Starting phenix.real_space_refine on Sat Feb 24 05:50:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8apx_15578/02_2024/8apx_15578_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8apx_15578/02_2024/8apx_15578.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8apx_15578/02_2024/8apx_15578_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8apx_15578/02_2024/8apx_15578_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8apx_15578/02_2024/8apx_15578_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8apx_15578/02_2024/8apx_15578.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8apx_15578/02_2024/8apx_15578.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8apx_15578/02_2024/8apx_15578_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8apx_15578/02_2024/8apx_15578_updated.pdb" } resolution = 3.2 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= 0.004 sd= 0.049 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: 6 Type Number sf(0) Gaussians Zn 12 6.06 5 P 12 5.49 5 S 324 5.16 5 C 26196 2.51 5 N 7272 2.21 5 O 7800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 146": "OD1" <-> "OD2" Residue "A TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 179": "OD1" <-> "OD2" Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 397": "OE1" <-> "OE2" Residue "A ASP 436": "OD1" <-> "OD2" Residue "A PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 36": "OD1" <-> "OD2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 146": "OD1" <-> "OD2" Residue "B TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 179": "OD1" <-> "OD2" Residue "B PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 397": "OE1" <-> "OE2" Residue "C PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 36": "OD1" <-> "OD2" Residue "C ASP 56": "OD1" <-> "OD2" Residue "C PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 277": "OD1" <-> "OD2" Residue "C TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 397": "OE1" <-> "OE2" Residue "C ASP 436": "OD1" <-> "OD2" Residue "C PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 146": "OD1" <-> "OD2" Residue "D TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 179": "OD1" <-> "OD2" Residue "D PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 397": "OE1" <-> "OE2" Residue "D ASP 436": "OD1" <-> "OD2" Residue "E PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 36": "OD1" <-> "OD2" Residue "E ASP 146": "OD1" <-> "OD2" Residue "E TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 353": "OE1" <-> "OE2" Residue "E GLU 397": "OE1" <-> "OE2" Residue "E ASP 436": "OD1" <-> "OD2" Residue "E PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 36": "OD1" <-> "OD2" Residue "F ASP 56": "OD1" <-> "OD2" Residue "F ASP 75": "OD1" <-> "OD2" Residue "F ASP 146": "OD1" <-> "OD2" Residue "F TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 179": "OD1" <-> "OD2" Residue "F TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 277": "OD1" <-> "OD2" Residue "F TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 397": "OE1" <-> "OE2" Residue "F ASP 436": "OD1" <-> "OD2" Residue "G PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 56": "OD1" <-> "OD2" Residue "G TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 146": "OD1" <-> "OD2" Residue "G TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 397": "OE1" <-> "OE2" Residue "G ASP 436": "OD1" <-> "OD2" Residue "G PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 36": "OD1" <-> "OD2" Residue "H ASP 146": "OD1" <-> "OD2" Residue "H TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 179": "OD1" <-> "OD2" Residue "H PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 353": "OE1" <-> "OE2" Residue "H GLU 397": "OE1" <-> "OE2" Residue "H TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 36": "OD1" <-> "OD2" Residue "I ASP 56": "OD1" <-> "OD2" Residue "I ASP 146": "OD1" <-> "OD2" Residue "I TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 179": "OD1" <-> "OD2" Residue "I PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 397": "OE1" <-> "OE2" Residue "I ASP 436": "OD1" <-> "OD2" Residue "J PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 56": "OD1" <-> "OD2" Residue "J ASP 146": "OD1" <-> "OD2" Residue "J TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 179": "OD1" <-> "OD2" Residue "J PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 436": "OD1" <-> "OD2" Residue "J PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 36": "OD1" <-> "OD2" Residue "K ASP 146": "OD1" <-> "OD2" Residue "K TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 397": "OE1" <-> "OE2" Residue "K TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 36": "OD1" <-> "OD2" Residue "L PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 56": "OD1" <-> "OD2" Residue "L TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 146": "OD1" <-> "OD2" Residue "L TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 179": "OD1" <-> "OD2" Residue "L TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 277": "OD1" <-> "OD2" Residue "L PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 397": "OE1" <-> "OE2" Residue "L ASP 436": "OD1" <-> "OD2" Residue "L PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 41616 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3441 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 418} Chain breaks: 3 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'PJ3:plan-3': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3441 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 418} Chain breaks: 3 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'PJ3:plan-3': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3441 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 418} Chain breaks: 3 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'PJ3:plan-3': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3441 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 418} Chain breaks: 3 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'PJ3:plan-3': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3441 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 418} Chain breaks: 3 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'PJ3:plan-3': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "F" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3441 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 418} Chain breaks: 3 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'PJ3:plan-3': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "G" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3441 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 418} Chain breaks: 3 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'PJ3:plan-3': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "H" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3441 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 418} Chain breaks: 3 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'PJ3:plan-3': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "I" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3441 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 418} Chain breaks: 3 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'PJ3:plan-3': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "J" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3441 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 418} Chain breaks: 3 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'PJ3:plan-3': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "K" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3441 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 418} Chain breaks: 3 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'PJ3:plan-3': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "L" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3441 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 418} Chain breaks: 3 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'PJ3:plan-3': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1036 SG CYS A 134 45.723 164.976 30.277 1.00139.66 S ATOM 1088 SG CYS A 141 43.256 162.169 30.655 1.00114.07 S ATOM 4477 SG CYS B 134 21.722 128.098 28.918 1.00140.48 S ATOM 4529 SG CYS B 141 19.712 125.219 30.722 1.00105.16 S ATOM 7918 SG CYS C 134 16.574 85.563 30.217 1.00137.95 S ATOM 7970 SG CYS C 141 17.812 82.003 30.646 1.00 99.47 S ATOM 11359 SG CYS D 134 36.691 46.336 28.990 1.00143.96 S ATOM 11411 SG CYS D 141 38.155 43.017 30.708 1.00112.38 S ATOM 14800 SG CYS E 134 71.008 20.351 30.350 1.00136.88 S ATOM 14852 SG CYS E 141 74.635 19.805 30.715 1.00111.98 S ATOM 18241 SG CYS F 134 114.678 18.133 28.838 1.00142.75 S ATOM 18293 SG CYS F 141 118.363 17.829 30.727 1.00109.17 S ATOM 21682 SG CYS G 134 154.395 35.145 30.290 1.00132.31 S ATOM 21734 SG CYS G 141 156.881 37.998 30.657 1.00112.21 S ATOM 25123 SG CYS H 134 179.804 71.018 30.371 1.00139.92 S ATOM 25175 SG CYS H 141 180.301 74.659 30.682 1.00108.89 S ATOM 28564 SG CYS I 134 183.786 114.626 30.076 1.00143.71 S ATOM 28616 SG CYS I 141 182.348 118.070 30.610 1.00105.56 S ATOM 32005 SG CYS J 134 165.025 154.332 30.304 1.00138.88 S ATOM 32057 SG CYS J 141 162.176 156.838 30.684 1.00120.23 S ATOM 35446 SG CYS K 134 128.111 178.352 29.033 1.00150.83 S ATOM 35498 SG CYS K 141 125.153 180.347 30.715 1.00118.88 S ATOM 38887 SG CYS L 134 85.502 183.551 30.226 1.00139.20 S ATOM 38939 SG CYS L 141 82.013 182.311 30.640 1.00106.65 S Time building chain proxies: 20.85, per 1000 atoms: 0.50 Number of scatterers: 41616 At special positions: 0 Unit cell: (200.925, 200.925, 88.065, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 12 29.99 S 324 16.00 P 12 15.00 O 7800 8.00 N 7272 7.00 C 26196 6.00 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=0, symmetry=0 Time building additional restraints: 16.03 Conformation dependent library (CDL) restraints added in 7.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 141 " pdb="ZN ZN A1001 " - pdb=" NE2 HIS A 79 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 134 " pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 134 " pdb="ZN ZN B1001 " - pdb=" NE2 HIS B 79 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 141 " pdb=" ZN C1001 " pdb="ZN ZN C1001 " - pdb=" NE2 HIS C 79 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 141 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 134 " pdb=" ZN D1001 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 134 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 141 " pdb="ZN ZN D1001 " - pdb=" NE2 HIS D 79 " pdb=" ZN E1001 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 141 " pdb="ZN ZN E1001 " - pdb=" NE2 HIS E 79 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 134 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 134 " pdb="ZN ZN F1001 " - pdb=" NE2 HIS F 79 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 141 " pdb=" ZN G1001 " pdb="ZN ZN G1001 " - pdb=" SG CYS G 141 " pdb="ZN ZN G1001 " - pdb=" NE2 HIS G 79 " pdb="ZN ZN G1001 " - pdb=" SG CYS G 134 " pdb=" ZN H1001 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 141 " pdb="ZN ZN H1001 " - pdb=" NE2 HIS H 79 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 134 " pdb=" ZN I1001 " pdb="ZN ZN I1001 " - pdb=" SG CYS I 141 " pdb="ZN ZN I1001 " - pdb=" NE2 HIS I 79 " pdb="ZN ZN I1001 " - pdb=" SG CYS I 134 " pdb=" ZN J1001 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 141 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 134 " pdb="ZN ZN J1001 " - pdb=" NE2 HIS J 79 " pdb=" ZN K1001 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 134 " pdb="ZN ZN K1001 " - pdb=" NE2 HIS K 79 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 141 " pdb=" ZN L1001 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 141 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 134 " pdb="ZN ZN L1001 " - pdb=" NE2 HIS L 79 " 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10056 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 169 helices and 61 sheets defined 27.9% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.97 Creating SS restraints... Processing helix chain 'A' and resid 13 through 21 Processing helix chain 'A' and resid 39 through 54 Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'A' and resid 89 through 102 Processing helix chain 'A' and resid 112 through 124 Processing helix chain 'A' and resid 138 through 140 No H-bonds generated for 'chain 'A' and resid 138 through 140' Processing helix chain 'A' and resid 158 through 168 removed outlier: 3.871A pdb=" N LYS A 168 " --> pdb=" O HIS A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 184 No H-bonds generated for 'chain 'A' and resid 181 through 184' Processing helix chain 'A' and resid 252 through 258 removed outlier: 3.863A pdb=" N TRP A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 341 Processing helix chain 'A' and resid 352 through 362 Processing helix chain 'A' and resid 381 through 383 No H-bonds generated for 'chain 'A' and resid 381 through 383' Processing helix chain 'A' and resid 386 through 402 Processing helix chain 'A' and resid 462 through 467 removed outlier: 3.591A pdb=" N THR A 466 " --> pdb=" O ILE A 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 21 Processing helix chain 'B' and resid 39 through 54 Processing helix chain 'B' and resid 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 through 72' Processing helix chain 'B' and resid 89 through 102 Processing helix chain 'B' and resid 112 through 124 Processing helix chain 'B' and resid 158 through 168 removed outlier: 4.072A pdb=" N LYS B 168 " --> pdb=" O HIS B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 184 No H-bonds generated for 'chain 'B' and resid 181 through 184' Processing helix chain 'B' and resid 252 through 258 removed outlier: 3.987A pdb=" N TRP B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 341 Processing helix chain 'B' and resid 352 through 362 Processing helix chain 'B' and resid 381 through 383 No H-bonds generated for 'chain 'B' and resid 381 through 383' Processing helix chain 'B' and resid 386 through 402 Processing helix chain 'B' and resid 462 through 467 removed outlier: 3.587A pdb=" N THR B 466 " --> pdb=" O ILE B 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 21 Processing helix chain 'C' and resid 39 through 54 Processing helix chain 'C' and resid 70 through 72 No H-bonds generated for 'chain 'C' and resid 70 through 72' Processing helix chain 'C' and resid 89 through 102 Processing helix chain 'C' and resid 112 through 124 Processing helix chain 'C' and resid 158 through 168 removed outlier: 3.973A pdb=" N LYS C 168 " --> pdb=" O HIS C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 184 No H-bonds generated for 'chain 'C' and resid 181 through 184' Processing helix chain 'C' and resid 252 through 258 removed outlier: 3.999A pdb=" N TRP C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 323 No H-bonds generated for 'chain 'C' and resid 321 through 323' Processing helix chain 'C' and resid 336 through 341 Processing helix chain 'C' and resid 352 through 362 Processing helix chain 'C' and resid 381 through 383 No H-bonds generated for 'chain 'C' and resid 381 through 383' Processing helix chain 'C' and resid 386 through 402 Processing helix chain 'C' and resid 462 through 467 removed outlier: 3.611A pdb=" N THR C 466 " --> pdb=" O ILE C 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 21 Processing helix chain 'D' and resid 39 through 54 Processing helix chain 'D' and resid 70 through 72 No H-bonds generated for 'chain 'D' and resid 70 through 72' Processing helix chain 'D' and resid 89 through 102 Processing helix chain 'D' and resid 112 through 124 Processing helix chain 'D' and resid 158 through 168 removed outlier: 3.860A pdb=" N LYS D 168 " --> pdb=" O HIS D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 184 No H-bonds generated for 'chain 'D' and resid 181 through 184' Processing helix chain 'D' and resid 252 through 258 removed outlier: 3.921A pdb=" N TRP D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 352 through 362 Processing helix chain 'D' and resid 381 through 383 No H-bonds generated for 'chain 'D' and resid 381 through 383' Processing helix chain 'D' and resid 386 through 402 Processing helix chain 'D' and resid 462 through 467 removed outlier: 3.586A pdb=" N THR D 466 " --> pdb=" O ILE D 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 21 Processing helix chain 'E' and resid 39 through 54 Processing helix chain 'E' and resid 70 through 72 No H-bonds generated for 'chain 'E' and resid 70 through 72' Processing helix chain 'E' and resid 89 through 102 Processing helix chain 'E' and resid 112 through 124 Processing helix chain 'E' and resid 138 through 140 No H-bonds generated for 'chain 'E' and resid 138 through 140' Processing helix chain 'E' and resid 158 through 168 removed outlier: 4.065A pdb=" N LYS E 168 " --> pdb=" O HIS E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 184 No H-bonds generated for 'chain 'E' and resid 181 through 184' Processing helix chain 'E' and resid 193 through 195 No H-bonds generated for 'chain 'E' and resid 193 through 195' Processing helix chain 'E' and resid 252 through 258 removed outlier: 4.003A pdb=" N TRP E 258 " --> pdb=" O LEU E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 323 No H-bonds generated for 'chain 'E' and resid 321 through 323' Processing helix chain 'E' and resid 336 through 341 Processing helix chain 'E' and resid 352 through 362 Processing helix chain 'E' and resid 381 through 383 No H-bonds generated for 'chain 'E' and resid 381 through 383' Processing helix chain 'E' and resid 386 through 402 Processing helix chain 'E' and resid 462 through 467 removed outlier: 3.595A pdb=" N THR E 466 " --> pdb=" O ILE E 462 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 21 Processing helix chain 'F' and resid 39 through 54 Processing helix chain 'F' and resid 70 through 72 No H-bonds generated for 'chain 'F' and resid 70 through 72' Processing helix chain 'F' and resid 89 through 102 Processing helix chain 'F' and resid 112 through 124 Processing helix chain 'F' and resid 138 through 140 No H-bonds generated for 'chain 'F' and resid 138 through 140' Processing helix chain 'F' and resid 158 through 168 removed outlier: 3.868A pdb=" N LYS F 168 " --> pdb=" O HIS F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 184 No H-bonds generated for 'chain 'F' and resid 181 through 184' Processing helix chain 'F' and resid 252 through 258 removed outlier: 4.002A pdb=" N TRP F 258 " --> pdb=" O LEU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 341 Processing helix chain 'F' and resid 352 through 362 Processing helix chain 'F' and resid 381 through 383 No H-bonds generated for 'chain 'F' and resid 381 through 383' Processing helix chain 'F' and resid 386 through 402 Processing helix chain 'F' and resid 462 through 467 removed outlier: 3.560A pdb=" N THR F 466 " --> pdb=" O ILE F 462 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 21 Processing helix chain 'G' and resid 39 through 54 Processing helix chain 'G' and resid 70 through 72 No H-bonds generated for 'chain 'G' and resid 70 through 72' Processing helix chain 'G' and resid 89 through 102 Processing helix chain 'G' and resid 112 through 124 Processing helix chain 'G' and resid 158 through 168 removed outlier: 3.866A pdb=" N LYS G 168 " --> pdb=" O HIS G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 184 No H-bonds generated for 'chain 'G' and resid 181 through 184' Processing helix chain 'G' and resid 193 through 195 No H-bonds generated for 'chain 'G' and resid 193 through 195' Processing helix chain 'G' and resid 252 through 258 removed outlier: 3.867A pdb=" N TRP G 258 " --> pdb=" O LEU G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 323 No H-bonds generated for 'chain 'G' and resid 321 through 323' Processing helix chain 'G' and resid 336 through 343 removed outlier: 3.767A pdb=" N THR G 343 " --> pdb=" O CYS G 339 " (cutoff:3.500A) Processing helix chain 'G' and resid 352 through 362 Processing helix chain 'G' and resid 381 through 383 No H-bonds generated for 'chain 'G' and resid 381 through 383' Processing helix chain 'G' and resid 386 through 402 Processing helix chain 'G' and resid 462 through 467 removed outlier: 3.558A pdb=" N THR G 466 " --> pdb=" O ILE G 462 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 21 Processing helix chain 'H' and resid 39 through 54 Processing helix chain 'H' and resid 70 through 72 No H-bonds generated for 'chain 'H' and resid 70 through 72' Processing helix chain 'H' and resid 89 through 102 Processing helix chain 'H' and resid 112 through 124 Processing helix chain 'H' and resid 138 through 140 No H-bonds generated for 'chain 'H' and resid 138 through 140' Processing helix chain 'H' and resid 158 through 166 Processing helix chain 'H' and resid 181 through 184 No H-bonds generated for 'chain 'H' and resid 181 through 184' Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'H' and resid 252 through 258 removed outlier: 3.979A pdb=" N TRP H 258 " --> pdb=" O LEU H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 336 through 341 Processing helix chain 'H' and resid 352 through 362 Processing helix chain 'H' and resid 381 through 383 No H-bonds generated for 'chain 'H' and resid 381 through 383' Processing helix chain 'H' and resid 386 through 402 Processing helix chain 'H' and resid 462 through 467 removed outlier: 3.570A pdb=" N THR H 466 " --> pdb=" O ILE H 462 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 21 Processing helix chain 'I' and resid 39 through 54 Processing helix chain 'I' and resid 70 through 72 No H-bonds generated for 'chain 'I' and resid 70 through 72' Processing helix chain 'I' and resid 89 through 102 Processing helix chain 'I' and resid 112 through 124 Processing helix chain 'I' and resid 158 through 168 removed outlier: 3.825A pdb=" N LYS I 168 " --> pdb=" O HIS I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 184 No H-bonds generated for 'chain 'I' and resid 181 through 184' Processing helix chain 'I' and resid 193 through 195 No H-bonds generated for 'chain 'I' and resid 193 through 195' Processing helix chain 'I' and resid 252 through 258 removed outlier: 3.951A pdb=" N TRP I 258 " --> pdb=" O LEU I 254 " (cutoff:3.500A) Processing helix chain 'I' and resid 336 through 341 Processing helix chain 'I' and resid 352 through 362 Processing helix chain 'I' and resid 381 through 383 No H-bonds generated for 'chain 'I' and resid 381 through 383' Processing helix chain 'I' and resid 386 through 402 Processing helix chain 'I' and resid 462 through 467 removed outlier: 3.568A pdb=" N THR I 466 " --> pdb=" O ILE I 462 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 21 Processing helix chain 'J' and resid 39 through 54 Processing helix chain 'J' and resid 70 through 72 No H-bonds generated for 'chain 'J' and resid 70 through 72' Processing helix chain 'J' and resid 89 through 102 Processing helix chain 'J' and resid 112 through 124 Processing helix chain 'J' and resid 158 through 168 removed outlier: 3.843A pdb=" N LYS J 168 " --> pdb=" O HIS J 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 184 No H-bonds generated for 'chain 'J' and resid 181 through 184' Processing helix chain 'J' and resid 252 through 258 removed outlier: 3.868A pdb=" N TRP J 258 " --> pdb=" O LEU J 254 " (cutoff:3.500A) Processing helix chain 'J' and resid 336 through 341 Processing helix chain 'J' and resid 352 through 362 Processing helix chain 'J' and resid 381 through 383 No H-bonds generated for 'chain 'J' and resid 381 through 383' Processing helix chain 'J' and resid 386 through 402 Processing helix chain 'J' and resid 462 through 467 removed outlier: 3.583A pdb=" N THR J 466 " --> pdb=" O ILE J 462 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 21 Processing helix chain 'K' and resid 39 through 54 Processing helix chain 'K' and resid 70 through 72 No H-bonds generated for 'chain 'K' and resid 70 through 72' Processing helix chain 'K' and resid 89 through 102 Processing helix chain 'K' and resid 112 through 124 Processing helix chain 'K' and resid 158 through 168 removed outlier: 4.067A pdb=" N LYS K 168 " --> pdb=" O HIS K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 184 No H-bonds generated for 'chain 'K' and resid 181 through 184' Processing helix chain 'K' and resid 252 through 258 removed outlier: 4.009A pdb=" N TRP K 258 " --> pdb=" O LEU K 254 " (cutoff:3.500A) Processing helix chain 'K' and resid 336 through 341 Processing helix chain 'K' and resid 352 through 362 Processing helix chain 'K' and resid 381 through 383 No H-bonds generated for 'chain 'K' and resid 381 through 383' Processing helix chain 'K' and resid 386 through 402 Processing helix chain 'K' and resid 462 through 467 removed outlier: 3.571A pdb=" N THR K 466 " --> pdb=" O ILE K 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 21 Processing helix chain 'L' and resid 39 through 54 Processing helix chain 'L' and resid 70 through 72 No H-bonds generated for 'chain 'L' and resid 70 through 72' Processing helix chain 'L' and resid 89 through 102 Processing helix chain 'L' and resid 112 through 124 Processing helix chain 'L' and resid 158 through 168 removed outlier: 3.898A pdb=" N LYS L 168 " --> pdb=" O HIS L 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 184 No H-bonds generated for 'chain 'L' and resid 181 through 184' Processing helix chain 'L' and resid 202 through 204 No H-bonds generated for 'chain 'L' and resid 202 through 204' Processing helix chain 'L' and resid 252 through 258 removed outlier: 3.956A pdb=" N TRP L 258 " --> pdb=" O LEU L 254 " (cutoff:3.500A) Processing helix chain 'L' and resid 321 through 323 No H-bonds generated for 'chain 'L' and resid 321 through 323' Processing helix chain 'L' and resid 336 through 341 Processing helix chain 'L' and resid 352 through 362 Processing helix chain 'L' and resid 381 through 383 No H-bonds generated for 'chain 'L' and resid 381 through 383' Processing helix chain 'L' and resid 386 through 402 Processing helix chain 'L' and resid 462 through 467 removed outlier: 3.587A pdb=" N THR L 466 " --> pdb=" O ILE L 462 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 4 through 6 Processing sheet with id= B, first strand: chain 'A' and resid 77 through 81 removed outlier: 6.642A pdb=" N VAL A 147 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ILE A 64 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE A 149 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU A 172 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N TYR A 150 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N TYR A 174 " --> pdb=" O TYR A 150 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL A 280 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG A 289 " --> pdb=" O THR A 278 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N THR A 278 " --> pdb=" O ARG A 289 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N THR A 291 " --> pdb=" O CYS A 276 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N CYS A 276 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N SER A 293 " --> pdb=" O CYS A 274 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N CYS A 274 " --> pdb=" O SER A 293 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 197 through 201 Processing sheet with id= D, first strand: chain 'A' and resid 303 through 307 Processing sheet with id= E, first strand: chain 'A' and resid 324 through 334 Processing sheet with id= F, first strand: chain 'B' and resid 4 through 6 Processing sheet with id= G, first strand: chain 'B' and resid 77 through 81 removed outlier: 6.633A pdb=" N VAL B 147 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ILE B 64 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE B 149 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU B 172 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N TYR B 150 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N TYR B 174 " --> pdb=" O TYR B 150 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL B 280 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ARG B 289 " --> pdb=" O THR B 278 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N THR B 278 " --> pdb=" O ARG B 289 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N THR B 291 " --> pdb=" O CYS B 276 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N CYS B 276 " --> pdb=" O THR B 291 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 197 through 201 Processing sheet with id= I, first