Starting phenix.real_space_refine (version: dev) on Wed Dec 21 19:10:11 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgh_31581/12_2022/7fgh_31581_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgh_31581/12_2022/7fgh_31581.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgh_31581/12_2022/7fgh_31581_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgh_31581/12_2022/7fgh_31581_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgh_31581/12_2022/7fgh_31581_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgh_31581/12_2022/7fgh_31581.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgh_31581/12_2022/7fgh_31581.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgh_31581/12_2022/7fgh_31581_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgh_31581/12_2022/7fgh_31581_updated.pdb" } resolution = 2.18 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.053 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 28": "OE1" <-> "OE2" Residue "A GLU 54": "OE1" <-> "OE2" Residue "A ARG 76": "NH1" <-> "NH2" Residue "A ARG 85": "NH1" <-> "NH2" Residue "A GLU 202": "OE1" <-> "OE2" Residue "A ARG 222": "NH1" <-> "NH2" Residue "A ARG 238": "NH1" <-> "NH2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "A ARG 275": "NH1" <-> "NH2" Residue "A ARG 289": "NH1" <-> "NH2" Residue "A TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 353": "OE1" <-> "OE2" Residue "A ARG 399": "NH1" <-> "NH2" Residue "A ARG 467": "NH1" <-> "NH2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B GLU 54": "OE1" <-> "OE2" Residue "B ARG 76": "NH1" <-> "NH2" Residue "B ARG 85": "NH1" <-> "NH2" Residue "B GLU 202": "OE1" <-> "OE2" Residue "B ARG 222": "NH1" <-> "NH2" Residue "B ARG 238": "NH1" <-> "NH2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "B ARG 275": "NH1" <-> "NH2" Residue "B ARG 289": "NH1" <-> "NH2" Residue "B TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 353": "OE1" <-> "OE2" Residue "B ARG 399": "NH1" <-> "NH2" Residue "B ARG 467": "NH1" <-> "NH2" Residue "C GLU 28": "OE1" <-> "OE2" Residue "C GLU 54": "OE1" <-> "OE2" Residue "C ARG 76": "NH1" <-> "NH2" Residue "C ARG 85": "NH1" <-> "NH2" Residue "C GLU 202": "OE1" <-> "OE2" Residue "C ARG 222": "NH1" <-> "NH2" Residue "C ARG 238": "NH1" <-> "NH2" Residue "C GLU 250": "OE1" <-> "OE2" Residue "C ARG 275": "NH1" <-> "NH2" Residue "C ARG 289": "NH1" <-> "NH2" Residue "C TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 353": "OE1" <-> "OE2" Residue "C ARG 399": "NH1" <-> "NH2" Residue "C ARG 467": "NH1" <-> "NH2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D GLU 54": "OE1" <-> "OE2" Residue "D ARG 76": "NH1" <-> "NH2" Residue "D ARG 85": "NH1" <-> "NH2" Residue "D GLU 202": "OE1" <-> "OE2" Residue "D ARG 222": "NH1" <-> "NH2" Residue "D ARG 238": "NH1" <-> "NH2" Residue "D GLU 250": "OE1" <-> "OE2" Residue "D ARG 275": "NH1" <-> "NH2" Residue "D ARG 289": "NH1" <-> "NH2" Residue "D TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 353": "OE1" <-> "OE2" Residue "D ARG 399": "NH1" <-> "NH2" Residue "D ARG 467": "NH1" <-> "NH2" Residue "E GLU 28": "OE1" <-> "OE2" Residue "E GLU 54": "OE1" <-> "OE2" Residue "E ARG 76": "NH1" <-> "NH2" Residue "E ARG 85": "NH1" <-> "NH2" Residue "E GLU 202": "OE1" <-> "OE2" Residue "E ARG 222": "NH1" <-> "NH2" Residue "E ARG 238": "NH1" <-> "NH2" Residue "E GLU 250": "OE1" <-> "OE2" Residue "E ARG 275": "NH1" <-> "NH2" Residue "E ARG 289": "NH1" <-> "NH2" Residue "E TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 353": "OE1" <-> "OE2" Residue "E ARG 399": "NH1" <-> "NH2" Residue "E ARG 467": "NH1" <-> "NH2" Residue "F GLU 28": "OE1" <-> "OE2" Residue "F GLU 54": "OE1" <-> "OE2" Residue "F ARG 76": "NH1" <-> "NH2" Residue "F ARG 85": "NH1" <-> "NH2" Residue "F GLU 202": "OE1" <-> "OE2" Residue "F ARG 222": "NH1" <-> "NH2" Residue "F ARG 238": "NH1" <-> "NH2" Residue "F GLU 250": "OE1" <-> "OE2" Residue "F ARG 275": "NH1" <-> "NH2" Residue "F ARG 289": "NH1" <-> "NH2" Residue "F TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 353": "OE1" <-> "OE2" Residue "F ARG 399": "NH1" <-> "NH2" Residue "F ARG 467": "NH1" <-> "NH2" Residue "G GLU 28": "OE1" <-> "OE2" Residue "G GLU 54": "OE1" <-> "OE2" Residue "G ARG 76": "NH1" <-> "NH2" Residue "G ARG 85": "NH1" <-> "NH2" Residue "G GLU 202": "OE1" <-> "OE2" Residue "G ARG 222": "NH1" <-> "NH2" Residue "G ARG 238": "NH1" <-> "NH2" Residue "G GLU 250": "OE1" <-> "OE2" Residue "G ARG 275": "NH1" <-> "NH2" Residue "G ARG 289": "NH1" <-> "NH2" Residue "G TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 353": "OE1" <-> "OE2" Residue "G ARG 399": "NH1" <-> "NH2" Residue "G ARG 467": "NH1" <-> "NH2" Residue "H GLU 28": "OE1" <-> "OE2" Residue "H GLU 54": "OE1" <-> "OE2" Residue "H ARG 76": "NH1" <-> "NH2" Residue "H ARG 85": "NH1" <-> "NH2" Residue "H GLU 202": "OE1" <-> "OE2" Residue "H ARG 222": "NH1" <-> "NH2" Residue "H ARG 238": "NH1" <-> "NH2" Residue "H GLU 250": "OE1" <-> "OE2" Residue "H ARG 275": "NH1" <-> "NH2" Residue "H ARG 289": "NH1" <-> "NH2" Residue "H TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 353": "OE1" <-> "OE2" Residue "H ARG 399": "NH1" <-> "NH2" Residue "H ARG 467": "NH1" <-> "NH2" Residue "I GLU 28": "OE1" <-> "OE2" Residue "I GLU 54": "OE1" <-> "OE2" Residue "I ARG 76": "NH1" <-> "NH2" Residue "I ARG 85": "NH1" <-> "NH2" Residue "I GLU 202": "OE1" <-> "OE2" Residue "I ARG 222": "NH1" <-> "NH2" Residue "I ARG 238": "NH1" <-> "NH2" Residue "I GLU 250": "OE1" <-> "OE2" Residue "I ARG 275": "NH1" <-> "NH2" Residue "I ARG 289": "NH1" <-> "NH2" Residue "I TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 353": "OE1" <-> "OE2" Residue "I ARG 399": "NH1" <-> "NH2" Residue "I ARG 467": "NH1" <-> "NH2" Residue "J GLU 28": "OE1" <-> "OE2" Residue "J GLU 54": "OE1" <-> "OE2" Residue "J ARG 76": "NH1" <-> "NH2" Residue "J ARG 85": "NH1" <-> "NH2" Residue "J GLU 202": "OE1" <-> "OE2" Residue "J ARG 222": "NH1" <-> "NH2" Residue "J ARG 238": "NH1" <-> "NH2" Residue "J GLU 250": "OE1" <-> "OE2" Residue "J ARG 275": "NH1" <-> "NH2" Residue "J ARG 289": "NH1" <-> "NH2" Residue "J TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 353": "OE1" <-> "OE2" Residue "J ARG 399": "NH1" <-> "NH2" Residue "J ARG 467": "NH1" <-> "NH2" Residue "K GLU 28": "OE1" <-> "OE2" Residue "K GLU 54": "OE1" <-> "OE2" Residue "K ARG 76": "NH1" <-> "NH2" Residue "K ARG 85": "NH1" <-> "NH2" Residue "K GLU 202": "OE1" <-> "OE2" Residue "K ARG 222": "NH1" <-> "NH2" Residue "K ARG 238": "NH1" <-> "NH2" Residue "K GLU 250": "OE1" <-> "OE2" Residue "K ARG 275": "NH1" <-> "NH2" Residue "K ARG 289": "NH1" <-> "NH2" Residue "K TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 353": "OE1" <-> "OE2" Residue "K ARG 399": "NH1" <-> "NH2" Residue "K ARG 467": "NH1" <-> "NH2" Residue "L GLU 28": "OE1" <-> "OE2" Residue "L GLU 54": "OE1" <-> "OE2" Residue "L ARG 76": "NH1" <-> "NH2" Residue "L ARG 85": "NH1" <-> "NH2" Residue "L GLU 202": "OE1" <-> "OE2" Residue "L ARG 222": "NH1" <-> "NH2" Residue "L ARG 238": "NH1" <-> "NH2" Residue "L GLU 250": "OE1" <-> "OE2" Residue "L ARG 275": "NH1" <-> "NH2" Residue "L ARG 289": "NH1" <-> "NH2" Residue "L TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 353": "OE1" <-> "OE2" Residue "L ARG 399": "NH1" <-> "NH2" Residue "L ARG 467": "NH1" <-> "NH2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 44532 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3542 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 3542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3542 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 3542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3542 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 3542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3542 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 3542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3542 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 3542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3542 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 3542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3542 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 3542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3542 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "I" Number of atoms: 3542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3542 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "J" Number of atoms: 3542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3542 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "K" Number of atoms: 3542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3542 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "L" Number of atoms: 3542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3542 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {' ZN': 1} Classifications: {'RNA': 1, 'peptide': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {' ZN': 1} Classifications: {'RNA': 1, 'peptide': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {' ZN': 1} Classifications: {'RNA': 1, 'peptide': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "D" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {' ZN': 1} Classifications: {'RNA': 1, 'peptide': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "E" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {' ZN': 1} Classifications: {'RNA': 1, 'peptide': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "F" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {' ZN': 1} Classifications: {'RNA': 1, 'peptide': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "G" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {' ZN': 1} Classifications: {'RNA': 1, 'peptide': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "H" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {' ZN': 1} Classifications: {'RNA': 1, 'peptide': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "I" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {' ZN': 1} Classifications: {'RNA': 1, 'peptide': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "J" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {' ZN': 1} Classifications: {'RNA': 1, 'peptide': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "K" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {' ZN': 1} Classifications: {'RNA': 1, 'peptide': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "L" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {' ZN': 1} Classifications: {'RNA': 1, 'peptide': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} Chain: "B" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} Chain: "C" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} Chain: "D" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} Chain: "E" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} Chain: "F" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} Chain: "G" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} Chain: "H" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} Chain: "I" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} Chain: "J" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} Chain: "K" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} Chain: "L" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1024 SG CYS A 134 46.090 168.911 60.711 1.00 0.00 S ATOM 1076 SG CYS A 141 48.875 171.684 59.981 1.00 0.00 S ATOM 4566 SG CYS B 134 20.777 131.262 60.711 1.00 0.00 S ATOM 4618 SG CYS B 141 21.803 135.056 59.981 1.00 0.00 S ATOM 8108 SG CYS C 134 17.689 85.992 60.711 1.00 0.00 S ATOM 8160 SG CYS C 141 16.680 89.790 59.981 1.00 0.00 S ATOM 11650 SG CYS D 134 37.639 45.240 60.711 1.00 0.00 S ATOM 11702 SG CYS D 141 34.866 48.025 59.981 1.00 0.00 S ATOM 15192 SG CYS E 134 75.296 19.933 60.711 1.00 0.00 S ATOM 15244 SG CYS E 141 71.502 20.958 59.981 1.00 0.00 S ATOM 18734 SG CYS F 134 120.567 16.835 60.711 1.00 0.00 S ATOM 18786 SG CYS F 141 116.769 15.826 59.981 1.00 0.00 S ATOM 22276 SG CYS G 134 161.310 36.790 60.711 1.00 0.00 S ATOM 22328 SG CYS G 141 158.525 34.016 59.981 1.00 0.00 S ATOM 25818 SG CYS H 134 186.626 74.453 60.711 1.00 0.00 S ATOM 25870 SG CYS H 141 185.600 70.659 59.981 1.00 0.00 S ATOM 29360 SG CYS I 134 189.724 119.713 60.711 1.00 0.00 S ATOM 29412 SG CYS I 141 190.733 115.915 59.981 1.00 0.00 S ATOM 32902 SG CYS J 134 169.760 160.461 60.711 1.00 0.00 S ATOM 32954 SG CYS J 141 172.533 157.676 59.981 1.00 0.00 S ATOM 36444 SG CYS K 134 132.106 185.782 60.711 1.00 0.00 S ATOM 36496 SG CYS K 141 135.900 184.757 59.981 1.00 0.00 S ATOM 39986 SG CYS L 134 86.846 188.870 60.711 1.00 0.00 S ATOM 40038 SG CYS L 141 90.644 189.879 59.981 1.00 0.00 S Time building chain proxies: 24.93, per 1000 atoms: 0.56 Number of scatterers: 44532 At special positions: 0 Unit cell: (208.25, 207.4, 89.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 12 29.99 S 336 16.00 P 12 15.00 O 9480 8.00 N 7512 7.00 C 27180 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 17.86 Conformation dependent library (CDL) restraints added in 6.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" NE2 HIS A 79 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 141 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 134 " pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" NE2 HIS B 79 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 141 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 134 " pdb=" ZN C1001 " pdb="ZN ZN C1001 " - pdb=" NE2 HIS C 79 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 141 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 134 " pdb=" ZN D1001 " pdb="ZN ZN D1001 " - pdb=" NE2 HIS D 79 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 141 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 134 " pdb=" ZN E1001 " pdb="ZN ZN E1001 " - pdb=" NE2 HIS E 79 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 141 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 134 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" NE2 HIS F 79 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 141 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 134 " pdb=" ZN G1001 " pdb="ZN ZN G1001 " - pdb=" NE2 HIS G 79 " pdb="ZN ZN G1001 " - pdb=" SG CYS G 141 " pdb="ZN ZN G1001 " - pdb=" SG CYS G 134 " pdb=" ZN H1001 " pdb="ZN ZN H1001 " - pdb=" NE2 HIS H 79 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 141 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 134 " pdb=" ZN I1001 " pdb="ZN ZN I1001 " - pdb=" NE2 HIS I 79 " pdb="ZN ZN I1001 " - pdb=" SG CYS I 141 " pdb="ZN ZN I1001 " - pdb=" SG CYS I 134 " pdb=" ZN J1001 " pdb="ZN ZN J1001 " - pdb=" NE2 HIS J 79 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 141 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 134 " pdb=" ZN K1001 " pdb="ZN ZN K1001 " - pdb=" NE2 HIS K 79 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 141 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 134 " pdb=" ZN L1001 " pdb="ZN ZN L1001 " - pdb=" NE2 HIS L 79 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 141 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 134 " 10680 Ramachandran restraints generated. 