Starting phenix.real_space_refine on Sun Mar 3 13:44:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv7_17956/03_2024/8pv7_17956_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv7_17956/03_2024/8pv7_17956.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv7_17956/03_2024/8pv7_17956_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv7_17956/03_2024/8pv7_17956_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv7_17956/03_2024/8pv7_17956_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv7_17956/03_2024/8pv7_17956.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv7_17956/03_2024/8pv7_17956.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv7_17956/03_2024/8pv7_17956_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv7_17956/03_2024/8pv7_17956_updated.pdb" } resolution = 2.12 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= 0.019 sd= 0.175 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 5 6.06 5 P 3441 5.49 5 Mg 3 5.21 5 S 254 5.16 5 C 85729 2.51 5 N 29147 2.21 5 O 38683 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "CB GLU 93": "OE1" <-> "OE2" Residue "CB GLU 210": "OE1" <-> "OE2" Residue "CB TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CB GLU 265": "OE1" <-> "OE2" Residue "CB TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CB GLU 303": "OE1" <-> "OE2" Residue "CF TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CF PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CF ASP 55": "OD1" <-> "OD2" Residue "CF TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CF ASP 183": "OD1" <-> "OD2" Residue "CF GLU 218": "OE1" <-> "OE2" Residue "CH PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH GLU 58": "OE1" <-> "OE2" Residue "CH GLU 229": "OE1" <-> "OE2" Residue "CH TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH GLU 300": "OE1" <-> "OE2" Residue "CH GLU 325": "OE1" <-> "OE2" Residue "CH GLU 341": "OE1" <-> "OE2" Residue "CH GLU 363": "OE1" <-> "OE2" Residue "CH GLU 409": "OE1" <-> "OE2" Residue "CH ASP 455": "OD1" <-> "OD2" Residue "CH GLU 466": "OE1" <-> "OE2" Residue "CH PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH GLU 486": "OE1" <-> "OE2" Residue "CH GLU 487": "OE1" <-> "OE2" Residue "CH ASP 540": "OD1" <-> "OD2" Residue "CI GLU 212": "OE1" <-> "OE2" Residue "CI ASP 237": "OD1" <-> "OD2" Residue "CI GLU 294": "OE1" <-> "OE2" Residue "CI GLU 310": "OE1" <-> "OE2" Residue "CI GLU 318": "OE1" <-> "OE2" Residue "CI GLU 326": "OE1" <-> "OE2" Residue "CJ GLU 114": "OE1" <-> "OE2" Residue "CJ GLU 410": "OE1" <-> "OE2" Residue "CK GLU 5": "OE1" <-> "OE2" Residue "CK TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CK GLU 22": "OE1" <-> "OE2" Residue "CK GLU 69": "OE1" <-> "OE2" Residue "CK ASP 84": "OD1" <-> "OD2" Residue "CK ASP 92": "OD1" <-> "OD2" Residue "CK ASP 160": "OD1" <-> "OD2" Residue "CK ASP 252": "OD1" <-> "OD2" Residue "CL GLU 44": "OE1" <-> "OE2" Residue "CL GLU 70": "OE1" <-> "OE2" Residue "CL GLU 72": "OE1" <-> "OE2" Residue "CM GLU 16": "OE1" <-> "OE2" Residue "CM GLU 31": "OE1" <-> "OE2" Residue "CM GLU 131": "OE1" <-> "OE2" Residue "CM ASP 171": "OD1" <-> "OD2" Residue "CM GLU 177": "OE1" <-> "OE2" Residue "CM PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CM GLU 230": "OE1" <-> "OE2" Residue "CM GLU 238": "OE1" <-> "OE2" Residue "CN PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CN GLU 124": "OE1" <-> "OE2" Residue "CN GLU 172": "OE1" <-> "OE2" Residue "CO GLU 12": "OE1" <-> "OE2" Residue "CO GLU 31": "OE1" <-> "OE2" Residue "CO ASP 95": "OD1" <-> "OD2" Residue "CQ ASP 66": "OD1" <-> "OD2" Residue "CQ GLU 94": "OE1" <-> "OE2" Residue "CQ GLU 131": "OE1" <-> "OE2" Residue "CQ GLU 141": "OE1" <-> "OE2" Residue "Cb ASP 20": "OD1" <-> "OD2" Residue "Cb GLU 23": "OE1" <-> "OE2" Residue "Cb ASP 43": "OD1" <-> "OD2" Residue "Cb GLU 62": "OE1" <-> "OE2" Residue "Cd GLU 64": "OE1" <-> "OE2" Residue "Cd ASP 119": "OD1" <-> "OD2" Residue "Cd GLU 139": "OE1" <-> "OE2" Residue "Cd GLU 169": "OE1" <-> "OE2" Residue "Cd GLU 180": "OE1" <-> "OE2" Residue "Cd PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cd ASP 312": "OD1" <-> "OD2" Residue "Cd GLU 391": "OE1" <-> "OE2" Residue "Cd ASP 392": "OD1" <-> "OD2" Residue "Cd GLU 408": "OE1" <-> "OE2" Residue "Cd ASP 458": "OD1" <-> "OD2" Residue "Cd GLU 481": "OE1" <-> "OE2" Residue "Ce ASP 89": "OD1" <-> "OD2" Residue "Ce ASP 221": "OD1" <-> "OD2" Residue "Ce GLU 231": "OE1" <-> "OE2" Residue "Ce ASP 362": "OD1" <-> "OD2" Residue "Ce PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ce ASP 387": "OD1" <-> "OD2" Residue "Ce ASP 391": "OD1" <-> "OD2" Residue "Ce GLU 399": "OE1" <-> "OE2" Residue "Cf TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cf PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cf ASP 121": "OD1" <-> "OD2" Residue "Cf GLU 150": "OE1" <-> "OE2" Residue "Cf ASP 264": "OD1" <-> "OD2" Residue "Cf GLU 270": "OE1" <-> "OE2" Residue "Cf GLU 280": "OE1" <-> "OE2" Residue "Cg ASP 24": "OD1" <-> "OD2" Residue "Cg ASP 32": "OD1" <-> "OD2" Residue "Cg ASP 77": "OD1" <-> "OD2" Residue "Cg GLU 93": "OE1" <-> "OE2" Residue "Cg GLU 102": "OE1" <-> "OE2" Residue "Cg GLU 135": "OE1" <-> "OE2" Residue "Cg GLU 148": "OE1" <-> "OE2" Residue "Cg ASP 150": "OD1" <-> "OD2" Residue "Cg GLU 154": "OE1" <-> "OE2" Residue "Cg GLU 160": "OE1" <-> "OE2" Residue "Cg GLU 197": "OE1" <-> "OE2" Residue "Ch TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ch ASP 177": "OD1" <-> "OD2" Residue "Ch GLU 219": "OE1" <-> "OE2" Residue "Ch TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ch GLU 345": "OE1" <-> "OE2" Residue "Ch GLU 350": "OE1" <-> "OE2" Residue "Ch GLU 359": "OE1" <-> "OE2" Residue "Ch PHE 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cz GLU 49": "OE1" <-> "OE2" Residue "Cz GLU 75": "OE1" <-> "OE2" Residue "Cz GLU 97": "OE1" <-> "OE2" Residue "LA GLU 74": "OE1" <-> "OE2" Residue "LA GLU 118": "OE1" <-> "OE2" Residue "LA GLU 143": "OE1" <-> "OE2" Residue "LB PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB GLU 74": "OE1" <-> "OE2" Residue "LB GLU 94": "OE1" <-> "OE2" Residue "LB PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB GLU 292": "OE1" <-> "OE2" Residue "LB GLU 298": "OE1" <-> "OE2" Residue "LB GLU 356": "OE1" <-> "OE2" Residue "LC ASP 154": "OD1" <-> "OD2" Residue "LC ASP 161": "OD1" <-> "OD2" Residue "LC ASP 238": "OD1" <-> "OD2" Residue "LC GLU 270": "OE1" <-> "OE2" Residue "LC PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LD TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LD PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LD GLU 189": "OE1" <-> "OE2" Residue "LD GLU 191": "OE1" <-> "OE2" Residue "LD ASP 216": "OD1" <-> "OD2" Residue "LD ASP 232": "OD1" <-> "OD2" Residue "LD ASP 233": "OD1" <-> "OD2" Residue "LD ASP 237": "OD1" <-> "OD2" Residue "LD GLU 241": "OE1" <-> "OE2" Residue "LE GLU 22": "OE1" <-> "OE2" Residue "LE GLU 31": "OE1" <-> "OE2" Residue "LE ASP 115": "OD1" <-> "OD2" Residue "LE TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LE ASP 161": "OD1" <-> "OD2" Residue "LE ASP 166": "OD1" <-> "OD2" Residue "LF GLU 26": "OE1" <-> "OE2" Residue "LF GLU 31": "OE1" <-> "OE2" Residue "LF GLU 45": "OE1" <-> "OE2" Residue "LF PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LF GLU 55": "OE1" <-> "OE2" Residue "LF GLU 65": "OE1" <-> "OE2" Residue "LF GLU 152": "OE1" <-> "OE2" Residue "LF GLU 177": "OE1" <-> "OE2" Residue "LF GLU 230": "OE1" <-> "OE2" Residue "LF GLU 239": "OE1" <-> "OE2" Residue "LG GLU 31": "OE1" <-> "OE2" Residue "LG TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG ASP 161": "OD1" <-> "OD2" Residue "LG PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LH TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LH GLU 65": "OE1" <-> "OE2" Residue "LH ASP 74": "OD1" <-> "OD2" Residue "LH GLU 141": "OE1" <-> "OE2" Residue "LH TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LH ASP 199": "OD1" <-> "OD2" Residue "LH TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LJ TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LJ ASP 112": "OD1" <-> "OD2" Residue "LJ GLU 158": "OE1" <-> "OE2" Residue "LJ ASP 169": "OD1" <-> "OD2" Residue "LK GLU 21": "OE1" <-> "OE2" Residue "LK GLU 95": "OE1" <-> "OE2" Residue "LK ASP 107": "OD1" <-> "OD2" Residue "LK ASP 124": "OD1" <-> "OD2" Residue "LK GLU 131": "OE1" <-> "OE2" Residue "LK ASP 144": "OD1" <-> "OD2" Residue "LK ASP 164": "OD1" <-> "OD2" Residue "LL GLU 78": "OE1" <-> "OE2" Residue "LL GLU 106": "OE1" <-> "OE2" Residue "LL GLU 107": "OE1" <-> "OE2" Residue "LL ASP 118": "OD1" <-> "OD2" Residue "LL ASP 137": "OD1" <-> "OD2" Residue "LL ASP 141": "OD1" <-> "OD2" Residue "LL GLU 146": "OE1" <-> "OE2" Residue "LL GLU 167": "OE1" <-> "OE2" Residue "LL ASP 191": "OD1" <-> "OD2" Residue "LM GLU 15": "OE1" <-> "OE2" Residue "LM GLU 32": "OE1" <-> "OE2" Residue "LM GLU 107": "OE1" <-> "OE2" Residue "LN ASP 17": "OD1" <-> "OD2" Residue "LN GLU 29": "OE1" <-> "OE2" Residue "LN TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN ASP 124": "OD1" <-> "OD2" Residue "LN PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO GLU 5": "OE1" <-> "OE2" Residue "LO ASP 115": "OD1" <-> "OD2" Residue "LO GLU 146": "OE1" <-> "OE2" Residue "LO GLU 160": "OE1" <-> "OE2" Residue "LO TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LP ASP 53": "OD1" <-> "OD2" Residue "LP GLU 99": "OE1" <-> "OE2" Residue "LP GLU 147": "OE1" <-> "OE2" Residue "LQ ASP 50": "OD1" <-> "OD2" Residue "LQ PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LQ GLU 104": "OE1" <-> "OE2" Residue "LQ GLU 127": "OE1" <-> "OE2" Residue "LQ GLU 142": "OE1" <-> "OE2" Residue "LQ ASP 152": "OD1" <-> "OD2" Residue "LR GLU 28": "OE1" <-> "OE2" Residue "LR GLU 65": "OE1" <-> "OE2" Residue "LR ASP 86": "OD1" <-> "OD2" Residue "LR ASP 116": "OD1" <-> "OD2" Residue "LR TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LR GLU 140": "OE1" <-> "OE2" Residue "LS TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS GLU 34": "OE1" <-> "OE2" Residue "LS ASP 82": "OD1" <-> "OD2" Residue "LS PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS GLU 128": "OE1" <-> "OE2" Residue "LT PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LT TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LT TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LT TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LT TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LT GLU 86": "OE1" <-> "OE2" Residue "LT GLU 103": "OE1" <-> "OE2" Residue "LT GLU 111": "OE1" <-> "OE2" Residue "LT GLU 137": "OE1" <-> "OE2" Residue "LT GLU 157": "OE1" <-> "OE2" Residue "LU ASP 31": "OD1" <-> "OD2" Residue "LU PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LU GLU 45": "OE1" <-> "OE2" Residue "LU ASP 50": "OD1" <-> "OD2" Residue "LU ASP 67": "OD1" <-> "OD2" Residue "LU GLU 71": "OE1" <-> "OE2" Residue "LU ASP 77": "OD1" <-> "OD2" Residue "LU GLU 111": "OE1" <-> "OE2" Residue "LU ASP 120": "OD1" <-> "OD2" Residue "LV GLU 70": "OE1" <-> "OE2" Residue "LV PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LV GLU 98": "OE1" <-> "OE2" Residue "LV GLU 110": "OE1" <-> "OE2" Residue "LX GLU 83": "OE1" <-> "OE2" Residue "LX PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LX ASP 100": "OD1" <-> "OD2" Residue "LX TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LX ASP 119": "OD1" <-> "OD2" Residue "LX ASP 130": "OD1" <-> "OD2" Residue "LX ASP 142": "OD1" <-> "OD2" Residue "LY GLU 37": "OE1" <-> "OE2" Residue "LY ASP 64": "OD1" <-> "OD2" Residue "LY GLU 66": "OE1" <-> "OE2" Residue "LY GLU 82": "OE1" <-> "OE2" Residue "LY ASP 111": "OD1" <-> "OD2" Residue "LY GLU 115": "OE1" <-> "OE2" Residue "LZ ASP 29": "OD1" <-> "OD2" Residue "LZ TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LZ PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LZ GLU 89": "OE1" <-> "OE2" Residue "LZ GLU 108": "OE1" <-> "OE2" Residue "LZ GLU 118": "OE1" <-> "OE2" Residue "LZ ASP 119": "OD1" <-> "OD2" Residue "La ASP 76": "OD1" <-> "OD2" Residue "La TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "La GLU 133": "OE1" <-> "OE2" Residue "La GLU 140": "OE1" <-> "OE2" Residue "Lc GLU 58": "OE1" <-> "OE2" Residue "Lc TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ld GLU 43": "OE1" <-> "OE2" Residue "Ld ASP 56": "OD1" <-> "OD2" Residue "Ld GLU 95": "OE1" <-> "OE2" Residue "Le PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Le ASP 30": "OD1" <-> "OD2" Residue "Le ASP 82": "OD1" <-> "OD2" Residue "Le GLU 84": "OE1" <-> "OE2" Residue "Le ASP 108": "OD1" <-> "OD2" Residue "Lf GLU 4": "OE1" <-> "OE2" Residue "Lf TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lf ASP 39": "OD1" <-> "OD2" Residue "Lf PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lf GLU 60": "OE1" <-> "OE2" Residue "Lg TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lg ASP 88": "OD1" <-> "OD2" Residue "Lg GLU 98": "OE1" <-> "OE2" Residue "Lh GLU 18": "OE1" <-> "OE2" Residue "Lh GLU 19": "OE1" <-> "OE2" Residue "Lh GLU 26": "OE1" <-> "OE2" Residue "Lh ASP 51": "OD1" <-> "OD2" Residue "Lh GLU 100": "OE1" <-> "OE2" Residue "Li ASP 75": "OD1" <-> "OD2" Residue "Li PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Li GLU 105": "OE1" <-> "OE2" Residue "Lj GLU 51": "OE1" <-> "OE2" Residue "Lk ASP 53": "OD1" <-> "OD2" Residue "Lk ASP 70": "OD1" <-> "OD2" Residue "Lp GLU 30": "OE1" <-> "OE2" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 157262 Number of models: 1 Model: "" Number of chains: 68 Chain: "C1" Number of atoms: 65888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3078, 65888 Classifications: {'RNA': 3078} Modifications used: {'rna2p': 1, 'rna2p_pur': 318, 'rna2p_pyr': 219, 'rna3p': 25, 'rna3p_pur': 1357, 'rna3p_pyr': 1150} Link IDs: {'rna2p': 538, 'rna3p': 2539} Chain breaks: 8 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 18 Chain: "C2" Number of atoms: 3319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3319 Classifications: {'RNA': 156} Modifications used: {'rna2p_pur': 18, 'rna2p_pyr': 12, 'rna3p_pur': 62, 'rna3p_pyr': 64} Link IDs: {'rna2p': 30, 'rna3p': 125} Chain: "C3" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1754 Classifications: {'RNA': 82} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 9, 'rna3p_pur': 31, 'rna3p_pyr': 31} Link IDs: {'rna2p': 19, 'rna3p': 62} Chain breaks: 1 Chain: "C4" Number of atoms: 2536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2536 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 54, 'rna3p_pyr': 53} Link IDs: {'rna2p': 12, 'rna3p': 106} Chain: "CB" Number of atoms: 2119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2119 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 246} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "CF" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1934 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 232} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "CH" Number of atoms: 5063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 5063 Classifications: {'peptide': 627} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 600} Chain breaks: 2 Chain: "CI" Number of atoms: 1234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1234 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 142} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "CJ" Number of atoms: 3116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3116 Classifications: {'peptide': 382} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 356} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "CK" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1903 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 221} Chain breaks: 2 Chain: "CL" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 622 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 72} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "CM" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1773 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 205} Chain breaks: 2 Chain: "CN" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1853 Classifications: {'peptide': 246} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 237} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "CO" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 468 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 2, 'TRANS': 59} Chain breaks: 2 Chain: "CQ" Number of atoms: 1480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1480 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 177} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "Lq" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1073 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 6, 'TRANS': 132} Chain: "Cb" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 830 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "Cd" Number of atoms: 3691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3691 Classifications: {'peptide': 462} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 30, 'TRANS': 431} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Ce" Number of atoms: 2148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2148 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 246} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Cf" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2282 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 267} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "Cg" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1478 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 19, 'TRANS': 168} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Ch" Number of atoms: 3812 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 485, 3809 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 466} Conformer: "B" Number of residues, atoms: 485, 3809 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 466} bond proxies already assigned to first conformer: 3904 Chain: "Cz" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 869 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "LA" Number of atoms: 1454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1454 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 175} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "LB" Number of atoms: 3104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3104 Classifications: {'peptide': 389} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 373} Chain: "LC" Number of atoms: 2751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2751 Classifications: {'peptide': 363} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 338} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "LD" Number of atoms: 2266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2266 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 6, 'TRANS': 279} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "LE" Number of atoms: 1477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1477 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 176} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "LF" Number of atoms: 2023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 2023 Classifications: {'peptide': 248} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 234} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "LG" Number of atoms: 1889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1889 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 223} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "LH" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1495 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain: "LJ" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1357 Classifications: {'peptide': 169} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 163} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "LK" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1184 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 149} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "LL" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1587 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 189} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 21 Chain: "LM" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1126 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "LN" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1704 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 193} Chain: "LO" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1611 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 192} Chain: "LP" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1343 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 164} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "LQ" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1200 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 7, 'TRANS': 142} Chain: "LR" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1241 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 151} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "LS" Number of atoms: 1426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1426 Classifications: {'peptide': 174} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 163} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "LT" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1027 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 121} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "LU" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 846 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "LV" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 991 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 125} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "LX" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1133 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 136} Chain: "LY" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1056 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 6, 'TRANS': 126} Chain: "LZ" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1112 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain: "La" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 872 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain breaks: 1 Chain: "Lc" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 705 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "Ld" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 875 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 105} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "Le" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1017 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "Lf" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 862 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "Lg" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 914 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 109} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Lh" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1003 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "Li" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 827 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 98} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS%COO:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Lj" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 698 Classifications: {'peptide': 88} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 83} Chain: "Lk" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 632 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 4, 'TRANS': 71} Chain: "Ll" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "Lp" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 698 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 89} Chain: "CH" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "CQ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Cb" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Cd" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' MG': 2, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Lg" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Lj" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Lp" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "CH" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Cd" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 93632 SG CYSCQ 6 146.508 179.577 99.778 1.00 38.97 S ATOM 93660 SG CYSCQ 9 150.138 180.515 100.400 1.00 39.12 S ATOM 93845 SG CYSCQ 32 149.434 177.351 98.650 1.00 37.00 S ATOM 93877 SG CYSCQ 36 148.716 177.752 102.410 1.00 36.62 S ATOM 96562 SG CYSCb 52 127.997 186.235 122.148 1.00 46.54 S ATOM 96585 SG CYSCb 55 131.424 184.445 122.077 1.00 46.84 S ATOM A14DQ SG CYSLg 45 142.231 159.393 198.005 1.00 39.52 S ATOM A14E8 SG CYSLg 48 140.023 161.270 195.653 1.00 41.41 S ATOM A14LG SG CYSLg 82 141.860 163.194 198.459 1.00 40.70 S ATOM A14LY SG CYSLg 85 139.076 161.027 199.394 1.00 42.48 S ATOM A16BV SG CYSLj 19 164.065 112.481 170.940 1.00 31.68 S ATOM A16CN SG CYSLj 22 164.985 110.177 167.996 1.00 31.77 S ATOM A16FD SG CYSLj 34 161.421 111.419 168.408 1.00 31.37 S ATOM A16FU SG CYSLj 37 162.899 108.967 170.940 1.00 31.50 S ATOM A17TK SG CYSLp 39 123.606 162.004 191.351 1.00 46.06 S ATOM A17U8 SG CYSLp 42 125.400 165.320 191.988 1.00 46.21 S ATOM A17XD SG CYSLp 57 126.586 162.997 189.308 1.00 45.54 S ATOM A17XY SG CYSLp 60 127.171 162.055 192.910 1.00 47.42 S Time building chain proxies: 60.26, per 1000 atoms: 0.38 Number of scatterers: 157262 At special positions: 0 Unit cell: (235.125, 228.855, 317.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 5 29.99 S 254 16.00 P 3441 15.00 Mg 3 11.99 O 38683 8.00 N 29147 7.00 C 85729 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: 60.67 Conformation dependent library (CDL) restraints added in 12.