strand: chain 'B' and resid 303 through 307 Processing sheet with id= J, first strand: chain 'B' and resid 324 through 334 Processing sheet with id= K, first strand: chain 'C' and resid 4 through 6 Processing sheet with id= L, first strand: chain 'C' and resid 77 through 81 removed outlier: 6.694A pdb=" N VAL C 147 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ILE C 64 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE C 149 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU C 172 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N TYR C 150 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N TYR C 174 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL C 280 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ARG C 289 " --> pdb=" O THR C 278 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N THR C 278 " --> pdb=" O ARG C 289 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N THR C 291 " --> pdb=" O CYS C 276 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N CYS C 276 " --> pdb=" O THR C 291 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 197 through 201 Processing sheet with id= N, first strand: chain 'C' and resid 303 through 307 Processing sheet with id= O, first strand: chain 'C' and resid 324 through 334 Processing sheet with id= P, first strand: chain 'D' and resid 4 through 6 Processing sheet with id= Q, first strand: chain 'D' and resid 77 through 81 removed outlier: 6.788A pdb=" N VAL D 147 " --> pdb=" O LEU D 62 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ILE D 64 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE D 149 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU D 172 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N TYR D 150 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N TYR D 174 " --> pdb=" O TYR D 150 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL D 280 " --> pdb=" O VAL D 287 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ARG D 289 " --> pdb=" O THR D 278 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N THR D 278 " --> pdb=" O ARG D 289 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 197 through 201 Processing sheet with id= S, first strand: chain 'D' and resid 263 through 266 Processing sheet with id= T, first strand: chain 'D' and resid 303 through 307 Processing sheet with id= U, first strand: chain 'D' and resid 324 through 334 Processing sheet with id= V, first strand: chain 'E' and resid 4 through 6 Processing sheet with id= W, first strand: chain 'E' and resid 77 through 81 removed outlier: 6.670A pdb=" N VAL E 147 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ILE E 64 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE E 149 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU E 172 " --> pdb=" O ALA E 148 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N TYR E 150 " --> pdb=" O LEU E 172 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N TYR E 174 " --> pdb=" O TYR E 150 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL E 280 " --> pdb=" O VAL E 287 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ARG E 289 " --> pdb=" O THR E 278 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N THR E 278 " --> pdb=" O ARG E 289 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N THR E 291 " --> pdb=" O CYS E 276 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N CYS E 276 " --> pdb=" O THR E 291 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N SER E 293 " --> pdb=" O CYS E 274 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N CYS E 274 " --> pdb=" O SER E 293 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 197 through 201 Processing sheet with id= Y, first strand: chain 'E' and resid 303 through 307 Processing sheet with id= Z, first strand: chain 'E' and resid 324 through 334 Processing sheet with id= AA, first strand: chain 'F' and resid 4 through 6 Processing sheet with id= AB, first strand: chain 'F' and resid 77 through 81 removed outlier: 6.744A pdb=" N VAL F 147 " --> pdb=" O LEU F 62 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ILE F 64 " --> pdb=" O VAL F 147 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE F 149 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU F 172 " --> pdb=" O ALA F 148 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N TYR F 150 " --> pdb=" O LEU F 172 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N TYR F 174 " --> pdb=" O TYR F 150 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL F 280 " --> pdb=" O VAL F 287 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ARG F 289 " --> pdb=" O THR F 278 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR F 278 " --> pdb=" O ARG F 289 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N THR F 291 " --> pdb=" O CYS F 276 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N CYS F 276 " --> pdb=" O THR F 291 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N SER F 293 " --> pdb=" O CYS F 274 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N CYS F 274 " --> pdb=" O SER F 293 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 197 through 201 Processing sheet with id= AD, first strand: chain 'F' and resid 303 through 307 Processing sheet with id= AE, first strand: chain 'F' and resid 324 through 334 Processing sheet with id= AF, first strand: chain 'G' and resid 4 through 6 Processing sheet with id= AG, first strand: chain 'G' and resid 77 through 81 removed outlier: 6.773A pdb=" N VAL G 147 " --> pdb=" O LEU G 62 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ILE G 64 " --> pdb=" O VAL G 147 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE G 149 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU G 172 " --> pdb=" O ALA G 148 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N TYR G 150 " --> pdb=" O LEU G 172 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N TYR G 174 " --> pdb=" O TYR G 150 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL G 280 " --> pdb=" O VAL G 287 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ARG G 289 " --> pdb=" O THR G 278 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N THR G 278 " --> pdb=" O ARG G 289 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N THR G 291 " --> pdb=" O CYS G 276 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N CYS G 276 " --> pdb=" O THR G 291 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'G' and resid 197 through 201 Processing sheet with id= AI, first strand: chain 'G' and resid 303 through 307 Processing sheet with id= AJ, first strand: chain 'G' and resid 324 through 334 Processing sheet with id= AK, first strand: chain 'H' and resid 4 through 6 Processing sheet with id= AL, first strand: chain 'H' and resid 77 through 81 removed outlier: 6.747A pdb=" N VAL H 147 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ILE H 64 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE H 149 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU H 172 " --> pdb=" O ALA H 148 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N TYR H 150 " --> pdb=" O LEU H 172 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N TYR H 174 " --> pdb=" O TYR H 150 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL H 280 " --> pdb=" O VAL H 287 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARG H 289 " --> pdb=" O THR H 278 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N THR H 278 " --> pdb=" O ARG H 289 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N THR H 291 " --> pdb=" O CYS H 276 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N CYS H 276 " --> pdb=" O THR H 291 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'H' and resid 197 through 201 Processing sheet with id= AN, first strand: chain 'H' and resid 303 through 307 Processing sheet with id= AO, first strand: chain 'H' and resid 324 through 334 Processing sheet with id= AP, first strand: chain 'I' and resid 4 through 6 Processing sheet with id= AQ, first strand: chain 'I' and resid 77 through 81 removed outlier: 6.655A pdb=" N VAL I 147 " --> pdb=" O LEU I 62 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ILE I 64 " --> pdb=" O VAL I 147 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE I 149 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU I 172 " --> pdb=" O ALA I 148 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N TYR I 150 " --> pdb=" O LEU I 172 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N TYR I 174 " --> pdb=" O TYR I 150 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL I 280 " --> pdb=" O VAL I 287 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ARG I 289 " --> pdb=" O THR I 278 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N THR I 278 " --> pdb=" O ARG I 289 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N THR I 291 " --> pdb=" O CYS I 276 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N CYS I 276 " --> pdb=" O THR I 291 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'I' and resid 197 through 201 Processing sheet with id= AS, first strand: chain 'I' and resid 303 through 307 Processing sheet with id= AT, first strand: chain 'I' and resid 324 through 334 Processing sheet with id= AU, first strand: chain 'J' and resid 4 through 6 Processing sheet with id= AV, first strand: chain 'J' and resid 77 through 81 removed outlier: 6.728A pdb=" N VAL J 147 " --> pdb=" O LEU J 62 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ILE J 64 " --> pdb=" O VAL J 147 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE J 149 " --> pdb=" O ILE J 64 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU J 172 " --> pdb=" O ALA J 148 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N TYR J 150 " --> pdb=" O LEU J 172 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TYR J 174 " --> pdb=" O TYR J 150 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL J 280 " --> pdb=" O VAL J 287 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ARG J 289 " --> pdb=" O THR J 278 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N THR J 278 " --> pdb=" O ARG J 289 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N THR J 291 " --> pdb=" O CYS J 276 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N CYS J 276 " --> pdb=" O THR J 291 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'J' and resid 197 through 201 Processing sheet with id= AX, first strand: chain 'J' and resid 303 through 307 Processing sheet with id= AY, first strand: chain 'J' and resid 324 through 334 Processing sheet with id= AZ, first strand: chain 'K' and resid 4 through 6 Processing sheet with id= BA, first strand: chain 'K' and resid 77 through 81 removed outlier: 6.690A pdb=" N VAL K 147 " --> pdb=" O LEU K 62 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ILE K 64 " --> pdb=" O VAL K 147 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE K 149 " --> pdb=" O ILE K 64 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU K 172 " --> pdb=" O ALA K 148 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N TYR K 150 " --> pdb=" O LEU K 172 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N TYR K 174 " --> pdb=" O TYR K 150 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL K 280 " --> pdb=" O VAL K 287 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ARG K 289 " --> pdb=" O THR K 278 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N THR K 278 " --> pdb=" O ARG K 289 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N THR K 291 " --> pdb=" O CYS K 276 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N CYS K 276 " --> pdb=" O THR K 291 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N SER K 293 " --> pdb=" O CYS K 274 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N CYS K 274 " --> pdb=" O SER K 293 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'K' and resid 197 through 201 Processing sheet with id= BC, first strand: chain 'K' and resid 303 through 307 Processing sheet with id= BD, first strand: chain 'K' and resid 324 through 334 Processing sheet with id= BE, first strand: chain 'L' and resid 4 through 6 Processing sheet with id= BF, first strand: chain 'L' and resid 77 through 81 removed outlier: 6.640A pdb=" N VAL L 147 " --> pdb=" O LEU L 62 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ILE L 64 " --> pdb=" O VAL L 147 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE L 149 " --> pdb=" O ILE L 64 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU L 172 " --> pdb=" O ALA L 148 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N TYR L 150 " --> pdb=" O LEU L 172 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N TYR L 174 " --> pdb=" O TYR L 150 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL L 280 " --> pdb=" O VAL L 287 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ARG L 289 " --> pdb=" O THR L 278 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N THR L 278 " --> pdb=" O ARG L 289 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N THR L 291 " --> pdb=" O CYS L 276 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N CYS L 276 " --> pdb=" O THR L 291 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'L' and resid 197 through 201 Processing sheet with id= BH, first strand: chain 'L' and resid 303 through 307 Processing sheet with id= BI, first strand: chain 'L' and resid 324 through 334 1404 hydrogen bonds defined for protein. 3783 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: 14.55 Time building geometry restraints manager: 17.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.28: 6732 1.28 - 1.43: 10786 1.43 - 1.58: 24446 1.58 - 1.73: 24 1.73 - 1.89: 516 Bond restraints: 42504 Sorted by residual: bond pdb=" CA PJ3 A 37 " pdb=" C PJ3 A 37 " ideal model delta sigma weight residual 1.522 1.864 -0.342 2.00e-02 2.50e+03 2.92e+02 bond pdb=" CA PJ3 G 37 " pdb=" C PJ3 G 37 " ideal model delta sigma weight residual 1.522 1.864 -0.342 2.00e-02 2.50e+03 2.92e+02 bond pdb=" CA PJ3 I 37 " pdb=" C PJ3 I 37 " ideal model delta sigma weight residual 1.522 1.863 -0.341 2.00e-02 2.50e+03 2.91e+02 bond pdb=" CA PJ3 L 37 " pdb=" C PJ3 L 37 " ideal model delta sigma weight residual 1.522 1.863 -0.341 2.00e-02 2.50e+03 2.91e+02 bond pdb=" CA PJ3 K 37 " pdb=" C PJ3 K 37 " ideal model delta sigma weight residual 1.522 1.863 -0.341 2.00e-02 2.50e+03 2.91e+02 ... (remaining 42499 not shown) Histogram of bond angle deviations from ideal: 89.36 - 98.46: 24 98.46 - 107.57: 1915 107.57 - 116.67: 28434 116.67 - 125.77: 26630 125.77 - 134.87: 681 Bond angle restraints: 57684 Sorted by residual: angle pdb=" CB PJ3 G 37 " pdb=" CG PJ3 G 37 " pdb=" ND1 PJ3 G 37 " ideal model delta sigma weight residual 92.64 128.92 -36.28 3.00e+00 1.11e-01 1.46e+02 angle pdb=" CB PJ3 B 37 " pdb=" CG PJ3 B 37 " pdb=" ND1 PJ3 B 37 " ideal model delta sigma weight residual 92.64 128.91 -36.27 3.00e+00 1.11e-01 1.46e+02 angle pdb=" CB PJ3 E 37 " pdb=" CG PJ3 E 37 " pdb=" ND1 PJ3 E 37 " ideal model delta sigma weight residual 92.64 128.91 -36.27 3.00e+00 1.11e-01 1.46e+02 angle pdb=" CB PJ3 D 37 " pdb=" CG PJ3 D 37 " pdb=" ND1 PJ3 D 37 " ideal model delta sigma weight residual 92.64 128.89 -36.25 3.00e+00 1.11e-01 1.46e+02 angle pdb=" CB PJ3 I 37 " pdb=" CG PJ3 I 37 " pdb=" ND1 PJ3 I 37 " ideal model delta sigma weight residual 92.64 128.87 -36.23 3.00e+00 1.11e-01 1.46e+02 ... (remaining 57679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 21652 17.81 - 35.63: 2889 35.63 - 53.44: 879 53.44 - 71.26: 143 71.26 - 89.07: 57 Dihedral angle restraints: 25620 sinusoidal: 10116 harmonic: 15504 Sorted by residual: dihedral pdb=" CA ILE J 384 " pdb=" C ILE J 384 " pdb=" N PRO J 385 " pdb=" CA PRO J 385 " ideal model delta harmonic sigma weight residual 180.00 144.02 35.98 0 5.00e+00 4.00e-02 5.18e+01 dihedral pdb=" CA ILE G 384 " pdb=" C ILE G 384 " pdb=" N PRO G 385 " pdb=" CA PRO G 385 " ideal model delta harmonic sigma weight residual 180.00 144.34 35.66 0 5.00e+00 4.00e-02 5.09e+01 dihedral pdb=" CA ILE D 384 " pdb=" C ILE D 384 " pdb=" N PRO D 385 " pdb=" CA PRO D 385 " ideal model delta harmonic sigma weight residual 180.00 145.12 34.88 0 5.00e+00 4.00e-02 4.87e+01 ... (remaining 25617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 5620 0.068 - 0.137: 889 0.137 - 0.205: 31 0.205 - 0.273: 12 0.273 - 0.342: 12 Chirality restraints: 6564 Sorted by residual: chirality pdb=" C2' PJ3 H 37 " pdb=" C1' PJ3 H 37 " pdb=" C3' PJ3 H 37 " pdb=" O2' PJ3 H 37 " both_signs ideal model delta sigma weight residual False -2.42 -2.76 0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" C2' PJ3 K 37 " pdb=" C1' PJ3 K 37 " pdb=" C3' PJ3 K 37 " pdb=" O2' PJ3 K 37 " both_signs ideal model delta sigma weight residual False -2.42 -2.76 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" C2' PJ3 C 37 " pdb=" C1' PJ3 C 37 " pdb=" C3' PJ3 C 37 " pdb=" O2' PJ3 C 37 " both_signs ideal model delta sigma weight residual False -2.42 -2.76 0.34 2.00e-01 2.50e+01 2.87e+00 ... (remaining 6561 not shown) Planarity restraints: 7260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' PJ3 B 37 " -0.132 2.00e-02 2.50e+03 2.79e-01 2.54e+03 pdb=" C2 PJ3 B 37 " 0.100 2.00e-02 2.50e+03 pdb=" C4 PJ3 B 37 " 0.034 2.00e-02 2.50e+03 pdb=" C5 PJ3 B 37 " -0.111 2.00e-02 2.50e+03 pdb=" C6 PJ3 B 37 " -0.156 2.00e-02 2.50e+03 pdb=" C8 PJ3 B 37 " -0.420 2.00e-02 2.50e+03 pdb=" CM7 PJ3 B 37 " 0.775 2.00e-02 2.50e+03 pdb=" N1 PJ3 B 37 " -0.039 2.00e-02 2.50e+03 pdb=" N2 PJ3 B 37 " 0.200 2.00e-02 2.50e+03 pdb=" N3 PJ3 B 37 " 0.141 2.00e-02 2.50e+03 pdb=" N7 PJ3 B 37 " -0.187 2.00e-02 2.50e+03 pdb=" N9 PJ3 B 37 " 0.063 2.00e-02 2.50e+03 pdb=" O6 PJ3 B 37 " -0.268 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' PJ3 H 37 " 0.161 2.00e-02 2.50e+03 2.79e-01 2.53e+03 pdb=" C2 PJ3 H 37 " -0.103 2.00e-02 2.50e+03 pdb=" C4 PJ3 H 37 " -0.039 2.00e-02 2.50e+03 pdb=" C5 PJ3 H 37 " 0.111 2.00e-02 2.50e+03 pdb=" C6 PJ3 H 37 " 0.161 2.00e-02 2.50e+03 pdb=" C8 PJ3 H 37 " 0.399 2.00e-02 2.50e+03 pdb=" CM7 PJ3 H 37 " -0.770 2.00e-02 2.50e+03 pdb=" N1 PJ3 H 37 " 0.043 2.00e-02 2.50e+03 pdb=" N2 PJ3 H 37 " -0.204 2.00e-02 2.50e+03 pdb=" N3 PJ3 H 37 " -0.148 2.00e-02 2.50e+03 pdb=" N7 PJ3 H 37 " 0.185 2.00e-02 2.50e+03 pdb=" N9 PJ3 H 37 " -0.075 2.00e-02 2.50e+03 pdb=" O6 PJ3 H 37 " 0.279 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' PJ3 K 37 " -0.138 2.00e-02 2.50e+03 2.69e-01 2.36e+03 pdb=" C2 PJ3 K 37 " 0.100 2.00e-02 2.50e+03 pdb=" C4 PJ3 K 37 " 0.032 2.00e-02 2.50e+03 pdb=" C5 PJ3 K 37 " -0.113 2.00e-02 2.50e+03 pdb=" C6 PJ3 K 37 " -0.156 2.00e-02 2.50e+03 pdb=" C8 PJ3 K 37 " -0.378 2.00e-02 2.50e+03 pdb=" CM7 PJ3 K 37 " 0.750 2.00e-02 2.50e+03 pdb=" N1 PJ3 K 37 " -0.039 2.00e-02 2.50e+03 pdb=" N2 PJ3 K 37 " 0.200 2.00e-02 2.50e+03 pdb=" N3 PJ3 K 37 " 0.139 2.00e-02 2.50e+03 pdb=" N7 PJ3 K 37 " -0.189 2.00e-02 2.50e+03 pdb=" N9 PJ3 K 37 " 0.059 2.00e-02 2.50e+03 pdb=" O6 PJ3 K 37 " -0.267 2.00e-02 2.50e+03 ... (remaining 7257 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 819 2.65 - 3.21: 38741 3.21 - 3.77: 66077 3.77 - 4.34: 90120 4.34 - 4.90: 145390 Nonbonded interactions: 341147 Sorted by model distance: nonbonded pdb=" OH TYR F 150 " pdb=" OE1 GLN F 165 " model vdw 2.086 2.440 nonbonded pdb=" OD2 ASP D 152 " pdb=" OH TYR D 285 " model vdw 2.089 2.440 nonbonded pdb=" OH TYR C 150 " pdb=" OE1 GLN C 165 " model vdw 2.100 2.440 nonbonded pdb=" OH TYR K 150 " pdb=" OE1 GLN K 165 " model vdw 2.110 2.440 nonbonded pdb=" OH TYR I 150 " pdb=" OE1 GLN I 165 " model vdw 2.112 2.440 ... (remaining 341142 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 2.010 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: 0.030 Extract box with map and model: 11.520 Check model and map are aligned: 0.580 Set scattering table: 0.370 Process input model: 110.160 Find NCS groups from input model: 2.840 Set up NCS constraints: 0.420 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: 0.020 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.342 42504 Z= 0.715 Angle : 1.240 36.276 57684 Z= 0.518 Chirality : 0.048 0.342 6564 Planarity : 0.013 0.279 7260 Dihedral : 18.042 89.072 15564 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 0.66 % Allowed : 34.99 % Favored : 64.36 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.06 % 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 (0.11), residues: 5148 helix: 0.49 (0.13), residues: 1524 sheet: -1.10 (0.13), residues: 1308 loop : -2.01 (0.11), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 258 HIS 0.003 0.000 HIS C 429 PHE 0.035 0.002 PHE I 43 TYR 0.029 0.002 TYR I 285 ARG 0.013 0.001 ARG F 325 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1863 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 1834 time to evaluate : 4.540 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: A 16 LYS cc_start: 0.8433 (mmtt) cc_final: 0.8137 (mmtt) REVERT: A 71 ARG cc_start: 0.7798 (mtm-85) cc_final: 0.7172 (ptp-110) REVERT: A 88 GLU cc_start: 0.7164 (tm-30) cc_final: 0.6423 (tm-30) REVERT: A 133 PHE cc_start: 0.7948 (t80) cc_final: 0.7657 (t80) REVERT: A 185 TYR cc_start: 0.8756 (m-80) cc_final: 0.8402 (m-80) REVERT: A 267 LYS cc_start: 0.8244 (mtmt) cc_final: 0.7878 (mtmt) REVERT: A 345 ILE cc_start: 0.9041 (mm) cc_final: 0.8821 (mm) REVERT: A 399 ARG cc_start: 0.7877 (tpp80) cc_final: 0.7664 (tpp80) REVERT: A 443 VAL cc_start: 0.8692 (t) cc_final: 0.8425 (p) REVERT: B 179 ASP cc_start: 0.8157 (t0) cc_final: 0.7699 (t0) REVERT: B 247 LEU cc_start: 0.8512 (tp) cc_final: 0.8294 (tt) REVERT: B 263 VAL cc_start: 0.8938 (m) cc_final: 0.8735 (t) REVERT: B 267 LYS cc_start: 0.8342 (mtpt) cc_final: 0.8082 (mtmm) REVERT: B 436 ASP cc_start: 0.8051 (t0) cc_final: 0.7767 (t70) REVERT: C 179 ASP cc_start: 0.8325 (t0) cc_final: 0.8098 (t0) REVERT: C 427 LYS cc_start: 0.7421 (mmmm) cc_final: 0.7189 (mmtm) REVERT: D 168 LYS cc_start: 0.8689 (mtmt) cc_final: 0.8231 (mtpp) REVERT: D 180 THR cc_start: 0.8285 (p) cc_final: 0.8031 (m) REVERT: D 197 THR cc_start: 0.8594 (p) cc_final: 0.8293 (t) REVERT: D 232 LYS cc_start: 0.8254 (ptmt) cc_final: 0.7940 (ptmt) REVERT: D 234 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7211 (mm-30) REVERT: D 272 PHE cc_start: 0.7664 (m-80) cc_final: 0.7393 (m-10) REVERT: D 274 CYS cc_start: 0.8189 (m) cc_final: 0.7877 (m) REVERT: D 345 ILE cc_start: 0.8951 (mm) cc_final: 0.8724 (mm) REVERT: E 20 ARG cc_start: 0.7969 (ttm-80) cc_final: 0.7722 (mtm-85) REVERT: E 28 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7349 (mm-30) REVERT: E 144 ARG cc_start: 0.8052 (ttm110) cc_final: 0.7651 (ttm110) REVERT: E 171 ARG cc_start: 0.7048 (mtm-85) cc_final: 0.6524 (mtm-85) REVERT: E 180 THR cc_start: 0.8413 (m) cc_final: 0.8132 (m) REVERT: E 195 TYR cc_start: 0.7831 (m-80) cc_final: 0.7573 (m-10) REVERT: E 219 GLU cc_start: 0.4760 (OUTLIER) cc_final: 0.4504 (pp20) REVERT: E 297 TYR cc_start: 0.7759 (m-10) cc_final: 0.7432 (m-10) REVERT: E 303 TYR cc_start: 0.7899 (m-80) cc_final: 0.7660 (m-10) REVERT: E 405 GLU cc_start: 0.7154 (tp30) cc_final: 0.6855 (tp30) REVERT: E 438 GLN cc_start: 0.7582 (mp10) cc_final: 0.7202 (mp10) REVERT: F 20 ARG cc_start: 0.7743 (ttm-80) cc_final: 0.7528 (mtm-85) REVERT: F 43 PHE cc_start: 0.8889 (t80) cc_final: 0.8627 (t80) REVERT: F 314 MET cc_start: 0.7813 (mtp) cc_final: 0.7533 (ttp) REVERT: F 436 ASP cc_start: 0.7839 (t0) cc_final: 0.7380 (t0) REVERT: G 16 LYS cc_start: 0.8440 (mmtt) cc_final: 0.8154 (mmtt) REVERT: G 76 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7547 (mtt90) REVERT: G 88 GLU cc_start: 0.7135 (tt0) cc_final: 0.6893 (tm-30) REVERT: G 150 TYR cc_start: 0.8621 (m-80) cc_final: 0.8417 (m-80) REVERT: G 183 PHE cc_start: 0.8497 (m-80) cc_final: 0.8188 (m-80) REVERT: G 274 CYS cc_start: 0.8246 (m) cc_final: 0.7588 (m) REVERT: G 400 LYS cc_start: 0.8448 (tppt) cc_final: 0.7871 (tppt) REVERT: G 438 GLN cc_start: 0.8036 (mp10) cc_final: 0.7351 (mp10) REVERT: G 442 LYS cc_start: 0.8352 (mttt) cc_final: 0.8043 (tttt) REVERT: H 16 LYS cc_start: 0.8422 (mmtt) cc_final: 0.8185 (mmtt) REVERT: H 28 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7372 (mm-30) REVERT: H 30 ARG cc_start: 0.7284 (ptp-170) cc_final: 0.7049 (mtm110) REVERT: H 106 LYS cc_start: 0.7920 (mtmm) cc_final: 0.7671 (mtmm) REVERT: H 171 ARG cc_start: 0.7098 (mtm-85) cc_final: 0.6620 (mtm-85) REVERT: H 176 VAL cc_start: 0.8668 (p) cc_final: 0.8397 (m) REVERT: H 180 THR cc_start: 0.8379 (m) cc_final: 0.8086 (m) REVERT: H 400 LYS cc_start: 0.8097 (tppt) cc_final: 0.7884 (tppt) REVERT: H 436 ASP cc_start: 0.8279 (t0) cc_final: 0.8047 (t70) REVERT: I 70 ARG cc_start: 0.7700 (ttm110) cc_final: 0.7264 (ttm110) REVERT: I 75 ASP cc_start: 0.8140 (p0) cc_final: 0.7862 (p0) REVERT: I 188 MET cc_start: 0.8420 (mmt) cc_final: 0.8018 (mmt) REVERT: I 204 VAL cc_start: 0.8879 (m) cc_final: 0.8668 (t) REVERT: I 255 LEU cc_start: 0.8686 (tp) cc_final: 0.8484 (tt) REVERT: I 289 ARG cc_start: 0.7959 (ttp80) cc_final: 0.7560 (mtp-110) REVERT: I 319 ASP cc_start: 0.7546 (m-30) cc_final: 0.7201 (m-30) REVERT: I 400 LYS cc_start: 0.8116 (tppt) cc_final: 0.7836 (tppt) REVERT: I 434 ARG cc_start: 0.8394 (mpp80) cc_final: 0.6829 (mpp80) REVERT: J 99 LYS cc_start: 0.8948 (mmmm) cc_final: 0.8700 (mmmm) REVERT: J 154 TYR cc_start: 0.8626 (m-80) cc_final: 0.8396 (m-80) REVERT: J 183 PHE cc_start: 0.8508 (m-80) cc_final: 0.8197 (m-80) REVERT: J 245 SER cc_start: 0.8476 (p) cc_final: 0.8265 (p) REVERT: J 314 MET cc_start: 0.8319 (mtp) cc_final: 0.8084 (ttp) REVERT: J 378 THR cc_start: 0.8043 (m) cc_final: 0.7733 (p) REVERT: J 400 LYS cc_start: 0.8364 (tppt) cc_final: 0.7785 (tppt) REVERT: K 76 ARG cc_start: 0.8292 (mtt90) cc_final: 0.7887 (mtt90) REVERT: K 204 VAL cc_start: 0.8620 (m) cc_final: 0.8419 (p) REVERT: K 264 PHE cc_start: 0.8121 (p90) cc_final: 0.7825 (p90) REVERT: K 313 LEU cc_start: 0.8430 (mt) cc_final: 0.8082 (mm) REVERT: K 340 ASP cc_start: 0.7670 (t0) cc_final: 0.7297 (t0) REVERT: K 341 GLN cc_start: 0.7753 (mt0) cc_final: 0.7273 (mt0) REVERT: L 71 ARG cc_start: 0.7744 (mtm-85) cc_final: 0.7152 (ptp-110) REVERT: L 245 SER cc_start: 0.8470 (t) cc_final: 0.8249 (p) outliers start: 29 outliers final: 10 residues processed: 1843 average time/residue: 0.6171 time to fit residues: 1746.1090 Evaluate side-chains 1808 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1796 time to evaluate : 4.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain E residue 219 GLU Chi-restraints excluded: chain G residue 76 ARG Chi-restraints excluded: chain G residue 236 CYS Chi-restraints excluded: chain I residue 53 GLN Chi-restraints excluded: chain I residue 403 GLU Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain L residue 20 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 445 optimal weight: 1.9990 chunk 400 optimal weight: 0.9980 chunk 222 optimal weight: 3.9990 chunk 136 optimal weight: 0.6980 chunk 269 optimal weight: 0.1980 chunk 213 optimal weight: 0.5980 chunk 413 optimal weight: 4.9990 chunk 160 optimal weight: 0.9980 chunk 251 optimal weight: 6.9990 chunk 308 optimal weight: 5.9990 chunk 479 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 HIS ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 GLN ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 GLN ** C 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 GLN F 389 GLN F 441 GLN ** G 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 364 GLN H 364 GLN I 198 ASN ** J 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 308 HIS J 356 GLN L 198 ASN L 389 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.0728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 42504 Z= 0.185 Angle : 0.616 8.265 57684 Z= 0.304 Chirality : 0.042 0.142 6564 Planarity : 0.006 0.126 7260 Dihedral : 6.121 50.135 5923 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 4.19 % Allowed : 30.68 % Favored : 65.