972 (ptp-170) REVERT: b 226 ASP cc_start: 0.6719 (t0) cc_final: 0.6311 (t0) REVERT: c 165 TRP cc_start: 0.8745 (m100) cc_final: 0.8481 (m100) REVERT: c 215 ARG cc_start: 0.6720 (ttp-170) cc_final: 0.6022 (tpt170) REVERT: c 221 MET cc_start: 0.7903 (tpt) cc_final: 0.7457 (tpt) REVERT: c 238 HIS cc_start: 0.6744 (t-90) cc_final: 0.6347 (t70) REVERT: c 254 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7549 (tt) REVERT: d 17 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.8068 (m-10) REVERT: d 117 LYS cc_start: 0.8846 (tttt) cc_final: 0.8611 (ttpt) REVERT: d 120 GLN cc_start: 0.8026 (tt0) cc_final: 0.7713 (tt0) REVERT: d 234 GLU cc_start: 0.3874 (OUTLIER) cc_final: 0.3366 (pt0) REVERT: e 169 GLU cc_start: 0.7751 (pt0) cc_final: 0.7454 (pt0) REVERT: e 249 LYS cc_start: 0.7972 (mttm) cc_final: 0.6847 (tptp) REVERT: e 284 ARG cc_start: 0.7591 (ttm-80) cc_final: 0.7342 (mtp85) REVERT: e 331 THR cc_start: 0.7931 (OUTLIER) cc_final: 0.7274 (t) REVERT: e 334 GLU cc_start: 0.6658 (OUTLIER) cc_final: 0.6330 (mp0) REVERT: f 247 ARG cc_start: 0.7302 (mtp-110) cc_final: 0.7081 (ptm160) REVERT: f 373 LYS cc_start: 0.8586 (mmmt) cc_final: 0.8111 (mtmt) REVERT: j 3 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8451 (mm) REVERT: j 126 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8511 (pt) REVERT: k 62 LYS cc_start: 0.8767 (mtpp) cc_final: 0.8539 (mtpp) REVERT: k 70 MET cc_start: 0.7639 (mmp) cc_final: 0.7274 (mtt) REVERT: k 125 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.7321 (mp-120) REVERT: l 138 ASP cc_start: 0.7211 (t0) cc_final: 0.6956 (t0) REVERT: l 243 ARG cc_start: 0.7828 (ptt180) cc_final: 0.7620 (ptt-90) REVERT: m 152 ARG cc_start: 0.8457 (ttt180) cc_final: 0.7808 (ttt180) REVERT: m 183 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.7406 (tm-30) REVERT: n 26 TYR cc_start: 0.8225 (t80) cc_final: 0.7870 (t80) outliers start: 198 outliers final: 157 residues processed: 1153 average time/residue: 0.5882 time to fit residues: 1123.1584 Evaluate side-chains 1165 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 994 time to evaluate : 5.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 239 GLU Chi-restraints excluded: chain H residue 243 ILE Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain I residue 90 SER Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 135 GLU Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 213 GLU Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 81 ASP Chi-restraints excluded: chain J residue 111 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain K residue 3 GLU Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain L residue 160 MET Chi-restraints excluded: chain L residue 232 ILE Chi-restraints excluded: chain L residue 286 ILE Chi-restraints excluded: chain M residue 183 GLN Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 256 THR Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 259 PHE Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 295 GLU Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 66 ASN Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 209 GLU Chi-restraints excluded: chain N residue 212 CYS Chi-restraints excluded: chain a residue 10 ILE Chi-restraints excluded: chain a residue 27 LYS Chi-restraints excluded: chain a residue 30 THR Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain a residue 58 MET Chi-restraints excluded: chain a residue 156 VAL Chi-restraints excluded: chain a residue 168 CYS Chi-restraints excluded: chain a residue 208 SER Chi-restraints excluded: chain b residue 18 ILE Chi-restraints excluded: chain b residue 118 GLU Chi-restraints excluded: chain b residue 184 ASP Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 50 MET Chi-restraints excluded: chain c residue 56 PHE Chi-restraints excluded: chain c residue 115 ASP Chi-restraints excluded: chain c residue 253 GLU Chi-restraints excluded: chain c residue 254 LEU Chi-restraints excluded: chain d residue 11 SER Chi-restraints excluded: chain d residue 17 PHE Chi-restraints excluded: chain d residue 40 SER Chi-restraints