Starting phenix.real_space_refine on Tue Mar 12 04:05:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bm1_16117/03_2024/8bm1_16117_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bm1_16117/03_2024/8bm1_16117.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bm1_16117/03_2024/8bm1_16117.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bm1_16117/03_2024/8bm1_16117.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bm1_16117/03_2024/8bm1_16117_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bm1_16117/03_2024/8bm1_16117_updated.pdb" } resolution = 2.7 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= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians K 14 8.98 5 P 42 5.49 5 Mg 14 5.21 5 S 287 5.16 5 C 36757 2.51 5 N 10255 2.21 5 O 14047 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 334": "OD1" <-> "OD2" Residue "I GLU 367": "OE1" <-> "OE2" Residue "W GLU 16": "OE1" <-> "OE2" Residue "W GLU 18": "OE1" <-> "OE2" Residue "W ASP 58": "OD1" <-> "OD2" Residue "W ASP 63": "OD1" <-> "OD2" Residue "W TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 96": "OE1" <-> "OE2" Residue "G ASP 398": "OD1" <-> "OD2" Residue "A ASP 52": "OD1" <-> "OD2" Residue "A ASP 188": "OD1" <-> "OD2" Residue "A PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 316": "OD1" <-> "OD2" Residue "A GLU 484": "OE1" <-> "OE2" Residue "B GLU 16": "OE1" <-> "OE2" Residue "B TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 398": "OD1" <-> "OD2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "C GLU 460": "OE1" <-> "OE2" Residue "D ASP 188": "OD1" <-> "OD2" Residue "D GLU 303": "OE1" <-> "OE2" Residue "D GLU 367": "OE1" <-> "OE2" Residue "E GLU 16": "OE1" <-> "OE2" Residue "E ASP 69": "OD1" <-> "OD2" Residue "E TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 398": "OD1" <-> "OD2" Residue "H ASP 52": "OD1" <-> "OD2" Residue "H GLU 216": "OE1" <-> "OE2" Residue "H PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 303": "OE1" <-> "OE2" Residue "H ASP 316": "OD1" <-> "OD2" Residue "H ASP 334": "OD1" <-> "OD2" Residue "H ASP 398": "OD1" <-> "OD2" Residue "J GLU 16": "OE1" <-> "OE2" Residue "K PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 398": "OD1" <-> "OD2" Residue "L PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 253": "OD1" <-> "OD2" Residue "L PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 16": "OE1" <-> "OE2" Residue "N ASP 398": "OD1" <-> "OD2" Residue "O ASP 52": "OD1" <-> "OD2" Residue "O GLU 216": "OE1" <-> "OE2" Residue "O PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 252": "OE1" <-> "OE2" Residue "O PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 473": "OD1" <-> "OD2" Residue "P GLU 16": "OE1" <-> "OE2" Residue "P GLU 96": "OE1" <-> "OE2" Residue "Q ASP 398": "OD1" <-> "OD2" Residue "Q ASP 428": "OD1" <-> "OD2" Residue "R TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 253": "OD1" <-> "OD2" Residue "R GLU 308": "OE1" <-> "OE2" Residue "R GLU 461": "OE1" <-> "OE2" Residue "S GLU 16": "OE1" <-> "OE2" Residue "S GLU 76": "OE1" <-> "OE2" Residue "T ASP 398": "OD1" <-> "OD2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 61416 Number of models: 1 Model: "" Number of chains: 56 Chain: "I" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "W" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 714 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 714 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 714 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 714 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 714 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 714 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 714 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 179 Classifications: {'water': 179} Link IDs: {None: 178} Chain: "W" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 112 Classifications: {'water': 112} Link IDs: {None: 111} Chain: "A" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 180 Classifications: {'water': 180} Link IDs: {None: 179} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 115 Classifications: {'water': 115} Link IDs: {None: 114} Chain: "D" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 169 Classifications: {'water': 169} Link IDs: {None: 168} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 107 Classifications: {'water': 107} Link IDs: {None: 106} Chain: "H" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 181 Classifications: {'water': 181} Link IDs: {None: 180} Chain: "J" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "K" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 104 Classifications: {'water': 104} Link IDs: {None: 103} Chain: "L" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 155 Classifications: {'water': 155} Link IDs: {None: 154} Chain: "M" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "N" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 120 Classifications: {'water': 120} Link IDs: {None: 119} Chain: "O" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 177 Classifications: {'water': 177} Link IDs: {None: 176} Chain: "P" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "Q" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 114 Classifications: {'water': 114} Link IDs: {None: 113} Chain: "R" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 178 Classifications: {'water': 178} Link IDs: {None: 177} Chain: "S" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "T" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 138 Classifications: {'water': 138} Link IDs: {None: 137} Residues with excluded nonbonded symmetry interactions: 7 residue: pdb="MG MG G 601 " occ=0.00 residue: pdb="MG MG C 601 " occ=0.00 residue: pdb="MG MG F 601 " occ=0.00 residue: pdb="MG MG K 601 " occ=0.00 residue: pdb="MG MG N 601 " occ=0.00 residue: pdb="MG MG Q 601 " occ=0.00 residue: pdb="MG MG T 601 " occ=0.00 Time building chain proxies: 23.72, per 1000 atoms: 0.39 Number of scatterers: 61416 At special positions: 0 Unit cell: (152.64, 150.72, 210.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 14 19.00 S 287 16.00 P 42 15.00 Mg 14 11.99 O 14047 8.00 N 10255 7.00 C 36757 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: 19.43 Conformation dependent library (CDL) restraints added in 8.0 seconds 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14462 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 270 helices and 108 sheets defined 49.1% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.27 Creating SS restraints... Processing helix chain 'I' and resid 9 through 30 removed outlier: 3.859A pdb=" N VAL I 29 " --> pdb=" O ASP I 25 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N THR I 30 " --> pdb=" O ALA I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 59 Processing helix chain 'I' and resid 65 through 84 removed outlier: 4.063A pdb=" N VAL I 77 " --> pdb=" O MET I 73 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA I 78 " --> pdb=" O VAL I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 108 Processing helix chain 'I' and resid 113 through 134 Processing helix chain 'I' and resid 141 through 151 Processing helix chain 'I' and resid 156 through 169 Processing helix chain 'I' and resid 202 through 204 No H-bonds generated for 'chain 'I' and resid 202 through 204' Processing helix chain 'I' and resid 234 through 243 Processing helix chain 'I' and resid 256 through 268 Processing helix chain 'I' and resid 285 through 296 Processing helix chain 'I' and resid 339 through 355 Processing helix chain 'I' and resid 359 through 372 Processing helix chain 'I' and resid 386 through 409 Processing helix chain 'I' and resid 417 through 425 Processing helix chain 'I' and resid 434 through 458 removed outlier: 3.751A pdb=" N GLU I 448 " --> pdb=" O LEU I 444 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA I 449 " --> pdb=" O ARG I 445 " (cutoff:3.500A) Proline residue: I 450 - end of helix Processing helix chain 'I' and resid 462 through 471 Processing helix chain 'I' and resid 497 through 516 removed outlier: 3.549A pdb=" N THR I 516 " --> pdb=" O GLY I 512 " (cutoff:3.500A) Processing helix chain 'W' and resid 29 through 31 No H-bonds generated for 'chain 'W' and resid 29 through 31' Processing helix chain 'G' and resid 9 through 30 removed outlier: 4.668A pdb=" N THR G 30 " --> pdb=" O ALA G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 59 Processing helix chain 'G' and resid 65 through 85 removed outlier: 3.952A pdb=" N VAL G 77 " --> pdb=" O MET G 73 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA G 78 " --> pdb=" O VAL G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 109 Processing helix chain 'G' and resid 113 through 134 Processing helix chain 'G' and resid 143 through 151 Processing helix chain 'G' and resid 156 through 169 Processing helix chain 'G' and resid 202 through 204 No H-bonds generated for 'chain 'G' and resid 202 through 204' Processing helix chain 'G' and resid 231 through 243 Proline residue: G 235 - end of helix Processing helix chain 'G' and resid 256 through 266 removed outlier: 4.729A pdb=" N THR G 261 " --> pdb=" O GLU G 257 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 296 Processing helix chain 'G' and resid 339 through 355 Processing helix chain 'G' and resid 359 through 374 Processing helix chain 'G' and resid 386 through 409 Processing helix chain 'G' and resid 417 through 425 Processing helix chain 'G' and resid 434 through 458 removed outlier: 3.819A pdb=" N GLU G 448 " --> pdb=" O LEU G 444 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA G 449 " --> pdb=" O ARG G 445 " (cutoff:3.500A) Proline residue: G 450 - end of helix Processing helix chain 'G' and resid 462 through 471 Processing helix chain 'G' and resid 488 through 491 No H-bonds generated for 'chain 'G' and resid 488 through 491' Processing helix chain 'G' and resid 497 through 516 removed outlier: 3.782A pdb=" N THR G 516 " --> pdb=" O GLY G 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 30 removed outlier: 3.884A pdb=" N VAL A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N THR A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 65 through 84 removed outlier: 4.043A pdb=" N VAL A 77 " --> pdb=" O MET A 73 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 108 Processing helix chain 'A' and resid 113 through 134 Processing helix chain 'A' and resid 141 through 151 Processing helix chain 'A' and resid 156 through 169 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 231 through 243 Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 284 through 296 Processing helix chain 'A' and resid 339 through 355 Processing helix chain 'A' and resid 359 through 372 Processing helix chain 'A' and resid 386 through 409 Processing helix chain 'A' and resid 417 through 425 Processing helix chain 'A' and resid 434 through 458 removed outlier: 3.704A pdb=" N GLU A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) Proline residue: A 450 - end of helix Processing helix chain 'A' and resid 462 through 471 Processing helix chain 'A' and resid 497 through 516 removed outlier: 3.689A pdb=" N THR A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 31 No H-bonds generated for 'chain 'B' and resid 29 through 31' Processing helix chain 'C' and resid 9 through 30 removed outlier: 4.680A pdb=" N THR C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 59 Processing helix chain 'C' and resid 65 through 85 removed outlier: 3.943A pdb=" N VAL C 77 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 109 Processing helix chain 'C' and resid 113 through 134 Processing helix chain 'C' and resid 138 through 141 No H-bonds generated for 'chain 'C' and resid 138 through 141' Processing helix chain 'C' and resid 144 through 151 Processing helix chain 'C' and resid 156 through 169 Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 230 through 242 Proline residue: C 235 - end of helix removed outlier: 4.091A pdb=" N LYS C 242 " --> pdb=" O GLU C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 266 removed outlier: 5.167A pdb=" N THR C 261 " --> pdb=" O GLU C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 296 Processing helix chain 'C' and resid 339 through 355 Processing helix chain 'C' and resid 359 through 374 Processing helix chain 'C' and resid 386 through 409 Processing helix chain 'C' and resid 417 through 425 Processing helix chain 'C' and resid 434 through 458 removed outlier: 3.803A pdb=" N GLU C 448 " --> pdb=" O LEU C 444 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA C 449 " --> pdb=" O ARG C 445 " (cutoff:3.500A) Proline residue: C 450 - end of helix Processing helix chain 'C' and resid 462 through 471 Processing helix chain 'C' and resid 488 through 491 No H-bonds generated for 'chain 'C' and resid 488 through 491' Processing helix chain 'C' and resid 497 through 516 removed outlier: 3.717A pdb=" N THR C 516 " --> pdb=" O GLY C 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 30 removed outlier: 3.882A pdb=" N VAL D 29 " --> pdb=" O ASP D 25 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N THR D 30 " --> pdb=" O ALA D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 59 Processing helix chain 'D' and resid 65 through 85 removed outlier: 3.633A pdb=" N GLU D 76 " --> pdb=" O GLN D 72 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL D 77 " --> pdb=" O MET D 73 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 108 Processing helix chain 'D' and resid 113 through 134 Processing helix chain 'D' and resid 141 