Starting phenix.real_space_refine on Thu Mar 14 21:11:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bkz_16099/03_2024/8bkz_16099_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bkz_16099/03_2024/8bkz_16099.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bkz_16099/03_2024/8bkz_16099.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bkz_16099/03_2024/8bkz_16099.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bkz_16099/03_2024/8bkz_16099_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bkz_16099/03_2024/8bkz_16099_updated.pdb" } resolution = 2.3 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= 0.008 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 294 5.16 5 C 39886 2.51 5 N 11130 2.21 5 O 16495 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "X PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 11": "OD1" <-> "OD2" Residue "X ASP 167": "OD1" <-> "OD2" Residue "Y GLU 16": "OE1" <-> "OE2" Residue "Y TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 79": "OD1" <-> "OD2" Residue "A PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 11": "OD1" <-> "OD2" Residue "A ASP 167": "OD1" <-> "OD2" Residue "B GLU 16": "OE1" <-> "OE2" Residue "B TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 79": "OD1" <-> "OD2" Residue "C PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 11": "OD1" <-> "OD2" Residue "C ASP 167": "OD1" <-> "OD2" Residue "D GLU 16": "OE1" <-> "OE2" Residue "D TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 79": "OD1" <-> "OD2" Residue "E PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 11": "OD1" <-> "OD2" Residue "E ASP 167": "OD1" <-> "OD2" Residue "F GLU 16": "OE1" <-> "OE2" Residue "F TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 79": "OD1" <-> "OD2" Residue "G PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 11": "OD1" <-> "OD2" Residue "G ASP 167": "OD1" <-> "OD2" Residue "H GLU 16": "OE1" <-> "OE2" Residue "H TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 79": "OD1" <-> "OD2" Residue "I PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 11": "OD1" <-> "OD2" Residue "I ASP 167": "OD1" <-> "OD2" Residue "J GLU 16": "OE1" <-> "OE2" Residue "J TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 79": "OD1" <-> "OD2" Residue "K PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 11": "OD1" <-> "OD2" Residue "K ASP 167": "OD1" <-> "OD2" Residue "L GLU 16": "OE1" <-> "OE2" Residue "L TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 79": "OD1" <-> "OD2" Residue "M PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 11": "OD1" <-> "OD2" Residue "M ASP 167": "OD1" <-> "OD2" Residue "N GLU 16": "OE1" <-> "OE2" Residue "N TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 79": "OD1" <-> "OD2" Residue "O PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 11": "OD1" <-> "OD2" Residue "O ASP 167": "OD1" <-> "OD2" Residue "P GLU 16": "OE1" <-> "OE2" Residue "P TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 79": "OD1" <-> "OD2" Residue "Q PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 11": "OD1" <-> "OD2" Residue "Q ASP 167": "OD1" <-> "OD2" Residue "R GLU 16": "OE1" <-> "OE2" Residue "R TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 79": "OD1" <-> "OD2" Residue "S PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 11": "OD1" <-> "OD2" Residue "S ASP 167": "OD1" <-> "OD2" Residue "T GLU 16": "OE1" <-> "OE2" Residue "T TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 79": "OD1" <-> "OD2" Residue "V PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 11": "OD1" <-> "OD2" Residue "V ASP 167": "OD1" <-> "OD2" Residue "W GLU 16": "OE1" <-> "OE2" Residue "W TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 79": "OD1" <-> "OD2" Residue "Z PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 11": "OD1" <-> "OD2" Residue "Z ASP 167": "OD1" <-> "OD2" Residue "AA GLU 16": "OE1" <-> "OE2" Residue "AA TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA ASP 79": "OD1" <-> "OD2" Residue "BA PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BA ASP 11": "OD1" <-> "OD2" Residue "BA ASP 167": "OD1" <-> "OD2" Residue "CA GLU 16": "OE1" <-> "OE2" Residue "CA TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA ASP 79": "OD1" <-> "OD2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 67875 Number of models: 1 Model: "" Number of chains: 70 Chain: "X" 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: "Y" 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: "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} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" 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: "E" 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: "F" 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: 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: "H" 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: "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: "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: 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: "L" 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: "M" 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: "N" 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: "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: 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: "R" 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: "S" 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: "T" 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: "V" 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: "Z" 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: "AA" 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: "BA" 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: "CA" 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: "X" 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: "E" 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: "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: "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: "M" 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: "S" 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: "V" 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: "Z" 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: "BA" 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: "X" Number of atoms: 247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 247 Classifications: {'water': 247} Link IDs: {None: 246} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 247 Classifications: {'water': 247} Link IDs: {None: 246} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 266 Classifications: {'water': 266} Link IDs: {None: 265} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 245 Classifications: {'water': 245} Link IDs: {None: 244} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 248 Classifications: {'water': 248} Link IDs: {None: 247} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 227 Classifications: {'water': 227} Link IDs: {None: 226} Chain: "J" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 249 Classifications: {'water': 249} Link IDs: {None: 248} Chain: "L" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 243 Classifications: {'water': 243} Link IDs: {None: 242} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 248 Classifications: {'water': 248} Link IDs: {None: 247} 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: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 275 Classifications: {'water': 275} Link IDs: {None: 274} Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 254 Classifications: {'water': 254} Link IDs: {None: 253} Chain: "T" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "V" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 252 Classifications: {'water': 252} Link IDs: {None: 251} 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: "Z" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 231 Classifications: {'water': 231} Link IDs: {None: 230} Chain: "AA" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "BA" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 234 Classifications: {'water': 234} Link IDs: {None: 233} Chain: "CA" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 26.91, per 1000 atoms: 0.40 Number of scatterers: 67875 At special positions: 0 Unit cell: (151.68, 154.56, 258.24, 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 294 16.00 P 42 15.00 Mg 14 11.99 O 16495 8.00 N 11130 7.00 C 39886 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: 21.81 Conformation dependent library (CDL) restraints added in 8.8 seconds 17248 Ramachandran restraints generated. 8624 Oldfield, 0 Emsley, 8624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15680 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 280 helices and 112 sheets defined 45.5% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.15 Creating SS restraints... Processing helix chain 'X' and resid 9 through 30 removed outlier: 3.940A pdb=" N VAL X 29 " --> pdb=" O ASP X 25 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N THR X 30 " --> pdb=" O ALA X 26 " (cutoff:3.500A) Processing helix chain 'X' and resid 53 through 59 Processing helix chain 'X' and resid 65 through 84 removed outlier: 3.597A pdb=" N GLU X 76 " --> pdb=" O GLN X 72 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL X 77 " --> pdb=" O MET X 73 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA X 78 " --> pdb=" O VAL X 74 " (cutoff:3.500A) Processing helix chain 'X' and resid 89 through 108 Processing helix chain 'X' and resid 113 through 134 Processing helix chain 'X' and resid 141 through 151 Processing helix chain 'X' and resid 156 through 169 Processing helix chain 'X' and resid 202 through 204 No H-bonds generated for 'chain 'X' and resid 202 through 204' Processing helix chain 'X' and resid 231 through 243 Proline residue: X 235 - end of helix Processing helix chain 'X' and resid 257 through 268 Processing helix chain 'X' and resid 285 through 296 Processing helix chain 'X' and resid 339 through 355 Processing helix chain 'X' and resid 359 through 372 Processing helix chain 'X' and resid 386 through 409 Processing helix chain 'X' and resid 417 through 426 Processing helix chain 'X' and resid 434 through 458 removed outlier: 3.778A pdb=" N GLU X 448 " --> pdb=" O LEU X 444 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA X 449 " --> pdb=" O ARG X 445 " (cutoff:3.500A) Proline residue: X 450 - end of helix Processing helix chain 'X' and resid 462 through 471 Processing helix chain 'X' and resid 497 through 516 removed outlier: 3.777A pdb=" N THR X 516 " --> pdb=" O GLY X 512 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 31 No H-bonds generated for 'chain 'Y' and resid 29 through 31' Processing helix chain 'Y' and resid 88 through 90 No H-bonds generated for 'chain 'Y' and resid 88 through 90' Processing helix chain 'A' and resid 9 through 30 removed outlier: 3.940A pdb=" N VAL A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) removed outlier: 5.076A 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: 3.597A pdb=" N GLU A 76 " --> pdb=" O GLN A 72 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL A 77 " --> pdb=" O MET A 73 " (cutoff:3.500A) removed outlier: 4.030A 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 257 through 268 Processing helix chain 'A' and resid 285 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 426 Processing helix chain 'A' and resid 434 through 458 removed outlier: 3.779A pdb=" N GLU A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.831A 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: 3.777A 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 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'C' and resid 9 through 30 removed outlier: 3.941A pdb=" N VAL C 29 " --> pdb=" O ASP C 25 " (cutoff:3.500A) removed outlier: 5.076A 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 84 removed outlier: 3.597A pdb=" N GLU C 76 " --> pdb=" O GLN C 72 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL C 77 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 108 Processing helix chain 'C' and resid 113 through 134 WARNING: missing atoms! Processing helix chain 'C' and resid 141 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 