Starting phenix.real_space_refine on Wed Mar 13 06:01:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmt_16125/03_2024/8bmt_16125_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmt_16125/03_2024/8bmt_16125.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmt_16125/03_2024/8bmt_16125.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmt_16125/03_2024/8bmt_16125.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmt_16125/03_2024/8bmt_16125_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmt_16125/03_2024/8bmt_16125_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 14331 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I GLU 76": "OE1" <-> "OE2" Residue "I GLU 102": "OE1" <-> "OE2" Residue "I GLU 186": "OE1" <-> "OE2" Residue "I GLU 363": "OE1" <-> "OE2" Residue "W GLU 96": "OE1" <-> "OE2" Residue "A GLU 76": "OE1" <-> "OE2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A GLU 363": "OE1" <-> "OE2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "C GLU 76": "OE1" <-> "OE2" Residue "C GLU 102": "OE1" <-> "OE2" Residue "C GLU 186": "OE1" <-> "OE2" Residue "C GLU 363": "OE1" <-> "OE2" Residue "D GLU 96": "OE1" <-> "OE2" Residue "E GLU 76": "OE1" <-> "OE2" Residue "E GLU 102": "OE1" <-> "OE2" Residue "E GLU 186": "OE1" <-> "OE2" Residue "E GLU 363": "OE1" <-> "OE2" Residue "F GLU 96": "OE1" <-> "OE2" Residue "G GLU 76": "OE1" <-> "OE2" Residue "G GLU 102": "OE1" <-> "OE2" Residue "G GLU 186": "OE1" <-> "OE2" Residue "G GLU 363": "OE1" <-> "OE2" Residue "H GLU 96": "OE1" <-> "OE2" Residue "J GLU 76": "OE1" <-> "OE2" Residue "J GLU 102": "OE1" <-> "OE2" Residue "J GLU 186": "OE1" <-> "OE2" Residue "J GLU 363": "OE1" <-> "OE2" Residue "K GLU 96": "OE1" <-> "OE2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "L GLU 102": "OE1" <-> "OE2" Residue "L GLU 186": "OE1" <-> "OE2" Residue "L GLU 363": "OE1" <-> "OE2" Residue "M GLU 96": "OE1" <-> "OE2" Residue "N GLU 76": "OE1" <-> "OE2" Residue "N GLU 102": "OE1" <-> "OE2" Residue "N GLU 186": "OE1" <-> "OE2" Residue "N GLU 363": "OE1" <-> "OE2" Residue "O GLU 96": "OE1" <-> "OE2" Residue "P GLU 76": "OE1" <-> "OE2" Residue "P GLU 102": "OE1" <-> "OE2" Residue "P GLU 186": "OE1" <-> "OE2" Residue "P GLU 363": "OE1" <-> "OE2" Residue "Q GLU 96": "OE1" <-> "OE2" Residue "R GLU 76": "OE1" <-> "OE2" Residue "R GLU 102": "OE1" <-> "OE2" Residue "R GLU 186": "OE1" <-> "OE2" Residue "R GLU 363": "OE1" <-> "OE2" Residue "S GLU 96": "OE1" <-> "OE2" Residue "T GLU 76": "OE1" <-> "OE2" Residue "T GLU 102": "OE1" <-> "OE2" Residue "T GLU 186": "OE1" <-> "OE2" Residue "T GLU 363": "OE1" <-> "OE2" Residue "V GLU 96": "OE1" <-> "OE2" Residue "X GLU 76": "OE1" <-> "OE2" Residue "X GLU 102": "OE1" <-> "OE2" Residue "X GLU 186": "OE1" <-> "OE2" Residue "X GLU 363": "OE1" <-> "OE2" Residue "Y GLU 96": "OE1" <-> "OE2" Residue "Z GLU 76": "OE1" <-> "OE2" Residue "Z GLU 102": "OE1" <-> "OE2" Residue "Z GLU 186": "OE1" <-> "OE2" Residue "Z GLU 363": "OE1" <-> "OE2" Residue "AA GLU 96": "OE1" <-> "OE2" Residue "BA GLU 76": "OE1" <-> "OE2" Residue "BA GLU 102": "OE1" <-> "OE2" Residue "BA GLU 186": "OE1" <-> "OE2" Residue "BA GLU 363": "OE1" <-> "OE2" Residue "CA GLU 96": "OE1" <-> "OE2" 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: 65711 Number of models: 1 Model: "" Number of chains: 56 Chain: "I" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "W" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 714 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "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: 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: "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: "J" 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: "K" 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: "L" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 714 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 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: "O" 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: "P" 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: "Q" 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: "R" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 714 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 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: "V" 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: 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: "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: "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: "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: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "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: "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: "I" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 98 Classifications: {'water': 98} Link IDs: {None: 97} Chain: "A" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 99 Classifications: {'water': 99} Link IDs: {None: 98} Chain: "C" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 92 Classifications: {'water': 92} Link IDs: {None: 91} Chain: "E" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 88 Classifications: {'water': 88} Link IDs: {None: 87} Chain: "G" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 102 Classifications: {'water': 102} Link IDs: {None: 101} Chain: "J" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "L" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 98 Classifications: {'water': 98} Link IDs: {None: 97} Chain: "N" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 98 Classifications: {'water': 98} Link IDs: {None: 97} Chain: "P" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 103 Classifications: {'water': 103} Link IDs: {None: 102} Chain: "R" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 92 Classifications: {'water': 92} Link IDs: {None: 91} Chain: "T" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 92 Classifications: {'water': 92} Link IDs: {None: 91} Chain: "X" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 99 Classifications: {'water': 99} Link IDs: {None: 98} Chain: "Z" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 97 Classifications: {'water': 97} Link IDs: {None: 96} Chain: "BA" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 88 Classifications: {'water': 88} Link IDs: {None: 87} Time building chain proxies: 25.17, per 1000 atoms: 0.38 Number of scatterers: 65711 At special positions: 0 Unit cell: (152.64, 151.68, 255.36, 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 14331 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: 21.54 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 46.0% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.84 Creating SS restraints... Processing helix chain 'I' and resid 9 through 30 removed outlier: 3.892A pdb=" N VAL I 29 " --> pdb=" O ASP I 25 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N THR I 30 " --> pdb=" O ALA I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 59 Processing helix chain 'I' and resid 65 through 84 removed outlier: 4.166A pdb=" N VAL I 77 " --> pdb=" O MET I 73 " (cutoff:3.500A) removed outlier: 3.988A 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 256 through 268 Processing helix chain 'I' and resid 285 through 296 Processing helix chain 'I' and resid 339 through 355 Processing helix chain 'I' and resid 359 through 372 Processing helix chain 'I' and resid 386 through 409 Processing helix chain 'I' and resid 417 through 428 removed outlier: 5.174A pdb=" N ASP I 428 " --> pdb=" O SER I 424 " (cutoff:3.500A) Processing helix chain 'I' and resid 434 through 458 removed outlier: 3.685A pdb=" N GLU I 448 " --> pdb=" O LEU I 444 " (cutoff:3.500A) removed outlier: 3.818A 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 488 through 491 No H-bonds generated for 'chain 'I' and resid 488 through 491' Processing helix chain 'I' and resid 497 through 515 Processing helix chain 'W' and resid 29 through 31 No H-bonds generated for 'chain 'W' and resid 29 through 31' Processing helix chain 'A' and resid 9 through 30 removed outlier: 3.892A pdb=" N VAL A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N THR A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 65 through 84 removed outlier: 4.166A pdb=" N VAL A 77 " --> pdb=" O MET A 73 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 108 Processing helix chain 'A' and resid 113 through 134 Processing helix chain 'A' and resid 141 through 151 Processing helix chain 'A' and resid 156 through 169 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 231 through 243 Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 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 428 removed outlier: 5.175A pdb=" N ASP A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 458 removed outlier: 3.685A pdb=" N GLU A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.817A 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 488 through 491 No H-bonds generated for 'chain 'A' and resid 488 through 491' Processing helix chain 'A' and resid 497 through 515 Processing helix chain 'B' and resid 29 through 31 No H-bonds generated for 'chain 'B' and resid 29 through 31' Processing helix chain 'C' and resid 9 through 30 removed outlier: 3.892A pdb=" N VAL C 29 " --> pdb=" O ASP C 25 " (cutoff:3.500A) removed outlier: 5.063A 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: 4.166A pdb=" N VAL C 77 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 3.988A 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 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 256 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 428 removed outlier: 5.175A pdb=" N ASP C 428 " --> pdb=" O SER C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 458 removed outlier: 3.685A pdb=" N GLU C 448 " --> pdb=" O LEU C 444 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA C 449 " --> pdb=" O ARG C 445 " (cutoff:3.500A) Proline residue: C 450 - end of helix Processing helix chain 'C' and resid 462 through 471 Processing helix chain 'C' and resid 488 through 491 No H-bonds generated for 'chain 'C' and resid 488 through 491' Processing helix chain 'C' and resid 497 through 515 Processing helix chain 'D' and resid 29 through 31 No H-bonds generated for 'chain 'D' and resid 29 through 31' Processing helix chain 'E' and resid 9 through 30 removed outlier: 3.892A pdb=" N VAL E 29 " --> pdb=" O ASP E 25 " (cutoff:3.500A) removed outlier: 5.063A 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: 4.166A pdb=" N VAL E 77 " --> pdb=" O MET E 73 " (cutoff:3.500A) removed outlier: 3.988A 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 256 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 428 removed outlier: 5.175A pdb=" N ASP E 428 " --> pdb=" O SER E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 434 through 458 removed outlier: 3.686A pdb=" N GLU E 448 " --> pdb=" O LEU E 444 " (cutoff:3.500A) removed outlier: 3.818A 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 488 through 491 No H-bonds generated for 'chain 'E' and resid 488 through 491' Processing helix chain 'E' and resid 497 through 515 Processing helix chain 'F' and resid 29 through 31 No H-bonds generated for 'chain 'F' and resid 29 through 31' Processing helix chain 'G' and resid 9 through 30 removed outlier: 3.891A pdb=" N VAL G 29 " --> pdb=" O ASP G 25 " (cutoff:3.500A) removed outlier: 5.063A 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: 4.166A pdb=" N VAL G 77 " --> pdb=" O MET G 73 " (cutoff:3.500A) removed outlier: 3.988A 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 256 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 428 removed outlier: 5.175A pdb=" N ASP G 428 " --> pdb=" O SER G 424 " (cutoff:3.500A) Processing helix chain 'G' and resid 434 through 458 removed outlier: 3.685A pdb=" N GLU G 448 " --> pdb=" O LEU G 444 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA G 449 " --> pdb=" O ARG G 445 " (cutoff:3.500A) Proline residue: G 450 - end of helix Processing helix chain 'G' and resid 462 through 471 Processing helix chain 'G' and resid 488 through 491 No H-bonds generated for 'chain 'G' and resid 488 through 491' Processing helix chain 'G' and resid 497 through 515 Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'J' and resid 9 through 30 removed outlier: 3.892A pdb=" N VAL J 29 " --> pdb=" O ASP J 25 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N THR J 30 " --> pdb=" O ALA J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 59 Processing helix chain 'J' and resid 65 through 84 removed outlier: 4.165A pdb=" N VAL J 77 " --> pdb=" O MET J 73 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA J 78 " --> pdb=" O VAL J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 108 Processing helix chain 'J' and resid 113 through 134 Processing helix chain 'J' and resid 141 through 151 Processing helix chain 'J' and resid 156 through 169 Processing helix chain 'J' and resid 202 through 204 No H-bonds generated for 'chain 'J' and resid 202 through 204' Processing helix chain 'J' and resid 231 through 243 Proline residue: J 235 - end of helix Processing helix chain 'J' and resid 256 through 268 Processing helix chain 'J' and resid 285 through 296 Processing helix chain 'J' and resid 339 through 355 Processing helix chain 'J' and resid 359 through 372 Processing helix chain 'J' and resid 386 through 409 Processing helix chain 'J' and resid 417 through 428 removed outlier: 5.175A pdb=" N ASP J 428 " --> pdb=" O SER J 424 " (cutoff:3.500A) Processing helix chain 'J' and resid 434 through 458 removed outlier: 3.685A pdb=" N GLU J 448 " --> pdb=" O LEU J 444 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA J 449 " --> pdb=" O ARG J 445 " (cutoff:3.500A) Proline residue: J 450 - end of helix Processing helix chain 'J' and resid 462 through 471 Processing helix chain 'J' and resid 488 through 491 No H-bonds generated for 'chain 'J' and resid 488 through 491' Processing helix chain 'J' and resid 497 through 515 Processing helix chain 'K' and resid 29 through 31 No H-bonds generated for 'chain 