through 151 Processing helix chain 'D' and resid 156 through 169 Processing helix chain 'D' and resid 202 through 204 No H-bonds generated for 'chain 'D' and resid 202 through 204' Processing helix chain 'D' and resid 231 through 243 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 256 through 268 Processing helix chain 'D' and resid 284 through 296 Processing helix chain 'D' and resid 339 through 355 Processing helix chain 'D' and resid 359 through 372 Processing helix chain 'D' and resid 386 through 409 Processing helix chain 'D' and resid 417 through 425 Processing helix chain 'D' and resid 434 through 458 removed outlier: 3.711A pdb=" N GLU D 448 " --> pdb=" O LEU D 444 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA D 449 " --> pdb=" O ARG D 445 " (cutoff:3.500A) Proline residue: D 450 - end of helix Processing helix chain 'D' and resid 462 through 471 Processing helix chain 'D' and resid 488 through 491 No H-bonds generated for 'chain 'D' and resid 488 through 491' Processing helix chain 'D' and resid 497 through 516 removed outlier: 3.726A pdb=" N THR D 516 " --> pdb=" O GLY D 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'F' and resid 9 through 30 removed outlier: 4.681A pdb=" N THR F 30 " --> pdb=" O ALA F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 59 Processing helix chain 'F' and resid 65 through 85 removed outlier: 3.931A pdb=" N VAL F 77 " --> pdb=" O MET F 73 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA F 78 " --> pdb=" O VAL F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 109 Processing helix chain 'F' and resid 113 through 134 Processing helix chain 'F' and resid 141 through 151 Processing helix chain 'F' and resid 156 through 169 Processing helix chain 'F' and resid 202 through 204 No H-bonds generated for 'chain 'F' and resid 202 through 204' Processing helix chain 'F' and resid 230 through 243 Proline residue: F 235 - end of helix removed outlier: 4.001A pdb=" N LYS F 242 " --> pdb=" O GLU F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 266 Processing helix chain 'F' and resid 282 through 296 Processing helix chain 'F' and resid 339 through 355 Processing helix chain 'F' and resid 359 through 374 Processing helix chain 'F' and resid 386 through 409 Processing helix chain 'F' and resid 417 through 425 Processing helix chain 'F' and resid 434 through 458 removed outlier: 3.812A pdb=" N GLU F 448 " --> pdb=" O LEU F 444 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA F 449 " --> pdb=" O ARG F 445 " (cutoff:3.500A) Proline residue: F 450 - end of helix Processing helix chain 'F' and resid 462 through 471 Processing helix chain 'F' and resid 488 through 491 No H-bonds generated for 'chain 'F' and resid 488 through 491' Processing helix chain 'F' and resid 497 through 516 removed outlier: 3.723A pdb=" N THR F 516 " --> pdb=" O GLY F 512 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 30 removed outlier: 3.899A pdb=" N VAL H 29 " --> pdb=" O ASP H 25 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N THR H 30 " --> pdb=" O ALA H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 59 Processing helix chain 'H' and resid 65 through 84 removed outlier: 4.068A pdb=" N VAL H 77 " --> pdb=" O MET H 73 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA H 78 " --> pdb=" O VAL H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 109 Processing helix chain 'H' and resid 113 through 134 Processing helix chain 'H' and resid 141 through 151 Processing helix chain 'H' and resid 156 through 169 Processing helix chain 'H' and resid 202 through 204 No H-bonds generated for 'chain 'H' and resid 202 through 204' Processing helix chain 'H' and resid 234 through 243 Processing helix chain 'H' and resid 256 through 268 Processing helix chain 'H' and resid 285 through 296 Processing helix chain 'H' and resid 339 through 355 Processing helix chain 'H' and resid 359 through 372 Processing helix chain 'H' and resid 386 through 409 Processing helix chain 'H' and resid 417 through 425 Processing helix chain 'H' and resid 434 through 458 removed outlier: 3.732A pdb=" N GLU H 448 " --> pdb=" O LEU H 444 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA H 449 " --> pdb=" O ARG H 445 " (cutoff:3.500A) Proline residue: H 450 - end of helix Processing helix chain 'H' and resid 462 through 471 Processing helix chain 'H' and resid 497 through 516 removed outlier: 3.604A pdb=" N THR H 516 " --> pdb=" O GLY H 512 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 31 No H-bonds generated for 'chain 'J' and resid 29 through 31' Processing helix chain 'K' and resid 9 through 30 removed outlier: 4.634A pdb=" N THR K 30 " --> pdb=" O ALA K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 59 Processing helix chain 'K' and resid 65 through 85 removed outlier: 3.918A pdb=" N VAL K 77 " --> pdb=" O MET K 73 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA K 78 " --> pdb=" O VAL K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 109 Processing helix chain 'K' and resid 113 through 134 Processing helix chain 'K' and resid 138 through 141 No H-bonds generated for 'chain 'K' and resid 138 through 141' Processing helix chain 'K' and resid 144 through 151 Processing helix chain 'K' and resid 156 through 169 Processing helix chain 'K' and resid 202 through 204 No H-bonds generated for 'chain 'K' and resid 202 through 204' Processing helix chain 'K' and resid 230 through 240 Proline residue: K 235 - end of helix Processing helix chain 'K' and resid 256 through 266 removed outlier: 4.235A pdb=" N THR K 261 " --> pdb=" O GLU K 257 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N LEU K 262 " --> pdb=" O ALA K 258 " (cutoff:3.500A) Processing helix chain 'K' and resid 282 through 296 Processing helix chain 'K' and resid 339 through 355 Processing helix chain 'K' and resid 359 through 374 Processing helix chain 'K' and resid 386 through 409 Processing helix chain 'K' and resid 417 through 425 Processing helix chain 'K' and resid 434 through 458 removed outlier: 3.825A pdb=" N GLU K 448 " --> pdb=" O LEU K 444 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA K 449 " --> pdb=" O ARG K 445 " (cutoff:3.500A) Proline residue: K 450 - end of helix Processing helix chain 'K' and resid 462 through 471 Processing helix chain 'K' and resid 488 through 491 No H-bonds generated for 'chain 'K' and resid 488 through 491' Processing helix chain 'K' and resid 497 through 516 removed outlier: 3.743A pdb=" N THR K 516 " --> pdb=" O GLY K 512 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 30 removed outlier: 3.910A pdb=" N VAL L 29 " --> pdb=" O ASP L 25 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N THR L 30 " --> pdb=" O ALA L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 59 Processing helix chain 'L' and resid 65 through 84 removed outlier: 3.951A pdb=" N VAL L 77 " --> pdb=" O MET L 73 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA L 78 " --> pdb=" O VAL L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 108 Processing helix chain 'L' and resid 113 through 134 Processing helix chain 'L' and resid 141 through 151 Processing helix chain 'L' and resid 156 through 169 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 231 through 243 Proline residue: L 235 - end of helix Processing helix chain 'L' and resid 256 through 268 Processing helix chain 'L' and resid 285 through 296 Processing helix chain 'L' and resid 339 through 355 Processing helix chain 'L' and resid 359 through 372 Processing helix chain 'L' and resid 386 through 409 Processing helix chain 'L' and resid 417 through 425 Processing helix chain 'L' and resid 434 through 458 removed outlier: 3.681A pdb=" N GLU L 448 " --> pdb=" O LEU L 444 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA L 449 " --> pdb=" O ARG L 445 " (cutoff:3.500A) Proline residue: L 450 - end of helix Processing helix chain 'L' and resid 462 through 471 Processing helix chain 'L' and resid 497 through 516 Processing helix chain 'M' and resid 29 through 31 No H-bonds generated for 'chain 'M' and resid 29 through 31' Processing helix chain 'N' and resid 9 through 30 removed outlier: 4.631A pdb=" N THR N 30 " --> pdb=" O ALA N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 59 Processing helix chain 'N' and resid 65 through 85 removed outlier: 3.928A pdb=" N VAL N 77 " --> pdb=" O MET N 73 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA N 78 " --> pdb=" O VAL N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 89 through 109 Processing helix chain 'N' and resid 113 through 134 Processing helix chain 'N' and resid 138 through 141 No H-bonds generated for 'chain 'N' and resid 138 through 141' Processing helix chain 'N' and resid 144 through 151 Processing helix chain 'N' and resid 156 through 169 Processing helix chain 'N' and resid 202 through 204 No H-bonds generated for 'chain 'N' and resid 202 through 204' Processing helix chain 'N' and resid 230 through 243 Proline residue: N 235 - end of helix Processing helix chain 'N' and resid 256 through 266 removed outlier: 5.085A pdb=" N THR N 261 " --> pdb=" O GLU N 257 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU N 262 " --> pdb=" O ALA N 258 " (cutoff:3.500A) Processing helix chain 'N' and resid 282 through 296 Processing helix chain 'N' and resid 339 through 355 Processing helix chain 'N' and resid 359 through 374 Processing helix chain 'N' and resid 386 through 409 Processing helix chain 'N' and resid 417 through 425 Processing helix chain 'N' and resid 434 through 457 removed outlier: 3.807A pdb=" N GLU N 448 " --> pdb=" O LEU N 444 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA N 449 " --> pdb=" O ARG N 445 " (cutoff:3.500A) Proline residue: N 450 - end of helix Processing helix chain 'N' and resid 462 through 471 Processing helix chain 'N' and resid 497 through 516 removed outlier: 3.726A pdb=" N THR N 516 " --> pdb=" O GLY N 512 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 30 removed outlier: 3.896A pdb=" N VAL O 29 " --> pdb=" O ASP O 25 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N THR O 30 " --> pdb=" O ALA O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 53 through 59 Processing helix chain 'O' and resid 65 through 84 removed outlier: 4.020A pdb=" N VAL O 77 " --> pdb=" O MET O 73 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA O 78 " --> pdb=" O VAL O 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 108 Processing helix chain 'O' and resid 113 through 134 Processing helix chain 'O' and resid 141 through 151 Processing helix chain 'O' and resid 156 through 169 Processing helix chain 'O' and resid 202 through 204 No H-bonds generated for 'chain 'O' and resid 202 through 204' Processing helix chain 'O' and resid 234 through 243 Processing helix chain 'O' and resid 256 through 268 Processing helix chain 'O' and resid 285 through 296 Processing helix chain 'O' and resid 339 through 355 Processing helix chain 'O' and resid 359 through 372 Processing helix chain 'O' and resid 386 through 409 Processing helix chain 'O' and resid 417 through 425 Processing helix chain 'O' and resid 434 through 458 removed outlier: 3.694A pdb=" N GLU O 448 " --> pdb=" O LEU O 444 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA O 449 " --> pdb=" O ARG O 445 " (cutoff:3.500A) Proline residue: O 450 - end of helix Processing helix chain 'O' and resid 462 through 471 Processing helix chain 'O' and resid 497 through 515 Processing helix chain 'P' and resid 29 through 31 No H-bonds generated for 'chain 'P' and resid 29 through 31' Processing helix chain 'Q' and resid 9 through 30 removed outlier: 4.645A pdb=" N THR Q 30 " --> pdb=" O ALA Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 53 through 59 Processing helix chain 'Q' and resid 65 through 85 removed outlier: 4.119A pdb=" N VAL Q 77 " --> pdb=" O MET Q 73 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA Q 78 " --> pdb=" O VAL Q 74 " (cutoff:3.500A) Processing helix chain 'Q' and resid 89 through 109 Processing helix chain 'Q' and resid 113 through 134 Processing helix chain 'Q' and resid 138 through 141 No H-bonds generated for 'chain 'Q' and resid 138 through 141' Processing helix chain 'Q' and resid 144 through 151 Processing helix chain 'Q' and resid 156 through 169 Processing helix chain 'Q' and resid 202 through 204 No H-bonds generated for 'chain 'Q' and resid 202 through 204' Processing helix chain 'Q' and resid 230 through 242 Proline residue: Q 235 - end of helix Processing helix chain 'Q' and resid 259 through 266 Processing helix chain 'Q' and resid 282 through 296 Processing helix chain 'Q' and resid 339 through 355 Processing helix chain 'Q' and resid 359 through 374 Processing helix chain 'Q' and resid 386 through 409 Processing helix chain 'Q' and resid 417 through 425 Processing helix chain 'Q' and resid 434 through 458 removed outlier: 3.804A pdb=" N GLU Q 448 " --> pdb=" O LEU Q 444 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA Q 449 " --> pdb=" O ARG Q 445 " (cutoff:3.500A) Proline residue: Q 450 - end of helix Processing helix chain 'Q' and resid 462 through 471 Processing helix chain 'Q' and resid 497 through 516 removed outlier: 3.766A pdb=" N THR Q 516 " --> pdb=" O GLY Q 512 " (cutoff:3.500A) Processing helix chain 'R' and resid 9 through 30 removed outlier: 3.903A pdb=" N VAL R 29 " --> pdb=" O ASP R 25 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N THR R 30 " --> pdb=" O ALA R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 53 through 59 Processing helix chain 'R' and resid 65 