Starting phenix.real_space_refine on Fri Mar 22 15:22:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlt_32592/03_2024/7wlt_32592_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlt_32592/03_2024/7wlt_32592.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlt_32592/03_2024/7wlt_32592_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlt_32592/03_2024/7wlt_32592_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlt_32592/03_2024/7wlt_32592_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlt_32592/03_2024/7wlt_32592.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlt_32592/03_2024/7wlt_32592.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlt_32592/03_2024/7wlt_32592_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlt_32592/03_2024/7wlt_32592_updated.pdb" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 27 5.49 5 S 195 5.16 5 C 22455 2.51 5 N 5466 2.21 5 O 5769 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 838": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 842": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 845": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 885": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 902": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 903": "NH1" <-> "NH2" Residue "A ARG 915": "NH1" <-> "NH2" Residue "A TYR 947": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 967": "NH1" <-> "NH2" Residue "A PHE 986": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1005": "NH1" <-> "NH2" Residue "A ARG 1024": "NH1" <-> "NH2" Residue "A ARG 1025": "NH1" <-> "NH2" Residue "A ARG 1031": "NH1" <-> "NH2" Residue "A TYR 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1084": "OD1" <-> "OD2" Residue "A PHE 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1086": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1087": "NH1" <-> "NH2" Residue "A PHE 1111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1134": "NH1" <-> "NH2" Residue "A ARG 1147": "NH1" <-> "NH2" Residue "A TYR 1149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1268": "OD1" <-> "OD2" Residue "A PHE 1297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1318": "NH1" <-> "NH2" Residue "A PHE 1333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1357": "OE1" <-> "OE2" Residue "A TYR 1412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1416": "OE1" <-> "OE2" Residue "A ARG 1518": "NH1" <-> "NH2" Residue "A GLU 1544": "OE1" <-> "OE2" Residue "A ARG 1547": "NH1" <-> "NH2" Residue "A ARG 1552": "NH1" <-> "NH2" Residue "A ARG 1553": "NH1" <-> "NH2" Residue "A GLU 1660": "OE1" <-> "OE2" Residue "A GLU 1661": "OE1" <-> "OE2" Residue "A ARG 1664": "NH1" <-> "NH2" Residue "A ARG 1671": "NH1" <-> "NH2" Residue "A PHE 1693": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1724": "NH1" <-> "NH2" Residue "A ARG 1728": "NH1" <-> "NH2" Residue "A TYR 1757": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1761": "NH1" <-> "NH2" Residue "A TYR 1763": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1777": "OE1" <-> "OE2" Residue "A TYR 1782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1785": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1786": "OD1" <-> "OD2" Residue "A PHE 1962": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1964": "OD1" <-> "OD2" Residue "A TYR 1970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1987": "OD1" <-> "OD2" Residue "A PHE 1993": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1998": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2034": "OD1" <-> "OD2" Residue "A PHE 2049": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2073": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2098": "NH1" <-> "NH2" Residue "A ARG 2104": "NH1" <-> "NH2" Residue "A ARG 2135": "NH1" <-> "NH2" Residue "A ASP 2225": "OD1" <-> "OD2" Residue "A TYR 2256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2318": "NH1" <-> "NH2" Residue "A PHE 2319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2343": "OE1" <-> "OE2" Residue "A GLU 2359": "OE1" <-> "OE2" Residue "A ARG 2377": "NH1" <-> "NH2" Residue "A GLU 2394": "OE1" <-> "OE2" Residue "A GLU 2395": "OE1" <-> "OE2" Residue "A ASP 2397": "OD1" <-> "OD2" Residue "A ARG 2402": "NH1" <-> "NH2" Residue "A ASP 2451": "OD1" <-> "OD2" Residue "A PHE 2484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2487": "OE1" <-> "OE2" Residue "A GLU 2524": "OE1" <-> "OE2" Residue "A TYR 2533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 838": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 842": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 845": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 885": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 902": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 903": "NH1" <-> "NH2" Residue "C ARG 915": "NH1" <-> "NH2" Residue "C TYR 947": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 967": "NH1" <-> "NH2" Residue "C PHE 986": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1005": "NH1" <-> "NH2" Residue "C ARG 1024": "NH1" <-> "NH2" Residue "C ARG 1025": "NH1" <-> "NH2" Residue "C ARG 1031": "NH1" <-> "NH2" Residue "C TYR 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1084": "OD1" <-> "OD2" Residue "C PHE 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1086": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1087": "NH1" <-> "NH2" Residue "C PHE 1111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1134": "NH1" <-> "NH2" Residue "C ARG 1147": "NH1" <-> "NH2" Residue "C TYR 1149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1268": "OD1" <-> "OD2" Residue "C PHE 1297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1318": "NH1" <-> "NH2" Residue "C PHE 1333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1357": "OE1" <-> "OE2" Residue "C TYR 1412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1416": "OE1" <-> "OE2" Residue "C ARG 1518": "NH1" <-> "NH2" Residue "C GLU 1544": "OE1" <-> "OE2" Residue "C ARG 1547": "NH1" <-> "NH2" Residue "C ARG 1552": "NH1" <-> "NH2" Residue "C ARG 1553": "NH1" <-> "NH2" Residue "C GLU 1660": "OE1" <-> "OE2" Residue "C GLU 1661": "OE1" <-> "OE2" Residue "C ARG 1664": "NH1" <-> "NH2" Residue "C ARG 1671": "NH1" <-> "NH2" Residue "C PHE 1693": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1724": "NH1" <-> "NH2" Residue "C ARG 1728": "NH1" <-> "NH2" Residue "C TYR 1757": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1761": "NH1" <-> "NH2" Residue "C TYR 1763": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1777": "OE1" <-> "OE2" Residue "C TYR 1782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1785": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1786": "OD1" <-> "OD2" Residue "C PHE 1962": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1964": "OD1" <-> "OD2" Residue "C TYR 1970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1987": "OD1" <-> "OD2" Residue "C PHE 1993": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1998": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 2034": "OD1" <-> "OD2" Residue "C PHE 2049": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2073": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 2098": "NH1" <-> "NH2" Residue "C ARG 2104": "NH1" <-> "NH2" Residue "C ARG 2135": "NH1" <-> "NH2" Residue "C ASP 2225": "OD1" <-> "OD2" Residue "C TYR 2256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 2318": "NH1" <-> "NH2" Residue "C PHE 2319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2343": "OE1" <-> "OE2" Residue "C GLU 2359": "OE1" <-> "OE2" Residue "C ARG 2377": "NH1" <-> "NH2" Residue "C GLU 2394": "OE1" <-> "OE2" Residue "C GLU 2395": "OE1" <-> "OE2" Residue "C ASP 2397": "OD1" <-> "OD2" Residue "C ARG 2402": "NH1" <-> "NH2" Residue "C ASP 2451": "OD1" <-> "OD2" Residue "C PHE 2484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2487": "OE1" <-> "OE2" Residue "C GLU 2524": "OE1" <-> "OE2" Residue "C TYR 2533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 838": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 842": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 845": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 885": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 902": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 903": "NH1" <-> "NH2" Residue "E ARG 915": "NH1" <-> "NH2" Residue "E TYR 947": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 967": "NH1" <-> "NH2" Residue "E PHE 986": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1005": "NH1" <-> "NH2" Residue "E ARG 1024": "NH1" <-> "NH2" Residue "E ARG 1025": "NH1" <-> "NH2" Residue "E ARG 1031": "NH1" <-> "NH2" Residue "E TYR 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 1084": "OD1" <-> "OD2" Residue "E PHE 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1086": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1087": "NH1" <-> "NH2" Residue "E PHE 1111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1134": "NH1" <-> "NH2" Residue "E ARG 1147": "NH1" <-> "NH2" Residue "E TYR 1149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 1268": "OD1" <-> "OD2" Residue "E PHE 1297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1318": "NH1" <-> "NH2" Residue "E PHE 1333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1357": "OE1" <-> "OE2" Residue "E TYR 1412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1416": "OE1" <-> "OE2" Residue "E ARG 1518": "NH1" <-> "NH2" Residue "E GLU 1544": "OE1" <-> "OE2" Residue "E ARG 1547": "NH1" <-> "NH2" Residue "E ARG 1552": "NH1" <-> "NH2" Residue "E ARG 1553": "NH1" <-> "NH2" Residue "E GLU 1660": "OE1" <-> "OE2" Residue "E GLU 1661": "OE1" <-> "OE2" Residue "E ARG 1664": "NH1" <-> "NH2" Residue "E ARG 1671": "NH1" <-> "NH2" Residue "E PHE 1693": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1724": "NH1" <-> "NH2" Residue "E ARG 1728": "NH1" <-> "NH2" Residue "E TYR 1757": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1761": "NH1" <-> "NH2" Residue "E TYR 1763": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1777": "OE1" <-> "OE2" Residue "E TYR 1782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1785": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 1786": "OD1" <-> "OD2" Residue "E PHE 1962": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 1964": "OD1" <-> "OD2" Residue "E TYR 1970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 1987": "OD1" <-> "OD2" Residue "E PHE 1993": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1998": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 2034": "OD1" <-> "OD2" Residue "E PHE 2049": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 2073": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 2098": "NH1" <-> "NH2" Residue "E ARG 2104": "NH1" <-> "NH2" Residue "E ARG 2135": "NH1" <-> "NH2" Residue "E ASP 2225": "OD1" <-> "OD2" Residue "E TYR 2256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 2266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 2318": "NH1" <-> "NH2" Residue "E PHE 2319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 2343": "OE1" <-> "OE2" Residue "E GLU 2359": "OE1" <-> "OE2" Residue "E ARG 2377": "NH1" <-> "NH2" Residue "E GLU 2394": "OE1" <-> "OE2" Residue "E