231 through 243 Proline residue: C 235 - end of helix Processing helix chain 'C' and resid 257 through 268 Processing helix chain 'C' and resid 285 through 296 Processing helix chain 'C' and resid 339 through 355 Processing helix chain 'C' and resid 359 through 372 Processing helix chain 'C' and resid 386 through 409 Processing helix chain 'C' and resid 417 through 426 Processing helix chain 'C' and resid 434 through 458 removed outlier: 3.778A pdb=" N GLU C 448 " --> pdb=" O LEU C 444 " (cutoff:3.500A) removed outlier: 3.831A 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 497 through 516 removed outlier: 3.777A pdb=" N THR C 516 " --> pdb=" O GLY C 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 31 No H-bonds generated for 'chain 'D' and resid 29 through 31' Processing helix chain 'D' and resid 88 through 90 No H-bonds generated for 'chain 'D' and resid 88 through 90' Processing helix chain 'E' and resid 9 through 30 removed outlier: 3.939A pdb=" N VAL E 29 " --> pdb=" O ASP E 25 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N THR E 30 " --> pdb=" O ALA E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 59 Processing helix chain 'E' and resid 65 through 84 removed outlier: 3.597A pdb=" N GLU E 76 " --> pdb=" O GLN E 72 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL E 77 " --> pdb=" O MET E 73 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 108 Processing helix chain 'E' and resid 113 through 134 Processing helix chain 'E' and resid 141 through 151 Processing helix chain 'E' and resid 156 through 169 Processing helix chain 'E' and resid 202 through 204 No H-bonds generated for 'chain 'E' and resid 202 through 204' Processing helix chain 'E' and resid 231 through 243 Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 257 through 268 Processing helix chain 'E' and resid 285 through 296 Processing helix chain 'E' and resid 339 through 355 Processing helix chain 'E' and resid 359 through 372 Processing helix chain 'E' and resid 386 through 409 Processing helix chain 'E' and resid 417 through 426 Processing helix chain 'E' and resid 434 through 458 removed outlier: 3.778A pdb=" N GLU E 448 " --> pdb=" O LEU E 444 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA E 449 " --> pdb=" O ARG E 445 " (cutoff:3.500A) Proline residue: E 450 - end of helix Processing helix chain 'E' and resid 462 through 471 Processing helix chain 'E' and resid 497 through 516 removed outlier: 3.777A pdb=" N THR E 516 " --> pdb=" O GLY E 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 31 No H-bonds generated for 'chain 'F' and resid 29 through 31' Processing helix chain 'F' and resid 88 through 90 No H-bonds generated for 'chain 'F' and resid 88 through 90' Processing helix chain 'G' and resid 9 through 30 removed outlier: 3.939A pdb=" N VAL G 29 " --> pdb=" O ASP G 25 " (cutoff:3.500A) removed outlier: 5.076A 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 84 removed outlier: 3.597A pdb=" N GLU G 76 " --> pdb=" O GLN G 72 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL G 77 " --> pdb=" O MET G 73 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA G 78 " --> pdb=" O VAL G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 108 Processing helix chain 'G' and resid 113 through 134 Processing helix chain 'G' and resid 141 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 257 through 268 Processing helix chain 'G' and resid 285 through 296 Processing helix chain 'G' and resid 339 through 355 Processing helix chain 'G' and resid 359 through 372 Processing helix chain 'G' and resid 386 through 409 Processing helix chain 'G' and resid 417 through 426 Processing helix chain 'G' and resid 434 through 458 removed outlier: 3.778A pdb=" N GLU G 448 " --> pdb=" O LEU G 444 " (cutoff:3.500A) removed outlier: 3.831A 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 497 through 516 removed outlier: 3.777A pdb=" N THR G 516 " --> pdb=" O GLY G 512 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'I' and resid 9 through 30 removed outlier: 3.940A pdb=" N VAL I 29 " --> pdb=" O ASP I 25 " (cutoff:3.500A) removed outlier: 5.076A 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: 3.597A pdb=" N GLU I 76 " --> pdb=" O GLN I 72 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL I 77 " --> pdb=" O MET I 73 " (cutoff:3.500A) removed outlier: 4.031A 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 231 through 243 Proline residue: I 235 - end of helix Processing helix chain 'I' and resid 257 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 426 Processing helix chain 'I' and resid 434 through 458 removed outlier: 3.778A pdb=" N GLU I 448 " --> pdb=" O LEU I 444 " (cutoff:3.500A) removed outlier: 3.831A 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: 3.777A pdb=" N THR I 516 " --> pdb=" O GLY I 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 'J' and resid 88 through 90 No H-bonds generated for 'chain 'J' and resid 88 through 90' Processing helix chain 'K' and resid 9 through 30 removed outlier: 3.940A pdb=" N VAL K 29 " --> pdb=" O ASP K 25 " (cutoff:3.500A) removed outlier: 5.075A 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 84 removed outlier: 3.598A pdb=" N GLU K 76 " --> pdb=" O GLN K 72 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL K 77 " --> pdb=" O MET K 73 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA K 78 " --> pdb=" O VAL K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 108 Processing helix chain 'K' and resid 113 through 134 Processing helix chain 'K' and resid 141 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 231 through 243 Proline residue: K 235 - end of helix Processing helix chain 'K' and resid 257 through 268 Processing helix chain 'K' and resid 285 through 296 Processing helix chain 'K' and resid 339 through 355 Processing helix chain 'K' and resid 359 through 372 Processing helix chain 'K' and resid 386 through 409 Processing helix chain 'K' and resid 417 through 426 Processing helix chain 'K' and resid 434 through 458 removed outlier: 3.778A pdb=" N GLU K 448 " --> pdb=" O LEU K 444 " (cutoff:3.500A) removed outlier: 3.831A 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 497 through 516 removed outlier: 3.777A pdb=" N THR K 516 " --> pdb=" O GLY K 512 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 31 No H-bonds generated for 'chain 'L' and resid 29 through 31' Processing helix chain 'L' and resid 88 through 90 No H-bonds generated for 'chain 'L' and resid 88 through 90' Processing helix chain 'M' and resid 9 through 30 removed outlier: 3.940A pdb=" N VAL M 29 " --> pdb=" O ASP M 25 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N THR M 30 " --> pdb=" O ALA M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 59 Processing helix chain 'M' and resid 65 through 84 removed outlier: 3.597A pdb=" N GLU M 76 " --> pdb=" O GLN M 72 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL M 77 " --> pdb=" O MET M 73 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA M 78 " --> pdb=" O VAL M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 108 Processing helix chain 'M' and resid 113 through 134 Processing helix chain 'M' and resid 141 through 151 Processing helix chain 'M' and resid 156 through 169 Processing helix chain 'M' and resid 202 through 204 No H-bonds generated for 'chain 'M' and resid 202 through 204' Processing helix chain 'M' and resid 231 through 243 Proline residue: M 235 - end of helix Processing helix chain 'M' and resid 257 through 268 Processing helix chain 'M' and resid 285 through 296 Processing helix chain 'M' and resid 339 through 355 Processing helix chain 'M' and resid 359 through 372 Processing helix chain 'M' and resid 386 through 409 Processing helix chain 'M' and resid 417 through 426 Processing helix chain 'M' and resid 434 through 458 removed outlier: 3.778A pdb=" N GLU M 448 " --> pdb=" O LEU M 444 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA M 449 " --> pdb=" O ARG M 445 " (cutoff:3.500A) Proline residue: M 450 - end of helix Processing helix chain 'M' and resid 462 through 471 Processing helix chain 'M' and resid 497 through 516 removed outlier: 3.777A pdb=" N THR M 516 " --> pdb=" O GLY M 512 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'O' and resid 9 through 30 removed outlier: 3.939A pdb=" N VAL O 29 " --> pdb=" O ASP O 25 " (cutoff:3.500A) removed outlier: 5.077A 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: 3.597A pdb=" N GLU O 76 " --> pdb=" O GLN O 72 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL O 77 " --> pdb=" O MET O 73 " (cutoff:3.500A) removed outlier: 4.030A 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 231 through 243 Proline residue: O 235 - end of helix Processing helix chain 'O' and resid 257 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 426 Processing helix chain 'O' and resid 434 through 458 removed outlier: 3.779A pdb=" N GLU O 448 " --> pdb=" O LEU O 444 " (cutoff:3.500A) removed outlier: 3.831A 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 516 removed outlier: 3.777A pdb=" N THR O 516 " --> pdb=" O GLY O 512 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 31 No H-bonds generated for 'chain 'P' and resid 29 through 31' Processing helix chain 'P' and resid 88 through 90 No H-bonds generated for 'chain 'P' and resid 88 through 90' Processing helix chain 'Q' and resid 9 through 30 removed outlier: 3.940A pdb=" N VAL Q 29 " --> pdb=" O ASP Q 25 " (cutoff:3.500A) removed outlier: 5.076A 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 84 removed outlier: 3.597A pdb=" N GLU Q 76 " --> pdb=" O GLN Q 72 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL Q 77 " --> pdb=" O MET Q 73 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA Q 78 " --> pdb=" O VAL Q 74 " (cutoff:3.500A) Processing helix chain 'Q' and resid 89 through 108 Processing helix chain 'Q' and resid 113 through 134 Processing helix chain 'Q' and resid 141 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 231 through 243 Proline residue: Q 235 - end of helix Processing helix chain 'Q' and resid 257 through 268 Processing helix chain 'Q' and resid 285 through 296 Processing helix chain 'Q' and resid 339 through 355 Processing helix chain 'Q' and resid 359 through 372 Processing helix chain 'Q' and resid 386 through 409 Processing helix chain 'Q' and resid 417 through 426 Processing helix chain 'Q' and resid 434 through 458 removed outlier: 3.778A pdb=" N GLU Q 448 " --> pdb=" O LEU Q 444 " (cutoff:3.500A) removed outlier: 3.831A 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: 3.777A pdb=" N THR Q 516 " --> pdb=" O GLY Q 512 " (cutoff:3.500A) Processing helix chain 'R' and resid 29 through 31 No H-bonds generated for 'chain 'R' and resid 29 through 31' Processing helix chain 'R' and resid 88 through 90 No H-bonds generated for 'chain 'R' and resid 88 through 90' Processing helix chain 'S' and resid 9 through 30 removed outlier: 3.940A pdb=" N VAL S 29 " --> pdb=" O ASP S 25 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N THR S 30 " --> pdb=" O ALA S 26 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 59 Processing helix chain 'S' and resid 65 through 84 removed outlier: 3.597A pdb=" N GLU S 76 " --> pdb=" O GLN S 72 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL S 77 " --> pdb=" O MET S 73 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA S 78 " --> pdb=" O VAL S 74 " (cutoff:3.500A) Processing helix chain 'S' and resid 89 through 108 Processing helix chain 'S' and resid 113 through 134 Processing helix chain 'S' and resid 141 through 151 Processing helix chain 'S' and resid 156 through 169 Processing helix chain 'S' and resid 202 through 204 No H-bonds generated for 'chain 'S' and resid 202 through 204' Processing helix chain 'S' and resid 231 through 243 Proline residue: S 235 - end of helix Processing helix chain 'S' and resid 257 through 268 Processing helix chain 'S' and resid 285 through 296 Processing helix chain 'S' and resid 339 through 355 Processing helix chain 'S' and resid 359 through 372 Processing helix chain 'S' and resid 386 through 409 Processing helix chain 'S' and resid 417 through 426 Processing helix chain 'S' and resid 434 through 458 removed outlier: 3.778A pdb=" N GLU S 448 " --> pdb=" O LEU S 