Starting phenix.real_space_refine on Sun Mar 24 23:15:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu5_33459/03_2024/7xu5_33459_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu5_33459/03_2024/7xu5_33459.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu5_33459/03_2024/7xu5_33459.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu5_33459/03_2024/7xu5_33459.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu5_33459/03_2024/7xu5_33459_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu5_33459/03_2024/7xu5_33459_trim_updated.pdb" } resolution = 3.1 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= 0.004 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 99 5.16 5 C 14532 2.51 5 N 3717 2.21 5 O 4395 1.98 5 H 21549 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 38": "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 GLU 156": "OE1" <-> "OE2" Residue "B ARG 190": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 198": "OD1" <-> "OD2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 GLU 281": "OE1" <-> "OE2" Residue "B ASP 287": "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 PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 583": "OE1" <-> "OE2" 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 663": "OD1" <-> "OD2" Residue "B GLU 748": "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 979": "OD1" <-> "OD2" Residue "B ASP 994": "OD1" <-> "OD2" 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 PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 1139": "OD1" <-> "OD2" Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 38": "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 GLU 156": "OE1" <-> "OE2" Residue "A ARG 190": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 GLU 281": "OE1" <-> "OE2" Residue "A ASP 287": "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 PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 583": "OE1" <-> "OE2" 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 663": "OD1" <-> "OD2" Residue "A GLU 748": "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 979": "OD1" <-> "OD2" Residue "A ASP 994": "OD1" <-> "OD2" 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 PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1139": "OD1" <-> "OD2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 38": "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 GLU 156": "OE1" <-> "OE2" Residue "C ARG 190": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 198": "OD1" <-> "OD2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 GLU 281": "OE1" <-> "OE2" Residue "C ASP 287": "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 PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 516": "OE1" <-> "OE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 583": "OE1" <-> "OE2" 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 663": "OD1" <-> "OD2" Residue "C GLU 748": "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 979": "OD1" <-> "OD2" Residue "C ASP 994": "OD1" <-> "OD2" 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 PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 1139": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 44292 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 14525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 938, 14525 Classifications: {'peptide': 938} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 45, 'TRANS': 892} Chain breaks: 14 Chain: "A" Number of atoms: 14525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 938, 14525 Classifications: {'peptide': 938} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 45, 'TRANS': 892} Chain breaks: 14 Chain: "C" Number of atoms: 14525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 938, 14525 Classifications: {'peptide': 938} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 45, 'TRANS': 892} Chain breaks: 14 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: "Z" 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: 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: "o" 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: "B" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 183 Unusual residues: {'BLA': 1, 'NAG': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "A" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 183 Unusual residues: {'BLA': 1, 'NAG': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 183 Unusual residues: {'BLA': 1, 'NAG': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 19.64, per 1000 atoms: 0.44 Number of scatterers: 44292 At special positions: 0 Unit cell: (126.259, 134.747, 158.089, 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 99 16.00 O 4395 8.00 N 3717 7.00 C 14532 6.00 H 21549 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 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=2.03 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=2.04 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=2.03 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=2.04 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 291 " - pdb=" SG CYS A 301 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " 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=2.03 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=2.02 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 291 " - pdb=" SG CYS C 301 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " 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=2.03 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 Z 1 " - " NAG Z 2 " " NAG b 1 " - " NAG b 2 " " NAG o 1 " - " NAG o 2 " " NAG q 1 " - " NAG q 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 A1098 " " NAG A1411 " - " 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 B1098 " " NAG B1411 " - " 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 C1098 " " NAG C1411 " - " ASN C1134 " " NAG K 1 " - " ASN B 717 " " NAG M 1 " - " ASN B 801 " " NAG Z 1 " - " ASN A 717 " " NAG b 1 " - " ASN A 801 " " NAG o 1 " - " ASN C 717 " " NAG q 1 " - " ASN C 801 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 31.66 Conformation dependent library (CDL) restraints added in 4.7 seconds 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5292 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 57 helices and 39 sheets defined 23.3% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.26 Creating SS restraints... Processing helix chain 'B' and resid 295 through 303 Processing helix chain 'B' and resid 339 through 342 No H-bonds generated for 'chain 'B' and resid 339 through 342' 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: 4.221A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 406 No H-bonds generated for 'chain 'B' and resid 404 through 406' Processing helix chain 'B' and resid 417 through 421 Processing helix chain 'B' and resid 738 through 742 Processing helix chain 'B' and resid 747 through 756 removed outlier: 3.877A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 782 removed outlier: 3.775A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 823 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 914 through 918 Processing helix chain 'B' and resid 920 through 940 removed outlier: 3.727A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 967 removed outlier: 3.579A pdb=" N GLY B 946 " --> pdb=" O SER B 943 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LYS B 947 " --> pdb=" O ALA B 944 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASP B 950 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN B 954 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN B 955 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN B 957 " --> pdb=" O GLN B 954 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA B 958 " --> pdb=" O ASN B 955 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN B 960 " --> pdb=" O GLN B 957 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR B 961 " --> pdb=" O ALA B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 983 Processing helix chain 'B' and resid 986 through 1032 removed outlier: 3.847A pdb=" N VAL B 991 " --> pdb=" O CYS B 987 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 6.158A 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 339 through 342 No H-bonds generated for 'chain 'A' and resid 339 through 342' 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: 4.222A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 406 No H-bonds generated for 'chain 'A' and resid 404 through 406' Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'A' and resid 738 through 742 Processing helix chain 'A' and resid 747 through 756 removed outlier: 3.877A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 782 removed outlier: 3.775A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 823 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 914 through 918 Processing helix chain 'A' and resid 920 through 940 removed outlier: 3.727A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 967 removed outlier: 3.579A pdb=" N GLY A 946 " --> pdb=" O SER A 943 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N LYS A 947 " --> pdb=" O ALA A 944 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASP A 950 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN A 954 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN A 955 " --> pdb=" O VAL A 952 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN A 957 " --> pdb=" O GLN A 954 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA A 958 " --> pdb=" O ASN A 955 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN A 960 " --> pdb=" O GLN A 957 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR A 961 " --> pdb=" O ALA A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 983 Processing helix chain 'A' and resid 986 through 1032 removed outlier: 3.847A pdb=" N VAL A 991 " --> pdb=" O CYS A 987 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 6.157A 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 339 through 342 No H-bonds generated for 'chain 'C' and resid 339 through 342' 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: 4.221A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 406 