Starting phenix.real_space_refine on Sun Mar 17 23:02:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tfk_41232/03_2024/8tfk_41232_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tfk_41232/03_2024/8tfk_41232.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tfk_41232/03_2024/8tfk_41232_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tfk_41232/03_2024/8tfk_41232_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tfk_41232/03_2024/8tfk_41232_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tfk_41232/03_2024/8tfk_41232.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tfk_41232/03_2024/8tfk_41232.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tfk_41232/03_2024/8tfk_41232_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tfk_41232/03_2024/8tfk_41232_trim_updated.pdb" } resolution = 2.66 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= 0.002 sd= 0.080 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 36 5.49 5 Mg 36 5.21 5 S 193 5.16 5 C 26718 2.51 5 N 7114 2.21 5 O 7845 1.98 5 H 39601 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 11": "OE1" <-> "OE2" Residue "A ASP 12": "OD1" <-> "OD2" Residue "A ASP 77": "OD1" <-> "OD2" Residue "A TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 104": "OD1" <-> "OD2" Residue "A ASP 174": "OD1" <-> "OD2" Residue "A ASP 176": "OD1" <-> "OD2" Residue "A GLU 180": "OE1" <-> "OE2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A ASP 201": "OD1" <-> "OD2" Residue "A PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 307": "OE1" <-> "OE2" Residue "A GLU 384": "OE1" <-> "OE2" Residue "A GLU 397": "OE1" <-> "OE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A GLU 439": "OE1" <-> "OE2" Residue "B GLU 11": "OE1" <-> "OE2" Residue "B ASP 12": "OD1" <-> "OD2" Residue "B GLU 19": "OE1" <-> "OE2" Residue "B ASP 21": "OD1" <-> "OD2" Residue "B GLU 69": "OE1" <-> "OE2" Residue "B GLU 124": "OE1" <-> "OE2" Residue "B GLU 137": "OE1" <-> "OE2" Residue "B PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 152": "OE1" <-> "OE2" Residue "B TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 174": "OD1" <-> "OD2" Residue "B ASP 176": "OD1" <-> "OD2" Residue "B GLU 180": "OE1" <-> "OE2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "B GLU 192": "OE1" <-> "OE2" Residue "B ASP 201": "OD1" <-> "OD2" Residue "B ASP 206": "OD1" <-> "OD2" Residue "B TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 336": "OE1" <-> "OE2" Residue "B ASP 341": "OD1" <-> "OD2" Residue "B GLU 382": "OE1" <-> "OE2" Residue "B GLU 397": "OE1" <-> "OE2" Residue "B GLU 410": "OE1" <-> "OE2" Residue "B GLU 425": "OE1" <-> "OE2" Residue "B GLU 427": "OE1" <-> "OE2" Residue "B ASP 429": "OD1" <-> "OD2" Residue "C PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 51": "OE1" <-> "OE2" Residue "C PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 71": "OD1" <-> "OD2" Residue "C PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 122": "OE1" <-> "OE2" Residue "C GLU 124": "OE1" <-> "OE2" Residue "C GLU 137": "OE1" <-> "OE2" Residue "C ASP 144": "OD1" <-> "OD2" Residue "C GLU 152": "OE1" <-> "OE2" Residue "C TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 256": "OD1" <-> "OD2" Residue "C TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "C ASP 400": "OD1" <-> "OD2" Residue "C PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 414": "OE1" <-> "OE2" Residue "C GLU 425": "OE1" <-> "OE2" Residue "D ASP 21": "OD1" <-> "OD2" Residue "D GLU 51": "OE1" <-> "OE2" Residue "D PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 99": "OD1" <-> "OD2" Residue "D ASP 104": "OD1" <-> "OD2" Residue "D GLU 124": "OE1" <-> "OE2" Residue "D GLU 135": "OE1" <-> "OE2" Residue "D GLU 152": "OE1" <-> "OE2" Residue "D TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 180": "OE1" <-> "OE2" Residue "D PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 206": "OD1" <-> "OD2" Residue "D ASP 256": "OD1" <-> "OD2" Residue "D ASP 265": "OD1" <-> "OD2" Residue "D TYR 276": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 307": "OE1" <-> "OE2" Residue "D ASP 341": "OD1" <-> "OD2" Residue "D GLU 384": "OE1" <-> "OE2" Residue "D GLU 385": "OE1" <-> "OE2" Residue "D GLU 397": "OE1" <-> "OE2" Residue "D ASP 400": "OD1" <-> "OD2" Residue "D GLU 410": "OE1" <-> "OE2" Residue "D GLU 414": "OE1" <-> "OE2" Residue "D GLU 425": "OE1" <-> "OE2" Residue "D ASP 429": "OD1" <-> "OD2" Residue "D GLU 430": "OE1" <-> "OE2" Residue "E ASP 12": "OD1" <-> "OD2" Residue "E ASP 21": "OD1" <-> "OD2" Residue "E GLU 68": "OE1" <-> "OE2" Residue "E ASP 71": "OD1" <-> "OD2" Residue "E PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 111": "OD1" <-> "OD2" Residue "E GLU 122": "OE1" <-> "OE2" Residue "E PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 152": "OE1" <-> "OE2" Residue "E TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 176": "OD1" <-> "OD2" Residue "E PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 187": "OE1" <-> "OE2" Residue "E ASP 201": "OD1" <-> "OD2" Residue "E ASP 206": "OD1" <-> "OD2" Residue "E ASP 256": "OD1" <-> "OD2" Residue "E ASP 394": "OD1" <-> "OD2" Residue "E GLU 414": "OE1" <-> "OE2" Residue "E GLU 425": "OE1" <-> "OE2" Residue "E ASP 429": "OD1" <-> "OD2" Residue "E TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 12": "OD1" <-> "OD2" Residue "F ASP 21": "OD1" <-> "OD2" Residue "F GLU 51": "OE1" <-> "OE2" Residue "F PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 122": "OE1" <-> "OE2" Residue "F GLU 124": "OE1" <-> "OE2" Residue "F GLU 152": "OE1" <-> "OE2" Residue "F GLU 180": "OE1" <-> "OE2" Residue "F PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 385": "OE1" <-> "OE2" Residue "F GLU 427": "OE1" <-> "OE2" Residue "F ASP 429": "OD1" <-> "OD2" Residue "F GLU 430": "OE1" <-> "OE2" Residue "G ASP 21": "OD1" <-> "OD2" Residue "G GLU 48": "OE1" <-> "OE2" Residue "G GLU 124": "OE1" <-> "OE2" Residue "G PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 135": "OE1" <-> "OE2" Residue "G PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 144": "OD1" <-> "OD2" Residue "G TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 180": "OE1" <-> "OE2" Residue "G GLU 187": "OE1" <-> "OE2" Residue "G TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 265": "OD1" <-> "OD2" Residue "G GLU 414": "OE1" <-> "OE2" Residue "G TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 425": "OE1" <-> "OE2" Residue "G ASP 429": "OD1" <-> "OD2" Residue "H GLU 51": "OE1" <-> "OE2" Residue "H PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 71": "OD1" <-> "OD2" Residue "H PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 124": "OE1" <-> "OE2" Residue "H GLU 187": "OE1" <-> "OE2" Residue "H ASP 341": "OD1" <-> "OD2" Residue "H ASP 366": "OD1" <-> "OD2" Residue "H GLU 384": "OE1" <-> "OE2" Residue "H ASP 400": "OD1" <-> "OD2" Residue "H GLU 414": "OE1" <-> "OE2" Residue "H GLU 427": "OE1" <-> "OE2" Residue "I GLU 11": "OE1" <-> "OE2" Residue "I ASP 12": "OD1" <-> "OD2" Residue "I ASP 21": "OD1" <-> "OD2" Residue "I GLU 44": "OE1" <-> "OE2" Residue "I GLU 48": "OE1" <-> "OE2" Residue "I GLU 51": "OE1" <-> "OE2" Residue "I ASP 71": "OD1" <-> "OD2" Residue "I PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 124": "OE1" <-> "OE2" Residue "I GLU 135": "OE1" <-> "OE2" Residue "I PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 152": "OE1" <-> "OE2" Residue "I TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 180": "OE1" <-> "OE2" Residue "I GLU 187": "OE1" <-> "OE2" Residue "I ASP 206": "OD1" <-> "OD2" Residue "I PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 307": "OE1" <-> "OE2" Residue "I GLU 336": "OE1" <-> "OE2" Residue "I GLU 385": "OE1" <-> "OE2" Residue "I GLU 425": "OE1" <-> "OE2" Residue "J GLU 11": "OE1" <-> "OE2" Residue "J ASP 12": "OD1" <-> "OD2" Residue "J GLU 68": "OE1" <-> "OE2" Residue "J ASP 71": "OD1" <-> "OD2" Residue "J ASP 99": "OD1" <-> "OD2" Residue "J TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 122": "OE1" <-> "OE2" Residue "J ASP 176": "OD1" <-> "OD2" Residue "J GLU 180": "OE1" <-> "OE2" Residue "J ASP 206": "OD1" <-> "OD2" Residue "J TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ASP 265": "OD1" <-> "OD2" Residue "J TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 384": "OE1" <-> "OE2" Residue "J PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 425": "OE1" <-> "OE2" Residue "K PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 122": "OE1" <-> "OE2" Residue "K ASP 144": "OD1" <-> "OD2" Residue "K TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 174": "OD1" <-> "OD2" Residue "K ASP 176": "OD1" <-> "OD2" Residue "K GLU 187": "OE1" <-> "OE2" Residue "K ASP 201": "OD1" <-> "OD2" Residue "K ARG 338": not complete - not flipped Residue "K ASP 341": "OD1" <-> "OD2" Residue "K GLU 382": "OE1" <-> "OE2" Residue "K GLU 397": "OE1" <-> "OE2" Residue "K PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 414": "OE1" <-> "OE2" Residue "K ASP 429": "OD1" <-> "OD2" Residue "K GLU 430": "OE1" <-> "OE2" Residue "L ASP 31": "OD1" <-> "OD2" Residue "L PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 152": "OE1" <-> "OE2" Residue "L TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 174": "OD1" <-> "OD2" Residue "L ASP 176": "OD1" <-> "OD2" Residue "L GLU 180": "OE1" <-> "OE2" Residue "L ASP 201": "OD1" <-> "OD2" Residue "L ASP 206": "OD1" <-> "OD2" Residue "L PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 384": "OE1" <-> "OE2" Residue "L GLU 397": "OE1" <-> "OE2" Residue "L GLU 425": "OE1" <-> "OE2" Residue "L GLU 430": "OE1" <-> "OE2" Residue "L GLU 439": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 81543 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 6734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 6734 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 413} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 6750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 6750 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 413} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 6779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 6779 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 413} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "D" Number of atoms: 6752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 6752 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 413} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "E" Number of atoms: 6725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 6725 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 413} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 7, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 42 Chain: "F" Number of atoms: 6755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 6755 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 413} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "G" Number of atoms: 6756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 6756 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 413} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "H" Number of atoms: 6750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 6750 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 413} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 41 Chain: "I" Number of atoms: 6764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 6764 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 413} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "J" Number of atoms: 6755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 6755 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 413} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "K" Number of atoms: 6755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 6755 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 413} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "L" Number of atoms: 6728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 6728 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 413} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 48 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 45 Unusual residues: {' MG': 3, 'ADP': 1} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 45 Unusual residues: {' MG': 3, 'ADP': 1} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 45 Unusual residues: {' MG': 3, 'ADP': 1} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 45 Unusual residues: {' MG': 3, 'ADP': 1} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Chain: "E" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 45 Unusual residues: {' MG': 3, 'ADP': 1} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Chain: "F" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 45 Unusual residues: {' MG': 3, 'ADP': 1} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Chain: "G" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 45 Unusual residues: {' MG': 3, 'ADP': 1} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Chain: "H" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 45 Unusual residues: {' MG': 3, 'ADP': 1} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Chain: "I" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 45 Unusual residues: {' MG': 3, 'ADP': 1} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Chain: "J" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 45 Unusual residues: {' MG': 3, 'ADP': 1} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Chain: "K" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 45 Unusual residues: {' MG': 3, 'ADP': 1} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Chain: "L" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 45 Unusual residues: {' MG': 3, 'ADP': 1} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Time building chain proxies: 27.13, per 1000 atoms: 0.33 Number of scatterers: 81543 At special positions: 0 Unit cell: (150.48, 161.04, 121.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 193 16.00 P 36 15.00 Mg 36 11.99 O 7845 8.00 N 7114 7.00 C 26718 6.00 H 39601 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 55.41 Conformation dependent library (CDL) restraints added in 7.6 seconds 10512 Ramachandran restraints generated. 5256 Oldfield, 0 Emsley, 5256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9840 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 197 helices and 58 sheets defined 37.9% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.62 Creating SS restraints... Processing helix chain 'A' and resid 10 through 19 removed outlier: 3.794A pdb=" N LEU A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 52 removed outlier: 4.435A pdb=" N GLU A 47 " --> pdb=" O GLU A 44 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN A 52 " --> pdb=" O ALA A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 80 No H-bonds generated for 'chain 'A' and resid 78 through 80' Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.181A pdb=" N MET A 126 " --> pdb=" O GLU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 182 Processing helix chain 'A' and resid 207 through 228 Processing helix chain 'A' and resid 267 through 269 No H-bonds generated for 'chain 'A' and resid 267 through 269' Processing helix chain 'A' and resid 272 through 292 removed outlier: 4.927A pdb=" N ARG A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N GLU A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE A 288 " --> pdb=" O HIS A 284 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ALA A 290 " --> pdb=" O ARG A 286 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N VAL A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 299 Processing helix chain 'A' and resid 346 through 362 Processing helix chain 'A' and resid 375 through 377 No H-bonds generated for 'chain 'A' and resid 375 through 377' Processing helix chain 'A' and resid 380 through 385 Processing helix chain 'A' and resid 395 through 403 Processing helix chain 'A' and resid 407 through 412 Processing helix chain 'A' and resid 414 through 432 Processing helix chain 'A' and resid 437 through 443 Processing helix chain 'B' and resid 10 through 19 Processing helix chain 'B' and resid 43 through 52 removed outlier: 4.577A pdb=" N GLU B 47 " --> pdb=" O GLU B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 80 No H-bonds generated for 'chain 'B' and resid 78 through 80' Processing helix chain 'B' and resid 112 through 126 Processing helix chain 'B' and resid 169 through 182 Processing helix chain 'B' and resid 207 through 228 removed outlier: 3.689A pdb=" N VAL B 215 " --> pdb=" O ALA B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 269 No H-bonds generated for 'chain 'B' and resid 267 through 269' Processing helix chain 'B' and resid 272 through 292 removed outlier: 4.985A pdb=" N ARG B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N GLU B 287 " --> pdb=" O LYS B 283 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE B 288 " --> pdb=" O HIS B 284 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ALA B 290 " --> pdb=" O ARG B 286 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N VAL B 291 " --> pdb=" O GLU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 299 Processing helix chain 'B' and resid 346 through 362 removed outlier: 3.528A pdb=" N GLY B 360 " --> pdb=" O ALA B 356 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE B 361 " --> pdb=" O GLY B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 386 Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 407 through 412 Processing helix chain 'B' and resid 414 through 432 Processing helix chain 'B' and resid 437 through 443 Processing helix chain 'C' and resid 10 through 19 removed outlier: 3.594A pdb=" N LEU C 14 " --> pdb=" O LYS C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 52 removed outlier: 4.580A pdb=" N GLU C 47 " --> pdb=" O GLU C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 60 No H-bonds generated for 'chain 'C' and resid 58 through 60' Processing helix chain 'C' and resid 67 through 69 No H-bonds generated for 'chain 'C' and resid 67 through 69' Processing helix chain 'C' and resid 78 through 80 No H-bonds generated for 'chain 'C' and resid 78 through 80' Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.545A pdb=" N LYS C 117 " --> pdb=" O ARG C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 181 Processing helix chain 'C' and resid 207 through 228 Processing helix chain 'C' and resid 267 through 269 No H-bonds generated for 'chain 'C' and resid 267 through 269' Processing helix chain 'C' and resid 272 through 292 removed outlier: 4.915A pdb=" N ARG C 286 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLU C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE C 288 " --> pdb=" O HIS C 284 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ALA C 290 " --> pdb=" O ARG C 286 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N VAL C 291 " --> pdb=" O GLU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 298 No H-bonds generated for 'chain 'C' and resid 296 through 298' Processing helix chain 'C' and resid 346 through 362 Processing helix chain 'C' and resid 375 through 377 No H-bonds generated for 'chain 'C' and resid 375 through 377' Processing helix chain 'C' and resid 380 through 385 Processing helix chain 'C' and resid 395 through 403 Processing helix chain 'C' and resid 407 through 412 Processing helix chain 'C' and resid 414 through 431 Processing helix chain 'C' and resid 437 through 443 Processing helix chain 'D' and resid 10 through 19 Processing helix chain 'D' and resid 43 through 52 removed outlier: 4.534A pdb=" N GLU D 47 " --> pdb=" O GLU D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 60 No H-bonds generated for 'chain 'D' and resid 58 through 60' Processing helix chain 'D' and resid 78 through 80 No H-bonds generated for 'chain 'D' and resid 78 through 80' Processing helix chain 'D' and resid 112 through 125 removed outlier: 3.582A pdb=" N LYS D 117 " --> pdb=" O ARG D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 181 Processing helix chain 'D' and resid 207 through 228 removed