444 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA S 449 " --> pdb=" O ARG S 445 " (cutoff:3.500A) Proline residue: S 450 - end of helix Processing helix chain 'S' and resid 462 through 471 Processing helix chain 'S' and resid 497 through 516 removed outlier: 3.777A pdb=" N THR S 516 " --> pdb=" O GLY S 512 " (cutoff:3.500A) Processing helix chain 'T' and resid 29 through 31 No H-bonds generated for 'chain 'T' and resid 29 through 31' Processing helix chain 'T' and resid 88 through 90 No H-bonds generated for 'chain 'T' and resid 88 through 90' Processing helix chain 'V' and resid 9 through 30 removed outlier: 3.940A pdb=" N VAL V 29 " --> pdb=" O ASP V 25 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N THR V 30 " --> pdb=" O ALA V 26 " (cutoff:3.500A) Processing helix chain 'V' and resid 53 through 59 Processing helix chain 'V' and resid 65 through 84 removed outlier: 3.597A pdb=" N GLU V 76 " --> pdb=" O GLN V 72 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL V 77 " --> pdb=" O MET V 73 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA V 78 " --> pdb=" O VAL V 74 " (cutoff:3.500A) Processing helix chain 'V' and resid 89 through 108 Processing helix chain 'V' and resid 113 through 134 Processing helix chain 'V' and resid 141 through 151 Processing helix chain 'V' and resid 156 through 169 Processing helix chain 'V' and resid 202 through 204 No H-bonds generated for 'chain 'V' and resid 202 through 204' Processing helix chain 'V' and resid 231 through 243 Proline residue: V 235 - end of helix Processing helix chain 'V' and resid 257 through 268 Processing helix chain 'V' and resid 285 through 296 Processing helix chain 'V' and resid 339 through 355 Processing helix chain 'V' and resid 359 through 372 Processing helix chain 'V' and resid 386 through 409 Processing helix chain 'V' and resid 417 through 426 Processing helix chain 'V' and resid 434 through 458 removed outlier: 3.778A pdb=" N GLU V 448 " --> pdb=" O LEU V 444 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA V 449 " --> pdb=" O ARG V 445 " (cutoff:3.500A) Proline residue: V 450 - end of helix Processing helix chain 'V' and resid 462 through 471 Processing helix chain 'V' and resid 497 through 516 removed outlier: 3.777A pdb=" N THR V 516 " --> pdb=" O GLY V 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 'W' and resid 88 through 90 No H-bonds generated for 'chain 'W' and resid 88 through 90' Processing helix chain 'Z' and resid 9 through 30 removed outlier: 3.940A pdb=" N VAL Z 29 " --> pdb=" O ASP Z 25 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N THR Z 30 " --> pdb=" O ALA Z 26 " (cutoff:3.500A) Processing helix chain 'Z' and resid 53 through 59 Processing helix chain 'Z' and resid 65 through 84 removed outlier: 3.597A pdb=" N GLU Z 76 " --> pdb=" O GLN Z 72 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL Z 77 " --> pdb=" O MET Z 73 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA Z 78 " --> pdb=" O VAL Z 74 " (cutoff:3.500A) Processing helix chain 'Z' and resid 89 through 108 Processing helix chain 'Z' and resid 113 through 134 Processing helix chain 'Z' and resid 141 through 151 Processing helix chain 'Z' and resid 156 through 169 Processing helix chain 'Z' and resid 202 through 204 No H-bonds generated for 'chain 'Z' and resid 202 through 204' Processing helix chain 'Z' and resid 231 through 243 Proline residue: Z 235 - end of helix Processing helix chain 'Z' and resid 257 through 268 Processing helix chain 'Z' and resid 285 through 296 Processing helix chain 'Z' and resid 339 through 355 Processing helix chain 'Z' and resid 359 through 372 Processing helix chain 'Z' and resid 386 through 409 Processing helix chain 'Z' and resid 417 through 426 Processing helix chain 'Z' and resid 434 through 458 removed outlier: 3.778A pdb=" N GLU Z 448 " --> pdb=" O LEU Z 444 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA Z 449 " --> pdb=" O ARG Z 445 " (cutoff:3.500A) Proline residue: Z 450 - end of helix Processing helix chain 'Z' and resid 462 through 471 Processing helix chain 'Z' and resid 497 through 516 removed outlier: 3.777A pdb=" N THR Z 516 " --> pdb=" O GLY Z 512 " (cutoff:3.500A) Processing helix chain 'AA' and resid 29 through 31 No H-bonds generated for 'chain 'AA' and resid 29 through 31' Processing helix chain 'AA' and resid 88 through 90 No H-bonds generated for 'chain 'AA' and resid 88 through 90' Processing helix chain 'BA' and resid 9 through 30 removed outlier: 3.940A pdb=" N VALBA 29 " --> pdb=" O ASPBA 25 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N THRBA 30 " --> pdb=" O ALABA 26 " (cutoff:3.500A) Processing helix chain 'BA' and resid 53 through 59 Processing helix chain 'BA' and resid 65 through 84 removed outlier: 3.597A pdb=" N GLUBA 76 " --> pdb=" O GLNBA 72 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VALBA 77 " --> pdb=" O METBA 73 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALABA 78 " --> pdb=" O VALBA 74 " (cutoff:3.500A) Processing helix chain 'BA' and resid 89 through 108 Processing helix chain 'BA' and resid 113 through 134 Processing helix chain 'BA' and resid 141 through 151 Processing helix chain 'BA' and resid 156 through 169 Processing helix chain 'BA' and resid 202 through 204 No H-bonds generated for 'chain 'BA' and resid 202 through 204' Processing helix chain 'BA' and resid 231 through 243 Proline residue: BA 235 - end of helix Processing helix chain 'BA' and resid 257 through 268 Processing helix chain 'BA' and resid 285 through 296 Processing helix chain 'BA' and resid 339 through 355 Processing helix chain 'BA' and resid 359 through 372 Processing helix chain 'BA' and resid 386 through 409 Processing helix chain 'BA' and resid 417 through 426 Processing helix chain 'BA' and resid 434 through 458 removed outlier: 3.778A pdb=" N GLUBA 448 " --> pdb=" O LEUBA 444 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALABA 449 " --> pdb=" O ARGBA 445 " (cutoff:3.500A) Proline residue: BA 450 - end of helix Processing helix chain 'BA' and resid 462 through 471 Processing helix chain 'BA' and resid 497 through 516 removed outlier: 3.777A pdb=" N THRBA 516 " --> pdb=" O GLYBA 512 " (cutoff:3.500A) Processing helix chain 'CA' and resid 29 through 31 No H-bonds generated for 'chain 'CA' and resid 29 through 31' Processing helix chain 'CA' and resid 88 through 90 No H-bonds generated for 'chain 'CA' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'X' and resid 4 through 8 Processing sheet with id= B, first strand: chain 'X' and resid 38 through 40 Processing sheet with id= C, first strand: chain 'X' and resid 174 through 179 Processing sheet with id= D, first strand: chain 'X' and resid 193 through 195 removed outlier: 3.635A pdb=" N MET X 193 " --> pdb=" O ILE X 332 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'X' and resid 219 through 223 Processing sheet with id= F, first strand: chain 'X' and resid 411 through 413 Processing sheet with id= G, first strand: chain 'X' and resid 476 through 479 Processing sheet with id= H, first strand: chain 'Y' and resid 74 through 78 removed outlier: 7.751A pdb=" N GLU Y 82 " --> pdb=" O ARG Y 14 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ARG Y 14 " --> pdb=" O GLU Y 82 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYS Y 13 " --> pdb=" O VAL Y 40 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL Y 40 " --> pdb=" O LYS Y 13 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE Y 64 " --> pdb=" O VAL Y 95 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 4 through 8 Processing sheet with id= J, first strand: chain 'A' and resid 38 through 40 Processing sheet with id= K, first strand: chain 'A' and resid 174 through 179 Processing sheet with id= L, first strand: chain 'A' and resid 193 through 195 removed outlier: 3.635A pdb=" N MET A 193 " --> pdb=" O ILE A 332 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 219 through 223 Processing sheet with id= N, first strand: chain 'A' and resid 411 through 413 Processing sheet with id= O, first strand: chain 'A' and resid 476 through 479 Processing sheet with id= P, first strand: chain 'B' and resid 74 through 78 removed outlier: 7.751A pdb=" N GLU B 82 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ARG B 14 " --> pdb=" O GLU B 82 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYS B 13 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL B 40 " --> pdb=" O LYS B 13 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE B 64 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 4 through 8 Processing sheet with id= R, first strand: chain 'C' and resid 38 through 40 Processing sheet with id= S, first strand: chain 'C' and resid 174 through 179 Processing sheet with id= T, first strand: chain 'C' and resid 193 through 195 removed outlier: 3.635A pdb=" N MET C 193 " --> pdb=" O ILE C 332 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 219 through 223 Processing sheet with id= V, first strand: chain 'C' and resid 411 through 413 Processing sheet with id= W, first strand: chain 'C' and resid 476 through 479 Processing sheet with id= X, first strand: chain 'D' and resid 74 through 78 removed outlier: 7.750A pdb=" N GLU D 82 " --> pdb=" O ARG D 14 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ARG D 14 " --> pdb=" O GLU D 82 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYS D 13 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL D 40 " --> pdb=" O LYS D 13 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE D 64 " --> pdb=" O VAL D 95 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 4 through 8 Processing sheet with id= Z, first strand: chain 'E' and resid 38 through 40 Processing sheet with id= AA, first strand: chain 'E' and resid 174 through 179 Processing sheet with id= AB, first strand: chain 'E' and resid 193 through 195 removed outlier: 3.635A pdb=" N MET E 193 " --> pdb=" O ILE E 332 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 219 through 223 Processing sheet with id= AD, first strand: chain 'E' and resid 411 through 413 Processing sheet with id= AE, first strand: chain 'E' and resid 476 through 479 Processing sheet with id= AF, first strand: chain 'F' and resid 74 through 78 removed outlier: 7.750A pdb=" N GLU F 82 " --> pdb=" O ARG F 14 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ARG F 14 " --> pdb=" O GLU F 82 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYS F 13 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL F 40 " --> pdb=" O LYS F 13 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE F 64 " --> pdb=" O VAL F 95 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 4 through 8 Processing sheet with id= AH, first strand: chain 'G' and resid 38 through 40 Processing sheet with id= AI, first strand: chain 'G' and resid 174 through 179 Processing sheet with id= AJ, first strand: chain 'G' and resid 193 through 195 removed outlier: 3.635A pdb=" N MET G 193 " --> pdb=" O ILE G 332 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'G' and resid 219 through 223 Processing sheet with id= AL, first strand: chain 'G' and resid 411 through 413 Processing sheet with id= AM, first strand: chain 'G' and resid 476 through 479 Processing sheet with id= AN, first strand: chain 'H' and resid 74 through 78 removed outlier: 7.750A pdb=" N GLU H 82 " --> pdb=" O ARG H 14 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ARG H 14 " --> pdb=" O GLU H 82 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYS H 13 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL H 40 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ILE H 64 " --> pdb=" O VAL H 95 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'I' and resid 4 through 8 Processing sheet with id= AP, first strand: chain 'I' and resid 38 through 40 Processing sheet with id= AQ, first strand: chain 'I' and resid 174 through 179 Processing sheet with id= AR, first strand: chain 'I' and resid 193 through 195 removed outlier: 3.635A pdb=" N MET I 193 " --> pdb=" O ILE I 332 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'I' and resid 219 through 223 Processing sheet with id= AT, first strand: chain 'I' and resid 411 through 413 Processing sheet with id= AU, first strand: chain 'I' and resid 476 through 479 Processing sheet with id= AV, first strand: chain 'J' and resid 74 through 78 removed outlier: 7.751A pdb=" N GLU J 82 " --> pdb=" O ARG J 14 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ARG J 14 " --> pdb=" O GLU J 82 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYS J 13 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL J 40 " --> pdb=" O LYS J 13 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE J 64 " --> pdb=" O VAL J 95 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'K' and resid 4 through 8 Processing sheet with id= AX, first strand: chain 'K' and resid 38 through 40 Processing sheet with id= AY, first strand: chain 'K' and resid 174 through 179 Processing sheet with id= AZ, first strand: chain 'K' and resid 193 through 195 removed outlier: 3.635A pdb=" N MET K 193 " --> pdb=" O ILE K 332 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'K' and resid 219 through 223 Processing sheet with id= BB, first strand: chain 'K' and resid 411 through 413 Processing sheet with id= BC, first strand: chain 'K' and resid 476 through 479 Processing sheet with id= BD, first strand: chain 'L' and resid 74 through 78 removed outlier: 7.750A pdb=" N GLU L 82 " --> pdb=" O ARG L 14 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ARG L 14 " --> pdb=" O GLU L 82 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYS L 13 " --> pdb=" O VAL L 40 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL L 40 " --> pdb=" O LYS L 13 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ILE L 64 " --> pdb=" O VAL L 95 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'M' and resid 4 through 8 Processing sheet with id= BF, first strand: chain 'M' and resid 38 through 40 Processing sheet with id= BG, first strand: chain 'M' and resid 174 through 179 Processing sheet with id= BH, first strand: chain 'M' and resid 193 through 195 removed outlier: 3.635A pdb=" N MET M 193 " --> pdb=" O ILE M 332 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'M' and resid 219 through 223 Processing sheet with id= BJ, first strand: chain 'M' and resid 411 through 413 Processing sheet with id= BK, first strand: chain 'M' and resid 476 through 479 Processing sheet with id= BL, first strand: chain 'N' and resid 74 through 78 removed outlier: 7.751A pdb=" N GLU N 82 " --> pdb=" O ARG N 14 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ARG N 14 " --> pdb=" O GLU N 82 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYS N 13 " --> pdb=" O VAL N 40 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL N 40 " --> pdb=" O LYS N 13 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE N 64 " --> pdb=" O VAL N 95 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'O' and resid 4 through 8 Processing sheet with id= BN, first strand: chain 'O' and resid 38 through 40 Processing sheet with id= BO, first strand: chain 'O' and resid 174 through 179 Processing sheet with id= BP, first strand: chain 'O' and resid 193 through 195 removed outlier: 3.635A pdb=" N MET O 193 " --> pdb=" O ILE O 332 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'O' and resid 219 through 223 Processing sheet with id= BR, first strand: chain 'O' and resid 411 through 413 Processing sheet with id= BS, first strand: chain 'O' and resid 476 through 479 Processing sheet with id= BT, first strand: chain 'P' and resid 74 through 78 removed outlier: 7.751A pdb=" N GLU P 82 " --> pdb=" O ARG P 14 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ARG P 14 " --> pdb=" O GLU P 82 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYS P 13 " --> pdb=" O VAL P 40 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL P 40 " --> pdb=" O LYS P 13 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE P 64 " --> pdb=" O VAL P 95 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'Q' and resid 4 through 8 Processing sheet with id= BV, first strand: chain 'Q' and resid 38 through 40 Processing sheet with id= BW, first strand: chain 'Q' and resid 174 through 179 Processing sheet with id= BX, first strand: chain 'Q' and resid 193 through 195 removed outlier: 3.635A pdb=" N MET Q 193 " --> pdb=" O ILE Q 332 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'Q' and resid 219 through 223 Processing sheet with id= BZ, first strand: chain 'Q' and resid 411 through 413 Processing sheet with id= CA, first strand: chain 'Q' and resid 476 through 479 Processing sheet with id= CB, first strand: chain 'R' and resid 74 through 78 removed outlier: 7.750A pdb=" N GLU R 82 " --> pdb=" O ARG R 14 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ARG R 14 " --> pdb=" O GLU R 82 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYS R 13 " --> pdb=" O VAL R 40 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL R 40 " --> pdb=" O LYS R 13 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ILE R 64 " --> pdb=" O VAL R 95 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'S' and resid 4 through 8 Processing sheet with id= CD, first strand: chain 'S' and resid 38 through 40 Processing sheet with id= CE, first strand: chain 'S' and resid 174 through 179 Processing sheet with id= CF, first strand: chain 'S' and resid 193 through 195 removed outlier: 3.635A pdb=" N MET S 193 " --> pdb=" O ILE S 332 " (cutoff:3.500A) Processing sheet with id= CG, first strand: chain 'S' and resid 219 through 223 Processing sheet with id= CH, first strand: chain 'S' and resid 411 through 413 Processing sheet with id= CI, first strand: chain 'S' and resid 476 through 479 Processing sheet with id= CJ, first strand: chain 'T' and resid 74 through 78 removed outlier: 7.751A pdb=" N GLU T 82 " --> pdb=" O ARG T 14 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ARG T 14 " --> pdb=" O GLU T 82 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYS T 13 " --> pdb=" O VAL T 40 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL T 40 " --> pdb=" O LYS T 13 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE T 64 " --> pdb=" O VAL T 95 " (cutoff:3.500A) Processing sheet with id= CK, first strand: chain 'V' and resid 4 through 8 Processing sheet with id= CL, first strand: chain 'V' and resid 38 through 40 Processing sheet with id= CM, first strand: chain 'V' and resid 174 through 179 Processing sheet with id= CN, first strand: chain 'V' and resid 193 through 195 removed outlier: 3.635A pdb=" N MET V 193 " --> pdb=" O ILE V 332 " (cutoff:3.500A) Processing sheet with id= CO, first strand: chain 'V' and resid 219 through 223 Processing sheet with id= CP, first strand: chain 'V' and resid 411 through 413 Processing sheet with id= CQ, first strand: chain 'V' and resid 476 through 479 Processing sheet with id= CR, first strand: chain 'W' and resid 74 through 78 removed outlier: 7.751A pdb=" N GLU W 82 " --> pdb=" O ARG W 14 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ARG W 14 " --> pdb=" O GLU W 82 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYS W 13 " --> pdb=" O VAL W 40 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL W 40 " --> pdb=" O LYS W 13 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE W 64 " --> pdb=" O VAL W 95 " (cutoff:3.500A) Processing sheet with id= CS, first strand: chain 'Z' and resid 4 through 8 Processing sheet with id= CT, first strand: chain 'Z' and resid 38 through 40 Processing sheet with id= CU, first strand: chain 'Z' and resid 174 through 179 Processing sheet with id= CV, first strand: chain 'Z' and resid 193 through 195 removed outlier: 3.635A pdb=" N MET Z 193 " --> pdb=" O ILE Z 332 " (cutoff:3.500A) Processing sheet with id= CW, first strand: chain 'Z' and resid 219 through 223 Processing sheet with id= CX, first strand: chain 'Z' and resid 411 through 413 Processing sheet with id= CY, first strand: chain 'Z' and resid 476 through 479 Processing sheet with id= CZ, first strand: chain 'AA' and resid 74 through 78 removed outlier: 7.750A pdb=" N GLUAA 82 " --> pdb=" O ARGAA 14 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ARGAA 14 " --> pdb=" O GLUAA 82 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYSAA 13 " --> pdb=" O VALAA 40 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VALAA 40 " --> pdb=" O LYSAA 13 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILEAA 64 " --> pdb=" O VALAA 95 " (cutoff:3.500A) Processing sheet with id= DA, first strand: chain 'BA' and resid 4 through 8 Processing sheet with id= DB, first strand: chain 'BA' and resid 38 through 40 Processing sheet with id= DC, first strand: chain 'BA' and resid 174 through 179 Processing sheet with id= DD, first strand: chain 'BA' and resid 193 through 195 removed outlier: 3.635A pdb=" N METBA 193 " --> pdb=" O ILEBA 332 " (cutoff:3.500A) Processing sheet with id= DE, first strand: chain 'BA' and resid 219 through 223 Processing sheet with id= DF, first strand: chain 'BA' and resid 411 through 413 Processing sheet with id= DG, first strand: chain 'BA' and resid 476 through 479 Processing sheet with id= DH, first strand: chain 'CA' and resid 74 through 78 removed outlier: 7.750A pdb=" N GLUCA 82 " --> pdb=" O ARGCA 14 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ARGCA 14 " --> pdb=" O GLUCA 82 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYSCA 13 " --> pdb=" O VALCA 40 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VALCA 40 " --> pdb=" O LYSCA 13 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ILECA 64 " --> pdb=" O VALCA 95 " (cutoff:3.500A) 3541 hydrogen bonds defined for protein. 10203 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: 27.05 Time building geometry restraints manager: 23.66 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: 19283 1.33 - 1.45: 6314 1.45 - 1.57: 38605 1.57 - 1.69: 70 1.69 - 1.81: 546 Bond restraints: 64818 Sorted by residual: bond pdb=" CB ASP B 79 " pdb=" CG ASP B 79 " ideal model delta sigma weight residual 1.516 1.554 -0.038 2.50e-02 1.60e+03 2.30e+00 bond pdb=" CB ASP D 79 " pdb=" CG ASP D 79 " ideal model delta sigma weight residual 1.516 1.554 -0.038 2.50e-02 1.60e+03 2.28e+00 bond pdb=" CB ASP R 79 " pdb=" CG ASP R 79 " ideal model delta sigma weight residual 1.516 1.554 -0.038 2.50e-02 1.60e+03 2.27e+00 bond pdb=" CB ASP T 79 " pdb=" CG ASP T 79 " ideal model delta sigma weight residual 1.516 1.554 -0.038 2.50e-02 1.60e+03 2.27e+00 bond pdb=" CA ASP L 79 " pdb=" CB ASP L 79 " ideal model delta sigma weight residual 1.529 1.553 -0.024 1.58e-02 4.01e+03 2.26e+00 ... (remaining 64813 not shown) Histogram of bond angle deviations from ideal: 96.57 - 105.22: 979 105.22 - 113.87: 38996 113.87 - 122.51: 39777 122.51 - 131.16: 7787 131.16 - 139.81: 69 Bond angle restraints: 87608 Sorted by residual: angle pdb=" C ASPAA 79 " pdb=" N ASNAA 80 " pdb=" CA ASNAA 80 " ideal model delta sigma weight residual 121.54 129.27 -7.73 1.91e+00 2.74e-01 1.64e+01 angle pdb=" C ASP R 79 " pdb=" N ASN R 80 " pdb=" CA ASN R 80 " ideal model delta sigma weight residual 121.54 129.27 -7.73 1.91e+00 2.74e-01 1.64e+01 angle pdb=" C ASP F 79 " pdb=" N ASN F 80 " pdb=" CA ASN F 80 " ideal model delta sigma weight residual 121.54 129.26 -7.72 1.91e+00 2.74e-01 1.64e+01 angle pdb=" C ASP J 79 " pdb=" N ASN J 80 " pdb=" CA ASN J 80 " ideal model delta sigma weight residual 121.54 129.25 -7.71 1.91e+00 2.74e-01 1.63e+01 angle pdb=" C ASP Y 79 " pdb=" N ASN Y 80 " pdb=" CA ASN Y 80 " ideal model delta sigma weight residual 121.54 129.24 -7.70 1.91e+00 2.74e-01 1.62e+01 ... (remaining 87603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 35069 17.54 - 35.09: 3750 35.09 - 52.63: 1221 52.63 - 70.17: 252 70.17 - 87.72: 126 Dihedral angle restraints: 40418 sinusoidal: 15974 harmonic: 24444 Sorted by residual: dihedral pdb=" CB GLU V 129 " pdb=" CG GLU V 129 " pdb=" CD GLU V 129 " pdb=" OE1 GLU V 129 " ideal model delta sinusoidal sigma weight residual 0.00 -85.26 85.26 1 3.00e+01 1.11e-03 9.79e+00 dihedral pdb=" CB GLU Q 129 " pdb=" CG GLU Q 129 " pdb=" CD GLU Q 129 " pdb=" OE1 GLU Q 129 " ideal model delta sinusoidal sigma weight residual 0.00 -85.26 85.26 1 3.00e+01 1.11e-03 9.79e+00 dihedral pdb=" CB GLU C 129 " pdb=" CG GLU C 129 " pdb=" CD GLU C 129 " pdb=" OE1 GLU C 129 " ideal model delta sinusoidal sigma weight residual 0.00 -85.26 85.26 1 3.00e+01 1.11e-03 9.79e+00 ... (remaining 40415 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 7454 0.036 - 0.072: 1956 0.072 - 0.108: 851 0.108 - 0.144: 295 0.144 - 