No H-bonds generated for 'chain 'C' and resid 404 through 406' Processing helix chain 'C' and resid 417 through 421 Processing helix chain 'C' and resid 738 through 742 Processing helix chain 'C' and resid 747 through 756 removed outlier: 3.876A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 782 removed outlier: 3.775A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 823 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 914 through 918 Processing helix chain 'C' and resid 920 through 940 removed outlier: 3.728A pdb=" N SER C 940 " --> pdb=" O ASP C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 967 removed outlier: 3.578A pdb=" N GLY C 946 " --> pdb=" O SER C 943 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N LYS C 947 " --> pdb=" O ALA C 944 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASP C 950 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN C 954 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN C 955 " --> pdb=" O VAL C 952 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN C 957 " --> pdb=" O GLN C 954 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA C 958 " --> pdb=" O ASN C 955 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN C 960 " --> pdb=" O GLN C 957 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR C 961 " --> pdb=" O ALA C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 983 Processing helix chain 'C' and resid 986 through 1032 removed outlier: 3.846A pdb=" N VAL C 991 " --> pdb=" O CYS C 987 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 47 through 55 Processing sheet with id= B, first strand: chain 'B' and resid 63 through 66 removed outlier: 3.599A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 117 through 121 Processing sheet with id= D, first strand: chain 'B' and resid 325 through 328 removed outlier: 6.324A pdb=" N ASN B 540 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ARG B 328 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 6.096A 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 Processing sheet with id= F, first strand: chain 'B' and resid 551 through 554 Processing sheet with id= G, first strand: chain 'B' and resid 642 through 645 removed outlier: 4.408A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 691 through 696 removed outlier: 6.209A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 711 through 715 Processing sheet with id= J, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.009A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 734 through 736 Processing sheet with id= L, first strand: chain 'B' and resid 1088 through 1090 Processing sheet with id= M, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id= N, first strand: chain 'A' and resid 47 through 55 Processing sheet with id= O, first strand: chain 'A' and resid 63 through 66 removed outlier: 3.598A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 117 through 121 Processing sheet with id= Q, first strand: chain 'A' and resid 325 through 328 removed outlier: 6.324A pdb=" N ASN A 540 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ARG A 328 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASN A 542 " --> pdb=" O ARG A 328 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 354 through 358 Processing sheet with id= S, first strand: chain 'A' and resid 551 through 554 Processing sheet with id= T, first strand: chain 'A' and resid 642 through 645 removed outlier: 4.408A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'A' and resid 691 through 696 removed outlier: 6.209A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'A' and resid 711 through 715 Processing sheet with id= W, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.009A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'A' and resid 734 through 736 Processing sheet with id= Y, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id= Z, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id= AA, first strand: chain 'C' and resid 47 through 55 Processing sheet with id= AB, first strand: chain 'C' and resid 63 through 66 removed outlier: 3.598A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 117 through 121 Processing sheet with id= AD, first strand: chain 'C' and resid 325 through 328 removed outlier: 6.324A pdb=" N ASN C 540 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ARG C 328 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ASN C 542 " --> pdb=" O ARG C 328 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 354 through 358 Processing sheet with id= AF, first strand: chain 'C' and resid 551 through 554 Processing sheet with id= AG, first strand: chain 'C' and resid 642 through 645 removed outlier: 4.407A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'C' and resid 691 through 696 removed outlier: 6.210A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 711 through 715 Processing sheet with id= AJ, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.009A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'C' and resid 734 through 736 Processing sheet with id= AL, first strand: chain 'C' and resid 1088 through 1090 Processing sheet with id= AM, first strand: chain 'C' and resid 1094 through 1097 780 hydrogen bonds defined for protein. 