'K' and resid 29 through 31' Processing helix chain 'L' and resid 9 through 30 removed outlier: 3.892A pdb=" N VAL L 29 " --> pdb=" O ASP L 25 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N THR L 30 " --> pdb=" O ALA L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 59 Processing helix chain 'L' and resid 65 through 84 removed outlier: 4.165A pdb=" N VAL L 77 " --> pdb=" O MET L 73 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA L 78 " --> pdb=" O VAL L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 108 Processing helix chain 'L' and resid 113 through 134 Processing helix chain 'L' and resid 141 through 151 Processing helix chain 'L' and resid 156 through 169 Processing helix chain 'L' and resid 202 through 204 No H-bonds generated for 'chain 'L' and resid 202 through 204' Processing helix chain 'L' and resid 231 through 243 Proline residue: L 235 - end of helix Processing helix chain 'L' and resid 256 through 268 Processing helix chain 'L' and resid 285 through 296 Processing helix chain 'L' and resid 339 through 355 Processing helix chain 'L' and resid 359 through 372 Processing helix chain 'L' and resid 386 through 409 Processing helix chain 'L' and resid 417 through 428 removed outlier: 5.175A pdb=" N ASP L 428 " --> pdb=" O SER L 424 " (cutoff:3.500A) Processing helix chain 'L' and resid 434 through 458 removed outlier: 3.685A pdb=" N GLU L 448 " --> pdb=" O LEU L 444 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA L 449 " --> pdb=" O ARG L 445 " (cutoff:3.500A) Proline residue: L 450 - end of helix Processing helix chain 'L' and resid 462 through 471 Processing helix chain 'L' and resid 488 through 491 No H-bonds generated for 'chain 'L' and resid 488 through 491' Processing helix chain 'L' and resid 497 through 515 Processing helix chain 'M' and resid 29 through 31 No H-bonds generated for 'chain 'M' and resid 29 through 31' Processing helix chain 'N' and resid 9 through 30 removed outlier: 3.892A pdb=" N VAL N 29 " --> pdb=" O ASP N 25 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N THR N 30 " --> pdb=" O ALA N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 59 Processing helix chain 'N' and resid 65 through 84 removed outlier: 4.166A pdb=" N VAL N 77 " --> pdb=" O MET N 73 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA N 78 " --> pdb=" O VAL N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 89 through 108 Processing helix chain 'N' and resid 113 through 134 Processing helix chain 'N' and resid 141 through 151 Processing helix chain 'N' and resid 156 through 169 Processing helix chain 'N' and resid 202 through 204 No H-bonds generated for 'chain 'N' and resid 202 through 204' Processing helix chain 'N' and resid 231 through 243 Proline residue: N 235 - end of helix Processing helix chain 'N' and resid 256 through 268 Processing helix chain 'N' and resid 285 through 296 Processing helix chain 'N' and resid 339 through 355 Processing helix chain 'N' and resid 359 through 372 Processing helix chain 'N' and resid 386 through 409 Processing helix chain 'N' and resid 417 through 428 removed outlier: 5.175A pdb=" N ASP N 428 " --> pdb=" O SER N 424 " (cutoff:3.500A) Processing helix chain 'N' and resid 434 through 458 removed outlier: 3.685A pdb=" N GLU N 448 " --> pdb=" O LEU N 444 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA N 449 " --> pdb=" O ARG N 445 " (cutoff:3.500A) Proline residue: N 450 - end of helix Processing helix chain 'N' and resid 462 through 471 Processing helix chain 'N' and resid 488 through 491 No H-bonds generated for 'chain 'N' and resid 488 through 491' Processing helix chain 'N' and resid 497 through 515 Processing helix chain 'O' and resid 29 through 31 No H-bonds generated for 'chain 'O' and resid 29 through 31' Processing helix chain 'P' and resid 9 through 30 removed outlier: 3.891A pdb=" N VAL P 29 " --> pdb=" O ASP P 25 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N THR P 30 " --> pdb=" O ALA P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 59 Processing helix chain 'P' and resid 65 through 84 removed outlier: 4.166A pdb=" N VAL P 77 " --> pdb=" O MET P 73 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA P 78 " --> pdb=" O VAL P 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 89 through 108 Processing helix chain 'P' and resid 113 through 134 Processing helix chain 'P' and resid 141 through 151 Processing helix chain 'P' and resid 156 through 169 Processing helix chain 'P' and resid 202 through 204 No H-bonds generated for 'chain 'P' and resid 202 through 204' Processing helix chain 'P' and resid 231 through 243 Proline residue: P 235 - end of helix Processing helix chain 'P' and resid 256 through 268 Processing helix chain 'P' and resid 285 through 296 Processing helix chain 'P' and resid 339 through 355 Processing helix chain 'P' and resid 359 through 372 Processing helix chain 'P' and resid 386 through 409 Processing helix chain 'P' and resid 417 through 428 removed outlier: 5.174A pdb=" N ASP P 428 " --> pdb=" O SER P 424 " (cutoff:3.500A) Processing helix chain 'P' and resid 434 through 458 removed outlier: 3.685A pdb=" N GLU P 448 " --> pdb=" O LEU P 444 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA P 449 " --> pdb=" O ARG P 445 " (cutoff:3.500A) Proline residue: P 450 - end of helix Processing helix chain 'P' and resid 462 through 471 Processing helix chain 'P' and resid 488 through 491 No H-bonds generated for 'chain 'P' and resid 488 through 491' Processing helix chain 'P' and resid 497 through 515 Processing helix chain 'Q' and resid 29 through 31 No H-bonds generated for 'chain 'Q' and resid 29 through 31' Processing helix chain 'R' and resid 9 through 30 removed outlier: 3.893A pdb=" N VAL R 29 " --> pdb=" O ASP R 25 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N THR R 30 " --> pdb=" O ALA R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 53 through 59 Processing helix chain 'R' and resid 65 through 84 removed outlier: 4.166A pdb=" N VAL R 77 " --> pdb=" O MET R 73 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA R 78 " --> pdb=" O VAL R 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 108 Processing helix chain 'R' and resid 113 through 134 Processing helix chain 'R' and resid 141 through 151 Processing helix chain 'R' and resid 156 through 169 Processing helix chain 'R' and resid 202 through 204 No H-bonds generated for 'chain 'R' and resid 202 through 204' Processing helix chain 'R' and resid 231 through 243 Proline residue: R 235 - end of helix Processing helix chain 'R' and resid 256 through 268 Processing helix chain 'R' and resid 285 through 296 Processing helix chain 'R' and resid 339 through 355 Processing helix chain 'R' and resid 359 through 372 Processing helix chain 'R' and resid 386 through 409 Processing helix chain 'R' and resid 417 through 428 removed outlier: 5.175A pdb=" N ASP R 428 " --> pdb=" O SER R 424 " (cutoff:3.500A) Processing helix chain 'R' and resid 434 through 458 removed outlier: 3.685A pdb=" N GLU R 448 " --> pdb=" O LEU R 444 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA R 449 " --> pdb=" O ARG R 445 " (cutoff:3.500A) Proline residue: R 450 - end of helix Processing helix chain 'R' and resid 462 through 471 Processing helix chain 'R' and resid 488 through 491 No H-bonds generated for 'chain 'R' and resid 488 through 491' Processing helix chain 'R' and resid 497 through 515 Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'T' and resid 9 through 30 removed outlier: 3.893A pdb=" N VAL T 29 " --> pdb=" O ASP T 25 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N THR T 30 " --> pdb=" O ALA T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 53 through 59 Processing helix chain 'T' and resid 65 through 84 removed outlier: 4.166A pdb=" N VAL T 77 " --> pdb=" O MET T 73 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA T 78 " --> pdb=" O VAL T 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 89 through 108 Processing helix chain 'T' and resid 113 through 134 Processing helix chain 'T' and resid 141 through 151 Processing helix chain 'T' and resid 156 through 169 Processing helix chain 'T' and resid 202 through 204 No H-bonds generated for 'chain 'T' and resid 202 through 204' Processing helix chain 'T' and resid 231 through 243 Proline residue: T 235 - end of helix Processing helix chain 'T' and resid 256 through 268 Processing helix chain 'T' and resid 285 through 296 Processing helix chain 'T' and resid 339 through 355 Processing helix chain 'T' and resid 359 through 372 Processing helix chain 'T' and resid 386 through 409 Processing helix chain 'T' and resid 417 through 428 removed outlier: 5.174A pdb=" N ASP T 428 " --> pdb=" O SER T 424 " (cutoff:3.500A) Processing helix chain 'T' and resid 434 through 458 removed outlier: 3.685A pdb=" N GLU T 448 " --> pdb=" O LEU T 444 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA T 449 " --> pdb=" O ARG T 445 " (cutoff:3.500A) Proline residue: T 450 - end of helix Processing helix chain 'T' and resid 462 through 471 Processing helix chain 'T' and resid 488 through 491 No H-bonds generated for 'chain 'T' and resid 488 through 491' Processing helix chain 'T' and resid 497 through 515 Processing helix chain 'V' and resid 29 through 31 No H-bonds generated for 'chain 'V' and resid 29 through 31' Processing helix chain 'X' and resid 9 through 30 removed outlier: 3.892A pdb=" N VAL X 29 " --> pdb=" O ASP X 25 " (cutoff:3.500A) removed outlier: 5.063A 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: 4.166A pdb=" N VAL X 77 " --> pdb=" O MET X 73 " (cutoff:3.500A) removed outlier: 3.988A 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 256 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 428 removed outlier: 5.174A pdb=" N ASP X 428 " --> pdb=" O SER X 424 " (cutoff:3.500A) Processing helix chain 'X' and resid 434 through 458 removed outlier: 3.686A pdb=" N GLU X 448 " --> pdb=" O LEU X 444 " (cutoff:3.500A) removed outlier: 3.818A 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 488 through 491 No H-bonds generated for 'chain 'X' and resid 488 through 491' Processing helix chain 'X' and resid 497 through 515 Processing helix chain 'Y' and resid 29 through 31 No H-bonds generated for 'chain 'Y' and resid 29 through 31' Processing helix chain 'Z' and resid 9 through 30 removed outlier: 3.892A pdb=" N VAL Z 29 " --> pdb=" O ASP Z 25 " (cutoff:3.500A) removed outlier: 5.062A 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: 4.165A pdb=" N VAL Z 77 " --> pdb=" O MET Z 73 " (cutoff:3.500A) removed outlier: 3.988A 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 256 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 428 removed outlier: 5.175A pdb=" N ASP Z 428 " --> pdb=" O SER Z 424 " (cutoff:3.500A) Processing helix chain 'Z' and resid 434 through 458 removed outlier: 3.686A pdb=" N GLU Z 448 " --> pdb=" O LEU Z 444 " (cutoff:3.500A) removed outlier: 3.817A 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 488 through 491 No H-bonds generated for 'chain 'Z' and resid 488 through 491' Processing helix chain 'Z' and resid 497 through 515 Processing helix chain 'AA' and resid 29 through 31 No H-bonds generated for 'chain 'AA' and resid 29 through 31' Processing helix chain 'BA' and resid 9 through 30 removed outlier: 3.892A pdb=" N VALBA 29 " --> pdb=" O ASPBA 25 " (cutoff:3.500A) removed outlier: 5.063A 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: 4.165A pdb=" N VALBA 77 " --> pdb=" O METBA 73 " (cutoff:3.500A) removed outlier: 3.988A 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 256 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 428 removed outlier: 5.174A pdb=" N ASPBA 428 " --> pdb=" O SERBA 424 " (cutoff:3.500A) Processing helix chain 'BA' and resid 434 through 458 removed outlier: 3.685A pdb=" N GLUBA 448 " --> pdb=" O LEUBA 444 " (cutoff:3.500A) removed outlier: 3.818A 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 488 through 491 No H-bonds generated for 'chain 'BA' and resid 488 through 491' Processing helix chain 'BA' and resid 497 through 515 Processing helix chain 'CA' and resid 29 through 31 No H-bonds generated for 'chain 'CA' and resid 29 through 31' Processing sheet with id= A, first strand: chain 'I' and resid 4 through 8 Processing sheet with id= B, first strand: chain 'I' and resid 38 through 40 Processing sheet with id= C, first strand: chain 'I' and resid 174 through 179 Processing sheet with id= D, first strand: chain 'I' and resid 213 through 216 Processing sheet with id= E, first strand: chain 'I' and resid 219 through 223 Processing sheet with id= F, first strand: chain 'I' and resid 411 through 413 Processing sheet with id= G, first strand: chain 'I' and resid 476 through 479 Processing sheet with id= H, first strand: chain 'W' and resid 74 through 78 removed outlier: 7.969A pdb=" N GLU W 82 " --> pdb=" O ARG W 14 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ARG W 14 " --> pdb=" O GLU W 82 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA W 42 " --> pdb=" O ILE W 11 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS W 13 " --> pdb=" O VAL W 40 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL W 40 " --> pdb=" O LYS W 13 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE W 64 " --> pdb=" O VAL W 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 213 through 216 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: 7.969A pdb=" N GLU B 82 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ARG B 14 " --> pdb=" O GLU B 82 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA B 42 " --> pdb=" O ILE B 11 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS B 13 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL B 40 " --> pdb=" O LYS B 13 " (cutoff:3.500A) removed outlier: 4.210A 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 213 through 216 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: 7.968A pdb=" N GLU D 82 " --> pdb=" O ARG D 14 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ARG D 14 " --> pdb=" O GLU D 82 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA