Starting phenix.real_space_refine on Sat Mar 23 10:29:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fer_31561/03_2024/7fer_31561_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fer_31561/03_2024/7fer_31561.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fer_31561/03_2024/7fer_31561.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fer_31561/03_2024/7fer_31561.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fer_31561/03_2024/7fer_31561_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fer_31561/03_2024/7fer_31561_updated.pdb" } resolution = 3.4 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= 0.022 sd= 0.132 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 98 5.16 5 C 11856 2.51 5 N 3070 2.21 5 O 3570 1.98 5 H 18142 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 26": "OD1" <-> "OD2" Residue "A ASP 36": "OD1" <-> "OD2" Residue "A TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A ASP 171": "OD1" <-> "OD2" Residue "A TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 26": "OD1" <-> "OD2" Residue "B ASP 36": "OD1" <-> "OD2" Residue "B TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B GLU 155": "OE1" <-> "OE2" Residue "B ASP 171": "OD1" <-> "OD2" Residue "B TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 26": "OD1" <-> "OD2" Residue "C ASP 36": "OD1" <-> "OD2" Residue "C TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "C ASP 171": "OD1" <-> "OD2" Residue "C TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 26": "OD1" <-> "OD2" Residue "D ASP 36": "OD1" <-> "OD2" Residue "D TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 107": "OE1" <-> "OE2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "D ASP 171": "OD1" <-> "OD2" Residue "D TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 26": "OD1" <-> "OD2" Residue "E ASP 36": "OD1" <-> "OD2" Residue "E TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 155": "OE1" <-> "OE2" Residue "E ASP 171": "OD1" <-> "OD2" Residue "E TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 26": "OD1" <-> "OD2" Residue "F ASP 36": "OD1" <-> "OD2" Residue "F TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 155": "OE1" <-> "OE2" Residue "F ASP 171": "OD1" <-> "OD2" Residue "F TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 26": "OD1" <-> "OD2" Residue "G ASP 36": "OD1" <-> "OD2" Residue "G TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 155": "OE1" <-> "OE2" Residue "G ASP 171": "OD1" <-> "OD2" Residue "G TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 26": "OD1" <-> "OD2" Residue "H ASP 36": "OD1" <-> "OD2" Residue "H TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 155": "OE1" <-> "OE2" Residue "H ASP 171": "OD1" <-> "OD2" Residue "H TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ASP 26": "OD1" <-> "OD2" Residue "I ASP 36": "OD1" <-> "OD2" Residue "I TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 155": "OE1" <-> "OE2" Residue "I ASP 171": "OD1" <-> "OD2" Residue "I TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ASP 26": "OD1" <-> "OD2" Residue "J ASP 36": "OD1" <-> "OD2" Residue "J TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 155": "OE1" <-> "OE2" Residue "J ASP 171": "OD1" <-> "OD2" Residue "J TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ASP 26": "OD1" <-> "OD2" Residue "K ASP 36": "OD1" <-> "OD2" Residue "K TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 155": "OE1" <-> "OE2" Residue "K ASP 171": "OD1" <-> "OD2" Residue "K TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ASP 26": "OD1" <-> "OD2" Residue "L ASP 36": "OD1" <-> "OD2" Residue "L TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 155": "OE1" <-> "OE2" Residue "L ASP 171": "OD1" <-> "OD2" Residue "L TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ASP 26": "OD1" <-> "OD2" Residue "M ASP 36": "OD1" <-> "OD2" Residue "M TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 155": "OE1" <-> "OE2" Residue "M ASP 171": "OD1" <-> "OD2" Residue "M TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ASP 26": "OD1" <-> "OD2" Residue "N ASP 36": "OD1" <-> "OD2" Residue "N TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N GLU 155": "OE1" <-> "OE2" Residue "N ASP 171": "OD1" <-> "OD2" Residue "N TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 36736 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 2568 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 6, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "B" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 2568 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 6, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "C" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 2568 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 6, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 2583 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 6, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 2568 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 6, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "F" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 2568 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 6, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "G" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 2568 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 6, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "H" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 2568 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 6, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "I" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 2568 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 6, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "J" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 2568 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 6, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "K" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 2568 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 6, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "L" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 2568 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 6, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "M" Number of atoms: 2609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 2609 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 6, 'TRANS': 161} Chain breaks: 1 Chain: "N" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 2568 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 6, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "O" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT O 1 " pdbres="PHE O 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "P" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT P 1 " pdbres="PHE P 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Q" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT Q 1 " pdbres="PHE Q 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT R 1 " pdbres="PHE R 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT S 1 " pdbres="PHE S 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "T" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT T 1 " pdbres="PHE T 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "U" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT U 1 " pdbres="PHE U 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "V" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT V 1 " pdbres="PHE V 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "W" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT W 1 " pdbres="PHE W 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "X" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT X 1 " pdbres="PHE X 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Y" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT Y 1 " pdbres="PHE Y 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Z" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT Z 1 " pdbres="PHE Z 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "a" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT a 1 " pdbres="PHE a 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "b" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT b 1 " pdbres="PHE b 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MAA:plan-1': 1, 'MP8:plan-1': 1, 'OTT:plan-1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 14.89, per 1000 atoms: 0.41 Number of scatterers: 36736 At special positions: 0 Unit cell: (120.4, 122.12, 103.2, 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 98 16.00 O 3570 8.00 N 3070 7.00 C 11856 6.00 H 18142 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=28, symmetry=0 Number of additional bonds: simple=28, symmetry=0 Coordination: Other bonds: Time building additional restraints: 26.48 Conformation dependent library (CDL) restraints added in 4.3 seconds 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4508 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 98 helices and 14 sheets defined 38.1% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.99 Creating SS restraints... Processing helix chain 'A' and resid 19 through 24 Processing helix chain 'A' and resid 37 through 51 removed outlier: 3.931A pdb=" N SER A 42 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN A 46 " --> pdb=" O SER A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 81 removed outlier: 3.547A pdb=" N MET A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA A 75 " --> pdb=" O THR A 71 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR A 77 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASP A 78 " --> pdb=" O MET A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 103 removed outlier: 3.816A pdb=" N LEU A 102 " --> pdb=" O MET A 98 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 157 removed outlier: 3.669A pdb=" N LEU A 144 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 149 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASN A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA A 154 " --> pdb=" O ASN A 150 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU A 155 " --> pdb=" O LYS A 151 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A 156 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 167 removed outlier: 4.391A pdb=" N ARG A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'B' and resid 19 through 24 Processing helix chain 'B' and resid 37 through 51 removed outlier: 3.932A pdb=" N SER B 42 " --> pdb=" O ASN B 38 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN B 46 " --> pdb=" O SER B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 81 removed outlier: 3.547A pdb=" N MET B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR B 77 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASP B 78 " --> pdb=" O MET B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 101 No H-bonds generated for 'chain 'B' and resid 99 through 101' Processing helix chain 'B' and resid 139 through 157 removed outlier: 3.669A pdb=" N LEU B 144 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP B 147 " --> pdb=" O LEU B 143 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU B 149 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN B 150 " --> pdb=" O ARG B 146 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA B 154 " --> pdb=" O ASN B 150 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU B 155 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG B 156 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR B 157 " --> pdb=" O LEU B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 167 removed outlier: 4.392A pdb=" N ARG B 166 " --> pdb=" O GLU B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 181 No H-bonds generated for 'chain 'B' and resid 179 through 181' Processing helix chain 'C' and resid 19 through 24 Processing helix chain 'C' and resid 37 through 51 removed outlier: 3.930A pdb=" N SER C 42 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN C 46 " --> pdb=" O SER C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 81 removed outlier: 3.547A pdb=" N MET C 74 " --> pdb=" O ILE C 70 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA C 75 " --> pdb=" O THR C 71 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE C 76 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR C 77 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASP C 78 " --> pdb=" O MET C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 103 Processing helix chain 'C' and resid 139 through 157 removed outlier: 3.669A pdb=" N LEU C 144 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP C 147 " --> pdb=" O LEU C 143 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN C 150 " --> pdb=" O ARG C 146 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA C 154 " --> pdb=" O ASN C 150 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU C 155 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG C 156 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR C 157 " --> pdb=" O LEU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 167 removed outlier: 4.392A pdb=" N ARG C 166 " --> pdb=" O GLU C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 181 No H-bonds generated for 'chain 'C' and resid 179 through 181' Processing helix chain 'D' and resid 19 through 24 Processing helix chain 'D' and resid 37 through 51 removed outlier: 3.930A pdb=" N SER D 42 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN D 46 " --> pdb=" O SER D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 81 removed outlier: 3.546A pdb=" N MET D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA D 75 " --> pdb=" O THR D 71 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR D 77 " --> pdb=" O GLY D 73 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASP D 78 " --> pdb=" O MET D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 103 removed outlier: 3.810A pdb=" N PHE D 101 " --> pdb=" O SER D 97 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU D 102 " --> pdb=" O MET D 98 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU D 103 " --> pdb=" O GLY D 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 103' Processing helix chain 'D' and resid 139 through 157 removed outlier: 3.670A pdb=" N LEU D 144 " --> pdb=" O LYS D 140 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP D 147 " --> pdb=" O LEU D 143 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU D 149 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN D 150 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU D 155 " --> pdb=" O LYS D 151 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG D 156 " --> pdb=" O VAL D 152 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR D 157 " --> pdb=" O LEU D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 167 removed outlier: 4.392A pdb=" N ARG D 166 " --> pdb=" O GLU D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 181 No H-bonds generated for 'chain 'D' and resid 179 through 181' Processing helix chain 'E' and resid 19 through 24 Processing helix chain 'E' and resid 37 through 51 removed outlier: 3.931A pdb=" N SER E 42 " --> pdb=" O ASN E 38 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN E 46 " --> pdb=" O SER E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 81 removed outlier: 3.547A pdb=" N MET E 74 " --> pdb=" O ILE E 70 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA E 75 " --> pdb=" O THR E 71 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE E 76 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR E 77 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASP E 78 " --> pdb=" O MET E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 103 Processing helix chain 'E' and resid 139 through 157 removed outlier: 3.669A pdb=" N LEU E 144 " --> pdb=" O LYS E 140 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU E 149 " --> pdb=" O LEU E 145 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASN E 150 " --> pdb=" O ARG E 146 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA E 154 " --> pdb=" O ASN E 150 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU E 155 " --> pdb=" O LYS E 151 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG E 156 " --> pdb=" O VAL E 152 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR E 157 " --> pdb=" O LEU E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 167 removed outlier: 4.392A pdb=" N ARG E 166 " --> pdb=" O GLU E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 181 No H-bonds generated for 'chain 'E' and resid 179 through 181' Processing helix chain 'F' and resid 19 through 24 Processing helix chain 'F' and resid 37 through 51 removed outlier: 3.931A pdb=" N SER F 42 " --> pdb=" O ASN F 38 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN F 46 " --> pdb=" O SER F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 81 removed outlier: 3.548A pdb=" N MET F 74 " --> pdb=" O ILE F 70 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA F 75 " --> pdb=" O THR F 71 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE F 76 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR F 77 " --> pdb=" O GLY F 73 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASP F 78 " --> pdb=" O MET F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 101 No H-bonds generated for 'chain 'F' and resid 99 through 101' Processing helix chain 'F' and resid 139 through 157 removed outlier: 3.670A pdb=" N LEU F 144 " --> pdb=" O LYS F 140 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP F 147 " --> pdb=" O LEU F 143 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU F 149 " --> pdb=" O LEU F 145 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASN F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA F 154 " --> pdb=" O ASN F 150 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU F 155 " --> pdb=" O LYS F 151 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG F 156 " --> pdb=" O VAL F 152 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR F 157 " --> pdb=" O LEU F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 167 removed outlier: 4.391A pdb=" N ARG F 166 " --> pdb=" O GLU F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 181 No H-bonds generated for 'chain 'F' and resid 179 through 181' Processing helix chain 'G' and resid 19 through 24 Processing helix chain 'G' and resid 37 through 51 removed outlier: 3.931A pdb=" N SER G 42 " --> pdb=" O ASN G 38 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN G 46 " --> pdb=" O SER G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 81 removed outlier: 3.547A pdb=" N MET G 74 " --> pdb=" O ILE G 70 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA G 75 " --> pdb=" O THR G 71 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE G 76 " --> pdb=" O ALA G 72 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR G 77 " --> pdb=" O GLY G 73 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ASP G 78 " --> pdb=" O MET G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 103 Processing helix chain 'G' and resid 139 through 157 removed outlier: 3.669A pdb=" N LEU G 144 " --> pdb=" O LYS G 140 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP G 147 " --> pdb=" O LEU G 143 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU G 149 " --> pdb=" O LEU G 145 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASN G 150 " --> pdb=" O ARG G 146 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA G 154 " --> pdb=" O ASN G 150 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU G 155 " --> pdb=" O LYS G 151 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG G 156 " --> pdb=" O VAL G 152 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR G 157 " --> pdb=" O LEU G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 161 through 167 removed outlier: 4.392A pdb=" N ARG G 166 " --> pdb=" O GLU G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 181 No H-bonds generated for 'chain 'G' and resid 179 through 181' Processing helix chain 'H' and resid 19 through 24 Processing helix chain 'H' and resid 37 through 51 removed outlier: 3.931A pdb=" N SER H 42 " --> pdb=" O ASN H 38 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN H 46 " --> pdb=" O SER H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 81 removed outlier: 3.546A pdb=" N MET H 74 " --> pdb=" O ILE H 70 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA H 75 " --> pdb=" O THR H 71 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE H 76 " --> pdb=" O ALA H 72 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR H 77 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASP H 78 " --> pdb=" O MET H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 103 removed outlier: 3.692A pdb=" N LEU H 103 " --> pdb=" O GLY H 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 99 through 103' Processing helix chain 'H' and resid 139 through 157 removed outlier: 3.669A pdb=" N LEU H 144 " --> pdb=" O LYS H 140 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP H 147 " --> pdb=" O LEU H 143 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU H 149 " --> pdb=" O LEU H 145 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASN H 150 " --> pdb=" O ARG H 146 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA H 154 " --> pdb=" O ASN H 150 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU H 155 " --> pdb=" O LYS H 151 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG H 156 " --> pdb=" O VAL H 152 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR H 157 " --> pdb=" O LEU H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 167 removed outlier: 4.392A pdb=" N ARG H 166 " --> pdb=" O GLU H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 181 No H-bonds generated for 'chain 'H' and resid 179 through 181' Processing helix chain 'I' and resid 19 through 24 Processing helix chain 'I' and resid 37 through 51 removed outlier: 3.931A pdb=" N SER I 42 " --> pdb=" O ASN I 38 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN I 46 " --> pdb=" O SER I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 81 removed outlier: 3.546A pdb=" N MET I 74 " --> pdb=" O ILE I 70 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA I 75 " --> pdb=" O THR I 71 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE I 76 " --> pdb=" O ALA I 72 