Starting phenix.real_space_refine on Fri Mar 15 23:46:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6muv_9257/03_2024/6muv_9257.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6muv_9257/03_2024/6muv_9257.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6muv_9257/03_2024/6muv_9257.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6muv_9257/03_2024/6muv_9257.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6muv_9257/03_2024/6muv_9257.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6muv_9257/03_2024/6muv_9257.pdb" } resolution = 3.8 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= 1.000 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: 4 Type Number sf(0) Gaussians S 310 5.16 5 C 45510 2.51 5 N 11816 2.21 5 O 13476 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 80": "OD1" <-> "OD2" Residue "A GLU 81": "OE1" <-> "OE2" Residue "A TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 199": "OE1" <-> "OE2" Residue "A ASP 223": "OD1" <-> "OD2" Residue "A GLU 246": "OE1" <-> "OE2" Residue "B PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 183": "OE1" <-> "OE2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B ASP 186": "OD1" <-> "OD2" Residue "C PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 69": "OD1" <-> "OD2" Residue "C ASP 82": "OD1" <-> "OD2" Residue "C TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 201": "OD1" <-> "OD2" Residue "C TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 13": "OD1" <-> "OD2" Residue "D ASP 66": "OD1" <-> "OD2" Residue "D GLU 67": "OE1" <-> "OE2" Residue "D ASP 79": "OD1" <-> "OD2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 173": "OE1" <-> "OE2" Residue "D GLU 181": "OE1" <-> "OE2" Residue "D ASP 213": "OD1" <-> "OD2" Residue "E GLU 60": "OE1" <-> "OE2" Residue "E GLU 95": "OE1" <-> "OE2" Residue "E TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 114": "OE1" <-> "OE2" Residue "E ASP 190": "OD1" <-> "OD2" Residue "E TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 7": "OD1" <-> "OD2" Residue "F GLU 16": "OE1" <-> "OE2" Residue "F TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 61": "OE1" <-> "OE2" Residue "F ASP 80": "OD1" <-> "OD2" Residue "F GLU 91": "OE1" <-> "OE2" Residue "F GLU 101": "OE1" <-> "OE2" Residue "F GLU 154": "OE1" <-> "OE2" Residue "G TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 97": "OE1" <-> "OE2" Residue "G PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 183": "OD1" <-> "OD2" Residue "H GLU 57": "OE1" <-> "OE2" Residue "H GLU 69": "OE1" <-> "OE2" Residue "H TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 175": "OE1" <-> "OE2" Residue "H PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 22": "OE1" <-> "OE2" Residue "I GLU 64": "OE1" <-> "OE2" Residue "I TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 104": "OD1" <-> "OD2" Residue "I TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 157": "OE1" <-> "OE2" Residue "I ASP 166": "OD1" <-> "OD2" Residue "I TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 26": "OD1" <-> "OD2" Residue "J PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 81": "OD1" <-> "OD2" Residue "J PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 131": "OE1" <-> "OE2" Residue "J ASP 138": "OD1" <-> "OD2" Residue "J GLU 178": "OE1" <-> "OE2" Residue "K TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 119": "OD1" <-> "OD2" Residue "K TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 36": "OE1" <-> "OE2" Residue "L TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 105": "OD1" <-> "OD2" Residue "L ASP 115": "OD1" <-> "OD2" Residue "L ASP 116": "OD1" <-> "OD2" Residue "L PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 150": "OD1" <-> "OD2" Residue "L ASP 167": "OD1" <-> "OD2" Residue "L PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 35": "OD1" <-> "OD2" Residue "M TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 153": "OD1" <-> "OD2" Residue "M ARG 180": "NH1" <-> "NH2" Residue "M ASP 213": "OD1" <-> "OD2" Residue "N ASP 84": "OD1" <-> "OD2" Residue "N ARG 97": "NH1" <-> "NH2" Residue "N ASP 128": "OD1" <-> "OD2" Residue "N PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 199": "OE1" <-> "OE2" Residue "N ARG 211": "NH1" <-> "NH2" Residue "N TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 183": "OE1" <-> "OE2" Residue "P GLU 185": "OE1" <-> "OE2" Residue "P ASP 186": "OD1" <-> "OD2" Residue "R ASP 13": "OD1" <-> "OD2" Residue "R ASP 66": "OD1" <-> "OD2" Residue "R GLU 67": "OE1" <-> "OE2" Residue "R ASP 79": "OD1" <-> "OD2" Residue "R PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 173": "OE1" <-> "OE2" Residue "R GLU 181": "OE1" <-> "OE2" Residue "R ASP 213": "OD1" <-> "OD2" Residue "S GLU 60": "OE1" <-> "OE2" Residue "S GLU 95": "OE1" <-> "OE2" Residue "S TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 114": "OE1" <-> "OE2" Residue "S ASP 190": "OD1" <-> "OD2" Residue "S TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 57": "OE1" <-> "OE2" Residue "V GLU 69": "OE1" <-> "OE2" Residue "V TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 175": "OE1" <-> "OE2" Residue "V PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 22": "OE1" <-> "OE2" Residue "W GLU 64": "OE1" <-> "OE2" Residue "W TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 104": "OD1" <-> "OD2" Residue "W TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 157": "OE1" <-> "OE2" Residue "W ASP 166": "OD1" <-> "OD2" Residue "W TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 119": "OD1" <-> "OD2" Residue "Y TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 35": "OD1" <-> "OD2" Residue "a TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 153": "OD1" <-> "OD2" Residue "a ARG 180": "NH1" <-> "NH2" Residue "a ASP 213": "OD1" <-> "OD2" Residue "c GLU 20": "OE1" <-> "OE2" Residue "c ASP 172": "OD1" <-> "OD2" Residue "c GLU 183": "OE1" <-> "OE2" Residue "c GLU 192": "OE1" <-> "OE2" Residue "c ASP 200": "OD1" <-> "OD2" Residue "c ASP 233": "OD1" <-> "OD2" Residue "c ASP 256": "OD1" <-> "OD2" Residue "d GLU 35": "OE1" <-> "OE2" Residue "d GLU 151": "OE1" <-> "OE2" Residue "d GLU 183": "OE1" <-> "OE2" Residue "d GLU 193": "OE1" <-> "OE2" Residue "d ASP 200": "OD1" <-> "OD2" Residue "d GLU 208": "OE1" <-> "OE2" Residue "d GLU 231": "OE1" <-> "OE2" Residue "d ASP 233": "OD1" <-> "OD2" Residue "e ASP 28": "OD1" <-> "OD2" Residue "e GLU 57": "OE1" <-> "OE2" Residue "e GLU 187": "OE1" <-> "OE2" Residue "e GLU 193": "OE1" <-> "OE2" Residue "e ASP 200": "OD1" <-> "OD2" Residue "e GLU 234": "OE1" <-> "OE2" Residue "e ASP 256": "OD1" <-> "OD2" Residue "f GLU 154": "OE1" <-> "OE2" Residue "f ASP 172": "OD1" <-> "OD2" Residue "f GLU 182": "OE1" <-> "OE2" Residue "f GLU 183": "OE1" <-> "OE2" Residue "f GLU 187": "OE1" <-> "OE2" Residue "f ASP 246": "OD1" <-> "OD2" Residue "g GLU 20": "OE1" <-> "OE2" Residue "g GLU 57": "OE1" <-> "OE2" Residue "g GLU 193": "OE1" <-> "OE2" Residue "g ASP 246": "OD1" <-> "OD2" Residue "g GLU 271": "OE1" <-> "OE2" Residue "h ASP 28": "OD1" <-> "OD2" Residue "h GLU 35": "OE1" <-> "OE2" Residue "h GLU 183": "OE1" <-> "OE2" Residue "i ASP 28": "OD1" <-> "OD2" Residue "i GLU 39": "OE1" <-> "OE2" Residue "i GLU 57": "OE1" <-> "OE2" Residue "i GLU 187": "OE1" <-> "OE2" Residue "i ASP 200": "OD1" <-> "OD2" Residue "i ASP 256": "OD1" <-> "OD2" Residue "j GLU 154": "OE1" <-> "OE2" Residue "j ASP 172": "OD1" <-> "OD2" Residue "j GLU 182": "OE1" <-> "OE2" Residue "j GLU 183": "OE1" <-> "OE2" Residue "j GLU 187": "OE1" <-> "OE2" Residue "j ASP 246": "OD1" <-> "OD2" Residue "k GLU 20": "OE1" <-> "OE2" Residue "k GLU 57": "OE1" <-> "OE2" Residue "k GLU 193": "OE1" <-> "OE2" Residue "k ASP 246": "OD1" <-> "OD2" Residue "k GLU 271": "OE1" <-> "OE2" Residue "l ASP 28": "OD1" <-> "OD2" Residue "l GLU 35": "OE1" <-> "OE2" Residue "l GLU 183": "OE1" <-> "OE2" Residue "m GLU 20": "OE1" <-> "OE2" Residue "m ASP 172": "OD1" <-> "OD2" Residue "m GLU 183": "OE1" <-> "OE2" Residue "m GLU 192": "OE1" <-> "OE2" Residue "m ASP 200": "OD1" <-> "OD2" Residue "m ASP 233": "OD1" <-> "OD2" Residue "m ASP 256": "OD1" <-> "OD2" Residue "n ASP 28": "OD1" <-> "OD2" Residue "n GLU 39": "OE1" <-> "OE2" Residue "n GLU 57": "OE1" <-> "OE2" Residue "n GLU 187": "OE1" <-> "OE2" Residue "n ASP 200": "OD1" <-> "OD2" Residue "n ASP 256": "OD1" <-> "OD2" Residue "o GLU 35": "OE1" <-> "OE2" Residue "o GLU 151": "OE1" <-> "OE2" Residue "o GLU 183": "OE1" <-> "OE2" Residue "o GLU 193": "OE1" <-> "OE2" Residue "o ASP 200": "OD1" <-> "OD2" Residue "o GLU 208": "OE1" <-> "OE2" Residue "o GLU 231": "OE1" <-> "OE2" Residue "o ASP 233": "OD1" <-> "OD2" Residue "p ASP 28": "OD1" <-> "OD2" Residue "p GLU 57": "OE1" <-> "OE2" Residue "p GLU 187": "OE1" <-> "OE2" Residue "p GLU 193": "OE1" <-> "OE2" Residue "p ASP 200": "OD1" <-> "OD2" Residue "p GLU 234": "OE1" <-> "OE2" Residue "p ASP 256": "OD1" <-> "OD2" Residue "b ASP 84": "OD1" <-> "OD2" Residue "b ARG 97": "NH1" <-> "NH2" Residue "b ASP 128": "OD1" <-> "OD2" Residue "b PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 199": "OE1" <-> "OE2" Residue "b ARG 211": "NH1" <-> "NH2" Residue "b TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 26": "OD1" <-> "OD2" Residue "X PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 81": "OD1" <-> "OD2" Residue "X PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 131": "OE1" <-> "OE2" Residue "X ASP 138": "OD1" <-> "OD2" Residue "X GLU 178": "OE1" <-> "OE2" Residue "Q PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 69": "OD1" <-> "OD2" Residue "Q ASP 82": "OD1" <-> "OD2" Residue "Q TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 201": "OD1" <-> "OD2" Residue "Q TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 7": "OD1" <-> "OD2" Residue "T GLU 16": "OE1" <-> "OE2" Residue "T TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 61": "OE1" <-> "OE2" Residue "T ASP 80": "OD1" <-> "OD2" Residue "T GLU 91": "OE1" <-> "OE2" Residue "T GLU 101": "OE1" <-> "OE2" Residue "T GLU 154": "OE1" <-> "OE2" Residue "O TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 80": "OD1" <-> "OD2" Residue "O GLU 81": "OE1" <-> "OE2" Residue "O TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 199": "OE1" <-> "OE2" Residue "O ASP 223": "OD1" <-> "OD2" Residue "O GLU 246": "OE1" <-> "OE2" Residue "Z PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 36": "OE1" <-> "OE2" Residue "Z TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 105": "OD1" <-> "OD2" Residue "Z ASP 115": "OD1" <-> "OD2" Residue "Z ASP 116": "OD1" <-> "OD2" Residue "Z PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 150": "OD1" <-> "OD2" Residue "Z ASP 167": "OD1" <-> "OD2" Residue "Z PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 97": "OE1" <-> "OE2" Residue "U PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 183": "OD1" <-> "OD2" 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: 71112 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 1943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1943 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 4, 'TRANS': 241} Chain breaks: 1 Chain: "B" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1782 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "C" Number of atoms: 1917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1917 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 5, 'TRANS': 234} Chain: "D" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1795 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 7, 'TRANS': 219} Chain: "E" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1760 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 5, 'TRANS': 221} Chain breaks: 1 Chain: "F" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1878 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 5, 'TRANS': 230} Chain: "G" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1906 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 5, 'TRANS': 227} Chain breaks: 1 Chain: "H" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1536 Classifications: {'peptide': 193} Link IDs: {'TRANS': 192} Chain breaks: 1 Chain: "I" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1676 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 11, 'TRANS': 207} Chain: "J" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1595 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 198} Chain breaks: 1 Chain: "K" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1614 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 193} Chain: "L" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1600 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 1, 'TRANS': 202} Chain: "M" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1676 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 205} Chain: "N" Number of atoms: 1845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1845 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 4, 'TRANS': 219} Chain breaks: 1 Chain: "P" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1782 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "R" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1795 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 7, 'TRANS': 219} Chain: "S" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1760 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 5, 'TRANS': 221} Chain breaks: 1 Chain: "V" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1536 Classifications: {'peptide': 193} Link IDs: {'TRANS': 192} Chain breaks: 1 Chain: "W" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1676 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 11, 'TRANS': 207} Chain: "Y" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1614 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 193} Chain: "a" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1676 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 205} Chain: "c" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1568 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 6, 'TRANS': 180} Chain breaks: 1 Chain: "d" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1568 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 6, 'TRANS': 180} Chain breaks: 1 Chain: "e" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1576 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 6, 'TRANS': 181} Chain breaks: 1 Chain: "f" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1618 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 6, 'TRANS': 186} Chain breaks: 1 Chain: "g" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1585 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "h" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1559 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 6, 'TRANS': 179} Chain breaks: 1 Chain: "i" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1559 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 6, 'TRANS': 179} Chain breaks: 1 Chain: "j" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1618 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 6, 'TRANS': 186} Chain breaks: 1 Chain: "k" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1585 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "l" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1559 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 6, 'TRANS': 179} Chain breaks: 1 Chain: "m" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1568 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 6, 'TRANS': 180} Chain breaks: 1 Chain: "n" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1559 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 6, 'TRANS': 179} Chain breaks: 1 Chain: "o" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1568 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 6, 'TRANS': 180} Chain breaks: 1 Chain: "p" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1576 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 6, 'TRANS': 181} Chain breaks: 1 Chain: "b" Number of atoms: 1845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1845 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 4, 'TRANS': 219} Chain breaks: 1 Chain: "X" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1595 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 198} Chain breaks: 1 Chain: "Q" Number of atoms: 1917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1917 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 5, 'TRANS': 234} Chain: "T" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1878 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 5, 'TRANS': 230} Chain: "O" Number of atoms: 1943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1943 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 4, 'TRANS': 241} Chain breaks: 1 Chain: "Z" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1600 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 1, 'TRANS': 202} Chain: "U" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1906 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 5, 'TRANS': 227} Chain breaks: 1 Time building chain proxies: 27.31, per 1000 atoms: 0.38 Number of scatterers: 71112 At special positions: 0 Unit cell: (134.93, 142.79, 299.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 310 16.00 O 13476 8.00 N 11816 7.00 C 45510 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: 19.97 Conformation dependent library (CDL) restraints added in 9.6 seconds 17320 Ramachandran restraints generated. 8660 Oldfield, 0 Emsley, 8660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16676 Finding SS restraints... Secondary structure from input PDB file: 262 helices and 72 sheets defined 50.5% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.26 Creating SS restraints... Processing helix chain 'A' and resid 22 through 34 removed outlier: 3.668A pdb=" N VAL A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 112 removed outlier: 4.231A pdb=" N GLU A 103 " --> pdb=" O LYS A 99 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 108 " --> pdb=" O ALA A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 134 removed outlier: 3.526A pdb=" N CYS A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 191 removed outlier: 4.169A pdb=" N ARG A 187 " --> pdb=" O SER A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 220 removed outlier: 4.518A pdb=" N ALA A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 229 removed outlier: 3.761A pdb=" N ILE A 229 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 254 removed outlier: 3.622A pdb=" N THR A 254 " --> pdb=" O ASP A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'B' and resid 19 through 30 removed outlier: 3.503A pdb=" N GLU B 23 " --> pdb=" O LEU B 19 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG B 28 " --> pdb=" O TYR B 24 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL B 29 " --> pdb=" O ALA B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 84 through 101 removed outlier: 3.792A pdb=" N SER B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 124 removed outlier: 3.817A pdb=" N ILE B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE B 121 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THR B 122 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN B 123 " --> pdb=" O GLN B 119 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 177 removed outlier: 4.231A pdb=" N SER B 172 " --> pdb=" O GLN B 168 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE B 173 " --> pdb=" O ASN B 169 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU B 174 " --> pdb=" O ASN B 170 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS B 176 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 197 removed outlier: 4.368A pdb=" N HIS B 189 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR B 190 " --> pdb=" O ASP B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 229 removed outlier: 3.704A pdb=" N ASP B 229 " --> pdb=" O ASN B 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 28 Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 79 through 102 removed outlier: 3.812A pdb=" N ASN C 84 " --> pdb=" O ASN C 80 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU C 86 " --> pdb=" O ASP C 82 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU C 92 " --> pdb=" O ASN C 88 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 120 removed outlier: 4.042A pdb=" N VAL C 112 " --> pdb=" O SER C 108 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN C 113 " --> pdb=" O GLN C 109 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE C 117 " --> pdb=" O GLN C 113 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS C 118 " --> pdb=" O ILE C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 178 removed outlier: 3.532A pdb=" N SER C 173 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL C 174 " --> pdb=" O THR C 170 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU C 175 " --> pdb=" O ALA C 171 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN C 177 " --> pdb=" O SER C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 198 removed outlier: 3.867A pdb=" N THR C 195 " --> pdb=" O LEU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 201 No H-bonds generated for 'chain 'C' and resid 199 through 201' Processing helix chain 'C' and resid 229 through 241 removed outlier: 4.110A pdb=" N GLU C 233 " --> pdb=" O GLU C 229 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU C 234 " --> pdb=" O LYS C 230 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR C 240 " --> pdb=" O ILE C 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 26 removed outlier: 3.563A pdb=" N VAL D 26 " --> pdb=" O ALA D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 78 through 99 removed outlier: 4.630A pdb=" N VAL D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU D 83 " --> pdb=" O ASP D 79 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU D 90 " --> pdb=" O LYS D 86 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR D 95 " --> pdb=" O CYS D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 120 removed outlier: 3.562A pdb=" N LYS D 113 " --> pdb=" O LYS D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 175 removed outlier: 3.899A pdb=" N VAL D 168 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE D 171 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN D 175 " --> pdb=" O PHE D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 190 Processing helix chain 'D' and resid 196 through 200 removed outlier: 3.778A pdb=" N LEU D 199 " --> pdb=" O VAL D 196 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER D 200 " --> pdb=" O VAL D 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 196 through 200' Processing helix chain 'D' and resid 218 through 227 removed outlier: 3.625A pdb=" N SER D 224 " --> pdb=" O GLN D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 233 removed outlier: 3.976A pdb=" N ARG D 233 " --> pdb=" O ASP D 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 29 removed outlier: 3.937A pdb=" N ALA E 27 " --> pdb=" O GLN E 23 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY E 29 " --> pdb=" O GLU E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 33 removed outlier: 3.657A pdb=" N LEU E 33 " --> pdb=" O ALA E 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 30 through 33' Processing helix chain 'E' and resid 81 through 103 removed outlier: 3.632A pdb=" N ARG E 86 " --> pdb=" O MET E 82 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N THR E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU E 88 " --> pdb=" O ASP E 84 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN E 97 " --> pdb=" O ARG E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 119 removed outlier: 3.683A pdb=" N GLU E 114 " --> pdb=" O LYS E 110 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU E 119 " --> pdb=" O LEU E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 185 removed outlier: 3.662A pdb=" N ALA E 179 " --> pdb=" O ALA E 175 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU E 181 " --> pdb=" O GLU E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 207 removed outlier: 3.767A pdb=" N ILE E 198 " --> pdb=" O GLU E 194 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU E 201 " --> pdb=" O GLU E 197 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL E 203 " --> pdb=" O LEU E 199 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU E 204 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL E 207 " --> pdb=" O VAL E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 242 removed outlier: 3.542A pdb=" N SER E 238 " --> pdb=" O THR E 234 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG E 239 " --> pdb=" O ASP E 235 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE E 240 " --> pdb=" O ASP E 236 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP E 242 " --> pdb=" O SER E 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 29 removed outlier: 3.788A pdb=" N ALA F 25 " --> pdb=" O GLN F 21 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU F 27 " --> pdb=" O GLU F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 32 No H-bonds generated for 'chain 'F' and resid 30 through 32' Processing helix chain 'F' and resid 77 through 99 removed outlier: 3.530A pdb=" N LYS F 82 " --> pdb=" O THR F 78 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL F 83 " --> pdb=" O SER F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 119 removed outlier: 3.963A pdb=" N SER F 111 " --> pdb=" O SER F 107 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 173 removed outlier: 3.796A pdb=" N TYR F 170 " --> pdb=" O ALA F 166 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS F 173 " --> pdb=" O THR F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 180 Processing helix chain 'F' and resid 182 through 196 removed outlier: 3.795A pdb=" N LEU F 194 " --> pdb=" O CYS F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 231 removed outlier: 3.583A pdb=" N GLU F 230 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N TYR F 231 " --> pdb=" O GLN F 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 226 through 231' Processing helix chain 'G' and resid 25 through 32 removed outlier: 3.793A pdb=" N LYS G 29 " --> pdb=" O GLU G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 106 removed outlier: 3.737A pdb=" N ARG G 88 " --> pdb=" O ASP G 84 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASN G 89 " --> pdb=" O GLY G 85 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE G 90 " --> pdb=" O ASP G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 125 removed outlier: 4.370A pdb=" N ASN G 116 " --> pdb=" O HIS G 112 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG G 117 " --> pdb=" O ILE G 113 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU G 120 " --> pdb=" O ASN G 116 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR G 125 " --> pdb=" O TYR G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 180 removed outlier: 3.858A pdb=" N LYS G 176 " --> pdb=" O LYS G 172 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N THR G 177 " --> pdb=" O GLU G 173 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU G 178 " --> pdb=" O MET G 174 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU G 180 " --> pdb=" O LYS G 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 187 removed outlier: 3.931A pdb=" N ASP G 186 " --> pdb=" O ASP G 183 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE G 187 " --> pdb=" O TYR G 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 183 through 187' Processing helix chain 'G' and resid 191 through 203 removed outlier: 3.515A pdb=" N LYS G 198 " --> pdb=" O GLU G 194 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU G 201 " --> pdb=" O TYR G 197 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR G 202 " --> pdb=" O LYS G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 238 Processing helix chain 'H' and resid 51 through 71 removed outlier: 3.540A pdb=" N MET H 66 " --> pdb=" O TYR H 62 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLU H 69 " --> pdb=" O SER H 65 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN H 70 " --> pdb=" O MET H 66 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG H 71 " --> pdb=" O LYS H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 removed outlier: 3.692A pdb=" N THR H 81 " --> pdb=" O HIS H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 188 removed outlier: 3.836A pdb=" N ILE H 187 " --> pdb=" O SER H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 189 through 197 removed outlier: 3.647A pdb=" N GLN H 194 " --> pdb=" O GLN H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 220 removed outlier: 3.816A pdb=" N ASN H 212 " --> pdb=" O ASN H 208 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN H 220 " --> pdb=" O TYR H 216 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 70 removed outlier: 3.569A pdb=" N LEU I 52 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU I 53 " --> pdb=" O ALA I 49 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N HIS I 54 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR I 55 " --> pdb=" O ASP I 51 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TRP I 58 " --> pdb=" O HIS I 54 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU I 59 " --> pdb=" O THR I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 88 removed outlier: 4.007A pdb=" N CYS I 79 " --> pdb=" O ARG I 75 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL I 80 " --> pdb=" O VAL I 76 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER I 81 " --> pdb=" O SER I 77 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR I 84 " --> pdb=" O VAL I 80 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N GLN I 85 " --> pdb=" O SER I 81 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU I 86 " --> pdb=" O ARG I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 141 removed outlier: 3.809A pdb=" N VAL I 137 " --> pdb=" O ASN I 133 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA I 140 " --> pdb=" O ALA I 136 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS I 141 " --> pdb=" O VAL I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 165 removed outlier: 3.896A pdb=" N LEU I 154 " --> pdb=" O GLU I 150 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY I 162 " --> pdb=" O ALA I 158 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 78 removed outlier: 3.653A pdb=" N GLN J 63 " --> pdb=" O ALA J 59 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N THR J 64 " --> pdb=" O THR J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 100 removed outlier: 3.563A pdb=" N ASN J 91 " --> pdb=" O GLU J 87 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET J 92 " --> pdb=" O CYS J 88 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER J 94 " --> pdb=" O ALA J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 156 through 161 removed outlier: 4.272A pdb=" N GLY J 161 " --> pdb=" O GLU J 157 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 189 removed outlier: 3.698A pdb=" N PHE J 177 " --> pdb=" O GLU J 173 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA J 187 " --> pdb=" O CYS J 183 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP J 189 " --> pdb=" O LEU J 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 72 removed outlier: 3.817A pdb=" N GLY K 58 " --> pdb=" O ARG K 54 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN K 64 " --> pdb=" O PHE K 60 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL K 65 " --> pdb=" O ILE K 61 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR K 68 " --> pdb=" O ASN K 64 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN K 72 " --> pdb=" O TYR K 68 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 92 removed outlier: 3.571A pdb=" N PHE K 83 " --> pdb=" O LYS K 79 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 140 Processing helix chain 'K' and resid 141 through 146 removed outlier: 3.699A pdb=" N LYS K 145 " --> pdb=" O ALA K 141 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR K 146 " --> pdb=" O ILE K 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 141 through 146' Processing helix chain 'K' and resid 152 through 171 removed outlier: 3.723A pdb=" N ALA K 156 " --> pdb=" O THR K 152 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU K 157 " --> pdb=" O VAL K 153 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP K 158 " --> pdb=" O