D 42 " --> pdb=" O ILE D 11 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS D 13 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N VAL D 40 " --> pdb=" O LYS D 13 " (cutoff:3.500A) removed outlier: 4.209A 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 213 through 216 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: 7.969A pdb=" N GLU F 82 " --> pdb=" O ARG F 14 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ARG F 14 " --> pdb=" O GLU F 82 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA F 42 " --> pdb=" O ILE F 11 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS F 13 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL F 40 " --> pdb=" O LYS F 13 " (cutoff:3.500A) removed outlier: 4.210A 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 213 through 216 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: 7.969A pdb=" N GLU H 82 " --> pdb=" O ARG H 14 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ARG H 14 " --> pdb=" O GLU H 82 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA H 42 " --> pdb=" O ILE H 11 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS H 13 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL H 40 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE H 64 " --> pdb=" O VAL H 95 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'J' and resid 4 through 8 Processing sheet with id= AP, first strand: chain 'J' and resid 38 through 40 Processing sheet with id= AQ, first strand: chain 'J' and resid 174 through 179 Processing sheet with id= AR, first strand: chain 'J' and resid 213 through 216 Processing sheet with id= AS, first strand: chain 'J' and resid 219 through 223 Processing sheet with id= AT, first strand: chain 'J' and resid 411 through 413 Processing sheet with id= AU, first strand: chain 'J' and resid 476 through 479 Processing sheet with id= AV, first strand: chain 'K' and resid 74 through 78 removed outlier: 7.969A pdb=" N GLU K 82 " --> pdb=" O ARG K 14 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ARG K 14 " --> pdb=" O GLU K 82 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA K 42 " --> pdb=" O ILE K 11 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS K 13 " --> pdb=" O VAL K 40 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL K 40 " --> pdb=" O LYS K 13 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE K 64 " --> pdb=" O VAL K 95 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'L' and resid 4 through 8 Processing sheet with id= AX, first strand: chain 'L' and resid 38 through 40 Processing sheet with id= AY, first strand: chain 'L' and resid 174 through 179 Processing sheet with id= AZ, first strand: chain 'L' and resid 213 through 216 Processing sheet with id= BA, first strand: chain 'L' and resid 219 through 223 Processing sheet with id= BB, first strand: chain 'L' and resid 411 through 413 Processing sheet with id= BC, first strand: chain 'L' and resid 476 through 479 Processing sheet with id= BD, first strand: chain 'M' and resid 74 through 78 removed outlier: 7.969A pdb=" N GLU M 82 " --> pdb=" O ARG M 14 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ARG M 14 " --> pdb=" O GLU M 82 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA M 42 " --> pdb=" O ILE M 11 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS M 13 " --> pdb=" O VAL M 40 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL M 40 " --> pdb=" O LYS M 13 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE M 64 " --> pdb=" O VAL M 95 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'N' and resid 4 through 8 Processing sheet with id= BF, first strand: chain 'N' and resid 38 through 40 Processing sheet with id= BG, first strand: chain 'N' and resid 174 through 179 Processing sheet with id= BH, first strand: chain 'N' and resid 213 through 216 Processing sheet with id= BI, first strand: chain 'N' and resid 219 through 223 Processing sheet with id= BJ, first strand: chain 'N' and resid 411 through 413 Processing sheet with id= BK, first strand: chain 'N' and resid 476 through 479 Processing sheet with id= BL, first strand: chain 'O' and resid 74 through 78 removed outlier: 7.969A pdb=" N GLU O 82 " --> pdb=" O ARG O 14 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ARG O 14 " --> pdb=" O GLU O 82 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA O 42 " --> pdb=" O ILE O 11 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS O 13 " --> pdb=" O VAL O 40 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL O 40 " --> pdb=" O LYS O 13 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE O 64 " --> pdb=" O VAL O 95 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'P' and resid 4 through 8 Processing sheet with id= BN, first strand: chain 'P' and resid 38 through 40 Processing sheet with id= BO, first strand: chain 'P' and resid 174 through 179 Processing sheet with id= BP, first strand: chain 'P' and resid 213 through 216 Processing sheet with id= BQ, first strand: chain 'P' and resid 219 through 223 Processing sheet with id= BR, first strand: chain 'P' and resid 411 through 413 Processing sheet with id= BS, first strand: chain 'P' and resid 476 through 479 Processing sheet with id= BT, first strand: chain 'Q' and resid 74 through 78 removed outlier: 7.969A pdb=" N GLU Q 82 " --> pdb=" O ARG Q 14 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ARG Q 14 " --> pdb=" O GLU Q 82 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA Q 42 " --> pdb=" O ILE Q 11 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS Q 13 " --> pdb=" O VAL Q 40 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL Q 40 " --> pdb=" O LYS Q 13 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE Q 64 " --> pdb=" O VAL Q 95 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'R' and resid 4 through 8 Processing sheet with id= BV, first strand: chain 'R' and resid 38 through 40 Processing sheet with id= BW, first strand: chain 'R' and resid 174 through 179 Processing sheet with id= BX, first strand: chain 'R' and resid 213 through 216 Processing sheet with id= BY, first strand: chain 'R' and resid 219 through 223 Processing sheet with id= BZ, first strand: chain 'R' and resid 411 through 413 Processing sheet with id= CA, first strand: chain 'R' and resid 476 through 479 Processing sheet with id= CB, first strand: chain 'S' and resid 74 through 78 removed outlier: 7.968A pdb=" N GLU S 82 " --> pdb=" O ARG S 14 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ARG S 14 " --> pdb=" O GLU S 82 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA S 42 " --> pdb=" O ILE S 11 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS S 13 " --> pdb=" O VAL S 40 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL S 40 " --> pdb=" O LYS S 13 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE S 64 " --> pdb=" O VAL S 95 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'T' and resid 4 through 8 Processing sheet with id= CD, first strand: chain 'T' and resid 38 through 40 Processing sheet with id= CE, first strand: chain 'T' and resid 174 through 179 Processing sheet with id= CF, first strand: chain 'T' and resid 213 through 216 Processing sheet with id= CG, first strand: chain 'T' and resid 219 through 223 Processing sheet with id= CH, first strand: chain 'T' and resid 411 through 413 Processing sheet with id= CI, first strand: chain 'T' and resid 476 through 479 Processing sheet with id= CJ, first strand: chain 'V' and resid 74 through 78 removed outlier: 7.969A pdb=" N GLU V 82 " --> pdb=" O ARG V 14 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ARG V 14 " --> pdb=" O GLU V 82 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA V 42 " --> pdb=" O ILE V 11 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LYS V 13 " --> pdb=" O VAL V 40 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL V 40 " --> pdb=" O LYS V 13 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE V 64 " --> pdb=" O VAL V 95 " (cutoff:3.500A) Processing sheet with id= CK, first strand: chain 'X' and resid 4 through 8 Processing sheet with id= CL, first strand: chain 'X' and resid 38 through 40 Processing sheet with id= CM, first strand: chain 'X' and resid 174 through 179 Processing sheet with id= CN, first strand: chain 'X' and resid 213 through 216 Processing sheet with id= CO, first strand: chain 'X' and resid 219 through 223 Processing sheet with id= CP, first strand: chain 'X' and resid 411 through 413 Processing sheet with id= CQ, first strand: chain 'X' and resid 476 through 479 Processing sheet with id= CR, first strand: chain 'Y' and resid 74 through 78 removed outlier: 7.969A pdb=" N GLU Y 82 " --> pdb=" O ARG Y 14 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ARG Y 14 " --> pdb=" O GLU Y 82 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA Y 42 " --> pdb=" O ILE Y 11 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS Y 13 " --> pdb=" O VAL Y 40 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL Y 40 " --> pdb=" O LYS Y 13 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE Y 64 " --> pdb=" O VAL Y 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 213 through 216 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: 7.969A pdb=" N GLUAA 82 " --> pdb=" O ARGAA 14 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ARGAA 14 " --> pdb=" O GLUAA 82 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALAAA 42 " --> pdb=" O ILEAA 11 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYSAA 13 " --> pdb=" O VALAA 40 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VALAA 40 " --> pdb=" O LYSAA 13 " (cutoff:3.500A) removed outlier: 4.211A 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 213 through 216 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: 7.969A pdb=" N GLUCA 82 " --> pdb=" O ARGCA 14 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ARGCA 14 " --> pdb=" O GLUCA 82 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALACA 42 " --> pdb=" O ILECA 11 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYSCA 13 " --> pdb=" O VALCA 40 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N VALCA 40 " --> pdb=" O LYSCA 13 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILECA 64 " --> pdb=" O VALCA 95 " (cutoff:3.500A) 3528 hydrogen bonds defined for protein. 10206 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: 27.46 Time building geometry restraints manager: 23.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 22330 1.34 - 1.46: 10917 1.46 - 1.58: 30957 1.58 - 1.69: 70 1.69 - 1.81: 546 Bond restraints: 64820 Sorted by residual: bond pdb=" N ASN H 2 " pdb=" CA ASN H 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.11e+00 bond pdb=" N ASN M 2 " pdb=" CA ASN M 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.09e+00 bond pdb=" N ASN D 2 " pdb=" CA ASN D 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.08e+00 bond pdb=" N ASN V 2 " pdb=" CA ASN V 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.08e+00 bond pdb=" N ASN O 2 " pdb=" CA ASN O 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 ... (remaining 64815 not shown) Histogram of bond angle deviations from ideal: 98.43 - 106.72: 1409 106.72 - 115.01: 40684 115.01 - 123.30: 43647 123.30 - 131.59: 1830 131.59 - 139.88: 42 Bond angle restraints: 87612 Sorted by residual: angle pdb=" N MET J 267 " pdb=" CA MET J 267 " pdb=" CB MET J 267 " ideal model delta sigma weight residual 110.01 115.13 -5.12 1.45e+00 4.76e-01 1.25e+01 angle pdb=" N MET N 267 " pdb=" CA MET N 267 " pdb=" CB MET N 267 " ideal model delta sigma weight residual 110.01 115.12 -5.11 1.45e+00 4.76e-01 1.24e+01 angle pdb=" N MET G 267 " pdb=" CA MET G 267 " pdb=" CB MET G 267 " ideal model delta sigma weight residual 110.01 115.12 -5.11 1.45e+00 4.76e-01 1.24e+01 angle pdb=" N METBA 267 " pdb=" CA METBA 267 " pdb=" CB METBA 267 " ideal model delta sigma weight residual 110.01 115.12 -5.11 1.45e+00 4.76e-01 1.24e+01 angle pdb=" N MET I 267 " pdb=" CA MET I 267 " pdb=" CB MET I 267 " ideal model delta sigma weight residual 110.01 115.11 -5.10 1.45e+00 4.76e-01 1.24e+01 ... (remaining 87607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 36076 17.84 - 35.69: 3222 35.69 - 53.53: 784 53.53 - 71.37: 280 71.37 - 89.21: 56 Dihedral angle restraints: 40418 sinusoidal: 15974 harmonic: 24444 Sorted by residual: dihedral pdb=" CB GLU N 172 " pdb=" CG GLU N 172 " pdb=" CD GLU N 172 " pdb=" OE1 GLU N 172 " ideal model delta sinusoidal sigma weight residual 0.00 -89.21 89.21 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU E 172 " pdb=" CG GLU E 172 " pdb=" CD GLU E 172 " pdb=" OE1 GLU E 172 " ideal model delta sinusoidal sigma weight residual 0.00 -89.21 89.21 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU L 172 " pdb=" CG GLU L 172 " pdb=" CD GLU L 172 " pdb=" OE1 GLU L 172 " ideal model delta sinusoidal sigma weight residual 0.00 -89.21 89.21 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 40415 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 9097 0.060 - 0.120: 1325 0.120 - 0.179: 162 0.179 - 0.239: 14 0.239 - 0.299: 42 Chirality restraints: 10640 Sorted by residual: chirality pdb=" C3' ATP A 603 " pdb=" C2' ATP A 603 " pdb=" C4' ATP A 603 " pdb=" O3' ATP A 603 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C3' ATP Z 603 " pdb=" C2' ATP Z 603 " pdb=" C4' ATP Z 603 " pdb=" O3' ATP Z 603 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C3' ATP C 603 " pdb=" C2' ATP C 603 " pdb=" C4' ATP C 603 " pdb=" O3' ATP C 603 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 10637 not shown) Planarity restraints: 11396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 44 " 0.018 2.00e-02 2.50e+03 1.55e-02 4.20e+00 pdb=" CG PHE A 44 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE A 44 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE A 44 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 44 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 PHE A 44 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 44 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE X 44 " -0.018 2.00e-02 2.50e+03 1.55e-02 4.19e+00 pdb=" CG PHE X 44 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE X 44 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE X 44 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE X 44 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 PHE X 44 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE X 44 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE L 44 " -0.018 2.00e-02 2.50e+03 1.54e-02 4.16e+00 pdb=" CG PHE L 44 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE L 44 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE L 44 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE L 44 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 PHE L 44 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE L 44 " -0.001 2.00e-02 2.50e+03 ... (remaining 11393 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.57: 1017 2.57 - 3.21: 66054 3.21 - 3.85: 143283 3.85 - 4.50: 195081 4.50 - 5.14: 297808 Nonbonded interactions: 703243 Sorted by model distance: nonbonded pdb=" OD1 ASP G 121 " pdb=" O HOH G 701 " model vdw 1.922 2.440 nonbonded pdb=" O LYSBA 470 " pdb=" O HOHBA 701 " model vdw 1.990 2.440 nonbonded pdb=" O GLY Z 35 " pdb=" O HOH Z 701 " model vdw 1.995 2.440 nonbonded pdb=" OE2 GLU L 102 " pdb=" O HOH L 701 " model vdw 1.998 2.440 nonbonded pdb=" O GLY P 35 " pdb=" O HOH P 701 " model vdw 1.999 2.440 ... (remaining 703238 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'BA' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'X' selection = chain 'Z' } ncs_group { reference = chain 'AA' selection = chain 'B' selection = chain 'CA' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'V' 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: 3.610 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: 0.060 Extract box with map and model: 13.740 Check model and map are aligned: 0.720 Set scattering table: 0.450 Process input model: 142.210 Find NCS groups from input model: 3.710 Set up NCS constraints: 0.700 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:10.