outlier: 3.538A pdb=" N LYS D 228 " --> pdb=" O ILE D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 269 No H-bonds generated for 'chain 'D' and resid 267 through 269' Processing helix chain 'D' and resid 272 through 282 Processing helix chain 'D' and resid 285 through 292 removed outlier: 5.262A pdb=" N ALA D 290 " --> pdb=" O ARG D 286 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N VAL D 291 " --> pdb=" O GLU D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 299 No H-bonds generated for 'chain 'D' and resid 297 through 299' Processing helix chain 'D' and resid 346 through 361 Processing helix chain 'D' and resid 380 through 385 Processing helix chain 'D' and resid 395 through 403 Processing helix chain 'D' and resid 407 through 412 Processing helix chain 'D' and resid 414 through 432 Processing helix chain 'D' and resid 437 through 443 Processing helix chain 'E' and resid 10 through 19 Processing helix chain 'E' and resid 43 through 52 removed outlier: 4.290A pdb=" N GLU E 47 " --> pdb=" O GLU E 44 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE E 50 " --> pdb=" O GLU E 47 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASN E 52 " --> pdb=" O ALA E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 125 Processing helix chain 'E' and resid 169 through 181 Processing helix chain 'E' and resid 207 through 228 Processing helix chain 'E' and resid 267 through 269 No H-bonds generated for 'chain 'E' and resid 267 through 269' Processing helix chain 'E' and resid 272 through 283 Processing helix chain 'E' and resid 285 through 292 removed outlier: 5.439A pdb=" N ALA E 290 " --> pdb=" O ARG E 286 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N VAL E 291 " --> pdb=" O GLU E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 298 No H-bonds generated for 'chain 'E' and resid 296 through 298' Processing helix chain 'E' and resid 330 through 332 No H-bonds generated for 'chain 'E' and resid 330 through 332' Processing helix chain 'E' and resid 346 through 362 Processing helix chain 'E' and resid 375 through 377 No H-bonds generated for 'chain 'E' and resid 375 through 377' Processing helix chain 'E' and resid 380 through 386 Processing helix chain 'E' and resid 395 through 403 Processing helix chain 'E' and resid 407 through 412 Processing helix chain 'E' and resid 414 through 429 removed outlier: 3.576A pdb=" N ALA E 423 " --> pdb=" O HIS E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 442 Processing helix chain 'F' and resid 10 through 19 Processing helix chain 'F' and resid 43 through 51 removed outlier: 4.512A pdb=" N GLU F 47 " --> pdb=" O GLU F 44 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU F 51 " --> pdb=" O GLU F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 60 No H-bonds generated for 'chain 'F' and resid 58 through 60' Processing helix chain 'F' and resid 78 through 80 No H-bonds generated for 'chain 'F' and resid 78 through 80' Processing helix chain 'F' and resid 112 through 125 Processing helix chain 'F' and resid 169 through 182 Processing helix chain 'F' and resid 207 through 228 removed outlier: 3.515A pdb=" N LYS F 228 " --> pdb=" O ILE F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 269 No H-bonds generated for 'chain 'F' and resid 267 through 269' Processing helix chain 'F' and resid 272 through 292 removed outlier: 4.982A pdb=" N ARG F 286 " --> pdb=" O LEU F 282 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N GLU F 287 " --> pdb=" O LYS F 283 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE F 288 " --> pdb=" O HIS F 284 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ALA F 290 " --> pdb=" O ARG F 286 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N VAL F 291 " --> pdb=" O GLU F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 301 Processing helix chain 'F' and resid 346 through 362 Processing helix chain 'F' and resid 375 through 377 No H-bonds generated for 'chain 'F' and resid 375 through 377' Processing helix chain 'F' and resid 380 through 386 Processing helix chain 'F' and resid 395 through 403 Processing helix chain 'F' and resid 406 through 412 Processing helix chain 'F' and resid 414 through 432 Processing helix chain 'F' and resid 437 through 443 Processing helix chain 'G' and resid 10 through 19 Processing helix chain 'G' and resid 43 through 51 removed outlier: 4.271A pdb=" N GLU G 47 " --> pdb=" O GLU G 44 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE G 50 " --> pdb=" O GLU G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 60 No H-bonds generated for 'chain 'G' and resid 58 through 60' Processing helix chain 'G' and resid 78 through 80 No H-bonds generated for 'chain 'G' and resid 78 through 80' Processing helix chain 'G' and resid 112 through 126 Processing helix chain 'G' and resid 169 through 181 Processing helix chain 'G' and resid 207 through 228 removed outlier: 3.635A pdb=" N VAL G 215 " --> pdb=" O ALA G 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 267 through 269 No H-bonds generated for 'chain 'G' and resid 267 through 269' Processing helix chain 'G' and resid 272 through 282 Processing helix chain 'G' and resid 285 through 292 removed outlier: 5.419A pdb=" N ALA G 290 " --> pdb=" O ARG G 286 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N VAL G 291 " --> pdb=" O GLU G 287 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 301 removed outlier: 3.596A pdb=" N TYR G 299 " --> pdb=" O VAL G 296 " (cutoff:3.500A) Processing helix chain 'G' and resid 330 through 332 No H-bonds generated for 'chain 'G' and resid 330 through 332' Processing helix chain 'G' and resid 346 through 362 Processing helix chain 'G' and resid 380 through 385 Processing helix chain 'G' and resid 395 through 403 Processing helix chain 'G' and resid 406 through 412 Processing helix chain 'G' and resid 414 through 432 Processing helix chain 'G' and resid 437 through 443 Processing helix chain 'H' and resid 10 through 19 Processing helix chain 'H' and resid 43 through 52 removed outlier: 4.460A pdb=" N GLU H 47 " --> pdb=" O GLU H 44 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASN H 52 " --> pdb=" O ALA H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 60 No H-bonds generated for 'chain 'H' and resid 58 through 60' Processing helix chain 'H' and resid 112 through 126 removed outlier: 3.552A pdb=" N GLU H 122 " --> pdb=" O THR H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 182 Processing helix chain 'H' and resid 207 through 228 Processing helix chain 'H' and resid 267 through 269 No H-bonds generated for 'chain 'H' and resid 267 through 269' Processing helix chain 'H' and resid 272 through 292 removed outlier: 3.528A pdb=" N HIS H 284 " --> pdb=" O GLY H 280 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ARG H 286 " --> pdb=" O LEU H 282 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N GLU H 287 " --> pdb=" O LYS H 283 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE H 288 " --> pdb=" O HIS H 284 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ALA H 290 " --> pdb=" O ARG H 286 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL H 291 " --> pdb=" O GLU H 287 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 298 No H-bonds generated for 'chain 'H' and resid 296 through 298' Processing helix chain 'H' and resid 346 through 362 Processing helix chain 'H' and resid 380 through 386 Processing helix chain 'H' and resid 395 through 403 Processing helix chain 'H' and resid 407 through 412 Processing helix chain 'H' and resid 414 through 432 removed outlier: 3.642A pdb=" N ALA H 423 " --> pdb=" O HIS H 419 " (cutoff:3.500A) Processing helix chain 'H' and resid 437 through 443 Processing helix chain 'I' and resid 10 through 20 Processing helix chain 'I' and resid 43 through 52 removed outlier: 4.130A pdb=" N GLU I 47 " --> pdb=" O GLU I 44 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE I 50 " --> pdb=" O GLU I 47 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASN I 52 " --> pdb=" O ALA I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 60 No H-bonds generated for 'chain 'I' and resid 58 through 60' Processing helix chain 'I' and resid 78 through 80 No H-bonds generated for 'chain 'I' and resid 78 through 80' Processing helix chain 'I' and resid 112 through 125 Processing helix chain 'I' and resid 169 through 182 Processing helix chain 'I' and resid 207 through 228 Processing helix chain 'I' and resid 267 through 269 No H-bonds generated for 'chain 'I' and resid 267 through 269' Processing helix chain 'I' and resid 272 through 292 removed outlier: 5.020A pdb=" N ARG I 286 " --> pdb=" O LEU I 282 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N GLU I 287 " --> pdb=" O LYS I 283 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE I 288 " --> pdb=" O HIS I 284 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ALA I 290 " --> pdb=" O ARG I 286 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N VAL I 291 " --> pdb=" O GLU I 287 " (cutoff:3.500A) Processing helix chain 'I' and resid 296 through 298 No H-bonds generated for 'chain 'I' and resid 296 through 298' Processing helix chain 'I' and resid 346 through 362 Processing helix chain 'I' and resid 380 through 385 Processing helix chain 'I' and resid 395 through 403 Processing helix chain 'I' and resid 406 through 412 Processing helix chain 'I' and resid 414 through 431 removed outlier: 3.575A pdb=" N ALA I 423 " --> pdb=" O HIS I 419 " (cutoff:3.500A) Processing helix chain 'I' and resid 437 through 442 Processing helix chain 'J' and resid 10 through 20 Processing helix chain 'J' and resid 43 through 52 removed outlier: 4.227A pdb=" N GLU J 47 " --> pdb=" O GLU J 44 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHE J 50 " --> pdb=" O GLU J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 60 No H-bonds generated for 'chain 'J' and resid 58 through 60' Processing helix chain 'J' and resid 78 through 80 No H-bonds generated for 'chain 'J' and resid 78 through 80' Processing helix chain 'J' and resid 112 through 126 removed outlier: 3.840A pdb=" N MET J 126 " --> pdb=" O GLU J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 169 through 181 Processing helix chain 'J' and resid 207 through 227 removed outlier: 3.600A pdb=" N VAL J 215 " --> pdb=" O ALA J 211 " (cutoff:3.500A) Processing helix chain 'J' and resid 267 through 269 No H-bonds generated for 'chain 'J' and resid 267 through 269' Processing helix chain 'J' and resid 272 through 287 removed outlier: 4.852A pdb=" N ARG J 286 " --> pdb=" O LEU J 282 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N GLU J 287 " --> pdb=" O LYS J 283 " (cutoff:3.500A) Processing helix chain 'J' and resid 289 through 292 No H-bonds generated for 'chain 'J' and resid 289 through 292' Processing helix chain 'J' and resid 296 through 298 No H-bonds generated for 'chain 'J' and resid 296 through 298' Processing helix chain 'J' and resid 346 through 362 Processing helix chain 'J' and resid 380 through 385 Processing helix chain 'J' and resid 395 through 403 Processing helix chain 'J' and resid 407 through 412 Processing helix chain 'J' and resid 414 through 431 Processing helix chain 'J' and resid 437 through 442 Processing helix chain 'K' and resid 10 through 19 Processing helix chain 'K' and resid 43 through 51 removed outlier: 4.452A pdb=" N GLU K 47 " --> pdb=" O GLU K 44 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 60 No H-bonds generated for 'chain 'K' and resid 58 through 60' Processing helix chain 'K' and resid 78 through 80 No H-bonds generated for 'chain 'K' and resid 78 through 80' Processing helix chain 'K' and resid 112 through 126 removed outlier: 3.515A pdb=" N GLU K 122 " --> pdb=" O THR K 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 169 through 181 Processing helix chain 'K' and resid 207 through 228 Processing helix chain 'K' and resid 267 through 269 No H-bonds generated for 'chain 'K' and resid 267 through 269' Processing helix chain 'K' and resid 272 through 292 removed outlier: 4.909A pdb=" N ARG K 286 " --> pdb=" O LEU K 282 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N GLU K 287 " --> pdb=" O LYS K 283 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE K 288 " --> pdb=" O HIS K 284 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ALA K 290 " --> pdb=" O ARG K 286 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N VAL K 291 " --> pdb=" O GLU K 287 " (cutoff:3.500A) Processing helix chain 'K' and resid 296 through 298 No H-bonds generated for 'chain 'K' and resid 296 through 298' Processing helix chain 'K' and resid 346 through 362 Processing helix chain 'K' and resid 380 through 385 Processing helix chain 'K' and resid 395 through 403 Processing helix chain 'K' and resid 407 through 412 Processing helix chain 'K' and resid 414 through 432 Processing helix chain 'K' and resid 437 through 443 Processing helix chain 'L' and resid 10 through 19 Processing helix chain 'L' and resid 43 through 52 removed outlier: 4.369A pdb=" N GLU L 47 " --> pdb=" O GLU L 44 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE L 50 " --> pdb=" O GLU L 47 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASN L 52 " --> pdb=" O ALA L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 80 No H-bonds generated for 'chain 'L' and resid 78 through 80' Processing helix chain 'L' and resid 112 through 126 Processing helix chain 'L' and resid 169 through 182 Processing helix chain 'L' and resid 207 through 228 Processing helix chain 'L' and resid 267 through 269 No H-bonds generated for 'chain 'L' and resid 267 through 269' Processing helix chain 'L' and resid 272 through 292 removed outlier: 4.956A pdb=" N ARG L 286 " --> pdb=" O LEU L 282 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N GLU L 287 " --> pdb=" O LYS L 283 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE L 288 " --> pdb=" O HIS L 284 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ALA L 290 " --> pdb=" O ARG L 286 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL L 291 " --> pdb=" O GLU L 287 " (cutoff:3.500A) Processing helix chain 'L' and resid 297 through 299 No H-bonds generated for 'chain 'L' and resid 297 through 299' Processing helix chain 'L' and resid 346 through 362 Processing helix chain 'L' and resid 380 through 385 Processing helix chain 'L' and resid 395 through 403 removed outlier: 3.563A pdb=" N GLU L 401 " --> pdb=" O GLU L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 407 through 412 Processing helix chain 'L' and resid 414 through 432 removed outlier: 3.542A pdb=" N ALA L 423 " --> pdb=" O HIS L 419 " (cutoff:3.500A) Processing helix chain 'L' and resid 437 through 443 Processing sheet with id= A, first strand: chain 'A' and resid 36 through 42 removed outlier: 7.165A pdb=" N ALA A 92 " --> pdb=" O LYS A 23 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ILE A 25 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALA A 94 " --> pdb=" O ILE A 25 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N THR A 27 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE A 96 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N PHE A 29 " --> pdb=" O ILE A 96 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 54 through 57 Processing sheet with id= C, first strand: chain 'A' and resid 129 through 135 removed outlier: 3.582A pdb=" N ASN A 250 " --> pdb=" O GLY A 133 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 230 through 233 removed outlier: 4.346A pdb=" N LEU A 136 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE A 200 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 188 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 36 through 42 removed outlier: 7.122A pdb=" N ALA B 92 " --> pdb=" O LYS B 23 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE B 25 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ALA B 94 " --> pdb=" O ILE B 25 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N THR B 27 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE B 96 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N PHE B 29 " --> pdb=" O ILE B 96 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 54 through 57 Processing sheet with id= G, first strand: chain 'B' and resid 129 through 134 Processing sheet with id= H, first strand: chain 'B' and resid 230 through 233 Processing sheet with id= I, first strand: chain 'B' and resid 314 through 316 removed outlier: 6.002A pdb=" N ILE B 323 " --> pdb=" O SER B 315 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'C' and resid 36 through 42 removed outlier: 7.180A pdb=" N ALA C 92 " --> pdb=" O LYS C 23 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N ILE C 25 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA C 94 " --> pdb=" O ILE C 25 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N THR C 27 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE C 96 " --> pdb=" O THR C 27 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N PHE C 29 " --> pdb=" O ILE C 96 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 54 through 57 Processing sheet with id= L, first strand: chain 'C' and resid 129 through 135 Processing sheet with id= M, first strand: chain 'C' and resid 230 through 233 removed outlier: 3.753A pdb=" N LEU C 136 " --> pdb=" O ILE C 200 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 314 through 316 removed outlier: 6.128A pdb=" N ILE C 323 " --> pdb=" O SER C 315 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'D' and resid 36 through 42 removed outlier: 7.125A pdb=" N ALA D 92 " --> pdb=" O LYS D 23 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ILE D 25 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA D 94 " --> pdb=" O ILE D 25 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N THR D 27 " --> pdb=" O ALA D 94 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE D 96 " --> pdb=" O THR D 27 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N PHE D 29 " --> pdb=" O ILE D 96 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 54 through 57 Processing sheet with id= Q, first strand: chain 'D' and resid 186 through 191 removed outlier: 6.963A pdb=" N ASP D 201 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N SER D 189 " --> pdb=" O GLU D 199 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N GLU D 199 " --> pdb=" O SER D 189 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N HIS D 191 " --> pdb=" O GLN D 197 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N GLN D 197 " --> pdb=" O HIS D 191 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU D 136 " --> pdb=" O ILE D 200 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N PHE D 202 " --> pdb=" O PRO D 134 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN D 250 " --> pdb=" O GLY D 133 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 139 through 142 Processing sheet with id= S, first strand: chain 'D' and resid 314 through 316 removed outlier: 6.218A pdb=" N ILE D 323 " --> pdb=" O SER D 315 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'E' and resid 36 through 42 removed outlier: 7.115A pdb=" N ALA E 92 " --> pdb=" O LYS E 23 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ILE E 25 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA E 94 " --> pdb=" O ILE E 25 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N THR E 27 " --> pdb=" O ALA E 94 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE E 96 " --> pdb=" O THR E 27 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N PHE E 29 " --> pdb=" O ILE E 96 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 54 through 57 Processing sheet with id= V, first strand: chain 'E' and resid 230 through 233 Processing sheet with id= W, first strand: chain 'E' and resid 249 through 251 Processing sheet with id= X, first strand: chain 'E' and resid 314 through 316 removed outlier: 6.084A pdb=" N ILE E 323 " --> pdb=" O SER E 315 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'F' and resid 36 through 42 removed outlier: 7.188A pdb=" N ALA F 92 " --> pdb=" O LYS F 23 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ILE