2052 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: 18.30 Time building geometry restraints manager: 33.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 21546 1.03 - 1.23: 558 1.23 - 1.43: 9491 1.43 - 1.63: 13057 1.63 - 1.83: 123 Bond restraints: 44775 Sorted by residual: bond pdb=" C4C BLA B1401 " pdb=" NC BLA B1401 " ideal model delta sigma weight residual 1.375 1.542 -0.167 2.00e-02 2.50e+03 6.96e+01 bond pdb=" C4C BLA A1401 " pdb=" NC BLA A1401 " ideal model delta sigma weight residual 1.375 1.541 -0.166 2.00e-02 2.50e+03 6.92e+01 bond pdb=" C4C BLA C1401 " pdb=" NC BLA C1401 " ideal model delta sigma weight residual 1.375 1.541 -0.166 2.00e-02 2.50e+03 6.89e+01 bond pdb=" C1C BLA C1401 " pdb=" NC BLA C1401 " ideal model delta sigma weight residual 1.368 1.530 -0.162 2.00e-02 2.50e+03 6.55e+01 bond pdb=" C1C BLA B1401 " pdb=" NC BLA B1401 " ideal model delta sigma weight residual 1.368 1.530 -0.162 2.00e-02 2.50e+03 6.54e+01 ... (remaining 44770 not shown) Histogram of bond angle deviations from ideal: 97.69 - 104.97: 405 104.97 - 112.25: 50218 112.25 - 119.53: 10996 119.53 - 126.82: 18478 126.82 - 134.10: 252 Bond angle restraints: 80349 Sorted by residual: angle pdb=" C1B BLA A1401 " pdb=" CHB BLA A1401 " pdb=" C4A BLA A1401 " ideal model delta sigma weight residual 128.06 116.30 11.76 3.00e+00 1.11e-01 1.54e+01 angle pdb=" C1B BLA B1401 " pdb=" CHB BLA B1401 " pdb=" C4A BLA B1401 " ideal model delta sigma weight residual 128.06 116.32 11.74 3.00e+00 1.11e-01 1.53e+01 angle pdb=" C1B BLA C1401 " pdb=" CHB BLA C1401 " pdb=" C4A BLA C1401 " ideal model delta sigma weight residual 128.06 116.37 11.69 3.00e+00 1.11e-01 1.52e+01 angle pdb=" SD MET B 740 " pdb=" CE MET B 740 " pdb=" HE1 MET B 740 " ideal model delta sigma weight residual 109.00 120.24 -11.24 3.00e+00 1.11e-01 1.40e+01 angle pdb=" C3B BLA B1401 " pdb=" CAB BLA B1401 " pdb=" CBB BLA B1401 " ideal model delta sigma weight residual 126.95 118.30 8.65 3.00e+00 1.11e-01 8.32e+00 ... (remaining 80344 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 19924 17.95 - 35.90: 1610 35.90 - 53.84: 368 53.84 - 71.79: 124 71.79 - 89.74: 27 Dihedral angle restraints: 22053 sinusoidal: 12210 harmonic: 9843 Sorted by residual: 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 93.00 -177.26 -89.74 1 1.00e+01 1.00e-02 9.56e+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 93.00 -177.26 -89.74 1 1.00e+01 1.00e-02 9.56e+01 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 93.00 -177.29 -89.71 1 1.00e+01 1.00e-02 9.55e+01 ... (remaining 22050 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3241 0.073 - 0.146: 449 0.146 - 0.220: 12 0.220 - 0.293: 0 0.293 - 0.366: 9 Chirality restraints: 3711 Sorted by residual: chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 4.55e+00 chirality pdb=" C1 NAG o 2 " pdb=" O4 NAG o 1 " pdb=" C2 NAG o 2 " pdb=" O5 NAG o 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 4.52e+00 chirality pdb=" C1 NAG Z 2 " pdb=" O4 NAG Z 1 " pdb=" C2 NAG Z 2 " pdb=" O5 NAG Z 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 4.24e+00 ... (remaining 3708 not shown) Planarity restraints: 6666 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" ND BLA A1401 " -0.032 2.00e-02 2.50e+03 4.75e-02 5.64e+01 pdb=" C1A BLA A1401 " 0.107 2.00e-02 2.50e+03 pdb=" C1D BLA A1401 " -0.007 2.00e-02 2.50e+03 pdb=" C2D BLA A1401 " 0.008 2.00e-02 2.50e+03 pdb=" C3D BLA A1401 " -0.015 2.00e-02 2.50e+03 pdb=" C4D BLA A1401 " -0.037 2.00e-02 2.50e+03 pdb=" CAD BLA A1401 " 0.011 2.00e-02 2.50e+03 pdb=" CHA BLA A1401 " -0.077 2.00e-02 2.50e+03 pdb=" CHD BLA A1401 " -0.006 2.00e-02 2.50e+03 pdb=" CMD BLA A1401 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BLA B1401 " -0.032 2.00e-02 2.50e+03 4.75e-02 5.64e+01 pdb=" C1A BLA B1401 " 0.107 2.00e-02 2.50e+03 pdb=" C1D BLA B1401 " -0.007 2.00e-02 2.50e+03 pdb=" C2D BLA B1401 " 0.008 2.00e-02 2.50e+03 pdb=" C3D BLA B1401 " -0.016 2.00e-02 2.50e+03 pdb=" C4D BLA B1401 " -0.037 2.00e-02 2.50e+03 pdb=" CAD BLA B1401 " 0.011 2.00e-02 2.50e+03 pdb=" CHA BLA B1401 " -0.076 2.00e-02 2.50e+03 pdb=" CHD BLA B1401 " -0.006 2.00e-02 2.50e+03 pdb=" CMD BLA B1401 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BLA C1401 " -0.032 2.00e-02 2.50e+03 4.74e-02 5.63e+01 pdb=" C1A BLA C1401 " 0.107 2.00e-02 2.50e+03 pdb=" C1D BLA C1401 " -0.007 2.00e-02 2.50e+03 pdb=" C2D BLA C1401 " 0.008 2.00e-02 2.50e+03 pdb=" C3D BLA C1401 " -0.016 2.00e-02 2.50e+03 pdb=" C4D BLA C1401 " -0.037 2.00e-02 2.50e+03 pdb=" CAD BLA C1401 " 0.012 2.00e-02 2.50e+03 pdb=" CHA BLA C1401 " -0.076 2.00e-02 2.50e+03 pdb=" CHD BLA C1401 " -0.006 2.00e-02 2.50e+03 pdb=" CMD BLA C1401 " 0.048 2.00e-02 2.50e+03 ... (remaining 6663 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 5706 2.25 - 2.84: 97228 2.84 - 3.43: 110409 3.43 - 4.01: 160766 4.01 - 4.60: 240382 Nonbonded interactions: 614491 Sorted by model distance: nonbonded pdb=" HZ2 LYS C 825 " pdb=" O LEU C 938 " model vdw 1.663 