Starting phenix.real_space_refine on Sat Feb 24 23:55:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu3_33457/02_2024/7xu3_33457_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu3_33457/02_2024/7xu3_33457.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu3_33457/02_2024/7xu3_33457.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu3_33457/02_2024/7xu3_33457.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu3_33457/02_2024/7xu3_33457_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu3_33457/02_2024/7xu3_33457_trim_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 114 5.16 5 C 15450 2.51 5 N 3951 2.21 5 O 4704 1.98 5 H 22838 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 294": "OD1" <-> "OD2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 357": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 364": "OD1" <-> "OD2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 574": "OD1" <-> "OD2" Residue "B ASP 578": "OD1" <-> "OD2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 614": "OD1" <-> "OD2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B ASP 737": "OD1" <-> "OD2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 1041": "OD1" <-> "OD2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 1118": "OD1" <-> "OD2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 357": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 574": "OD1" <-> "OD2" Residue "A ASP 578": "OD1" <-> "OD2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 614": "OD1" <-> "OD2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A ASP 737": "OD1" <-> "OD2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1041": "OD1" <-> "OD2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1118": "OD1" <-> "OD2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 294": "OD1" <-> "OD2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 357": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 364": "OD1" <-> "OD2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 574": "OD1" <-> "OD2" Residue "C ASP 578": "OD1" <-> "OD2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 614": "OD1" <-> "OD2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C ASP 737": "OD1" <-> "OD2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 1041": "OD1" <-> "OD2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 1118": "OD1" <-> "OD2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 47057 Number of models: 1 Model: "" Number of chains: 15 Chain: "B" Number of atoms: 15433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 15433 Classifications: {'peptide': 1002} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 47, 'TRANS': 954} Chain breaks: 9 Chain: "A" Number of atoms: 15433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 15433 Classifications: {'peptide': 1002} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 47, 'TRANS': 954} Chain breaks: 9 Chain: "C" Number of atoms: 15432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 15432 Classifications: {'peptide': 1002} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 47, 'TRANS': 954} Chain breaks: 9 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 169 Unusual residues: {'BLA': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 169 Unusual residues: {'BLA': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 169 Unusual residues: {'BLA': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 20.57, per 1000 atoms: 0.44 Number of scatterers: 47057 At special positions: 0 Unit cell: (131.564, 140.052, 164.455, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 114 16.00 O 4704 8.00 N 3951 7.00 C 15450 6.00 H 22838 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.06 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.06 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 427 " - pdb=" SG CYS C 987 " distance=2.08 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 987 " - pdb=" SG CYS A 427 " distance=2.01 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.06 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 987 " - pdb=" SG CYS C 427 " distance=2.01 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.06 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.06 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Links applied BETA1-4 " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG P 1 " - " NAG P 2 " " NAG a 1 " - " NAG a 2 " " NAG c 1 " - " NAG c 2 " " NAG f 1 " - " NAG f 2 " " NAG q 1 " - " NAG q 2 " " NAG s 1 " - " NAG s 2 " " NAG v 1 " - " NAG v 2 " NAG-ASN " NAG A1402 " - " ASN A 61 " " NAG A1403 " - " ASN A 282 " " NAG A1404 " - " ASN A 331 " " NAG A1405 " - " ASN A 343 " " NAG A1406 " - " ASN A 616 " " NAG A1407 " - " ASN A 657 " " NAG A1408 " - " ASN A 709 " " NAG A1409 " - " ASN A1074 " " NAG A1410 " - " ASN A1134 " " NAG B1402 " - " ASN B 61 " " NAG B1403 " - " ASN B 282 " " NAG B1404 " - " ASN B 331 " " NAG B1405 " - " ASN B 343 " " NAG B1406 " - " ASN B 