F 25 " --> pdb=" O ALA F 92 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA F 94 " --> pdb=" O ILE F 25 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N THR F 27 " --> pdb=" O ALA F 94 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE F 96 " --> pdb=" O THR F 27 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N PHE F 29 " --> pdb=" O ILE F 96 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 54 through 57 Processing sheet with id= AA, first strand: chain 'F' and resid 129 through 135 removed outlier: 3.590A pdb=" N ASN F 250 " --> pdb=" O GLY F 133 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 230 through 233 removed outlier: 3.664A pdb=" N LEU F 136 " --> pdb=" O ILE F 200 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 314 through 316 removed outlier: 6.048A pdb=" N ILE F 323 " --> pdb=" O SER F 315 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'G' and resid 36 through 42 removed outlier: 7.083A pdb=" N ALA G 92 " --> pdb=" O LYS G 23 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ILE G 25 " --> pdb=" O ALA G 92 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ALA G 94 " --> pdb=" O ILE G 25 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N THR G 27 " --> pdb=" O ALA G 94 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE G 96 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N PHE G 29 " --> pdb=" O ILE G 96 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 54 through 57 Processing sheet with id= AF, first strand: chain 'G' and resid 186 through 191 removed outlier: 6.815A pdb=" N ASP G 201 " --> pdb=" O GLU G 187 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N SER G 189 " --> pdb=" O GLU G 199 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N GLU G 199 " --> pdb=" O SER G 189 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N HIS G 191 " --> pdb=" O GLN G 197 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N GLN G 197 " --> pdb=" O HIS G 191 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE G 200 " --> pdb=" O LEU G 136 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU G 136 " --> pdb=" O ILE G 200 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N PHE G 202 " --> pdb=" O PRO G 134 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N HIS G 248 " --> pdb=" O GLU G 135 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 139 through 142 Processing sheet with id= AH, first strand: chain 'G' and resid 314 through 316 removed outlier: 6.116A pdb=" N ILE G 323 " --> pdb=" O SER G 315 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'H' and resid 36 through 42 removed outlier: 7.341A pdb=" N ALA H 92 " --> pdb=" O LYS H 23 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ILE H 25 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ALA H 94 " --> pdb=" O ILE H 25 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N THR H 27 " --> pdb=" O ALA H 94 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE H 96 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N PHE H 29 " --> pdb=" O ILE H 96 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'H' and resid 54 through 57 Processing sheet with id= AK, first strand: chain 'H' and resid 186 through 191 removed outlier: 6.662A pdb=" N ASP H 201 " --> pdb=" O GLU H 187 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N SER H 189 " --> pdb=" O GLU H 199 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLU H 199 " --> pdb=" O SER H 189 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N HIS H 191 " --> pdb=" O GLN H 197 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N GLN H 197 " --> pdb=" O HIS H 191 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE H 200 " --> pdb=" O LEU H 136 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU H 136 " --> pdb=" O ILE H 200 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N PHE H 202 " --> pdb=" O PRO H 134 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN H 250 " --> pdb=" O GLY H 133 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'H' and resid 139 through 142 Processing sheet with id= AM, first strand: chain 'H' and resid 314 through 316 removed outlier: 6.056A pdb=" N ILE H 323 " --> pdb=" O SER H 315 " (cutoff:3.500A) No H-bonds generated for sheet with id= AM Processing sheet with id= AN, first strand: chain 'I' and resid 36 through 42 removed outlier: 7.077A pdb=" N ALA I 92 " --> pdb=" O LYS I 23 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ILE I 25 " --> pdb=" O ALA I 92 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA I 94 " --> pdb=" O ILE I 25 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N THR I 27 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE I 96 " --> pdb=" O THR I 27 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N PHE I 29 " --> pdb=" O ILE I 96 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'I' and resid 54 through 57 Processing sheet with id= AP, first strand: chain 'I' and resid 186 through 191 removed outlier: 6.762A pdb=" N ASP I 201 " --> pdb=" O GLU I 187 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER I 189 " --> pdb=" O GLU I 199 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLU I 199 " --> pdb=" O SER I 189 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N HIS I 191 " --> pdb=" O GLN I 197 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N GLN I 197 " --> pdb=" O HIS I 191 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE I 200 " --> pdb=" O LEU I 136 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU I 136 " --> pdb=" O ILE I 200 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N PHE I 202 " --> pdb=" O PRO I 134 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN I 250 " --> pdb=" O GLY I 133 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N HIS I 248 " --> pdb=" O GLU I 135 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'I' and resid 139 through 142 Processing sheet with id= AR, first strand: chain 'J' and resid 36 through 42 removed outlier: 7.362A pdb=" N ALA J 92 " --> pdb=" O LYS J 23 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ILE J 25 " --> pdb=" O ALA J 92 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ALA J 94 " --> pdb=" O ILE J 25 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N THR J 27 " --> pdb=" O ALA J 94 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE J 96 " --> pdb=" O THR J 27 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N PHE J 29 " --> pdb=" O ILE J 96 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'J' and resid 54 through 57 Processing sheet with id= AT, first strand: chain 'J' and resid 186 through 191 removed outlier: 6.545A pdb=" N ASP J 201 " --> pdb=" O GLU J 187 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER J 189 " --> pdb=" O GLU J 199 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLU J 199 " --> pdb=" O SER J 189 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N HIS J 191 " --> pdb=" O GLN J 197 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N GLN J 197 " --> pdb=" O HIS J 191 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE J 200 " --> pdb=" O LEU J 136 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU J 136 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N PHE J 202 " --> pdb=" O PRO J 134 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'J' and resid 139 through 142 Processing sheet with id= AV, first strand: chain 'J' and resid 314 through 316 removed outlier: 6.090A pdb=" N ILE J 323 " --> pdb=" O SER J 315 " (cutoff:3.500A) No H-bonds generated for sheet with id= AV Processing sheet with id= AW, first strand: chain 'K' and resid 36 through 38 removed outlier: 7.342A pdb=" N ALA K 92 " --> pdb=" O LYS K 23 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ILE K 25 " --> pdb=" O ALA K 92 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA K 94 " --> pdb=" O ILE K 25 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N THR K 27 " --> pdb=" O ALA K 94 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE K 96 " --> pdb=" O THR K 27 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N PHE K 29 " --> pdb=" O ILE K 96 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'K' and resid 54 through 57 Processing sheet with id= AY, first strand: chain 'K' and resid 186 through 191 removed outlier: 6.766A pdb=" N ASP K 201 " --> pdb=" O GLU K 187 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SER K 189 " --> pdb=" O GLU K 199 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLU K 199 " --> pdb=" O SER K 189 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N HIS K 191 " --> pdb=" O GLN K 197 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N GLN K 197 " --> pdb=" O HIS K 191 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE K 200 " --> pdb=" O LEU K 136 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU K 136 " --> pdb=" O ILE K 200 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N PHE K 202 " --> pdb=" O PRO K 134 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASN K 250 " --> pdb=" O GLY K 133 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS K 248 " --> pdb=" O GLU K 135 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'K' and resid 139 through 142 Processing sheet with id= BA, first strand: chain 'K' and resid 314 through 316 removed outlier: 6.148A pdb=" N ILE K 323 " --> pdb=" O SER K 315 " (cutoff:3.500A) No H-bonds generated for sheet with id= BA Processing sheet with id= BB, first strand: chain 'L' and resid 36 through 42 removed outlier: 7.298A pdb=" N ALA L 92 " --> pdb=" O LYS L 23 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILE L 25 " --> pdb=" O ALA L 92 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA L 94 " --> pdb=" O ILE L 25 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N THR L 27 " --> pdb=" O ALA L 94 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE L 96 " --> pdb=" O THR L 27 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N PHE L 29 " --> pdb=" O ILE L 96 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'L' and resid 54 through 57 Processing sheet with id= BD, first strand: chain 'L' and resid 133 through 136 Processing sheet with id= BE, first strand: chain 'L' and resid 230 through 233 Processing sheet with id= BF, first strand: chain 'L' and resid 314 through 316 removed outlier: 6.272A pdb=" N ILE L 323 " --> pdb=" O SER L 315 " (cutoff:3.500A) No H-bonds generated for sheet with id= BF 1573 hydrogen bonds defined for protein. 4386 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: 32.57 Time building geometry restraints manager: 58.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 39553 1.03 - 1.23: 1927 1.23 - 1.43: 16640 1.43 - 1.63: 24129 1.63 - 1.83: 350 Bond restraints: 82599 Sorted by residual: bond pdb=" C TYR L 101 " pdb=" N LEU L 102 " ideal model delta sigma weight residual 1.329 1.269 0.060 1.86e-02 2.89e+03 1.05e+01 bond pdb=" C TYR C 101 " pdb=" N LEU C 102 " ideal model delta sigma weight residual 1.331 1.254 0.077 2.83e-02 1.25e+03 7.43e+00 bond pdb=" C ASN E 131 " pdb=" N VAL E 132 " ideal model delta sigma weight residual 1.334 1.303 0.031 1.24e-02 6.50e+03 6.17e+00 bond pdb=" CB CYS D 339 " pdb=" SG CYS D 339 " ideal model delta sigma weight residual 1.808 1.726 0.082 3.30e-02 9.18e+02 6.16e+00 bond pdb=" C LEU E 444 " pdb=" N SER E 445 " ideal model delta sigma weight residual 1.332 1.299 0.034 1.40e-02 5.10e+03 5.79e+00 ... (remaining 82594 not shown) Histogram of bond angle deviations from ideal: 72.63 - 86.35: 83 86.35 - 100.07: 13 100.07 - 113.79: 97388 113.79 - 127.51: 50706 127.51 - 141.23: 609 Bond angle restraints: 148799 Sorted by residual: angle pdb="HG21 VAL C 295 " pdb=" CG2 VAL C 295 " pdb="HG23 VAL C 295 " ideal model delta sigma weight residual 110.00 79.10 30.90 3.00e+00 1.11e-01 1.06e+02 angle pdb=" SD MET A 247 " pdb=" CE MET A 247 " pdb=" HE1 MET A 247 " ideal model delta sigma weight residual 109.00 78.68 30.32 3.00e+00 1.11e-01 1.02e+02 angle pdb=" CB VAL C 295 " pdb=" CG2 VAL C 295 " pdb="HG23 VAL C 295 " ideal model delta sigma weight residual 109.00 78.96 30.04 3.00e+00 1.11e-01 1.00e+02 angle pdb="HG21 VAL C 295 " pdb=" CG2 VAL C 295 " pdb="HG22 VAL C 295 " ideal model delta sigma weight residual 110.00 80.58 29.42 3.00e+00 1.11e-01 9.62e+01 angle pdb=" HE1 MET A 247 " pdb=" CE MET A 247 " pdb=" HE2 MET A 247 " ideal model delta sigma weight residual 110.00 80.65 29.35 3.00e+00 1.11e-01 9.57e+01 ... (remaining 148794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 37705 35.46 - 70.91: 1616 70.91 - 106.37: 81 106.37 - 141.83: 5 141.83 - 177.28: 4 Dihedral angle restraints: 39411 sinusoidal: 20903 harmonic: 18508 Sorted by residual: dihedral pdb=" CD ARG K 338 " pdb=" NE ARG K 338 " pdb=" CZ ARG K 338 " pdb=" NH1 ARG K 338 " ideal model delta sinusoidal sigma weight residual 0.00 177.28 -177.28 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" O2A ADP J 502 " pdb=" O3A ADP J 502 " pdb=" PA ADP J 502 " pdb=" PB ADP J 502 " ideal model delta sinusoidal sigma weight residual -60.00 113.30 -173.30 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O1B ADP L 502 " pdb=" O3A ADP L 502 " pdb=" PB ADP L 502 " pdb=" PA ADP L 502 " ideal model delta sinusoidal sigma weight residual 300.00 134.41 165.58 1 2.00e+01 2.50e-03 4.72e+01 ... (remaining 39408 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.390: 6257 0.390 - 0.779: 0 0.779 - 1.169: 0 1.169 - 1.559: 2 1.559 - 1.948: 16 Chirality restraints: 6275 Sorted by residual: chirality pdb=" CB VAL B 295 " pdb=" CA VAL B 295 " pdb=" CG1 VAL B 295 " pdb=" CG2 VAL B 295 " both_signs ideal model delta sigma weight residual False -2.63 -0.68 -1.95 2.00e-01 2.50e+01 9.49e+01 chirality pdb=" CB VAL C 295 " pdb=" CA VAL C 295 " pdb=" CG1 VAL C 295 " pdb=" CG2 VAL C 295 " both_signs ideal model delta sigma weight residual False -2.63 -0.72 -1.91 2.00e-01 2.50e+01 9.14e+01 chirality pdb=" CG LEU C 337 " pdb=" CB LEU C 337 " pdb=" CD1 LEU C 337 " pdb=" CD2 LEU C 337 " both_signs ideal model delta sigma weight residual False -2.59 -0.85 -1.74 2.00e-01 2.50e+01 7.57e+01 ... (remaining 6272 not shown) Planarity restraints: 12501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY J 133 " -0.052 5.00e-02 4.00e+02 8.00e-02 1.02e+01 pdb=" N PRO J 134 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO J 134 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO J 134 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN L 317 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.23e+00 pdb=" C GLN L 317 " -0.036 2.00e-02 2.50e+03 pdb=" O GLN L 317 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN L 318 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 341 " -0.009 2.00e-02 2.50e+03 1.86e-02 3.45e+00 pdb=" CG ASP D 341 " 0.032 2.00e-02 2.50e+03 pdb=" OD1 ASP D 341 " -0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP D 341 " -0.012 2.00e-02 2.50e+03 ... (remaining 12498 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 3463 2.14 - 2.75: 151286 2.75 - 3.37: 239964 3.37 - 3.98: 329130 3.98 - 4.60: 512809 Nonbonded interactions: 1236652 Sorted by model distance: nonbonded pdb=" HB VAL C 295 " pdb="HG22 VAL C 295 " model vdw 1.523 1.952 nonbonded pdb=" OD2 ASP K 57 " pdb=" HG SER K 60 " model vdw 1.527 1.850 nonbonded pdb=" OD2 ASP F 57 " pdb=" HG SER F 60 " model vdw 1.543 1.850 nonbonded pdb=" OE1 GLU H 11 " pdb=" H GLU H 11 " model vdw 1.553 1.850 nonbonded pdb=" O THR A 268 " pdb="HH21 ARG A 329 " model vdw 1.566 1.850 ... (remaining 1236647 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 8 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 20 through 43 or (resid 4 \ 4 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 45 through 50 or (resid 51 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 52 through 61 or (resid 62 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 63 \ through 72 or (resid 73 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 74 through 124 or (resid 125 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 126 through 1 \ 29 or (resid 130 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 131 through 162 or (resid 163 and (name N or name CA or \ name C or name O or name CB or name HA or name HB1 or name HB2 or name HB3)) or \ resid 164 through 169 or (resid 170 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 171 through 189 or (resid 190 and (na \ me N or name CA or name C or name O or name CB or name CG or name ND1 or name CD \ 2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name H \ D2 or name HE1)) or resid 191 through 247 or (resid 248 and (name N or name CA o \ r name C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or \ name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) \ or resid 249 or (resid 250 and (name N or name CA or name C or name O or name CB \ or name CG or name OD1 or name ND2 or name H or name HA or name HB2 or name HB3 \ )) or (resid 251 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 252 through 306 or (resid 307 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 308 through 337 or \ (resid 338 and (name N or name CA or name C or name O or name CB or name CG or n \ ame CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA or nam \ e HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or \ name HH11 or name HH21 or name HH22)) or resid 339 through 372 or (resid 373 and \ (name N or name CA or name C or name O or name CB )) or resid 374 through 377 o \ r (resid 378 and (name N or name CA or name C or name O or name CB or name CG or \ name CD1 or name CD2 or name H or name HA )) or resid 379 or (resid 380 through \ 381 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 382 or (resid 383 and (name N or name CA or name C or name O or name \ CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2 or name \ H or name HA )) or resid 384 through 447 or resid 503)) selection = (chain 'B' and (resid 8 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 20 through 47 or (resid 4 \ 8 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 49 through 50 or (resid 51 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 52 through 110 or (resid 111 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA )) or resid 1 \ 12 through 162 or (resid 163 and (name N or name CA or name C or name O or name \ CB or name HA or name HB1 or name HB2 or name HB3)) or resid 164 through 189 or \ (resid 190 and (name N or name CA or name C or name O or name CB or name CG or n \ ame ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or \ name HB3 or name HD2 or name HE1)) or (resid 191 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name H \ E2)) or resid 192 through 247 or (resid 248 and (name N or name CA or name C or \ name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or \ name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 249 \ or (resid 250 and (name N or name CA or name C or name O or name CB or name CG \ or name OD1 or name ND2 or name H or name HA or name HB2 or name HB3)) or (resid \ 251 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 252 through 255 or (resid 256 and (name N or name CA or name C or na \ me O or name CB or name H or name HA )) or resid 257 through 264 or (resid 265 a \ nd (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 266 through 306 or (resid 307 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 308 through 310 or (resid 311 and (na \ me N or name CA or name C or name O or name CB or name CG or name CD1 or name CD \ 2 or name CE1 or name CE2 or name CZ or name OH or name H or name HA )) or resid \ 312 through 337 or (resid 338 and (name N or name CA or name C or name O or nam \ e CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2 or name \ H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or nam \ e HD3 or name HE or name HH11 or name HH21 or name HH22)) or resid 339 through 3 \ 61 or (resid 362 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 363 or (resid 364 and (name N or name CA or name C or na \ me O or name CB or name H or name HA )) or resid 365 through 372 or (resid 