GLU 2395": "OE1" <-> "OE2" Residue "E ASP 2397": "OD1" <-> "OD2" Residue "E ARG 2402": "NH1" <-> "NH2" Residue "E ASP 2451": "OD1" <-> "OD2" Residue "E PHE 2484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 2485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 2487": "OE1" <-> "OE2" Residue "E GLU 2524": "OE1" <-> "OE2" Residue "E TYR 2533": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 33912 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1353, 10835 Classifications: {'peptide': 1353} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 57, 'TRANS': 1295} Chain breaks: 11 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 320 Unresolved non-hydrogen angles: 411 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 4, 'HIS:plan': 4, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 170 Chain: "C" Number of atoms: 10835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1353, 10835 Classifications: {'peptide': 1353} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 57, 'TRANS': 1295} Chain breaks: 11 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 320 Unresolved non-hydrogen angles: 411 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 4, 'HIS:plan': 4, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 170 Chain: "E" Number of atoms: 10835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1353, 10835 Classifications: {'peptide': 1353} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 57, 'TRANS': 1295} Chain breaks: 11 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 320 Unresolved non-hydrogen angles: 411 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 4, 'HIS:plan': 4, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 170 Chain: "A" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 469 Unusual residues: {'PEE': 1, 'PLX': 7} Classifications: {'peptide': 1, 'undetermined': 8} Link IDs: {None: 8} Chain: "C" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 469 Unusual residues: {'PEE': 1, 'PLX': 7} Classifications: {'peptide': 1, 'undetermined': 8} Link IDs: {None: 8} Chain: "E" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 469 Unusual residues: {'PEE': 1, 'PLX': 7} Classifications: {'peptide': 1, 'undetermined': 8} Link IDs: {None: 8} Time building chain proxies: 18.48, per 1000 atoms: 0.54 Number of scatterers: 33912 At special positions: 0 Unit cell: (198.738, 200.934, 157.014, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 195 16.00 P 27 15.00 O 5769 8.00 N 5466 7.00 C 22455 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A1243 " - pdb=" SG CYS A1271 " distance=2.04 Simple disulfide: pdb=" SG CYS C1243 " - pdb=" SG CYS C1271 " distance=2.04 Simple disulfide: pdb=" SG CYS E1243 " - pdb=" SG CYS E1271 " distance=2.04 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: 12.65 Conformation dependent library (CDL) restraints added in 5.9 seconds 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7794 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 156 helices and 9 sheets defined 62.1% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.99 Creating SS restraints... Processing helix chain 'A' and resid 785 through 823 removed outlier: 4.180A pdb=" N ARG A 803 " --> pdb=" O VAL A 799 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A 807 " --> pdb=" O ARG A 803 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N PHE A 810 " --> pdb=" O GLU A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 841 Proline residue: A 841 - end of helix Processing helix chain 'A' and resid 846 through 869 removed outlier: 3.990A pdb=" N THR A 854 " --> pdb=" O SER A 850 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU A 869 " --> pdb=" O MET A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 949 removed outlier: 3.598A pdb=" N GLN A 925 " --> pdb=" O GLY A 922 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ASN A 926 " --> pdb=" O TYR A 923 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N HIS A 927 " --> pdb=" O ILE A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 984 Processing helix chain 'A' and resid 990 through 1005 Processing helix chain 'A' and resid 1008 through 1022 Processing helix chain 'A' and resid 1026 through 1052 Proline residue: A1034 - end of helix Processing helix chain 'A' and resid 1074 through 1079 Processing helix chain 'A' and resid 1093 through 1113 Processing helix chain 'A' and resid 1149 through 1159 Processing helix chain 'A' and resid 1161 through 1175 Processing helix chain 'A' and resid 1181 through 1200 removed outlier: 5.645A pdb=" N THR A1196 " --> pdb=" O LEU A1192 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR A1197 " --> pdb=" O LEU A1193 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1231 removed outlier: 4.240A pdb=" N LEU A1229 " --> pdb=" O ASN A1225 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LEU A1230 " --> pdb=" O MET A1226 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER A1231 " --> pdb=" O LEU A1227 " (cutoff:3.500A) Processing helix chain 'A' and resid 1243 through 1249 Processing helix chain 'A' and resid 1264 through 1266 No H-bonds generated for 'chain 'A' and resid 1264 through 1266' Processing helix chain 'A' and resid 1281 through 1298 Processing helix chain 'A' and resid 1300 through 1364 removed outlier: 5.441A pdb=" N SER A1317 " --> pdb=" O ALA A1313 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ARG A1318 " --> pdb=" O LEU A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1407 Processing helix chain 'A' and resid 1412 through 1415 Processing helix chain 'A' and resid 1494 through 1547 removed outlier: 5.252A pdb=" N HIS A1526 " --> pdb=" O ALA A1522 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N HIS A1527 " --> pdb=" O PHE A1523 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN A1543 " --> pdb=" O TYR A1539 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLU A1544 " --> pdb=" O LEU A1540 " (cutoff:3.500A) Processing helix chain 'A' and resid 1553 through 1557 Processing helix chain 'A' and resid 1657 through 1668 Processing helix chain 'A' and resid 1673 through 1685 Processing helix chain 'A' and resid 1687 through 1700 Processing helix chain 'A' and resid 1705 through 1716 removed outlier: 4.895A pdb=" N LEU A1710 " --> pdb=" O ALA A1706 " (cutoff:3.500A) Proline residue: A1711 - end of helix Processing helix chain 'A' and resid 1727 through 1748 Processing helix chain 'A' and resid 1759 through 1762 No H-bonds generated for 'chain 'A' and resid 1759 through 1762' Processing helix chain 'A' and resid 1770 through 1774 Processing helix chain 'A' and resid 1787 through 1802 Processing helix chain 'A' and resid 1947 through 1967 Proline residue: A1957 - end of helix Processing helix chain 'A' and resid 1977 through 1996 Processing helix chain 'A' and resid 2017 through 2040 removed outlier: 3.994A pdb=" N PHE A2022 " --> pdb=" O GLN A2018 " (cutoff:3.500A) Processing helix chain 'A' and resid 2043 through 2062 Processing helix chain 'A' and resid 2064 through 2068 Processing helix chain 'A' and resid 2077 through 2099 Processing helix chain 'A' and resid 2109 through 2111 No H-bonds generated for 'chain 'A' and resid 2109 through 2111' Processing helix chain 'A' and resid 2116 through 2127 Processing helix chain 'A' and resid 2131 through 2142 Processing helix chain 'A' and resid 2149 through 2174 Processing helix chain 'A' and resid 2185 through 2213 Proline residue: A2206 - end of helix Processing helix chain 'A' and resid 2253 through 2262 Processing helix chain 'A' and resid 2267 through 2275 Processing helix chain 'A' and resid 2278 through 2280 No H-bonds generated for 'chain 'A' and resid 2278 through 2280' Processing helix chain 'A' and resid 2298 through 2309 Processing helix chain 'A' and resid 2349 through 2359 removed outlier: 3.884A pdb=" N GLU A2359 " --> pdb=" O ALA A2355 " (cutoff:3.500A) Processing helix chain 'A' and resid 2423 through 2425 No H-bonds generated for 'chain 'A' and resid 2423 through 2425' Processing helix chain 'A' and resid 2467 through 2484 removed outlier: 4.075A pdb=" N PHE A2484 " --> pdb=" O PHE A2480 " (cutoff:3.500A) Processing helix chain 'A' and resid 2489 through 2492 Processing helix chain 'A' and resid 2501 through 2516 Processing helix chain 'A' and resid 2519 through 2534 Processing helix chain 'A' and resid 2536 through 2542 Processing helix chain 'C' and resid 785 through 823 removed outlier: 4.180A pdb=" N ARG C 803 " --> pdb=" O VAL C 799 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU C 807 " --> pdb=" O ARG C 803 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N PHE C 810 " --> pdb=" O GLU C 806 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 841 Proline residue: C 841 - end of helix Processing helix chain 'C' and resid 846 through 869 removed outlier: 3.990A pdb=" N THR C 854 " --> pdb=" O SER C 850 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL C 855 " --> pdb=" O CYS C 851 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU C 869 " --> pdb=" O MET C 865 " (cutoff:3.500A) Processing helix chain 'C' and resid 922 through 949 removed outlier: 3.597A pdb=" N GLN C 925 " --> pdb=" O GLY C 922 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ASN C 926 " --> pdb=" O TYR C 923 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N HIS C 927 " --> pdb=" O ILE C 924 " (cutoff:3.500A) Processing helix chain 'C' and resid 974 through 984 Processing helix chain 'C' and resid 990 through 1005 Processing helix chain 'C' and resid 1008 through 1022 Processing helix chain 'C' and resid 1026 through 1052 Proline residue: C1034 - end of helix Processing helix chain 'C' and resid 1074 through 1079 Processing helix chain 'C' and resid 1093 through 1113 Processing helix chain 'C' and resid 1149 through 1159 Processing helix chain 'C' and resid 1161 through 1175 Processing helix chain 'C' and resid 1181 through 1200 removed outlier: 5.646A pdb=" N THR C1196 " --> pdb=" O LEU C1192 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N THR C1197 " --> pdb=" O LEU C1193 " (cutoff:3.500A) Processing helix chain 'C' and resid 1203 through 1231 removed outlier: 4.240A pdb=" N LEU C1229 " --> pdb=" O ASN C1225 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LEU C1230 " --> pdb=" O MET C1226 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER C1231 " --> pdb=" O LEU C1227 " (cutoff:3.500A) Processing helix chain 'C' and resid 1243 through 1249 Processing helix chain 'C' and resid 1264 through 1266 No H-bonds generated for 'chain 'C' and resid 1264 through 1266' Processing helix chain 'C' and resid 1281 through 1298 Processing helix chain 'C' and resid 1300 through 1364 removed outlier: 5.441A pdb=" N SER C1317 " --> pdb=" O ALA C1313 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ARG C1318 " --> pdb=" O LEU C1314 " (cutoff:3.500A) Processing helix chain 'C' and resid 1403 through 1407 Processing helix chain 'C' and resid 1412 through 1415 Processing helix chain 'C' and resid 1494 through 1547 removed outlier: 5.252A pdb=" N HIS C1526 " --> pdb=" O ALA C1522 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N HIS C1527 " --> pdb=" O PHE C1523 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN C1543 " --> pdb=" O TYR C1539 