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.37 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.11), residues: 5148 helix: 0.69 (0.13), residues: 1548 sheet: -1.09 (0.13), residues: 1320 loop : -2.08 (0.11), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 258 HIS 0.003 0.000 HIS F 79 PHE 0.027 0.002 PHE A 264 TYR 0.018 0.001 TYR D 154 ARG 0.009 0.001 ARG H 411 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2025 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1840 time to evaluate : 4.875 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: A 71 ARG cc_start: 0.7862 (mtm-85) cc_final: 0.7230 (ptp-110) REVERT: A 88 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6706 (tm-30) REVERT: A 92 ARG cc_start: 0.7428 (mmp80) cc_final: 0.7055 (mmp80) REVERT: A 115 LYS cc_start: 0.8765 (mptp) cc_final: 0.8341 (mptp) REVERT: A 133 PHE cc_start: 0.7836 (t80) cc_final: 0.7522 (t80) REVERT: A 135 LEU cc_start: 0.8617 (mt) cc_final: 0.8281 (mm) REVERT: A 142 ARG cc_start: 0.7613 (tpp80) cc_final: 0.7311 (ttm-80) REVERT: A 258 TRP cc_start: 0.8625 (m100) cc_final: 0.7371 (m100) REVERT: A 325 ARG cc_start: 0.7708 (ptp-110) cc_final: 0.7447 (ttm-80) REVERT: A 396 LYS cc_start: 0.8403 (mmmm) cc_final: 0.7943 (mmtm) REVERT: A 399 ARG cc_start: 0.7958 (tpp80) cc_final: 0.7577 (tpp80) REVERT: A 443 VAL cc_start: 0.8683 (t) cc_final: 0.8412 (p) REVERT: B 72 MET cc_start: 0.7908 (tmm) cc_final: 0.7477 (tmm) REVERT: B 115 LYS cc_start: 0.8681 (mptp) cc_final: 0.8339 (mptp) REVERT: B 179 ASP cc_start: 0.8142 (t0) cc_final: 0.7871 (t0) REVERT: B 274 CYS cc_start: 0.8182 (m) cc_final: 0.7881 (m) REVERT: B 396 LYS cc_start: 0.8497 (mmmm) cc_final: 0.7976 (mmtm) REVERT: B 434 ARG cc_start: 0.8416 (mpp80) cc_final: 0.7097 (mpp80) REVERT: B 436 ASP cc_start: 0.8160 (t0) cc_final: 0.7952 (t70) REVERT: C 133 PHE cc_start: 0.8080 (t80) cc_final: 0.7859 (t80) REVERT: C 144 ARG cc_start: 0.8264 (ttm-80) cc_final: 0.7998 (ttm-80) REVERT: C 146 ASP cc_start: 0.7363 (p0) cc_final: 0.6759 (p0) REVERT: C 219 GLU cc_start: 0.5327 (OUTLIER) cc_final: 0.4950 (pp20) REVERT: D 146 ASP cc_start: 0.7092 (p0) cc_final: 0.6700 (p0) REVERT: D 163 TYR cc_start: 0.8503 (t80) cc_final: 0.8271 (t80) REVERT: D 168 LYS cc_start: 0.8702 (mtmt) cc_final: 0.8318 (mtpp) REVERT: D 180 THR cc_start: 0.8264 (p) cc_final: 0.8043 (m) REVERT: D 232 LYS cc_start: 0.8269 (ptmt) cc_final: 0.7965 (ptmt) REVERT: D 234 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7186 (mm-30) REVERT: D 272 PHE cc_start: 0.7677 (m-80) cc_final: 0.7445 (m-10) REVERT: D 274 CYS cc_start: 0.8228 (m) cc_final: 0.7923 (m) REVERT: D 285 TYR cc_start: 0.8000 (OUTLIER) cc_final: 0.7453 (t80) REVERT: D 345 ILE cc_start: 0.8943 (mm) cc_final: 0.8698 (mm) REVERT: E 20 ARG cc_start: 0.7974 (ttm-80) cc_final: 0.7729 (mtm-85) REVERT: E 88 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6830 (tt0) REVERT: E 115 LYS cc_start: 0.8725 (mptp) cc_final: 0.8365 (mptp) REVERT: E 144 ARG cc_start: 0.8001 (ttm110) cc_final: 0.7773 (ttm110) REVERT: E 171 ARG cc_start: 0.7040 (mtm-85) cc_final: 0.6616 (mtm-85) REVERT: E 180 THR cc_start: 0.8386 (m) cc_final: 0.8121 (m) REVERT: E 275 ARG cc_start: 0.7672 (ttt180) cc_final: 0.7393 (ptt180) REVERT: E 291 THR cc_start: 0.8737 (OUTLIER) cc_final: 0.8458 (p) REVERT: E 297 TYR cc_start: 0.7788 (m-10) cc_final: 0.7480 (m-10) REVERT: F 30 ARG cc_start: 0.7133 (ptp-110) cc_final: 0.6342 (ttm110) REVERT: F 43 PHE cc_start: 0.8907 (t80) cc_final: 0.8618 (t80) REVERT: F 133 PHE cc_start: 0.7988 (t80) cc_final: 0.7600 (t80) REVERT: F 184 MET cc_start: 0.7637 (tpp) cc_final: 0.7425 (tpp) REVERT: F 314 MET cc_start: 0.7842 (mtp) cc_final: 0.7568 (ttp) REVERT: F 433 LYS cc_start: 0.8362 (mmmt) cc_final: 0.8061 (mmmt) REVERT: F 436 ASP cc_start: 0.7847 (t0) cc_final: 0.7530 (t0) REVERT: F 441 GLN cc_start: 0.7862 (mt0) cc_final: 0.7628 (mt0) REVERT: G 16 LYS cc_start: 0.8388 (mmtt) cc_final: 0.8096 (mmtt) REVERT: G 43 PHE cc_start: 0.8939 (t80) cc_final: 0.8717 (t80) REVERT: G 76 ARG cc_start: 0.8149 (mtt90) cc_final: 0.7548 (mtt90) REVERT: G 88 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.7040 (tm-30) REVERT: G 115 LYS cc_start: 0.8820 (mptp) cc_final: 0.8459 (mptp) REVERT: G 118 ASP cc_start: 0.7957 (m-30) cc_final: 0.7755 (m-30) REVERT: G 248 TYR cc_start: 0.7932 (m-10) cc_final: 0.7658 (m-10) REVERT: G 274 CYS cc_start: 0.8223 (m) cc_final: 0.7583 (m) REVERT: G 285 TYR cc_start: 0.8060 (OUTLIER) cc_final: 0.6988 (t80) REVERT: G 400 LYS cc_start: 0.8407 (tppt) cc_final: 0.7773 (tppt) REVERT: G 403 GLU cc_start: 0.7530 (mp0) cc_final: 0.7197 (mp0) REVERT: G 438 GLN cc_start: 0.7988 (mp10) cc_final: 0.7248 (mp10) REVERT: G 442 LYS cc_start: 0.8350 (mttt) cc_final: 0.8116 (tttm) REVERT: G 448 ASP cc_start: 0.7611 (t0) cc_final: 0.7390 (t0) REVERT: H 16 LYS cc_start: 0.8418 (mmtt) cc_final: 0.8179 (mmtt) REVERT: H 72 MET cc_start: 0.7942 (tmm) cc_final: 0.7515 (tmm) REVERT: H 76 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7529 (mtt90) REVERT: H 115 LYS cc_start: 0.8802 (mptp) cc_final: 0.8420 (mptp) REVERT: H 135 LEU cc_start: 0.8667 (mt) cc_final: 0.8436 (mm) REVERT: H 171 ARG cc_start: 0.7183 (mtm-85) cc_final: 0.6612 (mtm-85) REVERT: H 180 THR cc_start: 0.8364 (m) cc_final: 0.8103 (m) REVERT: H 291 THR cc_start: 0.8662 (OUTLIER) cc_final: 0.8386 (p) REVERT: H 436 ASP cc_start: 0.8244 (t0) cc_final: 0.8029 (t70) REVERT: I 5 TYR cc_start: 0.7804 (m-10) cc_final: 0.7580 (m-80) REVERT: I 30 ARG cc_start: 0.7090 (ptp90) cc_final: 0.5620 (ptp90) REVERT: I 72 MET cc_start: 0.7890 (tmm) cc_final: 0.7674 (tmm) REVERT: I 133 PHE cc_start: 0.7714 (t80) cc_final: 0.7446 (t80) REVERT: I 135 LEU cc_start: 0.8500 (mt) cc_final: 0.8280 (mm) REVERT: I 285 TYR cc_start: 0.7934 (OUTLIER) cc_final: 0.7404 (t80) REVERT: I 400 LYS cc_start: 0.8091 (tppt) cc_final: 0.7697 (tppt) REVERT: I 403 GLU cc_start: 0.7280 (mp0) cc_final: 0.7035 (mp0) REVERT: I 434 ARG cc_start: 0.8389 (mpp80) cc_final: 0.6824 (mpp80) REVERT: J 71 ARG cc_start: 0.7867 (mtm110) cc_final: 0.7581 (mtm-85) REVERT: J 76 ARG cc_start: 0.8260 (mtp85) cc_final: 0.8022 (mtt90) REVERT: J 99 LYS cc_start: 0.8932 (mmmm) cc_final: 0.8628 (mmmm) REVERT: J 115 LYS cc_start: 0.8792 (mptp) cc_final: 0.8399 (mptp) REVERT: J 183 PHE cc_start: 0.8598 (m-80) cc_final: 0.8233 (m-80) REVERT: J 240 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7985 (mp) REVERT: J 245 SER cc_start: 0.8504 (p) cc_final: 0.8267 (p) REVERT: J 314 MET cc_start: 0.8322 (mtp) cc_final: 0.8099 (ttp) REVERT: J 378 THR cc_start: 0.8061 (m) cc_final: 0.7773 (p) REVERT: J 383 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8073 (ppp) REVERT: J 400 LYS cc_start: 0.8343 (tppt) cc_final: 0.7895 (tppt) REVERT: J 433 LYS cc_start: 0.8425 (mmmt) cc_final: 0.8150 (mmmt) REVERT: K 76 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7908 (mtt90) REVERT: K 88 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6933 (tt0) REVERT: K 115 LYS cc_start: 0.8767 (mptp) cc_final: 0.8491 (mptp) REVERT: K 204 VAL cc_start: 0.8604 (m) cc_final: 0.8400 (p) REVERT: K 283 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7713 (tt0) REVERT: K 313 LEU cc_start: 0.8422 (mt) cc_final: 0.8083 (mm) REVERT: K 340 ASP cc_start: 0.7644 (t0) cc_final: 0.7293 (t0) REVERT: K 378 THR cc_start: 0.7901 (m) cc_final: 0.7648 (p) REVERT: L 20 ARG cc_start: 0.7769 (mtm-85) cc_final: 0.7394 (mtm-85) REVERT: L 171 ARG cc_start: 0.6741 (mtm-85) cc_final: 0.6318 (mtm-85) REVERT: L 202 GLU cc_start: 0.7992 (tp30) cc_final: 0.7469 (tp30) REVERT: L 238 ARG cc_start: 0.7491 (ttm110) cc_final: 0.7040 (mtm110) REVERT: L 271 SER cc_start: 0.7465 (p) cc_final: 0.7175 (m) REVERT: L 283 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7497 (mp0) REVERT: L 383 MET cc_start: 0.8724 (ttp) cc_final: 0.8248 (ttp) REVERT: L 427 LYS cc_start: 0.6884 (OUTLIER) cc_final: 0.6569 (mmtm) REVERT: L 434 ARG cc_start: 0.8259 (mpp80) cc_final: 0.6841 (mpp80) REVERT: L 446 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7363 (mm-30) outliers start: 185 outliers final: 103 residues processed: 1916 average time/residue: 0.6573 time to fit residues: 1958.3371 Evaluate side-chains 1934 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1814 time to evaluate : 5.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 236 CYS Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 342 MET Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 236 CYS Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 342 MET Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 403 GLU Chi-restraints excluded: chain F residue 16 LYS Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 134 CYS Chi-restraints excluded: chain F residue 245 SER Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 77 LYS Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 348 THR Chi-restraints excluded: chain G residue 397 GLU Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 236 CYS Chi-restraints excluded: chain H residue 291 THR Chi-restraints excluded: chain H residue 305 VAL Chi-restraints excluded: chain H residue 342 MET Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 403 GLU Chi-restraints excluded: chain H residue 429 HIS Chi-restraints excluded: chain I residue 73 MET Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 238 ARG Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 291 THR Chi-restraints excluded: chain I residue 348 THR Chi-restraints excluded: chain I residue 358 LEU Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 228 MET Chi-restraints excluded: chain J residue 236 CYS Chi-restraints excluded: chain J residue 240 LEU Chi-restraints excluded: chain J residue 291 THR Chi-restraints excluded: chain J residue 318 THR Chi-restraints excluded: chain J residue 348 THR Chi-restraints excluded: chain J residue 383 MET Chi-restraints excluded: chain K residue 76 ARG Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain K residue 202 GLU Chi-restraints excluded: chain K residue 236 CYS Chi-restraints excluded: chain K residue 283 GLU Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 362 LEU Chi-restraints excluded: chain K residue 403 GLU Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 146 ASP Chi-restraints excluded: chain L residue 167 ILE Chi-restraints excluded: chain L residue 194 SER Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 283 GLU Chi-restraints excluded: chain L residue 301 THR Chi-restraints excluded: chain L residue 348 THR Chi-restraints excluded: chain L residue 358 LEU Chi-restraints excluded: chain L residue 427 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 266 optimal weight: 0.9980 chunk 148 optimal weight: 4.9990 chunk 399 optimal weight: 3.9990 chunk 326 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 480 optimal weight: 8.9990 chunk 518 optimal weight: 5.9990 chunk 427 optimal weight: 4.9990 chunk 476 optimal weight: 6.9990 chunk 163 optimal weight: 4.9990 chunk 385 optimal weight: 2.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 HIS B 356 GLN ** C 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 GLN ** D 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 307 HIS G 31 GLN G 308 HIS ** G 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 364 GLN H 364 GLN ** I 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 308 HIS ** J 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 364 GLN J 441 GLN K 429 HIS ** L 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.093 42504 Z= 0.542 Angle : 0.754 11.980 57684 Z= 0.381 Chirality : 0.049 0.180 6564 Planarity : 0.006 0.117 7260 Dihedral : 6.304 38.920 5892 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 6.82 % Allowed : 28.31 % Favored : 64.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % 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: -1.66 (0.11), residues: 5148 helix: 0.38 (0.13), residues: 1620 sheet: -1.30 (0.14), residues: 1116 loop : -2.06 (0.11), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP K 258 HIS 0.007 0.001 HIS K 79 PHE 0.026 0.003 PHE K 264 TYR 0.037 0.003 TYR L 382 ARG 0.014 0.001 ARG G 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2314 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 301 poor density : 2013 time to evaluate : 4.567 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: A 41 ARG cc_start: 0.7892 (tpp-160) cc_final: 0.7462 (tpp-160) REVERT: A 52 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7612 (mt-10) REVERT: A 63 ASP cc_start: 0.7576 (t0) cc_final: 0.7042 (t0) REVERT: A 71 ARG cc_start: 0.7922 (mtm-85) cc_final: 0.7676 (mtm-85) REVERT: A 78 TYR cc_start: 0.8940 (m-80) cc_final: 0.8658 (m-80) REVERT: A 88 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.6802 (tm-30) REVERT: A 92 ARG cc_start: 0.7604 (mmp80) cc_final: 0.7239 (mmp80) REVERT: A 98 ARG cc_start: 0.8278 (mtm180) cc_final: 0.7738 (mtm180) REVERT: A 106 LYS cc_start: 0.8346 (mtmm) cc_final: 0.8038 (mtmm) REVERT: A 115 LYS cc_start: 0.8838 (mptp) cc_final: 0.8308 (mptp) REVERT: A 133 PHE cc_start: 0.7819 (t80) cc_final: 0.7505 (t80) REVERT: A 135 LEU cc_start: 0.8693 (mt) cc_final: 0.8316 (mm) REVERT: A 146 ASP cc_start: 0.7447 (p0) cc_final: 0.6829 (p0) REVERT: A 165 GLN cc_start: 0.8350 (mt0) cc_final: 0.8097 (mt0) REVERT: A 171 ARG cc_start: 0.7372 (mtm-85) cc_final: 0.6876 (mtm-85) REVERT: A 176 VAL cc_start: 0.8604 (OUTLIER) cc_final: 0.8318 (t) REVERT: A 185 TYR cc_start: 0.8744 (m-80) cc_final: 0.8406 (m-80) REVERT: A 188 MET cc_start: 0.8396 (mmt) cc_final: 0.8006 (mmt) REVERT: A 267 LYS cc_start: 0.8240 (mtmt) cc_final: 0.7975 (mtmt) REVERT: A 278 THR cc_start: 0.9015 (OUTLIER) cc_final: 0.8617 (p) REVERT: A 285 TYR cc_start: 0.8334 (OUTLIER) cc_final: 0.6916 (t80) REVERT: A 324 GLU cc_start: 0.7011 (tt0) cc_final: 0.6618 (tt0) REVERT: A 345 ILE cc_start: 0.9104 (mm) cc_final: 0.8887 (mm) REVERT: A 443 VAL cc_start: 0.8716 (t) cc_final: 0.8437 (p) REVERT: B 24 MET cc_start: 0.8637 (pmm) cc_final: 0.8338 (pmm) REVERT: B 41 ARG cc_start: 0.7881 (tpp-160) cc_final: 0.7397 (tpp-160) REVERT: B 84 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.7943 (mmm) REVERT: B 85 ARG cc_start: 0.7548 (mmp80) cc_final: 0.7312 (mmp80) REVERT: B 111 ASN cc_start: 0.8577 (t0) cc_final: 0.8362 (t0) REVERT: B 115 LYS cc_start: 0.8795 (mptp) cc_final: 0.8252 (mptp) REVERT: B 146 ASP cc_start: 0.7439 (p0) cc_final: 0.6941 (p0) REVERT: B 179 ASP cc_start: 0.8244 (t0) cc_final: 0.7725 (t70) REVERT: B 184 MET cc_start: 0.8621 (mmm) cc_final: 0.8007 (tpp) REVERT: B 234 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7361 (mm-30) REVERT: B 274 CYS cc_start: 0.8186 (m) cc_final: 0.7790 (m) REVERT: B 436 ASP cc_start: 0.8579 (t0) cc_final: 0.8084 (t70) REVERT: B 447 PHE cc_start: 0.8506 (m-80) cc_final: 0.8120 (m-10) REVERT: C 51 ILE cc_start: 0.8476 (mm) cc_final: 0.8207 (mm) REVERT: C 76 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7984 (mtt90) REVERT: C 92 ARG cc_start: 0.7891 (mmp80) cc_final: 0.7546 (mmp80) REVERT: C 144 ARG cc_start: 0.8335 (ttm-80) cc_final: 0.8087 (ttm110) REVERT: C 146 ASP cc_start: 0.7578 (p0) cc_final: 0.7119 (p0) REVERT: C 219 GLU cc_start: 0.5814 (OUTLIER) cc_final: 0.5603 (pp20) REVERT: C 258 TRP cc_start: 0.8714 (m100) cc_final: 0.7867 (m100) REVERT: C 325 ARG cc_start: 0.7878 (ttm-80) cc_final: 0.7490 (ttp-170) REVERT: C 396 LYS cc_start: 0.8501 (tppt) cc_final: 0.8089 (mmtm) REVERT: C 403 GLU cc_start: 0.7531 (mp0) cc_final: 0.7222 (mp0) REVERT: D 20 ARG cc_start: 0.7906 (mtm-85) cc_final: 0.7492 (mtm-85) REVERT: D 28 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7320 (mm-30) REVERT: D 63 ASP cc_start: 0.7588 (t0) cc_final: 0.7086 (t0) REVERT: D 88 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7234 (tm-30) REVERT: D 92 ARG cc_start: 0.8078 (mtp85) cc_final: 0.7383 (mtp85) REVERT: D 106 LYS cc_start: 0.8202 (mtmm) cc_final: 0.7984 (mtmm) REVERT: D 146 ASP cc_start: 0.7515 (p0) cc_final: 0.7008 (p0) REVERT: D 150 TYR cc_start: 0.8662 (m-80) cc_final: 0.8298 (m-10) REVERT: D 163 TYR cc_start: 0.8722 (t80) cc_final: 0.8421 (t80) REVERT: D 165 GLN cc_start: 0.8138 (mt0) cc_final: 0.7818 (mt0) REVERT: D 188 MET cc_start: 0.8354 (mmt) cc_final: 0.7876 (mmt) REVERT: D 197 THR cc_start: 0.8583 (p) cc_final: 0.8260 (t) REVERT: D 201 ASP cc_start: 0.8445 (t0) cc_final: 0.8240 (t0) REVERT: D 205 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8583 (mt) REVERT: D 232 LYS cc_start: 0.8360 (ptmt) cc_final: 0.8159 (ptmt) REVERT: D 234 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7310 (mm-30) REVERT: D 246 THR cc_start: 0.8608 (m) cc_final: 0.8120 (p) REVERT: D 274 CYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7921 (m) REVERT: D 285 TYR cc_start: 0.8366 (OUTLIER) cc_final: 0.7477 (t80) REVERT: D 297 TYR cc_start: 0.7722 (m-10) cc_final: 0.7452 (m-10) REVERT: D 314 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.7999 (ttp) REVERT: D 324 GLU cc_start: 0.7128 (tt0) cc_final: 0.6722 (tt0) REVERT: D 383 MET cc_start: 0.8735 (ttp) cc_final: 0.8262 (ttp) REVERT: D 448 ASP cc_start: 0.7710 (t0) cc_final: 0.7485 (t0) REVERT: E 6 VAL cc_start: 0.8159 (t) cc_final: 0.7933 (m) REVERT: E 24 MET cc_start: 0.8806 (pmm) cc_final: 0.8405 (pmm) REVERT: E 106 LYS cc_start: 0.8180 (mtmm) cc_final: 0.7929 (mtmm) REVERT: E 115 LYS cc_start: 0.8818 (mptp) cc_final: 0.8287 (mptp) REVERT: E 144 ARG cc_start: 0.8147 (ttm110) cc_final: 0.7684 (mmm-85) REVERT: E 146 ASP cc_start: 0.7523 (p0) cc_final: 0.7248 (p0) REVERT: E 171 ARG cc_start: 0.7531 (mtm-85) cc_final: 0.6976 (mtm-85) REVERT: E 180 THR cc_start: 0.8576 (m) cc_final: 0.8284 (m) REVERT: E 197 THR cc_start: 0.8483 (p) cc_final: 0.8183 (t) REVERT: E 201 ASP cc_start: 0.8444 (t0) cc_final: 0.8182 (t0) REVERT: E 243 VAL cc_start: 0.8421 (m) cc_final: 0.8115 (p) REVERT: E 275 ARG cc_start: 0.7654 (ttt180) cc_final: 0.7331 (ttp80) REVERT: E 289 ARG cc_start: 0.8220 (mtp-110) cc_final: 0.7869 (ttp80) REVERT: E 297 TYR cc_start: 0.7912 (m-10) cc_final: 0.7393 (m-10) REVERT: E 426 GLN cc_start: 0.7176 (mt0) cc_final: 0.6814 (mt0) REVERT: E 436 ASP cc_start: 0.8615 (t0) cc_final: 0.8160 (t70) REVERT: E 447 PHE cc_start: 0.8526 (m-80) cc_final: 0.8127 (m-10) REVERT: F 20 ARG cc_start: 0.7894 (ttm-80) cc_final: 0.7642 (mtm-85) REVERT: F 30 ARG cc_start: 0.7224 (ptp-110) cc_final: 0.7013 (ptp-170) REVERT: F 51 ILE cc_start: 0.8504 (mm) cc_final: 0.8245 (mm) REVERT: F 85 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.7172 (mmp80) REVERT: F 115 LYS cc_start: 0.8798 (mptp) cc_final: 0.8547 (mptp) REVERT: F 314 MET cc_start: 0.8289 (mtp) cc_final: 0.8002 (ttp) REVERT: F 316 LYS cc_start: 0.8263 (tppp) cc_final: 0.8046 (tppp) REVERT: F 325 ARG cc_start: 0.7642 (ptp-110) cc_final: 0.7341 (ttm110) REVERT: F 399 ARG cc_start: 0.7850 (tpp80) cc_final: 0.7541 (tpp80) REVERT: F 403 GLU cc_start: 0.7425 (mp0) cc_final: 0.7076 (mp0) REVERT: F 433 LYS cc_start: 0.8423 (mmmt) cc_final: 0.8128 (mmmt) REVERT: F 436 ASP cc_start: 0.8301 (t0) cc_final: 0.8046 (t0) REVERT: F 441 GLN cc_start: 0.7669 (mt0) cc_final: 0.7439 (mt0) REVERT: G 16 LYS cc_start: 0.8447 (mmtt) cc_final: 0.8167 (mmtt) REVERT: G 30 ARG cc_start: 0.7462 (pmt170) cc_final: 0.7009 (pmt170) REVERT: G 41 ARG cc_start: 0.7846 (tpp-160) cc_final: 0.7326 (tpp-160) REVERT: G 52 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7013 (mm-30) REVERT: G 63 ASP cc_start: 0.7463 (t0) cc_final: 0.6931 (t0) REVERT: G 76 ARG cc_start: 0.8244 (mtt90) cc_final: 0.7271 (mtt90) REVERT: G 88 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.6998 (tm-30) REVERT: G 92 ARG cc_start: 0.7722 (mmp80) cc_final: 0.7183 (mmp80) REVERT: G 106 LYS cc_start: 0.8139 (mtmm) cc_final: 0.7912 (mtmm) REVERT: G 111 ASN cc_start: 0.8769 (t0) cc_final: 0.8437 (t0) REVERT: G 115 LYS cc_start: 0.8855 (mptp) cc_final: 0.8331 (mptp) REVERT: G 135 LEU cc_start: 0.8790 (mt) cc_final: 0.8288 (mt) REVERT: G 163 TYR cc_start: 0.8639 (t80) cc_final: 0.8280 (t80) REVERT: G 184 MET cc_start: 0.8520 (mmm) cc_final: 0.8146 (mmm) REVERT: G 188 MET cc_start: 0.8360 (mmt) cc_final: 0.7629 (mmt) REVERT: G 201 ASP cc_start: 0.8443 (t0) cc_final: 0.8208 (t0) REVERT: G 234 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7303 (mm-30) REVERT: G 274 CYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7678 (m) REVERT: G 275 ARG cc_start: 0.7540 (OUTLIER) cc_final: 0.7123 (ptt180) REVERT: G 285 TYR cc_start: 0.8327 (OUTLIER) cc_final: 0.7081 (t80) REVERT: G 297 TYR cc_start: 0.7924 (m-10) cc_final: 0.7667 (m-10) REVERT: G 324 GLU cc_start: 0.7041 (tt0) cc_final: 0.6553 (tt0) REVERT: G 383 MET cc_start: 0.8621 (ttp) cc_final: 0.8376 (ttm) REVERT: G 397 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7811 (mm-30) REVERT: G 403 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7074 (mp0) REVERT: G 442 LYS cc_start: 0.8533 (mttt) cc_final: 0.8314 (tttm) REVERT: G 448 ASP cc_start: 0.7621 (t0) cc_final: 0.7401 (t0) REVERT: H 6 VAL cc_start: 0.7997 (t) cc_final: 0.7744 (m) REVERT: H 16 LYS cc_start: 0.8504 (mmtt) cc_final: 0.8200 (mmtt) REVERT: H 20 ARG cc_start: 0.8006 (ttm-80) cc_final: 0.7715 (mtm-85) REVERT: H 85 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.7159 (mmp80) REVERT: H 86 SER cc_start: 0.7469 (OUTLIER) cc_final: 0.7057 (p) REVERT: H 88 GLU cc_start: 0.7775 (tt0) cc_final: 0.7100 (tm-30) REVERT: H 111 ASN cc_start: 0.8621 (t0) cc_final: 0.8277 (t0) REVERT: H 115 LYS cc_start: 0.8746 (mptp) cc_final: 0.8241 (mptp) REVERT: H 146 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.6731 (p0) REVERT: H 171 ARG cc_start: 0.7656 (mtm-85) cc_final: 0.7083 (mtm-85) REVERT: H 180 THR cc_start: 0.8462 (m) cc_final: 0.8213 (m) REVERT: H 239 VAL cc_start: 0.8749 (t) cc_final: 0.8391 (p) REVERT: H 403 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.7073 (mp0) REVERT: H 405 GLU cc_start: 0.7843 (tp30) cc_final: 0.7498 (tp30) REVERT: H 406 LYS cc_start: 0.8953 (mmtp) cc_final: 0.8017 (mmtp) REVERT: H 436 ASP cc_start: 0.8560 (t0) cc_final: 0.8292 (t70) REVERT: H 447 PHE cc_start: 0.8518 (m-80) cc_final: 0.8182 (m-10) REVERT: I 16 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8306 (mtpt) REVERT: I 22 TYR cc_start: 0.8566 (m-80) cc_final: 0.8197 (m-80) REVERT: I 30 ARG cc_start: 0.7110 (ptp90) cc_final: 0.6471 (ptp90) REVERT: I 52 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7550 (mt-10) REVERT: I 72 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7704 (tmm) REVERT: I 106 LYS cc_start: 0.8223 (mtmm) cc_final: 0.8018 (mtmm) REVERT: I 135 LEU cc_start: 0.8645 (mt) cc_final: 0.8386 (mm) REVERT: I 150 TYR cc_start: 0.8707 (m-10) cc_final: 0.8479 (m-10) REVERT: I 165 GLN cc_start: 0.8183 (mt0) cc_final: 0.7892 (mt0) REVERT: I 192 TYR cc_start: 0.8975 (m-80) cc_final: 0.8454 (m-80) REVERT: I 203 GLN cc_start: 0.8610 (mt0) cc_final: 0.8346 (mt0) REVERT: I 258 TRP cc_start: 0.8647 (m100) cc_final: 0.8121 (m100) REVERT: I 266 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8481 (mt) REVERT: I 303 TYR cc_start: 0.8560 (m-10) cc_final: 0.8231 (m-80) REVERT: I 325 ARG cc_start: 0.7908 (ttm170) cc_final: 0.7422 (ttm170) REVERT: I 400 LYS cc_start: 0.8308 (tppt) cc_final: 0.7863 (tppt) REVERT: I 403 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7072 (mp0) REVERT: I 405 GLU cc_start: 0.7775 (mp0) cc_final: 0.7216 (mp0) REVERT: I 426 GLN cc_start: 0.7342 (mt0) cc_final: 0.7025 (mt0) REVERT: I 436 ASP cc_start: 0.8370 (t0) cc_final: 0.8111 (t0) REVERT: I 441 GLN cc_start: 0.7723 (mt0) cc_final: 0.7402 (mt0) REVERT: J 41 ARG cc_start: 0.7842 (tpp-160) cc_final: 0.7373 (tpp-160) REVERT: J 63 ASP cc_start: 0.7645 (t0) cc_final: 0.7391 (t0) REVERT: J 72 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.8167 (tmm) REVERT: J 92 ARG cc_start: 0.7727 (mmp80) cc_final: 0.7278 (mmp80) REVERT: J 99 LYS cc_start: 0.8861 (mmmm) cc_final: 0.8524 (mmmm) REVERT: J 106 LYS cc_start: 0.8325 (mtmm) cc_final: 0.8062 (mtmm) REVERT: J 115 LYS cc_start: 0.8823 (mptp) cc_final: 0.8314 (mptp) REVERT: J 171 ARG cc_start: 0.7447 (mtm-85) cc_final: 0.6878 (mtm-85) REVERT: J 248 TYR cc_start: 0.8008 (m-10) cc_final: 0.7360 (m-10) REVERT: J 275 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.6407 (ptt180) REVERT: J 285 TYR cc_start: 0.8291 (OUTLIER) cc_final: 0.6934 (t80) REVERT: J 288 LYS cc_start: 0.8793 (mttm) cc_final: 0.8586 (mttp) REVERT: J 305 VAL cc_start: 0.8703 (t) cc_final: 0.8483 (m) REVERT: J 314 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.8165 (ttp) REVERT: J 324 GLU cc_start: 0.7156 (tt0) cc_final: 0.6776 (tt0) REVERT: J 403 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7109 (mp0) REVERT: J 433 LYS cc_start: 0.8602 (mmmt) cc_final: 0.8249 (mmmt) REVERT: K 28 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7293 (mm-30) REVERT: K 41 ARG cc_start: 0.7908 (tpp-160) cc_final: 0.7326 (tpp-160) REVERT: K 63 ASP cc_start: 0.7496 (t0) cc_final: 0.7113 (t0) REVERT: K 76 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.8078 (mtt90) REVERT: K 88 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7242 (tt0) REVERT: K 115 LYS cc_start: 0.8796 (mptp) cc_final: 0.8440 (mptp) REVERT: K 143 GLN cc_start: 0.8413 (tt0) cc_final: 0.8207 (tt0) REVERT: K 171 ARG cc_start: 0.7392 (mtm-85) cc_final: 0.7076 (mtm-85) REVERT: K 184 MET cc_start: 0.8507 (mmm) cc_final: 0.8080 (mmm) REVERT: K 202 GLU cc_start: 0.8274 (tp30) cc_final: 0.8021 (tp30) REVERT: K 238 ARG cc_start: 0.7454 (ttm110) cc_final: 0.7115 (mtm110) REVERT: K 270 LEU cc_start: 0.8337 (mp) cc_final: 0.8110 (mt) REVERT: K 283 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7707 (tt0) REVERT: K 316 LYS cc_start: 0.8384 (tptm) cc_final: 0.7872 (ttmt) REVERT: K 396 LYS cc_start: 0.8345 (tppt) cc_final: 0.8052 (tppt) REVERT: K 403 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7171 (mp0) REVERT: K 441 GLN cc_start: 0.7543 (mt0) cc_final: 0.7242 (mt0) REVERT: L 20 ARG cc_start: 0.7919 (mtm-85) cc_final: 0.7533 (mtm-85) REVERT: L 92 ARG cc_start: 0.7669 (mmp80) cc_final: 0.7318 (mmp80) REVERT: L 106 LYS cc_start: 0.8339 (mtmm) cc_final: 0.8068 (mtmm) REVERT: L 135 LEU cc_start: 0.8642 (mt) cc_final: 0.8369 (mm) REVERT: L 168 LYS cc_start: 0.8935 (mtmt) cc_final: 0.8699 (mtmt) REVERT: L 232 LYS cc_start: 0.8261 (ptmt) cc_final: 0.7811 (ptmt) REVERT: L 238 ARG cc_start: 0.7512 (ttm110) cc_final: 0.7167 (mtm110) REVERT: L 245 SER cc_start: 0.8766 (p) cc_final: 0.8420 (t) REVERT: L 258 TRP cc_start: 0.8576 (m100) cc_final: 0.7813 (m100) REVERT: L 283 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7365 (mp0) REVERT: L 285 TYR cc_start: 0.8166 (OUTLIER) cc_final: 0.7369 (t80) REVERT: L 324 GLU cc_start: 0.7071 (tt0) cc_final: 0.6778 (tt0) REVERT: L 383 MET cc_start: 0.8617 (ttp) cc_final: 0.8364 (ttm) REVERT: L 403 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7128 (mp0) REVERT: L 427 LYS cc_start: 0.7137 (OUTLIER) cc_final: 0.6788 (mmtt) REVERT: L 429 HIS cc_start: 0.8579 (OUTLIER) cc_final: 0.8229 (m-70) REVERT: L 446 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7350 (mm-30) outliers start: 301 outliers final: 165 residues processed: 2123 average time/residue: 0.6296 time to fit residues: 2043.1063 Evaluate side-chains 2162 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 1957 time to evaluate : 4.