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR I 77 " --> pdb=" O GLY I 73 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASP I 78 " --> pdb=" O MET I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 104 Processing helix chain 'I' and resid 139 through 157 removed outlier: 3.669A pdb=" N LEU I 144 " --> pdb=" O LYS I 140 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP I 147 " --> pdb=" O LEU I 143 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU I 149 " --> pdb=" O LEU I 145 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASN I 150 " --> pdb=" O ARG I 146 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA I 154 " --> pdb=" O ASN I 150 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU I 155 " --> pdb=" O LYS I 151 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG I 156 " --> pdb=" O VAL I 152 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR I 157 " --> pdb=" O LEU I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 167 removed outlier: 4.391A pdb=" N ARG I 166 " --> pdb=" O GLU I 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 179 through 181 No H-bonds generated for 'chain 'I' and resid 179 through 181' Processing helix chain 'J' and resid 19 through 24 Processing helix chain 'J' and resid 37 through 51 removed outlier: 3.931A pdb=" N SER J 42 " --> pdb=" O ASN J 38 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN J 46 " --> pdb=" O SER J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 81 removed outlier: 3.547A pdb=" N MET J 74 " --> pdb=" O ILE J 70 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA J 75 " --> pdb=" O THR J 71 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE J 76 " --> pdb=" O ALA J 72 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR J 77 " --> pdb=" O GLY J 73 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASP J 78 " --> pdb=" O MET J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 101 No H-bonds generated for 'chain 'J' and resid 99 through 101' Processing helix chain 'J' and resid 139 through 157 removed outlier: 3.669A pdb=" N LEU J 144 " --> pdb=" O LYS J 140 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP J 147 " --> pdb=" O LEU J 143 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU J 149 " --> pdb=" O LEU J 145 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN J 150 " --> pdb=" O ARG J 146 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA J 154 " --> pdb=" O ASN J 150 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU J 155 " --> pdb=" O LYS J 151 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG J 156 " --> pdb=" O VAL J 152 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR J 157 " --> pdb=" O LEU J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 167 removed outlier: 4.392A pdb=" N ARG J 166 " --> pdb=" O GLU J 162 " (cutoff:3.500A) Processing helix chain 'J' and resid 179 through 181 No H-bonds generated for 'chain 'J' and resid 179 through 181' Processing helix chain 'K' and resid 19 through 24 Processing helix chain 'K' and resid 37 through 51 removed outlier: 3.931A pdb=" N SER K 42 " --> pdb=" O ASN K 38 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN K 46 " --> pdb=" O SER K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 81 removed outlier: 3.546A pdb=" N MET K 74 " --> pdb=" O ILE K 70 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE K 76 " --> pdb=" O ALA K 72 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR K 77 " --> pdb=" O GLY K 73 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASP K 78 " --> pdb=" O MET K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 101 No H-bonds generated for 'chain 'K' and resid 99 through 101' Processing helix chain 'K' and resid 139 through 152 removed outlier: 3.669A pdb=" N LEU K 144 " --> pdb=" O LYS K 140 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP K 147 " --> pdb=" O LEU K 143 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU K 149 " --> pdb=" O LEU K 145 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASN K 150 " --> pdb=" O ARG K 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 161 through 167 removed outlier: 4.347A pdb=" N GLU K 165 " --> pdb=" O GLU K 162 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 181 No H-bonds generated for 'chain 'K' and resid 179 through 181' Processing helix chain 'L' and resid 19 through 24 Processing helix chain 'L' and resid 37 through 51 removed outlier: 3.931A pdb=" N SER L 42 " --> pdb=" O ASN L 38 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN L 46 " --> pdb=" O SER L 42 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 81 removed outlier: 3.547A pdb=" N MET L 74 " --> pdb=" O ILE L 70 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA L 75 " --> pdb=" O THR L 71 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE L 76 " --> pdb=" O ALA L 72 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR L 77 " --> pdb=" O GLY L 73 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASP L 78 " --> pdb=" O MET L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 103 removed outlier: 3.807A pdb=" N LEU L 102 " --> pdb=" O MET L 98 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU L 103 " --> pdb=" O GLY L 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 98 through 103' Processing helix chain 'L' and resid 139 through 157 removed outlier: 3.670A pdb=" N LEU L 144 " --> pdb=" O LYS L 140 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP L 147 " --> pdb=" O LEU L 143 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU L 149 " --> pdb=" O LEU L 145 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASN L 150 " --> pdb=" O ARG L 146 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA L 154 " --> pdb=" O ASN L 150 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU L 155 " --> pdb=" O LYS L 151 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG L 156 " --> pdb=" O VAL L 152 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR L 157 " --> pdb=" O LEU L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 161 through 167 removed outlier: 4.392A pdb=" N ARG L 166 " --> pdb=" O GLU L 162 " (cutoff:3.500A) Processing helix chain 'L' and resid 179 through 181 No H-bonds generated for 'chain 'L' and resid 179 through 181' Processing helix chain 'M' and resid 19 through 24 Processing helix chain 'M' and resid 37 through 51 removed outlier: 3.931A pdb=" N SER M 42 " --> pdb=" O ASN M 38 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN M 46 " --> pdb=" O SER M 42 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 81 removed outlier: 3.546A pdb=" N MET M 74 " --> pdb=" O ILE M 70 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA M 75 " --> pdb=" O THR M 71 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE M 76 " --> pdb=" O ALA M 72 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR M 77 " --> pdb=" O GLY M 73 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASP M 78 " --> pdb=" O MET M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 101 No H-bonds generated for 'chain 'M' and resid 98 through 101' Processing helix chain 'M' and resid 139 through 152 removed outlier: 3.670A pdb=" N LEU M 144 " --> pdb=" O LYS M 140 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP M 147 " --> pdb=" O LEU M 143 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU M 149 " --> pdb=" O LEU M 145 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASN M 150 " --> pdb=" O ARG M 146 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 167 removed outlier: 4.392A pdb=" N ARG M 166 " --> pdb=" O GLU M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 179 through 181 No H-bonds generated for 'chain 'M' and resid 179 through 181' Processing helix chain 'N' and resid 19 through 24 Processing helix chain 'N' and resid 37 through 51 removed outlier: 3.931A pdb=" N SER N 42 " --> pdb=" O ASN N 38 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN N 46 " --> pdb=" O SER N 42 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 81 removed outlier: 3.547A pdb=" N MET N 74 " --> pdb=" O ILE N 70 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA N 75 " --> pdb=" O THR N 71 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE N 76 " --> pdb=" O ALA N 72 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR N 77 " --> pdb=" O GLY N 73 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASP N 78 " --> pdb=" O MET N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 103 removed outlier: 3.656A pdb=" N LEU N 102 " --> pdb=" O MET N 98 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU N 103 " --> pdb=" O GLY N 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 98 through 103' Processing helix chain 'N' and resid 139 through 157 removed outlier: 3.669A pdb=" N LEU N 144 " --> pdb=" O LYS N 140 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP N 147 " --> pdb=" O LEU N 143 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU N 149 " --> pdb=" O LEU N 145 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN N 150 " --> pdb=" O ARG N 146 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA N 154 " --> pdb=" O ASN N 150 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU N 155 " --> pdb=" O LYS N 151 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG N 156 " --> pdb=" O VAL N 152 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR N 157 " --> pdb=" O LEU N 153 " (cutoff:3.500A) Processing helix chain 'N' and resid 161 through 167 removed outlier: 4.391A pdb=" N ARG N 166 " --> pdb=" O GLU N 162 " (cutoff:3.500A) Processing helix chain 'N' and resid 179 through 181 No H-bonds generated for 'chain 'N' and resid 179 through 181' Processing sheet with id= A, first strand: chain 'A' and resid 59 through 63 Processing sheet with id= B, first strand: chain 'B' and resid 59 through 63 Processing sheet with id= C, first strand: chain 'C' and resid 59 through 63 Processing sheet with id= D, first strand: chain 'D' and resid 59 through 63 Processing sheet with id= E, first strand: chain 'E' and resid 59 through 63 Processing sheet with id= F, first strand: chain 'F' and resid 59 through 63 Processing sheet with id= G, first strand: chain 'G' and resid 59 through 63 Processing sheet with id= H, first strand: chain 'H' and resid 59 through 63 Processing sheet with id= I, first strand: chain 'I' and resid 59 through 63 Processing sheet with id= J, first strand: chain 'J' and resid 59 through 63 Processing sheet with id= K, first strand: chain 'K' and resid 28 through 31 removed outlier: 6.984A pdb=" N SER K 60 " --> pdb=" O ILE K 29 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N LEU K 31 " --> pdb=" O SER K 60 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N TYR K 62 " --> pdb=" O LEU K 31 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'L' and resid 59 through 63 Processing sheet with id= M, first strand: chain 'M' and resid 28 through 31 removed outlier: 6.983A pdb=" N SER M 60 " --> pdb=" O ILE M 29 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N LEU M 31 " --> pdb=" O SER M 60 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N TYR M 62 " --> pdb=" O LEU M 31 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'N' and resid 59 through 63 389 hydrogen bonds defined for protein. 