0.180: 84 Chirality restraints: 10640 Sorted by residual: chirality pdb=" CA ASP T 79 " pdb=" N ASP T 79 " pdb=" C ASP T 79 " pdb=" CB ASP T 79 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.14e-01 chirality pdb=" CA ASP B 79 " pdb=" N ASP B 79 " pdb=" C ASP B 79 " pdb=" CB ASP B 79 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.00e-01 chirality pdb=" CA ASP F 79 " pdb=" N ASP F 79 " pdb=" C ASP F 79 " pdb=" CB ASP F 79 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.99e-01 ... (remaining 10637 not shown) Planarity restraints: 11394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP C 11 " -0.012 2.00e-02 2.50e+03 2.51e-02 6.31e+00 pdb=" CG ASP C 11 " 0.043 2.00e-02 2.50e+03 pdb=" OD1 ASP C 11 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP C 11 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP G 11 " -0.012 2.00e-02 2.50e+03 2.51e-02 6.31e+00 pdb=" CG ASP G 11 " 0.043 2.00e-02 2.50e+03 pdb=" OD1 ASP G 11 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP G 11 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 11 " -0.012 2.00e-02 2.50e+03 2.51e-02 6.31e+00 pdb=" CG ASP A 11 " 0.043 2.00e-02 2.50e+03 pdb=" OD1 ASP A 11 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP A 11 " -0.016 2.00e-02 2.50e+03 ... (remaining 11391 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.70: 3225 2.70 - 3.31: 81045 3.31 - 3.92: 155252 3.92 - 4.53: 199780 4.53 - 5.14: 294776 Nonbonded interactions: 734078 Sorted by model distance: nonbonded pdb="MG MG I 601 " pdb=" O1G ATP I 603 " model vdw 2.085 2.170 nonbonded pdb="MG MGBA 601 " pdb=" O1G ATPBA 603 " model vdw 2.085 2.170 nonbonded pdb="MG MG S 601 " pdb=" O1G ATP S 603 " model vdw 2.085 2.170 nonbonded pdb="MG MG C 601 " pdb=" O1G ATP C 603 " model vdw 2.086 2.170 nonbonded pdb="MG MG Q 601 " pdb=" O1G ATP Q 603 " model vdw 2.086 2.170 ... (remaining 734073 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 123 or (resid 124 and (name N or name CA or name \ C or name CB or name CG1 or name CG2)) or resid 125 through 197 or (resid 198 a \ nd (name N or name CA or name C )) or resid 199 through 525 or resid 601 through \ 603)) selection = (chain 'BA' and (resid 2 through 123 or (resid 124 and (name N or name CA or nam \ e C or name CB or name CG1 or name CG2)) or resid 125 through 197 or (resid 198 \ and (name N or name CA or name C )) or resid 199 through 525 or resid 601 throug \ h 603)) selection = chain 'C' selection = (chain 'E' and (resid 2 through 123 or (resid 124 and (name N or name CA or name \ C or name CB or name CG1 or name CG2)) or resid 125 through 197 or (resid 198 a \ nd (name N or name CA or name C )) or resid 199 through 525 or resid 601 through \ 603)) selection = (chain 'G' and (resid 2 through 123 or (resid 124 and (name N or name CA or name \ C or name CB or name CG1 or name CG2)) or resid 125 through 197 or (resid 198 a \ nd (name N or name CA or name C )) or resid 199 through 525 or resid 601 through \ 603)) selection = (chain 'I' and (resid 2 through 123 or (resid 124 and (name N or name CA or name \ C or name CB or name CG1 or name CG2)) or resid 125 through 197 or (resid 198 a \ nd (name N or name CA or name C )) or resid 199 through 525 or resid 601 through \ 603)) selection = (chain 'K' and (resid 2 through 123 or (resid 124 and (name N or name CA or name \ C or name CB or name CG1 or name CG2)) or resid 125 through 197 or (resid 198 a \ nd (name N or name CA or name C )) or resid 199 through 525 or resid 601 through \ 603)) selection = (chain 'M' and (resid 2 through 123 or (resid 124 and (name N or name CA or name \ C or name CB or name CG1 or name CG2)) or resid 125 through 197 or (resid 198 a \ nd (name N or name CA or name C )) or resid 199 through 525 or resid 601 through \ 603)) selection = (chain 'O' and (resid 2 through 123 or (resid 124 and (name N or name CA or name \ C or name CB or name CG1 or name CG2)) or resid 125 through 197 or (resid 198 a \ nd (name N or name CA or name C )) or resid 199 through 525 or resid 601 through \ 603)) selection = (chain 'Q' and (resid 2 through 123 or (resid 124 and (name N or name CA or name \ C or name CB or name CG1 or name CG2)) or resid 125 through 197 or (resid 198 a \ nd (name N or name CA or name C )) or resid 199 through 525 or resid 601 through \ 603)) selection = (chain 'S' and (resid 2 through 123 or (resid 124 and (name N or name CA or name \ C or name CB or name CG1 or name CG2)) or resid 125 through 197 or (resid 198 a \ nd (name N or name CA or name C )) or resid 199 through 525 or resid 601 through \ 603)) selection = (chain 'V' and (resid 2 through 123 or (resid 124 and (name N or name CA or name \ C or name CB or name CG1 or name CG2)) or resid 125 through 197 or (resid 198 a \ nd (name N or name CA or name C )) or resid 199 through 525 or resid 601 through \ 603)) selection = (chain 'X' and (resid 2 through 123 or (resid 124 and (name N or name CA or name \ C or name CB or name CG1 or name CG2)) or resid 125 through 197 or (resid 198 a \ nd (name N or name CA or name C )) or resid 199 through 525 or resid 601 through \ 603)) selection = (chain 'Z' and (resid 2 through 123 or (resid 124 and (name N or name CA or name \ C or name CB or name CG1 or name CG2)) or resid 125 through 197 or (resid 198 a \ nd (name N or name CA or name C )) or resid 199 through 525 or resid 601 through \ 603)) } ncs_group { reference = chain 'AA' selection = chain 'B' selection = chain 'CA' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'W' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 13.850 Check model and map are aligned: 0.730 Set scattering table: 0.450 Process input model: 143.520 Find NCS groups from input model: 4.480 Set up NCS constraints: 0.710 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:9.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 175.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 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 : 0.003 0.038 64818 Z= 0.184 Angle : 0.516 9.980 87608 Z= 0.282 Chirality : 0.044 0.180 10640 Planarity : 0.003 0.025 11394 Dihedral : 17.155 87.718 24738 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.07 % Allowed : 22.43 % Favored : 77.50 % 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: 1.74 (0.08), residues: 8624 helix: 1.99 (0.07), residues: 4255 sheet: 1.04 (0.13), residues: 1204 loop : 0.12 (0.10), residues: 3165 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 7 PHE 0.006 0.001 PHE I 195 TYR 0.010 0.001 TYR W 71 ARG 0.004 0.000 ARG M 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17248 Ramachandran restraints generated. 8624 Oldfield, 0 Emsley, 8624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17248 Ramachandran restraints generated. 8624 Oldfield, 0 Emsley, 8624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 782 time to evaluate : 5.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 171 LYS cc_start: 0.7225 (mmmt) cc_final: 0.6932 (mmtp) REVERT: C 322 ARG cc_start: 0.8089 (mmm160) cc_final: 0.7875 (mtp85) REVERT: E 288 MET cc_start: 0.8484 (mtt) cc_final: 0.8251 (mpp) REVERT: G 322 ARG cc_start: 0.8126 (mmm160) cc_final: 0.7911 (mtp85) REVERT: G 329 THR cc_start: 0.9001 (p) cc_final: 0.8692 (p) REVERT: M 171 LYS cc_start: 0.7184 (mmmt) cc_final: 0.6898 (mmtp) REVERT: Q 322 ARG cc_start: 0.8094 (mmm160) cc_final: 0.7860 (mtp85) REVERT: S 288 MET cc_start: 0.8482 (mtt) cc_final: 0.8272 (mpp) REVERT: V 322 ARG cc_start: 0.8137 (mmm160) cc_final: 0.7912 (mtp85) REVERT: V 329 THR cc_start: 0.8946 (p) cc_final: 0.8652 (p) outliers start: 5 outliers final: 5 residues processed: 787 average time/residue: 1.4000 time to fit residues: 1454.8003 Evaluate side-chains 754 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 749 time to evaluate : 5.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain O residue 238 GLU Chi-restraints excluded: chain Q residue 238 GLU Chi-restraints excluded: chain S residue 238 GLU Chi-restraints excluded: chain V residue 238 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 721 optimal weight: 2.9990 chunk 647 optimal weight: 6.9990 chunk 359 optimal weight: 0.8980 chunk 221 optimal weight: 0.0870 chunk 436 optimal weight: 0.9980 chunk 345 optimal weight: 3.9990 chunk 669 optimal weight: 1.9990 chunk 259 optimal weight: 2.9990 chunk 407 optimal weight: 8.9990 chunk 498 optimal weight: 7.9990 chunk 775 optimal weight: 0.8980 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 352 GLN G 10 ASN G 343 GLN K 112 ASN M 352 GLN BA 112 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.0445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 64818 Z= 0.174 Angle : 0.452 7.249 87608 Z= 0.250 Chirality : 0.044 0.168 10640 Planarity : 0.003 0.040 11394 Dihedral : 8.446 89.920 9647 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.59 % Allowed : 19.60 % Favored : 78.81 % 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: 1.91 (0.09), residues: 8624 helix: 2.19 (0.07), residues: 4242 sheet: 1.08 (0.13), residues: 1204 loop : 0.15 (0.10), residues: 3178 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS L 7 PHE 0.006 0.001 PHE K 195 TYR 0.008 0.001 TYR Z 478 ARG 0.009 0.000 ARG J 9 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17248 Ramachandran restraints generated. 8624 Oldfield, 0 Emsley, 8624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17248 Ramachandran restraints generated. 8624 Oldfield, 0 Emsley, 8624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 890 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 783 time to evaluate : 7.054 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: C 322 ARG cc_start: 0.8092 (mmm160) cc_final: 0.7874 (mtp85) REVERT: E 16 MET cc_start: 0.9279 (ttp) cc_final: 0.8972 (ttp) REVERT: G 329 THR cc_start: 0.9035 (p) cc_final: 0.8763 (p) REVERT: K 267 MET cc_start: 0.8739 (mtt) cc_final: 0.8517 (mtt) REVERT: S 16 MET cc_start: 0.9254 (ttp) cc_final: 0.8950 (ttp) REVERT: V 329 THR cc_start: 0.8947 (p) cc_final: 0.8645 (p) REVERT: V 366 GLN cc_start: 0.7873 (mm-40) cc_final: 0.7631 (tp-100) REVERT: BA 267 MET cc_start: 0.8778 (mtt) cc_final: 0.8576 (mtt) outliers start: 107 outliers final: 28 residues processed: 849 average time/residue: 1.3831 time to fit residues: 1558.4927 Evaluate side-chains 778 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 750 time to evaluate : 5.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 141 SER Chi-restraints excluded: chain X residue 238 GLU Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 238 GLU Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 238 GLU Chi-restraints excluded: chain I residue 141 SER Chi-restraints excluded: chain I residue 238 GLU Chi-restraints excluded: chain J residue 85 ILE Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain K residue 238 GLU Chi-restraints excluded: chain M residue 141 SER Chi-restraints excluded: chain M residue 238 GLU Chi-restraints excluded: chain O residue 141 SER Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 234 LEU Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain S residue 141 SER Chi-restraints excluded: chain V residue 141 SER Chi-restraints excluded: chain Z residue 141 SER Chi-restraints excluded: chain Z residue 238 GLU Chi-restraints excluded: chain AA residue 85 ILE Chi-restraints excluded: chain BA residue 141 SER Chi-restraints excluded: chain BA residue 238 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 431 optimal weight: 0.7980 chunk 240 optimal weight: 9.9990 chunk 645 optimal weight: 9.9990 chunk 528 optimal weight: 3.9990 chunk 213 optimal weight: 0.0980 chunk 776 optimal weight: 0.7980 chunk 839 optimal weight: 2.9990 chunk 691 optimal weight: 7.9990 chunk 770 optimal weight: 2.9990 chunk 264 optimal weight: 20.0000 chunk 623 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 352 GLN O 366 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.0639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 64818 Z= 0.203 Angle : 0.461 9.670 87608 Z= 0.254 Chirality : 0.044 0.167 10640 Planarity : 0.003 0.031 11394 Dihedral : 8.574 89.957 9632 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.37 % Allowed : 19.90 % Favored : 78.74 % 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: 1.89 (0.09), residues: 8624 helix: 2.16 (0.07), residues: 4240 sheet: 1.05 (0.13), residues: 1204 loop : 0.16 (0.11), residues: 3180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS G 401 PHE 0.006 0.001 PHE A 195 TYR 0.008 0.001 TYR Z 478 ARG 0.007 0.000 ARG D 9 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17248 Ramachandran restraints generated. 