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 319 ASP Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 342 MET Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 398 CYS Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 411 ARG Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 274 CYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 396 LYS Chi-restraints excluded: chain D residue 398 CYS Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 120 GLN Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 292 MET Chi-restraints excluded: chain E residue 342 MET Chi-restraints excluded: chain E residue 398 CYS Chi-restraints excluded: chain E residue 403 GLU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 85 ARG Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 120 GLN Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain F residue 357 LYS Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 411 ARG Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain G residue 77 LYS Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain G residue 236 CYS Chi-restraints excluded: chain G residue 247 LEU Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 274 CYS Chi-restraints excluded: chain G residue 275 ARG Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 316 LYS Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 348 THR Chi-restraints excluded: chain G residue 403 GLU Chi-restraints excluded: chain G residue 411 ARG Chi-restraints excluded: chain G residue 440 ILE Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 85 ARG Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 146 ASP Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 245 SER Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 292 MET Chi-restraints excluded: chain H residue 342 MET Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 379 MET Chi-restraints excluded: chain H residue 398 CYS Chi-restraints excluded: chain H residue 403 GLU Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 75 ASP Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 120 GLN Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain I residue 215 THR Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 291 THR Chi-restraints excluded: chain I residue 301 THR Chi-restraints excluded: chain I residue 348 THR Chi-restraints excluded: chain I residue 358 LEU Chi-restraints excluded: chain I residue 403 GLU Chi-restraints excluded: chain I residue 408 LEU Chi-restraints excluded: chain J residue 72 MET Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 120 GLN Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 228 MET Chi-restraints excluded: chain J residue 236 CYS Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain J residue 275 ARG Chi-restraints excluded: chain J residue 277 ASP Chi-restraints excluded: chain J residue 278 THR Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 291 THR Chi-restraints excluded: chain J residue 314 MET Chi-restraints excluded: chain J residue 318 THR Chi-restraints excluded: chain J residue 348 THR Chi-restraints excluded: chain J residue 383 MET Chi-restraints excluded: chain J residue 403 GLU Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 55 ILE Chi-restraints excluded: chain K residue 76 ARG Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 277 ASP Chi-restraints excluded: chain K residue 283 GLU Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 292 MET Chi-restraints excluded: chain K residue 358 LEU Chi-restraints excluded: chain K residue 362 LEU Chi-restraints excluded: chain K residue 398 CYS Chi-restraints excluded: chain K residue 403 GLU Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 120 GLN Chi-restraints excluded: chain L residue 146 ASP Chi-restraints excluded: chain L residue 167 ILE Chi-restraints excluded: chain L residue 194 SER Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain L residue 283 GLU Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 301 THR Chi-restraints excluded: chain L residue 342 MET Chi-restraints excluded: chain L residue 348 THR Chi-restraints excluded: chain L residue 358 LEU Chi-restraints excluded: chain L residue 403 GLU Chi-restraints excluded: chain L residue 405 GLU Chi-restraints excluded: chain L residue 427 LYS Chi-restraints excluded: chain L residue 429 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 474 optimal weight: 0.9990 chunk 361 optimal weight: 0.8980 chunk 249 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 229 optimal weight: 0.9990 chunk 322 optimal weight: 2.9990 chunk 482 optimal weight: 3.9990 chunk 510 optimal weight: 6.9990 chunk 251 optimal weight: 2.9990 chunk 456 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 ASN ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 GLN ** C 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 GLN ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 389 GLN F 356 GLN F 389 GLN G 364 GLN G 438 GLN ** H 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 198 ASN H 364 GLN ** I 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 356 GLN J 364 GLN K 203 GLN ** K 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 42504 Z= 0.264 Angle : 0.633 8.182 57684 Z= 0.316 Chirality : 0.044 0.177 6564 Planarity : 0.005 0.097 7260 Dihedral : 6.019 36.615 5892 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 6.09 % Allowed : 30.48 % Favored : 63.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.37 % 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: -1.53 (0.11), residues: 5148 helix: 0.58 (0.14), residues: 1620 sheet: -1.24 (0.14), residues: 1116 loop : -2.04 (0.11), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 175 HIS 0.002 0.001 HIS A 308 PHE 0.038 0.002 PHE E 264 TYR 0.024 0.002 TYR G 5 ARG 0.009 0.001 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2198 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 1929 time to evaluate : 4.990 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: A 16 LYS cc_start: 0.8406 (mmtt) cc_final: 0.8080 (mmtt) REVERT: A 28 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7367 (mm-30) REVERT: A 41 ARG cc_start: 0.7737 (tpp-160) cc_final: 0.7286 (tpp-160) REVERT: A 85 ARG cc_start: 0.7492 (mmp80) cc_final: 0.7282 (mmp80) REVERT: A 88 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6576 (tm-30) REVERT: A 92 ARG cc_start: 0.7581 (mmp80) cc_final: 0.7211 (mmp80) REVERT: A 98 ARG cc_start: 0.8255 (mtm180) cc_final: 0.7738 (mtm180) REVERT: A 106 LYS cc_start: 0.8364 (mtmm) cc_final: 0.8075 (mtmm) REVERT: A 133 PHE cc_start: 0.7835 (t80) cc_final: 0.7493 (t80) REVERT: A 135 LEU cc_start: 0.8623 (mt) cc_final: 0.8202 (mm) REVERT: A 146 ASP cc_start: 0.7284 (p0) cc_final: 0.6485 (p0) REVERT: A 171 ARG cc_start: 0.7251 (mtm-85) cc_final: 0.6734 (mtm-85) REVERT: A 176 VAL cc_start: 0.8614 (OUTLIER) cc_final: 0.8339 (t) REVERT: A 184 MET cc_start: 0.8615 (mmm) cc_final: 0.8394 (mmm) REVERT: A 188 MET cc_start: 0.8378 (mmt) cc_final: 0.7899 (mmt) REVERT: A 242 SER cc_start: 0.8138 (t) cc_final: 0.7596 (p) REVERT: A 243 VAL cc_start: 0.7979 (t) cc_final: 0.7656 (t) REVERT: A 267 LYS cc_start: 0.8250 (mtmt) cc_final: 0.7984 (mtmt) REVERT: A 278 THR cc_start: 0.9011 (m) cc_final: 0.8591 (p) REVERT: A 285 TYR cc_start: 0.8239 (OUTLIER) cc_final: 0.6933 (t80) REVERT: A 345 ILE cc_start: 0.9075 (mm) cc_final: 0.8835 (mm) REVERT: A 383 MET cc_start: 0.8475 (ttm) cc_final: 0.8266 (ttm) REVERT: A 396 LYS cc_start: 0.8475 (mmmm) cc_final: 0.7987 (tppt) REVERT: A 443 VAL cc_start: 0.8659 (t) cc_final: 0.8388 (p) REVERT: B 84 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7744 (mmm) REVERT: B 85 ARG cc_start: 0.7497 (mmp80) cc_final: 0.7266 (mmp80) REVERT: B 111 ASN cc_start: 0.8616 (t0) cc_final: 0.8238 (t0) REVERT: B 115 LYS cc_start: 0.8745 (mptp) cc_final: 0.8140 (mptp) REVERT: B 146 ASP cc_start: 0.7460 (p0) cc_final: 0.7191 (p0) REVERT: B 179 ASP cc_start: 0.8144 (t0) cc_final: 0.7820 (t0) REVERT: B 184 MET cc_start: 0.8556 (mmm) cc_final: 0.8240 (mmm) REVERT: B 234 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7344 (mm-30) REVERT: B 274 CYS cc_start: 0.8200 (m) cc_final: 0.7806 (m) REVERT: B 396 LYS cc_start: 0.8452 (mmmm) cc_final: 0.7916 (mmtm) REVERT: B 436 ASP cc_start: 0.8418 (t0) cc_final: 0.8023 (t70) REVERT: B 447 PHE cc_start: 0.8563 (m-80) cc_final: 0.8136 (m-10) REVERT: C 51 ILE cc_start: 0.8418 (mm) cc_final: 0.8159 (mm) REVERT: C 76 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7909 (mtt90) REVERT: C 92 ARG cc_start: 0.7880 (mmp80) cc_final: 0.7529 (mmp80) REVERT: C 93 LEU cc_start: 0.8827 (tp) cc_final: 0.8619 (tp) REVERT: C 135 LEU cc_start: 0.8539 (mt) cc_final: 0.8097 (mm) REVERT: C 144 ARG cc_start: 0.8312 (ttm-80) cc_final: 0.8033 (ttm110) REVERT: C 146 ASP cc_start: 0.7493 (p0) cc_final: 0.6976 (p0) REVERT: C 258 TRP cc_start: 0.8686 (m100) cc_final: 0.7729 (m100) REVERT: C 383 MET cc_start: 0.8567 (ttp) cc_final: 0.8337 (ttm) REVERT: C 400 LYS cc_start: 0.8408 (tppt) cc_final: 0.8164 (tppt) REVERT: C 403 GLU cc_start: 0.7530 (mp0) cc_final: 0.7190 (mp0) REVERT: D 16 LYS cc_start: 0.8380 (mmtt) cc_final: 0.8009 (mmtt) REVERT: D 20 ARG cc_start: 0.7851 (mtm-85) cc_final: 0.7456 (mtm-85) REVERT: D 63 ASP cc_start: 0.7555 (t0) cc_final: 0.6497 (t0) REVERT: D 71 ARG cc_start: 0.7798 (mtm-85) cc_final: 0.7293 (ptp-110) REVERT: D 77 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7843 (pttm) REVERT: D 88 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7201 (tm-30) REVERT: D 98 ARG cc_start: 0.8327 (mtm180) cc_final: 0.7955 (mtm180) REVERT: D 106 LYS cc_start: 0.8238 (mtmm) cc_final: 0.8012 (mtmm) REVERT: D 146 ASP cc_start: 0.7043 (p0) cc_final: 0.6340 (p0) REVERT: D 150 TYR cc_start: 0.8671 (m-80) cc_final: 0.8326 (m-10) REVERT: D 163 TYR cc_start: 0.8670 (t80) cc_final: 0.8241 (t80) REVERT: D 165 GLN cc_start: 0.8047 (mt0) cc_final: 0.7772 (mt0) REVERT: D 171 ARG cc_start: 0.7295 (mtm-85) cc_final: 0.6773 (mtm-85) REVERT: D 179 ASP cc_start: 0.8369 (t0) cc_final: 0.7960 (t0) REVERT: D 197 THR cc_start: 0.8557 (p) cc_final: 0.8282 (t) REVERT: D 205 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8625 (mp) REVERT: D 234 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7334 (mm-30) REVERT: D 246 THR cc_start: 0.8589 (m) cc_final: 0.8103 (p) REVERT: D 274 CYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7975 (m) REVERT: D 285 TYR cc_start: 0.8300 (OUTLIER) cc_final: 0.7531 (t80) REVERT: D 297 TYR cc_start: 0.7669 (m-10) cc_final: 0.7453 (m-10) REVERT: D 383 MET cc_start: 0.8693 (ttp) cc_final: 0.8413 (ttm) REVERT: D 448 ASP cc_start: 0.7684 (t0) cc_final: 0.7453 (t0) REVERT: E 6 VAL cc_start: 0.8058 (t) cc_final: 0.7841 (m) REVERT: E 20 ARG cc_start: 0.8000 (mtm-85) cc_final: 0.7644 (mtm-85) REVERT: E 24 MET cc_start: 0.8729 (pmm) cc_final: 0.8251 (pmm) REVERT: E 115 LYS cc_start: 0.8773 (mptp) cc_final: 0.8208 (mptp) REVERT: E 171 ARG cc_start: 0.7322 (mtm-85) cc_final: 0.6764 (mtm-85) REVERT: E 180 THR cc_start: 0.8528 (m) cc_final: 0.8219 (m) REVERT: E 201 ASP cc_start: 0.8272 (t0) cc_final: 0.8049 (t0) REVERT: E 203 GLN cc_start: 0.8720 (mt0) cc_final: 0.8427 (mt0) REVERT: E 243 VAL cc_start: 0.8390 (m) cc_final: 0.8044 (p) REVERT: E 248 TYR cc_start: 0.7947 (m-80) cc_final: 0.7643 (m-80) REVERT: E 267 LYS cc_start: 0.8175 (pttp) cc_final: 0.7882 (mttp) REVERT: E 275 ARG cc_start: 0.7653 (ttt180) cc_final: 0.7301 (ptt180) REVERT: E 297 TYR cc_start: 0.7780 (m-10) cc_final: 0.7455 (m-10) REVERT: E 426 GLN cc_start: 0.7081 (mt0) cc_final: 0.6685 (mt0) REVERT: E 433 LYS cc_start: 0.8363 (mmmt) cc_final: 0.7975 (mmtt) REVERT: E 436 ASP cc_start: 0.8477 (t0) cc_final: 0.8088 (t70) REVERT: E 447 PHE cc_start: 0.8515 (m-80) cc_final: 0.8136 (m-10) REVERT: F 92 ARG cc_start: 0.7843 (mmp80) cc_final: 0.7539 (mmp80) REVERT: F 111 ASN cc_start: 0.8662 (t0) cc_final: 0.8408 (t0) REVERT: F 115 LYS cc_start: 0.8758 (mptp) cc_final: 0.8283 (mptp) REVERT: F 184 MET cc_start: 0.8180 (tpp) cc_final: 0.7635 (mmm) REVERT: F 232 LYS cc_start: 0.8171 (ptmt) cc_final: 0.7743 (ptmt) REVERT: F 297 TYR cc_start: 0.7788 (m-80) cc_final: 0.7580 (m-80) REVERT: F 303 TYR cc_start: 0.8127 (m-80) cc_final: 0.7773 (m-80) REVERT: F 325 ARG cc_start: 0.7611 (ptp-110) cc_final: 0.7231 (ttm110) REVERT: F 403 GLU cc_start: 0.7417 (mp0) cc_final: 0.7149 (mp0) REVERT: F 433 LYS cc_start: 0.8442 (mmmt) cc_final: 0.8105 (mmtt) REVERT: F 436 ASP cc_start: 0.8110 (t0) cc_final: 0.7860 (t0) REVERT: F 441 GLN cc_start: 0.7578 (mt0) cc_final: 0.7243 (mt0) REVERT: G 16 LYS cc_start: 0.8397 (mmtt) cc_final: 0.8136 (mmtt) REVERT: G 52 GLU cc_start: 0.7949 (mt-10) cc_final: 0.6954 (mm-30) REVERT: G 76 ARG cc_start: 0.8234 (mtt90) cc_final: 0.7243 (mtt90) REVERT: G 88 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6885 (tm-30) REVERT: G 92 ARG cc_start: 0.7695 (mmp80) cc_final: 0.7138 (mmp80) REVERT: G 106 LYS cc_start: 0.8160 (mtmm) cc_final: 0.7885 (mtmm) REVERT: G 111 ASN cc_start: 0.8748 (t0) cc_final: 0.8325 (t0) REVERT: G 115 LYS cc_start: 0.8865 (mptp) cc_final: 0.8294 (mptp) REVERT: G 163 TYR cc_start: 0.8597 (t80) cc_final: 0.8191 (t80) REVERT: G 165 GLN cc_start: 0.8224 (mt0) cc_final: 0.8020 (mt0) REVERT: G 234 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7217 (mm-30) REVERT: G 274 CYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7357 (m) REVERT: G 275 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.7006 (ptt180) REVERT: G 285 TYR cc_start: 0.8257 (OUTLIER) cc_final: 0.6893 (t80) REVERT: G 292 MET cc_start: 0.7909 (mmt) cc_final: 0.7692 (mmt) REVERT: G 293 SER cc_start: 0.8235 (m) cc_final: 0.7446 (p) REVERT: G 400 LYS cc_start: 0.8411 (tppt) cc_final: 0.7755 (tppt) REVERT: G 403 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7004 (mp0) REVERT: G 438 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7382 (mp10) REVERT: G 448 ASP cc_start: 0.7601 (t0) cc_final: 0.7366 (t0) REVERT: H 16 LYS cc_start: 0.8452 (mmtt) cc_final: 0.8145 (mmtt) REVERT: H 20 ARG cc_start: 0.7961 (mtm-85) cc_final: 0.7634 (mtm-85) REVERT: H 73 MET cc_start: 0.7896 (mmp) cc_final: 0.7657 (mmp) REVERT: H 76 ARG cc_start: 0.8216 (mtt90) cc_final: 0.7962 (mtt90) REVERT: H 88 GLU cc_start: 0.7677 (tt0) cc_final: 0.7090 (tm-30) REVERT: H 99 LYS cc_start: 0.8889 (mmmm) cc_final: 0.8612 (mmmm) REVERT: H 111 ASN cc_start: 0.8606 (t0) cc_final: 0.8268 (t0) REVERT: H 171 ARG cc_start: 0.7467 (mtm-85) cc_final: 0.6994 (mtm-85) REVERT: H 180 THR cc_start: 0.8418 (m) cc_final: 0.8132 (m) REVERT: H 239 VAL cc_start: 0.8732 (t) cc_final: 0.8388 (p) REVERT: H 341 GLN cc_start: 0.8014 (mt0) cc_final: 0.7781 (mt0) REVERT: H 436 ASP cc_start: 0.8488 (t0) cc_final: 0.8220 (t70) REVERT: H 447 PHE cc_start: 0.8513 (m-80) cc_final: 0.8074 (m-80) REVERT: I 16 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8280 (mtpt) REVERT: I 22 TYR cc_start: 0.8526 (m-80) cc_final: 0.8039 (m-80) REVERT: I 43 PHE cc_start: 0.8951 (t80) cc_final: 0.8408 (t80) REVERT: I 52 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7537 (mt-10) REVERT: I 72 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7769 (tmm) REVERT: I 76 ARG cc_start: 0.8385 (mmm-85) cc_final: 0.8007 (mtp85) REVERT: I 98 ARG cc_start: 0.8217 (mtm180) cc_final: 0.7761 (mtm180) REVERT: I 106 LYS cc_start: 0.8220 (mtmm) cc_final: 0.7900 (mtmm) REVERT: I 135 LEU cc_start: 0.8625 (mt) cc_final: 0.8404 (mm) REVERT: I 150 TYR cc_start: 0.8667 (m-10) cc_final: 0.8432 (m-10) REVERT: I 165 GLN cc_start: 0.8101 (mt0) cc_final: 0.7837 (mt0) REVERT: I 184 MET cc_start: 0.8273 (mmm) cc_final: 0.7593 (mmm) REVERT: I 188 MET cc_start: 0.8393 (mmt) cc_final: 0.8059 (mmt) REVERT: I 192 TYR cc_start: 0.8948 (m-80) cc_final: 0.8646 (m-80) REVERT: I 203 GLN cc_start: 0.8578 (mt0) cc_final: 0.8320 (mt0) REVERT: I 258 TRP cc_start: 0.8587 (m100) cc_final: 0.7999 (m100) REVERT: I 266 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8478 (mt) REVERT: I 303 TYR cc_start: 0.8518 (m-10) cc_final: 0.8156 (m-80) REVERT: I 325 ARG cc_start: 0.7778 (ttm170) cc_final: 0.7337 (ttm170) REVERT: I 400 LYS cc_start: 0.8238 (tppt) cc_final: 0.7967 (tppt) REVERT: I 405 GLU cc_start: 0.7762 (mp0) cc_final: 0.7200 (mp0) REVERT: I 436 ASP cc_start: 0.8251 (t0) cc_final: 0.8001 (t0) REVERT: I 441 GLN cc_start: 0.7689 (mt0) cc_final: 0.7203 (mt0) REVERT: J 41 ARG cc_start: 0.7682 (tpp-160) cc_final: 0.7305 (tpp-160) REVERT: J 76 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.8053 (mtt90) REVERT: J 92 ARG cc_start: 0.7681 (mmp80) cc_final: 0.7182 (mmp80) REVERT: J 98 ARG cc_start: 0.8310 (mtm180) cc_final: 0.7870 (mtm180) REVERT: J 99 LYS cc_start: 0.8850 (mmmm) cc_final: 0.8473 (mmmm) REVERT: J 106 LYS cc_start: 0.8336 (mtmm) cc_final: 0.8081 (mtmm) REVERT: J 111 ASN cc_start: 0.8686 (t0) cc_final: 0.8123 (t0) REVERT: J 115 LYS cc_start: 0.8814 (mptp) cc_final: 0.8209 (mptp) REVERT: J 171 ARG cc_start: 0.7366 (mtm-85) cc_final: 0.6772 (mtm-85) REVERT: J 215 THR cc_start: 0.8452 (OUTLIER) cc_final: 0.8149 (p) REVERT: J 248 TYR cc_start: 0.7897 (m-10) cc_final: 0.7607 (m-10) REVERT: J 258 TRP cc_start: 0.8729 (m100) cc_final: 0.7666 (m100) REVERT: J 275 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.6274 (ptt180) REVERT: J 285 TYR cc_start: 0.8245 (OUTLIER) cc_final: 0.6836 (t80) REVERT: J 324 GLU cc_start: 0.7059 (tt0) cc_final: 0.6659 (tt0) REVERT: J 400 LYS cc_start: 0.8382 (tppt) cc_final: 0.7615 (tppt) REVERT: J 403 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.7080 (mp0) REVERT: J 446 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7656 (mm-30) REVERT: K 76 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7881 (mtt90) REVERT: K 88 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7143 (tt0) REVERT: K 106 LYS cc_start: 0.8038 (mtmm) cc_final: 0.7757 (mtmm) REVERT: K 115 LYS cc_start: 0.8772 (mptp) cc_final: 0.8341 (mptp) REVERT: K 143 GLN cc_start: 0.8395 (tt0) cc_final: 0.8168 (tt0) REVERT: K 171 ARG cc_start: 0.7288 (mtm-85) cc_final: 0.6881 (mtm-85) REVERT: K 184 MET cc_start: 0.8382 (mmm) cc_final: 0.7830 (mmm) REVERT: K 224 LYS cc_start: 0.2170 (OUTLIER) cc_final: 0.1694 (pttm) REVERT: K 238 ARG cc_start: 0.7453 (ttm110) cc_final: 0.7095 (mtm110) REVERT: K 264 PHE cc_start: 0.8400 (p90) cc_final: 0.8180 (p90) REVERT: K 270 LEU cc_start: 0.8240 (mp) cc_final: 0.8031 (mt) REVERT: K 324 GLU cc_start: 0.7149 (tt0) cc_final: 0.6935 (tt0) REVERT: K 341 GLN cc_start: 0.7922 (mt0) cc_final: 0.7586 (mt0) REVERT: K 396 LYS cc_start: 0.8375 (tppt) cc_final: 0.8015 (tppt) REVERT: K 441 GLN cc_start: 0.7517 (mt0) cc_final: 0.7204 (mt0) REVERT: L 5 TYR cc_start: 0.8429 (m-10) cc_final: 0.8211 (m-10) REVERT: L 20 ARG cc_start: 0.7867 (mtm-85) cc_final: 0.7450 (mtm-85) REVERT: L 24 MET cc_start: 0.8798 (pmm) cc_final: 0.8252 (pmm) REVERT: L 43 PHE cc_start: 0.9014 (t80) cc_final: 0.8478 (t80) REVERT: L 51 ILE cc_start: 0.8615 (mm) cc_final: 0.8302 (mm) REVERT: L 56 ASP cc_start: 0.7863 (t0) cc_final: 0.7632 (t0) REVERT: L 76 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7953 (mtt90) REVERT: L 92 ARG cc_start: 0.7706 (mmp80) cc_final: 0.7412 (mmp80) REVERT: L 106 LYS cc_start: 0.8322 (mtmm) cc_final: 0.8037 (mtmm) REVERT: L 135 LEU cc_start: 0.8640 (mt) cc_final: 0.8354 (mm) REVERT: L 168 LYS cc_start: 0.8876 (mtmt) cc_final: 0.8455 (mtpp) REVERT: L 171 ARG cc_start: 0.7132 (mtm-85) cc_final: 0.6771 (mtm-85) REVERT: L 184 MET cc_start: 0.8440 (mmm) cc_final: 0.7829 (mmm) REVERT: L 232 LYS cc_start: 0.8299 (ptmt) cc_final: 0.7841 (ptmt) REVERT: L 238 ARG cc_start: 0.7485 (ttm110) cc_final: 0.7037 (mtm110) REVERT: L 245 SER cc_start: 0.8689 (p) cc_final: 0.8350 (t) REVERT: L 283 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7388 (mp0) REVERT: L 285 TYR cc_start: 0.8155 (OUTLIER) cc_final: 0.7002 (t80) REVERT: L 403 GLU cc_start: 0.7432 (mp0) cc_final: 0.7015 (mp0) REVERT: L 427 LYS cc_start: 0.7181 (OUTLIER) cc_final: 0.6896 (mmtt) REVERT: L 446 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7362 (mm-30) outliers start: 269 outliers final: 161 residues processed: 2029 average time/residue: 0.6265 time to fit residues: 1941.8035 Evaluate side-chains 2082 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1890 time to evaluate : 4.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain B residue 342 MET Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 411 ARG Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 274 CYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 396 LYS Chi-restraints excluded: chain D residue 442 LYS Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain E residue 19 GLN Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 277 ASP Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 292 MET Chi-restraints excluded: chain E residue 342 MET Chi-restraints excluded: chain E residue 398 CYS Chi-restraints excluded: chain E residue 403 GLU Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain F residue 397 GLU Chi-restraints excluded: chain F residue 411 ARG Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 77 LYS Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain G residue 236 CYS Chi-restraints excluded: chain G residue 245 SER Chi-restraints excluded: chain G residue 274 CYS Chi-restraints excluded: chain G residue 275 ARG Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 348 THR Chi-restraints excluded: chain G residue 403 GLU Chi-restraints excluded: chain G residue 411 ARG Chi-restraints excluded: chain G residue 430 THR Chi-restraints excluded: chain G residue 438 GLN Chi-restraints excluded: chain G residue 440 ILE Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 292 MET Chi-restraints excluded: chain H residue 342 MET Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 403 GLU Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 428 THR Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 73 MET Chi-restraints excluded: chain I residue 75 ASP Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 172 LEU Chi-restraints excluded: chain I residue 215 THR Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain I residue 271 SER Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 291 THR Chi-restraints excluded: chain I residue 348 THR Chi-restraints excluded: chain I residue 358 LEU Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain I residue 403 GLU Chi-restraints excluded: chain I residue 408 LEU Chi-restraints excluded: chain J residue 16 LYS Chi-restraints excluded: chain J residue 76 ARG Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 228 MET Chi-restraints excluded: chain J residue 236 CYS Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain J residue 275 ARG Chi-restraints excluded: chain J residue 277 ASP Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 291 THR Chi-restraints excluded: chain J residue 301 THR Chi-restraints excluded: chain J residue 348 THR Chi-restraints excluded: chain J residue 383 MET Chi-restraints excluded: chain J residue 403 GLU Chi-restraints excluded: chain K residue 76 ARG Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 120 GLN Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain K residue 203 GLN Chi-restraints excluded: chain K residue 224 LYS Chi-restraints excluded: chain K residue 259 HIS Chi-restraints excluded: chain K residue 277 ASP Chi-restraints excluded: chain K residue 283 GLU Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 292 MET Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 305 VAL Chi-restraints excluded: chain K residue 337 THR Chi-restraints excluded: chain K residue 348 THR Chi-restraints excluded: chain K residue 349 GLU Chi-restraints excluded: chain K residue 398 CYS Chi-restraints excluded: chain K residue 403 GLU Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain L residue 84 MET Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 146 ASP Chi-restraints excluded: chain L residue 167 ILE Chi-restraints excluded: chain L residue 194 SER Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 283 GLU Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 342 MET Chi-restraints excluded: chain L residue 348 THR Chi-restraints excluded: chain L residue 405 GLU Chi-restraints excluded: chain L residue 427 LYS Chi-restraints excluded: chain L residue 442 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 425 optimal weight: 0.9990 chunk 289 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 380 optimal weight: 3.9990 chunk 210 optimal weight: 4.9990 chunk 435 optimal weight: 9.9990 chunk 352 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 260 optimal weight: 0.6980 chunk 458 optimal weight: 2.9990 chunk 128 optimal weight: 0.3980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 GLN ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 GLN ** C 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 GLN ** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 389 GLN ** G 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 364 GLN ** I 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 364 GLN ** K 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 429 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 42504 Z= 0.320 Angle : 0.639 8.541 57684 Z= 0.321 Chirality : 0.045 0.154 6564 Planarity : 0.005 0.090 7260 Dihedral : 6.005 37.812 5892 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 6.77 % Allowed : 30.77 % Favored : 62.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.37 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.11), residues: 5148 helix: 0.65 (0.14), residues: 1620 sheet: -1.32 (0.14), residues: 1164 loop : -2.00 (0.11), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 258 HIS 0.003 0.001 HIS E 79 PHE 0.018 0.002 PHE A 183 TYR 0.030 0.002 TYR G 5 ARG 0.016 0.001 ARG I 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2232 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 299 poor density : 1933 time to evaluate : 4.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.7785 (tpp-160) cc_final: 0.7286 (tpp-160) REVERT: A 76 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8345 (mtt90) REVERT: A 85 ARG cc_start: 0.7492 (mmp80) cc_final: 0.7247 (mmp80) REVERT: A 88 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6559 (tm-30) REVERT: A 92 ARG cc_start: 0.7618 (mmp80) cc_final: 0.7257 (mmp80) REVERT: A 98 ARG cc_start: 0.8282 (mtm180) cc_final: 0.7857 (mtm180) REVERT: A 106 LYS cc_start: 0.8413 (mtmm) cc_final: 0.8122 (mtmm) REVERT: A 133 PHE cc_start: 0.7834 (t80) cc_final: 0.7519 (t80) REVERT: A 135 LEU cc_start: 0.8645 (mt) cc_final: 0.8140 (mm) REVERT: A 146 ASP cc_start: 0.7295 (p0) cc_final: 0.6384 (p0) REVERT: A 163 TYR cc_start: 0.8685 (t80) cc_final: 0.8402 (t80) REVERT: A 171 ARG cc_start: 0.7259 (mtm-85) cc_final: 0.6699 (mtm-85) REVERT: A 176 VAL cc_start: 0.8592 (OUTLIER) cc_final: 0.8336 (t) REVERT: A 188 MET cc_start: 0.8372 (mmt) cc_final: 0.7888 (mmt) REVERT: A 242 SER cc_start: 0.8157 (t) cc_final: 0.7603 (p) REVERT: A 243 VAL cc_start: 0.8025 (t) cc_final: 0.7722 (t) REVERT: A 266 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8610 (mt) REVERT: A 267 LYS cc_start: 0.8236 (mtmt) cc_final: 0.8002 (mtmt) REVERT: A 278 THR cc_start: 0.9017 (m) cc_final: 0.8529 (p) REVERT: A 285 TYR cc_start: 0.8304 (OUTLIER) cc_final: 0.6965 (t80) REVERT: A 345 ILE cc_start: 0.9092 (mm) cc_final: 0.8854 (mm) REVERT: A 383 MET cc_start: 0.8500 (ttm) cc_final: 0.8291 (ttm) REVERT: A 396 LYS cc_start: 0.8514 (mmmm) cc_final: 0.8045 (tppt) REVERT: B 85 ARG cc_start: 0.7529 (mmp80) cc_final: 0.7266 (mmp80) REVERT: B 111 ASN cc_start: 0.8669 (t0) cc_final: 0.8082 (t0) REVERT: B 115 LYS cc_start: 0.8771 (mptp) cc_final: 0.8050 (mptp) REVERT: B 146 ASP cc_start: 0.7532 (p0) cc_final: 0.7247 (p0) REVERT: B 184 MET cc_start: 0.8600 (mmm) cc_final: 0.8268 (mmm) REVERT: B 274 CYS cc_start: 0.8231 (m) cc_final: 0.7837 (m) REVERT: B 396 LYS cc_start: 0.8479 (mmmm) cc_final: 0.8113 (tppt) REVERT: B 436 ASP cc_start: 0.8448 (t0) cc_final: 0.8048 (t70) REVERT: B 447 PHE cc_start: 0.8574 (m-80) cc_final: 0.8353 (m-10) REVERT: C 51 ILE cc_start: 0.8513 (mm) cc_final: 0.8219 (mm) REVERT: C 76 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7982 (mtt90) REVERT: C 92 ARG cc_start: 0.7907 (mmp80) cc_final: 0.7524 (mmp80) REVERT: C 135 LEU cc_start: 0.8565 (mt) cc_final: 0.8065 (mm) REVERT: C 144 ARG cc_start: 0.8306 (ttm-80) cc_final: 0.8073 (ttm110) REVERT: C 146 ASP cc_start: 0.7526 (p0) cc_final: 0.7010 (p0) REVERT: C 258 TRP cc_start: 0.8680 (m100) cc_final: 0.7725 (m100) REVERT: C 324 GLU cc_start: 0.7144 (tt0) cc_final: 0.6907 (tt0) REVERT: C 325 ARG cc_start: 0.7943 (ttp-170) cc_final: 0.7555 (ttp-170) REVERT: C 396 LYS cc_start: 0.8424 (tppt) cc_final: 0.8168 (tppt) REVERT: C 400 LYS cc_start: 0.8398 (tppt) cc_final: 0.8174 (tppt) REVERT: C 403 GLU cc_start: 0.7548 (mp0) cc_final: 0.7157 (mp0) REVERT: D 16 LYS cc_start: 0.8387 (mmtt) cc_final: 0.8007 (mmtt) REVERT: D 20 ARG cc_start: 0.7848 (mtm-85) cc_final: 0.7454 (mtm-85) REVERT: D 28 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7403 (mm-30) REVERT: D 63 ASP cc_start: 0.7603 (t0) cc_final: 0.7017 (t0) REVERT: D 76 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.8044 (mtt90) REVERT: D 88 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7114 (tm-30) REVERT: D 98 ARG cc_start: 0.8375 (mtm180) cc_final: 0.7952 (mtm180) REVERT: D 150 TYR cc_start: 0.8688 (m-80) cc_final: 0.8337 (m-10) REVERT: D 163 TYR cc_start: 0.8685 (t80) cc_final: 0.8307 (t80) REVERT: D 165 GLN cc_start: 0.8028 (mt0) cc_final: 0.7760 (mt0) REVERT: D 179 ASP cc_start: 0.8396 (t0) cc_final: 0.7968 (t0) REVERT: D 197 THR cc_start: 0.8568 (p) cc_final: 0.8268 (t) REVERT: D 205 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8602 (mp) REVERT: D 234 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7301 (mm-30) REVERT: D 246 THR cc_start: 0.8568 (m) cc_final: 0.8041 (p) REVERT: D 274 CYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7956 (m) REVERT: D 285 TYR cc_start: 0.8325 (OUTLIER) cc_final: 0.7551 (t80) REVERT: D 297 TYR cc_start: 0.7712 (m-10) cc_final: 0.7483 (m-10) REVERT: D 331 CYS cc_start: 0.8384 (p) cc_final: 0.8174 (p) REVERT: D 448 ASP cc_start: 0.7685 (t0) cc_final: 0.7449 (t0) REVERT: E 6 VAL cc_start: 0.8133 (t) cc_final: 0.7916 (m) REVERT: E 20 ARG cc_start: 0.8009 (mtm-85) cc_final: 0.7652 (mtm-85) REVERT: E 24 MET cc_start: 0.8716 (pmm) cc_final: 0.8249 (pmm) REVERT: E 28 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7286 (mm-30) REVERT: E 98 ARG cc_start: 0.8262 (mtm180) cc_final: 0.7883 (mtm180) REVERT: E 115 LYS cc_start: 0.8815 (mptp) cc_final: 0.8207 (mptp) REVERT: E 144 ARG cc_start: 0.8138 (ttm110) cc_final: 0.7735 (mmm-85) REVERT: E 146 ASP cc_start: 0.7546 (p0) cc_final: 0.7075 (p0) REVERT: E 150 TYR cc_start: 0.8680 (m-10) cc_final: 0.8396 (m-10) REVERT: E 171 ARG cc_start: 0.7407 (mtm-85) cc_final: 0.6823 (mtm-85) REVERT: E 184 MET cc_start: 0.8278 (mmm) cc_final: 0.8001 (mmm) REVERT: E 197 THR cc_start: 0.8486 (p) cc_final: 0.8204 (t) REVERT: E 203 