through 84 removed outlier: 4.061A pdb=" N VAL R 77 " --> pdb=" O MET R 73 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA R 78 " --> pdb=" O VAL R 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 108 Processing helix chain 'R' and resid 113 through 134 Processing helix chain 'R' and resid 141 through 151 Processing helix chain 'R' and resid 156 through 169 Processing helix chain 'R' and resid 202 through 204 No H-bonds generated for 'chain 'R' and resid 202 through 204' Processing helix chain 'R' and resid 234 through 243 Processing helix chain 'R' and resid 256 through 268 Processing helix chain 'R' and resid 285 through 296 Processing helix chain 'R' and resid 339 through 355 Processing helix chain 'R' and resid 359 through 372 Processing helix chain 'R' and resid 386 through 409 Processing helix chain 'R' and resid 417 through 425 Processing helix chain 'R' and resid 434 through 458 removed outlier: 3.726A pdb=" N GLU R 448 " --> pdb=" O LEU R 444 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA R 449 " --> pdb=" O ARG R 445 " (cutoff:3.500A) Proline residue: R 450 - end of helix Processing helix chain 'R' and resid 462 through 471 Processing helix chain 'R' and resid 497 through 516 removed outlier: 3.516A pdb=" N THR R 516 " --> pdb=" O GLY R 512 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'T' and resid 9 through 30 removed outlier: 4.650A pdb=" N THR T 30 " --> pdb=" O ALA T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 53 through 59 Processing helix chain 'T' and resid 65 through 85 removed outlier: 3.818A pdb=" N VAL T 77 " --> pdb=" O MET T 73 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA T 78 " --> pdb=" O VAL T 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 89 through 109 Processing helix chain 'T' and resid 113 through 134 Processing helix chain 'T' and resid 138 through 141 No H-bonds generated for 'chain 'T' and resid 138 through 141' Processing helix chain 'T' and resid 144 through 151 Processing helix chain 'T' and resid 156 through 169 Processing helix chain 'T' and resid 202 through 204 No H-bonds generated for 'chain 'T' and resid 202 through 204' Processing helix chain 'T' and resid 230 through 240 Proline residue: T 235 - end of helix Processing helix chain 'T' and resid 256 through 266 removed outlier: 4.222A pdb=" N THR T 261 " --> pdb=" O GLU T 257 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N LEU T 262 " --> pdb=" O ALA T 258 " (cutoff:3.500A) Processing helix chain 'T' and resid 282 through 296 Processing helix chain 'T' and resid 339 through 355 Processing helix chain 'T' and resid 359 through 374 Processing helix chain 'T' and resid 386 through 409 Processing helix chain 'T' and resid 417 through 425 Processing helix chain 'T' and resid 434 through 458 removed outlier: 3.819A pdb=" N GLU T 448 " --> pdb=" O LEU T 444 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA T 449 " --> pdb=" O ARG T 445 " (cutoff:3.500A) Proline residue: T 450 - end of helix Processing helix chain 'T' and resid 462 through 471 Processing helix chain 'T' and resid 488 through 491 No H-bonds generated for 'chain 'T' and resid 488 through 491' Processing helix chain 'T' and resid 497 through 516 removed outlier: 3.774A pdb=" N THR T 516 " --> pdb=" O GLY T 512 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'I' and resid 4 through 8 Processing sheet with id= B, first strand: chain 'I' and resid 38 through 40 Processing sheet with id= C, first strand: chain 'I' and resid 174 through 179 Processing sheet with id= D, first strand: chain 'I' and resid 213 through 216 Processing sheet with id= E, first strand: chain 'I' and resid 219 through 223 removed outlier: 3.515A pdb=" N ALA I 251 " --> pdb=" O VAL I 276 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'I' and resid 411 through 413 Processing sheet with id= G, first strand: chain 'I' and resid 476 through 479 Processing sheet with id= H, first strand: chain 'W' and resid 74 through 78 removed outlier: 8.011A pdb=" N GLU W 82 " --> pdb=" O ARG W 14 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ARG W 14 " --> pdb=" O GLU W 82 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LYS W 13 " --> pdb=" O VAL W 40 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N VAL W 40 " --> pdb=" O LYS W 13 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE W 64 " --> pdb=" O VAL W 95 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 4 through 8 Processing sheet with id= J, first strand: chain 'G' and resid 38 through 40 Processing sheet with id= K, first strand: chain 'G' and resid 175 through 180 removed outlier: 6.310A pdb=" N ALA G 377 " --> pdb=" O THR G 176 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N GLU G 178 " --> pdb=" O ALA G 377 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ILE G 379 " --> pdb=" O GLU G 178 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N GLY G 180 " --> pdb=" O ILE G 379 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N VAL G 381 " --> pdb=" O GLY G 180 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 193 through 195 Processing sheet with id= M, first strand: chain 'G' and resid 213 through 216 Processing sheet with id= N, first strand: chain 'G' and resid 219 through 222 Processing sheet with id= O, first strand: chain 'G' and resid 411 through 413 Processing sheet with id= P, first strand: chain 'G' and resid 476 through 479 Processing sheet with id= Q, first strand: chain 'A' and resid 4 through 8 Processing sheet with id= R, first strand: chain 'A' and resid 38 through 40 Processing sheet with id= S, first strand: chain 'A' and resid 174 through 179 Processing sheet with id= T, first strand: chain 'A' and resid 213 through 216 Processing sheet with id= U, first strand: chain 'A' and resid 219 through 223 removed outlier: 3.602A pdb=" N ALA A 251 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'A' and resid 411 through 413 Processing sheet with id= W, first strand: chain 'A' and resid 476 through 479 Processing sheet with id= X, first strand: chain 'B' and resid 74 through 78 removed outlier: 7.959A pdb=" N GLU B 82 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ARG B 14 " --> pdb=" O GLU B 82 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LYS B 13 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N VAL B 40 " --> pdb=" O LYS B 13 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE B 64 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA B 93 " --> pdb=" O ILE B 66 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 4 through 8 Processing sheet with id= Z, first strand: chain 'C' and resid 38 through 40 Processing sheet with id= AA, first strand: chain 'C' and resid 175 through 180 removed outlier: 6.326A pdb=" N ALA C 377 " --> pdb=" O THR C 176 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLU C 178 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ILE C 379 " --> pdb=" O GLU C 178 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N GLY C 180 " --> pdb=" O ILE C 379 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N VAL C 381 " --> pdb=" O GLY C 180 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 193 through 195 removed outlier: 6.493A pdb=" N ARG C 322 " --> pdb=" O ILE C 333 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL C 323 " --> pdb=" O LEU C 215 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 219 through 222 removed outlier: 6.721A pdb=" N ALA C 274 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ALA C 251 " --> pdb=" O ALA C 274 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL C 276 " --> pdb=" O ALA C 251 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 411 through 413 Processing sheet with id= AE, first strand: chain 'C' and resid 476 through 479 Processing sheet with id= AF, first strand: chain 'D' and resid 4 through 8 Processing sheet with id= AG, first strand: chain 'D' and resid 38 through 40 Processing sheet with id= AH, first strand: chain 'D' and resid 174 through 179 Processing sheet with id= AI, first strand: chain 'D' and resid 213 through 216 Processing sheet with id= AJ, first strand: chain 'D' and resid 219 through 223 Processing sheet with id= AK, first strand: chain 'D' and resid 411 through 413 Processing sheet with id= AL, first strand: chain 'D' and resid 476 through 479 Processing sheet with id= AM, first strand: chain 'E' and resid 74 through 78 removed outlier: 7.992A pdb=" N GLU E 82 " --> pdb=" O ARG E 14 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ARG E 14 " --> pdb=" O GLU E 82 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LYS E 13 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N VAL E 40 " --> pdb=" O LYS E 13 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE E 64 " --> pdb=" O VAL E 95 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA E 93 " --> pdb=" O ILE E 66 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'F' and resid 4 through 8 Processing sheet with id= AO, first strand: chain 'F' and resid 38 through 40 Processing sheet with id= AP, first strand: chain 'F' and resid 174 through 180 Processing sheet with id= AQ, first strand: chain 'F' and resid 193 through 195 removed outlier: 6.422A pdb=" N ARG F 322 " --> pdb=" O ILE F 333 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL F 323 " --> pdb=" O LEU F 215 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'F' and resid 219 through 222 removed outlier: 6.708A pdb=" N ALA F 274 " --> pdb=" O ILE F 249 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N ALA F 251 " --> pdb=" O ALA F 274 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL F 276 " --> pdb=" O ALA F 251 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'F' and resid 411 through 413 Processing sheet with id= AT, first strand: chain 'F' and resid 476 through 479 Processing sheet with id= AU, first strand: chain 'H' and resid 4 through 8 Processing sheet with id= AV, first strand: chain 'H' and resid 38 through 40 Processing sheet with id= AW, first strand: chain 'H' and resid 174 through 179 Processing sheet with id= AX, first strand: chain 'H' and resid 213 through 216 Processing sheet with id= AY, first strand: chain 'H' and resid 219 through 223 Processing sheet with id= AZ, first strand: chain 'H' and resid 411 through 413 Processing sheet with id= BA, first strand: chain 'H' and resid 476 through 479 Processing sheet with id= BB, first strand: chain 'J' and resid 74 through 78 removed outlier: 7.660A pdb=" N GLU J 82 " --> pdb=" O ARG J 14 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ARG J 14 " --> pdb=" O GLU J 82 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LYS J 13 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N VAL J 40 " --> pdb=" O LYS J 13 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'K' and resid 4 through 8 Processing sheet with id= BD, first strand: chain 'K' and resid 38 through 40 Processing sheet with id= BE, first strand: chain 'K' and resid 175 through 179 removed outlier: 6.371A pdb=" N ALA K 377 " --> pdb=" O THR K 176 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N GLU K 178 " --> pdb=" O ALA K 377 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ILE K 379 " --> pdb=" O GLU K 178 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'K' and resid 193 through 195 removed outlier: 6.513A pdb=" N ARG K 322 " --> pdb=" O ILE K 333 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL K 323 " --> pdb=" O LEU K 215 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'K' and resid 219 through 222 removed outlier: 6.565A pdb=" N ALA K 274 " --> pdb=" O ILE K 249 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ALA K 251 " --> pdb=" O ALA K 274 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N VAL K 276 " --> pdb=" O ALA K 251 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'K' and resid 411 through 413 Processing sheet with id= BI, first strand: chain 'K' and resid 476 through 479 Processing sheet with id= BJ, first strand: chain 'L' and resid 4 through 8 Processing sheet with id= BK, first strand: chain 'L' and resid 38 through 40 Processing sheet with id= BL, first strand: chain 'L' and resid 174 through 179 Processing sheet with id= BM, first strand: chain 'L' and resid 213 through 216 Processing sheet with id= BN, first strand: chain 'L' and resid 219 through 222 Processing sheet with id= BO, first strand: chain 'L' and resid 411 through 413 Processing sheet with id= BP, first strand: chain 'L' and resid 476 through 479 Processing sheet with id= BQ, first strand: chain 'M' and resid 74 through 78 removed outlier: 7.819A pdb=" N GLU M 82 " --> pdb=" O ARG M 14 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ARG M 14 " --> pdb=" O GLU M 82 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LYS M 13 " --> pdb=" O VAL M 40 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL M 40 " --> pdb=" O LYS M 13 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'N' and resid 4 through 8 Processing sheet with id= BS, first strand: chain 'N' and resid 38 through 40 Processing sheet with id= BT, first strand: chain 'N' and resid 175 through 179 removed outlier: 6.407A pdb=" N ALA N 377 " --> pdb=" O THR N 176 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N GLU N 178 " --> pdb=" O ALA N 377 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ILE N 379 " --> pdb=" O GLU N 178 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'N' and resid 193 through 195 Processing sheet with id= BV, first strand: chain 'N' and resid 213 through 216 Processing