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLU C1544 " --> pdb=" O LEU C1540 " (cutoff:3.500A) Processing helix chain 'C' and resid 1553 through 1557 Processing helix chain 'C' and resid 1657 through 1668 Processing helix chain 'C' and resid 1673 through 1685 Processing helix chain 'C' and resid 1687 through 1700 Processing helix chain 'C' and resid 1705 through 1716 removed outlier: 4.895A pdb=" N LEU C1710 " --> pdb=" O ALA C1706 " (cutoff:3.500A) Proline residue: C1711 - end of helix Processing helix chain 'C' and resid 1727 through 1748 Processing helix chain 'C' and resid 1759 through 1762 No H-bonds generated for 'chain 'C' and resid 1759 through 1762' Processing helix chain 'C' and resid 1770 through 1774 Processing helix chain 'C' and resid 1787 through 1802 Processing helix chain 'C' and resid 1947 through 1967 Proline residue: C1957 - end of helix Processing helix chain 'C' and resid 1977 through 1996 Processing helix chain 'C' and resid 2017 through 2040 removed outlier: 3.994A pdb=" N PHE C2022 " --> pdb=" O GLN C2018 " (cutoff:3.500A) Processing helix chain 'C' and resid 2043 through 2062 Processing helix chain 'C' and resid 2064 through 2068 Processing helix chain 'C' and resid 2077 through 2099 Processing helix chain 'C' and resid 2109 through 2111 No H-bonds generated for 'chain 'C' and resid 2109 through 2111' Processing helix chain 'C' and resid 2116 through 2127 Processing helix chain 'C' and resid 2131 through 2142 Processing helix chain 'C' and resid 2149 through 2174 Processing helix chain 'C' and resid 2185 through 2213 Proline residue: C2206 - end of helix Processing helix chain 'C' and resid 2253 through 2262 Processing helix chain 'C' and resid 2267 through 2275 Processing helix chain 'C' and resid 2278 through 2280 No H-bonds generated for 'chain 'C' and resid 2278 through 2280' Processing helix chain 'C' and resid 2298 through 2309 Processing helix chain 'C' and resid 2349 through 2359 removed outlier: 3.884A pdb=" N GLU C2359 " --> pdb=" O ALA C2355 " (cutoff:3.500A) Processing helix chain 'C' and resid 2423 through 2425 No H-bonds generated for 'chain 'C' and resid 2423 through 2425' Processing helix chain 'C' and resid 2467 through 2484 removed outlier: 4.075A pdb=" N PHE C2484 " --> pdb=" O PHE C2480 " (cutoff:3.500A) Processing helix chain 'C' and resid 2489 through 2492 Processing helix chain 'C' and resid 2501 through 2516 Processing helix chain 'C' and resid 2519 through 2534 Processing helix chain 'C' and resid 2536 through 2542 Processing helix chain 'E' and resid 785 through 823 removed outlier: 4.180A pdb=" N ARG E 803 " --> pdb=" O VAL E 799 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU E 807 " --> pdb=" O ARG E 803 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N PHE E 810 " --> pdb=" O GLU E 806 " (cutoff:3.500A) Processing helix chain 'E' and resid 827 through 841 Proline residue: E 841 - end of helix Processing helix chain 'E' and resid 846 through 869 removed outlier: 3.989A pdb=" N THR E 854 " --> pdb=" O SER E 850 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL E 855 " --> pdb=" O CYS E 851 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU E 869 " --> pdb=" O MET E 865 " (cutoff:3.500A) Processing helix chain 'E' and resid 922 through 949 removed outlier: 3.597A pdb=" N GLN E 925 " --> pdb=" O GLY E 922 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ASN E 926 " --> pdb=" O TYR E 923 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N HIS E 927 " --> pdb=" O ILE E 924 " (cutoff:3.500A) Processing helix chain 'E' and resid 974 through 984 Processing helix chain 'E' and resid 990 through 1005 Processing helix chain 'E' and resid 1008 through 1022 Processing helix chain 'E' and resid 1026 through 1052 Proline residue: E1034 - end of helix Processing helix chain 'E' and resid 1074 through 1079 Processing helix chain 'E' and resid 1093 through 1113 Processing helix chain 'E' and resid 1149 through 1159 Processing helix chain 'E' and resid 1161 through 1175 Processing helix chain 'E' and resid 1181 through 1200 removed outlier: 5.645A pdb=" N THR E1196 " --> pdb=" O LEU E1192 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR E1197 " --> pdb=" O LEU E1193 " (cutoff:3.500A) Processing helix chain 'E' and resid 1203 through 1231 removed outlier: 4.240A pdb=" N LEU E1229 " --> pdb=" O ASN E1225 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LEU E1230 " --> pdb=" O MET E1226 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N SER E1231 " --> pdb=" O LEU E1227 " (cutoff:3.500A) Processing helix chain 'E' and resid 1243 through 1249 Processing helix chain 'E' and resid 1264 through 1266 No H-bonds generated for 'chain 'E' and resid 1264 through 1266' Processing helix chain 'E' and resid 1281 through 1298 Processing helix chain 'E' and resid 1300 through 1364 removed outlier: 5.441A pdb=" N SER E1317 " --> pdb=" O ALA E1313 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ARG E1318 " --> pdb=" O LEU E1314 " (cutoff:3.500A) Processing helix chain 'E' and resid 1403 through 1407 Processing helix chain 'E' and resid 1412 through 1415 Processing helix chain 'E' and resid 1494 through 1547 removed outlier: 5.251A pdb=" N HIS E1526 " --> pdb=" O ALA E1522 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N HIS E1527 " --> pdb=" O PHE E1523 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN E1543 " --> pdb=" O TYR E1539 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLU E1544 " --> pdb=" O LEU E1540 " (cutoff:3.500A) Processing helix chain 'E' and resid 1553 through 1557 Processing helix chain 'E' and resid 1657 through 1668 Processing helix chain 'E' and resid 1673 through 1685 Processing helix chain 'E' and resid 1687 through 1700 Processing helix chain 'E' and resid 1705 through 1716 removed outlier: 4.895A pdb=" N LEU E1710 " --> pdb=" O ALA E1706 " (cutoff:3.500A) Proline residue: E1711 - end of helix Processing helix chain 'E' and resid 1727 through 1748 Processing helix chain 'E' and resid 1759 through 1762 No H-bonds generated for 'chain 'E' and resid 1759 through 1762' Processing helix chain 'E' and resid 1770 through 1774 Processing helix chain 'E' and resid 1787 through 1802 Processing helix chain 'E' and resid 1947 through 1967 Proline residue: E1957 - end of helix Processing helix chain 'E' and resid 1977 through 1996 Processing helix chain 'E' and resid 2017 through 2040 removed outlier: 3.994A pdb=" N PHE E2022 " --> pdb=" O GLN E2018 " (cutoff:3.500A) Processing helix chain 'E' and resid 2043 through 2062 Processing helix chain 'E' and resid 2064 through 2068 Processing helix chain 'E' and resid 2077 through 2099 Processing helix chain 'E' and resid 2109 through 2111 No H-bonds generated for 'chain 'E' and resid 2109 through 2111' Processing helix chain 'E' and resid 2116 through 2127 Processing helix chain 'E' and resid 2131 through 2142 Processing helix chain 'E' and resid 2149 through 2174 Processing helix chain 'E' and resid 2185 through 2213 Proline residue: E2206 - end of helix Processing helix chain 'E' and resid 2253 through 2262 Processing helix chain 'E' and resid 2267 through 2275 Processing helix chain 'E' and resid 2278 through 2280 No H-bonds generated for 'chain 'E' and resid 2278 through 2280' Processing helix chain 'E' and resid 2298 through 2309 Processing helix chain 'E' and resid 2349 through 2359 removed outlier: 3.883A pdb=" N GLU E2359 " --> pdb=" O ALA E2355 " (cutoff:3.500A) Processing helix chain 'E' and resid 2423 through 2425 No H-bonds generated for 'chain 'E' and resid 2423 through 2425' Processing helix chain 'E' and resid 2467 through 2484 removed outlier: 4.075A pdb=" N PHE E2484 " --> pdb=" O PHE E2480 " (cutoff:3.500A) Processing helix chain 'E' and resid 2489 through 2492 Processing helix chain 'E' and resid 2501 through 2516 Processing helix chain 'E' and resid 2519 through 2534 Processing helix chain 'E' and resid 2536 through 2542 Processing sheet with id= A, first strand: chain 'A' and resid 2248 through 2250 Processing sheet with id= B, first strand: chain 'A' and resid 2335 through 2344 removed outlier: 6.926A pdb=" N LEU A2232 " --> pdb=" O PRO A2237 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 2366 through 2368 Processing sheet with id= D, first strand: chain 'C' and resid 2248 through 2250 Processing sheet with id= E, first strand: chain 'C' and resid 2335 through 2344 removed outlier: 6.926A pdb=" N LEU C2232 " --> pdb=" O PRO C2237 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 2366 through 2368 Processing sheet with id= G, first strand: chain 'E' and resid 2248 through 2250 Processing sheet with id= H, first strand: chain 'E' and resid 2335 through 2344 removed outlier: 6.926A pdb=" N LEU E2232 " --> pdb=" O PRO E2237 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 2366 through 2368 1938 hydrogen bonds defined for protein. 5409 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.27 Time building geometry restraints manager: 13.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6384 1.33 - 1.45: 8653 1.45 - 1.57: 19286 1.57 - 1.70: 78 1.70 - 1.82: 303 Bond restraints: 34704 Sorted by residual: bond pdb=" C30 PEE E2608 " pdb=" O3 PEE E2608 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C30 PEE C2607 " pdb=" O3 PEE C2607 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C30 PEE A2606 " pdb=" O3 PEE A2606 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" O4 PLX C2604 " pdb=" P1 PLX C2604 " ideal model delta sigma weight residual 1.680 1.609 0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" O1 PLX E2605 " pdb=" P1 PLX E2605 " ideal model delta sigma weight residual 1.680 1.610 0.070 2.00e-02 2.50e+03 1.24e+01 ... (remaining 34699 not shown) Histogram of bond angle deviations from ideal: 97.01 - 104.42: 566 104.42 - 111.84: 17238 111.84 - 119.25: 11520 119.25 - 126.66: 16947 126.66 - 134.08: 568 Bond angle restraints: 46839 Sorted by residual: angle pdb=" C GLY E2463 " pdb=" N TYR E2464 " pdb=" CA TYR E2464 " ideal model delta sigma weight residual 121.54 133.16 -11.62 1.91e+00 2.74e-01 3.70e+01 angle pdb=" C GLY A2463 " pdb=" N TYR A2464 " pdb=" CA TYR A2464 " ideal model delta sigma weight residual 121.54 133.14 -11.60 1.91e+00 2.74e-01 3.69e+01 angle pdb=" C GLY C2463 " pdb=" N TYR C2464 " pdb=" CA TYR C2464 " ideal model delta sigma weight residual 121.54 133.12 -11.58 1.91e+00 2.74e-01 3.68e+01 angle pdb=" N ASN E1142 " pdb=" CA ASN E1142 " pdb=" C ASN E1142 " ideal model delta sigma weight residual 110.70 119.18 -8.48 1.55e+00 4.16e-01 2.99e+01 angle pdb=" N ASN A1142 " pdb=" CA ASN A1142 " pdb=" C ASN A1142 " ideal model delta sigma weight residual 110.70 119.16 -8.46 1.55e+00 4.16e-01 2.98e+01 ... (remaining 46834 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.63: 19761 28.63 - 57.25: 888 57.25 - 85.88: 75 85.88 - 114.50: 18 114.50 - 143.13: 21 Dihedral angle restraints: 20763 sinusoidal: 8781 harmonic: 11982 Sorted by residual: dihedral pdb=" CA TYR E1259 " pdb=" C TYR E1259 " pdb=" N ASP E1260 " pdb=" CA ASP E1260 " ideal model delta harmonic sigma weight residual 180.00 158.04 21.96 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA TYR A1259 " pdb=" C TYR A1259 " pdb=" N ASP A1260 " pdb=" CA ASP A1260 " ideal