1.850 nonbonded pdb=" HZ2 LYS B 825 " pdb=" O LEU B 938 " model vdw 1.663 1.850 nonbonded pdb=" HZ2 LYS A 825 " pdb=" O LEU A 938 " model vdw 1.663 1.850 nonbonded pdb=" O GLN A 957 " pdb=" HG1 THR A 961 " model vdw 1.668 1.850 nonbonded pdb=" O GLN C 957 " pdb=" HG1 THR C 961 " model vdw 1.669 1.850 ... (remaining 614486 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'Z' selection = chain 'b' selection = chain 'o' selection = chain 'q' } 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: 2.490 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: 0.660 Extract box with map and model: 11.610 Check model and map are aligned: 0.640 Set scattering table: 0.380 Process input model: 135.960 Find NCS groups from input model: 1.770 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 156.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.167 23226 Z= 0.564 Angle : 0.763 11.763 31569 Z= 0.379 Chirality : 0.050 0.366 3711 Planarity : 0.005 0.059 3993 Dihedral : 13.698 88.024 8988 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.17 (0.15), residues: 2724 helix: 0.52 (0.20), residues: 654 sheet: -0.65 (0.19), residues: 642 loop : -1.46 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 436 HIS 0.005 0.001 HIS A 207 PHE 0.028 0.002 PHE C 906 TYR 0.013 0.001 TYR C1067 ARG 0.008 0.001 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 2460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 2.857 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 1.1101 time to fit residues: 91.5703 Evaluate side-chains 42 residues out of total 2460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 3.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 235 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 218 optimal weight: 0.2980 chunk 84 optimal weight: 0.5980 chunk 132 optimal weight: 3.9990 chunk 162 optimal weight: 0.6980 chunk 253 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.0485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23226 Z= 0.158 Angle : 0.483 5.165 31569 Z= 0.252 Chirality : 0.045 0.335 3711 Planarity : 0.004 0.054 3993 Dihedral : 7.475 65.244 3957 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.16 % Allowed : 1.75 % Favored : 98.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.87 (0.15), residues: 2724 helix: 0.92 (0.21), residues: 636 sheet: -0.72 (0.19), residues: 654 loop : -1.19 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.003 0.001 HIS C 66 PHE 0.009 0.001 PHE A 238 TYR 0.014 0.001 TYR A 170 ARG 0.001 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 2460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 3.174 Fit side-chains revert: symmetry clash REVERT: B 740 MET cc_start: 0.8474 (tpt) cc_final: 0.8210 (tpt) outliers start: 4 outliers final: 4 residues processed: 48 average time/residue: 1.1273 time to fit residues: 78.4964 Evaluate side-chains 48 residues out of total 2460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 3.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain C residue 449 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 140 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 210 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 253 optimal weight: 2.9990 chunk 274 optimal weight: 0.5980 chunk 226 optimal weight: 0.5980 chunk 251 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.0850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23226 Z= 0.228 Angle : 0.470 4.698 31569 Z= 0.244 Chirality : 0.044 0.306 3711 Planarity : 0.004 0.049 3993 Dihedral : 6.718 60.611 3957 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.12 % Allowed : 3.09 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.72 (0.16), residues: 2724 helix: 1.20 (0.21), residues: 636 sheet: -0.75 (0.19), residues: 654 loop : -1.10 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.003 0.001 HIS B 207 PHE 0.012 0.001 PHE B 906 TYR 0.013 0.001 TYR A1067 ARG 0.002 0.000 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 2460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 3.593 Fit side-chains revert: symmetry clash REVERT: B 740 MET cc_start: 0.8528 (tpt) cc_final: 0.8200 (tpt) outliers start: 3 outliers final: 3 residues processed: 48 average time/residue: 1.1633 time to fit residues: 81.9755 Evaluate side-chains 47 residues out of total 2460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 3.