373 a \ nd (name N or name CA or name C or name O or name CB )) or resid 374 through 377 \ or (resid 378 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2 or name H or name HA )) or resid 379 or (resid 380 throu \ gh 381 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 382 through 447 or resid 503)) selection = (chain 'C' and (resid 8 through 47 or (resid 48 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 49 through 50 or (resid 5 \ 1 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 52 through 72 or (resid 73 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 74 through 110 or (resid 111 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA )) or resid 1 \ 12 through 124 or (resid 125 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 126 through 162 or (resid 163 and (name N or \ name CA or name C or name O or name CB or name HA or name HB1 or name HB2 or na \ me HB3)) or resid 164 through 189 or (resid 190 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid \ 191 through 247 or (resid 248 and (name N or name CA or name C or name O or nam \ e CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or nam \ e HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 249 through 250 \ or (resid 251 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 252 through 255 or (resid 256 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 257 through 264 or (re \ sid 265 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 266 through 306 or (resid 307 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 308 through 310 or (resid 31 \ 1 and (name N or name CA or name C or name O or name CB or name CG or name CD1 o \ r name CD2 or name CE1 or name CE2 or name CZ or name OH or name H or name HA )) \ or resid 312 through 337 or (resid 338 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH \ 2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name H \ D2 or name HD3 or name HE or name HH11 or name HH21 or name HH22)) or resid 339 \ through 361 or (resid 362 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 363 or (resid 364 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 365 through 372 or (re \ sid 373 and (name N or name CA or name C or name O or name CB )) or resid 374 th \ rough 377 or (resid 378 and (name N or name CA or name C or name O or name CB or \ name CG or name CD1 or name CD2 or name H or name HA )) or resid 379 or (resid \ 380 through 381 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 382 or (resid 383 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name NE or name CZ or name NH1 or name N \ H2 or name H or name HA )) or resid 384 through 447 or resid 503)) selection = (chain 'D' and (resid 8 through 47 or (resid 48 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 49 through 50 or (resid 5 \ 1 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 52 through 72 or (resid 73 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 74 through 110 or (resid 111 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA )) or resid 1 \ 12 through 162 or (resid 163 and (name N or name CA or name C or name O or name \ CB or name HA or name HB1 or name HB2 or name HB3)) or resid 164 through 189 or \ (resid 190 and (name N or name CA or name C or name O or name CB or name CG or n \ ame ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or \ name HB3 or name HD2 or name HE1)) or resid 191 through 247 or (resid 248 and (n \ ame N or name CA or name C or name O or name CB or name CG or name ND1 or name C \ D2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name \ HD2 or name HE1)) or resid 249 or (resid 250 and (name N or name CA or name C or \ name O or name CB or name CG or name OD1 or name ND2 or name H or name HA or na \ me HB2 or name HB3)) or (resid 251 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 252 through 255 or (resid 256 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA )) or resid 2 \ 57 through 264 or (resid 265 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 266 through 306 or (resid 307 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 308 thr \ ough 310 or (resid 311 and (name N or name CA or name C or name O or name CB or \ name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH or \ name H or name HA )) or resid 312 through 337 or (resid 338 and (name N or name \ CA or name C or name O or name CB or name CG or name CD or name NE or name CZ o \ r name NH1 or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 \ or name HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH21 or name \ HH22)) or resid 339 through 361 or (resid 362 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 363 or (resid 364 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA )) or resid 3 \ 65 through 377 or (resid 378 and (name N or name CA or name C or name O or name \ CB or name CG or name CD1 or name CD2 or name H or name HA )) or resid 379 or (r \ esid 380 through 381 and (name N or name CA or name C or name O or name CB or na \ me H or name HA )) or resid 382 through 447 or resid 503)) selection = (chain 'E' and (resid 8 through 43 or (resid 44 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 45 through 47 or (resid 4 \ 8 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 49 through 110 or (resid 111 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 112 through 189 or (resid 190 and ( \ name N or name CA or name C or name O or name CB or name CG or name ND1 or name \ CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name \ HD2 or name HE1)) or resid 191 through 247 or (resid 248 and (name N or name CA \ or name C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 o \ r name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1) \ ) or resid 249 or (resid 250 and (name N or name CA or name C or name O or name \ CB or name CG or name OD1 or name ND2 or name H or name HA or name HB2 or name H \ B3)) or resid 251 through 255 or (resid 256 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 257 through 264 or (resid 265 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 266 through 306 or (resid 307 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 308 through 310 or (resid 311 and ( \ name N or name CA or name C or name O or name CB or name CG or name CD1 or name \ CD2 or name CE1 or name CE2 or name CZ or name OH or name H or name HA )) or res \ id 312 through 337 or (resid 338 and (name N or name CA or name C or name O or n \ ame CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2 or na \ me H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or n \ ame HD3 or name HE or name HH11 or name HH21 or name HH22)) or resid 339 through \ 361 or (resid 362 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 363 or (resid 364 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 365 through 372 or (resid 373 \ and (name N or name CA or name C or name O or name CB )) or resid 374 through 3 \ 77 or (resid 378 and (name N or name CA or name C or name O or name CB or name C \ G or name CD1 or name CD2 or name H or name HA )) or resid 379 or (resid 380 thr \ ough 381 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 382 through 447 or resid 503)) selection = (chain 'F' and (resid 8 through 47 or (resid 48 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 49 through 50 or (resid 5 \ 1 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 52 through 72 or (resid 73 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 74 through 110 or (resid 111 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA )) or resid 1 \ 12 through 162 or (resid 163 and (name N or name CA or name C or name O or name \ CB or name HA or name HB1 or name HB2 or name HB3)) or resid 164 through 189 or \ (resid 190 and (name N or name CA or name C or name O or name CB or name CG or n \ ame ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or \ name HB3 or name HD2 or name HE1)) or resid 191 through 247 or (resid 248 and (n \ ame N or name CA or name C or name O or name CB or name CG or name ND1 or name C \ D2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name \ HD2 or name HE1)) or resid 249 or (resid 250 and (name N or name CA or name C or \ name O or name CB or name CG or name OD1 or name ND2 or name H or name HA or na \ me HB2 or name HB3)) or (resid 251 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 252 through 255 or (resid 256 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA )) or resid 2 \ 57 through 264 or (resid 265 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 266 through 306 or (resid 307 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 308 thr \ ough 310 or (resid 311 and (name N or name CA or name C or name O or name CB or \ name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH or \ name H or name HA )) or resid 312 through 337 or (resid 338 and (name N or name \ CA or name C or name O or name CB or name CG or name CD or name NE or name CZ o \ r name NH1 or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 \ or name HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH21 or name \ HH22)) or resid 339 through 361 or (resid 362 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 363 or (resid 364 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA )) or resid 3 \ 65 through 372 or (resid 373 and (name N or name CA or name C or name O or name \ CB )) or resid 374 through 377 or (resid 378 and (name N or name CA or name C or \ name O or name CB or name CG or name CD1 or name CD2 or name H or name HA )) or \ resid 379 or (resid 380 through 381 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 382 through 447 or resid 603)) selection = (chain 'G' and (resid 8 through 43 or (resid 44 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 45 through 47 or (resid 4 \ 8 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 49 through 50 or (resid 51 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 52 through 110 or (resid 111 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA )) or resid 1 \ 12 through 162 or (resid 163 and (name N or name CA or name C or name O or name \ CB or name HA or name HB1 or name HB2 or name HB3)) or resid 164 through 189 or \ (resid 190 and (name N or name CA or name C or name O or name CB or name CG or n \ ame ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or \ name HB3 or name HD2 or name HE1)) or resid 191 through 247 or (resid 248 and (n \ ame N or name CA or name C or name O or name CB or name CG or name ND1 or name C \ D2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name \ HD2 or name HE1)) or resid 249 or (resid 250 and (name N or name CA or name C or \ name O or name CB or name CG or name OD1 or name ND2 or name H or name HA or na \ me HB2 or name HB3)) or (resid 251 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 252 through 255 or (resid 256 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA )) or resid 2 \ 57 through 264 or (resid 265 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 266 through 306 or (resid 307 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 308 thr \ ough 310 or (resid 311 and (name N or name CA or name C or name O or name CB or \ name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH or \ name H or name HA )) or resid 312 through 337 or (resid 338 and (name N or name \ CA or name C or name O or name CB or name CG or name CD or name NE or name CZ o \ r name NH1 or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 \ or name HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH21 or name \ HH22)) or resid 339 through 361 or (resid 362 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 363 or (resid 364 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA )) or resid 3 \ 65 through 372 or (resid 373 and (name N or name CA or name C or name O or name \ CB )) or resid 374 through 377 or (resid 378 and (name N or name CA or name C or \ name O or name CB or name CG or name CD1 or name CD2 or name H or name HA )) or \ resid 379 or (resid 380 through 381 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 382 or (resid 383 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD or name NE or name CZ \ or name NH1 or name NH2 or name H or name HA )) or resid 384 through 447 or resi \ d 603)) selection = (chain 'H' and (resid 8 through 47 or (resid 48 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 49 through 50 or (resid 5 \ 1 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 52 through 72 or (resid 73 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 74 through 162 or (resid 163 and (nam \ e N or name CA or name C or name O or name CB or name HA or name HB1 or name HB2 \ or name HB3)) or resid 164 through 189 or (resid 190 and (name N or name CA or \ name C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or na \ me NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or \ resid 191 through 247 or (resid 248 and (name N or name CA or name C or name O \ or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H \ or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 249 or (re \ sid 250 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3)) or (resid 251 an \ d (name N or name CA or name C or name O or name CB or name H or name HA )) or r \ esid 252 through 255 or (resid 256 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 257 through 264 or (resid 265 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA )) or resid 2 \ 66 through 306 or (resid 307 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 308 through 310 or (resid 311 and (name N or \ name CA or name C or name O or name CB or name CG or name CD1 or name CD2 or na \ me CE1 or name CE2 or name CZ or name OH or name H or name HA )) or resid 312 th \ rough 337 or (resid 338 and (name N or name CA or name C or name O or name CB or \ name CG or name CD or name NE or name CZ or name NH1 or name NH2 or name H or n \ ame HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 o \ r name HE or name HH11 or name HH21 or name HH22)) or resid 339 through 361 or ( \ resid 362 and (name N or name CA or name C or name O or name CB or name H or nam \ e HA )) or resid 363 or (resid 364 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 365 through 372 or (resid 373 and (nam \ e N or name CA or name C or name O or name CB )) or resid 374 through 377 or (re \ sid 378 and (name N or name CA or name C or name O or name CB or name CG or name \ CD1 or name CD2 or name H or name HA )) or resid 379 or (resid 380 through 381 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 382 through 447 or resid 603)) selection = (chain 'I' and (resid 8 through 43 or (resid 44 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 45 through 47 or (resid 4 \ 8 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 49 through 50 or (resid 51 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 52 through 61 or (resid 62 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 63 \ through 72 or (resid 73 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 74 through 110 or (resid 111 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 112 through 1 \ 62 or (resid 163 and (name N or name CA or name C or name O or name CB or name H \ A or name HB1 or name HB2 or name HB3)) or resid 164 through 189 or (resid 190 a \ nd (name N or name CA or name C or name O or name CB or name CG or name ND1 or n \ ame CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or \ name HD2 or name HE1)) or resid 191 through 247 or (resid 248 and (name N or nam \ e CA or name C or name O or name CB or name CG or name ND1 or name CD2 or name C \ E1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name \ HE1)) or resid 249 or (resid 250 and (name N or name CA or name C or name O or n \ ame CB or name CG or name OD1 or name ND2 or name H or name HA or name HB2 or na \ me HB3)) or (resid 251 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 252 through 255 or (resid 256 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 257 through 2 \ 64 or (resid 265 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 266 through 306 or (resid 307 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 308 through 310 or \ (resid 311 and (name N or name CA or name C or name O or name CB or name CG or n \ ame CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH or name H or n \ ame HA )) or resid 312 through 337 or (resid 338 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 o \ r name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 \ or name HD2 or name HD3 or name HE or name HH11 or name HH21 or name HH22)) or r \ esid 339 through 361 or (resid 362 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 363 or (resid 364 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 365 through 3 \ 72 or (resid 373 and (name N or name CA or name C or name O or name CB )) or res \ id 374 through 377 or (resid 378 and (name N or name CA or name C or name O or n \ ame CB or name CG or name CD1 or name CD2 or name H or name HA )) or resid 379 o \ r (resid 380 through 381 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 382 or (resid 383 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2 or name H or name HA )) or resid 384 through 447 or resid 503)) selection = (chain 'J' and (resid 8 through 47 or (resid 48 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 49 through 50 or (resid 5 \ 1 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 52 through 72 or (resid 73 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 74 through 110 or (resid 111 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA )) or resid 1 \ 12 through 162 or (resid 163 and (name N or name CA or name C or name O or name \ CB or name HA or name HB1 or name HB2 or name HB3)) or resid 164 through 189 or \ (resid 190 and (name N or name CA or name C or name O or name CB or name CG or n \ ame ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or \ name HB3 or name HD2 or name HE1)) or resid 191 through 247 or (resid 248 and (n \ ame N or name CA or name C or name O or name CB or name CG or name ND1 or name C \ D2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name \ HD2 or name HE1)) or resid 249 or (resid 250 and (name N or name CA or name C or \ name O or name CB or name CG or name OD1 or name ND2 or name H or name HA or na \ me HB2 or name HB3)) or (resid 251 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 252 through 255 or (resid 256 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA )) or resid 2 \ 57 through 264 or (resid 265 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 266 through 306 or (resid 307 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 308 thr \ ough 310 or (resid 311 and (name N or name CA or name C or name O or name CB or \ name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH or \ name H or name HA )) or resid 312 through 337 or (resid 338 and (name N or name \ CA or name C or name O or name CB or name CG or name CD or name NE or name CZ o \ r name NH1 or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 \ or name HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH21 or name \ HH22)) or resid 339 through 361 or (resid 362 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 363 or (resid 364 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA )) or resid 3 \ 65 through 372 or (resid 373 and (name N or name CA or name C or name O or name \ CB )) or resid 374 through 377 or (resid 378 and (name N or name CA or name C or \ name O or name CB or name CG or name CD1 or name CD2 or name H or name HA )) or \ resid 379 or (resid 380 through 381 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 382 through 447 or resid 503)) selection = (chain 'K' and (resid 8 through 47 or (resid 48 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 49 through 50 or (resid 5 \ 1 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 52 through 72 or (resid 73 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 74 through 110 or (resid 111 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA )) or resid 1 \ 12 through 162 or (resid 163 and (name