5340 Oldfield, 0 Emsley, 5340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10344 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 180 helices and 60 sheets defined 31.0% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.36 Creating SS restraints... Processing helix chain 'A' and resid 13 through 21 removed outlier: 3.538A pdb=" N LYS A 16 " --> pdb=" O ALA A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 54 Processing helix chain 'A' and resid 68 through 71 Processing helix chain 'A' and resid 89 through 102 Processing helix chain 'A' and resid 112 through 124 Processing helix chain 'A' and resid 158 through 168 removed outlier: 4.130A pdb=" N LYS A 168 " --> pdb=" O HIS A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 184 No H-bonds generated for 'chain 'A' and resid 181 through 184' Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' 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 252 through 258 removed outlier: 3.868A pdb=" N TRP A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 342 Processing helix chain 'A' and resid 345 through 347 No H-bonds generated for 'chain 'A' and resid 345 through 347' Processing helix chain 'A' and resid 352 through 363 Processing helix chain 'A' and resid 381 through 402 Proline residue: A 385 - end of helix removed outlier: 3.551A pdb=" N ALA A 388 " --> pdb=" O PRO A 385 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE A 391 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP A 394 " --> pdb=" O PHE A 391 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA A 395 " --> pdb=" O SER A 392 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N CYS A 398 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 473 Processing helix chain 'B' and resid 13 through 21 removed outlier: 3.538A pdb=" N LYS B 16 " --> pdb=" O ALA B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 54 Processing helix chain 'B' and resid 68 through 71 Processing helix chain 'B' and resid 89 through 102 Processing helix chain 'B' and resid 112 through 124 Processing helix chain 'B' and resid 158 through 168 removed outlier: 4.130A pdb=" N LYS B 168 " --> pdb=" O HIS B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 184 No H-bonds generated for 'chain 'B' and resid 181 through 184' Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 252 through 258 removed outlier: 3.867A pdb=" N TRP B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 342 Processing helix chain 'B' and resid 345 through 347 No H-bonds generated for 'chain 'B' and resid 345 through 347' Processing helix chain 'B' and resid 352 through 363 Processing helix chain 'B' and resid 381 through 402 Proline residue: B 385 - end of helix removed outlier: 3.551A pdb=" N ALA B 388 " --> pdb=" O PRO B 385 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE B 391 " --> pdb=" O ALA B 388 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP B 394 " --> pdb=" O PHE B 391 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA B 395 " --> pdb=" O SER B 392 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N CYS B 398 " --> pdb=" O ALA B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 473 Processing helix chain 'C' and resid 13 through 21 removed outlier: 3.538A pdb=" N LYS C 16 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 54 Processing helix chain 'C' and resid 68 through 71 Processing helix chain 'C' and resid 89 through 102 Processing helix chain 'C' and resid 112 through 124 Processing helix chain 'C' and resid 158 through 168 removed outlier: 4.130A pdb=" N LYS C 168 " --> pdb=" O HIS C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 184 No H-bonds generated for 'chain 'C' and resid 181 through 184' Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' 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 252 through 258 removed outlier: 3.868A pdb=" N TRP C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 342 Processing helix chain 'C' and resid 345 through 347 No H-bonds generated for 'chain 'C' and resid 345 through 347' Processing helix chain 'C' and resid 352 through 363 Processing helix chain 'C' and resid 381 through 402 Proline residue: C 385 - end of helix removed outlier: 3.550A pdb=" N ALA C 388 " --> pdb=" O PRO C 385 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE C 391 " --> pdb=" O ALA C 388 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP C 394 " --> pdb=" O PHE C 391 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA C 395 " --> pdb=" O SER C 392 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N CYS C 398 " --> pdb=" O ALA C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 473 Processing helix chain 'D' and resid 13 through 21 removed outlier: 3.538A pdb=" N LYS D 16 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 54 Processing helix chain 'D' and resid 68 through 71 Processing helix chain 'D' and resid 89 through 102 Processing helix chain 'D' and resid 112 through 124 Processing helix chain 'D' and resid 158 through 168 removed outlier: 4.130A pdb=" N LYS D 168 " --> pdb=" O HIS D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 184 No H-bonds generated for 'chain 'D' and resid 181 through 184' Processing helix chain 'D' and resid 193 through 195 No H-bonds generated for 'chain 'D' and resid 193 through 195' Processing helix chain 'D' and resid 202 through 204 No H-bonds generated for 'chain 'D' and resid 202 through 204' Processing helix chain 'D' and resid 252 through 258 removed outlier: 3.868A pdb=" N TRP D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 345 through 347 No H-bonds generated for 'chain 'D' and resid 345 through 347' Processing helix chain 'D' and resid 352 through 363 Processing helix chain 'D' and resid 381 through 402 Proline residue: D 385 - end of helix removed outlier: 3.551A pdb=" N ALA D 388 " --> pdb=" O PRO D 385 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE D 391 " --> pdb=" O ALA D 388 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP D 394 " --> pdb=" O PHE D 391 