616 " " NAG B1407 " - " ASN B 657 " " NAG B1408 " - " ASN B 709 " " NAG B1409 " - " ASN B1074 " " NAG B1410 " - " ASN B1134 " " NAG C1402 " - " ASN C 61 " " NAG C1403 " - " ASN C 282 " " NAG C1404 " - " ASN C 331 " " NAG C1405 " - " ASN C 343 " " NAG C1406 " - " ASN C 616 " " NAG C1407 " - " ASN C 657 " " NAG C1408 " - " ASN C 709 " " NAG C1409 " - " ASN C1074 " " NAG C1410 " - " ASN C1134 " " NAG K 1 " - " ASN B 717 " " NAG M 1 " - " ASN B 801 " " NAG P 1 " - " ASN B1098 " " NAG a 1 " - " ASN A 717 " " NAG c 1 " - " ASN A 801 " " NAG f 1 " - " ASN A1098 " " NAG q 1 " - " ASN C 717 " " NAG s 1 " - " ASN C 801 " " NAG v 1 " - " ASN C1098 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 39.56 Conformation dependent library (CDL) restraints added in 4.7 seconds 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5628 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 42 sheets defined 21.5% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.57 Creating SS restraints... Processing helix chain 'B' and resid 295 through 303 Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 384 through 389 removed outlier: 4.673A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 removed outlier: 5.040A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 421 No H-bonds generated for 'chain 'B' and resid 418 through 421' Processing helix chain 'B' and resid 738 through 741 No H-bonds generated for 'chain 'B' and resid 738 through 741' Processing helix chain 'B' and resid 747 through 756 removed outlier: 3.882A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 782 removed outlier: 3.546A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 824 Processing helix chain 'B' and resid 867 through 884 Processing helix chain 'B' and resid 887 through 889 No H-bonds generated for 'chain 'B' and resid 887 through 889' Processing helix chain 'B' and resid 898 through 909 Processing helix chain 'B' and resid 913 through 917 Processing helix chain 'B' and resid 920 through 939 Processing helix chain 'B' and resid 943 through 967 removed outlier: 4.687A pdb=" N LYS B 947 " --> pdb=" O ALA B 944 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASP B 950 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN B 965 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 983 Processing helix chain 'B' and resid 986 through 1031 removed outlier: 4.085A pdb=" N VAL B 991 " --> pdb=" O CYS B 987 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 384 through 389 removed outlier: 4.673A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 5.040A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 421 No H-bonds generated for 'chain 'A' and resid 418 through 421' Processing helix chain 'A' and resid 738 through 741 No H-bonds generated for 'chain 'A' and resid 738 through 741' Processing helix chain 'A' and resid 747 through 756 removed outlier: 3.882A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 782 removed outlier: 3.547A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 824 Processing helix chain 'A' and resid 867 through 884 Processing helix chain 'A' and resid 887 through 889 No H-bonds generated for 'chain 'A' and resid 887 through 889' Processing helix chain 'A' and resid 898 through 909 Processing helix chain 'A' and resid 913 through 917 Processing helix chain 'A' and resid 920 through 939 Processing helix chain 'A' and resid 943 through 967 removed outlier: 4.687A pdb=" N LYS A 947 " --> pdb=" O ALA A 944 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP A 950 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN A 965 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 983 Processing helix chain 'A' and resid 986 through 1031 removed outlier: 4.086A pdb=" N VAL A 991 " --> pdb=" O CYS A 987 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 303 Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 366 through 370 Processing helix chain 'C' and resid 384 through 389 removed outlier: 4.673A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 5.039A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 421 No H-bonds generated for 'chain 'C' and resid 418 through 421' Processing helix chain 'C' and resid 738 through 741 No H-bonds generated for 'chain 'C' and resid 738 through 741' Processing helix chain 'C' and resid 747 through 756 removed outlier: 3.882A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 782 removed outlier: 3.545A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 824 Processing helix chain 'C' and resid 867 through 884 Processing helix chain 'C' and resid 887 through 889 No H-bonds generated for 'chain 'C' and resid 887 through 889' Processing helix chain 'C' and resid 898 through 909 Processing helix chain 'C' and resid 913 through 917 Processing helix chain 'C' and resid 920 through 939 Processing helix chain 'C' and resid 943 through 967 removed outlier: 4.687A pdb=" N LYS C 947 " --> pdb=" O ALA C 944 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP C 950 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN C 965 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 983 Processing helix chain 'C' and resid 986 through 1031 removed outlier: 4.086A pdb=" N VAL C 991 " --> pdb=" O CYS C 987 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.801A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 63 through 65 Processing sheet with id= C, first strand: chain 'B' and resid 237 through 240 Processing sheet with id= D, first strand: chain 'B' and resid 325 through 328 removed outlier: 6.054A pdb=" N ASN B 540 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ARG B 328 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASN B 542 " --> pdb=" O ARG B 328 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.990A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 452 through 454 Processing sheet with id= G, first strand: chain 'B' and resid 551 through 554 Processing sheet with id= H, first strand: chain 'B' and resid 642 through 645 removed outlier: 4.957A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 691 through 696 removed outlier: 6.471A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 711 through 715 Processing sheet with id= K, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.127A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 734 through 736 Processing sheet with id= M, first strand: chain 'B' and resid 1088 through 1090 Processing sheet with id= N, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id= O, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.802A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 63 through 65 Processing sheet with id= Q, first strand: chain 'A' and resid 237 through 240 Processing sheet with id= R, first strand: chain 'A' and resid 325 through 328 removed outlier: 6.054A pdb=" N ASN A 540 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ARG A 328 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASN A 542 " --> pdb=" O ARG A 328 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.990A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'A' and resid 452 through 454 Processing sheet with id= U, first strand: chain 'A' and resid 551 through 554 Processing sheet with id= V, first strand: chain 'A' and resid 642 through 645 removed outlier: 4.957A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'A' and resid 691 through 696 removed outlier: 6.471A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'A' and resid 711 through 715 Processing sheet with id= Y, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.127A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'A' and resid 734 through 736 Processing sheet with id= AA, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id= AB, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id= AC, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.801A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 63 through 65 Processing sheet with id= AE, first strand: chain 'C' and resid 237 through 240 Processing sheet with id= AF, first strand: chain 'C' and resid 325 through 328 removed outlier: 6.055A pdb=" N ASN C 540 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ARG C 328 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ASN C 542 " --> pdb=" O ARG C 328 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.991A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'C' and resid 452 through 454 Processing sheet with id= AI, first strand: chain 'C' and resid 551 through 554 Processing sheet with id= AJ, first strand: chain 'C' and resid 642 through 645 removed outlier: 4.957A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'C' and resid 691 through 696 removed outlier: 6.471A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'C' and resid 711 through 715 Processing sheet with id= AM, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.128A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'C' and resid 734 through 736 Processing sheet with id= AO, first strand: chain 'C' and resid 1088 through 1090 Processing sheet with id= AP, first strand: chain 'C' and resid 1094 through 1097 846 hydrogen bonds defined for protein. 2124 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 20.35 Time building geometry restraints manager: 40.