model delta harmonic sigma weight residual 180.00 158.08 21.92 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" C41 PEE E2608 " pdb=" C42 PEE E2608 " pdb=" C43 PEE E2608 " pdb=" C44 PEE E2608 " ideal model delta sinusoidal sigma weight residual 179.49 36.36 143.13 1 3.00e+01 1.11e-03 1.92e+01 ... (remaining 20760 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 4677 0.096 - 0.191: 463 0.191 - 0.287: 38 0.287 - 0.383: 0 0.383 - 0.479: 3 Chirality restraints: 5181 Sorted by residual: chirality pdb=" CB ILE E1722 " pdb=" CA ILE E1722 " pdb=" CG1 ILE E1722 " pdb=" CG2 ILE E1722 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.48 2.00e-01 2.50e+01 5.73e+00 chirality pdb=" CB ILE A1722 " pdb=" CA ILE A1722 " pdb=" CG1 ILE A1722 " pdb=" CG2 ILE A1722 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" CB ILE C1722 " pdb=" CA ILE C1722 " pdb=" CG1 ILE C1722 " pdb=" CG2 ILE C1722 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.48 2.00e-01 2.50e+01 5.69e+00 ... (remaining 5178 not shown) Planarity restraints: 5667 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1244 " 0.020 2.00e-02 2.50e+03 2.10e-02 1.10e+01 pdb=" CG TRP A1244 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP A1244 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP A1244 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A1244 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A1244 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A1244 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1244 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1244 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A1244 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E1244 " 0.020 2.00e-02 2.50e+03 2.10e-02 1.10e+01 pdb=" CG TRP E1244 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP E1244 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP E1244 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E1244 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E1244 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E1244 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP E1244 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E1244 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP E1244 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C1244 " 0.020 2.00e-02 2.50e+03 2.09e-02 1.09e+01 pdb=" CG TRP C1244 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP C1244 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP C1244 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C1244 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C1244 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C1244 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP C1244 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C1244 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C1244 " -0.001 2.00e-02 2.50e+03 ... (remaining 5664 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 1218 2.69 - 3.25: 35538 3.25 - 3.80: 53925 3.80 - 4.35: 63005 4.35 - 4.90: 106925 Nonbonded interactions: 260611 Sorted by model distance: nonbonded pdb=" N GLU E2518 " pdb=" OE1 GLU E2518 " model vdw 2.142 2.520 nonbonded pdb=" N GLU A2518 " pdb=" OE1 GLU A2518 " model vdw 2.143 2.520 nonbonded pdb=" N GLU C2518 " pdb=" OE1 GLU C2518 " model vdw 2.143 2.520 nonbonded pdb=" O TRP E2542 " pdb=" NH2 ARG E2546 " model vdw 2.200 2.520 nonbonded pdb=" O TRP A2542 " pdb=" NH2 ARG A2546 " model vdw 2.200 2.520 ... (remaining 260606 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 784 through 2547 or resid 2601 through 2605)) selection = (chain 'C' and (resid 784 through 2547 or resid 2601 through 2605)) selection = (chain 'E' and (resid 784 through 2547 or resid 2601 through 2605)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 11.940 Check model and map are aligned: 0.500 Set scattering table: 0.320 Process input model: 86.350 Find NCS groups from input model: 2.620 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 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 : 0.011 0.079 34704 Z= 0.702 Angle : 1.112 14.030 46839 Z= 0.594 Chirality : 0.059 0.479 5181 Planarity : 0.007 0.074 5667 Dihedral : 16.102 143.128 12960 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 20.69 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.94 % Favored : 93.91 % Rotamer: Outliers : 0.89 % Allowed : 0.95 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.14), residues: 3987 helix: 2.60 (0.10), residues: 2646 sheet: -0.37 (0.33), residues: 261 loop : -1.97 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP E1244 HIS 0.014 0.002 HIS A1145 PHE 0.049 0.003 PHE E2426 TYR 0.029 0.003 TYR A1757 ARG 0.025 0.001 ARG C1664 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 407 time to evaluate : 3.735 Fit side-chains REVERT: A 897 ASN cc_start: 0.7354 (t0) cc_final: 0.7036 (t0) REVERT: A 1142 ASN cc_start: 0.6838 (p0) cc_final: 0.6431 (p0) REVERT: A 1144 ILE cc_start: 0.8167 (pt) cc_final: 0.7904 (pt) REVERT: A 1226 MET cc_start: 0.7733 (ttm) cc_final: 0.7343 (tpp) REVERT: A 2153 MET cc_start: 0.8458 (mmm) cc_final: 0.7957 (mtt) REVERT: A 2270 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7819 (mmm) REVERT: A 2446 MET cc_start: 0.8884 (ttt) cc_final: 0.8402 (ttt) REVERT: C 1226 MET cc_start: 0.7900 (ttm) cc_final: 0.7583 (tpp) REVERT: C 1264 MET cc_start: 0.6932 (mmt) cc_final: 0.5838 (mmt) REVERT: C 1323 TYR cc_start: 0.8440 (t80) cc_final: 0.7965 (t80) REVERT: C 1495 MET cc_start: 0.3070 (mpp) cc_final: 0.1924 (ttt) REVERT: C 2061 MET cc_start: 0.8676 (tpp) cc_final: 0.8388 (tpp) REVERT: C 2153 MET cc_start: 0.8358 (mmm) cc_final: 0.7820 (mtt) REVERT: E 2061 MET cc_start: 0.8572 (tpp) cc_final: 0.8222 (tpp) REVERT: E 2153 MET cc_start: 0.8370 (mmm) cc_final: 0.7792 (mtt) outliers start: 30 outliers final: 7 residues processed: 410 average time/residue: 0.4237 time to fit residues: 290.1364 Evaluate side-chains 341 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 333 time to evaluate : 3.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1143 PHE Chi-restraints excluded: chain A residue 1238 MET Chi-restraints excluded: chain A residue 2270 MET Chi-restraints excluded: chain C residue 1143 PHE Chi-restraints excluded: chain C residue 2270 MET Chi-restraints excluded: chain E residue 1143 PHE Chi-restraints excluded: chain E residue 2270 MET Chi-restraints excluded: chain E residue 2493 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 341 optimal weight: 0.9990 chunk 306 optimal weight: 5.9990 chunk 170 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 207 optimal weight: 0.0770 chunk 163 optimal weight: 1.9990 chunk 317 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 236 optimal weight: 2.9990 chunk 367 optimal weight: 0.8980 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1107 GLN ** A1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1967 HIS ** C1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1107 GLN C1967 HIS E1013 HIS E1047 GLN ** E1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1967 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34704 Z= 0.200 Angle : 0.649 7.775 46839 Z= 0.322 Chirality : 0.041 0.180 5181 Planarity : 0.005 0.055 5667 Dihedral : 13.806 127.701 5526 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.24 % Allowed : 8.95 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.13), residues: 3987 helix: 2.16 (0.10), residues: 2658 sheet: -0.24 (0.33), residues: 261 loop : -1.95 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C1244 HIS 0.010 0.001 HIS C1304 PHE 0.025 0.002 PHE A2426 TYR 0.022 0.001 TYR A1803 ARG 0.004 0.000 ARG C1664 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 416 time to evaluate : 3.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 816 TYR cc_start: 0.7592 (t80) cc_final: 0.7285 (t80) REVERT: A 1009 MET cc_start: 0.6214 (mmm) cc_final: 0.5757 (mmm) REVERT: A 1107 GLN cc_start: 0.7727 (tm130) cc_final: 0.7492 (tm-30) REVERT: A 1142 ASN cc_start: 0.7133 (p0) cc_final: 0.6655 (p0) REVERT: A 1336 GLN cc_start: 0.8857 (mm-40) cc_final: 0.8504 (mm-40) REVERT: A 1525 LYS cc_start: 0.8825 (tppt) cc_final: 0.8602 (tppt) REVERT: A 2139 ASP cc_start: 0.8805 (m-30) cc_final: 0.8524 (m-30) REVERT: A 2446 MET cc_start: 0.8556 (ttt) cc_final: 0.8053 (ttt) REVERT: A 2464 TYR cc_start: 0.6984 (OUTLIER) cc_final: 0.5790 (m-80) REVERT: C 1142 ASN cc_start: 0.7066 (p0) cc_final: 0.6597 (p0) REVERT: C 1144 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8179 (mp) REVERT: C 1323 TYR cc_start: 0.8308 (t80) cc_final: 0.7933 (t80) REVERT: C 1791 MET cc_start: 0.8329 (mmm) cc_final: 0.8128 (mmm) REVERT: C 2235 TYR cc_start: 0.7871 (m-80) cc_final: 0.7082 (m-80) REVERT: C 2464 TYR cc_start: 0.6896 (OUTLIER) cc_final: 0.5609 (m-80) REVERT: E 1142 ASN cc_start: 0.7021 (p0) cc_final: 0.6656 (p0) REVERT: E 1144 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8085 (mp) REVERT: E 1336 GLN cc_start: 0.8942 (mm-40) cc_final: 0.8606 (mm-40) REVERT: E 1494 MET cc_start: 0.5344 (mmp) cc_final: 0.4936 (mmt) REVERT: E 1791 MET cc_start: 0.8363 (mmm) cc_final: 0.8085 (mmm) REVERT: E 2235 TYR cc_start: 0.7854 (m-10) cc_final: 0.7202 (m-10) outliers start: 42 outliers final: 24 residues processed: 434 average time/residue: 0.4328 time to fit residues: 311.8683 Evaluate side-chains 393 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 365 time to evaluate : 3.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1709 VAL Chi-restraints excluded: chain A residue 1731 MET Chi-restraints excluded: chain A residue 1967 HIS Chi-restraints excluded: chain A residue 2464 TYR Chi-restraints excluded: chain A residue 2486 SER Chi-restraints excluded: chain C residue 813 VAL Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 1015 CYS Chi-restraints excluded: chain C residue 1144 ILE Chi-restraints excluded: chain C residue 1407 ILE Chi-restraints excluded: chain C residue 1709 VAL Chi-restraints excluded: chain C residue 1776 LEU Chi-restraints excluded: chain C residue 2033 ILE Chi-restraints excluded: chain C residue 2464 TYR Chi-restraints excluded: chain C residue 2486 SER Chi-restraints excluded: chain E residue 813 VAL Chi-restraints excluded: chain E residue 838 PHE Chi-restraints excluded: chain E residue 840 LEU Chi-restraints excluded: chain E residue 1013 HIS Chi-restraints excluded: chain E residue 1144 ILE Chi-restraints excluded: chain E residue 1407 ILE Chi-restraints excluded: chain E residue 1516 LEU Chi-restraints excluded: chain E residue 1709 VAL Chi-restraints excluded: chain E residue 1731 MET Chi-restraints excluded: chain E residue 2464 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 204 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 306 optimal weight: 7.9990 chunk 250 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 368 optimal weight: 3.9990 chunk 398 optimal weight: 0.8980 chunk 328 optimal weight: 0.9980 chunk 365 optimal weight: 0.2980 chunk 125 optimal weight: 0.0870 chunk 295 optimal weight: 4.