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain C residue 449 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 250 optimal weight: 2.9990 chunk 190 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 254 optimal weight: 2.9990 chunk 269 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 chunk 241 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 920 GLN A 920 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 920 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 23226 Z= 0.336 Angle : 0.499 5.569 31569 Z= 0.262 Chirality : 0.045 0.293 3711 Planarity : 0.004 0.049 3993 Dihedral : 6.545 58.110 3957 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.65 % Allowed : 3.21 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.79 (0.16), residues: 2724 helix: 1.16 (0.21), residues: 639 sheet: -0.81 (0.18), residues: 684 loop : -1.14 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 104 HIS 0.003 0.001 HIS B1048 PHE 0.018 0.001 PHE B 906 TYR 0.019 0.001 TYR C 170 ARG 0.002 0.000 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 2460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 44 time to evaluate : 3.475 Fit side-chains revert: symmetry clash REVERT: B 920 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8433 (tt0) outliers start: 16 outliers final: 6 residues processed: 57 average time/residue: 1.0312 time to fit residues: 87.4741 Evaluate side-chains 50 residues out of total 2460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 3.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 920 GLN Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 920 GLN Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 920 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 224 optimal weight: 5.9990 chunk 153 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 200 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 230 optimal weight: 0.7980 chunk 186 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 137 optimal weight: 0.6980 chunk 242 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 920 GLN B1005 GLN A 920 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 920 GLN C1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23226 Z= 0.188 Angle : 0.465 7.864 31569 Z= 0.244 Chirality : 0.044 0.282 3711 Planarity : 0.003 0.048 3993 Dihedral : 6.305 59.974 3957 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.45 % Allowed : 4.23 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.66 (0.16), residues: 2724 helix: 1.27 (0.21), residues: 639 sheet: -0.72 (0.18), residues: 678 loop : -1.08 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 104 HIS 0.002 0.001 HIS C 207 PHE 0.010 0.001 PHE A 898 TYR 0.015 0.001 TYR A 170 ARG 0.001 0.000 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 2460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 43 time to evaluate : 3.644 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 51 average time/residue: 1.1272 time to fit residues: 83.7248 Evaluate side-chains 50 residues out of total 2460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 3.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 552 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 90 optimal weight: 2.9990 chunk 242 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 269 optimal weight: 0.5980 chunk 224 optimal weight: 0.0970 chunk 124 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN A 920 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23226 Z= 0.140 Angle : 0.433 4.641 31569 Z= 0.224 Chirality : 0.044 0.277 3711 Planarity : 0.003 0.045 3993 Dihedral : 5.952 57.864 3957 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.28 % Allowed : 4.43 % Favored : 95.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.47 (0.16), residues: 2724 helix: 1.46 (0.22), residues: 639 sheet: -0.70 (0.18), residues: 693 loop : -0.92 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 64 HIS 0.002 0.000 HIS B 207 PHE 0.010 0.001 PHE A 898 TYR 0.010 0.001 TYR A 170 ARG 0.001 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 2460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 3.499 Fit side-chains revert: symmetry clash REVERT: B 740 MET cc_start: 0.8495 (tpt) cc_final: 0.8160 (tpt) REVERT: A 52 GLN cc_start: 0.8583 (pp30) cc_final: 0.8342 (pp30) outliers start: 7 outliers final: 6 residues processed: 48 average time/residue: 1.1519 time to fit residues: 80.3477 Evaluate side-chains 49 residues out of total 2460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 3.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 552 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 260 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 chunk 150 optimal weight: 0.7980 chunk 268 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23226 Z= 0.248 Angle : 0.451 4.837 31569 Z= 0.235 Chirality : 0.044 0.280 3711 Planarity : 0.003 0.045 3993 Dihedral : 5.878 55.463 3957 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.37 % Allowed : 4.76 % Favored : 94.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.51 (0.16), residues: 2724 helix: 1.47 (0.22), residues: 639 sheet: -0.71 (0.18), residues: 693 loop : -0.97 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 104 HIS 0.002 0.001 HIS B1048 PHE 0.011 0.001 PHE A 898 TYR 0.012 0.001 TYR C1067 ARG 0.005 0.000 ARG C1039 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 2460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 3.538 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 50 average time/residue: 1.1822 time to fit residues: 87.1823 Evaluate side-chains 52 residues out of total 2460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 3.