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNCQ1000 " pdb="ZN ZNCQ1000 " - pdb=" SG CYSCQ 36 " pdb="ZN ZNCQ1000 " - pdb=" SG CYSCQ 9 " pdb="ZN ZNCQ1000 " - pdb=" SG CYSCQ 32 " pdb="ZN ZNCQ1000 " - pdb=" SG CYSCQ 6 " pdb=" ZNCb1000 " pdb="ZN ZNCb1000 " - pdb=" ND1 HISCb 74 " pdb="ZN ZNCb1000 " - pdb=" NE2 HISCb 68 " pdb="ZN ZNCb1000 " - pdb=" SG CYSCb 52 " pdb="ZN ZNCb1000 " - pdb=" SG CYSCb 55 " pdb=" ZNLg1000 " pdb="ZN ZNLg1000 " - pdb=" SG CYSLg 82 " pdb="ZN ZNLg1000 " - pdb=" SG CYSLg 48 " pdb="ZN ZNLg1000 " - pdb=" SG CYSLg 85 " pdb="ZN ZNLg1000 " - pdb=" SG CYSLg 45 " pdb=" ZNLj1000 " pdb="ZN ZNLj1000 " - pdb=" SG CYSLj 34 " pdb="ZN ZNLj1000 " - pdb=" SG CYSLj 22 " pdb="ZN ZNLj1000 " - pdb=" SG CYSLj 19 " pdb="ZN ZNLj1000 " - pdb=" SG CYSLj 37 " pdb=" ZNLp 101 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 57 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 42 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 39 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 60 " Number of angles added : 26 20722 Ramachandran restraints generated. 10361 Oldfield, 0 Emsley, 10361 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 19708 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 380 helices and 106 sheets defined 45.4% alpha, 14.3% beta 1081 base pairs and 1855 stacking pairs defined. Time for finding SS restraints: 86.66 Creating SS restraints... Processing helix chain 'CB' and resid 19 through 40 removed outlier: 3.607A pdb=" N ALACB 40 " --> pdb=" O LYSCB 36 " (cutoff:3.500A) Processing helix chain 'CB' and resid 52 through 60 removed outlier: 4.467A pdb=" N GLUCB 59 " --> pdb=" O SERCB 55 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N THRCB 60 " --> pdb=" O THRCB 56 " (cutoff:3.500A) Processing helix chain 'CB' and resid 104 through 115 removed outlier: 4.299A pdb=" N TYRCB 108 " --> pdb=" O PROCB 104 " (cutoff:3.500A) Processing helix chain 'CB' and resid 117 through 125 removed outlier: 5.473A pdb=" N GLYCB 125 " --> pdb=" O ARGCB 121 " (cutoff:3.500A) Processing helix chain 'CB' and resid 129 through 137 Processing helix chain 'CB' and resid 139 through 151 removed outlier: 3.783A pdb=" N HISCB 150 " --> pdb=" O LEUCB 146 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ASPCB 151 " --> pdb=" O PHECB 147 " (cutoff:3.500A) Processing helix chain 'CB' and resid 159 through 168 removed outlier: 3.790A pdb=" N LEUCB 163 " --> pdb=" O ILECB 159 " (cutoff:3.500A) Proline residue: CB 164 - end of helix Processing helix chain 'CB' and resid 169 through 175 removed outlier: 5.535A pdb=" N THRCB 174 " --> pdb=" O THRCB 170 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N THRCB 175 " --> pdb=" O PHECB 171 " (cutoff:3.500A) Processing helix chain 'CB' and resid 216 through 230 Processing helix chain 'CB' and resid 251 through 269 Processing helix chain 'CB' and resid 274 through 279 removed outlier: 3.829A pdb=" N VALCB 278 " --> pdb=" O LYSCB 274 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ARGCB 279 " --> pdb=" O TRPCB 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'CB' and resid 274 through 279' Processing helix chain 'CB' and resid 302 through 307 removed outlier: 3.915A pdb=" N VALCB 306 " --> pdb=" O ASPCB 302 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N VALCB 307 " --> pdb=" O GLUCB 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'CB' and resid 302 through 307' Processing helix chain 'CF' and resid 19 through 37 removed outlier: 3.727A pdb=" N LYSCF 23 " --> pdb=" O GLYCF 19 " (cutoff:3.500A) Proline residue: CF 35 - end of helix Processing helix chain 'CF' and resid 50 through 61 removed outlier: 4.953A pdb=" N LYSCF 54 " --> pdb=" O ASNCF 50 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ASPCF 55 " --> pdb=" O ASNCF 51 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASNCF 61 " --> pdb=" O ARGCF 57 " (cutoff:3.500A) Processing helix chain 'CF' and resid 69 through 78 Processing helix chain 'CF' and resid 88 through 97 removed outlier: 4.360A pdb=" N LEUCF 92 " --> pdb=" O GLYCF 88 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THRCF 93 " --> pdb=" O LEUCF 89 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ARGCF 94 " --> pdb=" O HISCF 90 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N TYRCF 95 " --> pdb=" O ARGCF 91 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEUCF 96 " --> pdb=" O LEUCF 92 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N THRCF 97 " --> pdb=" O THRCF 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'CF' and resid 88 through 97' Processing helix chain 'CF' and resid 108 through 119 removed outlier: 3.514A pdb=" N ILECF 112 " --> pdb=" O ASPCF 108 " (cutoff:3.500A) Processing helix chain 'CF' and resid 158 through 169 removed outlier: 4.250A pdb=" N GLUCF 162 " --> pdb=" O SERCF 158 " (cutoff:3.500A) Proline residue: CF 163 - end of helix Processing helix chain 'CF' and resid 202 through 213 Processing helix chain 'CF' and resid 237 through 243 removed outlier: 3.687A pdb=" N THRCF 242 " --> pdb=" O GLUCF 238 " (cutoff:3.500A) Processing helix chain 'CH' and resid 12 through 27 Processing helix chain 'CH' and resid 37 through 66 Processing helix chain 'CH' and resid 69 through 74 removed outlier: 3.648A pdb=" N GLNCH 73 " --> pdb=" O VALCH 69 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N HISCH 74 " --> pdb=" O LEUCH 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'CH' and resid 69 through 74' Processing helix chain 'CH' and resid 75 through 85 Processing helix chain 'CH' and resid 86 through 118 removed outlier: 3.946A pdb=" N TYRCH 117 " --> pdb=" O ARGCH 113 " (cutoff:3.500A) Processing helix chain 'CH' and resid 120 through 143 removed outlier: 3.923A pdb=" N LEUCH 142 " --> pdb=" O LEUCH 138 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LYSCH 143 " --> pdb=" O ILECH 139 " (cutoff:3.500A) Processing helix chain 'CH' and resid 144 through 159 Processing helix chain 'CH' and resid 178 through 187 Processing helix chain 'CH' and resid 227 through 232 removed outlier: 3.675A pdb=" N METCH 231 " --> pdb=" O PROCH 227 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ASNCH 232 " --> pdb=" O LEUCH 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'CH' and resid 227 through 232' Processing helix chain 'CH' and resid 233 through 244 removed outlier: 3.917A pdb=" N SERCH 238 " --> pdb=" O ILECH 234 " (cutoff:3.500A) Processing helix chain 'CH' and resid 262 through 278 Proline residue: CH 275 - end of helix removed outlier: 4.113A pdb=" N ALACH 278 " --> pdb=" O LYSCH 274 " (cutoff:3.500A) Processing helix chain 'CH' and resid 293 through 298 removed outlier: 3.814A pdb=" N LEUCH 297 " --> pdb=" O LYSCH 293 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ASPCH 298 " --> pdb=" O PHECH 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'CH' and resid 293 through 298' Processing helix chain 'CH' and resid 299 through 311 removed outlier: 3.913A pdb=" N THRCH 309 " --> pdb=" O ILECH 305 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYSCH 310 " --> pdb=" O ASNCH 306 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N SERCH 311 " --> pdb=" O ASPCH 307 " (cutoff:3.500A) Processing helix chain 'CH' and resid 326 through 352 removed outlier: 4.833A pdb=" N GLYCH 350 " --> pdb=" O LYSCH 346 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THRCH 351 " --> pdb=" O LEUCH 347 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N HISCH 352 " --> pdb=" O LYSCH 348 " (cutoff:3.500A) Processing helix chain 'CH' and resid 358 through 369 Processing helix chain 'CH' and resid 384 through 390 removed outlier: 4.838A pdb=" N LYSCH 388 " --> pdb=" O PROCH 384 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASNCH 389 " --> pdb=" O GLUCH 385 " (cutoff:3.500A) Processing helix chain 'CH' and resid 403 through 412 Processing helix chain 'CH' and resid 445 through 450 removed outlier: 3.629A pdb=" N TYRCH 449 " --> pdb=" O ASNCH 445 " (cutoff:3.500A) Processing helix chain 'CH' and resid 453 through 472 removed outlier: 3.947A pdb=" N LYSCH 457 " --> pdb=" O ASPCH 453 " (cutoff:3.500A) Processing helix chain 'CH' and resid 482 through 510 Processing helix chain 'CH' and resid 519 through 524 removed outlier: 3.976A pdb=" N VALCH 523 " --> pdb=" O PROCH 519 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N LYSCH 524 " --> pdb=" O ARGCH 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'CH' and resid 519 through 524' Processing helix chain 'CH' and resid 526 through 538 Processing helix chain 'CH' and resid 540 through 545 removed outlier: 4.023A pdb=" N ILECH 544 " --> pdb=" O ASPCH 540 " (cutoff:3.500A) Processing helix chain 'CH' and resid 546 through 551 removed outlier: 5.676A pdb=" N GLNCH 551 " --> pdb=" O ARGCH 547 " (cutoff:3.500A) Processing helix chain 'CH' and resid 582 through 597 Processing helix chain 'CH' and resid 609 through 631 removed outlier: 3.968A pdb=" N GLNCH 624 " --> pdb=" O ALACH 620 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARGCH 625 " --> pdb=" O LYSCH 621 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LYSCH 626 " --> pdb=" O LEUCH 622 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N METCH 627 " --> pdb=" O ALACH 623 " (cutoff:3.500A) Processing helix chain 'CH' and resid 645 through 650 Processing helix chain 'CH' and resid 429 through 434 removed outlier: 4.675A pdb=" N TYRCH 434 " --> pdb=" O GLUCH 431 " (cutoff:3.500A) Processing helix chain 'CI' and resid 199 through 211 removed outlier: 3.846A pdb=" N GLNCI 209 " --> pdb=" O GLYCI 205 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N PHECI 210 " --> pdb=" O TYRCI 206 " (cutoff:3.500A) Processing helix chain 'CI' and resid 237 through 249 Processing helix chain 'CI' and resid 284 through 295 Processing helix chain 'CI' and resid 298 through 324 removed outlier: 4.151A pdb=" N GLUCI 322 " --> pdb=" O GLUCI 318 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N METCI 323 " --> pdb=" O LYSCI 319 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 11 through 16 Processing helix chain 'CJ' and resid 18 through 27 Processing helix chain 'CJ' and resid 29 through 41 Processing helix chain 'CJ' and resid 49 through 54 removed outlier: 3.919A pdb=" N VALCJ 53 " --> pdb=" O ASPCJ 49 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 65 through 75 removed outlier: 4.160A pdb=" N HISCJ 74 " --> pdb=" O GLNCJ 70 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLUCJ 75 " --> pdb=" O TYRCJ 71 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 76 through 98 removed outlier: 3.556A pdb=" N LYSCJ 80 " --> pdb=" O PROCJ 76 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 99 through 111 removed outlier: 3.866A pdb=" N ASNCJ 109 " --> pdb=" O ARGCJ 105 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALACJ 110 " --> pdb=" O LEUCJ 106 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASNCJ 111 " --> pdb=" O GLUCJ 107 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 112 through 117 Processing helix chain 'CJ' and resid 123 through 132 removed outlier: 3.729A pdb=" N ARGCJ 128 " --> pdb=" O ASNCJ 124 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLUCJ 129 " --> pdb=" O HISCJ 125 " (cutoff:3.500A) Proline residue: CJ 132 - end of helix Processing helix chain 'CJ' and resid 133 through 155 removed outlier: 4.693A pdb=" N ASPCJ 142 " --> pdb=" O LEUCJ 138 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ASPCJ 143 " --> pdb=" O ARGCJ 139 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ASNCJ 153 " --> pdb=" O PHECJ 149 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEUCJ 154 " --> pdb=" O LEUCJ 150 " (cutoff:3.500A) Proline residue: CJ 155 - end of helix Processing helix chain 'CJ' and resid 161 through 183 Processing helix chain 'CJ' and resid 223 through 250 removed outlier: 3.668A pdb=" N PHECJ 240 " --> pdb=" O THRCJ 236 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 258 through 265 Processing helix chain 'CJ' and resid 362 through 367 removed outlier: 3.901A pdb=" N LEUCJ 366 " --> pdb=" O ASPCJ 362 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N PHECJ 367 " --> pdb=" O PROCJ 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'CJ' and resid 362 through 367' Processing helix chain 'CJ' and resid 379 through 391 Processing helix chain 'CJ' and resid 457 through 468 removed outlier: 4.525A pdb=" N VALCJ 461 " --> pdb=" O GLNCJ 457 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TRPCJ 462 " --> pdb=" O PROCJ 458 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 472 through 477 removed outlier: 4.246A pdb=" N TYRCJ 476 " --> pdb=" O PROCJ 472 " (cutoff:3.500A) Processing helix chain 'CK' and resid 5 through 14 Processing helix chain 'CK' and resid 19 through 41 removed outlier: 4.853A pdb=" N GLYCK 32 " --> pdb=" O ALACK 28 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N HISCK 33 " --> pdb=" O ALACK 29 " (cutoff:3.500A) Processing helix chain 'CK' and resid 44 through 72 removed outlier: 5.101A pdb=" N ASNCK 72 " --> pdb=" O HISCK 68 " (cutoff:3.500A) Processing helix chain 'CK' and resid 128 through 133 Processing helix chain 'CK' and resid 174 through 179 removed outlier: 3.521A pdb=" N ARGCK 178 " --> pdb=" O PROCK 174 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N TYRCK 179 " --> pdb=" O METCK 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'CK' and resid 174 through 179' Processing helix chain 'CK' and resid 206 through 213 Processing helix chain 'CK' and resid 248 through 253 Processing helix chain 'CL' and resid 17 through 42 Processing helix chain 'CL' and resid 61 through 80 Processing helix chain 'CM' and resid 14 through 35 Processing helix chain 'CM' and resid 53 through 78 Processing helix chain 'CM' and resid 102 through 113 Processing helix chain 'CM' and resid 126 through 137 Processing helix chain 'CM' and resid 146 through 156 Processing helix chain 'CM' and resid 171 through 179 removed outlier: 4.640A pdb=" N ILECM 175 " --> pdb=" O ASPCM 171 " (cutoff:3.500A) Processing helix chain 'CM' and resid 186 through 197 Processing helix chain 'CM' and resid 200 through 209 removed outlier: 5.133A pdb=" N TRPCM 209 " --> pdb=" O ALACM 205 " (cutoff:3.500A) Processing helix chain 'CM' and resid 215 through 221 removed outlier: 4.556A pdb=" N GLYCM 219 " --> pdb=" O ASNCM 215 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N PHECM 220 " --> pdb=" O PROCM 216 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ARGCM 221 " --> pdb=" O ASNCM 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'CM' and resid 215 through 221' Processing helix chain 'CM' and resid 239 through 249 removed outlier: 4.598A pdb=" N ALACM 243 " --> pdb=" O GLUCM 239 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEUCM 244 " --> pdb=" O HISCM 240 " (cutoff:3.500A) Processing helix chain 'CN' and resid 12 through 17 removed outlier: 3.786A pdb=" N PHECN 16 " --> pdb=" O GLUCN 12 " (cutoff:3.500A) Processing helix chain 'CN' and resid 32 through 43 removed outlier: 3.658A pdb=" N PHECN 38 " --> pdb=" O PHECN 34 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLNCN 43 " --> pdb=" O GLUCN 39 " (cutoff:3.500A) Processing helix chain 'CN' and resid 58 through 63 Processing helix chain 'CN' and resid 77 through 89 Proline residue: CN 89 - end of helix Processing helix chain 'CN' and resid 103 through 108 Processing helix chain 'CN' and resid 122 through 133 Processing helix chain 'CN' and resid 147 through 152 Processing helix chain 'CN' and resid 166 through 178 Processing helix chain 'CN' and resid 192 through 197 Processing helix chain 'CN' and resid 211 through 223 Processing helix chain 'CN' and resid 229 through 236 removed outlier: 4.455A pdb=" N ILECN 233 " --> pdb=" O GLYCN 229 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASNCN 234 " --> pdb=" O PROCN 230 " (cutoff:3.500A) Processing helix chain 'CN' and resid 237 through 246 Processing helix chain 'CO' and resid 7 through 21 Processing helix chain 'CO' and resid 22 through 43 Processing helix chain 'CO' and resid 83 through 88 Processing helix chain 'CQ' and resid 33 through 43 Processing helix chain 'CQ' and resid 45 through 50 removed outlier: 5.304A pdb=" N LYSCQ 50 " --> pdb=" O PROCQ 46 " (cutoff:3.500A) Processing helix chain 'CQ' and resid 52 through 60 Processing helix chain 'CQ' and resid 66 through 71 removed outlier: 4.301A pdb=" N GLNCQ 70 " --> pdb=" O ASPCQ 66 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N PHECQ 71 " --> pdb=" O SERCQ 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'CQ' and resid 66 through 71' Processing helix chain 'CQ' and resid 82 through 131 removed outlier: 5.827A pdb=" N GLYCQ 114 " --> pdb=" O LYSCQ 110 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LYSCQ 115 " --> pdb=" O ARGCQ 111 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ARGCQ 116 " --> pdb=" O METCQ 112 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ALACQ 117 " --> pdb=" O ALACQ 113 " (cutoff:3.500A) Processing helix chain 'CQ' and resid 138 through 153 Processing helix chain 'CQ' and resid 155 through 171 removed outlier: 4.621A pdb=" N LYSCQ 171 " --> pdb=" O LEUCQ 167 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 5 through 14 Processing helix chain 'Lq' and resid 44 through 49 removed outlier: 5.443A pdb=" N ASPLq 49 " --> pdb=" O GLYLq 45 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 86 through 99 Processing helix chain 'Lq' and resid 104 through 123 removed outlier: 4.006A pdb=" N ARGLq 108 " --> pdb=" O ARGLq 104 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N GLNLq 109 " --> pdb=" O ALALq 105 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ALALq 110 " --> pdb=" O ASPLq 106 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARGLq 123 " --> pdb=" O LEULq 119 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 135 through 140 removed outlier: 5.223A pdb=" N ARGLq 140 " --> pdb=" O GLYLq 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'Lq' and resid 135 through 140' Processing helix chain 'Cb' and resid 5 through 10 removed outlier: 3.760A pdb=" N METCb 9 " --> pdb=" O ALACb 5 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N THRCb 10 " --> pdb=" O LYSCb 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'Cb' and resid 5 through 10' Processing helix chain 'Cb' and resid 18 through 28 Processing helix chain 'Cb' and resid 29 through 40 removed outlier: 3.970A pdb=" N LYSCb 39 " --> pdb=" O TYRCb 35 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ALACb 40 " --> pdb=" O LYSCb 36 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 61 through 72 removed outlier: 3.783A pdb=" N LYSCb 70 " --> pdb=" O VALCb 66 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLYCb 71 " --> pdb=" O GLYCb 67 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LYSCb 72 " --> pdb=" O HISCb 68 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 73 through 84 Processing helix chain 'Cb' and resid 87 through 96 removed outlier: 3.646A pdb=" N ILECb 95 " --> pdb=" O ALACb 91 " (cutoff:3.500A) Processing helix chain 'Cd' and resid 6 through 15 Processing helix chain 'Cd' and resid 31 through 43 removed outlier: 3.969A pdb=" N LEUCd 41 " --> pdb=" O THRCd 37 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYSCd 42 " --> pdb=" O LEUCd 38 " (cutoff:3.500A) Processing helix chain 'Cd' and resid 73 through 79 removed outlier: 4.684A pdb=" N PHECd 77 " --> pdb=" O ASNCd 73 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THRCd 78 " --> pdb=" O ARGCd 74 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ASNCd 79 " --> pdb=" O LYSCd 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'Cd' and resid 73 through 79' Processing helix chain 'Cd' and resid 84 through 98 Processing helix chain 'Cd' and resid 113 through 118 removed outlier: 3.554A pdb=" N ILECd 117 " --> pdb=" O PROCd 113 " (cutoff:3.500A) Processing helix chain 'Cd' and resid 122 through 139 removed outlier: 3.855A pdb=" N HISCd 130 " --> pdb=" O GLYCd 126 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ALACd 132 " --> pdb=" O LYSCd 128 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N LYSCd 133 " --> pdb=" O LYSCd 129 " (cutoff:3.500A) Processing helix chain 'Cd' and resid 140 through 145 Processing helix chain 'Cd' and resid 160 through 185 Processing helix chain 'Cd' and resid 211 through 216 removed outlier: 4.354A pdb=" N ASNCd 215 " --> pdb=" O GLUCd 211 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYSCd 216 " --> pdb=" O ALACd 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'Cd' and resid 211 through 216' Processing helix chain 'Cd' and resid 219 through 233 Processing helix chain 'Cd' and resid 244 through 249 Processing helix chain 'Cd' and resid 250 through 260 Processing helix chain 'Cd' and resid 272 through 277 removed outlier: 4.335A pdb=" N VALCd 276 " --> pdb=" O LYSCd 272 " (cutoff:3.500A) Proline residue: Cd 277 - end of helix No H-bonds generated for 'chain 'Cd' and resid 272 through 277' Processing helix chain 'Cd' and resid 278 through 292 removed outlier: 3.861A pdb=" N LYSCd 290 " --> pdb=" O ARGCd 286 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASPCd 291 " --> pdb=" O ILECd 287 " (cutoff:3.500A) Processing helix chain 'Cd' and resid 306 through 322 Processing helix chain 'Cd' and resid 338 through 348 Processing helix chain 'Cd' and resid 389 through 397 Processing helix chain 'Cd' and resid 400 through 405 removed outlier: 4.173A pdb=" N VALCd 404 " --> pdb=" O ARGCd 400 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLUCd 405 " --> pdb=" O VALCd 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'Cd' and resid 400 through 405' Processing helix chain 'Cd' and resid 406 through 419 removed outlier: 4.739A pdb=" N TYRCd 410 " --> pdb=" O HISCd 406 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILECd 411 " --> pdb=" O PROCd 407 " (cutoff:3.500A) Proline residue: Cd 412 - end of helix removed outlier: 5.116A pdb=" N LYSCd 419 " --> pdb=" O LEUCd 415 " (cutoff:3.500A) Processing helix chain 'Cd' and resid 420 through 428 Processing helix chain 'Cd' and resid 434 through 447 Processing helix chain 'Cd' and resid 456 through 471 removed outlier: 3.531A pdb=" N GLYCd 471 " --> pdb=" O ASPCd 467 " (cutoff:3.500A) Processing helix chain 'Ce' and resid 86 through 94 Processing helix chain 'Ce' and resid 186 through 192 removed outlier: 5.719A pdb=" N LYSCe 192 " --> pdb=" O THRCe 188 " (cutoff:3.500A) Processing helix chain 'Ce' and resid 218 through 269 Processing helix chain 'Ce' and resid 300 through 333 Processing helix chain 'Ce' and resid 334 through 353 Processing helix chain 'Ce' and resid 401 through 414 Processing helix chain 'Ce' and resid 435 through 441 Processing helix chain 'Cf' and resid 9 through 20 Processing helix chain 'Cf' and resid 39 through 54 Processing helix chain 'Cf' and resid 72 through 83 Processing helix chain 'Cf' and resid 155 through 169 Processing helix chain 'Cf' and resid 264 through 273 Processing helix chain 'Cf' and resid 314 through 319 removed outlier: 3.692A pdb=" N LYSCf 318 " --> pdb=" O METCf 314 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ARGCf 319 " --> pdb=" O LYSCf 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'Cf' and resid 314 through 319' Processing helix chain 'Cf' and resid 177 through 182 removed outlier: 3.884A pdb=" N LEUCf 181 " --> pdb=" O VALCf 178 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ARGCf 182 " --> pdb=" O GLUCf 179 " (cutoff:3.500A) Processing helix chain 'Cg' and resid 43 through 69 Processing helix chain 'Cg' and resid 103 through 113 Processing helix chain 'Cg' and resid 118 through 123 removed outlier: 3.513A pdb=" N ARGCg 123 " --> pdb=" O ARGCg 119 " (cutoff:3.500A) Processing helix chain 'Cg' and resid 156 through 163 Processing helix chain 'Cg' and resid 168 through 198 removed outlier: 4.146A pdb=" N ASPCg 172 " --> pdb=" O SERCg 168 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LYSCg 173 " --> pdb=" O VALCg 169 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ARGCg 174 " --> pdb=" O ARGCg 170 " (cutoff:3.500A) Processing helix chain 'Ch' and resid 61 through 74 Processing helix chain 'Ch' and resid 102 through 111 Processing helix chain 'Ch' and resid 331 through 338 removed outlier: 3.760A pdb=" N THRCh 337 " --> pdb=" O HISCh 333 " (cutoff:3.500A) Processing helix chain 'Ch' and resid 349 through 366 Processing helix chain 'Ch' and resid 388 through 393 Processing helix chain 'Cz' and resid 48 through 103 Processing helix chain 'Cz' and resid 104 through 121 Processing helix chain 'LA' and resid 33 through 39 Processing helix chain 'LA' and resid 103 through 108 removed outlier: 3.936A pdb=" N VALLA 107 " --> pdb=" O PROLA 103 " (cutoff:3.500A) Proline residue: LA 108 - end of helix No H-bonds generated for 'chain 'LA' and resid 103 through 108' Processing helix chain 'LA' and resid 181 through 193 removed outlier: 4.024A pdb=" N VALLA 191 " --> pdb=" O HISLA 187 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYSLA 192 " --> pdb=" O LYSLA 188 " (cutoff:3.500A) Processing helix chain 'LA' and resid 200 through 205 removed outlier: 3.833A pdb=" N METLA 204 " --> pdb=" O ARGLA 200 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ASNLA 205 " --> pdb=" O GLYLA 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'LA' and resid 200 through 205' Processing helix chain 'LB' and resid 13 through 18 removed outlier: 4.606A pdb=" N LEULB 17 " --> pdb=" O SERLB 13 " (cutoff:3.500A) Proline residue: LB 18 - end of helix No H-bonds generated for 'chain 'LB' and resid 13 through 18' Processing helix chain 'LB' and resid 111 through 120 removed outlier: 4.112A pdb=" N ARGLB 117 " --> pdb=" O GLULB 113 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHELB 118 " --> pdb=" O VALLB 114 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N TYRLB 119 " --> pdb=" O LYSLB 115 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LYSLB 120 " --> pdb=" O ARGLB 116 " (cutoff:3.500A) Processing helix chain 'LB' and resid 130 through 139 removed outlier: 4.010A pdb=" N LYSLB 135 " --> pdb=" O