sheet with id= BW, first strand: chain 'N' and resid 219 through 223 Processing sheet with id= BX, first strand: chain 'N' and resid 411 through 413 Processing sheet with id= BY, first strand: chain 'N' and resid 476 through 479 Processing sheet with id= BZ, first strand: chain 'O' and resid 4 through 8 Processing sheet with id= CA, first strand: chain 'O' and resid 38 through 40 Processing sheet with id= CB, first strand: chain 'O' and resid 174 through 179 Processing sheet with id= CC, first strand: chain 'O' and resid 213 through 216 Processing sheet with id= CD, first strand: chain 'O' and resid 219 through 223 removed outlier: 3.529A pdb=" N ALA O 251 " --> pdb=" O VAL O 276 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'O' and resid 411 through 413 Processing sheet with id= CF, first strand: chain 'O' and resid 476 through 479 Processing sheet with id= CG, first strand: chain 'P' and resid 74 through 78 removed outlier: 7.738A pdb=" N GLU P 82 " --> pdb=" O ARG P 14 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ARG P 14 " --> pdb=" O GLU P 82 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N LYS P 13 " --> pdb=" O VAL P 40 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N VAL P 40 " --> pdb=" O LYS P 13 " (cutoff:3.500A) Processing sheet with id= CH, first strand: chain 'Q' and resid 4 through 8 Processing sheet with id= CI, first strand: chain 'Q' and resid 38 through 40 Processing sheet with id= CJ, first strand: chain 'Q' and resid 175 through 179 removed outlier: 6.362A pdb=" N ALA Q 377 " --> pdb=" O THR Q 176 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N GLU Q 178 " --> pdb=" O ALA Q 377 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ILE Q 379 " --> pdb=" O GLU Q 178 " (cutoff:3.500A) Processing sheet with id= CK, first strand: chain 'Q' and resid 193 through 195 Processing sheet with id= CL, first strand: chain 'Q' and resid 213 through 216 removed outlier: 3.661A pdb=" N VAL Q 323 " --> pdb=" O LEU Q 215 " (cutoff:3.500A) Processing sheet with id= CM, first strand: chain 'Q' and resid 219 through 222 removed outlier: 6.747A pdb=" N ALA Q 274 " --> pdb=" O ILE Q 249 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ALA Q 251 " --> pdb=" O ALA Q 274 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL Q 276 " --> pdb=" O ALA Q 251 " (cutoff:3.500A) Processing sheet with id= CN, first strand: chain 'Q' and resid 411 through 413 Processing sheet with id= CO, first strand: chain 'Q' and resid 476 through 479 Processing sheet with id= CP, first strand: chain 'R' and resid 4 through 8 Processing sheet with id= CQ, first strand: chain 'R' and resid 38 through 40 Processing sheet with id= CR, first strand: chain 'R' and resid 174 through 179 Processing sheet with id= CS, first strand: chain 'R' and resid 213 through 216 Processing sheet with id= CT, first strand: chain 'R' and resid 219 through 223 removed outlier: 3.518A pdb=" N ALA R 251 " --> pdb=" O VAL R 276 " (cutoff:3.500A) Processing sheet with id= CU, first strand: chain 'R' and resid 411 through 413 Processing sheet with id= CV, first strand: chain 'R' and resid 476 through 479 Processing sheet with id= CW, first strand: chain 'S' and resid 74 through 78 removed outlier: 7.800A pdb=" N GLU S 82 " --> pdb=" O ARG S 14 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ARG S 14 " --> pdb=" O GLU S 82 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LYS S 13 " --> pdb=" O VAL S 40 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N VAL S 40 " --> pdb=" O LYS S 13 " (cutoff:3.500A) Processing sheet with id= CX, first strand: chain 'T' and resid 4 through 8 Processing sheet with id= CY, first strand: chain 'T' and resid 38 through 40 Processing sheet with id= CZ, first strand: chain 'T' and resid 174 through 180 Processing sheet with id= DA, first strand: chain 'T' and resid 193 through 195 removed outlier: 6.397A pdb=" N ARG T 322 " --> pdb=" O ILE T 333 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL T 323 " --> pdb=" O LEU T 215 " (cutoff:3.500A) Processing sheet with id= DB, first strand: chain 'T' and resid 219 through 222 removed outlier: 6.620A pdb=" N ALA T 274 " --> pdb=" O ILE T 249 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ALA T 251 " --> pdb=" O ALA T 274 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N VAL T 276 " --> pdb=" O ALA T 251 " (cutoff:3.500A) Processing sheet with id= DC, first strand: chain 'T' and resid 411 through 413 Processing sheet with id= DD, first strand: chain 'T' and resid 476 through 479 3341 hydrogen bonds defined for protein. 9666 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: 23.95 Time building geometry restraints manager: 21.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 17955 1.33 - 1.45: 5849 1.45 - 1.57: 35368 1.57 - 1.69: 69 1.69 - 1.81: 532 Bond restraints: 59773 Sorted by residual: bond pdb=" C GLY K 244 " pdb=" N LYS K 245 " ideal model delta sigma weight residual 1.332 1.315 0.016 7.50e-03 1.78e+04 4.72e+00 bond pdb=" CG LYS G 242 " pdb=" CD LYS G 242 " ideal model delta sigma weight residual 1.520 1.462 0.058 3.00e-02 1.11e+03 3.75e+00 bond pdb=" CB ASN M 80 " pdb=" CG ASN M 80 " ideal model delta sigma weight residual 1.516 1.562 -0.046 2.50e-02 1.60e+03 3.44e+00 bond pdb=" CB VAL N 236 " pdb=" CG2 VAL N 236 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.25e+00 bond pdb=" C GLY G 244 " pdb=" N LYS G 245 " ideal model delta sigma weight residual 1.340 1.236 0.104 5.87e-02 2.90e+02 3.17e+00 ... (remaining 59768 not shown) Histogram of bond angle deviations from ideal: 96.18 - 104.93: 884 104.93 - 113.68: 35328 113.68 - 122.43: 37272 122.43 - 131.18: 7259 131.18 - 139.93: 58 Bond angle restraints: 80801 Sorted by residual: angle pdb=" CA GLU T 255 " pdb=" CB GLU T 255 " pdb=" CG GLU T 255 " ideal model delta sigma weight residual 114.10 130.88 -16.78 2.00e+00 2.50e-01 7.04e+01 angle pdb=" CA GLU K 255 " pdb=" CB GLU K 255 " pdb=" CG GLU K 255 " ideal model delta sigma weight residual 114.10 130.35 -16.25 2.00e+00 2.50e-01 6.60e+01 angle pdb=" N GLU K 255 " pdb=" CA GLU K 255 " pdb=" CB GLU K 255 " ideal model delta sigma weight residual 109.71 119.35 -9.64 1.54e+00 4.22e-01 3.92e+01 angle pdb=" C LYS K 245 " pdb=" CA LYS K 245 " pdb=" CB LYS K 245 " ideal model delta sigma weight residual 111.01 118.54 -7.53 1.38e+00 5.25e-01 2.98e+01 angle pdb=" N GLU T 255 " pdb=" CA GLU T 255 " pdb=" CB GLU T 255 " ideal model delta sigma weight residual 109.60 118.48 -8.88 1.64e+00 3.72e-01 2.93e+01 ... (remaining 80796 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 33213 17.89 - 35.78: 2895 35.78 - 53.67: 874 53.67 - 71.56: 229 71.56 - 89.45: 78 Dihedral angle restraints: 37289 sinusoidal: 14742 harmonic: 22547 Sorted by residual: dihedral pdb=" CG ARG I 284 " pdb=" CD ARG I 284 " pdb=" NE ARG I 284 " pdb=" CZ ARG I 284 " ideal model delta sinusoidal sigma weight residual -90.00 -39.96 -50.04 2 1.50e+01 4.44e-03 1.25e+01 dihedral pdb=" CG ARG F 404 " pdb=" CD ARG F 404 " pdb=" NE ARG F 404 " pdb=" CZ ARG F 404 " ideal model delta sinusoidal sigma weight residual -90.00 -40.28 -49.72 2 1.50e+01 4.44e-03 1.24e+01 dihedral pdb=" CA PHE T 8 " pdb=" C PHE T 8 " pdb=" N GLY T 9 " pdb=" CA GLY T 9 " ideal model delta harmonic sigma weight residual 180.00 162.78 17.22 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 37286 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 7993 0.058 - 0.116: 1569 0.116 - 0.174: 215 0.174 - 0.232: 25 0.232 - 0.290: 5 Chirality restraints: 9807 Sorted by residual: chirality pdb=" CB ILE K 227 " pdb=" CA ILE K 227 " pdb=" CG1 ILE K 227 " pdb=" CG2 ILE K 227 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CG LEU R 365 " pdb=" CB LEU R 365 " pdb=" CD1 LEU R 365 " pdb=" CD2 LEU R 365 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CG LEU H 365 " pdb=" CB LEU H 365 " pdb=" CD1 LEU H 365 " pdb=" CD2 LEU H 365 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 9804 not shown) Planarity restraints: 10507 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP K 253 " -0.024 2.00e-02 2.50e+03 4.90e-02 2.40e+01 pdb=" C ASP K 253 " 0.085 2.00e-02 2.50e+03 pdb=" O ASP K 253 " -0.032 2.00e-02 2.50e+03 pdb=" N VAL K 254 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU T 255 " -0.019 2.00e-02 2.50e+03 3.81e-02 1.45e+01 pdb=" CD GLU T 255 " 0.066 2.00e-02 2.50e+03 pdb=" OE1 GLU T 255 " -0.024 2.00e-02 2.50e+03 pdb=" OE2 GLU T 255 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU K 255 " 0.018 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" CD GLU K 255 " -0.065 2.00e-02 2.50e+03 pdb=" OE1 GLU K 255 " 0.024 2.00e-02 2.50e+03 pdb=" OE2 GLU K 255 " 0.023 2.00e-02 2.50e+03 ... (remaining 10504 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.59: 1062 2.59 - 3.23: 62873 3.23 - 3.86: 136416 3.86 - 4.50: 183616 4.50 - 5.14: 278515 Nonbonded interactions: 662482 Sorted by model distance: nonbonded pdb=" O ASN M 80 " pdb=" ND2 ASN M 80 " model vdw 1.948 2.520 nonbonded pdb=" O ASN E 80 " pdb=" ND2 ASN E 80 " model vdw 1.971 2.520 nonbonded pdb=" O ASN J 80 " pdb=" ND2 ASN J 80 " model vdw 1.972 2.520 nonbonded pdb=" O ASN P 80 " pdb=" ND2 ASN P 80 " model vdw 1.975 2.520 nonbonded pdb=" O ASN B 80 " pdb=" ND2 ASN B 80 " model vdw 2.029 2.520 ... (remaining 662477 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 524 or resid 601)) selection = (chain 'C' and (resid 2 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 524 or resid 601)) selection = (chain 'D' and (resid 2 through 524 or resid 601)) selection = (chain 'F' and (resid 2 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 524 or resid 601)) selection = (chain 'G' and (resid 2 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 524 or resid 601)) selection = (chain 'H' and (resid 2 through 524 or resid 601)) selection = (chain 'I' and (resid 2 through 524 or resid 601)) selection = (chain 'K' and (resid 2 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 524 or resid 601)) selection = (chain 'L' and (resid 2 through 524 or resid 601)) selection = (chain 'N' and (resid 2 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 524 or resid 601)) selection = (chain 'O' and (resid 2 through 524 or resid 601)) selection = (chain 'Q' and (resid 2 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 524 or resid 601)) selection = (chain 'R' and (resid 2 through 524 or resid 601)) selection = (chain 'T' and (resid 2 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 524 or resid 601)) } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'S' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 13.750 Check model and map are aligned: 0.670 Set scattering table: 0.430 Process input model: 128.880 Find NCS groups from input model: 3.810 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 163.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 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 : 0.004 0.104 59773 Z= 0.256 Angle : 0.727 16.777 80801 Z= 0.400 Chirality : 0.047 0.290 9807 Planarity : 0.005 0.088 10507 Dihedral : 15.947 89.449 22827 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.82 % Favored : 98.05 % Rotamer: Outliers : 0.81 % Allowed : 18.38 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.09), residues: 7959 helix: 1.49 (0.08), residues: 4193 sheet: 0.77 (0.16), residues: 1008 loop : -0.38 (0.11), residues: 2758 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 7 PHE 0.021 0.001 PHE I 219 TYR 0.016 0.002 TYR G 478 ARG 0.019 0.001 ARG R 362 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 700 time to evaluate : 5.092 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: I 69 MET cc_start: 0.8971 (mtp) cc_final: 0.8725 (mtp) REVERT: W 64 ILE cc_start: 0.9129 (mp) cc_final: 0.8922 (mm) REVERT: G 288 MET cc_start: 0.5371 (mpt) cc_final: 0.4444 (ptt) REVERT: C 288 MET cc_start: 0.6504 (mpt) cc_final: 0.5126 (ptt) REVERT: D 73 MET cc_start: 0.8914 (mtm) cc_final: 0.8665 (mtm) REVERT: E 21 SER cc_start: 0.8256 (t) cc_final: 0.7971 (p) REVERT: E 35 SER cc_start: 0.8753 (t) cc_final: 0.8546 (t) REVERT: J 20 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7843 (ttmm) REVERT: J 35 SER cc_start: 0.8811 (t) cc_final: 0.8490 (p) REVERT: J 74 LYS cc_start: 0.8516 (mptm) cc_final: 0.8276 (tttm) REVERT: J 77 LYS cc_start: 0.8695 (tppp) cc_final: 0.8270 (mmmm) REVERT: M 35 SER cc_start: 0.8714 (t) cc_final: 0.8380 (p) REVERT: M 76 GLU cc_start: 0.7547 (tp30) cc_final: 0.7161 (tp30) REVERT: N 288 MET cc_start: 0.4589 (mpt) cc_final: 0.3990 (ptt) REVERT: P 35 SER cc_start: 0.8800 (t) cc_final: 0.8447 (p) REVERT: Q 491 MET cc_start: 0.9430 (mtm) cc_final: 0.9213 (mtp) REVERT: S 76 GLU cc_start: 0.7817 (tp30) cc_final: 0.7581 (tp30) outliers start: 50 outliers final: 14 residues processed: 728 average time/residue: 1.4471 time to fit residues: 1377.7211 Evaluate side-chains 665 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 650 time to evaluate : 5.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 52 ASP Chi-restraints excluded: chain G residue 43 SER Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain H residue 184 GLN Chi-restraints excluded: chain H residue 307 MET Chi-restraints excluded: chain J residue 20 LYS Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 80 ASN Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain Q residue 138 CYS Chi-restraints excluded: chain R residue 184 GLN Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 299 THR Chi-restraints excluded: chain S residue 64 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 667 optimal weight: 6.9990 chunk 599 optimal weight: 8.9990 chunk 332 optimal weight: 0.6980 chunk 204 optimal weight: 30.0000 chunk 404 optimal weight: 5.9990 chunk 320 optimal weight: 9.9990 chunk 619 optimal weight: 0.3980 chunk 239 optimal weight: 0.0060 chunk 376 optimal weight: 5.9990 chunk 461 optimal weight: 2.9990 chunk 718 optimal weight: 3.9990 overall best weight: 1.