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.05: 22833 1.05 - 1.26: 3926 1.26 - 1.48: 10390 1.48 - 1.70: 10301 1.70 - 1.91: 141 Bond restraints: 47591 Sorted by residual: bond pdb=" NB BLA B1401 " pdb=" C4B BLA B1401 " ideal model delta sigma weight residual 1.371 1.534 -0.163 2.00e-02 2.50e+03 6.64e+01 bond pdb=" C1C BLA C1401 " pdb=" NC BLA C1401 " ideal model delta sigma weight residual 1.368 1.531 -0.163 2.00e-02 2.50e+03 6.61e+01 bond pdb=" C1C BLA A1401 " pdb=" NC BLA A1401 " ideal model delta sigma weight residual 1.368 1.530 -0.162 2.00e-02 2.50e+03 6.59e+01 bond pdb=" NB BLA A1401 " pdb=" C4B BLA A1401 " ideal model delta sigma weight residual 1.371 1.533 -0.162 2.00e-02 2.50e+03 6.58e+01 bond pdb=" NB BLA C1401 " pdb=" C4B BLA C1401 " ideal model delta sigma weight residual 1.371 1.533 -0.162 2.00e-02 2.50e+03 6.56e+01 ... (remaining 47586 not shown) Histogram of bond angle deviations from ideal: 82.10 - 97.58: 14 97.58 - 113.05: 54819 113.05 - 128.53: 30329 128.53 - 144.00: 213 144.00 - 159.48: 1 Bond angle restraints: 85376 Sorted by residual: angle pdb=" CG ASN B 907 " pdb=" ND2 ASN B 907 " pdb="HD22 ASN B 907 " ideal model delta sigma weight residual 120.00 159.48 -39.48 3.00e+00 1.11e-01 1.73e+02 angle pdb="HD21 ASN B 907 " pdb=" ND2 ASN B 907 " pdb="HD22 ASN B 907 " ideal model delta sigma weight residual 120.00 82.10 37.90 3.00e+00 1.11e-01 1.60e+02 angle pdb=" CG ASN B 907 " pdb=" ND2 ASN B 907 " pdb="HD21 ASN B 907 " ideal model delta sigma weight residual 120.00 87.75 32.25 3.00e+00 1.11e-01 1.16e+02 angle pdb=" CG PHE B 86 " pdb=" CB PHE B 86 " pdb=" HB3 PHE B 86 " ideal model delta sigma weight residual 108.00 83.54 24.46 3.00e+00 1.11e-01 6.65e+01 angle pdb=" CA CYS C 432 " pdb=" CB CYS C 432 " pdb=" SG CYS C 432 " ideal model delta sigma weight residual 114.40 132.39 -17.99 2.30e+00 1.89e-01 6.12e+01 ... (remaining 85371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 21084 17.86 - 35.71: 1806 35.71 - 53.57: 432 53.57 - 71.43: 160 71.43 - 89.28: 19 Dihedral angle restraints: 23501 sinusoidal: 12977 harmonic: 10524 Sorted by residual: dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual -86.00 -22.06 -63.94 1 1.00e+01 1.00e-02 5.38e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -22.08 -63.92 1 1.00e+01 1.00e-02 5.38e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual -86.00 -22.09 -63.91 1 1.00e+01 1.00e-02 5.38e+01 ... (remaining 23498 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 3539 0.083 - 0.167: 373 0.167 - 0.250: 21 0.250 - 0.334: 3 0.334 - 0.417: 6 Chirality restraints: 3942 Sorted by residual: chirality pdb=" C1 NAG C1404 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1404 " pdb=" O5 NAG C1404 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.35e+00 chirality pdb=" C1 NAG B1404 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B1404 " pdb=" O5 NAG B1404 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.32e+00 chirality pdb=" C1 NAG A1404 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1404 " pdb=" O5 NAG A1404 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.28e+00 ... (remaining 3939 not shown) Planarity restraints: 7158 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" ND BLA A1401 " -0.059 2.00e-02 2.50e+03 7.32e-02 1.34e+02 pdb=" C1A BLA A1401 " 0.166 2.00e-02 2.50e+03 pdb=" C1D BLA A1401 " -0.009 2.00e-02 2.50e+03 pdb=" C2D BLA A1401 " 0.013 2.00e-02 2.50e+03 pdb=" C3D BLA A1401 " -0.017 2.00e-02 2.50e+03 pdb=" C4D BLA A1401 " -0.062 2.00e-02 2.50e+03 pdb=" CAD BLA A1401 " 0.008 2.00e-02 2.50e+03 pdb=" CHA BLA A1401 " -0.111 2.00e-02 2.50e+03 pdb=" CHD BLA A1401 " -0.005 2.00e-02 2.50e+03 pdb=" CMD BLA A1401 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BLA B1401 " -0.059 2.00e-02 2.50e+03 7.32e-02 1.34e+02 pdb=" C1A BLA B1401 " 0.166 2.00e-02 2.50e+03 pdb=" C1D BLA B1401 " -0.009 2.00e-02 2.50e+03 pdb=" C2D BLA B1401 " 0.014 2.00e-02 2.50e+03 pdb=" C3D BLA B1401 " -0.018 2.00e-02 2.50e+03 pdb=" C4D BLA B1401 " -0.062 2.00e-02 2.50e+03 pdb=" CAD BLA B1401 " 0.008 2.00e-02 2.50e+03 pdb=" CHA BLA B1401 " -0.110 2.00e-02 2.50e+03 pdb=" CHD BLA B1401 " -0.005 2.00e-02 2.50e+03 pdb=" CMD BLA B1401 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BLA C1401 " -0.059 2.00e-02 2.50e+03 7.31e-02 1.33e+02 pdb=" C1A BLA C1401 " 0.166 2.00e-02 2.50e+03 pdb=" C1D BLA C1401 " -0.009 2.00e-02 2.50e+03 pdb=" C2D BLA C1401 " 0.014 2.00e-02 2.50e+03 pdb=" C3D BLA C1401 " -0.018 2.00e-02 2.50e+03 pdb=" C4D BLA C1401 " -0.061 2.00e-02 2.50e+03 pdb=" CAD BLA C1401 " 0.008 2.00e-02 2.50e+03 pdb=" CHA BLA C1401 " -0.110 2.00e-02 2.50e+03 pdb=" CHD BLA C1401 " -0.005 2.00e-02 2.50e+03 pdb=" CMD BLA C1401 " 0.076 2.00e-02 2.50e+03 ... (remaining 7155 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 2697 2.19 - 2.79: 95472 2.79 - 3.40: 124535 3.40 - 4.00: 172361 4.00 - 4.60: 260940 Nonbonded interactions: 656005 Sorted by model distance: nonbonded pdb="HH12 ARG A 403 " pdb=" OD1 ASP A 405 " model vdw 1.591 1.850 nonbonded pdb="HH12 ARG C 403 " pdb=" OD1 ASP C 405 " model vdw 1.622 1.850 nonbonded pdb="HH12 ARG B 403 " pdb=" OD1 ASP B 405 " model vdw 1.622 1.850 nonbonded pdb=" O THR B 124 " pdb=" H PHE B 175 " model vdw 1.640 1.850 nonbonded pdb=" O THR A 124 " pdb=" H PHE A 175 " model vdw 1.640 1.850 ... (remaining 656000 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 27 through 426 or (resid 427 and (name N or name CA or nam \ e C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3 \ )) or resid 428 through 1140 or resid 1401 through 1410)) selection = (chain 'B' and (resid 27 through 986 or (resid 987 and (name N or name CA or nam \ e C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3 \ )) or resid 988 through 1140 or resid 1401 through 1410)) selection = chain 'C' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'P' selection = chain 'a' selection = chain 'c' selection = chain 'f' selection = chain 'q' selection = chain 's' selection = chain 'v' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.730 Extract box with map and model: 12.040 Check model and map are aligned: 0.730 Set scattering table: 0.470 Process input model: 151.560 Find NCS groups from input model: 2.240 Set up NCS constraints: 0.310 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:12.