THRLB 131 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYSLB 136 " --> pdb=" O LYSLB 132 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TYRLB 137 " --> pdb=" O TYRLB 133 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALALB 138 " --> pdb=" O ALALB 134 " (cutoff:3.500A) Processing helix chain 'LB' and resid 142 through 155 Processing helix chain 'LB' and resid 166 through 171 removed outlier: 4.319A pdb=" N THRLB 170 " --> pdb=" O GLNLB 166 " (cutoff:3.500A) Proline residue: LB 171 - end of helix No H-bonds generated for 'chain 'LB' and resid 166 through 171' Processing helix chain 'LB' and resid 188 through 200 Processing helix chain 'LB' and resid 205 through 210 removed outlier: 3.995A pdb=" N ILELB 209 " --> pdb=" O THRLB 205 " (cutoff:3.500A) Processing helix chain 'LB' and resid 229 through 234 Processing helix chain 'LB' and resid 348 through 353 removed outlier: 3.949A pdb=" N LEULB 352 " --> pdb=" O SERLB 348 " (cutoff:3.500A) Processing helix chain 'LB' and resid 373 through 382 Processing helix chain 'LB' and resid 384 through 390 removed outlier: 3.630A pdb=" N LEULB 388 " --> pdb=" O LEULB 384 " (cutoff:3.500A) Processing helix chain 'LC' and resid 24 through 30 removed outlier: 4.562A pdb=" N SERLC 28 " --> pdb=" O PROLC 24 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALALC 29 " --> pdb=" O LYSLC 25 " (cutoff:3.500A) Proline residue: LC 30 - end of helix No H-bonds generated for 'chain 'LC' and resid 24 through 30' Processing helix chain 'LC' and resid 32 through 47 removed outlier: 4.153A pdb=" N LYSLC 45 " --> pdb=" O THRLC 41 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASNLC 46 " --> pdb=" O GLYLC 42 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LYSLC 47 " --> pdb=" O METLC 43 " (cutoff:3.500A) Processing helix chain 'LC' and resid 115 through 133 removed outlier: 3.678A pdb=" N ALALC 131 " --> pdb=" O LEULC 127 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VALLC 132 " --> pdb=" O ALALC 128 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ALALC 133 " --> pdb=" O ALALC 129 " (cutoff:3.500A) Processing helix chain 'LC' and resid 134 through 140 Processing helix chain 'LC' and resid 154 through 159 removed outlier: 3.983A pdb=" N VALLC 158 " --> pdb=" O ASPLC 154 " (cutoff:3.500A) Processing helix chain 'LC' and resid 165 through 177 Processing helix chain 'LC' and resid 178 through 189 removed outlier: 4.009A pdb=" N LYSLC 189 " --> pdb=" O VALLC 185 " (cutoff:3.500A) Processing helix chain 'LC' and resid 194 through 200 removed outlier: 4.696A pdb=" N METLC 198 " --> pdb=" O GLYLC 194 " (cutoff:3.500A) Processing helix chain 'LC' and resid 220 through 228 removed outlier: 4.027A pdb=" N LYSLC 224 " --> pdb=" O LYSLC 220 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASNLC 228 " --> pdb=" O LYSLC 224 " (cutoff:3.500A) Processing helix chain 'LC' and resid 241 through 247 Proline residue: LC 247 - end of helix Processing helix chain 'LC' and resid 258 through 272 removed outlier: 4.927A pdb=" N ASPLC 266 " --> pdb=" O ILELC 262 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ALALC 267 " --> pdb=" O LYSLC 263 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYSLC 272 " --> pdb=" O VALLC 268 " (cutoff:3.500A) Processing helix chain 'LC' and resid 286 through 293 Processing helix chain 'LC' and resid 294 through 300 removed outlier: 4.449A pdb=" N VALLC 299 " --> pdb=" O GLULC 295 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEULC 300 " --> pdb=" O ILELC 296 " (cutoff:3.500A) Processing helix chain 'LC' and resid 318 through 323 removed outlier: 4.592A pdb=" N LYSLC 323 " --> pdb=" O PROLC 319 " (cutoff:3.500A) Processing helix chain 'LC' and resid 324 through 330 Processing helix chain 'LC' and resid 331 through 340 removed outlier: 4.619A pdb=" N THRLC 335 " --> pdb=" O PROLC 331 " (cutoff:3.500A) Processing helix chain 'LC' and resid 355 through 364 Processing helix chain 'LC' and resid 214 through 219 removed outlier: 3.743A pdb=" N GLYLC 219 " --> pdb=" O SERLC 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'LC' and resid 214 through 219' Processing helix chain 'LD' and resid 9 through 16 Processing helix chain 'LD' and resid 20 through 26 Processing helix chain 'LD' and resid 29 through 38 removed outlier: 3.710A pdb=" N ARGLD 35 " --> pdb=" O TYRLD 31 " (cutoff:3.500A) Processing helix chain 'LD' and resid 79 through 87 removed outlier: 4.206A pdb=" N LEULD 83 " --> pdb=" O TYRLD 79 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ARGLD 84 " --> pdb=" O SERLD 80 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ALALD 85 " --> pdb=" O HISLD 81 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N TYRLD 86 " --> pdb=" O GLULD 82 " (cutoff:3.500A) Processing helix chain 'LD' and resid 94 through 114 Processing helix chain 'LD' and resid 130 through 136 Processing helix chain 'LD' and resid 160 through 173 removed outlier: 3.621A pdb=" N GLYLD 164 " --> pdb=" O ALALD 160 " (cutoff:3.500A) Processing helix chain 'LD' and resid 194 through 204 Processing helix chain 'LD' and resid 205 through 218 Processing helix chain 'LD' and resid 219 through 227 Processing helix chain 'LD' and resid 228 through 233 Processing helix chain 'LD' and resid 235 through 253 removed outlier: 3.996A pdb=" N LEULD 239 " --> pdb=" O GLULD 235 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N GLULD 240 " --> pdb=" O ALALD 236 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N GLULD 241 " --> pdb=" O ASPLD 237 " (cutoff:3.500A) Processing helix chain 'LD' and resid 266 through 278 removed outlier: 3.795A pdb=" N TYRLD 277 " --> pdb=" O GLULD 273 " (cutoff:3.500A) Processing helix chain 'LD' and resid 283 through 300 Processing helix chain 'LE' and resid 98 through 103 removed outlier: 3.910A pdb=" N VALLE 102 " --> pdb=" O ASNLE 98 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILELE 103 " --> pdb=" O ALALE 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'LE' and resid 98 through 103' Processing helix chain 'LE' and resid 115 through 124 Processing helix chain 'LE' and resid 131 through 140 Processing helix chain 'LE' and resid 155 through 174 removed outlier: 4.778A pdb=" N ALALE 168 " --> pdb=" O ALALE 164 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEULE 169 " --> pdb=" O ILELE 165 " (cutoff:3.500A) Processing helix chain 'LE' and resid 178 through 186 removed outlier: 5.343A pdb=" N SERLE 186 " --> pdb=" O TYRLE 182 " (cutoff:3.500A) Processing helix chain 'LF' and resid 8 through 14 removed outlier: 3.643A pdb=" N ILELF 12 " --> pdb=" O THRLF 8 " (cutoff:3.500A) Processing helix chain 'LF' and resid 15 through 34 removed outlier: 5.135A pdb=" N GLULF 31 " --> pdb=" O LYSLF 27 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ARGLF 32 " --> pdb=" O ALALF 28 " (cutoff:3.500A) Processing helix chain 'LF' and resid 35 through 79 removed outlier: 3.609A pdb=" N GLULF 45 " --> pdb=" O GLNLF 41 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLNLF 48 " --> pdb=" O LYSLF 44 " (cutoff:3.500A) Processing helix chain 'LF' and resid 102 through 113 Processing helix chain 'LF' and resid 126 through 137 removed outlier: 4.299A pdb=" N METLF 132 " --> pdb=" O ALALF 128 " (cutoff:3.500A) Processing helix chain 'LF' and resid 146 through 157 Processing helix chain 'LF' and resid 171 through 179 removed outlier: 4.121A pdb=" N ILELF 175 " --> pdb=" O ASPLF 171 " (cutoff:3.500A) Processing helix chain 'LF' and resid 186 through 197 Processing helix chain 'LF' and resid 200 through 209 removed outlier: 5.158A pdb=" N TRPLF 209 " --> pdb=" O ALALF 205 " (cutoff:3.500A) Processing helix chain 'LF' and resid 240 through 249 removed outlier: 3.769A pdb=" N LEULF 244 " --> pdb=" O HISLF 240 " (cutoff:3.500A) Processing helix chain 'LG' and resid 56 through 72 Processing helix chain 'LG' and resid 75 through 83 removed outlier: 5.105A pdb=" N PHELG 81 " --> pdb=" O ALALG 77 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLNLG 82 " --> pdb=" O ILELG 78 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N TYRLG 83 " --> pdb=" O ALALG 79 " (cutoff:3.500A) Processing helix chain 'LG' and resid 86 through 101 removed outlier: 4.268A pdb=" N LYSLG 99 " --> pdb=" O LYSLG 95 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N TYRLG 100 " --> pdb=" O LEULG 96 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARGLG 101 " --> pdb=" O LEULG 97 " (cutoff:3.500A) Processing helix chain 'LG' and resid 104 through 122 Processing helix chain 'LG' and resid 124 through 129 removed outlier: 4.004A pdb=" N VALLG 128 " --> pdb=" O LYSLG 124 " (cutoff:3.500A) Processing helix chain 'LG' and resid 138 through 149 Processing helix chain 'LG' and resid 168 through 177 Processing helix chain 'LG' and resid 185 through 194 removed outlier: 3.547A pdb=" N LEULG 192 " --> pdb=" O ARGLG 188 " (cutoff:3.500A) Processing helix chain 'LG' and resid 207 through 230 removed outlier: 4.758A pdb=" N ASNLG 212 " --> pdb=" O SERLG 208 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N GLULG 213 " --> pdb=" O GLULG 209 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEULG 226 " --> pdb=" O LYSLG 222 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLULG 227 " --> pdb=" O GLULG 223 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N LYSLG 228 " --> pdb=" O GLYLG 224 " (cutoff:3.500A) Processing helix chain 'LG' and resid 231 through 236 removed outlier: 4.157A pdb=" N ARGLG 235 " --> pdb=" O ASPLG 231 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N TRPLG 236 " --> pdb=" O THRLG 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'LG' and resid 231 through 236' Processing helix chain 'LG' and resid 242 through 259 Processing helix chain 'LH' and resid 98 through 121 removed outlier: 3.951A pdb=" N LEULH 105 " --> pdb=" O ASPLH 101 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ARGLH 106 " --> pdb=" O VALLH 102 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N THRLH 107 " --> pdb=" O ALALH 103 " (cutoff:3.500A) Processing helix chain 'LH' and resid 189 through 205 removed outlier: 3.783A pdb=" N CYSLH 204 " --> pdb=" O ILELH 200 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LYSLH 205 " --> pdb=" O GLNLH 201 " (cutoff:3.500A) Processing helix chain 'LH' and resid 210 through 215 removed outlier: 5.199A pdb=" N LEULH 215 " --> pdb=" O ILELH 211 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 28 through 43 Processing helix chain 'LJ' and resid 74 through 89 Processing helix chain 'LJ' and resid 109 through 114 removed outlier: 4.782A pdb=" N LEULJ 113 " --> pdb=" O GLULJ 109 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLYLJ 114 " --> pdb=" O HISLJ 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'LJ' and resid 109 through 114' Processing helix chain 'LJ' and resid 136 through 142 removed outlier: 4.908A pdb=" N ALALJ 140 " --> pdb=" O GLYLJ 136 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYSLJ 141 " --> pdb=" O GLULJ 137 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 150 through 155 removed outlier: 3.542A pdb=" N ARGLJ 154 " --> pdb=" O GLYLJ 150 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ILELJ 155 " --> pdb=" O ALALJ 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'LJ' and resid 150 through 155' Processing helix chain 'LJ' and resid 156 through 168 Processing helix chain 'LJ' and resid 93 through 98 removed outlier: 5.177A pdb=" N SERLJ 98 " --> pdb=" O ARGLJ 95 " (cutoff:3.500A) Processing helix chain 'LK' and resid 22 through 33 removed outlier: 4.784A pdb=" N SERLK 26 " --> pdb=" O VALLK 22 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ALALK 27 " --> pdb=" O GLYLK 23 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEULK 28 " --> pdb=" O ALALK 24 " (cutoff:3.500A) Proline residue: LK 30 - end of helix Processing helix chain 'LK' and resid 38 through 51 Processing helix chain 'LK' and resid 76 through 86 removed outlier: 3.905A pdb=" N LYSLK 86 " --> pdb=" O ILELK 82 " (cutoff:3.500A) Processing helix chain 'LK' and resid 105 through 121 removed outlier: 4.986A pdb=" N PHELK 118 " --> pdb=" O ARGLK 114 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N LYSLK 119 " --> pdb=" O THRLK 115 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N PHELK 121 " --> pdb=" O ARGLK 117 " (cutoff:3.500A) Processing helix chain 'LK' and resid 124 through 140 Processing helix chain 'LK' and resid 147 through 158 Processing helix chain 'LL' and resid 17 through 22 removed outlier: 4.424A pdb=" N ARGLL 21 " --> pdb=" O HISLL 17 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VALLL 22 " --> pdb=" O TRPLL 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'LL' and resid 17 through 22' Processing helix chain 'LL' and resid 27 through 47 Processing helix chain 'LL' and resid 76 through 84 Processing helix chain 'LL' and resid 86 through 94 Proline residue: LL 91 - end of helix removed outlier: 3.722A pdb=" N GLYLL 94 " --> pdb=" O ALALL 90 " (cutoff:3.500A) Processing helix chain 'LL' and resid 105 through 123 removed outlier: 3.793A pdb=" N LEULL 109 " --> pdb=" O SERLL 105 " (cutoff:3.500A) Processing helix chain 'LL' and resid 139 through 144 removed outlier: 4.254A pdb=" N THRLL 144 " --> pdb=" O LYSLL 140 " (cutoff:3.500A) Processing helix chain 'LL' and resid 150 through 155 Processing helix chain 'LL' and resid 180 through 195 Processing helix chain 'LL' and resid 196 through 213 Processing helix chain 'LM' and resid 58 through 63 removed outlier: 3.613A pdb=" N ALALM 62 " --> pdb=" O PROLM 58 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEULM 63 " --> pdb=" O LEULM 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'LM' and resid 58 through 63' Processing helix chain 'LM' and resid 77 through 89 Processing helix chain 'LM' and resid 90 through 98 removed outlier: 5.466A pdb=" N ASNLM 98 " --> pdb=" O TRPLM 94 " (cutoff:3.500A) Processing helix chain 'LM' and resid 99 through 112 removed outlier: 3.954A pdb=" N LEULM 112 " --> pdb=" O ARGLM 108 " (cutoff:3.500A) Processing helix chain 'LM' and resid 113 through 140 Processing helix chain 'LN' and resid 2 through 14 removed outlier: 4.710A pdb=" N TYRLN 6 " --> pdb=" O GLYLN 2 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYSLN 13 " --> pdb=" O GLULN 9 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LYSLN 14 " --> pdb=" O LEULN 10 " (cutoff:3.500A) Processing helix chain 'LN' and resid 16 through 34 removed outlier: 4.911A pdb=" N ASNLN 34 " --> pdb=" O TYRLN 30 " (cutoff:3.500A) Processing helix chain 'LN' and resid 44 through 52 Processing helix chain 'LN' and resid 88 through 93 removed outlier: 4.021A pdb=" N LEULN 92 " --> pdb=" O GLYLN 88 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LYSLN 93 " --> pdb=" O VALLN 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'LN' and resid 88 through 93' Processing helix chain 'LN' and resid 97 through 111 Processing helix chain 'LN' and resid 139 through 146 removed outlier: 3.910A pdb=" N ASPLN 145 " --> pdb=" O ALALN 141 " (cutoff:3.500A) Proline residue: LN 146 - end of helix Processing helix chain 'LN' and resid 148 through 153 removed outlier: 4.424A pdb=" N CYSLN 152 " --> pdb=" O ILELN 148 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASNLN 153 " --> pdb=" O ASNLN 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'LN' and resid 148 through 153' Processing helix chain 'LN' and resid 158 through 163 removed outlier: 3.590A pdb=" N ARGLN 162 " --> pdb=" O HISLN 158 " (cutoff:3.500A) Processing helix chain 'LN' and resid 165 through 173 Processing helix chain 'LN' and resid 186 through 196 Processing helix chain 'LO' and resid 16 through 31 Processing helix chain 'LO' and resid 47 through 61 removed outlier: 3.569A pdb=" N ALALO 51 " --> pdb=" O GLULO 47 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYSLO 61 " --> pdb=" O ALALO 57 " (cutoff:3.500A) Processing helix chain 'LO' and resid 77 through 91 removed outlier: 3.780A pdb=" N METLO 89 " --> pdb=" O ALALO 85 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILELO 90 " --> pdb=" O VALLO 86 " (cutoff:3.500A) Proline residue: LO 91 - end of helix Processing helix chain 'LO' and resid 94 through 105 removed outlier: 3.668A pdb=" N ARGLO 103 " --> pdb=" O ALALO 99 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEULO 104 " --> pdb=" O ALALO 100 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N LYSLO 105 " --> pdb=" O LEULO 101 " (cutoff:3.500A) Processing helix chain 'LO' and resid 112 through 118 removed outlier: 7.881A pdb=" N LYSLO 116 " --> pdb=" O PROLO 112 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYSLO 117 " --> pdb=" O PROLO 113 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LYSLO 118 " --> pdb=" O TYRLO 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'LO' and resid 112 through 118' Processing helix chain 'LO' and resid 126 through 131 Processing helix chain 'LO' and resid 139 through 148 Processing helix chain 'LO' and resid 153 through 188 Processing helix chain 'LO' and resid 192 through 203 Processing helix chain 'LP' and resid 25 through 37 Processing helix chain 'LP' and resid 40 through 54 Processing helix chain 'LP' and resid 70 through 77 removed outlier: 4.783A pdb=" N LYSLP 74 " --> pdb=" O THRLP 70 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N GLNLP 75 " --> pdb=" O ALALP 71 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N TRPLP 76 " --> pdb=" O GLNLP 72 " (cutoff:3.500A) Processing helix chain 'LP' and resid 84 through 106 Processing helix chain 'LP' and resid 172 through 185 Processing helix chain 'LQ' and resid 51 through 68 Processing helix chain 'LQ' and resid 70 through 83 removed outlier: 3.951A pdb=" N LYSLQ 74 " --> pdb=" O ALALQ 70 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N METLQ 82 " --> pdb=" O ARGLQ 78 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N SERLQ 83 " --> pdb=" O ARGLQ 79 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 91 through 100 removed outlier: 3.850A pdb=" N LYSLQ 100 " --> pdb=" O ALALQ 96 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 134 through 145 Processing helix chain 'LQ' and resid 150 through 158 Processing helix chain 'LQ' and resid 174 through 180 Processing helix chain 'LR' and resid 4 through 16 Processing helix chain 'LR' and resid 18 through 23 removed outlier: 3.716A pdb=" N VALLR 22 " --> pdb=" O GLYLR 18 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N TRPLR 23 " --> pdb=" O GLULR 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'LR' and resid 18 through 23' Processing helix chain 'LR' and resid 28 through 36 removed outlier: 3.742A pdb=" N ALALR 35 " --> pdb=" O GLULR 31 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ASNLR 36 " --> pdb=" O ILELR 32 " (cutoff:3.500A) Processing helix chain 'LR' and resid 37 through 48 Processing helix chain 'LR' and resid 60 through 73 Processing helix chain 'LR' and resid 77 through 82 removed outlier: 5.831A pdb=" N LYSLR 82 " --> pdb=" O PHELR 78 " (cutoff:3.500A) Processing helix chain 'LR' and resid 84 through 113 Proline residue: LR 90 - end of helix removed outlier: 6.652A pdb=" N VALLR 93 " --> pdb=" O METLR 89 " (cutoff:3.500A) Processing helix chain 'LR' and resid 116 through 130 Processing helix chain 'LR' and resid 134 through 156 Processing helix chain 'LS' and resid 33 through 49 Processing helix chain 'LS' and resid 98 through 114 Processing helix chain 'LS' and resid 117 through 122 removed outlier: 3.659A pdb=" N ILELS 121 " --> pdb=" O ARGLS 117 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N HISLS 122 " --> pdb=" O PHELS 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'LS' and resid 117 through 122' Processing helix chain 'LS' and resid 137 through 145 removed outlier: 4.579A pdb=" N LEULS 143 " --> pdb=" O TYRLS 139 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALALS 145 " --> pdb=" O LYSLS 141 " (cutoff:3.500A) Processing helix chain 'LT' and resid 92 through 97 removed outlier: 3.999A pdb=" N VALLT 96 " --> pdb=" O ARGLT 92 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N LYSLT 97 " --> pdb=" O ILELT 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'LT' and resid 92 through 97' Processing helix chain 'LT' and resid 102 through 123 Processing helix chain 'LT' and resid 155 through 160 Processing helix chain 'LU' and resid 25 through 32 Processing helix chain 'LU' and resid 35 through 47 Processing helix chain 'LU' and resid 79 through 95 Processing helix chain 'LV' and resid 68 through 73 removed outlier: 3.758A pdb=" N ARGLV 72 " --> pdb=" O LYSLV 68 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYSLV 73 " --> pdb=" O PROLV 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'LV' and resid 68 through 73' Processing helix chain 'LV' and resid 121 through 129 Proline residue: LV 129 - end of helix Processing helix chain 'LV' and resid 130 through 135 Processing helix chain 'LX' and resid 12 through 29 Processing helix chain 'LX' and resid 71 through 77 removed outlier: 5.073A pdb=" N ILELX 77 " --> pdb=" O HISLX 73 " (cutoff:3.500A) Processing helix chain 'LX' and resid 82 through 92 removed outlier: 4.283A pdb=" N GLULX 90 " --> pdb=" O LEULX 86 " (cutoff:3.500A) Processing helix chain 'LX' and resid 104 through 116 Processing helix chain 'LX' and resid 144 through 152 Processing helix chain 'LY' and resid 10 through 21 Processing helix chain 'LY' and resid 22 through 31 removed outlier: 3.569A pdb=" N VALLY 28 " --> pdb=" O SERLY 24 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N SERLY 31 " --> pdb=" O ARGLY 27 " (cutoff:3.500A) Processing helix chain 'LY' and resid 35 through 43 Processing helix chain 'LY' and resid 99 through 104 removed outlier: 4.040A pdb=" N VALLY 103 " --> pdb=" O HISLY 99 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N VALLY 104 " --> pdb=" O PROLY 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'LY' and resid 99 through 104' Processing helix chain 'LY' and resid 111 through 133 Processing helix chain 'LZ' and resid 57 through 66 removed outlier: 4.038A pdb=" N LYSLZ 66 " --> pdb=" O GLULZ 62 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 75 through 80 removed outlier: 3.749A pdb=" N LEULZ 79 " --> pdb=" O ASNLZ 75 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N METLZ 80 " --> pdb=" O TYRLZ 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'LZ' and resid 75 through 80' Processing helix chain 'LZ' and resid 96 through 103 removed outlier: 4.233A pdb=" N PHELZ 100 " --> pdb=" O ASNLZ 96 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LYSLZ 101 " --> pdb=" O ALALZ 97 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLULZ 102 " --> pdb=" O ASPLZ 98 " (cutoff:3.500A) Proline residue: LZ 103 - end of helix No H-bonds generated for 'chain 'LZ' and resid 96 through 103' Processing helix chain 'LZ' and resid 104 through 124 removed outlier: 3.604A pdb=" N GLYLZ 124 " --> pdb=" O ARGLZ 120 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 126 through 132 removed outlier: 3.674A pdb=" N PHELZ 130 " --> pdb=" O ASNLZ 126 " (cutoff:3.500A) Proline residue: LZ 132 - end of helix Processing helix chain 'La' and resid 6 through 12 removed outlier: 3.967A pdb=" N LYSLa 10 " --> pdb=" O SERLa 6 " (cutoff:3.500A) Processing helix chain 'La' and resid 64 through 69 removed outlier: 4.327A pdb=" N TYRLa 68 " --> pdb=" O LEULa 64 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TRPLa 69 " --> pdb=" O ARGLa 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'La' and resid 64 through 69' Processing helix chain 'La' and resid 74 through 83 removed outlier: 3.575A pdb=" N LEULa 78 " --> pdb=" O ASNLa 74 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N TRPLa 79 " --> pdb=" O ILELa 75 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N SERLa 80 " --> pdb=" O ASPLa 76 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEULa 81 " --> pdb=" O LYSLa 77 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VALLa 82 " --> pdb=" O LEULa 78 " (cutoff:3.500A) Proline residue: La 83 - end of helix No H-bonds generated for 'chain 'La' and resid 74 through 83' Processing helix chain 'La' and resid 84 through 93 Processing helix chain 'La' and resid 103 through 108 removed outlier: 3.593A pdb=" N HISLa 107 " --> pdb=" O ASPLa 103 " (cutoff:3.500A) Processing helix chain 'La' and resid 131 through 142 Processing helix chain 'Lc' and resid 12 through 24 Processing helix chain 'Lc' and resid 29 through 40 Processing helix chain 'Lc' and resid 52 through 67 Processing helix chain 'Lc' and resid 76 through 85 Processing helix chain 'Ld' and resid 23 through 29 removed outlier: 3.993A pdb=" N ARGLd 27 " --> pdb=" O HISLd 23 " (cutoff:3.500A) Processing helix chain 'Ld' and resid 35 through 53 Processing helix chain 'Ld' and resid 60 through 69 Processing helix chain 'Le' and resid 22 through 27 removed outlier: 4.981A pdb=" N LYSLe 27 " --> pdb=" O SERLe 23 " (cutoff:3.500A) Processing helix chain 'Le' and resid 41 through 46 Processing helix chain 'Le' and resid 79 through 87 removed outlier: 3.659A pdb=" N LEULe 85 " --> pdb=" O LYSLe 81 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEULe 86 " --> pdb=" O ASPLe 82 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEULe 87 " --> pdb=" O VALLe 83 " (cutoff:3.500A) Processing helix chain 'Le' and resid 102 through 117 Processing helix chain 'Lf' and resid 39 through 47 removed outlier: 4.073A pdb=" N PHELf 45 " --> pdb=" O ALALf 41 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N TYRLf 46 " --> pdb=" O ALALf 42 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEULf 47 " --> pdb=" O ALALf 43 " (cutoff:3.500A) Processing helix chain 'Lg' and resid 59 through 67 removed outlier: 3.970A pdb=" N TYRLg 63 " --> pdb=" O ARGLg 59 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ALALg 64 " --> pdb=" O PROLg 60 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THRLg 65 " --> pdb=" O ARGLg 61 