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 112 ASN I 319 GLN I 366 GLN W 45 ASN ** W 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 GLN B 45 ASN B 80 ASN C 37 ASN D 82 ASN E 45 ASN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 319 GLN J 45 ASN M 45 ASN N 37 ASN O 112 ASN O 194 GLN O 366 GLN R 319 GLN S 45 ASN T 37 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.0725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 59773 Z= 0.261 Angle : 0.545 7.230 80801 Z= 0.295 Chirality : 0.044 0.190 9807 Planarity : 0.004 0.050 10507 Dihedral : 9.083 88.569 8942 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.01 % Favored : 98.98 % Rotamer: Outliers : 2.67 % Allowed : 15.18 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.09), residues: 7959 helix: 1.73 (0.08), residues: 4200 sheet: 0.83 (0.16), residues: 1008 loop : -0.45 (0.10), residues: 2751 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 7 PHE 0.011 0.001 PHE K 219 TYR 0.015 0.001 TYR G 478 ARG 0.023 0.001 ARG M 4 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 681 time to evaluate : 5.143 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: G 200 LEU cc_start: 0.2385 (OUTLIER) cc_final: 0.1989 (pt) REVERT: G 267 MET cc_start: 0.3125 (OUTLIER) cc_final: 0.2870 (ppp) REVERT: G 288 MET cc_start: 0.5346 (OUTLIER) cc_final: 0.4577 (ptt) REVERT: B 35 SER cc_start: 0.8556 (t) cc_final: 0.8295 (p) REVERT: C 200 LEU cc_start: 0.3369 (OUTLIER) cc_final: 0.2789 (pt) REVERT: C 288 MET cc_start: 0.6592 (OUTLIER) cc_final: 0.5357 (ptt) REVERT: D 73 MET cc_start: 0.8957 (mtm) cc_final: 0.8701 (mtm) REVERT: D 321 LYS cc_start: 0.8486 (mppt) cc_final: 0.8185 (mppt) REVERT: E 35 SER cc_start: 0.8772 (t) cc_final: 0.8570 (t) REVERT: F 193 MET cc_start: 0.5272 (OUTLIER) cc_final: 0.4740 (tmt) REVERT: F 267 MET cc_start: 0.2773 (OUTLIER) cc_final: 0.2400 (ppp) REVERT: F 288 MET cc_start: 0.4390 (ptt) cc_final: 0.4122 (mpm) REVERT: F 307 MET cc_start: 0.4803 (mmm) cc_final: 0.4393 (tpt) REVERT: H 233 MET cc_start: 0.7292 (OUTLIER) cc_final: 0.6984 (ttp) REVERT: H 362 ARG cc_start: 0.7609 (ptp90) cc_final: 0.7280 (ttm110) REVERT: J 35 SER cc_start: 0.8859 (t) cc_final: 0.8495 (p) REVERT: J 74 LYS cc_start: 0.8479 (mptm) cc_final: 0.8261 (tttm) REVERT: J 80 ASN cc_start: 0.7619 (OUTLIER) cc_final: 0.7391 (t0) REVERT: L 184 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8014 (mp10) REVERT: L 322 ARG cc_start: 0.8044 (mmm-85) cc_final: 0.7655 (ttp80) REVERT: L 325 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8380 (mm) REVERT: L 362 ARG cc_start: 0.7560 (ptp90) cc_final: 0.7353 (ttp-110) REVERT: M 35 SER cc_start: 0.8718 (t) cc_final: 0.8376 (p) REVERT: N 200 LEU cc_start: 0.2330 (OUTLIER) cc_final: 0.2059 (pt) REVERT: N 288 MET cc_start: 0.4590 (OUTLIER) cc_final: 0.4053 (ptt) REVERT: N 404 ARG cc_start: 0.7914 (mtt-85) cc_final: 0.7575 (mmm160) REVERT: O 160 LYS cc_start: 0.8738 (tmmt) cc_final: 0.8379 (mptp) REVERT: O 184 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8030 (mp10) REVERT: O 220 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8302 (mm) REVERT: P 35 SER cc_start: 0.8819 (t) cc_final: 0.8459 (p) REVERT: P 74 LYS cc_start: 0.8499 (tmtt) cc_final: 0.8205 (tmtt) REVERT: Q 267 MET cc_start: 0.2074 (OUTLIER) cc_final: 0.1611 (ppp) REVERT: Q 491 MET cc_start: 0.9441 (mtm) cc_final: 0.9213 (mtp) REVERT: T 200 LEU cc_start: 0.2368 (OUTLIER) cc_final: 0.1976 (pt) REVERT: T 288 MET cc_start: 0.4903 (OUTLIER) cc_final: 0.4532 (ptt) outliers start: 165 outliers final: 43 residues processed: 767 average time/residue: 1.4878 time to fit residues: 1487.6092 Evaluate side-chains 718 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 657 time to evaluate : 5.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 299 THR Chi-restraints excluded: chain I residue 343 GLN Chi-restraints excluded: chain W residue 21 SER Chi-restraints excluded: chain W residue 87 SER Chi-restraints excluded: chain G residue 200 LEU Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 288 MET Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 184 GLN Chi-restraints excluded: chain H residue 233 MET Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 80 ASN Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain L residue 184 GLN Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 294 THR Chi-restraints excluded: chain L residue 299 THR Chi-restraints excluded: chain L residue 307 MET Chi-restraints excluded: chain L residue 325 ILE Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 288 MET Chi-restraints excluded: chain O residue 176 THR Chi-restraints excluded: chain O residue 184 GLN Chi-restraints excluded: chain O residue 220 ILE Chi-restraints excluded: chain O residue 234 LEU Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain Q residue 138 CYS Chi-restraints excluded: chain Q residue 267 MET Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain R residue 184 GLN Chi-restraints excluded: chain R residue 233 MET Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain R residue 294 THR Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 87 SER Chi-restraints excluded: chain T residue 200 LEU Chi-restraints excluded: chain T residue 288 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 399 optimal weight: 5.9990 chunk 222 optimal weight: 1.9990 chunk 597 optimal weight: 6.9990 chunk 489 optimal weight: 9.9990 chunk 198 optimal weight: 30.0000 chunk 719 optimal weight: 4.9990 chunk 777 optimal weight: 0.9990 chunk 640 optimal weight: 0.5980 chunk 713 optimal weight: 8.9990 chunk 245 optimal weight: 0.0270 chunk 577 optimal weight: 1.9990 overall best weight: 1.1244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 366 GLN W 45 ASN W 80 ASN A 352 GLN B 45 ASN E 45 ASN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 319 GLN J 45 ASN M 45 ASN N 37 ASN O 319 GLN R 319 GLN S 45 ASN T 37 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 59773 Z= 0.204 Angle : 0.495 6.738 80801 Z= 0.268 Chirality : 0.042 0.195 9807 Planarity : 0.003 0.049 10507 Dihedral : 8.703 89.920 8924 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.60 % Allowed : 15.86 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.09), residues: 7959 helix: 1.86 (0.08), residues: 4207 sheet: 0.81 (0.15), residues: 1099 loop : -0.49 (0.11), residues: 2653 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS I 401 PHE 0.010 0.001 PHE I 219 TYR 0.012 0.001 TYR T 478 ARG 0.007 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 680 time to evaluate : 5.053 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: G 200 LEU cc_start: 0.2316 (OUTLIER) cc_final: 0.1960 (pt) REVERT: G 288 MET cc_start: 0.5336 (OUTLIER) cc_final: 0.4571 (ptt) REVERT: A 111 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.7952 (mtp) REVERT: B 35 SER cc_start: 0.8537 (t) cc_final: 0.8291 (p) REVERT: C 193 MET cc_start: 0.5505 (OUTLIER) cc_final: 0.4598 (tmt) REVERT: C 200 LEU cc_start: 0.3350 (OUTLIER) cc_final: 0.2792 (pt) REVERT: C 267 MET cc_start: 0.2657 (OUTLIER) cc_final: 0.2093 (ppp) REVERT: C 288 MET cc_start: 0.6628 (OUTLIER) cc_final: 0.5390 (ptt) REVERT: D 284 ARG cc_start: 0.7179 (mtp-110) cc_final: 0.6860 (mtp85) REVERT: D 321 LYS cc_start: 0.8443 (mppt) cc_final: 0.8068 (mppt) REVERT: E 35 SER cc_start: 0.8768 (t) cc_final: 0.8245 (p) REVERT: F 267 MET cc_start: 0.2624 (OUTLIER) cc_final: 0.2205 (ppp) REVERT: F 307 MET cc_start: 0.4793 (mmm) cc_final: 0.4371 (tpt) REVERT: H 233 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.7087 (ttm) REVERT: H 267 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8353 (mtt) REVERT: H 307 MET cc_start: 0.7471 (OUTLIER) cc_final: 0.7058 (ptm) REVERT: J 35 SER cc_start: 0.8857 (t) cc_final: 0.8494 (p) REVERT: J 80 ASN cc_start: 0.7606 (OUTLIER) cc_final: 0.7386 (t0) REVERT: K 267 MET cc_start: 0.1815 (OUTLIER) cc_final: 0.1288 (ppp) REVERT: K 404 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7549 (mpt90) REVERT: L 184 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.7970 (mp10) REVERT: L 322 ARG cc_start: 0.8037 (mmm-85) cc_final: 0.7745 (ttp80) REVERT: L 325 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8380 (mm) REVERT: M 35 SER cc_start: 0.8699 (t) cc_final: 0.8368 (p) REVERT: N 193 MET cc_start: 0.4832 (OUTLIER) cc_final: 0.4209 (tmt) REVERT: N 200 LEU cc_start: 0.2272 (OUTLIER) cc_final: 0.1991 (pt) REVERT: N 288 MET cc_start: 0.4639 (OUTLIER) cc_final: 0.4079 (ptt) REVERT: N 404 ARG cc_start: 0.7879 (mtt-85) cc_final: 0.7549 (mmm160) REVERT: O 160 LYS cc_start: 0.8747 (tmmt) cc_final: 0.8416 (mptp) REVERT: O 184 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8042 (mp10) REVERT: O 322 ARG cc_start: 0.8156 (mmm-85) cc_final: 0.7731 (ttp80) REVERT: P 35 SER cc_start: 0.8817 (t) cc_final: 0.8471 (p) REVERT: P 74 LYS cc_start: 0.8530 (tmtt) cc_final: 0.8178 (tmtt) REVERT: Q 227 ILE cc_start: -0.2478 (OUTLIER) cc_final: -0.3438 (tt) REVERT: Q 267 MET cc_start: 0.1794 (OUTLIER) cc_final: 0.1281 (ppp) REVERT: Q 491 MET cc_start: 0.9414 (mtm) cc_final: 0.9190 (mtp) REVERT: T 200 LEU cc_start: 0.2228 (OUTLIER) cc_final: 0.1840 (pt) REVERT: T 267 MET cc_start: 0.1957 (OUTLIER) cc_final: 0.1519 (ppp) REVERT: T 288 MET cc_start: 0.4983 (OUTLIER) cc_final: 0.4629 (ptt) outliers start: 161 outliers final: 46 residues processed: 761 average time/residue: 1.4532 time to fit residues: 1442.9759 Evaluate side-chains 728 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 657 time to evaluate : 5.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 343 GLN Chi-restraints excluded: chain G residue 132 LYS Chi-restraints excluded: chain G residue 200 LEU Chi-restraints excluded: chain G residue 288 MET Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 74 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 184 GLN Chi-restraints excluded: chain H residue 233 MET Chi-restraints excluded: chain H residue 267 MET Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain H residue 307 MET Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 80 ASN Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 267 MET Chi-restraints excluded: chain K residue 404 ARG Chi-restraints excluded: chain L residue 184 GLN Chi-restraints excluded: chain L residue 188 ASP Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 294 THR Chi-restraints excluded: chain L residue 325 ILE Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 219 PHE Chi-restraints excluded: chain N residue 288 MET Chi-restraints excluded: chain O residue 176 THR Chi-restraints excluded: chain O residue 184 GLN Chi-restraints excluded: chain O residue 234 LEU Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 27 LEU Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain Q residue 138 CYS Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 227 ILE Chi-restraints excluded: chain Q residue 267 MET Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain R residue 184 GLN Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain R residue 294 THR Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 87 SER Chi-restraints excluded: chain T residue 200 LEU Chi-restraints excluded: chain T residue 245 LYS Chi-restraints excluded: chain T residue 267 MET Chi-restraints excluded: chain T residue 288 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 710 optimal weight: 5.9990 chunk 541 optimal weight: 7.9990 chunk 373 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 343 optimal weight: 1.9990 chunk 483 optimal weight: 5.9990 chunk 722 optimal weight: 0.9990 chunk 764 optimal weight: 40.0000 chunk 377 optimal weight: 6.9990 chunk 684 optimal weight: 2.9990 chunk 206 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 319 GLN I 343 GLN I 366 GLN W 45 ASN G 37 ASN A 82 ASN A 352 GLN B 7 HIS B 45 ASN D 112 ASN E 2 ASN E 45 ASN F 37 ASN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 319 GLN J 45 ASN K 37 ASN L 194 GLN M 45 ASN N 37 ASN O 366 GLN P 2 ASN Q 37 ASN R 194 GLN R 319 GLN R 348 GLN S 45 ASN T 37 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 59773 Z= 0.375 Angle : 0.565 7.477 80801 Z= 0.303 Chirality : 0.046 0.260 9807 Planarity : 0.004 0.055 10507 Dihedral : 9.217 88.715 8924 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.15 % Allowed : 15.61 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.09), residues: 7959 helix: 1.50 (0.08), residues: 4221 sheet: 0.63 (0.14), residues: 1078 loop : -0.59 (0.10), residues: 2660 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 401 PHE 0.018 0.001 PHE G 219 TYR 0.015 0.002 TYR T 478 ARG 0.009 0.001 ARG L 284 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 680 time to evaluate : 5.116 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: G 200 LEU cc_start: 0.2302 (OUTLIER) cc_final: 0.1929 (pt) REVERT: G 267 MET cc_start: 0.3304 (OUTLIER) cc_final: 0.3060 (ppp) REVERT: G 288 MET cc_start: 0.5355 (OUTLIER) cc_final: 0.4461 (ptt) REVERT: G 307 MET cc_start: 0.2617 (OUTLIER) cc_final: 0.2106 (mmm) REVERT: G 404 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7499 (mpt90) REVERT: B 21 SER cc_start: 0.8196 (t) cc_final: 0.7985 (m) REVERT: C 193 MET cc_start: 0.5520 (OUTLIER) cc_final: 