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 552 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 166 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 170 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 211 optimal weight: 5.9990 chunk 244 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23226 Z= 0.237 Angle : 0.453 4.998 31569 Z= 0.236 Chirality : 0.044 0.280 3711 Planarity : 0.003 0.045 3993 Dihedral : 5.738 56.218 3957 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.41 % Allowed : 5.20 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.16), residues: 2724 helix: 1.47 (0.22), residues: 639 sheet: -0.71 (0.18), residues: 693 loop : -0.98 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 64 HIS 0.002 0.001 HIS B1064 PHE 0.012 0.001 PHE A 906 TYR 0.012 0.001 TYR A1067 ARG 0.003 0.000 ARG C1039 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 2460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 44 time to evaluate : 3.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 740 MET cc_start: 0.8490 (tpt) cc_final: 0.8169 (tpt) outliers start: 10 outliers final: 8 residues processed: 51 average time/residue: 1.1073 time to fit residues: 83.3791 Evaluate side-chains 52 residues out of total 2460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 3.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 552 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 257 optimal weight: 2.9990 chunk 235 optimal weight: 1.9990 chunk 250 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 196 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 226 optimal weight: 1.9990 chunk 237 optimal weight: 2.9990 chunk 249 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23226 Z= 0.290 Angle : 0.469 5.368 31569 Z= 0.245 Chirality : 0.044 0.284 3711 Planarity : 0.003 0.046 3993 Dihedral : 5.737 57.059 3957 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.33 % Allowed : 5.24 % Favored : 94.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.58 (0.16), residues: 2724 helix: 1.42 (0.21), residues: 639 sheet: -0.77 (0.18), residues: 699 loop : -1.01 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 104 HIS 0.003 0.001 HIS B1048 PHE 0.013 0.001 PHE A 906 TYR 0.013 0.001 TYR A1067 ARG 0.002 0.000 ARG A 995 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 2460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 3.566 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 8 residues processed: 50 average time/residue: 1.2157 time to fit residues: 86.5188 Evaluate side-chains 50 residues out of total 2460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 3.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 552 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 264 optimal weight: 0.1980 chunk 161 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 184 optimal weight: 0.4980 chunk 277 optimal weight: 0.5980 chunk 255 optimal weight: 0.9980 chunk 221 optimal weight: 9.9990 chunk 22 optimal weight: 0.7980 chunk 170 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 23226 Z= 0.146 Angle : 0.431 4.872 31569 Z= 0.223 Chirality : 0.044 0.277 3711 Planarity : 0.003 0.042 3993 Dihedral : 5.504 56.406 3957 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.24 % Allowed : 5.49 % Favored : 94.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.40 (0.16), residues: 2724 helix: 1.56 (0.22), residues: 639 sheet: -0.62 (0.19), residues: 675 loop : -0.91 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 104 HIS 0.001 0.000 HIS B 519 PHE 0.010 0.001 PHE A 898 TYR 0.010 0.001 TYR A1067 ARG 0.003 0.000 ARG A 319 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 2460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 3.093 Fit side-chains revert: symmetry clash REVERT: B 740 MET cc_start: 0.8479 (tpt) cc_final: 0.8156 (tpt) outliers start: 6 outliers final: 6 residues processed: 51 average time/residue: 1.1956 time to fit residues: 87.1317 Evaluate side-chains 50 residues out of total 2460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 3.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain C residue 552 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 235 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 221 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 227 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.086820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.064280 restraints weight = 162940.155| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.80 r_work: 0.2951 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23226 Z= 0.253 Angle : 0.452 5.123 31569 Z= 0.235 Chirality : 0.044 0.279 3711 Planarity : 0.003 0.044 3993 Dihedral : 5.554 56.659 3957 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.28 % Allowed : 5.53 % Favored : 94.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.46 (0.16), residues: 2724 helix: 1.53 (0.22), residues: 639 sheet: -0.65 (0.19), residues: 675 loop : -0.97 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 104 HIS 0.002 0.001 HIS C1048 PHE 0.011 0.001 PHE A 898 TYR 0.012 0.001 TYR A1067 ARG 0.006 0.000 ARG C 319 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6806.98 seconds wall clock time: 129 minutes 4.38 seconds (7744.38 seconds total)