ASP K 154 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU K 165 " --> pdb=" O LYS K 161 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLU K 166 " --> pdb=" O LEU K 162 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE K 171 " --> pdb=" O LEU K 167 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 70 removed outlier: 3.842A pdb=" N TYR L 54 " --> pdb=" O ALA L 50 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N TRP L 55 " --> pdb=" O ASP L 51 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY L 60 " --> pdb=" O GLU L 56 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS L 61 " --> pdb=" O LYS L 57 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN L 70 " --> pdb=" O TYR L 66 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 86 removed outlier: 3.876A pdb=" N LEU L 83 " --> pdb=" O ALA L 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 91 Processing helix chain 'L' and resid 131 through 142 removed outlier: 4.286A pdb=" N ALA L 135 " --> pdb=" O GLY L 131 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER L 137 " --> pdb=" O THR L 133 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU L 139 " --> pdb=" O ALA L 135 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASP L 140 " --> pdb=" O TYR L 136 " (cutoff:3.500A) Processing helix chain 'L' and resid 148 through 165 removed outlier: 4.708A pdb=" N GLU L 154 " --> pdb=" O ASP L 150 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU L 155 " --> pdb=" O GLN L 151 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA L 163 " --> pdb=" O ALA L 159 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 108 removed outlier: 3.949A pdb=" N THR M 91 " --> pdb=" O SER M 87 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU M 92 " --> pdb=" O ASP M 88 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE M 103 " --> pdb=" O LYS M 99 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU M 106 " --> pdb=" O LEU M 102 " (cutoff:3.500A) Processing helix chain 'M' and resid 112 through 126 removed outlier: 3.502A pdb=" N ARG M 118 " --> pdb=" O HIS M 114 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL M 122 " --> pdb=" O ARG M 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 169 through 179 Proline residue: M 175 - end of helix Processing helix chain 'M' and resid 194 through 213 removed outlier: 3.736A pdb=" N ASN M 200 " --> pdb=" O GLY M 196 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU M 211 " --> pdb=" O THR M 207 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG M 212 " --> pdb=" O SER M 208 " (cutoff:3.500A) Processing helix chain 'N' and resid 58 through 77 removed outlier: 4.099A pdb=" N GLN N 62 " --> pdb=" O LEU N 58 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N TYR N 63 " --> pdb=" O ALA N 59 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LEU N 64 " --> pdb=" O ASP N 60 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU N 67 " --> pdb=" O TYR N 63 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LYS N 71 " --> pdb=" O LEU N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 85 removed outlier: 3.807A pdb=" N MET N 85 " --> pdb=" O LYS N 82 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 105 removed outlier: 3.864A pdb=" N ARG N 105 " --> pdb=" O VAL N 101 " (cutoff:3.500A) Processing helix chain 'N' and resid 179 through 183 removed outlier: 3.543A pdb=" N ARG N 182 " --> pdb=" O GLY N 179 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR N 183 " --> pdb=" O TYR N 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 179 through 183' Processing helix chain 'N' and resid 184 through 193 removed outlier: 3.645A pdb=" N LEU N 188 " --> pdb=" O PHE N 184 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASP N 191 " --> pdb=" O THR N 187 " (cutoff:3.500A) Processing helix chain 'N' and resid 198 through 211 removed outlier: 3.536A pdb=" N ARG N 211 " --> pdb=" O ASN N 207 " (cutoff:3.500A) Processing helix chain 'N' and resid 211 through 216 removed outlier: 3.807A pdb=" N PHE N 215 " --> pdb=" O ARG N 211 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG N 216 " --> pdb=" O ILE N 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 211 through 216' Processing helix chain 'P' and resid 19 through 30 removed outlier: 3.503A pdb=" N GLU P 23 " --> pdb=" O LEU P 19 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG P 28 " --> pdb=" O TYR P 24 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL P 29 " --> pdb=" O ALA P 25 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 83 Processing helix chain 'P' and resid 84 through 101 removed outlier: 3.792A pdb=" N SER P 98 " --> pdb=" O ALA P 94 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN P 100 " --> pdb=" O ARG P 96 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 124 removed outlier: 3.817A pdb=" N ILE P 113 " --> pdb=" O GLU P 109 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE P 121 " --> pdb=" O ILE P 117 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THR P 122 " --> pdb=" O VAL P 118 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN P 123 " --> pdb=" O GLN P 119 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR P 124 " --> pdb=" O GLU P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 166 through 177 removed outlier: 4.233A pdb=" N SER P 172 " --> pdb=" O GLN P 168 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE P 173 " --> pdb=" O ASN P 169 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU P 174 " --> pdb=" O ASN P 170 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS P 176 " --> pdb=" O SER P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 183 through 197 removed outlier: 4.367A pdb=" N HIS P 189 " --> pdb=" O GLU P 185 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR P 190 " --> pdb=" O ASP P 186 " (cutoff:3.500A) Processing helix chain 'P' and resid 223 through 229 removed outlier: 3.705A pdb=" N ASP P 229 " --> pdb=" O ASN P 225 " (cutoff:3.500A) Processing helix chain 'R' and resid 19 through 26 removed outlier: 3.564A pdb=" N VAL R 26 " --> pdb=" O ALA R 22 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 60 Processing helix chain 'R' and resid 78 through 99 removed outlier: 4.629A pdb=" N VAL R 82 " --> pdb=" O ALA R 78 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU R 83 " --> pdb=" O ASP R 79 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLU R 90 " --> pdb=" O LYS R 86 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR R 95 " --> pdb=" O CYS R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 120 removed outlier: 3.562A pdb=" N LYS R 113 " --> pdb=" O LYS R 109 " (cutoff:3.500A) Processing helix chain 'R' and resid 164 through 175 removed outlier: 3.898A pdb=" N VAL R 168 " --> pdb=" O ASN R 164 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE R 171 " --> pdb=" O ILE R 167 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS R 174 " --> pdb=" O GLU R 170 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN R 175 " --> pdb=" O PHE R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 190 Processing helix chain 'R' and resid 196 through 200 removed outlier: 3.779A pdb=" N LEU R 199 " --> pdb=" O VAL R 196 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N SER R 200 " --> pdb=" O VAL R 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 196 through 200' Processing helix chain 'R' and resid 218 through 227 removed outlier: 3.626A pdb=" N SER R 224 " --> pdb=" O GLN R 220 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 233 removed outlier: 3.976A pdb=" N ARG R 233 " --> pdb=" O ASP R 230 " (cutoff:3.500A) Processing helix chain 'S' and resid 22 through 29 removed outlier: 3.938A pdb=" N ALA S 27 " --> pdb=" O GLN S 23 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLY S 29 " --> pdb=" O GLU S 25 " (cutoff:3.500A) Processing helix chain 'S' and resid 30 through 33 removed outlier: 3.657A pdb=" N LEU S 33 " --> pdb=" O ALA S 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 30 through 33' Processing helix chain 'S' and resid 81 through 103 removed outlier: 3.632A pdb=" N ARG S 86 " --> pdb=" O MET S 82 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N THR S 87 " --> pdb=" O ALA S 83 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN S 97 " --> pdb=" O ARG S 93 " (cutoff:3.500A) Processing helix chain 'S' and resid 108 through 119 removed outlier: 3.683A pdb=" N GLU S 114 " --> pdb=" O LYS S 110 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU S 115 " --> pdb=" O SER S 111 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU S 119 " --> pdb=" O LEU S 115 " (cutoff:3.500A) Processing helix chain 'S' and resid 175 through 185 removed outlier: 3.662A pdb=" N ALA S 179 " --> pdb=" O ALA S 175 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU S 181 " --> pdb=" O GLU S 177 " (cutoff:3.500A) Processing helix chain 'S' and resid 192 through 207 removed outlier: 3.766A pdb=" N ILE S 198 " --> pdb=" O GLU S 194 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU S 201 " --> pdb=" O GLU S 197 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL S 203 " --> pdb=" O LEU S 199 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU S 204 " --> pdb=" O ALA S 200 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL S 207 " --> pdb=" O VAL S 203 " (cutoff:3.500A) Processing helix chain 'S' and resid 233 through 242 removed outlier: 3.542A pdb=" N SER S 238 " --> pdb=" O THR S 234 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG S 239 " --> pdb=" O ASP S 235 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE S 240 " --> pdb=" O ASP S 236 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP S 242 " --> pdb=" O SER S 238 " (cutoff:3.500A) Processing helix chain 'V' and resid 51 through 71 removed outlier: 3.541A pdb=" N MET V 66 " --> pdb=" O TYR V 62 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLU V 69 " --> pdb=" O SER V 65 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN V 70 " --> pdb=" O MET V 66 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG V 71 " --> pdb=" O LYS V 67 " (cutoff:3.500A) Processing helix chain 'V' and resid 77 through 87 removed outlier: 3.693A pdb=" N THR V 81 " --> pdb=" O HIS V 77 " (cutoff:3.500A) Processing helix chain 'V' and resid 184 through 188 removed outlier: 3.836A pdb=" N ILE V 187 " --> pdb=" O SER V 184 " (cutoff:3.500A) Processing helix chain 'V' and resid 189 through 197 removed outlier: 3.646A pdb=" N GLN V 194 " --> pdb=" O GLN V 190 " (cutoff:3.500A) Processing helix chain 'V' and resid 202 through 220 removed outlier: 3.816A pdb=" N ASN V 212 " --> pdb=" O ASN V 208 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN V 220 " --> pdb=" O TYR V 216 " (cutoff:3.500A) Processing helix chain 'W' and resid 48 through 70 removed outlier: 3.569A pdb=" N LEU W 52 " --> pdb=" O VAL W 48 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU W 53 " --> pdb=" O ALA W 49 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N HIS W 54 " --> pdb=" O GLY W 50 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR W 55 " --> pdb=" O ASP W 51 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TRP W 58 " --> pdb=" O HIS W 54 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU W 59 " --> pdb=" O THR W 55 " (cutoff:3.500A) Processing helix chain 'W' and resid 75 through 88 removed outlier: 4.007A pdb=" N CYS W 79 " --> pdb=" O ARG W 75 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL W 80 " --> pdb=" O VAL W 76 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER W 81 " --> pdb=" O SER W 77 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR W 84 " --> pdb=" O VAL W 80 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N GLN W 85 " --> pdb=" O SER W 81 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU W 86 " --> pdb=" O ARG W 82 " (cutoff:3.500A) Processing helix chain 'W' and resid 130 through 141 removed outlier: 3.808A pdb=" N VAL W 137 " --> pdb=" O ASN W 133 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS W 141 " --> pdb=" O VAL W 137 " (cutoff:3.500A) Processing helix chain 'W' and resid 147 through 165 removed outlier: 3.896A pdb=" N LEU W 154 " --> pdb=" O GLU W 150 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY W 162 " --> pdb=" O ALA W 158 " (cutoff:3.500A) Processing helix chain 'Y' and resid 50 through 72 removed outlier: 3.816A pdb=" N GLY Y 58 " --> pdb=" O ARG Y 54 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN Y 64 " --> pdb=" O PHE Y 60 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL Y 65 " --> pdb=" O ILE Y 61 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR Y 68 " --> pdb=" O ASN Y 64 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN Y 72 " --> pdb=" O TYR Y 68 " (cutoff:3.500A) Processing helix chain 'Y' and resid 77 through 92 removed outlier: 3.571A pdb=" N PHE Y 83 " --> pdb=" O LYS Y 79 " (cutoff:3.500A) Processing helix chain 'Y' and resid 135 through 140 Processing helix chain 'Y' and resid 141 through 146 removed outlier: 3.699A pdb=" N LYS Y 145 " --> pdb=" O ALA Y 141 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR Y 146 " --> pdb=" O ILE Y 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 141 through 146' Processing helix chain 'Y' and resid 152 through 171 removed outlier: 3.723A pdb=" N ALA Y 156 " --> pdb=" O THR Y 152 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU Y 157 " --> pdb=" O VAL Y 153 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP Y 158 " --> pdb=" O ASP Y 154 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU Y 165 " --> pdb=" O LYS Y 161 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLU Y 166 " --> pdb=" O LEU Y 162 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE Y 171 " --> pdb=" O LEU Y 167 " (cutoff:3.500A) Processing helix chain 'a' and resid 86 through 108 removed outlier: 3.949A pdb=" N THR a 91 " --> pdb=" O SER a 87 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU a 92 " --> pdb=" O ASP a 88 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE a 103 " --> pdb=" O LYS a 99 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU a 106 " --> pdb=" O LEU a 102 " (cutoff:3.500A) Processing helix chain 'a' and resid 112 through 126 removed outlier: 3.503A pdb=" N ARG a 118 " --> pdb=" O HIS a 114 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL a 122 " --> pdb=" O ARG a 118 " (cutoff:3.500A) Processing helix chain 'a' and resid 169 through 179 Proline residue: a 175 - end of helix Processing helix chain 'a' and resid 194 through 213 removed outlier: 3.736A pdb=" N ASN a 200 " --> pdb=" O GLY a 196 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU a 211 " --> pdb=" O THR a 207 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG a 212 " --> pdb=" O SER a 208 " (cutoff:3.500A) Processing helix chain 'c' and resid 19 through 39 Processing helix chain 'c' and resid 39 through 52 removed outlier: 3.566A pdb=" N LEU c 51 " --> pdb=" O PHE c 47 " (cutoff:3.500A) Processing helix chain 'c' and resid 135 through 166 removed outlier: 3.805A pdb=" N ASN c 158 " --> pdb=" O GLU c 154 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE c 159 " --> pdb=" O ILE c 155 " (cutoff:3.500A) Processing helix chain 'c' and resid 175 through 219 removed outlier: 3.802A pdb=" N GLY c 179 " --> pdb=" O ASN c 175 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU c 198 " --> pdb=" O SER c 194 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N TYR c 199 " --> pdb=" O ALA c 195 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASP c 200 " --> pdb=" O PHE c 196 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL c 203 " --> pdb=" O TYR c 199 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR c 206 " --> pdb=" O ILE c 202 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE c 212 " --> pdb=" O GLU c 208 " (cutoff:3.500A) Processing helix chain 'c' and resid 222 through 261 removed outlier: 4.350A pdb=" N GLN c 226 " --> pdb=" O VAL c 222 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN c 261 " --> pdb=" O LEU c 257 " (cutoff:3.500A) Processing helix chain 'c' and resid 261 through 267 Processing helix chain 'd' and resid 19 through 39 Processing helix chain 'd' and resid 39 through 52 removed outlier: 3.603A pdb=" N ARG d 44 " --> pdb=" O ARG d 40 " (cutoff:3.500A) Processing helix chain 'd' and resid 135 through 166 removed outlier: 3.761A pdb=" N GLU d 141 " --> pdb=" O GLN d 137 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN d 158 " --> pdb=" O GLU d 154 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE d 159 " --> pdb=" O ILE d 155 " (cutoff:3.500A) Processing helix chain 'd' and resid 175 through 219 removed outlier: 3.964A pdb=" N GLY d 179 " --> pdb=" O ASN d 175 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU d 198 " --> pdb=" O SER d 194 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TYR d 199 " --> pdb=" O ALA d 195 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP d 200 " --> pdb=" O PHE d 196 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR d 206 " --> pdb=" O ILE d 202 " (cutoff:3.500A) Processing helix chain 'd' and resid 222 through 261 removed outlier: 4.154A pdb=" N GLN d 226 " --> pdb=" O VAL d 222 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU d 234 " --> pdb=" O ARG d 230 " (cutoff:3.500A) Processing helix chain 'd' and resid 261 through 267 Processing helix chain 'e' and resid 19 through 39 removed outlier: 3.677A pdb=" N THR e 30 " --> pdb=" O LYS e 26 " (cutoff:3.500A) Processing helix chain 'e' and resid 39 through 52 Processing helix chain 'e' and resid 135 through 166 removed outlier: 3.507A pdb=" N LYS e 144 " --> pdb=" O LEU e 140 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN e 158 " --> pdb=" O GLU e 154 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE e 159 " --> pdb=" O ILE e 155 " (cutoff:3.500A) Processing helix chain 'e' and resid 175 through 219 removed outlier: 3.701A pdb=" N GLY e 179 " --> pdb=" O ASN e 175 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU e 198 " --> pdb=" O SER e 194 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR e 199 " --> pdb=" O ALA e 195 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASP e 200 " --> pdb=" O PHE e 196 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL e 203 " --> pdb=" O TYR e 199 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR e 206 " --> pdb=" O ILE e 202 " (cutoff:3.500A) Processing helix chain 'e' and resid 222 through 261 removed outlier: 4.128A pdb=" N GLN e 226 " --> pdb=" O VAL e 222 " (cutoff:3.500A) Processing helix chain 'e' and resid 261 through 267 Processing helix chain 'f' and resid 19 through 39 Processing helix chain 'f' and resid 39 through 52 Processing helix chain 'f' and resid 135 through 166 removed outlier: 3.620A pdb=" N GLU f 141 " --> pdb=" O GLN f 137 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN f 158 " --> pdb=" O GLU f 154 " (cutoff:3.500A) Processing helix chain 'f' and resid 175 through 219 removed outlier: 3.684A pdb=" N GLY f 179 " --> pdb=" O ASN f 175 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU f 198 " --> pdb=" O SER f 194 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TYR f 199 " --> pdb=" O ALA f 195 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASP f 200 " --> pdb=" O PHE f 196 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL f 203 " --> pdb=" O TYR f 199 " (cutoff:3.500A) Processing helix chain 'f' and resid 222 through 261 removed outlier: 4.181A pdb=" N GLN f 226 " --> pdb=" O VAL f 222 " (cutoff:3.500A) Processing helix chain 'f' and resid 261 through 267 Processing helix chain 'g' and resid 19 through 39 Processing helix chain 'g' and resid 39 through 52 Processing helix chain 'g' and resid 135 through 166 removed outlier: 3.593A pdb=" N GLU g 141 " --> pdb=" O GLN g 137 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS g 144 " --> pdb=" O LEU g 140 " (cutoff:3.500A) Processing helix chain 'g' and resid 175 through 219 removed outlier: 4.245A pdb=" N LEU g 198 " --> pdb=" O SER g 194 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N TYR g 199 " --> pdb=" O ALA g 195 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASP g 200 " --> pdb=" O PHE g 196 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL g 203 " --> pdb=" O TYR g 199 " (cutoff:3.500A) Processing helix chain 'g' and resid 223 through 261 Processing helix chain 'g' and resid 261 through 267 Processing helix chain 'h' and resid 19 through 39 Processing helix chain 'h' and resid 39 through 52 removed outlier: 3.522A pdb=" N ARG h 44 " --> pdb=" O ARG h 40 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU h 51 " --> pdb=" O PHE h 47 " (cutoff:3.500A) Processing helix chain 'h' and resid 135 through 166 removed outlier: 3.604A pdb=" N GLU h 141 " --> pdb=" O GLN h 137 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS h 144 " --> pdb=" O LEU h 140 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN h 158 " --> pdb=" O GLU h 154 " (cutoff:3.500A) Processing helix chain 'h' and resid 175 through 219 removed outlier: 3.865A pdb=" N GLY h 179 " --> pdb=" O ASN h 175 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU h 198 " --> pdb=" O SER h 194 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TYR h 199 " --> pdb=" O ALA h 195 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP h 200 " --> pdb=" O PHE h 196 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL h 203 " --> pdb=" O TYR h 199 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR h 206 " --> pdb=" O ILE h 202 " (cutoff:3.500A) Processing helix chain 'h' and resid 223 through 261 Processing helix chain 'h' and resid 261 through 267 removed outlier: 3.583A pdb=" N VAL h 266 " --> pdb=" O TRP h 262 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS h 267 " --> pdb=" O GLU h 263 " (cutoff:3.500A) Processing helix chain 'i' and resid 19 through 39 removed outlier: 3.628A pdb=" N THR i 30 " --> pdb=" O LYS i 26 " (cutoff:3.500A) Processing helix chain 'i' and resid 39 through 52 removed outlier: 3.680A pdb=" N LEU i 51 " --> pdb=" O PHE i 47 " (cutoff:3.500A) Processing helix chain 'i' and resid 135 through 166 removed outlier: 4.002A pdb=" N GLU i 141 " --> pdb=" O GLN i 137 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN i 158 " --> pdb=" O GLU i 154 " (cutoff:3.500A) Processing helix chain 'i' and resid 175 through 197 removed outlier: 3.991A pdb=" N GLY i 179 " --> pdb=" O ASN i 175 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE i 180 " --> pdb=" O PHE i 176 " (cutoff:3.500A) Processing helix chain 'i' and resid 197 through 219 removed outlier: 3.651A pdb=" N VAL i 203 " --> pdb=" O TYR i 199 " (cutoff:3.500A) Processing helix chain 'i' and resid 223 through 261 Processing helix chain 'i' and resid 261 through 267 removed outlier: 3.736A pdb=" N VAL i 266 " --> pdb=" O TRP i 262 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS i 267 " --> pdb=" O GLU i 263 " (cutoff:3.500A) Processing helix chain 'j' and resid 19 through 39 Processing helix chain 'j' and resid 39 through 52 Processing helix chain 'j' and resid 135 through 166 removed outlier: 3.620A pdb=" N GLU j 141 " --> pdb=" O GLN j 137 " (cutoff:3.500A) Processing helix chain 'j' and resid 175 through 219 removed outlier: 3.684A pdb=" N GLY j 179 " --> pdb=" O ASN j 175 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU j 198 " --> pdb=" O SER j 194 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TYR j 199 " --> pdb=" O ALA j 195 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASP j 200 " --> pdb=" O PHE j 196 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL j 203 " --> pdb=" O TYR j 199 " (cutoff:3.500A) Processing helix chain 'j' and resid 222 through 261 removed outlier: 4.181A pdb=" N GLN j 226 " --> pdb=" O VAL j 222 " (cutoff:3.500A) Processing helix chain 'j' and resid 261 through 267 Processing helix chain 'k' and resid 19 through 39 Processing helix chain 'k' and resid 39 through 52 Processing helix chain 'k' and resid 135 through 166 removed outlier: 3.593A pdb=" N GLU k 141 " --> pdb=" O GLN k 137 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS k 144 " --> pdb=" O LEU k 140 " (cutoff:3.500A) Processing helix chain 'k' and resid 175 through 219 removed outlier: 4.246A pdb=" N LEU k 198 " --> pdb=" O SER k 194 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N TYR k 199 " --> pdb=" O ALA k 195 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASP k 200 " --> pdb=" O PHE k 196 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL k 203 " --> pdb=" O TYR k 199 " (cutoff:3.500A) Processing helix chain 'k' and resid 223 through 261 Processing helix chain 'k' and resid 261 through 267 Processing helix chain 'l' and resid 19 through 39 Processing helix chain 'l' and resid 39 through 52 removed outlier: 3.521A pdb=" N ARG l 44 " --> pdb=" O ARG l 40 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU l 51 " --> pdb=" O PHE l 47 " (cutoff:3.500A) Processing helix chain 'l' and resid 135 through 166 removed outlier: 3.605A pdb=" N GLU l 141 " --> pdb=" O GLN l 137 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS l 144 " --> pdb=" O LEU l 140 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN l 158 " --> pdb=" O GLU l 154 " (cutoff:3.500A) Processing helix chain 'l' and resid 175 through 219 removed outlier: 3.866A pdb=" N GLY l 179 " --> pdb=" O ASN l 175 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU l 198 " --> pdb=" O SER l 194 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TYR l 199 " --> pdb=" O ALA l 195 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP l 200 " --> pdb=" O PHE l 196 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL l 203 " --> pdb=" O TYR l 199 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR l 206 " --> pdb=" O ILE l 202 " (cutoff:3.500A) Processing helix chain 'l' and resid 223 through 261 Processing helix chain 'l' and resid 261 through 267 removed outlier: 3.583A pdb=" N VAL l 266 " --> pdb=" O TRP l 262 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS l 267 " --> pdb=" O GLU l 263 " (cutoff:3.500A) Processing helix chain 'm' and resid 19 through 39 Processing helix chain 'm' and resid 39 through 52 removed outlier: 3.566A pdb=" N LEU m 51 " --> pdb=" O PHE m 47 " (cutoff:3.500A) Processing helix chain 'm' and resid 135 through 166 removed outlier: 3.804A pdb=" N ASN m 158 " --> pdb=" O GLU m 154 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE m 159 " --> pdb=" O ILE m 155 " (cutoff:3.500A) Processing helix chain 'm' and resid 175 through 219 removed outlier: 3.801A pdb=" N GLY m 179 " --> pdb=" O ASN m 175 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU m 198 " --> pdb=" O SER m 194 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N TYR m 199 " --> pdb=" O ALA m 195 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP m 200 " --> pdb=" O PHE m 196 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL m 203 " --> pdb=" O TYR m 199 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR m 206 " --> pdb=" O ILE m 202 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE m 212 " --> pdb=" O GLU m 208 " (cutoff:3.500A) Processing helix chain 'm' and resid 222 through 261 removed outlier: 4.349A pdb=" N GLN m 226 " --> pdb=" O VAL m 222 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN m 261 " --> pdb=" O LEU m 257 " (cutoff:3.500A) Processing helix chain 'm' and resid 261 through 267 Processing helix chain 'n' and resid 19 through 39 removed outlier: 3.627A pdb=" N THR n 30 " --> pdb=" O LYS n 26 " (cutoff:3.500A) Processing helix chain 'n' and resid 39 through 52 removed outlier: 3.681A pdb=" N LEU n 51 " --> pdb=" O PHE n 47 " (cutoff:3.500A) Processing helix chain 'n' and resid 135 through 166 removed outlier: 4.002A pdb=" N GLU n 141 " --> pdb=" O GLN n 137 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN n 158 " --> pdb=" O GLU n 154 " (cutoff:3.500A) Processing helix chain 'n' and resid 175 through 197 removed outlier: 3.991A pdb=" N GLY n 179 " --> pdb=" O ASN n 175 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE n 180 " --> pdb=" O PHE n 176 " (cutoff:3.500A) Processing helix chain 'n' and resid 197 through 219 removed outlier: 3.651A pdb=" N VAL n 203 " --> pdb=" O TYR n 199 " (cutoff:3.500A) Processing helix chain 'n' and resid 223 through 261 Processing helix chain 'n' and resid 261 through 267 removed outlier: 3.737A pdb=" N VAL n 266 " --> pdb=" O TRP n 262 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS n 267 " --> pdb=" O GLU n 263 " (cutoff:3.500A) Processing helix chain 'o' and resid 19 through 39 Processing helix chain 'o' and resid 39 through 52 removed outlier: 3.604A pdb=" N ARG o 44 " --> pdb=" O ARG o 40 " (cutoff:3.500A) Processing helix chain 'o' and resid 135 through 166 removed outlier: 3.760A pdb=" N GLU o 141 " --> pdb=" O GLN o 137 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN o 158 " --> pdb=" O GLU o 154 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE o 159 " --> pdb=" O ILE o 155 " (cutoff:3.500A) Processing helix chain 'o' and resid 175 through 219 removed outlier: 3.964A pdb=" N GLY o 179 " --> pdb=" O ASN o 175 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU o 198 " --> pdb=" O SER o 194 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TYR o 199 " --> pdb=" O ALA o 195 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASP o 200 " --> pdb=" O PHE o 196 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR o 206 " --> pdb=" O ILE o 202 " (cutoff:3.500A) Processing helix chain 'o' and resid 222 through 261 removed outlier: 4.154A pdb=" N GLN o 226 " --> pdb=" O VAL o 222 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU o 234 " --> pdb=" O ARG o 230 " (cutoff:3.500A) Processing helix chain 'o' and resid 261 through 267 Processing helix chain 'p' and resid 19 through 39 removed outlier: 3.677A pdb=" N THR p 30 " --> pdb=" O LYS p 26 " (cutoff:3.500A) Processing helix chain 'p' and resid 39 through 52 Processing helix chain 'p' and resid 135 through 166 removed outlier: 3.507A pdb=" N LYS p 144 " --> pdb=" O LEU p 140 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN p 158 " --> pdb=" O GLU p 154 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE p 159 " --> pdb=" O ILE p 155 " (cutoff:3.500A) Processing helix chain 'p' and resid 175 through 219 removed outlier: 3.701A pdb=" N GLY p 179 " --> pdb=" O ASN p 175 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU p 198 " --> pdb=" O SER p 194 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR p 199 " --> pdb=" O ALA p 195 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ASP p 200 " --> pdb=" O PHE p 196 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL p 203 " --> pdb=" O TYR p 199 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR p 206 " --> pdb=" O ILE p 202 " (cutoff:3.500A) Processing helix chain 'p' and resid 222 through 261 removed outlier: 4.129A pdb=" N GLN p 226 " --> pdb=" O VAL p 222 " (cutoff:3.500A) Processing helix chain 'p' and resid 261 through 267 Processing helix chain 'b' and resid 58 through 77 removed outlier: 4.099A pdb=" N GLN b 62 " --> pdb=" O LEU b 58 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N TYR b 63 " --> pdb=" O ALA b 59 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LEU b 64 " --> pdb=" O ASP b 60 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LEU b 67 " --> pdb=" O TYR b 63 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LYS b 71 " --> pdb=" O LEU b 67 " (cutoff:3.500A) Processing helix chain 'b' and resid 81 through 85 removed outlier: 3.807A pdb=" N MET b 85 " --> pdb=" O LYS b 82 " (cutoff:3.500A) Processing helix chain 'b' and resid 87 through 105 removed outlier: 3.863A pdb=" N ARG b 105 " --> pdb=" O VAL b 101 " (cutoff:3.500A) Processing helix chain 'b' and resid 179 through 183 removed outlier: 3.542A pdb=" N ARG b 182 " --> pdb=" O GLY b 179 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR b 183 " --> pdb=" O TYR b 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 179 through 183' Processing helix chain 'b' and resid 184 through 193 removed outlier: 3.645A pdb=" N LEU b 188 " --> pdb=" O PHE b 184 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASP b 191 " --> pdb=" O THR b 187 " (cutoff:3.500A) Processing helix chain 'b' and resid 198 through 211 removed outlier: 3.535A pdb=" N ARG b 211 " --> pdb=" O ASN b 207 " (cutoff:3.500A) Processing helix chain 'b' and resid 211 through 216 removed outlier: 3.806A pdb=" N PHE b 