excluded: chain d residue 42 VAL Chi-restraints excluded: chain d residue 119 THR Chi-restraints excluded: chain d residue 147 THR Chi-restraints excluded: chain d residue 169 ILE Chi-restraints excluded: chain d residue 183 ASP Chi-restraints excluded: chain d residue 197 VAL Chi-restraints excluded: chain d residue 211 TYR Chi-restraints excluded: chain d residue 234 GLU Chi-restraints excluded: chain e residue 147 VAL Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 282 THR Chi-restraints excluded: chain e residue 289 MET Chi-restraints excluded: chain e residue 331 THR Chi-restraints excluded: chain e residue 334 GLU Chi-restraints excluded: chain f residue 171 ASP Chi-restraints excluded: chain f residue 199 THR Chi-restraints excluded: chain f residue 221 LEU Chi-restraints excluded: chain f residue 245 ASP Chi-restraints excluded: chain f residue 324 THR Chi-restraints excluded: chain f residue 380 VAL Chi-restraints excluded: chain g residue 9 ASP Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 42 CYS Chi-restraints excluded: chain g residue 163 VAL Chi-restraints excluded: chain g residue 171 VAL Chi-restraints excluded: chain g residue 216 VAL Chi-restraints excluded: chain h residue 56 THR Chi-restraints excluded: chain h residue 129 ASN Chi-restraints excluded: chain h residue 201 MET Chi-restraints excluded: chain h residue 230 THR Chi-restraints excluded: chain h residue 231 ILE Chi-restraints excluded: chain h residue 243 ILE Chi-restraints excluded: chain h residue 263 THR Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain i residue 135 GLU Chi-restraints excluded: chain i residue 148 THR Chi-restraints excluded: chain i residue 212 THR Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 37 THR Chi-restraints excluded: chain j residue 39 VAL Chi-restraints excluded: chain j residue 58 THR Chi-restraints excluded: chain j residue 81 ASP Chi-restraints excluded: chain j residue 111 SER Chi-restraints excluded: chain j residue 126 LEU Chi-restraints excluded: chain j residue 166 ILE Chi-restraints excluded: chain j residue 189 ILE Chi-restraints excluded: chain k residue 3 GLU Chi-restraints excluded: chain k residue 4 THR Chi-restraints excluded: chain k residue 14 VAL Chi-restraints excluded: chain k residue 44 LEU Chi-restraints excluded: chain k residue 121 VAL Chi-restraints excluded: chain k residue 125 GLN Chi-restraints excluded: chain l residue 232 ILE Chi-restraints excluded: chain l residue 286 ILE Chi-restraints excluded: chain m residue 183 GLN Chi-restraints excluded: chain m residue 237 VAL Chi-restraints excluded: chain m residue 256 THR Chi-restraints excluded: chain m residue 257 GLU Chi-restraints excluded: chain m residue 259 PHE Chi-restraints excluded: chain m residue 263 THR Chi-restraints excluded: chain m residue 295 GLU Chi-restraints excluded: chain m residue 300 MET Chi-restraints excluded: chain m residue 329 VAL Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain n residue 77 ASP Chi-restraints excluded: chain n residue 116 THR Chi-restraints excluded: chain n residue 212 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 366 optimal weight: 8.9990 chunk 590 optimal weight: 0.0570 chunk 360 optimal weight: 7.9990 chunk 280 optimal weight: 9.9990 chunk 410 optimal weight: 4.9990 chunk 619 optimal weight: 1.9990 chunk 570 optimal weight: 0.4980 chunk 493 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 381 optimal weight: 9.9990 chunk 302 optimal weight: 3.9990 overall best weight: 1.4902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN B 187 HIS B 207 GLN ** E 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 194 ASN ** F 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 ASN ** M 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 66 ASN a 72 ASN ** a 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 207 GLN ** e 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 194 ASN ** f 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 137 ASN m 165 GLN m 170 GLN ** m 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 280 