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILELg 66 " --> pdb=" O GLULg 62 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N SERLg 67 " --> pdb=" O TYRLg 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'Lg' and resid 59 through 67' Processing helix chain 'Lg' and resid 82 through 119 Processing helix chain 'Lh' and resid 8 through 16 removed outlier: 3.590A pdb=" N LEULh 12 " --> pdb=" O LYSLh 8 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N SERLh 14 " --> pdb=" O GLYLh 10 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYSLh 15 " --> pdb=" O GLNLh 11 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ASNLh 16 " --> pdb=" O LEULh 12 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 17 through 41 removed outlier: 3.674A pdb=" N ILELh 36 " --> pdb=" O SERLh 32 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 44 through 76 removed outlier: 4.122A pdb=" N LYSLh 48 " --> pdb=" O ALALh 44 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 82 through 87 Proline residue: Lh 87 - end of helix Processing helix chain 'Lh' and resid 90 through 96 Processing helix chain 'Lh' and resid 98 through 104 Processing helix chain 'Lh' and resid 106 through 116 Processing helix chain 'Li' and resid 34 through 39 removed outlier: 4.038A pdb=" N ARGLi 38 " --> pdb=" O ARGLi 34 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LYSLi 39 " --> pdb=" O PROLi 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'Li' and resid 34 through 39' Processing helix chain 'Li' and resid 43 through 58 Processing helix chain 'Li' and resid 60 through 73 Processing helix chain 'Li' and resid 74 through 87 Processing helix chain 'Li' and resid 88 through 110 Processing helix chain 'Lj' and resid 4 through 11 removed outlier: 3.646A pdb=" N GLYLj 9 " --> pdb=" O THRLj 5 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LYSLj 10 " --> pdb=" O SERLj 6 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ARGLj 11 " --> pdb=" O SERLj 7 " (cutoff:3.500A) Processing helix chain 'Lj' and resid 50 through 58 removed outlier: 3.660A pdb=" N LYSLj 57 " --> pdb=" O ALALj 53 " (cutoff:3.500A) Processing helix chain 'Lj' and resid 65 through 77 removed outlier: 5.421A pdb=" N THRLj 69 " --> pdb=" O ARGLj 65 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VALLj 70 " --> pdb=" O TYRLj 66 " (cutoff:3.500A) Proline residue: Lj 71 - end of helix Processing helix chain 'Lk' and resid 7 through 17 Processing helix chain 'Lk' and resid 52 through 63 removed outlier: 4.178A pdb=" N LYSLk 59 " --> pdb=" O ALALk 55 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLNLk 60 " --> pdb=" O GLULk 56 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SERLk 61 " --> pdb=" O LYSLk 57 " (cutoff:3.500A) Proline residue: Lk 63 - end of helix Processing helix chain 'Ll' and resid 6 through 21 removed outlier: 5.356A pdb=" N ARGLl 21 " --> pdb=" O GLNLl 17 " (cutoff:3.500A) Processing helix chain 'Ll' and resid 24 through 30 removed outlier: 4.478A pdb=" N ARGLl 28 " --> pdb=" O PROLl 24 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEULl 29 " --> pdb=" O GLNLl 25 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARGLl 30 " --> pdb=" O TRPLl 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ll' and resid 24 through 30' Processing helix chain 'Lp' and resid 19 through 35 removed outlier: 3.816A pdb=" N LYSLp 28 " --> pdb=" O LYSLp 24 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLNLp 29 " --> pdb=" O LEULp 25 " (cutoff:3.500A) Processing helix chain 'Lp' and resid 73 through 92 Processing sheet with id= 1, first strand: chain 'CB' and resid 80 through 83 Processing sheet with id= 2, first strand: chain 'CB' and resid 97 through 101 Processing sheet with id= 3, first strand: chain 'CB' and resid 239 through 245 removed outlier: 5.680A pdb=" N THRCB 239 " --> pdb=" O THRCB 68 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILECB 62 " --> pdb=" O VALCB 245 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N PHECB 281 " --> pdb=" O ILECB 293 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'CF' and resid 63 through 67 removed outlier: 6.759A pdb=" N VALCF 42 " --> pdb=" O LEUCF 224 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'CF' and resid 135 through 138 removed outlier: 6.758A pdb=" N VALCF 135 " --> pdb=" O ILECF 194 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'CF' and resid 172 through 175 Processing sheet with id= 7, first strand: chain 'CF' and resid 232 through 236 removed outlier: 3.636A pdb=" N GLUCF 233 " --> pdb=" O SERCF 228 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'CF' and resid 38 through 42 removed outlier: 8.236A pdb=" N GLNCF 38 " --> pdb=" O SERCF 229 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLYCF 225 " --> pdb=" O VALCF 42 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'CH' and resid 203 through 209 removed outlier: 4.961A pdb=" N ARGCH 167 " --> pdb=" O ARGCH 214 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THRCH 220 " --> pdb=" O VALCH 171 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLYCH 173 " --> pdb=" O THRCH 220 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N METCH 281 " --> pdb=" O ALACH 247 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'CI' and resid 214 through 219 removed outlier: 5.057A pdb=" N ARGCI 230 " --> pdb=" O VALCI 219 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VALCI 188 " --> pdb=" O VALCI 263 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'CJ' and resid 186 through 191 removed outlier: 3.913A pdb=" N GLYCJ 194 " --> pdb=" O SERCJ 191 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'CJ' and resid 394 through 398 Processing sheet with id= 13, first strand: chain 'CK' and resid 148 through 151 Processing sheet with id= 14, first strand: chain 'CK' and resid 190 through 195 removed outlier: 3.700A pdb=" N VALCK 191 " --> pdb=" O HISCK 186 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ASNCK 256 " --> pdb=" O THRCK 246 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N TYRCK 242 " --> pdb=" O LEUCK 260 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N THRCK 219 " --> pdb=" O ILECK 245 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'CM' and resid 139 through 144 removed outlier: 5.388A pdb=" N TRPCM 139 " --> pdb=" O ILECM 95 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYSCM 88 " --> pdb=" O VALCM 125 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ASNCM 119 " --> pdb=" O ARGCM 94 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ASNCM 118 " --> pdb=" O LEUCM 213 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'CM' and resid 158 through 161 removed outlier: 6.773A pdb=" N GLYCM 158 " --> pdb=" O LEUCM 169 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'CN' and resid 1 through 4 Processing sheet with id= 18, first strand: chain 'CN' and resid 23 through 27 Processing sheet with id= 19, first strand: chain 'CN' and resid 69 through 73 Processing sheet with id= 20, first strand: chain 'CN' and resid 158 through 161 Processing sheet with id= 21, first strand: chain 'CQ' and resid 3 through 6 removed outlier: 4.673A pdb=" N ARGCQ 11 " --> pdb=" O CYSCQ 6 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'CQ' and resid 18 through 23 removed outlier: 3.627A pdb=" N LYSCQ 27 " --> pdb=" O ARGCQ 23 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'Lq' and resid 19 through 22 removed outlier: 6.851A pdb=" N PHELq 19 " --> pdb=" O ARGLq 30 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'Lq' and resid 51 through 56 removed outlier: 5.331A pdb=" N ALALq 51 " --> pdb=" O LYSLq 66 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N SERLq 77 " --> pdb=" O LYSLq 67 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'Cb' and resid 50 through 53 removed outlier: 4.539A pdb=" N TYRCb 50 " --> pdb=" O PHECb 59 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'Cd' and resid 293 through 297 removed outlier: 3.860A pdb=" N CYSCd 378 " --> pdb=" O LEUCd 331 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLYCd 333 " --> pdb=" O CYSCd 378 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILECd 373 " --> pdb=" O LEUCd 369 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'Cf' and resid 56 through 60 removed outlier: 5.711A pdb=" N ARGCf 34 " --> pdb=" O PHECf 60 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N SERCf 92 " --> pdb=" O GLYCf 35 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N HISCf 98 " --> pdb=" O LEUCf 118 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ASPCf 254 " --> pdb=" O ASPCf 119 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'Cf' and resid 287 through 290 removed outlier: 4.621A pdb=" N ASPCf 294 " --> pdb=" O ASPCf 290 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'Cf' and resid 111 through 116 removed outlier: 8.783A pdb=" N LEUCf 111 " --> pdb=" O PROCf 263 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ARGCf 259 " --> pdb=" O GLUCf 115 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'Cf' and resid 229 through 232 removed outlier: 6.732A pdb=" N VALCf 229 " --> pdb=" O HISCf 249 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'Cg' and resid 21 through 25 Processing sheet with id= 32, first strand: chain 'Cg' and resid 71 through 75 removed outlier: 4.446A pdb=" N THRCg 71 " --> pdb=" O THRCg 82 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'Cg' and resid 124 through 129 removed outlier: 8.667A pdb=" N ASNCg 124 " --> pdb=" O LYSCg 137 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LYSCg 137 " --> pdb=" O ASNCg 124 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'Ch' and resid 52 through 56 removed outlier: 4.087A pdb=" N THRCh 121 " --> pdb=" O HISCh 88 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N LEUCh 94 " --> pdb=" O ILECh 89 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'Ch' and resid 139 through 143 removed outlier: 5.152A pdb=" N ALACh 511 " --> pdb=" O GLYCh 507 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N GLYCh 507 " --> pdb=" O ALACh 511 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N LEUCh 502 " --> pdb=" O ALACh 497 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'Ch' and resid 151 through 155 removed outlier: 6.427A pdb=" N ARGCh 161 " --> pdb=" O SERCh 155 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N SERCh 160 " --> pdb=" O THRCh 176 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THRCh 170 " --> pdb=" O SERCh 166 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILECh 173 " --> pdb=" O LYSCh 182 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'Ch' and resid 193 through 198 removed outlier: 5.445A pdb=" N TYRCh 203 " --> pdb=" O SERCh 198 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N THRCh 212 " --> pdb=" O SERCh 208 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N VALCh 215 " --> pdb=" O VALCh 224 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYSCh 222 " --> pdb=" O ASPCh 217 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'Ch' and resid 236 through 241 removed outlier: 5.772A pdb=" N ARGCh 252 " --> pdb=" O GLNCh 241 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ALACh 251 " --> pdb=" O VALCh 267 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THRCh 261 " --> pdb=" O SERCh 257 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILECh 264 " --> pdb=" O GLUCh 273 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARGCh 271 " --> pdb=" O LEUCh 266 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'Ch' and resid 284 through 288 removed outlier: 3.617A pdb=" N CYSCh 285 " --> pdb=" O GLYCh 297 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N ASPCh 292 " --> pdb=" O ALACh 308 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SERCh 302 " --> pdb=" O SERCh 298 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VALCh 305 " --> pdb=" O VALCh 314 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'Ch' and resid 326 through 330 removed outlier: 3.556A pdb=" N HISCh 326 " --> pdb=" O ALACh 378 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ARGCh 374 " --> pdb=" O SERCh 330 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THRCh 383 " --> pdb=" O SERCh 379 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALACh 398 " --> pdb=" O LEUCh 386 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'Ch' and resid 408 through 413 removed outlier: 3.567A pdb=" N HISCh 409 " --> pdb=" O ALACh 422 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LEUCh 418 " --> pdb=" O SERCh 413 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THRCh 417 " --> pdb=" O ALACh 433 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SERCh 427 " --> pdb=" O GLYCh 423 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEUCh 430 " --> pdb=" O ILECh 439 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYSCh 437 " --> pdb=" O ASNCh 432 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'Ch' and resid 451 through 455 removed outlier: 5.801A pdb=" N LEUCh 460 " --> pdb=" O SERCh 455 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N ARGCh 459 " --> pdb=" O VALCh 475 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N THRCh 469 " --> pdb=" O SERCh 465 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VALCh 472 " --> pdb=" O ALACh 481 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'Ch' and resid 170 through 173 Processing sheet with id= 44, first strand: chain 'Ch' and resid 261 through 264 removed outlier: 3.777A pdb=" N HISCh 274 " --> pdb=" O ILECh 264 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'Ch' and resid 302 through 305 Processing sheet with id= 46, first strand: chain 'Ch' and resid 469 through 472 Processing sheet with id= 47, first strand: chain 'LA' and resid 47 through 50 removed outlier: 3.630A pdb=" N GLULA 47 " --> pdb=" O ARGLA 60 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ARGLA 60 " --> pdb=" O LYSLA 46 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLNLA 86 " --> pdb=" O VALLA 45 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'LA' and resid 110 through 114 removed outlier: 4.257A pdb=" N THRLA 111 " --> pdb=" O VALLA 136 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARGLA 147 " --> pdb=" O VALLA 137 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'LA' and resid 58 through 64 No H-bonds generated for sheet with id= 49 Processing sheet with id= 50, first strand: chain 'LA' and resid 145 through 150 removed outlier: 4.240A pdb=" N ALALA 154 " --> pdb=" O LEULA 150 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'LB' and resid 41 through 44 removed outlier: 6.499A pdb=" N GLNLB 183 " --> pdb=" O THRLB 44 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N HISLB 178 " --> pdb=" O THRLB 165 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N VALLB 159 " --> pdb=" O ILELB 184 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ARGLB 160 " --> pdb=" O LEULB 89 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEULB 89 " --> pdb=" O ARGLB 160 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEULB 162 " --> pdb=" O VALLB 87 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLYLB 91 " --> pdb=" O LEULB 102 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'LB' and resid 53 through 58 removed outlier: 6.751A pdb=" N ILELB 78 " --> pdb=" O ALALB 51 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ARGLB 335 " --> pdb=" O LYSLB 50 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ILELB 336 " --> pdb=" O VALLB 221 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N VALLB 221 " --> pdb=" O ILELB 336 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N HISLB 274 " --> pdb=" O THRLB 222 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'LB' and resid 285 through 289 removed outlier: 3.716A pdb=" N ARGLB 285 " --> pdb=" O METLB 324 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLYLB 289 " --> pdb=" O ASNLB 320 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ASNLB 320 " --> pdb=" O GLYLB 289 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'LB' and resid 76 through 80 Processing sheet with id= 55, first strand: chain 'LB' and resid 87 through 91 removed outlier: 7.863A pdb=" N VALLB 87 " --> pdb=" O ALALB 107 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THRLB 103 " --> pdb=" O GLYLB 91 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'LB' and resid 84 through 87 removed outlier: 3.751A pdb=" N LYSLB 202 " --> pdb=" O VALLB 86 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'LB' and resid 213 through 217 removed outlier: 4.385A pdb=" N GLULB 214 " --> pdb=" O ILELB 283 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'LC' and resid 5 through 9 removed outlier: 4.842A pdb=" N ALALC 19 " --> pdb=" O VALLC 9 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'LC' and resid 209 through 212 Processing sheet with id= 60, first strand: chain 'LD' and resid 60 through 66 Processing sheet with id= 61, first strand: chain 'LE' and resid 5 through 9 Processing sheet with id= 62, first strand: chain 'LE' and resid 56 through 61 removed outlier: 4.111A pdb=" N THRLE 56 " --> pdb=" O LEULE 72 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYSLE 68 " --> pdb=" O LEULE 60 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'LF' and resid 139 through 144 removed outlier: 7.453A pdb=" N TRPLF 139 " --> pdb=" O ILELF 95 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LYSLF 88 " --> pdb=" O VALLF 125 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASNLF 119 " --> pdb=" O ARGLF 94 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ASNLF 118 " --> pdb=" O LEULF 213 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'LF' and resid 158 through 162 removed outlier: 6.403A pdb=" N GLYLF 158 " --> pdb=" O LEULF 169 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'LG' and resid 179 through 184 Processing sheet with id= 66, first strand: chain 'LH' and resid 5 through 12 removed outlier: 5.726A pdb=" N GLYLH 88 " --> pdb=" O VALLH 12 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'LH' and resid 54 through 57 Processing sheet with id= 68, first strand: chain 'LH' and resid 137 through 144 removed outlier: 3.820A pdb=" N CYSLH 148 " --> pdb=" O ASNLH 143 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N TYRLH 149 " --> pdb=" O METLH 167 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'LH' and resid 181 through 188 removed outlier: 5.631A pdb=" N ASPLH 181 " --> pdb=" O TYRLH 129 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'LJ' and resid 46 through 50 removed outlier: 3.516A pdb=" N ALALJ 67 " --> pdb=" O SERLJ 49 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ILELJ 66 " --> pdb=" O VALLJ 24 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYSLJ 17 " --> pdb=" O CYSLJ 131 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N SERLJ 23 " --> pdb=" O GLYLJ 125 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N GLYLJ 125 " --> pdb=" O SERLJ 23 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'LK' and resid 11 through 16 removed outlier: 4.247A pdb=" N THRLK 59 " --> pdb=" O VALLK 74 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'LL' and resid 56 through 59 Processing sheet with id= 73, first strand: chain 'LM' and resid 18 through 21 removed outlier: 4.617A pdb=" N ARGLM 18 " --> pdb=" O ILELM 30 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEULM 40 " --> pdb=" O VALLM 31 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLYLM 43 " --> pdb=" O PROLM 53 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'LN' and resid 35 through 39 removed outlier: 6.506A pdb=" N VALLN 35 " --> pdb=" O ARGLN 65 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ILELN 61 " --> pdb=" O ALALN 39 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLYLN 58 " --> pdb=" O ASPLN 136 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILELN 133 " --> pdb=" O LEULN 116 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'LN' and resid 117 through 121 removed outlier: 3.632A pdb=" N ASNLN 117 " --> pdb=" O ILELN 133 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TYRLN 129 " --> pdb=" O VALLN 121 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'LO' and resid 7 through 11 Processing sheet with id= 77, first strand: chain 'LP' and resid 14 through 20 removed outlier: 6.603A pdb=" N ILELP 149 " --> pdb=" O LYSLP 115 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'LP' and resid 57 through 60 removed outlier: 5.424A pdb=" N ARGLP 80 " --> pdb=" O METLP 60 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'LP' and resid 116 through 122 Processing sheet with id= 80, first strand: chain 'LP' and resid 124 through 131 removed outlier: 3.960A pdb=" N ARGLP 127 " --> pdb=" O TYRLP 139 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARGLP 135 " --> pdb=" O ARGLP 131 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'LQ' and resid 106 through 110 Processing sheet with id= 82, first strand: chain 'LQ' and resid 126 through 129 Processing sheet with id= 83, first strand: chain 'LS' and resid 24 through 30 removed outlier: 6.632A pdb=" N ILELS 10 " --> pdb=" O VALLS 59 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'LS' and resid 86 through 96 removed outlier: 5.135A pdb=" N ASNLS 74 " --> pdb=" O LEULS 129 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'LS' and resid 6 through 10 removed outlier: 4.629A pdb=" N GLULS 6 " --> pdb=" O ILELS 64 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'LT' and resid 40 through 43 removed outlier: 3.759A pdb=" N LYSLT 60 " --> pdb=" O ILELT 42 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'LT' and resid 72 through 79 Processing sheet with id= 88, first strand: chain 'LU' and resid 60 through 64 removed outlier: 5.541A pdb=" N GLYLU 108 " --> pdb=" O LYSLU 20 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'LV' and resid 23 through 26 removed outlier: 4.430A pdb=" N ALALV 23 " --> pdb=" O ILELV 38 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'LV' and resid 58 through 62 removed outlier: 4.297A pdb=" N ASPLV 58 " --> pdb=" O ILELV 80 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASPLV 99 " --> pdb=" O ALALV 84 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALALV 84 " --> pdb=" O ASPLV 99 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 'LV' and resid 86 through 89 removed outlier: 3.878A pdb=" N VALLV 93 " --> pdb=" O ARGLV 89 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'LX' and resid 93 through 99 removed outlier: 6.658A pdb=" N ASNLX 93 " --> pdb=" O LEULX 139 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYSLX 133 " --> pdb=" O VALLX 99 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THRLX 132 " --> pdb=" O ARGLX 128 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYSLX 122 " --> pdb=" O ARGLX 138 " (cutoff:3.500A) Processing sheet with id= 93, first strand: chain 'LY' and resid 55 through 58 removed outlier: 4.251A pdb=" N LYSLY 65 " --> pdb=" O ILELY 57 " (cutoff:3.500A) Processing sheet with id= 94, first strand: chain 'LY' and resid 71 through 74 removed outlier: 3.621A pdb=" N SERLY 71 " --> pdb=" O HISLY 80 " (cutoff:3.500A) Processing sheet with id= 95, first strand: chain 'LY' and resid 85 through 88 removed outlier: 4.727A pdb=" N GLNLY 92 " --> pdb=" O LYSLY 88 " (cutoff:3.500A) Processing sheet with id= 96, first strand: chain 'LZ' and resid 8 through 13 removed outlier: 4.524A pdb=" N ARGLZ 8 " --> pdb=" O ILELZ 24 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYSLZ 20 " --> pdb=" O VALLZ 12 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEULZ 41 " --> pdb=" O ILELZ 25 " (cutoff:3.500A) Processing sheet with id= 97, first strand: chain 'LZ' and resid 41 through 44 Processing sheet with id= 98, first strand: chain 'La' and resid 99 through 102 Processing sheet with id= 99, first strand: chain 'Lc' and resid 25 through 28 removed outlier: 6.155A pdb=" N LYSLc 25 " --> pdb=" O LEULc 96 " (cutoff:3.500A) Processing sheet with id=100, first strand: chain 'Ld' and resid 56 through 59 removed outlier: 5.014A pdb=" N ASPLd 56 " --> pdb=" O LEULd 97 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ALALd 17 " --> pdb=" O VALLd 117 " (cutoff:3.500A) Processing sheet with id=101, first strand: chain 'Le' and resid 72 through 78 Processing sheet with id=102, first strand: chain 'Lf' and resid 12 through 17 removed outlier: 6.089A pdb=" N LYSLf 12 " --> pdb=" O GLULf 35 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEULf 31 " --> pdb=" O LEULf 16 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ARGLf 84 " --> pdb=" O THRLf 74 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LYSLf 65 " --> pdb=" O ALALf 57 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYSLf 49 " --> pdb=" O ILELf 73 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ARGLf 50 " --> pdb=" O METLf 103 " (cutoff:3.500A) Processing sheet with id=103, first strand: chain 'Lf' and resid 10 through 16 removed outlier: 4.130A pdb=" N ALALf 98 " --> pdb=" O HISLf 15 " (cutoff:3.500A) Processing sheet with id=104, first strand: chain 'Lg' and resid 20 through 25 removed outlier: 4.447A pdb=" N ARGLg 20 " --> pdb=" O ILELg 36 " (cutoff:3.500A) Processing sheet with id=105, first strand: chain 'Lk' and resid 2 through 5 removed outlier: 4.534A pdb=" N VALLk 48 " --> pdb=" O VALLk 5 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SERLk 22 " --> pdb=" O ARGLk 39 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N LYSLk 27 " --> pdb=" O VALLk 71 " (cutoff:3.500A) Processing sheet with id=106, first strand: chain 'Lp' and resid 47 through 50 removed outlier: 6.942A pdb=" N ILELp 54 " --> pdb=" O THRLp 50 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLYLp 53 " --> pdb=" O GLYLp 66 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LYSLp 62 " --> pdb=" O CYSLp 57 " (cutoff:3.500A) 3747 hydrogen bonds defined for protein. 