215 " --> pdb=" O ARG b 211 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG b 216 " --> pdb=" O ILE b 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 211 through 216' Processing helix chain 'X' and resid 58 through 78 removed outlier: 3.652A pdb=" N GLN X 63 " --> pdb=" O ALA X 59 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N THR X 64 " --> pdb=" O THR X 60 " (cutoff:3.500A) Processing helix chain 'X' and resid 85 through 100 removed outlier: 3.563A pdb=" N ASN X 91 " --> pdb=" O GLU X 87 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET X 92 " --> pdb=" O CYS X 88 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER X 94 " --> pdb=" O ALA X 90 " (cutoff:3.500A) Processing helix chain 'X' and resid 156 through 161 removed outlier: 4.271A pdb=" N GLY X 161 " --> pdb=" O GLU X 157 " (cutoff:3.500A) Processing helix chain 'X' and resid 172 through 189 removed outlier: 3.699A pdb=" N PHE X 177 " --> pdb=" O GLU X 173 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA X 187 " --> pdb=" O CYS X 183 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP X 189 " --> pdb=" O LEU X 185 " (cutoff:3.500A) Processing helix chain 'Q' and resid 19 through 28 Processing helix chain 'Q' and resid 29 through 31 No H-bonds generated for 'chain 'Q' and resid 29 through 31' Processing helix chain 'Q' and resid 79 through 102 removed outlier: 3.811A pdb=" N ASN Q 84 " --> pdb=" O ASN Q 80 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE Q 85 " --> pdb=" O ALA Q 81 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU Q 86 " --> pdb=" O ASP Q 82 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU Q 92 " --> pdb=" O ASN Q 88 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU Q 98 " --> pdb=" O ALA Q 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 120 removed outlier: 4.042A pdb=" N VAL Q 112 " --> pdb=" O SER Q 108 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN Q 113 " --> pdb=" O GLN Q 109 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE Q 117 " --> pdb=" O GLN Q 113 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS Q 118 " --> pdb=" O ILE Q 114 " (cutoff:3.500A) Processing helix chain 'Q' and resid 167 through 178 removed outlier: 3.532A pdb=" N SER Q 173 " --> pdb=" O LEU Q 169 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL Q 174 " --> pdb=" O THR Q 170 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU Q 175 " --> pdb=" O ALA Q 171 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN Q 177 " --> pdb=" O SER Q 173 " (cutoff:3.500A) Processing helix chain 'Q' and resid 184 through 198 removed outlier: 3.867A pdb=" N THR Q 195 " --> pdb=" O LEU Q 191 " (cutoff:3.500A) Processing helix chain 'Q' and resid 199 through 201 No H-bonds generated for 'chain 'Q' and resid 199 through 201' Processing helix chain 'Q' and resid 229 through 241 removed outlier: 4.109A pdb=" N GLU Q 233 " --> pdb=" O GLU Q 229 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU Q 234 " --> pdb=" O LYS Q 230 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR Q 239 " --> pdb=" O LEU Q 235 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR Q 240 " --> pdb=" O ILE Q 236 " (cutoff:3.500A) Processing helix chain 'T' and resid 19 through 29 removed outlier: 3.788A pdb=" N ALA T 25 " --> pdb=" O GLN T 21 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU T 27 " --> pdb=" O GLU T 23 " (cutoff:3.500A) Processing helix chain 'T' and resid 30 through 32 No H-bonds generated for 'chain 'T' and resid 30 through 32' Processing helix chain 'T' and resid 77 through 99 removed outlier: 3.530A pdb=" N LYS T 82 " --> pdb=" O THR T 78 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL T 83 " --> pdb=" O SER T 79 " (cutoff:3.500A) Processing helix chain 'T' and resid 104 through 119 removed outlier: 3.963A pdb=" N SER T 111 " --> pdb=" O SER T 107 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN T 119 " --> pdb=" O LYS T 115 " (cutoff:3.500A) Processing helix chain 'T' and resid 163 through 173 removed outlier: 3.796A pdb=" N TYR T 170 " --> pdb=" O ALA T 166 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS T 173 " --> pdb=" O THR T 169 " (cutoff:3.500A) Processing helix chain 'T' and resid 176 through 180 Processing helix chain 'T' and resid 182 through 196 removed outlier: 3.795A pdb=" N LEU T 194 " --> pdb=" O CYS T 190 " (cutoff:3.500A) Processing helix chain 'T' and resid 226 through 231 removed outlier: 3.582A pdb=" N GLU T 230 " --> pdb=" O LEU T 226 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N TYR T 231 " --> pdb=" O GLN T 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 226 through 231' Processing helix chain 'O' and resid 22 through 34 removed outlier: 3.668A pdb=" N VAL O 32 " --> pdb=" O ALA O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 112 removed outlier: 4.232A pdb=" N GLU O 103 " --> pdb=" O LYS O 99 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU O 106 " --> pdb=" O SER O 102 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU O 108 " --> pdb=" O ALA O 104 " (cutoff:3.500A) Processing helix chain 'O' and resid 116 through 134 removed outlier: 3.526A pdb=" N CYS O 121 " --> pdb=" O ALA O 117 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS O 127 " --> pdb=" O ASN O 123 " (cutoff:3.500A) Processing helix chain 'O' and resid 181 through 191 removed outlier: 4.169A pdb=" N ARG O 187 " --> pdb=" O SER O 183 " (cutoff:3.500A) Processing helix chain 'O' and resid 209 through 220 removed outlier: 4.518A pdb=" N ALA O 215 " --> pdb=" O LEU O 211 " (cutoff:3.500A) Processing helix chain 'O' and resid 225 through 229 removed outlier: 3.761A pdb=" N ILE O 229 " --> pdb=" O ALA O 226 " (cutoff:3.500A) Processing helix chain 'O' and resid 245 through 254 removed outlier: 3.621A pdb=" N THR O 254 " --> pdb=" O ASP O 250 " (cutoff:3.500A) Processing helix chain 'O' and resid 255 through 257 No H-bonds generated for 'chain 'O' and resid 255 through 257' Processing helix chain 'Z' and resid 49 through 70 removed outlier: 3.842A pdb=" N TYR Z 54 " --> pdb=" O ALA Z 50 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N TRP Z 55 " --> pdb=" O ASP Z 51 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY Z 60 " --> pdb=" O GLU Z 56 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS Z 61 " --> pdb=" O LYS Z 57 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN Z 70 " --> pdb=" O TYR Z 66 " (cutoff:3.500A) Processing helix chain 'Z' and resid 75 through 86 removed outlier: 3.876A pdb=" N LEU Z 83 " --> pdb=" O ALA Z 79 " (cutoff:3.500A) Processing helix chain 'Z' and resid 87 through 91 Processing helix chain 'Z' and resid 131 through 142 removed outlier: 4.285A pdb=" N ALA Z 135 " --> pdb=" O GLY Z 131 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER Z 137 " --> pdb=" O THR Z 133 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU Z 139 " --> pdb=" O ALA Z 135 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASP Z 140 " --> pdb=" O TYR Z 136 " (cutoff:3.500A) Processing helix chain 'Z' and resid 148 through 165 removed outlier: 4.708A pdb=" N GLU Z 154 " --> pdb=" O ASP Z 150 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU Z 155 " --> pdb=" O GLN Z 151 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA Z 163 " --> pdb=" O ALA Z 159 " (cutoff:3.500A) Processing helix chain 'U' and resid 25 through 32 removed outlier: 3.793A pdb=" N LYS U 29 " --> pdb=" O GLU U 25 " (cutoff:3.500A) Processing helix chain 'U' and resid 83 through 106 removed outlier: 3.737A pdb=" N ARG U 88 " --> pdb=" O ASP U 84 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASN U 89 " --> pdb=" O GLY U 85 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE U 90 " --> pdb=" O ASP U 86 " (cutoff:3.500A) Processing helix chain 'U' and resid 110 through 125 removed outlier: 4.369A pdb=" N ASN U 116 " --> pdb=" O HIS U 112 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG U 117 " --> pdb=" O ILE U 113 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU U 120 " --> pdb=" O ASN U 116 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR U 125 " --> pdb=" O TYR U 121 " (cutoff:3.500A) Processing helix chain 'U' and resid 171 through 180 removed outlier: 3.859A pdb=" N LYS U 176 " --> pdb=" O LYS U 172 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N THR U 177 " --> pdb=" O GLU U 173 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU U 178 " --> pdb=" O MET U 174 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU U 180 " --> pdb=" O LYS U 176 " (cutoff:3.500A) Processing helix chain 'U' and resid 183 through 187 removed outlier: 3.931A pdb=" N ASP U 186 " --> pdb=" O ASP U 183 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE U 187 " --> pdb=" O TYR U 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 183 through 187' Processing helix chain 'U' and resid 191 through 203 removed outlier: 3.516A pdb=" N LYS U 198 " --> pdb=" O GLU U 194 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU U 201 " --> pdb=" O TYR U 197 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR U 202 " --> pdb=" O LYS U 198 " (cutoff:3.500A) Processing helix chain 'U' and resid 233 through 238 Processing sheet with id=AA1, first strand: chain 'A' and resid 171 through 174 Processing sheet with id=AA2, first strand: chain 'A' and resid 75 through 77 removed outlier: 3.733A pdb=" N MET A 145 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER A 143 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 77 removed outlier: 3.733A pdb=" N MET A 145 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A 144 " --> pdb=" O PHE A 160 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 160 through 162 removed outlier: 3.534A pdb=" N LYS B 220 " --> pdb=" O VAL B 212 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 65 through 67 removed outlier: 4.430A pdb=" N LEU B 146 " --> pdb=" O TRP B 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 36 through 38 removed outlier: 3.556A pdb=" N TYR C 214 " --> pdb=" O GLN C 224 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 72 through 78 Processing sheet with id=AA8, first strand: chain 'D' and resid 158 through 161 removed outlier: 3.556A pdb=" N LEU D 209 " --> pdb=" O ALA D 41 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA D 207 " --> pdb=" O LEU D 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 63 through 64 Processing sheet with id=AB1, first strand: chain 'D' and resid 74 through 75 Processing sheet with id=AB2, first strand: chain 'E' and resid 169 through 172 removed outlier: 3.667A pdb=" N CYS E 220 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 74 through 75 Processing sheet with id=AB4, first strand: chain 'F' and resid 35 through 39 removed outlier: 7.480A pdb=" N LEU F 211 " --> pdb=" O GLU F 222 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N GLU F 222 " --> pdb=" O LEU F 211 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL F 213 " --> pdb=" O TRP F 220 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N TRP F 220 " --> pdb=" O VAL F 213 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 70 through 72 Processing sheet with id=AB6, first strand: chain 'G' and resid 46 through 51 removed outlier: 3.529A pdb=" N ILE G 47 " --> pdb=" O LEU G 40 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR G 36 " --> pdb=" O ILE G 51 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 69 through 73 removed outlier: 7.164A pdb=" N ILE G 76 " --> pdb=" O VAL G 72 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE G 139 " --> pdb=" O THR G 79 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE G 151 " --> pdb=" O TYR G 163 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 181 through 182 Processing sheet with id=AB9, first strand: chain 'H' and resid 34 through 36 removed outlier: 3.510A pdb=" N GLY H 154 " --> pdb=" O TYR H 42 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 124 through 127 Processing sheet with id=AC2, first strand: chain 'I' and resid 20 through 21 removed outlier: 6.692A pdb=" N ALA I 20 " --> pdb=" O ALA I 27 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 41 through 47 removed outlier: 4.152A pdb=" N TRP I 42 " --> pdb=" O GLY I 101 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS I 120 " --> pdb=" O GLY I 112 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 212 through 213 removed outlier: 3.912A pdb=" N ILE I 212 " --> pdb=" O LYS J 212 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ALA J 198 " --> pdb=" O LEU J 213 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N CYS J 25 " --> pdb=" O GLU J 199 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 44 through 46 removed outlier: 3.609A pdb=" N LEU J 134 " --> pdb=" O THR J 146 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 4 through 8 Processing sheet with id=AC7, first strand: chain 'K' and resid 20 through 22 removed outlier: 7.181A pdb=" N SER K 21 " --> pdb=" O LYS K 29 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 36 through 39 removed outlier: 3.881A pdb=" N LYS K 43 " --> pdb=" O ILE K 39 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA K 105 " --> pdb=" O CYS K 44 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY K 106 " --> pdb=" O GLN K 114 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP K 108 " --> pdb=" O GLY K 112 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 13 through 17 Processing sheet with id=AD1, first strand: chain 'L' and resid 20 through 22 removed outlier: 7.106A pdb=" N ALA L 20 " --> pdb=" O SER L 27 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 34 through 36 Processing sheet with id=AD3, first strand: chain 'L' and resid 98 through 99 Processing sheet with id=AD4, first strand: chain 'M' and resid 164 through 167 removed outlier: 5.398A pdb=" N THR M 39 " --> pdb=" O ASP M 54 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP M 54 " --> pdb=" O THR M 39 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA M 53 " --> pdb=" O LEU M 221 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU M 221 " --> pdb=" O ALA M 53 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN M 233 " --> pdb=" O ILE M 222 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 57 through 58 removed outlier: 3.848A pdb=" N THR M 65 " --> pdb=" O LEU M 57 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 71 through 73 removed outlier: 4.071A pdb=" N ASN M 136 " --> pdb=" O TYR M 152 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR M 152 " --> pdb=" O ASN M 136 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 175 through 177 removed outlier: 3.737A pdb=" N GLY N 233 " --> pdb=" O THR N 230 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 29 through 30 Processing sheet with id=AD9, first strand: chain 'N' and resid 44 through 45 removed outlier: 3.503A pdb=" N ILE N 114 " --> pdb=" O GLY N 53 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'P' and resid 160 through 162 removed outlier: 3.534A pdb=" N LYS P 220 " --> pdb=" O VAL P 212 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 65 through 67 removed outlier: 4.431A pdb=" N LEU P 146 " --> pdb=" O TRP P 158 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'R' and resid 158 through 161 removed outlier: 3.556A pdb=" N LEU R 209 " --> pdb=" O ALA R 41 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA R 207 " --> pdb=" O LEU R 43 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'R' and resid 63 through 64 Processing sheet with id=AE5, first strand: chain 'R' and resid 74 through 75 Processing sheet with id=AE6, first strand: chain 'S' and resid 169 through 172 removed outlier: 3.666A pdb=" N CYS S 220 " --> pdb=" O LEU S 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'S' and resid 74 through 75 Processing sheet with id=AE8, first strand: chain 'V' and resid 181 through 182 Processing sheet with id=AE9, first strand: chain 'V' and resid 34 through 36 removed outlier: 3.509A pdb=" N GLY V 154 " --> pdb=" O TYR V 42 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'W' and resid 124 through 127 Processing sheet with id=AF2, first strand: chain 'W' and resid 20 through 21 removed outlier: 6.692A pdb=" N ALA W 20 " --> pdb=" O ALA W 27 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'W' and resid 41 through 47 removed outlier: 4.152A pdb=" N TRP W 42 " --> pdb=" O GLY W 101 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS W 120 " --> pdb=" O GLY W 112 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'W' and resid 212 through 213 removed outlier: 4.072A pdb=" N ILE W 212 " --> pdb=" O LYS X 212 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS X 212 " --> pdb=" O ILE W 212 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA X 198 " --> pdb=" O LEU X 213 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N CYS X 25 " --> pdb=" O GLU X 199 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Y' and resid 4 through 8 Processing sheet with id=AF6, first strand: chain 'Y' and resid 20 through 22 removed outlier: 7.180A pdb=" N SER Y 21 " --> pdb=" O LYS Y 29 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Y' and resid 36 through 39 removed outlier: 3.881A pdb=" N LYS Y 43 " --> pdb=" O ILE Y 39 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA Y 105 " --> pdb=" O CYS Y 44 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY Y 106 " --> pdb=" O GLN Y 114 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP Y 108 " --> pdb=" O GLY Y 112 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'a' and resid 164 through 167 removed outlier: 5.398A pdb=" N THR a 39 " --> pdb=" O ASP a 54 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP a 54 " --> pdb=" O THR a 39 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA a 53 " --> pdb=" O LEU a 221 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU a 221 " --> pdb=" O ALA a 53 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN a 233 " --> pdb=" O ILE a 222 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'a' and resid 57 through 58 removed outlier: 3.849A pdb=" N THR a 65 " --> pdb=" O LEU a 57 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'a' and resid 71 through 73 removed outlier: 4.070A pdb=" N ASN a 136 " --> pdb=" O TYR a 152 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR a 152 " --> pdb=" O ASN a 136 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'b' and resid 175 through 177 removed outlier: 3.738A pdb=" N GLY b 233 " --> pdb=" O THR b 230 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'b' and resid 29 through 30 Processing sheet with id=AG4, first strand: chain 'b' and resid 44 through 45 removed outlier: 3.503A pdb=" N ILE b 114 " --> pdb=" O GLY b 53 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 44 through 46 removed outlier: 3.610A pdb=" N LEU X 134 " --> pdb=" O THR X 146 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Q' and resid 36 through 38 removed outlier: 3.555A pdb=" N TYR Q 214 " --> pdb=" O GLN Q 224 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Q' and resid 72 through 78 Processing sheet with id=AG8, first strand: chain 'T' and resid 35 through 39 removed outlier: 7.480A pdb=" N LEU T 211 " --> pdb=" O GLU T 222 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N GLU T 222 " --> pdb=" O LEU T 211 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL T 213 " --> pdb=" O TRP T 220 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N TRP T 220 " --> pdb=" O VAL T 213 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'T' and resid 70 through 72 Processing sheet with id=AH1, first strand: chain 'O' and resid 171 through 174 Processing sheet with id=AH2, first strand: chain 'O' and resid 75 through 77 removed outlier: 3.733A pdb=" N MET O 145 " --> pdb=" O SER O 85 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER O 143 " --> pdb=" O VAL O 87 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'O' and resid 75 through 77 removed outlier: 3.733A pdb=" N MET O 145 " --> pdb=" O SER O 85 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY O 144 " --> pdb=" O PHE O 160 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Z' and resid 13 through 17 Processing sheet with id=AH5, first strand: chain 'Z' and resid 20 through 22 removed outlier: 7.106A pdb=" N ALA Z 20 " --> pdb=" O SER Z 27 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'Z' and resid 34 through 36 Processing sheet with id=AH7, first strand: chain 'Z' and resid 98 through 99 Processing sheet with id=AH8, first strand: chain 'U' and resid 46 through 51 removed outlier: 3.529A pdb=" N ILE U 47 " --> pdb=" O LEU U 40 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR U 36 " --> pdb=" O ILE U 51 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'U' and resid 69 through 73 removed outlier: 7.163A pdb=" N ILE U 76 " --> pdb=" O VAL U 72 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE U 139 " --> pdb=" O THR U 79 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE U 151 " --> pdb=" O TYR U 163 " (cutoff:3.500A) 3537 hydrogen bonds defined for protein. 10251 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: 23.95 Time building geometry restraints manager: 22.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 14779 1.33 - 1.45: 17148 1.45 - 1.57: 40015 1.57 - 1.70: 4 1.70 - 1.82: 462 Bond restraints: 72408 Sorted by residual: bond pdb=" CA GLY J 30 " pdb=" C GLY J 30 " ideal model delta sigma weight residual 1.517 1.493 0.024 7.00e-03 2.04e+04 1.19e+01 bond pdb=" CA GLY X 30 " pdb=" C GLY X 30 " ideal model delta sigma weight residual 1.517 1.494 0.024 7.00e-03 2.04e+04 1.13e+01 bond pdb=" CB PHE L 8 " pdb=" CG PHE L 8 " ideal model delta sigma weight residual 1.502 1.436 0.066 2.30e-02 1.89e+03 8.33e+00 bond pdb=" CB PHE Z 8 " pdb=" CG PHE Z 8 " ideal model delta sigma weight residual 1.502 1.436 0.066 2.30e-02 1.89e+03 8.16e+00 bond pdb=" CB TYR F 152 " pdb=" CG TYR F 152 " ideal model delta sigma weight residual 1.512 1.455 0.057 2.20e-02 2.07e+03 6.68e+00 ... (remaining 72403 not shown) Histogram of bond angle deviations from ideal: 97.19 - 106.10: 1192 106.10 - 115.01: 43499 115.01 - 123.92: 51333 123.92 - 132.83: 1634 132.83 - 141.74: 88 Bond angle restraints: 97746 Sorted by residual: angle pdb=" CA VAL M 232 " pdb=" CB VAL M 232 " pdb=" CG1 VAL M 232 " ideal model delta sigma weight residual 110.40 122.44 -12.04 1.70e+00 3.46e-01 5.02e+01 angle pdb=" CA VAL a 232 " pdb=" CB VAL a 232 " pdb=" CG1 VAL a 232 " ideal model delta sigma weight residual 110.40 122.42 -12.02 1.70e+00 3.46e-01 5.00e+01 angle pdb=" N GLY T 161 " pdb=" CA GLY T 161 " pdb=" C GLY T 161 " ideal model delta sigma weight residual 113.18 129.47 -16.29 2.37e+00 1.78e-01 4.72e+01 angle pdb=" N GLY F 161 " pdb=" CA GLY F 161 " pdb=" C GLY F 161 " ideal model delta sigma weight residual 113.18 129.42 -16.24 2.37e+00 1.78e-01 4.70e+01 angle pdb=" N ILE Z 188 " pdb=" CA ILE Z 188 " pdb=" C ILE Z 188 " ideal model delta sigma weight residual 109.34 123.29 -13.95 2.08e+00 2.31e-01 4.50e+01 ... (remaining 97741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 38690 17.81 - 35.61: 4131 35.61 - 53.42: 775 53.42 - 71.22: 188 71.22 - 89.03: 44 Dihedral angle restraints: 43828 sinusoidal: 17870 harmonic: 25958 Sorted by residual: dihedral pdb=" N ASN m 174 " pdb=" C ASN m 174 " pdb=" CA ASN m 174 " pdb=" CB ASN m 174 " ideal model delta harmonic sigma weight residual 122.80 132.81 -10.01 0 2.50e+00 1.60e-01 1.60e+01 dihedral pdb=" N ASN c 174 " pdb=" C ASN c 174 " pdb=" CA ASN c 174 " pdb=" CB ASN c 174 " ideal model delta harmonic sigma weight residual 122.80 132.77 -9.97 0 2.50e+00 1.60e-01 1.59e+01 dihedral pdb=" C VAL h 222 " pdb=" N VAL h 222 " pdb=" CA VAL h 222 " pdb=" CB VAL h 222 " ideal model delta harmonic sigma weight residual -122.00 -131.88 9.88 0 2.50e+00 1.60e-01 1.56e+01 ... (remaining 43825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 9885 0.109 - 0.218: 949 0.218 - 0.327: 90 0.327 - 0.436: 10 0.436 - 0.546: 2 Chirality restraints: 10936 Sorted by residual: chirality pdb=" CB VAL m 167 " pdb=" CA VAL m 167 " pdb=" CG1 VAL m 167 " pdb=" CG2 VAL m 167 " both_signs ideal model delta sigma weight residual False -2.63 -2.08 -0.55 2.00e-01 2.50e+01 7.44e+00 chirality pdb=" CB VAL c 167 " pdb=" CA VAL c 167 " pdb=" CG1 VAL c 167 " pdb=" CG2 VAL c 167 " both_signs ideal model delta sigma weight residual False -2.63 -2.09 -0.54 2.00e-01 2.50e+01 7.37e+00 chirality pdb=" CB ILE G 187 " pdb=" CA ILE G 187 " pdb=" CG1 ILE G 187 " pdb=" CG2 ILE G 187 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.24e+00 ... (remaining 10933 not shown) Planarity restraints: 12412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY W 23 " -0.060 5.00e-02 4.00e+02 9.02e-02 1.30e+01 pdb=" N PRO W 24 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO W 24 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO W 24 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY I 23 " 0.060 5.00e-02 4.00e+02 9.01e-02 1.30e+01 pdb=" N PRO I 24 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO I 24 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO I 24 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 161 " -0.058 5.00e-02 4.00e+02 8.64e-02 1.19e+01 pdb=" N PRO A 162 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO A 162 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 162 " -0.048 5.00e-02 4.00e+02 ... (remaining 12409 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 14259 2.77 - 3.30: 68615 3.30 - 3.83: 118558 3.83 - 4.37: 134448 4.37 - 4.90: 231478 Nonbonded interactions: 567358 Sorted by model distance: nonbonded pdb=" OG1 THR b 10 " pdb=" OD1 ASP b 26 " model vdw 2.233 2.440 nonbonded pdb=" OG1 THR N 10 " pdb=" OD1 ASP N 26 " model vdw 2.233 2.440 nonbonded pdb=" OG SER S 168 " pdb=" O LEU T 56 " model vdw 2.263 2.440 nonbonded pdb=" OG SER S 16 " pdb=" OD2 ASP o 172 " model vdw 2.263 2.440 nonbonded pdb=" OH TYR U 184 " pdb=" OD2 ASP U 195 " model vdw 2.264 2.440 ... (remaining 567353 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 'O' } ncs_group { reference = chain 'B' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'Q' } ncs_group { reference = chain 'D' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'S' } ncs_group { reference = chain 'F' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'V' } ncs_group { reference = chain 'I' selection = chain 'W' } ncs_group { reference = chain 'J' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'Z' } ncs_group { reference = chain 'M' selection = chain 'a' } ncs_group { reference = chain 'N' selection = chain 'b' } ncs_group { reference = (chain 'c' and resid 18 through 268) selection = (chain 'd' and resid 18 through 268) selection = (chain 'e' and resid 18 through 268) selection = (chain 'f' and resid 18 through 268) selection = (chain 'g' and resid 18 through 268) selection = chain 'h' selection = chain 'i' selection = (chain 'j' and resid 18 through 268) selection = (chain 'k' and resid 18 through 268) selection = chain 'l' selection = (chain 'm' and resid 18 through 268) selection = chain 'n' selection = (chain 'o' and resid 18 through 268) selection = (chain 'p' and resid 18 through 268) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.100 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: 10.990 Check model and map are aligned: 0.840 Set scattering table: 0.480 Process input model: 136.610 Find NCS groups from input model: 5.810 Set up NCS constraints: 0.520 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:2.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 159.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 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 : 0.008 0.075 72408 Z= 0.545 Angle : 1.222 20.330 97746 Z= 0.689 Chirality : 0.068 0.546 10936 Planarity : 0.006 0.090 12412 Dihedral : 14.934 89.030 27152 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.13 % Favored : 90.73 % Rotamer: Outliers : 1.10 % Allowed : 10.32 % Favored : 88.59 % Cbeta Deviations : 0.07 % 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: -3.64 (0.07), residues: 8660 helix: -1.89 (0.06), residues: 3998 sheet: -2.85 (0.13), residues: 1292 loop : -2.68 (0.10), residues: 3370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP l 237 HIS 0.015 0.002 HIS V 77 PHE 0.031 0.003 PHE i 176 TYR 0.035 0.003 TYR C 214 ARG 0.012 0.001 ARG m 248 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17320 Ramachandran restraints generated. 8660 Oldfield, 0 Emsley, 8660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17320 Ramachandran restraints generated. 8660 Oldfield, 0 Emsley, 8660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1894 residues out of total 7852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 1808 time to evaluate : 6.