0.4601 (tmt) REVERT: C 200 LEU cc_start: 0.3176 (OUTLIER) cc_final: 0.2668 (pt) REVERT: C 267 MET cc_start: 0.2665 (OUTLIER) cc_final: 0.2121 (ppp) REVERT: C 288 MET cc_start: 0.6531 (OUTLIER) cc_final: 0.5276 (ptt) REVERT: D 63 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7169 (tm-30) REVERT: D 366 GLN cc_start: 0.8186 (mm-40) cc_final: 0.7809 (tp40) REVERT: E 35 SER cc_start: 0.8833 (t) cc_final: 0.8631 (t) REVERT: F 193 MET cc_start: 0.5379 (OUTLIER) cc_final: 0.4771 (tmt) REVERT: F 267 MET cc_start: 0.2513 (OUTLIER) cc_final: 0.1967 (ppp) REVERT: F 307 MET cc_start: 0.4789 (mmm) cc_final: 0.4358 (tpt) REVERT: H 63 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7199 (tm-30) REVERT: H 233 MET cc_start: 0.7418 (OUTLIER) cc_final: 0.7164 (ttm) REVERT: H 267 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8361 (mtt) REVERT: J 80 ASN cc_start: 0.7610 (OUTLIER) cc_final: 0.7406 (t0) REVERT: K 267 MET cc_start: 0.1618 (OUTLIER) cc_final: 0.0713 (pmt) REVERT: K 404 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7588 (mpt90) REVERT: L 325 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8577 (mm) REVERT: M 35 SER cc_start: 0.8773 (t) cc_final: 0.8350 (p) REVERT: N 193 MET cc_start: 0.4815 (OUTLIER) cc_final: 0.4136 (tmt) REVERT: N 200 LEU cc_start: 0.2331 (OUTLIER) cc_final: 0.2022 (pt) REVERT: N 288 MET cc_start: 0.4658 (OUTLIER) cc_final: 0.4076 (ptt) REVERT: O 63 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7299 (tm-30) REVERT: O 184 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.7942 (mp10) REVERT: O 220 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8433 (mm) REVERT: O 322 ARG cc_start: 0.8161 (mmm-85) cc_final: 0.7857 (ttp80) REVERT: P 35 SER cc_start: 0.8858 (t) cc_final: 0.8451 (p) REVERT: P 74 LYS cc_start: 0.8566 (tmtt) cc_final: 0.8210 (tmtt) REVERT: Q 227 ILE cc_start: -0.2697 (OUTLIER) cc_final: -0.3329 (tt) REVERT: Q 267 MET cc_start: 0.1796 (OUTLIER) cc_final: 0.1208 (ppp) REVERT: Q 491 MET cc_start: 0.9422 (mtm) cc_final: 0.9174 (mtp) REVERT: R 63 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7241 (tm-30) REVERT: R 491 MET cc_start: 0.9270 (mtm) cc_final: 0.9030 (mtp) REVERT: T 200 LEU cc_start: 0.2310 (OUTLIER) cc_final: 0.1897 (pt) REVERT: T 267 MET cc_start: 0.1572 (OUTLIER) cc_final: 0.1001 (ppp) REVERT: T 288 MET cc_start: 0.5020 (OUTLIER) cc_final: 0.4566 (ptt) outliers start: 195 outliers final: 68 residues processed: 782 average time/residue: 1.5319 time to fit residues: 1547.2076 Evaluate side-chains 761 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 662 time to evaluate : 5.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 299 THR Chi-restraints excluded: chain W residue 21 SER Chi-restraints excluded: chain W residue 87 SER Chi-restraints excluded: chain G residue 200 LEU Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 288 MET Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 404 ARG Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 233 MET Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 74 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 184 GLN Chi-restraints excluded: chain H residue 233 MET Chi-restraints excluded: chain H residue 234 LEU Chi-restraints excluded: chain H residue 267 MET Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain J residue 80 ASN Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain K residue 132 LYS Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 267 MET Chi-restraints excluded: chain K residue 404 ARG Chi-restraints excluded: chain L residue 14 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 188 ASP Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 294 THR Chi-restraints excluded: chain L residue 299 THR Chi-restraints excluded: chain L residue 325 ILE Chi-restraints excluded: chain L residue 483 GLU Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 288 MET Chi-restraints excluded: chain O residue 14 VAL Chi-restraints excluded: chain O residue 63 GLU Chi-restraints excluded: chain O residue 176 THR Chi-restraints excluded: chain O residue 184 GLN Chi-restraints excluded: chain O residue 220 ILE Chi-restraints excluded: chain O residue 234 LEU Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 27 LEU Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain Q residue 138 CYS Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 227 ILE Chi-restraints excluded: chain Q residue 267 MET Chi-restraints excluded: chain R residue 63 GLU Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain R residue 184 GLN Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 294 THR Chi-restraints excluded: chain R residue 307 MET Chi-restraints excluded: chain S residue 87 SER Chi-restraints excluded: chain T residue 200 LEU Chi-restraints excluded: chain T residue 245 LYS Chi-restraints excluded: chain T residue 267 MET Chi-restraints excluded: chain T residue 288 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 636 optimal weight: 0.8980 chunk 434 optimal weight: 40.0000 chunk 11 optimal weight: 0.1980 chunk 569 optimal weight: 0.4980 chunk 315 optimal weight: 3.9990 chunk 652 optimal weight: 50.0000 chunk 528 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 390 optimal weight: 0.6980 chunk 686 optimal weight: 1.9990 chunk 192 optimal weight: 0.0970 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 366 GLN W 45 ASN G 37 ASN A 352 GLN A 432 GLN B 45 ASN E 45 ASN F 37 ASN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 ASN H 319 GLN J 45 ASN K 37 ASN L 194 GLN M 45 ASN N 37 ASN Q 37 ASN S 45 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 59773 Z= 0.153 Angle : 0.469 7.524 80801 Z= 0.254 Chirality : 0.041 0.206 9807 Planarity : 0.003 0.053 10507 Dihedral : 8.092 89.761 8922 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.99 % Allowed : 17.15 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.09), residues: 7959 helix: 1.90 (0.08), residues: 4179 sheet: 0.66 (0.15), residues: 1092 loop : -0.48 (0.11), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS M 7 PHE 0.020 0.001 PHE G 219 TYR 0.012 0.001 TYR R 199 ARG 0.010 0.000 ARG L 284 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 688 time to evaluate : 5.672 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: G 200 LEU cc_start: 0.2372 (OUTLIER) cc_final: 0.1970 (pt) REVERT: G 267 MET cc_start: 0.3326 (OUTLIER) cc_final: 0.3072 (ppp) REVERT: G 288 MET cc_start: 0.5363 (OUTLIER) cc_final: 0.4480 (ptt) REVERT: G 307 MET cc_start: 0.2467 (OUTLIER) cc_final: 0.1712 (mmt) REVERT: G 404 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7443 (mpt90) REVERT: B 15 LYS cc_start: 0.7562 (OUTLIER) cc_final: 0.7263 (mttm) REVERT: B 35 SER cc_start: 0.8574 (t) cc_final: 0.8304 (p) REVERT: C 200 LEU cc_start: 0.3109 (OUTLIER) cc_final: 0.2622 (pt) REVERT: C 267 MET cc_start: 0.2552 (OUTLIER) cc_final: 0.1876 (ppp) REVERT: C 288 MET cc_start: 0.6610 (OUTLIER) cc_final: 0.5389 (ptt) REVERT: C 365 LEU cc_start: 0.6679 (OUTLIER) cc_final: 0.6400 (pp) REVERT: D 63 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7087 (tm-30) REVERT: D 321 LYS cc_start: 0.8568 (mppt) cc_final: 0.8187 (mppt) REVERT: D 366 GLN cc_start: 0.8129 (mm-40) cc_final: 0.7786 (tp40) REVERT: E 35 SER cc_start: 0.8852 (t) cc_final: 0.8274 (p) REVERT: F 193 MET cc_start: 0.5261 (OUTLIER) cc_final: 0.4673 (tmt) REVERT: F 267 MET cc_start: 0.2305 (OUTLIER) cc_final: 0.1742 (ppp) REVERT: F 307 MET cc_start: 0.4761 (mmm) cc_final: 0.4338 (tpt) REVERT: H 63 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7061 (tm-30) REVERT: H 184 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8453 (mp10) REVERT: H 267 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8348 (mtt) REVERT: J 80 ASN cc_start: 0.7577 (OUTLIER) cc_final: 0.7370 (t0) REVERT: K 267 MET cc_start: 0.1596 (pmm) cc_final: 0.1311 (pmt) REVERT: K 404 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7580 (mpt90) REVERT: L 325 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8320 (mm) REVERT: M 35 SER cc_start: 0.8719 (t) cc_final: 0.8343 (p) REVERT: N 193 MET cc_start: 0.4790 (OUTLIER) cc_final: 0.4176 (tmt) REVERT: N 200 LEU cc_start: 0.1984 (OUTLIER) cc_final: 0.1710 (pt) REVERT: N 288 MET cc_start: 0.4577 (OUTLIER) cc_final: 0.4049 (ptt) REVERT: O 160 LYS cc_start: 0.8627 (ttpp) cc_final: 0.8408 (mptp) REVERT: O 184 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.7935 (mp10) REVERT: O 267 MET cc_start: 0.8522 (mtt) cc_final: 0.7814 (mtt) REVERT: P 35 SER cc_start: 0.8796 (t) cc_final: 0.8440 (p) REVERT: P 74 LYS cc_start: 0.8536 (tmtt) cc_final: 0.8206 (tmtt) REVERT: Q 227 ILE cc_start: -0.2848 (OUTLIER) cc_final: -0.3396 (mp) REVERT: Q 267 MET cc_start: 0.1883 (OUTLIER) cc_final: 0.1301 (ppp) REVERT: Q 288 MET cc_start: 0.5174 (mmt) cc_final: 0.4530 (ptt) REVERT: Q 491 MET cc_start: 0.9380 (mtm) cc_final: 0.9176 (mtp) REVERT: R 171 LYS cc_start: 0.6870 (mmmt) cc_final: 0.6583 (mmmt) REVERT: R 491 MET cc_start: 0.9244 (mtm) cc_final: 0.8970 (mtt) REVERT: S 74 LYS cc_start: 0.8368 (tmtt) cc_final: 0.7930 (tmtt) REVERT: T 200 LEU cc_start: 0.2291 (OUTLIER) cc_final: 0.1913 (pt) REVERT: T 288 MET cc_start: 0.5261 (OUTLIER) cc_final: 0.4785 (ptt) outliers start: 123 outliers final: 28 residues processed: 757 average time/residue: 1.5164 time to fit residues: 1487.1505 Evaluate side-chains 707 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 652 time to evaluate : 5.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain W residue 21 SER Chi-restraints excluded: chain W residue 87 SER Chi-restraints excluded: chain G residue 200 LEU Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 288 MET Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 404 ARG Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain E residue 74 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 184 GLN Chi-restraints excluded: chain H residue 267 MET Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 319 GLN Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 80 ASN Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 404 ARG Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 325 ILE Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 288 MET Chi-restraints excluded: chain O residue 184 GLN Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain Q residue 138 CYS Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 227 ILE Chi-restraints excluded: chain Q residue 267 MET Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain R residue 307 MET Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain T residue 200 LEU Chi-restraints excluded: chain T residue 245 LYS Chi-restraints excluded: chain T residue 288 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 257 optimal weight: 7.9990 chunk 688 optimal weight: 0.5980 chunk 151 optimal weight: 0.0060 chunk 448 optimal weight: 2.9990 chunk 188 optimal weight: 0.0040 chunk 765 optimal weight: 4.9990 chunk 635 optimal weight: 3.9990 chunk 354 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 253 optimal weight: 6.9990 chunk 401 optimal weight: 0.6980 overall best weight: 0.8610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 366 GLN W 45 ASN G 82 ASN G 229 ASN ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 ASN F 37 ASN F 82 ASN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 319 GLN J 45 ASN N 37 ASN Q 37 ASN S 45 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 59773 Z= 0.182 Angle : 0.482 11.289 80801 Z= 0.257 Chirality : 0.042 0.209 9807 Planarity : 0.003 0.053 10507 Dihedral : 8.147 89.916 8919 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.01 % Allowed : 17.52 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.09), residues: 7959 helix: 1.98 (0.08), residues: 4172 sheet: 0.58 (0.15), residues: 1106 loop : -0.45 (0.11), residues: 2681 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 401 PHE 0.016 0.001 PHE G 219 TYR 0.010 0.001 TYR T 478 ARG 0.010 0.000 ARG I 362 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 668 time to evaluate : 5.