11127 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2736 hydrogen bonds 4560 hydrogen bond angles 0 basepair planarities 1081 basepair parallelities 1855 stacking parallelities Total time for adding SS restraints: 207.30 Time building geometry restraints manager: 65.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 21236 1.32 - 1.45: 62715 1.45 - 1.57: 76273 1.57 - 1.70: 6888 1.70 - 1.82: 421 Bond restraints: 167533 Sorted by residual: bond pdb=" C3' A2MC12289 " pdb=" C2' A2MC12289 " ideal model delta sigma weight residual 1.544 1.237 0.307 2.00e-02 2.50e+03 2.36e+02 bond pdb=" C3' A2MC1 858 " pdb=" C2' A2MC1 858 " ideal model delta sigma weight residual 1.544 1.239 0.305 2.00e-02 2.50e+03 2.33e+02 bond pdb=" C3' A2MC1 637 " pdb=" C2' A2MC1 637 " ideal model delta sigma weight residual 1.544 1.241 0.303 2.00e-02 2.50e+03 2.29e+02 bond pdb=" C3' A2MC11223 " pdb=" C2' A2MC11223 " ideal model delta sigma weight residual 1.544 1.242 0.302 2.00e-02 2.50e+03 2.29e+02 bond pdb=" C3' A2MC11432 " pdb=" C2' A2MC11432 " ideal model delta sigma weight residual 1.544 1.243 0.301 2.00e-02 2.50e+03 2.27e+02 ... (remaining 167528 not shown) Histogram of bond angle deviations from ideal: 95.94 - 105.88: 19730 105.88 - 115.83: 114400 115.83 - 125.77: 95900 125.77 - 135.71: 12816 135.71 - 145.65: 8 Bond angle restraints: 242854 Sorted by residual: angle pdb=" C1' OMGC11433 " pdb=" N9 OMGC11433 " pdb=" C4 OMGC11433 " ideal model delta sigma weight residual 108.29 128.43 -20.14 3.00e+00 1.11e-01 4.51e+01 angle pdb=" C1' A2MC11223 " pdb=" N9 A2MC11223 " pdb=" C8 A2MC11223 " ideal model delta sigma weight residual 88.50 108.60 -20.10 3.00e+00 1.11e-01 4.49e+01 angle pdb=" C1' OMGC1 385 " pdb=" N9 OMGC1 385 " pdb=" C4 OMGC1 385 " ideal model delta sigma weight residual 108.29 128.35 -20.06 3.00e+00 1.11e-01 4.47e+01 angle pdb=" C1' A2MC12289 " pdb=" N9 A2MC12289 " pdb=" C8 A2MC12289 " ideal model delta sigma weight residual 88.50 108.39 -19.89 3.00e+00 1.11e-01 4.40e+01 angle pdb=" C1' OMGC12881 " pdb=" N9 OMGC12881 " pdb=" C4 OMGC12881 " ideal model delta sigma weight residual 108.29 127.95 -19.66 3.00e+00 1.11e-01 4.29e+01 ... (remaining 242849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 96395 35.99 - 71.98: 8927 71.98 - 107.97: 986 107.97 - 143.96: 24 143.96 - 179.95: 36 Dihedral angle restraints: 106368 sinusoidal: 75924 harmonic: 30444 Sorted by residual: dihedral pdb=" C4' CC13324 " pdb=" C3' CC13324 " pdb=" C2' CC13324 " pdb=" C1' CC13324 " ideal model delta sinusoidal sigma weight residual -35.00 33.94 -68.94 1 8.00e+00 1.56e-02 9.61e+01 dihedral pdb=" C5' CC13324 " pdb=" C4' CC13324 " pdb=" C3' CC13324 " pdb=" O3' CC13324 " ideal model delta sinusoidal sigma weight residual 147.00 78.90 68.10 1 8.00e+00 1.56e-02 9.41e+01 dihedral pdb=" O4' CC1 961 " pdb=" C1' CC1 961 " pdb=" N1 CC1 961 " pdb=" C2 CC1 961 " ideal model delta sinusoidal sigma weight residual 200.00 24.16 175.84 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 106365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 26808 0.072 - 0.145: 2666 0.145 - 0.217: 153 0.217 - 0.290: 25 0.290 - 0.362: 6 Chirality restraints: 29658 Sorted by residual: chirality pdb=" C3' CC13324 " pdb=" C4' CC13324 " pdb=" O3' CC13324 " pdb=" C2' CC13324 " both_signs ideal model delta sigma weight residual False -2.74 -2.38 -0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" C3' UC11537 " pdb=" C4' UC11537 " pdb=" O3' UC11537 " pdb=" C2' UC11537 " both_signs ideal model delta sigma weight residual False -2.74 -2.39 -0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" C3' CC11267 " pdb=" C4' CC11267 " pdb=" O3' CC11267 " pdb=" C2' CC11267 " both_signs ideal model delta sigma weight residual False -2.48 -2.15 -0.33 2.00e-01 2.50e+01 2.70e+00 ... (remaining 29655 not shown) Planarity restraints: 18146 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMGC12578 " 0.081 2.00e-02 2.50e+03 6.01e-01 8.13e+03 pdb=" C4' OMGC12578 " 0.430 2.00e-02 2.50e+03 pdb=" O4' OMGC12578 " 0.595 2.00e-02 2.50e+03 pdb=" C3' OMGC12578 " -0.601 2.00e-02 2.50e+03 pdb=" O3' OMGC12578 " -0.659 2.00e-02 2.50e+03 pdb=" C2' OMGC12578 " -0.160 2.00e-02 2.50e+03 pdb=" O2' OMGC12578 " 0.999 2.00e-02 2.50e+03 pdb=" C1' OMGC12578 " 0.229 2.00e-02 2.50e+03 pdb=" N9 OMGC12578 " -0.914 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMGC1 627 " 0.089 2.00e-02 2.50e+03 6.00e-01 8.11e+03 pdb=" C4' OMGC1 627 " 0.411 2.00e-02 2.50e+03 pdb=" O4' OMGC1 627 " 0.565 2.00e-02 2.50e+03 pdb=" C3' OMGC1 627 " -0.614 2.00e-02 2.50e+03 pdb=" O3' OMGC1 627 " -0.667 2.00e-02 2.50e+03 pdb=" C2' OMGC1 627 " -0.151 2.00e-02 2.50e+03 pdb=" O2' OMGC1 627 " 1.028 2.00e-02 2.50e+03 pdb=" C1' OMGC1 627 " 0.229 2.00e-02 2.50e+03 pdb=" N9 OMGC1 627 " -0.890 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMCC11420 " -0.019 2.00e-02 2.50e+03 5.91e-01 7.87e+03 pdb=" C4' OMCC11420 " -0.450 2.00e-02 2.50e+03 pdb=" O4' OMCC11420 " -0.761 2.00e-02 2.50e+03 pdb=" C3' OMCC11420 " 0.597 2.00e-02 2.50e+03 pdb=" O3' OMCC11420 " 0.562 2.00e-02 2.50e+03 pdb=" C2' OMCC11420 " 0.243 2.00e-02 2.50e+03 pdb=" O2' OMCC11420 " -0.880 2.00e-02 2.50e+03 pdb=" C1' OMCC11420 " -0.198 2.00e-02 2.50e+03 pdb=" N1 OMCC11420 " 0.906 2.00e-02 2.50e+03 ... (remaining 18143 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 6411 2.68 - 3.24: 131561 3.24 - 3.79: 309008 3.79 - 4.35: 407306 4.35 - 4.90: 562797 Nonbonded interactions: 1417083 Sorted by model distance: nonbonded pdb="MG MGCd1002 " pdb=" O HOHCd1102 " model vdw 2.127 2.170 nonbonded pdb=" O2G GTPCd1000 " pdb="MG MGCd1002 " model vdw 2.130 2.170 nonbonded pdb=" O1B GTPCd1000 " pdb="MG MGCd1002 " model vdw 2.178 2.170 nonbonded pdb=" NH1 ARGLT 79 " pdb=" O LYSLT 81 " model vdw 2.181 2.520 nonbonded pdb=" NH1 ARGLp 85 " pdb=" OE1 GLULp 88 " model vdw 2.192 2.520 ... (remaining 1417078 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 'CM' selection = (chain 'LF' and (resid 13 through 35 or resid 49 through 79 or resid 87 through \ 249)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.21 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.130 Extract box with map and model: 29.110 Check model and map are aligned: 1.700 Set scattering table: 1.050 Process input model: 555.470 Find NCS groups from input model: 4.010 Set up NCS constraints: 0.460 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: 0.020 Load rotamer database and sin/cos tables:9.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 611.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.307 167533 Z= 0.410 Angle : 0.795 20.138 242854 Z= 0.403 Chirality : 0.044 0.362 29658 Planarity : 0.019 0.601 18146 Dihedral : 21.720 179.948 86660 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.91 % Allowed : 13.46 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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 (0.08), residues: 10361 helix: 1.06 (0.08), residues: 4000 sheet: 0.18 (0.13), residues: 1500 loop : 0.21 (0.08), residues: 4861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRPLM 11 HIS 0.012 0.002 HISLT 82 PHE 0.028 0.002 PHELO 49 TYR 0.028 0.002 TYRCI 251 ARG 0.019 0.001 ARGLS 117 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20722 Ramachandran restraints generated. 10361 Oldfield, 0 Emsley, 10361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20722 Ramachandran restraints generated. 10361 Oldfield, 0 Emsley, 10361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1235 residues out of total 8941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 1156 time to evaluate : 9.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CB 36 LYS cc_start: 0.9055 (ttpp) cc_final: 0.8706 (tmmt) REVERT: CB 213 ASN cc_start: 0.8630 (t0) cc_final: 0.8413 (t0) REVERT: CF 10 TYR cc_start: 0.8835 (t80) cc_final: 0.8503 (t80) REVERT: CF 121 GLN cc_start: 0.8566 (mm-40) cc_final: 0.8346 (tp40) REVERT: CH 303 GLN cc_start: 0.8108 (tp40) cc_final: 0.7883 (tp-100) REVERT: CH 395 LYS cc_start: 0.8288 (mppt) cc_final: 0.7939 (mptt) REVERT: CI 310 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7683 (mp0) REVERT: CK 53 GLN cc_start: 0.8199 (tm130) cc_final: 0.7865 (tm-30) REVERT: Lq 7 ASP cc_start: 0.8374 (m-30) cc_final: 0.8048 (m-30) REVERT: Lq 131 LYS cc_start: 0.8414 (mmtt) cc_final: 0.8176 (mmmt) REVERT: Cf 319 ARG cc_start: 0.6290 (mpp-170) cc_final: 0.6084 (mpp-170) REVERT: Cz 76 ARG cc_start: 0.7627 (ttt-90) cc_final: 0.7169 (ttt-90) REVERT: LC 100 MET cc_start: 0.9058 (ptm) cc_final: 0.8841 (ptp) REVERT: LC 270 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.7072 (mp0) REVERT: LO 89 MET cc_start: 0.9370 (mtt) cc_final: 0.9097 (mtt) REVERT: LY 130 LYS cc_start: 0.8505 (ttpm) cc_final: 0.8176 (ttpp) REVERT: Lh 16 ASN cc_start: 0.8903 (p0) cc_final: 0.8527 (p0) outliers start: 79 outliers final: 52 residues processed: 1212 average time/residue: 2.5297 time to fit residues: 4282.2928 Evaluate side-chains 1167 residues out of total 8941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 1113 time to evaluate : 8.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CB residue 255 LEU Chi-restraints excluded: chain CF residue 149 VAL Chi-restraints excluded: chain CH residue 85 TYR Chi-restraints excluded: chain CH residue 168 THR Chi-restraints excluded: chain CH residue 364 VAL Chi-restraints excluded: chain CH residue 469 GLU Chi-restraints excluded: chain CH residue 655 ILE Chi-restraints excluded: chain CI residue 198 PHE Chi-restraints excluded: chain CI residue 263 VAL Chi-restraints excluded: chain CI residue 310 GLU Chi-restraints excluded: chain CJ residue 381 GLN Chi-restraints excluded: chain CK residue 98 THR Chi-restraints excluded: chain CK residue 185 THR Chi-restraints excluded: chain CM residue 162 VAL Chi-restraints excluded: chain CN residue 168 GLN Chi-restraints excluded: chain CQ residue 173 SER Chi-restraints excluded: chain Cb residue 27 ARG Chi-restraints excluded: chain Cb residue 68 HIS Chi-restraints excluded: chain Ce residue 102 SER Chi-restraints excluded: chain Ce residue 396 LEU Chi-restraints excluded: chain Cf residue 166 ASP Chi-restraints excluded: chain Cg residue 19 THR Chi-restraints excluded: chain Cg residue 71 THR Chi-restraints excluded: chain Ch residue 426 ASN Chi-restraints excluded: chain LA residue 114 SER Chi-restraints excluded: chain LC residue 270 GLU Chi-restraints excluded: chain LD residue 51 LEU Chi-restraints excluded: chain LD residue 242 LEU Chi-restraints excluded: chain LE residue 6 THR Chi-restraints excluded: chain LE residue 165 ILE Chi-restraints excluded: chain LF residue 90 VAL Chi-restraints excluded: chain LG residue 169 LEU Chi-restraints excluded: chain LH residue 56 SER Chi-restraints excluded: chain LH residue 85 VAL Chi-restraints excluded: chain LJ residue 45 THR Chi-restraints excluded: chain LJ residue 171 ILE Chi-restraints excluded: chain LL residue 177 ILE Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LN residue 64 VAL Chi-restraints excluded: chain LQ residue 41 SER Chi-restraints excluded: chain LT residue 72 VAL Chi-restraints excluded: chain LU residue 106 SER Chi-restraints excluded: chain LX residue 37 THR Chi-restraints excluded: chain LY residue 46 SER Chi-restraints excluded: chain LY residue 78 VAL Chi-restraints excluded: chain LY residue 93 THR Chi-restraints excluded: chain Lc residue 101 SER Chi-restraints excluded: chain Lf residue 3 SER Chi-restraints excluded: chain Lf residue 51 VAL Chi-restraints excluded: chain Lj residue 6 SER Chi-restraints excluded: chain Lj residue 7 SER Chi-restraints excluded: chain Lk residue 22 SER Chi-restraints excluded: chain Lp residue 11 SER Chi-restraints excluded: chain Lp residue 72 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1368 random chunks: chunk 1155 optimal weight: 1.9990 chunk 1036 optimal weight: 2.9990 chunk 575 optimal weight: 5.9990 chunk 354 optimal weight: 5.9990 chunk 699 optimal weight: 1.9990 chunk 553 optimal weight: 5.9990 chunk 1072 optimal weight: 2.9990 chunk 414 optimal weight: 0.6980 chunk 651 optimal weight: 5.9990 chunk 798 optimal weight: 0.9990 chunk 1242 optimal weight: 0.2980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CF 14 GLN CF 118 ASN CH 345 GLN CH 362 GLN CH 399 ASN CH 536 GLN CI 267 GLN CI 303 GLN CK 190 ASN ** CL 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CM 99 ASN CN 43 GLN CQ 130 ASN Lq 97 GLN Cg 31 ASN LB 379 GLN LC 118 GLN LD 17 GLN LD 39 GLN LE 172 ASN LH 5 HIS LH 72 GLN LJ 16 GLN ** LK 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LK 70 GLN LM 106 GLN LP 75 GLN LP 111 ASN LP 170 HIS LT 82 HIS LU 55 ASN LX 81 ASN LX 124 ASN LY 127 GLN Ld 49 GLN Ld 70 GLN Lg 30 GLN Lh 33 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.0569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 167533 Z= 0.160 Angle : 0.632 17.093 242854 Z= 0.339 Chirality : 0.036 0.279 29658 Planarity : 0.006 0.128 18146 Dihedral : 22.687 179.773 65226 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.76 % Allowed : 12.48 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: 1.41 (0.08), residues: 10361 helix: 1.89 (0.08), residues: 4029 sheet: 0.29 (0.13), residues: 1488 loop : 0.45 (0.09), residues: 4844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRPCg 105 HIS 0.006 0.001 HISLT 54 PHE 0.016 0.001 PHELO 49 TYR 0.017 0.001 TYRLQ 61 ARG 0.007 0.000 ARGCL 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20722 Ramachandran restraints generated. 10361 Oldfield, 0 Emsley, 10361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20722 Ramachandran restraints generated. 10361 Oldfield, 0 Emsley, 10361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1293 residues out of total 8941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1139 time to evaluate : 8.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CB 36 LYS cc_start: 0.9022 (ttpp) cc_final: 0.8631 (tmmt) REVERT: CB 213 ASN cc_start: 0.8603 (t0) cc_final: 0.8396 (t0) REVERT: CF 10 TYR cc_start: 0.8835 (t80) cc_final: 0.8532 (t80) REVERT: CF 121 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8314 (tp40) REVERT: CH 303 GLN cc_start: 0.8058 (tp40) cc_final: 0.7803 (tp-100) REVERT: CH 549 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7779 (mtt180) REVERT: CI 309 GLU cc_start: 0.8388 (tp30) cc_final: 0.8036 (tp30) REVERT: CI 310 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7707 (mp0) REVERT: CI 318 GLU cc_start: 0.7914 (pm20) cc_final: 0.7604 (pm20) REVERT: CM 238 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7488 (mp0) REVERT: Lq 131 LYS cc_start: 0.8409 (mmtt) cc_final: 0.8180 (mmmt) REVERT: Cb 27 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7826 (mtm-85) REVERT: Cd 12 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8842 (mm) REVERT: Cd 64 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7217 (tm-30) REVERT: Ce 310 ARG cc_start: 0.8400 (ttm110) cc_final: 0.8196 (ttm170) REVERT: Cg 49 GLN cc_start: 0.7990 (tm-30) cc_final: 0.7693 (tp40) REVERT: Cz 95 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.7761 (ttm170) REVERT: LC 270 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6976 (mp0) REVERT: LD 192 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7072 (mm-30) REVERT: LE 31 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7183 (mt-10) REVERT: LF 23 LYS cc_start: 0.8434 (ttpp) cc_final: 0.8215 (pptt) REVERT: LG 251 LYS cc_start: 0.7697 (ttmm) cc_final: 0.7381 (mptp) REVERT: LH 141 GLU cc_start: 0.6900 (pm20) cc_final: 0.6552 (pm20) REVERT: LL 23 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7755 (tpp-160) REVERT: LL 135 LYS cc_start: 0.8372 (ptpt) cc_final: 0.8157 (ptpt) REVERT: LO 89 MET cc_start: 0.9400 (mtt) cc_final: 0.8988 (mtt) REVERT: LU 31 ASP cc_start: 0.8438 (m-30) cc_final: 0.8047 (m-30) REVERT: LY 73 TYR cc_start: 0.9148 (OUTLIER) cc_final: 0.6698 (m-80) REVERT: LZ 5 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8590 (mttp) REVERT: Lh 112 ARG cc_start: 0.7826 (ttm110) cc_final: 0.7589 (ttm-80) REVERT: Lk 10 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8353 (mttp) outliers start: 154 outliers final: 64 residues processed: 1234 average time/residue: 2.5284 time to fit residues: 4363.3249 Evaluate side-chains 1192 residues out of total 8941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 1113 time to evaluate : 8.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CB residue 35 LYS Chi-restraints excluded: chain CB residue 209 LEU Chi-restraints excluded: chain CF residue 121 GLN Chi-restraints excluded: chain CF residue 149 VAL Chi-restraints excluded: chain CH residue 85 TYR Chi-restraints excluded: chain CH residue 168 THR Chi-restraints excluded: chain CH residue 344 SER Chi-restraints excluded: chain CH residue 363 GLU Chi-restraints excluded: chain CH residue 364 VAL Chi-restraints excluded: chain CH residue 469 GLU Chi-restraints excluded: chain CH residue 549 ARG Chi-restraints excluded: chain CI residue 198 PHE Chi-restraints excluded: chain CI residue 310 GLU Chi-restraints excluded: chain CJ residue 381 GLN Chi-restraints excluded: chain CJ residue 393 LYS Chi-restraints excluded: chain CJ residue 408 THR Chi-restraints excluded: chain CK residue 98 THR Chi-restraints excluded: chain CK residue 185 THR Chi-restraints excluded: chain CL residue 67 GLN Chi-restraints excluded: chain CL residue 73 ARG Chi-restraints excluded: chain CM residue 162 VAL Chi-restraints excluded: chain CM residue 187 ILE Chi-restraints excluded: chain CM residue 238 GLU Chi-restraints excluded: chain CN residue 51 THR Chi-restraints excluded: chain CQ residue 64 VAL Chi-restraints excluded: chain Cb residue 27 ARG Chi-restraints excluded: chain Cb residue 68 HIS Chi-restraints excluded: chain Cd residue 12 LEU Chi-restraints excluded: chain Cd residue 64 GLU Chi-restraints excluded: chain Cd residue 206 VAL Chi-restraints excluded: chain Ce residue 349 LEU Chi-restraints excluded: chain Cf residue 16 LEU Chi-restraints excluded: chain Cf residue 166 ASP Chi-restraints excluded: chain Cg residue 71 THR Chi-restraints excluded: chain Ch residue 142 ILE Chi-restraints excluded: chain Ch residue 426 ASN Chi-restraints excluded: chain Cz residue 22 ASN Chi-restraints excluded: chain Cz residue 95 ARG Chi-restraints excluded: chain LC residue 198 MET Chi-restraints excluded: chain LC residue 270 GLU Chi-restraints excluded: chain LD residue 51 LEU Chi-restraints excluded: chain LD residue 188 ILE Chi-restraints excluded: chain LD residue 192 GLU Chi-restraints excluded: chain LD residue 282 LEU Chi-restraints excluded: chain LE residue 31 GLU Chi-restraints excluded: chain LE residue 155 SER Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LF residue 90 VAL Chi-restraints excluded: chain LG residue 169 LEU Chi-restraints excluded: chain LG residue 246 GLN Chi-restraints excluded: chain LH residue 85 VAL Chi-restraints excluded: chain LH residue 157 ILE Chi-restraints excluded: chain LJ residue 45 THR Chi-restraints excluded: chain LJ residue 49 SER Chi-restraints excluded: chain LL residue 23 ARG Chi-restraints excluded: chain LL residue 148 THR Chi-restraints excluded: chain LM residue 9 THR Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LN residue 64 VAL Chi-restraints excluded: chain LP residue 169 SER Chi-restraints excluded: chain LT residue 72 VAL Chi-restraints excluded: chain LT residue 115 LEU Chi-restraints excluded: chain LU residue 30 SER Chi-restraints excluded: chain LU residue 37 SER Chi-restraints excluded: chain LU residue 59 VAL Chi-restraints excluded: chain LV residue 74 LYS Chi-restraints excluded: chain LX residue 37 THR Chi-restraints excluded: chain LX residue 83 GLU Chi-restraints excluded: chain LY residue 73 TYR Chi-restraints excluded: chain LY residue 78 VAL Chi-restraints excluded: chain LZ residue 5 LYS Chi-restraints excluded: chain La residue 85 ASP Chi-restraints excluded: chain Lc residue 23 SER Chi-restraints excluded: chain Li residue 105 GLU Chi-restraints excluded: chain Lk residue 10 LYS Chi-restraints excluded: chain Lk residue 38 VAL Chi-restraints excluded: chain Lk residue 51 ASP Chi-restraints excluded: chain Lk residue 62 LEU Chi-restraints excluded: chain Ll residue 34 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1368 random chunks: chunk 690 optimal weight: 9.9990 chunk 385 optimal weight: 10.0000 chunk 1033 optimal weight: 3.9990 chunk 845 optimal weight: 4.9990 chunk 342 optimal weight: 6.9990 chunk 1244 optimal weight: 8.9990 chunk 1344 optimal weight: 6.9990 chunk 1108 optimal weight: 6.9990 chunk 1234 optimal weight: 10.0000 chunk 424 optimal weight: 6.9990 chunk 998 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CB 132 HIS CF 118 ASN CH 345 GLN CH 362 GLN CH 399 ASN CH 536 GLN ** CI 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CK 190 ASN ** CL 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CM 99 ASN CM 165 GLN ** CM 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CN 170 GLN CQ 130 ASN Lq 97 GLN Cg 31 ASN ** LA 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 141 ASN ** LB 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LB 379 GLN LC 118 GLN LD 17 GLN LD 39 GLN LE 172 ASN LF 10 ASN LF 200 ASN LH 139 ASN LH 201 GLN LJ 16 GLN LK 65 GLN LK 70 GLN LL 17 HIS LM 106 GLN LN 138 ASN LP 111 ASN LT 82 HIS ** LT 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LU 55 ASN LX 81 ASN LY 127 GLN Ld 49 GLN Ld 70 GLN Lg 30 GLN Lh 33 GLN Lk 41 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.0826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.100 167533 Z= 0.539 Angle : 0.864 22.859 242854 Z= 0.441 Chirality : 0.050 0.311 29658 Planarity : 0.009 0.155 18146 Dihedral : 22.762 179.532 65190 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.38 % Allowed : 12.03 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: 1.19 (0.08), residues: 10361 helix: 1.61 (0.08), residues: 4038 sheet: 0.08 (0.13), residues: 1503 loop : 0.47 (0.09), residues: 4820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRPCg 105 HIS 0.013 0.002 HISLR 125 PHE 0.028 0.003 PHELO 49 TYR 0.030 0.003 TYRLO 55 ARG 0.016 0.001 ARGLN 105 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20722 Ramachandran restraints generated. 10361 Oldfield, 0 Emsley, 10361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20722 Ramachandran restraints generated. 10361 Oldfield, 0 Emsley, 10361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1355 residues out of total 8941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 1146 time to evaluate : 9.035 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: CB 36 LYS cc_start: 0.9018 (ttpp) cc_final: 0.8629 (tmmt) REVERT: CB 274 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8216 (mptt) REVERT: CB 277 ASN cc_start: 0.9016 (t0) cc_final: 0.8756 (t160) REVERT: CF 10 TYR cc_start: 0.8889 (t80) cc_final: 0.8581 (t80) REVERT: CH 303 GLN cc_start: 0.8156 (tp40) cc_final: 0.7927 (tp-100) REVERT: CH 549 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.7857 (mtt180) REVERT: CH 617 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6768 (tm-30) REVERT: CI 309 GLU cc_start: 0.8401 (tp30) cc_final: 0.7950 (tp30) REVERT: CI 310 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7715 (mp0) REVERT: CM 238 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7541 (mp0) REVERT: CN 142 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8922 (mt) REVERT: Lq 131 LYS cc_start: 0.8462 (mmtt) cc_final: 0.8230 (mmmt) REVERT: Cd 12 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8933 (mm) REVERT: Ch 177 ASP cc_start: 0.8209 (m-30) cc_final: 0.7988 (m-30) REVERT: Cz 95 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.7808 (ttm170) REVERT: LC 100 MET cc_start: 0.9124 (ptm) cc_final: 0.8863 (ptp) REVERT: LC 270 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7177 (mp0) REVERT: LD 192 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7099 (mm-30) REVERT: LE 31 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7184 (mt-10) REVERT: LH 100 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8691 (ttmt) REVERT: LJ 52 ARG cc_start: 0.8444 (mtm180) cc_final: 0.8094 (mtp180) REVERT: LL 146 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7036 (tm-30) REVERT: LO 89 MET cc_start: 0.9435 (mtt) cc_final: 0.9099 (mtt) REVERT: LQ 105 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7499 (mtmm) REVERT: LT 89 ILE cc_start: 0.9295 (OUTLIER) cc_final: 0.9025 (pt) REVERT: LT 115 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8186 (mp) REVERT: LU 93 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8854 (tttm) REVERT: LY 111 ASP cc_start: 0.8610 (p0) cc_final: 0.8393 (p0) REVERT: LZ 5 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8543 (mttp) REVERT: Lh 112 ARG cc_start: 0.7950 (ttm110) cc_final: 0.7661 (ttm-80) REVERT: Lj 27 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9155 (tm) outliers start: 209 outliers final: 117 residues processed: 1266 average time/residue: 2.4957 time to fit residues: 4432.0005 Evaluate side-chains 1260 residues out of total 8941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1124 time to evaluate : 8.