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1047 GLN ** A1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1503 GLN C1047 GLN ** C1304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1315 GLN C1503 GLN C1543 GLN C1967 HIS E1225 ASN E1315 GLN E1503 GLN E1967 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 34704 Z= 0.176 Angle : 0.578 7.346 46839 Z= 0.291 Chirality : 0.039 0.173 5181 Planarity : 0.004 0.073 5667 Dihedral : 12.850 111.453 5505 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.57 % Allowed : 12.83 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.14), residues: 3987 helix: 2.17 (0.10), residues: 2658 sheet: -0.16 (0.33), residues: 261 loop : -2.04 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1519 HIS 0.023 0.001 HIS E1013 PHE 0.037 0.001 PHE A1954 TYR 0.026 0.001 TYR C1803 ARG 0.004 0.000 ARG A1664 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 395 time to evaluate : 3.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1009 MET cc_start: 0.6100 (mmm) cc_final: 0.5877 (mmm) REVERT: A 1107 GLN cc_start: 0.7924 (tm130) cc_final: 0.7144 (tm-30) REVERT: A 1142 ASN cc_start: 0.7052 (p0) cc_final: 0.6670 (p0) REVERT: A 1143 PHE cc_start: 0.6481 (m-80) cc_final: 0.6068 (m-80) REVERT: A 1525 LYS cc_start: 0.8890 (tppt) cc_final: 0.8638 (tppt) REVERT: A 1664 ARG cc_start: 0.8754 (ptt-90) cc_final: 0.8411 (ptt-90) REVERT: A 2139 ASP cc_start: 0.8768 (m-30) cc_final: 0.8488 (m-30) REVERT: A 2228 VAL cc_start: 0.9164 (OUTLIER) cc_final: 0.8956 (t) REVERT: A 2388 LYS cc_start: 0.8364 (mmpt) cc_final: 0.8109 (mmmt) REVERT: A 2464 TYR cc_start: 0.7124 (OUTLIER) cc_final: 0.5941 (m-80) REVERT: C 1142 ASN cc_start: 0.7222 (p0) cc_final: 0.6634 (p0) REVERT: C 1495 MET cc_start: 0.2144 (mpp) cc_final: 0.0945 (ttt) REVERT: C 1664 ARG cc_start: 0.8654 (pmt170) cc_final: 0.8449 (ptt-90) REVERT: C 1791 MET cc_start: 0.8472 (mmm) cc_final: 0.8233 (mmm) REVERT: C 2033 ILE cc_start: 0.9398 (OUTLIER) cc_final: 0.9180 (mp) REVERT: C 2153 MET cc_start: 0.8366 (mmm) cc_final: 0.7349 (mtt) REVERT: C 2235 TYR cc_start: 0.7860 (m-80) cc_final: 0.7125 (m-80) REVERT: C 2464 TYR cc_start: 0.6832 (OUTLIER) cc_final: 0.5586 (m-80) REVERT: E 1107 GLN cc_start: 0.7693 (tm-30) cc_final: 0.7200 (tm-30) REVERT: E 1142 ASN cc_start: 0.7033 (p0) cc_final: 0.6341 (p0) REVERT: E 1143 PHE cc_start: 0.6310 (m-80) cc_final: 0.5887 (m-80) REVERT: E 1264 MET cc_start: 0.6664 (mmt) cc_final: 0.6120 (mmt) REVERT: E 1494 MET cc_start: 0.5402 (mmp) cc_final: 0.4990 (mmt) REVERT: E 2228 VAL cc_start: 0.9204 (OUTLIER) cc_final: 0.8955 (m) REVERT: E 2235 TYR cc_start: 0.7819 (m-80) cc_final: 0.7176 (m-10) REVERT: E 2464 TYR cc_start: 0.7060 (OUTLIER) cc_final: 0.6046 (m-80) outliers start: 53 outliers final: 28 residues processed: 427 average time/residue: 0.4676 time to fit residues: 333.6865 Evaluate side-chains 389 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 355 time to evaluate : 3.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 1013 HIS Chi-restraints excluded: chain A residue 1350 LYS Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1709 VAL Chi-restraints excluded: chain A residue 1731 MET Chi-restraints excluded: chain A residue 1967 HIS Chi-restraints excluded: chain A residue 2191 MET Chi-restraints excluded: chain A residue 2228 VAL Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain A residue 2464 TYR Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 1013 HIS Chi-restraints excluded: chain C residue 1246 ILE Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1407 ILE Chi-restraints excluded: chain C residue 1546 LEU Chi-restraints excluded: chain C residue 1709 VAL Chi-restraints excluded: chain C residue 2033 ILE Chi-restraints excluded: chain C residue 2295 ARG Chi-restraints excluded: chain C residue 2464 TYR Chi-restraints excluded: chain E residue 838 PHE Chi-restraints excluded: chain E residue 840 LEU Chi-restraints excluded: chain E residue 981 PHE Chi-restraints excluded: chain E residue 1246 ILE Chi-restraints excluded: chain E residue 1407 ILE Chi-restraints excluded: chain E residue 1516 LEU Chi-restraints excluded: chain E residue 1709 VAL Chi-restraints excluded: chain E residue 1731 MET Chi-restraints excluded: chain E residue 1967 HIS Chi-restraints excluded: chain E residue 2228 VAL Chi-restraints excluded: chain E residue 2448 ILE Chi-restraints excluded: chain E residue 2464 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 364 optimal weight: 1.9990 chunk 277 optimal weight: 4.9990 chunk 191 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 247 optimal weight: 2.9990 chunk 369 optimal weight: 7.9990 chunk 391 optimal weight: 2.9990 chunk 193 optimal weight: 0.9990 chunk 350 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1543 GLN A1967 HIS C1503 GLN C1967 HIS E1543 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 34704 Z= 0.267 Angle : 0.608 8.303 46839 Z= 0.307 Chirality : 0.040 0.172 5181 Planarity : 0.005 0.052 5667 Dihedral : 12.405 97.076 5505 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.45 % Allowed : 14.63 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.14), residues: 3987 helix: 2.12 (0.10), residues: 2661 sheet: -0.26 (0.33), residues: 264 loop : -1.96 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E1754 HIS 0.037 0.002 HIS E1967 PHE 0.046 0.002 PHE E1954 TYR 0.027 0.001 TYR E1803 ARG 0.009 0.000 ARG A1664 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 382 time to evaluate : 3.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1107 GLN cc_start: 0.8023 (tm130) cc_final: 0.7674 (tm-30) REVERT: A 1142 ASN cc_start: 0.7504 (p0) cc_final: 0.7163 (p0) REVERT: A 1495 MET cc_start: 0.3251 (mpp) cc_final: 0.2175 (ttt) REVERT: A 2034 ASP cc_start: 0.8673 (OUTLIER) cc_final: 0.8365 (m-30) REVERT: A 2139 ASP cc_start: 0.8853 (m-30) cc_final: 0.8582 (m-30) REVERT: A 2464 TYR cc_start: 0.7043 (OUTLIER) cc_final: 0.5937 (m-80) REVERT: C 1142 ASN cc_start: 0.7293 (p0) cc_final: 0.6859 (p0) REVERT: C 1495 MET cc_start: 0.2234 (mpp) cc_final: 0.1011 (ttt) REVERT: C 1791 MET cc_start: 0.8474 (mmm) cc_final: 0.8260 (mmm) REVERT: C 2153 MET cc_start: 0.8481 (mmm) cc_final: 0.7630 (mtt) REVERT: C 2308 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8247 (mp) REVERT: C 2464 TYR cc_start: 0.6908 (OUTLIER) cc_final: 0.5660 (m-80) REVERT: E 1107 GLN cc_start: 0.7664 (tm-30) cc_final: 0.7089 (tm-30) REVERT: E 1142 ASN cc_start: 0.7286 (p0) cc_final: 0.6671 (p0) REVERT: E 2153 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.8047 (mtt) REVERT: E 2228 VAL cc_start: 0.9287 (OUTLIER) cc_final: 0.9050 (m) REVERT: E 2235 TYR cc_start: 0.8226 (m-80) cc_final: 0.7698 (m-80) REVERT: E 2464 TYR cc_start: 0.7103 (OUTLIER) cc_final: 0.6077 (m-80) outliers start: 83 outliers final: 47 residues processed: 437 average time/residue: 0.4319 time to fit residues: 311.4140 Evaluate side-chains 400 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 346 time to evaluate : 3.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 1013 HIS Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain A residue 1709 VAL Chi-restraints excluded: chain A residue 1731 MET Chi-restraints excluded: chain A residue 1967 HIS Chi-restraints excluded: chain A residue 2034 ASP Chi-restraints excluded: chain A residue 2191 MET Chi-restraints excluded: chain A residue 2228 VAL Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain A residue 2464 TYR Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 981 PHE Chi-restraints excluded: chain C residue 1013 HIS Chi-restraints excluded: chain C residue 1018 VAL Chi-restraints excluded: chain C residue 1144 ILE Chi-restraints excluded: chain C residue 1246 ILE Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1407 ILE Chi-restraints excluded: chain C residue 1546 LEU Chi-restraints excluded: chain C residue 1701 VAL Chi-restraints excluded: chain C residue 1709 VAL Chi-restraints excluded: chain C residue 1755 ASN Chi-restraints excluded: chain C residue 1776 LEU Chi-restraints excluded: chain C residue 1803 TYR Chi-restraints excluded: chain C residue 2308 LEU Chi-restraints excluded: chain C residue 2464 TYR Chi-restraints excluded: chain C residue 2472 SER Chi-restraints excluded: chain C residue 2513 VAL Chi-restraints excluded: chain C residue 2518 GLU Chi-restraints excluded: chain E residue 825 VAL Chi-restraints excluded: chain E residue 838 PHE Chi-restraints excluded: chain E residue 840 LEU Chi-restraints excluded: chain E residue 981 PHE Chi-restraints excluded: chain E residue 1167 VAL Chi-restraints excluded: chain E residue 1192 LEU Chi-restraints excluded: chain E residue 1246 ILE Chi-restraints excluded: chain E residue 1407 ILE Chi-restraints excluded: chain E residue 1516 LEU Chi-restraints excluded: chain E residue 1701 VAL Chi-restraints excluded: chain E residue 1709 VAL Chi-restraints excluded: chain E residue 1731 MET Chi-restraints excluded: chain E residue 2034 ASP Chi-restraints excluded: chain E residue 2153 MET Chi-restraints excluded: chain E residue 2228 VAL Chi-restraints excluded: chain E residue 2448 ILE Chi-restraints excluded: chain E residue 2464 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 326 optimal weight: 6.9990 chunk 222 optimal weight: 2.9990 chunk 5 optimal weight: 0.0570 chunk 291 optimal weight: 20.0000 chunk 161 optimal weight: 8.9990 chunk 334 optimal weight: 7.9990 chunk 270 optimal weight: 60.0000 chunk 0 optimal weight: 60.0000 chunk 199 optimal weight: 5.9990 chunk 351 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 overall best weight: 2.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1107 GLN ** A1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1967 HIS C1967 HIS E1503 GLN E1967 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 34704 Z= 0.342 Angle : 0.648 10.138 46839 Z= 0.329 Chirality : 0.041 0.188 5181 Planarity : 0.005 0.053 5667 Dihedral : 12.270 101.344 5505 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.10 % Allowed : 16.70 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.14), residues: 3987 helix: 2.03 (0.10), residues: 2658 sheet: -0.29 (0.34), residues: 264 loop : -2.07 (0.18), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2429 HIS 0.035 0.002 HIS A1967 PHE 0.054 0.002 PHE E1954 TYR 0.022 0.002 TYR E1803 ARG 0.005 0.000 ARG A1664 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 372 time to evaluate : 4.089 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 838 PHE cc_start: 0.7926 (OUTLIER) cc_final: 0.7631 (m-80) REVERT: A 1107 GLN cc_start: 0.8109 (tm-30) cc_final: 0.7784 (tm-30) REVERT: A 1142 ASN cc_start: 0.7511 (p0) cc_final: 0.7201 (p0) REVERT: A 1495 MET cc_start: 0.3434 (mpp) cc_final: 0.2401 (ttt) REVERT: A 2034 ASP cc_start: 0.8727 (OUTLIER) cc_final: 0.8419 (m-30) REVERT: A 2139 ASP cc_start: 0.8848 (m-30) cc_final: 0.8639 (m-30) REVERT: A 2308 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8419 (mp) REVERT: A 2446 MET cc_start: 0.8858 (ttt) cc_final: 0.8372 (ttt) REVERT: A 2464 TYR cc_start: 0.7060 (OUTLIER) cc_final: 0.5918 (m-80) REVERT: C 1142 ASN cc_start: 0.7567 (p0) cc_final: 0.7202 (p0) REVERT: C 1206 GLN cc_start: 0.7329 (mt0) cc_final: 0.6972 (mt0) REVERT: C 1264 MET cc_start: 0.6540 (mmt) cc_final: 0.5561 (mmt) REVERT: C 1495 MET cc_start: 0.2211 (mpp) cc_final: 0.0870 (ttt) REVERT: C 1502 MET cc_start: 0.6878 (ppp) cc_final: 0.6352 (ppp) REVERT: C 1546 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8598 (tt) REVERT: C 1780 ASP cc_start: 0.8477 (p0) cc_final: 0.8228 (p0) REVERT: C 1791 MET cc_start: 0.8492 (mmm) cc_final: 0.8261 (mmm) REVERT: C 2153 MET cc_start: 0.8444 (mmm) cc_final: 0.7677 (mtt) REVERT: C 2270 MET cc_start: 0.7684 (mmm) cc_final: 0.7311 (mmm) REVERT: C 2308 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8271 (mp) REVERT: C 2464 TYR cc_start: 0.6860 (OUTLIER) cc_final: 0.5602 (m-80) REVERT: E 1107 GLN cc_start: 0.7669 (tm-30) cc_final: 0.7110 (tm-30) REVERT: E 1264 MET cc_start: 0.6776 (mmt) cc_final: 0.6170 (mmt) REVERT: E 1494 MET cc_start: 0.5409 (mmp) cc_final: 0.4561 (mmt) REVERT: E 1495 MET cc_start: 0.3052 (OUTLIER) cc_final: 0.1312 (ttt) REVERT: E 1525 LYS cc_start: 0.8710 (pptt) cc_final: 0.8432 (tppt) REVERT: E 1768 TYR cc_start: 0.8287 (m-80) cc_final: 0.7873 (m-80) REVERT: E 2061 MET cc_start: 0.8712 (tpt) cc_final: 0.8502 (tpp) REVERT: E 2228 VAL cc_start: 0.9335 (OUTLIER) cc_final: 0.9097 (m) REVERT: E 2308 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8431 (mp) REVERT: E 2464 TYR cc_start: 0.7103 (OUTLIER) cc_final: 0.6018 (m-80) outliers start: 105 outliers final: 67 residues processed: 448 average time/residue: 0.4251 time to fit residues: 317.7012 Evaluate side-chains 433 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 355 time to evaluate : 3.