8624 Oldfield, 0 Emsley, 8624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17248 Ramachandran restraints generated. 8624 Oldfield, 0 Emsley, 8624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 878 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 786 time to evaluate : 5.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8198 (mtp) REVERT: C 322 ARG cc_start: 0.8101 (mmm160) cc_final: 0.7882 (mtp85) REVERT: E 16 MET cc_start: 0.9285 (ttp) cc_final: 0.8966 (ttp) REVERT: G 329 THR cc_start: 0.9026 (p) cc_final: 0.8750 (p) REVERT: O 267 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8161 (mtp) REVERT: Q 322 ARG cc_start: 0.8087 (mmm160) cc_final: 0.7863 (mtp85) REVERT: S 16 MET cc_start: 0.9260 (ttp) cc_final: 0.8953 (ttp) REVERT: V 329 THR cc_start: 0.8955 (p) cc_final: 0.8678 (p) REVERT: V 366 GLN cc_start: 0.7833 (mm-40) cc_final: 0.7592 (tp-100) REVERT: Z 389 MET cc_start: 0.9198 (tpp) cc_final: 0.8942 (tpp) outliers start: 92 outliers final: 33 residues processed: 847 average time/residue: 1.3518 time to fit residues: 1524.1641 Evaluate side-chains 801 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 766 time to evaluate : 5.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 141 SER Chi-restraints excluded: chain X residue 238 GLU Chi-restraints excluded: chain X residue 267 MET Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 238 GLU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 238 GLU Chi-restraints excluded: chain I residue 141 SER Chi-restraints excluded: chain I residue 238 GLU Chi-restraints excluded: chain J residue 85 ILE Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain K residue 238 GLU Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain M residue 141 SER Chi-restraints excluded: chain M residue 238 GLU Chi-restraints excluded: chain M residue 267 MET Chi-restraints excluded: chain O residue 141 SER Chi-restraints excluded: chain O residue 267 MET Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 234 LEU Chi-restraints excluded: chain S residue 141 SER Chi-restraints excluded: chain T residue 85 ILE Chi-restraints excluded: chain V residue 141 SER Chi-restraints excluded: chain Z residue 141 SER Chi-restraints excluded: chain Z residue 238 GLU Chi-restraints excluded: chain BA residue 141 SER Chi-restraints excluded: chain BA residue 238 GLU Chi-restraints excluded: chain CA residue 94 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 767 optimal weight: 1.9990 chunk 584 optimal weight: 10.0000 chunk 403 optimal weight: 2.9990 chunk 85 optimal weight: 20.0000 chunk 370 optimal weight: 5.9990 chunk 521 optimal weight: 20.0000 chunk 779 optimal weight: 3.9990 chunk 825 optimal weight: 8.9990 chunk 407 optimal weight: 9.9990 chunk 738 optimal weight: 0.9990 chunk 222 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 112 ASN X 319 GLN X 352 GLN C 112 ASN E 319 GLN G 343 GLN K 319 GLN M 112 ASN M 319 GLN O 319 GLN Q 112 ASN S 319 GLN Z 319 GLN Z 366 GLN BA 319 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 64818 Z= 0.309 Angle : 0.519 8.291 87608 Z= 0.285 Chirality : 0.047 0.228 10640 Planarity : 0.003 0.034 11394 Dihedral : 8.894 89.356 9632 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.62 % Allowed : 19.15 % Favored : 79.23 % 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: 1.73 (0.08), residues: 8624 helix: 1.98 (0.07), residues: 4227 sheet: 0.94 (0.13), residues: 1204 loop : 0.20 (0.11), residues: 3193 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS V 401 PHE 0.008 0.001 PHEBA 195 TYR 0.012 0.002 TYR G 506 ARG 0.007 0.001 ARG C 36 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17248 Ramachandran restraints generated. 8624 Oldfield, 0 Emsley, 8624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17248 Ramachandran restraints generated. 8624 Oldfield, 0 Emsley, 8624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 776 time to evaluate : 5.609 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: X 267 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8749 (mtt) REVERT: X 488 MET cc_start: 0.9507 (mmm) cc_final: 0.8895 (mmm) REVERT: C 307 MET cc_start: 0.7767 (OUTLIER) cc_final: 0.7334 (pmt) REVERT: C 366 GLN cc_start: 0.7887 (mm-40) cc_final: 0.7444 (mt0) REVERT: E 16 MET cc_start: 0.9301 (ttp) cc_final: 0.8984 (ttp) REVERT: G 329 THR cc_start: 0.9028 (p) cc_final: 0.8740 (p) REVERT: I 267 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.7933 (mtp) REVERT: I 322 ARG cc_start: 0.8260 (mmm160) cc_final: 0.8045 (mtp85) REVERT: M 267 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8769 (mtt) REVERT: M 488 MET cc_start: 0.9505 (mmm) cc_final: 0.8667 (mmm) REVERT: O 366 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7172 (tm-30) REVERT: Q 307 MET cc_start: 0.7767 (OUTLIER) cc_final: 0.7325 (pmt) REVERT: Q 322 ARG cc_start: 0.8140 (mmm160) cc_final: 0.7920 (mtp85) REVERT: S 16 MET cc_start: 0.9277 (ttp) cc_final: 0.8973 (ttp) REVERT: V 329 THR cc_start: 0.8975 (p) cc_final: 0.8691 (p) REVERT: V 366 GLN cc_start: 0.8011 (mm-40) cc_final: 0.7711 (tp-100) REVERT: Z 52 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.8246 (m-30) REVERT: BA 193 MET cc_start: 0.8764 (tpp) cc_final: 0.8491 (tpp) outliers start: 109 outliers final: 38 residues processed: 835 average time/residue: 1.4299 time to fit residues: 1567.9997 Evaluate side-chains 800 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 755 time to evaluate : 5.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 141 SER Chi-restraints excluded: chain X residue 238 GLU Chi-restraints excluded: chain X residue 267 MET Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 238 GLU Chi-restraints excluded: chain C residue 307 MET Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 238 GLU Chi-restraints excluded: chain I residue 141 SER Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 238 GLU Chi-restraints excluded: chain I residue 267 MET Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain K residue 238 GLU Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain M residue 141 SER Chi-restraints excluded: chain M residue 267 MET Chi-restraints excluded: chain O residue 141 SER Chi-restraints excluded: chain O residue 366 GLN Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 222 LEU Chi-restraints excluded: chain Q residue 234 LEU Chi-restraints excluded: chain Q residue 307 MET Chi-restraints excluded: chain S residue 141 SER Chi-restraints excluded: chain S residue 234 LEU Chi-restraints excluded: chain T residue 85 ILE Chi-restraints excluded: chain V residue 52 ASP Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain V residue 141 SER Chi-restraints excluded: chain Z residue 52 ASP Chi-restraints excluded: chain Z residue 141 SER Chi-restraints excluded: chain AA residue 85 ILE Chi-restraints excluded: chain BA residue 141 SER Chi-restraints excluded: chain BA residue 238 GLU Chi-restraints excluded: chain CA residue 66 ILE Chi-restraints excluded: chain CA residue 94 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 687 optimal weight: 0.7980 chunk 468 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 614 optimal weight: 0.6980 chunk 340 optimal weight: 1.9990 chunk 704 optimal weight: 8.9990 chunk 570 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 421 optimal weight: 4.9990 chunk 740 optimal weight: 2.9990 chunk 208 optimal weight: 7.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 10 ASN M 352 GLN O 319 GLN BA 319 GLN BA 343 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 64818 Z= 0.232 Angle : 0.488 9.483 87608 Z= 0.267 Chirality : 0.045 0.175 10640 Planarity : 0.003 0.034 11394 Dihedral : 8.738 89.586 9632 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.24 % Allowed : 19.14 % Favored : 79.63 % 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: 1.76 (0.08), residues: 8624 helix: 2.01 (0.07), residues: 4227 sheet: 0.90 (0.13), residues: 1204 loop : 0.22 (0.11), residues: 3193 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HISCA 7 PHE 0.007 0.001 PHE I 195 TYR 0.009 0.001 TYR G 506 ARG 0.006 0.000 ARG F 9 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17248 Ramachandran restraints generated. 8624 Oldfield, 0 Emsley, 8624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17248 Ramachandran restraints generated. 8624 Oldfield, 0 Emsley, 8624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 770 time to evaluate : 5.583 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: X 267 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8779 (mtt) REVERT: X 488 MET cc_start: 0.9518 (mmm) cc_final: 0.8882 (mmm) REVERT: C 307 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7165 (pmt) REVERT: E 16 MET cc_start: 0.9296 (ttp) cc_final: 0.8990 (ttp) REVERT: G 329 THR cc_start: 0.8985 (p) cc_final: 0.8714 (p) REVERT: I 267 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8003 (mtp) REVERT: I 322 ARG cc_start: 0.8244 (mmm160) cc_final: 0.8038 (mtp85) REVERT: M 267 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8784 (mtt) REVERT: M 488 MET cc_start: 0.9517 (mmm) cc_final: 0.8834 (mmm) REVERT: O 366 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7120 (tm-30) REVERT: Q 307 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.7163 (pmt) REVERT: S 16 MET cc_start: 0.9282 (ttp) cc_final: 0.8992 (ttp) REVERT: V 329 THR cc_start: 0.8934 (p) cc_final: 0.8702 (p) REVERT: V 366 GLN cc_start: 0.8002 (mm-40) cc_final: 0.7699 (tp-100) REVERT: Z 52 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.8219 (m-30) outliers start: 83 outliers final: 39 residues processed: 817 average time/residue: 1.4332 time to fit residues: 1537.3441 Evaluate side-chains 803 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 757 time to evaluate : 5.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 141 SER Chi-restraints excluded: chain X residue 238 GLU Chi-restraints excluded: chain X residue 267 MET Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 238 GLU Chi-restraints excluded: chain C residue 307 MET Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 319 GLN Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 238 GLU Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain I residue 141 SER Chi-restraints excluded: chain I residue 238 GLU Chi-restraints excluded: chain I residue 267 MET Chi-restraints excluded: chain J residue 85 ILE Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain K residue 238 GLU Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain M residue 141 SER Chi-restraints excluded: chain M residue 222 LEU Chi-restraints excluded: chain M residue 238 GLU Chi-restraints excluded: chain M residue 267 MET Chi-restraints excluded: chain M residue 346 VAL Chi-restraints excluded: chain O residue 141 SER Chi-restraints excluded: chain O residue 366 GLN Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 222 LEU Chi-restraints excluded: chain Q residue 234 LEU Chi-restraints excluded: chain Q residue 307 MET Chi-restraints excluded: chain S residue 141 SER Chi-restraints excluded: chain T residue 85 ILE Chi-restraints excluded: chain V residue 52 ASP Chi-restraints excluded: chain V residue 141 SER Chi-restraints excluded: chain Z residue 52 ASP Chi-restraints excluded: chain Z residue 141 SER Chi-restraints excluded: chain BA residue 141 SER Chi-restraints excluded: chain BA residue 238 GLU Chi-restraints excluded: chain BA residue 295 LEU Chi-restraints excluded: chain CA residue 94 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 277 optimal weight: 20.0000 chunk 743 optimal weight: 2.9990 chunk 163 optimal weight: 10.0000 chunk 484 optimal weight: 8.9990 chunk 203 optimal weight: 20.0000 chunk 826 optimal weight: 10.0000 chunk 685 optimal weight: 1.9990 chunk 382 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 273 optimal weight: 2.9990 chunk 433 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 352 GLN G 343 GLN M 352 GLN O 319 GLN Z 366 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 64818 Z= 0.254 Angle : 0.500 9.939 87608 Z= 0.273 Chirality : 0.046 0.192 10640 Planarity : 0.003 0.034 11394 Dihedral : 8.786 89.992 9632 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.71 % Allowed : 18.29 % Favored : 80.00 % 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: 1.74 (0.08), residues: 8624 helix: 1.97 (0.07), residues: 4227 sheet: 0.86 (0.13), residues: 1204 loop : 0.26 (0.11), residues: 3193 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS L 7 PHE 0.007 0.001 PHE X 195 TYR 0.010 0.002 TYR I 478 ARG 0.007 0.000 ARG T 9 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17248 Ramachandran restraints generated. 