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CB residue 35 LYS Chi-restraints excluded: chain CB residue 115 GLU Chi-restraints excluded: chain CB residue 185 MET Chi-restraints excluded: chain CB residue 209 LEU Chi-restraints excluded: chain CB residue 238 SER Chi-restraints excluded: chain CB residue 241 THR Chi-restraints excluded: chain CB residue 274 LYS Chi-restraints excluded: chain CB residue 301 LEU Chi-restraints excluded: chain CF residue 45 VAL Chi-restraints excluded: chain CF residue 149 VAL Chi-restraints excluded: chain CF residue 231 SER Chi-restraints excluded: chain CF residue 233 GLU Chi-restraints excluded: chain CH residue 79 ASP Chi-restraints excluded: chain CH residue 85 TYR Chi-restraints excluded: chain CH residue 168 THR Chi-restraints excluded: chain CH residue 344 SER Chi-restraints excluded: chain CH residue 363 GLU Chi-restraints excluded: chain CH residue 364 VAL Chi-restraints excluded: chain CH residue 549 ARG Chi-restraints excluded: chain CH residue 617 GLU Chi-restraints excluded: chain CH residue 655 ILE Chi-restraints excluded: chain CI residue 198 PHE Chi-restraints excluded: chain CI residue 263 VAL Chi-restraints excluded: chain CI residue 267 GLN Chi-restraints excluded: chain CI residue 310 GLU Chi-restraints excluded: chain CJ residue 222 VAL Chi-restraints excluded: chain CJ residue 364 SER Chi-restraints excluded: chain CJ residue 381 GLN Chi-restraints excluded: chain CJ residue 393 LYS Chi-restraints excluded: chain CJ residue 408 THR Chi-restraints excluded: chain CJ residue 465 ILE Chi-restraints excluded: chain CK residue 66 LYS Chi-restraints excluded: chain CK residue 73 VAL Chi-restraints excluded: chain CK residue 98 THR Chi-restraints excluded: chain CK residue 185 THR Chi-restraints excluded: chain CL residue 19 ARG Chi-restraints excluded: chain CL residue 68 GLN Chi-restraints excluded: chain CL residue 73 ARG Chi-restraints excluded: chain CM residue 110 GLN Chi-restraints excluded: chain CM residue 111 LEU Chi-restraints excluded: chain CM residue 162 VAL Chi-restraints excluded: chain CM residue 187 ILE Chi-restraints excluded: chain CM residue 238 GLU Chi-restraints excluded: chain CN residue 51 THR Chi-restraints excluded: chain CN residue 91 ASP Chi-restraints excluded: chain CN residue 142 ILE Chi-restraints excluded: chain CQ residue 64 VAL Chi-restraints excluded: chain CQ residue 173 SER Chi-restraints excluded: chain Cb residue 28 SER Chi-restraints excluded: chain Cb residue 68 HIS Chi-restraints excluded: chain Cd residue 12 LEU Chi-restraints excluded: chain Cd residue 64 GLU Chi-restraints excluded: chain Cd residue 139 GLU Chi-restraints excluded: chain Cd residue 206 VAL Chi-restraints excluded: chain Cd residue 219 SER Chi-restraints excluded: chain Cd residue 278 SER Chi-restraints excluded: chain Ce residue 98 LEU Chi-restraints excluded: chain Ce residue 102 SER Chi-restraints excluded: chain Ce residue 349 LEU Chi-restraints excluded: chain Ce residue 396 LEU Chi-restraints excluded: chain Cf residue 16 LEU Chi-restraints excluded: chain Cf residue 166 ASP Chi-restraints excluded: chain Cf residue 280 GLU Chi-restraints excluded: chain Cg residue 19 THR Chi-restraints excluded: chain Cg residue 22 THR Chi-restraints excluded: chain Cg residue 62 LEU Chi-restraints excluded: chain Cg residue 71 THR Chi-restraints excluded: chain Ch residue 426 ASN Chi-restraints excluded: chain Cz residue 72 LYS Chi-restraints excluded: chain Cz residue 95 ARG Chi-restraints excluded: chain LA residue 114 SER Chi-restraints excluded: chain LC residue 270 GLU Chi-restraints excluded: chain LD residue 51 LEU Chi-restraints excluded: chain LD residue 129 TYR Chi-restraints excluded: chain LD residue 188 ILE Chi-restraints excluded: chain LD residue 192 GLU Chi-restraints excluded: chain LD residue 242 LEU Chi-restraints excluded: chain LD residue 256 ARG Chi-restraints excluded: chain LE residue 6 THR Chi-restraints excluded: chain LE residue 31 GLU Chi-restraints excluded: chain LE residue 155 SER Chi-restraints excluded: chain LE residue 165 ILE Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LF residue 90 VAL Chi-restraints excluded: chain LF residue 136 VAL Chi-restraints excluded: chain LG residue 169 LEU Chi-restraints excluded: chain LG residue 246 GLN Chi-restraints excluded: chain LG residue 248 ARG Chi-restraints excluded: chain LH residue 85 VAL Chi-restraints excluded: chain LH residue 100 LYS Chi-restraints excluded: chain LH residue 157 ILE Chi-restraints excluded: chain LJ residue 45 THR Chi-restraints excluded: chain LJ residue 49 SER Chi-restraints excluded: chain LL residue 63 VAL Chi-restraints excluded: chain LL residue 146 GLU Chi-restraints excluded: chain LL residue 166 THR Chi-restraints excluded: chain LL residue 177 ILE Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LN residue 7 LEU Chi-restraints excluded: chain LN residue 35 VAL Chi-restraints excluded: chain LP residue 109 THR Chi-restraints excluded: chain LP residue 169 SER Chi-restraints excluded: chain LQ residue 105 LYS Chi-restraints excluded: chain LQ residue 136 LYS Chi-restraints excluded: chain LR residue 29 VAL Chi-restraints excluded: chain LS residue 45 LEU Chi-restraints excluded: chain LS residue 90 MET Chi-restraints excluded: chain LT residue 33 THR Chi-restraints excluded: chain LT residue 72 VAL Chi-restraints excluded: chain LT residue 89 ILE Chi-restraints excluded: chain LT residue 93 ILE Chi-restraints excluded: chain LT residue 115 LEU Chi-restraints excluded: chain LT residue 151 LEU Chi-restraints excluded: chain LU residue 30 SER Chi-restraints excluded: chain LU residue 37 SER Chi-restraints excluded: chain LU residue 59 VAL Chi-restraints excluded: chain LU residue 93 LYS Chi-restraints excluded: chain LX residue 37 THR Chi-restraints excluded: chain LX residue 83 GLU Chi-restraints excluded: chain LY residue 78 VAL Chi-restraints excluded: chain LY residue 93 THR Chi-restraints excluded: chain LZ residue 5 LYS Chi-restraints excluded: chain La residue 85 ASP Chi-restraints excluded: chain Lf residue 51 VAL Chi-restraints excluded: chain Lf residue 59 LYS Chi-restraints excluded: chain Li residue 67 ILE Chi-restraints excluded: chain Li residue 105 GLU Chi-restraints excluded: chain Lj residue 27 LEU Chi-restraints excluded: chain Lk residue 21 SER Chi-restraints excluded: chain Lk residue 34 ILE Chi-restraints excluded: chain Lk residue 51 ASP Chi-restraints excluded: chain Ll residue 34 THR Chi-restraints excluded: chain Lp residue 6 LYS Chi-restraints excluded: chain Lp residue 56 SER Chi-restraints excluded: chain Lp residue 72 SER Chi-restraints excluded: chain Lp residue 73 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1368 random chunks: chunk 1229 optimal weight: 0.7980 chunk 935 optimal weight: 7.9990 chunk 645 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 593 optimal weight: 7.9990 chunk 835 optimal weight: 0.0980 chunk 1248 optimal weight: 0.8980 chunk 1322 optimal weight: 3.9990 chunk 652 optimal weight: 6.9990 chunk 1183 optimal weight: 3.9990 chunk 356 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CB 87 HIS CF 118 ASN CH 244 HIS CH 345 GLN CH 362 GLN CH 399 ASN CH 536 GLN CI 267 GLN ** CI 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CI 303 GLN CJ 365 GLN CK 190 ASN CM 99 ASN CM 165 GLN ** CM 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CQ 130 ASN Lq 97 GLN Cg 31 ASN Cg 98 GLN Cg 133 GLN Cg 192 GLN ** LA 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 379 GLN LC 118 GLN LC 315 GLN LD 17 GLN LD 39 GLN LE 53 GLN LE 116 GLN LH 201 GLN LJ 16 GLN ** LK 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LK 70 GLN LM 106 GLN LP 111 ASN LT 82 HIS LU 27 GLN LU 55 ASN LU 95 GLN LX 81 ASN LY 127 GLN Ld 49 GLN Ld 70 GLN Lg 30 GLN Lh 33 GLN Lk 33 GLN Lk 41 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.0753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 167533 Z= 0.165 Angle : 0.628 17.374 242854 Z= 0.340 Chirality : 0.036 0.293 29658 Planarity : 0.006 0.128 18146 Dihedral : 22.663 179.855 65182 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.69 % Allowed : 13.03 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: 1.61 (0.08), residues: 10361 helix: 2.09 (0.08), residues: 4031 sheet: 0.25 (0.13), residues: 1459 loop : 0.58 (0.09), residues: 4871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRPCg 105 HIS 0.008 0.001 HISCd 252 PHE 0.017 0.001 PHECH 90 TYR 0.018 0.001 TYRLS 43 ARG 0.010 0.000 ARGCH 549 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20722 Ramachandran restraints generated. 10361 Oldfield, 0 Emsley, 10361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20722 Ramachandran restraints generated. 10361 Oldfield, 0 Emsley, 10361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1299 residues out of total 8941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1151 time to evaluate : 8.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CB 36 LYS cc_start: 0.9020 (ttpp) cc_final: 0.8631 (tmmt) REVERT: CF 10 TYR cc_start: 0.8846 (t80) cc_final: 0.8505 (t80) REVERT: CH 303 GLN cc_start: 0.8088 (tp40) cc_final: 0.7842 (tp-100) REVERT: CH 617 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6713 (tm-30) REVERT: CI 279 ARG cc_start: 0.7288 (OUTLIER) cc_final: 0.7043 (mtm-85) REVERT: CI 309 GLU cc_start: 0.8355 (tp30) cc_final: 0.7949 (tp30) REVERT: CI 310 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7625 (mp0) REVERT: CI 318 GLU cc_start: 0.7955 (pm20) cc_final: 0.7633 (pm20) REVERT: CM 248 MET cc_start: 0.9325 (mtp) cc_final: 0.9022 (mtp) REVERT: Lq 131 LYS cc_start: 0.8453 (mmtt) cc_final: 0.8221 (mmmt) REVERT: Cd 12 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8869 (mm) REVERT: Cd 425 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7452 (mtp180) REVERT: Ce 310 ARG cc_start: 0.8409 (ttm110) cc_final: 0.8189 (ttm170) REVERT: Ce 331 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7012 (mp0) REVERT: Ch 86 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7976 (mtp180) REVERT: Ch 177 ASP cc_start: 0.8228 (m-30) cc_final: 0.8002 (m-30) REVERT: Cz 95 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.7862 (ttm170) REVERT: LC 270 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.7003 (mp0) REVERT: LD 192 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7093 (mm-30) REVERT: LE 31 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7130 (mt-10) REVERT: LG 150 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8456 (mmtp) REVERT: LJ 52 ARG cc_start: 0.8415 (mtm180) cc_final: 0.8091 (mtp180) REVERT: LJ 132 MET cc_start: 0.8481 (mmm) cc_final: 0.8220 (mmm) REVERT: LL 19 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.7954 (mp10) REVERT: LL 23 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7741 (tpp-160) REVERT: LL 146 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7039 (tm-30) REVERT: LO 89 MET cc_start: 0.9497 (mtt) cc_final: 0.9054 (mtt) REVERT: LT 89 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.8985 (pt) REVERT: LT 111 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7488 (mt-10) REVERT: LT 115 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8300 (mp) REVERT: LU 95 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.7861 (mt0) REVERT: LZ 5 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8599 (mttp) REVERT: Lh 112 ARG cc_start: 0.7891 (ttm110) cc_final: 0.7586 (ttm-80) REVERT: Lj 27 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9142 (tm) outliers start: 148 outliers final: 68 residues processed: 1229 average time/residue: 2.5778 time to fit residues: 4424.2585 Evaluate side-chains 1224 residues out of total 8941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1135 time to evaluate : 8.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CB residue 35 LYS Chi-restraints excluded: chain CB residue 115 GLU Chi-restraints excluded: chain CB residue 209 LEU Chi-restraints excluded: chain CB residue 306 VAL Chi-restraints excluded: chain CF residue 149 VAL Chi-restraints excluded: chain CF residue 233 GLU Chi-restraints excluded: chain CH residue 85 TYR Chi-restraints excluded: chain CH residue 168 THR Chi-restraints excluded: chain CH residue 344 SER Chi-restraints excluded: chain CH residue 363 GLU Chi-restraints excluded: chain CH residue 364 VAL Chi-restraints excluded: chain CH residue 617 GLU Chi-restraints excluded: chain CH residue 655 ILE Chi-restraints excluded: chain CI residue 198 PHE Chi-restraints excluded: chain CI residue 263 VAL Chi-restraints excluded: chain CI residue 267 GLN Chi-restraints excluded: chain CI residue 279 ARG Chi-restraints excluded: chain CI residue 310 GLU Chi-restraints excluded: chain CJ residue 381 GLN Chi-restraints excluded: chain CJ residue 393 LYS Chi-restraints excluded: chain CJ residue 408 THR Chi-restraints excluded: chain CK residue 66 LYS Chi-restraints excluded: chain CK residue 98 THR Chi-restraints excluded: chain CK residue 185 THR Chi-restraints excluded: chain CL residue 67 GLN Chi-restraints excluded: chain CL residue 73 ARG Chi-restraints excluded: chain CM residue 111 LEU Chi-restraints excluded: chain CM residue 162 VAL Chi-restraints excluded: chain CM residue 187 ILE Chi-restraints excluded: chain CN residue 51 THR Chi-restraints excluded: chain CN residue 91 ASP Chi-restraints excluded: chain CQ residue 64 VAL Chi-restraints excluded: chain Cb residue 68 HIS Chi-restraints excluded: chain Cd residue 12 LEU Chi-restraints excluded: chain Cd residue 425 ARG Chi-restraints excluded: chain Ce residue 331 GLU Chi-restraints excluded: chain Ce residue 349 LEU Chi-restraints excluded: chain Ce residue 397 LYS Chi-restraints excluded: chain Cf residue 16 LEU Chi-restraints excluded: chain Cf residue 166 ASP Chi-restraints excluded: chain Cg residue 22 THR Chi-restraints excluded: chain Cg residue 71 THR Chi-restraints excluded: chain Ch residue 86 ARG Chi-restraints excluded: chain Ch residue 142 ILE Chi-restraints excluded: chain Ch residue 426 ASN Chi-restraints excluded: chain Cz residue 95 ARG Chi-restraints excluded: chain LC residue 198 MET Chi-restraints excluded: chain LC residue 270 GLU Chi-restraints excluded: chain LD residue 51 LEU Chi-restraints excluded: chain LD residue 188 ILE Chi-restraints excluded: chain LD residue 192 GLU Chi-restraints excluded: chain LD residue 282 LEU Chi-restraints excluded: chain LE residue 31 GLU Chi-restraints excluded: chain LE residue 155 SER Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LF residue 90 VAL Chi-restraints excluded: chain LG residue 150 LYS Chi-restraints excluded: chain LG residue 169 LEU Chi-restraints excluded: chain LG residue 246 GLN Chi-restraints excluded: chain LH residue 85 VAL Chi-restraints excluded: chain LH residue 157 ILE Chi-restraints excluded: chain LJ residue 45 THR Chi-restraints excluded: chain LJ residue 49 SER Chi-restraints excluded: chain LJ residue 63 ASN Chi-restraints excluded: chain LL residue 19 GLN Chi-restraints excluded: chain LL residue 23 ARG Chi-restraints excluded: chain LL residue 146 GLU Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LP residue 169 SER Chi-restraints excluded: chain LR residue 29 VAL Chi-restraints excluded: chain LR residue 133 LYS Chi-restraints excluded: chain LS residue 90 MET Chi-restraints excluded: chain LT residue 72 VAL Chi-restraints excluded: chain LT residue 89 ILE Chi-restraints excluded: chain LT residue 111 GLU Chi-restraints excluded: chain LT residue 115 LEU Chi-restraints excluded: chain LU residue 30 SER Chi-restraints excluded: chain LU residue 59 VAL Chi-restraints excluded: chain LU residue 95 GLN Chi-restraints excluded: chain LX residue 37 THR Chi-restraints excluded: chain LX residue 83 GLU Chi-restraints excluded: chain LX residue 92 GLN Chi-restraints excluded: chain LY residue 78 VAL Chi-restraints excluded: chain LY residue 88 LYS Chi-restraints excluded: chain LY residue 93 THR Chi-restraints excluded: chain LZ residue 5 LYS Chi-restraints excluded: chain La residue 85 ASP Chi-restraints excluded: chain Li residue 105 GLU Chi-restraints excluded: chain Lj residue 27 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1368 random chunks: chunk 1101 optimal weight: 2.9990 chunk 750 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 984 optimal weight: 3.9990 chunk 545 optimal weight: 2.9990 chunk 1128 optimal weight: 7.9990 chunk 914 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 675 optimal weight: 10.0000 chunk 1186 optimal weight: 6.9990 chunk 333 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CF 118 ASN CH 345 GLN CH 362 GLN CH 399 ASN CH 536 GLN ** CI 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 365 GLN CK 190 ASN ** CL 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CM 99 ASN CM 165 GLN ** CM 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CQ 130 ASN Lq 97 GLN Cg 31 ASN Cg 133 GLN Cg 192 GLN ** LA 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 141 ASN LB 379 GLN LC 118 GLN LD 17 GLN LD 39 GLN LE 53 GLN LE 172 ASN LF 10 ASN LH 201 GLN LH 225 ASN LJ 16 GLN ** LK 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LK 70 GLN LM 106 GLN LP 75 GLN LP 111 ASN LT 82 HIS ** LT 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LX 81 ASN LY 127 GLN Ld 49 GLN Ld 70 GLN Lg 30 GLN Lh 33 GLN Lk 33 GLN Lk 75 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.0777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 167533 Z= 0.334 Angle : 0.716 18.020 242854 Z= 0.378 Chirality : 0.042 0.293 29658 Planarity : 0.007 0.142 18146 Dihedral : 22.654 179.458 65182 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.11 % Allowed : 12.82 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: 1.51 (0.08), residues: 10361 helix: 1.96 (0.08), residues: 4038 sheet: 0.17 (0.13), residues: 1485 loop : 0.58 (0.09), residues: 4838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRPCg 105 HIS 0.010 0.001 HISLR 125 PHE 0.022 0.002 PHELO 49 TYR 0.025 0.002 TYRLO 55 ARG 0.010 0.001 ARGCz 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20722 Ramachandran restraints generated. 10361 Oldfield, 0 Emsley, 10361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20722 Ramachandran restraints generated. 10361 Oldfield, 0 Emsley, 10361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1330 residues out of total 8941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1145 time to evaluate : 9.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CB 36 LYS cc_start: 0.9017 (ttpp) cc_final: 0.8622 (tmmt) REVERT: CF 10 TYR cc_start: 0.8861 (t80) cc_final: 0.8586 (t80) REVERT: CH 617 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6757 (tm-30) REVERT: CI 279 ARG cc_start: 0.7316 (OUTLIER) cc_final: 0.7072 (ttm-80) REVERT: CI 309 GLU cc_start: 0.8367 (tp30) cc_final: 0.7925 (tp30) REVERT: CI 310 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7595 (mp0) REVERT: CJ 381 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7687 (mm-40) REVERT: CL 33 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.7365 (mtp180) REVERT: CM 238 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7520 (mp0) REVERT: Lq 131 LYS cc_start: 0.8459 (mmtt) cc_final: 0.8233 (mmmt) REVERT: Cb 76 ARG cc_start: 0.9187 (OUTLIER) cc_final: 0.7645 (ttp-170) REVERT: Cd 12 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8904 (mm) REVERT: Cg 135 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8447 (pt0) REVERT: Ch 177 ASP cc_start: 0.8206 (m-30) cc_final: 0.7982 (m-30) REVERT: Cz 95 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.7877 (ttm170) REVERT: LB 358 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.9014 (mttt) REVERT: LC 100 MET cc_start: 0.9105 (ptm) cc_final: 0.8850 (ptp) REVERT: LD 192 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7079 (mm-30) REVERT: LE 31 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.7148 (mt-10) REVERT: LJ 52 ARG cc_start: 0.8445 (mtm180) cc_final: 0.8099 (mtp180) REVERT: LJ 132 MET cc_start: 0.8492 (mmm) cc_final: 0.8239 (mmm) REVERT: LL 146 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7032 (tm-30) REVERT: LO 89 MET cc_start: 0.9504 (mtt) cc_final: 0.9076 (mtt) REVERT: LT 89 ILE cc_start: 0.9313 (OUTLIER) cc_final: 0.9058 (pt) REVERT: LT 111 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7516 (mt-10) REVERT: LT 115 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8352 (mp) REVERT: LZ 5 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8568 (mttp) REVERT: Lh 112 ARG cc_start: 0.7929 (ttm110) cc_final: 0.7623 (ttm-80) REVERT: Lj 27 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9145 (tm) REVERT: Lp 3 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7956 (mtpt) outliers start: 185 outliers final: 107 residues processed: 1249 average time/residue: 2.5832 time to fit residues: 4496.5117 Evaluate side-chains 1258 residues out of total 8941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 1131 time to evaluate : 8.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CB residue 35 LYS Chi-restraints excluded: chain CB residue 115 GLU Chi-restraints excluded: chain CB residue 209 LEU Chi-restraints excluded: chain CB residue 301 LEU Chi-restraints excluded: chain CF residue 149 VAL Chi-restraints excluded: chain CF residue 233 GLU Chi-restraints excluded: chain CH residue 79 ASP Chi-restraints excluded: chain CH residue 85 TYR Chi-restraints excluded: chain CH residue 168 THR Chi-restraints excluded: chain CH residue 344 SER Chi-restraints excluded: chain CH residue 363 GLU Chi-restraints excluded: chain CH residue 364 VAL Chi-restraints excluded: chain CH residue 392 LYS Chi-restraints excluded: chain CH residue 610 THR Chi-restraints excluded: chain CH residue 617 GLU Chi-restraints excluded: chain CH residue 655 ILE Chi-restraints excluded: chain CI residue 198 PHE Chi-restraints excluded: chain CI residue 263 VAL Chi-restraints excluded: chain CI residue 279 ARG Chi-restraints excluded: chain CI residue 310 GLU Chi-restraints excluded: chain CI residue 332 LEU Chi-restraints excluded: chain CJ residue 222 VAL Chi-restraints excluded: chain CJ residue 364 SER Chi-restraints excluded: chain CJ residue 381 GLN Chi-restraints excluded: chain CJ residue 393 LYS Chi-restraints excluded: chain CJ residue 408 THR Chi-restraints excluded: chain CK residue 66 LYS Chi-restraints excluded: chain CK residue 73 VAL Chi-restraints excluded: chain CK residue 98 THR Chi-restraints excluded: chain CK residue 185 THR Chi-restraints excluded: chain CL residue 19 ARG Chi-restraints excluded: chain CL residue 33 ARG Chi-restraints excluded: chain CL residue 67 GLN Chi-restraints excluded: chain CL residue 73 ARG Chi-restraints excluded: chain CM residue 111 LEU Chi-restraints excluded: chain CM residue 162 VAL Chi-restraints excluded: chain CM residue 187 ILE Chi-restraints excluded: chain CM residue 238 GLU Chi-restraints excluded: chain CN residue 51 THR Chi-restraints excluded: chain CN residue 91 ASP Chi-restraints excluded: chain CQ residue 64 VAL Chi-restraints excluded: chain CQ residue 173 SER Chi-restraints excluded: chain Cb residue 68 HIS Chi-restraints excluded: chain Cb residue 76 ARG Chi-restraints excluded: chain Cd residue 12 LEU Chi-restraints excluded: chain Cd residue 206 VAL Chi-restraints excluded: chain Cd residue 278 SER Chi-restraints excluded: chain Ce residue 102 SER Chi-restraints excluded: chain Ce residue 349 LEU Chi-restraints excluded: chain Ce residue 397 LYS Chi-restraints excluded: chain Cf residue 16 LEU Chi-restraints excluded: chain Cf residue 166 ASP Chi-restraints excluded: chain Cf residue 306 LEU Chi-restraints excluded: chain Cg residue 19 THR Chi-restraints excluded: chain Cg residue 22 THR Chi-restraints excluded: chain Cg residue 71 THR Chi-restraints excluded: chain Cg residue 135 GLU Chi-restraints excluded: chain Ch residue 142 ILE Chi-restraints excluded: chain Ch residue 426 ASN Chi-restraints excluded: chain Cz residue 22 ASN Chi-restraints excluded: chain Cz residue 72 LYS Chi-restraints excluded: chain Cz residue 95 ARG Chi-restraints excluded: chain LB residue 358 LYS Chi-restraints excluded: chain LB residue 386 LYS Chi-restraints excluded: chain LC residue 198 MET Chi-restraints excluded: chain LD residue 51 LEU Chi-restraints excluded: chain LD residue 188 ILE Chi-restraints excluded: chain LD residue 192 GLU Chi-restraints excluded: chain LD residue 282 LEU Chi-restraints excluded: chain LE residue 6 THR Chi-restraints excluded: chain LE residue 31 GLU Chi-restraints excluded: chain LE residue 155 SER Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LF residue 90 VAL Chi-restraints excluded: chain LF residue 136 VAL Chi-restraints excluded: chain LG residue 169 LEU Chi-restraints excluded: chain LG residue 246 GLN Chi-restraints excluded: chain LH residue 56 SER Chi-restraints excluded: chain LH residue 85 VAL Chi-restraints excluded: chain LH residue 157 ILE Chi-restraints excluded: chain LH residue 203 ILE Chi-restraints excluded: chain LJ residue 45 THR Chi-restraints excluded: chain LJ residue 49 SER Chi-restraints excluded: chain LJ residue 63 ASN Chi-restraints excluded: chain LK residue 78 SER Chi-restraints excluded: chain LK residue 151 ILE Chi-restraints excluded: chain LL residue 63 VAL Chi-restraints excluded: chain LL residue 146 GLU Chi-restraints excluded: chain LL residue 177 ILE Chi-restraints excluded: chain LM residue 9 THR Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LM residue 71 LYS Chi-restraints excluded: chain LN residue 7 LEU Chi-restraints excluded: chain LP residue 109 THR Chi-restraints excluded: chain LP residue 169 SER Chi-restraints excluded: chain LR residue 29 VAL Chi-restraints excluded: chain LR residue 51 ILE Chi-restraints excluded: chain LS residue 45 LEU Chi-restraints excluded: chain LS residue 90 MET Chi-restraints excluded: chain LT residue 72 VAL Chi-restraints excluded: chain LT residue 89 ILE Chi-restraints excluded: chain LT residue 93 ILE Chi-restraints excluded: chain LT residue 111 GLU Chi-restraints excluded: chain LT residue 115 LEU Chi-restraints excluded: chain LU residue 30 SER Chi-restraints excluded: chain LU residue 37 SER Chi-restraints excluded: chain LU residue 59 VAL Chi-restraints excluded: chain LX residue 37 THR Chi-restraints excluded: chain LX residue 83 GLU Chi-restraints excluded: chain LY residue 78 VAL Chi-restraints excluded: chain LY residue 88 LYS Chi-restraints excluded: chain LY residue 93 THR Chi-restraints excluded: chain LY residue 130 LYS Chi-restraints excluded: chain LZ residue 5 LYS Chi-restraints excluded: chain La residue 85 ASP Chi-restraints excluded: chain Lf residue 51 VAL Chi-restraints excluded: chain Lf residue 59 LYS Chi-restraints excluded: chain Lg residue 68 LYS Chi-restraints excluded: chain Lg residue 104 LYS Chi-restraints excluded: chain Li residue 67 ILE Chi-restraints excluded: chain Li residue 105 GLU Chi-restraints excluded: chain Lj residue 27 LEU Chi-restraints excluded: chain Ll residue 34 THR Chi-restraints excluded: chain Lp residue 3 LYS Chi-restraints excluded: chain Lp residue 56 SER Chi-restraints excluded: chain Lp residue 72 SER Chi-restraints excluded: chain Lp residue 73 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1368 random chunks: chunk 444 optimal weight: 0.9980 chunk 1190 optimal weight: 4.9990 chunk 261 optimal weight: 5.9990 chunk 776 optimal weight: 5.9990 chunk 326 optimal weight: 10.0000 chunk 1323 optimal weight: 6.9990 chunk 1098 optimal weight: 5.9990 chunk 612 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 chunk 437 optimal weight: 5.9990 chunk 694 optimal weight: 0.0670 overall best weight: 3.