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 175.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 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 0.085 64820 Z= 0.231 Angle : 0.624 7.115 87612 Z= 0.343 Chirality : 0.047 0.299 10640 Planarity : 0.004 0.053 11396 Dihedral : 15.402 89.214 24738 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.12 % Allowed : 17.43 % Favored : 81.46 % 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: 1.86 (0.09), residues: 8624 helix: 2.31 (0.08), residues: 4242 sheet: 0.11 (0.13), residues: 1218 loop : 0.31 (0.11), residues: 3164 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS H 7 PHE 0.022 0.003 PHE A 44 TYR 0.014 0.001 TYR L 203 ARG 0.004 0.001 ARG D 9 *********************** 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 845 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 770 time to evaluate : 5.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 362 ARG cc_start: 0.6237 (ptp-110) cc_final: 0.5975 (ptp-110) REVERT: I 520 MET cc_start: 0.9160 (mtp) cc_final: 0.8958 (mtm) REVERT: W 90 ASP cc_start: 0.9523 (m-30) cc_final: 0.9265 (m-30) REVERT: A 193 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.8000 (mmm) REVERT: B 90 ASP cc_start: 0.9492 (m-30) cc_final: 0.9199 (m-30) REVERT: C 193 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7985 (mmm) REVERT: C 195 PHE cc_start: 0.8726 (p90) cc_final: 0.8517 (p90) REVERT: C 362 ARG cc_start: 0.6342 (ptp-110) cc_final: 0.6101 (ptp-110) REVERT: D 11 ILE cc_start: 0.9172 (mm) cc_final: 0.8945 (mp) REVERT: D 90 ASP cc_start: 0.9504 (m-30) cc_final: 0.9229 (m-30) REVERT: E 362 ARG cc_start: 0.6198 (ptp-110) cc_final: 0.5941 (ptp-110) REVERT: E 514 MET cc_start: 0.9104 (mtp) cc_final: 0.8748 (mtp) REVERT: F 90 ASP cc_start: 0.9499 (m-30) cc_final: 0.9249 (m-30) REVERT: G 193 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.8032 (mmm) REVERT: G 195 PHE cc_start: 0.8725 (p90) cc_final: 0.8510 (p90) REVERT: G 514 MET cc_start: 0.9087 (mtp) cc_final: 0.8516 (mtp) REVERT: H 90 ASP cc_start: 0.9499 (m-30) cc_final: 0.9245 (m-30) REVERT: J 195 PHE cc_start: 0.8709 (p90) cc_final: 0.8467 (p90) REVERT: J 362 ARG cc_start: 0.6168 (ptp-110) cc_final: 0.5956 (ptp-110) REVERT: J 514 MET cc_start: 0.9051 (mtp) cc_final: 0.8720 (mtp) REVERT: K 87 SER cc_start: 0.8982 (m) cc_final: 0.8771 (p) REVERT: K 90 ASP cc_start: 0.9525 (m-30) cc_final: 0.9237 (m-30) REVERT: L 195 PHE cc_start: 0.8743 (p90) cc_final: 0.8477 (p90) REVERT: L 322 ARG cc_start: 0.7976 (tmm-80) cc_final: 0.7751 (tpt-90) REVERT: L 362 ARG cc_start: 0.6309 (ptp-110) cc_final: 0.6086 (ptp-110) REVERT: M 11 ILE cc_start: 0.9150 (mm) cc_final: 0.8912 (mp) REVERT: M 90 ASP cc_start: 0.9525 (m-30) cc_final: 0.9282 (m-30) REVERT: N 73 MET cc_start: 0.8804 (mtm) cc_final: 0.8347 (mtp) REVERT: N 195 PHE cc_start: 0.8631 (p90) cc_final: 0.8193 (p90) REVERT: P 195 PHE cc_start: 0.8662 (p90) cc_final: 0.8297 (p90) REVERT: R 69 MET cc_start: 0.9182 (mtp) cc_final: 0.8934 (mtm) REVERT: R 195 PHE cc_start: 0.8584 (p90) cc_final: 0.7920 (p90) REVERT: T 195 PHE cc_start: 0.8575 (p90) cc_final: 0.8191 (p90) REVERT: X 141 SER cc_start: 0.7982 (m) cc_final: 0.7508 (p) REVERT: X 195 PHE cc_start: 0.8685 (p90) cc_final: 0.8129 (p90) REVERT: Z 16 MET cc_start: 0.8884 (ttp) cc_final: 0.8682 (ttp) REVERT: Z 59 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8360 (mm-30) REVERT: Z 195 PHE cc_start: 0.8558 (p90) cc_final: 0.8226 (p90) REVERT: Z 219 PHE cc_start: 0.7374 (m-80) cc_final: 0.7138 (m-80) REVERT: BA 195 PHE cc_start: 0.8547 (p90) cc_final: 0.8213 (p90) outliers start: 75 outliers final: 23 residues processed: 813 average time/residue: 1.4217 time to fit residues: 1510.6610 Evaluate side-chains 661 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 635 time to evaluate : 5.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 473 ASP Chi-restraints excluded: chain W residue 4 ARG Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain B residue 4 ARG Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain D residue 4 ARG Chi-restraints excluded: chain E residue 473 ASP Chi-restraints excluded: chain F residue 4 ARG Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 473 ASP Chi-restraints excluded: chain H residue 4 ARG Chi-restraints excluded: chain J residue 473 ASP Chi-restraints excluded: chain K residue 4 ARG Chi-restraints excluded: chain L residue 473 ASP Chi-restraints excluded: chain M residue 4 ARG Chi-restraints excluded: chain O residue 4 ARG Chi-restraints excluded: chain Q residue 4 ARG Chi-restraints excluded: chain R residue 428 ASP Chi-restraints excluded: chain S residue 4 ARG Chi-restraints excluded: chain T residue 428 ASP Chi-restraints excluded: chain V residue 4 ARG Chi-restraints excluded: chain Y residue 4 ARG Chi-restraints excluded: chain AA residue 4 ARG Chi-restraints excluded: chain CA residue 4 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 721 optimal weight: 3.9990 chunk 647 optimal weight: 10.0000 chunk 359 optimal weight: 2.9990 chunk 221 optimal weight: 6.9990 chunk 436 optimal weight: 2.9990 chunk 345 optimal weight: 4.9990 chunk 669 optimal weight: 40.0000 chunk 259 optimal weight: 7.9990 chunk 407 optimal weight: 1.9990 chunk 498 optimal weight: 0.8980 chunk 775 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 64820 Z= 0.305 Angle : 0.587 7.422 87612 Z= 0.315 Chirality : 0.047 0.214 10640 Planarity : 0.004 0.050 11396 Dihedral : 7.870 102.102 9715 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.20 % Allowed : 17.11 % Favored : 79.69 % 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: 1.56 (0.09), residues: 8624 helix: 1.90 (0.08), residues: 4214 sheet: 0.13 (0.14), residues: 1218 loop : 0.35 (0.10), residues: 3192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 7 PHE 0.022 0.003 PHE C 219 TYR 0.014 0.002 TYR X 478 ARG 0.007 0.001 ARG P 445 *********************** 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 874 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 659 time to evaluate : 5.474 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: I 44 PHE cc_start: 0.6148 (p90) cc_final: 0.5778 (p90) REVERT: I 193 MET cc_start: 0.8750 (mmm) cc_final: 0.8491 (mmm) REVERT: I 362 ARG cc_start: 0.6525 (ptp-110) cc_final: 0.6212 (ptp-110) REVERT: I 514 MET cc_start: 0.9222 (mtp) cc_final: 0.8850 (mtp) REVERT: W 7 HIS cc_start: 0.7621 (OUTLIER) cc_final: 0.7253 (m90) REVERT: A 193 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7953 (mmm) REVERT: A 267 MET cc_start: 0.8598 (mpt) cc_final: 0.8323 (mpt) REVERT: A 271 VAL cc_start: 0.7632 (OUTLIER) cc_final: 0.7394 (m) REVERT: A 360 TYR cc_start: 0.7058 (OUTLIER) cc_final: 0.6534 (m-80) REVERT: B 7 HIS cc_start: 0.7831 (OUTLIER) cc_final: 0.7395 (m90) REVERT: B 90 ASP cc_start: 0.9668 (m-30) cc_final: 0.9428 (m-30) REVERT: C 193 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.8144 (mmm) REVERT: C 195 PHE cc_start: 0.8826 (p90) cc_final: 0.8619 (p90) REVERT: C 267 MET cc_start: 0.8540 (mpt) cc_final: 0.8278 (mpt) REVERT: C 362 ARG cc_start: 0.6682 (ptp-110) cc_final: 0.6377 (ptp-110) REVERT: C 389 MET cc_start: 0.8964 (tpp) cc_final: 0.8606 (tpp) REVERT: D 7 HIS cc_start: 0.7816 (m90) cc_final: 0.7465 (m90) REVERT: E 267 MET cc_start: 0.8768 (mpt) cc_final: 0.8568 (mpt) REVERT: E 290 GLN cc_start: 0.9109 (tp-100) cc_final: 0.8846 (tp-100) REVERT: E 348 GLN cc_start: 0.8036 (tp-100) cc_final: 0.7670 (tp-100) REVERT: E 352 GLN cc_start: 0.8722 (mt0) cc_final: 0.8449 (mt0) REVERT: E 362 ARG cc_start: 0.6652 (ptp-110) cc_final: 0.6230 (ptp-110) REVERT: E 389 MET cc_start: 0.8959 (tpp) cc_final: 0.8636 (tpp) REVERT: F 7 HIS cc_start: 0.7848 (OUTLIER) cc_final: 0.7412 (m90) REVERT: G 193 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.8041 (mmm) REVERT: G 362 ARG cc_start: 0.6608 (ptp-110) cc_final: 0.6342 (ptp-110) REVERT: H 6 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8391 (mp) REVERT: H 7 HIS cc_start: 0.7690 (OUTLIER) cc_final: 0.7321 (m90) REVERT: H 90 ASP cc_start: 0.9621 (m-30) cc_final: 0.9383 (m-30) REVERT: J 193 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.8015 (mmm) REVERT: J 271 VAL cc_start: 0.7706 (OUTLIER) cc_final: 0.7462 (m) REVERT: J 348 GLN cc_start: 0.7878 (tp-100) cc_final: 0.7585 (tp-100) REVERT: J 362 ARG cc_start: 0.6413 (ptp-110) cc_final: 0.6166 (ptp-110) REVERT: K 11 ILE cc_start: 0.8585 (mm) cc_final: 0.8304 (mm) REVERT: K 90 ASP cc_start: 0.9678 (m-30) cc_final: 0.9430 (m-30) REVERT: L 193 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.8088 (mmm) REVERT: L 267 MET cc_start: 0.8625 (mpt) cc_final: 0.8101 (mpt) REVERT: L 271 VAL cc_start: 0.7692 (OUTLIER) cc_final: 0.7469 (m) REVERT: L 348 GLN cc_start: 0.7796 (tp-100) cc_final: 0.7573 (tp-100) REVERT: M 90 ASP cc_start: 0.9679 (m-30) cc_final: 0.9445 (m-30) REVERT: N 195 PHE cc_start: 0.8676 (p90) cc_final: 0.8419 (p90) REVERT: O 71 TYR cc_start: 0.5989 (OUTLIER) cc_final: 0.5251 (m-80) REVERT: P 195 PHE cc_start: 0.8655 (p90) cc_final: 0.8213 (p90) REVERT: P 219 PHE cc_start: 0.7567 (m-80) cc_final: 0.7355 (m-80) REVERT: R 205 ILE cc_start: 0.7975 (mt) cc_final: 0.7748 (tt) REVERT: S 71 TYR cc_start: 0.5918 (OUTLIER) cc_final: 0.4670 (m-80) REVERT: T 267 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8295 (pmm) REVERT: X 233 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8250 (pmm) REVERT: Y 71 TYR cc_start: 0.6010 (OUTLIER) cc_final: 0.5072 (m-80) REVERT: Z 59 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8414 (mm-30) REVERT: BA 233 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.8035 (mpp) REVERT: BA 267 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8648 (pmm) outliers start: 215 outliers final: 44 residues processed: 784 average time/residue: 1.1945 time to fit residues: 1278.2017 Evaluate side-chains 681 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 616 time to evaluate : 5.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain W residue 7 HIS Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain B residue 7 HIS Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain C residue 360 TYR Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain F residue 7 HIS Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 325 ILE Chi-restraints excluded: chain G residue 326 ASN Chi-restraints excluded: chain G residue 360 TYR Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 7 HIS Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain J residue 271 VAL Chi-restraints excluded: chain J residue 325 ILE Chi-restraints excluded: chain J residue 326 ASN Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 193 MET Chi-restraints excluded: chain L residue 271 VAL Chi-restraints excluded: chain L residue 360 TYR Chi-restraints excluded: chain M residue 66 ILE Chi-restraints excluded: chain N residue 273 VAL Chi-restraints excluded: chain O residue 6 LEU Chi-restraints excluded: chain O residue 71 TYR Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain Q residue 6 LEU Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 71 TYR Chi-restraints excluded: chain T residue 174 VAL Chi-restraints excluded: chain T residue 267 MET Chi-restraints excluded: chain T residue 273 VAL Chi-restraints excluded: chain V residue 6 LEU Chi-restraints excluded: chain V residue 71 TYR Chi-restraints excluded: chain X residue 233 MET Chi-restraints excluded: chain X residue 273 VAL Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 71 TYR Chi-restraints excluded: chain Z residue 193 MET Chi-restraints excluded: chain Z residue 273 VAL Chi-restraints excluded: chain Z residue 473 ASP Chi-restraints excluded: chain AA residue 6 LEU Chi-restraints excluded: chain BA residue 233 MET Chi-restraints excluded: chain BA residue 267 MET Chi-restraints excluded: chain BA residue 273 VAL Chi-restraints excluded: chain CA residue 6 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 431 optimal weight: 0.1980 chunk 240 optimal weight: 30.0000 chunk 645 optimal weight: 3.9990 chunk 528 optimal weight: 4.9990 chunk 213 optimal weight: 20.0000 chunk 776 optimal weight: 1.9990 chunk 839 optimal weight: 3.9990 chunk 691 optimal weight: 0.0570 chunk 770 optimal weight: 5.9990 chunk 264 optimal weight: 0.2980 chunk 623 optimal weight: 5.9990 overall best weight: 1.