N or name CA or name C or name O or name \ CB or name HA or name HB1 or name HB2 or name HB3)) or resid 164 through 189 or \ (resid 190 and (name N or name CA or name C or name O or name CB or name CG or n \ ame ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or \ name HB3 or name HD2 or name HE1)) or resid 191 through 247 or (resid 248 and (n \ ame N or name CA or name C or name O or name CB or name CG or name ND1 or name C \ D2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name \ HD2 or name HE1)) or resid 249 or (resid 250 and (name N or name CA or name C or \ name O or name CB or name CG or name OD1 or name ND2 or name H or name HA or na \ me HB2 or name HB3)) or (resid 251 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 252 through 255 or (resid 256 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA )) or resid 2 \ 57 through 264 or (resid 265 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 266 through 306 or (resid 307 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 308 thr \ ough 310 or (resid 311 and (name N or name CA or name C or name O or name CB or \ name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH or \ name H or name HA )) or resid 312 through 361 or (resid 362 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 363 or (resi \ d 364 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 365 through 372 or (resid 373 and (name N or name CA or name C or n \ ame O or name CB )) or resid 374 through 377 or (resid 378 and (name N or name C \ A or name C or name O or name CB or name CG or name CD1 or name CD2 or name H or \ name HA )) or resid 379 or (resid 380 through 381 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 382 through 447 or res \ id 503)) selection = (chain 'L' and (resid 8 through 47 or (resid 48 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 49 through 50 or (resid 5 \ 1 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 52 through 72 or (resid 73 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 74 through 162 or (resid 163 and (nam \ e N or name CA or name C or name O or name CB or name HA or name HB1 or name HB2 \ or name HB3)) or resid 164 through 189 or (resid 190 and (name N or name CA or \ name C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or na \ me NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or \ resid 191 through 247 or (resid 248 and (name N or name CA or name C or name O \ or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H \ or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 249 or (re \ sid 250 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3)) or (resid 251 an \ d (name N or name CA or name C or name O or name CB or name H or name HA )) or r \ esid 252 through 255 or (resid 256 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 257 through 264 or (resid 265 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA )) or resid 2 \ 66 through 310 or (resid 311 and (name N or name CA or name C or name O or name \ CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name \ OH or name H or name HA )) or resid 312 through 337 or (resid 338 and (name N o \ r name CA or name C or name O or name CB or name CG or name CD or name NE or nam \ e CZ or name NH1 or name NH2 or name H or name HA or name HB2 or name HB3 or nam \ e HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH21 o \ r name HH22)) or resid 339 through 361 or (resid 362 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 363 or (resid 364 an \ d (name N or name CA or name C or name O or name CB or name H or name HA )) or r \ esid 365 through 372 or (resid 373 and (name N or name CA or name C or name O or \ name CB )) or resid 374 through 447 or resid 503)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.960 Extract box with map and model: 8.760 Check model and map are aligned: 0.930 Set scattering table: 0.600 Process input model: 216.780 Find NCS groups from input model: 4.170 Set up NCS constraints: 0.250 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:11.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 244.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3238 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 : 0.006 0.082 42998 Z= 0.368 Angle : 0.805 12.331 58428 Z= 0.423 Chirality : 0.101 1.948 6275 Planarity : 0.004 0.080 7559 Dihedral : 18.761 177.284 15688 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.68 % Allowed : 27.43 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.11), residues: 5256 helix: 0.24 (0.12), residues: 1980 sheet: -0.98 (0.18), residues: 864 loop : -1.11 (0.12), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 39 HIS 0.011 0.002 HIS L 198 PHE 0.019 0.002 PHE G 288 TYR 0.022 0.002 TYR E 219 ARG 0.009 0.001 ARG B 338 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10512 Ramachandran restraints generated. 5256 Oldfield, 0 Emsley, 5256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10512 Ramachandran restraints generated. 5256 Oldfield, 0 Emsley, 5256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue TYR 311 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LEU 378 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Evaluate side-chains 730 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 614 time to evaluate : 4.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 ASN cc_start: 0.4351 (OUTLIER) cc_final: 0.3928 (t0) REVERT: A 438 TRP cc_start: 0.5088 (t60) cc_final: 0.3596 (t60) REVERT: B 331 ASN cc_start: 0.0454 (OUTLIER) cc_final: 0.0123 (p0) REVERT: D 12 ASP cc_start: 0.6495 (OUTLIER) cc_final: 0.6238 (m-30) REVERT: E 261 PHE cc_start: 0.5478 (m-10) cc_final: 0.5233 (m-10) REVERT: G 12 ASP cc_start: 0.2242 (OUTLIER) cc_final: 0.0812 (t70) REVERT: G 321 SER cc_start: 0.4295 (OUTLIER) cc_final: 0.4010 (t) REVERT: K 402 MET cc_start: 0.5421 (ttt) cc_final: 0.5107 (ttt) REVERT: L 135 GLU cc_start: 0.4354 (pt0) cc_final: 0.3552 (pt0) outliers start: 116 outliers final: 37 residues processed: 719 average time/residue: 1.9462 time to fit residues: 1857.5964 Evaluate side-chains 468 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 426 time to evaluate : 4.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain D residue 250 ASN Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain F residue 201 ASP Chi-restraints excluded: chain G residue 12 ASP Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 321 SER Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain H residue 96 ILE Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 337 LEU Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 250 ASN Chi-restraints excluded: chain I residue 443 TYR Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain J residue 335 ILE Chi-restraints excluded: chain J residue 337 LEU Chi-restraints excluded: chain K residue 201 ASP Chi-restraints excluded: chain K residue 322 LEU Chi-restraints excluded: chain K residue 337 LEU Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain L residue 57 ASP Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 252 SER Chi-restraints excluded: chain L residue 298 SER Chi-restraints excluded: chain L residue 447 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 445 optimal weight: 2.9990 chunk 400 optimal weight: 5.9990 chunk 222 optimal weight: 0.6980 chunk 136 optimal weight: 4.9990 chunk 269 optimal weight: 2.9990 chunk 213 optimal weight: 10.0000 chunk 413 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 chunk 251 optimal weight: 5.9990 chunk 308 optimal weight: 10.0000 chunk 479 optimal weight: 3.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 197 GLN ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN B 28 GLN B 45 GLN B 284 HIS C 197 GLN C 259 ASN D 363 ASN D 419 HIS F 198 HIS F 272 GLN F 293 ASN F 317 GLN G 146 ASN ** G 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 293 ASN ** H 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 243 ASN ** I 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 28 GLN J 131 ASN ** J 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 250 ASN J 272 GLN J 284 HIS K 52 ASN ** K 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 250 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 1.0799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.116 42998 Z= 0.494 Angle : 1.062 17.456 58428 Z= 0.540 Chirality : 0.105 1.930 6275 Planarity : 0.008 0.146 7559 Dihedral : 10.060 162.229 6023 Min Nonbonded Distance : 1.573 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.93 % Favored : 95.03 % Rotamer: Outliers : 6.79 % Allowed : 23.22 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.10), residues: 5256 helix: -1.12 (0.10), residues: 1980 sheet: -1.30 (0.20), residues: 660 loop : -1.77 (0.11), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 86 HIS 0.019 0.003 HIS K 198 PHE 0.043 0.003 PHE F 64 TYR 0.039 0.003 TYR A 219 ARG 0.014 0.001 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10512 Ramachandran restraints generated. 5256 Oldfield, 0 Emsley, 5256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10512 Ramachandran restraints generated. 5256 Oldfield, 0 Emsley, 5256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue TYR 311 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LEU 378 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Evaluate side-chains 1342 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 294 poor density : 1048 time to evaluate : 5.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.8030 (p90) REVERT: A 278 ILE cc_start: 0.6092 (mt) cc_final: 0.5667 (mt) REVERT: A 328 THR cc_start: 0.7519 (p) cc_final: 0.7301 (t) REVERT: A 338 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7310 (mtp180) REVERT: A 394 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8481 (p0) REVERT: B 128 PHE cc_start: 0.6265 (OUTLIER) cc_final: 0.5173 (p90) REVERT: B 362 LYS cc_start: 0.7047 (tttm) cc_final: 0.6556 (ttpt) REVERT: C 151 THR cc_start: 0.8261 (m) cc_final: 0.7954 (p) REVERT: C 335 ILE cc_start: 0.7625 (pt) cc_final: 0.6674 (tt) REVERT: D 95 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.8428 (ptt-90) REVERT: D 406 LYS cc_start: 0.7817 (mmpt) cc_final: 0.7536 (mtpm) REVERT: E 13 VAL cc_start: 0.8275 (t) cc_final: 0.8069 (t) REVERT: E 71 ASP cc_start: 0.7786 (m-30) cc_final: 0.7465 (m-30) REVERT: E 132 VAL cc_start: 0.8591 (OUTLIER) cc_final: 0.8332 (p) REVERT: E 201 ASP cc_start: 0.9036 (OUTLIER) cc_final: 0.8778 (m-30) REVERT: F 286 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.8161 (ttt-90) REVERT: F 366 ASP cc_start: 0.7538 (OUTLIER) cc_final: 0.7335 (p0) REVERT: H 54 VAL cc_start: 0.7033 (t) cc_final: 0.6723 (t) REVERT: H 207 VAL cc_start: 0.4609 (OUTLIER) cc_final: 0.4062 (m) REVERT: H 226 TYR cc_start: 0.6688 (t80) cc_final: 0.6130 (t80) REVERT: H 311 TYR cc_start: 0.6829 (m-80) cc_final: 0.6304 (m-80) REVERT: H 403 LYS cc_start: 0.6988 (ptpp) cc_final: 0.6698 (ptpp) REVERT: I 207 VAL cc_start: 0.5568 (OUTLIER) cc_final: 0.4977 (m) REVERT: I 446 MET cc_start: 0.6929 (mmt) cc_final: 0.6397 (ttm) REVERT: J 69 GLU cc_start: 0.7766 (pt0) cc_final: 0.7542 (pp20) REVERT: J 71 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.7669 (m-30) REVERT: J 146 ASN cc_start: 0.7329 (m-40) cc_final: 0.7086 (m110) REVERT: J 201 ASP cc_start: 0.8804 (OUTLIER) cc_final: 0.8585 (m-30) REVERT: J 394 ASP cc_start: 0.8332 (p0) cc_final: 0.8120 (p0) REVERT: J 403 LYS cc_start: 0.7915 (mtmm) cc_final: 0.7598 (mtmt) REVERT: J 426 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7566 (ptp) REVERT: J 446 MET cc_start: 0.7092 (OUTLIER) cc_final: 0.6458 (mtp) REVERT: K 176 ASP cc_start: 0.7769 (m-30) cc_final: 0.7497 (m-30) REVERT: L 38 SER cc_start: 0.8774 (OUTLIER) cc_final: 0.8556 (t) REVERT: L 176 ASP cc_start: 0.7981 (m-30) cc_final: 0.7672 (m-30) REVERT: L 426 MET cc_start: 0.7889 (mtp) cc_final: 0.7665 (mtm) outliers start: 294 outliers final: 52 residues processed: 1226 average time/residue: 2.4438 time to fit residues: 3774.5601 Evaluate side-chains 742 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 674 time to evaluate : 4.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain F residue 286 ARG Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 366 ASP Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 429 ASP Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain H residue 50 PHE Chi-restraints excluded: chain H residue 96 ILE Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 249 SER Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 207 VAL Chi-restraints excluded: chain I residue 250 ASN Chi-restraints excluded: chain I residue 443 TYR Chi-restraints excluded: chain J residue 71 ASP Chi-restraints excluded: chain J residue 201 ASP Chi-restraints excluded: chain J residue 426 MET Chi-restraints excluded: chain J residue 446 MET Chi-restraints excluded: chain J residue 447 LEU Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 207 VAL Chi-restraints excluded: chain K residue 322 LEU Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 447 LEU Chi-restraints excluded: chain L residue 28 GLN Chi-restraints excluded: chain L residue 38 SER Chi-restraints excluded: chain L residue 59 SER Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 135 GLU Chi-restraints excluded: chain L residue 201 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 266 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 chunk 399 optimal weight: 2.9990 chunk 326 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 480 optimal weight: 4.9990 chunk 518 optimal weight: 2.9990 chunk 427 optimal weight: 3.9990 chunk 476 optimal weight: 6.9990 chunk 163 optimal weight: 0.0000 chunk 385 optimal weight: 0.8980 overall best weight: 1.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 ASN B 250 ASN C 243 ASN C 259 ASN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 HIS D 251 GLN D 272 GLN E 243 ASN E 250 ASN F 198 HIS F 250 ASN F 293 ASN G 284 HIS I 62 GLN I 243 ASN J 185 GLN J 251 GLN K 284 HIS L 169 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 1.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 42998 Z= 0.252 Angle : 0.721 12.175 58428 Z= 0.347 Chirality : 0.097 1.758 6275 Planarity : 0.005 0.081 7559 Dihedral : 8.100 177.164 5968 Min Nonbonded Distance : 1.641 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.97 % Allowed : 25.79 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.11), residues: 5256 helix: 0.32 (0.12), residues: 1932 sheet: -1.00 (0.18), residues: 876 loop : -1.17 (0.12), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 438 HIS 0.008 0.002 HIS L 248 PHE 0.020 0.002 PHE F 64 TYR 0.047 0.002 TYR G 177 ARG 0.008 0.001 ARG I 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10512 Ramachandran restraints generated. 5256 Oldfield, 0 Emsley, 5256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10512 Ramachandran restraints generated. 5256 Oldfield, 0 Emsley, 5256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue TYR 311 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LEU 378 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Evaluate side-chains 907 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 735 time to evaluate : 5.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8277 (mp) REVERT: B 128 PHE cc_start: 0.6938 (OUTLIER) cc_final: 0.5706 (p90) REVERT: B 353 MET cc_start: 0.8834 (mtm) cc_final: 0.8608 (mtt) REVERT: B 380 ASP cc_start: 0.7195 (t0) cc_final: 0.6670 (m-30) REVERT: B 422 CYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8126 (m) REVERT: C 64 PHE cc_start: 0.8454 (OUTLIER) cc_final: 0.7650 (t80) REVERT: C 247 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8436 (ttp) REVERT: C 362 LYS cc_start: 0.7654 (ttmt) cc_final: 0.7297 (tttt) REVERT: D 95 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.7806 (ppt-90) REVERT: D 121 LYS cc_start: 0.8458 (mttp) cc_final: 0.8150 (mttm) REVERT: D 182 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7066 (mtt) REVERT: D 375 ILE cc_start: 0.8290 (tt) cc_final: 0.8062 (mt) REVERT: D 394 ASP cc_start: 0.8748 (p0) cc_final: 0.8487 (p0) REVERT: E 12 ASP cc_start: 0.7979 (m-30) cc_final: 0.7584 (m-30) REVERT: E 71 ASP cc_start: 0.7981 (m-30) cc_final: 0.7485 (m-30) REVERT: E 385 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6826 (mp0) REVERT: E 439 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8623 (mt-10) REVERT: F 20 ARG cc_start: 0.7589 (mmm160) cc_final: 0.7382 (mmm160) REVERT: F 111 ASP cc_start: 0.8336 (p0) cc_final: 0.7962 (p0) REVERT: F 295 VAL cc_start: 0.8364 (OUTLIER) cc_final: 0.8139 (t) REVERT: F 445 SER cc_start: 0.8264 (OUTLIER) cc_final: 0.8051 (p) REVERT: G 39 TRP cc_start: 0.7148 (p-90) cc_final: 0.6940 (p90) REVERT: G 82 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7373 (mpt180) REVERT: G 180 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7105 (tt0) REVERT: H 64 PHE cc_start: 0.7637 (OUTLIER) cc_final: 0.7184 (t80) REVERT: H 180 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6800 (tt0) REVERT: H 207 VAL cc_start: 0.6619 (OUTLIER) cc_final: 0.6186 (m) REVERT: H 226 TYR cc_start: 0.7619 (t80) cc_final: 0.7168 (t80) REVERT: H 403 LYS cc_start: 0.7815 (ptpp) cc_final: 0.7537 (pttt) REVERT: I 18 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7539 (ttmm) REVERT: I 207 VAL cc_start: 0.6878 (OUTLIER) cc_final: 0.6490 (m) REVERT: I 389 ARG cc_start: 0.7275 (mpp-170) cc_final: 0.7032 (mtm180) REVERT: J 69 GLU cc_start: 0.7710 (pt0) cc_final: 0.7086 (pp20) REVERT: K 23 LYS cc_start: 0.7498 (mmtp) cc_final: 0.7237 (mmmt) REVERT: K 122 GLU cc_start: 0.7719 (mp0) cc_final: 0.7512 (mm-30) REVERT: K 406 LYS cc_start: 0.8240 (tttm) cc_final: 0.7631 (mmtm) REVERT: L 121 LYS cc_start: 0.7709 (mptt) cc_final: 0.7403 (mtpm) outliers start: 172 outliers final: 37 residues processed: 834 average time/residue: 2.5864 time to fit residues: 2691.9740 Evaluate side-chains 646 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 593 time to evaluate : 5.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 422 CYS Chi-restraints excluded: chain C residue 64 PHE Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 341 ASP Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain F residue 201 ASP Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 180 GLU Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain H residue 64 PHE Chi-restraints excluded: chain H residue 96 ILE Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 418 SER Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 18 LYS Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 207 VAL Chi-restraints excluded: chain I residue 337 LEU Chi-restraints excluded: chain I residue 443 TYR Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 339 CYS Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 390 SER Chi-restraints excluded: chain K residue 418 SER Chi-restraints excluded: chain L residue 28 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 474 optimal weight: 5.9990 chunk 361 optimal weight: 3.9990 chunk 249 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 229 optimal weight: 6.9990 chunk 322 optimal weight: 4.9990 chunk 482 optimal weight: 5.9990 chunk 510 optimal weight: 4.9990 chunk 251 optimal weight: 6.9990 chunk 456 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN A 198 HIS B 250 ASN C 250 ASN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 HIS E 250 ASN F 185 GLN F 250 ASN G 156 GLN G 317 GLN H 250 ASN I 250 ASN I 284 HIS I 297 ASN J 251 GLN J 259 ASN J 374 ASN L 190 HIS L 198 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 1.5137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 42998 Z= 0.416 Angle : 0.815 11.589 58428 Z= 0.401 Chirality : 0.100 1.874 6275 Planarity : 0.006 0.076 7559 Dihedral : 9.254 173.160 5963 Min Nonbonded Distance : 1.680 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.19 % Favored : 95.80 % Rotamer: Outliers : 4.62 % Allowed : 23.94 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.11), residues: 5256 helix: 0.28 (0.11), residues: 2004 sheet: -0.82 (0.18), residues: 876 loop : -1.14 (0.12), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 39 HIS 0.010 0.002 HIS L 191 PHE 0.030 0.002 PHE H 288 TYR 0.030 0.002 TYR A 219 ARG 0.007 0.001 ARG E 324 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10512 Ramachandran restraints generated. 