1131 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.89 Time building geometry restraints manager: 27.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.79 - 0.99: 18071 0.99 - 1.20: 62 1.20 - 1.40: 7121 1.40 - 1.61: 11510 1.61 - 1.81: 196 Bond restraints: 36960 Sorted by residual: bond pdb=" C ALA b 6 " pdb=" N MP8 b 7 " ideal model delta sigma weight residual 1.329 1.467 -0.138 1.40e-02 5.10e+03 9.71e+01 bond pdb=" C ALA Y 6 " pdb=" N MP8 Y 7 " ideal model delta sigma weight residual 1.329 1.467 -0.138 1.40e-02 5.10e+03 9.71e+01 bond pdb=" C ALA P 6 " pdb=" N MP8 P 7 " ideal model delta sigma weight residual 1.329 1.467 -0.138 1.40e-02 5.10e+03 9.70e+01 bond pdb=" C ALA O 6 " pdb=" N MP8 O 7 " ideal model delta sigma weight residual 1.329 1.467 -0.138 1.40e-02 5.10e+03 9.66e+01 bond pdb=" C ALA R 6 " pdb=" N MP8 R 7 " ideal model delta sigma weight residual 1.329 1.467 -0.138 1.40e-02 5.10e+03 9.65e+01 ... (remaining 36955 not shown) Histogram of bond angle deviations from ideal: 56.80 - 74.36: 63 74.36 - 91.92: 65 91.92 - 109.49: 24954 109.49 - 127.05: 41451 127.05 - 144.61: 203 Bond angle restraints: 66736 Sorted by residual: angle pdb=" C ALA M 104 " pdb=" N ALA M 105 " pdb=" H ALA M 105 " ideal model delta sigma weight residual 124.24 66.09 58.16 3.00e+00 1.11e-01 3.76e+02 angle pdb=" C LEU J 161 " pdb=" N GLU J 162 " pdb=" H GLU J 162 " ideal model delta sigma weight residual 124.39 66.50 57.89 3.00e+00 1.11e-01 3.72e+02 angle pdb=" C ASN J 116 " pdb=" N SER J 117 " pdb=" H SER J 117 " ideal model delta sigma weight residual 124.11 66.38 57.73 3.00e+00 1.11e-01 3.70e+02 angle pdb=" C ASP J 169 " pdb=" N ARG J 170 " pdb=" H ARG J 170 " ideal model delta sigma weight residual 123.49 66.13 57.36 3.00e+00 1.11e-01 3.66e+02 angle pdb=" CA GLU J 162 " pdb=" N GLU J 162 " pdb=" H GLU J 162 " ideal model delta sigma weight residual 114.09 56.80 57.29 3.00e+00 1.11e-01 3.65e+02 ... (remaining 66731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.03: 14658 16.03 - 32.06: 1722 32.06 - 48.09: 541 48.09 - 64.11: 262 64.11 - 80.14: 29 Dihedral angle restraints: 17212 sinusoidal: 9568 harmonic: 7644 Sorted by residual: dihedral pdb=" CA ASP F 26 " pdb=" C ASP F 26 " pdb=" N ARG F 27 " pdb=" CA ARG F 27 " ideal model delta harmonic sigma weight residual 180.00 153.07 26.93 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA ASP H 26 " pdb=" C ASP H 26 " pdb=" N ARG H 27 " pdb=" CA ARG H 27 " ideal model delta harmonic sigma weight residual 180.00 153.08 26.92 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA ASP K 26 " pdb=" C ASP K 26 " pdb=" N ARG K 27 " pdb=" CA ARG K 27 " ideal model delta harmonic sigma weight residual 180.00 153.08 26.92 0 5.00e+00 4.00e-02 2.90e+01 ... (remaining 17209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2391 0.069 - 0.139: 476 0.139 - 0.208: 31 0.208 - 0.277: 28 0.277 - 0.347: 28 Chirality restraints: 2954 Sorted by residual: chirality pdb=" CA PRO Z 4 " pdb=" N PRO Z 4 " pdb=" C PRO Z 4 " pdb=" CB PRO Z 4 " both_signs ideal model delta sigma weight residual False 2.72 3.07 -0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA PRO Q 4 " pdb=" N PRO Q 4 " pdb=" C PRO Q 4 " pdb=" CB PRO Q 4 " both_signs ideal model delta sigma weight residual False 2.72 3.06 -0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CA PRO b 4 " pdb=" N PRO b 4 " pdb=" C PRO b 4 " pdb=" CB PRO b 4 " both_signs ideal model delta sigma weight residual False 2.72 3.06 -0.35 2.00e-01 2.50e+01 2.98e+00 ... (remaining 2951 not shown) Planarity restraints: 5530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN K 159 " -0.244 2.00e-02 2.50e+03 2.96e-01 1.31e+03 pdb=" CD GLN K 159 " 0.015 2.00e-02 2.50e+03 pdb=" OE1 GLN K 159 " 0.237 2.00e-02 2.50e+03 pdb=" NE2 GLN K 159 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN K 159 " 0.448 2.00e-02 2.50e+03 pdb="HE22 GLN K 159 " -0.457 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY G 99 " 0.045 2.00e-02 2.50e+03 8.98e-02 8.07e+01 pdb=" N ALA G 100 " -0.154 2.00e-02 2.50e+03 pdb=" CA ALA G 100 " 0.036 2.00e-02 2.50e+03 pdb=" H ALA G 100 " 0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 99 " -0.041 2.00e-02 2.50e+03 7.91e-02 6.25e+01 pdb=" N ALA C 100 " 0.136 2.00e-02 2.50e+03 pdb=" CA ALA C 100 " -0.033 2.00e-02 2.50e+03 pdb=" H ALA C 100 " -0.062 2.00e-02 2.50e+03 ... (remaining 5527 not shown) Histogram of nonbonded interaction distances: 1.34 - 1.99: 374 1.99 - 2.65: 49749 2.65 - 3.30: 98167 3.30 - 3.95: 123493 3.95 - 4.60: 199310 Nonbonded interactions: 471093 Sorted by model distance: nonbonded pdb=" O GLU M 107 " pdb=" H GLY M 109 " model vdw 1.343 1.850 nonbonded pdb=" H ALA M 105 " pdb=" HA ALA M 105 " model vdw 1.450 1.816 nonbonded pdb=" O GLY B 99 " pdb=" H LEU B 102 " model vdw 1.453 1.850 nonbonded pdb=" H ARG J 170 " pdb=" HA ARG J 170 " model vdw 1.473 1.816 nonbonded pdb=" H SER J 117 " pdb=" HA SER J 117 " model vdw 1.501 1.816 ... (remaining 471088 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 17 through 106 or (resid 107 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H \ or name HA )) or resid 108 through 189)) selection = (chain 'B' and (resid 17 through 106 or (resid 107 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H \ or name HA )) or resid 108 through 189)) selection = (chain 'C' and (resid 17 through 106 or (resid 107 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H \ or name HA )) or resid 108 through 189)) selection = (chain 'D' and (resid 17 through 83 or (resid 84 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 85 through 106 or (resid \ 107 and (name N or name CA or name C or name O or name CB or name CG or name CD \ or name OE1 or name OE2 or name H or name HA )) or resid 108 through 189)) selection = (chain 'E' and (resid 17 through 106 or (resid 107 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H \ or name HA )) or resid 108 through 189)) selection = (chain 'F' and (resid 17 through 106 or (resid 107 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H \ or name HA )) or resid 108 through 189)) selection = (chain 'G' and (resid 17 through 106 or (resid 107 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H \ or name HA )) or resid 108 through 189)) selection = (chain 'H' and (resid 17 through 106 or (resid 107 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H \ or name HA )) or resid 108 through 189)) selection = (chain 'I' and (resid 17 through 106 or (resid 107 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H \ or name HA )) or resid 108 through 189)) selection = (chain 'J' and (resid 17 through 106 or (resid 107 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H \ or name HA )) or resid 108 through 189)) selection = (chain 'K' and (resid 17 through 106 or (resid 107 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H \ or name HA )) or resid 108 through 189)) selection = (chain 'L' and (resid 17 through 106 or (resid 107 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H \ or name HA )) or resid 108 through 189)) selection = (chain 'M' and (resid 17 through 83 or (resid 84 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 85 through 139 or (resid \ 140 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 141 through 186 or (resid 187 and (name N or name CA or name C or na \ me O or name CB or name H or name HA )) or resid 188 through 189)) selection = (chain 'N' and (resid 17 through 106 or (resid 107 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H \ or name HA )) or resid 108 through 189)) } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.500 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: 0.610 Extract box with map and model: 3.370 Check model and map are aligned: 0.430 Set scattering table: 0.250 Process input model: 105.940 Find NCS groups from input model: 2.070 Set up NCS constraints: 0.340 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:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 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 : 0.015 0.138 18818 Z= 0.935 Angle : 1.252 9.412 25328 Z= 0.689 Chirality : 0.065 0.347 2954 Planarity : 0.005 0.065 3290 Dihedral : 14.273 80.143 7030 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 1.04 % Allowed : 8.61 % Favored : 90.35 % Rotamer: Outliers : 2.03 % Allowed : 0.62 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 1.22 % 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: -5.31 (0.13), residues: 2310 helix: -3.80 (0.10), residues: 1008 sheet: -3.79 (0.24), residues: 238 loop : -3.05 (0.16), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS L 122 PHE 0.008 0.002 PHE H 49 TYR 0.010 0.001 TYR N 20 ARG 0.002 0.000 ARG E 146 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Evaluate side-chains 1102 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 1063 time to evaluate : 2.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASP cc_start: 0.8570 (t0) cc_final: 0.8295 (t70) REVERT: A 78 ASP cc_start: 0.8263 (m-30) cc_final: 0.7613 (m-30) REVERT: A 116 ASN cc_start: 0.8589 (m-40) cc_final: 0.8374 (m110) REVERT: A 123 GLN cc_start: 0.8240 (pt0) cc_final: 0.7688 (pt0) REVERT: A 136 GLU cc_start: 0.6561 (pm20) cc_final: 0.6174 (pm20) REVERT: A 165 GLU cc_start: 0.8690 (mt-10) cc_final: 0.7862 (mt-10) REVERT: A 174 LYS cc_start: 0.8533 (mtmm) cc_final: 0.8178 (mtpp) REVERT: B 41 ASN cc_start: 0.9521 (m-40) cc_final: 0.9288 (m110) REVERT: B 78 ASP cc_start: 0.8229 (m-30) cc_final: 0.7517 (m-30) REVERT: B 116 ASN cc_start: 0.8594 (m-40) cc_final: 0.8268 (m110) REVERT: B 121 ILE cc_start: 0.8998 (pt) cc_final: 0.8764 (pt) REVERT: B 123 GLN cc_start: 0.8030 (pt0) cc_final: 0.7565 (pt0) REVERT: B 137 ILE cc_start: 0.8739 (mm) cc_final: 0.8191 (mm) REVERT: B 165 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8245 (mt-10) REVERT: C 18 ASP cc_start: 0.8441 (t0) cc_final: 0.7902 (t70) REVERT: C 78 ASP cc_start: 0.8194 (m-30) cc_final: 0.7844 (m-30) REVERT: C 98 MET cc_start: 0.9201 (tpp) cc_final: 0.8965 (tpp) REVERT: C 116 ASN cc_start: 0.8575 (m-40) cc_final: 0.8157 (m110) REVERT: C 117 SER cc_start: 0.8900 (m) cc_final: 0.8649 (p) REVERT: C 123 GLN cc_start: 0.8514 (pt0) cc_final: 0.7600 (pt0) REVERT: C 165 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8435 (tm-30) REVERT: C 174 LYS cc_start: 0.8412 (mtmm) cc_final: 0.8107 (mtpp) REVERT: D 18 ASP cc_start: 0.8103 (t0) cc_final: 0.7690 (t70) REVERT: D 56 GLU cc_start: 0.8588 (pm20) cc_final: 0.8148 (pp20) REVERT: D 78 ASP cc_start: 0.8229 (m-30) cc_final: 0.7623 (m-30) REVERT: D 116 ASN cc_start: 0.8433 (m-40) cc_final: 0.8182 (m110) REVERT: D 123 GLN cc_start: 0.8659 (pt0) cc_final: 0.7887 (pt0) REVERT: D 165 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8318 (mt-10) REVERT: D 174 LYS cc_start: 0.8423 (mtmm) cc_final: 0.8042 (mtpp) REVERT: E 18 ASP cc_start: 0.8246 (t0) cc_final: 0.7893 (t70) REVERT: E 56 GLU cc_start: 0.8408 (pm20) cc_final: 0.7907 (pp20) REVERT: E 98 MET cc_start: 0.9172 (tpp) cc_final: 0.8784 (tpp) REVERT: E 123 GLN cc_start: 0.8599 (pt0) cc_final: 0.7629 (pt0) REVERT: E 