GLN cc_start: 0.8629 (mt0) cc_final: 0.8427 (mt0) REVERT: E 243 VAL cc_start: 0.8386 (m) cc_final: 0.8118 (p) REVERT: E 248 TYR cc_start: 0.7969 (m-80) cc_final: 0.7669 (m-80) REVERT: E 289 ARG cc_start: 0.7982 (mtp-110) cc_final: 0.7618 (ttp80) REVERT: E 297 TYR cc_start: 0.7772 (m-10) cc_final: 0.7430 (m-10) REVERT: E 426 GLN cc_start: 0.7198 (mt0) cc_final: 0.6647 (mt0) REVERT: E 433 LYS cc_start: 0.8395 (mmmt) cc_final: 0.8051 (mmtt) REVERT: E 436 ASP cc_start: 0.8498 (t0) cc_final: 0.8123 (t70) REVERT: E 447 PHE cc_start: 0.8504 (m-80) cc_final: 0.8084 (m-10) REVERT: F 30 ARG cc_start: 0.7334 (ptp-170) cc_final: 0.6943 (ptp-170) REVERT: F 111 ASN cc_start: 0.8702 (t0) cc_final: 0.8345 (t0) REVERT: F 115 LYS cc_start: 0.8789 (mptp) cc_final: 0.8234 (mptp) REVERT: F 184 MET cc_start: 0.8309 (tpp) cc_final: 0.7690 (mmm) REVERT: F 192 TYR cc_start: 0.8921 (m-80) cc_final: 0.8612 (m-80) REVERT: F 232 LYS cc_start: 0.8204 (ptmt) cc_final: 0.7771 (ptmt) REVERT: F 275 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.7217 (ptt90) REVERT: F 297 TYR cc_start: 0.7881 (m-80) cc_final: 0.7672 (m-80) REVERT: F 303 TYR cc_start: 0.8152 (m-80) cc_final: 0.7945 (m-80) REVERT: F 325 ARG cc_start: 0.7605 (ptp-110) cc_final: 0.7179 (ttm110) REVERT: F 346 LEU cc_start: 0.8714 (mt) cc_final: 0.8402 (tt) REVERT: F 399 ARG cc_start: 0.7785 (tpp80) cc_final: 0.7308 (tpp80) REVERT: F 400 LYS cc_start: 0.8380 (tppt) cc_final: 0.7671 (tppt) REVERT: F 403 GLU cc_start: 0.7476 (mp0) cc_final: 0.6970 (mp0) REVERT: F 433 LYS cc_start: 0.8439 (mmmt) cc_final: 0.8097 (mmtt) REVERT: F 441 GLN cc_start: 0.7627 (mt0) cc_final: 0.7279 (mt0) REVERT: G 16 LYS cc_start: 0.8410 (mmtt) cc_final: 0.8151 (mmtt) REVERT: G 32 VAL cc_start: 0.8402 (t) cc_final: 0.8010 (p) REVERT: G 41 ARG cc_start: 0.7799 (tpp-160) cc_final: 0.7224 (tpp-160) REVERT: G 52 GLU cc_start: 0.7951 (mt-10) cc_final: 0.6964 (mm-30) REVERT: G 76 ARG cc_start: 0.8229 (mtt90) cc_final: 0.7285 (mtt90) REVERT: G 88 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7161 (tm-30) REVERT: G 106 LYS cc_start: 0.8236 (mtmm) cc_final: 0.7899 (mtmm) REVERT: G 111 ASN cc_start: 0.8782 (t0) cc_final: 0.8220 (t0) REVERT: G 115 LYS cc_start: 0.8872 (mptp) cc_final: 0.8286 (mptp) REVERT: G 135 LEU cc_start: 0.8759 (mt) cc_final: 0.8269 (mt) REVERT: G 163 TYR cc_start: 0.8619 (t80) cc_final: 0.8200 (t80) REVERT: G 171 ARG cc_start: 0.7568 (mtm-85) cc_final: 0.7072 (mtm-85) REVERT: G 179 ASP cc_start: 0.8337 (t0) cc_final: 0.7767 (t0) REVERT: G 234 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7316 (mm-30) REVERT: G 274 CYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7152 (m) REVERT: G 275 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.7054 (ptt180) REVERT: G 285 TYR cc_start: 0.8282 (OUTLIER) cc_final: 0.6818 (t80) REVERT: G 292 MET cc_start: 0.7934 (mmt) cc_final: 0.7674 (mmt) REVERT: G 400 LYS cc_start: 0.8403 (tppt) cc_final: 0.7756 (tppt) REVERT: G 403 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7065 (mp0) REVERT: G 406 LYS cc_start: 0.8885 (mmmm) cc_final: 0.8549 (mmtp) REVERT: G 433 LYS cc_start: 0.8389 (mmmt) cc_final: 0.8034 (mmtt) REVERT: G 448 ASP cc_start: 0.7570 (t0) cc_final: 0.7329 (t0) REVERT: H 16 LYS cc_start: 0.8438 (mmtt) cc_final: 0.8135 (mmtt) REVERT: H 20 ARG cc_start: 0.7978 (mtm-85) cc_final: 0.7667 (mtm-85) REVERT: H 76 ARG cc_start: 0.8223 (mtt90) cc_final: 0.7988 (mtt90) REVERT: H 88 GLU cc_start: 0.7633 (tt0) cc_final: 0.7042 (tm-30) REVERT: H 99 LYS cc_start: 0.8863 (mmmm) cc_final: 0.8565 (mmmm) REVERT: H 111 ASN cc_start: 0.8655 (t0) cc_final: 0.8291 (t0) REVERT: H 146 ASP cc_start: 0.7738 (OUTLIER) cc_final: 0.6985 (p0) REVERT: H 171 ARG cc_start: 0.7495 (mtm-85) cc_final: 0.7023 (mtm-85) REVERT: H 239 VAL cc_start: 0.8731 (t) cc_final: 0.8401 (p) REVERT: H 341 GLN cc_start: 0.8035 (mt0) cc_final: 0.7803 (mt0) REVERT: H 436 ASP cc_start: 0.8524 (t0) cc_final: 0.8074 (t70) REVERT: H 447 PHE cc_start: 0.8509 (m-80) cc_final: 0.8182 (m-10) REVERT: I 5 TYR cc_start: 0.8058 (m-10) cc_final: 0.7785 (m-10) REVERT: I 16 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8288 (mtpt) REVERT: I 22 TYR cc_start: 0.8534 (m-80) cc_final: 0.8015 (m-80) REVERT: I 43 PHE cc_start: 0.8923 (t80) cc_final: 0.8362 (t80) REVERT: I 72 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7773 (tmm) REVERT: I 98 ARG cc_start: 0.8248 (mtm180) cc_final: 0.7787 (mtm180) REVERT: I 106 LYS cc_start: 0.8263 (mtmm) cc_final: 0.7839 (mtmm) REVERT: I 135 LEU cc_start: 0.8660 (mt) cc_final: 0.8427 (mm) REVERT: I 150 TYR cc_start: 0.8695 (m-10) cc_final: 0.8484 (m-10) REVERT: I 165 GLN cc_start: 0.8112 (mt0) cc_final: 0.7826 (mt0) REVERT: I 184 MET cc_start: 0.8351 (mmm) cc_final: 0.7844 (mmm) REVERT: I 192 TYR cc_start: 0.8952 (m-80) cc_final: 0.8598 (m-80) REVERT: I 203 GLN cc_start: 0.8589 (mt0) cc_final: 0.8347 (mt0) REVERT: I 266 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8492 (mt) REVERT: I 303 TYR cc_start: 0.8569 (m-10) cc_final: 0.8130 (m-80) REVERT: I 383 MET cc_start: 0.8597 (ttp) cc_final: 0.8303 (ttm) REVERT: I 405 GLU cc_start: 0.7798 (mp0) cc_final: 0.7248 (mp0) REVERT: I 436 ASP cc_start: 0.8314 (t0) cc_final: 0.8073 (t0) REVERT: I 441 GLN cc_start: 0.7692 (mt0) cc_final: 0.7264 (mt0) REVERT: J 28 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7350 (mm-30) REVERT: J 30 ARG cc_start: 0.7652 (ptp-170) cc_final: 0.7103 (ptp-170) REVERT: J 41 ARG cc_start: 0.7743 (tpp-160) cc_final: 0.7294 (tpp-160) REVERT: J 76 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.8164 (mtt90) REVERT: J 92 ARG cc_start: 0.7716 (mmp80) cc_final: 0.7274 (mmp80) REVERT: J 98 ARG cc_start: 0.8335 (mtm180) cc_final: 0.7906 (mtm180) REVERT: J 106 LYS cc_start: 0.8384 (mtmm) cc_final: 0.8094 (mtmm) REVERT: J 111 ASN cc_start: 0.8706 (t0) cc_final: 0.8068 (t0) REVERT: J 115 LYS cc_start: 0.8827 (mptp) cc_final: 0.8232 (mptp) REVERT: J 165 GLN cc_start: 0.8276 (mt0) cc_final: 0.8040 (mt0) REVERT: J 171 ARG cc_start: 0.7410 (mtm-85) cc_final: 0.6843 (mtm-85) REVERT: J 248 TYR cc_start: 0.7946 (m-10) cc_final: 0.7634 (m-10) REVERT: J 258 TRP cc_start: 0.8732 (m100) cc_final: 0.7704 (m100) REVERT: J 275 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.6346 (ptt180) REVERT: J 285 TYR cc_start: 0.8278 (OUTLIER) cc_final: 0.6933 (t80) REVERT: J 324 GLU cc_start: 0.7077 (tt0) cc_final: 0.6742 (tt0) REVERT: J 400 LYS cc_start: 0.8330 (tppt) cc_final: 0.7592 (tppt) REVERT: J 403 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7118 (mp0) REVERT: J 446 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7579 (mm-30) REVERT: K 76 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7920 (mtt90) REVERT: K 88 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7146 (tt0) REVERT: K 115 LYS cc_start: 0.8749 (mptp) cc_final: 0.8275 (mptp) REVERT: K 143 GLN cc_start: 0.8421 (tt0) cc_final: 0.8174 (tt0) REVERT: K 146 ASP cc_start: 0.7522 (p0) cc_final: 0.6809 (p0) REVERT: K 171 ARG cc_start: 0.7343 (mtm-85) cc_final: 0.6857 (mtm-85) REVERT: K 202 GLU cc_start: 0.8248 (tp30) cc_final: 0.7936 (tp30) REVERT: K 203 GLN cc_start: 0.8552 (mt0) cc_final: 0.8324 (mt0) REVERT: K 238 ARG cc_start: 0.7445 (ttm110) cc_final: 0.7098 (mtm110) REVERT: K 267 LYS cc_start: 0.8352 (pttp) cc_final: 0.8045 (mttp) REVERT: K 396 LYS cc_start: 0.8360 (tppt) cc_final: 0.7994 (tppt) REVERT: L 5 TYR cc_start: 0.8436 (m-10) cc_final: 0.7682 (m-10) REVERT: L 20 ARG cc_start: 0.7869 (mtm-85) cc_final: 0.7452 (mtm-85) REVERT: L 24 MET cc_start: 0.8812 (pmm) cc_final: 0.8295 (pmm) REVERT: L 43 PHE cc_start: 0.9006 (t80) cc_final: 0.8698 (t80) REVERT: L 51 ILE cc_start: 0.8644 (mm) cc_final: 0.8320 (mm) REVERT: L 56 ASP cc_start: 0.7878 (t0) cc_final: 0.7640 (t0) REVERT: L 76 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.8012 (mtt90) REVERT: L 135 LEU cc_start: 0.8690 (mt) cc_final: 0.8473 (mm) REVERT: L 168 LYS cc_start: 0.8857 (mtmt) cc_final: 0.8445 (mtpp) REVERT: L 171 ARG cc_start: 0.7223 (mtm-85) cc_final: 0.6958 (mtm-85) REVERT: L 184 MET cc_start: 0.8463 (mmm) cc_final: 0.7898 (mmm) REVERT: L 245 SER cc_start: 0.8706 (p) cc_final: 0.8353 (t) REVERT: L 283 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7382 (mp0) REVERT: L 403 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7082 (mp0) REVERT: L 426 GLN cc_start: 0.7301 (OUTLIER) cc_final: 0.7028 (mt0) REVERT: L 446 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7391 (mm-30) outliers start: 299 outliers final: 199 residues processed: 2038 average time/residue: 0.6480 time to fit residues: 2039.8560 Evaluate side-chains 2129 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 1899 time to evaluate : 4.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 398 CYS Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 411 ARG Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 342 MET Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 411 ARG Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 80 CYS Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 274 CYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain E residue 19 GLN Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 92 ARG Chi-restraints excluded: chain E residue 106 LYS Chi-restraints excluded: chain E residue 120 GLN Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 277 ASP Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 292 MET Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 342 MET Chi-restraints excluded: chain E residue 398 CYS Chi-restraints excluded: chain E residue 403 GLU Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 120 GLN Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 216 ASP Chi-restraints excluded: chain F residue 275 ARG Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain F residue 397 GLU Chi-restraints excluded: chain F residue 411 ARG Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 77 LYS Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain G residue 236 CYS Chi-restraints excluded: chain G residue 245 SER Chi-restraints excluded: chain G residue 274 CYS Chi-restraints excluded: chain G residue 275 ARG Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 348 THR Chi-restraints excluded: chain G residue 403 GLU Chi-restraints excluded: chain G residue 411 ARG Chi-restraints excluded: chain G residue 430 THR Chi-restraints excluded: chain G residue 440 ILE Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 146 ASP Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 277 ASP Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 292 MET Chi-restraints excluded: chain H residue 301 THR Chi-restraints excluded: chain H residue 342 MET Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 398 CYS Chi-restraints excluded: chain H residue 403 GLU Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 428 THR Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 73 MET Chi-restraints excluded: chain I residue 75 ASP Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 120 GLN Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain I residue 172 LEU Chi-restraints excluded: chain I residue 215 THR Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain I residue 271 SER Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 291 THR Chi-restraints excluded: chain I residue 348 THR Chi-restraints excluded: chain I residue 358 LEU Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain I residue 403 GLU Chi-restraints excluded: chain J residue 76 ARG Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain J residue 88 GLU Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 120 GLN Chi-restraints excluded: chain J residue 134 CYS Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 228 MET Chi-restraints excluded: chain J residue 236 CYS Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain J residue 275 ARG Chi-restraints excluded: chain J residue 277 ASP Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 291 THR Chi-restraints excluded: chain J residue 301 THR Chi-restraints excluded: chain J residue 315 CYS Chi-restraints excluded: chain J residue 318 THR Chi-restraints excluded: chain J residue 348 THR Chi-restraints excluded: chain J residue 383 MET Chi-restraints excluded: chain J residue 398 CYS Chi-restraints excluded: chain J residue 403 GLU Chi-restraints excluded: chain K residue 76 ARG Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 120 GLN Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain K residue 232 LYS Chi-restraints excluded: chain K residue 259 HIS Chi-restraints excluded: chain K residue 277 ASP Chi-restraints excluded: chain K residue 283 GLU Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 292 MET Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 305 VAL Chi-restraints excluded: chain K residue 316 LYS Chi-restraints excluded: chain K residue 348 THR Chi-restraints excluded: chain K residue 349 GLU Chi-restraints excluded: chain K residue 358 LEU Chi-restraints excluded: chain K residue 397 GLU Chi-restraints excluded: chain K residue 398 CYS Chi-restraints excluded: chain K residue 403 GLU Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain L residue 120 GLN Chi-restraints excluded: chain L residue 146 ASP Chi-restraints excluded: chain L residue 167 ILE Chi-restraints excluded: chain L residue 194 SER Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain L residue 277 ASP Chi-restraints excluded: chain L residue 283 GLU Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 292 MET Chi-restraints excluded: chain L residue 301 THR Chi-restraints excluded: chain L residue 314 MET Chi-restraints excluded: chain L residue 342 MET Chi-restraints excluded: chain L residue 348 THR Chi-restraints excluded: chain L residue 403 GLU Chi-restraints excluded: chain L residue 405 GLU Chi-restraints excluded: chain L residue 426 GLN Chi-restraints excluded: chain L residue 427 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 171 optimal weight: 10.0000 chunk 459 optimal weight: 0.6980 chunk 100 optimal weight: 0.2980 chunk 299 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 510 optimal weight: 5.9990 chunk 424 optimal weight: 0.8980 chunk 236 optimal weight: 0.0870 chunk 42 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 chunk 268 optimal weight: 0.6980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 ASN A 364 GLN ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 GLN ** C 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 ASN ** C 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 GLN D 356 GLN ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 GLN ** G 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 364 GLN G 438 GLN H 364 GLN ** I 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 389 GLN ** J 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 364 GLN ** K 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 42504 Z= 0.182 Angle : 0.590 6.756 57684 Z= 0.296 Chirality : 0.042 0.137 6564 Planarity : 0.005 0.098 7260 Dihedral : 5.850 35.968 5892 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 5.98 % Allowed : 32.65 % Favored : 61.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.97 % 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: -1.34 (0.11), residues: 5148 helix: 0.77 (0.14), residues: 1632 sheet: -1.15 (0.13), residues: 1308 loop : -1.97 (0.11), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 258 HIS 0.002 0.000 HIS B 429 PHE 0.033 0.002 PHE K 264 TYR 0.021 0.001 TYR K 174 ARG 0.010 0.001 ARG K 411 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2152 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 1888 time to evaluate : 4.678 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: A 16 LYS cc_start: 0.8357 (mmtt) cc_final: 0.8090 (mmtt) REVERT: A 28 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7347 (mm-30) REVERT: A 76 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8176 (mtt90) REVERT: A 85 ARG cc_start: 0.7482 (mmp80) cc_final: 0.7227 (mmp80) REVERT: A 88 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6397 (tm-30) REVERT: A 92 ARG cc_start: 0.7580 (mmp80) cc_final: 0.7186 (mmp80) REVERT: A 98 ARG cc_start: 0.8233 (mtm180) cc_final: 0.7721 (mtm180) REVERT: A 133 PHE cc_start: 0.7862 (t80) cc_final: 0.7495 (t80) REVERT: A 135 LEU cc_start: 0.8592 (mt) cc_final: 0.8053 (mm) REVERT: A 146 ASP cc_start: 0.7197 (p0) cc_final: 0.6323 (p0) REVERT: A 171 ARG cc_start: 0.7128 (mtm-85) cc_final: 0.6627 (mtm-85) REVERT: A 188 MET cc_start: 0.8385 (mmt) cc_final: 0.7822 (mmt) REVERT: A 242 SER cc_start: 0.8127 (t) cc_final: 0.7688 (p) REVERT: A 243 VAL cc_start: 0.7897 (t) cc_final: 0.7615 (t) REVERT: A 258 TRP cc_start: 0.8702 (m100) cc_final: 0.7686 (m100) REVERT: A 266 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8596 (mt) REVERT: A 267 LYS cc_start: 0.8231 (mtmt) cc_final: 0.8012 (mtmt) REVERT: A 278 THR cc_start: 0.8995 (m) cc_final: 0.8534 (p) REVERT: A 285 TYR cc_start: 0.8218 (OUTLIER) cc_final: 0.7063 (t80) REVERT: A 345 ILE cc_start: 0.9065 (mm) cc_final: 0.8798 (mm) REVERT: B 72 MET cc_start: 0.8224 (tmm) cc_final: 0.7631 (tmm) REVERT: B 73 MET cc_start: 0.7726 (mmp) cc_final: 0.6983 (mmp) REVERT: B 85 ARG cc_start: 0.7507 (mmp80) cc_final: 0.7306 (mmp80) REVERT: B 110 ARG cc_start: 0.8209 (mmt-90) cc_final: 0.7605 (mmt-90) REVERT: B 115 LYS cc_start: 0.8720 (mptp) cc_final: 0.8176 (mptp) REVERT: B 184 MET cc_start: 0.8525 (mmm) cc_final: 0.7928 (tpp) REVERT: B 396 LYS cc_start: 0.8463 (mmmm) cc_final: 0.7922 (mmtm) REVERT: B 447 PHE cc_start: 0.8529 (m-80) cc_final: 0.8113 (m-10) REVERT: C 5 TYR cc_start: 0.8399 (m-10) cc_final: 0.8185 (m-10) REVERT: C 51 ILE cc_start: 0.8491 (mm) cc_final: 0.8231 (mm) REVERT: C 76 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7962 (mtt90) REVERT: C 92 ARG cc_start: 0.7895 (mmp80) cc_final: 0.7481 (mmp80) REVERT: C 93 LEU cc_start: 0.8811 (tp) cc_final: 0.8586 (tp) REVERT: C 135 LEU cc_start: 0.8528 (mt) cc_final: 0.8045 (mm) REVERT: C 146 ASP cc_start: 0.7502 (p0) cc_final: 0.6951 (p0) REVERT: C 325 ARG cc_start: 0.7885 (ttp-170) cc_final: 0.7607 (ttm-80) REVERT: C 396 LYS cc_start: 0.8345 (tppt) cc_final: 0.7942 (tppt) REVERT: C 400 LYS cc_start: 0.8327 (tppt) cc_final: 0.8085 (tppt) REVERT: C 403 GLU cc_start: 0.7539 (mp0) cc_final: 0.7152 (mp0) REVERT: D 16 LYS cc_start: 0.8356 (mmtt) cc_final: 0.7970 (mmtt) REVERT: D 20 ARG cc_start: 0.7802 (mtm-85) cc_final: 0.7429 (mtm-85) REVERT: D 28 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7390 (mm-30) REVERT: D 71 ARG cc_start: 0.7792 (mtm-85) cc_final: 0.7224 (ptp90) REVERT: D 76 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8037 (mtt90) REVERT: D 88 GLU cc_start: 0.7449 (tt0) cc_final: 0.7071 (tm-30) REVERT: D 98 ARG cc_start: 0.8322 (mtm180) cc_final: 0.7856 (mtm180) REVERT: D 137 THR cc_start: 0.8381 (p) cc_final: 0.8135 (p) REVERT: D 163 TYR cc_start: 0.8628 (t80) cc_final: 0.8213 (t80) REVERT: D 165 GLN cc_start: 0.7987 (mt0) cc_final: 0.7742 (mt0) REVERT: D 179 ASP cc_start: 0.8424 (t0) cc_final: 0.8038 (t0) REVERT: D 197 THR cc_start: 0.8494 (p) cc_final: 0.8204 (t) REVERT: D 234 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7311 (mm-30) REVERT: D 246 THR cc_start: 0.8582 (m) cc_final: 0.8063 (p) REVERT: D 274 CYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7897 (m) REVERT: D 285 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.7584 (t80) REVERT: D 404 ASP cc_start: 0.7931 (OUTLIER) cc_final: 0.7562 (t0) REVERT: D 448 ASP cc_start: 0.7655 (t0) cc_final: 0.7393 (t0) REVERT: E 6 VAL cc_start: 0.8026 (t) cc_final: 0.7774 (m) REVERT: E 20 ARG cc_start: 0.7959 (mtm-85) cc_final: 0.7605 (mtm-85) REVERT: E 24 MET cc_start: 0.8680 (pmm) cc_final: 0.8229 (pmm) REVERT: E 53 GLN cc_start: 0.8396 (tp40) cc_final: 0.7727 (tt0) REVERT: E 73 MET cc_start: 0.7727 (mmp) cc_final: 0.7516 (mmp) REVERT: E 98 ARG cc_start: 0.8190 (mtm180) cc_final: 0.7818 (mtm180) REVERT: E 115 LYS cc_start: 0.8806 (mptp) cc_final: 0.8211 (mptp) REVERT: E 146 ASP cc_start: 0.7475 (p0) cc_final: 0.6614 (p0) REVERT: E 150 TYR cc_start: 0.8656 (m-10) cc_final: 0.8402 (m-10) REVERT: E 165 GLN cc_start: 0.8198 (mt0) cc_final: 0.7998 (mt0) REVERT: E 171 ARG cc_start: 0.7182 (mtm-85) cc_final: 0.6630 (mtm-85) REVERT: E 184 MET cc_start: 0.8104 (mmm) cc_final: 0.7838 (mmm) REVERT: E 197 THR cc_start: 0.8454 (p) cc_final: 0.8185 (t) REVERT: E 243 VAL cc_start: 0.8314 (m) cc_final: 0.8041 (p) REVERT: E 248 TYR cc_start: 0.7926 (m-80) cc_final: 0.7618 (m-10) REVERT: E 405 GLU cc_start: 0.7501 (tp30) cc_final: 0.7054 (tp30) REVERT: E 426 GLN cc_start: 0.7088 (mt0) cc_final: 0.6487 (mt0) REVERT: E 433 LYS cc_start: 0.8336 (mmmt) cc_final: 0.7927 (mmtt) REVERT: E 436 ASP cc_start: 0.8410 (t0) cc_final: 0.8052 (t70) REVERT: F 30 ARG cc_start: 0.7240 (ptp-170) cc_final: 0.6888 (ttm110) REVERT: F 51 ILE cc_start: 0.8353 (mm) cc_final: 0.8124 (mm) REVERT: F 75 ASP cc_start: 0.8028 (p0) cc_final: 0.7825 (p0) REVERT: F 111 ASN cc_start: 0.8674 (t0) cc_final: 0.8278 (t0) REVERT: F 115 LYS cc_start: 0.8804 (mptp) cc_final: 0.8227 (mptp) REVERT: F 192 TYR cc_start: 0.8893 (m-80) cc_final: 0.8612 (m-80) REVERT: F 232 LYS cc_start: 0.8172 (ptmt) cc_final: 0.7754 (ptmt) REVERT: F 303 TYR cc_start: 0.7949 (m-80) cc_final: 0.7652 (m-80) REVERT: F 325 ARG cc_start: 0.7516 (ptp-110) cc_final: 0.6964 (ttm110) REVERT: F 346 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8312 (tt) REVERT: F 362 LEU cc_start: 0.8662 (mm) cc_final: 0.8459 (mt) REVERT: F 396 LYS cc_start: 0.8259 (mmtm) cc_final: 0.7868 (mmmm) REVERT: F 403 GLU cc_start: 0.7485 (mp0) cc_final: 0.7163 (mp0) REVERT: F 433 LYS cc_start: 0.8438 (mmmt) cc_final: 0.8072 (mmtt) REVERT: F 436 ASP cc_start: 0.8018 (t0) cc_final: 0.7780 (t0) REVERT: F 441 GLN cc_start: 0.7557 (mt0) cc_final: 0.7316 (mt0) REVERT: G 16 LYS cc_start: 0.8363 (mmtt) cc_final: 0.8116 (mmtt) REVERT: G 52 GLU cc_start: 0.7915 (mt-10) cc_final: 0.6924 (mm-30) REVERT: G 76 ARG cc_start: 0.8209 (mtt90) cc_final: 0.7282 (mtt90) REVERT: G 88 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7094 (tm-30) REVERT: G 106 LYS cc_start: 0.8266 (mtmm) cc_final: 0.7958 (mtmm) REVERT: G 111 ASN cc_start: 0.8744 (t0) cc_final: 0.8213 (t0) REVERT: G 115 LYS cc_start: 0.8887 (mptp) cc_final: 0.8285 (mptp) REVERT: G 150 TYR cc_start: 0.8719 (m-80) cc_final: 0.8474 (m-80) REVERT: G 163 TYR cc_start: 0.8576 (t80) cc_final: 0.8190 (t80) REVERT: G 171 ARG cc_start: 0.7507 (mtm-85) cc_final: 0.7000 (mtm-85) REVERT: G 179 ASP cc_start: 0.8312 (t0) cc_final: 0.7658 (t0) REVERT: G 274 CYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7204 (m) REVERT: G 275 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.7073 (ptt180) REVERT: G 285 TYR cc_start: 0.8195 (OUTLIER) cc_final: 0.6892 (t80) REVERT: G 293 SER cc_start: 0.8260 (m) cc_final: 0.7483 (p) REVERT: G 400 LYS cc_start: 0.8379 (tppt) cc_final: 0.7774 (tppt) REVERT: G 448 ASP cc_start: 0.7527 (t0) cc_final: 0.7307 (t0) REVERT: H 16 LYS cc_start: 0.8409 (mmtt) cc_final: 0.8097 (mmtt) REVERT: H 20 ARG cc_start: 0.7862 (mtm-85) cc_final: 0.7573 (mtm-85) REVERT: H 88 GLU cc_start: 0.7519 (tt0) cc_final: 0.6909 (tm-30) REVERT: H 99 LYS cc_start: 0.8846 (mmmm) cc_final: 0.8540 (mmmm) REVERT: H 111 ASN cc_start: 0.8652 (t0) cc_final: 0.7962 (t0) REVERT: H 115 LYS cc_start: 0.8790 (mptp) cc_final: 0.8106 (mptp) REVERT: H 171 ARG cc_start: 0.7335 (mtm-85) cc_final: 0.6907 (mtm-85) REVERT: H 179 ASP cc_start: 0.8078 (t0) cc_final: 0.7329 (t70) REVERT: H 239 VAL cc_start: 0.8724 (t) cc_final: 0.8390 (p) REVERT: H 341 GLN cc_start: 0.7971 (mt0) cc_final: 0.7728 (mt0) REVERT: H 436 ASP cc_start: 0.8431 (t0) cc_final: 0.8172 (t70) REVERT: H 447 PHE cc_start: 0.8532 (m-80) cc_final: 0.8157 (m-80) REVERT: I 16 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8246 (mtpt) REVERT: I 22 TYR cc_start: 0.8501 (m-80) cc_final: 0.8047 (m-80) REVERT: I 43 PHE cc_start: 0.8884 (t80) cc_final: 0.8642 (t80) REVERT: I 52 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7431 (mt-10) REVERT: I 98 ARG cc_start: 0.8213 (mtm180) cc_final: 0.7754 (mtm180) REVERT: I 106 LYS cc_start: 0.8258 (mtmm) cc_final: 0.7815 (mtmm) REVERT: I 135 LEU cc_start: 0.8640 (mt) cc_final: 0.8410 (mm) REVERT: I 165 GLN cc_start: 0.8016 (mt0) cc_final: 0.7727 (mt0) REVERT: I 184 MET cc_start: 0.8216 (mmm) cc_final: 0.7877 (mmm) REVERT: I 192 TYR cc_start: 0.8922 (m-80) cc_final: 0.8683 (m-80) REVERT: I 266 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8473 (mt) REVERT: I 383 MET cc_start: 0.8591 (ttp) cc_final: 0.8271 (ttm) REVERT: I 400 LYS cc_start: 0.8205 (tppt) cc_final: 0.7729 (ttpt) REVERT: I 405 GLU cc_start: 0.7769 (mp0) cc_final: 0.7272 (mp0) REVERT: I 441 GLN cc_start: 0.7700 (mt0) cc_final: 0.7329 (mt0) REVERT: J 5 TYR cc_start: 0.8229 (m-10) cc_final: 0.7740 (m-10) REVERT: J 16 LYS cc_start: 0.8362 (mmtt) cc_final: 0.8151 (mmpt) REVERT: J 51 ILE cc_start: 0.8602 (mm) cc_final: 0.8400 (mm) REVERT: J 76 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.8149 (mtt90) REVERT: J 92 ARG cc_start: 0.7681 (mmp80) cc_final: 0.7239 (mmp80) REVERT: J 98 ARG cc_start: 0.8282 (mtm180) cc_final: 0.7897 (mtm180) REVERT: J 106 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8131 (mtmm) REVERT: J 115 LYS cc_start: 0.8836 (mptp) cc_final: 0.8275 (mptp) REVERT: J 165 GLN cc_start: 0.8201 (mt0) cc_final: 0.7946 (mt0) REVERT: J 171 ARG cc_start: 0.7310 (mtm-85) cc_final: 0.6756 (mtm-85) REVERT: J 213 CYS cc_start: 0.7944 (p) cc_final: 0.7684 (p) REVERT: J 248 TYR cc_start: 0.7935 (m-10) cc_final: 0.7666 (m-10) REVERT: J 258 TRP cc_start: 0.8693 (m100) cc_final: 0.7584 (m100) REVERT: J 275 ARG cc_start: 0.7309 (ttt180) cc_final: 0.6692 (ptt180) REVERT: J 285 TYR cc_start: 0.8217 (OUTLIER) cc_final: 0.6749 (t80) REVERT: J 400 LYS cc_start: 0.8277 (tppt) cc_final: 0.7570 (tppt) REVERT: J 403 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7068 (mp0) REVERT: K 28 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7246 (mm-30) REVERT: K 76 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7725 (mtt90) REVERT: K 88 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7170 (tt0) REVERT: K 111 ASN cc_start: 0.8586 (t0) cc_final: 0.8353 (t0) REVERT: K 115 LYS cc_start: 0.8755 (mptp) cc_final: 0.8136 (mptp) REVERT: K 143 GLN cc_start: 0.8343 (tt0) cc_final: 0.8089 (tt0) REVERT: K 171 ARG cc_start: 0.7180 (mtm-85) cc_final: 0.6774 (mtm-85) REVERT: K 184 MET cc_start: 0.8309 (mmm) cc_final: 0.8101 (mmm) REVERT: K 203 GLN cc_start: 0.8497 (mt0) cc_final: 0.8280 (mt0) REVERT: K 221 ARG cc_start: 0.7803 (ttp80) cc_final: 0.7388 (ttp80) REVERT: K 238 ARG cc_start: 0.7441 (ttm110) cc_final: 0.7088 (mtm110) REVERT: K 267 LYS cc_start: 0.8310 (pttp) cc_final: 0.8088 (pttp) REVERT: K 313 LEU cc_start: 0.8449 (mt) cc_final: 0.8096 (mm) REVERT: K 378 THR cc_start: 0.7931 (m) cc_final: 0.7607 (p) REVERT: K 396 LYS cc_start: 0.8343 (tppt) cc_final: 0.7975 (tppt) REVERT: L 5 TYR cc_start: 0.8188 (m-10) cc_final: 0.7518 (m-10) REVERT: L 20 ARG cc_start: 0.7820 (mtm-85) cc_final: 0.7386 (mtm-85) REVERT: L 24 MET cc_start: 0.8779 (pmm) cc_final: 0.8244 (pmm) REVERT: L 43 PHE cc_start: 0.8959 (t80) cc_final: 0.8612 (t80) REVERT: L 76 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7939 (mtt90) REVERT: L 92 ARG cc_start: 0.7742 (mmp80) cc_final: 0.7361 (mmp80) REVERT: L 98 ARG cc_start: 0.8182 (mtm180) cc_final: 0.7699 (mtm180) REVERT: L 106 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8156 (mtmm) REVERT: L 135 LEU cc_start: 0.8648 (mt) cc_final: 0.8404 (mm) REVERT: L 168 LYS cc_start: 0.8827 (mtmt) cc_final: 0.8382 (mtpp) REVERT: L 171 ARG cc_start: 0.7013 (mtm-85) cc_final: 0.6728 (mtm-85) REVERT: L 179 ASP cc_start: 0.8225 (t0) cc_final: 0.7698 (t0) REVERT: L 240 LEU cc_start: 0.8083 (mm) cc_final: 0.7693 (mp) REVERT: L 245 SER cc_start: 0.8601 (p) cc_final: 0.8260 (t) REVERT: L 258 TRP cc_start: 0.8585 (m100) cc_final: 0.7553 (m100) REVERT: L 283 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7374 (mp0) REVERT: L 328 PHE cc_start: 0.8047 (p90) cc_final: 0.7827 (p90) REVERT: L 400 LYS cc_start: 0.8160 (tppt) cc_final: 0.7585 (ttpt) REVERT: L 403 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6920 (mp0) REVERT: L 426 GLN cc_start: 0.7130 (OUTLIER) cc_final: 0.6785 (mt0) REVERT: L 446 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7437 (mm-30) outliers start: 264 outliers final: 169 residues processed: 1977 average time/residue: 0.6196 time to fit residues: 1875.6535 Evaluate side-chains 2032 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1836 time to evaluate : 4.