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 GLN cc_start: 0.8466 (tm-30) cc_final: 0.8244 (tm-30) REVERT: C 41 ASP cc_start: 0.6877 (t0) cc_final: 0.6654 (t70) REVERT: C 48 ASP cc_start: 0.8106 (OUTLIER) cc_final: 0.7806 (m-30) REVERT: C 142 LYS cc_start: 0.8332 (mttt) cc_final: 0.8055 (tptt) REVERT: D 12 PRO cc_start: 0.9168 (Cg_exo) cc_final: 0.8941 (Cg_endo) REVERT: D 116 GLN cc_start: 0.8592 (tm-30) cc_final: 0.8209 (tm-30) REVERT: D 121 ARG cc_start: 0.7970 (mtt180) cc_final: 0.7567 (ttp-170) REVERT: E 97 ASN cc_start: 0.8954 (t0) cc_final: 0.8695 (t0) REVERT: E 198 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8712 (tt) REVERT: E 233 ASN cc_start: 0.8275 (p0) cc_final: 0.7693 (t0) REVERT: F 9 ASP cc_start: 0.8459 (m-30) cc_final: 0.8161 (m-30) REVERT: F 106 GLU cc_start: 0.7635 (pm20) cc_final: 0.7341 (pm20) REVERT: F 117 GLN cc_start: 0.8775 (tp-100) cc_final: 0.8530 (tp40) REVERT: F 152 TYR cc_start: 0.7407 (m-80) cc_final: 0.7142 (m-80) REVERT: F 154 GLU cc_start: 0.7155 (tt0) cc_final: 0.6834 (tt0) REVERT: F 190 CYS cc_start: 0.8502 (t) cc_final: 0.7987 (t) REVERT: F 227 GLN cc_start: 0.7544 (tm-30) cc_final: 0.7083 (tm-30) REVERT: G 38 LEU cc_start: 0.8305 (tt) cc_final: 0.7953 (tt) REVERT: G 86 ASP cc_start: 0.8417 (m-30) cc_final: 0.8119 (m-30) REVERT: G 128 TYR cc_start: 0.8471 (m-80) cc_final: 0.8138 (m-80) REVERT: G 199 PHE cc_start: 0.7895 (m-10) cc_final: 0.7617 (m-10) REVERT: H 8 TYR cc_start: 0.6650 (m-10) cc_final: 0.6437 (m-10) REVERT: H 59 ILE cc_start: 0.9503 (mm) cc_final: 0.9302 (mm) REVERT: H 62 TYR cc_start: 0.8331 (m-80) cc_final: 0.8098 (m-80) REVERT: H 173 ILE cc_start: 0.5061 (OUTLIER) cc_final: 0.4713 (mt) REVERT: I 166 ASP cc_start: 0.8799 (t70) cc_final: 0.8593 (t70) REVERT: J 180 ILE cc_start: 0.9549 (tt) cc_final: 0.9321 (tt) REVERT: J 191 ASP cc_start: 0.7635 (t0) cc_final: 0.7273 (t0) REVERT: K 114 GLN cc_start: 0.8030 (mm-40) cc_final: 0.7755 (mt0) REVERT: K 120 TYR cc_start: 0.7496 (m-80) cc_final: 0.7137 (m-80) REVERT: K 125 ASP cc_start: 0.8281 (t70) cc_final: 0.8063 (t70) REVERT: K 166 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8375 (tm-30) REVERT: K 178 TYR cc_start: 0.8509 (m-80) cc_final: 0.8242 (m-10) REVERT: L 6 PHE cc_start: 0.8083 (m-80) cc_final: 0.7563 (m-10) REVERT: M 30 TRP cc_start: 0.8183 (t-100) cc_final: 0.7644 (t-100) REVERT: M 57 LEU cc_start: 0.8719 (tp) cc_final: 0.8455 (tt) REVERT: M 146 LYS cc_start: 0.7983 (mmmt) cc_final: 0.7773 (mmmt) REVERT: M 204 ASP cc_start: 0.7554 (t0) cc_final: 0.7343 (t0) REVERT: N 54 PHE cc_start: 0.6641 (m-80) cc_final: 0.6096 (m-10) REVERT: N 89 GLN cc_start: 0.8936 (tp-100) cc_final: 0.8699 (tp-100) REVERT: N 128 ASP cc_start: 0.7150 (m-30) cc_final: 0.6895 (m-30) REVERT: N 184 PHE cc_start: 0.7910 (m-80) cc_final: 0.7691 (m-80) REVERT: R 12 PRO cc_start: 0.9163 (Cg_exo) cc_final: 0.8952 (Cg_endo) REVERT: R 121 ARG cc_start: 0.7872 (mtt180) cc_final: 0.7570 (mtm-85) REVERT: R 225 MET cc_start: 0.8192 (mtt) cc_final: 0.7960 (mtp) REVERT: S 28 LEU cc_start: 0.8846 (mm) cc_final: 0.8602 (mm) REVERT: S 78 MET cc_start: 0.7825 (mtm) cc_final: 0.7419 (mtm) REVERT: S 115 LEU cc_start: 0.9005 (pp) cc_final: 0.8301 (pp) REVERT: S 233 ASN cc_start: 0.8102 (p0) cc_final: 0.7791 (p0) REVERT: V 59 ILE cc_start: 0.9475 (mm) cc_final: 0.9244 (mm) REVERT: V 62 TYR cc_start: 0.8275 (m-80) cc_final: 0.7889 (m-80) REVERT: V 173 ILE cc_start: 0.4698 (OUTLIER) cc_final: 0.4301 (mt) REVERT: V 201 MET cc_start: 0.8179 (mtt) cc_final: 0.7960 (mtp) REVERT: W 122 LEU cc_start: 0.9015 (mt) cc_final: 0.8638 (mt) REVERT: W 166 ASP cc_start: 0.8797 (t70) cc_final: 0.8581 (t70) REVERT: Y 99 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7305 (tm-30) REVERT: Y 114 GLN cc_start: 0.8123 (mm-40) cc_final: 0.7708 (mt0) REVERT: Y 120 TYR cc_start: 0.7414 (m-80) cc_final: 0.6996 (m-80) REVERT: Y 125 ASP cc_start: 0.8254 (t70) cc_final: 0.8031 (t70) REVERT: a 30 TRP cc_start: 0.8257 (t-100) cc_final: 0.7662 (t-100) REVERT: a 57 LEU cc_start: 0.8764 (tp) cc_final: 0.8462 (tt) REVERT: a 239 GLN cc_start: 0.8269 (mt0) cc_final: 0.8043 (mt0) REVERT: c 192 GLU cc_start: 0.8388 (tt0) cc_final: 0.8160 (tt0) REVERT: c 209 ARG cc_start: 0.8261 (ttt90) cc_final: 0.8040 (ttm170) REVERT: c 237 TRP cc_start: 0.7945 (t-100) cc_final: 0.7297 (t-100) REVERT: c 247 MET cc_start: 0.8397 (ttm) cc_final: 0.7905 (ttm) REVERT: d 35 GLU cc_start: 0.6968 (tp30) cc_final: 0.6372 (tp30) REVERT: d 164 GLN cc_start: 0.8328 (tm-30) cc_final: 0.7363 (tm-30) REVERT: d 212 ILE cc_start: 0.8091 (pt) cc_final: 0.7890 (tp) REVERT: d 256 ASP cc_start: 0.7696 (t0) cc_final: 0.7393 (t0) REVERT: e 162 TRP cc_start: 0.8636 (t60) cc_final: 0.7677 (t60) REVERT: e 172 ASP cc_start: 0.6894 (p0) cc_final: 0.6662 (p0) REVERT: f 176 PHE cc_start: 0.8385 (t80) cc_final: 0.7888 (t80) REVERT: f 196 PHE cc_start: 0.8449 (t80) cc_final: 0.8158 (t80) REVERT: f 200 ASP cc_start: 0.8826 (t0) cc_final: 0.8607 (t0) REVERT: f 247 MET cc_start: 0.8631 (tpp) cc_final: 0.7628 (ttm) REVERT: g 207 MET cc_start: 0.9521 (tpt) cc_final: 0.9297 (tpp) REVERT: g 219 TYR cc_start: 0.7451 (m-80) cc_final: 0.7064 (m-80) REVERT: g 224 ASP cc_start: 0.6776 (m-30) cc_final: 0.6175 (m-30) REVERT: g 247 MET cc_start: 0.8572 (mmt) cc_final: 0.8369 (mmm) REVERT: g 248 ARG cc_start: 0.8205 (ttp-170) cc_final: 0.7927 (ttp-110) REVERT: h 187 GLU cc_start: 0.7452 (pp20) cc_final: 0.7019 (mt-10) REVERT: h 188 LEU cc_start: 0.8179 (tt) cc_final: 0.7841 (tt) REVERT: h 207 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7647 (mmp) REVERT: i 38 ARG cc_start: 0.8228 (mtt90) cc_final: 0.7650 (mmt180) REVERT: i 161 LEU cc_start: 0.9060 (tp) cc_final: 0.8810 (tp) REVERT: i 165 LEU cc_start: 0.7865 (mp) cc_final: 0.7268 (tt) REVERT: i 229 VAL cc_start: 0.8804 (t) cc_final: 0.8539 (t) REVERT: i 243 THR cc_start: 0.8489 (m) cc_final: 0.8118 (m) REVERT: i 262 TRP cc_start: 0.6697 (t-100) cc_final: 0.6486 (t-100) REVERT: j 164 GLN cc_start: 0.9474 (mm-40) cc_final: 0.8845 (mm-40) REVERT: j 176 PHE cc_start: 0.7814 (t80) cc_final: 0.7484 (t80) REVERT: j 196 PHE cc_start: 0.8363 (t80) cc_final: 0.8031 (t80) REVERT: j 200 ASP cc_start: 0.8724 (t0) cc_final: 0.8449 (t0) REVERT: j 224 ASP cc_start: 0.7918 (m-30) cc_final: 0.6909 (t0) REVERT: j 247 MET cc_start: 0.8797 (tpp) cc_final: 0.8018 (tpp) REVERT: k 136 LYS cc_start: 0.7015 (tttt) cc_final: 0.6769 (mmmt) REVERT: k 172 ASP cc_start: 0.7150 (t70) cc_final: 0.6930 (t70) REVERT: k 205 TYR cc_start: 0.7396 (t80) cc_final: 0.6970 (t80) REVERT: k 253 MET cc_start: 0.8381 (mtp) cc_final: 0.7985 (tpt) REVERT: k 255 TYR cc_start: 0.8071 (t80) cc_final: 0.7434 (t80) REVERT: k 256 ASP cc_start: 0.8176 (p0) cc_final: 0.7951 (p0) REVERT: l 187 GLU cc_start: 0.7496 (pp20) cc_final: 0.6837 (pp20) REVERT: l 247 MET cc_start: 0.8612 (mmt) cc_final: 0.8252 (mmm) REVERT: l 263 GLU cc_start: 0.8375 (mp0) cc_final: 0.8045 (mm-30) REVERT: m 181 GLN cc_start: 0.8313 (mm-40) cc_final: 0.8064 (mm-40) REVERT: m 226 GLN cc_start: 0.8934 (mp10) cc_final: 0.8612 (mp10) REVERT: m 259 TYR cc_start: 0.7750 (t80) cc_final: 0.7452 (t80) REVERT: m 269 LYS cc_start: 0.5691 (OUTLIER) cc_final: 0.5337 (tptp) REVERT: n 38 ARG cc_start: 0.8241 (mtt90) cc_final: 0.7644 (mmt180) REVERT: n 164 GLN cc_start: 0.8008 (mt0) cc_final: 0.7316 (mt0) REVERT: n 176 PHE cc_start: 0.7756 (t80) cc_final: 0.7119 (t80) REVERT: n 209 ARG cc_start: 0.7704 (ttt90) cc_final: 0.7221 (ttm-80) REVERT: n 243 THR cc_start: 0.8568 (m) cc_final: 0.8199 (m) REVERT: n 262 TRP cc_start: 0.6653 (t-100) cc_final: 0.6360 (t-100) REVERT: o 35 GLU cc_start: 0.7040 (tp30) cc_final: 0.6270 (tp30) REVERT: o 190 ARG cc_start: 0.7227 (ttp80) cc_final: 0.7013 (ttt-90) REVERT: o 212 ILE cc_start: 0.7881 (pt) cc_final: 0.7675 (tt) REVERT: p 162 TRP cc_start: 0.8736 (t60) cc_final: 0.7500 (t60) REVERT: p 182 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7895 (tm-30) REVERT: p 186 GLN cc_start: 0.8257 (tm-30) cc_final: 0.7727 (tm-30) REVERT: p 187 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8295 (mm-30) REVERT: b 54 PHE cc_start: 0.6745 (m-80) cc_final: 0.6368 (m-10) REVERT: b 89 GLN cc_start: 0.8968 (tp-100) cc_final: 0.8732 (tp-100) REVERT: X 61 ASP cc_start: 0.8277 (m-30) cc_final: 0.8067 (m-30) REVERT: X 80 GLN cc_start: 0.8811 (mp10) cc_final: 0.8559 (mp10) REVERT: X 180 ILE cc_start: 0.9516 (tt) cc_final: 0.9289 (tt) REVERT: X 191 ASP cc_start: 0.7502 (t0) cc_final: 0.7164 (t0) REVERT: Q 41 ASP cc_start: 0.7133 (t0) cc_final: 0.6869 (t70) REVERT: Q 119 GLN cc_start: 0.8864 (tp40) cc_final: 0.8579 (tm-30) REVERT: Q 134 PHE cc_start: 0.8607 (p90) cc_final: 0.8400 (p90) REVERT: T 9 ASP cc_start: 0.8566 (m-30) cc_final: 0.8325 (m-30) REVERT: T 68 ASP cc_start: 0.7926 (p0) cc_final: 0.7585 (p0) REVERT: T 82 LYS cc_start: 0.8831 (ttmt) cc_final: 0.8603 (tppt) REVERT: T 106 GLU cc_start: 0.7677 (pm20) cc_final: 0.7380 (pm20) REVERT: T 152 TYR cc_start: 0.7338 (m-80) cc_final: 0.7019 (m-80) REVERT: T 154 GLU cc_start: 0.7185 (tt0) cc_final: 0.6787 (tt0) REVERT: T 190 CYS cc_start: 0.8524 (t) cc_final: 0.8027 (t) REVERT: T 227 GLN cc_start: 0.7582 (tm-30) cc_final: 0.7166 (tm-30) REVERT: O 145 MET cc_start: 0.6973 (mtp) cc_final: 0.6732 (mtt) REVERT: Z 6 PHE cc_start: 0.8058 (m-80) cc_final: 0.7510 (m-10) REVERT: Z 72 GLU cc_start: 0.7635 (pt0) cc_final: 0.7229 (pt0) REVERT: U 38 LEU cc_start: 0.8064 (tt) cc_final: 0.7662 (tt) REVERT: U 60 MET cc_start: 0.7864 (mmm) cc_final: 0.7512 (mmp) REVERT: U 128 TYR cc_start: 0.8499 (m-80) cc_final: 0.8121 (m-80) REVERT: U 137 SER cc_start: 0.9275 (m) cc_final: 0.8935 (t) REVERT: U 199 PHE cc_start: 0.7816 (m-10) cc_final: 0.7544 (m-10) outliers start: 86 outliers final: 19 residues processed: 1872 average time/residue: 0.6999 time to fit residues: 2178.5098 Evaluate side-chains 1188 residues out of total 7852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 1163 time to evaluate : 6.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain C residue 48 ASP Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain M residue 232 VAL Chi-restraints excluded: chain R residue 55 ASN Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain V residue 173 ILE Chi-restraints excluded: chain Y residue 50 SER Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain a residue 232 VAL Chi-restraints excluded: chain e residue 64 VAL Chi-restraints excluded: chain e residue 258 LEU Chi-restraints excluded: chain g residue 266 VAL Chi-restraints excluded: chain h residue 207 MET Chi-restraints excluded: chain k residue 266 VAL Chi-restraints excluded: chain l residue 60 SER Chi-restraints excluded: chain m residue 269 LYS Chi-restraints excluded: chain p residue 64 VAL Chi-restraints excluded: chain O residue 81 GLU Chi-restraints excluded: chain O residue 227 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 724 optimal weight: 0.8980 chunk 650 optimal weight: 6.9990 chunk 360 optimal weight: 0.2980 chunk 222 optimal weight: 0.8980 chunk 438 optimal weight: 2.9990 chunk 347 optimal weight: 4.9990 chunk 672 optimal weight: 5.9990 chunk 260 optimal weight: 0.9980 chunk 408 optimal weight: 0.8980 chunk 500 optimal weight: 3.9990 chunk 779 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 46 ASN ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 ASN A 197 GLN B 21 GLN ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 ASN ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN C 146 GLN D 18 GLN D 97 ASN ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 23 GLN ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN ** E 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN F 189 HIS G 23 GLN G 35 ASN G 54 ASN G 104 ASN G 123 HIS G 144 ASN G 157 ASN G 211 ASN H 53 GLN H 68 ASN H 212 ASN I 35 HIS I 69 ASN I 71 ASN I 133 ASN J 63 GLN J 91 ASN K 69 GLN ** L 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 ASN L 162 HIS ** M 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 75 ASN N 92 HIS N 121 GLN P 21 GLN P 157 ASN P 204 ASN P 207 ASN ** P 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN R 138 ASN ** R 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 23 GLN ** S 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 97 ASN S 104 ASN S 186 ASN V 68 ASN V 212 ASN W 35 HIS W 71 ASN W 133 ASN ** W 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 69 GLN ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 166 ASN c 197 ASN c 239 HIS d 53 ASN d 65 ASN d 250 ASN d 261 ASN e 249 ASN e 250 ASN f 158 ASN f 261 ASN g 23 ASN g 239 HIS h 32 GLN h 158 ASN h 250 ASN h 261 ASN j 261 ASN j 275 HIS k 23 ASN k 239 HIS ** l 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 164 GLN l 250 ASN l 261 ASN m 166 ASN m 197 ASN ** n 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 23 ASN o 65 ASN o 250 ASN o 261 ASN p 249 ASN p 250 ASN ** b 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 75 ASN b 92 HIS b 121 GLN b 225 GLN X 63 GLN X 91 ASN Q 29 ASN Q 113 GLN Q 146 GLN T 189 HIS O 46 ASN O 71 ASN O 140 HIS O 153 ASN ** Z 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 85 ASN Z 162 HIS U 23 GLN U 35 ASN U 54 ASN U 104 ASN U 123 HIS U 144 ASN U 157 ASN U 211 ASN Total number of N/Q/H flips: 109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 72408 Z= 0.186 Angle : 0.644 24.492 97746 Z= 0.338 Chirality : 0.043 0.282 10936 Planarity : 0.005 0.094 12412 Dihedral : 4.776 88.120 9654 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.12 % Favored : 94.84 % Rotamer: Outliers : 2.74 % Allowed : 16.76 % Favored : 80.50 % 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: -1.81 (0.09), residues: 8660 helix: 0.18 (0.08), residues: 4056 sheet: -2.39 (0.13), residues: 1294 loop : -2.39 (0.10), residues: 3310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP c 162 HIS 0.010 0.001 HIS d 239 PHE 0.027 0.002 PHE M 201 TYR 0.033 0.001 TYR V 156 ARG 0.016 0.001 ARG h 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17320 Ramachandran restraints generated. 8660 Oldfield, 0 Emsley, 8660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17320 Ramachandran restraints generated. 8660 Oldfield, 0 Emsley, 8660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1660 residues out of total 7852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 1445 time to evaluate : 6.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8170 (tp30) cc_final: 0.7779 (tm-30) REVERT: A 129 GLN cc_start: 0.8585 (tm-30) cc_final: 0.8286 (tm-30) REVERT: B 54 ASN cc_start: 0.8172 (OUTLIER) cc_final: 0.7937 (p0) REVERT: B 159 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.8087 (mpp) REVERT: C 17 ARG cc_start: 0.7759 (mtt180) cc_final: 0.7283 (mtp85) REVERT: C 41 ASP cc_start: 0.6854 (t0) cc_final: 0.6566 (t0) REVERT: C 48 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7629 (m-30) REVERT: C 119 GLN cc_start: 0.8934 (tp40) cc_final: 0.8318 (tm-30) REVERT: C 142 LYS cc_start: 0.8143 (mttt) cc_final: 0.7918 (tptt) REVERT: C 216 THR cc_start: 0.7589 (t) cc_final: 0.7025 (t) REVERT: C 224 GLN cc_start: 0.7114 (mt0) cc_final: 0.6810 (mt0) REVERT: C 225 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8428 (mtmm) REVERT: D 46 GLU cc_start: 0.6914 (mp0) cc_final: 0.6604 (mm-30) REVERT: D 116 GLN cc_start: 0.8305 (tm-30) cc_final: 0.7932 (tm-30) REVERT: D 117 LYS cc_start: 0.6720 (mttt) cc_final: 0.5911 (ttmt) REVERT: D 121 ARG cc_start: 0.7738 (mtt180) cc_final: 0.7367 (ttp-170) REVERT: D 170 GLU cc_start: 0.7762 (tp30) cc_final: 0.7441 (tm-30) REVERT: E 28 LEU cc_start: 0.8882 (mm) cc_final: 0.8573 (mm) REVERT: E 164 ASN cc_start: 0.8353 (m110) cc_final: 0.8111 (m-40) REVERT: E 233 ASN cc_start: 0.8497 (p0) cc_final: 0.7639 (t0) REVERT: F 68 ASP cc_start: 0.7858 (p0) cc_final: 0.7441 (p0) REVERT: F 82 LYS cc_start: 0.8655 (tppt) cc_final: 0.8433 (tptt) REVERT: F 154 GLU cc_start: 0.6942 (tt0) cc_final: 0.6697 (tt0) REVERT: F 177 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8222 (mt) REVERT: F 190 CYS cc_start: 0.8459 (t) cc_final: 0.7984 (t) REVERT: F 227 GLN cc_start: 0.7664 (tm-30) cc_final: 0.7163 (tm-30) REVERT: G 118 ILE cc_start: 0.9502 (OUTLIER) cc_final: 0.9173 (tt) REVERT: G 125 TYR cc_start: 0.8116 (m-10) cc_final: 0.7863 (m-80) REVERT: G 128 TYR cc_start: 0.8321 (m-80) cc_final: 0.7943 (m-80) REVERT: H 19 ARG cc_start: 0.7916 (tpp80) cc_final: 0.7680 (tpt-90) REVERT: H 78 GLU cc_start: 0.7996 (tt0) cc_final: 0.7616 (tt0) REVERT: H 173 ILE cc_start: 0.4730 (OUTLIER) cc_final: 0.4290 (mt) REVERT: H 177 HIS cc_start: 0.6409 (OUTLIER) cc_final: 0.5928 (t-170) REVERT: I 82 ARG cc_start: 0.8493 (mtp85) cc_final: 0.7917 (mtp85) REVERT: I 122 LEU cc_start: 0.8884 (mt) cc_final: 0.8627 (mt) REVERT: J 101 ARG cc_start: 0.8261 (ttp80) cc_final: 0.7520 (ttp80) REVERT: J 188 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7664 (tp) REVERT: J 191 ASP cc_start: 0.7378 (t0) cc_final: 0.6784 (t0) REVERT: K 92 TYR cc_start: 0.7182 (m-10) cc_final: 0.6601 (m-10) REVERT: K 114 GLN cc_start: 0.7978 (mm-40) cc_final: 0.7483 (mt0) REVERT: L 58 TYR cc_start: 0.8277 (t80) cc_final: 0.8054 (t80) REVERT: L 67 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7400 (mm-30) REVERT: M 30 TRP cc_start: 0.7978 (t-100) cc_final: 0.7315 (t60) REVERT: M 112 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.8004 (m-30) REVERT: M 190 ASN cc_start: 0.7658 (t0) cc_final: 0.7379 (t0) REVERT: N 54 PHE cc_start: 0.6606 (m-80) cc_final: 0.5805 (m-80) REVERT: P 79 MET cc_start: 0.8023 (mtp) cc_final: 0.7819 (mtp) REVERT: P 147 TYR cc_start: 0.8517 (m-80) cc_final: 0.8097 (m-80) REVERT: R 12 PRO cc_start: 0.8969 (Cg_exo) cc_final: 0.8749 (Cg_endo) REVERT: R 46 GLU cc_start: 0.6857 (mp0) cc_final: 0.6575 (mm-30) REVERT: R 99 ASP cc_start: 0.8436 (t0) cc_final: 0.8196 (t0) REVERT: R 116 GLN cc_start: 0.8138 (tm-30) cc_final: 0.7884 (tm-30) REVERT: R 117 LYS cc_start: 0.6871 (mttt) cc_final: 0.6204 (ttmt) REVERT: S 28 LEU cc_start: 0.8877 (mm) cc_final: 0.8560 (mm) REVERT: S 104 ASN cc_start: 0.8086 (OUTLIER) cc_final: 0.7883 (m-40) REVERT: V 41 LEU cc_start: 0.8152 (pp) cc_final: 0.7818 (pt) REVERT: V 173 ILE cc_start: 0.4669 (OUTLIER) cc_final: 0.4199 (mt) REVERT: V 177 HIS cc_start: 0.6564 (OUTLIER) cc_final: 0.6035 (t-170) REVERT: W 25 ILE cc_start: 0.8814 (pt) cc_final: 0.8531 (mm) REVERT: W 82 ARG cc_start: 0.8535 (mtp85) cc_final: 0.8080 (mtp85) REVERT: W 122 LEU cc_start: 0.8897 (mt) cc_final: 0.8573 (mt) REVERT: Y 92 TYR cc_start: 0.7156 (m-10) cc_final: 0.6670 (m-10) REVERT: Y 114 GLN cc_start: 0.7987 (mm-40) cc_final: 0.7456 (mt0) REVERT: Y 166 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8136 (tm-30) REVERT: a 30 TRP cc_start: 0.7839 (t-100) cc_final: 0.7250 (t60) REVERT: a 57 LEU cc_start: 0.8630 (tp) cc_final: 0.8397 (tt) REVERT: c 207 MET cc_start: 0.7619 (tmm) cc_final: 0.7341 (tmm) REVERT: c 209 ARG cc_start: 0.8113 (ttt90) cc_final: 0.7866 (ttt180) REVERT: c 226 GLN cc_start: 0.8759 (mp10) cc_final: 0.8418 (mp10) REVERT: c 237 TRP cc_start: 0.7642 (t-100) cc_final: 0.7158 (t-100) REVERT: c 248 ARG cc_start: 0.7691 (ttp-170) cc_final: 0.7231 (ptm-80) REVERT: d 222 VAL cc_start: 0.8672 (OUTLIER) cc_final: 0.8328 (p) REVERT: e 162 TRP cc_start: 0.8671 (t60) cc_final: 0.8418 (t60) REVERT: e 182 GLU cc_start: 0.8267 (tm-30) cc_final: 0.8009 (tm-30) REVERT: e 250 ASN cc_start: 0.8464 (m-40) cc_final: 0.8159 (m110) REVERT: e 262 TRP cc_start: 0.7301 (t-100) cc_final: 0.7084 (t-100) REVERT: f 164 GLN cc_start: 0.9430 (mm-40) cc_final: 0.9215 (mt0) REVERT: f 176 PHE cc_start: 0.7831 (t80) cc_final: 0.7435 (t80) REVERT: f 190 ARG cc_start: 0.8527 (ttp-170) cc_final: 0.8257 (ptm-80) REVERT: g 207 MET cc_start: 0.9417 (tpt) cc_final: 0.9089 (tpt) REVERT: g 253 MET cc_start: 0.8813 (ttm) cc_final: 0.8504 (ttm) REVERT: h 164 GLN cc_start: 0.8606 (mm-40) cc_final: 0.8365 (mm-40) REVERT: h 188 LEU cc_start: 0.7864 (tt) cc_final: 0.7198 (tt) REVERT: h 190 ARG cc_start: 0.7774 (ttp80) cc_final: 0.7276 (ttp80) REVERT: h 194 SER cc_start: 0.8075 (p) cc_final: 0.7696 (p) REVERT: h 263 GLU cc_start: 0.8461 (mp0) cc_final: 0.7953 (mm-30) REVERT: i 38 ARG cc_start: 0.8400 (mtt90) cc_final: 0.8165 (mpt180) REVERT: i 164 GLN cc_start: 0.8349 (mt0) cc_final: 0.7916 (mt0) REVERT: i 176 PHE cc_start: 0.7600 (t80) cc_final: 0.7171 (t80) REVERT: i 226 GLN cc_start: 0.7903 (tt0) cc_final: 0.7311 (tm-30) REVERT: i 243 THR cc_start: 0.8465 (m) cc_final: 0.8252 (m) REVERT: i 262 TRP cc_start: 0.6551 (t-100) cc_final: 0.6295 (t-100) REVERT: j 158 ASN cc_start: 0.8161 (OUTLIER) cc_final: 0.7870 (p0) REVERT: j 164 GLN cc_start: 0.9412 (mm-40) cc_final: 0.9206 (tp40) REVERT: j 176 PHE cc_start: 0.7394 (t80) cc_final: 0.6903 (t80) REVERT: j 224 ASP cc_start: 0.7942 (m-30) cc_final: 0.6979 (t0) REVERT: j 247 MET cc_start: 0.8661 (tpp) cc_final: 0.8404 (mtt) REVERT: k 139 TYR cc_start: 0.8706 (t80) cc_final: 0.8503 (t80) REVERT: k 183 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8250 (tm-30) REVERT: k 239 HIS cc_start: 0.8604 (m170) cc_final: 0.8078 (m90) REVERT: k 255 TYR cc_start: 0.7439 (t80) cc_final: 0.6597 (t80) REVERT: k 259 TYR cc_start: 0.6173 (OUTLIER) cc_final: 0.4938 (m-80) REVERT: l 230 ARG cc_start: 0.7459 (ttp-110) cc_final: 0.7254 (ptm-80) REVERT: l 247 MET cc_start: 0.8554 (mmt) cc_final: 0.8172 (mmm) REVERT: l 262 TRP cc_start: 0.7736 (t-100) cc_final: 0.7364 (t-100) REVERT: l 263 GLU cc_start: 0.8466 (mp0) cc_final: 0.8247 (mm-30) REVERT: m 176 PHE cc_start: 0.7970 (t80) cc_final: 0.7623 (t80) REVERT: m 182 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7516 (mt-10) REVERT: m 204 LYS cc_start: 0.8962 (mmtm) cc_final: 0.8734 (mmtm) REVERT: m 207 MET cc_start: 0.7225 (tpp) cc_final: 0.6430 (tmm) REVERT: m 226 GLN cc_start: 0.9052 (mp10) cc_final: 0.8452 (mp10) REVERT: n 38 ARG cc_start: 0.8423 (mtt90) cc_final: 0.8159 (mpt180) REVERT: n 176 PHE cc_start: 0.7535 (t80) cc_final: 0.7145 (t80) REVERT: n 209 ARG cc_start: 0.7599 (ttt90) cc_final: 0.7203 (tpp80) REVERT: n 262 TRP cc_start: 0.6580 (t-100) cc_final: 0.6327 (t-100) REVERT: o 35 GLU cc_start: 0.7259 (tp30) cc_final: 0.6989 (tp30) REVERT: o 212 ILE cc_start: 0.8270 (pt) cc_final: 0.8008 (tp) REVERT: p 162 TRP cc_start: 0.8721 (t60) cc_final: 0.7515 (t60) REVERT: p 175 ASN cc_start: 0.7346 (OUTLIER) cc_final: 0.6669 (p0) REVERT: p 182 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7931 (tm-30) REVERT: p 186 GLN cc_start: 0.8442 (tm-30) cc_final: 0.8130 (tm-30) REVERT: p 239 HIS cc_start: 0.8656 (m90) cc_final: 0.8364 (m90) REVERT: p 248 ARG cc_start: 0.7592 (tmm-80) cc_final: 0.7358 (ttp-170) REVERT: p 250 ASN cc_start: 0.8379 (m-40) cc_final: 0.8128 (m110) REVERT: p 256 ASP cc_start: 0.8066 (t0) cc_final: 0.7601 (t0) REVERT: X 15 MET cc_start: 0.8214 (tpp) cc_final: 0.7896 (tpp) REVERT: X 92 MET cc_start: 0.8616 (ttp) cc_final: 0.8279 (ttm) REVERT: X 95 SER cc_start: 0.9129 (t) cc_final: 0.8926 (p) REVERT: X 101 ARG cc_start: 0.8243 (ttp80) cc_final: 0.7596 (ttp80) REVERT: X 188 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7586 (tp) REVERT: X 191 ASP cc_start: 0.7321 (t0) cc_final: 0.6718 (t0) REVERT: Q 82 ASP cc_start: 0.7742 (m-30) cc_final: 0.7443 (m-30) REVERT: Q 111 VAL cc_start: 0.9441 (m) cc_final: 0.9193 (t) REVERT: Q 119 GLN cc_start: 0.8798 (tp40) cc_final: 0.8454 (tm-30) REVERT: Q 216 THR cc_start: 0.7320 (t) cc_final: 0.6394 (t) REVERT: T 68 ASP cc_start: 0.7794 (p0) cc_final: 0.7497 (p0) REVERT: T 154 GLU cc_start: 0.7040 (tt0) cc_final: 0.6702 (tt0) REVERT: T 177 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8242 (mt) REVERT: T 190 CYS cc_start: 0.8493 (t) cc_final: 0.8008 (t) REVERT: T 227 GLN cc_start: 0.7658 (tm-30) cc_final: 0.7139 (tm-30) REVERT: O 26 GLU cc_start: 0.8161 (tp30) cc_final: 0.7816 (tm-30) REVERT: O 145 MET cc_start: 0.6793 (mtp) cc_final: 0.6483 (mtt) REVERT: Z 22 MET cc_start: 0.7714 (tmm) cc_final: 0.7504 (tmm) REVERT: U 49 CYS cc_start: 0.8136 (t) cc_final: 0.7854 (t) REVERT: U 118 ILE cc_start: 0.9429 (mm) cc_final: 0.9142 (tt) REVERT: U 125 TYR cc_start: 0.8101 (m-10) cc_final: 0.7850 (m-10) REVERT: U 128 TYR cc_start: 0.8357 (m-80) cc_final: 0.7980 (m-80) REVERT: U 137 SER cc_start: 0.9004 (m) cc_final: 0.8715 (t) outliers start: 215 outliers final: 100 residues processed: 1590 average time/residue: 0.6608 time to fit residues: 1788.4922 Evaluate side-chains 1272 residues out of total 7852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1152 time to evaluate : 6.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain C residue 48 ASP Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 176 HIS Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 177 HIS Chi-restraints excluded: chain I residue 13 ILE Chi-restraints excluded: chain I residue 181 ASP Chi-restraints excluded: chain I residue 198 HIS Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 68 ILE Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 159 ILE Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 26 ASP Chi-restraints excluded: chain P residue 12 THR Chi-restraints excluded: chain P residue 16 THR Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 215 ASP Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 129 ILE Chi-restraints excluded: chain S residue 13 ASN Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 104 ASN Chi-restraints excluded: chain S residue 141 VAL Chi-restraints excluded: chain S residue 198 ILE Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 87 THR Chi-restraints excluded: chain V residue 173 ILE Chi-restraints excluded: chain V residue 177 HIS Chi-restraints excluded: chain W residue 13 ILE Chi-restraints excluded: chain W residue 181 ASP Chi-restraints excluded: chain W residue 198 HIS Chi-restraints excluded: chain W residue 213 LEU Chi-restraints excluded: chain Y residue 50 SER Chi-restraints excluded: chain Y residue 55 LEU Chi-restraints excluded: chain Y residue 74 THR Chi-restraints excluded: chain Y residue 153 VAL Chi-restraints excluded: chain Y residue 173 LEU Chi-restraints excluded: chain a residue 63 ILE Chi-restraints excluded: chain a residue 89 ILE Chi-restraints excluded: chain a residue 112 ASP Chi-restraints excluded: chain d residue 172 ASP Chi-restraints excluded: chain d residue 222 VAL Chi-restraints excluded: chain e residue 64 VAL Chi-restraints excluded: chain e residue 222 VAL Chi-restraints excluded: chain f residue 28 ASP Chi-restraints excluded: chain f residue 158 ASN Chi-restraints excluded: chain f residue 275 HIS Chi-restraints excluded: chain g residue 222 VAL Chi-restraints excluded: chain g residue 254 LEU Chi-restraints excluded: chain j residue 28 ASP Chi-restraints excluded: chain j residue 158 ASN Chi-restraints excluded: chain j residue 254 LEU Chi-restraints excluded: chain j residue 258 LEU Chi-restraints excluded: chain k residue 254 LEU Chi-restraints excluded: chain k residue 259 TYR Chi-restraints excluded: chain m residue 178 VAL Chi-restraints excluded: chain m residue 182 GLU Chi-restraints excluded: chain m residue 239 HIS Chi-restraints excluded: chain o residue 172 ASP Chi-restraints excluded: chain p residue 64 VAL Chi-restraints excluded: chain p residue 139 TYR Chi-restraints excluded: chain p residue 175 ASN Chi-restraints excluded: chain p residue 222 VAL Chi-restraints excluded: chain b residue 12 VAL Chi-restraints excluded: chain b residue 26 ASP Chi-restraints excluded: chain X residue 139 LEU Chi-restraints excluded: chain X residue 184 LEU Chi-restraints excluded: chain X residue 188 LEU Chi-restraints excluded: chain X residue 199 GLU Chi-restraints excluded: chain Q residue 21 VAL Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 52 ILE Chi-restraints excluded: chain Q residue 60 ASN Chi-restraints excluded: chain Q residue 196 LEU Chi-restraints excluded: chain T residue 112 VAL Chi-restraints excluded: chain T residue 176 HIS Chi-restraints excluded: chain T residue 177 LEU Chi-restraints excluded: chain O residue 29 ILE Chi-restraints excluded: chain O residue 105 SER Chi-restraints excluded: chain O residue 130 VAL Chi-restraints excluded: chain O residue 139 LEU Chi-restraints excluded: chain O residue 165 PHE Chi-restraints excluded: chain O residue 196 ILE Chi-restraints excluded: chain Z residue 176 VAL Chi-restraints excluded: chain U residue 47 ILE Chi-restraints excluded: chain U residue 238 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 433 optimal weight: 0.6980 chunk 241 optimal weight: 10.0000 chunk 648 optimal weight: 9.9990 chunk 530 optimal weight: 9.9990 chunk 214 optimal weight: 6.9990 chunk 780 optimal weight: 0.0770 chunk 843 optimal weight: 0.8980 chunk 695 optimal weight: 0.9980 chunk 774 optimal weight: 2.9990 chunk 266 optimal weight: 1.9990 chunk 626 optimal weight: 6.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 HIS ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 HIS E 43 ASN E 97 ASN E 104 ASN ** E 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 HIS ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 ASN H 53 GLN H 61 HIS K 23 ASN K 69 GLN K 72 ASN ** L 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 158 ASN ** M 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN ** P 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 138 ASN ** R 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 43 ASN S 97 ASN S 104 ASN V 61 HIS W 66 HIS ** W 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 23 ASN e 261 ASN ** h 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 181 GLN j 239 HIS j 275 HIS l 158 ASN l 164 GLN l 181 GLN n 32 GLN ** n 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 53 ASN o 239 HIS b 89 GLN ** Q 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 138 HIS O 36 ASN ** O 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 144 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 72408 Z= 0.174 Angle : 0.593 24.828 97746 Z= 0.307 Chirality : 0.042 0.222 10936 Planarity : 0.004 0.099 12412 Dihedral : 4.258 74.127 9624 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.58 % Favored : 94.38 % Rotamer: Outliers : 3.13 % Allowed : 19.38 % Favored : 77.48 % 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: -1.11 (0.09), residues: 8660 helix: 0.87 (0.08), residues: 4042 sheet: -2.01 (0.13), residues: 1298 loop : -2.22 (0.10), residues: 3320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP h 162 HIS 0.009 0.001 HIS o 239 PHE 0.023 0.001 PHE U 199 TYR 0.035 0.001 TYR V 156 ARG 0.012 0.000 ARG J 101 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17320 Ramachandran restraints generated. 8660 Oldfield, 0 Emsley, 8660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17320 Ramachandran restraints generated. 8660 Oldfield, 0 Emsley, 8660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1539 residues out of total 7852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 1293 time to evaluate : 6.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7319 (mt-10) REVERT: B 159 MET cc_start: 0.8445 (tpp) cc_final: 0.8078 (mpp) REVERT: B 171 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7870 (ttm) REVERT: C 17 ARG cc_start: 0.7801 (mtt180) cc_final: 0.6903 (mtp85) REVERT: C 48 ASP cc_start: 0.8100 (t0) cc_final: 0.7545 (m-30) REVERT: C 119 GLN cc_start: 0.8924 (tp40) cc_final: 0.8292 (tm-30) REVERT: C 216 THR cc_start: 0.7510 (t) cc_final: 0.6951 (t) REVERT: C 225 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8148 (mtmm) REVERT: D 46 GLU cc_start: 0.6969 (mp0) cc_final: 0.6636 (mm-30) REVERT: D 117 LYS cc_start: 0.6474 (mttt) cc_final: 0.5940 (ttmt) REVERT: D 121 ARG cc_start: 0.7669 (mtt180) cc_final: 0.7330 (ttp-170) REVERT: D 205 GLU cc_start: 0.6830 (mp0) cc_final: 0.6628 (mp0) REVERT: E 20 ARG cc_start: 0.7396 (mtm180) cc_final: 0.7090 (mtm180) REVERT: E 28 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8631 (mm) REVERT: E 88 LEU cc_start: 0.8969 (mt) cc_final: 0.8758 (mt) REVERT: E 164 ASN cc_start: 0.8385 (m110) cc_final: 0.8119 (m-40) REVERT: E 172 ILE cc_start: 0.8863 (mp) cc_final: 0.8415 (mm) REVERT: E 233 ASN cc_start: 0.8532 (p0) cc_final: 0.7686 (t0) REVERT: F 9 ASP cc_start: 0.8360 (m-30) cc_final: 0.8157 (m-30) REVERT: F 68 ASP cc_start: 0.7821 (p0) cc_final: 0.7517 (p0) REVERT: F 82 LYS cc_start: 0.8621 (tppt) cc_final: 0.8342 (tptt) REVERT: F 117 GLN cc_start: 0.8909 (tp40) cc_final: 0.8539 (tp40) REVERT: F 154 GLU cc_start: 0.6969 (tt0) cc_final: 0.6669 (tt0) REVERT: F 177 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8374 (mt) REVERT: F 190 CYS cc_start: 0.8367 (t) cc_final: 0.7909 (t) REVERT: F 227 GLN cc_start: 0.7715 (tm-30) cc_final: 0.7192 (tm-30) REVERT: G 86 ASP cc_start: 0.8292 (m-30) cc_final: 0.7973 (m-30) REVERT: G 118 ILE cc_start: 0.9439 (OUTLIER) cc_final: 0.9021 (tt) REVERT: G 128 TYR cc_start: 0.8270 (m-80) cc_final: 0.8010 (m-80) REVERT: G 199 PHE cc_start: 0.7612 (m-10) cc_final: 0.7405 (m-80) REVERT: H 78 GLU cc_start: 0.8095 (tt0) cc_final: 0.7686 (tt0) REVERT: H 173 ILE cc_start: 0.4881 (OUTLIER) cc_final: 0.4431 (mt) REVERT: H 177 HIS cc_start: 0.6435 (OUTLIER) cc_final: 0.5919 (t-170) REVERT: I 122 LEU cc_start: 0.8867 (mt) cc_final: 0.8610 (mt) REVERT: J 191 ASP cc_start: 0.7357 (t0) cc_final: 0.6904 (t0) REVERT: K 92 TYR cc_start: 0.7137 (m-10) cc_final: 0.6575 (m-10) REVERT: K 98 PHE cc_start: 0.7548 (OUTLIER) cc_final: 0.7109 (t80) REVERT: K 114 GLN cc_start: 0.7992 (mm-40) cc_final: 0.7563 (mt0) REVERT: L 67 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7592 (mm-30) REVERT: R 46 GLU cc_start: 0.6922 (mp0) cc_final: 0.6705 (mm-30) REVERT: R 117 LYS cc_start: 0.6880 (mttt) cc_final: 0.6041 (ttmt) REVERT: S 28 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8609 (mm) REVERT: V 89 ASP cc_start: 0.7257 (p0) cc_final: 0.6864 (p0) REVERT: V 173 ILE cc_start: 0.4821 (OUTLIER) cc_final: 0.4328 (mt) REVERT: V 177 HIS cc_start: 0.6621 (OUTLIER) cc_final: 0.6085 (t-170) REVERT: W 86 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7492 (pm20) REVERT: W 122 LEU cc_start: 0.8854 (mt) cc_final: 0.8548 (mt) REVERT: W 144 ASP cc_start: 0.7889 (m-30) cc_final: 0.7580 (m-30) REVERT: Y 92 TYR cc_start: 0.7220 (m-10) cc_final: 0.6768 (m-10) REVERT: Y 114 GLN cc_start: 0.8042 (mm-40) cc_final: 0.7616 (mt0) REVERT: Y 166 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8211 (tm-30) REVERT: a 57 LEU cc_start: 0.8598 (tp) cc_final: 0.8358 (tt) REVERT: c 207 MET cc_start: 0.7587 (tmm) cc_final: 0.6913 (tmm) REVERT: c 209 ARG cc_start: 0.8099 (ttt90) cc_final: 0.7846 (ttt180) REVERT: c 237 TRP cc_start: 0.7560 (t-100) cc_final: 0.6400 (t60) REVERT: c 253 MET cc_start: 0.9138 (mmm) cc_final: 0.8903 (tpp) REVERT: d 27 TYR cc_start: 0.7887 (t80) cc_final: 0.7407 (t80) REVERT: e 162 TRP cc_start: 0.8656 (t60) cc_final: 0.7982 (t60) REVERT: e 176 PHE cc_start: 0.7775 (t80) cc_final: 0.7395 (t80) REVERT: f 190 ARG cc_start: 0.8503 (ttp-170) cc_final: 0.8230 (ptm-80) REVERT: f 224 ASP cc_start: 0.7892 (m-30) cc_final: 0.6851 (t0) REVERT: g 248 ARG cc_start: 0.8750 (ttp-110) cc_final: 0.8546 (ttp-110) REVERT: h 194 SER cc_start: 0.8098 (p) cc_final: 0.7799 (p) REVERT: h 263 GLU cc_start: 0.8438 (mp0) cc_final: 0.7962 (mm-30) REVERT: i 164 GLN cc_start: 0.8169 (mt0) cc_final: 0.7528 (mt0) REVERT: i 176 PHE cc_start: 0.7696 (t80) cc_final: 0.7334 (t80) REVERT: i 226 GLN cc_start: 0.7826 (tt0) cc_final: 0.7162 (tm-30) REVERT: j 44 ARG cc_start: 0.7776 (mmp-170) cc_final: 0.7426 (mmp-170) REVERT: j 224 ASP cc_start: 0.7881 (m-30) cc_final: 0.7242 (t0) REVERT: j 247 MET cc_start: 0.8635 (tpp) cc_final: 0.8415 (mtt) REVERT: j 253 MET cc_start: 0.8421 (mtt) cc_final: 0.8098 (ttp) REVERT: k 255 TYR cc_start: 0.7689 (t80) cc_final: 0.6435 (t80) REVERT: k 259 TYR cc_start: 0.6256 (OUTLIER) cc_final: 0.5176 (m-80) REVERT: l 37 LEU cc_start: 0.8508 (mt) cc_final: 0.8281 (tt) REVERT: l 194 SER cc_start: 0.8154 (p) cc_final: 0.7807 (p) REVERT: m 204 LYS cc_start: 0.8873 (mmtm) cc_final: 0.8616 (mmtm) REVERT: m 207 MET cc_start: 0.7220 (tpp) cc_final: 0.6294 (tmm) REVERT: m 226 GLN cc_start: 0.8962 (mp10) cc_final: 0.8598 (mp10) REVERT: m 247 MET cc_start: 0.8610 (ttm) cc_final: 0.8077 (mtt) REVERT: m 248 ARG cc_start: 0.8469 (tmm-80) cc_final: 0.7681 (ttp80) REVERT: n 38 ARG cc_start: 0.8403 (mtt90) cc_final: 0.8070 (mpt180) REVERT: n 150 SER cc_start: 0.8911 (t) cc_final: 0.8354 (p) REVERT: n 164 GLN cc_start: 0.7930 (mt0) cc_final: 0.7476 (mt0) REVERT: n 176 PHE cc_start: 0.7662 (t80) cc_final: 0.7309 (t80) REVERT: n 226 GLN cc_start: 0.8093 (tt0) cc_final: 0.7524 (tm-30) REVERT: n 262 TRP cc_start: 0.6599 (t-100) cc_final: 0.6364 (t-100) REVERT: o 35 GLU cc_start: 0.7287 (tp30) cc_final: 0.7053 (tp30) REVERT: o 209 ARG cc_start: 0.7775 (ttm170) cc_final: 0.7568 (ttm170) REVERT: p 162 TRP cc_start: 0.8704 (t60) cc_final: 0.8178 (t60) REVERT: p 175 ASN cc_start: 0.7406 (OUTLIER) cc_final: 0.6468 (p0) REVERT: p 182 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7800 (tm-30) REVERT: p 186 GLN cc_start: 0.8518 (tm-30) cc_final: 0.8290 (tm-30) REVERT: p 256 ASP cc_start: 0.8107 (t0) cc_final: 0.7775 (t0) REVERT: b 89 GLN cc_start: 0.8682 (tp-100) cc_final: 0.8394 (tm-30) REVERT: b 128 ASP cc_start: 0.6806 (m-30) cc_final: 0.6485 (m-30) REVERT: X 188 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7594 (tp) REVERT: X 191 ASP cc_start: 0.7283 (t0) cc_final: 0.6781 (t0) REVERT: Q 119 GLN cc_start: 0.8913 (tp40) cc_final: 0.8437 (tm-30) REVERT: T 3 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.7150 (ptp-170) REVERT: T 68 ASP cc_start: 0.7787 (p0) cc_final: 0.7502 (p0) REVERT: T 154 GLU cc_start: 0.7088 (tt0) cc_final: 0.6763 (tt0) REVERT: T 177 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8336 (mt) REVERT: T 190 CYS cc_start: 0.8409 (t) cc_final: 0.7924 (t) REVERT: T 221 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7808 (pt0) REVERT: T 227 GLN cc_start: 0.7719 (tm-30) cc_final: 0.7147 (tm-30) REVERT: O 26 GLU cc_start: 0.8233 (tp30) cc_final: 0.7904 (tm-30) REVERT: Z 22 MET cc_start: 0.7848 (tmm) cc_final: 0.7550 (tmm) REVERT: U 125 TYR cc_start: 0.8179 (m-10) cc_final: 0.7940 (m-80) REVERT: U 128 TYR cc_start: 0.8291 (m-80) cc_final: 0.8036 (m-80) REVERT: U 199 PHE cc_start: 0.7781 (m-10) cc_final: 0.7575 (m-10) outliers start: 246 outliers final: 137 residues processed: 1463 average time/residue: 0.6542 time to fit residues: 1636.5308 Evaluate side-chains 1276 residues out of total 7852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1121 time to evaluate : 6.