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 254 VAL cc_start: 0.2797 (OUTLIER) cc_final: 0.2550 (m) REVERT: G 267 MET cc_start: 0.3353 (OUTLIER) cc_final: 0.3068 (ppp) REVERT: G 288 MET cc_start: 0.5364 (OUTLIER) cc_final: 0.4508 (ptt) REVERT: G 307 MET cc_start: 0.2518 (OUTLIER) cc_final: 0.2067 (mmm) REVERT: G 404 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7455 (mpt90) REVERT: B 15 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7380 (mttm) REVERT: B 35 SER cc_start: 0.8598 (t) cc_final: 0.8265 (p) REVERT: C 193 MET cc_start: 0.5346 (OUTLIER) cc_final: 0.4439 (tmt) REVERT: C 200 LEU cc_start: 0.3097 (OUTLIER) cc_final: 0.2594 (pt) REVERT: C 262 LEU cc_start: -0.2341 (OUTLIER) cc_final: -0.2930 (pp) REVERT: C 267 MET cc_start: 0.2339 (OUTLIER) cc_final: 0.1762 (ppp) REVERT: C 288 MET cc_start: 0.6615 (OUTLIER) cc_final: 0.5394 (ptt) REVERT: C 365 LEU cc_start: 0.6674 (OUTLIER) cc_final: 0.6412 (pp) REVERT: D 63 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7087 (tm-30) REVERT: D 321 LYS cc_start: 0.8540 (mppt) cc_final: 0.8145 (mppt) REVERT: D 366 GLN cc_start: 0.8058 (mm-40) cc_final: 0.7739 (tp40) REVERT: E 35 SER cc_start: 0.8832 (t) cc_final: 0.8258 (p) REVERT: F 193 MET cc_start: 0.5361 (OUTLIER) cc_final: 0.4737 (tmt) REVERT: F 267 MET cc_start: 0.2300 (OUTLIER) cc_final: 0.1746 (ppp) REVERT: F 288 MET cc_start: 0.4480 (ptt) cc_final: 0.4167 (mpt) REVERT: F 307 MET cc_start: 0.4752 (mmm) cc_final: 0.4322 (tpt) REVERT: H 63 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7070 (tm-30) REVERT: H 184 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8444 (mp10) REVERT: H 322 ARG cc_start: 0.8158 (mmm-85) cc_final: 0.7852 (ttp80) REVERT: H 483 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.6813 (mm-30) REVERT: J 80 ASN cc_start: 0.7652 (OUTLIER) cc_final: 0.7436 (t0) REVERT: K 267 MET cc_start: 0.1444 (OUTLIER) cc_final: 0.1177 (pmt) REVERT: K 404 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7522 (mpt90) REVERT: L 184 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8038 (mp10) REVERT: L 194 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.6407 (tm-30) REVERT: L 483 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.7705 (mt-10) REVERT: M 35 SER cc_start: 0.8711 (t) cc_final: 0.8340 (p) REVERT: N 288 MET cc_start: 0.4620 (OUTLIER) cc_final: 0.4142 (ptt) REVERT: O 160 LYS cc_start: 0.8628 (ttpp) cc_final: 0.8407 (mptp) REVERT: O 184 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.7974 (mp10) REVERT: O 194 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7185 (tm-30) REVERT: O 220 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8245 (mm) REVERT: P 35 SER cc_start: 0.8784 (t) cc_final: 0.8433 (p) REVERT: P 74 LYS cc_start: 0.8527 (tmtt) cc_final: 0.8190 (tmtt) REVERT: P 91 ILE cc_start: 0.9156 (mt) cc_final: 0.8896 (mt) REVERT: Q 227 ILE cc_start: -0.2966 (OUTLIER) cc_final: -0.3500 (mp) REVERT: Q 267 MET cc_start: 0.1850 (OUTLIER) cc_final: 0.1247 (ppp) REVERT: Q 288 MET cc_start: 0.5058 (mmt) cc_final: 0.4599 (ptt) REVERT: Q 491 MET cc_start: 0.9381 (mtm) cc_final: 0.9179 (mtp) REVERT: R 171 LYS cc_start: 0.6798 (mmmt) cc_final: 0.6449 (mmmt) REVERT: R 194 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.6436 (tm-30) REVERT: R 491 MET cc_start: 0.9223 (mtm) cc_final: 0.8960 (mtt) REVERT: T 200 LEU cc_start: 0.2306 (OUTLIER) cc_final: 0.1927 (pt) REVERT: T 267 MET cc_start: 0.1627 (OUTLIER) cc_final: 0.1389 (pmt) REVERT: T 288 MET cc_start: 0.5209 (OUTLIER) cc_final: 0.4772 (ptt) outliers start: 124 outliers final: 39 residues processed: 738 average time/residue: 1.5334 time to fit residues: 1462.2928 Evaluate side-chains 724 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 651 time to evaluate : 5.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain W residue 21 SER Chi-restraints excluded: chain W residue 87 SER Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 288 MET Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 404 ARG Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 184 GLN Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 483 GLU Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 80 ASN Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 267 MET Chi-restraints excluded: chain K residue 404 ARG Chi-restraints excluded: chain L residue 14 VAL Chi-restraints excluded: chain L residue 184 GLN Chi-restraints excluded: chain L residue 194 GLN Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 307 MET Chi-restraints excluded: chain L residue 483 GLU Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain N residue 288 MET Chi-restraints excluded: chain O residue 184 GLN Chi-restraints excluded: chain O residue 194 GLN Chi-restraints excluded: chain O residue 220 ILE Chi-restraints excluded: chain O residue 273 VAL Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain Q residue 138 CYS Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 227 ILE Chi-restraints excluded: chain Q residue 267 MET Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain R residue 184 GLN Chi-restraints excluded: chain R residue 194 GLN Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain R residue 307 MET Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain T residue 200 LEU Chi-restraints excluded: chain T residue 245 LYS Chi-restraints excluded: chain T residue 267 MET Chi-restraints excluded: chain T residue 288 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 737 optimal weight: 0.0270 chunk 86 optimal weight: 40.0000 chunk 436 optimal weight: 7.9990 chunk 558 optimal weight: 1.9990 chunk 433 optimal weight: 40.0000 chunk 644 optimal weight: 8.9990 chunk 427 optimal weight: 30.0000 chunk 762 optimal weight: 8.9990 chunk 477 optimal weight: 8.9990 chunk 464 optimal weight: 3.9990 chunk 351 optimal weight: 4.9990 overall best weight: 3.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 194 GLN I 366 GLN W 45 ASN G 37 ASN B 2 ASN B 7 HIS B 45 ASN E 7 HIS ** H 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 ASN K 37 ASN L 112 ASN L 194 GLN L 319 GLN P 7 HIS R 112 ASN R 194 GLN R 348 GLN S 45 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 59773 Z= 0.484 Angle : 0.615 11.092 80801 Z= 0.326 Chirality : 0.049 0.323 9807 Planarity : 0.005 0.076 10507 Dihedral : 9.440 89.850 8919 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.39 % Allowed : 17.49 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.09), residues: 7959 helix: 1.37 (0.08), residues: 4214 sheet: 0.45 (0.14), residues: 1078 loop : -0.59 (0.11), residues: 2667 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS I 401 PHE 0.016 0.001 PHE G 204 TYR 0.015 0.002 TYR T 478 ARG 0.010 0.001 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 693 time to evaluate : 5.134 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: G 254 VAL cc_start: 0.3009 (OUTLIER) cc_final: 0.2650 (m) REVERT: G 267 MET cc_start: 0.3345 (OUTLIER) cc_final: 0.3095 (ppp) REVERT: G 307 MET cc_start: 0.2652 (OUTLIER) cc_final: 0.1860 (mmt) REVERT: G 404 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7555 (mpt90) REVERT: A 491 MET cc_start: 0.9409 (mtm) cc_final: 0.9061 (mtp) REVERT: B 15 LYS cc_start: 0.7848 (mmtp) cc_final: 0.7584 (mttm) REVERT: C 193 MET cc_start: 0.5400 (OUTLIER) cc_final: 0.4475 (tmt) REVERT: C 200 LEU cc_start: 0.3158 (OUTLIER) cc_final: 0.2649 (pt) REVERT: C 262 LEU cc_start: -0.2292 (OUTLIER) cc_final: -0.2716 (pp) REVERT: C 267 MET cc_start: 0.2216 (OUTLIER) cc_final: 0.1613 (ppp) REVERT: C 288 MET cc_start: 0.6526 (OUTLIER) cc_final: 0.5254 (ptt) REVERT: C 365 LEU cc_start: 0.6684 (OUTLIER) cc_final: 0.6402 (pp) REVERT: D 63 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7189 (tm-30) REVERT: E 35 SER cc_start: 0.8893 (t) cc_final: 0.8689 (t) REVERT: F 193 MET cc_start: 0.5238 (OUTLIER) cc_final: 0.4633 (tmt) REVERT: F 267 MET cc_start: 0.2321 (OUTLIER) cc_final: 0.1782 (ppp) REVERT: F 307 MET cc_start: 0.4874 (mmm) cc_final: 0.4397 (tpt) REVERT: H 63 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7288 (tm-30) REVERT: H 322 ARG cc_start: 0.8185 (mmm-85) cc_final: 0.7927 (ttp80) REVERT: H 362 ARG cc_start: 0.7733 (ptp-110) cc_final: 0.7461 (ttp-110) REVERT: H 483 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.6995 (mm-30) REVERT: J 80 ASN cc_start: 0.7705 (OUTLIER) cc_final: 0.7483 (t0) REVERT: J 85 ILE cc_start: 0.8706 (mm) cc_final: 0.8478 (mm) REVERT: K 267 MET cc_start: 0.1428 (OUTLIER) cc_final: 0.1062 (pmt) REVERT: K 404 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7644 (mpt90) REVERT: L 63 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7330 (tm-30) REVERT: N 200 LEU cc_start: 0.2124 (OUTLIER) cc_final: 0.1450 (pt) REVERT: N 288 MET cc_start: 0.4618 (OUTLIER) cc_final: 0.4043 (ptt) REVERT: O 18 ARG cc_start: 0.8476 (ttm110) cc_final: 0.8274 (ttm110) REVERT: O 52 ASP cc_start: 0.8499 (OUTLIER) cc_final: 0.8290 (t70) REVERT: O 63 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7443 (tm-30) REVERT: O 184 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.7906 (mp10) REVERT: O 220 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8546 (mm) REVERT: P 35 SER cc_start: 0.8867 (t) cc_final: 0.8423 (p) REVERT: P 74 LYS cc_start: 0.8565 (tmtt) cc_final: 0.8191 (tmtt) REVERT: P 91 ILE cc_start: 0.9296 (mt) cc_final: 0.9064 (mt) REVERT: Q 227 ILE cc_start: -0.2985 (OUTLIER) cc_final: -0.3508 (mp) REVERT: Q 267 MET cc_start: 0.1862 (OUTLIER) cc_final: 0.1302 (ppp) REVERT: Q 288 MET cc_start: 0.5050 (mmt) cc_final: 0.4629 (ptt) REVERT: Q 491 MET cc_start: 0.9426 (mtm) cc_final: 0.9192 (mtp) REVERT: R 63 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7292 (tm-30) REVERT: R 491 MET cc_start: 0.9268 (mtm) cc_final: 0.9012 (mtp) REVERT: T 200 LEU cc_start: 0.2312 (OUTLIER) cc_final: 0.1928 (pt) REVERT: T 267 MET cc_start: 0.1719 (OUTLIER) cc_final: 0.1473 (pmt) REVERT: T 288 MET cc_start: 0.5206 (OUTLIER) cc_final: 0.4759 (ptt) outliers start: 148 outliers final: 53 residues processed: 776 average time/residue: 1.5448 time to fit residues: 1543.3091 Evaluate side-chains 755 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 671 time to evaluate : 4.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 299 THR Chi-restraints excluded: chain W residue 21 SER Chi-restraints excluded: chain W residue 87 SER Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 404 ARG Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 233 MET Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 483 GLU Chi-restraints excluded: chain J residue 80 ASN Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 267 MET Chi-restraints excluded: chain K residue 404 ARG Chi-restraints excluded: chain L residue 14 VAL Chi-restraints excluded: chain L residue 63 GLU Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 233 MET Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 294 THR Chi-restraints excluded: chain L residue 483 GLU Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 288 MET Chi-restraints excluded: chain O residue 52 ASP Chi-restraints excluded: chain O residue 63 GLU Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 176 THR Chi-restraints excluded: chain O residue 184 GLN Chi-restraints excluded: chain O residue 220 ILE Chi-restraints excluded: chain P residue 27 LEU Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain Q residue 136 VAL Chi-restraints excluded: chain Q residue 138 CYS Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 227 ILE Chi-restraints excluded: chain Q residue 267 MET Chi-restraints excluded: chain R residue 63 GLU Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain R residue 294 THR Chi-restraints excluded: chain R residue 307 MET Chi-restraints excluded: chain S residue 87 SER Chi-restraints excluded: chain T residue 200 LEU Chi-restraints excluded: chain T residue 245 LYS Chi-restraints excluded: chain T residue 267 MET Chi-restraints excluded: chain T residue 288 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 471 optimal weight: 0.6980 chunk 304 optimal weight: 9.9990 chunk 455 optimal weight: 0.8980 chunk 229 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 484 optimal weight: 5.9990 chunk 519 optimal weight: 0.5980 chunk 376 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 599 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 366 GLN W 45 ASN G 37 ASN J 45 ASN K 37 ASN L 194 GLN O 194 GLN O 366 GLN R 194 GLN R 348 GLN S 45 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 59773 Z= 0.187 Angle : 0.506 10.867 80801 Z= 0.268 Chirality : 0.042 0.238 9807 Planarity : 0.003 0.059 10507 Dihedral : 8.273 87.669 8916 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.54 % Allowed : 18.65 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.09), residues: 7959 helix: 1.75 (0.08), residues: 4186 sheet: 0.48 (0.14), residues: 1092 loop : -0.52 (0.11), residues: 2681 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 7 PHE 0.015 0.001 PHE G 219 TYR 0.011 0.001 TYR T 478 ARG 0.013 0.000 ARG O 362 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 682 time to evaluate : 5.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 254 VAL cc_start: 0.2486 (OUTLIER) cc_final: 0.2236 (m) REVERT: G 267 MET cc_start: 0.3421 (OUTLIER) cc_final: 0.3220 (ppp) REVERT: G 307 MET cc_start: 0.2604 (OUTLIER) cc_final: 0.1811 (mmt) REVERT: G 404 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.7540 (mpt90) REVERT: A 491 MET cc_start: 0.9332 (mtm) cc_final: 0.8975 (mtp) REVERT: B 15 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.7460 (mttm) REVERT: C 200 LEU cc_start: 0.3108 (OUTLIER) cc_final: 0.2609 (pt) REVERT: C 262 LEU cc_start: -0.2149 (OUTLIER) cc_final: -0.2544 (pp) REVERT: C 267 MET cc_start: 0.2279 (OUTLIER) cc_final: 0.1779 (ppp) REVERT: C 288 MET cc_start: 0.6558 (OUTLIER) cc_final: 0.5357 (ptt) REVERT: D 63 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7104 (tm-30) REVERT: D 321 LYS cc_start: 0.8572 (mppt) cc_final: 0.8252 (mppt) REVERT: D 366 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7832 (tp40) REVERT: F 193 MET cc_start: 0.5219 (OUTLIER) cc_final: 0.4592 (tmt) REVERT: F 267 MET cc_start: 0.2237 (OUTLIER) cc_final: 0.1677 (ppp) REVERT: F 288 MET cc_start: 0.4502 (ptt) cc_final: 0.4261 (mpt) REVERT: F 307 MET cc_start: 0.4885 (mmm) cc_final: 0.4393 (tpt) REVERT: H 63 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7175 (tm-30) REVERT: H 322 ARG cc_start: 0.8134 (mmm-85) cc_final: 0.7928 (ttp80) REVERT: H 362 ARG cc_start: 0.7660 (ptp-110) cc_final: 0.7381 (ttp-110) REVERT: K 267 MET cc_start: 0.1671 (OUTLIER) cc_final: 0.1428 (pmt) REVERT: K 404 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7572 (mpt90) REVERT: L 483 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7848 (mt-10) REVERT: N 200 LEU cc_start: 0.2140 (OUTLIER) cc_final: 0.1553 (pt) REVERT: N 288 MET cc_start: 0.4634 (OUTLIER) cc_final: 0.4144 (ptt) REVERT: O 160 LYS cc_start: 0.8614 (ttpp) cc_final: 0.8399 (mptp) REVERT: O 184 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.7932 (mp10) REVERT: P 35 SER cc_start: 0.8817 (t) cc_final: 0.8416 (p) REVERT: P 74 LYS cc_start: 0.8536 (tmtt) cc_final: 0.8236 (tmtt) REVERT: P 91 ILE cc_start: 0.9183 (mt) cc_final: 0.8969 (mt) REVERT: Q 227 ILE cc_start: -0.2904 (OUTLIER) cc_final: -0.3423 (mp) REVERT: Q 267 MET cc_start: 0.1798 (OUTLIER) cc_final: 0.1225 (ppp) REVERT: Q 288 MET cc_start: 0.5157 (mmt) cc_final: 0.4806 (ptt) REVERT: Q 491 MET cc_start: 0.9387 (mtm) cc_final: 0.9110 (mtm) REVERT: R 52 ASP cc_start: 0.8484 (t0) cc_final: 0.8247 (m-30) REVERT: R 171 LYS cc_start: 0.7107 (mmmt) cc_final: 0.6787 (mmmt) REVERT: R 491 MET cc_start: 0.9269 (mtm) cc_final: 0.8955 (mtp) REVERT: T 200 LEU cc_start: 0.2273 (OUTLIER) cc_final: 0.1928 (pt) REVERT: T 267 MET cc_start: 0.1482 (OUTLIER) cc_final: 0.1256 (pmt) REVERT: T 288 MET cc_start: 0.5140 (OUTLIER) cc_final: 0.4753 (ptt) outliers start: 95 outliers final: 35 residues processed: 732 average time/residue: 1.5729 time to fit residues: 1481.9245 Evaluate side-chains 726 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 666 time to evaluate : 5.