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA D 395 " --> pdb=" O SER D 392 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N CYS D 398 " --> pdb=" O ALA D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 473 Processing helix chain 'E' and resid 14 through 21 Processing helix chain 'E' and resid 38 through 54 Processing helix chain 'E' and resid 68 through 71 Processing helix chain 'E' and resid 89 through 102 Processing helix chain 'E' and resid 112 through 124 Processing helix chain 'E' and resid 158 through 168 removed outlier: 4.130A pdb=" N LYS E 168 " --> pdb=" O HIS E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 184 No H-bonds generated for 'chain 'E' and resid 181 through 184' Processing helix chain 'E' and resid 193 through 195 No H-bonds generated for 'chain 'E' and resid 193 through 195' Processing helix chain 'E' and resid 202 through 204 No H-bonds generated for 'chain 'E' and resid 202 through 204' Processing helix chain 'E' and resid 252 through 258 removed outlier: 3.868A pdb=" N TRP E 258 " --> pdb=" O LEU E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 342 Processing helix chain 'E' and resid 345 through 347 No H-bonds generated for 'chain 'E' and resid 345 through 347' Processing helix chain 'E' and resid 352 through 363 Processing helix chain 'E' and resid 381 through 402 Proline residue: E 385 - end of helix removed outlier: 3.551A pdb=" N ALA E 388 " --> pdb=" O PRO E 385 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE E 391 " --> pdb=" O ALA E 388 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP E 394 " --> pdb=" O PHE E 391 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA E 395 " --> pdb=" O SER E 392 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS E 398 " --> pdb=" O ALA E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 473 Processing helix chain 'F' and resid 13 through 21 removed outlier: 3.538A pdb=" N LYS F 16 " --> pdb=" O ALA F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 54 Processing helix chain 'F' and resid 68 through 71 Processing helix chain 'F' and resid 89 through 102 Processing helix chain 'F' and resid 112 through 124 Processing helix chain 'F' and resid 158 through 168 removed outlier: 4.130A pdb=" N LYS F 168 " --> pdb=" O HIS F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 184 No H-bonds generated for 'chain 'F' and resid 181 through 184' Processing helix chain 'F' and resid 193 through 195 No H-bonds generated for 'chain 'F' and resid 193 through 195' Processing helix chain 'F' and resid 202 through 204 No H-bonds generated for 'chain 'F' and resid 202 through 204' Processing helix chain 'F' and resid 252 through 258 removed outlier: 3.868A pdb=" N TRP F 258 " --> pdb=" O LEU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 342 Processing helix chain 'F' and resid 345 through 347 No H-bonds generated for 'chain 'F' and resid 345 through 347' Processing helix chain 'F' and resid 352 through 363 Processing helix chain 'F' and resid 381 through 402 Proline residue: F 385 - end of helix removed outlier: 3.551A pdb=" N ALA F 388 " --> pdb=" O PRO F 385 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE F 391 " --> pdb=" O ALA F 388 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP F 394 " --> pdb=" O PHE F 391 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA F 395 " --> pdb=" O SER F 392 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N CYS F 398 " --> pdb=" O ALA F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 473 Processing helix chain 'G' and resid 14 through 21 Processing helix chain 'G' and resid 38 through 54 Processing helix chain 'G' and resid 68 through 71 Processing helix chain 'G' and resid 89 through 102 Processing helix chain 'G' and resid 112 through 124 Processing helix chain 'G' and resid 158 through 168 removed outlier: 4.130A pdb=" N LYS G 168 " --> pdb=" O HIS G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 184 No H-bonds generated for 'chain 'G' and resid 181 through 184' Processing helix chain 'G' and resid 193 through 195 No H-bonds generated for 'chain 'G' and resid 193 through 195' Processing helix chain 'G' and resid 202 through 204 No H-bonds generated for 'chain 'G' and resid 202 through 204' Processing helix chain 'G' and resid 252 through 258 removed outlier: 3.868A pdb=" N TRP G 258 " --> pdb=" O LEU G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 336 through 342 Processing helix chain 'G' and resid 345 through 347 No H-bonds generated for 'chain 'G' and resid 345 through 347' Processing helix chain 'G' and resid 352 through 363 Processing helix chain 'G' and resid 381 through 402 Proline residue: G 385 - end of helix removed outlier: 3.551A pdb=" N ALA G 388 " --> pdb=" O PRO G 385 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE G 391 " --> pdb=" O ALA G 388 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP G 394 " --> pdb=" O PHE G 391 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA G 395 " --> pdb=" O SER G 392 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N CYS G 398 " --> pdb=" O ALA G 395 " (cutoff:3.500A) Processing helix chain 'G' and resid 462 through 473 Processing helix chain 'H' and resid 13 through 21 removed outlier: 3.538A pdb=" N LYS H 16 " --> pdb=" O ALA H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 54 Processing helix chain 'H' and resid 68 through 71 Processing helix chain 'H' and resid 89 through 102 Processing helix chain 'H' and resid 112 through 124 Processing helix chain 'H' and resid 158 through 168 removed outlier: 4.130A pdb=" N LYS H 168 " --> pdb=" O HIS H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 184 No H-bonds generated for 'chain 'H' and resid 181 through 184' Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'H' and resid 202 through 204 No H-bonds generated for 'chain 'H' and resid 202 through 204' Processing helix chain 'H' and resid 252 through 258 removed outlier: 3.868A pdb=" N TRP H 258 " --> pdb=" O LEU H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 336 through 342 Processing helix chain 'H' and resid 345 through 347 No H-bonds generated for 'chain 'H' and resid 345 through 347' Processing helix chain 'H' and resid 352 through 363 Processing helix chain 'H' and resid 381 through 402 Proline residue: H 385 - end of helix removed outlier: 3.551A pdb=" N ALA H 388 " --> pdb=" O PRO H 385 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE H 391 " --> pdb=" O ALA H 388 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP H 394 " --> pdb=" O PHE H 391 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA H 395 " --> pdb=" O SER H 392 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N CYS H 398 " --> pdb=" O ALA H 395 " (cutoff:3.500A) Processing helix chain 'H' and resid 462 through 473 Processing helix chain 'I' and resid 13 through 21 removed outlier: 3.538A pdb=" N LYS I 16 " --> pdb=" O ALA I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 54 Processing helix chain 'I' and resid 68 through 71 Processing helix chain 'I' and resid 89 through 102 