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 1013 HIS Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain A residue 1709 VAL Chi-restraints excluded: chain A residue 1731 MET Chi-restraints excluded: chain A residue 1755 ASN Chi-restraints excluded: chain A residue 1798 SER Chi-restraints excluded: chain A residue 1967 HIS Chi-restraints excluded: chain A residue 1989 ILE Chi-restraints excluded: chain A residue 1992 ILE Chi-restraints excluded: chain A residue 2034 ASP Chi-restraints excluded: chain A residue 2191 MET Chi-restraints excluded: chain A residue 2228 VAL Chi-restraints excluded: chain A residue 2308 LEU Chi-restraints excluded: chain A residue 2332 THR Chi-restraints excluded: chain A residue 2426 PHE Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain A residue 2464 TYR Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 981 PHE Chi-restraints excluded: chain C residue 1013 HIS Chi-restraints excluded: chain C residue 1018 VAL Chi-restraints excluded: chain C residue 1221 ILE Chi-restraints excluded: chain C residue 1246 ILE Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1407 ILE Chi-restraints excluded: chain C residue 1530 MET Chi-restraints excluded: chain C residue 1546 LEU Chi-restraints excluded: chain C residue 1697 LEU Chi-restraints excluded: chain C residue 1701 VAL Chi-restraints excluded: chain C residue 1709 VAL Chi-restraints excluded: chain C residue 1731 MET Chi-restraints excluded: chain C residue 1755 ASN Chi-restraints excluded: chain C residue 1776 LEU Chi-restraints excluded: chain C residue 1798 SER Chi-restraints excluded: chain C residue 1803 TYR Chi-restraints excluded: chain C residue 1992 ILE Chi-restraints excluded: chain C residue 2228 VAL Chi-restraints excluded: chain C residue 2308 LEU Chi-restraints excluded: chain C residue 2464 TYR Chi-restraints excluded: chain C residue 2472 SER Chi-restraints excluded: chain C residue 2493 MET Chi-restraints excluded: chain E residue 825 VAL Chi-restraints excluded: chain E residue 838 PHE Chi-restraints excluded: chain E residue 840 LEU Chi-restraints excluded: chain E residue 981 PHE Chi-restraints excluded: chain E residue 1013 HIS Chi-restraints excluded: chain E residue 1018 VAL Chi-restraints excluded: chain E residue 1167 VAL Chi-restraints excluded: chain E residue 1192 LEU Chi-restraints excluded: chain E residue 1246 ILE Chi-restraints excluded: chain E residue 1251 LEU Chi-restraints excluded: chain E residue 1407 ILE Chi-restraints excluded: chain E residue 1495 MET Chi-restraints excluded: chain E residue 1516 LEU Chi-restraints excluded: chain E residue 1523 PHE Chi-restraints excluded: chain E residue 1676 LEU Chi-restraints excluded: chain E residue 1701 VAL Chi-restraints excluded: chain E residue 1709 VAL Chi-restraints excluded: chain E residue 1731 MET Chi-restraints excluded: chain E residue 1755 ASN Chi-restraints excluded: chain E residue 1982 LEU Chi-restraints excluded: chain E residue 1992 ILE Chi-restraints excluded: chain E residue 2034 ASP Chi-restraints excluded: chain E residue 2228 VAL Chi-restraints excluded: chain E residue 2308 LEU Chi-restraints excluded: chain E residue 2332 THR Chi-restraints excluded: chain E residue 2448 ILE Chi-restraints excluded: chain E residue 2464 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 131 optimal weight: 1.9990 chunk 352 optimal weight: 0.0370 chunk 77 optimal weight: 0.8980 chunk 229 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 391 optimal weight: 1.9990 chunk 325 optimal weight: 9.9990 chunk 181 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 205 optimal weight: 0.5980 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 910 ASN ** A1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1967 HIS C 910 ASN ** C1363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1967 HIS E 910 ASN E1503 GLN E1543 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34704 Z= 0.171 Angle : 0.570 9.437 46839 Z= 0.285 Chirality : 0.038 0.162 5181 Planarity : 0.004 0.051 5667 Dihedral : 11.589 100.110 5505 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.42 % Allowed : 18.35 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.14), residues: 3987 helix: 2.16 (0.10), residues: 2664 sheet: -0.07 (0.33), residues: 261 loop : -2.02 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C2429 HIS 0.023 0.001 HIS A1967 PHE 0.048 0.001 PHE E1954 TYR 0.024 0.001 TYR E1803 ARG 0.004 0.000 ARG A1664 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 400 time to evaluate : 3.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 838 PHE cc_start: 0.8038 (OUTLIER) cc_final: 0.7785 (m-80) REVERT: A 972 GLN cc_start: 0.8504 (mp10) cc_final: 0.8055 (mp10) REVERT: A 1495 MET cc_start: 0.3511 (mpp) cc_final: 0.2327 (ttt) REVERT: A 1525 LYS cc_start: 0.8871 (tppt) cc_final: 0.8552 (tppt) REVERT: A 1745 TYR cc_start: 0.8508 (t80) cc_final: 0.8199 (t80) REVERT: A 2228 VAL cc_start: 0.9183 (OUTLIER) cc_final: 0.8951 (t) REVERT: A 2464 TYR cc_start: 0.7172 (OUTLIER) cc_final: 0.5805 (m-80) REVERT: C 838 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.7605 (m-80) REVERT: C 1142 ASN cc_start: 0.7419 (p0) cc_final: 0.7083 (p0) REVERT: C 1264 MET cc_start: 0.6532 (mmt) cc_final: 0.5517 (mmt) REVERT: C 1495 MET cc_start: 0.1793 (mpp) cc_final: 0.0753 (ttt) REVERT: C 1502 MET cc_start: 0.6677 (ppp) cc_final: 0.6391 (ppp) REVERT: C 1546 LEU cc_start: 0.8876 (tt) cc_final: 0.8650 (tt) REVERT: C 1791 MET cc_start: 0.8451 (mmm) cc_final: 0.8191 (mmm) REVERT: C 2153 MET cc_start: 0.8435 (mmm) cc_final: 0.7645 (mtt) REVERT: C 2235 TYR cc_start: 0.7893 (m-80) cc_final: 0.7122 (m-80) REVERT: C 2270 MET cc_start: 0.7444 (mmm) cc_final: 0.7129 (mmm) REVERT: C 2464 TYR cc_start: 0.6787 (OUTLIER) cc_final: 0.5592 (m-80) REVERT: E 1264 MET cc_start: 0.6791 (mmt) cc_final: 0.6017 (mmt) REVERT: E 1363 GLN cc_start: 0.6802 (pp30) cc_final: 0.6564 (pp30) REVERT: E 1494 MET cc_start: 0.5519 (mmp) cc_final: 0.4713 (mmt) REVERT: E 1495 MET cc_start: 0.2956 (mpp) cc_final: 0.1308 (ttt) REVERT: E 1525 LYS cc_start: 0.8695 (pptt) cc_final: 0.8380 (ptpt) REVERT: E 2228 VAL cc_start: 0.9222 (OUTLIER) cc_final: 0.8957 (m) REVERT: E 2235 TYR cc_start: 0.8081 (m-80) cc_final: 0.7559 (m-80) REVERT: E 2270 MET cc_start: 0.7102 (mmm) cc_final: 0.6869 (mmm) REVERT: E 2436 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7906 (p0) REVERT: E 2464 TYR cc_start: 0.6988 (OUTLIER) cc_final: 0.5980 (m-80) outliers start: 82 outliers final: 48 residues processed: 454 average time/residue: 0.4429 time to fit residues: 328.9476 Evaluate side-chains 406 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 350 time to evaluate : 3.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 1013 HIS Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1697 LEU Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain A residue 1709 VAL Chi-restraints excluded: chain A residue 1731 MET Chi-restraints excluded: chain A residue 1755 ASN Chi-restraints excluded: chain A residue 1798 SER Chi-restraints excluded: chain A residue 1967 HIS Chi-restraints excluded: chain A residue 2034 ASP Chi-restraints excluded: chain A residue 2228 VAL Chi-restraints excluded: chain A residue 2332 THR Chi-restraints excluded: chain A residue 2436 ASP Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain A residue 2464 TYR Chi-restraints excluded: chain C residue 838 PHE Chi-restraints excluded: chain C residue 981 PHE Chi-restraints excluded: chain C residue 1013 HIS Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1407 ILE Chi-restraints excluded: chain C residue 1530 MET Chi-restraints excluded: chain C residue 1709 VAL Chi-restraints excluded: chain C residue 1731 MET Chi-restraints excluded: chain C residue 1776 LEU Chi-restraints excluded: chain C residue 1798 SER Chi-restraints excluded: chain C residue 1803 TYR Chi-restraints excluded: chain C residue 2228 VAL Chi-restraints excluded: chain C residue 2251 PHE Chi-restraints excluded: chain C residue 2464 TYR Chi-restraints excluded: chain C residue 2472 SER Chi-restraints excluded: chain C residue 2493 MET Chi-restraints excluded: chain C residue 2513 VAL Chi-restraints excluded: chain E residue 838 PHE Chi-restraints excluded: chain E residue 840 LEU Chi-restraints excluded: chain E residue 981 PHE Chi-restraints excluded: chain E residue 1192 LEU Chi-restraints excluded: chain E residue 1233 VAL Chi-restraints excluded: chain E residue 1246 ILE Chi-restraints excluded: chain E residue 1407 ILE Chi-restraints excluded: chain E residue 1516 LEU Chi-restraints excluded: chain E residue 1697 LEU Chi-restraints excluded: chain E residue 1701 VAL Chi-restraints excluded: chain E residue 1709 VAL Chi-restraints excluded: chain E residue 1731 MET Chi-restraints excluded: chain E residue 2228 VAL Chi-restraints excluded: chain E residue 2332 THR Chi-restraints excluded: chain E residue 2436 ASP Chi-restraints excluded: chain E residue 2448 ILE Chi-restraints excluded: chain E residue 2464 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 377 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 223 optimal weight: 9.9990 chunk 286 optimal weight: 5.9990 chunk 221 optimal weight: 2.9990 chunk 329 optimal weight: 6.9990 chunk 218 optimal weight: 2.9990 chunk 390 optimal weight: 0.2980 chunk 244 optimal weight: 0.1980 chunk 237 optimal weight: 0.9990 chunk 180 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1967 HIS C1107 GLN ** C1363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1503 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 34704 Z= 0.161 Angle : 0.565 10.512 46839 Z= 0.281 Chirality : 0.038 0.164 5181 Planarity : 0.004 0.050 5667 Dihedral : 11.115 102.606 5505 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.19 % Allowed : 19.44 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.14), residues: 3987 helix: 2.21 (0.10), residues: 2658 sheet: -0.01 (0.33), residues: 261 loop : -2.02 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C2429 HIS 0.016 0.001 HIS A1967 PHE 0.043 0.001 PHE E1954 TYR 0.028 0.001 TYR A1539 ARG 0.006 0.000 ARG E2407 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 386 time to evaluate : 4.