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 398 CYS Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 342 MET Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 398 CYS Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 292 MET Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 411 ARG Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 274 CYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 404 ASP Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain E residue 19 GLN Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 106 LYS Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 292 MET Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 342 MET Chi-restraints excluded: chain E residue 398 CYS Chi-restraints excluded: chain E residue 403 GLU Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 120 GLN Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 321 VAL Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 397 GLU Chi-restraints excluded: chain F residue 411 ARG Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 77 LYS Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain G residue 236 CYS Chi-restraints excluded: chain G residue 245 SER Chi-restraints excluded: chain G residue 274 CYS Chi-restraints excluded: chain G residue 275 ARG Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 340 ASP Chi-restraints excluded: chain G residue 348 THR Chi-restraints excluded: chain G residue 403 GLU Chi-restraints excluded: chain G residue 411 ARG Chi-restraints excluded: chain G residue 430 THR Chi-restraints excluded: chain G residue 438 GLN Chi-restraints excluded: chain G residue 440 ILE Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 73 MET Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 146 ASP Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 301 THR Chi-restraints excluded: chain H residue 342 MET Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 398 CYS Chi-restraints excluded: chain H residue 403 GLU Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain I residue 36 ASP Chi-restraints excluded: chain I residue 73 MET Chi-restraints excluded: chain I residue 75 ASP Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 120 GLN Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 291 THR Chi-restraints excluded: chain I residue 314 MET Chi-restraints excluded: chain I residue 348 THR Chi-restraints excluded: chain I residue 358 LEU Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain I residue 403 GLU Chi-restraints excluded: chain I residue 408 LEU Chi-restraints excluded: chain J residue 53 GLN Chi-restraints excluded: chain J residue 76 ARG Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain J residue 120 GLN Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 228 MET Chi-restraints excluded: chain J residue 236 CYS Chi-restraints excluded: chain J residue 243 VAL Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 291 THR Chi-restraints excluded: chain J residue 301 THR Chi-restraints excluded: chain J residue 348 THR Chi-restraints excluded: chain J residue 383 MET Chi-restraints excluded: chain J residue 403 GLU Chi-restraints excluded: chain K residue 76 ARG Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 149 ILE Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 283 GLU Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 292 MET Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 305 VAL Chi-restraints excluded: chain K residue 337 THR Chi-restraints excluded: chain K residue 348 THR Chi-restraints excluded: chain K residue 349 GLU Chi-restraints excluded: chain K residue 397 GLU Chi-restraints excluded: chain K residue 403 GLU Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain L residue 120 GLN Chi-restraints excluded: chain L residue 167 ILE Chi-restraints excluded: chain L residue 202 GLU Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain L residue 283 GLU Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 314 MET Chi-restraints excluded: chain L residue 318 THR Chi-restraints excluded: chain L residue 348 THR Chi-restraints excluded: chain L residue 403 GLU Chi-restraints excluded: chain L residue 405 GLU Chi-restraints excluded: chain L residue 426 GLN Chi-restraints excluded: chain L residue 427 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 492 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 291 optimal weight: 4.9990 chunk 373 optimal weight: 2.9990 chunk 289 optimal weight: 1.9990 chunk 430 optimal weight: 0.6980 chunk 285 optimal weight: 5.9990 chunk 508 optimal weight: 6.9990 chunk 318 optimal weight: 0.4980 chunk 310 optimal weight: 1.9990 chunk 234 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 GLN ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 GLN ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 356 GLN G 31 GLN ** G 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 308 HIS ** G 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 364 GLN G 381 ASN G 438 GLN ** H 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 389 GLN ** J 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 364 GLN ** K 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 429 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 42504 Z= 0.249 Angle : 0.620 9.026 57684 Z= 0.310 Chirality : 0.044 0.151 6564 Planarity : 0.005 0.101 7260 Dihedral : 5.862 36.015 5892 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 5.89 % Allowed : 33.08 % Favored : 61.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.37 % 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: -1.32 (0.11), residues: 5148 helix: 0.84 (0.14), residues: 1632 sheet: -1.11 (0.13), residues: 1332 loop : -2.05 (0.11), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 258 HIS 0.004 0.001 HIS G 308 PHE 0.020 0.002 PHE C 133 TYR 0.035 0.002 TYR J 5 ARG 0.009 0.001 ARG B 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2136 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 1876 time to evaluate : 5.389 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: A 16 LYS cc_start: 0.8388 (mmtt) cc_final: 0.8041 (mmtt) REVERT: A 30 ARG cc_start: 0.6067 (ptt-90) cc_final: 0.5802 (ptt-90) REVERT: A 41 ARG cc_start: 0.7779 (tpp-160) cc_final: 0.7329 (tpp-160) REVERT: A 76 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.8306 (mtt90) REVERT: A 85 ARG cc_start: 0.7514 (mmp80) cc_final: 0.7232 (mmp80) REVERT: A 88 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6487 (tm-30) REVERT: A 98 ARG cc_start: 0.8297 (mtm180) cc_final: 0.7798 (mtm180) REVERT: A 110 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7760 (tpp-160) REVERT: A 133 PHE cc_start: 0.7836 (t80) cc_final: 0.7607 (t80) REVERT: A 135 LEU cc_start: 0.8625 (mt) cc_final: 0.8372 (mt) REVERT: A 146 ASP cc_start: 0.7265 (p0) cc_final: 0.6285 (p0) REVERT: A 163 TYR cc_start: 0.8631 (t80) cc_final: 0.8341 (t80) REVERT: A 171 ARG cc_start: 0.7193 (mtm-85) cc_final: 0.6663 (mtm-85) REVERT: A 176 VAL cc_start: 0.8665 (OUTLIER) cc_final: 0.8432 (t) REVERT: A 188 MET cc_start: 0.8330 (mmt) cc_final: 0.7764 (mmt) REVERT: A 242 SER cc_start: 0.8149 (t) cc_final: 0.7602 (p) REVERT: A 243 VAL cc_start: 0.7987 (t) cc_final: 0.7653 (t) REVERT: A 266 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8591 (mt) REVERT: A 267 LYS cc_start: 0.8205 (mtmt) cc_final: 0.7912 (mtmt) REVERT: A 278 THR cc_start: 0.9017 (m) cc_final: 0.8542 (p) REVERT: A 285 TYR cc_start: 0.8262 (OUTLIER) cc_final: 0.7040 (t80) REVERT: A 345 ILE cc_start: 0.9049 (mm) cc_final: 0.8813 (mm) REVERT: B 72 MET cc_start: 0.8278 (tmm) cc_final: 0.7704 (tmm) REVERT: B 76 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.8135 (mtt90) REVERT: B 85 ARG cc_start: 0.7515 (mmp80) cc_final: 0.7307 (mmp80) REVERT: B 115 LYS cc_start: 0.8761 (mptp) cc_final: 0.8183 (mptp) REVERT: B 184 MET cc_start: 0.8572 (mmm) cc_final: 0.8244 (mmm) REVERT: B 217 LEU cc_start: 0.8019 (mt) cc_final: 0.7764 (mp) REVERT: B 219 GLU cc_start: 0.5784 (OUTLIER) cc_final: 0.5409 (pp20) REVERT: B 396 LYS cc_start: 0.8471 (mmmm) cc_final: 0.8005 (tppt) REVERT: B 447 PHE cc_start: 0.8532 (m-80) cc_final: 0.8096 (m-10) REVERT: C 24 MET cc_start: 0.8706 (pmm) cc_final: 0.8494 (pmm) REVERT: C 51 ILE cc_start: 0.8559 (mm) cc_final: 0.8329 (mm) REVERT: C 76 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.8051 (mtt90) REVERT: C 110 ARG cc_start: 0.8205 (mmt-90) cc_final: 0.7364 (mmt-90) REVERT: C 135 LEU cc_start: 0.8558 (mt) cc_final: 0.8053 (mm) REVERT: C 146 ASP cc_start: 0.7541 (p0) cc_final: 0.7005 (p0) REVERT: C 324 GLU cc_start: 0.7159 (tt0) cc_final: 0.6934 (tt0) REVERT: C 396 LYS cc_start: 0.8385 (tppt) cc_final: 0.7995 (tppt) REVERT: C 400 LYS cc_start: 0.8359 (tppt) cc_final: 0.8102 (tppt) REVERT: C 403 GLU cc_start: 0.7540 (mp0) cc_final: 0.7163 (mp0) REVERT: D 16 LYS cc_start: 0.8372 (mmtt) cc_final: 0.7997 (mmtt) REVERT: D 20 ARG cc_start: 0.7827 (mtm-85) cc_final: 0.7438 (mtm-85) REVERT: D 28 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7385 (mm-30) REVERT: D 43 PHE cc_start: 0.8889 (t80) cc_final: 0.8630 (t80) REVERT: D 63 ASP cc_start: 0.7628 (t0) cc_final: 0.7147 (t0) REVERT: D 76 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8052 (mtt90) REVERT: D 88 GLU cc_start: 0.7485 (tt0) cc_final: 0.7115 (tm-30) REVERT: D 98 ARG cc_start: 0.8362 (mtm180) cc_final: 0.7895 (mtm180) REVERT: D 99 LYS cc_start: 0.8896 (mmmm) cc_final: 0.8642 (mmmm) REVERT: D 137 THR cc_start: 0.8376 (p) cc_final: 0.8131 (p) REVERT: D 146 ASP cc_start: 0.7133 (p0) cc_final: 0.6781 (p0) REVERT: D 150 TYR cc_start: 0.8759 (m-80) cc_final: 0.8519 (m-80) REVERT: D 163 TYR cc_start: 0.8643 (t80) cc_final: 0.8221 (t80) REVERT: D 179 ASP cc_start: 0.8461 (t0) cc_final: 0.8006 (t0) REVERT: D 188 MET cc_start: 0.8350 (mmt) cc_final: 0.7787 (mmt) REVERT: D 197 THR cc_start: 0.8494 (p) cc_final: 0.8198 (t) REVERT: D 234 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7339 (mm-30) REVERT: D 246 THR cc_start: 0.8570 (m) cc_final: 0.8012 (p) REVERT: D 274 CYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7937 (m) REVERT: D 285 TYR cc_start: 0.8335 (OUTLIER) cc_final: 0.7467 (t80) REVERT: D 393 LYS cc_start: 0.8516 (mttp) cc_final: 0.8315 (mttp) REVERT: D 404 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7582 (t0) REVERT: D 448 ASP cc_start: 0.7642 (t0) cc_final: 0.7371 (t0) REVERT: E 6 VAL cc_start: 0.8036 (t) cc_final: 0.7774 (m) REVERT: E 20 ARG cc_start: 0.7981 (mtm-85) cc_final: 0.7649 (mtm-85) REVERT: E 24 MET cc_start: 0.8682 (pmm) cc_final: 0.8237 (pmm) REVERT: E 98 ARG cc_start: 0.8249 (mtm180) cc_final: 0.7900 (mtm180) REVERT: E 115 LYS cc_start: 0.8847 (mptp) cc_final: 0.8231 (mptp) REVERT: E 144 ARG cc_start: 0.8018 (ttm110) cc_final: 0.7700 (mmm-85) REVERT: E 146 ASP cc_start: 0.7561 (p0) cc_final: 0.6767 (p0) REVERT: E 150 TYR cc_start: 0.8658 (m-10) cc_final: 0.8410 (m-10) REVERT: E 171 ARG cc_start: 0.7267 (mtm-85) cc_final: 0.6709 (mtm-85) REVERT: E 180 THR cc_start: 0.8548 (m) cc_final: 0.8228 (m) REVERT: E 184 MET cc_start: 0.8176 (mmm) cc_final: 0.7902 (mmm) REVERT: E 197 THR cc_start: 0.8495 (p) cc_final: 0.8218 (t) REVERT: E 243 VAL cc_start: 0.8349 (m) cc_final: 0.8061 (p) REVERT: E 248 TYR cc_start: 0.7965 (m-80) cc_final: 0.7728 (m-10) REVERT: E 289 ARG cc_start: 0.7957 (mtp-110) cc_final: 0.7623 (ttp80) REVERT: E 405 GLU cc_start: 0.7539 (tp30) cc_final: 0.7074 (tp30) REVERT: E 426 GLN cc_start: 0.7131 (mt0) cc_final: 0.6419 (mt0) REVERT: E 433 LYS cc_start: 0.8425 (mmmt) cc_final: 0.8105 (mmtt) REVERT: E 436 ASP cc_start: 0.8444 (t0) cc_final: 0.8078 (t70) REVERT: E 447 PHE cc_start: 0.8555 (m-80) cc_final: 0.8275 (m-10) REVERT: F 111 ASN cc_start: 0.8695 (t0) cc_final: 0.8270 (t0) REVERT: F 115 LYS cc_start: 0.8821 (mptp) cc_final: 0.8259 (mptp) REVERT: F 232 LYS cc_start: 0.8147 (ptmt) cc_final: 0.7731 (ptmt) REVERT: F 303 TYR cc_start: 0.8050 (m-80) cc_final: 0.7798 (m-80) REVERT: F 325 ARG cc_start: 0.7568 (ptp-110) cc_final: 0.6978 (ttm110) REVERT: F 328 PHE cc_start: 0.8004 (p90) cc_final: 0.7755 (p90) REVERT: F 346 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8402 (tt) REVERT: F 360 VAL cc_start: 0.8986 (OUTLIER) cc_final: 0.8778 (t) REVERT: F 362 LEU cc_start: 0.8695 (mm) cc_final: 0.8453 (mt) REVERT: F 399 ARG cc_start: 0.7714 (tpp80) cc_final: 0.7180 (tpp80) REVERT: F 403 GLU cc_start: 0.7466 (mp0) cc_final: 0.7003 (mp0) REVERT: F 433 LYS cc_start: 0.8443 (mmmt) cc_final: 0.8094 (mmtt) REVERT: F 441 GLN cc_start: 0.7618 (mt0) cc_final: 0.7306 (mt0) REVERT: G 16 LYS cc_start: 0.8379 (mmtt) cc_final: 0.8129 (mmtt) REVERT: G 24 MET cc_start: 0.7812 (ptp) cc_final: 0.7609 (ptp) REVERT: G 52 GLU cc_start: 0.7941 (mt-10) cc_final: 0.6963 (mm-30) REVERT: G 76 ARG cc_start: 0.8226 (mtt90) cc_final: 0.7293 (mtt90) REVERT: G 88 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7091 (tm-30) REVERT: G 106 LYS cc_start: 0.8312 (mtmm) cc_final: 0.7962 (mtmm) REVERT: G 111 ASN cc_start: 0.8759 (t0) cc_final: 0.8153 (t0) REVERT: G 115 LYS cc_start: 0.8900 (mptp) cc_final: 0.8249 (mptp) REVERT: G 163 TYR cc_start: 0.8584 (t80) cc_final: 0.8184 (t80) REVERT: G 171 ARG cc_start: 0.7505 (mtm-85) cc_final: 0.7026 (mtm-85) REVERT: G 179 ASP cc_start: 0.8313 (t0) cc_final: 0.7662 (t0) REVERT: G 234 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7196 (mm-30) REVERT: G 274 CYS cc_start: 0.8311 (OUTLIER) cc_final: 0.8059 (m) REVERT: G 275 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.6965 (ptt180) REVERT: G 285 TYR cc_start: 0.8271 (OUTLIER) cc_final: 0.6845 (t80) REVERT: G 293 SER cc_start: 0.8200 (m) cc_final: 0.7428 (p) REVERT: G 400 LYS cc_start: 0.8372 (tppt) cc_final: 0.7779 (tppt) REVERT: G 406 LYS cc_start: 0.8853 (mmmm) cc_final: 0.8543 (mmtp) REVERT: G 433 LYS cc_start: 0.8340 (mmmt) cc_final: 0.8012 (mmtt) REVERT: H 16 LYS cc_start: 0.8426 (mmtt) cc_final: 0.8111 (mmtt) REVERT: H 20 ARG cc_start: 0.7935 (mtm-85) cc_final: 0.7647 (mtm-85) REVERT: H 88 GLU cc_start: 0.7562 (tt0) cc_final: 0.6911 (tm-30) REVERT: H 99 LYS cc_start: 0.8845 (mmmm) cc_final: 0.8568 (mmmm) REVERT: H 111 ASN cc_start: 0.8670 (t0) cc_final: 0.7940 (t0) REVERT: H 115 LYS cc_start: 0.8825 (mptp) cc_final: 0.8114 (mptp) REVERT: H 146 ASP cc_start: 0.7707 (OUTLIER) cc_final: 0.6875 (p0) REVERT: H 171 ARG cc_start: 0.7382 (mtm-85) cc_final: 0.6909 (mtm-85) REVERT: H 239 VAL cc_start: 0.8729 (t) cc_final: 0.8395 (p) REVERT: H 264 PHE cc_start: 0.8280 (p90) cc_final: 0.7932 (p90) REVERT: H 436 ASP cc_start: 0.8457 (t0) cc_final: 0.8172 (t70) REVERT: H 447 PHE cc_start: 0.8508 (m-80) cc_final: 0.8115 (m-80) REVERT: I 16 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8221 (mtpt) REVERT: I 22 TYR cc_start: 0.8521 (m-80) cc_final: 0.7965 (m-80) REVERT: I 43 PHE cc_start: 0.8892 (t80) cc_final: 0.8287 (t80) REVERT: I 56 ASP cc_start: 0.7914 (t0) cc_final: 0.7630 (t0) REVERT: I 98 ARG cc_start: 0.8261 (mtm180) cc_final: 0.7800 (mtm180) REVERT: I 106 LYS cc_start: 0.8310 (mtmm) cc_final: 0.7900 (mtmm) REVERT: I 135 LEU cc_start: 0.8655 (mt) cc_final: 0.8422 (mm) REVERT: I 150 TYR cc_start: 0.8715 (m-10) cc_final: 0.8514 (m-10) REVERT: I 165 GLN cc_start: 0.7994 (mt0) cc_final: 0.7698 (mt0) REVERT: I 184 MET cc_start: 0.8314 (mmm) cc_final: 0.7881 (mmm) REVERT: I 192 TYR cc_start: 0.8942 (m-80) cc_final: 0.8646 (m-80) REVERT: I 303 TYR cc_start: 0.8348 (m-80) cc_final: 0.7861 (m-80) REVERT: I 383 MET cc_start: 0.8585 (ttp) cc_final: 0.8309 (ttm) REVERT: I 400 LYS cc_start: 0.8210 (tppt) cc_final: 0.7756 (ttpt) REVERT: I 405 GLU cc_start: 0.7800 (mp0) cc_final: 0.7297 (mp0) REVERT: I 426 GLN cc_start: 0.7137 (mt0) cc_final: 0.6566 (mt0) REVERT: I 436 ASP cc_start: 0.8258 (t0) cc_final: 0.7803 (t0) REVERT: I 441 GLN cc_start: 0.7723 (mt0) cc_final: 0.7310 (mt0) REVERT: J 16 LYS cc_start: 0.8362 (mmtt) cc_final: 0.8135 (mmpt) REVERT: J 28 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7369 (mm-30) REVERT: J 41 ARG cc_start: 0.7689 (tpp-160) cc_final: 0.7224 (tpp-160) REVERT: J 72 MET cc_start: 0.8402 (tmm) cc_final: 0.8114 (tmm) REVERT: J 76 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.8183 (mtt90) REVERT: J 92 ARG cc_start: 0.7684 (mmp80) cc_final: 0.7286 (mmp80) REVERT: J 98 ARG cc_start: 0.8329 (mtm180) cc_final: 0.7881 (mtm180) REVERT: J 99 LYS cc_start: 0.8853 (mmmm) cc_final: 0.8473 (mmmm) REVERT: J 106 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8144 (mtmm) REVERT: J 115 LYS cc_start: 0.8854 (mptp) cc_final: 0.8232 (mptp) REVERT: J 165 GLN cc_start: 0.8258 (mt0) cc_final: 0.7988 (mt0) REVERT: J 171 ARG cc_start: 0.7272 (mtm-85) cc_final: 0.6742 (mtm-85) REVERT: J 185 TYR cc_start: 0.8694 (m-80) cc_final: 0.8001 (m-80) REVERT: J 248 TYR cc_start: 0.7959 (m-10) cc_final: 0.7622 (m-10) REVERT: J 258 TRP cc_start: 0.8703 (m100) cc_final: 0.7645 (m100) REVERT: J 275 ARG cc_start: 0.7359 (ttt180) cc_final: 0.6735 (ptt180) REVERT: J 285 TYR cc_start: 0.8257 (OUTLIER) cc_final: 0.6806 (t80) REVERT: J 313 LEU cc_start: 0.8302 (mt) cc_final: 0.8002 (mp) REVERT: J 324 GLU cc_start: 0.7033 (tt0) cc_final: 0.6683 (tt0) REVERT: J 397 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7880 (mm-30) REVERT: J 400 LYS cc_start: 0.8267 (tppt) cc_final: 0.7565 (tppt) REVERT: J 403 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7082 (mp0) REVERT: K 6 VAL cc_start: 0.7994 (t) cc_final: 0.7701 (p) REVERT: K 28 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7220 (mm-30) REVERT: K 30 ARG cc_start: 0.7434 (mtm110) cc_final: 0.7200 (ttm110) REVERT: K 76 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7802 (mtt90) REVERT: K 88 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7192 (tt0) REVERT: K 110 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7956 (tpp-160) REVERT: K 111 ASN cc_start: 0.8619 (t0) cc_final: 0.8338 (t0) REVERT: K 115 LYS cc_start: 0.8775 (mptp) cc_final: 0.8126 (mptp) REVERT: K 143 GLN cc_start: 0.8368 (tt0) cc_final: 0.8090 (tt0) REVERT: K 171 ARG cc_start: 0.7226 (mtm-85) cc_final: 0.6829 (mtm-85) REVERT: K 203 GLN cc_start: 0.8494 (mt0) cc_final: 0.8251 (mt0) REVERT: K 221 ARG cc_start: 0.7800 (ttp80) cc_final: 0.7392 (ttp80) REVERT: K 238 ARG cc_start: 0.7455 (ttm110) cc_final: 0.7099 (mtm110) REVERT: K 267 LYS cc_start: 0.8292 (pttp) cc_final: 0.8070 (pttp) REVERT: K 313 LEU cc_start: 0.8451 (mt) cc_final: 0.8096 (mm) REVERT: K 396 LYS cc_start: 0.8362 (tppt) cc_final: 0.7970 (tppt) REVERT: L 20 ARG cc_start: 0.7838 (mtm-85) cc_final: 0.7410 (mtm-85) REVERT: L 24 MET cc_start: 0.8790 (pmm) cc_final: 0.8247 (pmm) REVERT: L 43 PHE cc_start: 0.8959 (t80) cc_final: 0.8600 (t80) REVERT: L 76 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.8009 (mtt90) REVERT: L 98 ARG cc_start: 0.8208 (mtm180) cc_final: 0.7734 (mtm180) REVERT: L 135 LEU cc_start: 0.8681 (mt) cc_final: 0.8444 (mm) REVERT: L 146 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.6845 (p0) REVERT: L 168 LYS cc_start: 0.8846 (mtmt) cc_final: 0.8425 (mtpp) REVERT: L 171 ARG cc_start: 0.7092 (mtm-85) cc_final: 0.6785 (mtm-85) REVERT: L 179 ASP cc_start: 0.8220 (t0) cc_final: 0.7714 (t0) REVERT: L 245 SER cc_start: 0.8656 (p) cc_final: 0.8286 (t) REVERT: L 258 TRP cc_start: 0.8625 (m100) cc_final: 0.7554 (m100) REVERT: L 283 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7339 (mp0) REVERT: L 303 TYR cc_start: 0.8249 (m-80) cc_final: 0.8045 (m-80) REVERT: L 400 LYS cc_start: 0.8146 (tppt) cc_final: 0.7529 (ttpt) REVERT: L 403 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6946 (mp0) REVERT: L 427 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.7251 (mmtt) REVERT: L 446 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7482 (mm-30) outliers start: 260 outliers final: 175 residues processed: 1956 average time/residue: 0.6238 time to fit residues: 1875.8134 Evaluate side-chains 2060 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 1852 time to evaluate : 4.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 110 ARG Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 398 CYS Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 342 MET Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 398 CYS Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 411 ARG Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 274 CYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 404 ASP Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain E residue 19 GLN Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 92 ARG Chi-restraints excluded: chain E residue 106 LYS Chi-restraints excluded: chain E residue 120 GLN Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 277 ASP Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 292 MET Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 342 MET Chi-restraints excluded: chain E residue 398 CYS Chi-restraints excluded: chain E residue 403 GLU Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 120 GLN Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 321 VAL Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 411 ARG Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 236 CYS Chi-restraints excluded: chain G residue 274 CYS Chi-restraints excluded: chain G residue 275 ARG Chi-restraints excluded: chain G residue 283 GLU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 340 ASP Chi-restraints excluded: chain G residue 348 THR Chi-restraints excluded: chain G residue 403 GLU Chi-restraints excluded: chain G residue 411 ARG Chi-restraints excluded: chain G residue 430 THR Chi-restraints excluded: chain G residue 440 ILE Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 146 ASP Chi-restraints excluded: chain H residue 277 ASP Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 301 THR Chi-restraints excluded: chain H residue 342 MET Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 398 CYS Chi-restraints excluded: chain H residue 403 GLU Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain I residue 36 ASP Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 120 GLN Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 291 THR Chi-restraints excluded: chain I residue 301 THR Chi-restraints excluded: chain I residue 348 THR Chi-restraints excluded: chain I residue 358 LEU Chi-restraints excluded: chain I residue 403 GLU Chi-restraints excluded: chain I residue 437 THR Chi-restraints excluded: chain J residue 53 GLN Chi-restraints excluded: chain J residue 76 ARG Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain J residue 120 GLN Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 236 CYS Chi-restraints excluded: chain J residue 243 VAL Chi-restraints excluded: chain J residue 277 ASP Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 291 THR Chi-restraints excluded: chain J residue 301 THR Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 348 THR Chi-restraints excluded: chain J residue 379 MET Chi-restraints excluded: chain J residue 383 MET Chi-restraints excluded: chain J residue 403 GLU Chi-restraints excluded: chain K residue 76 ARG Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 110 ARG Chi-restraints excluded: chain K residue 120 GLN Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 277 ASP Chi-restraints excluded: chain K residue 283 GLU Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 292 MET Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 305 VAL Chi-restraints excluded: chain K residue 348 THR Chi-restraints excluded: chain K residue 398 CYS Chi-restraints excluded: chain K residue 403 GLU Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain L residue 120 GLN Chi-restraints excluded: chain L residue 146 ASP Chi-restraints excluded: chain L residue 167 ILE Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain L residue 283 GLU Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 301 THR Chi-restraints excluded: chain L residue 314 MET Chi-restraints excluded: chain L residue 318 THR Chi-restraints excluded: chain L residue 348 THR Chi-restraints excluded: chain L residue 403 GLU Chi-restraints excluded: chain L residue 405 GLU Chi-restraints excluded: chain L residue 427 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 314 optimal weight: 0.3980 chunk 203 optimal weight: 4.9990 chunk 303 optimal weight: 0.4980 chunk 153 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 323 optimal weight: 0.2980 chunk 346 optimal weight: 0.7980 chunk 251 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 400 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 ASN A 364 GLN ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 GLN ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 GLN ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN ** F 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 GLN ** G 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 364 GLN ** I 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 364 GLN ** K 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 429 HIS K 441 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 42504 Z= 0.183 Angle : 0.601 8.663 57684 Z= 0.302 Chirality : 0.043 0.140 6564 Planarity : 0.005 0.099 7260 Dihedral : 5.807 37.664 5892 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 5.48 % Allowed : 33.45 % Favored : 61.