Processing helix chain 'I' and resid 112 through 124 Processing helix chain 'I' and resid 158 through 168 removed outlier: 4.130A pdb=" N LYS I 168 " --> pdb=" O HIS I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 184 No H-bonds generated for 'chain 'I' and resid 181 through 184' Processing helix chain 'I' and resid 193 through 195 No H-bonds generated for 'chain 'I' and resid 193 through 195' Processing helix chain 'I' and resid 202 through 204 No H-bonds generated for 'chain 'I' and resid 202 through 204' Processing helix chain 'I' and resid 252 through 258 removed outlier: 3.868A pdb=" N TRP I 258 " --> pdb=" O LEU I 254 " (cutoff:3.500A) Processing helix chain 'I' and resid 336 through 342 Processing helix chain 'I' and resid 345 through 347 No H-bonds generated for 'chain 'I' and resid 345 through 347' Processing helix chain 'I' and resid 352 through 363 Processing helix chain 'I' and resid 381 through 402 Proline residue: I 385 - end of helix removed outlier: 3.551A pdb=" N ALA I 388 " --> pdb=" O PRO I 385 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE I 391 " --> pdb=" O ALA I 388 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP I 394 " --> pdb=" O PHE I 391 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA I 395 " --> pdb=" O SER I 392 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N CYS I 398 " --> pdb=" O ALA I 395 " (cutoff:3.500A) Processing helix chain 'I' and resid 462 through 473 Processing helix chain 'J' and resid 13 through 21 removed outlier: 3.538A pdb=" N LYS J 16 " --> pdb=" O ALA J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 54 Processing helix chain 'J' and resid 68 through 71 Processing helix chain 'J' and resid 89 through 102 Processing helix chain 'J' and resid 112 through 124 Processing helix chain 'J' and resid 158 through 168 removed outlier: 4.130A pdb=" N LYS J 168 " --> pdb=" O HIS J 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 184 No H-bonds generated for 'chain 'J' and resid 181 through 184' Processing helix chain 'J' and resid 193 through 195 No H-bonds generated for 'chain 'J' and resid 193 through 195' 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 252 through 258 removed outlier: 3.868A pdb=" N TRP J 258 " --> pdb=" O LEU J 254 " (cutoff:3.500A) Processing helix chain 'J' and resid 336 through 342 Processing helix chain 'J' and resid 345 through 347 No H-bonds generated for 'chain 'J' and resid 345 through 347' Processing helix chain 'J' and resid 352 through 363 Processing helix chain 'J' and resid 381 through 402 Proline residue: J 385 - end of helix removed outlier: 3.551A pdb=" N ALA J 388 " --> pdb=" O PRO J 385 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE J 391 " --> pdb=" O ALA J 388 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP J 394 " --> pdb=" O PHE J 391 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA J 395 " --> pdb=" O SER J 392 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N CYS J 398 " --> pdb=" O ALA J 395 " (cutoff:3.500A) Processing helix chain 'J' and resid 462 through 473 Processing helix chain 'K' and resid 13 through 21 removed outlier: 3.538A pdb=" N LYS K 16 " --> pdb=" O ALA K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 54 Processing helix chain 'K' and resid 68 through 71 Processing helix chain 'K' and resid 89 through 102 Processing helix chain 'K' and resid 112 through 124 Processing helix chain 'K' and resid 158 through 168 removed outlier: 4.130A pdb=" N LYS K 168 " --> pdb=" O HIS K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 184 No H-bonds generated for 'chain 'K' and resid 181 through 184' Processing helix chain 'K' and resid 193 through 195 No H-bonds generated for 'chain 'K' and resid 193 through 195' Processing helix chain 'K' and resid 202 through 204 No H-bonds generated for 'chain 'K' and resid 202 through 204' Processing helix chain 'K' and resid 252 through 258 removed outlier: 3.868A pdb=" N TRP K 258 " --> pdb=" O LEU K 254 " (cutoff:3.500A) Processing helix chain 'K' and resid 336 through 342 Processing helix chain 'K' and resid 345 through 347 No H-bonds generated for 'chain 'K' and resid 345 through 347' Processing helix chain 'K' and resid 352 through 363 Processing helix chain 'K' and resid 381 through 402 Proline residue: K 385 - end of helix removed outlier: 3.551A pdb=" N ALA K 388 " --> pdb=" O PRO K 385 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE K 391 " --> pdb=" O ALA K 388 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TRP K 394 " --> pdb=" O PHE K 391 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA K 395 " --> pdb=" O SER K 392 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS K 398 " --> pdb=" O ALA K 395 " (cutoff:3.500A) Processing helix chain 'K' and resid 462 through 473 Processing helix chain 'L' and resid 13 through 21 removed outlier: 3.538A pdb=" N LYS L 16 " --> pdb=" O ALA L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 54 Processing helix chain 'L' and resid 68 through 71 Processing helix chain 'L' and resid 89 through 102 Processing helix chain 'L' and resid 112 through 124 Processing helix chain 'L' and resid 158 through 168 removed outlier: 4.130A pdb=" N LYS L 168 " --> pdb=" O HIS L 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 184 No H-bonds generated for 'chain 'L' and resid 181 through 184' Processing helix chain 'L' and resid 193 through 195 No H-bonds generated for 'chain 'L' and resid 193 through 195' Processing helix chain 'L' and resid 202 through 204 No H-bonds generated for 'chain 'L' and resid 202 through 204' Processing helix chain 'L' and resid 252 through 258 removed outlier: 3.868A pdb=" N TRP L 258 " --> pdb=" O LEU L 254 " (cutoff:3.500A) Processing helix chain 'L' and resid 336 through 342 Processing helix chain 'L' and resid 345 through 347 No H-bonds generated for 'chain 'L' and resid 345 through 347' Processing helix chain 'L' and resid 352 through 363 Processing helix chain 'L' and resid 381 through 402 Proline residue: L 385 - end of helix removed outlier: 3.550A pdb=" N ALA L 388 " --> pdb=" O PRO L 385 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE L 391 " --> pdb=" O ALA L 388 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP L 394 " --> pdb=" O PHE L 391 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA L 395 " --> pdb=" O SER L 392 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N CYS L 398 " --> pdb=" O ALA L 395 " (cutoff:3.500A) Processing helix chain 'L' and resid 462 through 473 Processing sheet with id= A, first strand: chain 'A' and resid 3 through 6 removed outlier: 6.179A pdb=" N GLU A 26 " --> pdb=" O VAL A 4 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL A 6 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLU A 28 " --> pdb=" O VAL A 6 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 77 through 81 removed outlier: 6.803A pdb=" N VAL A 147 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE A 64 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE A 149 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU A 172 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N TYR A 150 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N TYR A 174 " --> pdb=" O TYR A 150 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 280 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ARG A 289 " --> pdb=" O THR A 278 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N THR A 278 " --> pdb=" O ARG A 289 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N THR A 291 " --> pdb=" O CYS A 276 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N CYS A 276 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N SER A 293 " --> pdb=" O CYS A 274 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N CYS A 274 " --> pdb=" O SER A 293 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 189 through 192 Processing sheet with id= D, first strand: chain 'A' and resid 303 through 307 Processing sheet with id= E, first strand: chain 'A' and resid 324 through 334 Processing sheet with id= F, first strand: chain 'B' and resid 3 through 6 removed outlier: 6.179A pdb=" N GLU B 26 " --> pdb=" O VAL B 4 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N VAL B 6 " --> pdb=" O GLU B 26 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLU B 28 " --> pdb=" O VAL B 6 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 77 through 81 removed outlier: 6.803A pdb=" N VAL B 147 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE B 64 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE B 149 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU B 172 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N TYR B 150 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TYR B 174 " --> pdb=" O TYR B 150 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 280 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ARG B 289 " --> pdb=" O THR B 278 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N THR B 278 " --> pdb=" O ARG B 289 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N THR B 291 " --> pdb=" O CYS B 276 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N CYS B 276 " --> pdb=" O THR B 291 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N SER B 293 " --> pdb=" O CYS B 274 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N CYS B 274 " --> pdb=" O SER B 293 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 189 through 192 Processing sheet with id= I, first strand: chain 'B' and resid 303 through 307 Processing sheet with id= J, first strand: chain 'B' and resid 324 through 334 Processing sheet with id= K, first strand: chain 'C' and resid 3 through 6 removed outlier: 6.180A pdb=" N GLU C 26 " --> pdb=" O VAL C 4 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL C 6 " --> pdb=" O GLU C 26 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLU C 28 " --> pdb=" O VAL C 6 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 77 through 81 removed outlier: 6.803A pdb=" N VAL C 147 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE C 64 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE C 149 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU C 172 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N TYR C 150 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N TYR C 174 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL C 280 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ARG C 289 " --> pdb=" O THR C 278 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N THR C 278 " --> pdb=" O ARG C 289 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N THR C 291 " --> pdb=" O CYS C 276 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N CYS C 276 " --> pdb=" O THR C 291 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N SER C 293 " --> pdb=" O CYS C 274 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N CYS C 274 " --> pdb=" O SER C 293 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 189 through 192 Processing sheet with id= N, first strand: chain 'C' and resid 303 through 307 Processing sheet with id= O, first strand: chain 'C' and resid 324 through 334 Processing sheet with id= P, first strand: chain 'D' and resid 3 through 6 removed outlier: 6.179A pdb=" N GLU D 26 " --> pdb=" O VAL D 4 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL D 6 " --> pdb=" O GLU D 26 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLU D 28 " --> pdb=" O VAL D 6 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'D' and resid 77 through 81 removed outlier: 6.803A pdb=" N VAL D 147 " --> pdb=" O LEU D 62 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE D 64 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE D 149 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU D 172 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N TYR D 150 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N TYR D 174 " --> pdb=" O TYR D 150 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL D 280 " --> pdb=" O VAL D 287 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ARG D 289 " --> pdb=" O THR D 278 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N THR D 278 " --> pdb=" O ARG D 289 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N THR D 291 " --> pdb=" O CYS D 276 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N CYS D 276 " --> pdb=" O THR D 291 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N SER D 293 " --> pdb=" O CYS D 274 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N CYS D 274 " --> pdb=" O SER D 293 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 189 through 192 Processing sheet with id= S, first strand: chain 'D' and resid 303 through 307 Processing sheet with id= T, first strand: chain 'D' and resid 324 through 334 Processing sheet with id= U, first strand: chain 'E' and resid 3 through 6 removed outlier: 6.179A pdb=" N GLU E 26 " --> pdb=" O VAL E 4 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL E 6 " --> pdb=" O GLU E 26 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLU E 28 " --> pdb=" O VAL E 6 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'E' and resid 77 through 81 removed outlier: 6.803A pdb=" N VAL E 147 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE E 64 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE E 149 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU E 172 " --> pdb=" O ALA E 148 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N TYR E 150 " --> pdb=" O LEU E 172 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TYR E 174 " --> pdb=" O TYR E 150 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL E 280 " --> pdb=" O VAL E 287 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ARG E 289 " --> pdb=" O THR E 278 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N THR E 278 " --> pdb=" O ARG E 289 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N THR E 291 " --> pdb=" O CYS E 276 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N CYS E 276 " --> pdb=" O THR E 291 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N SER E 293 " --> pdb=" O CYS E 