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 194 GLN ** R 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 194 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 64820 Z= 0.230 Angle : 0.555 9.018 87612 Z= 0.294 Chirality : 0.045 0.212 10640 Planarity : 0.003 0.036 11396 Dihedral : 7.424 82.129 9641 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.29 % Allowed : 18.27 % Favored : 79.43 % 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: 1.57 (0.09), residues: 8624 helix: 1.86 (0.08), residues: 4214 sheet: 0.39 (0.13), residues: 1330 loop : 0.33 (0.11), residues: 3080 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS M 7 PHE 0.022 0.001 PHEBA 195 TYR 0.011 0.002 TYR I 478 ARG 0.006 0.000 ARG B 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 803 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 649 time to evaluate : 5.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 44 PHE cc_start: 0.6203 (p90) cc_final: 0.5825 (p90) REVERT: I 111 MET cc_start: 0.8531 (mtt) cc_final: 0.8285 (mtt) REVERT: I 193 MET cc_start: 0.8596 (mmm) cc_final: 0.8313 (tpt) REVERT: I 220 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.7913 (mp) REVERT: I 362 ARG cc_start: 0.6607 (ptp-110) cc_final: 0.6406 (ptp-110) REVERT: I 514 MET cc_start: 0.9224 (mtp) cc_final: 0.8945 (mtp) REVERT: W 11 ILE cc_start: 0.8514 (mm) cc_final: 0.8174 (mp) REVERT: A 193 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7882 (mmm) REVERT: A 342 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8614 (pp) REVERT: B 7 HIS cc_start: 0.7917 (m90) cc_final: 0.7714 (m90) REVERT: C 76 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8023 (tt0) REVERT: C 195 PHE cc_start: 0.8784 (p90) cc_final: 0.8556 (p90) REVERT: C 284 ARG cc_start: 0.7351 (pmt170) cc_final: 0.7117 (pmt170) REVERT: C 389 MET cc_start: 0.8937 (tpp) cc_final: 0.8556 (tpp) REVERT: D 7 HIS cc_start: 0.7901 (m90) cc_final: 0.7654 (m90) REVERT: E 111 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8095 (mpt) REVERT: E 290 GLN cc_start: 0.9035 (tp-100) cc_final: 0.8817 (tp-100) REVERT: E 343 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8482 (mm-40) REVERT: E 348 GLN cc_start: 0.7983 (tp-100) cc_final: 0.7641 (tp-100) REVERT: E 362 ARG cc_start: 0.6723 (ptp-110) cc_final: 0.6451 (ptp-110) REVERT: E 389 MET cc_start: 0.8966 (tpp) cc_final: 0.8686 (tpp) REVERT: F 7 HIS cc_start: 0.7858 (m90) cc_final: 0.7657 (m90) REVERT: G 76 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8109 (tt0) REVERT: G 193 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.7984 (mmm) REVERT: G 195 PHE cc_start: 0.8827 (p90) cc_final: 0.8450 (p90) REVERT: G 220 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.8080 (mp) REVERT: G 305 ILE cc_start: 0.8667 (tp) cc_final: 0.8360 (tp) REVERT: G 514 MET cc_start: 0.9164 (mtp) cc_final: 0.8684 (mtp) REVERT: H 11 ILE cc_start: 0.8479 (mm) cc_final: 0.8144 (mp) REVERT: J 111 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8610 (mpt) REVERT: J 193 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.8123 (mmm) REVERT: J 343 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8444 (mm-40) REVERT: J 348 GLN cc_start: 0.7826 (tp-100) cc_final: 0.7445 (tp-100) REVERT: J 514 MET cc_start: 0.9271 (mtp) cc_final: 0.8966 (mtp) REVERT: K 11 ILE cc_start: 0.8558 (mm) cc_final: 0.8348 (mp) REVERT: L 193 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7963 (mmm) REVERT: L 195 PHE cc_start: 0.8793 (p90) cc_final: 0.8504 (p90) REVERT: L 267 MET cc_start: 0.8520 (mpt) cc_final: 0.8311 (mpt) REVERT: L 348 GLN cc_start: 0.7812 (tp-100) cc_final: 0.7519 (tp-100) REVERT: L 362 ARG cc_start: 0.6641 (ptp-110) cc_final: 0.6394 (ptp-110) REVERT: N 284 ARG cc_start: 0.8275 (ptp-170) cc_final: 0.8028 (pmm-80) REVERT: N 285 ARG cc_start: 0.8403 (ttp-170) cc_final: 0.7832 (mtt-85) REVERT: P 195 PHE cc_start: 0.8716 (p90) cc_final: 0.8372 (p90) REVERT: P 219 PHE cc_start: 0.7594 (m-80) cc_final: 0.7322 (m-80) REVERT: P 290 GLN cc_start: 0.8962 (tm-30) cc_final: 0.8662 (tm-30) REVERT: P 362 ARG cc_start: 0.6470 (ptp-110) cc_final: 0.6153 (ptp90) REVERT: R 285 ARG cc_start: 0.8197 (mtm-85) cc_final: 0.7930 (mtt-85) REVERT: T 267 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8229 (pmm) REVERT: T 285 ARG cc_start: 0.8036 (mtm-85) cc_final: 0.7688 (mtt90) REVERT: T 290 GLN cc_start: 0.8968 (tm-30) cc_final: 0.8741 (tm-30) REVERT: T 467 ASN cc_start: 0.8859 (m-40) cc_final: 0.8585 (m-40) REVERT: V 11 ILE cc_start: 0.9236 (mm) cc_final: 0.8981 (mm) REVERT: X 16 MET cc_start: 0.8959 (ttp) cc_final: 0.8674 (ttm) REVERT: X 285 ARG cc_start: 0.8477 (mtt180) cc_final: 0.8152 (mtt-85) REVERT: X 290 GLN cc_start: 0.8943 (tm-30) cc_final: 0.8698 (tm-30) REVERT: Z 59 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8406 (mm-30) REVERT: BA 267 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8740 (pmm) REVERT: BA 285 ARG cc_start: 0.8171 (mtt-85) cc_final: 0.7949 (mtt-85) REVERT: BA 290 GLN cc_start: 0.8956 (tm-30) cc_final: 0.8717 (tm-30) outliers start: 154 outliers final: 53 residues processed: 731 average time/residue: 1.2076 time to fit residues: 1202.5088 Evaluate side-chains 679 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 611 time to evaluate : 5.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain I residue 325 ILE Chi-restraints excluded: chain I residue 326 ASN Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 90 ASP Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 343 GLN Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 90 ASP Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 111 MET Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 331 THR Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain J residue 111 MET Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 325 ILE Chi-restraints excluded: chain J residue 328 ASP Chi-restraints excluded: chain J residue 343 GLN Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 193 MET Chi-restraints excluded: chain M residue 66 ILE Chi-restraints excluded: chain N residue 248 LEU Chi-restraints excluded: chain N residue 273 VAL Chi-restraints excluded: chain O residue 6 LEU Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 494 LEU Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain T residue 174 VAL Chi-restraints excluded: chain T residue 248 LEU Chi-restraints excluded: chain T residue 267 MET Chi-restraints excluded: chain T residue 273 VAL Chi-restraints excluded: chain V residue 6 LEU Chi-restraints excluded: chain X residue 174 VAL Chi-restraints excluded: chain X residue 273 VAL Chi-restraints excluded: chain X residue 494 LEU Chi-restraints excluded: chain Z residue 199 TYR Chi-restraints excluded: chain Z residue 273 VAL Chi-restraints excluded: chain BA residue 174 VAL Chi-restraints excluded: chain BA residue 267 MET Chi-restraints excluded: chain BA residue 273 VAL Chi-restraints excluded: chain CA residue 6 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 767 optimal weight: 9.9990 chunk 584 optimal weight: 2.9990 chunk 403 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 370 optimal weight: 0.1980 chunk 521 optimal weight: 10.0000 chunk 779 optimal weight: 2.9990 chunk 825 optimal weight: 8.9990 chunk 407 optimal weight: 0.6980 chunk 738 optimal weight: 0.9990 chunk 222 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 194 GLN Z 194 GLN AA 68 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 64820 Z= 0.220 Angle : 0.562 11.294 87612 Z= 0.294 Chirality : 0.045 0.266 10640 Planarity : 0.003 0.032 11396 Dihedral : 7.370 83.074 9638 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.79 % Allowed : 19.15 % Favored : 79.06 % 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: 1.53 (0.09), residues: 8624 helix: 1.84 (0.08), residues: 4214 sheet: 0.39 (0.13), residues: 1330 loop : 0.28 (0.11), residues: 3080 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS Q 7 PHE 0.020 0.002 PHE C 219 TYR 0.012 0.001 TYR I 478 ARG 0.007 0.000 ARG R 362 *********************** 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 754 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 634 time to evaluate : 5.468 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: I 44 PHE cc_start: 0.6199 (p90) cc_final: 0.5833 (p90) REVERT: I 111 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.8281 (mtt) REVERT: I 514 MET cc_start: 0.9210 (mtp) cc_final: 0.8956 (mtp) REVERT: W 11 ILE cc_start: 0.8545 (mm) cc_final: 0.8273 (mp) REVERT: A 111 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.7947 (mtt) REVERT: A 267 MET cc_start: 0.8565 (mpt) cc_final: 0.8138 (mpt) REVERT: A 342 ILE cc_start: 0.8883 (tt) cc_final: 0.8674 (pp) REVERT: C 76 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8012 (tt0) REVERT: C 193 MET cc_start: 0.8608 (mmm) cc_final: 0.8319 (tpt) REVERT: C 267 MET cc_start: 0.8650 (mpt) cc_final: 0.8340 (mpt) REVERT: C 284 ARG cc_start: 0.7243 (pmt170) cc_final: 0.7024 (pmt170) REVERT: C 348 GLN cc_start: 0.7886 (tp-100) cc_final: 0.7613 (tp-100) REVERT: C 362 ARG cc_start: 0.6870 (ptp-110) cc_final: 0.6600 (ptp-110) REVERT: C 389 MET cc_start: 0.8930 (tpp) cc_final: 0.8552 (tpp) REVERT: E 111 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8034 (mtm) REVERT: E 267 MET cc_start: 0.8711 (mpt) cc_final: 0.8366 (mpt) REVERT: E 290 GLN cc_start: 0.9036 (tp-100) cc_final: 0.8817 (tp-100) REVERT: E 348 GLN cc_start: 0.8017 (tp-100) cc_final: 0.7656 (tp-100) REVERT: E 362 ARG cc_start: 0.6691 (ptp-110) cc_final: 0.6439 (ptp-110) REVERT: E 389 MET cc_start: 0.8961 (tpp) cc_final: 0.8688 (tpp) REVERT: G 76 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8124 (tt0) REVERT: G 193 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7974 (mmm) REVERT: G 195 PHE cc_start: 0.8861 (p90) cc_final: 0.8486 (p90) REVERT: H 11 ILE cc_start: 0.8573 (mm) cc_final: 0.8293 (mp) REVERT: J 111 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8622 (mpt) REVERT: J 193 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8176 (mmm) REVERT: J 343 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8479 (mm-40) REVERT: J 348 GLN cc_start: 0.7854 (tp-100) cc_final: 0.7440 (tp-100) REVERT: J 514 MET cc_start: 0.9235 (mtp) cc_final: 0.8907 (mtp) REVERT: L 193 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.8015 (mmm) REVERT: L 195 PHE cc_start: 0.8793 (p90) cc_final: 0.8463 (p90) REVERT: L 348 GLN cc_start: 0.7822 (tp-100) cc_final: 0.7507 (tp-100) REVERT: N 285 ARG cc_start: 0.8424 (ttp-170) cc_final: 0.7782 (mtt-85) REVERT: N 290 GLN cc_start: 0.8917 (tm-30) cc_final: 0.8708 (tm-30) REVERT: N 362 ARG cc_start: 0.7613 (mtm110) cc_final: 0.7085 (mtp180) REVERT: P 195 PHE cc_start: 0.8706 (p90) cc_final: 0.8148 (p90) REVERT: P 219 PHE cc_start: 0.7666 (m-80) cc_final: 0.7360 (m-80) REVERT: P 290 GLN cc_start: 0.8967 (tm-30) cc_final: 0.8688 (tm-30) REVERT: P 362 ARG cc_start: 0.6534 (ptp-110) cc_final: 0.5718 (mtm-85) REVERT: R 285 ARG cc_start: 0.8131 (mtm-85) cc_final: 0.7898 (mtt-85) REVERT: R 290 GLN cc_start: 0.8949 (tm-30) cc_final: 0.8662 (tm-30) REVERT: R 362 ARG cc_start: 0.7423 (mtm110) cc_final: 0.6974 (mtp-110) REVERT: T 267 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.8197 (pmm) REVERT: T 284 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.8014 (pmm-80) REVERT: T 285 ARG cc_start: 0.8046 (mtm-85) cc_final: 0.7676 (mtt90) REVERT: T 290 GLN cc_start: 0.8974 (tm-30) cc_final: 0.8729 (tm-30) REVERT: V 11 ILE cc_start: 0.9299 (mm) cc_final: 0.9067 (mm) REVERT: X 16 MET cc_start: 0.8892 (ttp) cc_final: 0.8664 (ttm) REVERT: X 285 ARG cc_start: 0.8428 (mtt180) cc_final: 0.7929 (mtt-85) REVERT: X 290 GLN cc_start: 0.8927 (tm-30) cc_final: 0.8705 (tm-30) REVERT: Z 59 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8414 (mm-30) REVERT: Z 193 MET cc_start: 0.8235 (mmm) cc_final: 0.8035 (mmm) REVERT: Z 290 GLN cc_start: 0.8923 (tm-30) cc_final: 0.8610 (tm-30) REVERT: BA 290 GLN cc_start: 0.8921 (tm-30) cc_final: 0.8676 (tm-30) REVERT: BA 467 ASN cc_start: 0.8746 (m-40) cc_final: 0.8477 (m-40) outliers start: 120 outliers final: 51 residues processed: 705 average time/residue: 1.2301 time to fit residues: 1175.1733 Evaluate side-chains 668 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 605 time to evaluate : 5.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 111 MET Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 325 ILE Chi-restraints excluded: chain I residue 326 ASN Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 111 MET Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 331 THR Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain J residue 111 MET Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain J residue 325 ILE Chi-restraints excluded: chain J residue 343 GLN Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 193 MET Chi-restraints excluded: chain M residue 66 ILE Chi-restraints excluded: chain M residue 90 ASP Chi-restraints excluded: chain N residue 273 VAL Chi-restraints excluded: chain N residue 294 THR Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 301 ILE Chi-restraints excluded: chain P residue 494 LEU Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain T residue 174 VAL Chi-restraints excluded: chain T residue 185 ASP Chi-restraints excluded: chain T residue 267 MET Chi-restraints excluded: chain T residue 273 VAL Chi-restraints excluded: chain T residue 284 ARG Chi-restraints excluded: chain V residue 6 LEU Chi-restraints excluded: chain X residue 273 VAL Chi-restraints excluded: chain Z residue 144 ILE Chi-restraints excluded: chain Z residue 185 ASP Chi-restraints excluded: chain Z residue 273 VAL Chi-restraints excluded: chain BA residue 174 VAL Chi-restraints excluded: chain BA residue 273 VAL Chi-restraints excluded: chain CA residue 6 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 687 optimal weight: 1.9990 chunk 468 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 614 optimal weight: 5.9990 chunk 340 optimal weight: 10.0000 chunk 704 optimal weight: 10.0000 chunk 570 optimal weight: 20.0000 chunk 0 optimal weight: 5.9990 chunk 421 optimal weight: 0.7980 chunk 740 optimal weight: 0.0980 chunk 208 optimal weight: 6.