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CB 249 ASN CF 118 ASN CH 345 GLN CH 362 GLN CH 399 ASN CH 536 GLN CI 267 GLN CJ 365 GLN ** CL 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CM 99 ASN CM 165 GLN ** CM 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CQ 130 ASN Lq 97 GLN Cg 31 ASN Cg 49 GLN Cg 98 GLN Cg 133 GLN Cg 192 GLN ** LA 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 244 HIS LB 379 GLN LD 17 GLN LD 39 GLN LE 172 ASN LF 10 ASN LH 201 GLN LJ 16 GLN ** LK 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LK 70 GLN LM 106 GLN LP 75 GLN LP 111 ASN LT 82 HIS ** LT 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LU 95 GLN LX 81 ASN LY 127 GLN Ld 49 GLN Ld 70 GLN Lg 30 GLN Lh 33 GLN Lk 33 GLN Lk 75 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.0854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 167533 Z= 0.354 Angle : 0.732 18.219 242854 Z= 0.385 Chirality : 0.042 0.303 29658 Planarity : 0.007 0.142 18146 Dihedral : 22.669 179.418 65179 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.33 % Allowed : 12.65 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: 1.43 (0.08), residues: 10361 helix: 1.89 (0.08), residues: 4039 sheet: 0.10 (0.13), residues: 1500 loop : 0.57 (0.09), residues: 4822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRPCg 105 HIS 0.009 0.002 HISCh 342 PHE 0.022 0.002 PHELO 49 TYR 0.025 0.002 TYRLG 100 ARG 0.011 0.001 ARGCz 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20722 Ramachandran restraints generated. 10361 Oldfield, 0 Emsley, 10361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20722 Ramachandran restraints generated. 10361 Oldfield, 0 Emsley, 10361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1352 residues out of total 8941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 1147 time to evaluate : 9.198 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: CB 36 LYS cc_start: 0.9033 (ttpp) cc_final: 0.8626 (tmmt) REVERT: CB 277 ASN cc_start: 0.9041 (t0) cc_final: 0.8791 (t160) REVERT: CF 10 TYR cc_start: 0.8862 (t80) cc_final: 0.8617 (t80) REVERT: CH 303 GLN cc_start: 0.8111 (tp40) cc_final: 0.7726 (tp-100) REVERT: CH 307 ASP cc_start: 0.7966 (m-30) cc_final: 0.7717 (m-30) REVERT: CH 617 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6755 (tm-30) REVERT: CI 279 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.7070 (mtm-85) REVERT: CI 309 GLU cc_start: 0.8370 (tp30) cc_final: 0.7941 (tp30) REVERT: CI 310 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7607 (mp0) REVERT: CJ 381 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7732 (mm-40) REVERT: CL 33 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.7367 (mtp180) REVERT: CM 238 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7516 (mp0) REVERT: Lq 131 LYS cc_start: 0.8463 (mmtt) cc_final: 0.8239 (mmmt) REVERT: Cb 76 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.7639 (ttp-170) REVERT: Cd 12 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8886 (mm) REVERT: Cd 64 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7393 (tm-30) REVERT: Cg 135 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8453 (pt0) REVERT: Cg 197 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7705 (mt-10) REVERT: Ch 86 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7946 (mtp180) REVERT: Ch 177 ASP cc_start: 0.8197 (m-30) cc_final: 0.7971 (m-30) REVERT: Cz 95 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7906 (ttm170) REVERT: LB 245 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8604 (mtpt) REVERT: LC 100 MET cc_start: 0.9119 (ptm) cc_final: 0.8851 (ptp) REVERT: LD 50 ARG cc_start: 0.9368 (OUTLIER) cc_final: 0.8729 (ptm-80) REVERT: LD 192 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.7069 (mm-30) REVERT: LE 31 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7162 (mt-10) REVERT: LG 150 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8477 (mmtp) REVERT: LJ 52 ARG cc_start: 0.8462 (mtm180) cc_final: 0.8104 (mtp180) REVERT: LK 57 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.7830 (mmm160) REVERT: LL 23 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.7726 (tpp-160) REVERT: LL 146 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7019 (tm-30) REVERT: LO 89 MET cc_start: 0.9514 (mtt) cc_final: 0.9073 (mtt) REVERT: LT 89 ILE cc_start: 0.9281 (OUTLIER) cc_final: 0.9016 (pt) REVERT: LT 111 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7498 (mt-10) REVERT: LT 115 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8499 (mp) REVERT: LY 130 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8261 (ttpp) REVERT: LZ 5 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8570 (mttp) REVERT: Lh 112 ARG cc_start: 0.7943 (ttm110) cc_final: 0.7633 (ttm-80) REVERT: Lj 27 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9147 (tm) REVERT: Lp 3 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7954 (mtpt) outliers start: 205 outliers final: 118 residues processed: 1264 average time/residue: 2.5681 time to fit residues: 4529.3717 Evaluate side-chains 1277 residues out of total 8941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 1132 time to evaluate : 8.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CB residue 35 LYS Chi-restraints excluded: chain CB residue 115 GLU Chi-restraints excluded: chain CB residue 209 LEU Chi-restraints excluded: chain CB residue 238 SER Chi-restraints excluded: chain CB residue 301 LEU Chi-restraints excluded: chain CB residue 306 VAL Chi-restraints excluded: chain CF residue 108 ASP Chi-restraints excluded: chain CF residue 149 VAL Chi-restraints excluded: chain CF residue 233 GLU Chi-restraints excluded: chain CH residue 79 ASP Chi-restraints excluded: chain CH residue 85 TYR Chi-restraints excluded: chain CH residue 168 THR Chi-restraints excluded: chain CH residue 344 SER Chi-restraints excluded: chain CH residue 363 GLU Chi-restraints excluded: chain CH residue 364 VAL Chi-restraints excluded: chain CH residue 392 LYS Chi-restraints excluded: chain CH residue 610 THR Chi-restraints excluded: chain CH residue 617 GLU Chi-restraints excluded: chain CH residue 655 ILE Chi-restraints excluded: chain CI residue 198 PHE Chi-restraints excluded: chain CI residue 263 VAL Chi-restraints excluded: chain CI residue 279 ARG Chi-restraints excluded: chain CI residue 310 GLU Chi-restraints excluded: chain CI residue 332 LEU Chi-restraints excluded: chain CJ residue 222 VAL Chi-restraints excluded: chain CJ residue 364 SER Chi-restraints excluded: chain CJ residue 381 GLN Chi-restraints excluded: chain CJ residue 393 LYS Chi-restraints excluded: chain CJ residue 408 THR Chi-restraints excluded: chain CK residue 53 GLN Chi-restraints excluded: chain CK residue 66 LYS Chi-restraints excluded: chain CK residue 73 VAL Chi-restraints excluded: chain CK residue 98 THR Chi-restraints excluded: chain CK residue 185 THR Chi-restraints excluded: chain CL residue 33 ARG Chi-restraints excluded: chain CL residue 67 GLN Chi-restraints excluded: chain CM residue 111 LEU Chi-restraints excluded: chain CM residue 162 VAL Chi-restraints excluded: chain CM residue 187 ILE Chi-restraints excluded: chain CM residue 238 GLU Chi-restraints excluded: chain CN residue 51 THR Chi-restraints excluded: chain CN residue 75 THR Chi-restraints excluded: chain CN residue 91 ASP Chi-restraints excluded: chain CQ residue 64 VAL Chi-restraints excluded: chain Cb residue 28 SER Chi-restraints excluded: chain Cb residue 68 HIS Chi-restraints excluded: chain Cb residue 76 ARG Chi-restraints excluded: chain Cd residue 12 LEU Chi-restraints excluded: chain Cd residue 64 GLU Chi-restraints excluded: chain Cd residue 139 GLU Chi-restraints excluded: chain Cd residue 206 VAL Chi-restraints excluded: chain Cd residue 219 SER Chi-restraints excluded: chain Cd residue 278 SER Chi-restraints excluded: chain Ce residue 98 LEU Chi-restraints excluded: chain Ce residue 102 SER Chi-restraints excluded: chain Ce residue 349 LEU Chi-restraints excluded: chain Ce residue 397 LYS Chi-restraints excluded: chain Cf residue 16 LEU Chi-restraints excluded: chain Cf residue 166 ASP Chi-restraints excluded: chain Cf residue 280 GLU Chi-restraints excluded: chain Cf residue 306 LEU Chi-restraints excluded: chain Cg residue 19 THR Chi-restraints excluded: chain Cg residue 22 THR Chi-restraints excluded: chain Cg residue 71 THR Chi-restraints excluded: chain Cg residue 135 GLU Chi-restraints excluded: chain Ch residue 86 ARG Chi-restraints excluded: chain Ch residue 142 ILE Chi-restraints excluded: chain Ch residue 426 ASN Chi-restraints excluded: chain Cz residue 22 ASN Chi-restraints excluded: chain Cz residue 95 ARG Chi-restraints excluded: chain LA residue 199 THR Chi-restraints excluded: chain LB residue 245 LYS Chi-restraints excluded: chain LC residue 198 MET Chi-restraints excluded: chain LD residue 50 ARG Chi-restraints excluded: chain LD residue 51 LEU Chi-restraints excluded: chain LD residue 129 TYR Chi-restraints excluded: chain LD residue 188 ILE Chi-restraints excluded: chain LD residue 192 GLU Chi-restraints excluded: chain LD residue 242 LEU Chi-restraints excluded: chain LD residue 282 LEU Chi-restraints excluded: chain LE residue 6 THR Chi-restraints excluded: chain LE residue 31 GLU Chi-restraints excluded: chain LE residue 155 SER Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LF residue 90 VAL Chi-restraints excluded: chain LF residue 136 VAL Chi-restraints excluded: chain LG residue 150 LYS Chi-restraints excluded: chain LG residue 169 LEU Chi-restraints excluded: chain LG residue 246 GLN Chi-restraints excluded: chain LG residue 248 ARG Chi-restraints excluded: chain LH residue 56 SER Chi-restraints excluded: chain LH residue 85 VAL Chi-restraints excluded: chain LH residue 157 ILE Chi-restraints excluded: chain LH residue 203 ILE Chi-restraints excluded: chain LJ residue 45 THR Chi-restraints excluded: chain LJ residue 49 SER Chi-restraints excluded: chain LJ residue 100 THR Chi-restraints excluded: chain LK residue 57 ARG Chi-restraints excluded: chain LK residue 78 SER Chi-restraints excluded: chain LK residue 139 VAL Chi-restraints excluded: chain LK residue 151 ILE Chi-restraints excluded: chain LL residue 23 ARG Chi-restraints excluded: chain LL residue 63 VAL Chi-restraints excluded: chain LL residue 146 GLU Chi-restraints excluded: chain LM residue 9 THR Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LN residue 7 LEU Chi-restraints excluded: chain LN residue 35 VAL Chi-restraints excluded: chain LN residue 64 VAL Chi-restraints excluded: chain LO residue 196 SER Chi-restraints excluded: chain LP residue 109 THR Chi-restraints excluded: chain LP residue 169 SER Chi-restraints excluded: chain LR residue 29 VAL Chi-restraints excluded: chain LR residue 51 ILE Chi-restraints excluded: chain LR residue 133 LYS Chi-restraints excluded: chain LS residue 45 LEU Chi-restraints excluded: chain LS residue 90 MET Chi-restraints excluded: chain LT residue 72 VAL Chi-restraints excluded: chain LT residue 89 ILE Chi-restraints excluded: chain LT residue 93 ILE Chi-restraints excluded: chain LT residue 111 GLU Chi-restraints excluded: chain LT residue 115 LEU Chi-restraints excluded: chain LU residue 30 SER Chi-restraints excluded: chain LU residue 37 SER Chi-restraints excluded: chain LU residue 59 VAL Chi-restraints excluded: chain LX residue 37 THR Chi-restraints excluded: chain LX residue 83 GLU Chi-restraints excluded: chain LX residue 92 GLN Chi-restraints excluded: chain LY residue 78 VAL Chi-restraints excluded: chain LY residue 93 THR Chi-restraints excluded: chain LY residue 130 LYS Chi-restraints excluded: chain LZ residue 5 LYS Chi-restraints excluded: chain La residue 85 ASP Chi-restraints excluded: chain Lf residue 51 VAL Chi-restraints excluded: chain Lf residue 59 LYS Chi-restraints excluded: chain Lg residue 68 LYS Chi-restraints excluded: chain Li residue 67 ILE Chi-restraints excluded: chain Li residue 105 GLU Chi-restraints excluded: chain Lj residue 27 LEU Chi-restraints excluded: chain Lj residue 84 LYS Chi-restraints excluded: chain Ll residue 34 THR Chi-restraints excluded: chain Lp residue 3 LYS Chi-restraints excluded: chain Lp residue 56 SER Chi-restraints excluded: chain Lp residue 72 SER Chi-restraints excluded: chain Lp residue 73 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1368 random chunks: chunk 1276 optimal weight: 0.9980 chunk 149 optimal weight: 6.9990 chunk 754 optimal weight: 5.9990 chunk 966 optimal weight: 0.9980 chunk 748 optimal weight: 10.0000 chunk 1114 optimal weight: 0.7980 chunk 739 optimal weight: 3.9990 chunk 1318 optimal weight: 0.9990 chunk 825 optimal weight: 8.9990 chunk 803 optimal weight: 6.9990 chunk 608 optimal weight: 0.0670 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CF 118 ASN CH 345 GLN CH 362 GLN CH 399 ASN CH 633 GLN CI 267 GLN ** CI 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CL 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CM 25 GLN CM 99 ASN CM 165 GLN ** CM 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CQ 130 ASN Lq 97 GLN Cf 40 GLN Cg 31 ASN Cg 192 GLN Cz 56 GLN ** LA 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 244 HIS LB 379 GLN LC 118 GLN LD 17 GLN LD 39 GLN LE 53 GLN LF 10 ASN LJ 16 GLN LJ 63 ASN ** LK 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LK 70 GLN LM 106 GLN LP 75 GLN ** LP 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LT 82 HIS LX 81 ASN LY 127 GLN Ld 49 GLN Ld 70 GLN Lg 30 GLN Lh 33 GLN Lk 33 GLN Lk 75 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 167533 Z= 0.139 Angle : 0.611 17.027 242854 Z= 0.332 Chirality : 0.035 0.280 29658 Planarity : 0.006 0.127 18146 Dihedral : 22.585 179.686 65179 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.53 % Allowed : 13.56 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: 1.76 (0.08), residues: 10361 helix: 2.24 (0.08), residues: 4042 sheet: 0.25 (0.13), residues: 1460 loop : 0.66 (0.09), residues: 4859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRPCg 105 HIS 0.008 0.001 HISCd 252 PHE 0.019 0.001 PHECH 90 TYR 0.017 0.001 TYRLH 129 ARG 0.011 0.000 ARGCz 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20722 Ramachandran restraints generated. 10361 Oldfield, 0 Emsley, 10361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20722 Ramachandran restraints generated. 10361 Oldfield, 0 Emsley, 10361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1276 residues out of total 8941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1142 time to evaluate : 9.208 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: CB 36 LYS cc_start: 0.9044 (ttpp) cc_final: 0.8620 (tmmt) REVERT: CF 10 TYR cc_start: 0.8815 (t80) cc_final: 0.8582 (t80) REVERT: CF 121 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8275 (tp40) REVERT: CH 303 GLN cc_start: 0.8049 (tp40) cc_final: 0.7616 (tp-100) REVERT: CH 307 ASP cc_start: 0.7878 (m-30) cc_final: 0.7640 (m-30) REVERT: CH 591 ARG cc_start: 0.8189 (mmm-85) cc_final: 0.7910 (mtm-85) REVERT: CH 617 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6710 (tm-30) REVERT: CI 279 ARG cc_start: 0.7274 (OUTLIER) cc_final: 0.6880 (mtm-85) REVERT: CI 310 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7631 (mp0) REVERT: CJ 381 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7669 (mm-40) REVERT: CM 248 MET cc_start: 0.9344 (mtp) cc_final: 0.9058 (mtp) REVERT: Lq 131 LYS cc_start: 0.8453 (mmtt) cc_final: 0.8229 (mmmt) REVERT: Cd 12 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8870 (mm) REVERT: Cd 297 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8203 (ttm) REVERT: Cd 425 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7582 (mtp180) REVERT: Ce 331 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.6927 (mp0) REVERT: Ch 86 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.7928 (mtp180) REVERT: Ch 177 ASP cc_start: 0.8235 (m-30) cc_final: 0.8018 (m-30) REVERT: LE 31 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.7139 (mt-10) REVERT: LG 150 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8452 (mmtp) REVERT: LJ 52 ARG cc_start: 0.8430 (mtm180) cc_final: 0.8096 (mtp180) REVERT: LL 23 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7754 (tpp-160) REVERT: LL 146 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7060 (tm-30) REVERT: LT 115 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8443 (mp) REVERT: LY 130 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8231 (ttpp) REVERT: Lh 112 ARG cc_start: 0.7884 (ttm110) cc_final: 0.7566 (ttm-80) REVERT: Lj 27 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9136 (tm) outliers start: 134 outliers final: 72 residues processed: 1215 average time/residue: 2.6132 time to fit residues: 4463.8515 Evaluate side-chains 1202 residues out of total 8941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1113 time to evaluate : 8.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CB residue 35 LYS Chi-restraints excluded: chain CB residue 115 GLU Chi-restraints excluded: chain CB residue 209 LEU Chi-restraints excluded: chain CB residue 306 VAL Chi-restraints excluded: chain CF residue 121 GLN Chi-restraints excluded: chain CF residue 149 VAL Chi-restraints excluded: chain CH residue 85 TYR Chi-restraints excluded: chain CH residue 168 THR Chi-restraints excluded: chain CH residue 363 GLU Chi-restraints excluded: chain CH residue 364 VAL Chi-restraints excluded: chain CH residue 392 LYS Chi-restraints excluded: chain CH residue 469 GLU Chi-restraints excluded: chain CH residue 617 GLU Chi-restraints excluded: chain CI residue 198 PHE Chi-restraints excluded: chain CI residue 263 VAL Chi-restraints excluded: chain CI residue 279 ARG Chi-restraints excluded: chain CI residue 310 GLU Chi-restraints excluded: chain CJ residue 222 VAL Chi-restraints excluded: chain CJ residue 364 SER Chi-restraints excluded: chain CJ residue 381 GLN Chi-restraints excluded: chain CJ residue 393 LYS Chi-restraints excluded: chain CJ residue 408 THR Chi-restraints excluded: chain CK residue 66 LYS Chi-restraints excluded: chain CK residue 73 VAL Chi-restraints excluded: chain CK residue 98 THR Chi-restraints excluded: chain CK residue 185 THR Chi-restraints excluded: chain CL residue 67 GLN Chi-restraints excluded: chain CM residue 111 LEU Chi-restraints excluded: chain CM residue 162 VAL Chi-restraints excluded: chain CM residue 187 ILE Chi-restraints excluded: chain CN residue 51 THR Chi-restraints excluded: chain CN residue 75 THR Chi-restraints excluded: chain CQ residue 64 VAL Chi-restraints excluded: chain CQ residue 173 SER Chi-restraints excluded: chain Cb residue 28 SER Chi-restraints excluded: chain Cb residue 68 HIS Chi-restraints excluded: chain Cd residue 12 LEU Chi-restraints excluded: chain Cd residue 297 MET Chi-restraints excluded: chain Cd residue 425 ARG Chi-restraints excluded: chain Ce residue 331 GLU Chi-restraints excluded: chain Ce residue 349 LEU Chi-restraints excluded: chain Ce residue 397 LYS Chi-restraints excluded: chain Cf residue 16 LEU Chi-restraints excluded: chain Cf residue 166 ASP Chi-restraints excluded: chain Cg residue 19 THR Chi-restraints excluded: chain Cg residue 22 THR Chi-restraints excluded: chain Cg residue 71 THR Chi-restraints excluded: chain Ch residue 86 ARG Chi-restraints excluded: chain Ch residue 142 ILE Chi-restraints excluded: chain Ch residue 426 ASN Chi-restraints excluded: chain Cz residue 72 LYS Chi-restraints excluded: chain LC residue 198 MET Chi-restraints excluded: chain LD residue 282 LEU Chi-restraints excluded: chain LE residue 31 GLU Chi-restraints excluded: chain LE residue 155 SER Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LF residue 90 VAL Chi-restraints excluded: chain LG residue 150 LYS Chi-restraints excluded: chain LG residue 169 LEU Chi-restraints excluded: chain LG residue 246 GLN Chi-restraints excluded: chain LH residue 85 VAL Chi-restraints excluded: chain LJ residue 45 THR Chi-restraints excluded: chain LJ residue 49 SER Chi-restraints excluded: chain LL residue 23 ARG Chi-restraints excluded: chain LL residue 146 GLU Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LM residue 71 LYS Chi-restraints excluded: chain LN residue 64 VAL Chi-restraints excluded: chain LP residue 109 THR Chi-restraints excluded: chain LP residue 169 SER Chi-restraints excluded: chain LR residue 51 ILE Chi-restraints excluded: chain LR residue 133 LYS Chi-restraints excluded: chain LS residue 45 LEU Chi-restraints excluded: chain LS residue 90 MET Chi-restraints excluded: chain LT residue 72 VAL Chi-restraints excluded: chain LT residue 115 LEU Chi-restraints excluded: chain LU residue 30 SER Chi-restraints excluded: chain LU residue 59 VAL Chi-restraints excluded: chain LX residue 37 THR Chi-restraints excluded: chain LX residue 83 GLU Chi-restraints excluded: chain LY residue 78 VAL Chi-restraints excluded: chain LY residue 88 LYS Chi-restraints excluded: chain LY residue 93 THR Chi-restraints excluded: chain LY residue 130 LYS Chi-restraints excluded: chain La residue 85 ASP Chi-restraints excluded: chain Li residue 105 GLU Chi-restraints excluded: chain Lj residue 27 LEU Chi-restraints excluded: chain Lj residue 84 LYS Chi-restraints excluded: chain Ll residue 34 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1368 random chunks: chunk 815 optimal weight: 6.9990 chunk 526 optimal weight: 3.9990 chunk 787 optimal weight: 0.5980 chunk 397 optimal weight: 0.0030 chunk 259 optimal weight: 6.9990 chunk 255 optimal weight: 10.0000 chunk 838 optimal weight: 0.9990 chunk 898 optimal weight: 3.9990 chunk 651 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 1036 optimal weight: 4.9990 overall best weight: 1.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CB 79 GLN CF 118 ASN CH 362 GLN CH 399 ASN CI 267 GLN ** CI 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CL 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CM 99 ASN CM 165 GLN ** CM 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CN 82 GLN CQ 130 ASN Lq 97 GLN Cf 40 GLN Cg 31 ASN Cg 98 GLN Cg 133 GLN Cg 192 GLN ** LA 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 244 HIS LB 379 GLN LC 118 GLN LD 17 GLN LD 39 GLN LE 53 GLN LE 172 ASN LF 10 ASN LH 72 GLN LH 201 GLN ** LK 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LK 70 GLN LM 106 GLN LP 75 GLN LT 82 HIS LX 81 ASN LY 127 GLN Ld 49 GLN Lg 30 GLN Lh 33 GLN Lk 33 GLN Lk 41 GLN Lk 75 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 167533 Z= 0.197 Angle : 0.629 17.367 242854 Z= 0.339 Chirality : 0.037 0.275 29658 Planarity : 0.006 0.131 18146 Dihedral : 22.537 178.701 65177 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.50 % Allowed : 13.82 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: 1.77 (0.08), residues: 10361 helix: 2.27 (0.08), residues: 4030 sheet: 0.26 (0.13), residues: 1468 loop : 0.67 (0.09), residues: 4863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRPCg 105 HIS 0.011 0.001 HISLT 54 PHE 0.017 0.001 PHECH 90 TYR 0.019 0.002 TYRLG 100 ARG 0.014 0.000 ARGCz 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20722 Ramachandran restraints generated. 10361 Oldfield, 0 Emsley, 10361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20722 Ramachandran restraints generated. 10361 Oldfield, 0 Emsley, 10361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1255 residues out of total 8941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 1124 time to evaluate : 9.134 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: CB 36 LYS cc_start: 0.9034 (ttpp) cc_final: 0.8650 (tmmt) REVERT: CF 10 TYR cc_start: 0.8842 (t80) cc_final: 0.8580 (t80) REVERT: CF 121 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8218 (tp40) REVERT: CH 303 GLN cc_start: 0.8084 (tp40) cc_final: 0.7617 (tp-100) REVERT: CH 307 ASP cc_start: 0.7861 (m-30) cc_final: 0.7620 (m-30) REVERT: CH 591 ARG cc_start: 0.8195 (mmm-85) cc_final: 0.7922 (mtm-85) REVERT: CH 617 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6738 (tm-30) REVERT: CI 279 ARG cc_start: 0.7292 (OUTLIER) cc_final: 0.6863 (mtm-85) REVERT: CI 310 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7684 (mp0) REVERT: CJ 381 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7703 (mm-40) REVERT: Lq 131 LYS cc_start: 0.8454 (mmtt) cc_final: 0.8228 (mmmt) REVERT: Cd 12 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8850 (mm) REVERT: Ch 86 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7925 (mtp180) REVERT: LD 192 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7084 (mm-30) REVERT: LE 31 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7146 (mt-10) REVERT: LJ 52 ARG cc_start: 0.8442 (mtm180) cc_final: 0.8105 (mtp180) REVERT: LL 23 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7748 (tpp-160) REVERT: LL 146 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7031 (tm-30) REVERT: LT 115 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8426 (mp) REVERT: LY 130 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8232 (ttpp) REVERT: Lh 112 ARG cc_start: 0.7900 (ttm110) cc_final: 0.7579 (ttm-80) REVERT: Lj 27 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9144 (tm) REVERT: Lp 3 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7978 (mtpt) outliers start: 131 outliers final: 80 residues processed: 1206 average time/residue: 2.6247 time to fit residues: 4414.0388 Evaluate side-chains 1217 residues out of total 8941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 1122 time to evaluate : 8.