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 182.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 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 : 0.009 0.163 24753 Z= 0.589 Angle : 0.884 17.995 33675 Z= 0.446 Chirality : 0.052 0.417 3942 Planarity : 0.005 0.073 4287 Dihedral : 13.993 89.283 9555 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.34 % Allowed : 0.46 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.15), residues: 2946 helix: -0.25 (0.20), residues: 639 sheet: -0.68 (0.17), residues: 732 loop : -1.36 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 886 HIS 0.004 0.001 HIS A1048 PHE 0.064 0.002 PHE A 86 TYR 0.056 0.002 TYR B 756 ARG 0.031 0.001 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 182 time to evaluate : 3.831 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: B 505 TYR cc_start: 0.6571 (t80) cc_final: 0.6330 (t80) REVERT: B 574 ASP cc_start: 0.8172 (t70) cc_final: 0.7880 (t0) REVERT: A 360 ASN cc_start: 0.8536 (m-40) cc_final: 0.8194 (p0) REVERT: A 574 ASP cc_start: 0.8129 (t70) cc_final: 0.7807 (t0) REVERT: A 646 ARG cc_start: 0.7980 (tpt90) cc_final: 0.7779 (mmm160) REVERT: C 360 ASN cc_start: 0.8615 (m-40) cc_final: 0.8157 (p0) REVERT: C 574 ASP cc_start: 0.8058 (t70) cc_final: 0.7730 (t0) outliers start: 9 outliers final: 5 residues processed: 187 average time/residue: 3.3639 time to fit residues: 714.1193 Evaluate side-chains 140 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 135 time to evaluate : 3.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain C residue 403 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 0.5980 chunk 227 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 121 optimal weight: 0.0470 chunk 235 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 142 optimal weight: 0.0980 chunk 175 optimal weight: 1.9990 chunk 272 optimal weight: 0.9990 overall best weight: 0.5482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.0757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 24753 Z= 0.190 Angle : 0.555 12.632 33675 Z= 0.290 Chirality : 0.045 0.321 3942 Planarity : 0.003 0.040 4287 Dihedral : 8.446 59.496 4249 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.42 % Allowed : 4.24 % Favored : 95.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.15), residues: 2946 helix: 0.30 (0.21), residues: 642 sheet: -0.50 (0.18), residues: 708 loop : -1.24 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.002 0.000 HIS C 207 PHE 0.013 0.001 PHE A 106 TYR 0.011 0.001 TYR B1067 ARG 0.006 0.000 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 137 time to evaluate : 3.651 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: B 346 ARG cc_start: 0.7701 (ptm-80) cc_final: 0.7405 (ptm-80) REVERT: B 360 ASN cc_start: 0.8446 (m-40) cc_final: 0.8156 (p0) REVERT: B 505 TYR cc_start: 0.6802 (t80) cc_final: 0.6486 (t80) REVERT: B 574 ASP cc_start: 0.8190 (t70) cc_final: 0.7848 (t0) REVERT: A 360 ASN cc_start: 0.8501 (m-40) cc_final: 0.8210 (p0) REVERT: A 574 ASP cc_start: 0.8116 (t70) cc_final: 0.7809 (t0) REVERT: A 646 ARG cc_start: 0.7976 (tpt90) cc_final: 0.7773 (mmm160) REVERT: C 360 ASN cc_start: 0.8514 (m-40) cc_final: 0.8107 (p0) REVERT: C 574 ASP cc_start: 0.8071 (t70) cc_final: 0.7732 (t0) REVERT: C 646 ARG cc_start: 0.8000 (mmm160) cc_final: 0.7526 (tpt-90) outliers start: 11 outliers final: 3 residues processed: 139 average time/residue: 3.2971 time to fit residues: 522.6638 Evaluate side-chains 125 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 122 time to evaluate : 3.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain C residue 572 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 151 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 226 optimal weight: 5.9990 chunk 185 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 272 optimal weight: 0.5980 chunk 294 optimal weight: 0.5980 chunk 243 optimal weight: 0.5980 chunk 270 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 218 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 24753 Z= 0.195 Angle : 0.523 12.600 33675 Z= 0.272 Chirality : 0.045 0.304 3942 Planarity : 0.004 0.094 4287 Dihedral : 7.388 60.380 4233 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.50 % Allowed : 5.35 % Favored : 94.