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 115 CYS Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 221 GLN Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 221 ILE Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 177 HIS Chi-restraints excluded: chain H residue 221 ASP Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 79 CYS Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 198 HIS Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 172 ASP Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain K residue 159 ILE Chi-restraints excluded: chain K residue 188 VAL Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 197 HIS Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 15 ILE Chi-restraints excluded: chain N residue 26 ASP Chi-restraints excluded: chain P residue 12 THR Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 169 ASN Chi-restraints excluded: chain P residue 215 ASP Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 55 ASN Chi-restraints excluded: chain R residue 129 ILE Chi-restraints excluded: chain S residue 13 ASN Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 43 ASN Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 141 VAL Chi-restraints excluded: chain S residue 198 ILE Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 44 CYS Chi-restraints excluded: chain V residue 62 TYR Chi-restraints excluded: chain V residue 87 THR Chi-restraints excluded: chain V residue 173 ILE Chi-restraints excluded: chain V residue 177 HIS Chi-restraints excluded: chain V residue 221 ASP Chi-restraints excluded: chain W residue 2 THR Chi-restraints excluded: chain W residue 41 ILE Chi-restraints excluded: chain W residue 79 CYS Chi-restraints excluded: chain W residue 86 GLU Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 198 HIS Chi-restraints excluded: chain Y residue 74 THR Chi-restraints excluded: chain Y residue 188 VAL Chi-restraints excluded: chain a residue 63 ILE Chi-restraints excluded: chain a residue 65 THR Chi-restraints excluded: chain a residue 112 ASP Chi-restraints excluded: chain c residue 54 VAL Chi-restraints excluded: chain c residue 203 VAL Chi-restraints excluded: chain c residue 239 HIS Chi-restraints excluded: chain d residue 172 ASP Chi-restraints excluded: chain e residue 64 VAL Chi-restraints excluded: chain e residue 222 VAL Chi-restraints excluded: chain e residue 243 THR Chi-restraints excluded: chain f residue 28 ASP Chi-restraints excluded: chain f residue 39 GLU Chi-restraints excluded: chain g residue 52 VAL Chi-restraints excluded: chain g residue 254 LEU Chi-restraints excluded: chain i residue 28 ASP Chi-restraints excluded: chain j residue 28 ASP Chi-restraints excluded: chain k residue 28 ASP Chi-restraints excluded: chain k residue 52 VAL Chi-restraints excluded: chain k residue 205 TYR Chi-restraints excluded: chain k residue 254 LEU Chi-restraints excluded: chain k residue 259 TYR Chi-restraints excluded: chain m residue 178 VAL Chi-restraints excluded: chain m residue 239 HIS Chi-restraints excluded: chain o residue 172 ASP Chi-restraints excluded: chain p residue 64 VAL Chi-restraints excluded: chain p residue 175 ASN Chi-restraints excluded: chain p residue 222 VAL Chi-restraints excluded: chain p residue 243 THR Chi-restraints excluded: chain b residue 12 VAL Chi-restraints excluded: chain b residue 26 ASP Chi-restraints excluded: chain b residue 84 ASP Chi-restraints excluded: chain b residue 101 VAL Chi-restraints excluded: chain X residue 68 ILE Chi-restraints excluded: chain X residue 139 LEU Chi-restraints excluded: chain X residue 172 ASP Chi-restraints excluded: chain X residue 184 LEU Chi-restraints excluded: chain X residue 188 LEU Chi-restraints excluded: chain X residue 199 GLU Chi-restraints excluded: chain Q residue 21 VAL Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 52 ILE Chi-restraints excluded: chain Q residue 60 ASN Chi-restraints excluded: chain Q residue 115 CYS Chi-restraints excluded: chain Q residue 189 LEU Chi-restraints excluded: chain Q residue 196 LEU Chi-restraints excluded: chain T residue 3 ARG Chi-restraints excluded: chain T residue 177 LEU Chi-restraints excluded: chain T residue 221 GLN Chi-restraints excluded: chain O residue 16 PHE Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 139 LEU Chi-restraints excluded: chain O residue 165 PHE Chi-restraints excluded: chain O residue 172 CYS Chi-restraints excluded: chain O residue 196 ILE Chi-restraints excluded: chain Z residue 76 VAL Chi-restraints excluded: chain Z residue 83 LEU Chi-restraints excluded: chain Z residue 176 VAL Chi-restraints excluded: chain Z residue 197 HIS Chi-restraints excluded: chain U residue 47 ILE Chi-restraints excluded: chain U residue 115 VAL Chi-restraints excluded: chain U residue 118 ILE Chi-restraints excluded: chain U residue 221 ILE Chi-restraints excluded: chain U residue 238 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 771 optimal weight: 0.9990 chunk 586 optimal weight: 5.9990 chunk 405 optimal weight: 0.9990 chunk 86 optimal weight: 0.0060 chunk 372 optimal weight: 2.9990 chunk 524 optimal weight: 0.9980 chunk 783 optimal weight: 1.9990 chunk 829 optimal weight: 6.9990 chunk 409 optimal weight: 3.9990 chunk 742 optimal weight: 9.9990 chunk 223 optimal weight: 0.0060 overall best weight: 0.6016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN ** E 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 HIS ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 GLN J 152 ASN K 56 GLN K 69 GLN ** L 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 107 HIS ** M 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 167 HIS ** P 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 104 ASN V 53 GLN ** W 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 56 GLN Y 69 GLN ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 164 GLN f 23 ASN h 174 ASN i 23 ASN i 197 ASN j 23 ASN ** j 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 275 HIS k 239 HIS l 164 GLN l 174 ASN n 23 ASN n 135 HIS n 197 ASN ** p 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 72 ASN b 167 HIS ** X 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 138 HIS ** Z 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 72408 Z= 0.154 Angle : 0.565 24.377 97746 Z= 0.291 Chirality : 0.042 0.213 10936 Planarity : 0.004 0.101 12412 Dihedral : 4.169 74.141 9620 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.50 % Allowed : 20.11 % Favored : 76.39 % 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: -0.73 (0.09), residues: 8660 helix: 1.20 (0.08), residues: 4074 sheet: -1.82 (0.13), residues: 1304 loop : -2.10 (0.10), residues: 3282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP h 162 HIS 0.006 0.001 HIS f 275 PHE 0.035 0.001 PHE m 25 TYR 0.040 0.001 TYR V 156 ARG 0.018 0.000 ARG h 190 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17320 Ramachandran restraints generated. 8660 Oldfield, 0 Emsley, 8660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17320 Ramachandran restraints generated. 8660 Oldfield, 0 Emsley, 8660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1535 residues out of total 7852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 275 poor density : 1260 time to evaluate : 6.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 MET cc_start: 0.7935 (ptt) cc_final: 0.7725 (ttp) REVERT: A 156 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7305 (mt-10) REVERT: B 159 MET cc_start: 0.8501 (tpp) cc_final: 0.8135 (mpp) REVERT: B 171 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7795 (ttm) REVERT: C 17 ARG cc_start: 0.7721 (mtt180) cc_final: 0.6867 (mtp85) REVERT: C 48 ASP cc_start: 0.8005 (t0) cc_final: 0.7473 (m-30) REVERT: C 119 GLN cc_start: 0.8901 (tp40) cc_final: 0.8268 (tm-30) REVERT: C 194 LYS cc_start: 0.8501 (tptt) cc_final: 0.8299 (tptt) REVERT: C 225 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8086 (mtmm) REVERT: D 46 GLU cc_start: 0.6855 (mp0) cc_final: 0.6602 (mm-30) REVERT: D 66 ASP cc_start: 0.7337 (t0) cc_final: 0.6929 (t0) REVERT: D 117 LYS cc_start: 0.6495 (mttt) cc_final: 0.5810 (ttmt) REVERT: D 121 ARG cc_start: 0.7734 (mtt180) cc_final: 0.7341 (ttp-170) REVERT: E 20 ARG cc_start: 0.7443 (mtm180) cc_final: 0.7099 (mtm180) REVERT: E 28 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8617 (mm) REVERT: E 88 LEU cc_start: 0.8925 (mt) cc_final: 0.8712 (mt) REVERT: E 164 ASN cc_start: 0.8346 (m110) cc_final: 0.8078 (m-40) REVERT: E 172 ILE cc_start: 0.8831 (mp) cc_final: 0.8388 (mm) REVERT: E 233 ASN cc_start: 0.8537 (p0) cc_final: 0.7690 (t0) REVERT: F 68 ASP cc_start: 0.7984 (p0) cc_final: 0.7525 (p0) REVERT: F 82 LYS cc_start: 0.8576 (tppt) cc_final: 0.8241 (tptt) REVERT: F 147 ARG cc_start: 0.8299 (mtt90) cc_final: 0.7881 (mtt-85) REVERT: F 154 GLU cc_start: 0.6917 (tt0) cc_final: 0.6630 (tt0) REVERT: F 190 CYS cc_start: 0.8320 (t) cc_final: 0.7941 (t) REVERT: F 227 GLN cc_start: 0.7708 (tm-30) cc_final: 0.7245 (tm-30) REVERT: G 118 ILE cc_start: 0.9446 (OUTLIER) cc_final: 0.8954 (tt) REVERT: G 128 TYR cc_start: 0.8304 (m-80) cc_final: 0.8078 (m-80) REVERT: H 62 TYR cc_start: 0.7855 (OUTLIER) cc_final: 0.7255 (t80) REVERT: H 78 GLU cc_start: 0.8073 (tt0) cc_final: 0.7680 (tt0) REVERT: H 173 ILE cc_start: 0.4889 (OUTLIER) cc_final: 0.4388 (mt) REVERT: H 177 HIS cc_start: 0.6376 (OUTLIER) cc_final: 0.5822 (t-170) REVERT: H 248 MET cc_start: 0.7107 (tpp) cc_final: 0.6721 (mtp) REVERT: I 78 MET cc_start: 0.8173 (ttt) cc_final: 0.7590 (ttm) REVERT: I 82 ARG cc_start: 0.8375 (mtp85) cc_final: 0.7938 (ttm-80) REVERT: I 122 LEU cc_start: 0.8813 (mt) cc_final: 0.8578 (mt) REVERT: J 191 ASP cc_start: 0.7209 (t0) cc_final: 0.6730 (t0) REVERT: K 92 TYR cc_start: 0.7120 (m-10) cc_final: 0.6315 (m-10) REVERT: K 98 PHE cc_start: 0.7497 (OUTLIER) cc_final: 0.7189 (t80) REVERT: K 114 GLN cc_start: 0.7946 (mm-40) cc_final: 0.7551 (mt0) REVERT: L 67 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7530 (mm-30) REVERT: M 190 ASN cc_start: 0.7690 (t0) cc_final: 0.7473 (t0) REVERT: N 89 GLN cc_start: 0.8668 (tp-100) cc_final: 0.8327 (tm-30) REVERT: N 184 PHE cc_start: 0.8014 (m-80) cc_final: 0.7635 (m-80) REVERT: R 117 LYS cc_start: 0.6601 (mttt) cc_final: 0.5829 (ttmt) REVERT: R 121 ARG cc_start: 0.7615 (mtt180) cc_final: 0.7330 (mtm-85) REVERT: S 28 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8618 (mm) REVERT: S 104 ASN cc_start: 0.8125 (OUTLIER) cc_final: 0.7554 (m110) REVERT: S 172 ILE cc_start: 0.8905 (mp) cc_final: 0.8519 (mm) REVERT: V 86 THR cc_start: 0.9002 (m) cc_final: 0.8739 (m) REVERT: V 89 ASP cc_start: 0.7161 (p0) cc_final: 0.6847 (p0) REVERT: V 173 ILE cc_start: 0.4824 (OUTLIER) cc_final: 0.4396 (mt) REVERT: V 177 HIS cc_start: 0.6629 (OUTLIER) cc_final: 0.6053 (t-170) REVERT: W 86 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7419 (pm20) REVERT: W 122 LEU cc_start: 0.8840 (mt) cc_final: 0.8578 (mt) REVERT: W 144 ASP cc_start: 0.7756 (m-30) cc_final: 0.7446 (m-30) REVERT: Y 76 MET cc_start: 0.8488 (ttt) cc_final: 0.8275 (tpp) REVERT: Y 92 TYR cc_start: 0.7164 (m-10) cc_final: 0.6689 (m-10) REVERT: Y 114 GLN cc_start: 0.7951 (mm-40) cc_final: 0.7507 (mt0) REVERT: Y 166 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8205 (tm-30) REVERT: c 207 MET cc_start: 0.7680 (tmm) cc_final: 0.7015 (tmm) REVERT: c 226 GLN cc_start: 0.8753 (mp10) cc_final: 0.7694 (tm-30) REVERT: c 237 TRP cc_start: 0.7588 (t-100) cc_final: 0.6454 (t60) REVERT: c 247 MET cc_start: 0.8550 (ttm) cc_final: 0.8089 (ttt) REVERT: c 262 TRP cc_start: 0.7580 (t-100) cc_final: 0.7222 (t60) REVERT: d 27 TYR cc_start: 0.7803 (t80) cc_final: 0.7278 (t80) REVERT: d 226 GLN cc_start: 0.6396 (mt0) cc_final: 0.5845 (tt0) REVERT: d 266 VAL cc_start: 0.6946 (t) cc_final: 0.6727 (m) REVERT: e 162 TRP cc_start: 0.8730 (t60) cc_final: 0.8400 (t60) REVERT: f 190 ARG cc_start: 0.8534 (ttp-170) cc_final: 0.8279 (ptm-80) REVERT: f 224 ASP cc_start: 0.7663 (m-30) cc_final: 0.6699 (t0) REVERT: g 248 ARG cc_start: 0.8529 (ttp-110) cc_final: 0.8257 (ttp-110) REVERT: h 194 SER cc_start: 0.8248 (p) cc_final: 0.7957 (p) REVERT: h 196 PHE cc_start: 0.8113 (t80) cc_final: 0.7882 (t80) REVERT: h 263 GLU cc_start: 0.8605 (mp0) cc_final: 0.8160 (mm-30) REVERT: i 164 GLN cc_start: 0.8171 (mt0) cc_final: 0.7798 (mt0) REVERT: i 176 PHE cc_start: 0.7631 (t80) cc_final: 0.7327 (t80) REVERT: i 226 GLN cc_start: 0.7769 (tt0) cc_final: 0.7262 (tm-30) REVERT: i 262 TRP cc_start: 0.4998 (t-100) cc_final: 0.4762 (t60) REVERT: j 190 ARG cc_start: 0.8199 (ptm-80) cc_final: 0.7856 (ptm-80) REVERT: j 224 ASP cc_start: 0.7890 (m-30) cc_final: 0.7237 (t0) REVERT: k 190 ARG cc_start: 0.8031 (ttt-90) cc_final: 0.7720 (ttt180) REVERT: k 207 MET cc_start: 0.9331 (tpp) cc_final: 0.8827 (tpt) REVERT: k 255 TYR cc_start: 0.7757 (t80) cc_final: 0.6319 (t80) REVERT: k 259 TYR cc_start: 0.6272 (OUTLIER) cc_final: 0.5227 (m-80) REVERT: l 37 LEU cc_start: 0.8620 (mt) cc_final: 0.8243 (tt) REVERT: l 194 SER cc_start: 0.8170 (p) cc_final: 0.7808 (p) REVERT: l 247 MET cc_start: 0.7835 (mmm) cc_final: 0.7385 (mtp) REVERT: m 176 PHE cc_start: 0.7320 (t80) cc_final: 0.7082 (t80) REVERT: m 226 GLN cc_start: 0.8878 (mp10) cc_final: 0.8405 (mp10) REVERT: m 247 MET cc_start: 0.8639 (ttm) cc_final: 0.8177 (mtt) REVERT: m 248 ARG cc_start: 0.8536 (tmm-80) cc_final: 0.7621 (ttp80) REVERT: n 150 SER cc_start: 0.8947 (t) cc_final: 0.8413 (p) REVERT: n 176 PHE cc_start: 0.7658 (t80) cc_final: 0.7356 (t80) REVERT: n 226 GLN cc_start: 0.8104 (tt0) cc_final: 0.7441 (tm-30) REVERT: o 226 GLN cc_start: 0.6284 (mt0) cc_final: 0.5967 (tt0) REVERT: p 162 TRP cc_start: 0.8676 (t60) cc_final: 0.8037 (t60) REVERT: p 182 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7694 (tm-30) REVERT: p 186 GLN cc_start: 0.8607 (tm-30) cc_final: 0.8312 (tm-30) REVERT: p 256 ASP cc_start: 0.8097 (t0) cc_final: 0.7712 (t0) REVERT: b 89 GLN cc_start: 0.8672 (tp-100) cc_final: 0.8331 (tm-30) REVERT: b 128 ASP cc_start: 0.6616 (m-30) cc_final: 0.6319 (m-30) REVERT: X 188 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7335 (tp) REVERT: X 191 ASP cc_start: 0.7208 (t0) cc_final: 0.6669 (t0) REVERT: Q 119 GLN cc_start: 0.8935 (tp40) cc_final: 0.8612 (tt0) REVERT: T 68 ASP cc_start: 0.7865 (p0) cc_final: 0.7549 (p0) REVERT: T 147 ARG cc_start: 0.8243 (mtt90) cc_final: 0.7797 (mtt-85) REVERT: T 154 GLU cc_start: 0.7065 (tt0) cc_final: 0.6730 (tt0) REVERT: T 190 CYS cc_start: 0.8337 (t) cc_final: 0.7940 (t) REVERT: T 221 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7758 (pt0) REVERT: T 227 GLN cc_start: 0.7686 (tm-30) cc_final: 0.7224 (tm-30) REVERT: Z 35 ILE cc_start: 0.9251 (mp) cc_final: 0.9003 (mt) REVERT: Z 56 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7266 (mp0) REVERT: U 128 TYR cc_start: 0.8459 (m-80) cc_final: 0.8170 (m-80) outliers start: 275 outliers final: 148 residues processed: 1445 average time/residue: 0.6490 time to fit residues: 1610.9985 Evaluate side-chains 1286 residues out of total 7852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 1122 time to evaluate : 6.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 115 CYS Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 221 ILE Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain H residue 76 PHE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 177 HIS Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 79 CYS Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 198 HIS Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 68 ILE Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain K residue 159 ILE Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 188 VAL Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 197 HIS Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain M residue 185 ASN Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 15 ILE Chi-restraints excluded: chain N residue 26 ASP Chi-restraints excluded: chain P residue 12 THR Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 169 ASN Chi-restraints excluded: chain P residue 215 ASP Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 55 ASN Chi-restraints excluded: chain R residue 68 HIS Chi-restraints excluded: chain R residue 129 ILE Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 159 GLN Chi-restraints excluded: chain S residue 13 ASN Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 104 ASN Chi-restraints excluded: chain S residue 141 VAL Chi-restraints excluded: chain S residue 198 ILE Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 44 CYS Chi-restraints excluded: chain V residue 62 TYR Chi-restraints excluded: chain V residue 76 PHE Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain V residue 87 THR Chi-restraints excluded: chain V residue 173 ILE Chi-restraints excluded: chain V residue 177 HIS Chi-restraints excluded: chain W residue 2 THR Chi-restraints excluded: chain W residue 41 ILE Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 79 CYS Chi-restraints excluded: chain W residue 86 GLU Chi-restraints excluded: chain W residue 198 HIS Chi-restraints excluded: chain Y residue 153 VAL Chi-restraints excluded: chain Y residue 173 LEU Chi-restraints excluded: chain Y residue 188 VAL Chi-restraints excluded: chain a residue 63 ILE Chi-restraints excluded: chain a residue 65 THR Chi-restraints excluded: chain a residue 112 ASP Chi-restraints excluded: chain a residue 185 ASN Chi-restraints excluded: chain a residue 236 ASP Chi-restraints excluded: chain c residue 183 GLU Chi-restraints excluded: chain d residue 172 ASP Chi-restraints excluded: chain d residue 217 LEU Chi-restraints excluded: chain e residue 64 VAL Chi-restraints excluded: chain e residue 222 VAL Chi-restraints excluded: chain e residue 243 THR Chi-restraints excluded: chain f residue 28 ASP Chi-restraints excluded: chain f residue 39 GLU Chi-restraints excluded: chain g residue 52 VAL Chi-restraints excluded: chain g residue 254 LEU Chi-restraints excluded: chain i residue 48 PHE Chi-restraints excluded: chain j residue 28 ASP Chi-restraints excluded: chain j residue 254 LEU Chi-restraints excluded: chain k residue 52 VAL Chi-restraints excluded: chain k residue 205 TYR Chi-restraints excluded: chain k residue 254 LEU Chi-restraints excluded: chain k residue 259 TYR Chi-restraints excluded: chain l residue 239 HIS Chi-restraints excluded: chain m residue 178 VAL Chi-restraints excluded: chain m residue 239 HIS Chi-restraints excluded: chain o residue 172 ASP Chi-restraints excluded: chain o residue 251 TYR Chi-restraints excluded: chain p residue 64 VAL Chi-restraints excluded: chain p residue 222 VAL Chi-restraints excluded: chain p residue 243 THR Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 12 VAL Chi-restraints excluded: chain b residue 26 ASP Chi-restraints excluded: chain b residue 84 ASP Chi-restraints excluded: chain b residue 101 VAL Chi-restraints excluded: chain X residue 44 ILE Chi-restraints excluded: chain X residue 139 LEU Chi-restraints excluded: chain X residue 172 ASP Chi-restraints excluded: chain X residue 188 LEU Chi-restraints excluded: chain X residue 199 GLU Chi-restraints excluded: chain Q residue 21 VAL Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 52 ILE Chi-restraints excluded: chain Q residue 60 ASN Chi-restraints excluded: chain Q residue 115 CYS Chi-restraints excluded: chain T residue 221 GLN Chi-restraints excluded: chain O residue 16 PHE Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 139 LEU Chi-restraints excluded: chain O residue 165 PHE Chi-restraints excluded: chain O residue 196 ILE Chi-restraints excluded: chain Z residue 76 VAL Chi-restraints excluded: chain Z residue 83 LEU Chi-restraints excluded: chain Z residue 176 VAL Chi-restraints excluded: chain Z residue 197 HIS Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 111 LEU Chi-restraints excluded: chain U residue 115 VAL Chi-restraints excluded: chain U residue 118 ILE Chi-restraints excluded: chain U residue 221 ILE Chi-restraints excluded: chain U residue 238 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 690 optimal weight: 0.8980 chunk 470 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 chunk 617 optimal weight: 10.0000 chunk 342 optimal weight: 9.9990 chunk 707 optimal weight: 0.2980 chunk 573 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 423 optimal weight: 2.9990 chunk 744 optimal weight: 7.9990 chunk 209 optimal weight: 5.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN ** E 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 HIS G 35 ASN G 54 ASN ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 ASN ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 56 GLN K 69 GLN M 36 ASN ** M 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 72 ASN ** P 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 163 GLN ** W 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 23 ASN ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 239 HIS ** d 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 197 ASN f 239 HIS ** h 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 32 GLN i 197 ASN ** j 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 275 HIS k 239 HIS ** l 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 239 HIS ** n 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 197 ASN ** o 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 197 ASN b 72 ASN X 152 ASN Q 71 HIS ** Q 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 138 HIS Z 158 ASN U 35 ASN U 54 ASN U 144 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 72408 Z= 0.256 Angle : 0.624 26.241 97746 Z= 0.321 Chirality : 0.043 0.316 10936 Planarity : 0.004 0.107 12412 Dihedral : 4.366 75.326 9620 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.12 % Favored : 93.87 % Rotamer: Outliers : 4.25 % Allowed : 21.12 % Favored : 74.63 % 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: -0.65 (0.09), residues: 8660 helix: 1.28 (0.08), residues: 4068 sheet: -1.89 (0.13), residues: 1348 loop : -2.01 (0.11), residues: 3244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP h 162 HIS 0.005 0.001 HIS f 275 PHE 0.024 0.002 PHE m 176 TYR 0.041 0.001 TYR V 156 ARG 0.008 0.001 ARG Y 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17320 Ramachandran restraints generated. 8660 Oldfield, 0 Emsley, 8660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17320 Ramachandran restraints generated. 8660 Oldfield, 0 Emsley, 8660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1495 residues out of total 7852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 334 poor density : 1161 time to evaluate : 6.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 MET cc_start: 0.7698 (ptt) cc_final: 0.7330 (ttp) REVERT: B 159 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.8010 (mpp) REVERT: B 168 GLN cc_start: 0.8903 (tp-100) cc_final: 0.8677 (tp-100) REVERT: C 17 ARG cc_start: 0.7913 (mtt180) cc_final: 0.7383 (mtp180) REVERT: C 48 ASP cc_start: 0.8120 (t0) cc_final: 0.7532 (m-30) REVERT: C 225 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8357 (mtmm) REVERT: D 117 LYS cc_start: 0.6571 (mttt) cc_final: 0.5848 (ttmt) REVERT: D 121 ARG cc_start: 0.7747 (mtt180) cc_final: 0.7437 (mtm-85) REVERT: E 20 ARG cc_start: 0.7463 (mtm180) cc_final: 0.7147 (mtm180) REVERT: E 28 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8626 (mm) REVERT: E 99 TYR cc_start: 0.8825 (t80) cc_final: 0.8618 (t80) REVERT: E 233 ASN cc_start: 0.8568 (p0) cc_final: 0.7734 (t0) REVERT: F 68 ASP cc_start: 0.8035 (p0) cc_final: 0.7468 (p0) REVERT: F 82 LYS cc_start: 0.8654 (tppt) cc_final: 0.8303 (tptt) REVERT: F 154 GLU cc_start: 0.7099 (tt0) cc_final: 0.6747 (tt0) REVERT: F 190 CYS cc_start: 0.8341 (t) cc_final: 0.7939 (t) REVERT: F 227 GLN cc_start: 0.7766 (tm-30) cc_final: 0.7488 (tm-30) REVERT: G 118 ILE cc_start: 0.9535 (OUTLIER) cc_final: 0.9063 (tt) REVERT: G 128 TYR cc_start: 0.8278 (m-80) cc_final: 0.7942 (m-80) REVERT: G 199 PHE cc_start: 0.7704 (m-10) cc_final: 0.7477 (m-10) REVERT: H 62 TYR cc_start: 0.7873 (OUTLIER) cc_final: 0.7236 (t80) REVERT: H 78 GLU cc_start: 0.8158 (tt0) cc_final: 0.7828 (tt0) REVERT: H 173 ILE cc_start: 0.4811 (OUTLIER) cc_final: 0.4315 (mt) REVERT: H 177 HIS cc_start: 0.6704 (OUTLIER) cc_final: 0.6244 (t-170) REVERT: H 248 MET cc_start: 0.7270 (tpp) cc_final: 0.6789 (mtp) REVERT: I 122 LEU cc_start: 0.8838 (mt) cc_final: 0.8531 (mt) REVERT: J 191 ASP cc_start: 0.7297 (t0) cc_final: 0.6827 (t0) REVERT: J 196 TRP cc_start: 0.6917 (t60) cc_final: 0.6571 (t60) REVERT: K 92 TYR cc_start: 0.7267 (m-10) cc_final: 0.6819 (m-10) REVERT: K 114 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7655 (mt0) REVERT: K 166 GLU cc_start: 0.8567 (tm-30) cc_final: 0.7943 (tm-30) REVERT: L 67 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7548 (mm-30) REVERT: L 88 TYR cc_start: 0.7312 (t80) cc_final: 0.7090 (t80) REVERT: M 101 GLN cc_start: 0.8738 (mm110) cc_final: 0.8511 (mm-40) REVERT: N 184 PHE cc_start: 0.8162 (m-80) cc_final: 0.7770 (m-80) REVERT: P 10 LEU cc_start: 0.7282 (mt) cc_final: 0.6690 (pp) REVERT: P 168 GLN cc_start: 0.8902 (tp-100) cc_final: 0.8699 (tp-100) REVERT: R 66 ASP cc_start: 0.7617 (t0) cc_final: 0.7139 (t0) REVERT: R 117 LYS cc_start: 0.6724 (mttt) cc_final: 0.5946 (ttmt) REVERT: R 121 ARG cc_start: 0.7751 (mtt180) cc_final: 0.7275 (mtm180) REVERT: S 28 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8617 (mm) REVERT: V 62 TYR cc_start: 0.7731 (OUTLIER) cc_final: 0.7238 (t80) REVERT: V 173 ILE cc_start: 0.5002 (OUTLIER) cc_final: 0.4654 (mt) REVERT: V 177 HIS cc_start: 0.6787 (OUTLIER) cc_final: 0.6363 (t-170) REVERT: W 122 LEU cc_start: 0.8869 (mt) cc_final: 0.8557 (mt) REVERT: W 144 ASP cc_start: 0.7936 (m-30) cc_final: 0.7592 (m-30) REVERT: Y 114 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7681 (mt0) REVERT: Y 166 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8344 (tm-30) REVERT: Y 178 TYR cc_start: 0.7583 (OUTLIER) cc_final: 0.7288 (m-80) REVERT: a 101 GLN cc_start: 0.8736 (mm110) cc_final: 0.8462 (mm-40) REVERT: a 186 GLN cc_start: 0.8161 (tp40) cc_final: 0.7805 (tm-30) REVERT: a 194 ASN cc_start: 0.8531 (OUTLIER) cc_final: 0.8306 (p0) REVERT: a 213 ASP cc_start: 0.7718 (t0) cc_final: 0.7462 (t0) REVERT: a 236 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7603 (p0) REVERT: c 207 MET cc_start: 0.7580 (tmm) cc_final: 0.6895 (tmm) REVERT: c 237 TRP cc_start: 0.7739 (t-100) cc_final: 0.6494 (t60) REVERT: c 247 MET cc_start: 0.8608 (ttm) cc_final: 0.8062 (ttt) REVERT: d 27 TYR cc_start: 0.7768 (t80) cc_final: 0.7207 (t80) REVERT: d 226 GLN cc_start: 0.6348 (mt0) cc_final: 0.5822 (tt0) REVERT: d 266 VAL cc_start: 0.7086 (t) cc_final: 0.6867 (m) REVERT: e 162 TRP cc_start: 0.8748 (t60) cc_final: 0.8424 (t60) REVERT: f 190 ARG cc_start: 0.8559 (ttp-170) cc_final: 0.8290 (ptm-80) REVERT: f 224 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.6823 (t0) REVERT: g 248 ARG cc_start: 0.8600 (ttp-110) cc_final: 0.8270 (ttp-110) REVERT: h 190 ARG cc_start: 0.8426 (ptm-80) cc_final: 0.8225 (ptm-80) REVERT: h 194 SER cc_start: 0.8296 (p) cc_final: 0.7938 (p) REVERT: h 196 PHE cc_start: 0.8250 (t80) cc_final: 0.8013 (t80) REVERT: h 263 GLU cc_start: 0.8520 (mp0) cc_final: 0.8184 (mm-30) REVERT: i 164 GLN cc_start: 0.8209 (mt0) cc_final: 0.7910 (mt0) REVERT: i 176 PHE cc_start: 0.7464 (t80) cc_final: 0.7137 (t80) REVERT: i 226 GLN cc_start: 0.7799 (tt0) cc_final: 0.7245 (tm-30) REVERT: j 224 ASP cc_start: 0.7700 (m-30) cc_final: 0.7187 (t0) REVERT: j 248 ARG cc_start: 0.8041 (ptt180) cc_final: 0.7550 (ttp-110) REVERT: k 259 TYR cc_start: 0.6433 (OUTLIER) cc_final: 0.5097 (m-80) REVERT: l 37 LEU cc_start: 0.8726 (mt) cc_final: 0.8247 (tt) REVERT: l 194 SER cc_start: 0.8360 (p) cc_final: 0.8027 (p) REVERT: l 237 TRP cc_start: 0.7167 (t-100) cc_final: 0.6719 (t-100) REVERT: l 247 MET cc_start: 0.7856 (mmm) cc_final: 0.7388 (mtp) REVERT: m 204 LYS cc_start: 0.8629 (mmtm) cc_final: 0.8365 (mmtm) REVERT: m 226 GLN cc_start: 0.8894 (mp10) cc_final: 0.8523 (mp10) REVERT: m 247 MET cc_start: 0.8639 (ttm) cc_final: 0.8145 (mtt) REVERT: m 248 ARG cc_start: 0.8575 (tmm-80) cc_final: 0.7827 (ptm-80) REVERT: n 150 SER cc_start: 0.8890 (OUTLIER) cc_final: 0.8302 (p) REVERT: n 176 PHE cc_start: 0.7698 (t80) cc_final: 0.7414 (t80) REVERT: n 226 GLN cc_start: 0.8162 (tt0) cc_final: 0.7468 (tm-30) REVERT: p 162 TRP cc_start: 0.8811 (t60) cc_final: 0.8126 (t60) REVERT: p 175 ASN cc_start: 0.7397 (OUTLIER) cc_final: 0.7035 (p0) REVERT: p 182 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7772 (tm-30) REVERT: p 186 GLN cc_start: 0.8530 (tm-30) cc_final: 0.8321 (tm-30) REVERT: p 187 GLU cc_start: 0.9032 (mp0) cc_final: 0.8583 (mp0) REVERT: p 256 ASP cc_start: 0.8054 (t0) cc_final: 0.7687 (t0) REVERT: X 188 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.7682 (tp) REVERT: X 191 ASP cc_start: 0.7269 (t0) cc_final: 0.6730 (t0) REVERT: Q 119 GLN cc_start: 0.9099 (tp40) cc_final: 0.8467 (tp40) REVERT: T 3 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.7083 (ptp-170) REVERT: T 68 ASP cc_start: 0.7991 (p0) cc_final: 0.7458 (p0) REVERT: T 154 GLU cc_start: 0.7131 (tt0) cc_final: 0.6785 (tt0) REVERT: T 190 CYS cc_start: 0.8373 (t) cc_final: 0.7954 (t) REVERT: T 221 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7601 (pt0) REVERT: T 227 GLN cc_start: 0.7744 (tm-30) cc_final: 0.7457 (tm-30) REVERT: Z 35 ILE cc_start: 0.9289 (mp) cc_final: 0.9021 (mt) REVERT: U 128 TYR cc_start: 0.8321 (m-80) cc_final: 0.8046 (m-80) REVERT: U 199 PHE cc_start: 0.7959 (m-10) cc_final: 0.7745 (m-80) outliers start: 334 outliers final: 215 residues processed: 1387 average time/residue: 0.6439 time to fit residues: 1537.3836 Evaluate side-chains 1302 residues out of total 7852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 1066 time to evaluate : 6.