ASN n 66 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 50188 Z= 0.183 Angle : 0.532 10.931 67898 Z= 0.279 Chirality : 0.042 0.177 7548 Planarity : 0.004 0.054 8804 Dihedral : 4.264 31.450 6994 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.42 % Allowed : 23.91 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.11), residues: 6306 helix: 1.39 (0.11), residues: 2216 sheet: -0.50 (0.13), residues: 1488 loop : -1.45 (0.11), residues: 2602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP c 165 HIS 0.005 0.001 HIS D 164 PHE 0.018 0.001 PHE D 188 TYR 0.024 0.001 TYR D 21 ARG 0.008 0.000 ARG m 225 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1199 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 1020 time to evaluate : 5.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8348 (mmt) cc_final: 0.7511 (mmt) REVERT: A 87 LEU cc_start: 0.8954 (tp) cc_final: 0.8693 (tp) REVERT: A 141 ASP cc_start: 0.7906 (p0) cc_final: 0.7597 (p0) REVERT: A 155 THR cc_start: 0.8330 (m) cc_final: 0.8059 (m) REVERT: B 18 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8194 (pt) REVERT: B 107 GLN cc_start: 0.8258 (mm110) cc_final: 0.7995 (mm-40) REVERT: B 174 LYS cc_start: 0.7170 (pptt) cc_final: 0.6298 (pttp) REVERT: B 210 ARG cc_start: 0.7824 (ptt90) cc_final: 0.7287 (ptt90) REVERT: B 215 ARG cc_start: 0.6585 (ptt-90) cc_final: 0.5962 (ptp-170) REVERT: B 226 ASP cc_start: 0.6760 (t0) cc_final: 0.6346 (t0) REVERT: C 8 ARG cc_start: 0.7735 (mtm-85) cc_final: 0.7523 (mtm-85) REVERT: C 26 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7727 (mm-30) REVERT: C 165 TRP cc_start: 0.8703 (m100) cc_final: 0.8360 (m100) REVERT: C 215 ARG cc_start: 0.6744 (ttp-170) cc_final: 0.6051 (tpt170) REVERT: C 221 MET cc_start: 0.7947 (tpt) cc_final: 0.7421 (tpt) REVERT: C 238 HIS cc_start: 0.6525 (t-90) cc_final: 0.6314 (t70) REVERT: C 254 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7386 (tt) REVERT: D 4 ASP cc_start: 0.7294 (p0) cc_final: 0.7065 (p0) REVERT: D 24 GLU cc_start: 0.8170 (tp30) cc_final: 0.7827 (tm-30) REVERT: D 117 LYS cc_start: 0.8841 (tttt) cc_final: 0.8587 (ttpt) REVERT: D 120 GLN cc_start: 0.7989 (tt0) cc_final: 0.7756 (tt0) REVERT: D 212 LYS cc_start: 0.7913 (mmtt) cc_final: 0.7579 (mmtm) REVERT: E 204 ASN cc_start: 0.9460 (t0) cc_final: 0.9222 (t0) REVERT: E 249 LYS cc_start: 0.7930 (mttm) cc_final: 0.6811 (tptp) REVERT: E 263 THR cc_start: 0.8821 (m) cc_final: 0.8580 (p) REVERT: F 373 LYS cc_start: 0.8843 (mmmm) cc_final: 0.8427 (mmtm) REVERT: G 57 ARG cc_start: 0.7004 (ptm160) cc_final: 0.6795 (ptm-80) REVERT: G 231 MET cc_start: 0.5718 (tpt) cc_final: 0.5468 (tpp) REVERT: J 99 ARG cc_start: 0.8662 (ttt-90) cc_final: 0.8208 (ttt-90) REVERT: J 126 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8561 (pt) REVERT: J 127 ILE cc_start: 0.8736 (pt) cc_final: 0.8483 (mt) REVERT: L 138 ASP cc_start: 0.7254 (t0) cc_final: 0.6997 (t0) REVERT: M 152 ARG cc_start: 0.8081 (ttt180) cc_final: 0.7806 (ttt180) REVERT: M 183 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.7331 (tm-30) REVERT: N 26 TYR cc_start: 0.8245 (t80) cc_final: 0.7851 (t80) REVERT: N 94 GLN cc_start: 0.8283 (tp40) cc_final: 0.7980 (tp40) REVERT: a 77 MET cc_start: 0.8374 (mmt) cc_final: 0.7427 (mmt) REVERT: a 87 LEU cc_start: 0.8916 (tp) cc_final: 0.8624 (tp) REVERT: a 98 TYR cc_start: 0.9009 (t80) cc_final: 0.8708 (t80) REVERT: a 141 ASP cc_start: 0.7904 (p0) cc_final: 0.7631 (p0) REVERT: b 18 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8153 (pt) REVERT: b 100 ASN cc_start: 0.8646 (t0) cc_final: 0.8372 (t0) REVERT: b 107 GLN cc_start: 0.8274 (mm110) cc_final: 0.8013 (mm-40) REVERT: b 174 LYS cc_start: 0.7292 (pptt) cc_final: 0.6393 (pttp) REVERT: b 210 ARG cc_start: 0.7634 (ptm-80) cc_final: 0.7298 (ptt90) REVERT: b 215 ARG cc_start: 0.6555 (ptt-90) cc_final: 0.5906 (ptp-170) REVERT: b 226 ASP cc_start: 0.6731 (t0) cc_final: 0.6301 (t0) REVERT: c 8 ARG cc_start: 0.7803 (mtm-85) cc_final: 0.6808 (mtm-85) REVERT: c 165 TRP cc_start: 0.8718 (m100) cc_final: 0.8437 (m100) REVERT: c 215 ARG cc_start: 0.6729 (ttp-170) cc_final: 0.5997 (tpt170) REVERT: c 221 MET cc_start: 0.7935 (tpt) cc_final: 0.7442 (tpt) REVERT: c 238 HIS cc_start: 0.6605 (t-90) cc_final: 0.6301 (t70) REVERT: c 254 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7515 (tt) REVERT: d 117 LYS cc_start: 0.8851 (tttt) cc_final: 0.8633 (ttpt) REVERT: d 120 GLN cc_start: 0.7885 (tt0) cc_final: 0.7657 (tt0) REVERT: d 172 MET cc_start: 0.8777 (ptm) cc_final: 0.8537 (ptm) REVERT: d 234 GLU cc_start: 0.3893 (OUTLIER) cc_final: 0.3389 (pt0) REVERT: e 169 GLU cc_start: 0.7830 (pt0) cc_final: 0.7548 (pt0) REVERT: e 249 LYS cc_start: 0.7959 (mttm) cc_final: 0.6894 (tptp) REVERT: e 263 THR cc_start: 0.8741 (m) cc_final: 0.8474 (p) REVERT: e 331 THR cc_start: 0.7986 (OUTLIER) cc_final: 0.7341 (t) REVERT: e 334 GLU cc_start: 0.6628 (OUTLIER) cc_final: 0.6334 (mp0) REVERT: f 247 ARG cc_start: 0.7267 (mtp-110) cc_final: 0.7057 (ptm160) REVERT: f 321 TYR cc_start: 0.8081 (m-80) cc_final: 0.7858 (m-80) REVERT: f 373 LYS cc_start: 0.8582 (mmmt) cc_final: 0.7929 (mtmm) REVERT: j 3 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8420 (mm) REVERT: j 126 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8505 (pt) REVERT: k 62 LYS cc_start: 0.8750 (mtpp) cc_final: 0.8536 (mtpp) REVERT: k 125 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.7210 (mp-120) REVERT: l 138 ASP cc_start: 0.7182 (t0) cc_final: 0.6921 (t0) REVERT: m 152 ARG cc_start: 0.8447 (ttt180) cc_final: 0.7827 (ttt180) REVERT: m 183 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.7354 (tm-30) REVERT: m 317 ASP cc_start: 0.7150 (m-30) cc_final: 0.6770 (m-30) REVERT: n 26 TYR cc_start: 0.8164 (t80) cc_final: 0.7805 (t80) outliers start: 179 outliers final: 147 residues processed: 1140 average time/residue: 0.6018 time to fit residues: 1142.2991 Evaluate side-chains 1160 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 1000 time to evaluate : 5.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 239 GLU Chi-restraints excluded: chain H residue 243 ILE Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain I residue 90 SER Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 111 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain L residue 232 ILE Chi-restraints excluded: chain L residue 286 ILE Chi-restraints excluded: chain M residue 183 GLN Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 256 THR Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 259 PHE Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 295 GLU Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 66 ASN Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 209 GLU Chi-restraints excluded: chain N residue 212 CYS Chi-restraints excluded: chain a residue 10 ILE Chi-restraints excluded: chain a residue 27 LYS Chi-restraints excluded: chain a residue 30 THR Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain a residue 58 MET Chi-restraints excluded: chain a residue 156 VAL Chi-restraints excluded: chain a residue 168 CYS Chi-restraints excluded: chain b residue 18 ILE Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 118 GLU Chi-restraints excluded: chain b residue 184 ASP Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 50 MET Chi-restraints excluded: chain c residue 56 PHE Chi-restraints excluded: chain c residue 253 GLU Chi-restraints excluded: chain c residue 254 LEU Chi-restraints excluded: chain d residue 11 SER Chi-restraints excluded: chain d residue 40 SER Chi-restraints excluded: chain d residue 42 VAL Chi-restraints excluded: chain d residue 119 THR Chi-restraints excluded: chain d residue 147 THR Chi-restraints excluded: chain d residue 169 ILE Chi-restraints excluded: chain d residue 183 ASP Chi-restraints excluded: chain d residue 197 VAL Chi-restraints excluded: chain d residue 211 TYR Chi-restraints excluded: chain d residue 234 GLU Chi-restraints excluded: chain e residue 147 VAL Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 282 THR Chi-restraints excluded: chain e residue 289 MET Chi-restraints excluded: chain e residue 331 THR Chi-restraints excluded: chain e residue 334 GLU