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.15), residues: 2946 helix: 0.65 (0.22), residues: 642 sheet: -0.62 (0.17), residues: 732 loop : -1.21 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 104 HIS 0.002 0.000 HIS C1088 PHE 0.013 0.001 PHE C 238 TYR 0.029 0.001 TYR A 170 ARG 0.005 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 133 time to evaluate : 3.634 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: B 346 ARG cc_start: 0.7757 (ptm-80) cc_final: 0.7453 (ptm-80) REVERT: B 360 ASN cc_start: 0.8433 (m-40) cc_final: 0.8228 (p0) REVERT: B 505 TYR cc_start: 0.6876 (t80) cc_final: 0.6519 (t80) REVERT: B 574 ASP cc_start: 0.8160 (t70) cc_final: 0.7812 (t0) REVERT: A 360 ASN cc_start: 0.8497 (m-40) cc_final: 0.8232 (p0) REVERT: A 574 ASP cc_start: 0.8088 (t70) cc_final: 0.7752 (t0) REVERT: A 646 ARG cc_start: 0.7977 (tpt90) cc_final: 0.7774 (mmm160) REVERT: C 360 ASN cc_start: 0.8509 (m-40) cc_final: 0.8113 (p0) REVERT: C 574 ASP cc_start: 0.8027 (t70) cc_final: 0.7719 (t0) outliers start: 13 outliers final: 5 residues processed: 139 average time/residue: 2.9136 time to fit residues: 471.5583 Evaluate side-chains 128 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 123 time to evaluate : 3.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1123 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 269 optimal weight: 0.8980 chunk 205 optimal weight: 0.9990 chunk 141 optimal weight: 8.9990 chunk 30 optimal weight: 0.3980 chunk 130 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 273 optimal weight: 0.9980 chunk 289 optimal weight: 0.9990 chunk 143 optimal weight: 0.6980 chunk 259 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 24753 Z= 0.191 Angle : 0.503 12.514 33675 Z= 0.263 Chirality : 0.045 0.297 3942 Planarity : 0.003 0.055 4287 Dihedral : 6.824 60.029 4233 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.34 % Allowed : 6.72 % Favored : 92.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.15), residues: 2946 helix: 0.83 (0.22), residues: 642 sheet: -0.45 (0.18), residues: 696 loop : -1.14 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.002 0.000 HIS C1088 PHE 0.014 0.001 PHE B 238 TYR 0.019 0.001 TYR C1138 ARG 0.005 0.000 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 134 time to evaluate : 4.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.7301 (mmt) cc_final: 0.7091 (mmm) REVERT: B 346 ARG cc_start: 0.7837 (ptm-80) cc_final: 0.7547 (ptm-80) REVERT: B 505 TYR cc_start: 0.6875 (t80) cc_final: 0.6454 (t80) REVERT: B 574 ASP cc_start: 0.8145 (t70) cc_final: 0.7790 (t0) REVERT: A 360 ASN cc_start: 0.8499 (m-40) cc_final: 0.8250 (p0) REVERT: A 574 ASP cc_start: 0.8090 (t70) cc_final: 0.7747 (t0) REVERT: C 360 ASN cc_start: 0.8487 (m-40) cc_final: 0.8153 (p0) REVERT: C 574 ASP cc_start: 0.7983 (t70) cc_final: 0.7664 (t0) REVERT: C 646 ARG cc_start: 0.8029 (mmm160) cc_final: 0.7507 (tpt-90) REVERT: C 900 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.7846 (mtt) outliers start: 9 outliers final: 4 residues processed: 139 average time/residue: 2.8247 time to fit residues: 465.4877 Evaluate side-chains 132 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 127 time to evaluate : 3.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1123 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 241 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 247 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 260 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 24753 Z= 0.306 Angle : 0.526 12.798 33675 Z= 0.276 Chirality : 0.045 0.292 3942 Planarity : 0.003 0.046 4287 Dihedral : 6.568 59.563 4233 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.61 % Allowed : 7.64 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.15), residues: 2946 helix: 0.82 (0.22), residues: 642 sheet: -0.46 (0.18), residues: 696 loop : -1.19 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 886 HIS 0.003 0.001 HIS A1058 PHE 0.010 0.001 PHE B 275 TYR 0.011 0.001 TYR B1067 ARG 0.008 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 3.770 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: B 153 MET cc_start: 0.7286 (mmt) cc_final: 0.7060 (mmm) REVERT: B 346 ARG cc_start: 0.7912 (ptm-80) cc_final: 0.7609 (ptm-80) REVERT: B 574 ASP cc_start: 0.8170 (t70) cc_final: 0.7829 (t0) REVERT: A 360 ASN cc_start: 0.8505 (m-40) cc_final: 0.8247 (p0) REVERT: A 574 ASP cc_start: 0.8125 (t70) cc_final: 0.7779 (t0) REVERT: A 646 ARG cc_start: 0.7990 (mmm160) cc_final: 0.7431 (tpt170) REVERT: C 360 ASN cc_start: 0.8550 (m-40) cc_final: 0.8168 (p0) REVERT: C 574 ASP cc_start: 0.8027 (t70) cc_final: 0.7731 (t0) REVERT: C 900 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.7993 (mtt) outliers start: 16 outliers final: 10 residues processed: 137 average time/residue: 2.7784 time to fit residues: 446.1984 Evaluate side-chains 136 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 125 time to evaluate : 3.