274 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N CYS E 274 " --> pdb=" O SER E 293 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 189 through 192 Processing sheet with id= X, first strand: chain 'E' and resid 303 through 307 Processing sheet with id= Y, first strand: chain 'E' and resid 324 through 334 Processing sheet with id= Z, first strand: chain 'F' and resid 3 through 6 removed outlier: 6.179A pdb=" N GLU F 26 " --> pdb=" O VAL F 4 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL F 6 " --> pdb=" O GLU F 26 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLU F 28 " --> pdb=" O VAL F 6 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'F' and resid 77 through 81 removed outlier: 6.802A pdb=" N VAL F 147 " --> pdb=" O LEU F 62 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE F 64 " --> pdb=" O VAL F 147 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE F 149 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU F 172 " --> pdb=" O ALA F 148 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N TYR F 150 " --> pdb=" O LEU F 172 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N TYR F 174 " --> pdb=" O TYR F 150 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL F 280 " --> pdb=" O VAL F 287 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ARG F 289 " --> pdb=" O THR F 278 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N THR F 278 " --> pdb=" O ARG F 289 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N THR F 291 " --> pdb=" O CYS F 276 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N CYS F 276 " --> pdb=" O THR F 291 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N SER F 293 " --> pdb=" O CYS F 274 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N CYS F 274 " --> pdb=" O SER F 293 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 189 through 192 Processing sheet with id= AC, first strand: chain 'F' and resid 303 through 307 Processing sheet with id= AD, first strand: chain 'F' and resid 324 through 334 Processing sheet with id= AE, first strand: chain 'G' and resid 3 through 6 removed outlier: 6.179A pdb=" N GLU G 26 " --> pdb=" O VAL G 4 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL G 6 " --> pdb=" O GLU G 26 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLU G 28 " --> pdb=" O VAL G 6 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'G' and resid 77 through 81 removed outlier: 6.804A pdb=" N VAL G 147 " --> pdb=" O LEU G 62 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE G 64 " --> pdb=" O VAL G 147 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE G 149 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU G 172 " --> pdb=" O ALA G 148 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N TYR G 150 " --> pdb=" O LEU G 172 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TYR G 174 " --> pdb=" O TYR G 150 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL G 280 " --> pdb=" O VAL G 287 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ARG G 289 " --> pdb=" O THR G 278 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N THR G 278 " --> pdb=" O ARG G 289 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N THR G 291 " --> pdb=" O CYS G 276 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N CYS G 276 " --> pdb=" O THR G 291 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N SER G 293 " --> pdb=" O CYS G 274 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N CYS G 274 " --> pdb=" O SER G 293 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 189 through 192 Processing sheet with id= AH, first strand: chain 'G' and resid 303 through 307 Processing sheet with id= AI, first strand: chain 'G' and resid 324 through 334 Processing sheet with id= AJ, first strand: chain 'H' and resid 3 through 6 removed outlier: 6.179A pdb=" N GLU H 26 " --> pdb=" O VAL H 4 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL H 6 " --> pdb=" O GLU H 26 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLU H 28 " --> pdb=" O VAL H 6 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ Processing sheet with id= AK, first strand: chain 'H' and resid 77 through 81 removed outlier: 6.803A pdb=" N VAL H 147 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE H 64 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE H 149 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU H 172 " --> pdb=" O ALA H 148 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N TYR H 150 " --> pdb=" O LEU H 172 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TYR H 174 " --> pdb=" O TYR H 150 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL H 280 " --> pdb=" O VAL H 287 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ARG H 289 " --> pdb=" O THR H 278 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N THR H 278 " --> pdb=" O ARG H 289 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N THR H 291 " --> pdb=" O CYS H 276 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N CYS H 276 " --> pdb=" O THR H 291 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N SER H 293 " --> pdb=" O CYS H 274 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N CYS H 274 " --> pdb=" O SER H 293 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'H' and resid 189 through 192 Processing sheet with id= AM, first strand: chain 'H' and resid 303 through 307 Processing sheet with id= AN, first strand: chain 'H' and resid 324 through 334 Processing sheet with id= AO, first strand: chain 'I' and resid 3 through 6 removed outlier: 6.179A pdb=" N GLU I 26 " --> pdb=" O VAL I 4 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL I 6 " --> pdb=" O GLU I 26 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLU I 28 " --> pdb=" O VAL I 6 " (cutoff:3.500A) No H-bonds generated for sheet with id= AO Processing sheet with id= AP, first strand: chain 'I' and resid 77 through 81 removed outlier: 6.803A pdb=" N VAL I 147 " --> pdb=" O LEU I 62 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ILE I 64 " --> pdb=" O VAL I 147 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE I 149 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU I 172 " --> pdb=" O ALA I 148 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N TYR I 150 " --> pdb=" O LEU I 172 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N TYR I 174 " --> pdb=" O TYR I 150 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL I 280 " --> pdb=" O VAL I 287 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ARG I 289 " --> pdb=" O THR I 278 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N THR I 278 " --> pdb=" O ARG I 289 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N THR I 291 " --> pdb=" O CYS I 276 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N CYS I 276 " --> pdb=" O THR I 291 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N SER I 293 " --> pdb=" O CYS I 274 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N CYS I 274 " --> pdb=" O SER I 293 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'I' and resid 189 through 