165 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8378 (mt-10) REVERT: E 174 LYS cc_start: 0.8513 (mtmm) cc_final: 0.8260 (mtpp) REVERT: F 18 ASP cc_start: 0.8528 (t0) cc_final: 0.8128 (t70) REVERT: F 78 ASP cc_start: 0.8363 (m-30) cc_final: 0.7756 (m-30) REVERT: F 123 GLN cc_start: 0.8490 (pt0) cc_final: 0.8196 (pt0) REVERT: F 141 ARG cc_start: 0.9124 (tpt90) cc_final: 0.8885 (tpp80) REVERT: F 165 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8240 (tm-30) REVERT: F 174 LYS cc_start: 0.8300 (mtmm) cc_final: 0.8058 (mtpp) REVERT: G 18 ASP cc_start: 0.8437 (t0) cc_final: 0.8152 (t70) REVERT: G 56 GLU cc_start: 0.8380 (pm20) cc_final: 0.8135 (pp20) REVERT: G 78 ASP cc_start: 0.8273 (m-30) cc_final: 0.7789 (m-30) REVERT: G 123 GLN cc_start: 0.8541 (pt0) cc_final: 0.7683 (pt0) REVERT: G 165 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8086 (tm-30) REVERT: G 174 LYS cc_start: 0.8501 (mtmm) cc_final: 0.8143 (mtpp) REVERT: H 57 LYS cc_start: 0.7692 (mmmm) cc_final: 0.7466 (mmmt) REVERT: H 81 GLN cc_start: 0.8897 (mt0) cc_final: 0.8647 (mt0) REVERT: H 141 ARG cc_start: 0.8363 (tpt90) cc_final: 0.7864 (tpt170) REVERT: H 151 LYS cc_start: 0.8963 (tptp) cc_final: 0.8548 (ttpt) REVERT: H 178 GLU cc_start: 0.8544 (pt0) cc_final: 0.8268 (pt0) REVERT: I 81 GLN cc_start: 0.8933 (mt0) cc_final: 0.8656 (mt0) REVERT: I 129 GLN cc_start: 0.7790 (pm20) cc_final: 0.7579 (pm20) REVERT: I 151 LYS cc_start: 0.8982 (tptp) cc_final: 0.8681 (tppt) REVERT: I 165 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8071 (tt0) REVERT: I 167 ASP cc_start: 0.8305 (m-30) cc_final: 0.7806 (m-30) REVERT: I 178 GLU cc_start: 0.8473 (pt0) cc_final: 0.8163 (pt0) REVERT: J 57 LYS cc_start: 0.7669 (mmmm) cc_final: 0.7469 (mmmt) REVERT: J 141 ARG cc_start: 0.8401 (tpt90) cc_final: 0.7700 (tpt170) REVERT: J 188 ILE cc_start: 0.8924 (tt) cc_final: 0.8718 (mt) REVERT: K 81 GLN cc_start: 0.8901 (mt0) cc_final: 0.8579 (mt0) REVERT: K 129 GLN cc_start: 0.7735 (pm20) cc_final: 0.7459 (pm20) REVERT: K 151 LYS cc_start: 0.8986 (tptp) cc_final: 0.8634 (ttpt) REVERT: K 165 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8300 (tt0) REVERT: L 18 ASP cc_start: 0.9354 (t0) cc_final: 0.9005 (t0) REVERT: L 57 LYS cc_start: 0.7751 (mmmm) cc_final: 0.7550 (mmmt) REVERT: L 81 GLN cc_start: 0.8881 (mt0) cc_final: 0.8587 (mt0) REVERT: L 123 GLN cc_start: 0.8569 (pt0) cc_final: 0.8329 (pt0) REVERT: M 57 LYS cc_start: 0.7758 (mmmm) cc_final: 0.7512 (mmmt) REVERT: M 81 GLN cc_start: 0.8803 (mt0) cc_final: 0.8493 (mt0) REVERT: M 97 SER cc_start: 0.8725 (p) cc_final: 0.8382 (t) REVERT: M 118 GLU cc_start: 0.8308 (pt0) cc_final: 0.7657 (pt0) REVERT: M 165 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8185 (tt0) REVERT: M 178 GLU cc_start: 0.8601 (pt0) cc_final: 0.8305 (pt0) REVERT: N 97 SER cc_start: 0.8717 (p) cc_final: 0.8308 (t) REVERT: N 167 ASP cc_start: 0.8390 (m-30) cc_final: 0.8108 (m-30) outliers start: 39 outliers final: 25 residues processed: 1076 average time/residue: 0.8078 time to fit residues: 1242.6122 Evaluate side-chains 683 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 658 time to evaluate : 4.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain I residue 37 ASP Chi-restraints excluded: chain I residue 98 MET Chi-restraints excluded: chain J residue 37 ASP Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain K residue 37 ASP Chi-restraints excluded: chain K residue 97 SER Chi-restraints excluded: chain K residue 161 LEU Chi-restraints excluded: chain K residue 174 LYS Chi-restraints excluded: chain L residue 37 ASP Chi-restraints excluded: chain L residue 98 MET Chi-restraints excluded: chain M residue 37 ASP Chi-restraints excluded: chain M residue 98 MET Chi-restraints excluded: chain N residue 98 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 6.9990 chunk 169 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 175 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 203 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN B 38 ASN ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN H 41 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18818 Z= 0.196 Angle : 0.751 26.228 25328 Z= 0.382 Chirality : 0.087 1.754 2954 Planarity : 0.004 0.085 3290 Dihedral : 6.845 51.761 2696 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.35 % Favored : 91.26 % Rotamer: Outliers : 3.12 % Allowed : 16.75 % Favored : 80.12 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 1.22 % 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: -4.01 (0.16), residues: 2310 helix: -2.98 (0.14), residues: 966 sheet: -3.36 (0.26), residues: 238 loop : -2.04 (0.19), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 122 PHE 0.016 0.001 PHE T 2 TYR 0.011 0.001 TYR D 77 ARG 0.007 0.000 ARG D 141 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Evaluate side-chains 728 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 668 time to evaluate : 2.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8237 (m-30) cc_final: 0.7379 (m-30) REVERT: A 98 MET cc_start: 0.9375 (tpp) cc_final: 0.9037 (tpp) REVERT: A 157 THR cc_start: 0.9332 (p) cc_final: 0.9031 (t) REVERT: A 165 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8277 (mt-10) REVERT: B 78 ASP cc_start: 0.8221 (m-30) cc_final: 0.7269 (m-30) REVERT: B 116 ASN cc_start: 0.8502 (m-40) cc_final: 0.8165 (m110) REVERT: B 118 GLU cc_start: 0.7535 (pt0) cc_final: 0.7241 (pt0) REVERT: B 150 ASN cc_start: 0.8403 (p0) cc_final: 0.8042 (m-40) REVERT: B 152 VAL cc_start: 0.8818 (t) cc_final: 0.8568 (p) REVERT: B 165 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8141 (tm-30) REVERT: C 78 ASP cc_start: 0.8112 (m-30) cc_final: 0.7465 (m-30) REVERT: C 98 MET cc_start: 0.9258 (tpp) cc_final: 0.9015 (tpp) REVERT: C 116 ASN cc_start: 0.8406 (m-40) cc_final: 0.8096 (m110) REVERT: C 123 GLN cc_start: 0.7711 (pt0) cc_final: 0.7461 (pt0) REVERT: C 164 ILE cc_start: 0.8293 (mt) cc_final: 0.8072 (mt) REVERT: C 165 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8455 (tm-30) REVERT: D 56 GLU cc_start: 0.8531 (pm20) cc_final: 0.8130 (pp20) REVERT: D 116 ASN cc_start: 0.8283 (m-40) cc_final: 0.7888 (m110) REVERT: D 123 GLN cc_start: 0.8341 (pt0) cc_final: 0.7823 (pt0) REVERT: D 165 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8267 (mt-10) REVERT: D 169 ASP cc_start: 0.8002 (t0) cc_final: 0.7589 (t0) REVERT: E 56 GLU cc_start: 0.8424 (pm20) cc_final: 0.7975 (pp20) REVERT: E 98 MET cc_start: 0.9167 (tpp) cc_final: 0.8899 (tpp) REVERT: E 123 GLN cc_start: 0.8030 (pt0) cc_final: 0.7518 (pt0) REVERT: E 165 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8301 (mt-10) REVERT: F 123 GLN cc_start: 0.8448 (pt0) cc_final: 0.8173 (pt0) REVERT: F 165 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8367 (tm-30) REVERT: G 78 ASP cc_start: 0.8412 (m-30) cc_final: 0.7693 (m-30) REVERT: G 152 VAL cc_start: 0.9127 (t) cc_final: 0.8870 (p) REVERT: G 165 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8236 (tm-30) REVERT: G 170 ARG cc_start: 0.7773 (ptm-80) cc_final: 0.7453 (ptm160) REVERT: H 57 LYS cc_start: 0.7822 (mmmm) cc_final: 0.7569 (mmmt) REVERT: H 81 GLN cc_start: 0.8823 (mt0) cc_final: 0.8408 (mt0) REVERT: H 159 GLN cc_start: 0.8542 (mm-40) cc_final: 0.8015 (mp10) REVERT: H 167 ASP cc_start: 0.8190 (m-30) cc_final: 0.7881 (m-30) REVERT: I 81 GLN cc_start: 0.8857 (mt0) cc_final: 0.8473 (mt0) REVERT: I 129 GLN cc_start: 0.7890 (pm20) cc_final: 0.7632 (pm20) REVERT: I 165 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8242 (tt0) REVERT: J 57 LYS cc_start: 0.7896 (mmmm) cc_final: 0.7652 (mmmt) REVERT: J 159 GLN cc_start: 0.8531 (mm-40) cc_final: 0.7627 (mp10) REVERT: K 81 GLN cc_start: 0.8824 (mt0) cc_final: 0.8448 (mt0) REVERT: K 118 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7782 (mt-10) REVERT: K 123 GLN cc_start: 0.8487 (pt0) cc_final: 0.8277 (pt0) REVERT: L 18 ASP cc_start: 0.9250 (t0) cc_final: 0.8944 (t0) REVERT: L 57 LYS cc_start: 0.7864 (mmmm) cc_final: 0.7653 (mmmt) REVERT: L 81 GLN cc_start: 0.8822 (mt0) cc_final: 0.8421 (mt0) REVERT: M 81 GLN cc_start: 0.8799 (mt0) cc_final: 0.8350 (mt0) REVERT: M 97 SER cc_start: 0.8751 (p) cc_final: 0.8230 (m) REVERT: M 118 GLU cc_start: 0.8387 (pt0) cc_final: 0.7600 (pt0) REVERT: M 150 ASN cc_start: 0.9197 (m-40) cc_final: 0.8945 (m-40) REVERT: M 165 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8007 (tm-30) REVERT: M 167 ASP cc_start: 0.8393 (m-30) cc_final: 0.8143 (m-30) REVERT: N 148 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8276 (tmtt) outliers start: 60 outliers final: 44 residues processed: 696 average time/residue: 0.6133 time to fit residues: 660.3095 Evaluate side-chains 637 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 591 time to evaluate : 3.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain K residue 97 SER Chi-restraints excluded: chain K residue 118 GLU Chi-restraints excluded: chain L residue 148 LYS Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 98 MET Chi-restraints excluded: chain N residue 98 MET Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 148 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 169 optimal weight: 9.9990 chunk 138 optimal weight: 8.9990 chunk 56 optimal weight: 8.9990 chunk 203 optimal weight: 9.9990 chunk 220 optimal weight: 7.9990 chunk 181 optimal weight: 9.9990 chunk 202 optimal weight: 8.9990 chunk 69 optimal weight: 0.9980 chunk 163 optimal weight: 2.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN B 38 ASN ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN J 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.5939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 18818 Z= 0.307 Angle : 0.779 32.869 25328 Z= 0.394 Chirality : 0.090 1.713 2954 Planarity : 0.004 0.040 3290 Dihedral : 6.306 53.302 2667 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.74 % Favored : 90.00 % Rotamer: Outliers : 3.49 % Allowed : 19.93 % Favored : 76.59 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 1.22 % 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: -3.94 (0.15), residues: 2310 helix: -2.63 (0.13), residues: 1078 sheet: -2.74 (0.27), residues: 238 loop : -2.37 (0.18), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS L 122 PHE 0.014 0.002 PHE I 101 TYR 0.019 0.001 TYR E 182 ARG 0.005 0.001 ARG D 141 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Evaluate side-chains 631 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 564 time to evaluate : 3.