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1123 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 97 optimal weight: 0.7980 chunk 261 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 290 optimal weight: 1.9990 chunk 240 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 24753 Z= 0.291 Angle : 0.521 12.926 33675 Z= 0.272 Chirality : 0.045 0.286 3942 Planarity : 0.003 0.041 4287 Dihedral : 6.378 58.482 4233 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.65 % Allowed : 8.25 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.15), residues: 2946 helix: 0.79 (0.22), residues: 645 sheet: -0.49 (0.18), residues: 696 loop : -1.22 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 886 HIS 0.003 0.001 HIS C1088 PHE 0.013 0.001 PHE C 275 TYR 0.020 0.001 TYR C1138 ARG 0.006 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 3.700 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: B 153 MET cc_start: 0.7233 (mmt) cc_final: 0.6996 (mmm) REVERT: B 574 ASP cc_start: 0.8168 (t70) cc_final: 0.7829 (t0) REVERT: A 574 ASP cc_start: 0.8142 (t70) cc_final: 0.7789 (t0) REVERT: C 360 ASN cc_start: 0.8502 (m-40) cc_final: 0.8190 (p0) REVERT: C 574 ASP cc_start: 0.8058 (t70) cc_final: 0.7742 (t0) outliers start: 17 outliers final: 12 residues processed: 139 average time/residue: 2.7996 time to fit residues: 458.4937 Evaluate side-chains 136 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 3.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 1123 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 279 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 165 optimal weight: 0.9980 chunk 211 optimal weight: 0.7980 chunk 164 optimal weight: 1.9990 chunk 244 optimal weight: 0.2980 chunk 162 optimal weight: 1.9990 chunk 289 optimal weight: 1.9990 chunk 180 optimal weight: 0.0010 chunk 176 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 24753 Z= 0.170 Angle : 0.493 12.609 33675 Z= 0.257 Chirality : 0.044 0.282 3942 Planarity : 0.003 0.036 4287 Dihedral : 6.179 58.931 4233 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.53 % Allowed : 9.01 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.15), residues: 2946 helix: 0.94 (0.22), residues: 645 sheet: -0.45 (0.18), residues: 696 loop : -1.12 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 104 HIS 0.002 0.000 HIS A1088 PHE 0.012 0.001 PHE B 238 TYR 0.009 0.001 TYR C1067 ARG 0.004 0.000 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 133 time to evaluate : 3.780 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: B 153 MET cc_start: 0.7225 (mmt) cc_final: 0.6994 (mmm) REVERT: B 574 ASP cc_start: 0.8145 (t70) cc_final: 0.7799 (t0) REVERT: A 346 ARG cc_start: 0.7883 (ptm-80) cc_final: 0.7565 (ptm-80) REVERT: A 574 ASP cc_start: 0.8115 (t70) cc_final: 0.7766 (t0) REVERT: C 360 ASN cc_start: 0.8527 (m-40) cc_final: 0.8291 (p0) REVERT: C 574 ASP cc_start: 0.8028 (t70) cc_final: 0.7722 (t0) outliers start: 14 outliers final: 8 residues processed: 141 average time/residue: 2.8960 time to fit residues: 478.3159 Evaluate side-chains 136 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 128 time to evaluate : 3.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain C residue 301 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 178 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 172 optimal weight: 0.2980 chunk 87 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 183 optimal weight: 1.9990 chunk 196 optimal weight: 0.9980 chunk 142 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 227 optimal weight: 3.9990 chunk 263 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN C1002 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 24753 Z= 0.195 Angle : 0.494 12.525 33675 Z= 0.257 Chirality : 0.044 0.276 3942 Planarity : 0.003 0.034 4287 Dihedral : 6.050 58.590 4233 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.65 % Allowed : 9.13 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.15), residues: 2946 helix: 1.01 (0.22), residues: 645 sheet: -0.41 (0.18), residues: 696 loop : -1.08 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 104 HIS 0.002 0.000 HIS C1088 PHE 0.016 0.001 PHE A 106 TYR 0.020 0.001 TYR C1138 ARG 0.005 0.000 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 135 time to evaluate : 3.740 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: B 153 MET cc_start: 0.7223 (mmt) cc_final: 0.6995 (mmm) REVERT: B 505 TYR cc_start: 0.7102 (t80) cc_final: 0.6582 (t80) REVERT: B 574 ASP cc_start: 0.8127 (t70) cc_final: 0.7781 (t0) REVERT: A 346 ARG cc_start: 0.7889 (ptm-80) cc_final: 0.7589 (ptm-80) REVERT: A 574 ASP cc_start: 0.8095 (t70) cc_final: 0.7741 (t0) REVERT: C 574 ASP cc_start: 0.8050 (t70) cc_final: 0.7710 (t0) outliers start: 17 outliers final: 10 residues processed: 146 average time/residue: 2.9070 time to fit residues: 497.6902 Evaluate side-chains 137 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 127 time to evaluate : 3.