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 194 GLN Z 194 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 64820 Z= 0.235 Angle : 0.562 9.607 87612 Z= 0.292 Chirality : 0.044 0.205 10640 Planarity : 0.003 0.038 11396 Dihedral : 7.391 83.759 9635 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.85 % Allowed : 19.21 % Favored : 78.94 % 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: 1.48 (0.09), residues: 8624 helix: 1.83 (0.08), residues: 4200 sheet: 0.37 (0.13), residues: 1330 loop : 0.20 (0.10), residues: 3094 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS O 7 PHE 0.020 0.001 PHE C 195 TYR 0.012 0.002 TYR J 478 ARG 0.005 0.000 ARG R 362 *********************** 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 743 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 619 time to evaluate : 5.472 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: I 44 PHE cc_start: 0.6183 (p90) cc_final: 0.5845 (p90) REVERT: I 171 LYS cc_start: 0.8132 (mmmt) cc_final: 0.7789 (mmpt) REVERT: I 193 MET cc_start: 0.8424 (tpt) cc_final: 0.8109 (mmm) REVERT: I 220 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.8116 (mp) REVERT: I 301 ILE cc_start: 0.9295 (mp) cc_final: 0.8434 (mm) REVERT: I 362 ARG cc_start: 0.6650 (ptp-110) cc_final: 0.6321 (ptp-110) REVERT: W 11 ILE cc_start: 0.8542 (mm) cc_final: 0.8316 (mp) REVERT: A 193 MET cc_start: 0.8381 (tpt) cc_final: 0.8114 (mmm) REVERT: A 342 ILE cc_start: 0.8872 (tt) cc_final: 0.8668 (pp) REVERT: C 76 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8008 (tt0) REVERT: C 193 MET cc_start: 0.8635 (mmm) cc_final: 0.8268 (tpt) REVERT: C 348 GLN cc_start: 0.7928 (tp-100) cc_final: 0.7641 (tp-100) REVERT: C 389 MET cc_start: 0.8927 (tpp) cc_final: 0.8550 (tpp) REVERT: E 111 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8012 (mtm) REVERT: E 195 PHE cc_start: 0.8784 (p90) cc_final: 0.8531 (p90) REVERT: E 348 GLN cc_start: 0.8048 (tp-100) cc_final: 0.7668 (tp-100) REVERT: E 362 ARG cc_start: 0.6746 (ptp-110) cc_final: 0.6521 (ptp-110) REVERT: E 389 MET cc_start: 0.8958 (tpp) cc_final: 0.8615 (tpp) REVERT: G 76 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8135 (tt0) REVERT: G 193 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7949 (mmm) REVERT: H 11 ILE cc_start: 0.8615 (mm) cc_final: 0.8408 (mp) REVERT: J 193 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8135 (mmm) REVERT: J 331 THR cc_start: 0.8862 (m) cc_final: 0.8660 (p) REVERT: J 348 GLN cc_start: 0.7858 (tp-100) cc_final: 0.7426 (tp-100) REVERT: J 362 ARG cc_start: 0.6821 (ptp-110) cc_final: 0.6607 (ptp-110) REVERT: L 193 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7929 (mmm) REVERT: L 195 PHE cc_start: 0.8867 (p90) cc_final: 0.8557 (p90) REVERT: L 267 MET cc_start: 0.8540 (mpt) cc_final: 0.8097 (mpt) REVERT: L 348 GLN cc_start: 0.7861 (tp-100) cc_final: 0.7561 (tp-100) REVERT: N 111 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8087 (mpt) REVERT: N 199 TYR cc_start: 0.6720 (OUTLIER) cc_final: 0.6486 (p90) REVERT: N 285 ARG cc_start: 0.8400 (ttp-170) cc_final: 0.7786 (mtt-85) REVERT: N 290 GLN cc_start: 0.8900 (tm-30) cc_final: 0.8609 (tm-30) REVERT: N 362 ARG cc_start: 0.7643 (mtm110) cc_final: 0.7207 (mtp180) REVERT: P 219 PHE cc_start: 0.7732 (m-80) cc_final: 0.7392 (m-80) REVERT: P 281 PHE cc_start: 0.7943 (m-10) cc_final: 0.7538 (m-10) REVERT: P 290 GLN cc_start: 0.8968 (tm-30) cc_final: 0.8665 (tm-30) REVERT: P 362 ARG cc_start: 0.6659 (ptp-110) cc_final: 0.5968 (mtm-85) REVERT: R 285 ARG cc_start: 0.8104 (mtm-85) cc_final: 0.7851 (mtt-85) REVERT: R 290 GLN cc_start: 0.8979 (tm-30) cc_final: 0.8672 (tm-30) REVERT: R 362 ARG cc_start: 0.7524 (mtm110) cc_final: 0.7184 (mtm-85) REVERT: T 290 GLN cc_start: 0.8977 (tm-30) cc_final: 0.8655 (tm-30) REVERT: V 11 ILE cc_start: 0.9307 (mm) cc_final: 0.9081 (mm) REVERT: X 16 MET cc_start: 0.8886 (ttp) cc_final: 0.8668 (ttm) REVERT: X 285 ARG cc_start: 0.8409 (mtt180) cc_final: 0.7986 (mtt-85) REVERT: X 290 GLN cc_start: 0.8937 (tm-30) cc_final: 0.8690 (tm-30) REVERT: Z 290 GLN cc_start: 0.8954 (tm-30) cc_final: 0.8616 (tm-30) REVERT: Z 322 ARG cc_start: 0.7792 (tpp80) cc_final: 0.7586 (tpp80) REVERT: AA 11 ILE cc_start: 0.9320 (mm) cc_final: 0.9086 (mm) REVERT: BA 267 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8747 (pmm) REVERT: BA 285 ARG cc_start: 0.8176 (mtt-85) cc_final: 0.7786 (mtp85) REVERT: BA 290 GLN cc_start: 0.8939 (tm-30) cc_final: 0.8678 (tm-30) REVERT: BA 362 ARG cc_start: 0.6846 (ptp-110) cc_final: 0.6278 (mtm-85) REVERT: BA 467 ASN cc_start: 0.8778 (m-40) cc_final: 0.8509 (m-40) REVERT: CA 11 ILE cc_start: 0.9457 (mm) cc_final: 0.9247 (tp) outliers start: 124 outliers final: 47 residues processed: 697 average time/residue: 1.2321 time to fit residues: 1162.7791 Evaluate side-chains 652 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 595 time to evaluate : 5.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain I residue 326 ASN Chi-restraints excluded: chain I residue 360 TYR Chi-restraints excluded: chain W residue 90 ASP Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 90 ASP Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 111 MET Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain J residue 325 ILE Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 193 MET Chi-restraints excluded: chain L residue 422 VAL Chi-restraints excluded: chain M residue 66 ILE Chi-restraints excluded: chain M residue 90 ASP Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 144 ILE Chi-restraints excluded: chain N residue 199 TYR Chi-restraints excluded: chain N residue 273 VAL Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 494 LEU Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 185 ASP Chi-restraints excluded: chain T residue 273 VAL Chi-restraints excluded: chain X residue 273 VAL Chi-restraints excluded: chain Z residue 144 ILE Chi-restraints excluded: chain Z residue 185 ASP Chi-restraints excluded: chain Z residue 273 VAL Chi-restraints excluded: chain BA residue 174 VAL Chi-restraints excluded: chain BA residue 267 MET Chi-restraints excluded: chain BA residue 273 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 277 optimal weight: 0.0170 chunk 743 optimal weight: 0.0980 chunk 163 optimal weight: 3.9990 chunk 484 optimal weight: 5.9990 chunk 203 optimal weight: 6.9990 chunk 826 optimal weight: 6.9990 chunk 685 optimal weight: 4.9990 chunk 382 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 273 optimal weight: 5.9990 chunk 433 optimal weight: 4.9990 overall best weight: 1.3822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 ASN Q 68 ASN V 68 ASN Z 194 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 64820 Z= 0.238 Angle : 0.577 10.406 87612 Z= 0.300 Chirality : 0.045 0.216 10640 Planarity : 0.003 0.041 11396 Dihedral : 7.412 84.010 9635 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.86 % Allowed : 19.39 % Favored : 78.75 % 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: 1.45 (0.09), residues: 8624 helix: 1.83 (0.08), residues: 4200 sheet: 0.33 (0.13), residues: 1330 loop : 0.16 (0.10), residues: 3094 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HISCA 7 PHE 0.026 0.002 PHE J 204 TYR 0.013 0.001 TYR J 478 ARG 0.005 0.000 ARG P 285 *********************** 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 746 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 621 time to evaluate : 5.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 44 PHE cc_start: 0.6224 (p90) cc_final: 0.5889 (p90) REVERT: I 111 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8268 (mtt) REVERT: I 171 LYS cc_start: 0.8156 (mmmt) cc_final: 0.7808 (mmpt) REVERT: I 193 MET cc_start: 0.8404 (tpt) cc_final: 0.8178 (mmm) REVERT: I 362 ARG cc_start: 0.6716 (ptp-110) cc_final: 0.6402 (ptp-110) REVERT: B 6 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7699 (tt) REVERT: C 76 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8028 (tt0) REVERT: C 193 MET cc_start: 0.8631 (mmm) cc_final: 0.8260 (tpt) REVERT: C 348 GLN cc_start: 0.7933 (tp-100) cc_final: 0.7640 (tp-100) REVERT: C 362 ARG cc_start: 0.6859 (ptp-110) cc_final: 0.6525 (ptp-110) REVERT: C 389 MET cc_start: 0.8923 (tpp) cc_final: 0.8546 (tpp) REVERT: E 111 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.7998 (mtm) REVERT: E 193 MET cc_start: 0.8371 (mmm) cc_final: 0.7932 (mmm) REVERT: E 290 GLN cc_start: 0.9123 (tp-100) cc_final: 0.8902 (tp-100) REVERT: E 348 GLN cc_start: 0.8078 (tp-100) cc_final: 0.7695 (tp-100) REVERT: E 362 ARG cc_start: 0.6761 (ptp-110) cc_final: 0.6543 (ptp-110) REVERT: E 389 MET cc_start: 0.8953 (tpp) cc_final: 0.8608 (tpp) REVERT: F 66 ILE cc_start: 0.9169 (OUTLIER) cc_final: 0.8885 (tp) REVERT: G 76 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8157 (tt0) REVERT: G 193 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7940 (mmm) REVERT: G 514 MET cc_start: 0.9178 (mtp) cc_final: 0.8826 (mtp) REVERT: J 193 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.8007 (mmm) REVERT: J 343 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8587 (mm-40) REVERT: J 348 GLN cc_start: 0.7847 (tp-100) cc_final: 0.7431 (tp-100) REVERT: J 362 ARG cc_start: 0.6882 (ptp-110) cc_final: 0.6660 (ptp-110) REVERT: K 6 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7675 (tt) REVERT: L 193 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7933 (mmm) REVERT: L 195 PHE cc_start: 0.8894 (p90) cc_final: 0.8581 (p90) REVERT: L 267 MET cc_start: 0.8630 (mpt) cc_final: 0.8261 (mpt) REVERT: L 348 GLN cc_start: 0.7851 (tp-100) cc_final: 0.7551 (tp-100) REVERT: L 360 TYR cc_start: 0.7027 (OUTLIER) cc_final: 0.6526 (t80) REVERT: M 6 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.7825 (tt) REVERT: M 66 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8893 (tp) REVERT: N 111 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8085 (mpt) REVERT: N 199 TYR cc_start: 0.6852 (OUTLIER) cc_final: 0.6404 (p90) REVERT: N 285 ARG cc_start: 0.8383 (ttp-170) cc_final: 0.7800 (mtt-85) REVERT: N 290 GLN cc_start: 0.8914 (tm-30) cc_final: 0.8662 (tm-30) REVERT: N 362 ARG cc_start: 0.7610 (mtm110) cc_final: 0.7232 (mtp180) REVERT: P 219 PHE cc_start: 0.7705 (m-80) cc_final: 0.7381 (m-80) REVERT: P 290 GLN cc_start: 0.8981 (tm-30) cc_final: 0.8638 (tm-30) REVERT: P 322 ARG cc_start: 0.7962 (tpp80) cc_final: 0.7670 (tpp80) REVERT: P 362 ARG cc_start: 0.6749 (ptp-110) cc_final: 0.6046 (mtm-85) REVERT: R 290 GLN cc_start: 0.8987 (tm-30) cc_final: 0.8663 (tm-30) REVERT: R 362 ARG cc_start: 0.7530 (mtm110) cc_final: 0.7192 (mtm-85) REVERT: T 284 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7971 (pmm-80) REVERT: T 362 ARG cc_start: 0.6583 (ptp-110) cc_final: 0.5989 (mtm-85) REVERT: V 11 ILE cc_start: 0.9315 (mm) cc_final: 0.9108 (mm) REVERT: X 285 ARG cc_start: 0.8372 (mtt180) cc_final: 0.7903 (mtt-85) REVERT: X 290 GLN cc_start: 0.8948 (tm-30) cc_final: 0.8684 (tm-30) REVERT: Z 290 GLN cc_start: 0.8976 (tm-30) cc_final: 0.8756 (tm-30) REVERT: AA 11 ILE cc_start: 0.9328 (mm) cc_final: 0.9098 (mm) REVERT: BA 285 ARG cc_start: 0.8115 (mtt-85) cc_final: 0.7823 (mtp85) REVERT: BA 467 ASN cc_start: 0.8787 (m-40) cc_final: 0.8517 (m-40) outliers start: 125 outliers final: 58 residues processed: 703 average time/residue: 1.2472 time to fit residues: 1186.0026 Evaluate side-chains 665 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 590 time to evaluate : 5.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 111 MET Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 326 ASN Chi-restraints excluded: chain I residue 422 VAL Chi-restraints excluded: chain W residue 6 LEU Chi-restraints excluded: chain W residue 90 ASP Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 90 ASP Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 111 MET Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 326 ASN Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 325 ILE Chi-restraints excluded: chain J residue 343 GLN Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 193 MET Chi-restraints excluded: chain L residue 360 TYR Chi-restraints excluded: chain L residue 422 VAL Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 66 ILE Chi-restraints excluded: chain M residue 90 ASP Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 199 TYR Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 273 VAL Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 301 ILE Chi-restraints excluded: chain P residue 494 LEU Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 185 ASP Chi-restraints excluded: chain T residue 273 VAL Chi-restraints excluded: chain T residue 284 ARG Chi-restraints excluded: chain T residue 301 ILE Chi-restraints excluded: chain X residue 144 ILE Chi-restraints excluded: chain X residue 273 VAL Chi-restraints excluded: chain Z residue 144 ILE Chi-restraints excluded: chain Z residue 185 ASP Chi-restraints excluded: chain Z residue 273 VAL Chi-restraints excluded: chain BA residue 174 VAL Chi-restraints excluded: chain BA residue 273 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 796 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 470 optimal weight: 0.7980 chunk 603 optimal weight: 9.9990 chunk 467 optimal weight: 0.9980 chunk 695 optimal weight: 20.0000 chunk 461 optimal weight: 5.9990 chunk 823 optimal weight: 1.9990 chunk 515 optimal weight: 20.0000 chunk 501 optimal weight: 3.9990 chunk 380 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 64820 Z= 0.307 Angle : 0.609 9.767 87612 Z= 0.316 Chirality : 0.046 0.253 10640 Planarity : 0.004 0.045 11396 Dihedral : 7.714 86.397 9635 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.95 % Allowed : 19.49 % Favored : 78.56 % 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: 1.27 (0.09), residues: 8624 helix: 1.70 (0.08), residues: 4200 sheet: 0.15 (0.13), residues: 1358 loop : 0.11 (0.10), residues: 3066 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 401 PHE 0.024 0.001 PHE I 204 TYR 0.015 0.002 TYR J 478 ARG 0.006 0.001 ARG X 362 *********************** 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 763 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 632 time to evaluate : 5.