5256 Oldfield, 0 Emsley, 5256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10512 Ramachandran restraints generated. 5256 Oldfield, 0 Emsley, 5256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue TYR 311 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LEU 378 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Evaluate side-chains 853 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 653 time to evaluate : 5.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LYS cc_start: 0.8173 (mtmm) cc_final: 0.7941 (mtpp) REVERT: A 21 ASP cc_start: 0.7732 (t0) cc_final: 0.7511 (t0) REVERT: A 55 MET cc_start: 0.8644 (mpp) cc_final: 0.8419 (mmt) REVERT: A 69 GLU cc_start: 0.7829 (pp20) cc_final: 0.7503 (pp20) REVERT: A 95 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.7811 (ppt-90) REVERT: A 122 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7224 (tt0) REVERT: A 130 MET cc_start: 0.8687 (ttt) cc_final: 0.8383 (ttt) REVERT: B 25 ILE cc_start: 0.8324 (tt) cc_final: 0.8034 (mt) REVERT: B 65 THR cc_start: 0.8255 (t) cc_final: 0.8033 (p) REVERT: B 69 GLU cc_start: 0.7362 (pm20) cc_final: 0.6963 (pp20) REVERT: B 128 PHE cc_start: 0.7986 (OUTLIER) cc_final: 0.6722 (p90) REVERT: B 182 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8515 (tpp) REVERT: B 317 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8561 (mp10) REVERT: C 64 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.8250 (t80) REVERT: C 104 ASP cc_start: 0.7505 (OUTLIER) cc_final: 0.7262 (m-30) REVERT: C 121 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.7882 (mttp) REVERT: C 362 LYS cc_start: 0.7633 (ttmt) cc_final: 0.7357 (tttt) REVERT: C 426 MET cc_start: 0.8139 (mtm) cc_final: 0.7878 (ttm) REVERT: D 69 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7165 (pm20) REVERT: D 121 LYS cc_start: 0.8327 (mttp) cc_final: 0.8003 (mttp) REVERT: D 185 GLN cc_start: 0.8349 (mm-40) cc_final: 0.8092 (mt0) REVERT: D 247 MET cc_start: 0.8620 (tmm) cc_final: 0.8374 (ttp) REVERT: D 414 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7167 (tm-30) REVERT: E 12 ASP cc_start: 0.8257 (m-30) cc_final: 0.7908 (m-30) REVERT: E 64 PHE cc_start: 0.8505 (OUTLIER) cc_final: 0.8054 (t80) REVERT: E 69 GLU cc_start: 0.7655 (pt0) cc_final: 0.7210 (pm20) REVERT: E 95 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8034 (ppt-90) REVERT: E 122 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7417 (mp0) REVERT: E 185 GLN cc_start: 0.8233 (mm110) cc_final: 0.8028 (mt0) REVERT: F 9 THR cc_start: 0.7926 (OUTLIER) cc_final: 0.7705 (p) REVERT: F 20 ARG cc_start: 0.8109 (mmm160) cc_final: 0.7840 (mmm160) REVERT: F 69 GLU cc_start: 0.7621 (pm20) cc_final: 0.7351 (OUTLIER) REVERT: F 111 ASP cc_start: 0.8478 (p0) cc_final: 0.7878 (p0) REVERT: F 169 GLN cc_start: 0.8252 (mt0) cc_final: 0.8027 (pt0) REVERT: F 366 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7753 (p0) REVERT: F 385 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6542 (mp0) REVERT: G 23 LYS cc_start: 0.8481 (mmmt) cc_final: 0.7657 (mptm) REVERT: G 48 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6905 (tp30) REVERT: G 52 ASN cc_start: 0.8726 (m110) cc_final: 0.8347 (m110) REVERT: G 121 LYS cc_start: 0.8333 (mtpm) cc_final: 0.7766 (mttt) REVERT: G 180 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.8009 (mt-10) REVERT: G 402 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.6915 (tpt) REVERT: H 21 ASP cc_start: 0.7745 (t0) cc_final: 0.7473 (t70) REVERT: H 26 ARG cc_start: 0.8387 (mtt-85) cc_final: 0.7941 (mtt180) REVERT: H 275 MET cc_start: 0.8389 (mmm) cc_final: 0.8142 (mmm) REVERT: H 389 ARG cc_start: 0.7814 (mtm180) cc_final: 0.7572 (mtm110) REVERT: I 18 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8391 (ttmm) REVERT: I 146 ASN cc_start: 0.7842 (m110) cc_final: 0.7616 (m-40) REVERT: J 12 ASP cc_start: 0.8186 (m-30) cc_final: 0.7929 (m-30) REVERT: J 69 GLU cc_start: 0.7940 (pt0) cc_final: 0.7418 (pp20) REVERT: J 122 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7419 (tp30) REVERT: J 362 LYS cc_start: 0.7843 (mmmt) cc_final: 0.7244 (mtmt) REVERT: J 389 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7223 (ppt170) REVERT: K 122 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7571 (mm-30) REVERT: K 124 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6976 (mt-10) REVERT: K 146 ASN cc_start: 0.7867 (m-40) cc_final: 0.7621 (m-40) REVERT: K 187 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8110 (mt-10) REVERT: K 206 ASP cc_start: 0.8365 (m-30) cc_final: 0.7850 (t70) REVERT: K 331 ASN cc_start: 0.8299 (OUTLIER) cc_final: 0.8053 (t0) REVERT: K 384 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6561 (pp20) REVERT: K 389 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7154 (ptt180) REVERT: K 406 LYS cc_start: 0.8252 (tttm) cc_final: 0.7772 (mmtm) REVERT: L 55 MET cc_start: 0.8780 (mmm) cc_final: 0.8573 (mmm) REVERT: L 64 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.8303 (t80) REVERT: L 69 GLU cc_start: 0.7556 (pt0) cc_final: 0.6541 (pp20) REVERT: L 121 LYS cc_start: 0.8170 (mptt) cc_final: 0.7764 (mttt) outliers start: 200 outliers final: 56 residues processed: 783 average time/residue: 2.7920 time to fit residues: 2685.9075 Evaluate side-chains 633 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 552 time to evaluate : 5.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 317 GLN Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain C residue 64 PHE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 445 SER Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain F residue 286 ARG Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 366 ASP Chi-restraints excluded: chain F residue 385 GLU Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain G residue 180 GLU Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 402 MET Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain H residue 96 ILE Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 18 LYS Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 82 ARG Chi-restraints excluded: chain I residue 207 VAL Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 443 TYR Chi-restraints excluded: chain J residue 122 GLU Chi-restraints excluded: chain J residue 291 VAL Chi-restraints excluded: chain J residue 389 ARG Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 122 GLU Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 187 GLU Chi-restraints excluded: chain K residue 207 VAL Chi-restraints excluded: chain K residue 235 MET Chi-restraints excluded: chain K residue 250 ASN Chi-restraints excluded: chain K residue 331 ASN Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 384 GLU Chi-restraints excluded: chain K residue 389 ARG Chi-restraints excluded: chain K residue 418 SER Chi-restraints excluded: chain L residue 64 PHE Chi-restraints excluded: chain L residue 137 GLU Chi-restraints excluded: chain L residue 151 THR Chi-restraints excluded: chain L residue 363 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 425 optimal weight: 4.9990 chunk 289 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 380 optimal weight: 3.9990 chunk 210 optimal weight: 3.9990 chunk 435 optimal weight: 8.9990 chunk 352 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 260 optimal weight: 5.9990 chunk 458 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 250 ASN C 284 HIS ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 ASN H 52 ASN H 318 ASN H 363 ASN K 363 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 1.5292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 42998 Z= 0.321 Angle : 0.713 11.329 58428 Z= 0.343 Chirality : 0.098 1.797 6275 Planarity : 0.005 0.067 7559 Dihedral : 8.738 177.769 5963 Min Nonbonded Distance : 1.677 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.47 % Allowed : 24.61 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.11), residues: 5256 helix: 0.72 (0.12), residues: 1980 sheet: -0.64 (0.18), residues: 876 loop : -1.06 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 39 HIS 0.006 0.001 HIS E 191 PHE 0.017 0.002 PHE H 288 TYR 0.025 0.002 TYR B 219 ARG 0.005 0.001 ARG H 26 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10512 Ramachandran restraints generated. 5256 Oldfield, 0 Emsley, 5256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10512 Ramachandran restraints generated. 5256 Oldfield, 0 Emsley, 5256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue TYR 311 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LEU 378 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Evaluate side-chains 728 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 578 time to evaluate : 5.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LYS cc_start: 0.8233 (mtmm) cc_final: 0.8005 (mtpp) REVERT: A 31 ASP cc_start: 0.8540 (p0) cc_final: 0.8222 (p0) REVERT: A 55 MET cc_start: 0.8772 (mpp) cc_final: 0.8388 (mmt) REVERT: A 69 GLU cc_start: 0.8073 (pp20) cc_final: 0.7606 (pp20) REVERT: A 130 MET cc_start: 0.8573 (ttt) cc_final: 0.8235 (ttt) REVERT: B 10 LYS cc_start: 0.8099 (mtmt) cc_final: 0.7862 (mtmm) REVERT: B 23 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.7996 (tmtm) REVERT: B 25 ILE cc_start: 0.8415 (tt) cc_final: 0.8207 (mt) REVERT: B 128 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.6909 (p90) REVERT: B 317 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8595 (mp10) REVERT: C 64 PHE cc_start: 0.8602 (OUTLIER) cc_final: 0.8038 (t80) REVERT: C 65 THR cc_start: 0.8686 (OUTLIER) cc_final: 0.8451 (t) REVERT: C 121 LYS cc_start: 0.8371 (mtpm) cc_final: 0.7905 (mttp) REVERT: C 307 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7033 (mp0) REVERT: C 353 MET cc_start: 0.8915 (mtt) cc_final: 0.8693 (mtt) REVERT: C 362 LYS cc_start: 0.7615 (ttmt) cc_final: 0.7406 (tttm) REVERT: C 426 MET cc_start: 0.8163 (mtm) cc_final: 0.7867 (ttm) REVERT: D 95 ARG cc_start: 0.9075 (OUTLIER) cc_final: 0.7801 (ppt-90) REVERT: D 185 GLN cc_start: 0.8366 (mm-40) cc_final: 0.8102 (mt0) REVERT: D 247 MET cc_start: 0.8542 (tmm) cc_final: 0.8312 (ttp) REVERT: D 414 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7110 (tm-30) REVERT: E 12 ASP cc_start: 0.8357 (m-30) cc_final: 0.7982 (m-30) REVERT: E 23 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8313 (tmtm) REVERT: E 64 PHE cc_start: 0.8489 (OUTLIER) cc_final: 0.8059 (t80) REVERT: E 69 GLU cc_start: 0.7630 (pt0) cc_final: 0.7241 (pm20) REVERT: E 95 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8110 (ppt-90) REVERT: E 122 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7421 (mp0) REVERT: E 185 GLN cc_start: 0.8204 (mm110) cc_final: 0.7971 (mt0) REVERT: F 11 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7671 (mp0) REVERT: F 20 ARG cc_start: 0.8051 (mmm160) cc_final: 0.7813 (mmm160) REVERT: F 48 GLU cc_start: 0.7586 (pt0) cc_final: 0.7177 (pm20) REVERT: F 69 GLU cc_start: 0.7633 (pm20) cc_final: 0.7340 (OUTLIER) REVERT: F 152 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8245 (mt-10) REVERT: F 291 VAL cc_start: 0.8684 (OUTLIER) cc_final: 0.8382 (t) REVERT: G 23 LYS cc_start: 0.8477 (mmmt) cc_final: 0.7645 (mptm) REVERT: G 48 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6873 (tp30) REVERT: G 51 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7784 (tt0) REVERT: G 95 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.7412 (ppt-90) REVERT: G 121 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7853 (mttt) REVERT: G 180 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7952 (mt-10) REVERT: G 272 GLN cc_start: 0.8227 (tp-100) cc_final: 0.7992 (mm-40) REVERT: H 23 LYS cc_start: 0.8200 (tptp) cc_final: 0.7771 (mmtp) REVERT: H 48 GLU cc_start: 0.7313 (pt0) cc_final: 0.7080 (tp30) REVERT: H 69 GLU cc_start: 0.7520 (pt0) cc_final: 0.7172 (pm20) REVERT: H 275 MET cc_start: 0.8419 (mmm) cc_final: 0.8186 (mmm) REVERT: H 389 ARG cc_start: 0.7902 (mtm180) cc_final: 0.7668 (mtm110) REVERT: H 406 LYS cc_start: 0.8283 (tttm) cc_final: 0.7573 (mmtm) REVERT: I 82 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.6805 (mpt180) REVERT: I 122 GLU cc_start: 0.7177 (mp0) cc_final: 0.6861 (tp30) REVERT: I 146 ASN cc_start: 0.8036 (m110) cc_final: 0.7827 (m-40) REVERT: J 12 ASP cc_start: 0.8179 (m-30) cc_final: 0.7931 (m-30) REVERT: J 69 GLU cc_start: 0.7843 (pt0) cc_final: 0.7185 (pp20) REVERT: J 122 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7400 (tp30) REVERT: J 362 LYS cc_start: 0.7806 (mmmt) cc_final: 0.7271 (mttp) REVERT: K 122 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7555 (mm-30) REVERT: K 187 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8099 (mt-10) REVERT: K 206 ASP cc_start: 0.8299 (m-30) cc_final: 0.7815 (t70) REVERT: K 331 ASN cc_start: 0.8303 (OUTLIER) cc_final: 0.8022 (t0) REVERT: K 406 LYS cc_start: 0.8199 (tttm) cc_final: 0.7754 (mmtm) REVERT: L 64 PHE cc_start: 0.8560 (OUTLIER) cc_final: 0.8256 (t80) REVERT: L 69 GLU cc_start: 0.7477 (pt0) cc_final: 0.6431 (pp20) REVERT: L 121 LYS cc_start: 0.8100 (mptt) cc_final: 0.7681 (mttt) REVERT: L 137 GLU cc_start: 0.9127 (OUTLIER) cc_final: 0.8825 (mt-10) REVERT: L 172 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.7826 (ttp80) outliers start: 150 outliers final: 66 residues processed: 670 average time/residue: 2.8213 time to fit residues: 2317.8994 Evaluate side-chains 636 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 545 time to evaluate : 5.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLN Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 317 GLN Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain C residue 50 PHE Chi-restraints excluded: chain C residue 64 PHE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain D residue 55 MET Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 445 SER Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 429 ASP Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain F residue 286 ARG Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 429 ASP Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 121 LYS Chi-restraints excluded: chain G residue 180 GLU Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain H residue 96 ILE Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 82 ARG Chi-restraints excluded: chain I residue 135 GLU Chi-restraints excluded: chain I residue 207 VAL Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 429 ASP Chi-restraints excluded: chain I residue 443 TYR Chi-restraints excluded: chain J residue 8 THR Chi-restraints excluded: chain J residue 51 GLU Chi-restraints excluded: chain J residue 122 GLU Chi-restraints excluded: chain J residue 242 VAL Chi-restraints excluded: chain J residue 291 VAL Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 122 GLU Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 187 GLU Chi-restraints excluded: chain K residue 250 ASN Chi-restraints excluded: chain K residue 331 ASN Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain L residue 64 PHE Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 137 GLU Chi-restraints excluded: chain L residue 151 THR Chi-restraints excluded: chain L residue 172 ARG Chi-restraints excluded: chain L residue 363 ASN Chi-restraints excluded: chain L residue 418 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 171 optimal weight: 6.9990 chunk 459 optimal weight: 7.9990 chunk 100 optimal weight: 7.9990 chunk 299 optimal weight: 8.9990 chunk 125 optimal weight: 8.9990 chunk 510 optimal weight: 9.9990 chunk 424 optimal weight: 2.9990 chunk 236 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 268 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 250 ASN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 318 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 1.5534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 42998 Z= 0.457 Angle : 0.777 11.557 58428 Z= 0.380 Chirality : 0.100 1.860 6275 Planarity : 0.005 0.069 7559 Dihedral : 9.256 175.262 5963 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.07 % Allowed : 23.71 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.11), residues: 5256 helix: 0.54 (0.11), residues: 2004 sheet: -0.60 (0.18), residues: 876 loop : -1.13 (0.12), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP H 39 HIS 0.009 0.002 HIS K 284 PHE 0.024 0.002 PHE H 288 TYR 0.027 0.002 TYR B 219 ARG 0.006 0.001 ARG E 324 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10512 Ramachandran restraints generated. 5256 Oldfield, 0 Emsley, 5256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10512 Ramachandran restraints generated. 5256 Oldfield, 0 Emsley, 5256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue TYR 311 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LEU 378 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Evaluate side-chains 738 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 562 time to evaluate : 5.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LYS cc_start: 0.8272 (mtmm) cc_final: 0.8071 (mtpp) REVERT: A 31 ASP cc_start: 0.8638 (p0) cc_final: 0.8341 (p0) REVERT: A 55 MET cc_start: 0.8867 (mpp) cc_final: 0.8385 (mmt) REVERT: A 69 GLU cc_start: 0.8020 (pp20) cc_final: 0.7475 (pp20) REVERT: B 10 LYS cc_start: 0.8245 (mtmt) cc_final: 0.8036 (mtmm) REVERT: B 23 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8193 (tmtm) REVERT: B 69 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7041 (pp20) REVERT: B 121 LYS cc_start: 0.8060 (mptt) cc_final: 0.7721 (mttt) REVERT: B 128 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.7073 (p90) REVERT: B 317 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8614 (mp10) REVERT: C 64 PHE cc_start: 0.8743 (OUTLIER) cc_final: 0.8374 (t80) REVERT: C 121 LYS cc_start: 0.8494 (mtpm) cc_final: 0.7987 (mttp) REVERT: C 307 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.7280 (mp0) REVERT: C 353 MET cc_start: 0.8905 (mtt) cc_final: 0.8653 (mtt) REVERT: C 426 MET cc_start: 0.8184 (mtm) cc_final: 0.7915 (ttm) REVERT: D 95 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.7820 (ppt-90) REVERT: D 121 LYS cc_start: 0.8343 (mttt) cc_final: 0.7876 (mttp) REVERT: D 185 GLN cc_start: 0.8432 (mm-40) cc_final: 0.8170 (mt0) REVERT: D 247 MET cc_start: 0.8622 (tmm) cc_final: 0.8417 (ttp) REVERT: D 414 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7183 (tm-30) REVERT: E 12 ASP cc_start: 0.8470 (m-30) cc_final: 0.8162 (m-30) REVERT: E 23 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8312 (tmtm) REVERT: E 55 MET cc_start: 0.8905 (mmm) cc_final: 0.8637 (mmm) REVERT: E 64 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.8023 (t80) REVERT: E 69 GLU cc_start: 0.7820 (pt0) cc_final: 0.7349 (pm20) REVERT: E 95 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8068 (ppt-90) REVERT: E 122 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7457 (mp0) REVERT: E 185 GLN cc_start: 0.8262 (mm110) cc_final: 0.8013 (mt0) REVERT: F 20 ARG cc_start: 0.8020 (mmm160) cc_final: 0.7802 (mmm160) REVERT: F 69 GLU cc_start: 0.7644 (pm20) cc_final: 0.7336 (pp20) REVERT: F 111 ASP cc_start: 0.8407 (p0) cc_final: 0.7972 (p0) REVERT: F 152 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8320 (mt-10) REVERT: G 51 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7855 (tt0) REVERT: G 69 GLU cc_start: 0.7668 (pm20) cc_final: 0.7099 (pp20) REVERT: G 82 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7946 (mpt180) REVERT: G 95 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.7484 (ppt-90) REVERT: G 121 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.7947 (mttp) REVERT: G 122 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6708 (mp0) REVERT: G 180 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7934 (mt-10) REVERT: H 21 ASP cc_start: 0.7997 (t0) cc_final: 0.7780 (t70) REVERT: H 23 LYS cc_start: 0.8251 (tptp) cc_final: 0.7777 (mmtp) REVERT: H 69 GLU cc_start: 0.7657 (pt0) cc_final: 0.7203 (pm20) REVERT: H 122 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6753 (mp0) REVERT: H 389 ARG cc_start: 0.8007 (mtm180) cc_final: 0.7806 (mtm110) REVERT: H 406 LYS cc_start: 0.8364 (tttm) cc_final: 0.7720 (mmtm) REVERT: I 121 LYS cc_start: 0.8093 (mptt) cc_final: 0.7763 (mttt) REVERT: I 122 GLU cc_start: 0.7503 (mp0) cc_final: 0.7277 (mp0) REVERT: I 146 ASN cc_start: 0.8016 (m110) cc_final: 0.7805 (m-40) REVERT: I 406 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7332 (mmtm) REVERT: J 12 ASP cc_start: 0.8184 (m-30) cc_final: 0.7906 (m-30) REVERT: J 69 GLU cc_start: 0.7969 (pt0) cc_final: 0.7282 (pp20) REVERT: J 95 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.7681 (ppt-90) REVERT: J 122 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7449 (tp30) REVERT: J 362 LYS cc_start: 0.7890 (mmmt) cc_final: 0.7369 (mttp) REVERT: K 18 LYS cc_start: 0.8618 (ttpp) cc_final: 0.8366 (ttmm) REVERT: K 122 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7449 (mm-30) REVERT: K 187 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8068 (mt-10) REVERT: K 206 ASP cc_start: 0.8343 (m-30) cc_final: 0.7887 (t70) REVERT: K 331 ASN cc_start: 0.8273 (OUTLIER) cc_final: 0.7949 (t0) REVERT: K 389 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7375 (ptt180) REVERT: K 406 LYS cc_start: 0.8194 (tttm) cc_final: 0.7748 (mmtm) REVERT: L 31 ASP cc_start: 0.8525 (p0) cc_final: 0.7878 (p0) REVERT: L 69 GLU cc_start: 0.7550 (pt0) cc_final: 0.6586 (pp20) REVERT: L 172 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.7742 (ttp80) REVERT: L 403 LYS cc_start: 0.8541 (tttp) cc_final: 0.8255 (mttp) outliers start: 176 outliers final: 82 residues processed: 674 average time/residue: 2.7821 time to fit residues: 2304.5515 Evaluate side-chains 650 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 541 time to evaluate : 5.