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CB residue 35 LYS Chi-restraints excluded: chain CB residue 115 GLU Chi-restraints excluded: chain CB residue 209 LEU Chi-restraints excluded: chain CF residue 121 GLN Chi-restraints excluded: chain CF residue 149 VAL Chi-restraints excluded: chain CH residue 85 TYR Chi-restraints excluded: chain CH residue 168 THR Chi-restraints excluded: chain CH residue 344 SER Chi-restraints excluded: chain CH residue 363 GLU Chi-restraints excluded: chain CH residue 364 VAL Chi-restraints excluded: chain CH residue 392 LYS Chi-restraints excluded: chain CH residue 469 GLU Chi-restraints excluded: chain CH residue 617 GLU Chi-restraints excluded: chain CI residue 198 PHE Chi-restraints excluded: chain CI residue 263 VAL Chi-restraints excluded: chain CI residue 279 ARG Chi-restraints excluded: chain CI residue 310 GLU Chi-restraints excluded: chain CJ residue 222 VAL Chi-restraints excluded: chain CJ residue 364 SER Chi-restraints excluded: chain CJ residue 381 GLN Chi-restraints excluded: chain CJ residue 393 LYS Chi-restraints excluded: chain CJ residue 408 THR Chi-restraints excluded: chain CK residue 66 LYS Chi-restraints excluded: chain CK residue 73 VAL Chi-restraints excluded: chain CK residue 98 THR Chi-restraints excluded: chain CK residue 185 THR Chi-restraints excluded: chain CL residue 19 ARG Chi-restraints excluded: chain CL residue 67 GLN Chi-restraints excluded: chain CM residue 111 LEU Chi-restraints excluded: chain CM residue 162 VAL Chi-restraints excluded: chain CM residue 187 ILE Chi-restraints excluded: chain CN residue 51 THR Chi-restraints excluded: chain CN residue 75 THR Chi-restraints excluded: chain CQ residue 63 MET Chi-restraints excluded: chain CQ residue 64 VAL Chi-restraints excluded: chain CQ residue 173 SER Chi-restraints excluded: chain Cb residue 28 SER Chi-restraints excluded: chain Cb residue 68 HIS Chi-restraints excluded: chain Cd residue 12 LEU Chi-restraints excluded: chain Ce residue 349 LEU Chi-restraints excluded: chain Ce residue 397 LYS Chi-restraints excluded: chain Cf residue 16 LEU Chi-restraints excluded: chain Cf residue 166 ASP Chi-restraints excluded: chain Cg residue 19 THR Chi-restraints excluded: chain Cg residue 22 THR Chi-restraints excluded: chain Cg residue 71 THR Chi-restraints excluded: chain Ch residue 86 ARG Chi-restraints excluded: chain Ch residue 142 ILE Chi-restraints excluded: chain Ch residue 426 ASN Chi-restraints excluded: chain Cz residue 22 ASN Chi-restraints excluded: chain Cz residue 72 LYS Chi-restraints excluded: chain Cz residue 86 ARG Chi-restraints excluded: chain LC residue 198 MET Chi-restraints excluded: chain LD residue 192 GLU Chi-restraints excluded: chain LD residue 256 ARG Chi-restraints excluded: chain LD residue 282 LEU Chi-restraints excluded: chain LE residue 31 GLU Chi-restraints excluded: chain LE residue 155 SER Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LF residue 90 VAL Chi-restraints excluded: chain LG residue 169 LEU Chi-restraints excluded: chain LG residue 246 GLN Chi-restraints excluded: chain LH residue 85 VAL Chi-restraints excluded: chain LH residue 157 ILE Chi-restraints excluded: chain LJ residue 45 THR Chi-restraints excluded: chain LJ residue 49 SER Chi-restraints excluded: chain LJ residue 100 THR Chi-restraints excluded: chain LL residue 23 ARG Chi-restraints excluded: chain LL residue 146 GLU Chi-restraints excluded: chain LL residue 177 ILE Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LM residue 71 LYS Chi-restraints excluded: chain LN residue 64 VAL Chi-restraints excluded: chain LP residue 109 THR Chi-restraints excluded: chain LP residue 169 SER Chi-restraints excluded: chain LR residue 51 ILE Chi-restraints excluded: chain LS residue 45 LEU Chi-restraints excluded: chain LS residue 90 MET Chi-restraints excluded: chain LT residue 72 VAL Chi-restraints excluded: chain LT residue 115 LEU Chi-restraints excluded: chain LU residue 30 SER Chi-restraints excluded: chain LU residue 59 VAL Chi-restraints excluded: chain LX residue 37 THR Chi-restraints excluded: chain LX residue 83 GLU Chi-restraints excluded: chain LX residue 92 GLN Chi-restraints excluded: chain LY residue 78 VAL Chi-restraints excluded: chain LY residue 88 LYS Chi-restraints excluded: chain LY residue 93 THR Chi-restraints excluded: chain LY residue 130 LYS Chi-restraints excluded: chain La residue 85 ASP Chi-restraints excluded: chain Li residue 105 GLU Chi-restraints excluded: chain Lj residue 27 LEU Chi-restraints excluded: chain Lj residue 84 LYS Chi-restraints excluded: chain Ll residue 34 THR Chi-restraints excluded: chain Lp residue 3 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1368 random chunks: chunk 1199 optimal weight: 2.9990 chunk 1263 optimal weight: 0.9980 chunk 1152 optimal weight: 0.8980 chunk 1228 optimal weight: 2.9990 chunk 1262 optimal weight: 2.9990 chunk 739 optimal weight: 0.9980 chunk 535 optimal weight: 4.9990 chunk 964 optimal weight: 1.9990 chunk 377 optimal weight: 7.9990 chunk 1110 optimal weight: 0.9990 chunk 1162 optimal weight: 10.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CF 118 ASN CH 362 GLN CH 399 ASN CI 267 GLN ** CI 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CL 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CM 99 ASN CM 165 GLN ** CM 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CQ 130 ASN Lq 97 GLN Cf 40 GLN Cg 31 ASN Cg 192 GLN ** LA 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 244 HIS LB 379 GLN LC 118 GLN LD 17 GLN LD 39 GLN LE 53 GLN LE 172 ASN LF 10 ASN LH 201 GLN ** LK 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LK 70 GLN LM 106 GLN LP 75 GLN ** LP 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LX 81 ASN LY 127 GLN Ld 49 GLN Ld 70 GLN Lg 30 GLN Lh 33 GLN Lk 33 GLN Lk 75 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.0875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 167533 Z= 0.163 Angle : 0.621 17.371 242854 Z= 0.336 Chirality : 0.036 0.273 29658 Planarity : 0.006 0.129 18146 Dihedral : 22.543 178.885 65177 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.31 % Allowed : 14.11 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: 1.80 (0.08), residues: 10361 helix: 2.30 (0.08), residues: 4029 sheet: 0.26 (0.13), residues: 1453 loop : 0.68 (0.09), residues: 4879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRPCg 105 HIS 0.009 0.001 HISLT 54 PHE 0.020 0.001 PHELJ 58 TYR 0.018 0.001 TYRLO 55 ARG 0.021 0.000 ARGCz 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20722 Ramachandran restraints generated. 10361 Oldfield, 0 Emsley, 10361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20722 Ramachandran restraints generated. 10361 Oldfield, 0 Emsley, 10361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1243 residues out of total 8941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 1128 time to evaluate : 9.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CB 36 LYS cc_start: 0.9030 (ttpp) cc_final: 0.8643 (tmmt) REVERT: CF 10 TYR cc_start: 0.8843 (t80) cc_final: 0.8581 (t80) REVERT: CF 121 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.8297 (tp40) REVERT: CH 303 GLN cc_start: 0.8068 (tp40) cc_final: 0.7592 (tp-100) REVERT: CH 307 ASP cc_start: 0.7850 (m-30) cc_final: 0.7608 (m-30) REVERT: CH 591 ARG cc_start: 0.8189 (mmm-85) cc_final: 0.7919 (mtm-85) REVERT: CH 617 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6735 (tm-30) REVERT: CI 279 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.6862 (mtm-85) REVERT: CI 309 GLU cc_start: 0.8316 (tp30) cc_final: 0.7904 (tp30) REVERT: CI 310 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7674 (mp0) REVERT: CJ 381 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7700 (mm-40) REVERT: CL 41 LYS cc_start: 0.7606 (mmpt) cc_final: 0.7350 (mmpt) REVERT: CM 248 MET cc_start: 0.9303 (mtp) cc_final: 0.8972 (mtp) REVERT: Lq 131 LYS cc_start: 0.8454 (mmtt) cc_final: 0.8228 (mmmt) REVERT: Cd 12 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8838 (mm) REVERT: Ce 310 ARG cc_start: 0.8366 (ttm110) cc_final: 0.8139 (ttm170) REVERT: Ce 331 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6871 (mp0) REVERT: Cg 154 GLU cc_start: 0.7762 (mp0) cc_final: 0.6991 (mp0) REVERT: Ch 86 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.7923 (mtp180) REVERT: Cz 95 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.7908 (ttm170) REVERT: LE 31 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7141 (mt-10) REVERT: LJ 52 ARG cc_start: 0.8439 (mtm180) cc_final: 0.8106 (mtp180) REVERT: LL 23 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.7733 (tpp-160) REVERT: LL 135 LYS cc_start: 0.8394 (ptpt) cc_final: 0.8066 (ptpp) REVERT: LL 146 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7029 (tm-30) REVERT: LT 115 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8401 (mp) REVERT: LY 130 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8229 (ttpp) REVERT: Lh 112 ARG cc_start: 0.7891 (ttm110) cc_final: 0.7570 (ttm-80) REVERT: Lj 27 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9143 (tm) REVERT: Lp 3 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7977 (mtpt) outliers start: 115 outliers final: 82 residues processed: 1193 average time/residue: 2.5444 time to fit residues: 4233.0757 Evaluate side-chains 1219 residues out of total 8941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 1121 time to evaluate : 8.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CB residue 35 LYS Chi-restraints excluded: chain CB residue 115 GLU Chi-restraints excluded: chain CB residue 209 LEU Chi-restraints excluded: chain CF residue 121 GLN Chi-restraints excluded: chain CF residue 149 VAL Chi-restraints excluded: chain CH residue 79 ASP Chi-restraints excluded: chain CH residue 85 TYR Chi-restraints excluded: chain CH residue 140 LYS Chi-restraints excluded: chain CH residue 168 THR Chi-restraints excluded: chain CH residue 344 SER Chi-restraints excluded: chain CH residue 363 GLU Chi-restraints excluded: chain CH residue 364 VAL Chi-restraints excluded: chain CH residue 392 LYS Chi-restraints excluded: chain CH residue 469 GLU Chi-restraints excluded: chain CH residue 617 GLU Chi-restraints excluded: chain CI residue 198 PHE Chi-restraints excluded: chain CI residue 263 VAL Chi-restraints excluded: chain CI residue 279 ARG Chi-restraints excluded: chain CI residue 310 GLU Chi-restraints excluded: chain CJ residue 222 VAL Chi-restraints excluded: chain CJ residue 364 SER Chi-restraints excluded: chain CJ residue 381 GLN Chi-restraints excluded: chain CJ residue 393 LYS Chi-restraints excluded: chain CJ residue 408 THR Chi-restraints excluded: chain CK residue 66 LYS Chi-restraints excluded: chain CK residue 73 VAL Chi-restraints excluded: chain CK residue 98 THR Chi-restraints excluded: chain CK residue 185 THR Chi-restraints excluded: chain CL residue 67 GLN Chi-restraints excluded: chain CM residue 111 LEU Chi-restraints excluded: chain CM residue 162 VAL Chi-restraints excluded: chain CM residue 187 ILE Chi-restraints excluded: chain CN residue 51 THR Chi-restraints excluded: chain CN residue 75 THR Chi-restraints excluded: chain CQ residue 63 MET Chi-restraints excluded: chain CQ residue 64 VAL Chi-restraints excluded: chain CQ residue 173 SER Chi-restraints excluded: chain Cb residue 28 SER Chi-restraints excluded: chain Cb residue 68 HIS Chi-restraints excluded: chain Cd residue 12 LEU Chi-restraints excluded: chain Ce residue 331 GLU Chi-restraints excluded: chain Ce residue 349 LEU Chi-restraints excluded: chain Ce residue 397 LYS Chi-restraints excluded: chain Cf residue 16 LEU Chi-restraints excluded: chain Cf residue 166 ASP Chi-restraints excluded: chain Cg residue 19 THR Chi-restraints excluded: chain Cg residue 22 THR Chi-restraints excluded: chain Cg residue 71 THR Chi-restraints excluded: chain Ch residue 86 ARG Chi-restraints excluded: chain Ch residue 142 ILE Chi-restraints excluded: chain Ch residue 426 ASN Chi-restraints excluded: chain Cz residue 72 LYS Chi-restraints excluded: chain Cz residue 95 ARG Chi-restraints excluded: chain LC residue 198 MET Chi-restraints excluded: chain LD residue 282 LEU Chi-restraints excluded: chain LE residue 31 GLU Chi-restraints excluded: chain LE residue 155 SER Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LF residue 90 VAL Chi-restraints excluded: chain LG residue 169 LEU Chi-restraints excluded: chain LG residue 246 GLN Chi-restraints excluded: chain LH residue 85 VAL Chi-restraints excluded: chain LH residue 157 ILE Chi-restraints excluded: chain LJ residue 45 THR Chi-restraints excluded: chain LJ residue 49 SER Chi-restraints excluded: chain LJ residue 100 THR Chi-restraints excluded: chain LK residue 78 SER Chi-restraints excluded: chain LK residue 151 ILE Chi-restraints excluded: chain LL residue 23 ARG Chi-restraints excluded: chain LL residue 146 GLU Chi-restraints excluded: chain LL residue 148 THR Chi-restraints excluded: chain LL residue 177 ILE Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LM residue 71 LYS Chi-restraints excluded: chain LN residue 64 VAL Chi-restraints excluded: chain LP residue 109 THR Chi-restraints excluded: chain LP residue 169 SER Chi-restraints excluded: chain LR residue 51 ILE Chi-restraints excluded: chain LS residue 45 LEU Chi-restraints excluded: chain LS residue 90 MET Chi-restraints excluded: chain LT residue 72 VAL Chi-restraints excluded: chain LT residue 115 LEU Chi-restraints excluded: chain LU residue 30 SER Chi-restraints excluded: chain LU residue 59 VAL Chi-restraints excluded: chain LX residue 37 THR Chi-restraints excluded: chain LX residue 83 GLU Chi-restraints excluded: chain LX residue 92 GLN Chi-restraints excluded: chain LY residue 78 VAL Chi-restraints excluded: chain LY residue 88 LYS Chi-restraints excluded: chain LY residue 93 THR Chi-restraints excluded: chain LY residue 130 LYS Chi-restraints excluded: chain La residue 85 ASP Chi-restraints excluded: chain Lf residue 22 ARG Chi-restraints excluded: chain Li residue 105 GLU Chi-restraints excluded: chain Lj residue 27 LEU Chi-restraints excluded: chain Lj residue 84 LYS Chi-restraints excluded: chain Ll residue 34 THR Chi-restraints excluded: chain Lp residue 3 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1368 random chunks: chunk 1224 optimal weight: 10.0000 chunk 806 optimal weight: 10.0000 chunk 1299 optimal weight: 0.9990 chunk 793 optimal weight: 5.9990 chunk 616 optimal weight: 5.9990 chunk 903 optimal weight: 0.6980 chunk 1362 optimal weight: 4.9990 chunk 1254 optimal weight: 1.9990 chunk 1085 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 838 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CF 118 ASN CH 362 GLN CH 399 ASN CH 459 GLN CI 267 GLN ** CI 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CL 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CM 99 ASN CM 165 GLN ** CM 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CQ 130 ASN Lq 97 GLN Cf 40 GLN Cg 31 ASN Cg 49 GLN Cg 98 GLN Cg 133 GLN Cg 192 GLN ** LA 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 244 HIS LB 379 GLN LC 118 GLN LD 17 GLN LD 39 GLN LE 53 GLN LE 172 ASN LF 10 ASN LH 201 GLN ** LK 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LK 70 GLN LM 106 GLN LP 75 GLN LU 95 GLN ** LX 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LY 127 GLN Ld 49 GLN Ld 70 GLN Lg 30 GLN Lh 33 GLN Lk 33 GLN Lk 75 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 167533 Z= 0.198 Angle : 0.633 17.424 242854 Z= 0.341 Chirality : 0.037 0.276 29658 Planarity : 0.006 0.130 18146 Dihedral : 22.512 178.775 65177 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.30 % Allowed : 14.13 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: 1.79 (0.08), residues: 10361 helix: 2.27 (0.08), residues: 4022 sheet: 0.25 (0.13), residues: 1470 loop : 0.69 (0.09), residues: 4869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRPCg 105 HIS 0.014 0.001 HISLT 54 PHE 0.016 0.001 PHECH 90 TYR 0.019 0.002 TYRLS 43 ARG 0.019 0.000 ARGCz 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20722 Ramachandran restraints generated. 10361 Oldfield, 0 Emsley, 10361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20722 Ramachandran restraints generated. 10361 Oldfield, 0 Emsley, 10361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1240 residues out of total 8941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 1126 time to evaluate : 9.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CB 36 LYS cc_start: 0.9023 (ttpp) cc_final: 0.8627 (tmmt) REVERT: CF 10 TYR cc_start: 0.8858 (t80) cc_final: 0.8616 (t80) REVERT: CF 121 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8303 (tp40) REVERT: CH 303 GLN cc_start: 0.8086 (tp40) cc_final: 0.7696 (tp-100) REVERT: CH 591 ARG cc_start: 0.8190 (mmm-85) cc_final: 0.7917 (mtm-85) REVERT: CH 617 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6744 (tm-30) REVERT: CI 279 ARG cc_start: 0.7295 (OUTLIER) cc_final: 0.6862 (ttm-80) REVERT: CI 310 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7617 (mp0) REVERT: CJ 381 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7647 (mm-40) REVERT: CN 140 GLN cc_start: 0.8574 (tp40) cc_final: 0.8309 (tp40) REVERT: Lq 131 LYS cc_start: 0.8454 (mmtt) cc_final: 0.8225 (mmmt) REVERT: Cd 12 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8847 (mm) REVERT: Ch 86 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7897 (mtp180) REVERT: Cz 95 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.7953 (ttm170) REVERT: LD 192 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7042 (mm-30) REVERT: LE 31 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7141 (mt-10) REVERT: LF 36 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8342 (tm) REVERT: LJ 52 ARG cc_start: 0.8444 (mtm180) cc_final: 0.8106 (mtp180) REVERT: LL 23 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7759 (tpp-160) REVERT: LL 146 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7026 (tm-30) REVERT: LT 115 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8509 (mp) REVERT: LU 95 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.7841 (mt0) REVERT: Lh 112 ARG cc_start: 0.7903 (ttm110) cc_final: 0.7577 (ttm-80) REVERT: Lj 27 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9141 (tm) REVERT: Lp 3 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7965 (mtpt) outliers start: 114 outliers final: 77 residues processed: 1193 average time/residue: 2.5232 time to fit residues: 4210.1439 Evaluate side-chains 1213 residues out of total 8941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 1119 time to evaluate : 8.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CB residue 35 LYS Chi-restraints excluded: chain CB residue 115 GLU Chi-restraints excluded: chain CB residue 209 LEU Chi-restraints excluded: chain CF residue 121 GLN Chi-restraints excluded: chain CF residue 149 VAL Chi-restraints excluded: chain CH residue 79 ASP Chi-restraints excluded: chain CH residue 85 TYR Chi-restraints excluded: chain CH residue 168 THR Chi-restraints excluded: chain CH residue 344 SER Chi-restraints excluded: chain CH residue 363 GLU Chi-restraints excluded: chain CH residue 364 VAL Chi-restraints excluded: chain CH residue 469 GLU Chi-restraints excluded: chain CH residue 617 GLU Chi-restraints excluded: chain CI residue 198 PHE Chi-restraints excluded: chain CI residue 263 VAL Chi-restraints excluded: chain CI residue 279 ARG Chi-restraints excluded: chain CI residue 310 GLU Chi-restraints excluded: chain CJ residue 222 VAL Chi-restraints excluded: chain CJ residue 364 SER Chi-restraints excluded: chain CJ residue 381 GLN Chi-restraints excluded: chain CJ residue 393 LYS Chi-restraints excluded: chain CJ residue 408 THR Chi-restraints excluded: chain CK residue 66 LYS Chi-restraints excluded: chain CK residue 73 VAL Chi-restraints excluded: chain CK residue 98 THR Chi-restraints excluded: chain CK residue 185 THR Chi-restraints excluded: chain CL residue 19 ARG Chi-restraints excluded: chain CL residue 67 GLN Chi-restraints excluded: chain CM residue 162 VAL Chi-restraints excluded: chain CM residue 187 ILE Chi-restraints excluded: chain CN residue 51 THR Chi-restraints excluded: chain CN residue 75 THR Chi-restraints excluded: chain CQ residue 64 VAL Chi-restraints excluded: chain CQ residue 173 SER Chi-restraints excluded: chain Cb residue 28 SER Chi-restraints excluded: chain Cb residue 68 HIS Chi-restraints excluded: chain Cd residue 12 LEU Chi-restraints excluded: chain Ce residue 98 LEU Chi-restraints excluded: chain Ce residue 349 LEU Chi-restraints excluded: chain Ce residue 397 LYS Chi-restraints excluded: chain Cf residue 16 LEU Chi-restraints excluded: chain Cf residue 166 ASP Chi-restraints excluded: chain Cg residue 19 THR Chi-restraints excluded: chain Cg residue 71 THR Chi-restraints excluded: chain Ch residue 86 ARG Chi-restraints excluded: chain Ch residue 142 ILE Chi-restraints excluded: chain Ch residue 426 ASN Chi-restraints excluded: chain Cz residue 95 ARG Chi-restraints excluded: chain LA residue 114 SER Chi-restraints excluded: chain LC residue 198 MET Chi-restraints excluded: chain LD residue 192 GLU Chi-restraints excluded: chain LD residue 256 ARG Chi-restraints excluded: chain LD residue 282 LEU Chi-restraints excluded: chain LE residue 31 GLU Chi-restraints excluded: chain LE residue 155 SER Chi-restraints excluded: chain LF residue 36 LEU Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LF residue 90 VAL Chi-restraints excluded: chain LG residue 169 LEU Chi-restraints excluded: chain LG residue 246 GLN Chi-restraints excluded: chain LH residue 85 VAL Chi-restraints excluded: chain LH residue 157 ILE Chi-restraints excluded: chain LJ residue 45 THR Chi-restraints excluded: chain LJ residue 49 SER Chi-restraints excluded: chain LJ residue 100 THR Chi-restraints excluded: chain LK residue 78 SER Chi-restraints excluded: chain LK residue 151 ILE Chi-restraints excluded: chain LL residue 23 ARG Chi-restraints excluded: chain LL residue 146 GLU Chi-restraints excluded: chain LL residue 148 THR Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LN residue 64 VAL Chi-restraints excluded: chain LP residue 109 THR Chi-restraints excluded: chain LP residue 169 SER Chi-restraints excluded: chain LR residue 51 ILE Chi-restraints excluded: chain LS residue 45 LEU Chi-restraints excluded: chain LS residue 90 MET Chi-restraints excluded: chain LT residue 72 VAL Chi-restraints excluded: chain LT residue 115 LEU Chi-restraints excluded: chain LU residue 30 SER Chi-restraints excluded: chain LU residue 59 VAL Chi-restraints excluded: chain LU residue 95 GLN Chi-restraints excluded: chain LX residue 37 THR Chi-restraints excluded: chain LX residue 83 GLU Chi-restraints excluded: chain LY residue 78 VAL Chi-restraints excluded: chain LY residue 93 THR Chi-restraints excluded: chain LY residue 130 LYS Chi-restraints excluded: chain La residue 85 ASP Chi-restraints excluded: chain Lf residue 22 ARG Chi-restraints excluded: chain Li residue 105 GLU Chi-restraints excluded: chain Lj residue 27 LEU Chi-restraints excluded: chain Lj residue 84 LYS Chi-restraints excluded: chain Ll residue 34 THR Chi-restraints excluded: chain Lp residue 3 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1368 random chunks: chunk 665 optimal weight: 6.9990 chunk 862 optimal weight: 7.9990 chunk 1156 optimal weight: 1.9990 chunk 332 optimal weight: 8.9990 chunk 1000 optimal weight: 0.9990 chunk 160 optimal weight: 7.9990 chunk 301 optimal weight: 7.9990 chunk 1086 optimal weight: 5.9990 chunk 454 optimal weight: 5.9990 chunk 1116 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CF 118 ASN CH 362 GLN CH 399 ASN CI 267 GLN ** CI 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CL 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CM 99 ASN CM 165 GLN ** CM 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CQ 130 ASN Lq 97 GLN Cf 40 GLN Cg 31 ASN Cg 192 GLN ** LA 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 244 HIS LB 379 GLN LC 118 GLN LD 17 GLN LD 39 GLN LE 53 GLN LE 172 ASN LF 10 ASN LH 201 GLN ** LK 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LK 70 GLN LM 106 GLN LP 75 GLN LR 91 GLN ** LT 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LY 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ld 49 GLN Ld 70 GLN Lg 30 GLN Lh 33 GLN Lk 33 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.090307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.064745 restraints weight = 235697.863| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 0.99 r_work: 0.2789 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.203 167533 Z= 0.286 Angle : 0.664 59.200 242854 Z= 0.360 Chirality : 0.040 0.280 29658 Planarity : 0.006 0.130 18146 Dihedral : 22.512 178.756 65177 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.30 % Allowed : 14.28 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: 1.78 (0.08), residues: 10361 helix: 2.26 (0.08), residues: 4022 sheet: 0.26 (0.13), residues: 1469 loop : 0.69 (0.09), residues: 4870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRPCg 105 HIS 0.047 0.001 HISLT 54 PHE 0.016 0.002 PHECH 90 TYR 0.019 0.002 TYRCI 251 ARG 0.021 0.001 ARGCL 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 62601.59 seconds wall clock time: 1081 minutes 30.89 seconds (64890.89 seconds total)