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 972 GLN cc_start: 0.8514 (mp10) cc_final: 0.8053 (mp10) REVERT: A 1107 GLN cc_start: 0.7713 (tp40) cc_final: 0.6840 (tm-30) REVERT: A 1363 GLN cc_start: 0.6673 (pp30) cc_final: 0.6316 (pp30) REVERT: A 1495 MET cc_start: 0.3484 (mpp) cc_final: 0.2318 (ttt) REVERT: A 1745 TYR cc_start: 0.8473 (t80) cc_final: 0.8124 (t80) REVERT: A 2464 TYR cc_start: 0.7131 (OUTLIER) cc_final: 0.5621 (m-80) REVERT: C 838 PHE cc_start: 0.8049 (OUTLIER) cc_final: 0.7702 (m-80) REVERT: C 1107 GLN cc_start: 0.7820 (tp-100) cc_final: 0.7572 (tm-30) REVERT: C 1360 ARG cc_start: 0.8105 (ttm-80) cc_final: 0.7900 (mtm-85) REVERT: C 1495 MET cc_start: 0.1780 (mpp) cc_final: 0.0745 (ttt) REVERT: C 1546 LEU cc_start: 0.8844 (tt) cc_final: 0.8603 (tt) REVERT: C 1791 MET cc_start: 0.8451 (mmm) cc_final: 0.8187 (mmm) REVERT: C 2153 MET cc_start: 0.8460 (mmm) cc_final: 0.7630 (mtt) REVERT: C 2235 TYR cc_start: 0.7807 (m-80) cc_final: 0.7043 (m-80) REVERT: C 2270 MET cc_start: 0.7432 (mmm) cc_final: 0.7140 (mmm) REVERT: C 2464 TYR cc_start: 0.6904 (OUTLIER) cc_final: 0.5681 (m-80) REVERT: E 1264 MET cc_start: 0.6736 (mmt) cc_final: 0.6025 (mmt) REVERT: E 1494 MET cc_start: 0.5580 (mmp) cc_final: 0.4783 (mmt) REVERT: E 1495 MET cc_start: 0.2999 (mpp) cc_final: 0.1458 (ttt) REVERT: E 1525 LYS cc_start: 0.8722 (pptt) cc_final: 0.8412 (ptpt) REVERT: E 1995 PHE cc_start: 0.8092 (t80) cc_final: 0.7891 (t80) REVERT: E 2228 VAL cc_start: 0.9214 (OUTLIER) cc_final: 0.8936 (m) REVERT: E 2235 TYR cc_start: 0.7915 (m-80) cc_final: 0.7368 (m-80) REVERT: E 2436 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7804 (p0) REVERT: E 2464 TYR cc_start: 0.7178 (OUTLIER) cc_final: 0.5698 (m-80) outliers start: 74 outliers final: 49 residues processed: 434 average time/residue: 0.4461 time to fit residues: 322.4142 Evaluate side-chains 418 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 363 time to evaluate : 3.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1530 MET Chi-restraints excluded: chain A residue 1697 LEU Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain A residue 1709 VAL Chi-restraints excluded: chain A residue 1731 MET Chi-restraints excluded: chain A residue 1755 ASN Chi-restraints excluded: chain A residue 1798 SER Chi-restraints excluded: chain A residue 1967 HIS Chi-restraints excluded: chain A residue 2034 ASP Chi-restraints excluded: chain A residue 2332 THR Chi-restraints excluded: chain A residue 2436 ASP Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain A residue 2464 TYR Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 838 PHE Chi-restraints excluded: chain C residue 981 PHE Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1407 ILE Chi-restraints excluded: chain C residue 1697 LEU Chi-restraints excluded: chain C residue 1709 VAL Chi-restraints excluded: chain C residue 1731 MET Chi-restraints excluded: chain C residue 1776 LEU Chi-restraints excluded: chain C residue 1798 SER Chi-restraints excluded: chain C residue 1803 TYR Chi-restraints excluded: chain C residue 2228 VAL Chi-restraints excluded: chain C residue 2432 ILE Chi-restraints excluded: chain C residue 2464 TYR Chi-restraints excluded: chain C residue 2472 SER Chi-restraints excluded: chain C residue 2493 MET Chi-restraints excluded: chain C residue 2513 VAL Chi-restraints excluded: chain E residue 825 VAL Chi-restraints excluded: chain E residue 838 PHE Chi-restraints excluded: chain E residue 840 LEU Chi-restraints excluded: chain E residue 981 PHE Chi-restraints excluded: chain E residue 1095 ILE Chi-restraints excluded: chain E residue 1192 LEU Chi-restraints excluded: chain E residue 1246 ILE Chi-restraints excluded: chain E residue 1407 ILE Chi-restraints excluded: chain E residue 1516 LEU Chi-restraints excluded: chain E residue 1697 LEU Chi-restraints excluded: chain E residue 1701 VAL Chi-restraints excluded: chain E residue 1709 VAL Chi-restraints excluded: chain E residue 1731 MET Chi-restraints excluded: chain E residue 1967 HIS Chi-restraints excluded: chain E residue 2228 VAL Chi-restraints excluded: chain E residue 2436 ASP Chi-restraints excluded: chain E residue 2448 ILE Chi-restraints excluded: chain E residue 2464 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 241 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 233 optimal weight: 0.0060 chunk 117 optimal weight: 0.6980 chunk 76 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 chunk 265 optimal weight: 2.9990 chunk 192 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 306 optimal weight: 0.7980 overall best weight: 1.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1967 HIS ** C1363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1967 HIS E1107 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34704 Z= 0.187 Angle : 0.577 10.167 46839 Z= 0.286 Chirality : 0.038 0.197 5181 Planarity : 0.004 0.050 5667 Dihedral : 10.883 105.044 5505 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.36 % Allowed : 19.98 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.14), residues: 3987 helix: 2.17 (0.10), residues: 2679 sheet: 0.03 (0.33), residues: 261 loop : -2.05 (0.19), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C1754 HIS 0.017 0.001 HIS A1967 PHE 0.043 0.001 PHE A1954 TYR 0.021 0.001 TYR E1803 ARG 0.005 0.000 ARG E2407 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 374 time to evaluate : 3.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 838 PHE cc_start: 0.7948 (OUTLIER) cc_final: 0.7714 (m-80) REVERT: A 972 GLN cc_start: 0.8509 (mp10) cc_final: 0.8041 (mp10) REVERT: A 1107 GLN cc_start: 0.7660 (tp40) cc_final: 0.7041 (tm-30) REVERT: A 1363 GLN cc_start: 0.6615 (pp30) cc_final: 0.6316 (pp30) REVERT: A 1495 MET cc_start: 0.3465 (mpp) cc_final: 0.2314 (ttt) REVERT: A 2446 MET cc_start: 0.8782 (ttm) cc_final: 0.8558 (ttt) REVERT: A 2464 TYR cc_start: 0.7096 (OUTLIER) cc_final: 0.5596 (m-80) REVERT: C 838 PHE cc_start: 0.8082 (OUTLIER) cc_final: 0.7722 (m-80) REVERT: C 972 GLN cc_start: 0.8305 (mp10) cc_final: 0.7987 (mp10) REVERT: C 1360 ARG cc_start: 0.8113 (ttm-80) cc_final: 0.7847 (mtm-85) REVERT: C 1495 MET cc_start: 0.2036 (mpp) cc_final: 0.0944 (ttt) REVERT: C 1546 LEU cc_start: 0.8834 (tt) cc_final: 0.8573 (tt) REVERT: C 1791 MET cc_start: 0.8464 (mmm) cc_final: 0.8193 (mmm) REVERT: C 2235 TYR cc_start: 0.7873 (m-80) cc_final: 0.7109 (m-80) REVERT: C 2270 MET cc_start: 0.7524 (mmm) cc_final: 0.7233 (mmm) REVERT: C 2464 TYR cc_start: 0.6924 (OUTLIER) cc_final: 0.5599 (m-80) REVERT: E 1143 PHE cc_start: 0.5845 (m-80) cc_final: 0.5417 (m-10) REVERT: E 1264 MET cc_start: 0.6624 (mmt) cc_final: 0.5900 (mmt) REVERT: E 1494 MET cc_start: 0.5648 (mmp) cc_final: 0.5415 (mmp) REVERT: E 1495 MET cc_start: 0.2943 (mpp) cc_final: 0.1451 (ttt) REVERT: E 1525 LYS cc_start: 0.8689 (pptt) cc_final: 0.8425 (ptpt) REVERT: E 1791 MET cc_start: 0.8533 (mmm) cc_final: 0.8141 (mmm) REVERT: E 1995 PHE cc_start: 0.8145 (t80) cc_final: 0.7933 (t80) REVERT: E 2228 VAL cc_start: 0.9232 (OUTLIER) cc_final: 0.8974 (m) REVERT: E 2235 TYR cc_start: 0.7987 (m-80) cc_final: 0.7453 (m-80) REVERT: E 2436 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7823 (p0) REVERT: E 2464 TYR cc_start: 0.7065 (OUTLIER) cc_final: 0.5624 (m-80) outliers start: 80 outliers final: 55 residues processed: 429 average time/residue: 0.4319 time to fit residues: 306.3128 Evaluate side-chains 419 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 357 time to evaluate : 3.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 1013 HIS Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1697 LEU Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain A residue 1709 VAL Chi-restraints excluded: chain A residue 1731 MET Chi-restraints excluded: chain A residue 1755 ASN Chi-restraints excluded: chain A residue 1798 SER Chi-restraints excluded: chain A residue 1803 TYR Chi-restraints excluded: chain A residue 1967 HIS Chi-restraints excluded: chain A residue 2034 ASP Chi-restraints excluded: chain A residue 2332 THR Chi-restraints excluded: chain A residue 2436 ASP Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain A residue 2464 TYR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 838 PHE Chi-restraints excluded: chain C residue 1013 HIS Chi-restraints excluded: chain C residue 1153 LEU Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1407 ILE Chi-restraints excluded: chain C residue 1697 LEU Chi-restraints excluded: chain C residue 1701 VAL Chi-restraints excluded: chain C residue 1709 VAL Chi-restraints excluded: chain C residue 1731 MET Chi-restraints excluded: chain C residue 1776 LEU Chi-restraints excluded: chain C residue 1798 SER Chi-restraints excluded: chain C residue 1803 TYR Chi-restraints excluded: chain C residue 2228 VAL Chi-restraints excluded: chain C residue 2251 PHE Chi-restraints excluded: chain C residue 2432 ILE Chi-restraints excluded: chain C residue 2464 TYR Chi-restraints excluded: chain C residue 2472 SER Chi-restraints excluded: chain C residue 2493 MET Chi-restraints excluded: chain C residue 2513 VAL Chi-restraints excluded: chain E residue 825 VAL Chi-restraints excluded: chain E residue 838 PHE Chi-restraints excluded: chain E residue 840 LEU Chi-restraints excluded: chain E residue 981 PHE Chi-restraints excluded: chain E residue 1095 ILE Chi-restraints excluded: chain E residue 1192 LEU Chi-restraints excluded: chain E residue 1233 VAL Chi-restraints excluded: chain E residue 1407 ILE Chi-restraints excluded: chain E residue 1516 LEU Chi-restraints excluded: chain E residue 1697 LEU Chi-restraints excluded: chain E residue 1701 VAL Chi-restraints excluded: chain E residue 1709 VAL Chi-restraints excluded: chain E residue 1731 MET Chi-restraints excluded: chain E residue 1803 TYR Chi-restraints excluded: chain E residue 2228 VAL Chi-restraints excluded: chain E residue 2436 ASP Chi-restraints excluded: chain E residue 2448 ILE Chi-restraints excluded: chain E residue 2464 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 355 optimal weight: 5.9990 chunk 373 optimal weight: 0.0770 chunk 341 optimal weight: 0.6980 chunk 363 optimal weight: 0.8980 chunk 218 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 chunk 285 optimal weight: 2.9990 chunk 111 optimal weight: 0.2980 chunk 328 optimal weight: 7.9990 chunk 344 optimal weight: 0.9990 chunk 362 optimal weight: 6.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1967 HIS C1107 GLN ** C1363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1967 HIS E1526 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 34704 Z= 0.155 Angle : 0.570 9.895 46839 Z= 0.282 Chirality : 0.038 0.186 5181 Planarity : 0.004 0.050 5667 Dihedral : 10.524 105.837 5505 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.01 % Allowed : 20.30 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.14), residues: 3987 helix: 2.19 (0.10), residues: 2667 sheet: 0.16 (0.33), residues: 258 loop : -1.99 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C1754 HIS 0.023 0.001 HIS A1967 PHE 0.044 0.001 PHE A1954 TYR 0.032 0.001 TYR E1539 ARG 0.007 0.000 ARG C2407 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 394 time to evaluate : 3.