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8167 (m-30) cc_final: 0.7629 (m-30) REVERT: A 98 MET cc_start: 0.9409 (tpp) cc_final: 0.9036 (tpp) REVERT: A 165 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8337 (mt-10) REVERT: B 78 ASP cc_start: 0.8221 (m-30) cc_final: 0.7788 (m-30) REVERT: B 116 ASN cc_start: 0.8415 (m-40) cc_final: 0.8097 (m-40) REVERT: B 118 GLU cc_start: 0.7898 (pt0) cc_final: 0.7237 (pt0) REVERT: B 165 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8400 (tm-30) REVERT: C 78 ASP cc_start: 0.8076 (m-30) cc_final: 0.7444 (m-30) REVERT: C 98 MET cc_start: 0.9417 (tpp) cc_final: 0.9194 (tpp) REVERT: C 116 ASN cc_start: 0.8323 (m-40) cc_final: 0.8122 (m110) REVERT: C 165 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8591 (tm-30) REVERT: D 56 GLU cc_start: 0.8569 (pm20) cc_final: 0.8187 (pp20) REVERT: D 116 ASN cc_start: 0.8297 (m-40) cc_final: 0.7960 (m-40) REVERT: D 123 GLN cc_start: 0.8233 (pt0) cc_final: 0.7688 (pt0) REVERT: D 165 GLU cc_start: 0.8475 (mt-10) cc_final: 0.7996 (mt-10) REVERT: D 169 ASP cc_start: 0.8255 (t0) cc_final: 0.7846 (t0) REVERT: E 56 GLU cc_start: 0.8385 (pm20) cc_final: 0.8002 (pp20) REVERT: E 123 GLN cc_start: 0.8074 (pt0) cc_final: 0.7650 (pt0) REVERT: F 116 ASN cc_start: 0.8330 (m-40) cc_final: 0.7867 (m110) REVERT: F 123 GLN cc_start: 0.8363 (pt0) cc_final: 0.8102 (pt0) REVERT: F 152 VAL cc_start: 0.9161 (t) cc_final: 0.8961 (p) REVERT: F 165 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8506 (tm-30) REVERT: G 165 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8534 (tm-30) REVERT: G 170 ARG cc_start: 0.7855 (ptm-80) cc_final: 0.7316 (ptm160) REVERT: H 81 GLN cc_start: 0.8760 (mt0) cc_final: 0.8447 (mt0) REVERT: H 107 GLU cc_start: 0.7384 (tp30) cc_final: 0.7175 (mm-30) REVERT: H 167 ASP cc_start: 0.8078 (m-30) cc_final: 0.7774 (m-30) REVERT: I 81 GLN cc_start: 0.8826 (mt0) cc_final: 0.8502 (mt0) REVERT: I 165 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8162 (tm-30) REVERT: I 167 ASP cc_start: 0.8126 (m-30) cc_final: 0.7835 (m-30) REVERT: J 136 GLU cc_start: 0.4946 (pt0) cc_final: 0.4501 (pt0) REVERT: J 159 GLN cc_start: 0.8568 (mm-40) cc_final: 0.7642 (mp10) REVERT: K 81 GLN cc_start: 0.8774 (mt0) cc_final: 0.8465 (mt0) REVERT: K 123 GLN cc_start: 0.8497 (pt0) cc_final: 0.8266 (pt0) REVERT: L 18 ASP cc_start: 0.9127 (t0) cc_final: 0.8868 (t0) REVERT: L 81 GLN cc_start: 0.8787 (mt0) cc_final: 0.8380 (mt0) REVERT: L 165 GLU cc_start: 0.8512 (pt0) cc_final: 0.8237 (pt0) REVERT: M 120 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.8169 (ptm) REVERT: M 165 GLU cc_start: 0.8311 (mt-10) cc_final: 0.8038 (tm-30) REVERT: N 148 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8483 (tmtt) REVERT: N 181 GLU cc_start: 0.8080 (mp0) cc_final: 0.7732 (mp0) outliers start: 67 outliers final: 50 residues processed: 606 average time/residue: 0.6199 time to fit residues: 589.7785 Evaluate side-chains 562 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 510 time to evaluate : 3.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 178 GLU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 129 GLN Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain J residue 26 ASP Chi-restraints excluded: chain J residue 37 ASP Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain K residue 23 LEU Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 97 SER Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 120 MET Chi-restraints excluded: chain N residue 26 ASP Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 148 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 chunk 97 optimal weight: 8.9990 chunk 136 optimal weight: 10.0000 chunk 204 optimal weight: 7.9990 chunk 216 optimal weight: 10.0000 chunk 106 optimal weight: 6.9990 chunk 193 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.6424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18818 Z= 0.250 Angle : 0.738 33.918 25328 Z= 0.368 Chirality : 0.089 1.726 2954 Planarity : 0.003 0.028 3290 Dihedral : 5.677 55.497 2648 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.52 % Favored : 90.22 % Rotamer: Outliers : 3.02 % Allowed : 21.80 % Favored : 75.18 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 1.22 % 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: -3.21 (0.16), residues: 2310 helix: -1.98 (0.14), residues: 1078 sheet: -2.43 (0.28), residues: 238 loop : -2.05 (0.20), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 122 PHE 0.009 0.001 PHE J 101 TYR 0.007 0.001 TYR I 17 ARG 0.004 0.000 ARG D 141 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Evaluate side-chains 580 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 522 time to evaluate : 3.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8192 (m-30) cc_final: 0.7645 (m-30) REVERT: A 98 MET cc_start: 0.9382 (tpp) cc_final: 0.8979 (tpp) REVERT: A 170 ARG cc_start: 0.7636 (ptm-80) cc_final: 0.7366 (ptm-80) REVERT: B 78 ASP cc_start: 0.8294 (m-30) cc_final: 0.7874 (m-30) REVERT: B 116 ASN cc_start: 0.8464 (m-40) cc_final: 0.8106 (m-40) REVERT: B 118 GLU cc_start: 0.8005 (pt0) cc_final: 0.7365 (pt0) REVERT: B 162 GLU cc_start: 0.8386 (tp30) cc_final: 0.8178 (tp30) REVERT: B 165 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8442 (tm-30) REVERT: C 78 ASP cc_start: 0.8050 (m-30) cc_final: 0.7451 (m-30) REVERT: C 98 MET cc_start: 0.9395 (tpp) cc_final: 0.9137 (tpp) REVERT: C 116 ASN cc_start: 0.8360 (m-40) cc_final: 0.8013 (m110) REVERT: C 165 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8598 (tm-30) REVERT: D 56 GLU cc_start: 0.8552 (pm20) cc_final: 0.8210 (pp20) REVERT: D 116 ASN cc_start: 0.8307 (m-40) cc_final: 0.8104 (m-40) REVERT: D 123 GLN cc_start: 0.8255 (pt0) cc_final: 0.7794 (pt0) REVERT: D 165 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8013 (mt-10) REVERT: D 169 ASP cc_start: 0.8338 (t0) cc_final: 0.7840 (t0) REVERT: E 56 GLU cc_start: 0.8419 (pm20) cc_final: 0.8007 (pp20) REVERT: E 123 GLN cc_start: 0.8044 (pt0) cc_final: 0.7486 (pt0) REVERT: F 116 ASN cc_start: 0.8378 (m-40) cc_final: 0.7903 (m110) REVERT: F 123 GLN cc_start: 0.8380 (pt0) cc_final: 0.8102 (pt0) REVERT: F 165 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8640 (tm-30) REVERT: G 165 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8537 (tm-30) REVERT: G 169 ASP cc_start: 0.7967 (t70) cc_final: 0.7528 (t0) REVERT: G 170 ARG cc_start: 0.7655 (ptm-80) cc_final: 0.7278 (ptm160) REVERT: H 81 GLN cc_start: 0.8770 (mt0) cc_final: 0.8408 (mt0) REVERT: I 81 GLN cc_start: 0.8826 (mt0) cc_final: 0.8475 (mt0) REVERT: J 136 GLU cc_start: 0.4456 (pt0) cc_final: 0.4015 (pt0) REVERT: K 81 GLN cc_start: 0.8787 (mt0) cc_final: 0.8430 (mt0) REVERT: L 18 ASP cc_start: 0.9085 (t0) cc_final: 0.8832 (t0) REVERT: L 54 ASP cc_start: 0.8531 (m-30) cc_final: 0.8318 (m-30) REVERT: L 81 GLN cc_start: 0.8785 (mt0) cc_final: 0.8332 (mt0) REVERT: M 120 MET cc_start: 0.8475 (ptt) cc_final: 0.8234 (ptm) REVERT: M 165 GLU cc_start: 0.8285 (mt-10) cc_final: 0.8046 (tm-30) REVERT: N 120 MET cc_start: 0.8698 (ptm) cc_final: 0.8433 (ppp) REVERT: N 181 GLU cc_start: 0.8139 (mp0) cc_final: 0.7794 (mp0) outliers start: 58 outliers final: 51 residues processed: 564 average time/residue: 0.6153 time to fit residues: 546.4525 Evaluate side-chains 542 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 491 time to evaluate : 2.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 178 GLU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain J residue 26 ASP Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain K residue 23 LEU Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain K residue 97 SER Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 107 GLU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 119 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 161 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 184 optimal weight: 8.9990 chunk 149 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.7125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 18818 Z= 0.367 Angle : 0.785 25.745 25328 Z= 0.404 Chirality : 0.091 1.775 2954 Planarity : 0.004 0.032 3290 Dihedral : 6.196 54.871 2648 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.22 % Allowed : 11.13 % Favored : 88.66 % Rotamer: Outliers : 4.16 % Allowed : 22.63 % Favored : 73.20 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 1.22 % 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: -3.18 (0.16), residues: 2310 helix: -1.91 (0.14), residues: 1092 sheet: -2.40 (0.26), residues: 238 loop : -2.11 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 122 PHE 0.015 0.002 PHE I 101 TYR 0.013 0.001 TYR D 77 ARG 0.005 0.001 ARG D 141 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Evaluate side-chains 540 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 460 time to evaluate : 2.914 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: A 78 ASP cc_start: 0.8202 (m-30) cc_final: 0.7713 (m-30) REVERT: A 118 GLU cc_start: 0.8425 (pt0) cc_final: 0.8195 (pt0) REVERT: A 165 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8306 (mt-10) REVERT: A 169 ASP cc_start: 0.7773 (t70) cc_final: 0.7167 (t0) REVERT: B 78 ASP cc_start: 0.8252 (m-30) cc_final: 0.7639 (m-30) REVERT: B 116 ASN cc_start: 0.8383 (m-40) cc_final: 0.7991 (m-40) REVERT: B 118 GLU cc_start: 0.8290 (pt0) cc_final: 0.7511 (pt0) REVERT: B 165 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8500 (tm-30) REVERT: B 168 THR cc_start: 0.9199 (m) cc_final: 0.8783 (p) REVERT: B 177 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8677 (tp30) REVERT: C 78 ASP cc_start: 0.8089 (m-30) cc_final: 0.7469 (m-30) REVERT: C 98 MET cc_start: 0.9390 (tpp) cc_final: 0.9087 (tpp) REVERT: C 116 ASN cc_start: 0.8295 (m-40) cc_final: 0.7949 (m110) REVERT: C 169 ASP cc_start: 0.8129 (t0) cc_final: 0.7887 (t0) REVERT: C 170 ARG cc_start: 0.7757 (ptm-80) cc_final: 0.7382 (ptm160) REVERT: D 56 GLU cc_start: 0.8543 (pm20) cc_final: 0.8276 (pp20) REVERT: D 116 ASN cc_start: 0.8270 (m-40) cc_final: 0.8066 (m-40) REVERT: D 167 ASP cc_start: 0.9163 (m-30) cc_final: 0.8938 (m-30) REVERT: D 169 ASP cc_start: 0.8507 (t0) cc_final: 0.8114 (t0) REVERT: E 56 GLU cc_start: 0.8418 (pm20) cc_final: 0.8128 (pp20) REVERT: E 123 GLN cc_start: 0.8030 (pt0) cc_final: 0.7548 (pt0) REVERT: E 169 ASP cc_start: 0.8304 (t0) cc_final: 0.7802 (t0) REVERT: F 116 ASN cc_start: 0.8316 (m-40) cc_final: 0.7920 (m110) REVERT: F 147 ASP cc_start: 0.9191 (t70) cc_final: 0.8982 (t0) REVERT: F 169 ASP cc_start: 0.7681 (t0) cc_final: 0.7458 (t0) REVERT: G 118 GLU cc_start: 0.8419 (pt0) cc_final: 0.7906 (pt0) REVERT: G 165 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8573 (tm-30) REVERT: G 169 ASP cc_start: 0.8116 (t70) cc_final: 0.7535 (t0) REVERT: I 81 GLN cc_start: 0.8825 (mt0) cc_final: 0.8367 (mt0) REVERT: J 136 GLU cc_start: 0.4663 (pt0) cc_final: 0.4223 (pt0) REVERT: J 167 ASP cc_start: 0.8049 (m-30) cc_final: 0.7747 (m-30) REVERT: L 18 ASP cc_start: 0.9097 (t0) cc_final: 0.8896 (t0) REVERT: M 54 ASP cc_start: 0.8713 (m-30) cc_final: 0.8491 (m-30) REVERT: M 120 MET cc_start: 0.8326 (ptt) cc_final: 0.8070 (ptm) REVERT: N 120 MET cc_start: 0.8701 (ptm) cc_final: 0.8381 (ppp) REVERT: N 162 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8449 (tp30) REVERT: N 165 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8144 (tt0) outliers start: 80 outliers final: 59 residues processed: 519 average time/residue: 0.5998 time to fit residues: 488.4071 Evaluate side-chains 490 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 430 time to evaluate : 2.