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 115 CYS Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 159 GLN Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 184 GLN Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 221 ILE Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain H residue 76 PHE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 177 HIS Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 13 ILE Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 79 CYS Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 181 ASP Chi-restraints excluded: chain I residue 198 HIS Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 138 ASP Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 160 PHE Chi-restraints excluded: chain J residue 172 ASP Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 159 ILE Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 188 VAL Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 197 HIS Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain M residue 185 ASN Chi-restraints excluded: chain M residue 187 LEU Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 15 ILE Chi-restraints excluded: chain N residue 26 ASP Chi-restraints excluded: chain N residue 84 ASP Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain P residue 12 THR Chi-restraints excluded: chain P residue 16 THR Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 169 ASN Chi-restraints excluded: chain P residue 215 ASP Chi-restraints excluded: chain R residue 31 CYS Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 55 ASN Chi-restraints excluded: chain R residue 68 HIS Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 129 ILE Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain S residue 13 ASN Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain S residue 141 VAL Chi-restraints excluded: chain S residue 164 ASN Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 184 GLN Chi-restraints excluded: chain S residue 198 ILE Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 62 TYR Chi-restraints excluded: chain V residue 76 PHE Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain V residue 87 THR Chi-restraints excluded: chain V residue 157 ASP Chi-restraints excluded: chain V residue 173 ILE Chi-restraints excluded: chain V residue 177 HIS Chi-restraints excluded: chain V residue 209 LEU Chi-restraints excluded: chain W residue 2 THR Chi-restraints excluded: chain W residue 13 ILE Chi-restraints excluded: chain W residue 18 THR Chi-restraints excluded: chain W residue 41 ILE Chi-restraints excluded: chain W residue 79 CYS Chi-restraints excluded: chain W residue 80 VAL Chi-restraints excluded: chain W residue 181 ASP Chi-restraints excluded: chain W residue 198 HIS Chi-restraints excluded: chain Y residue 74 THR Chi-restraints excluded: chain Y residue 173 LEU Chi-restraints excluded: chain Y residue 178 TYR Chi-restraints excluded: chain Y residue 188 VAL Chi-restraints excluded: chain a residue 63 ILE Chi-restraints excluded: chain a residue 65 THR Chi-restraints excluded: chain a residue 89 ILE Chi-restraints excluded: chain a residue 112 ASP Chi-restraints excluded: chain a residue 185 ASN Chi-restraints excluded: chain a residue 187 LEU Chi-restraints excluded: chain a residue 194 ASN Chi-restraints excluded: chain a residue 236 ASP Chi-restraints excluded: chain c residue 183 GLU Chi-restraints excluded: chain c residue 203 VAL Chi-restraints excluded: chain c residue 222 VAL Chi-restraints excluded: chain c residue 239 HIS Chi-restraints excluded: chain d residue 172 ASP Chi-restraints excluded: chain d residue 217 LEU Chi-restraints excluded: chain e residue 64 VAL Chi-restraints excluded: chain e residue 222 VAL Chi-restraints excluded: chain e residue 243 THR Chi-restraints excluded: chain f residue 28 ASP Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain f residue 39 GLU Chi-restraints excluded: chain f residue 224 ASP Chi-restraints excluded: chain f residue 275 HIS Chi-restraints excluded: chain g residue 52 VAL Chi-restraints excluded: chain g residue 63 ASN Chi-restraints excluded: chain g residue 254 LEU Chi-restraints excluded: chain h residue 52 VAL Chi-restraints excluded: chain i residue 28 ASP Chi-restraints excluded: chain j residue 28 ASP Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 254 LEU Chi-restraints excluded: chain j residue 258 LEU Chi-restraints excluded: chain k residue 52 VAL Chi-restraints excluded: chain k residue 205 TYR Chi-restraints excluded: chain k residue 254 LEU Chi-restraints excluded: chain k residue 259 TYR Chi-restraints excluded: chain l residue 239 HIS Chi-restraints excluded: chain l residue 242 ILE Chi-restraints excluded: chain m residue 67 LEU Chi-restraints excluded: chain m residue 178 VAL Chi-restraints excluded: chain m residue 222 VAL Chi-restraints excluded: chain m residue 239 HIS Chi-restraints excluded: chain n residue 150 SER Chi-restraints excluded: chain n residue 170 ILE Chi-restraints excluded: chain n residue 252 ILE Chi-restraints excluded: chain o residue 251 TYR Chi-restraints excluded: chain p residue 64 VAL Chi-restraints excluded: chain p residue 175 ASN Chi-restraints excluded: chain p residue 222 VAL Chi-restraints excluded: chain p residue 243 THR Chi-restraints excluded: chain b residue 12 VAL Chi-restraints excluded: chain b residue 26 ASP Chi-restraints excluded: chain b residue 84 ASP Chi-restraints excluded: chain b residue 101 VAL Chi-restraints excluded: chain b residue 109 LEU Chi-restraints excluded: chain X residue 44 ILE Chi-restraints excluded: chain X residue 60 THR Chi-restraints excluded: chain X residue 99 SER Chi-restraints excluded: chain X residue 138 ASP Chi-restraints excluded: chain X residue 139 LEU Chi-restraints excluded: chain X residue 160 PHE Chi-restraints excluded: chain X residue 172 ASP Chi-restraints excluded: chain X residue 188 LEU Chi-restraints excluded: chain Q residue 21 VAL Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 60 ASN Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 115 CYS Chi-restraints excluded: chain Q residue 143 ASP Chi-restraints excluded: chain Q residue 201 ASP Chi-restraints excluded: chain T residue 3 ARG Chi-restraints excluded: chain T residue 221 GLN Chi-restraints excluded: chain O residue 16 PHE Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 139 LEU Chi-restraints excluded: chain O residue 142 CYS Chi-restraints excluded: chain O residue 165 PHE Chi-restraints excluded: chain O residue 196 ILE Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain Z residue 76 VAL Chi-restraints excluded: chain Z residue 83 LEU Chi-restraints excluded: chain Z residue 176 VAL Chi-restraints excluded: chain Z residue 197 HIS Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 61 ILE Chi-restraints excluded: chain U residue 77 ILE Chi-restraints excluded: chain U residue 111 LEU Chi-restraints excluded: chain U residue 115 VAL Chi-restraints excluded: chain U residue 147 ASP Chi-restraints excluded: chain U residue 150 ASP Chi-restraints excluded: chain U residue 221 ILE Chi-restraints excluded: chain U residue 238 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 279 optimal weight: 2.9990 chunk 746 optimal weight: 4.9990 chunk 163 optimal weight: 6.9990 chunk 486 optimal weight: 0.9980 chunk 204 optimal weight: 0.6980 chunk 830 optimal weight: 0.7980 chunk 689 optimal weight: 7.9990 chunk 384 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 274 optimal weight: 6.9990 chunk 435 optimal weight: 0.6980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 GLN ** E 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN F 138 HIS ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 152 ASN K 23 ASN L 158 ASN ** M 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 207 ASN R 116 GLN ** S 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 104 ASN ** W 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 69 GLN ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 239 HIS ** d 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 197 ASN j 135 HIS ** j 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 275 HIS k 239 HIS ** l 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 197 ASN ** o 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 72 ASN ** X 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 138 HIS Z 158 ASN ** U 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 72408 Z= 0.188 Angle : 0.585 24.792 97746 Z= 0.300 Chirality : 0.042 0.251 10936 Planarity : 0.004 0.101 12412 Dihedral : 4.303 74.825 9620 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.10 % Favored : 94.88 % Rotamer: Outliers : 3.81 % Allowed : 22.30 % Favored : 73.89 % 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: -0.52 (0.09), residues: 8660 helix: 1.40 (0.08), residues: 4078 sheet: -1.77 (0.13), residues: 1342 loop : -1.99 (0.11), residues: 3240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP h 162 HIS 0.016 0.001 HIS m 239 PHE 0.035 0.001 PHE N 44 TYR 0.035 0.001 TYR C 223 ARG 0.008 0.000 ARG i 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17320 Ramachandran restraints generated. 8660 Oldfield, 0 Emsley, 8660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17320 Ramachandran restraints generated. 8660 Oldfield, 0 Emsley, 8660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1475 residues out of total 7852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 299 poor density : 1176 time to evaluate : 6.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 MET cc_start: 0.7547 (ptt) cc_final: 0.7194 (ttp) REVERT: B 159 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8074 (mmm) REVERT: B 168 GLN cc_start: 0.8901 (tp-100) cc_final: 0.8686 (tp-100) REVERT: C 17 ARG cc_start: 0.7849 (mtt180) cc_final: 0.6994 (mtp85) REVERT: C 48 ASP cc_start: 0.8051 (t0) cc_final: 0.7510 (m-30) REVERT: C 194 LYS cc_start: 0.8562 (tptt) cc_final: 0.8329 (tptt) REVERT: C 225 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8238 (mtmm) REVERT: D 117 LYS cc_start: 0.6522 (mttt) cc_final: 0.5787 (ttmt) REVERT: D 121 ARG cc_start: 0.7795 (mtt180) cc_final: 0.7395 (mtm-85) REVERT: E 20 ARG cc_start: 0.7374 (mtm180) cc_final: 0.7047 (mtm180) REVERT: E 28 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8618 (mm) REVERT: E 233 ASN cc_start: 0.8493 (p0) cc_final: 0.7616 (t0) REVERT: F 31 GLN cc_start: 0.8453 (mm110) cc_final: 0.7802 (tp40) REVERT: F 68 ASP cc_start: 0.8044 (p0) cc_final: 0.7503 (p0) REVERT: F 82 LYS cc_start: 0.8622 (tppt) cc_final: 0.8277 (tptt) REVERT: F 117 GLN cc_start: 0.8744 (tp40) cc_final: 0.8334 (tp40) REVERT: F 154 GLU cc_start: 0.7019 (tt0) cc_final: 0.6687 (tt0) REVERT: F 190 CYS cc_start: 0.8379 (t) cc_final: 0.7910 (t) REVERT: F 227 GLN cc_start: 0.7777 (tm-30) cc_final: 0.7190 (tm-30) REVERT: G 118 ILE cc_start: 0.9492 (OUTLIER) cc_final: 0.9034 (tt) REVERT: G 128 TYR cc_start: 0.8313 (m-80) cc_final: 0.8036 (m-80) REVERT: H 62 TYR cc_start: 0.7782 (OUTLIER) cc_final: 0.7283 (t80) REVERT: H 78 GLU cc_start: 0.8179 (tt0) cc_final: 0.7877 (tt0) REVERT: H 173 ILE cc_start: 0.4976 (OUTLIER) cc_final: 0.4445 (mt) REVERT: H 177 HIS cc_start: 0.6541 (OUTLIER) cc_final: 0.5879 (t-170) REVERT: I 122 LEU cc_start: 0.8859 (mt) cc_final: 0.8531 (mt) REVERT: I 215 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8404 (tm-30) REVERT: J 191 ASP cc_start: 0.7145 (t0) cc_final: 0.6535 (t0) REVERT: K 92 TYR cc_start: 0.7210 (m-10) cc_final: 0.6443 (m-10) REVERT: K 98 PHE cc_start: 0.7537 (OUTLIER) cc_final: 0.7330 (t80) REVERT: K 114 GLN cc_start: 0.8067 (mm-40) cc_final: 0.7717 (mt0) REVERT: K 166 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8031 (tm-30) REVERT: L 67 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7548 (mm-30) REVERT: L 72 GLU cc_start: 0.8005 (pp20) cc_final: 0.7450 (pp20) REVERT: L 88 TYR cc_start: 0.7203 (t80) cc_final: 0.6960 (t80) REVERT: M 101 GLN cc_start: 0.8730 (mm110) cc_final: 0.8472 (mm-40) REVERT: M 135 PHE cc_start: 0.8652 (OUTLIER) cc_final: 0.8442 (m-80) REVERT: M 186 GLN cc_start: 0.8134 (tp40) cc_final: 0.7736 (tm-30) REVERT: N 62 GLN cc_start: 0.8815 (mm110) cc_final: 0.8522 (mm110) REVERT: N 184 PHE cc_start: 0.8143 (m-80) cc_final: 0.7734 (m-80) REVERT: P 168 GLN cc_start: 0.8906 (tp-100) cc_final: 0.8704 (tp-100) REVERT: R 117 LYS cc_start: 0.6823 (mttt) cc_final: 0.5982 (ttmt) REVERT: R 121 ARG cc_start: 0.7677 (mtt180) cc_final: 0.7229 (mtm180) REVERT: S 28 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8604 (mm) REVERT: S 233 ASN cc_start: 0.8405 (p0) cc_final: 0.8012 (p0) REVERT: V 89 ASP cc_start: 0.7456 (p0) cc_final: 0.7241 (p0) REVERT: V 165 TYR cc_start: 0.6580 (OUTLIER) cc_final: 0.5970 (p90) REVERT: V 173 ILE cc_start: 0.4914 (OUTLIER) cc_final: 0.4645 (mt) REVERT: V 177 HIS cc_start: 0.6633 (OUTLIER) cc_final: 0.5992 (t-170) REVERT: W 122 LEU cc_start: 0.8890 (mt) cc_final: 0.8629 (mt) REVERT: W 144 ASP cc_start: 0.7963 (m-30) cc_final: 0.7637 (m-30) REVERT: Y 92 TYR cc_start: 0.7205 (m-10) cc_final: 0.6743 (m-10) REVERT: Y 114 GLN cc_start: 0.8097 (mm-40) cc_final: 0.7737 (mt0) REVERT: a 101 GLN cc_start: 0.8695 (mm110) cc_final: 0.8470 (mm-40) REVERT: a 186 GLN cc_start: 0.8106 (tp40) cc_final: 0.7727 (tm-30) REVERT: a 194 ASN cc_start: 0.8508 (OUTLIER) cc_final: 0.8301 (p0) REVERT: a 213 ASP cc_start: 0.7716 (t0) cc_final: 0.7444 (t0) REVERT: a 236 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7514 (p0) REVERT: c 207 MET cc_start: 0.7729 (tmm) cc_final: 0.7029 (tmm) REVERT: c 226 GLN cc_start: 0.8769 (mp10) cc_final: 0.7699 (tm-30) REVERT: c 237 TRP cc_start: 0.7810 (t-100) cc_final: 0.7338 (t-100) REVERT: c 247 MET cc_start: 0.8577 (ttm) cc_final: 0.8101 (ttt) REVERT: d 27 TYR cc_start: 0.7823 (t80) cc_final: 0.7273 (t80) REVERT: d 226 GLN cc_start: 0.6318 (mt0) cc_final: 0.5815 (tt0) REVERT: d 266 VAL cc_start: 0.7266 (t) cc_final: 0.7064 (m) REVERT: e 58 PRO cc_start: 0.4197 (Cg_endo) cc_final: 0.3970 (Cg_exo) REVERT: e 162 TRP cc_start: 0.8722 (t60) cc_final: 0.8377 (t60) REVERT: e 239 HIS cc_start: 0.8423 (m-70) cc_final: 0.8215 (m-70) REVERT: e 250 ASN cc_start: 0.8458 (m-40) cc_final: 0.8205 (m110) REVERT: f 161 LEU cc_start: 0.9184 (tp) cc_final: 0.8959 (mt) REVERT: f 190 ARG cc_start: 0.8584 (ttp-170) cc_final: 0.8322 (ptm-80) REVERT: f 224 ASP cc_start: 0.7563 (OUTLIER) cc_final: 0.6811 (t0) REVERT: f 248 ARG cc_start: 0.8032 (ptt90) cc_final: 0.7824 (ptt90) REVERT: g 247 MET cc_start: 0.8671 (mmm) cc_final: 0.8412 (mmt) REVERT: g 248 ARG cc_start: 0.8640 (ttp-110) cc_final: 0.8326 (ttp-110) REVERT: g 259 TYR cc_start: 0.6143 (OUTLIER) cc_final: 0.4938 (m-80) REVERT: h 196 PHE cc_start: 0.8132 (t80) cc_final: 0.7857 (t80) REVERT: h 237 TRP cc_start: 0.7497 (t-100) cc_final: 0.6745 (t-100) REVERT: h 263 GLU cc_start: 0.8593 (mp0) cc_final: 0.8260 (mm-30) REVERT: i 176 PHE cc_start: 0.7446 (t80) cc_final: 0.7160 (t80) REVERT: i 190 ARG cc_start: 0.8274 (ttp80) cc_final: 0.7725 (ttp80) REVERT: i 226 GLN cc_start: 0.8046 (tt0) cc_final: 0.7464 (tm-30) REVERT: j 224 ASP cc_start: 0.7665 (m-30) cc_final: 0.7168 (t0) REVERT: k 207 MET cc_start: 0.9318 (tpp) cc_final: 0.8904 (tpt) REVERT: k 259 TYR cc_start: 0.6453 (OUTLIER) cc_final: 0.5138 (m-80) REVERT: l 164 GLN cc_start: 0.8967 (mm-40) cc_final: 0.8657 (mm-40) REVERT: l 194 SER cc_start: 0.8355 (p) cc_final: 0.8011 (p) REVERT: l 237 TRP cc_start: 0.7032 (t-100) cc_final: 0.6583 (t-100) REVERT: l 247 MET cc_start: 0.7940 (mmm) cc_final: 0.7720 (mtp) REVERT: m 186 GLN cc_start: 0.8740 (tp40) cc_final: 0.8488 (mm-40) REVERT: m 204 LYS cc_start: 0.8656 (mmtm) cc_final: 0.8390 (mmtm) REVERT: m 226 GLN cc_start: 0.8924 (mp10) cc_final: 0.8568 (mp10) REVERT: m 237 TRP cc_start: 0.7426 (t-100) cc_final: 0.7083 (t-100) REVERT: m 247 MET cc_start: 0.8567 (ttm) cc_final: 0.8179 (ttt) REVERT: m 248 ARG cc_start: 0.8496 (tmm-80) cc_final: 0.7795 (ptm-80) REVERT: n 150 SER cc_start: 0.8873 (OUTLIER) cc_final: 0.8291 (p) REVERT: n 176 PHE cc_start: 0.7469 (t80) cc_final: 0.7236 (t80) REVERT: n 226 GLN cc_start: 0.8087 (tt0) cc_final: 0.7419 (tm-30) REVERT: o 251 TYR cc_start: 0.8259 (OUTLIER) cc_final: 0.7854 (t80) REVERT: p 162 TRP cc_start: 0.8839 (t60) cc_final: 0.8133 (t60) REVERT: p 175 ASN cc_start: 0.7639 (OUTLIER) cc_final: 0.6987 (p0) REVERT: p 182 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7697 (tm-30) REVERT: p 187 GLU cc_start: 0.9032 (mp0) cc_final: 0.8597 (mp0) REVERT: p 256 ASP cc_start: 0.8032 (t0) cc_final: 0.7733 (t0) REVERT: X 188 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7672 (tp) REVERT: X 191 ASP cc_start: 0.7242 (t0) cc_final: 0.6777 (t0) REVERT: Q 119 GLN cc_start: 0.9089 (tp40) cc_final: 0.8494 (tm-30) REVERT: T 3 ARG cc_start: 0.7274 (OUTLIER) cc_final: 0.7051 (ptp-170) REVERT: T 68 ASP cc_start: 0.8002 (p0) cc_final: 0.7461 (p0) REVERT: T 117 GLN cc_start: 0.8742 (tp40) cc_final: 0.8312 (tp40) REVERT: T 154 GLU cc_start: 0.7075 (tt0) cc_final: 0.6751 (tt0) REVERT: T 190 CYS cc_start: 0.8380 (t) cc_final: 0.7914 (t) REVERT: T 227 GLN cc_start: 0.7760 (tm-30) cc_final: 0.7176 (tm-30) REVERT: O 22 LEU cc_start: 0.8748 (mt) cc_final: 0.7500 (mt) REVERT: O 96 MET cc_start: 0.8800 (mmm) cc_final: 0.8580 (mpp) REVERT: O 193 LYS cc_start: 0.8379 (tptt) cc_final: 0.8080 (tptt) REVERT: Z 35 ILE cc_start: 0.9224 (mp) cc_final: 0.8952 (mt) REVERT: U 128 TYR cc_start: 0.8417 (m-80) cc_final: 0.7995 (m-80) REVERT: U 199 PHE cc_start: 0.7621 (m-10) cc_final: 0.7397 (m-80) REVERT: U 201 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8204 (mm) outliers start: 299 outliers final: 207 residues processed: 1390 average time/residue: 0.6380 time to fit residues: 1531.6375 Evaluate side-chains 1310 residues out of total 7852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 1079 time to evaluate : 7.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 115 CYS Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 159 GLN Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 184 GLN Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 221 ILE Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain H residue 76 PHE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 177 HIS Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 79 CYS Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 181 ASP Chi-restraints excluded: chain I residue 198 HIS Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 96 ILE Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 163 CYS Chi-restraints excluded: chain J residue 172 ASP Chi-restraints excluded: chain J residue 185 LEU Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain K residue 159 ILE Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 188 VAL Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 158 ASN Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 197 HIS Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain M residue 135 PHE Chi-restraints excluded: chain M residue 185 ASN Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 15 ILE Chi-restraints excluded: chain N residue 26 ASP Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain P residue 12 THR Chi-restraints excluded: chain P residue 16 THR Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 36 LEU Chi-restraints excluded: chain P residue 60 ASN Chi-restraints excluded: chain P residue 114 ILE Chi-restraints excluded: chain P residue 169 ASN Chi-restraints excluded: chain P residue 215 ASP Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 55 ASN Chi-restraints excluded: chain R residue 68 HIS Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 159 GLN Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain S residue 13 ASN Chi-restraints excluded: chain S residue 24 VAL Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 141 VAL Chi-restraints excluded: chain S residue 164 ASN Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 184 GLN Chi-restraints excluded: chain S residue 198 ILE Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 62 TYR Chi-restraints excluded: chain V residue 87 THR Chi-restraints excluded: chain V residue 165 TYR Chi-restraints excluded: chain V residue 173 ILE Chi-restraints excluded: chain V residue 177 HIS Chi-restraints excluded: chain V residue 209 LEU Chi-restraints excluded: chain W residue 2 THR Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 41 ILE Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 52 LEU Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 79 CYS Chi-restraints excluded: chain W residue 198 HIS Chi-restraints excluded: chain Y residue 74 THR Chi-restraints excluded: chain Y residue 173 LEU Chi-restraints excluded: chain Y residue 188 VAL Chi-restraints excluded: chain a residue 63 ILE Chi-restraints excluded: chain a residue 65 THR Chi-restraints excluded: chain a residue 89 ILE Chi-restraints excluded: chain a residue 112 ASP Chi-restraints excluded: chain a residue 185 ASN Chi-restraints excluded: chain a residue 187 LEU Chi-restraints excluded: chain a residue 194 ASN Chi-restraints excluded: chain a residue 236 ASP Chi-restraints excluded: chain c residue 54 VAL Chi-restraints excluded: chain c residue 178 VAL Chi-restraints excluded: chain c residue 183 GLU Chi-restraints excluded: chain c residue 222 VAL Chi-restraints excluded: chain d residue 214 THR Chi-restraints excluded: chain d residue 217 LEU Chi-restraints excluded: chain e residue 64 VAL Chi-restraints excluded: chain e residue 222 VAL Chi-restraints excluded: chain e residue 243 THR Chi-restraints excluded: chain f residue 28 ASP Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain f residue 224 ASP Chi-restraints excluded: chain f residue 275 HIS Chi-restraints excluded: chain g residue 52 VAL Chi-restraints excluded: chain g residue 254 LEU Chi-restraints excluded: chain g residue 259 TYR Chi-restraints excluded: chain h residue 52 VAL Chi-restraints excluded: chain h residue 191 VAL Chi-restraints excluded: chain i residue 28 ASP Chi-restraints excluded: chain j residue 28 ASP Chi-restraints excluded: chain j residue 254 LEU Chi-restraints excluded: chain k residue 52 VAL Chi-restraints excluded: chain k residue 205 TYR Chi-restraints excluded: chain k residue 254 LEU Chi-restraints excluded: chain k residue 259 TYR Chi-restraints excluded: chain l residue 239 HIS Chi-restraints excluded: chain l residue 242 ILE Chi-restraints excluded: chain m residue 67 LEU Chi-restraints excluded: chain m residue 178 VAL Chi-restraints excluded: chain m residue 222 VAL Chi-restraints excluded: chain n residue 150 SER Chi-restraints excluded: chain n residue 170 ILE Chi-restraints excluded: chain n residue 242 ILE Chi-restraints excluded: chain n residue 252 ILE Chi-restraints excluded: chain o residue 251 TYR Chi-restraints excluded: chain p residue 64 VAL Chi-restraints excluded: chain p residue 175 ASN Chi-restraints excluded: chain p residue 222 VAL Chi-restraints excluded: chain p residue 243 THR Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 10 THR Chi-restraints excluded: chain b residue 12 VAL Chi-restraints excluded: chain b residue 26 ASP Chi-restraints excluded: chain b residue 84 ASP Chi-restraints excluded: chain b residue 101 VAL Chi-restraints excluded: chain b residue 109 LEU Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 36 THR Chi-restraints excluded: chain X residue 44 ILE Chi-restraints excluded: chain X residue 60 THR Chi-restraints excluded: chain X residue 139 LEU Chi-restraints excluded: chain X residue 160 PHE Chi-restraints excluded: chain X residue 172 ASP Chi-restraints excluded: chain X residue 185 LEU Chi-restraints excluded: chain X residue 188 LEU Chi-restraints excluded: chain Q residue 21 VAL Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 52 ILE Chi-restraints excluded: chain Q residue 60 ASN Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 115 CYS Chi-restraints excluded: chain Q residue 143 ASP Chi-restraints excluded: chain T residue 3 ARG Chi-restraints excluded: chain T residue 214 VAL Chi-restraints excluded: chain O residue 16 PHE Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 139 LEU Chi-restraints excluded: chain O residue 142 CYS Chi-restraints excluded: chain O residue 165 PHE Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain Z residue 76 VAL Chi-restraints excluded: chain Z residue 83 LEU Chi-restraints excluded: chain Z residue 158 ASN Chi-restraints excluded: chain Z residue 176 VAL Chi-restraints excluded: chain Z residue 197 HIS Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 61 ILE Chi-restraints excluded: chain U residue 77 ILE Chi-restraints excluded: chain U residue 80 TYR Chi-restraints excluded: chain U residue 111 LEU Chi-restraints excluded: chain U residue 115 VAL Chi-restraints excluded: chain U residue 147 ASP Chi-restraints excluded: chain U residue 150 ASP Chi-restraints excluded: chain U residue 201 LEU Chi-restraints excluded: chain U residue 221 ILE Chi-restraints excluded: chain U residue 238 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 800 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 472 optimal weight: 9.9990 chunk 606 optimal weight: 6.9990 chunk 469 optimal weight: 8.9990 chunk 698 optimal weight: 20.0000 chunk 463 optimal weight: 9.9990 chunk 826 optimal weight: 1.9990 chunk 517 optimal weight: 5.9990 chunk 504 optimal weight: 4.9990 chunk 381 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN F 138 HIS ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 GLN K 23 ASN K 177 ASN L 158 ASN ** M 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 72 ASN ** P 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 69 ASN ** W 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 69 GLN a 36 ASN ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 239 HIS c 261 ASN ** d 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 197 ASN ** j 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 275 HIS ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 239 HIS ** l 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 261 ASN ** n 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 197 ASN ** o 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 72 ASN ** X 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 138 HIS T 221 GLN ** U 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 72408 Z= 0.381 Angle : 0.708 25.322 97746 Z= 0.365 Chirality : 0.045 0.238 10936 Planarity : 0.004 0.113 12412 Dihedral : 4.700 75.694 9620 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.07 % Favored : 92.90 % Rotamer: Outliers : 4.57 % Allowed : 22.54 % Favored : 72.89 % 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: -0.70 (0.09), residues: 8660 helix: 1.25 (0.08), residues: 4068 sheet: -1.94 (0.14), residues: 1298 loop : -2.05 (0.11), residues: 3294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP c 162 HIS 0.006 0.001 HIS f 275 PHE 0.046 0.002 PHE N 44 TYR 0.043 0.002 TYR C 223 ARG 0.012 0.001 ARG X 147 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17320 Ramachandran restraints generated. 8660 Oldfield, 0 Emsley, 8660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17320 Ramachandran restraints generated. 8660 Oldfield, 0 Emsley, 8660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1418 residues out of total 7852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 359 poor density : 1059 time to evaluate : 6.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 TYR cc_start: 0.7827 (m-10) cc_final: 0.7580 (m-80) REVERT: B 159 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8009 (mpp) REVERT: C 48 ASP cc_start: 0.8203 (t0) cc_final: 0.7709 (m-30) REVERT: C 225 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8454 (mtmm) REVERT: D 116 GLN cc_start: 0.8689 (tm-30) cc_final: 0.8325 (tm-30) REVERT: D 117 LYS cc_start: 0.6709 (mttt) cc_final: 0.5819 (ttmt) REVERT: D 121 ARG cc_start: 0.7858 (mtt180) cc_final: 0.7527 (mtm-85) REVERT: E 28 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8659 (mm) REVERT: E 193 PHE cc_start: 0.7962 (OUTLIER) cc_final: 0.7178 (t80) REVERT: E 233 ASN cc_start: 0.8484 (p0) cc_final: 0.7658 (t0) REVERT: F 68 ASP cc_start: 0.8149 (p0) cc_final: 0.7603 (p0) REVERT: F 82 LYS cc_start: 0.8760 (tppt) cc_final: 0.8399 (tptt) REVERT: F 117 GLN cc_start: 0.8903 (tp40) cc_final: 0.8703 (tp40) REVERT: F 154 GLU cc_start: 0.7103 (tt0) cc_final: 0.6731 (tt0) REVERT: F 227 GLN cc_start: 0.7855 (tm-30) cc_final: 0.7126 (tm-30) REVERT: G 38 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8280 (pp) REVERT: G 118 ILE cc_start: 0.9562 (OUTLIER) cc_final: 0.9076 (tt) REVERT: G 128 TYR cc_start: 0.8382 (m-80) cc_final: 0.8004 (m-80) REVERT: G 201 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8274 (mm) REVERT: G 233 HIS cc_start: 0.7068 (OUTLIER) cc_final: 0.6414 (t-90) REVERT: H 62 TYR cc_start: 0.8016 (OUTLIER) cc_final: 0.7449 (t80) REVERT: H 66 MET cc_start: 0.8065 (tmm) cc_final: 0.7558 (tmm) REVERT: H 78 GLU cc_start: 0.8284 (tt0) cc_final: 0.7951 (tt0) REVERT: H 173 ILE cc_start: 0.4910 (OUTLIER) cc_final: 0.4595 (mt) REVERT: H 177 HIS cc_start: 0.6818 (OUTLIER) cc_final: 0.6321 (t-170) REVERT: H 218 MET cc_start: 0.8868 (mmm) cc_final: 0.8314 (mmm) REVERT: H 221 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7877 (t70) REVERT: I 122 LEU cc_start: 0.8909 (mt) cc_final: 0.8558 (mt) REVERT: J 163 CYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7167 (m) REVERT: J 191 ASP cc_start: 0.7270 (t0) cc_final: 0.6706 (t0) REVERT: K 98 PHE cc_start: 0.7766 (OUTLIER) cc_final: 0.7403 (t80) REVERT: K 114 GLN cc_start: 0.8110 (mm-40) cc_final: 0.7670 (mt0) REVERT: K 166 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8040 (tm-30) REVERT: L 32 GLU cc_start: 0.8167 (mp0) cc_final: 0.7954 (mp0) REVERT: L 72 GLU cc_start: 0.8067 (pp20) cc_final: 0.7754 (pp20) REVERT: M 110 TYR cc_start: 0.7923 (OUTLIER) cc_final: 0.6998 (m-80) REVERT: M 135 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.8437 (m-80) REVERT: M 186 GLN cc_start: 0.8251 (tp40) cc_final: 0.7917 (tm-30) REVERT: M 190 ASN cc_start: 0.7920 (t0) cc_final: 0.7630 (t0) REVERT: N 70 ARG cc_start: 0.7994 (ttp-170) cc_final: 0.7783 (ttp-170) REVERT: N 184 PHE cc_start: 0.8273 (m-80) cc_final: 0.7851 (m-80) REVERT: P 10 LEU cc_start: 0.7522 (mt) cc_final: 0.7017 (pp) REVERT: R 117 LYS cc_start: 0.6814 (mttt) cc_final: 0.5966 (ttmt) REVERT: R 121 ARG cc_start: 0.7820 (mtt180) cc_final: 0.7519 (mtm-85) REVERT: R 184 ASP cc_start: 0.8506 (t0) cc_final: 0.8287 (t0) REVERT: S 28 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8605 (mm) REVERT: V 61 HIS cc_start: 0.8926 (OUTLIER) cc_final: 0.8254 (t70) REVERT: V 62 TYR cc_start: 0.7937 (OUTLIER) cc_final: 0.7368 (t80) REVERT: V 66 MET cc_start: 0.8059 (tmm) cc_final: 0.7539 (tmm) REVERT: V 165 TYR cc_start: 0.7028 (OUTLIER) cc_final: 0.6570 (p90) REVERT: V 173 ILE cc_start: 0.5213 (OUTLIER) cc_final: 0.4946 (mt) REVERT: V 177 HIS cc_start: 0.6873 (OUTLIER) cc_final: 0.6369 (t-170) REVERT: W 82 ARG cc_start: 0.8714 (mtp85) cc_final: 0.8484 (mtp85) REVERT: W 122 LEU cc_start: 0.8915 (mt) cc_final: 0.8559 (mt) REVERT: Y 114 GLN cc_start: 0.8148 (mm-40) cc_final: 0.7756 (mt0) REVERT: a 186 GLN cc_start: 0.8262 (tp40) cc_final: 0.7941 (tm-30) REVERT: a 213 ASP cc_start: 0.8001 (t0) cc_final: 0.7681 (t70) REVERT: a 236 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7768 (p0) REVERT: c 207 MET cc_start: 0.7759 (tmm) cc_final: 0.7061 (tmm) REVERT: c 226 GLN cc_start: 0.8740 (mp10) cc_final: 0.7968 (tm-30) REVERT: c 237 TRP cc_start: 0.7901 (t-100) cc_final: 0.7618 (t-100) REVERT: c 247 MET cc_start: 0.8591 (ttm) cc_final: 0.8175 (ttt) REVERT: d 27 TYR cc_start: 0.7891 (t80) cc_final: 0.7383 (t80) REVERT: d 226 GLN cc_start: 0.6381 (mt0) cc_final: 0.5832 (tt0) REVERT: d 251 TYR cc_start: 0.8305 (OUTLIER) cc_final: 0.7471 (t80) REVERT: d 266 VAL cc_start: 0.7067 (t) cc_final: 0.6848 (m) REVERT: e 32 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7892 (tm-30) REVERT: e 58 PRO cc_start: 0.4335 (Cg_endo) cc_final: 0.4107 (Cg_exo) REVERT: e 162 TRP cc_start: 0.8776 (t60) cc_final: 0.8208 (t60) REVERT: e 239 HIS cc_start: 0.8417 (m-70) cc_final: 0.8201 (m-70) REVERT: f 190 ARG cc_start: 0.8566 (ttp-170) cc_final: 0.8340 (ptm-80) REVERT: f 224 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7019 (t0) REVERT: g 259 TYR cc_start: 0.6484 (OUTLIER) cc_final: 0.5240 (m-80) REVERT: h 237 TRP cc_start: 0.7639 (t-100) cc_final: 0.6969 (t-100) REVERT: h 263 GLU cc_start: 0.8602 (mp0) cc_final: 0.8271 (mm-30) REVERT: i 164 GLN cc_start: 0.7956 (mt0) cc_final: 0.7637 (mt0) REVERT: i 176 PHE cc_start: 0.7457 (t80) cc_final: 0.7161 (t80) REVERT: i 226 GLN cc_start: 0.7965 (tt0) cc_final: 0.7408 (tm-30) REVERT: j 224 ASP cc_start: 0.7599 (m-30) cc_final: 0.7031 (t0) REVERT: j 236 GLU cc_start: 0.8591 (tp30) cc_final: 0.8248 (mm-30) REVERT: k 207 MET cc_start: 0.9344 (tpp) cc_final: 0.8925 (tpt) REVERT: k 259 TYR cc_start: 0.6593 (OUTLIER) cc_final: 0.5269 (m-80) REVERT: l 194 SER cc_start: 0.8408 (p) cc_final: 0.8098 (p) REVERT: l 207 MET cc_start: 0.7645 (mmp) cc_final: 0.7380 (mmm) REVERT: l 237 TRP cc_start: 0.7550 (t-100) cc_final: 0.7202 (t-100) REVERT: l 247 MET cc_start: 0.7929 (mmm) cc_final: 0.7568 (mtp) REVERT: m 204 LYS cc_start: 0.8674 (mmtm) cc_final: 0.8399 (mmtm) REVERT: m 226 GLN cc_start: 0.8961 (mp10) cc_final: 0.8548 (mp10) REVERT: m 237 TRP cc_start: 0.7262 (t-100) cc_final: 0.6980 (t-100) REVERT: m 247 MET cc_start: 0.8554 (ttm) cc_final: 0.8220 (mtt) REVERT: m 248 ARG cc_start: 0.8584 (tmm-80) cc_final: 0.8089 (ptm-80) REVERT: m 253 MET cc_start: 0.8825 (tpt) cc_final: 0.8610 (mmm) REVERT: n 150 SER cc_start: 0.8910 (OUTLIER) cc_final: 0.8339 (p) REVERT: n 164 GLN cc_start: 0.8147 (mt0) cc_final: 0.7813 (mt0) REVERT: n 226 GLN cc_start: 0.8147 (tt0) cc_final: 0.7458 (tm-30) REVERT: o 251 TYR cc_start: 0.8389 (OUTLIER) cc_final: 0.7954 (t80) REVERT: o 266 VAL cc_start: 0.7060 (t) cc_final: 0.6856 (m) REVERT: p 162 TRP cc_start: 0.8821 (t60) cc_final: 0.8168 (t60) REVERT: p 182 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7747 (tm-30) REVERT: p 256 ASP cc_start: 0.7984 (t0) cc_final: 0.7581 (t0) REVERT: b 128 ASP cc_start: 0.6760 (m-30) cc_final: 0.6523 (m-30) REVERT: X 191 ASP cc_start: 0.7282 (t0) cc_final: 0.6864 (t0) REVERT: X 196 TRP cc_start: 0.6777 (t60) cc_final: 0.6388 (t60) REVERT: Q 119 GLN cc_start: 0.9142 (tp40) cc_final: 0.8458 (tp40) REVERT: T 3 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.7056 (ptp-170) REVERT: T 9 ASP cc_start: 0.8487 (m-30) cc_final: 0.8151 (m-30) REVERT: T 68 ASP cc_start: 0.8135 (p0) cc_final: 0.7562 (p0) REVERT: T 154 GLU cc_start: 0.7162 (tt0) cc_final: 0.6788 (tt0) REVERT: T 227 GLN cc_start: 0.7859 (tm-30) cc_final: 0.7125 (tm-30) REVERT: O 26 GLU cc_start: 0.7856 (mp0) cc_final: 0.7395 (mp0) REVERT: O 96 MET cc_start: 0.8871 (mmm) cc_final: 0.8641 (tpp) REVERT: O 193 LYS cc_start: 0.8489 (tptt) cc_final: 0.8171 (tptt) REVERT: Z 88 TYR cc_start: 0.7311 (t80) cc_final: 0.6792 (t80) REVERT: U 128 TYR cc_start: 0.8403 (m-80) cc_final: 0.8021 (m-80) REVERT: U 233 HIS cc_start: 0.7006 (OUTLIER) cc_final: 0.6335 (t-90) outliers start: 359 outliers final: 246 residues processed: 1316 average time/residue: 0.6462 time to fit residues: 1465.3276 Evaluate side-chains 1294 residues out of total 7852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 278 poor density : 1016 time to evaluate : 6.