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLN Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 317 GLN Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 422 CYS Chi-restraints excluded: chain C residue 50 PHE Chi-restraints excluded: chain C residue 64 PHE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain D residue 55 MET Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 445 SER Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 429 ASP Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 169 GLN Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain F residue 286 ARG Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 366 ASP Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 121 LYS Chi-restraints excluded: chain G residue 122 GLU Chi-restraints excluded: chain G residue 180 GLU Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 445 SER Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 82 ARG Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 135 GLU Chi-restraints excluded: chain I residue 137 GLU Chi-restraints excluded: chain I residue 207 VAL Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 372 ASN Chi-restraints excluded: chain I residue 406 LYS Chi-restraints excluded: chain I residue 418 SER Chi-restraints excluded: chain I residue 443 TYR Chi-restraints excluded: chain J residue 8 THR Chi-restraints excluded: chain J residue 95 ARG Chi-restraints excluded: chain J residue 122 GLU Chi-restraints excluded: chain J residue 242 VAL Chi-restraints excluded: chain J residue 256 ASP Chi-restraints excluded: chain J residue 291 VAL Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 122 GLU Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 187 GLU Chi-restraints excluded: chain K residue 207 VAL Chi-restraints excluded: chain K residue 250 ASN Chi-restraints excluded: chain K residue 331 ASN Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 382 GLU Chi-restraints excluded: chain K residue 389 ARG Chi-restraints excluded: chain K residue 418 SER Chi-restraints excluded: chain K residue 429 ASP Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 151 THR Chi-restraints excluded: chain L residue 172 ARG Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain L residue 418 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 492 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 291 optimal weight: 5.9990 chunk 373 optimal weight: 4.9990 chunk 289 optimal weight: 3.9990 chunk 430 optimal weight: 0.9980 chunk 285 optimal weight: 5.9990 chunk 508 optimal weight: 5.9990 chunk 318 optimal weight: 5.9990 chunk 310 optimal weight: 1.9990 chunk 234 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 318 ASN K 146 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 1.5567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 42998 Z= 0.237 Angle : 0.671 11.142 58428 Z= 0.319 Chirality : 0.097 1.702 6275 Planarity : 0.004 0.061 7559 Dihedral : 8.486 177.887 5961 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.68 % Allowed : 24.63 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.11), residues: 5256 helix: 1.01 (0.12), residues: 1980 sheet: -0.49 (0.18), residues: 876 loop : -1.01 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 39 HIS 0.005 0.001 HIS H 198 PHE 0.013 0.001 PHE H 288 TYR 0.022 0.001 TYR B 219 ARG 0.004 0.000 ARG H 26 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10512 Ramachandran restraints generated. 5256 Oldfield, 0 Emsley, 5256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10512 Ramachandran restraints generated. 5256 Oldfield, 0 Emsley, 5256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue TYR 311 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LEU 378 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Evaluate side-chains 689 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 573 time to evaluate : 5.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.8521 (p0) cc_final: 0.8181 (p0) REVERT: A 55 MET cc_start: 0.8836 (mpp) cc_final: 0.8346 (mmt) REVERT: A 69 GLU cc_start: 0.7956 (pp20) cc_final: 0.7511 (pp20) REVERT: A 182 MET cc_start: 0.8391 (ptm) cc_final: 0.8036 (ptm) REVERT: A 394 ASP cc_start: 0.9087 (p0) cc_final: 0.8871 (p0) REVERT: B 23 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8191 (tmtm) REVERT: B 69 GLU cc_start: 0.7460 (pm20) cc_final: 0.6738 (pp20) REVERT: B 121 LYS cc_start: 0.8014 (mptt) cc_final: 0.7667 (mttt) REVERT: B 128 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.7010 (p90) REVERT: B 317 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8610 (mp10) REVERT: C 64 PHE cc_start: 0.8531 (OUTLIER) cc_final: 0.7802 (t80) REVERT: C 65 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.8405 (t) REVERT: C 121 LYS cc_start: 0.8388 (mtpm) cc_final: 0.7890 (mptt) REVERT: C 172 ARG cc_start: 0.9254 (OUTLIER) cc_final: 0.8472 (ttp80) REVERT: C 307 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7032 (mp0) REVERT: C 426 MET cc_start: 0.8108 (mtm) cc_final: 0.7847 (ttm) REVERT: D 95 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.7798 (ppt-90) REVERT: D 121 LYS cc_start: 0.8317 (mttt) cc_final: 0.7842 (mttp) REVERT: D 122 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7179 (mp0) REVERT: D 185 GLN cc_start: 0.8370 (mm-40) cc_final: 0.8106 (mt0) REVERT: D 247 MET cc_start: 0.8489 (tmm) cc_final: 0.8251 (ttp) REVERT: D 414 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7129 (tm-30) REVERT: E 12 ASP cc_start: 0.8477 (m-30) cc_final: 0.8180 (m-30) REVERT: E 23 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8306 (tmtm) REVERT: E 55 MET cc_start: 0.8900 (mmm) cc_final: 0.8656 (mmm) REVERT: E 64 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.8061 (t80) REVERT: E 69 GLU cc_start: 0.7680 (pt0) cc_final: 0.7262 (pm20) REVERT: E 95 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8106 (ppt-90) REVERT: E 185 GLN cc_start: 0.8193 (mm110) cc_final: 0.7965 (mt0) REVERT: F 48 GLU cc_start: 0.7631 (pt0) cc_final: 0.7154 (tp30) REVERT: F 69 GLU cc_start: 0.7650 (pm20) cc_final: 0.7310 (pp20) REVERT: F 111 ASP cc_start: 0.8401 (p0) cc_final: 0.7981 (p0) REVERT: F 152 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8323 (mt-10) REVERT: F 353 MET cc_start: 0.8944 (mtt) cc_final: 0.8658 (mtt) REVERT: G 23 LYS cc_start: 0.8430 (mmmt) cc_final: 0.7680 (mptm) REVERT: G 69 GLU cc_start: 0.7515 (pm20) cc_final: 0.7050 (pp20) REVERT: G 82 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7986 (mpt180) REVERT: G 121 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7885 (mttt) REVERT: G 122 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6580 (mp0) REVERT: H 8 THR cc_start: 0.6899 (p) cc_final: 0.6587 (p) REVERT: H 23 LYS cc_start: 0.8237 (tptp) cc_final: 0.7783 (mmtp) REVERT: H 69 GLU cc_start: 0.7565 (pt0) cc_final: 0.7109 (pm20) REVERT: H 406 LYS cc_start: 0.8318 (tttm) cc_final: 0.7714 (mmtm) REVERT: I 82 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.6858 (mpt180) REVERT: I 122 GLU cc_start: 0.7437 (mp0) cc_final: 0.7086 (tp30) REVERT: I 135 GLU cc_start: 0.9019 (OUTLIER) cc_final: 0.8750 (pt0) REVERT: I 146 ASN cc_start: 0.8023 (m110) cc_final: 0.7799 (m-40) REVERT: I 247 MET cc_start: 0.8773 (tmm) cc_final: 0.8535 (ttt) REVERT: I 406 LYS cc_start: 0.8106 (pttm) cc_final: 0.7296 (mmtm) REVERT: J 12 ASP cc_start: 0.8204 (m-30) cc_final: 0.7935 (m-30) REVERT: J 31 ASP cc_start: 0.8529 (p0) cc_final: 0.8189 (p0) REVERT: J 69 GLU cc_start: 0.7824 (pt0) cc_final: 0.7154 (pp20) REVERT: J 95 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.7642 (ppt-90) REVERT: J 122 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7326 (tp30) REVERT: J 362 LYS cc_start: 0.7875 (mmmt) cc_final: 0.7375 (mttp) REVERT: J 446 MET cc_start: 0.7813 (mmt) cc_final: 0.6919 (ptm) REVERT: K 21 ASP cc_start: 0.8351 (t0) cc_final: 0.8144 (t0) REVERT: K 23 LYS cc_start: 0.8410 (mptm) cc_final: 0.8172 (tptp) REVERT: K 122 GLU cc_start: 0.7634 (mp0) cc_final: 0.7335 (mm-30) REVERT: K 206 ASP cc_start: 0.8264 (m-30) cc_final: 0.7823 (t70) REVERT: K 331 ASN cc_start: 0.8252 (OUTLIER) cc_final: 0.7971 (t0) REVERT: K 389 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7183 (ptt180) REVERT: K 406 LYS cc_start: 0.8138 (tttm) cc_final: 0.7722 (mmtm) REVERT: L 21 ASP cc_start: 0.8282 (t0) cc_final: 0.7938 (t0) REVERT: L 69 GLU cc_start: 0.7517 (pt0) cc_final: 0.6566 (pp20) REVERT: L 137 GLU cc_start: 0.9145 (OUTLIER) cc_final: 0.8845 (mt-10) REVERT: L 172 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.7893 (ttp80) outliers start: 116 outliers final: 50 residues processed: 647 average time/residue: 2.8363 time to fit residues: 2254.9836 Evaluate side-chains 632 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 558 time to evaluate : 4.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 317 GLN Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain C residue 50 PHE Chi-restraints excluded: chain C residue 64 PHE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain D residue 55 MET Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 445 SER Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 429 ASP Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 286 ARG Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 429 ASP Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain G residue 121 LYS Chi-restraints excluded: chain G residue 122 GLU Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 418 SER Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 82 ARG Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 135 GLU Chi-restraints excluded: chain I residue 207 VAL Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 429 ASP Chi-restraints excluded: chain I residue 443 TYR Chi-restraints excluded: chain J residue 95 ARG Chi-restraints excluded: chain J residue 122 GLU Chi-restraints excluded: chain J residue 291 VAL Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 72 MET Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 250 ASN Chi-restraints excluded: chain K residue 331 ASN Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 389 ARG Chi-restraints excluded: chain K residue 418 SER Chi-restraints excluded: chain K residue 429 ASP Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 137 GLU Chi-restraints excluded: chain L residue 172 ARG Chi-restraints excluded: chain L residue 418 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 314 optimal weight: 7.9990 chunk 203 optimal weight: 3.9990 chunk 303 optimal weight: 8.9990 chunk 153 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 323 optimal weight: 7.9990 chunk 346 optimal weight: 2.9990 chunk 251 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 400 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN G 131 ASN H 318 ASN K 146 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 1.5616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 42998 Z= 0.267 Angle : 0.680 11.276 58428 Z= 0.323 Chirality : 0.097 1.725 6275 Planarity : 0.004 0.060 7559 Dihedral : 8.405 177.697 5959 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.70 % Allowed : 24.49 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.11), residues: 5256 helix: 1.14 (0.12), residues: 1980 sheet: -0.43 (0.19), residues: 876 loop : -0.96 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 39 HIS 0.005 0.001 HIS H 198 PHE 0.015 0.001 PHE H 288 TYR 0.023 0.002 TYR B 219 ARG 0.003 0.000 ARG H 26 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10512 Ramachandran restraints generated. 5256 Oldfield, 0 Emsley, 5256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10512 Ramachandran restraints generated. 5256 Oldfield, 0 Emsley, 5256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue TYR 311 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LEU 378 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Evaluate side-chains 678 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 561 time to evaluate : 5.515 Fit side-chains revert: symmetry clash REVERT: A 18 LYS cc_start: 0.8628 (mtpp) cc_final: 0.7980 (mtmm) REVERT: A 31 ASP cc_start: 0.8564 (p0) cc_final: 0.8238 (p0) REVERT: A 55 MET cc_start: 0.8838 (mpp) cc_final: 0.8330 (mmt) REVERT: A 69 GLU cc_start: 0.7973 (pp20) cc_final: 0.7511 (pp20) REVERT: A 95 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.7743 (ppt-90) REVERT: A 182 MET cc_start: 0.8348 (ptm) cc_final: 0.8073 (ptm) REVERT: A 394 ASP cc_start: 0.9084 (p0) cc_final: 0.8865 (p0) REVERT: B 23 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8187 (tmtm) REVERT: B 69 GLU cc_start: 0.7598 (pm20) cc_final: 0.7004 (pp20) REVERT: B 121 LYS cc_start: 0.7975 (mptt) cc_final: 0.7665 (mttt) REVERT: B 128 PHE cc_start: 0.8301 (OUTLIER) cc_final: 0.6917 (p90) REVERT: B 317 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8661 (mp10) REVERT: C 64 PHE cc_start: 0.8603 (OUTLIER) cc_final: 0.8050 (t80) REVERT: C 121 LYS cc_start: 0.8411 (mtpm) cc_final: 0.7925 (mptt) REVERT: C 172 ARG cc_start: 0.9263 (OUTLIER) cc_final: 0.8479 (ttp80) REVERT: C 307 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7057 (mp0) REVERT: C 426 MET cc_start: 0.8145 (mtm) cc_final: 0.7894 (ttm) REVERT: D 95 ARG cc_start: 0.9085 (OUTLIER) cc_final: 0.7817 (ppt-90) REVERT: D 121 LYS cc_start: 0.8345 (mttt) cc_final: 0.7869 (mttp) REVERT: D 122 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7163 (mp0) REVERT: D 185 GLN cc_start: 0.8374 (mm-40) cc_final: 0.8118 (mt0) REVERT: D 247 MET cc_start: 0.8505 (tmm) cc_final: 0.8276 (ttp) REVERT: D 414 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7162 (tm-30) REVERT: E 12 ASP cc_start: 0.8479 (m-30) cc_final: 0.8194 (m-30) REVERT: E 23 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8295 (tmtm) REVERT: E 55 MET cc_start: 0.8891 (mmm) cc_final: 0.8664 (mmm) REVERT: E 64 PHE cc_start: 0.8526 (OUTLIER) cc_final: 0.8112 (t80) REVERT: E 69 GLU cc_start: 0.7638 (pt0) cc_final: 0.7238 (pm20) REVERT: E 95 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8095 (ppt-90) REVERT: E 122 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7237 (tp30) REVERT: E 185 GLN cc_start: 0.8192 (mm110) cc_final: 0.7989 (mt0) REVERT: F 48 GLU cc_start: 0.7616 (pt0) cc_final: 0.7165 (tp30) REVERT: F 69 GLU cc_start: 0.7672 (pm20) cc_final: 0.7134 (pp20) REVERT: F 111 ASP cc_start: 0.8415 (p0) cc_final: 0.7998 (p0) REVERT: F 152 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8315 (mt-10) REVERT: F 353 MET cc_start: 0.8954 (mtt) cc_final: 0.8686 (mtt) REVERT: G 23 LYS cc_start: 0.8450 (mmmt) cc_final: 0.7700 (mptm) REVERT: G 69 GLU cc_start: 0.7592 (pm20) cc_final: 0.7136 (pp20) REVERT: G 82 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7884 (mpt180) REVERT: G 95 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.7670 (ppt-90) REVERT: G 121 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7906 (mttt) REVERT: G 122 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6534 (mp0) REVERT: G 270 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8534 (mp) REVERT: H 8 THR cc_start: 0.7016 (p) cc_final: 0.6747 (p) REVERT: H 23 LYS cc_start: 0.8251 (tptp) cc_final: 0.7788 (mmtt) REVERT: H 69 GLU cc_start: 0.7567 (pt0) cc_final: 0.7141 (pm20) REVERT: H 406 LYS cc_start: 0.8265 (tttm) cc_final: 0.7652 (mmtm) REVERT: I 82 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.6850 (mpt180) REVERT: I 146 ASN cc_start: 0.8026 (m110) cc_final: 0.7772 (m-40) REVERT: I 247 MET cc_start: 0.8777 (tmm) cc_final: 0.8525 (ttt) REVERT: I 406 LYS cc_start: 0.8111 (pttm) cc_final: 0.7294 (mmtm) REVERT: J 12 ASP cc_start: 0.8202 (m-30) cc_final: 0.7936 (m-30) REVERT: J 31 ASP cc_start: 0.8571 (p0) cc_final: 0.8244 (p0) REVERT: J 69 GLU cc_start: 0.7749 (pt0) cc_final: 0.7093 (pp20) REVERT: J 95 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.7632 (ppt-90) REVERT: J 122 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7322 (tp30) REVERT: J 362 LYS cc_start: 0.7875 (mmmt) cc_final: 0.7437 (mttp) REVERT: J 446 MET cc_start: 0.7795 (mmt) cc_final: 0.6952 (ptm) REVERT: K 122 GLU cc_start: 0.7571 (mp0) cc_final: 0.7316 (mm-30) REVERT: K 206 ASP cc_start: 0.8266 (m-30) cc_final: 0.7792 (t70) REVERT: K 331 ASN cc_start: 0.8224 (OUTLIER) cc_final: 0.7949 (t0) REVERT: K 389 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7190 (ptt180) REVERT: K 406 LYS cc_start: 0.8116 (tttm) cc_final: 0.7714 (mmtm) REVERT: L 21 ASP cc_start: 0.8268 (t0) cc_final: 0.7948 (t0) REVERT: L 69 GLU cc_start: 0.7504 (pt0) cc_final: 0.6749 (pp20) REVERT: L 122 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7211 (mp0) REVERT: L 172 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.7868 (ttp80) outliers start: 117 outliers final: 68 residues processed: 643 average time/residue: 2.8876 time to fit residues: 2300.8360 Evaluate side-chains 647 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 553 time to evaluate : 5.