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 116 ASN Chi-restraints excluded: chain E residue 129 GLN Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain J residue 37 ASP Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain K residue 97 SER Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 107 GLU Chi-restraints excluded: chain N residue 70 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 8.9990 chunk 194 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 127 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 216 optimal weight: 8.9990 chunk 179 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 113 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 122 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.7385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18818 Z= 0.217 Angle : 0.694 25.482 25328 Z= 0.356 Chirality : 0.090 1.733 2954 Planarity : 0.003 0.029 3290 Dihedral : 5.555 56.384 2648 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.31 % Favored : 90.52 % Rotamer: Outliers : 2.81 % Allowed : 24.40 % Favored : 72.79 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 1.22 % 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: -2.68 (0.17), residues: 2310 helix: -1.56 (0.15), residues: 1078 sheet: -2.04 (0.28), residues: 238 loop : -1.80 (0.20), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 122 PHE 0.012 0.001 PHE I 101 TYR 0.009 0.001 TYR C 77 ARG 0.003 0.000 ARG D 141 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Evaluate side-chains 520 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 466 time to evaluate : 3.296 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: A 78 ASP cc_start: 0.8237 (m-30) cc_final: 0.7608 (m-30) REVERT: A 118 GLU cc_start: 0.8424 (pt0) cc_final: 0.8208 (pt0) REVERT: A 165 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8186 (mt-10) REVERT: A 169 ASP cc_start: 0.7798 (t70) cc_final: 0.7487 (t70) REVERT: B 78 ASP cc_start: 0.8262 (m-30) cc_final: 0.7658 (m-30) REVERT: B 116 ASN cc_start: 0.8376 (m-40) cc_final: 0.7983 (m110) REVERT: B 118 GLU cc_start: 0.8386 (pt0) cc_final: 0.7637 (pt0) REVERT: B 147 ASP cc_start: 0.8676 (t70) cc_final: 0.8397 (t0) REVERT: B 165 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8469 (tm-30) REVERT: C 78 ASP cc_start: 0.8055 (m-30) cc_final: 0.7354 (m-30) REVERT: C 116 ASN cc_start: 0.8297 (m-40) cc_final: 0.7917 (m110) REVERT: C 169 ASP cc_start: 0.8188 (t0) cc_final: 0.7804 (t0) REVERT: C 170 ARG cc_start: 0.7781 (ptm-80) cc_final: 0.7335 (ptm160) REVERT: D 56 GLU cc_start: 0.8579 (pm20) cc_final: 0.8296 (pp20) REVERT: D 116 ASN cc_start: 0.8233 (m-40) cc_final: 0.7928 (m-40) REVERT: D 123 GLN cc_start: 0.8119 (pt0) cc_final: 0.7885 (pt0) REVERT: D 169 ASP cc_start: 0.8486 (t0) cc_final: 0.8085 (t0) REVERT: E 56 GLU cc_start: 0.8410 (pm20) cc_final: 0.8142 (pp20) REVERT: E 169 ASP cc_start: 0.8330 (t0) cc_final: 0.7759 (t0) REVERT: E 177 GLU cc_start: 0.8811 (tt0) cc_final: 0.8590 (mm-30) REVERT: F 116 ASN cc_start: 0.8303 (m-40) cc_final: 0.7906 (m-40) REVERT: F 118 GLU cc_start: 0.8443 (pt0) cc_final: 0.8206 (pt0) REVERT: F 147 ASP cc_start: 0.9120 (t70) cc_final: 0.8871 (t0) REVERT: F 169 ASP cc_start: 0.7785 (t0) cc_final: 0.7481 (t0) REVERT: G 118 GLU cc_start: 0.8550 (pt0) cc_final: 0.7878 (pt0) REVERT: G 165 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8594 (tm-30) REVERT: G 169 ASP cc_start: 0.8108 (t70) cc_final: 0.7513 (t0) REVERT: I 81 GLN cc_start: 0.8797 (mt0) cc_final: 0.8290 (mt0) REVERT: J 167 ASP cc_start: 0.7875 (m-30) cc_final: 0.7648 (m-30) REVERT: L 118 GLU cc_start: 0.8674 (pt0) cc_final: 0.8347 (pt0) REVERT: M 120 MET cc_start: 0.8349 (ptt) cc_final: 0.7952 (ptm) REVERT: N 120 MET cc_start: 0.8646 (ptm) cc_final: 0.8395 (ppp) outliers start: 54 outliers final: 50 residues processed: 507 average time/residue: 0.6337 time to fit residues: 506.4035 Evaluate side-chains 492 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 442 time to evaluate : 3.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain J residue 182 TYR Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain K residue 97 SER Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 107 GLU Chi-restraints excluded: chain N residue 70 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 158 optimal weight: 8.9990 chunk 122 optimal weight: 0.5980 chunk 182 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 215 optimal weight: 8.9990 chunk 135 optimal weight: 3.9990 chunk 131 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 overall best weight: 5.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN M 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.7628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 18818 Z= 0.268 Angle : 0.709 25.744 25328 Z= 0.364 Chirality : 0.090 1.743 2954 Planarity : 0.004 0.031 3290 Dihedral : 5.580 58.802 2648 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.82 % Favored : 89.00 % Rotamer: Outliers : 3.43 % Allowed : 24.30 % Favored : 72.27 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 1.22 % 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: -2.62 (0.17), residues: 2310 helix: -1.43 (0.15), residues: 1064 sheet: -1.89 (0.28), residues: 238 loop : -1.90 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 122 PHE 0.014 0.001 PHE H 101 TYR 0.013 0.001 TYR C 77 ARG 0.004 0.000 ARG F 141 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Evaluate side-chains 510 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 444 time to evaluate : 2.694 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: A 78 ASP cc_start: 0.8268 (m-30) cc_final: 0.7709 (m-30) REVERT: A 163 VAL cc_start: 0.8514 (OUTLIER) cc_final: 0.8303 (p) REVERT: A 165 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8191 (mt-10) REVERT: A 168 THR cc_start: 0.8850 (m) cc_final: 0.8587 (m) REVERT: A 169 ASP cc_start: 0.7959 (t70) cc_final: 0.7332 (t0) REVERT: B 78 ASP cc_start: 0.8254 (m-30) cc_final: 0.7689 (m-30) REVERT: B 116 ASN cc_start: 0.8345 (m-40) cc_final: 0.7952 (m110) REVERT: B 118 GLU cc_start: 0.8492 (pt0) cc_final: 0.7857 (pt0) REVERT: B 147 ASP cc_start: 0.8659 (t70) cc_final: 0.8377 (t0) REVERT: B 165 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8431 (tm-30) REVERT: C 78 ASP cc_start: 0.8060 (m-30) cc_final: 0.7426 (m-30) REVERT: C 116 ASN cc_start: 0.8272 (m-40) cc_final: 0.7883 (m110) REVERT: C 118 GLU cc_start: 0.8486 (pt0) cc_final: 0.7826 (pt0) REVERT: C 169 ASP cc_start: 0.8427 (t0) cc_final: 0.7921 (t0) REVERT: C 170 ARG cc_start: 0.7830 (ptm-80) cc_final: 0.7448 (ptm160) REVERT: D 56 GLU cc_start: 0.8511 (pm20) cc_final: 0.8291 (pp20) REVERT: D 116 ASN cc_start: 0.8211 (m-40) cc_final: 0.7903 (m-40) REVERT: D 118 GLU cc_start: 0.8484 (pt0) cc_final: 0.8032 (pt0) REVERT: D 123 GLN cc_start: 0.8102 (pt0) cc_final: 0.7866 (pt0) REVERT: D 169 ASP cc_start: 0.8614 (t0) cc_final: 0.8216 (t0) REVERT: E 56 GLU cc_start: 0.8427 (pm20) cc_final: 0.8163 (pp20) REVERT: E 123 GLN cc_start: 0.7849 (pt0) cc_final: 0.7472 (pt0) REVERT: E 163 VAL cc_start: 0.8315 (OUTLIER) cc_final: 0.8090 (p) REVERT: E 169 ASP cc_start: 0.8456 (t0) cc_final: 0.7657 (t0) REVERT: F 116 ASN cc_start: 0.8270 (m-40) cc_final: 0.7800 (m-40) REVERT: F 147 ASP cc_start: 0.9134 (t70) cc_final: 0.8867 (t0) REVERT: F 165 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8416 (tm-30) REVERT: F 169 ASP cc_start: 0.7819 (t0) cc_final: 0.7525 (t0) REVERT: G 118 GLU cc_start: 0.8677 (pt0) cc_final: 0.8299 (pt0) REVERT: G 169 ASP cc_start: 0.8321 (t70) cc_final: 0.7688 (t0) REVERT: J 167 ASP cc_start: 0.7927 (m-30) cc_final: 0.7692 (m-30) REVERT: K 143 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8949 (mp) REVERT: L 155 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7665 (mp0) REVERT: M 54 ASP cc_start: 0.8694 (m-30) cc_final: 0.8482 (m-30) REVERT: M 120 MET cc_start: 0.8294 (ptt) cc_final: 0.7878 (ptm) outliers start: 66 outliers final: 57 residues processed: 493 average time/residue: 0.5980 time to fit residues: 465.6435 Evaluate side-chains 493 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 433 time to evaluate : 3.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 170 ARG Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain J residue 60 SER Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 182 TYR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain K residue 97 SER Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 70 ILE Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 107 GLU Chi-restraints excluded: chain N residue 70 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 0.4980 chunk 86 optimal weight: 5.9990 chunk 128 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 147 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 169 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.7716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18818 Z= 0.155 Angle : 0.663 25.625 25328 Z= 0.334 Chirality : 0.089 1.717 2954 Planarity : 0.003 0.028 3290 Dihedral : 4.962 57.876 2647 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.06 % Favored : 92.77 % Rotamer: Outliers : 1.30 % Allowed : 26.53 % Favored : 72.16 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 1.22 % 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: -1.75 (0.17), residues: 2310 helix: -0.65 (0.17), residues: 1036 sheet: -1.44 (0.29), residues: 238 loop : -1.52 (0.20), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS A 122 PHE 0.013 0.001 PHE H 101 TYR 0.006 0.001 TYR G 77 ARG 0.006 0.000 ARG F 141 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Evaluate side-chains 513 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 488 time to evaluate : 3.231 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: A 78 ASP cc_start: 0.8212 (m-30) cc_final: 0.7567 (m-30) REVERT: A 163 VAL cc_start: 0.8514 (OUTLIER) cc_final: 0.8261 (p) REVERT: A 164 ILE cc_start: 0.8766 (mm) cc_final: 0.8467 (mt) REVERT: A 165 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8176 (mt-10) REVERT: A 169 ASP cc_start: 0.8121 (t70) cc_final: 0.7498 (t0) REVERT: B 78 ASP cc_start: 0.8309 (m-30) cc_final: 0.7797 (m-30) REVERT: B 116 ASN cc_start: 0.8375 (m-40) cc_final: 0.7930 (m110) REVERT: B 118 GLU cc_start: 0.8425 (pt0) cc_final: 0.7700 (pt0) REVERT: B 141 ARG cc_start: 0.9060 (tpt90) cc_final: 0.8840 (tpp80) REVERT: B 147 ASP cc_start: 0.8504 (t70) cc_final: 0.8248 (t0) REVERT: B 165 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8387 (tm-30) REVERT: B 169 ASP cc_start: 0.7707 (t70) cc_final: 0.7408 (t0) REVERT: C 78 ASP cc_start: 0.8047 (m-30) cc_final: 0.7423 (m-30) REVERT: C 116 ASN cc_start: 0.8269 (m-40) cc_final: 0.8014 (m-40) REVERT: C 169 ASP cc_start: 0.8424 (t0) cc_final: 0.7869 (t0) REVERT: C 170 ARG cc_start: 0.7743 (ptm-80) cc_final: 0.7446 (ptm160) REVERT: D 56 GLU cc_start: 0.8559 (pm20) cc_final: 0.8305 (pp20) REVERT: D 116 ASN cc_start: 0.8215 (m-40) cc_final: 0.7874 (m-40) REVERT: D 118 GLU cc_start: 0.8317 (pt0) cc_final: 0.7961 (pt0) REVERT: D 141 ARG cc_start: 0.8817 (tpp80) cc_final: 0.8612 (tpp80) REVERT: D 169 ASP cc_start: 0.8607 (t0) cc_final: 0.8161 (t0) REVERT: E 56 GLU cc_start: 0.8423 (pm20) cc_final: 0.8139 (pp20) REVERT: E 123 GLN cc_start: 0.7758 (pt0) cc_final: 0.7443 (pt0) REVERT: E 147 ASP cc_start: 0.9087 (t0) cc_final: 0.8881 (t0) REVERT: E 169 ASP cc_start: 0.8478 (t0) cc_final: 0.7688 (t0) REVERT: E 178 GLU cc_start: 0.8346 (mp0) cc_final: 0.8001 (mp0) REVERT: F 81 GLN cc_start: 0.8340 (tm-30) cc_final: 0.8121 (tm-30) REVERT: F 116 ASN cc_start: 0.8308 (m-40) cc_final: 0.7802 (m-40) REVERT: F 147 ASP cc_start: 0.9105 (t70) cc_final: 0.8861 (t0) REVERT: F 165 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8415 (tm-30) REVERT: F 169 ASP cc_start: 0.7778 (t0) cc_final: 0.7502 (t0) REVERT: G 118 GLU cc_start: 0.8561 (pt0) cc_final: 0.7896 (pt0) REVERT: G 169 ASP cc_start: 0.8324 (t70) cc_final: 0.7611 (t0) REVERT: I 81 GLN cc_start: 0.8813 (mt0) cc_final: 0.8293 (mt0) REVERT: J 167 ASP cc_start: 0.7880 (m-30) cc_final: 0.7639 (m-30) REVERT: K 26 ASP cc_start: 0.7689 (OUTLIER) cc_final: 0.7267 (p0) REVERT: K 167 ASP cc_start: 0.8004 (m-30) cc_final: 0.7713 (m-30) outliers start: 25 outliers final: 20 residues processed: 505 average time/residue: 0.6039 time to fit residues: 476.3464 Evaluate side-chains 490 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 468 time to evaluate : 2.