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 44 PHE cc_start: 0.6292 (p90) cc_final: 0.5960 (p90) REVERT: I 171 LYS cc_start: 0.8183 (mmmm) cc_final: 0.7835 (mmpt) REVERT: I 290 GLN cc_start: 0.9045 (tp-100) cc_final: 0.8819 (tp-100) REVERT: I 348 GLN cc_start: 0.8039 (tp-100) cc_final: 0.7644 (tp-100) REVERT: W 11 ILE cc_start: 0.8603 (mp) cc_final: 0.8375 (mp) REVERT: B 6 LEU cc_start: 0.8173 (mp) cc_final: 0.7772 (tt) REVERT: C 76 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8027 (tt0) REVERT: C 193 MET cc_start: 0.8624 (mmm) cc_final: 0.8262 (tpt) REVERT: C 343 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8462 (mm-40) REVERT: C 348 GLN cc_start: 0.7966 (tp-100) cc_final: 0.7643 (tp-100) REVERT: C 389 MET cc_start: 0.8947 (tpp) cc_final: 0.8624 (tpp) REVERT: D 6 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.7984 (tt) REVERT: E 111 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8015 (mpt) REVERT: E 193 MET cc_start: 0.8434 (mmm) cc_final: 0.8023 (mmm) REVERT: E 348 GLN cc_start: 0.8141 (tp-100) cc_final: 0.7737 (tp-100) REVERT: E 389 MET cc_start: 0.8946 (tpp) cc_final: 0.8667 (tpp) REVERT: F 6 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7970 (tt) REVERT: F 66 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8979 (tp) REVERT: G 76 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8183 (tt0) REVERT: G 193 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7904 (mmm) REVERT: G 514 MET cc_start: 0.9164 (mtp) cc_final: 0.8824 (mtp) REVERT: H 6 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7597 (tp) REVERT: H 66 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8967 (tp) REVERT: J 193 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7942 (mmm) REVERT: J 343 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8597 (mm-40) REVERT: J 348 GLN cc_start: 0.7895 (tp-100) cc_final: 0.7444 (tp-100) REVERT: K 6 LEU cc_start: 0.8283 (mp) cc_final: 0.7850 (tt) REVERT: L 171 LYS cc_start: 0.8352 (mmmm) cc_final: 0.7923 (mmpt) REVERT: L 348 GLN cc_start: 0.7893 (tp-100) cc_final: 0.7567 (tp-100) REVERT: L 360 TYR cc_start: 0.6971 (OUTLIER) cc_final: 0.6481 (t80) REVERT: M 6 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.7798 (tp) REVERT: M 66 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8848 (tp) REVERT: N 199 TYR cc_start: 0.7163 (OUTLIER) cc_final: 0.6500 (p90) REVERT: N 215 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8520 (mp) REVERT: N 285 ARG cc_start: 0.8360 (ttp-170) cc_final: 0.7762 (mtt-85) REVERT: N 290 GLN cc_start: 0.8924 (tm-30) cc_final: 0.8629 (tm-30) REVERT: N 362 ARG cc_start: 0.7602 (mtm110) cc_final: 0.7240 (mtp180) REVERT: P 69 MET cc_start: 0.9242 (mtt) cc_final: 0.9029 (mtp) REVERT: P 219 PHE cc_start: 0.7765 (m-80) cc_final: 0.7428 (m-80) REVERT: P 290 GLN cc_start: 0.9007 (tm-30) cc_final: 0.8782 (tm-30) REVERT: R 285 ARG cc_start: 0.8163 (mtm-85) cc_final: 0.7884 (mtt-85) REVERT: R 290 GLN cc_start: 0.8993 (tm-30) cc_final: 0.8779 (tm-30) REVERT: R 362 ARG cc_start: 0.7534 (mtm110) cc_final: 0.7214 (mtm-85) REVERT: T 111 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8050 (mtm) REVERT: T 290 GLN cc_start: 0.8997 (tm-30) cc_final: 0.8771 (tm-30) REVERT: T 362 ARG cc_start: 0.6613 (ptp-110) cc_final: 0.5991 (mtm-85) REVERT: V 11 ILE cc_start: 0.9342 (mm) cc_final: 0.9120 (mm) REVERT: X 285 ARG cc_start: 0.8362 (mtt180) cc_final: 0.7878 (mtt-85) REVERT: X 290 GLN cc_start: 0.8972 (tm-30) cc_final: 0.8693 (tm-30) REVERT: X 362 ARG cc_start: 0.7672 (mtm110) cc_final: 0.7108 (mtp180) REVERT: Z 290 GLN cc_start: 0.8993 (tm-30) cc_final: 0.8770 (tm-30) REVERT: BA 267 MET cc_start: 0.8401 (pmm) cc_final: 0.7973 (pmm) REVERT: BA 285 ARG cc_start: 0.8126 (mtt-85) cc_final: 0.7845 (mtp85) REVERT: BA 290 GLN cc_start: 0.8937 (tm-30) cc_final: 0.8694 (tm-30) REVERT: BA 362 ARG cc_start: 0.6809 (ptp-110) cc_final: 0.6512 (mtp180) REVERT: BA 467 ASN cc_start: 0.8821 (m-40) cc_final: 0.8524 (m-40) outliers start: 131 outliers final: 63 residues processed: 719 average time/residue: 1.3186 time to fit residues: 1277.4400 Evaluate side-chains 690 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 609 time to evaluate : 5.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 301 ILE Chi-restraints excluded: chain I residue 422 VAL Chi-restraints excluded: chain W residue 6 LEU Chi-restraints excluded: chain W residue 90 ASP Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 360 TYR Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 90 ASP Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 111 MET Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 326 ASN Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 325 ILE Chi-restraints excluded: chain J residue 343 GLN Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 193 MET Chi-restraints excluded: chain L residue 360 TYR Chi-restraints excluded: chain L residue 422 VAL Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 66 ILE Chi-restraints excluded: chain M residue 90 ASP Chi-restraints excluded: chain N residue 144 ILE Chi-restraints excluded: chain N residue 199 TYR Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 215 LEU Chi-restraints excluded: chain N residue 273 VAL Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 301 ILE Chi-restraints excluded: chain P residue 494 LEU Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain T residue 111 MET Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 185 ASP Chi-restraints excluded: chain T residue 273 VAL Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 144 ILE Chi-restraints excluded: chain X residue 273 VAL Chi-restraints excluded: chain Z residue 144 ILE Chi-restraints excluded: chain Z residue 185 ASP Chi-restraints excluded: chain Z residue 213 VAL Chi-restraints excluded: chain Z residue 273 VAL Chi-restraints excluded: chain Z residue 301 ILE Chi-restraints excluded: chain BA residue 174 VAL Chi-restraints excluded: chain BA residue 213 VAL Chi-restraints excluded: chain BA residue 273 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 509 optimal weight: 10.0000 chunk 328 optimal weight: 10.0000 chunk 491 optimal weight: 2.9990 chunk 247 optimal weight: 0.8980 chunk 161 optimal weight: 0.8980 chunk 159 optimal weight: 9.9990 chunk 523 optimal weight: 3.9990 chunk 560 optimal weight: 0.7980 chunk 406 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 646 optimal weight: 20.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 68 ASN Y 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 64820 Z= 0.198 Angle : 0.605 13.636 87612 Z= 0.309 Chirality : 0.044 0.252 10640 Planarity : 0.003 0.043 11396 Dihedral : 7.345 80.718 9635 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.34 % Allowed : 20.24 % Favored : 78.42 % 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: 1.34 (0.09), residues: 8624 helix: 1.83 (0.08), residues: 4200 sheet: 0.16 (0.14), residues: 1358 loop : 0.02 (0.10), residues: 3066 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HISCA 7 PHE 0.022 0.002 PHE C 219 TYR 0.011 0.001 TYR J 478 ARG 0.008 0.000 ARG I 362 *********************** 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 720 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 630 time to evaluate : 5.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 44 PHE cc_start: 0.6231 (p90) cc_final: 0.5916 (p90) REVERT: I 171 LYS cc_start: 0.8175 (mmmm) cc_final: 0.7819 (mmpt) REVERT: I 322 ARG cc_start: 0.8108 (mmm160) cc_final: 0.7838 (mmm160) REVERT: I 348 GLN cc_start: 0.8088 (tp-100) cc_final: 0.7741 (tp-100) REVERT: W 6 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7616 (tp) REVERT: B 6 LEU cc_start: 0.8196 (mp) cc_final: 0.7591 (tp) REVERT: B 66 ILE cc_start: 0.9298 (OUTLIER) cc_final: 0.9033 (tp) REVERT: C 193 MET cc_start: 0.8619 (mmm) cc_final: 0.8182 (tpt) REVERT: C 343 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8457 (mm-40) REVERT: C 348 GLN cc_start: 0.7914 (tp-100) cc_final: 0.7581 (tp-100) REVERT: C 389 MET cc_start: 0.8907 (tpp) cc_final: 0.8538 (tpp) REVERT: D 6 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.7754 (tp) REVERT: E 193 MET cc_start: 0.8260 (mmm) cc_final: 0.7813 (mmm) REVERT: E 348 GLN cc_start: 0.8133 (tp-100) cc_final: 0.7716 (tp-100) REVERT: E 389 MET cc_start: 0.8934 (tpp) cc_final: 0.8593 (tpp) REVERT: F 6 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7750 (tp) REVERT: F 66 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8950 (tp) REVERT: G 322 ARG cc_start: 0.8026 (mmm160) cc_final: 0.7645 (mmm160) REVERT: G 514 MET cc_start: 0.9174 (mtp) cc_final: 0.8821 (mtp) REVERT: H 6 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7830 (tp) REVERT: H 66 ILE cc_start: 0.9163 (OUTLIER) cc_final: 0.8912 (tp) REVERT: J 193 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.7991 (mmm) REVERT: J 331 THR cc_start: 0.8918 (m) cc_final: 0.8672 (p) REVERT: J 343 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8595 (mm-40) REVERT: J 348 GLN cc_start: 0.7866 (tp-100) cc_final: 0.7408 (tp-100) REVERT: K 6 LEU cc_start: 0.8214 (mp) cc_final: 0.7651 (tp) REVERT: L 171 LYS cc_start: 0.8344 (mmmm) cc_final: 0.7907 (mmpt) REVERT: L 348 GLN cc_start: 0.7873 (tp-100) cc_final: 0.7547 (tp-100) REVERT: L 360 TYR cc_start: 0.7004 (OUTLIER) cc_final: 0.6500 (t80) REVERT: M 6 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.7799 (tp) REVERT: M 66 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8872 (tp) REVERT: N 199 TYR cc_start: 0.7230 (OUTLIER) cc_final: 0.6274 (p90) REVERT: N 285 ARG cc_start: 0.8340 (ttp-170) cc_final: 0.7763 (mtt-85) REVERT: N 290 GLN cc_start: 0.8917 (tm-30) cc_final: 0.8613 (tm-30) REVERT: N 362 ARG cc_start: 0.7564 (mtm110) cc_final: 0.7254 (mtp180) REVERT: P 219 PHE cc_start: 0.7779 (m-80) cc_final: 0.7430 (m-80) REVERT: P 290 GLN cc_start: 0.8991 (tm-30) cc_final: 0.8754 (tm-30) REVERT: R 285 ARG cc_start: 0.8142 (mtm-85) cc_final: 0.7852 (mtt-85) REVERT: R 290 GLN cc_start: 0.8983 (tm-30) cc_final: 0.8760 (tm-30) REVERT: R 362 ARG cc_start: 0.7499 (mtm110) cc_final: 0.7236 (mtm-85) REVERT: T 111 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8034 (mtm) REVERT: T 362 ARG cc_start: 0.6725 (ptp-110) cc_final: 0.6117 (mtm-85) REVERT: X 285 ARG cc_start: 0.8334 (mtt180) cc_final: 0.7847 (mtt-85) REVERT: X 290 GLN cc_start: 0.8961 (tm-30) cc_final: 0.8667 (tm-30) REVERT: X 362 ARG cc_start: 0.7651 (mtm110) cc_final: 0.7144 (mtp180) REVERT: Z 290 GLN cc_start: 0.8987 (tm-30) cc_final: 0.8744 (tm-30) REVERT: Z 362 ARG cc_start: 0.7093 (ptp90) cc_final: 0.6779 (ptp-110) REVERT: BA 267 MET cc_start: 0.8468 (pmm) cc_final: 0.8084 (pmm) REVERT: BA 285 ARG cc_start: 0.8063 (mtt-85) cc_final: 0.7774 (mtp85) REVERT: BA 290 GLN cc_start: 0.8933 (tm-30) cc_final: 0.8718 (tm-30) REVERT: BA 362 ARG cc_start: 0.6757 (ptp-110) cc_final: 0.6227 (mtm-85) REVERT: BA 467 ASN cc_start: 0.8785 (m-40) cc_final: 0.8525 (m-40) REVERT: CA 11 ILE cc_start: 0.9140 (mp) cc_final: 0.8896 (pp) outliers start: 90 outliers final: 49 residues processed: 690 average time/residue: 1.2624 time to fit residues: 1173.7429 Evaluate side-chains 672 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 608 time to evaluate : 5.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 301 ILE Chi-restraints excluded: chain I residue 360 TYR Chi-restraints excluded: chain I residue 422 VAL Chi-restraints excluded: chain W residue 6 LEU Chi-restraints excluded: chain W residue 90 ASP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 360 TYR Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 90 ASP Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 325 ILE Chi-restraints excluded: chain J residue 343 GLN Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 193 MET Chi-restraints excluded: chain L residue 360 TYR Chi-restraints excluded: chain L residue 422 VAL Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 66 ILE Chi-restraints excluded: chain M residue 90 ASP Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain N residue 144 ILE Chi-restraints excluded: chain N residue 199 TYR Chi-restraints excluded: chain N residue 273 VAL Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 301 ILE Chi-restraints excluded: chain P residue 494 LEU Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain T residue 111 MET Chi-restraints excluded: chain T residue 273 VAL Chi-restraints excluded: chain X residue 144 ILE Chi-restraints excluded: chain X residue 213 VAL Chi-restraints excluded: chain X residue 273 VAL Chi-restraints excluded: chain Z residue 213 VAL Chi-restraints excluded: chain Z residue 273 VAL Chi-restraints excluded: chain Z residue 301 ILE Chi-restraints excluded: chain BA residue 213 VAL Chi-restraints excluded: chain BA residue 273 VAL Chi-restraints excluded: chain BA residue 301 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 748 optimal weight: 0.8980 chunk 788 optimal weight: 40.0000 chunk 719 optimal weight: 0.9990 chunk 767 optimal weight: 20.0000 chunk 461 optimal weight: 6.9990 chunk 334 optimal weight: 5.9990 chunk 602 optimal weight: 50.0000 chunk 235 optimal weight: 10.0000 chunk 693 optimal weight: 30.0000 chunk 725 optimal weight: 20.0000 chunk 764 optimal weight: 20.0000 overall best weight: 4.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 37 ASN BA 37 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.073 64820 Z= 0.576 Angle : 0.734 11.651 87612 Z= 0.381 Chirality : 0.053 0.318 10640 Planarity : 0.005 0.070 11396 Dihedral : 8.596 89.661 9632 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.55 % Allowed : 20.31 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.08), residues: 8624 helix: 1.15 (0.08), residues: 4242 sheet: 0.16 (0.14), residues: 1316 loop : -0.07 (0.10), residues: 3066 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 401 PHE 0.024 0.002 PHE Z 195 TYR 0.022 0.003 TYR C 478 ARG 0.011 0.001 ARG G 362 *********************** 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 740 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 636 time to evaluate : 5.