8624 Oldfield, 0 Emsley, 8624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17248 Ramachandran restraints generated. 8624 Oldfield, 0 Emsley, 8624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 770 time to evaluate : 5.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 267 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8731 (mtt) REVERT: X 488 MET cc_start: 0.9540 (mmm) cc_final: 0.8952 (mmm) REVERT: A 267 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8394 (mtt) REVERT: A 366 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7437 (mm-40) REVERT: C 307 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7392 (pmt) REVERT: C 366 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7490 (mt0) REVERT: E 16 MET cc_start: 0.9301 (ttp) cc_final: 0.9000 (ttp) REVERT: G 329 THR cc_start: 0.8947 (p) cc_final: 0.8656 (p) REVERT: M 267 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8741 (mtt) REVERT: M 488 MET cc_start: 0.9537 (mmm) cc_final: 0.9019 (mmm) REVERT: O 267 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8357 (mtt) REVERT: O 366 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7133 (tm-30) REVERT: Q 307 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.7307 (pmt) REVERT: Q 366 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7481 (mt0) REVERT: S 16 MET cc_start: 0.9282 (ttp) cc_final: 0.8949 (ttp) REVERT: V 329 THR cc_start: 0.8919 (p) cc_final: 0.8585 (p) REVERT: V 366 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7690 (tp-100) REVERT: Z 322 ARG cc_start: 0.8196 (mmm160) cc_final: 0.7933 (mtp85) outliers start: 115 outliers final: 51 residues processed: 841 average time/residue: 1.4297 time to fit residues: 1580.0820 Evaluate side-chains 819 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 757 time to evaluate : 5.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 141 SER Chi-restraints excluded: chain X residue 238 GLU Chi-restraints excluded: chain X residue 267 MET Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 238 GLU Chi-restraints excluded: chain C residue 307 MET Chi-restraints excluded: chain C residue 366 GLN Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 222 LEU Chi-restraints excluded: chain G residue 238 GLU Chi-restraints excluded: chain I residue 141 SER Chi-restraints excluded: chain I residue 238 GLU Chi-restraints excluded: chain J residue 85 ILE Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain K residue 238 GLU Chi-restraints excluded: chain L residue 91 ILE Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain M residue 141 SER Chi-restraints excluded: chain M residue 222 LEU Chi-restraints excluded: chain M residue 238 GLU Chi-restraints excluded: chain M residue 267 MET Chi-restraints excluded: chain M residue 346 VAL Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain O residue 141 SER Chi-restraints excluded: chain O residue 267 MET Chi-restraints excluded: chain O residue 366 GLN Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 222 LEU Chi-restraints excluded: chain Q residue 234 LEU Chi-restraints excluded: chain Q residue 307 MET Chi-restraints excluded: chain Q residue 366 GLN Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain S residue 141 SER Chi-restraints excluded: chain T residue 85 ILE Chi-restraints excluded: chain V residue 52 ASP Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain V residue 141 SER Chi-restraints excluded: chain V residue 222 LEU Chi-restraints excluded: chain V residue 366 GLN Chi-restraints excluded: chain Z residue 141 SER Chi-restraints excluded: chain BA residue 139 SER Chi-restraints excluded: chain BA residue 141 SER Chi-restraints excluded: chain BA residue 238 GLU Chi-restraints excluded: chain BA residue 295 LEU Chi-restraints excluded: chain CA residue 94 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 796 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 470 optimal weight: 7.9990 chunk 603 optimal weight: 20.0000 chunk 467 optimal weight: 4.9990 chunk 695 optimal weight: 6.9990 chunk 461 optimal weight: 5.9990 chunk 823 optimal weight: 10.0000 chunk 515 optimal weight: 0.7980 chunk 501 optimal weight: 5.9990 chunk 380 optimal weight: 1.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN G 319 GLN I 352 GLN M 352 GLN O 319 GLN Q 319 GLN V 319 GLN Z 319 GLN Z 366 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 64818 Z= 0.323 Angle : 0.542 9.855 87608 Z= 0.296 Chirality : 0.048 0.232 10640 Planarity : 0.004 0.044 11394 Dihedral : 8.950 89.098 9632 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.70 % Allowed : 17.95 % Favored : 80.36 % 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: 1.60 (0.09), residues: 8624 helix: 1.85 (0.07), residues: 4214 sheet: 0.56 (0.13), residues: 1288 loop : 0.33 (0.11), residues: 3122 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS V 401 PHE 0.009 0.001 PHE I 195 TYR 0.012 0.002 TYR I 478 ARG 0.011 0.001 ARG M 322 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17248 Ramachandran restraints generated. 8624 Oldfield, 0 Emsley, 8624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17248 Ramachandran restraints generated. 8624 Oldfield, 0 Emsley, 8624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 886 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 772 time to evaluate : 5.712 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: X 488 MET cc_start: 0.9540 (mmm) cc_final: 0.9118 (mmm) REVERT: A 366 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7495 (mm-40) REVERT: C 366 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7503 (mt0) REVERT: E 16 MET cc_start: 0.9298 (ttp) cc_final: 0.8999 (ttp) REVERT: G 329 THR cc_start: 0.8953 (p) cc_final: 0.8696 (p) REVERT: G 366 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7699 (tp-100) REVERT: I 366 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7783 (tp-100) REVERT: K 205 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8729 (mt) REVERT: M 488 MET cc_start: 0.9535 (mmm) cc_final: 0.8954 (mmm) REVERT: O 366 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7104 (tm-30) REVERT: Q 288 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8413 (mtm) REVERT: Q 307 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.7451 (pmt) REVERT: Q 366 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7474 (mt0) REVERT: S 16 MET cc_start: 0.9278 (ttp) cc_final: 0.8988 (ttp) REVERT: V 193 MET cc_start: 0.8860 (tpp) cc_final: 0.8512 (tpt) REVERT: V 329 THR cc_start: 0.8944 (p) cc_final: 0.8664 (p) REVERT: V 366 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7674 (tp-100) outliers start: 114 outliers final: 56 residues processed: 847 average time/residue: 1.4638 time to fit residues: 1624.3603 Evaluate side-chains 828 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 762 time to evaluate : 5.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 141 SER Chi-restraints excluded: chain X residue 222 LEU Chi-restraints excluded: chain X residue 238 GLU Chi-restraints excluded: chain X residue 346 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 238 GLU Chi-restraints excluded: chain C residue 366 GLN Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 222 LEU Chi-restraints excluded: chain G residue 238 GLU Chi-restraints excluded: chain G residue 366 GLN Chi-restraints excluded: chain I residue 141 SER Chi-restraints excluded: chain I residue 238 GLU Chi-restraints excluded: chain I residue 366 GLN Chi-restraints excluded: chain J residue 85 ILE Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain K residue 205 ILE Chi-restraints excluded: chain K residue 238 GLU Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain M residue 141 SER Chi-restraints excluded: chain M residue 222 LEU Chi-restraints excluded: chain M residue 238 GLU Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 346 VAL Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain O residue 141 SER Chi-restraints excluded: chain O residue 222 LEU Chi-restraints excluded: chain O residue 366 GLN Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 222 LEU Chi-restraints excluded: chain Q residue 234 LEU Chi-restraints excluded: chain Q residue 288 MET Chi-restraints excluded: chain Q residue 307 MET Chi-restraints excluded: chain Q residue 366 GLN Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain S residue 141 SER Chi-restraints excluded: chain T residue 85 ILE Chi-restraints excluded: chain V residue 52 ASP Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain V residue 141 SER Chi-restraints excluded: chain V residue 222 LEU Chi-restraints excluded: chain V residue 366 GLN Chi-restraints excluded: chain Z residue 141 SER Chi-restraints excluded: chain BA residue 139 SER Chi-restraints excluded: chain BA residue 141 SER Chi-restraints excluded: chain BA residue 238 GLU Chi-restraints excluded: chain BA residue 259 LEU Chi-restraints excluded: chain BA residue 295 LEU Chi-restraints excluded: chain CA residue 94 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 509 optimal weight: 6.9990 chunk 328 optimal weight: 2.9990 chunk 491 optimal weight: 1.9990 chunk 247 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 159 optimal weight: 9.9990 chunk 523 optimal weight: 10.0000 chunk 560 optimal weight: 0.2980 chunk 406 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 646 optimal weight: 6.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN M 352 GLN O 319 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 64818 Z= 0.233 Angle : 0.504 10.866 87608 Z= 0.274 Chirality : 0.045 0.173 10640 Planarity : 0.003 0.040 11394 Dihedral : 8.759 89.823 9632 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.32 % Allowed : 18.24 % Favored : 80.43 % 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: 1.72 (0.09), residues: 8624 helix: 1.92 (0.07), residues: 4227 sheet: 0.81 (0.14), residues: 1074 loop : 0.34 (0.10), residues: 3323 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS G 401 PHE 0.007 0.001 PHE I 195 TYR 0.009 0.001 TYR I 478 ARG 0.009 0.000 ARG M 322 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17248 Ramachandran restraints generated. 8624 Oldfield, 0 Emsley, 8624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17248 Ramachandran restraints generated. 8624 Oldfield, 0 Emsley, 8624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 849 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 760 time to evaluate : 5.677 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: X 488 MET cc_start: 0.9542 (mmm) cc_final: 0.9009 (mmm) REVERT: A 366 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7456 (mm-40) REVERT: C 366 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7499 (mt0) REVERT: E 16 MET cc_start: 0.9307 (ttp) cc_final: 0.9021 (ttp) REVERT: G 329 THR cc_start: 0.8851 (p) cc_final: 0.8614 (p) REVERT: G 366 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7697 (tp-100) REVERT: I 366 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7739 (tp-100) REVERT: M 488 MET cc_start: 0.9537 (mmm) cc_final: 0.8823 (mmm) REVERT: O 366 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7106 (tm-30) REVERT: Q 307 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.7329 (pmt) REVERT: Q 366 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7537 (mt0) REVERT: S 16 MET cc_start: 0.9280 (ttp) cc_final: 0.8958 (ttp) REVERT: V 193 MET cc_start: 0.8859 (tpp) cc_final: 0.8508 (tpt) REVERT: V 366 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7700 (tp-100) outliers start: 89 outliers final: 49 residues processed: 827 average time/residue: 1.4430 time to fit residues: 1569.5489 Evaluate side-chains 808 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 751 time to evaluate : 5.