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.17 % 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: -1.32 (0.11), residues: 5148 helix: 0.80 (0.14), residues: 1620 sheet: -1.10 (0.13), residues: 1332 loop : -2.00 (0.11), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 258 HIS 0.002 0.000 HIS G 308 PHE 0.034 0.002 PHE K 264 TYR 0.034 0.001 TYR J 5 ARG 0.009 0.001 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2100 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 1858 time to evaluate : 4.800 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: A 41 ARG cc_start: 0.7706 (tpp-160) cc_final: 0.7244 (tpp-160) REVERT: A 85 ARG cc_start: 0.7518 (mmp80) cc_final: 0.7202 (mmp80) REVERT: A 88 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6473 (tm-30) REVERT: A 98 ARG cc_start: 0.8267 (mtm180) cc_final: 0.7747 (mtm180) REVERT: A 110 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7743 (tpp-160) REVERT: A 133 PHE cc_start: 0.7819 (t80) cc_final: 0.7596 (t80) REVERT: A 146 ASP cc_start: 0.7204 (p0) cc_final: 0.6286 (p0) REVERT: A 163 TYR cc_start: 0.8563 (t80) cc_final: 0.8285 (t80) REVERT: A 171 ARG cc_start: 0.7098 (mtm-85) cc_final: 0.6660 (mtm-85) REVERT: A 188 MET cc_start: 0.8392 (mmt) cc_final: 0.7850 (mmt) REVERT: A 242 SER cc_start: 0.8131 (t) cc_final: 0.7661 (p) REVERT: A 243 VAL cc_start: 0.7896 (t) cc_final: 0.7609 (t) REVERT: A 266 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8575 (mt) REVERT: A 267 LYS cc_start: 0.8213 (mtmt) cc_final: 0.7946 (mtmt) REVERT: A 278 THR cc_start: 0.9009 (m) cc_final: 0.8547 (p) REVERT: A 285 TYR cc_start: 0.8213 (OUTLIER) cc_final: 0.7120 (t80) REVERT: A 345 ILE cc_start: 0.9035 (mm) cc_final: 0.8790 (mm) REVERT: B 76 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8157 (mtt90) REVERT: B 115 LYS cc_start: 0.8759 (mptp) cc_final: 0.8179 (mptp) REVERT: B 176 VAL cc_start: 0.8603 (p) cc_final: 0.8382 (m) REVERT: B 184 MET cc_start: 0.8527 (mmm) cc_final: 0.7914 (tpp) REVERT: B 283 GLU cc_start: 0.7786 (tp30) cc_final: 0.7350 (tp30) REVERT: B 396 LYS cc_start: 0.8451 (mmmm) cc_final: 0.8063 (tppt) REVERT: B 400 LYS cc_start: 0.8199 (tppt) cc_final: 0.7568 (tppt) REVERT: B 447 PHE cc_start: 0.8534 (m-80) cc_final: 0.8084 (m-10) REVERT: C 5 TYR cc_start: 0.8369 (m-10) cc_final: 0.8142 (m-10) REVERT: C 51 ILE cc_start: 0.8520 (mm) cc_final: 0.8256 (mm) REVERT: C 76 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.8026 (mtt90) REVERT: C 92 ARG cc_start: 0.7891 (mmp80) cc_final: 0.7467 (mmp80) REVERT: C 135 LEU cc_start: 0.8562 (mt) cc_final: 0.8089 (mm) REVERT: C 146 ASP cc_start: 0.7540 (p0) cc_final: 0.6966 (p0) REVERT: C 258 TRP cc_start: 0.8668 (m100) cc_final: 0.7537 (m100) REVERT: C 325 ARG cc_start: 0.7855 (ttp-170) cc_final: 0.7437 (ttp-170) REVERT: C 380 LYS cc_start: 0.8663 (mmtp) cc_final: 0.8448 (mmtp) REVERT: C 396 LYS cc_start: 0.8337 (tppt) cc_final: 0.7913 (tppt) REVERT: C 400 LYS cc_start: 0.8283 (tppt) cc_final: 0.8046 (tppt) REVERT: C 403 GLU cc_start: 0.7531 (mp0) cc_final: 0.7144 (mp0) REVERT: D 16 LYS cc_start: 0.8347 (mmtt) cc_final: 0.7999 (mmtt) REVERT: D 20 ARG cc_start: 0.7795 (mtm-85) cc_final: 0.7425 (mtm-85) REVERT: D 28 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7412 (mm-30) REVERT: D 43 PHE cc_start: 0.8831 (t80) cc_final: 0.8597 (t80) REVERT: D 60 THR cc_start: 0.8565 (p) cc_final: 0.7759 (m) REVERT: D 76 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7986 (mtt90) REVERT: D 98 ARG cc_start: 0.8345 (mtm180) cc_final: 0.7962 (mtm180) REVERT: D 99 LYS cc_start: 0.8918 (mmmm) cc_final: 0.8653 (mmmm) REVERT: D 163 TYR cc_start: 0.8580 (t80) cc_final: 0.8167 (t80) REVERT: D 179 ASP cc_start: 0.8452 (t0) cc_final: 0.8000 (t0) REVERT: D 197 THR cc_start: 0.8444 (p) cc_final: 0.8154 (t) REVERT: D 234 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7321 (mm-30) REVERT: D 274 CYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7931 (m) REVERT: D 285 TYR cc_start: 0.8316 (OUTLIER) cc_final: 0.7506 (t80) REVERT: D 404 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7664 (t0) REVERT: D 448 ASP cc_start: 0.7632 (t0) cc_final: 0.7335 (t0) REVERT: E 20 ARG cc_start: 0.7955 (mtm-85) cc_final: 0.7614 (mtm-85) REVERT: E 24 MET cc_start: 0.8661 (pmm) cc_final: 0.8254 (pmm) REVERT: E 28 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7379 (mm-30) REVERT: E 53 GLN cc_start: 0.8412 (tp40) cc_final: 0.7789 (tt0) REVERT: E 76 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.8228 (mtt90) REVERT: E 98 ARG cc_start: 0.8199 (mtm180) cc_final: 0.7851 (mtm180) REVERT: E 115 LYS cc_start: 0.8836 (mptp) cc_final: 0.8219 (mptp) REVERT: E 146 ASP cc_start: 0.7561 (p0) cc_final: 0.6723 (p0) REVERT: E 171 ARG cc_start: 0.7140 (mtm-85) cc_final: 0.6555 (mtm-85) REVERT: E 180 THR cc_start: 0.8495 (m) cc_final: 0.8162 (m) REVERT: E 184 MET cc_start: 0.8051 (mmm) cc_final: 0.7793 (mmm) REVERT: E 197 THR cc_start: 0.8469 (p) cc_final: 0.8189 (t) REVERT: E 243 VAL cc_start: 0.8290 (m) cc_final: 0.8025 (p) REVERT: E 405 GLU cc_start: 0.7523 (tp30) cc_final: 0.7126 (tp30) REVERT: E 406 LYS cc_start: 0.8531 (mmtp) cc_final: 0.7668 (mmtp) REVERT: E 426 GLN cc_start: 0.7075 (mt0) cc_final: 0.6281 (mt0) REVERT: E 436 ASP cc_start: 0.8357 (t0) cc_final: 0.8024 (t70) REVERT: F 51 ILE cc_start: 0.8192 (mm) cc_final: 0.7943 (mm) REVERT: F 75 ASP cc_start: 0.8006 (p0) cc_final: 0.7799 (p0) REVERT: F 85 ARG cc_start: 0.7320 (mmp80) cc_final: 0.6898 (mmp80) REVERT: F 98 ARG cc_start: 0.8219 (mtm180) cc_final: 0.7849 (mtm180) REVERT: F 111 ASN cc_start: 0.8682 (t0) cc_final: 0.8285 (t0) REVERT: F 115 LYS cc_start: 0.8819 (mptp) cc_final: 0.8255 (mptp) REVERT: F 192 TYR cc_start: 0.8852 (m-80) cc_final: 0.8639 (m-80) REVERT: F 232 LYS cc_start: 0.8137 (ptmt) cc_final: 0.7844 (ptmt) REVERT: F 303 TYR cc_start: 0.7945 (m-80) cc_final: 0.7509 (m-80) REVERT: F 312 PHE cc_start: 0.8080 (t80) cc_final: 0.7879 (t80) REVERT: F 324 GLU cc_start: 0.7001 (tt0) cc_final: 0.6549 (tt0) REVERT: F 325 ARG cc_start: 0.7441 (ptp-110) cc_final: 0.6892 (ttm110) REVERT: F 346 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8305 (tt) REVERT: F 360 VAL cc_start: 0.8954 (OUTLIER) cc_final: 0.8742 (t) REVERT: F 396 LYS cc_start: 0.8253 (mmtm) cc_final: 0.7855 (mmmm) REVERT: F 403 GLU cc_start: 0.7484 (mp0) cc_final: 0.7129 (mp0) REVERT: F 433 LYS cc_start: 0.8443 (mmmt) cc_final: 0.8086 (mmtt) REVERT: F 441 GLN cc_start: 0.7534 (mt0) cc_final: 0.7195 (mt0) REVERT: G 16 LYS cc_start: 0.8370 (mmtt) cc_final: 0.8108 (mmtt) REVERT: G 24 MET cc_start: 0.7700 (ptp) cc_final: 0.7466 (ptp) REVERT: G 60 THR cc_start: 0.8539 (p) cc_final: 0.7705 (m) REVERT: G 76 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7835 (mtt90) REVERT: G 88 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.7069 (tm-30) REVERT: G 98 ARG cc_start: 0.8310 (mtm180) cc_final: 0.7995 (mtm180) REVERT: G 106 LYS cc_start: 0.8302 (mtmm) cc_final: 0.7959 (mtmm) REVERT: G 111 ASN cc_start: 0.8735 (t0) cc_final: 0.8247 (t0) REVERT: G 115 LYS cc_start: 0.8899 (mptp) cc_final: 0.8215 (mptp) REVERT: G 163 TYR cc_start: 0.8534 (t80) cc_final: 0.8165 (t80) REVERT: G 171 ARG cc_start: 0.7437 (mtm-85) cc_final: 0.7001 (mtm-85) REVERT: G 234 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7241 (mm-30) REVERT: G 274 CYS cc_start: 0.8289 (OUTLIER) cc_final: 0.8034 (m) REVERT: G 275 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.7269 (ptt180) REVERT: G 285 TYR cc_start: 0.8210 (OUTLIER) cc_final: 0.6892 (t80) REVERT: G 293 SER cc_start: 0.8223 (m) cc_final: 0.7445 (p) REVERT: G 400 LYS cc_start: 0.8366 (tppt) cc_final: 0.7759 (tppt) REVERT: G 406 LYS cc_start: 0.8838 (mmmm) cc_final: 0.8547 (mmtp) REVERT: G 430 THR cc_start: 0.8757 (OUTLIER) cc_final: 0.8408 (p) REVERT: G 433 LYS cc_start: 0.8312 (mmmt) cc_final: 0.7960 (mmtt) REVERT: H 16 LYS cc_start: 0.8408 (mmtt) cc_final: 0.8085 (mmtt) REVERT: H 20 ARG cc_start: 0.7876 (mtm-85) cc_final: 0.7593 (mtm-85) REVERT: H 28 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7308 (mm-30) REVERT: H 56 ASP cc_start: 0.7648 (t70) cc_final: 0.7345 (t70) REVERT: H 92 ARG cc_start: 0.7700 (mmp80) cc_final: 0.7199 (mmp80) REVERT: H 99 LYS cc_start: 0.8852 (mmmm) cc_final: 0.8549 (mmmm) REVERT: H 111 ASN cc_start: 0.8664 (t0) cc_final: 0.7972 (t0) REVERT: H 115 LYS cc_start: 0.8826 (mptp) cc_final: 0.8119 (mptp) REVERT: H 146 ASP cc_start: 0.7677 (OUTLIER) cc_final: 0.6784 (p0) REVERT: H 171 ARG cc_start: 0.7279 (mtm-85) cc_final: 0.6857 (mtm-85) REVERT: H 178 PHE cc_start: 0.8897 (m-10) cc_final: 0.8657 (m-10) REVERT: H 179 ASP cc_start: 0.8068 (t0) cc_final: 0.7606 (t0) REVERT: H 264 PHE cc_start: 0.8179 (p90) cc_final: 0.7880 (p90) REVERT: H 447 PHE cc_start: 0.8519 (m-80) cc_final: 0.8149 (m-80) REVERT: I 16 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8190 (mtpt) REVERT: I 22 TYR cc_start: 0.8505 (m-80) cc_final: 0.7892 (m-80) REVERT: I 43 PHE cc_start: 0.8858 (t80) cc_final: 0.8210 (t80) REVERT: I 56 ASP cc_start: 0.7868 (t0) cc_final: 0.7561 (t0) REVERT: I 72 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7765 (tmm) REVERT: I 98 ARG cc_start: 0.8206 (mtm180) cc_final: 0.7748 (mtm180) REVERT: I 106 LYS cc_start: 0.8295 (mtmm) cc_final: 0.7894 (mtmm) REVERT: I 135 LEU cc_start: 0.8657 (mt) cc_final: 0.8413 (mm) REVERT: I 165 GLN cc_start: 0.7954 (mt0) cc_final: 0.7692 (mt0) REVERT: I 184 MET cc_start: 0.8199 (mmm) cc_final: 0.7761 (mmm) REVERT: I 192 TYR cc_start: 0.8917 (m-80) cc_final: 0.8676 (m-80) REVERT: I 258 TRP cc_start: 0.8496 (m100) cc_final: 0.7960 (m100) REVERT: I 289 ARG cc_start: 0.7975 (ttp80) cc_final: 0.7591 (mtp-110) REVERT: I 328 PHE cc_start: 0.8078 (p90) cc_final: 0.7820 (p90) REVERT: I 383 MET cc_start: 0.8610 (ttp) cc_final: 0.8338 (ttm) REVERT: I 400 LYS cc_start: 0.8160 (tppt) cc_final: 0.7439 (ttpt) REVERT: I 405 GLU cc_start: 0.7777 (mp0) cc_final: 0.7275 (mp0) REVERT: I 426 GLN cc_start: 0.6672 (mt0) cc_final: 0.6440 (mt0) REVERT: I 441 GLN cc_start: 0.7715 (mt0) cc_final: 0.7270 (mt0) REVERT: J 16 LYS cc_start: 0.8354 (mmtt) cc_final: 0.8115 (mmpt) REVERT: J 28 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7306 (mm-30) REVERT: J 41 ARG cc_start: 0.7610 (tpp-160) cc_final: 0.7157 (tpp-160) REVERT: J 49 LYS cc_start: 0.8654 (tppt) cc_final: 0.8000 (mppt) REVERT: J 76 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.8119 (mtt90) REVERT: J 88 GLU cc_start: 0.6445 (OUTLIER) cc_final: 0.6027 (tm-30) REVERT: J 92 ARG cc_start: 0.7675 (mmp80) cc_final: 0.7139 (mmp80) REVERT: J 98 ARG cc_start: 0.8299 (mtm180) cc_final: 0.7892 (mtm180) REVERT: J 99 LYS cc_start: 0.8896 (mmmm) cc_final: 0.8535 (mmmm) REVERT: J 106 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8139 (mtmm) REVERT: J 115 LYS cc_start: 0.8844 (mptp) cc_final: 0.8218 (mptp) REVERT: J 151 GLN cc_start: 0.8233 (tp40) cc_final: 0.7977 (tp40) REVERT: J 163 TYR cc_start: 0.8585 (t80) cc_final: 0.8313 (t80) REVERT: J 165 GLN cc_start: 0.8187 (mt0) cc_final: 0.7932 (mt0) REVERT: J 171 ARG cc_start: 0.7207 (mtm-85) cc_final: 0.6727 (mtm-85) REVERT: J 185 TYR cc_start: 0.8685 (m-80) cc_final: 0.7989 (m-80) REVERT: J 248 TYR cc_start: 0.7943 (m-10) cc_final: 0.7645 (m-10) REVERT: J 258 TRP cc_start: 0.8671 (m100) cc_final: 0.7633 (m100) REVERT: J 275 ARG cc_start: 0.7347 (ttt180) cc_final: 0.6762 (ptt180) REVERT: J 285 TYR cc_start: 0.8216 (OUTLIER) cc_final: 0.6803 (t80) REVERT: J 313 LEU cc_start: 0.8281 (mt) cc_final: 0.7982 (mp) REVERT: J 400 LYS cc_start: 0.8249 (tppt) cc_final: 0.7569 (tppt) REVERT: J 403 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6999 (mp0) REVERT: K 6 VAL cc_start: 0.7975 (t) cc_final: 0.7675 (p) REVERT: K 30 ARG cc_start: 0.7425 (mtm110) cc_final: 0.7192 (ttm110) REVERT: K 76 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7690 (mtt90) REVERT: K 88 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7097 (tt0) REVERT: K 110 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7953 (tpp-160) REVERT: K 111 ASN cc_start: 0.8576 (t0) cc_final: 0.8328 (t0) REVERT: K 115 LYS cc_start: 0.8747 (mptp) cc_final: 0.8136 (mptp) REVERT: K 118 ASP cc_start: 0.8094 (m-30) cc_final: 0.7729 (m-30) REVERT: K 143 GLN cc_start: 0.8324 (tt0) cc_final: 0.8066 (tt0) REVERT: K 171 ARG cc_start: 0.7136 (mtm-85) cc_final: 0.6730 (mtm-85) REVERT: K 238 ARG cc_start: 0.7438 (ttm110) cc_final: 0.7083 (mtm110) REVERT: K 242 SER cc_start: 0.8108 (t) cc_final: 0.7504 (t) REVERT: K 267 LYS cc_start: 0.8268 (pttp) cc_final: 0.7972 (pttp) REVERT: K 313 LEU cc_start: 0.8450 (mt) cc_final: 0.8104 (mm) REVERT: K 378 THR cc_start: 0.7926 (m) cc_final: 0.7603 (p) REVERT: K 396 LYS cc_start: 0.8346 (tppt) cc_final: 0.7953 (tppt) REVERT: K 434 ARG cc_start: 0.8560 (mpp80) cc_final: 0.7412 (mpp80) REVERT: L 20 ARG cc_start: 0.7793 (mtm-85) cc_final: 0.7379 (mtm-85) REVERT: L 24 MET cc_start: 0.8771 (pmm) cc_final: 0.8288 (pmm) REVERT: L 36 ASP cc_start: 0.7995 (m-30) cc_final: 0.7686 (t0) REVERT: L 76 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7939 (mtt90) REVERT: L 98 ARG cc_start: 0.8182 (mtm180) cc_final: 0.7711 (mtm180) REVERT: L 135 LEU cc_start: 0.8664 (mt) cc_final: 0.8440 (mm) REVERT: L 171 ARG cc_start: 0.6967 (mtm-85) cc_final: 0.6691 (mtm-85) REVERT: L 179 ASP cc_start: 0.8218 (t0) cc_final: 0.7705 (t0) REVERT: L 240 LEU cc_start: 0.8036 (mm) cc_final: 0.7683 (mp) REVERT: L 245 SER cc_start: 0.8578 (p) cc_final: 0.8200 (t) REVERT: L 258 TRP cc_start: 0.8609 (m100) cc_final: 0.7390 (m100) REVERT: L 271 SER cc_start: 0.7615 (p) cc_final: 0.7325 (m) REVERT: L 283 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7416 (mp0) REVERT: L 362 LEU cc_start: 0.8840 (mm) cc_final: 0.8574 (tt) REVERT: L 380 LYS cc_start: 0.8582 (mmmm) cc_final: 0.8170 (mmmm) REVERT: L 400 LYS cc_start: 0.8075 (tppt) cc_final: 0.7477 (ttpt) REVERT: L 403 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6903 (mp0) REVERT: L 426 GLN cc_start: 0.6935 (mt0) cc_final: 0.6645 (mt0) REVERT: L 446 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7455 (mm-30) outliers start: 242 outliers final: 170 residues processed: 1933 average time/residue: 0.6373 time to fit residues: 1892.7529 Evaluate side-chains 2033 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 1830 time to evaluate : 4.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 110 ARG Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 398 CYS Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 342 MET Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 398 CYS Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 411 ARG Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 80 CYS Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 274 CYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 398 CYS Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 404 ASP Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 92 ARG Chi-restraints excluded: chain E residue 106 LYS Chi-restraints excluded: chain E residue 120 GLN Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 203 GLN Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 342 MET Chi-restraints excluded: chain E residue 398 CYS Chi-restraints excluded: chain E residue 403 GLU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 120 GLN Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 315 CYS Chi-restraints excluded: chain F residue 342 MET Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 411 ARG Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 76 ARG Chi-restraints excluded: chain G residue 77 LYS Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 236 CYS Chi-restraints excluded: chain G residue 274 CYS Chi-restraints excluded: chain G residue 275 ARG Chi-restraints excluded: chain G residue 283 GLU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 340 ASP Chi-restraints excluded: chain G residue 348 THR Chi-restraints excluded: chain G residue 403 GLU Chi-restraints excluded: chain G residue 411 ARG Chi-restraints excluded: chain G residue 430 THR Chi-restraints excluded: chain G residue 440 ILE Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 146 ASP Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 301 THR Chi-restraints excluded: chain H residue 342 MET Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 398 CYS Chi-restraints excluded: chain H residue 403 GLU Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 429 HIS Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain I residue 36 ASP Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 120 GLN Chi-restraints excluded: chain I residue 215 THR Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 291 THR Chi-restraints excluded: chain I residue 301 THR Chi-restraints excluded: chain I residue 348 THR Chi-restraints excluded: chain I residue 358 LEU Chi-restraints excluded: chain I residue 362 LEU Chi-restraints excluded: chain I residue 403 GLU Chi-restraints excluded: chain I residue 408 LEU Chi-restraints excluded: chain I residue 437 THR Chi-restraints excluded: chain J residue 72 MET Chi-restraints excluded: chain J residue 76 ARG Chi-restraints excluded: chain J residue 88 GLU Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain J residue 120 GLN Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 243 VAL Chi-restraints excluded: chain J residue 277 ASP Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 291 THR Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 348 THR Chi-restraints excluded: chain J residue 403 GLU Chi-restraints excluded: chain K residue 76 ARG Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 110 ARG Chi-restraints excluded: chain K residue 120 GLN Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 283 GLU Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 305 VAL Chi-restraints excluded: chain K residue 337 THR Chi-restraints excluded: chain K residue 348 THR Chi-restraints excluded: chain K residue 349 GLU Chi-restraints excluded: chain K residue 403 GLU Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 120 GLN Chi-restraints excluded: chain L residue 167 ILE Chi-restraints excluded: chain L residue 202 GLU Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain L residue 283 GLU Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 314 MET Chi-restraints excluded: chain L residue 318 THR Chi-restraints excluded: chain L residue 348 THR Chi-restraints excluded: chain L residue 403 GLU Chi-restraints excluded: chain L residue 405 GLU Chi-restraints excluded: chain L residue 427 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 462 optimal weight: 0.8980 chunk 487 optimal weight: 3.9990 chunk 444 optimal weight: 0.9980 chunk 474 optimal weight: 2.9990 chunk 285 optimal weight: 0.8980 chunk 206 optimal weight: 0.5980 chunk 372 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 428 optimal weight: 0.6980 chunk 448 optimal weight: 0.3980 chunk 472 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 HIS A 364 GLN ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 GLN ** D 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN ** F 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 GLN ** G 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 308 HIS G 364 GLN H 377 ASN H 381 ASN ** I 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 308 HIS ** J 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 364 GLN ** K 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 203 GLN K 356 GLN ** L 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 42504 Z= 0.199 Angle : 0.616 10.520 57684 Z= 0.308 Chirality : 0.043 0.142 6564 Planarity : 0.005 0.102 7260 Dihedral : 5.811 37.946 5892 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 5.21 % Allowed : 33.67 % Favored : 61.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.11), residues: 5148 helix: 0.85 (0.14), residues: 1620 sheet: -0.97 (0.14), residues: 1284 loop : -2.02 (0.11), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 175 HIS 0.003 0.000 HIS A 308 PHE 0.025 0.002 PHE C 133 TYR 0.023 0.001 TYR K 174 ARG 0.014 0.001 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2080 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 1850 time to evaluate : 4.390 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: A 16 LYS cc_start: 0.8373 (mmtt) cc_final: 0.8076 (mmtt) REVERT: A 41 ARG cc_start: 0.7730 (tpp-160) cc_final: 0.7260 (tpp-160) REVERT: A 85 ARG cc_start: 0.7521 (mmp80) cc_final: 0.7184 (mmp80) REVERT: A 88 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6468 (tm-30) REVERT: A 98 ARG cc_start: 0.8291 (mtm180) cc_final: 0.7769 (mtm180) REVERT: A 99 LYS cc_start: 0.8869 (mmmm) cc_final: 0.8608 (mmmm) REVERT: A 110 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7724 (tpp-160) REVERT: A 146 ASP cc_start: 0.7253 (p0) cc_final: 0.6324 (p0) REVERT: A 163 TYR cc_start: 0.8558 (t80) cc_final: 0.8302 (t80) REVERT: A 171 ARG cc_start: 0.7115 (mtm-85) cc_final: 0.6644 (mtm-85) REVERT: A 184 MET cc_start: 0.8535 (mmm) cc_final: 0.8043 (mmm) REVERT: A 188 MET cc_start: 0.8412 (mmt) cc_final: 0.7840 (mmt) REVERT: A 242 SER cc_start: 0.8138 (t) cc_final: 0.7640 (p) REVERT: A 243 VAL cc_start: 0.7942 (t) cc_final: 0.7602 (t) REVERT: A 248 TYR cc_start: 0.8073 (m-10) cc_final: 0.7837 (m-10) REVERT: A 266 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8561 (mt) REVERT: A 267 LYS cc_start: 0.8188 (mtmt) cc_final: 0.7913 (mtmt) REVERT: A 278 THR cc_start: 0.9024 (m) cc_final: 0.8566 (p) REVERT: A 285 TYR cc_start: 0.8237 (OUTLIER) cc_final: 0.7067 (t80) REVERT: A 312 PHE cc_start: 0.8246 (t80) cc_final: 0.7908 (t80) REVERT: A 345 ILE cc_start: 0.9013 (mm) cc_final: 0.8791 (mm) REVERT: B 53 GLN cc_start: 0.8396 (tp40) cc_final: 0.7818 (tt0) REVERT: B 76 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.8234 (mtt90) REVERT: B 84 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.7960 (mmm) REVERT: B 115 LYS cc_start: 0.8753 (mptp) cc_final: 0.8175 (mptp) REVERT: B 176 VAL cc_start: 0.8682 (p) cc_final: 0.8423 (m) REVERT: B 184 MET cc_start: 0.8540 (mmm) cc_final: 0.7915 (tpp) REVERT: B 283 GLU cc_start: 0.7800 (tp30) cc_final: 0.7398 (tp30) REVERT: B 313 LEU cc_start: 0.8401 (mt) cc_final: 0.8076 (mm) REVERT: B 396 LYS cc_start: 0.8445 (mmmm) cc_final: 0.7950 (tppt) REVERT: B 400 LYS cc_start: 0.8136 (tppt) cc_final: 0.7512 (tppt) REVERT: C 51 ILE cc_start: 0.8494 (mm) cc_final: 0.8279 (mm) REVERT: C 76 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.8027 (mtt90) REVERT: C 92 ARG cc_start: 0.7904 (mmp80) cc_final: 0.7474 (mmp80) REVERT: C 110 ARG cc_start: 0.8169 (mmt-90) cc_final: 0.7400 (mmt-90) REVERT: C 135 LEU cc_start: 0.8559 (mt) cc_final: 0.8071 (mm) REVERT: C 146 ASP cc_start: 0.7565 (p0) cc_final: 0.7008 (p0) REVERT: C 258 TRP cc_start: 0.8667 (m100) cc_final: 0.7528 (m100) REVERT: C 325 ARG cc_start: 0.7857 (ttp-170) cc_final: 0.7428 (ttp-170) REVERT: C 396 LYS cc_start: 0.8330 (tppt) cc_final: 0.7921 (tppt) REVERT: C 400 LYS cc_start: 0.8266 (tppt) cc_final: 0.8021 (tppt) REVERT: C 403 GLU cc_start: 0.7516 (mp0) cc_final: 0.7144 (mp0) REVERT: D 16 LYS cc_start: 0.8348 (mmtt) cc_final: 0.8111 (mmtt) REVERT: D 20 ARG cc_start: 0.7796 (mtm-85) cc_final: 0.7425 (mtm-85) REVERT: D 28 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7381 (mm-30) REVERT: D 60 THR cc_start: 0.8559 (p) cc_final: 0.7760 (m) REVERT: D 76 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7983 (mtt90) REVERT: D 98 ARG cc_start: 0.8362 (mtm180) cc_final: 0.7985 (mtm180) REVERT: D 99 LYS cc_start: 0.8920 (mmmm) cc_final: 0.8643 (mmmm) REVERT: D 163 TYR cc_start: 0.8584 (t80) cc_final: 0.8204 (t80) REVERT: D 179 ASP cc_start: 0.8455 (t0) cc_final: 0.7991 (t0) REVERT: D 188 MET cc_start: 0.8349 (mmt) cc_final: 0.7838 (mmt) REVERT: D 234 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7337 (mm-30) REVERT: D 274 CYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7954 (m) REVERT: D 285 TYR cc_start: 0.8279 (OUTLIER) cc_final: 0.7573 (t80) REVERT: D 316 LYS cc_start: 0.7966 (tppp) cc_final: 0.7713 (tppp) REVERT: D 404 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.7647 (t0) REVERT: D 448 ASP cc_start: 0.7619 (t0) cc_final: 0.7365 (t0) REVERT: E 6 VAL cc_start: 0.7973 (t) cc_final: 0.7704 (m) REVERT: E 20 ARG cc_start: 0.7956 (mtm-85) cc_final: 0.7634 (mtm-85) REVERT: E 24 MET cc_start: 0.8660 (pmm) cc_final: 0.8255 (pmm) REVERT: E 28 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7308 (mm-30) REVERT: E 53 GLN cc_start: 0.8365 (tp40) cc_final: 0.7743 (tt0) REVERT: E 76 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.8153 (mtt90) REVERT: E 98 ARG cc_start: 0.8238 (mtm180) cc_final: 0.7894 (mtm180) REVERT: E 115 LYS cc_start: 0.8850 (mptp) cc_final: 0.8229 (mptp) REVERT: E 146 ASP cc_start: 0.7586 (p0) cc_final: 0.6758 (p0) REVERT: E 171 ARG cc_start: 0.7132 (mtm-85) cc_final: 0.6541 (mtm-85) REVERT: E 180 THR cc_start: 0.8501 (m) cc_final: 0.8197 (m) REVERT: E 184 MET cc_start: 0.8053 (mmm) cc_final: 0.7789 (mmm) REVERT: E 243 VAL cc_start: 0.8261 (m) cc_final: 0.7939 (p) REVERT: E 405 GLU cc_start: 0.7494 (tp30) cc_final: 0.7094 (tp30) REVERT: E 426 GLN cc_start: 0.7059 (mt0) cc_final: 0.6331 (mt0) REVERT: E 436 ASP cc_start: 0.8367 (t0) cc_final: 0.8013 (t70) REVERT: E 447 PHE cc_start: 0.8501 (m-10) cc_final: 0.8203 (m-10) REVERT: F 51 ILE cc_start: 0.8294 (mm) cc_final: 0.8048 (mm) REVERT: F 85 ARG cc_start: 0.7318 (mmp80) cc_final: 0.6898 (mmp80) REVERT: F 98 ARG cc_start: 0.8202 (mtm180) cc_final: 0.7854 (mtm180) REVERT: F 111 ASN cc_start: 0.8689 (t0) cc_final: 0.8265 (t0) REVERT: F 115 LYS cc_start: 0.8821 (mptp) cc_final: 0.8253 (mptp) REVERT: F 232 LYS cc_start: 0.8152 (ptmt) cc_final: 0.7861 (ptmt) REVERT: F 303 TYR cc_start: 0.7948 (m-80) cc_final: 0.7516 (m-80) REVERT: F 312 PHE cc_start: 0.8008 (t80) cc_final: 0.7780 (t80) REVERT: F 324 GLU cc_start: 0.7024 (tt0) cc_final: 0.6568 (tt0) REVERT: F 325 ARG cc_start: 0.7433 (ptp-110) cc_final: 0.6838 (ttm110) REVERT: F 346 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8325 (tt) REVERT: F 396 LYS cc_start: 0.8249 (mmtm) cc_final: 0.7866 (mmmm) REVERT: F 399 ARG cc_start: 0.7610 (tpp80) cc_final: 0.7104 (tpp80) REVERT: F 403 GLU cc_start: 0.7479 (mp0) cc_final: 0.7003 (mp0) REVERT: F 441 GLN cc_start: 0.7507 (mt0) cc_final: 0.7162 (mt0) REVERT: G 16 LYS cc_start: 0.8386 (mmtt) cc_final: 0.8133 (mmtt) REVERT: G 20 ARG cc_start: 0.7753 (mtm-85) cc_final: 0.7505 (mtm-85) REVERT: G 24 MET cc_start: 0.7713 (ptp) cc_final: 0.7481 (ptp) REVERT: G 43 PHE cc_start: 0.8885 (t80) cc_final: 0.8447 (t80) REVERT: G 60 THR cc_start: 0.8531 (p) cc_final: 0.7730 (m) REVERT: G 76 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7833 (mtt90) REVERT: G 88 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.7068 (tm-30) REVERT: G 98 ARG cc_start: 0.8337 (mtm180) cc_final: 0.8025 (mtm180) REVERT: G 106 LYS cc_start: 0.8316 (mtmm) cc_final: 0.7973 (mtmm) REVERT: G 111 ASN cc_start: 0.8733 (t0) cc_final: 0.8202 (t0) REVERT: G 115 LYS cc_start: 0.8899 (mptp) cc_final: 0.8211 (mptp) REVERT: G 163 TYR cc_start: 0.8509 (t80) cc_final: 0.8114 (t80) REVERT: G 171 ARG cc_start: 0.7394 (mtm-85) cc_final: 0.6967 (mtm-85) REVERT: G 179 ASP cc_start: 0.8340 (t0) cc_final: 0.7739 (t0) REVERT: G 185 TYR cc_start: 0.8816 (m-80) cc_final: 0.8127 (m-80) REVERT: G 217 LEU cc_start: 0.6919 (mp) cc_final: 0.6715 (mt) REVERT: G 234 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7205 (mm-30) REVERT: G 274 CYS cc_start: 0.8298 (OUTLIER) cc_final: 0.8033 (m) REVERT: G 275 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.7300 (ptt180) REVERT: G 285 TYR cc_start: 0.8248 (OUTLIER) cc_final: 0.6731 (t80) REVERT: G 293 SER cc_start: 0.8197 (m) cc_final: 0.7421 (p) REVERT: G 384 ILE cc_start: 0.8984 (pt) cc_final: 0.8723 (mt) REVERT: G 400 LYS cc_start: 0.8355 (tppt) cc_final: 0.7686 (tppt) REVERT: G 403 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7011 (mp0) REVERT: G 406 LYS cc_start: 0.8835 (mmmm) cc_final: 0.8547 (mmtp) REVERT: G 430 THR cc_start: 0.8755 (OUTLIER) cc_final: 0.8408 (p) REVERT: G 433 LYS cc_start: 0.8328 (mmmt) cc_final: 0.7959 (mmtt) REVERT: H 16 LYS cc_start: 0.8411 (mmtt) cc_final: 0.8090 (mmtt) REVERT: H 20 ARG cc_start: 0.7880 (mtm-85) cc_final: 0.7595 (mtm-85) REVERT: H 56 ASP cc_start: 0.7650 (t70) cc_final: 0.7359 (t70) REVERT: H 92 ARG cc_start: 0.7691 (mmp80) cc_final: 0.7177 (mmp80) REVERT: H 99 LYS cc_start: 0.8846 (mmmm) cc_final: 0.8581 (mmmm) REVERT: H 111 ASN cc_start: 0.8666 (t0) cc_final: 0.7950 (t0) REVERT: H 115 LYS cc_start: 0.8841 (mptp) cc_final: 0.8118 (mptp) REVERT: H 146 ASP cc_start: 0.7709 (OUTLIER) cc_final: 0.6814 (p0) REVERT: H 171 ARG cc_start: 0.7268 (mtm-85) cc_final: 0.6864 (mtm-85) REVERT: H 264 PHE cc_start: 0.8169 (p90) cc_final: 0.7881 (p90) REVERT: H 400 LYS cc_start: 0.8218 (tppt) cc_final: 0.7650 (tppt) REVERT: H 447 PHE cc_start: 0.8505 (m-80) cc_final: 0.8149 (m-80) REVERT: I 16 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8186 (mtpt) REVERT: I 22 TYR cc_start: 0.8509 (m-80) cc_final: 0.8036 (m-80) REVERT: I 43 PHE cc_start: 0.8853 (t80) cc_final: 0.8624 (t80) REVERT: I 52 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7231 (mt-10) REVERT: I 72 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7847 (tmm) REVERT: I 98 ARG cc_start: 0.8232 (mtm180) cc_final: 0.7781 (mtm180) REVERT: I 106 LYS cc_start: 0.8312 (mtmm) cc_final: 0.7914 (mtmm) REVERT: I 135 LEU cc_start: 0.8684 (mt) cc_final: 0.8453 (mm) REVERT: I 150 TYR cc_start: 0.8665 (m-10) cc_final: 0.8443 (m-10) REVERT: I 165 GLN cc_start: 0.7960 (mt0) cc_final: 0.7699 (mt0) REVERT: I 184 MET cc_start: 0.8236 (mmm) cc_final: 0.7729 (mmm) REVERT: I 192 TYR cc_start: 0.8922 (m-80) cc_final: 0.8700 (m-80) REVERT: I 234 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7133 (mm-30) REVERT: I 289 ARG cc_start: 0.7959 (ttp80) cc_final: 0.7616 (mtp-110) REVERT: I 328 PHE cc_start: 0.8133 (p90) cc_final: 0.7866 (p90) REVERT: I 383 MET cc_start: 0.8617 (ttp) cc_final: 0.8266 (ttm) REVERT: I 400 LYS cc_start: 0.7923 (tppt) cc_final: 0.7464 (ttpt) REVERT: I 405 GLU cc_start: 0.7790 (mp0) cc_final: 0.7290 (mp0) REVERT: I 441 GLN cc_start: 0.7753 (mt0) cc_final: 0.7287 (mt0) REVERT: J 16 LYS cc_start: 0.8378 (mmtt) cc_final: 0.8154 (mmpt) REVERT: J 41 ARG cc_start: 0.7646 (tpp-160) cc_final: 0.7191 (tpp-160) REVERT: J 43 PHE cc_start: 0.8856 (t80) cc_final: 0.8602 (t80) REVERT: J 76 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.8106 (mtt90) REVERT: J 88 GLU cc_start: 0.6493 (tm-30) cc_final: 0.6103 (tm-30) REVERT: J 92 ARG cc_start: 0.7685 (mmp80) cc_final: 0.7149 (mmp80) REVERT: J 98 ARG cc_start: 0.8314 (mtm180) cc_final: 0.7897 (mtm180) REVERT: J 99 LYS cc_start: 0.8904 (mmmm) cc_final: 0.8541 (mmmm) REVERT: J 106 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8218 (mtmm) REVERT: J 115 LYS cc_start: 0.8851 (mptp) cc_final: 0.8230 (mptp) REVERT: J 163 TYR cc_start: 0.8575 (t80) cc_final: 0.8315 (t80) REVERT: J 165 GLN cc_start: 0.8206 (mt0) cc_final: 0.7938 (mt0) REVERT: J 171 ARG cc_start: 0.7223 (mtm-85) cc_final: 0.6747 (mtm-85) REVERT: J 185 TYR cc_start: 0.8676 (m-80) cc_final: 0.8005 (m-80) REVERT: J 248 TYR cc_start: 0.7944 (m-10) cc_final: 0.7648 (m-10) REVERT: J 258 TRP cc_start: 0.8674 (m100) cc_final: 0.7654 (m100) REVERT: J 275 ARG cc_start: 0.7355 (ttt180) cc_final: 0.6763 (ptt180) REVERT: J 285 TYR cc_start: 0.8226 (OUTLIER) cc_final: 0.6623 (t80) REVERT: J 313 LEU cc_start: 0.8263 (mt) cc_final: 0.7962 (mp) REVERT: J 400 LYS cc_start: 0.8226 (tppt) cc_final: 0.7530 (tppt) REVERT: J 403 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.7007 (mp0) REVERT: K 6 VAL cc_start: 0.7973 (t) cc_final: 0.7672 (p) REVERT: K 28 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7189 (mm-30) REVERT: K 76 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7730 (mtt90) REVERT: K 88 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7081 (tt0) REVERT: K 110 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7976 (tpp-160) REVERT: K 111 ASN cc_start: 0.8581 (t0) cc_final: 0.8312 (t0) REVERT: K 115 LYS cc_start: 0.8758 (mptp) cc_final: 0.8105 (mptp) REVERT: K 143 GLN cc_start: 0.8311 (tt0) cc_final: 0.8053 (tt0) REVERT: K 171 ARG cc_start: 0.7110 (mtm-85) cc_final: 0.6678 (mtm-85) REVERT: K 221 ARG cc_start: 0.7899 (ttp80) cc_final: 0.7492 (ttp80) REVERT: K 238 ARG cc_start: 0.7405 (ttm110) cc_final: 0.7056 (mtm110) REVERT: K 242 SER cc_start: 0.8061 (t) cc_final: 0.7484 (t) REVERT: K 264 PHE cc_start: 0.8120 (p90) cc_final: 0.7736 (p90) REVERT: K 267 LYS cc_start: 0.8239 (pttp) cc_final: 0.7916 (pttp) REVERT: K 313 LEU cc_start: 0.8448 (mt) cc_final: 0.8106 (mm) REVERT: K 378 THR cc_start: 0.7944 (m) cc_final: 0.7625 (p) REVERT: K 396 LYS cc_start: 0.8351 (tppt) cc_final: 0.7941 (tppt) REVERT: L 20 ARG cc_start: 0.7803 (mtm-85) cc_final: 0.7386 (mtm-85) REVERT: L 36 ASP cc_start: 0.7992 (m-30) cc_final: 0.7665 (t0) REVERT: L 60 THR cc_start: 0.8521 (p) cc_final: 0.7844 (m) REVERT: L 76 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7943 (mtt90) REVERT: L 98 ARG cc_start: 0.8197 (mtm180) cc_final: 0.7717 (mtm180) REVERT: L 135 LEU cc_start: 0.8705 (mt) cc_final: 0.8483 (mm) REVERT: L 168 LYS cc_start: 0.8816 (mtmt) cc_final: 0.8397 (mtpp) REVERT: L 171 ARG cc_start: 0.6955 (mtm-85) cc_final: 0.6614 (mtm-85) REVERT: L 179 ASP cc_start: 0.8223 (t0) cc_final: 0.7690 (t0) REVERT: L 240 LEU cc_start: 0.8078 (mm) cc_final: 0.7720 (mp) REVERT: L 245 SER cc_start: 0.8561 (p) cc_final: 0.8178 (t) REVERT: L 271 SER cc_start: 0.7686 (p) cc_final: 0.7391 (m) REVERT: L 283 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7327 (mp0) REVERT: L 362 LEU cc_start: 0.8842 (mm) cc_final: 0.8608 (tt) REVERT: L 400 LYS cc_start: 0.8065 (tppt) cc_final: 0.7460 (ttpt) REVERT: L 403 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6863 (mp0) REVERT: L 427 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7470 (mmtt) REVERT: L 446 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7462 (mm-30) outliers start: 230 outliers final: 172 residues processed: 1921 average time/residue: 0.6156 time to fit residues: 1809.6363 Evaluate side-chains 2053 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 1847 time to evaluate : 4.