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain W residue 21 SER Chi-restraints excluded: chain W residue 87 SER Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 404 ARG Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 366 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 267 MET Chi-restraints excluded: chain K residue 404 ARG Chi-restraints excluded: chain L residue 14 VAL Chi-restraints excluded: chain L residue 63 GLU Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 483 GLU Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain M residue 92 LEU Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 288 MET Chi-restraints excluded: chain O residue 184 GLN Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain Q residue 138 CYS Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 227 ILE Chi-restraints excluded: chain Q residue 267 MET Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain R residue 307 MET Chi-restraints excluded: chain S residue 87 SER Chi-restraints excluded: chain T residue 200 LEU Chi-restraints excluded: chain T residue 245 LYS Chi-restraints excluded: chain T residue 267 MET Chi-restraints excluded: chain T residue 288 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 693 optimal weight: 0.9980 chunk 730 optimal weight: 0.8980 chunk 666 optimal weight: 9.9990 chunk 710 optimal weight: 0.7980 chunk 427 optimal weight: 4.9990 chunk 309 optimal weight: 4.9990 chunk 557 optimal weight: 0.9980 chunk 218 optimal weight: 0.6980 chunk 641 optimal weight: 0.9980 chunk 671 optimal weight: 6.9990 chunk 707 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 194 GLN I 366 GLN W 45 ASN B 45 ASN ** H 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 ASN L 343 GLN L 366 GLN O 194 GLN R 194 GLN S 45 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 59773 Z= 0.190 Angle : 0.511 13.601 80801 Z= 0.269 Chirality : 0.042 0.220 9807 Planarity : 0.003 0.063 10507 Dihedral : 8.193 89.234 8914 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.39 % Allowed : 19.06 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.09), residues: 7959 helix: 1.84 (0.08), residues: 4193 sheet: 0.45 (0.15), residues: 1113 loop : -0.45 (0.11), residues: 2653 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS P 7 PHE 0.015 0.001 PHE H 219 TYR 0.010 0.001 TYR T 478 ARG 0.014 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 677 time to evaluate : 5.157 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: G 307 MET cc_start: 0.2578 (OUTLIER) cc_final: 0.1821 (mmt) REVERT: G 404 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7527 (mpt90) REVERT: A 491 MET cc_start: 0.9331 (mtm) cc_final: 0.8981 (mtp) REVERT: B 15 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.7439 (mttm) REVERT: C 200 LEU cc_start: 0.3074 (OUTLIER) cc_final: 0.2590 (pt) REVERT: C 267 MET cc_start: 0.2242 (OUTLIER) cc_final: 0.1741 (ppp) REVERT: C 288 MET cc_start: 0.6646 (OUTLIER) cc_final: 0.5428 (ptt) REVERT: C 365 LEU cc_start: 0.6736 (OUTLIER) cc_final: 0.6499 (pp) REVERT: D 63 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7083 (tm-30) REVERT: D 111 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8088 (mtt) REVERT: F 193 MET cc_start: 0.5281 (OUTLIER) cc_final: 0.4653 (tmt) REVERT: F 267 MET cc_start: 0.2265 (OUTLIER) cc_final: 0.1676 (ppp) REVERT: F 288 MET cc_start: 0.4499 (ptt) cc_final: 0.4296 (mpt) REVERT: F 307 MET cc_start: 0.4875 (mmm) cc_final: 0.4373 (tpt) REVERT: H 63 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7101 (tm-30) REVERT: H 322 ARG cc_start: 0.8153 (mmm-85) cc_final: 0.7929 (ttp80) REVERT: H 362 ARG cc_start: 0.7665 (ptp-110) cc_final: 0.7383 (ttp-110) REVERT: K 267 MET cc_start: 0.1295 (OUTLIER) cc_final: 0.0731 (pmt) REVERT: K 404 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7551 (mpt90) REVERT: N 200 LEU cc_start: 0.2471 (OUTLIER) cc_final: 0.1753 (pt) REVERT: N 267 MET cc_start: 0.1582 (OUTLIER) cc_final: 0.0874 (ppp) REVERT: N 288 MET cc_start: 0.4631 (OUTLIER) cc_final: 0.4143 (ptt) REVERT: P 35 SER cc_start: 0.8790 (t) cc_final: 0.8415 (p) REVERT: P 74 LYS cc_start: 0.8536 (tmtt) cc_final: 0.8215 (tmtt) REVERT: P 91 ILE cc_start: 0.9122 (mt) cc_final: 0.8919 (mt) REVERT: Q 227 ILE cc_start: -0.2978 (OUTLIER) cc_final: -0.3711 (tt) REVERT: Q 267 MET cc_start: 0.1611 (OUTLIER) cc_final: 0.1016 (pmt) REVERT: Q 288 MET cc_start: 0.5141 (mmt) cc_final: 0.4844 (ptt) REVERT: Q 491 MET cc_start: 0.9373 (mtm) cc_final: 0.9116 (mtm) REVERT: R 52 ASP cc_start: 0.8483 (t0) cc_final: 0.8255 (m-30) REVERT: R 171 LYS cc_start: 0.6832 (mmmt) cc_final: 0.6461 (mmmt) REVERT: R 491 MET cc_start: 0.9243 (mtm) cc_final: 0.8954 (mtt) REVERT: T 200 LEU cc_start: 0.2271 (OUTLIER) cc_final: 0.1936 (pt) REVERT: T 288 MET cc_start: 0.5131 (OUTLIER) cc_final: 0.4717 (ptt) outliers start: 86 outliers final: 36 residues processed: 722 average time/residue: 1.5677 time to fit residues: 1457.4160 Evaluate side-chains 724 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 667 time to evaluate : 5.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain W residue 87 SER Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 404 ARG Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 520 MET Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 267 MET Chi-restraints excluded: chain K residue 404 ARG Chi-restraints excluded: chain L residue 14 VAL Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 483 GLU Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 267 MET Chi-restraints excluded: chain N residue 288 MET Chi-restraints excluded: chain O residue 176 THR Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain Q residue 136 VAL Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 227 ILE Chi-restraints excluded: chain Q residue 267 MET Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain R residue 294 THR Chi-restraints excluded: chain R residue 307 MET Chi-restraints excluded: chain S residue 87 SER Chi-restraints excluded: chain T residue 200 LEU Chi-restraints excluded: chain T residue 288 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 466 optimal weight: 2.9990 chunk 751 optimal weight: 2.9990 chunk 458 optimal weight: 0.8980 chunk 356 optimal weight: 5.9990 chunk 522 optimal weight: 5.9990 chunk 788 optimal weight: 1.9990 chunk 725 optimal weight: 2.9990 chunk 627 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 484 optimal weight: 7.9990 chunk 384 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 194 GLN W 45 ASN ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 ASN ** L 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 194 GLN R 194 GLN R 348 GLN S 45 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 59773 Z= 0.288 Angle : 0.556 12.421 80801 Z= 0.291 Chirality : 0.044 0.236 9807 Planarity : 0.004 0.067 10507 Dihedral : 8.658 89.654 8913 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.13 % Allowed : 19.69 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.09), residues: 7959 helix: 1.63 (0.08), residues: 4221 sheet: 0.45 (0.14), residues: 1099 loop : -0.50 (0.11), residues: 2639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 401 PHE 0.013 0.001 PHE G 219 TYR 0.012 0.001 TYR T 478 ARG 0.014 0.001 ARG L 362 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 672 time to evaluate : 5.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 483 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7238 (mm-30) REVERT: G 307 MET cc_start: 0.2667 (OUTLIER) cc_final: 0.1879 (mmt) REVERT: G 404 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7554 (mpt90) REVERT: A 491 MET cc_start: 0.9354 (mtm) cc_final: 0.9010 (mtp) REVERT: B 15 LYS cc_start: 0.7684 (mmtp) cc_final: 0.7471 (mttm) REVERT: C 200 LEU cc_start: 0.3077 (OUTLIER) cc_final: 0.2599 (pt) REVERT: C 267 MET cc_start: 0.2155 (OUTLIER) cc_final: 0.1742 (ppp) REVERT: C 288 MET cc_start: 0.6510 (OUTLIER) cc_final: 0.5311 (ptt) REVERT: C 365 LEU cc_start: 0.6732 (OUTLIER) cc_final: 0.6499 (pp) REVERT: D 63 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7195 (tm-30) REVERT: D 111 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8117 (mtt) REVERT: D 321 LYS cc_start: 0.8529 (mppt) cc_final: 0.8153 (mppt) REVERT: F 193 MET cc_start: 0.5285 (OUTLIER) cc_final: 0.4662 (tmt) REVERT: F 267 MET cc_start: 0.2395 (OUTLIER) cc_final: 0.1797 (ppp) REVERT: F 307 MET cc_start: 0.4874 (mmm) cc_final: 0.4339 (tpt) REVERT: H 63 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7103 (tm-30) REVERT: H 322 ARG cc_start: 0.8164 (mmm-85) cc_final: 0.7946 (ttp80) REVERT: H 362 ARG cc_start: 0.7696 (ptp-110) cc_final: 0.7421 (ttm110) REVERT: H 483 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.6886 (mm-30) REVERT: K 267 MET cc_start: 0.1353 (OUTLIER) cc_final: 0.0800 (pmt) REVERT: K 404 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7606 (mpt90) REVERT: L 194 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.6729 (tm-30) REVERT: N 200 LEU cc_start: 0.2530 (OUTLIER) cc_final: 0.1821 (pt) REVERT: N 288 MET cc_start: 0.4647 (OUTLIER) cc_final: 0.4162 (ptt) REVERT: P 35 SER cc_start: 0.8812 (t) cc_final: 0.8411 (p) REVERT: P 74 LYS cc_start: 0.8544 (tmtt) cc_final: 0.8200 (tmtt) REVERT: P 91 ILE cc_start: 0.9179 (mt) cc_final: 0.8965 (mt) REVERT: Q 227 ILE cc_start: -0.3013 (OUTLIER) cc_final: -0.3749 (tt) REVERT: Q 267 MET cc_start: 0.1794 (OUTLIER) cc_final: 0.1231 (pmt) REVERT: Q 288 MET cc_start: 0.5121 (mmt) cc_final: 0.4854 (ptt) REVERT: Q 491 MET cc_start: 0.9414 (mtm) cc_final: 0.9200 (mtp) REVERT: R 171 LYS cc_start: 0.6878 (mmmt) cc_final: 0.6555 (mmmt) REVERT: R 491 MET cc_start: 0.9258 (mtm) cc_final: 0.8982 (mtp) REVERT: T 200 LEU cc_start: 0.2314 (OUTLIER) cc_final: 0.1969 (pt) REVERT: T 288 MET cc_start: 0.5107 (OUTLIER) cc_final: 0.4706 (ptt) outliers start: 70 outliers final: 34 residues processed: 711 average time/residue: 1.5608 time to fit residues: 1429.2150 Evaluate side-chains 720 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 664 time to evaluate : 5.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 483 GLU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 404 ARG Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 483 GLU Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 267 MET Chi-restraints excluded: chain K residue 404 ARG Chi-restraints excluded: chain L residue 14 VAL Chi-restraints excluded: chain L residue 194 GLN Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 483 GLU Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 288 MET Chi-restraints excluded: chain O residue 176 THR Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain Q residue 136 VAL Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 227 ILE Chi-restraints excluded: chain Q residue 267 MET Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain R residue 294 THR Chi-restraints excluded: chain R residue 307 MET Chi-restraints excluded: chain S residue 87 SER Chi-restraints excluded: chain T residue 200 LEU Chi-restraints excluded: chain T residue 288 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 498 optimal weight: 0.6980 chunk 668 optimal weight: 2.9990 chunk 192 optimal weight: 6.9990 chunk 578 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 chunk 628 optimal weight: 3.9990 chunk 263 optimal weight: 0.4980 chunk 645 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 115 optimal weight: 0.9980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 194 GLN W 45 ASN A 319 GLN ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 ASN H 319 GLN J 45 ASN O 194 GLN R 194 GLN R 348 GLN S 45 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.162605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.115768 restraints weight = 72199.395| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.57 r_work: 0.2945 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 59773 Z= 0.258 Angle : 0.544 12.545 80801 Z= 0.284 Chirality : 0.043 0.253 9807 Planarity : 0.003 0.070 10507 Dihedral : 8.538 89.402 8913 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.25 % Allowed : 19.67 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.09), residues: 7959 helix: 1.64 (0.08), residues: 4221 sheet: 0.44 (0.14), residues: 1099 loop : -0.50 (0.11), residues: 2639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS D 401 PHE 0.023 0.001 PHE A 219 TYR 0.011 0.001 TYR T 478 ARG 0.015 0.001 ARG A 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21196.04 seconds wall clock time: 369 minutes 2.65 seconds (22142.65 seconds total)