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 115 CYS Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 159 GLN Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 184 GLN Chi-restraints excluded: chain E residue 193 PHE Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 176 HIS Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 221 ILE Chi-restraints excluded: chain G residue 233 HIS Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain H residue 76 PHE Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 177 HIS Chi-restraints excluded: chain H residue 221 ASP Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 13 ILE Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 79 CYS Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 181 ASP Chi-restraints excluded: chain I residue 198 HIS Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 68 ILE Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 96 ILE Chi-restraints excluded: chain J residue 99 SER Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 160 PHE Chi-restraints excluded: chain J residue 163 CYS Chi-restraints excluded: chain J residue 172 ASP Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain K residue 159 ILE Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 188 VAL Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 158 ASN Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 197 HIS Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 110 TYR Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain M residue 135 PHE Chi-restraints excluded: chain M residue 185 ASN Chi-restraints excluded: chain M residue 187 LEU Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 15 ILE Chi-restraints excluded: chain N residue 26 ASP Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain P residue 12 THR Chi-restraints excluded: chain P residue 16 THR Chi-restraints excluded: chain P residue 36 LEU Chi-restraints excluded: chain P residue 60 ASN Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 169 ASN Chi-restraints excluded: chain P residue 215 ASP Chi-restraints excluded: chain R residue 31 CYS Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 55 ASN Chi-restraints excluded: chain R residue 68 HIS Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 159 GLN Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain S residue 13 ASN Chi-restraints excluded: chain S residue 24 VAL Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain S residue 164 ASN Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 184 GLN Chi-restraints excluded: chain S residue 198 ILE Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 61 HIS Chi-restraints excluded: chain V residue 62 TYR Chi-restraints excluded: chain V residue 76 PHE Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain V residue 87 THR Chi-restraints excluded: chain V residue 157 ASP Chi-restraints excluded: chain V residue 165 TYR Chi-restraints excluded: chain V residue 173 ILE Chi-restraints excluded: chain V residue 177 HIS Chi-restraints excluded: chain V residue 209 LEU Chi-restraints excluded: chain W residue 2 THR Chi-restraints excluded: chain W residue 13 ILE Chi-restraints excluded: chain W residue 18 THR Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 41 ILE Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 79 CYS Chi-restraints excluded: chain W residue 80 VAL Chi-restraints excluded: chain W residue 181 ASP Chi-restraints excluded: chain W residue 198 HIS Chi-restraints excluded: chain Y residue 74 THR Chi-restraints excluded: chain Y residue 124 MET Chi-restraints excluded: chain Y residue 173 LEU Chi-restraints excluded: chain Y residue 188 VAL Chi-restraints excluded: chain a residue 63 ILE Chi-restraints excluded: chain a residue 65 THR Chi-restraints excluded: chain a residue 89 ILE Chi-restraints excluded: chain a residue 112 ASP Chi-restraints excluded: chain a residue 185 ASN Chi-restraints excluded: chain a residue 187 LEU Chi-restraints excluded: chain a residue 236 ASP Chi-restraints excluded: chain c residue 67 LEU Chi-restraints excluded: chain c residue 178 VAL Chi-restraints excluded: chain c residue 183 GLU Chi-restraints excluded: chain c residue 222 VAL Chi-restraints excluded: chain c residue 239 HIS Chi-restraints excluded: chain c residue 261 ASN Chi-restraints excluded: chain d residue 214 THR Chi-restraints excluded: chain d residue 217 LEU Chi-restraints excluded: chain d residue 251 TYR Chi-restraints excluded: chain e residue 32 GLN Chi-restraints excluded: chain e residue 64 VAL Chi-restraints excluded: chain e residue 222 VAL Chi-restraints excluded: chain e residue 243 THR Chi-restraints excluded: chain f residue 28 ASP Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain f residue 224 ASP Chi-restraints excluded: chain f residue 275 HIS Chi-restraints excluded: chain g residue 52 VAL Chi-restraints excluded: chain g residue 259 TYR Chi-restraints excluded: chain h residue 191 VAL Chi-restraints excluded: chain i residue 28 ASP Chi-restraints excluded: chain i residue 242 ILE Chi-restraints excluded: chain j residue 28 ASP Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 156 ILE Chi-restraints excluded: chain j residue 247 MET Chi-restraints excluded: chain j residue 254 LEU Chi-restraints excluded: chain j residue 258 LEU Chi-restraints excluded: chain k residue 52 VAL Chi-restraints excluded: chain k residue 205 TYR Chi-restraints excluded: chain k residue 243 THR Chi-restraints excluded: chain k residue 259 TYR Chi-restraints excluded: chain l residue 242 ILE Chi-restraints excluded: chain m residue 178 VAL Chi-restraints excluded: chain m residue 222 VAL Chi-restraints excluded: chain m residue 239 HIS Chi-restraints excluded: chain n residue 150 SER Chi-restraints excluded: chain n residue 170 ILE Chi-restraints excluded: chain n residue 242 ILE Chi-restraints excluded: chain o residue 175 ASN Chi-restraints excluded: chain o residue 251 TYR Chi-restraints excluded: chain p residue 64 VAL Chi-restraints excluded: chain p residue 222 VAL Chi-restraints excluded: chain p residue 243 THR Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 12 VAL Chi-restraints excluded: chain b residue 26 ASP Chi-restraints excluded: chain b residue 101 VAL Chi-restraints excluded: chain b residue 109 LEU Chi-restraints excluded: chain b residue 166 MET Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 44 ILE Chi-restraints excluded: chain X residue 60 THR Chi-restraints excluded: chain X residue 68 ILE Chi-restraints excluded: chain X residue 96 ILE Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain X residue 138 ASP Chi-restraints excluded: chain X residue 139 LEU Chi-restraints excluded: chain X residue 160 PHE Chi-restraints excluded: chain X residue 172 ASP Chi-restraints excluded: chain Q residue 21 VAL Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 52 ILE Chi-restraints excluded: chain Q residue 60 ASN Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 115 CYS Chi-restraints excluded: chain Q residue 143 ASP Chi-restraints excluded: chain Q residue 201 ASP Chi-restraints excluded: chain T residue 3 ARG Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 152 TYR Chi-restraints excluded: chain T residue 176 HIS Chi-restraints excluded: chain T residue 214 VAL Chi-restraints excluded: chain O residue 9 TYR Chi-restraints excluded: chain O residue 16 PHE Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 89 MET Chi-restraints excluded: chain O residue 93 CYS Chi-restraints excluded: chain O residue 139 LEU Chi-restraints excluded: chain O residue 142 CYS Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain Z residue 83 LEU Chi-restraints excluded: chain Z residue 107 THR Chi-restraints excluded: chain Z residue 176 VAL Chi-restraints excluded: chain Z residue 197 HIS Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 77 ILE Chi-restraints excluded: chain U residue 80 TYR Chi-restraints excluded: chain U residue 111 LEU Chi-restraints excluded: chain U residue 115 VAL Chi-restraints excluded: chain U residue 147 ASP Chi-restraints excluded: chain U residue 150 ASP Chi-restraints excluded: chain U residue 221 ILE Chi-restraints excluded: chain U residue 233 HIS Chi-restraints excluded: chain U residue 238 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 511 optimal weight: 0.0970 chunk 330 optimal weight: 3.9990 chunk 493 optimal weight: 9.9990 chunk 249 optimal weight: 4.9990 chunk 162 optimal weight: 0.4980 chunk 160 optimal weight: 0.9980 chunk 525 optimal weight: 6.9990 chunk 563 optimal weight: 9.9990 chunk 408 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 650 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN E 104 ASN F 138 HIS ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 23 ASN K 177 ASN L 158 ASN ** M 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 72 ASN P 123 GLN ** P 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 53 GLN ** W 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 261 ASN ** d 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 197 ASN ** j 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 158 ASN j 275 HIS k 239 HIS ** n 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 197 ASN n 221 ASN ** o 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 152 ASN Q 109 GLN T 138 HIS T 221 GLN Z 158 ASN ** U 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 72408 Z= 0.165 Angle : 0.599 23.608 97746 Z= 0.307 Chirality : 0.042 0.280 10936 Planarity : 0.004 0.099 12412 Dihedral : 4.410 74.216 9620 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.08 % Allowed : 24.08 % Favored : 72.83 % 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 (0.09), residues: 8660 helix: 1.46 (0.08), residues: 4080 sheet: -1.73 (0.14), residues: 1284 loop : -1.92 (0.11), residues: 3296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP c 162 HIS 0.005 0.001 HIS c 239 PHE 0.036 0.001 PHE R 187 TYR 0.039 0.001 TYR C 223 ARG 0.012 0.000 ARG j 248 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17320 Ramachandran restraints generated. 8660 Oldfield, 0 Emsley, 8660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17320 Ramachandran restraints generated. 8660 Oldfield, 0 Emsley, 8660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1479 residues out of total 7852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 1237 time to evaluate : 6.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.7778 (tp30) cc_final: 0.7122 (tp30) REVERT: B 121 PHE cc_start: 0.8234 (m-10) cc_final: 0.8008 (m-10) REVERT: B 159 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.8074 (mmm) REVERT: C 17 ARG cc_start: 0.7922 (mtt180) cc_final: 0.7082 (mtp85) REVERT: C 48 ASP cc_start: 0.8050 (t0) cc_final: 0.7653 (m-30) REVERT: C 225 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.7938 (mtmm) REVERT: D 116 GLN cc_start: 0.8634 (tm-30) cc_final: 0.8211 (tm-30) REVERT: D 117 LYS cc_start: 0.6476 (mttt) cc_final: 0.5663 (ttmt) REVERT: D 118 PHE cc_start: 0.9050 (m-80) cc_final: 0.8709 (m-10) REVERT: D 121 ARG cc_start: 0.7816 (mtt180) cc_final: 0.7369 (mtm-85) REVERT: D 180 MET cc_start: 0.6542 (mmt) cc_final: 0.6204 (mmp) REVERT: E 28 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8742 (mm) REVERT: E 91 TYR cc_start: 0.8748 (t80) cc_final: 0.8537 (t80) REVERT: E 233 ASN cc_start: 0.8470 (p0) cc_final: 0.7602 (t0) REVERT: F 31 GLN cc_start: 0.8400 (mm110) cc_final: 0.7816 (tp40) REVERT: F 82 LYS cc_start: 0.8614 (tppt) cc_final: 0.8223 (tptt) REVERT: F 117 GLN cc_start: 0.8792 (tp40) cc_final: 0.8229 (tp40) REVERT: F 154 GLU cc_start: 0.7001 (tt0) cc_final: 0.6685 (tt0) REVERT: F 227 GLN cc_start: 0.7855 (tm-30) cc_final: 0.7233 (tm-30) REVERT: G 118 ILE cc_start: 0.9452 (OUTLIER) cc_final: 0.8980 (tt) REVERT: G 128 TYR cc_start: 0.8268 (m-80) cc_final: 0.7957 (m-80) REVERT: G 199 PHE cc_start: 0.7815 (m-80) cc_final: 0.7595 (m-80) REVERT: G 201 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8080 (mm) REVERT: H 66 MET cc_start: 0.7981 (tmm) cc_final: 0.7397 (tmm) REVERT: H 78 GLU cc_start: 0.8261 (tt0) cc_final: 0.7908 (tt0) REVERT: H 173 ILE cc_start: 0.4910 (OUTLIER) cc_final: 0.4399 (mt) REVERT: H 177 HIS cc_start: 0.6717 (OUTLIER) cc_final: 0.5986 (t-170) REVERT: H 218 MET cc_start: 0.8807 (mmm) cc_final: 0.8339 (mmm) REVERT: I 82 ARG cc_start: 0.8732 (mtp85) cc_final: 0.8243 (mtp85) REVERT: I 122 LEU cc_start: 0.8865 (mt) cc_final: 0.8569 (mt) REVERT: J 191 ASP cc_start: 0.7105 (t0) cc_final: 0.6428 (t0) REVERT: K 56 GLN cc_start: 0.8209 (mt0) cc_final: 0.7935 (mt0) REVERT: K 92 TYR cc_start: 0.7211 (m-10) cc_final: 0.6448 (m-10) REVERT: K 114 GLN cc_start: 0.7978 (mm-40) cc_final: 0.7604 (mt0) REVERT: K 166 GLU cc_start: 0.8588 (tm-30) cc_final: 0.7966 (tm-30) REVERT: L 35 ILE cc_start: 0.9265 (mp) cc_final: 0.9018 (mt) REVERT: L 72 GLU cc_start: 0.7855 (pp20) cc_final: 0.7613 (pp20) REVERT: L 88 TYR cc_start: 0.7223 (t80) cc_final: 0.6742 (t80) REVERT: M 110 TYR cc_start: 0.7600 (OUTLIER) cc_final: 0.6761 (m-80) REVERT: M 127 ARG cc_start: 0.8437 (mtp85) cc_final: 0.8124 (mtp85) REVERT: M 135 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.8386 (m-80) REVERT: M 186 GLN cc_start: 0.8106 (tp40) cc_final: 0.7723 (tm-30) REVERT: N 62 GLN cc_start: 0.8769 (mm110) cc_final: 0.8473 (mm110) REVERT: N 70 ARG cc_start: 0.7739 (ttp-170) cc_final: 0.7149 (ttp80) REVERT: N 89 GLN cc_start: 0.8763 (tp-100) cc_final: 0.8368 (tm-30) REVERT: P 130 PHE cc_start: 0.8282 (m-80) cc_final: 0.8033 (m-80) REVERT: P 147 TYR cc_start: 0.8631 (m-80) cc_final: 0.8217 (m-10) REVERT: R 66 ASP cc_start: 0.7187 (t0) cc_final: 0.6945 (t0) REVERT: R 117 LYS cc_start: 0.6740 (mttt) cc_final: 0.6007 (ttmt) REVERT: R 121 ARG cc_start: 0.7747 (mtt180) cc_final: 0.7371 (mtm-85) REVERT: S 20 ARG cc_start: 0.7696 (mtm180) cc_final: 0.7400 (mtm180) REVERT: S 28 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8599 (mm) REVERT: S 172 ILE cc_start: 0.8988 (mp) cc_final: 0.8623 (mm) REVERT: V 61 HIS cc_start: 0.8834 (OUTLIER) cc_final: 0.8050 (t70) REVERT: V 62 TYR cc_start: 0.7655 (OUTLIER) cc_final: 0.7231 (t80) REVERT: V 66 MET cc_start: 0.8017 (tmm) cc_final: 0.7377 (tmm) REVERT: V 165 TYR cc_start: 0.6450 (OUTLIER) cc_final: 0.5612 (p90) REVERT: V 173 ILE cc_start: 0.4997 (OUTLIER) cc_final: 0.4723 (mt) REVERT: V 177 HIS cc_start: 0.6643 (OUTLIER) cc_final: 0.5986 (t-170) REVERT: W 122 LEU cc_start: 0.8879 (mt) cc_final: 0.8596 (mt) REVERT: Y 92 TYR cc_start: 0.7350 (m-10) cc_final: 0.6908 (m-10) REVERT: Y 114 GLN cc_start: 0.7950 (mm-40) cc_final: 0.7617 (mt0) REVERT: a 127 ARG cc_start: 0.8380 (mtp85) cc_final: 0.8063 (mtp85) REVERT: a 186 GLN cc_start: 0.8116 (tp40) cc_final: 0.7721 (tm-30) REVERT: a 236 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7548 (p0) REVERT: c 207 MET cc_start: 0.7926 (tmm) cc_final: 0.7198 (tmm) REVERT: c 226 GLN cc_start: 0.8627 (mp10) cc_final: 0.7887 (tm-30) REVERT: c 237 TRP cc_start: 0.7815 (t-100) cc_final: 0.7449 (t-100) REVERT: c 247 MET cc_start: 0.8552 (ttm) cc_final: 0.8018 (mtt) REVERT: c 256 ASP cc_start: 0.8148 (t70) cc_final: 0.7490 (t0) REVERT: c 262 TRP cc_start: 0.7738 (t-100) cc_final: 0.7286 (t60) REVERT: d 27 TYR cc_start: 0.7987 (t80) cc_final: 0.7391 (t80) REVERT: d 226 GLN cc_start: 0.6361 (mt0) cc_final: 0.5835 (tt0) REVERT: d 251 TYR cc_start: 0.8211 (OUTLIER) cc_final: 0.7186 (t80) REVERT: d 266 VAL cc_start: 0.7028 (t) cc_final: 0.6828 (m) REVERT: e 58 PRO cc_start: 0.3698 (Cg_endo) cc_final: 0.3379 (Cg_exo) REVERT: e 162 TRP cc_start: 0.8735 (t60) cc_final: 0.8390 (t60) REVERT: e 224 ASP cc_start: 0.6729 (m-30) cc_final: 0.5553 (t0) REVERT: e 250 ASN cc_start: 0.8330 (m-40) cc_final: 0.8124 (m110) REVERT: f 44 ARG cc_start: 0.7758 (mmp-170) cc_final: 0.7404 (mmp-170) REVERT: f 190 ARG cc_start: 0.8596 (ttp-170) cc_final: 0.8383 (ptm-80) REVERT: f 224 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.7010 (t0) REVERT: f 248 ARG cc_start: 0.7929 (ptt90) cc_final: 0.7718 (ptt90) REVERT: g 248 ARG cc_start: 0.8610 (ttp-110) cc_final: 0.8342 (ttp-110) REVERT: g 259 TYR cc_start: 0.6398 (OUTLIER) cc_final: 0.5139 (m-80) REVERT: h 237 TRP cc_start: 0.7426 (t-100) cc_final: 0.6819 (t-100) REVERT: h 263 GLU cc_start: 0.8751 (mp0) cc_final: 0.8474 (mm-30) REVERT: i 176 PHE cc_start: 0.7433 (t80) cc_final: 0.7138 (t80) REVERT: i 190 ARG cc_start: 0.8290 (ttp80) cc_final: 0.8075 (ttp80) REVERT: i 192 GLU cc_start: 0.8321 (tm-30) cc_final: 0.7793 (pp20) REVERT: i 193 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8611 (mm-30) REVERT: i 226 GLN cc_start: 0.8053 (tt0) cc_final: 0.7457 (tm-30) REVERT: j 224 ASP cc_start: 0.7680 (m-30) cc_final: 0.7160 (t0) REVERT: j 236 GLU cc_start: 0.8560 (tp30) cc_final: 0.8237 (mm-30) REVERT: k 207 MET cc_start: 0.9290 (tpp) cc_final: 0.8892 (tpt) REVERT: k 208 GLU cc_start: 0.8326 (tm-30) cc_final: 0.7255 (tm-30) REVERT: k 259 TYR cc_start: 0.6440 (OUTLIER) cc_final: 0.5214 (m-80) REVERT: l 196 PHE cc_start: 0.8376 (t80) cc_final: 0.8162 (t80) REVERT: m 186 GLN cc_start: 0.8793 (tp40) cc_final: 0.8564 (mm-40) REVERT: m 204 LYS cc_start: 0.8648 (mmtm) cc_final: 0.8383 (mmtm) REVERT: m 226 GLN cc_start: 0.8917 (mp10) cc_final: 0.8541 (mp10) REVERT: m 237 TRP cc_start: 0.7516 (t-100) cc_final: 0.7066 (t60) REVERT: m 247 MET cc_start: 0.8575 (ttm) cc_final: 0.8149 (mtt) REVERT: m 248 ARG cc_start: 0.8514 (tmm-80) cc_final: 0.7806 (ptm-80) REVERT: n 150 SER cc_start: 0.8826 (OUTLIER) cc_final: 0.8277 (p) REVERT: n 164 GLN cc_start: 0.8185 (mt0) cc_final: 0.7845 (mt0) REVERT: n 226 GLN cc_start: 0.8086 (tt0) cc_final: 0.7378 (tm-30) REVERT: o 226 GLN cc_start: 0.6065 (mt0) cc_final: 0.5547 (tt0) REVERT: o 251 TYR cc_start: 0.8404 (OUTLIER) cc_final: 0.7924 (t80) REVERT: o 253 MET cc_start: 0.7228 (mmt) cc_final: 0.7022 (mmt) REVERT: p 44 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7324 (mtm-85) REVERT: p 162 TRP cc_start: 0.8739 (t60) cc_final: 0.8283 (t60) REVERT: p 190 ARG cc_start: 0.8634 (tmm-80) cc_final: 0.8417 (ptt-90) REVERT: b 89 GLN cc_start: 0.8738 (tp-100) cc_final: 0.8341 (tm-30) REVERT: X 191 ASP cc_start: 0.7230 (t0) cc_final: 0.6673 (t0) REVERT: Q 109 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7949 (mm-40) REVERT: Q 119 GLN cc_start: 0.9087 (tp40) cc_final: 0.8396 (tm-30) REVERT: T 3 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.7054 (ptp-170) REVERT: T 9 ASP cc_start: 0.8449 (m-30) cc_final: 0.8225 (m-30) REVERT: T 31 GLN cc_start: 0.8291 (mm110) cc_final: 0.7736 (tp40) REVERT: T 68 ASP cc_start: 0.8076 (p0) cc_final: 0.7555 (p0) REVERT: T 154 GLU cc_start: 0.7081 (tt0) cc_final: 0.6735 (tt0) REVERT: T 227 GLN cc_start: 0.7838 (tm-30) cc_final: 0.7216 (tm-30) REVERT: O 22 LEU cc_start: 0.8609 (mt) cc_final: 0.7713 (mt) REVERT: O 26 GLU cc_start: 0.7916 (mp0) cc_final: 0.7594 (mp0) REVERT: O 96 MET cc_start: 0.8750 (mmm) cc_final: 0.8410 (mpp) REVERT: Z 35 ILE cc_start: 0.9274 (mp) cc_final: 0.9017 (mt) REVERT: Z 56 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7328 (mp0) REVERT: Z 88 TYR cc_start: 0.7062 (t80) cc_final: 0.6699 (t80) REVERT: U 128 TYR cc_start: 0.8277 (m-80) cc_final: 0.7956 (m-80) REVERT: U 199 PHE cc_start: 0.7974 (m-80) cc_final: 0.7750 (m-80) REVERT: U 233 HIS cc_start: 0.6751 (OUTLIER) cc_final: 0.6166 (t-90) outliers start: 242 outliers final: 167 residues processed: 1408 average time/residue: 0.6439 time to fit residues: 1566.3718 Evaluate side-chains 1315 residues out of total 7852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 1122 time to evaluate : 7.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain B residue 214 TYR Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 115 CYS Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 184 GLN Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 221 ILE Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 44 CYS Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 177 HIS Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 198 HIS Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 172 ASP Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain K residue 159 ILE Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 188 VAL Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 158 ASN Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 197 HIS Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 110 TYR Chi-restraints excluded: chain M residue 135 PHE Chi-restraints excluded: chain M residue 185 ASN Chi-restraints excluded: chain M residue 187 LEU Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 15 ILE Chi-restraints excluded: chain N residue 26 ASP Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain P residue 12 THR Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 60 ASN Chi-restraints excluded: chain P residue 169 ASN Chi-restraints excluded: chain P residue 215 ASP Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 55 ASN Chi-restraints excluded: chain R residue 68 HIS Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 129 ILE Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 159 GLN Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain S residue 13 ASN Chi-restraints excluded: chain S residue 24 VAL Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 184 GLN Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 61 HIS Chi-restraints excluded: chain V residue 62 TYR Chi-restraints excluded: chain V residue 76 PHE Chi-restraints excluded: chain V residue 87 THR Chi-restraints excluded: chain V residue 165 TYR Chi-restraints excluded: chain V residue 173 ILE Chi-restraints excluded: chain V residue 177 HIS Chi-restraints excluded: chain V residue 209 LEU Chi-restraints excluded: chain V residue 227 LEU Chi-restraints excluded: chain V residue 245 ASN Chi-restraints excluded: chain W residue 2 THR Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 41 ILE Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 79 CYS Chi-restraints excluded: chain W residue 80 VAL Chi-restraints excluded: chain W residue 198 HIS Chi-restraints excluded: chain Y residue 124 MET Chi-restraints excluded: chain Y residue 173 LEU Chi-restraints excluded: chain a residue 63 ILE Chi-restraints excluded: chain a residue 65 THR Chi-restraints excluded: chain a residue 89 ILE Chi-restraints excluded: chain a residue 185 ASN Chi-restraints excluded: chain a residue 187 LEU Chi-restraints excluded: chain a residue 236 ASP Chi-restraints excluded: chain c residue 67 LEU Chi-restraints excluded: chain c residue 178 VAL Chi-restraints excluded: chain c residue 183 GLU Chi-restraints excluded: chain c residue 222 VAL Chi-restraints excluded: chain c residue 261 ASN Chi-restraints excluded: chain d residue 214 THR Chi-restraints excluded: chain d residue 217 LEU Chi-restraints excluded: chain d residue 251 TYR Chi-restraints excluded: chain e residue 64 VAL Chi-restraints excluded: chain e residue 232 LEU Chi-restraints excluded: chain f residue 28 ASP Chi-restraints excluded: chain f residue 158 ASN Chi-restraints excluded: chain f residue 224 ASP Chi-restraints excluded: chain g residue 52 VAL Chi-restraints excluded: chain g residue 259 TYR Chi-restraints excluded: chain h residue 191 VAL Chi-restraints excluded: chain i residue 28 ASP Chi-restraints excluded: chain j residue 28 ASP Chi-restraints excluded: chain j residue 254 LEU Chi-restraints excluded: chain k residue 52 VAL Chi-restraints excluded: chain k residue 205 TYR Chi-restraints excluded: chain k residue 259 TYR Chi-restraints excluded: chain l residue 242 ILE Chi-restraints excluded: chain m residue 178 VAL Chi-restraints excluded: chain m residue 222 VAL Chi-restraints excluded: chain n residue 150 SER Chi-restraints excluded: chain n residue 170 ILE Chi-restraints excluded: chain o residue 251 TYR Chi-restraints excluded: chain p residue 44 ARG Chi-restraints excluded: chain p residue 64 VAL Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 10 THR Chi-restraints excluded: chain b residue 12 VAL Chi-restraints excluded: chain b residue 26 ASP Chi-restraints excluded: chain b residue 101 VAL Chi-restraints excluded: chain b residue 109 LEU Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 44 ILE Chi-restraints excluded: chain X residue 60 THR Chi-restraints excluded: chain X residue 139 LEU Chi-restraints excluded: chain Q residue 21 VAL Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 44 ILE Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 52 ILE Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 109 GLN Chi-restraints excluded: chain Q residue 115 CYS Chi-restraints excluded: chain Q residue 132 VAL Chi-restraints excluded: chain Q residue 143 ASP Chi-restraints excluded: chain T residue 3 ARG Chi-restraints excluded: chain O residue 16 PHE Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 93 CYS Chi-restraints excluded: chain O residue 139 LEU Chi-restraints excluded: chain O residue 142 CYS Chi-restraints excluded: chain Z residue 83 LEU Chi-restraints excluded: chain Z residue 107 THR Chi-restraints excluded: chain Z residue 158 ASN Chi-restraints excluded: chain Z residue 176 VAL Chi-restraints excluded: chain Z residue 197 HIS Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 61 ILE Chi-restraints excluded: chain U residue 77 ILE Chi-restraints excluded: chain U residue 80 TYR Chi-restraints excluded: chain U residue 111 LEU Chi-restraints excluded: chain U residue 147 ASP Chi-restraints excluded: chain U residue 150 ASP Chi-restraints excluded: chain U residue 221 ILE Chi-restraints excluded: chain U residue 233 HIS Chi-restraints excluded: chain U residue 238 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 752 optimal weight: 1.9990 chunk 792 optimal weight: 4.9990 chunk 722 optimal weight: 0.6980 chunk 770 optimal weight: 5.9990 chunk 463 optimal weight: 7.9990 chunk 335 optimal weight: 2.9990 chunk 605 optimal weight: 7.9990 chunk 236 optimal weight: 1.9990 chunk 696 optimal weight: 20.0000 chunk 728 optimal weight: 0.8980 chunk 767 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN F 138 HIS ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 HIS ** H 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 109 GLN ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 158 ASN ** M 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 109 GLN ** W 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 239 HIS ** d 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 239 HIS ** g 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 275 HIS ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 239 HIS ** n 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 197 ASN ** o 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 109 GLN T 138 HIS Z 158 ASN ** U 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 112 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 72408 Z= 0.226 Angle : 0.629 23.837 97746 Z= 0.322 Chirality : 0.043 0.363 10936 Planarity : 0.004 0.110 12412 Dihedral : 4.374 75.203 9620 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.94 % Favored : 94.05 % Rotamer: Outliers : 3.20 % Allowed : 24.61 % Favored : 72.20 % 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: -0.36 (0.09), residues: 8660 helix: 1.50 (0.08), residues: 4082 sheet: -1.64 (0.14), residues: 1282 loop : -1.90 (0.11), residues: 3296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP c 162 HIS 0.009 0.001 HIS d 239 PHE 0.033 0.002 PHE R 187 TYR 0.040 0.001 TYR C 223 ARG 0.010 0.000 ARG n 190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17320 Ramachandran restraints generated. 8660 Oldfield, 0 Emsley, 8660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17320 Ramachandran restraints generated. 8660 Oldfield, 0 Emsley, 8660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1371 residues out of total 7852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 1120 time to evaluate : 6.