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 972 GLN cc_start: 0.8510 (mp10) cc_final: 0.8001 (mp10) REVERT: A 1107 GLN cc_start: 0.7609 (tp40) cc_final: 0.7054 (tm-30) REVERT: A 1495 MET cc_start: 0.3529 (mpp) cc_final: 0.2438 (ttt) REVERT: A 1745 TYR cc_start: 0.8450 (t80) cc_final: 0.8087 (t80) REVERT: A 2446 MET cc_start: 0.8604 (ttm) cc_final: 0.8279 (ttt) REVERT: A 2464 TYR cc_start: 0.7052 (OUTLIER) cc_final: 0.5617 (m-80) REVERT: C 838 PHE cc_start: 0.8157 (OUTLIER) cc_final: 0.7855 (m-80) REVERT: C 972 GLN cc_start: 0.8304 (mp10) cc_final: 0.8005 (mp10) REVERT: C 1107 GLN cc_start: 0.7835 (tp-100) cc_final: 0.7618 (tm-30) REVERT: C 1360 ARG cc_start: 0.8055 (ttm-80) cc_final: 0.7755 (mtm-85) REVERT: C 1495 MET cc_start: 0.1996 (mpp) cc_final: 0.1002 (ttt) REVERT: C 1546 LEU cc_start: 0.8811 (tt) cc_final: 0.8536 (tt) REVERT: C 1791 MET cc_start: 0.8446 (mmm) cc_final: 0.8181 (mmm) REVERT: C 2153 MET cc_start: 0.8395 (mmm) cc_final: 0.7433 (mtt) REVERT: C 2270 MET cc_start: 0.7453 (mmm) cc_final: 0.7195 (mmm) REVERT: C 2464 TYR cc_start: 0.6957 (OUTLIER) cc_final: 0.5622 (m-80) REVERT: E 1264 MET cc_start: 0.6575 (mmt) cc_final: 0.5798 (mmt) REVERT: E 1494 MET cc_start: 0.5652 (mmp) cc_final: 0.5411 (mmp) REVERT: E 1495 MET cc_start: 0.2928 (mpp) cc_final: 0.1441 (ttt) REVERT: E 1791 MET cc_start: 0.8521 (mmm) cc_final: 0.8196 (mmm) REVERT: E 1995 PHE cc_start: 0.8210 (t80) cc_final: 0.7991 (t80) REVERT: E 2228 VAL cc_start: 0.9211 (OUTLIER) cc_final: 0.8938 (m) REVERT: E 2235 TYR cc_start: 0.7824 (m-80) cc_final: 0.7269 (m-80) REVERT: E 2436 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7783 (p0) REVERT: E 2464 TYR cc_start: 0.7061 (OUTLIER) cc_final: 0.5641 (m-80) outliers start: 68 outliers final: 48 residues processed: 441 average time/residue: 0.4426 time to fit residues: 326.7910 Evaluate side-chains 420 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 366 time to evaluate : 3.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1697 LEU Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain A residue 1709 VAL Chi-restraints excluded: chain A residue 1731 MET Chi-restraints excluded: chain A residue 1798 SER Chi-restraints excluded: chain A residue 1967 HIS Chi-restraints excluded: chain A residue 2332 THR Chi-restraints excluded: chain A residue 2436 ASP Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain A residue 2464 TYR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 838 PHE Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1407 ILE Chi-restraints excluded: chain C residue 1697 LEU Chi-restraints excluded: chain C residue 1709 VAL Chi-restraints excluded: chain C residue 1731 MET Chi-restraints excluded: chain C residue 1776 LEU Chi-restraints excluded: chain C residue 1798 SER Chi-restraints excluded: chain C residue 1803 TYR Chi-restraints excluded: chain C residue 2228 VAL Chi-restraints excluded: chain C residue 2432 ILE Chi-restraints excluded: chain C residue 2448 ILE Chi-restraints excluded: chain C residue 2464 TYR Chi-restraints excluded: chain C residue 2472 SER Chi-restraints excluded: chain C residue 2493 MET Chi-restraints excluded: chain C residue 2513 VAL Chi-restraints excluded: chain E residue 825 VAL Chi-restraints excluded: chain E residue 838 PHE Chi-restraints excluded: chain E residue 981 PHE Chi-restraints excluded: chain E residue 1095 ILE Chi-restraints excluded: chain E residue 1192 LEU Chi-restraints excluded: chain E residue 1246 ILE Chi-restraints excluded: chain E residue 1407 ILE Chi-restraints excluded: chain E residue 1516 LEU Chi-restraints excluded: chain E residue 1697 LEU Chi-restraints excluded: chain E residue 1701 VAL Chi-restraints excluded: chain E residue 1709 VAL Chi-restraints excluded: chain E residue 1731 MET Chi-restraints excluded: chain E residue 2228 VAL Chi-restraints excluded: chain E residue 2332 THR Chi-restraints excluded: chain E residue 2434 LEU Chi-restraints excluded: chain E residue 2436 ASP Chi-restraints excluded: chain E residue 2448 ILE Chi-restraints excluded: chain E residue 2464 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 238 optimal weight: 9.9990 chunk 384 optimal weight: 0.8980 chunk 234 optimal weight: 9.9990 chunk 182 optimal weight: 0.9990 chunk 267 optimal weight: 0.7980 chunk 403 optimal weight: 0.7980 chunk 371 optimal weight: 0.8980 chunk 321 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 197 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1967 HIS ** C1363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1503 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 34704 Z= 0.174 Angle : 0.585 9.868 46839 Z= 0.290 Chirality : 0.038 0.179 5181 Planarity : 0.004 0.050 5667 Dihedral : 10.416 106.838 5505 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.95 % Allowed : 20.83 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.14), residues: 3987 helix: 2.15 (0.10), residues: 2685 sheet: -0.01 (0.33), residues: 264 loop : -2.04 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C1754 HIS 0.015 0.001 HIS A1967 PHE 0.059 0.001 PHE C1954 TYR 0.031 0.001 TYR E1539 ARG 0.007 0.000 ARG C2407 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 386 time to evaluate : 3.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 972 GLN cc_start: 0.8504 (mp10) cc_final: 0.7990 (mp10) REVERT: A 1107 GLN cc_start: 0.7524 (tp40) cc_final: 0.6975 (tm-30) REVERT: A 1360 ARG cc_start: 0.8270 (ttm-80) cc_final: 0.7927 (mtm-85) REVERT: A 1495 MET cc_start: 0.3362 (mpp) cc_final: 0.2277 (ttt) REVERT: A 2446 MET cc_start: 0.8640 (ttm) cc_final: 0.8312 (ttt) REVERT: A 2464 TYR cc_start: 0.7029 (OUTLIER) cc_final: 0.5602 (m-80) REVERT: C 838 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.7852 (m-80) REVERT: C 972 GLN cc_start: 0.8297 (mp10) cc_final: 0.7996 (mp10) REVERT: C 1264 MET cc_start: 0.6799 (mmm) cc_final: 0.6200 (mmm) REVERT: C 1360 ARG cc_start: 0.8042 (ttm-80) cc_final: 0.7756 (mtm-85) REVERT: C 1495 MET cc_start: 0.1971 (mpp) cc_final: 0.1001 (ttt) REVERT: C 1546 LEU cc_start: 0.8819 (tt) cc_final: 0.8541 (tt) REVERT: C 1791 MET cc_start: 0.8460 (mmm) cc_final: 0.8176 (mmm) REVERT: C 2153 MET cc_start: 0.8442 (mmm) cc_final: 0.7480 (mtt) REVERT: C 2235 TYR cc_start: 0.7821 (m-80) cc_final: 0.7000 (m-80) REVERT: C 2270 MET cc_start: 0.7489 (mmm) cc_final: 0.7213 (mmm) REVERT: C 2464 TYR cc_start: 0.6994 (OUTLIER) cc_final: 0.5609 (m-80) REVERT: E 1264 MET cc_start: 0.6591 (mmt) cc_final: 0.5848 (mmt) REVERT: E 1494 MET cc_start: 0.5661 (mmp) cc_final: 0.5417 (mmp) REVERT: E 1495 MET cc_start: 0.2919 (mpp) cc_final: 0.1441 (ttt) REVERT: E 1525 LYS cc_start: 0.8782 (ptpt) cc_final: 0.8475 (ptpt) REVERT: E 1791 MET cc_start: 0.8525 (mmm) cc_final: 0.8208 (mmm) REVERT: E 1995 PHE cc_start: 0.8231 (t80) cc_final: 0.8005 (t80) REVERT: E 2228 VAL cc_start: 0.9232 (OUTLIER) cc_final: 0.8974 (m) REVERT: E 2235 TYR cc_start: 0.7917 (m-80) cc_final: 0.7367 (m-80) REVERT: E 2436 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7790 (p0) REVERT: E 2464 TYR cc_start: 0.7031 (OUTLIER) cc_final: 0.5565 (m-80) outliers start: 66 outliers final: 50 residues processed: 429 average time/residue: 0.4481 time to fit residues: 315.4011 Evaluate side-chains 423 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 367 time to evaluate : 3.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1359 TYR Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1697 LEU Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain A residue 1709 VAL Chi-restraints excluded: chain A residue 1731 MET Chi-restraints excluded: chain A residue 1798 SER Chi-restraints excluded: chain A residue 2332 THR Chi-restraints excluded: chain A residue 2436 ASP Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain A residue 2464 TYR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 838 PHE Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1407 ILE Chi-restraints excluded: chain C residue 1697 LEU Chi-restraints excluded: chain C residue 1701 VAL Chi-restraints excluded: chain C residue 1709 VAL Chi-restraints excluded: chain C residue 1731 MET Chi-restraints excluded: chain C residue 1776 LEU Chi-restraints excluded: chain C residue 1798 SER Chi-restraints excluded: chain C residue 1803 TYR Chi-restraints excluded: chain C residue 2228 VAL Chi-restraints excluded: chain C residue 2251 PHE Chi-restraints excluded: chain C residue 2332 THR Chi-restraints excluded: chain C residue 2432 ILE Chi-restraints excluded: chain C residue 2448 ILE Chi-restraints excluded: chain C residue 2464 TYR Chi-restraints excluded: chain C residue 2472 SER Chi-restraints excluded: chain C residue 2493 MET Chi-restraints excluded: chain C residue 2513 VAL Chi-restraints excluded: chain E residue 825 VAL Chi-restraints excluded: chain E residue 838 PHE Chi-restraints excluded: chain E residue 981 PHE Chi-restraints excluded: chain E residue 1095 ILE Chi-restraints excluded: chain E residue 1192 LEU Chi-restraints excluded: chain E residue 1246 ILE Chi-restraints excluded: chain E residue 1407 ILE Chi-restraints excluded: chain E residue 1697 LEU Chi-restraints excluded: chain E residue 1701 VAL Chi-restraints excluded: chain E residue 1709 VAL Chi-restraints excluded: chain E residue 1731 MET Chi-restraints excluded: chain E residue 2228 VAL Chi-restraints excluded: chain E residue 2332 THR Chi-restraints excluded: chain E residue 2434 LEU Chi-restraints excluded: chain E residue 2436 ASP Chi-restraints excluded: chain E residue 2448 ILE Chi-restraints excluded: chain E residue 2464 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 255 optimal weight: 5.9990 chunk 342 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 296 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 321 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 330 optimal weight: 20.0000 chunk 40 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1239 GLN ** A1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1107 GLN ** C1363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1503 GLN C1967 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.132898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.101654 restraints weight = 63672.509| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 3.03 r_work: 0.3048 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 34704 Z= 0.233 Angle : 0.608 9.875 46839 Z= 0.303 Chirality : 0.039 0.179 5181 Planarity : 0.004 0.050 5667 Dihedral : 10.525 117.560 5505 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.95 % Allowed : 20.89 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.14), residues: 3987 helix: 2.14 (0.10), residues: 2685 sheet: -0.13 (0.32), residues: 264 loop : -2.01 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C1754 HIS 0.010 0.001 HIS A1304 PHE 0.053 0.002 PHE C1954 TYR 0.027 0.001 TYR E1539 ARG 0.005 0.000 ARG E2546 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7548.61 seconds wall clock time: 136 minutes 57.38 seconds (8217.38 seconds total)