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 141 SER Chi-restraints excluded: chain X residue 222 LEU Chi-restraints excluded: chain X residue 238 GLU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 238 GLU Chi-restraints excluded: chain C residue 366 GLN Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 222 LEU Chi-restraints excluded: chain G residue 238 GLU Chi-restraints excluded: chain G residue 366 GLN Chi-restraints excluded: chain I residue 141 SER Chi-restraints excluded: chain I residue 238 GLU Chi-restraints excluded: chain I residue 366 GLN Chi-restraints excluded: chain J residue 85 ILE Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain K residue 238 GLU Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain M residue 141 SER Chi-restraints excluded: chain M residue 222 LEU Chi-restraints excluded: chain M residue 238 GLU Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain O residue 141 SER Chi-restraints excluded: chain O residue 222 LEU Chi-restraints excluded: chain O residue 366 GLN Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 222 LEU Chi-restraints excluded: chain Q residue 234 LEU Chi-restraints excluded: chain Q residue 307 MET Chi-restraints excluded: chain Q residue 366 GLN Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain S residue 141 SER Chi-restraints excluded: chain T residue 85 ILE Chi-restraints excluded: chain V residue 52 ASP Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain V residue 141 SER Chi-restraints excluded: chain V residue 366 GLN Chi-restraints excluded: chain Z residue 141 SER Chi-restraints excluded: chain BA residue 139 SER Chi-restraints excluded: chain BA residue 141 SER Chi-restraints excluded: chain BA residue 238 GLU Chi-restraints excluded: chain BA residue 295 LEU Chi-restraints excluded: chain CA residue 94 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 748 optimal weight: 0.9980 chunk 788 optimal weight: 10.0000 chunk 719 optimal weight: 4.9990 chunk 767 optimal weight: 20.0000 chunk 461 optimal weight: 10.0000 chunk 334 optimal weight: 9.9990 chunk 602 optimal weight: 20.0000 chunk 235 optimal weight: 6.9990 chunk 693 optimal weight: 9.9990 chunk 725 optimal weight: 2.9990 chunk 764 optimal weight: 1.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN C 319 GLN G 343 GLN I 112 ASN O 319 GLN V 343 GLN Z 319 GLN Z 352 GLN Z 366 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 64818 Z= 0.394 Angle : 0.586 11.167 87608 Z= 0.319 Chirality : 0.050 0.272 10640 Planarity : 0.004 0.040 11394 Dihedral : 9.113 88.782 9632 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.22 % Allowed : 18.62 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.09), residues: 8624 helix: 1.72 (0.07), residues: 4201 sheet: 0.50 (0.13), residues: 1288 loop : 0.34 (0.11), residues: 3135 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS V 401 PHE 0.010 0.001 PHE M 195 TYR 0.013 0.002 TYR I 478 ARG 0.010 0.001 ARG M 322 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17248 Ramachandran restraints generated. 8624 Oldfield, 0 Emsley, 8624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17248 Ramachandran restraints generated. 8624 Oldfield, 0 Emsley, 8624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 848 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 766 time to evaluate : 8.328 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: X 171 LYS cc_start: 0.7751 (mmmt) cc_final: 0.7544 (mmtt) REVERT: X 488 MET cc_start: 0.9538 (mmm) cc_final: 0.9070 (mmm) REVERT: A 366 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7486 (mm-40) REVERT: C 366 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7471 (mt0) REVERT: E 16 MET cc_start: 0.9300 (ttp) cc_final: 0.8996 (ttp) REVERT: E 322 ARG cc_start: 0.8284 (mmm160) cc_final: 0.8029 (mtp85) REVERT: G 329 THR cc_start: 0.8908 (p) cc_final: 0.8694 (p) REVERT: G 366 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7713 (tp-100) REVERT: I 366 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7780 (tp-100) REVERT: K 205 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8697 (mt) REVERT: M 171 LYS cc_start: 0.7696 (mmmt) cc_final: 0.7490 (mmtt) REVERT: M 238 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7456 (mm-30) REVERT: M 488 MET cc_start: 0.9524 (mmm) cc_final: 0.8946 (mmm) REVERT: O 366 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7121 (tm-30) REVERT: Q 307 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7505 (pmt) REVERT: Q 366 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7472 (mt0) REVERT: S 16 MET cc_start: 0.9275 (ttp) cc_final: 0.8982 (ttp) REVERT: S 322 ARG cc_start: 0.8283 (mmm160) cc_final: 0.7999 (mtp85) REVERT: V 366 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7690 (tp-100) outliers start: 82 outliers final: 51 residues processed: 830 average time/residue: 1.4737 time to fit residues: 1600.0648 Evaluate side-chains 818 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 757 time to evaluate : 5.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 141 SER Chi-restraints excluded: chain X residue 222 LEU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 238 GLU Chi-restraints excluded: chain C residue 366 GLN Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 238 GLU Chi-restraints excluded: chain G residue 366 GLN Chi-restraints excluded: chain I residue 141 SER Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 238 GLU Chi-restraints excluded: chain I residue 366 GLN Chi-restraints excluded: chain J residue 85 ILE Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain K residue 205 ILE Chi-restraints excluded: chain K residue 238 GLU Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain M residue 141 SER Chi-restraints excluded: chain M residue 222 LEU Chi-restraints excluded: chain M residue 238 GLU Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain O residue 141 SER Chi-restraints excluded: chain O residue 222 LEU Chi-restraints excluded: chain O residue 366 GLN Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 222 LEU Chi-restraints excluded: chain Q residue 234 LEU Chi-restraints excluded: chain Q residue 307 MET Chi-restraints excluded: chain Q residue 366 GLN Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain S residue 141 SER Chi-restraints excluded: chain T residue 85 ILE Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain V residue 52 ASP Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain V residue 141 SER Chi-restraints excluded: chain V residue 366 GLN Chi-restraints excluded: chain Z residue 141 SER Chi-restraints excluded: chain BA residue 139 SER Chi-restraints excluded: chain BA residue 141 SER Chi-restraints excluded: chain BA residue 238 GLU Chi-restraints excluded: chain CA residue 94 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 503 optimal weight: 0.8980 chunk 811 optimal weight: 6.9990 chunk 495 optimal weight: 0.4980 chunk 384 optimal weight: 0.8980 chunk 563 optimal weight: 0.9980 chunk 850 optimal weight: 7.9990 chunk 783 optimal weight: 0.9980 chunk 677 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 523 optimal weight: 20.0000 chunk 415 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN E 112 ASN O 319 GLN S 112 ASN Z 10 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 64818 Z= 0.182 Angle : 0.494 11.417 87608 Z= 0.268 Chirality : 0.045 0.201 10640 Planarity : 0.003 0.039 11394 Dihedral : 8.566 89.973 9632 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 0.88 % Allowed : 19.14 % Favored : 79.99 % 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: 1.73 (0.09), residues: 8624 helix: 1.92 (0.07), residues: 4239 sheet: 0.77 (0.14), residues: 1074 loop : 0.38 (0.11), residues: 3311 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS N 7 PHE 0.007 0.001 PHE X 195 TYR 0.008 0.001 TYR G 478 ARG 0.009 0.000 ARG M 322 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17248 Ramachandran restraints generated. 8624 Oldfield, 0 Emsley, 8624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17248 Ramachandran restraints generated. 8624 Oldfield, 0 Emsley, 8624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 761 time to evaluate : 5.709 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: X 488 MET cc_start: 0.9543 (mmm) cc_final: 0.9001 (mmm) REVERT: A 322 ARG cc_start: 0.8274 (mmm160) cc_final: 0.8012 (mtp85) REVERT: A 520 MET cc_start: 0.9328 (mtp) cc_final: 0.9108 (mtp) REVERT: C 366 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7522 (mt0) REVERT: E 16 MET cc_start: 0.9300 (ttp) cc_final: 0.8984 (ttp) REVERT: G 366 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7705 (tp-100) REVERT: M 488 MET cc_start: 0.9536 (mmm) cc_final: 0.8796 (mmm) REVERT: O 366 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7131 (tm-30) REVERT: Q 307 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.7233 (pmt) REVERT: Q 366 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7528 (mt0) REVERT: S 16 MET cc_start: 0.9283 (ttp) cc_final: 0.8974 (ttp) REVERT: V 366 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7725 (tp-100) REVERT: W 92 LEU cc_start: 0.9408 (mm) cc_final: 0.9122 (mt) outliers start: 59 outliers final: 38 residues processed: 810 average time/residue: 1.4508 time to fit residues: 1543.6677 Evaluate side-chains 794 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 750 time to evaluate : 5.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 141 SER Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 238 GLU Chi-restraints excluded: chain C residue 366 GLN Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 238 GLU Chi-restraints excluded: chain G residue 366 GLN Chi-restraints excluded: chain I residue 141 SER Chi-restraints excluded: chain I residue 238 GLU Chi-restraints excluded: chain J residue 85 ILE Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 141 SER Chi-restraints excluded: chain K residue 238 GLU Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain M residue 141 SER Chi-restraints excluded: chain M residue 238 GLU Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain O residue 141 SER Chi-restraints excluded: chain O residue 366 GLN Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 222 LEU Chi-restraints excluded: chain Q residue 307 MET Chi-restraints excluded: chain Q residue 366 GLN Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain S residue 141 SER Chi-restraints excluded: chain T residue 85 ILE Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain V residue 141 SER Chi-restraints excluded: chain V residue 366 GLN Chi-restraints excluded: chain Z residue 141 SER Chi-restraints excluded: chain BA residue 139 SER Chi-restraints excluded: chain BA residue 141 SER Chi-restraints excluded: chain BA residue 238 GLU Chi-restraints excluded: chain CA residue 94 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 538 optimal weight: 0.9990 chunk 721 optimal weight: 0.9990 chunk 207 optimal weight: 0.1980 chunk 624 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 188 optimal weight: 0.9980 chunk 678 optimal weight: 0.7980 chunk 283 optimal weight: 0.8980 chunk 696 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 124 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 352 GLN A 319 GLN G 343 GLN G 352 GLN M 352 GLN O 319 GLN S 82 ASN V 343 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.163090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.109696 restraints weight = 66102.542| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.18 r_work: 0.2904 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 64818 Z= 0.172 Angle : 0.487 11.208 87608 Z= 0.263 Chirality : 0.044 0.179 10640 Planarity : 0.003 0.041 11394 Dihedral : 8.438 89.947 9632 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.98 % Allowed : 19.29 % Favored : 79.73 % 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: 1.84 (0.09), residues: 8624 helix: 2.04 (0.08), residues: 4239 sheet: 0.85 (0.13), residues: 1204 loop : 0.35 (0.11), residues: 3181 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS G 401 PHE 0.007 0.001 PHE X 195 TYR 0.008 0.001 TYR I 199 ARG 0.010 0.000 ARG M 322 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23378.65 seconds wall clock time: 407 minutes 21.05 seconds (24441.05 seconds total)