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 572 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 277 optimal weight: 0.9980 chunk 252 optimal weight: 0.6980 chunk 269 optimal weight: 0.7980 chunk 276 optimal weight: 0.6980 chunk 162 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 211 optimal weight: 1.9990 chunk 82 optimal weight: 0.2980 chunk 243 optimal weight: 2.9990 chunk 254 optimal weight: 3.9990 chunk 268 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 24753 Z= 0.163 Angle : 0.490 12.374 33675 Z= 0.255 Chirality : 0.044 0.269 3942 Planarity : 0.003 0.035 4287 Dihedral : 5.922 58.819 4233 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.50 % Allowed : 9.74 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.15), residues: 2946 helix: 0.91 (0.22), residues: 663 sheet: -0.40 (0.18), residues: 696 loop : -0.96 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 104 HIS 0.002 0.000 HIS A1088 PHE 0.012 0.001 PHE B 238 TYR 0.018 0.001 TYR A1138 ARG 0.006 0.000 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 135 time to evaluate : 4.099 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: B 153 MET cc_start: 0.7246 (mmt) cc_final: 0.7038 (mmm) REVERT: B 505 TYR cc_start: 0.7069 (t80) cc_final: 0.6554 (t80) REVERT: B 574 ASP cc_start: 0.8108 (t70) cc_final: 0.7779 (t0) REVERT: A 346 ARG cc_start: 0.7911 (ptm-80) cc_final: 0.7617 (ptm-80) REVERT: A 574 ASP cc_start: 0.8077 (t70) cc_final: 0.7718 (t0) REVERT: C 574 ASP cc_start: 0.8004 (t70) cc_final: 0.7696 (t0) outliers start: 13 outliers final: 8 residues processed: 144 average time/residue: 2.7994 time to fit residues: 470.3929 Evaluate side-chains 136 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 128 time to evaluate : 3.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 902 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 176 optimal weight: 0.9990 chunk 284 optimal weight: 1.9990 chunk 173 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 198 optimal weight: 0.6980 chunk 298 optimal weight: 2.9990 chunk 275 optimal weight: 1.9990 chunk 237 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 145 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN A1002 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1005 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 24753 Z= 0.227 Angle : 0.503 12.545 33675 Z= 0.261 Chirality : 0.044 0.267 3942 Planarity : 0.003 0.035 4287 Dihedral : 5.896 58.519 4233 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.73 % Allowed : 9.70 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.15), residues: 2946 helix: 0.83 (0.22), residues: 672 sheet: -0.39 (0.18), residues: 696 loop : -0.98 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 886 HIS 0.002 0.000 HIS A1088 PHE 0.015 0.001 PHE A 106 TYR 0.019 0.001 TYR C1138 ARG 0.006 0.000 ARG A 646 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 129 time to evaluate : 3.580 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: B 153 MET cc_start: 0.7259 (mmt) cc_final: 0.7046 (mmm) REVERT: B 505 TYR cc_start: 0.7122 (t80) cc_final: 0.6632 (t80) REVERT: B 574 ASP cc_start: 0.8125 (t70) cc_final: 0.7775 (t0) REVERT: B 786 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8338 (pmtt) REVERT: A 346 ARG cc_start: 0.7939 (ptm-80) cc_final: 0.7653 (ptm-80) REVERT: A 574 ASP cc_start: 0.8072 (t70) cc_final: 0.7707 (t0) REVERT: C 574 ASP cc_start: 0.8026 (t70) cc_final: 0.7718 (t0) outliers start: 19 outliers final: 10 residues processed: 141 average time/residue: 2.8544 time to fit residues: 473.1028 Evaluate side-chains 139 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 128 time to evaluate : 4.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 572 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 189 optimal weight: 1.9990 chunk 253 optimal weight: 1.9990 chunk 72 optimal weight: 0.4980 chunk 219 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 238 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 244 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.125759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.087989 restraints weight = 132885.563| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.99 r_work: 0.2913 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.260 24753 Z= 0.257 Angle : 0.650 59.108 33675 Z= 0.370 Chirality : 0.045 0.424 3942 Planarity : 0.003 0.034 4287 Dihedral : 5.898 58.520 4233 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.53 % Allowed : 9.81 % Favored : 89.65 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.15), residues: 2946 helix: 0.81 (0.22), residues: 672 sheet: -0.39 (0.18), residues: 696 loop : -0.98 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 104 HIS 0.001 0.000 HIS A1088 PHE 0.009 0.001 PHE A 106 TYR 0.010 0.001 TYR A 449 ARG 0.004 0.000 ARG A 646 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11614.31 seconds wall clock time: 206 minutes 56.46 seconds (12416.46 seconds total)