Chi-restraints excluded: chain f residue 171 ASP Chi-restraints excluded: chain f residue 199 THR Chi-restraints excluded: chain f residue 245 ASP Chi-restraints excluded: chain f residue 324 THR Chi-restraints excluded: chain f residue 380 VAL Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 42 CYS Chi-restraints excluded: chain g residue 163 VAL Chi-restraints excluded: chain g residue 171 VAL Chi-restraints excluded: chain g residue 216 VAL Chi-restraints excluded: chain h residue 56 THR Chi-restraints excluded: chain h residue 129 ASN Chi-restraints excluded: chain h residue 201 MET Chi-restraints excluded: chain h residue 230 THR Chi-restraints excluded: chain h residue 243 ILE Chi-restraints excluded: chain h residue 263 THR Chi-restraints excluded: chain h residue 266 GLN Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain i residue 148 THR Chi-restraints excluded: chain i residue 212 THR Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 37 THR Chi-restraints excluded: chain j residue 39 VAL Chi-restraints excluded: chain j residue 58 THR Chi-restraints excluded: chain j residue 111 SER Chi-restraints excluded: chain j residue 126 LEU Chi-restraints excluded: chain j residue 166 ILE Chi-restraints excluded: chain j residue 189 ILE Chi-restraints excluded: chain k residue 3 GLU Chi-restraints excluded: chain k residue 4 THR Chi-restraints excluded: chain k residue 14 VAL Chi-restraints excluded: chain k residue 44 LEU Chi-restraints excluded: chain k residue 121 VAL Chi-restraints excluded: chain k residue 125 GLN Chi-restraints excluded: chain l residue 232 ILE Chi-restraints excluded: chain l residue 286 ILE Chi-restraints excluded: chain m residue 183 GLN Chi-restraints excluded: chain m residue 234 ASN Chi-restraints excluded: chain m residue 237 VAL Chi-restraints excluded: chain m residue 256 THR Chi-restraints excluded: chain m residue 257 GLU Chi-restraints excluded: chain m residue 259 PHE Chi-restraints excluded: chain m residue 263 THR Chi-restraints excluded: chain m residue 295 GLU Chi-restraints excluded: chain m residue 300 MET Chi-restraints excluded: chain m residue 329 VAL Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain n residue 66 ASN Chi-restraints excluded: chain n residue 77 ASP Chi-restraints excluded: chain n residue 116 THR Chi-restraints excluded: chain n residue 212 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 391 optimal weight: 5.9990 chunk 525 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 454 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 137 optimal weight: 7.9990 chunk 494 optimal weight: 8.9990 chunk 206 optimal weight: 4.9990 chunk 507 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN ** E 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 194 ASN ** F 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 ASN M 280 ASN N 66 ASN N 148 GLN a 72 ASN ** a 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 207 GLN d 15 HIS ** e 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 194 ASN ** f 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 137 ASN m 165 GLN m 280 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.142775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.118147 restraints weight = 65424.801| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.03 r_work: 0.3164 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 50188 Z= 0.272 Angle : 0.569 10.606 67898 Z= 0.298 Chirality : 0.044 0.176 7548 Planarity : 0.004 0.055 8804 Dihedral : 4.409 34.113 6994 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.63 % Allowed : 23.87 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.11), residues: 6306 helix: 1.32 (0.11), residues: 2206 sheet: -0.52 (0.13), residues: 1494 loop : -1.49 (0.11), residues: 2606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP c 165 HIS 0.005 0.001 HIS D 164 PHE 0.018 0.001 PHE K 8 TYR 0.034 0.001 TYR D 21 ARG 0.008 0.000 ARG m 225 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17857.26 seconds wall clock time: 317 minutes 32.71 seconds (19052.71 seconds total)