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 317 GLN Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain C residue 64 PHE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain D residue 55 MET Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 445 SER Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 429 ASP Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 286 ARG Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 429 ASP Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain G residue 12 ASP Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 121 LYS Chi-restraints excluded: chain G residue 122 GLU Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 405 SER Chi-restraints excluded: chain G residue 445 SER Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 331 ASN Chi-restraints excluded: chain H residue 418 SER Chi-restraints excluded: chain H residue 429 ASP Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 82 ARG Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 135 GLU Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 429 ASP Chi-restraints excluded: chain I residue 443 TYR Chi-restraints excluded: chain J residue 8 THR Chi-restraints excluded: chain J residue 95 ARG Chi-restraints excluded: chain J residue 122 GLU Chi-restraints excluded: chain J residue 242 VAL Chi-restraints excluded: chain J residue 291 VAL Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 72 MET Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 207 VAL Chi-restraints excluded: chain K residue 250 ASN Chi-restraints excluded: chain K residue 331 ASN Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 389 ARG Chi-restraints excluded: chain K residue 418 SER Chi-restraints excluded: chain K residue 429 ASP Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain L residue 121 LYS Chi-restraints excluded: chain L residue 122 GLU Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 172 ARG Chi-restraints excluded: chain L residue 418 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 462 optimal weight: 5.9990 chunk 487 optimal weight: 6.9990 chunk 444 optimal weight: 5.9990 chunk 474 optimal weight: 4.9990 chunk 285 optimal weight: 4.9990 chunk 206 optimal weight: 0.5980 chunk 372 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 428 optimal weight: 7.9990 chunk 448 optimal weight: 0.0470 chunk 472 optimal weight: 6.9990 overall best weight: 3.1284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 ASN H 318 ASN K 146 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 1.5658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 42998 Z= 0.271 Angle : 0.678 11.250 58428 Z= 0.322 Chirality : 0.097 1.721 6275 Planarity : 0.004 0.060 7559 Dihedral : 8.346 177.710 5959 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.59 % Allowed : 24.61 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.11), residues: 5256 helix: 1.20 (0.12), residues: 1980 sheet: -0.42 (0.19), residues: 876 loop : -0.95 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 39 HIS 0.005 0.001 HIS D 181 PHE 0.015 0.001 PHE H 288 TYR 0.023 0.002 TYR B 219 ARG 0.003 0.000 ARG H 26 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10512 Ramachandran restraints generated. 5256 Oldfield, 0 Emsley, 5256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10512 Ramachandran restraints generated. 5256 Oldfield, 0 Emsley, 5256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue TYR 311 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LEU 378 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Evaluate side-chains 667 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 555 time to evaluate : 5.110 Fit side-chains revert: symmetry clash REVERT: A 18 LYS cc_start: 0.8609 (mtpp) cc_final: 0.7948 (mtmm) REVERT: A 31 ASP cc_start: 0.8555 (p0) cc_final: 0.8225 (p0) REVERT: A 55 MET cc_start: 0.8841 (mpp) cc_final: 0.8337 (mmt) REVERT: A 69 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7484 (pp20) REVERT: A 95 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.7731 (ppt-90) REVERT: A 394 ASP cc_start: 0.9077 (p0) cc_final: 0.8855 (p0) REVERT: B 23 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8189 (tmtm) REVERT: B 69 GLU cc_start: 0.7610 (pm20) cc_final: 0.7040 (pp20) REVERT: B 121 LYS cc_start: 0.8008 (mptt) cc_final: 0.7692 (mttt) REVERT: B 128 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.6917 (p90) REVERT: B 317 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8650 (mp10) REVERT: C 18 LYS cc_start: 0.8613 (mtpp) cc_final: 0.8107 (mttp) REVERT: C 64 PHE cc_start: 0.8539 (OUTLIER) cc_final: 0.7909 (t80) REVERT: C 65 THR cc_start: 0.8654 (OUTLIER) cc_final: 0.8411 (t) REVERT: C 121 LYS cc_start: 0.8422 (mtpm) cc_final: 0.7916 (mptt) REVERT: C 172 ARG cc_start: 0.9258 (OUTLIER) cc_final: 0.8472 (ttp80) REVERT: C 307 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7049 (mp0) REVERT: C 426 MET cc_start: 0.8142 (mtm) cc_final: 0.7898 (ttm) REVERT: D 69 GLU cc_start: 0.7436 (pm20) cc_final: 0.7178 (pt0) REVERT: D 95 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.7795 (ppt-90) REVERT: D 121 LYS cc_start: 0.8310 (mttt) cc_final: 0.7844 (mttp) REVERT: D 185 GLN cc_start: 0.8359 (mm-40) cc_final: 0.8105 (mt0) REVERT: D 247 MET cc_start: 0.8489 (tmm) cc_final: 0.8252 (ttp) REVERT: D 414 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7159 (tm-30) REVERT: E 12 ASP cc_start: 0.8448 (m-30) cc_final: 0.8164 (m-30) REVERT: E 23 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8335 (tmtm) REVERT: E 55 MET cc_start: 0.8892 (mmm) cc_final: 0.8681 (mmm) REVERT: E 64 PHE cc_start: 0.8481 (OUTLIER) cc_final: 0.8064 (t80) REVERT: E 69 GLU cc_start: 0.7646 (pt0) cc_final: 0.7204 (pm20) REVERT: E 95 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8092 (ppt-90) REVERT: E 122 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7194 (tp30) REVERT: E 185 GLN cc_start: 0.8206 (mm110) cc_final: 0.7994 (mt0) REVERT: F 48 GLU cc_start: 0.7599 (pt0) cc_final: 0.7168 (tp30) REVERT: F 69 GLU cc_start: 0.7676 (pm20) cc_final: 0.7122 (pp20) REVERT: F 111 ASP cc_start: 0.8409 (p0) cc_final: 0.7838 (p0) REVERT: F 152 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8326 (mt-10) REVERT: F 385 GLU cc_start: 0.7067 (mp0) cc_final: 0.6857 (mp0) REVERT: G 18 LYS cc_start: 0.8555 (mtpp) cc_final: 0.8040 (mttp) REVERT: G 23 LYS cc_start: 0.8435 (mmmt) cc_final: 0.7687 (mptm) REVERT: G 31 ASP cc_start: 0.8418 (p0) cc_final: 0.8129 (p0) REVERT: G 69 GLU cc_start: 0.7594 (pm20) cc_final: 0.7212 (pp20) REVERT: G 82 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7896 (mpt180) REVERT: G 95 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.7469 (ppt-90) REVERT: G 121 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7898 (mttt) REVERT: G 122 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6517 (mp0) REVERT: H 8 THR cc_start: 0.7110 (p) cc_final: 0.6831 (p) REVERT: H 69 GLU cc_start: 0.7545 (pt0) cc_final: 0.7127 (pm20) REVERT: H 122 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6767 (mp0) REVERT: H 406 LYS cc_start: 0.8265 (tttm) cc_final: 0.7651 (mmtm) REVERT: I 82 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.6883 (mpt180) REVERT: I 122 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7111 (tp30) REVERT: I 146 ASN cc_start: 0.8050 (m110) cc_final: 0.7782 (m-40) REVERT: I 247 MET cc_start: 0.8776 (tmm) cc_final: 0.8523 (ttt) REVERT: I 406 LYS cc_start: 0.8126 (pttm) cc_final: 0.7300 (mmtm) REVERT: J 12 ASP cc_start: 0.8212 (m-30) cc_final: 0.7946 (m-30) REVERT: J 31 ASP cc_start: 0.8560 (p0) cc_final: 0.8232 (p0) REVERT: J 69 GLU cc_start: 0.7746 (pt0) cc_final: 0.7085 (pp20) REVERT: J 95 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.7628 (ppt-90) REVERT: J 122 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7361 (tp30) REVERT: J 362 LYS cc_start: 0.7907 (mmmt) cc_final: 0.7524 (mttp) REVERT: J 364 LYS cc_start: 0.8278 (mmtp) cc_final: 0.7698 (mmtm) REVERT: J 446 MET cc_start: 0.7806 (mmt) cc_final: 0.6936 (ptm) REVERT: K 10 LYS cc_start: 0.8338 (ttpt) cc_final: 0.8137 (ptpt) REVERT: K 122 GLU cc_start: 0.7390 (mp0) cc_final: 0.7186 (mm-30) REVERT: K 206 ASP cc_start: 0.8262 (m-30) cc_final: 0.7784 (t70) REVERT: K 331 ASN cc_start: 0.8219 (OUTLIER) cc_final: 0.7935 (t0) REVERT: K 389 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7148 (ptt180) REVERT: K 406 LYS cc_start: 0.8129 (tttm) cc_final: 0.7720 (mmtm) REVERT: L 21 ASP cc_start: 0.8330 (t0) cc_final: 0.8018 (t0) REVERT: L 69 GLU cc_start: 0.7583 (pt0) cc_final: 0.6786 (pp20) REVERT: L 122 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: L 172 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.7864 (ttp80) outliers start: 112 outliers final: 68 residues processed: 628 average time/residue: 3.0250 time to fit residues: 2358.6456 Evaluate side-chains 643 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 547 time to evaluate : 5.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 317 GLN Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain C residue 64 PHE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain D residue 55 MET Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 445 SER Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 429 ASP Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 286 ARG Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 429 ASP Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain G residue 12 ASP Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 121 LYS Chi-restraints excluded: chain G residue 122 GLU Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 405 SER Chi-restraints excluded: chain G residue 445 SER Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 331 ASN Chi-restraints excluded: chain H residue 418 SER Chi-restraints excluded: chain H residue 429 ASP Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 82 ARG Chi-restraints excluded: chain I residue 122 GLU Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 135 GLU Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 418 SER Chi-restraints excluded: chain I residue 429 ASP Chi-restraints excluded: chain I residue 443 TYR Chi-restraints excluded: chain J residue 8 THR Chi-restraints excluded: chain J residue 95 ARG Chi-restraints excluded: chain J residue 122 GLU Chi-restraints excluded: chain J residue 242 VAL Chi-restraints excluded: chain J residue 291 VAL Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 72 MET Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 207 VAL Chi-restraints excluded: chain K residue 250 ASN Chi-restraints excluded: chain K residue 331 ASN Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 389 ARG Chi-restraints excluded: chain K residue 418 SER Chi-restraints excluded: chain K residue 429 ASP Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain L residue 121 LYS Chi-restraints excluded: chain L residue 122 GLU Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 172 ARG Chi-restraints excluded: chain L residue 418 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 311 optimal weight: 2.9990 chunk 501 optimal weight: 6.9990 chunk 306 optimal weight: 5.9990 chunk 237 optimal weight: 5.9990 chunk 348 optimal weight: 7.9990 chunk 526 optimal weight: 6.9990 chunk 484 optimal weight: 7.9990 chunk 418 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 323 optimal weight: 6.9990 chunk 256 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 318 ASN K 146 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 1.5664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.147 42998 Z= 0.307 Angle : 0.746 59.188 58428 Z= 0.377 Chirality : 0.097 1.722 6275 Planarity : 0.004 0.060 7559 Dihedral : 8.348 177.678 5959 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.43 % Allowed : 24.61 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.11), residues: 5256 helix: 1.20 (0.12), residues: 1980 sheet: -0.42 (0.19), residues: 876 loop : -0.95 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 39 HIS 0.005 0.001 HIS H 198 PHE 0.015 0.001 PHE H 288 TYR 0.023 0.002 TYR B 219 ARG 0.003 0.000 ARG F 329 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10512 Ramachandran restraints generated. 5256 Oldfield, 0 Emsley, 5256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10512 Ramachandran restraints generated. 5256 Oldfield, 0 Emsley, 5256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue TYR 311 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue THR 8 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue LEU 140 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue ALA 290 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LEU 378 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Evaluate side-chains 650 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 545 time to evaluate : 5.049 Fit side-chains revert: symmetry clash REVERT: A 18 LYS cc_start: 0.8611 (mtpp) cc_final: 0.7948 (mtmm) REVERT: A 31 ASP cc_start: 0.8556 (p0) cc_final: 0.8228 (p0) REVERT: A 55 MET cc_start: 0.8842 (mpp) cc_final: 0.8338 (mmt) REVERT: A 69 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7489 (pp20) REVERT: A 95 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.7740 (ppt-90) REVERT: A 182 MET cc_start: 0.8379 (ptm) cc_final: 0.8053 (ptm) REVERT: A 394 ASP cc_start: 0.9076 (p0) cc_final: 0.8855 (p0) REVERT: B 23 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8190 (tmtm) REVERT: B 69 GLU cc_start: 0.7614 (pm20) cc_final: 0.7060 (pp20) REVERT: B 121 LYS cc_start: 0.8009 (mptt) cc_final: 0.7694 (mttt) REVERT: B 128 PHE cc_start: 0.8306 (OUTLIER) cc_final: 0.6921 (p90) REVERT: B 317 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8659 (mp10) REVERT: C 64 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.7913 (t80) REVERT: C 65 THR cc_start: 0.8655 (OUTLIER) cc_final: 0.8412 (t) REVERT: C 121 LYS cc_start: 0.8414 (mtpm) cc_final: 0.7917 (mptt) REVERT: C 172 ARG cc_start: 0.9259 (OUTLIER) cc_final: 0.8473 (ttp80) REVERT: C 307 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7052 (mp0) REVERT: C 426 MET cc_start: 0.8125 (mtm) cc_final: 0.7898 (ttm) REVERT: D 69 GLU cc_start: 0.7442 (pm20) cc_final: 0.7183 (pt0) REVERT: D 95 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.7798 (ppt-90) REVERT: D 121 LYS cc_start: 0.8311 (mttt) cc_final: 0.7846 (mttp) REVERT: D 185 GLN cc_start: 0.8362 (mm-40) cc_final: 0.8109 (mt0) REVERT: D 247 MET cc_start: 0.8493 (tmm) cc_final: 0.8256 (ttp) REVERT: D 414 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7161 (tm-30) REVERT: E 12 ASP cc_start: 0.8450 (m-30) cc_final: 0.8169 (m-30) REVERT: E 23 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8335 (tmtm) REVERT: E 55 MET cc_start: 0.8893 (mmm) cc_final: 0.8683 (mmm) REVERT: E 64 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.8067 (t80) REVERT: E 69 GLU cc_start: 0.7650 (pt0) cc_final: 0.7208 (pm20) REVERT: E 95 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8094 (ppt-90) REVERT: E 122 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7187 (tp30) REVERT: E 185 GLN cc_start: 0.8207 (mm110) cc_final: 0.7981 (mt0) REVERT: F 48 GLU cc_start: 0.7599 (pt0) cc_final: 0.7171 (tp30) REVERT: F 69 GLU cc_start: 0.7679 (pm20) cc_final: 0.7126 (pp20) REVERT: F 111 ASP cc_start: 0.8414 (p0) cc_final: 0.7830 (p0) REVERT: F 152 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8327 (mt-10) REVERT: F 385 GLU cc_start: 0.7074 (mp0) cc_final: 0.6843 (mp0) REVERT: G 23 LYS cc_start: 0.8435 (mmmt) cc_final: 0.7686 (mptm) REVERT: G 31 ASP cc_start: 0.8419 (p0) cc_final: 0.8131 (p0) REVERT: G 69 GLU cc_start: 0.7599 (pm20) cc_final: 0.7217 (pp20) REVERT: G 82 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7904 (mpt180) REVERT: G 95 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.7671 (ppt-90) REVERT: G 121 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.7899 (mttt) REVERT: G 122 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6519 (mp0) REVERT: H 8 THR cc_start: 0.7115 (p) cc_final: 0.6843 (p) REVERT: H 69 GLU cc_start: 0.7554 (pt0) cc_final: 0.7072 (pm20) REVERT: H 122 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6770 (mp0) REVERT: H 406 LYS cc_start: 0.8264 (tttm) cc_final: 0.7651 (mmtm) REVERT: I 82 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.6887 (mpt180) REVERT: I 122 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7114 (tp30) REVERT: I 146 ASN cc_start: 0.8049 (m110) cc_final: 0.7783 (m-40) REVERT: I 247 MET cc_start: 0.8777 (tmm) cc_final: 0.8525 (ttt) REVERT: I 406 LYS cc_start: 0.8126 (pttm) cc_final: 0.7302 (mmtm) REVERT: J 12 ASP cc_start: 0.8213 (m-30) cc_final: 0.7949 (m-30) REVERT: J 31 ASP cc_start: 0.8562 (p0) cc_final: 0.8234 (p0) REVERT: J 69 GLU cc_start: 0.7750 (pt0) cc_final: 0.7087 (pp20) REVERT: J 95 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.7632 (ppt-90) REVERT: J 122 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7363 (tp30) REVERT: J 362 LYS cc_start: 0.7904 (mmmt) cc_final: 0.7530 (mttp) REVERT: J 364 LYS cc_start: 0.8277 (mmtp) cc_final: 0.7697 (mmtm) REVERT: J 446 MET cc_start: 0.7802 (mmt) cc_final: 0.6936 (ptm) REVERT: K 10 LYS cc_start: 0.8339 (ttpt) cc_final: 0.8138 (ptpt) REVERT: K 122 GLU cc_start: 0.7393 (mp0) cc_final: 0.7185 (mm-30) REVERT: K 206 ASP cc_start: 0.8264 (m-30) cc_final: 0.7786 (t70) REVERT: K 331 ASN cc_start: 0.8222 (OUTLIER) cc_final: 0.7938 (t0) REVERT: K 389 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7149 (ptt180) REVERT: K 406 LYS cc_start: 0.8130 (tttm) cc_final: 0.7722 (mmtm) REVERT: L 21 ASP cc_start: 0.8332 (t0) cc_final: 0.8019 (t0) REVERT: L 69 GLU cc_start: 0.7586 (pt0) cc_final: 0.6790 (pp20) REVERT: L 122 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7184 (mp0) REVERT: L 172 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.7865 (ttp80) outliers start: 105 outliers final: 70 residues processed: 616 average time/residue: 2.8863 time to fit residues: 2169.8655 Evaluate side-chains 642 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 544 time to evaluate : 5.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 317 GLN Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain C residue 64 PHE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain D residue 55 MET Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 445 SER Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 429 ASP Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 286 ARG Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 429 ASP Chi-restraints excluded: chain F residue 445 SER Chi-restraints excluded: chain G residue 12 ASP Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 121 LYS Chi-restraints excluded: chain G residue 122 GLU Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 405 SER Chi-restraints excluded: chain G residue 445 SER Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 331 ASN Chi-restraints excluded: chain H residue 418 SER Chi-restraints excluded: chain H residue 429 ASP Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 82 ARG Chi-restraints excluded: chain I residue 122 GLU Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 135 GLU Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 418 SER Chi-restraints excluded: chain I residue 429 ASP Chi-restraints excluded: chain I residue 443 TYR Chi-restraints excluded: chain J residue 8 THR Chi-restraints excluded: chain J residue 95 ARG Chi-restraints excluded: chain J residue 122 GLU Chi-restraints excluded: chain J residue 242 VAL Chi-restraints excluded: chain J residue 291 VAL Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 72 MET Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 207 VAL Chi-restraints excluded: chain K residue 250 ASN Chi-restraints excluded: chain K residue 331 ASN Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 389 ARG Chi-restraints excluded: chain K residue 418 SER Chi-restraints excluded: chain K residue 429 ASP Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain L residue 121 LYS Chi-restraints excluded: chain L residue 122 GLU Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 172 ARG Chi-restraints excluded: chain L residue 418 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 332 optimal weight: 4.9990 chunk 446 optimal weight: 7.9990 chunk 128 optimal weight: 5.9990 chunk 386 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 419 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 430 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 318 ASN K 146 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.113649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.100042 restraints weight = 136369.309| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.23 r_work: 0.3029 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2934 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 1.5664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.147 42998 Z= 0.307 Angle : 0.746 59.200 58428 Z= 0.377 Chirality : 0.097 1.722 6275 Planarity : 0.004 0.060 7559 Dihedral : 8.348 177.678 5959 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.29 % Allowed : 24.77 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.11), residues: 5256 helix: 1.20 (0.12), residues: 1980 sheet: -0.42 (0.19), residues: 876 loop : -0.95 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 39 HIS 0.005 0.001 HIS H 198 PHE 0.015 0.001 PHE H 288 TYR 0.023 0.002 TYR B 219 ARG 0.003 0.000 ARG F 329 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31901.23 seconds wall clock time: 547 minutes 35.22 seconds (32855.22 seconds total)