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 182 TYR Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain K residue 97 SER Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 70 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 4.9990 chunk 206 optimal weight: 9.9990 chunk 188 optimal weight: 8.9990 chunk 201 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 157 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 181 optimal weight: 10.0000 chunk 190 optimal weight: 10.0000 chunk 200 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.7915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 18818 Z= 0.331 Angle : 0.737 26.081 25328 Z= 0.379 Chirality : 0.092 1.762 2954 Planarity : 0.004 0.033 3290 Dihedral : 5.613 57.586 2647 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.91 % Favored : 88.92 % Rotamer: Outliers : 2.08 % Allowed : 25.55 % Favored : 72.37 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 1.22 % 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: -2.50 (0.16), residues: 2310 helix: -1.36 (0.15), residues: 1106 sheet: -1.57 (0.28), residues: 238 loop : -1.89 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 122 PHE 0.017 0.001 PHE I 101 TYR 0.013 0.001 TYR M 77 ARG 0.008 0.001 ARG E 141 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Evaluate side-chains 481 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 441 time to evaluate : 2.682 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: A 78 ASP cc_start: 0.8260 (m-30) cc_final: 0.7770 (m-30) REVERT: A 163 VAL cc_start: 0.8628 (OUTLIER) cc_final: 0.8425 (p) REVERT: A 165 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8178 (mt-10) REVERT: A 169 ASP cc_start: 0.8303 (t70) cc_final: 0.7696 (t0) REVERT: A 178 GLU cc_start: 0.9177 (pt0) cc_final: 0.8899 (mp0) REVERT: B 78 ASP cc_start: 0.8293 (m-30) cc_final: 0.7825 (m-30) REVERT: B 116 ASN cc_start: 0.8366 (m-40) cc_final: 0.7967 (m-40) REVERT: B 118 GLU cc_start: 0.8664 (pt0) cc_final: 0.8435 (pt0) REVERT: B 147 ASP cc_start: 0.8660 (t70) cc_final: 0.8380 (t0) REVERT: B 169 ASP cc_start: 0.7897 (t70) cc_final: 0.7660 (t0) REVERT: C 78 ASP cc_start: 0.8058 (m-30) cc_final: 0.7438 (m-30) REVERT: C 116 ASN cc_start: 0.8352 (m-40) cc_final: 0.7908 (m-40) REVERT: C 118 GLU cc_start: 0.8644 (pt0) cc_final: 0.7948 (pt0) REVERT: C 163 VAL cc_start: 0.8497 (m) cc_final: 0.8276 (p) REVERT: C 165 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8351 (tm-30) REVERT: C 169 ASP cc_start: 0.8560 (t0) cc_final: 0.7967 (t0) REVERT: D 56 GLU cc_start: 0.8490 (pm20) cc_final: 0.8265 (pp20) REVERT: D 116 ASN cc_start: 0.8166 (m-40) cc_final: 0.7846 (m-40) REVERT: D 118 GLU cc_start: 0.8433 (pt0) cc_final: 0.8027 (pt0) REVERT: D 169 ASP cc_start: 0.8634 (t0) cc_final: 0.8109 (t0) REVERT: E 56 GLU cc_start: 0.8473 (pm20) cc_final: 0.8211 (pp20) REVERT: E 123 GLN cc_start: 0.7764 (pt0) cc_final: 0.7451 (pt0) REVERT: E 163 VAL cc_start: 0.8490 (OUTLIER) cc_final: 0.8290 (p) REVERT: E 169 ASP cc_start: 0.8525 (t0) cc_final: 0.7748 (t0) REVERT: E 178 GLU cc_start: 0.8551 (mp0) cc_final: 0.8168 (mp0) REVERT: F 81 GLN cc_start: 0.8338 (tm-30) cc_final: 0.8129 (tm-30) REVERT: F 116 ASN cc_start: 0.8266 (m-40) cc_final: 0.7807 (m-40) REVERT: F 147 ASP cc_start: 0.9138 (t70) cc_final: 0.8886 (t0) REVERT: F 165 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8428 (tm-30) REVERT: F 169 ASP cc_start: 0.7850 (t0) cc_final: 0.7554 (t0) REVERT: G 118 GLU cc_start: 0.8736 (pt0) cc_final: 0.8347 (pt0) REVERT: G 163 VAL cc_start: 0.8617 (m) cc_final: 0.8406 (p) REVERT: G 169 ASP cc_start: 0.8487 (t70) cc_final: 0.7815 (t0) REVERT: I 94 MET cc_start: 0.8153 (tpp) cc_final: 0.7904 (tpp) REVERT: I 182 TYR cc_start: 0.7390 (m-80) cc_final: 0.7164 (m-80) REVERT: J 167 ASP cc_start: 0.8026 (m-30) cc_final: 0.7795 (m-30) REVERT: K 97 SER cc_start: 0.7800 (OUTLIER) cc_final: 0.7414 (m) REVERT: K 143 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8978 (mp) REVERT: M 54 ASP cc_start: 0.8710 (m-30) cc_final: 0.8483 (m-30) REVERT: N 54 ASP cc_start: 0.8541 (m-30) cc_final: 0.8280 (m-30) outliers start: 40 outliers final: 33 residues processed: 472 average time/residue: 0.6072 time to fit residues: 455.6028 Evaluate side-chains 467 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 430 time to evaluate : 2.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 116 ASN Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 116 ASN Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain J residue 60 SER Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 182 TYR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain K residue 97 SER Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 70 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 9.9990 chunk 212 optimal weight: 9.9990 chunk 129 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 147 optimal weight: 0.0370 chunk 223 optimal weight: 9.9990 chunk 205 optimal weight: 10.0000 chunk 177 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 overall best weight: 3.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.7987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18818 Z= 0.189 Angle : 0.682 25.730 25328 Z= 0.346 Chirality : 0.090 1.728 2954 Planarity : 0.003 0.030 3290 Dihedral : 5.194 54.867 2647 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.10 % Favored : 91.73 % Rotamer: Outliers : 1.61 % Allowed : 25.86 % Favored : 72.53 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 1.22 % 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: -1.96 (0.17), residues: 2310 helix: -0.84 (0.16), residues: 1050 sheet: -1.28 (0.29), residues: 238 loop : -1.71 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS G 122 PHE 0.017 0.001 PHE M 101 TYR 0.014 0.001 TYR M 77 ARG 0.008 0.000 ARG F 141 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Evaluate side-chains 484 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 453 time to evaluate : 2.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8251 (m-30) cc_final: 0.7691 (m-30) REVERT: A 163 VAL cc_start: 0.8598 (OUTLIER) cc_final: 0.8390 (p) REVERT: A 165 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8160 (mt-10) REVERT: A 169 ASP cc_start: 0.8373 (t70) cc_final: 0.7766 (t0) REVERT: B 78 ASP cc_start: 0.8272 (m-30) cc_final: 0.7747 (m-30) REVERT: B 116 ASN cc_start: 0.8337 (m-40) cc_final: 0.7932 (m110) REVERT: B 118 GLU cc_start: 0.8656 (pt0) cc_final: 0.8399 (pt0) REVERT: B 147 ASP cc_start: 0.8599 (t70) cc_final: 0.8338 (t0) REVERT: B 169 ASP cc_start: 0.8037 (t70) cc_final: 0.7825 (t0) REVERT: C 78 ASP cc_start: 0.8059 (m-30) cc_final: 0.7399 (m-30) REVERT: C 116 ASN cc_start: 0.8411 (m-40) cc_final: 0.7960 (m-40) REVERT: C 118 GLU cc_start: 0.8584 (pt0) cc_final: 0.7793 (pt0) REVERT: C 163 VAL cc_start: 0.8445 (m) cc_final: 0.8208 (p) REVERT: C 165 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8351 (tm-30) REVERT: C 169 ASP cc_start: 0.8568 (t0) cc_final: 0.7986 (t0) REVERT: D 56 GLU cc_start: 0.8541 (pm20) cc_final: 0.8318 (pp20) REVERT: D 116 ASN cc_start: 0.8153 (m-40) cc_final: 0.7840 (m-40) REVERT: D 118 GLU cc_start: 0.8448 (pt0) cc_final: 0.8065 (pt0) REVERT: D 169 ASP cc_start: 0.8632 (t0) cc_final: 0.8115 (t0) REVERT: E 56 GLU cc_start: 0.8460 (pm20) cc_final: 0.8187 (pp20) REVERT: E 123 GLN cc_start: 0.7703 (pt0) cc_final: 0.7435 (pt0) REVERT: E 169 ASP cc_start: 0.8509 (t0) cc_final: 0.7743 (t0) REVERT: E 178 GLU cc_start: 0.8505 (mp0) cc_final: 0.8112 (mp0) REVERT: F 81 GLN cc_start: 0.8329 (tm-30) cc_final: 0.8115 (tm-30) REVERT: F 116 ASN cc_start: 0.8201 (m-40) cc_final: 0.7709 (m-40) REVERT: F 123 GLN cc_start: 0.8019 (pt0) cc_final: 0.7783 (pt0) REVERT: F 147 ASP cc_start: 0.9116 (t70) cc_final: 0.8874 (t0) REVERT: F 165 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8308 (tm-30) REVERT: F 169 ASP cc_start: 0.7886 (t0) cc_final: 0.7552 (t0) REVERT: G 118 GLU cc_start: 0.8722 (pt0) cc_final: 0.8316 (pt0) REVERT: G 163 VAL cc_start: 0.8586 (m) cc_final: 0.8362 (p) REVERT: G 169 ASP cc_start: 0.8477 (t70) cc_final: 0.7779 (t0) REVERT: K 97 SER cc_start: 0.7799 (OUTLIER) cc_final: 0.7447 (m) REVERT: N 54 ASP cc_start: 0.8518 (m-30) cc_final: 0.8261 (m-30) REVERT: N 81 GLN cc_start: 0.8792 (mt0) cc_final: 0.8511 (mt0) outliers start: 31 outliers final: 28 residues processed: 474 average time/residue: 0.5918 time to fit residues: 437.3893 Evaluate side-chains 474 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 444 time to evaluate : 2.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 182 TYR Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain K residue 97 SER Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 70 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 0.0770 chunk 189 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 163 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 177 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 182 optimal weight: 0.0980 chunk 22 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 overall best weight: 2.6344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 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 = 0.3447 r_free = 0.3447 target = 0.103291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.087954 restraints weight = 124553.377| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 4.75 r_work: 0.3056 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.8065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18818 Z= 0.171 Angle : 0.676 25.908 25328 Z= 0.341 Chirality : 0.090 1.726 2954 Planarity : 0.003 0.034 3290 Dihedral : 4.997 47.419 2647 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.35 % Favored : 91.47 % Rotamer: Outliers : 1.51 % Allowed : 26.17 % Favored : 72.32 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 1.22 % 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: -1.55 (0.17), residues: 2310 helix: -0.54 (0.17), residues: 1036 sheet: -1.03 (0.30), residues: 238 loop : -1.44 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 122 PHE 0.016 0.001 PHE M 101 TYR 0.005 0.001 TYR J 182 ARG 0.008 0.000 ARG F 141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9984.61 seconds wall clock time: 175 minutes 17.37 seconds (10517.37 seconds total)