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 44 PHE cc_start: 0.6350 (p90) cc_final: 0.6026 (p90) REVERT: I 171 LYS cc_start: 0.8238 (mmmm) cc_final: 0.7896 (mmpt) REVERT: I 322 ARG cc_start: 0.8224 (mmm160) cc_final: 0.7982 (mmm160) REVERT: I 348 GLN cc_start: 0.8108 (tp-100) cc_final: 0.7677 (tp-100) REVERT: W 6 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.7834 (tp) REVERT: A 171 LYS cc_start: 0.8304 (mmmt) cc_final: 0.7982 (mmpt) REVERT: B 6 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.7798 (tp) REVERT: B 66 ILE cc_start: 0.9351 (OUTLIER) cc_final: 0.9108 (tp) REVERT: C 193 MET cc_start: 0.8688 (mmm) cc_final: 0.8298 (mmm) REVERT: C 343 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8501 (mm-40) REVERT: C 348 GLN cc_start: 0.7999 (tp-100) cc_final: 0.7581 (tp-100) REVERT: C 389 MET cc_start: 0.8965 (tpp) cc_final: 0.8685 (tpp) REVERT: D 6 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8087 (tp) REVERT: E 171 LYS cc_start: 0.8218 (mmmm) cc_final: 0.7845 (mmpt) REVERT: E 193 MET cc_start: 0.8434 (mmm) cc_final: 0.7899 (mmm) REVERT: E 348 GLN cc_start: 0.8215 (tp-100) cc_final: 0.7755 (tp-100) REVERT: E 380 LYS cc_start: 0.8712 (mtpt) cc_final: 0.8424 (mmmt) REVERT: E 389 MET cc_start: 0.8908 (tpp) cc_final: 0.8623 (tpp) REVERT: F 6 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.7874 (tp) REVERT: F 66 ILE cc_start: 0.9281 (OUTLIER) cc_final: 0.9063 (tp) REVERT: G 171 LYS cc_start: 0.8103 (mmmm) cc_final: 0.7814 (mmpt) REVERT: G 193 MET cc_start: 0.8303 (mmt) cc_final: 0.8045 (mmm) REVERT: G 259 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8856 (tt) REVERT: G 514 MET cc_start: 0.9200 (mtp) cc_final: 0.8800 (mtp) REVERT: H 6 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.7977 (tp) REVERT: H 66 ILE cc_start: 0.9227 (OUTLIER) cc_final: 0.8988 (tp) REVERT: J 193 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.7975 (mmm) REVERT: J 322 ARG cc_start: 0.8154 (mmm160) cc_final: 0.7763 (mmm160) REVERT: J 348 GLN cc_start: 0.8032 (tp-100) cc_final: 0.7524 (tp-100) REVERT: K 6 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.7806 (tp) REVERT: L 171 LYS cc_start: 0.8428 (mmmm) cc_final: 0.8034 (mmpt) REVERT: L 348 GLN cc_start: 0.8055 (tp-100) cc_final: 0.7663 (tp-100) REVERT: L 360 TYR cc_start: 0.7091 (OUTLIER) cc_final: 0.6551 (t80) REVERT: M 6 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.7959 (tp) REVERT: M 66 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8923 (tp) REVERT: N 285 ARG cc_start: 0.8371 (ttp-170) cc_final: 0.7639 (mtt-85) REVERT: N 362 ARG cc_start: 0.7647 (mtm110) cc_final: 0.7335 (mtm-85) REVERT: P 219 PHE cc_start: 0.7960 (m-80) cc_final: 0.7612 (m-80) REVERT: P 290 GLN cc_start: 0.9029 (tm-30) cc_final: 0.8818 (tm-30) REVERT: P 491 MET cc_start: 0.9369 (mtm) cc_final: 0.9067 (mtm) REVERT: R 285 ARG cc_start: 0.8306 (mtm-85) cc_final: 0.7972 (mtt-85) REVERT: R 290 GLN cc_start: 0.9059 (tm-30) cc_final: 0.8847 (tm-30) REVERT: R 362 ARG cc_start: 0.7598 (mtm110) cc_final: 0.7279 (mtm-85) REVERT: T 111 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8672 (mtp) REVERT: T 288 MET cc_start: 0.8908 (mtt) cc_final: 0.8672 (mtp) REVERT: T 362 ARG cc_start: 0.6429 (ptp-110) cc_final: 0.6030 (mtm-85) REVERT: X 199 TYR cc_start: 0.7595 (OUTLIER) cc_final: 0.6827 (p90) REVERT: X 285 ARG cc_start: 0.8408 (mtt180) cc_final: 0.7916 (mtt-85) REVERT: X 290 GLN cc_start: 0.9001 (tm-30) cc_final: 0.8698 (tm-30) REVERT: X 362 ARG cc_start: 0.7548 (mtm110) cc_final: 0.7230 (mtm-85) REVERT: Z 114 MET cc_start: 0.8951 (tpp) cc_final: 0.8726 (tpp) REVERT: Z 290 GLN cc_start: 0.9052 (tm-30) cc_final: 0.8817 (tm-30) REVERT: BA 267 MET cc_start: 0.8436 (pmm) cc_final: 0.8005 (pmm) REVERT: BA 285 ARG cc_start: 0.8099 (mtt-85) cc_final: 0.7742 (mtt-85) outliers start: 104 outliers final: 60 residues processed: 718 average time/residue: 1.3067 time to fit residues: 1268.5315 Evaluate side-chains 685 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 608 time to evaluate : 5.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 301 ILE Chi-restraints excluded: chain I residue 360 TYR Chi-restraints excluded: chain I residue 422 VAL Chi-restraints excluded: chain W residue 6 LEU Chi-restraints excluded: chain W residue 90 ASP Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain E residue 360 TYR Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 467 ASN Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain J residue 325 ILE Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 360 TYR Chi-restraints excluded: chain L residue 422 VAL Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 66 ILE Chi-restraints excluded: chain M residue 90 ASP Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain N residue 144 ILE Chi-restraints excluded: chain N residue 273 VAL Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 494 LEU Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain T residue 111 MET Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 185 ASP Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 273 VAL Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 199 TYR Chi-restraints excluded: chain X residue 213 VAL Chi-restraints excluded: chain X residue 273 VAL Chi-restraints excluded: chain Z residue 139 SER Chi-restraints excluded: chain Z residue 144 ILE Chi-restraints excluded: chain Z residue 185 ASP Chi-restraints excluded: chain Z residue 213 VAL Chi-restraints excluded: chain Z residue 273 VAL Chi-restraints excluded: chain Z residue 301 ILE Chi-restraints excluded: chain BA residue 213 VAL Chi-restraints excluded: chain BA residue 273 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 503 optimal weight: 0.9980 chunk 811 optimal weight: 2.9990 chunk 495 optimal weight: 4.9990 chunk 384 optimal weight: 6.9990 chunk 563 optimal weight: 4.9990 chunk 850 optimal weight: 10.0000 chunk 783 optimal weight: 0.9980 chunk 677 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 523 optimal weight: 8.9990 chunk 415 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 37 ASN BA 37 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 64820 Z= 0.264 Angle : 0.664 11.919 87612 Z= 0.339 Chirality : 0.046 0.226 10640 Planarity : 0.003 0.052 11396 Dihedral : 7.930 86.596 9632 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.12 % Allowed : 21.35 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.09), residues: 8624 helix: 1.44 (0.08), residues: 4186 sheet: 0.04 (0.14), residues: 1344 loop : -0.03 (0.10), residues: 3094 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS L 401 PHE 0.025 0.002 PHE A 204 TYR 0.014 0.002 TYR J 478 ARG 0.014 0.001 ARG E 362 ********************** 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 721 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 646 time to evaluate : 5.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 44 PHE cc_start: 0.6285 (p90) cc_final: 0.5978 (p90) REVERT: I 111 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8351 (mtt) REVERT: I 171 LYS cc_start: 0.8217 (mmmm) cc_final: 0.7878 (mmpt) REVERT: I 322 ARG cc_start: 0.8235 (mmm160) cc_final: 0.7982 (mmm160) REVERT: I 348 GLN cc_start: 0.8130 (tp-100) cc_final: 0.7661 (tp-100) REVERT: I 352 GLN cc_start: 0.8674 (mt0) cc_final: 0.8384 (mt0) REVERT: W 6 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.7867 (tp) REVERT: A 171 LYS cc_start: 0.8320 (mmmt) cc_final: 0.7970 (mmpt) REVERT: B 6 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.7834 (tp) REVERT: B 66 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.9086 (tp) REVERT: C 193 MET cc_start: 0.8661 (mmm) cc_final: 0.8326 (mmm) REVERT: C 343 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8509 (mm-40) REVERT: C 348 GLN cc_start: 0.8009 (tp-100) cc_final: 0.7589 (tp-100) REVERT: C 362 ARG cc_start: 0.7080 (ptp-110) cc_final: 0.6722 (ptp-110) REVERT: C 389 MET cc_start: 0.8978 (tpp) cc_final: 0.8657 (tpp) REVERT: D 6 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8150 (tp) REVERT: E 171 LYS cc_start: 0.8243 (mmmm) cc_final: 0.7917 (mmpt) REVERT: E 193 MET cc_start: 0.8407 (mmm) cc_final: 0.7836 (mmm) REVERT: E 288 MET cc_start: 0.9081 (mtp) cc_final: 0.8726 (mmm) REVERT: E 348 GLN cc_start: 0.8173 (tp-100) cc_final: 0.7722 (tp-100) REVERT: E 389 MET cc_start: 0.8904 (tpp) cc_final: 0.8602 (tpp) REVERT: F 6 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.7971 (tp) REVERT: F 66 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.9001 (tp) REVERT: G 193 MET cc_start: 0.8251 (mmt) cc_final: 0.8021 (mmm) REVERT: G 514 MET cc_start: 0.9159 (mtp) cc_final: 0.8760 (mtp) REVERT: H 6 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.7939 (tp) REVERT: H 66 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8974 (tp) REVERT: J 193 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.7968 (mmm) REVERT: J 348 GLN cc_start: 0.7988 (tp-100) cc_final: 0.7497 (tp-100) REVERT: K 6 LEU cc_start: 0.8439 (mp) cc_final: 0.7764 (tp) REVERT: L 171 LYS cc_start: 0.8403 (mmmm) cc_final: 0.7984 (mmpt) REVERT: L 348 GLN cc_start: 0.8032 (tp-100) cc_final: 0.7630 (tp-100) REVERT: M 6 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.7980 (tp) REVERT: M 66 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8908 (tp) REVERT: N 285 ARG cc_start: 0.8361 (ttp-170) cc_final: 0.7641 (mtt-85) REVERT: N 362 ARG cc_start: 0.7624 (mtm110) cc_final: 0.7389 (mtm-85) REVERT: P 219 PHE cc_start: 0.8007 (m-80) cc_final: 0.7610 (m-80) REVERT: P 290 GLN cc_start: 0.9011 (tm-30) cc_final: 0.8787 (tm-30) REVERT: P 491 MET cc_start: 0.9334 (mtm) cc_final: 0.9012 (mtm) REVERT: R 285 ARG cc_start: 0.8208 (mtm-85) cc_final: 0.7897 (mtt-85) REVERT: R 290 GLN cc_start: 0.9045 (tm-30) cc_final: 0.8823 (tm-30) REVERT: R 362 ARG cc_start: 0.7592 (mtm110) cc_final: 0.7376 (mtm-85) REVERT: T 111 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8037 (mtm) REVERT: T 288 MET cc_start: 0.8947 (mtt) cc_final: 0.8710 (mtp) REVERT: T 362 ARG cc_start: 0.6658 (ptp-110) cc_final: 0.6108 (mtm-85) REVERT: X 199 TYR cc_start: 0.7588 (OUTLIER) cc_final: 0.6964 (p90) REVERT: X 285 ARG cc_start: 0.8372 (mtt180) cc_final: 0.7817 (mtt-85) REVERT: X 290 GLN cc_start: 0.8988 (tm-30) cc_final: 0.8786 (tm-30) REVERT: X 362 ARG cc_start: 0.7613 (mtm110) cc_final: 0.7270 (mtm-85) REVERT: Y 11 ILE cc_start: 0.8935 (mm) cc_final: 0.8674 (mm) REVERT: Z 290 GLN cc_start: 0.8979 (tm-30) cc_final: 0.8738 (tm-30) REVERT: AA 11 ILE cc_start: 0.9150 (mm) cc_final: 0.8847 (mm) REVERT: BA 267 MET cc_start: 0.8418 (pmm) cc_final: 0.7974 (pmm) REVERT: BA 285 ARG cc_start: 0.8306 (mtt-85) cc_final: 0.7910 (mtt-85) REVERT: BA 362 ARG cc_start: 0.7013 (ttm-80) cc_final: 0.6248 (mtm-85) outliers start: 75 outliers final: 53 residues processed: 697 average time/residue: 1.2825 time to fit residues: 1203.7828 Evaluate side-chains 692 residues out of total 6762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 624 time to evaluate : 5.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 111 MET Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 301 ILE Chi-restraints excluded: chain I residue 360 TYR Chi-restraints excluded: chain I residue 422 VAL Chi-restraints excluded: chain W residue 6 LEU Chi-restraints excluded: chain W residue 90 ASP Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 325 ILE Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain J residue 325 ILE Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 422 VAL Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 66 ILE Chi-restraints excluded: chain M residue 90 ASP Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain N residue 144 ILE Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 273 VAL Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 281 PHE Chi-restraints excluded: chain P residue 494 LEU Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain T residue 111 MET Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 185 ASP Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 273 VAL Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 199 TYR Chi-restraints excluded: chain X residue 213 VAL Chi-restraints excluded: chain X residue 273 VAL Chi-restraints excluded: chain Z residue 144 ILE Chi-restraints excluded: chain Z residue 213 VAL Chi-restraints excluded: chain Z residue 273 VAL Chi-restraints excluded: chain Z residue 281 PHE Chi-restraints excluded: chain Z residue 301 ILE Chi-restraints excluded: chain BA residue 144 ILE Chi-restraints excluded: chain BA residue 213 VAL Chi-restraints excluded: chain BA residue 273 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 538 optimal weight: 1.9990 chunk 721 optimal weight: 0.5980 chunk 207 optimal weight: 7.9990 chunk 624 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 188 optimal weight: 0.6980 chunk 678 optimal weight: 1.9990 chunk 283 optimal weight: 0.6980 chunk 696 optimal weight: 20.0000 chunk 85 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.169386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.104773 restraints weight = 95411.174| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.87 r_work: 0.3107 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 64820 Z= 0.219 Angle : 0.651 12.458 87612 Z= 0.330 Chirality : 0.045 0.222 10640 Planarity : 0.003 0.057 11396 Dihedral : 7.510 81.951 9632 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.04 % Allowed : 21.70 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.09), residues: 8624 helix: 1.66 (0.08), residues: 4172 sheet: 0.21 (0.14), residues: 1232 loop : -0.22 (0.10), residues: 3220 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HISAA 7 PHE 0.023 0.001 PHE E 204 TYR 0.012 0.001 TYR E 203 ARG 0.011 0.000 ARG I 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21000.01 seconds wall clock time: 366 minutes 19.44 seconds (21979.44 seconds total)