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 110 ARG Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 342 MET Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 398 CYS Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 411 ARG Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 274 CYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 403 GLU Chi-restraints excluded: chain D residue 404 ASP Chi-restraints excluded: chain D residue 442 LYS Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 106 LYS Chi-restraints excluded: chain E residue 120 GLN Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 203 GLN Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 342 MET Chi-restraints excluded: chain E residue 396 LYS Chi-restraints excluded: chain E residue 398 CYS Chi-restraints excluded: chain E residue 403 GLU Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 120 GLN Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain F residue 321 VAL Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain F residue 411 ARG Chi-restraints excluded: chain F residue 428 THR Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 76 ARG Chi-restraints excluded: chain G residue 77 LYS Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 236 CYS Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 274 CYS Chi-restraints excluded: chain G residue 275 ARG Chi-restraints excluded: chain G residue 283 GLU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 340 ASP Chi-restraints excluded: chain G residue 348 THR Chi-restraints excluded: chain G residue 403 GLU Chi-restraints excluded: chain G residue 411 ARG Chi-restraints excluded: chain G residue 430 THR Chi-restraints excluded: chain G residue 440 ILE Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 146 ASP Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 301 THR Chi-restraints excluded: chain H residue 342 MET Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 398 CYS Chi-restraints excluded: chain H residue 403 GLU Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 429 HIS Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 120 GLN Chi-restraints excluded: chain I residue 215 THR Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 291 THR Chi-restraints excluded: chain I residue 301 THR Chi-restraints excluded: chain I residue 314 MET Chi-restraints excluded: chain I residue 348 THR Chi-restraints excluded: chain I residue 358 LEU Chi-restraints excluded: chain I residue 403 GLU Chi-restraints excluded: chain J residue 72 MET Chi-restraints excluded: chain J residue 76 ARG Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain J residue 120 GLN Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 243 VAL Chi-restraints excluded: chain J residue 277 ASP Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 291 THR Chi-restraints excluded: chain J residue 301 THR Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 348 THR Chi-restraints excluded: chain J residue 403 GLU Chi-restraints excluded: chain K residue 76 ARG Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 110 ARG Chi-restraints excluded: chain K residue 120 GLN Chi-restraints excluded: chain K residue 149 ILE Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 277 ASP Chi-restraints excluded: chain K residue 283 GLU Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 305 VAL Chi-restraints excluded: chain K residue 337 THR Chi-restraints excluded: chain K residue 348 THR Chi-restraints excluded: chain K residue 349 GLU Chi-restraints excluded: chain K residue 403 GLU Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain L residue 53 GLN Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain L residue 120 GLN Chi-restraints excluded: chain L residue 167 ILE Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain L residue 283 GLU Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 314 MET Chi-restraints excluded: chain L residue 318 THR Chi-restraints excluded: chain L residue 348 THR Chi-restraints excluded: chain L residue 403 GLU Chi-restraints excluded: chain L residue 405 GLU Chi-restraints excluded: chain L residue 427 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 311 optimal weight: 2.9990 chunk 501 optimal weight: 4.9990 chunk 306 optimal weight: 2.9990 chunk 237 optimal weight: 1.9990 chunk 348 optimal weight: 0.5980 chunk 526 optimal weight: 7.9990 chunk 484 optimal weight: 5.9990 chunk 418 optimal weight: 50.0000 chunk 43 optimal weight: 0.0470 chunk 323 optimal weight: 0.5980 chunk 256 optimal weight: 0.3980 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 HIS A 364 GLN ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 GLN ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 GLN ** C 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 GLN ** D 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 GLN ** G 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 364 GLN ** H 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 308 HIS ** J 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 364 GLN ** K 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 203 GLN ** L 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 42504 Z= 0.204 Angle : 0.623 9.429 57684 Z= 0.312 Chirality : 0.043 0.146 6564 Planarity : 0.005 0.106 7260 Dihedral : 5.800 38.372 5892 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 5.10 % Allowed : 34.26 % Favored : 60.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.17 % 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: -1.23 (0.11), residues: 5148 helix: 0.86 (0.14), residues: 1620 sheet: -0.93 (0.14), residues: 1284 loop : -2.01 (0.11), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 258 HIS 0.004 0.000 HIS A 308 PHE 0.030 0.002 PHE C 133 TYR 0.029 0.002 TYR G 5 ARG 0.013 0.001 ARG H 30 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2059 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 1834 time to evaluate : 4.912 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: A 16 LYS cc_start: 0.8391 (mmtt) cc_final: 0.8058 (mmtt) REVERT: A 41 ARG cc_start: 0.7718 (tpp-160) cc_final: 0.7246 (tpp-160) REVERT: A 85 ARG cc_start: 0.7532 (mmp80) cc_final: 0.7191 (mmp80) REVERT: A 88 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6465 (tm-30) REVERT: A 98 ARG cc_start: 0.8284 (mtm180) cc_final: 0.7761 (mtm180) REVERT: A 99 LYS cc_start: 0.8880 (mmmm) cc_final: 0.8620 (mmmm) REVERT: A 110 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7731 (tpp-160) REVERT: A 146 ASP cc_start: 0.7310 (p0) cc_final: 0.6307 (p0) REVERT: A 154 TYR cc_start: 0.8837 (m-80) cc_final: 0.8517 (m-80) REVERT: A 163 TYR cc_start: 0.8568 (t80) cc_final: 0.8306 (t80) REVERT: A 171 ARG cc_start: 0.7110 (mtm-85) cc_final: 0.6639 (mtm-85) REVERT: A 184 MET cc_start: 0.8489 (mmm) cc_final: 0.8144 (mmm) REVERT: A 188 MET cc_start: 0.8435 (mmt) cc_final: 0.7856 (mmt) REVERT: A 242 SER cc_start: 0.8167 (t) cc_final: 0.7613 (p) REVERT: A 243 VAL cc_start: 0.7942 (t) cc_final: 0.7602 (t) REVERT: A 248 TYR cc_start: 0.8069 (m-10) cc_final: 0.7840 (m-10) REVERT: A 266 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8559 (mt) REVERT: A 267 LYS cc_start: 0.8183 (mtmt) cc_final: 0.7904 (mtmt) REVERT: A 278 THR cc_start: 0.9028 (m) cc_final: 0.8544 (p) REVERT: A 285 TYR cc_start: 0.8221 (OUTLIER) cc_final: 0.7092 (t80) REVERT: A 312 PHE cc_start: 0.8229 (t80) cc_final: 0.7932 (t80) REVERT: B 25 PHE cc_start: 0.8179 (m-10) cc_final: 0.7669 (m-10) REVERT: B 53 GLN cc_start: 0.8399 (tp40) cc_final: 0.7863 (tt0) REVERT: B 115 LYS cc_start: 0.8752 (mptp) cc_final: 0.8179 (mptp) REVERT: B 171 ARG cc_start: 0.7465 (mtm-85) cc_final: 0.7064 (mtm-85) REVERT: B 176 VAL cc_start: 0.8666 (p) cc_final: 0.8411 (m) REVERT: B 184 MET cc_start: 0.8558 (mmm) cc_final: 0.7920 (tpp) REVERT: B 283 GLU cc_start: 0.7786 (tp30) cc_final: 0.7400 (tp30) REVERT: B 312 PHE cc_start: 0.8030 (t80) cc_final: 0.7795 (t80) REVERT: B 313 LEU cc_start: 0.8401 (mt) cc_final: 0.8079 (mm) REVERT: B 396 LYS cc_start: 0.8441 (mmmm) cc_final: 0.8044 (tppt) REVERT: B 400 LYS cc_start: 0.8096 (tppt) cc_final: 0.7452 (tppt) REVERT: B 447 PHE cc_start: 0.8528 (m-80) cc_final: 0.8070 (m-10) REVERT: C 51 ILE cc_start: 0.8506 (mm) cc_final: 0.8300 (mm) REVERT: C 76 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.8025 (mtt90) REVERT: C 92 ARG cc_start: 0.7915 (mmp80) cc_final: 0.7480 (mmp80) REVERT: C 110 ARG cc_start: 0.8160 (mmt-90) cc_final: 0.7383 (mmt-90) REVERT: C 135 LEU cc_start: 0.8563 (mt) cc_final: 0.8077 (mm) REVERT: C 146 ASP cc_start: 0.7557 (p0) cc_final: 0.6998 (p0) REVERT: C 258 TRP cc_start: 0.8668 (m100) cc_final: 0.7523 (m100) REVERT: C 325 ARG cc_start: 0.7862 (ttp-170) cc_final: 0.7422 (ttp-170) REVERT: C 396 LYS cc_start: 0.8326 (tppt) cc_final: 0.7913 (tppt) REVERT: C 400 LYS cc_start: 0.8249 (tppt) cc_final: 0.8011 (tppt) REVERT: C 403 GLU cc_start: 0.7531 (mp0) cc_final: 0.7148 (mp0) REVERT: C 436 ASP cc_start: 0.8140 (t0) cc_final: 0.7858 (t0) REVERT: D 16 LYS cc_start: 0.8344 (mmtt) cc_final: 0.8102 (mmtt) REVERT: D 20 ARG cc_start: 0.7794 (mtm-85) cc_final: 0.7414 (mtm-85) REVERT: D 28 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7358 (mm-30) REVERT: D 76 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7995 (mtt90) REVERT: D 98 ARG cc_start: 0.8344 (mtm180) cc_final: 0.7970 (mtm180) REVERT: D 99 LYS cc_start: 0.8923 (mmmm) cc_final: 0.8654 (mmmm) REVERT: D 163 TYR cc_start: 0.8592 (t80) cc_final: 0.8191 (t80) REVERT: D 168 LYS cc_start: 0.8771 (mtmt) cc_final: 0.8321 (mtmm) REVERT: D 179 ASP cc_start: 0.8449 (t0) cc_final: 0.7986 (t0) REVERT: D 188 MET cc_start: 0.8352 (mmt) cc_final: 0.7823 (mmt) REVERT: D 197 THR cc_start: 0.8429 (p) cc_final: 0.8091 (t) REVERT: D 234 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7336 (mm-30) REVERT: D 274 CYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7917 (m) REVERT: D 285 TYR cc_start: 0.8279 (OUTLIER) cc_final: 0.7586 (t80) REVERT: D 316 LYS cc_start: 0.7972 (tppp) cc_final: 0.7756 (tppp) REVERT: D 404 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7626 (t0) REVERT: D 448 ASP cc_start: 0.7611 (t0) cc_final: 0.7356 (t0) REVERT: E 6 VAL cc_start: 0.7968 (t) cc_final: 0.7700 (m) REVERT: E 20 ARG cc_start: 0.7955 (mtm-85) cc_final: 0.7626 (mtm-85) REVERT: E 24 MET cc_start: 0.8653 (pmm) cc_final: 0.8260 (pmm) REVERT: E 28 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7305 (mm-30) REVERT: E 53 GLN cc_start: 0.8381 (tp40) cc_final: 0.7752 (tt0) REVERT: E 76 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.8098 (mtt90) REVERT: E 98 ARG cc_start: 0.8245 (mtm180) cc_final: 0.7914 (mtm180) REVERT: E 115 LYS cc_start: 0.8851 (mptp) cc_final: 0.8237 (mptp) REVERT: E 146 ASP cc_start: 0.7593 (p0) cc_final: 0.6758 (p0) REVERT: E 171 ARG cc_start: 0.7129 (mtm-85) cc_final: 0.6548 (mtm-85) REVERT: E 180 THR cc_start: 0.8483 (m) cc_final: 0.8183 (m) REVERT: E 184 MET cc_start: 0.8034 (mmm) cc_final: 0.7786 (mmm) REVERT: E 197 THR cc_start: 0.8417 (p) cc_final: 0.8145 (t) REVERT: E 243 VAL cc_start: 0.8216 (m) cc_final: 0.7977 (p) REVERT: E 405 GLU cc_start: 0.7472 (tp30) cc_final: 0.7077 (tp30) REVERT: E 406 LYS cc_start: 0.8527 (mmtp) cc_final: 0.7685 (mmtp) REVERT: E 426 GLN cc_start: 0.7060 (mt0) cc_final: 0.6321 (mt0) REVERT: E 436 ASP cc_start: 0.8352 (t0) cc_final: 0.8003 (t70) REVERT: E 447 PHE cc_start: 0.8500 (m-10) cc_final: 0.8203 (m-10) REVERT: F 30 ARG cc_start: 0.6864 (ptp90) cc_final: 0.6424 (ptp-170) REVERT: F 51 ILE cc_start: 0.8236 (mm) cc_final: 0.7996 (mm) REVERT: F 85 ARG cc_start: 0.7300 (mmp80) cc_final: 0.6874 (mmp80) REVERT: F 98 ARG cc_start: 0.8220 (mtm180) cc_final: 0.7846 (mtm180) REVERT: F 111 ASN cc_start: 0.8688 (t0) cc_final: 0.8303 (t0) REVERT: F 115 LYS cc_start: 0.8802 (mptp) cc_final: 0.8228 (mptp) REVERT: F 232 LYS cc_start: 0.8155 (ptmt) cc_final: 0.7865 (ptmt) REVERT: F 303 TYR cc_start: 0.7950 (m-80) cc_final: 0.7513 (m-80) REVERT: F 312 PHE cc_start: 0.8001 (t80) cc_final: 0.7793 (t80) REVERT: F 324 GLU cc_start: 0.7031 (tt0) cc_final: 0.6568 (tt0) REVERT: F 325 ARG cc_start: 0.7431 (ptp-110) cc_final: 0.6827 (ttm110) REVERT: F 346 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8372 (tt) REVERT: F 396 LYS cc_start: 0.8253 (mmtm) cc_final: 0.7861 (mmmm) REVERT: F 399 ARG cc_start: 0.7594 (tpp80) cc_final: 0.7164 (tpp80) REVERT: F 403 GLU cc_start: 0.7495 (mp0) cc_final: 0.7081 (mp0) REVERT: F 441 GLN cc_start: 0.7470 (mt0) cc_final: 0.7161 (mt0) REVERT: G 16 LYS cc_start: 0.8399 (mmtt) cc_final: 0.8131 (mmtt) REVERT: G 20 ARG cc_start: 0.7755 (mtm-85) cc_final: 0.7506 (mtm-85) REVERT: G 24 MET cc_start: 0.7696 (ptp) cc_final: 0.7464 (ptp) REVERT: G 60 THR cc_start: 0.8533 (p) cc_final: 0.7635 (m) REVERT: G 76 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7879 (mtt90) REVERT: G 88 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7078 (tm-30) REVERT: G 98 ARG cc_start: 0.8342 (mtm180) cc_final: 0.8025 (mtm180) REVERT: G 106 LYS cc_start: 0.8305 (mtmm) cc_final: 0.7965 (mtmm) REVERT: G 111 ASN cc_start: 0.8735 (t0) cc_final: 0.8222 (t0) REVERT: G 115 LYS cc_start: 0.8903 (mptp) cc_final: 0.8206 (mptp) REVERT: G 135 LEU cc_start: 0.8763 (mt) cc_final: 0.8512 (mm) REVERT: G 163 TYR cc_start: 0.8519 (t80) cc_final: 0.8162 (t80) REVERT: G 171 ARG cc_start: 0.7422 (mtm-85) cc_final: 0.6998 (mtm-85) REVERT: G 185 TYR cc_start: 0.8819 (m-80) cc_final: 0.8151 (m-80) REVERT: G 234 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7210 (mm-30) REVERT: G 275 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.7270 (ptt180) REVERT: G 285 TYR cc_start: 0.8231 (OUTLIER) cc_final: 0.6942 (t80) REVERT: G 293 SER cc_start: 0.8188 (m) cc_final: 0.7399 (p) REVERT: G 325 ARG cc_start: 0.7684 (ttm-80) cc_final: 0.7438 (ttm170) REVERT: G 384 ILE cc_start: 0.9054 (pt) cc_final: 0.8698 (mt) REVERT: G 400 LYS cc_start: 0.8365 (tppt) cc_final: 0.7709 (tppt) REVERT: G 403 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7025 (mp0) REVERT: G 406 LYS cc_start: 0.8828 (mmmm) cc_final: 0.8523 (mmtp) REVERT: G 430 THR cc_start: 0.8763 (OUTLIER) cc_final: 0.8414 (p) REVERT: G 433 LYS cc_start: 0.8324 (mmmt) cc_final: 0.7962 (mmtt) REVERT: H 16 LYS cc_start: 0.8403 (mmtt) cc_final: 0.8083 (mmtt) REVERT: H 20 ARG cc_start: 0.7880 (mtm-85) cc_final: 0.7594 (mtm-85) REVERT: H 28 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7331 (mm-30) REVERT: H 56 ASP cc_start: 0.7657 (t70) cc_final: 0.7365 (t70) REVERT: H 92 ARG cc_start: 0.7701 (mmp80) cc_final: 0.7192 (mmp80) REVERT: H 99 LYS cc_start: 0.8849 (mmmm) cc_final: 0.8575 (mmmm) REVERT: H 111 ASN cc_start: 0.8651 (t0) cc_final: 0.7941 (t0) REVERT: H 115 LYS cc_start: 0.8841 (mptp) cc_final: 0.8105 (mptp) REVERT: H 146 ASP cc_start: 0.7717 (OUTLIER) cc_final: 0.6815 (p0) REVERT: H 171 ARG cc_start: 0.7290 (mtm-85) cc_final: 0.6877 (mtm-85) REVERT: H 264 PHE cc_start: 0.8219 (p90) cc_final: 0.7908 (p90) REVERT: H 274 CYS cc_start: 0.8074 (m) cc_final: 0.7830 (m) REVERT: H 400 LYS cc_start: 0.8224 (tppt) cc_final: 0.7666 (tppt) REVERT: H 447 PHE cc_start: 0.8489 (m-80) cc_final: 0.8268 (m-80) REVERT: I 16 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8187 (mtpt) REVERT: I 22 TYR cc_start: 0.8497 (m-80) cc_final: 0.7969 (m-80) REVERT: I 43 PHE cc_start: 0.8824 (t80) cc_final: 0.8599 (t80) REVERT: I 72 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7763 (tmm) REVERT: I 98 ARG cc_start: 0.8232 (mtm180) cc_final: 0.7769 (mtm180) REVERT: I 106 LYS cc_start: 0.8325 (mtmm) cc_final: 0.7911 (mtmm) REVERT: I 135 LEU cc_start: 0.8686 (mt) cc_final: 0.8445 (mm) REVERT: I 165 GLN cc_start: 0.8014 (mt0) cc_final: 0.7807 (mt0) REVERT: I 184 MET cc_start: 0.8227 (mmm) cc_final: 0.7714 (mmm) REVERT: I 234 GLU cc_start: 0.7462 (mm-30) cc_final: 0.7144 (mm-30) REVERT: I 328 PHE cc_start: 0.8156 (p90) cc_final: 0.7892 (p90) REVERT: I 383 MET cc_start: 0.8618 (ttp) cc_final: 0.8265 (ttm) REVERT: I 400 LYS cc_start: 0.7903 (tppt) cc_final: 0.7448 (ttpt) REVERT: I 405 GLU cc_start: 0.7785 (mp0) cc_final: 0.7298 (mp0) REVERT: I 436 ASP cc_start: 0.8232 (t0) cc_final: 0.8023 (t0) REVERT: I 441 GLN cc_start: 0.7764 (mt0) cc_final: 0.7278 (mt0) REVERT: J 16 LYS cc_start: 0.8377 (mmtt) cc_final: 0.8157 (mmpt) REVERT: J 41 ARG cc_start: 0.7640 (tpp-160) cc_final: 0.7176 (tpp-160) REVERT: J 43 PHE cc_start: 0.8854 (t80) cc_final: 0.8603 (t80) REVERT: J 76 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.8091 (mtt90) REVERT: J 88 GLU cc_start: 0.6437 (OUTLIER) cc_final: 0.6074 (tm-30) REVERT: J 92 ARG cc_start: 0.7702 (mmp80) cc_final: 0.7135 (mmp80) REVERT: J 98 ARG cc_start: 0.8305 (mtm180) cc_final: 0.7888 (mtm180) REVERT: J 99 LYS cc_start: 0.8906 (mmmm) cc_final: 0.8538 (mmmm) REVERT: J 106 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8212 (mtmm) REVERT: J 115 LYS cc_start: 0.8857 (mptp) cc_final: 0.8233 (mptp) REVERT: J 163 TYR cc_start: 0.8571 (t80) cc_final: 0.8314 (t80) REVERT: J 165 GLN cc_start: 0.8203 (mt0) cc_final: 0.7930 (mt0) REVERT: J 171 ARG cc_start: 0.7206 (mtm-85) cc_final: 0.6748 (mtm-85) REVERT: J 185 TYR cc_start: 0.8684 (m-80) cc_final: 0.7991 (m-80) REVERT: J 213 CYS cc_start: 0.8001 (p) cc_final: 0.7669 (p) REVERT: J 248 TYR cc_start: 0.7947 (m-10) cc_final: 0.7655 (m-10) REVERT: J 258 TRP cc_start: 0.8678 (m100) cc_final: 0.7648 (m100) REVERT: J 275 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.6783 (ptt180) REVERT: J 285 TYR cc_start: 0.8223 (OUTLIER) cc_final: 0.6617 (t80) REVERT: J 313 LEU cc_start: 0.8252 (mt) cc_final: 0.7943 (mp) REVERT: J 400 LYS cc_start: 0.8204 (tppt) cc_final: 0.7519 (tppt) REVERT: J 403 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6998 (mp0) REVERT: K 6 VAL cc_start: 0.7977 (t) cc_final: 0.7671 (p) REVERT: K 28 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7188 (mm-30) REVERT: K 71 ARG cc_start: 0.7881 (mtm-85) cc_final: 0.7309 (ptp-110) REVERT: K 76 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7749 (mtt90) REVERT: K 88 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7073 (tt0) REVERT: K 110 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7980 (tpp-160) REVERT: K 111 ASN cc_start: 0.8583 (t0) cc_final: 0.8298 (t0) REVERT: K 115 LYS cc_start: 0.8756 (mptp) cc_final: 0.8100 (mptp) REVERT: K 143 GLN cc_start: 0.8276 (tt0) cc_final: 0.8020 (tt0) REVERT: K 171 ARG cc_start: 0.7040 (mtm-85) cc_final: 0.6644 (mtm-85) REVERT: K 221 ARG cc_start: 0.7813 (ttp80) cc_final: 0.7440 (ttp80) REVERT: K 238 ARG cc_start: 0.7424 (ttm110) cc_final: 0.7077 (mtm110) REVERT: K 242 SER cc_start: 0.8089 (t) cc_final: 0.7498 (t) REVERT: K 264 PHE cc_start: 0.8105 (p90) cc_final: 0.7703 (p90) REVERT: K 267 LYS cc_start: 0.8227 (pttp) cc_final: 0.7894 (pttp) REVERT: K 312 PHE cc_start: 0.8094 (t80) cc_final: 0.7733 (t80) REVERT: K 313 LEU cc_start: 0.8444 (mt) cc_final: 0.8101 (mm) REVERT: K 340 ASP cc_start: 0.7660 (t0) cc_final: 0.7305 (t0) REVERT: K 378 THR cc_start: 0.7940 (m) cc_final: 0.7620 (p) REVERT: K 396 LYS cc_start: 0.8358 (tppt) cc_final: 0.7978 (tppt) REVERT: L 20 ARG cc_start: 0.7803 (mtm-85) cc_final: 0.7382 (mtm-85) REVERT: L 36 ASP cc_start: 0.8003 (m-30) cc_final: 0.7675 (t0) REVERT: L 60 THR cc_start: 0.8511 (p) cc_final: 0.7621 (m) REVERT: L 76 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7904 (mtt90) REVERT: L 98 ARG cc_start: 0.8219 (mtm180) cc_final: 0.7742 (mtm180) REVERT: L 135 LEU cc_start: 0.8706 (mt) cc_final: 0.8473 (mm) REVERT: L 146 ASP cc_start: 0.7585 (OUTLIER) cc_final: 0.6416 (p0) REVERT: L 168 LYS cc_start: 0.8812 (mtmt) cc_final: 0.8398 (mtpp) REVERT: L 171 ARG cc_start: 0.6942 (mtm-85) cc_final: 0.6487 (mtm-85) REVERT: L 240 LEU cc_start: 0.8077 (mm) cc_final: 0.7724 (mp) REVERT: L 245 SER cc_start: 0.8616 (p) cc_final: 0.8234 (t) REVERT: L 258 TRP cc_start: 0.8560 (m100) cc_final: 0.7463 (m100) REVERT: L 271 SER cc_start: 0.7705 (p) cc_final: 0.7422 (m) REVERT: L 283 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7418 (mp0) REVERT: L 303 TYR cc_start: 0.8138 (m-80) cc_final: 0.7904 (m-10) REVERT: L 313 LEU cc_start: 0.8519 (mt) cc_final: 0.8164 (mp) REVERT: L 362 LEU cc_start: 0.8822 (mm) cc_final: 0.8610 (tt) REVERT: L 400 LYS cc_start: 0.8044 (tppt) cc_final: 0.7449 (ttpt) REVERT: L 403 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6838 (mp0) REVERT: L 427 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7560 (mmtt) REVERT: L 436 ASP cc_start: 0.8249 (t0) cc_final: 0.7904 (t0) REVERT: L 446 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7497 (mm-30) outliers start: 225 outliers final: 169 residues processed: 1901 average time/residue: 0.6399 time to fit residues: 1866.8065 Evaluate side-chains 2027 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 1824 time to evaluate : 4.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 110 ARG Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 398 CYS Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 411 ARG Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 274 CYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 398 CYS Chi-restraints excluded: chain D residue 404 ASP Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 106 LYS Chi-restraints excluded: chain E residue 120 GLN Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 342 MET Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 398 CYS Chi-restraints excluded: chain E residue 403 GLU Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 120 GLN Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain F residue 321 VAL Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain F residue 411 ARG Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 76 ARG Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 236 CYS Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 275 ARG Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 291 THR Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 348 THR Chi-restraints excluded: chain G residue 403 GLU Chi-restraints excluded: chain G residue 430 THR Chi-restraints excluded: chain G residue 440 ILE Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 146 ASP Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 301 THR Chi-restraints excluded: chain H residue 342 MET Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 398 CYS Chi-restraints excluded: chain H residue 403 GLU Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 429 HIS Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain I residue 36 ASP Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 120 GLN Chi-restraints excluded: chain I residue 203 GLN Chi-restraints excluded: chain I residue 215 THR Chi-restraints excluded: chain I residue 267 LYS Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 291 THR Chi-restraints excluded: chain I residue 301 THR Chi-restraints excluded: chain I residue 314 MET Chi-restraints excluded: chain I residue 348 THR Chi-restraints excluded: chain I residue 358 LEU Chi-restraints excluded: chain I residue 403 GLU Chi-restraints excluded: chain I residue 408 LEU Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 72 MET Chi-restraints excluded: chain J residue 76 ARG Chi-restraints excluded: chain J residue 88 GLU Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain J residue 120 GLN Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 243 VAL Chi-restraints excluded: chain J residue 275 ARG Chi-restraints excluded: chain J residue 277 ASP Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 291 THR Chi-restraints excluded: chain J residue 301 THR Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 348 THR Chi-restraints excluded: chain J residue 403 GLU Chi-restraints excluded: chain K residue 76 ARG Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 110 ARG Chi-restraints excluded: chain K residue 120 GLN Chi-restraints excluded: chain K residue 149 ILE Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain K residue 203 GLN Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 255 LEU Chi-restraints excluded: chain K residue 277 ASP Chi-restraints excluded: chain K residue 283 GLU Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 305 VAL Chi-restraints excluded: chain K residue 337 THR Chi-restraints excluded: chain K residue 348 THR Chi-restraints excluded: chain K residue 349 GLU Chi-restraints excluded: chain K residue 398 CYS Chi-restraints excluded: chain K residue 403 GLU Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain L residue 73 MET Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain L residue 120 GLN Chi-restraints excluded: chain L residue 146 ASP Chi-restraints excluded: chain L residue 167 ILE Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain L residue 283 GLU Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 314 MET Chi-restraints excluded: chain L residue 318 THR Chi-restraints excluded: chain L residue 348 THR Chi-restraints excluded: chain L residue 403 GLU Chi-restraints excluded: chain L residue 405 GLU Chi-restraints excluded: chain L residue 427 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 332 optimal weight: 2.9990 chunk 446 optimal weight: 0.0050 chunk 128 optimal weight: 9.9990 chunk 386 optimal weight: 0.1980 chunk 61 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 419 optimal weight: 2.9990 chunk 175 optimal weight: 0.9980 chunk 430 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 HIS A 364 GLN ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 GLN ** C 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 308 HIS G 364 GLN ** H 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 308 HIS ** J 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 364 GLN ** K 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 203 GLN ** K 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.135047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.118756 restraints weight = 63885.214| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.82 r_work: 0.3432 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 42504 Z= 0.197 Angle : 0.626 9.960 57684 Z= 0.314 Chirality : 0.043 0.184 6564 Planarity : 0.005 0.109 7260 Dihedral : 5.792 38.689 5892 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 4.96 % Allowed : 34.38 % Favored : 60.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.17 % 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: -1.21 (0.11), residues: 5148 helix: 0.89 (0.14), residues: 1620 sheet: -0.93 (0.13), residues: 1284 loop : -2.00 (0.11), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 258 HIS 0.003 0.000 HIS A 308 PHE 0.024 0.002 PHE L 264 TYR 0.023 0.001 TYR B 174 ARG 0.013 0.001 ARG H 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23124.03 seconds wall clock time: 409 minutes 45.73 seconds (24585.73 seconds total)