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.7858 (tp30) cc_final: 0.7186 (tp30) REVERT: B 159 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8073 (mmm) REVERT: C 17 ARG cc_start: 0.7889 (mtt180) cc_final: 0.7383 (mtp180) REVERT: C 48 ASP cc_start: 0.8214 (t0) cc_final: 0.7654 (m-30) REVERT: C 225 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8010 (mtmm) REVERT: D 116 GLN cc_start: 0.8657 (tm-30) cc_final: 0.8179 (tm-30) REVERT: D 117 LYS cc_start: 0.6553 (mttt) cc_final: 0.5730 (ttmt) REVERT: D 121 ARG cc_start: 0.7861 (mtt180) cc_final: 0.7444 (mtm-85) REVERT: D 180 MET cc_start: 0.6694 (mmt) cc_final: 0.6358 (mmp) REVERT: E 28 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8590 (mm) REVERT: E 233 ASN cc_start: 0.8453 (p0) cc_final: 0.7616 (t0) REVERT: F 31 GLN cc_start: 0.8404 (mm110) cc_final: 0.7895 (tp40) REVERT: F 82 LYS cc_start: 0.8683 (tppt) cc_final: 0.8329 (tptt) REVERT: F 117 GLN cc_start: 0.8810 (tp40) cc_final: 0.8303 (tp40) REVERT: F 154 GLU cc_start: 0.7029 (tt0) cc_final: 0.6684 (tt0) REVERT: F 227 GLN cc_start: 0.7877 (tm-30) cc_final: 0.7176 (tm-30) REVERT: G 118 ILE cc_start: 0.9477 (OUTLIER) cc_final: 0.9012 (tt) REVERT: G 128 TYR cc_start: 0.8310 (m-80) cc_final: 0.7984 (m-80) REVERT: G 199 PHE cc_start: 0.7821 (m-80) cc_final: 0.7589 (m-80) REVERT: G 201 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8124 (mm) REVERT: H 62 TYR cc_start: 0.7752 (OUTLIER) cc_final: 0.7280 (t80) REVERT: H 66 MET cc_start: 0.8011 (tmm) cc_final: 0.7406 (tmm) REVERT: H 78 GLU cc_start: 0.8243 (tt0) cc_final: 0.7578 (tt0) REVERT: H 173 ILE cc_start: 0.4931 (OUTLIER) cc_final: 0.4434 (mt) REVERT: H 177 HIS cc_start: 0.6594 (OUTLIER) cc_final: 0.6021 (t-170) REVERT: H 218 MET cc_start: 0.8817 (mmm) cc_final: 0.8345 (mmm) REVERT: I 82 ARG cc_start: 0.8701 (mtp85) cc_final: 0.8247 (mtp85) REVERT: I 109 GLN cc_start: 0.8186 (tt0) cc_final: 0.7938 (tt0) REVERT: I 122 LEU cc_start: 0.8870 (mt) cc_final: 0.8541 (mt) REVERT: J 163 CYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7741 (m) REVERT: J 191 ASP cc_start: 0.7162 (t0) cc_final: 0.6585 (t0) REVERT: K 92 TYR cc_start: 0.7267 (m-10) cc_final: 0.6564 (m-10) REVERT: K 114 GLN cc_start: 0.8106 (mm-40) cc_final: 0.7735 (mt0) REVERT: K 166 GLU cc_start: 0.8633 (tm-30) cc_final: 0.7959 (tm-30) REVERT: L 35 ILE cc_start: 0.9309 (mp) cc_final: 0.9059 (mt) REVERT: L 72 GLU cc_start: 0.8032 (pp20) cc_final: 0.7714 (pp20) REVERT: L 88 TYR cc_start: 0.7396 (t80) cc_final: 0.6953 (t80) REVERT: M 110 TYR cc_start: 0.7914 (OUTLIER) cc_final: 0.7056 (m-80) REVERT: M 135 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.8465 (m-80) REVERT: M 186 GLN cc_start: 0.8121 (tp40) cc_final: 0.7735 (tm-30) REVERT: N 70 ARG cc_start: 0.7881 (ttp-170) cc_final: 0.7571 (ttp80) REVERT: N 184 PHE cc_start: 0.8179 (m-80) cc_final: 0.7804 (m-80) REVERT: P 147 TYR cc_start: 0.8686 (m-80) cc_final: 0.8272 (m-10) REVERT: R 116 GLN cc_start: 0.8550 (tm-30) cc_final: 0.8335 (tm-30) REVERT: R 117 LYS cc_start: 0.6829 (mttt) cc_final: 0.5891 (ttmt) REVERT: R 121 ARG cc_start: 0.7751 (mtt180) cc_final: 0.7381 (mtm-85) REVERT: S 20 ARG cc_start: 0.7707 (mtm180) cc_final: 0.7459 (mtm180) REVERT: S 28 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8591 (mm) REVERT: S 193 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7359 (t80) REVERT: S 233 ASN cc_start: 0.8461 (p0) cc_final: 0.7572 (t0) REVERT: V 61 HIS cc_start: 0.8834 (OUTLIER) cc_final: 0.8106 (t70) REVERT: V 62 TYR cc_start: 0.7734 (OUTLIER) cc_final: 0.7250 (t80) REVERT: V 66 MET cc_start: 0.8062 (tmm) cc_final: 0.7423 (tmm) REVERT: V 165 TYR cc_start: 0.6624 (OUTLIER) cc_final: 0.5853 (p90) REVERT: V 173 ILE cc_start: 0.4903 (OUTLIER) cc_final: 0.4581 (mt) REVERT: V 177 HIS cc_start: 0.6578 (OUTLIER) cc_final: 0.5910 (t-170) REVERT: W 94 LYS cc_start: 0.7334 (mttt) cc_final: 0.6659 (mttp) REVERT: W 109 GLN cc_start: 0.8105 (tt0) cc_final: 0.7812 (tt0) REVERT: W 122 LEU cc_start: 0.8903 (mt) cc_final: 0.8596 (mt) REVERT: Y 114 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7728 (mt0) REVERT: a 127 ARG cc_start: 0.8440 (mtp85) cc_final: 0.7921 (mtp85) REVERT: a 186 GLN cc_start: 0.8177 (tp40) cc_final: 0.7767 (tm-30) REVERT: a 236 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7695 (p0) REVERT: c 204 LYS cc_start: 0.8929 (mmtm) cc_final: 0.8688 (mmtm) REVERT: c 207 MET cc_start: 0.7991 (tmm) cc_final: 0.7259 (tmm) REVERT: c 226 GLN cc_start: 0.8592 (mp10) cc_final: 0.7831 (tm-30) REVERT: c 237 TRP cc_start: 0.7580 (t-100) cc_final: 0.7301 (t-100) REVERT: c 247 MET cc_start: 0.8631 (ttm) cc_final: 0.8274 (ttt) REVERT: c 253 MET cc_start: 0.8673 (tpt) cc_final: 0.8428 (mmm) REVERT: c 256 ASP cc_start: 0.8158 (t70) cc_final: 0.7578 (t0) REVERT: d 27 TYR cc_start: 0.7923 (t80) cc_final: 0.7318 (t80) REVERT: d 226 GLN cc_start: 0.6380 (mt0) cc_final: 0.5836 (tt0) REVERT: d 251 TYR cc_start: 0.8319 (OUTLIER) cc_final: 0.7436 (t80) REVERT: e 58 PRO cc_start: 0.3270 (Cg_endo) cc_final: 0.3069 (Cg_exo) REVERT: e 162 TRP cc_start: 0.8768 (t60) cc_final: 0.8279 (t60) REVERT: f 190 ARG cc_start: 0.8602 (ttp-170) cc_final: 0.8354 (ptm-80) REVERT: f 224 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.7025 (t0) REVERT: f 248 ARG cc_start: 0.7930 (ptt90) cc_final: 0.7721 (ptt90) REVERT: g 248 ARG cc_start: 0.8387 (ttp-110) cc_final: 0.8145 (ptt-90) REVERT: g 259 TYR cc_start: 0.6456 (OUTLIER) cc_final: 0.5195 (m-80) REVERT: h 237 TRP cc_start: 0.7424 (t-100) cc_final: 0.6809 (t-100) REVERT: h 247 MET cc_start: 0.8047 (mmm) cc_final: 0.7273 (mmp) REVERT: h 263 GLU cc_start: 0.8775 (mp0) cc_final: 0.8486 (mm-30) REVERT: i 164 GLN cc_start: 0.7935 (mt0) cc_final: 0.7635 (mt0) REVERT: i 176 PHE cc_start: 0.7430 (t80) cc_final: 0.7152 (t80) REVERT: i 193 GLU cc_start: 0.9104 (mm-30) cc_final: 0.8814 (mm-30) REVERT: i 226 GLN cc_start: 0.8033 (tt0) cc_final: 0.7458 (tm-30) REVERT: i 253 MET cc_start: 0.8401 (tpp) cc_final: 0.8166 (tpp) REVERT: j 224 ASP cc_start: 0.7532 (m-30) cc_final: 0.6985 (t0) REVERT: j 236 GLU cc_start: 0.8616 (tp30) cc_final: 0.8291 (mm-30) REVERT: k 172 ASP cc_start: 0.7645 (t70) cc_final: 0.7150 (t70) REVERT: k 207 MET cc_start: 0.9304 (tpp) cc_final: 0.8883 (tpt) REVERT: k 208 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7267 (tm-30) REVERT: k 259 TYR cc_start: 0.6454 (OUTLIER) cc_final: 0.5192 (m-80) REVERT: l 196 PHE cc_start: 0.8336 (t80) cc_final: 0.8126 (t80) REVERT: m 186 GLN cc_start: 0.8765 (tp40) cc_final: 0.8511 (mm-40) REVERT: m 204 LYS cc_start: 0.8667 (mmtm) cc_final: 0.8397 (mmtm) REVERT: m 226 GLN cc_start: 0.8893 (mp10) cc_final: 0.8511 (mp10) REVERT: m 237 TRP cc_start: 0.7347 (t-100) cc_final: 0.6937 (t60) REVERT: m 247 MET cc_start: 0.8562 (ttm) cc_final: 0.8203 (mtt) REVERT: m 248 ARG cc_start: 0.8531 (tmm-80) cc_final: 0.7767 (tmm-80) REVERT: n 150 SER cc_start: 0.8943 (OUTLIER) cc_final: 0.8371 (p) REVERT: n 193 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8723 (mm-30) REVERT: n 226 GLN cc_start: 0.8067 (tt0) cc_final: 0.7393 (tm-30) REVERT: o 251 TYR cc_start: 0.8397 (OUTLIER) cc_final: 0.7937 (t80) REVERT: p 162 TRP cc_start: 0.8881 (t60) cc_final: 0.8415 (t60) REVERT: p 172 ASP cc_start: 0.6513 (OUTLIER) cc_final: 0.6214 (p0) REVERT: X 101 ARG cc_start: 0.8478 (ttp80) cc_final: 0.7846 (ttp80) REVERT: X 191 ASP cc_start: 0.7173 (t0) cc_final: 0.6658 (t0) REVERT: Q 109 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.8063 (mm-40) REVERT: Q 119 GLN cc_start: 0.9118 (tp40) cc_final: 0.8609 (tp40) REVERT: T 3 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.7061 (ptp-170) REVERT: T 31 GLN cc_start: 0.8365 (mm110) cc_final: 0.7799 (tp40) REVERT: T 154 GLU cc_start: 0.7064 (tt0) cc_final: 0.6713 (tt0) REVERT: T 227 GLN cc_start: 0.7885 (tm-30) cc_final: 0.7180 (tm-30) REVERT: O 22 LEU cc_start: 0.8645 (mt) cc_final: 0.7695 (mt) REVERT: O 26 GLU cc_start: 0.7991 (mp0) cc_final: 0.7717 (mp0) REVERT: O 96 MET cc_start: 0.8817 (mmm) cc_final: 0.8506 (tpp) REVERT: O 193 LYS cc_start: 0.8302 (tptt) cc_final: 0.8005 (tptt) REVERT: Z 35 ILE cc_start: 0.9268 (mp) cc_final: 0.9047 (mt) REVERT: Z 56 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7417 (mp0) REVERT: Z 88 TYR cc_start: 0.7259 (t80) cc_final: 0.6876 (t80) REVERT: U 128 TYR cc_start: 0.8314 (m-80) cc_final: 0.7991 (m-80) REVERT: U 199 PHE cc_start: 0.7976 (m-80) cc_final: 0.7557 (m-80) REVERT: U 233 HIS cc_start: 0.6824 (OUTLIER) cc_final: 0.6213 (t-90) outliers start: 251 outliers final: 188 residues processed: 1295 average time/residue: 0.6488 time to fit residues: 1448.2463 Evaluate side-chains 1281 residues out of total 7852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 1063 time to evaluate : 6.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 115 CYS Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 184 GLN Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 221 ILE Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 177 HIS Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 198 HIS Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 160 PHE Chi-restraints excluded: chain J residue 163 CYS Chi-restraints excluded: chain J residue 172 ASP Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 159 ILE Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 188 VAL Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 158 ASN Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 197 HIS Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 110 TYR Chi-restraints excluded: chain M residue 135 PHE Chi-restraints excluded: chain M residue 185 ASN Chi-restraints excluded: chain M residue 187 LEU Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 15 ILE Chi-restraints excluded: chain N residue 26 ASP Chi-restraints excluded: chain N residue 101 VAL Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain P residue 12 THR Chi-restraints excluded: chain P residue 36 LEU Chi-restraints excluded: chain P residue 60 ASN Chi-restraints excluded: chain P residue 169 ASN Chi-restraints excluded: chain P residue 215 ASP Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 55 ASN Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 129 ILE Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 159 GLN Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain S residue 13 ASN Chi-restraints excluded: chain S residue 24 VAL Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 184 GLN Chi-restraints excluded: chain S residue 193 PHE Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 61 HIS Chi-restraints excluded: chain V residue 62 TYR Chi-restraints excluded: chain V residue 76 PHE Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain V residue 87 THR Chi-restraints excluded: chain V residue 165 TYR Chi-restraints excluded: chain V residue 173 ILE Chi-restraints excluded: chain V residue 177 HIS Chi-restraints excluded: chain V residue 209 LEU Chi-restraints excluded: chain V residue 245 ASN Chi-restraints excluded: chain W residue 2 THR Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 41 ILE Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 79 CYS Chi-restraints excluded: chain W residue 80 VAL Chi-restraints excluded: chain W residue 198 HIS Chi-restraints excluded: chain Y residue 72 ASN Chi-restraints excluded: chain Y residue 124 MET Chi-restraints excluded: chain Y residue 173 LEU Chi-restraints excluded: chain a residue 63 ILE Chi-restraints excluded: chain a residue 65 THR Chi-restraints excluded: chain a residue 89 ILE Chi-restraints excluded: chain a residue 185 ASN Chi-restraints excluded: chain a residue 187 LEU Chi-restraints excluded: chain a residue 236 ASP Chi-restraints excluded: chain c residue 67 LEU Chi-restraints excluded: chain c residue 178 VAL Chi-restraints excluded: chain c residue 183 GLU Chi-restraints excluded: chain c residue 222 VAL Chi-restraints excluded: chain c residue 239 HIS Chi-restraints excluded: chain d residue 214 THR Chi-restraints excluded: chain d residue 217 LEU Chi-restraints excluded: chain d residue 251 TYR Chi-restraints excluded: chain e residue 64 VAL Chi-restraints excluded: chain e residue 232 LEU Chi-restraints excluded: chain f residue 28 ASP Chi-restraints excluded: chain f residue 158 ASN Chi-restraints excluded: chain f residue 224 ASP Chi-restraints excluded: chain g residue 52 VAL Chi-restraints excluded: chain g residue 254 LEU Chi-restraints excluded: chain g residue 259 TYR Chi-restraints excluded: chain h residue 188 LEU Chi-restraints excluded: chain h residue 191 VAL Chi-restraints excluded: chain i residue 28 ASP Chi-restraints excluded: chain i residue 242 ILE Chi-restraints excluded: chain j residue 28 ASP Chi-restraints excluded: chain j residue 254 LEU Chi-restraints excluded: chain k residue 52 VAL Chi-restraints excluded: chain k residue 205 TYR Chi-restraints excluded: chain k residue 208 GLU Chi-restraints excluded: chain k residue 259 TYR Chi-restraints excluded: chain l residue 242 ILE Chi-restraints excluded: chain m residue 178 VAL Chi-restraints excluded: chain m residue 222 VAL Chi-restraints excluded: chain n residue 150 SER Chi-restraints excluded: chain n residue 170 ILE Chi-restraints excluded: chain o residue 251 TYR Chi-restraints excluded: chain p residue 64 VAL Chi-restraints excluded: chain p residue 172 ASP Chi-restraints excluded: chain p residue 187 GLU Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 10 THR Chi-restraints excluded: chain b residue 12 VAL Chi-restraints excluded: chain b residue 26 ASP Chi-restraints excluded: chain b residue 101 VAL Chi-restraints excluded: chain b residue 109 LEU Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 44 ILE Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain X residue 139 LEU Chi-restraints excluded: chain X residue 160 PHE Chi-restraints excluded: chain X residue 172 ASP Chi-restraints excluded: chain X residue 185 LEU Chi-restraints excluded: chain Q residue 21 VAL Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 44 ILE Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 52 ILE Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 109 GLN Chi-restraints excluded: chain Q residue 115 CYS Chi-restraints excluded: chain Q residue 117 ILE Chi-restraints excluded: chain Q residue 132 VAL Chi-restraints excluded: chain Q residue 143 ASP Chi-restraints excluded: chain T residue 3 ARG Chi-restraints excluded: chain T residue 199 SER Chi-restraints excluded: chain T residue 214 VAL Chi-restraints excluded: chain O residue 16 PHE Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 93 CYS Chi-restraints excluded: chain O residue 139 LEU Chi-restraints excluded: chain O residue 142 CYS Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain Z residue 83 LEU Chi-restraints excluded: chain Z residue 107 THR Chi-restraints excluded: chain Z residue 158 ASN Chi-restraints excluded: chain Z residue 176 VAL Chi-restraints excluded: chain Z residue 197 HIS Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 61 ILE Chi-restraints excluded: chain U residue 77 ILE Chi-restraints excluded: chain U residue 80 TYR Chi-restraints excluded: chain U residue 111 LEU Chi-restraints excluded: chain U residue 115 VAL Chi-restraints excluded: chain U residue 147 ASP Chi-restraints excluded: chain U residue 150 ASP Chi-restraints excluded: chain U residue 221 ILE Chi-restraints excluded: chain U residue 233 HIS Chi-restraints excluded: chain U residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 506 optimal weight: 20.0000 chunk 814 optimal weight: 10.0000 chunk 497 optimal weight: 8.9990 chunk 386 optimal weight: 0.7980 chunk 566 optimal weight: 6.9990 chunk 854 optimal weight: 0.0870 chunk 786 optimal weight: 8.9990 chunk 680 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 525 optimal weight: 7.9990 chunk 417 optimal weight: 0.8980 overall best weight: 1.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN E 164 ASN F 138 HIS ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 152 ASN L 158 ASN ** M 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 43 ASN ** S 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 239 HIS ** d 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 239 HIS ** e 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 275 HIS k 239 HIS ** n 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 197 ASN ** o 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 109 GLN ** T 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 138 HIS Z 158 ASN ** U 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 72408 Z= 0.190 Angle : 0.619 23.647 97746 Z= 0.316 Chirality : 0.043 0.368 10936 Planarity : 0.004 0.106 12412 Dihedral : 4.343 74.563 9620 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.98 % Favored : 95.00 % Rotamer: Outliers : 2.98 % Allowed : 24.97 % Favored : 72.05 % 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: -0.31 (0.09), residues: 8660 helix: 1.51 (0.08), residues: 4092 sheet: -1.52 (0.14), residues: 1266 loop : -1.89 (0.11), residues: 3302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP l 162 HIS 0.010 0.001 HIS d 239 PHE 0.038 0.001 PHE D 187 TYR 0.042 0.001 TYR C 223 ARG 0.012 0.000 ARG n 190 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17320 Ramachandran restraints generated. 8660 Oldfield, 0 Emsley, 8660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17320 Ramachandran restraints generated. 8660 Oldfield, 0 Emsley, 8660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1382 residues out of total 7852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 1148 time to evaluate : 6.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.7865 (tp30) cc_final: 0.7220 (tp30) REVERT: B 159 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8055 (mmm) REVERT: C 17 ARG cc_start: 0.7854 (mtt180) cc_final: 0.7011 (mtp85) REVERT: C 48 ASP cc_start: 0.8158 (t0) cc_final: 0.7612 (m-30) REVERT: C 225 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.7874 (mtmm) REVERT: D 116 GLN cc_start: 0.8639 (tm-30) cc_final: 0.8198 (tm-30) REVERT: D 117 LYS cc_start: 0.6498 (mttt) cc_final: 0.5674 (ttmt) REVERT: D 118 PHE cc_start: 0.9064 (m-80) cc_final: 0.8800 (m-10) REVERT: D 121 ARG cc_start: 0.7838 (mtt180) cc_final: 0.7389 (mtm-85) REVERT: D 180 MET cc_start: 0.6600 (mmt) cc_final: 0.6285 (mmp) REVERT: E 20 ARG cc_start: 0.7669 (mtm180) cc_final: 0.7420 (mtm180) REVERT: E 28 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8612 (mm) REVERT: E 233 ASN cc_start: 0.8448 (p0) cc_final: 0.7604 (t0) REVERT: F 82 LYS cc_start: 0.8645 (tppt) cc_final: 0.8270 (tptt) REVERT: F 117 GLN cc_start: 0.8770 (tp40) cc_final: 0.8276 (tp40) REVERT: F 154 GLU cc_start: 0.6962 (tt0) cc_final: 0.6677 (tt0) REVERT: F 227 GLN cc_start: 0.7880 (tm-30) cc_final: 0.7185 (tm-30) REVERT: G 118 ILE cc_start: 0.9462 (OUTLIER) cc_final: 0.9006 (tt) REVERT: G 128 TYR cc_start: 0.8280 (m-80) cc_final: 0.7973 (m-80) REVERT: G 199 PHE cc_start: 0.7853 (m-80) cc_final: 0.7593 (m-80) REVERT: G 201 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7996 (mm) REVERT: H 66 MET cc_start: 0.7988 (tmm) cc_final: 0.7387 (tmm) REVERT: H 78 GLU cc_start: 0.8239 (tt0) cc_final: 0.7901 (tt0) REVERT: H 80 GLU cc_start: 0.7339 (tm-30) cc_final: 0.6971 (tm-30) REVERT: H 173 ILE cc_start: 0.4939 (OUTLIER) cc_final: 0.4478 (mt) REVERT: H 177 HIS cc_start: 0.6775 (OUTLIER) cc_final: 0.6009 (t-170) REVERT: H 218 MET cc_start: 0.8819 (mmm) cc_final: 0.8331 (mmm) REVERT: I 82 ARG cc_start: 0.8658 (mtp85) cc_final: 0.8199 (mtp85) REVERT: I 122 LEU cc_start: 0.8842 (mt) cc_final: 0.8588 (mt) REVERT: J 163 CYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7725 (m) REVERT: J 191 ASP cc_start: 0.7131 (t0) cc_final: 0.6484 (t0) REVERT: K 92 TYR cc_start: 0.7228 (m-10) cc_final: 0.6506 (m-10) REVERT: K 114 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7708 (mt0) REVERT: K 166 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8043 (tm-30) REVERT: L 35 ILE cc_start: 0.9296 (mp) cc_final: 0.9055 (mt) REVERT: L 72 GLU cc_start: 0.7948 (pp20) cc_final: 0.7640 (pp20) REVERT: L 88 TYR cc_start: 0.7292 (t80) cc_final: 0.6962 (t80) REVERT: M 110 TYR cc_start: 0.7645 (OUTLIER) cc_final: 0.6842 (m-80) REVERT: M 127 ARG cc_start: 0.8450 (mtp85) cc_final: 0.7961 (mtp85) REVERT: M 135 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.8437 (m-80) REVERT: M 186 GLN cc_start: 0.8079 (tp40) cc_final: 0.7685 (tm-30) REVERT: N 52 MET cc_start: 0.8106 (ptm) cc_final: 0.7860 (ppp) REVERT: N 70 ARG cc_start: 0.7785 (ttp-170) cc_final: 0.7254 (ttp80) REVERT: N 184 PHE cc_start: 0.8111 (m-80) cc_final: 0.7725 (m-80) REVERT: P 147 TYR cc_start: 0.8656 (m-80) cc_final: 0.8281 (m-10) REVERT: R 117 LYS cc_start: 0.6766 (mttt) cc_final: 0.6001 (ttmt) REVERT: R 121 ARG cc_start: 0.7725 (mtt180) cc_final: 0.7339 (ttp-170) REVERT: S 20 ARG cc_start: 0.7662 (mtm180) cc_final: 0.7435 (mtm180) REVERT: S 28 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8585 (mm) REVERT: S 193 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7340 (t80) REVERT: S 233 ASN cc_start: 0.8521 (p0) cc_final: 0.7666 (t0) REVERT: V 61 HIS cc_start: 0.8872 (OUTLIER) cc_final: 0.8087 (t70) REVERT: V 62 TYR cc_start: 0.7700 (OUTLIER) cc_final: 0.7294 (t80) REVERT: V 66 MET cc_start: 0.8044 (tmm) cc_final: 0.7409 (tmm) REVERT: V 165 TYR cc_start: 0.6388 (OUTLIER) cc_final: 0.5681 (p90) REVERT: V 173 ILE cc_start: 0.4968 (OUTLIER) cc_final: 0.4648 (mt) REVERT: V 177 HIS cc_start: 0.6690 (OUTLIER) cc_final: 0.6086 (t-170) REVERT: W 82 ARG cc_start: 0.8571 (mtp85) cc_final: 0.8098 (mtp85) REVERT: W 122 LEU cc_start: 0.8891 (mt) cc_final: 0.8623 (mt) REVERT: Y 92 TYR cc_start: 0.7338 (m-10) cc_final: 0.6983 (m-10) REVERT: Y 114 GLN cc_start: 0.8030 (mm-40) cc_final: 0.7704 (mt0) REVERT: a 127 ARG cc_start: 0.8275 (mtp85) cc_final: 0.7828 (mtp85) REVERT: a 186 GLN cc_start: 0.8055 (tp40) cc_final: 0.7690 (tm-30) REVERT: a 236 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7624 (p0) REVERT: c 204 LYS cc_start: 0.8881 (mmtm) cc_final: 0.8639 (mmtm) REVERT: c 207 MET cc_start: 0.7970 (tmm) cc_final: 0.7236 (tmm) REVERT: c 226 GLN cc_start: 0.8575 (mp10) cc_final: 0.7650 (tm-30) REVERT: c 237 TRP cc_start: 0.7612 (t-100) cc_final: 0.7303 (t-100) REVERT: c 247 MET cc_start: 0.8635 (ttm) cc_final: 0.8280 (ttt) REVERT: c 256 ASP cc_start: 0.8133 (t70) cc_final: 0.7514 (t0) REVERT: c 262 TRP cc_start: 0.7710 (t-100) cc_final: 0.7241 (t60) REVERT: d 27 TYR cc_start: 0.7915 (t80) cc_final: 0.7359 (t80) REVERT: d 226 GLN cc_start: 0.6372 (mt0) cc_final: 0.5847 (tt0) REVERT: d 251 TYR cc_start: 0.8290 (OUTLIER) cc_final: 0.7388 (t80) REVERT: d 262 TRP cc_start: 0.7623 (t-100) cc_final: 0.7340 (t-100) REVERT: e 162 TRP cc_start: 0.8752 (t60) cc_final: 0.7622 (t60) REVERT: f 190 ARG cc_start: 0.8600 (ttp-170) cc_final: 0.8359 (ptm-80) REVERT: f 224 ASP cc_start: 0.7578 (OUTLIER) cc_final: 0.7084 (t0) REVERT: g 259 TYR cc_start: 0.6426 (OUTLIER) cc_final: 0.5214 (m-80) REVERT: h 237 TRP cc_start: 0.7412 (t-100) cc_final: 0.6814 (t-100) REVERT: h 247 MET cc_start: 0.8008 (mmm) cc_final: 0.7247 (mmp) REVERT: h 263 GLU cc_start: 0.8774 (mp0) cc_final: 0.8509 (mm-30) REVERT: i 176 PHE cc_start: 0.7478 (t80) cc_final: 0.7236 (t80) REVERT: i 190 ARG cc_start: 0.8246 (ttp80) cc_final: 0.7378 (ttp80) REVERT: i 193 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8205 (pp20) REVERT: i 226 GLN cc_start: 0.8011 (tt0) cc_final: 0.7458 (tm-30) REVERT: i 253 MET cc_start: 0.8407 (tpp) cc_final: 0.8169 (tpp) REVERT: j 224 ASP cc_start: 0.7502 (m-30) cc_final: 0.6986 (t0) REVERT: j 236 GLU cc_start: 0.8603 (tp30) cc_final: 0.8285 (mm-30) REVERT: j 248 ARG cc_start: 0.7805 (ppt170) cc_final: 0.7285 (pmt-80) REVERT: k 172 ASP cc_start: 0.7716 (t70) cc_final: 0.7319 (t70) REVERT: k 207 MET cc_start: 0.9294 (tpp) cc_final: 0.8923 (tpt) REVERT: k 208 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7266 (tm-30) REVERT: k 259 TYR cc_start: 0.6450 (OUTLIER) cc_final: 0.5198 (m-80) REVERT: l 196 PHE cc_start: 0.8310 (t80) cc_final: 0.8074 (t80) REVERT: m 204 LYS cc_start: 0.8700 (mmtm) cc_final: 0.8424 (mmtm) REVERT: m 226 GLN cc_start: 0.8918 (mp10) cc_final: 0.8545 (mp10) REVERT: m 237 TRP cc_start: 0.7377 (t-100) cc_final: 0.6978 (t60) REVERT: m 247 MET cc_start: 0.8574 (ttm) cc_final: 0.8133 (mtt) REVERT: m 248 ARG cc_start: 0.8530 (tmm-80) cc_final: 0.7476 (ptm-80) REVERT: m 255 TYR cc_start: 0.7342 (t80) cc_final: 0.6691 (t80) REVERT: n 150 SER cc_start: 0.8952 (OUTLIER) cc_final: 0.8376 (p) REVERT: n 193 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8666 (mm-30) REVERT: n 226 GLN cc_start: 0.8070 (tt0) cc_final: 0.7396 (tm-30) REVERT: o 251 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.7929 (t80) REVERT: p 58 PRO cc_start: 0.3874 (Cg_endo) cc_final: 0.3505 (Cg_exo) REVERT: p 162 TRP cc_start: 0.8853 (t60) cc_final: 0.8365 (t60) REVERT: p 172 ASP cc_start: 0.6468 (OUTLIER) cc_final: 0.6135 (p0) REVERT: p 250 ASN cc_start: 0.8240 (m-40) cc_final: 0.7956 (m110) REVERT: X 101 ARG cc_start: 0.8466 (ttp80) cc_final: 0.7938 (ttp80) REVERT: X 191 ASP cc_start: 0.7226 (t0) cc_final: 0.6679 (t0) REVERT: Q 109 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.8061 (mm-40) REVERT: Q 119 GLN cc_start: 0.9085 (tp40) cc_final: 0.8607 (tt0) REVERT: T 3 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.7056 (ptp-170) REVERT: T 31 GLN cc_start: 0.8347 (mm110) cc_final: 0.7810 (tp40) REVERT: T 154 GLU cc_start: 0.6982 (tt0) cc_final: 0.6684 (tt0) REVERT: T 227 GLN cc_start: 0.7882 (tm-30) cc_final: 0.7181 (tm-30) REVERT: O 22 LEU cc_start: 0.8557 (mt) cc_final: 0.7604 (mt) REVERT: O 26 GLU cc_start: 0.7965 (mp0) cc_final: 0.7669 (mp0) REVERT: O 96 MET cc_start: 0.8778 (mmm) cc_final: 0.8383 (mpp) REVERT: O 193 LYS cc_start: 0.8342 (tptt) cc_final: 0.8003 (tptt) REVERT: Z 35 ILE cc_start: 0.9258 (mp) cc_final: 0.9032 (mt) REVERT: Z 56 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7281 (mp0) REVERT: Z 88 TYR cc_start: 0.7205 (t80) cc_final: 0.6891 (t80) REVERT: U 128 TYR cc_start: 0.8204 (m-80) cc_final: 0.7937 (m-80) REVERT: U 199 PHE cc_start: 0.7930 (m-80) cc_final: 0.7547 (m-80) outliers start: 234 outliers final: 184 residues processed: 1304 average time/residue: 0.6422 time to fit residues: 1447.0873 Evaluate side-chains 1326 residues out of total 7852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1114 time to evaluate : 6.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain B residue 214 TYR Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 115 CYS Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 184 GLN Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 221 ILE Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 177 HIS Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 198 HIS Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 148 ASP Chi-restraints excluded: chain J residue 163 CYS Chi-restraints excluded: chain J residue 172 ASP Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 159 ILE Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain K residue 188 VAL Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 158 ASN Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 197 HIS Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 110 TYR Chi-restraints excluded: chain M residue 135 PHE Chi-restraints excluded: chain M residue 185 ASN Chi-restraints excluded: chain M residue 187 LEU Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 15 ILE Chi-restraints excluded: chain N residue 26 ASP Chi-restraints excluded: chain N residue 101 VAL Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain P residue 12 THR Chi-restraints excluded: chain P residue 36 LEU Chi-restraints excluded: chain P residue 60 ASN Chi-restraints excluded: chain P residue 169 ASN Chi-restraints excluded: chain P residue 215 ASP Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 159 GLN Chi-restraints excluded: chain S residue 13 ASN Chi-restraints excluded: chain S residue 24 VAL Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 43 ASN Chi-restraints excluded: chain S residue 184 GLN Chi-restraints excluded: chain S residue 193 PHE Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 61 HIS Chi-restraints excluded: chain V residue 62 TYR Chi-restraints excluded: chain V residue 76 PHE Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain V residue 87 THR Chi-restraints excluded: chain V residue 165 TYR Chi-restraints excluded: chain V residue 173 ILE Chi-restraints excluded: chain V residue 177 HIS Chi-restraints excluded: chain V residue 209 LEU Chi-restraints excluded: chain V residue 227 LEU Chi-restraints excluded: chain V residue 245 ASN Chi-restraints excluded: chain W residue 2 THR Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 41 ILE Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 79 CYS Chi-restraints excluded: chain W residue 198 HIS Chi-restraints excluded: chain Y residue 124 MET Chi-restraints excluded: chain Y residue 173 LEU Chi-restraints excluded: chain a residue 63 ILE Chi-restraints excluded: chain a residue 65 THR Chi-restraints excluded: chain a residue 185 ASN Chi-restraints excluded: chain a residue 187 LEU Chi-restraints excluded: chain a residue 236 ASP Chi-restraints excluded: chain c residue 67 LEU Chi-restraints excluded: chain c residue 178 VAL Chi-restraints excluded: chain c residue 183 GLU Chi-restraints excluded: chain c residue 222 VAL Chi-restraints excluded: chain c residue 239 HIS Chi-restraints excluded: chain d residue 214 THR Chi-restraints excluded: chain d residue 217 LEU Chi-restraints excluded: chain d residue 251 TYR Chi-restraints excluded: chain e residue 64 VAL Chi-restraints excluded: chain e residue 232 LEU Chi-restraints excluded: chain f residue 28 ASP Chi-restraints excluded: chain f residue 158 ASN Chi-restraints excluded: chain f residue 224 ASP Chi-restraints excluded: chain g residue 52 VAL Chi-restraints excluded: chain g residue 254 LEU Chi-restraints excluded: chain g residue 259 TYR Chi-restraints excluded: chain h residue 188 LEU Chi-restraints excluded: chain h residue 191 VAL Chi-restraints excluded: chain i residue 28 ASP Chi-restraints excluded: chain i residue 242 ILE Chi-restraints excluded: chain j residue 28 ASP Chi-restraints excluded: chain j residue 254 LEU Chi-restraints excluded: chain k residue 52 VAL Chi-restraints excluded: chain k residue 205 TYR Chi-restraints excluded: chain k residue 208 GLU Chi-restraints excluded: chain k residue 259 TYR Chi-restraints excluded: chain l residue 242 ILE Chi-restraints excluded: chain m residue 178 VAL Chi-restraints excluded: chain m residue 222 VAL Chi-restraints excluded: chain n residue 150 SER Chi-restraints excluded: chain n residue 170 ILE Chi-restraints excluded: chain o residue 251 TYR Chi-restraints excluded: chain p residue 64 VAL Chi-restraints excluded: chain p residue 172 ASP Chi-restraints excluded: chain p residue 187 GLU Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 10 THR Chi-restraints excluded: chain b residue 12 VAL Chi-restraints excluded: chain b residue 26 ASP Chi-restraints excluded: chain b residue 101 VAL Chi-restraints excluded: chain b residue 109 LEU Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 44 ILE Chi-restraints excluded: chain X residue 110 ILE Chi-restraints excluded: chain X residue 139 LEU Chi-restraints excluded: chain X residue 172 ASP Chi-restraints excluded: chain X residue 185 LEU Chi-restraints excluded: chain Q residue 21 VAL Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 44 ILE Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 52 ILE Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 109 GLN Chi-restraints excluded: chain Q residue 115 CYS Chi-restraints excluded: chain Q residue 132 VAL Chi-restraints excluded: chain Q residue 143 ASP Chi-restraints excluded: chain T residue 3 ARG Chi-restraints excluded: chain T residue 214 VAL Chi-restraints excluded: chain O residue 16 PHE Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 93 CYS Chi-restraints excluded: chain O residue 139 LEU Chi-restraints excluded: chain O residue 142 CYS Chi-restraints excluded: chain Z residue 83 LEU Chi-restraints excluded: chain Z residue 107 THR Chi-restraints excluded: chain Z residue 158 ASN Chi-restraints excluded: chain Z residue 176 VAL Chi-restraints excluded: chain Z residue 197 HIS Chi-restraints excluded: chain Z residue 201 THR Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 61 ILE Chi-restraints excluded: chain U residue 77 ILE Chi-restraints excluded: chain U residue 80 TYR Chi-restraints excluded: chain U residue 111 LEU Chi-restraints excluded: chain U residue 147 ASP Chi-restraints excluded: chain U residue 150 ASP Chi-restraints excluded: chain U residue 221 ILE Chi-restraints excluded: chain U residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 540 optimal weight: 8.9990 chunk 725 optimal weight: 0.0980 chunk 208 optimal weight: 0.9990 chunk 627 optimal weight: 20.0000 chunk 100 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 chunk 681 optimal weight: 20.0000 chunk 285 optimal weight: 4.9990 chunk 700 optimal weight: 9.9990 chunk 86 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN F 138 HIS F 221 GLN ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 158 ASN ** M 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 239 HIS ** d 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 239 HIS ** e 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 275 HIS k 239 HIS n 197 ASN ** o 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 138 HIS Z 158 ASN ** U 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 112 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.149002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.111800 restraints weight = 144973.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.113472 restraints weight = 73445.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.114611 restraints weight = 46586.107| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 72408 Z= 0.235 Angle : 0.636 23.447 97746 Z= 0.326 Chirality : 0.043 0.367 10936 Planarity : 0.004 0.111 12412 Dihedral : 4.387 74.866 9620 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.92 % Favored : 94.05 % Rotamer: Outliers : 3.36 % Allowed : 24.72 % Favored : 71.92 % 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: -0.29 (0.09), residues: 8660 helix: 1.53 (0.08), residues: 4094 sheet: -1.56 (0.14), residues: 1296 loop : -1.87 (0.11), residues: 3270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP l 162 HIS 0.014 0.001 HIS c 239 PHE 0.032 0.002 PHE R 187 TYR 0.044 0.001 TYR C 223 ARG 0.012 0.001 ARG n 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21443.07 seconds wall clock time: 376 minutes 3.68 seconds (22563.68 seconds total)