192 Processing sheet with id= AR, first strand: chain 'I' and resid 303 through 307 Processing sheet with id= AS, first strand: chain 'I' and resid 324 through 334 Processing sheet with id= AT, first strand: chain 'J' and resid 3 through 6 removed outlier: 6.179A pdb=" N GLU J 26 " --> pdb=" O VAL J 4 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL J 6 " --> pdb=" O GLU J 26 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLU J 28 " --> pdb=" O VAL J 6 " (cutoff:3.500A) No H-bonds generated for sheet with id= AT Processing sheet with id= AU, first strand: chain 'J' and resid 77 through 81 removed outlier: 6.803A pdb=" N VAL J 147 " --> pdb=" O LEU J 62 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE J 64 " --> pdb=" O VAL J 147 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE J 149 " --> pdb=" O ILE J 64 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU J 172 " --> pdb=" O ALA J 148 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N TYR J 150 " --> pdb=" O LEU J 172 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N TYR J 174 " --> pdb=" O TYR J 150 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL J 280 " --> pdb=" O VAL J 287 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ARG J 289 " --> pdb=" O THR J 278 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N THR J 278 " --> pdb=" O ARG J 289 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N THR J 291 " --> pdb=" O CYS J 276 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N CYS J 276 " --> pdb=" O THR J 291 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N SER J 293 " --> pdb=" O CYS J 274 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N CYS J 274 " --> pdb=" O SER J 293 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'J' and resid 189 through 192 Processing sheet with id= AW, first strand: chain 'J' and resid 303 through 307 Processing sheet with id= AX, first strand: chain 'J' and resid 324 through 334 Processing sheet with id= AY, first strand: chain 'K' and resid 3 through 6 removed outlier: 6.179A pdb=" N GLU K 26 " --> pdb=" O VAL K 4 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL K 6 " --> pdb=" O GLU K 26 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLU K 28 " --> pdb=" O VAL K 6 " (cutoff:3.500A) No H-bonds generated for sheet with id= AY Processing sheet with id= AZ, first strand: chain 'K' and resid 77 through 81 removed outlier: 6.803A pdb=" N VAL K 147 " --> pdb=" O LEU K 62 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE K 64 " --> pdb=" O VAL K 147 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE K 149 " --> pdb=" O ILE K 64 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU K 172 " --> pdb=" O ALA K 148 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N TYR K 150 " --> pdb=" O LEU K 172 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TYR K 174 " --> pdb=" O TYR K 150 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL K 280 " --> pdb=" O VAL K 287 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ARG K 289 " --> pdb=" O THR K 278 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N THR K 278 " --> pdb=" O ARG K 289 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N THR K 291 " --> pdb=" O CYS K 276 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N CYS K 276 " --> pdb=" O THR K 291 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N SER K 293 " --> pdb=" O CYS K 274 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N CYS K 274 " --> pdb=" O SER K 293 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'K' and resid 189 through 192 Processing sheet with id= BB, first strand: chain 'K' and resid 303 through 307 Processing sheet with id= BC, first strand: chain 'K' and resid 324 through 334 Processing sheet with id= BD, first strand: chain 'L' and resid 3 through 6 removed outlier: 6.180A pdb=" N GLU L 26 " --> pdb=" O VAL L 4 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL L 6 " --> pdb=" O GLU L 26 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLU L 28 " --> pdb=" O VAL L 6 " (cutoff:3.500A) No H-bonds generated for sheet with id= BD Processing sheet with id= BE, first strand: chain 'L' and resid 77 through 81 removed outlier: 6.803A pdb=" N VAL L 147 " --> pdb=" O LEU L 62 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE L 64 " --> pdb=" O VAL L 147 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE L 149 " --> pdb=" O ILE L 64 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU L 172 " --> pdb=" O ALA L 148 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N TYR L 150 " --> pdb=" O LEU L 172 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N TYR L 174 " --> pdb=" O TYR L 150 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL L 280 " --> pdb=" O VAL L 287 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ARG L 289 " --> pdb=" O THR L 278 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N THR L 278 " --> pdb=" O ARG L 289 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N THR L 291 " --> pdb=" O CYS L 276 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N CYS L 276 " --> pdb=" O THR L 291 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N SER L 293 " --> pdb=" O CYS L 274 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N CYS L 274 " --> pdb=" O SER L 293 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'L' and resid 189 through 192 Processing sheet with id= BG, first strand: chain 'L' and resid 303 through 307 Processing sheet with id= BH, first strand: chain 'L' and resid 324 through 334 1522 hydrogen bonds defined for protein. 3804 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: 18.06 Time building geometry restraints manager: 18.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 6996 1.30 - 1.43: 11766 1.43 - 1.56: 24750 1.56 - 1.69: 36 1.69 - 1.82: 516 Bond restraints: 44064 Sorted by residual: bond pdb=" C4' G7M E1003 " pdb=" C3' G7M E1003 " ideal model delta sigma weight residual 1.521 1.289 0.232 1.50e-02 4.44e+03 2.39e+02 bond pdb=" C4' G7M I1003 " pdb=" C3' G7M I1003 " ideal model delta sigma weight residual 1.521 1.289 0.232 1.50e-02 4.44e+03 2.39e+02 bond pdb=" C4' G7M D1003 " pdb=" C3' G7M D1003 " ideal model delta sigma weight residual 1.521 1.290 0.231 1.50e-02 4.44e+03 2.38e+02 bond pdb=" C4' G7M A1003 " pdb=" C3' G7M A1003 " ideal model delta sigma weight residual 1.521 1.290 0.231 1.50e-02 4.44e+03 2.38e+02 bond pdb=" C4' G7M J1003 " pdb=" C3' G7M J1003 " ideal model delta sigma weight residual 1.521 1.290 0.231 1.50e-02 4.44e+03 2.38e+02 ... (remaining 44059 not shown) Histogram of bond angle deviations from ideal: 91.42 - 100.27: 60 100.27 - 109.12: 3935 109.12 - 117.97: 29243 117.97 - 126.82: 25793 126.82 - 135.66: 741 Bond angle restraints: 59772 Sorted by residual: angle pdb=" OP1 G7M K1003 " pdb=" P G7M K1003 " pdb=" OP2 G7M K1003 " ideal model delta sigma weight residual 119.60 100.07 19.53 3.00e+00 1.11e-01 4.24e+01 angle pdb=" OP1 G7M I1003 " pdb=" P G7M I1003 " pdb=" OP2 G7M I1003 " ideal model delta sigma weight residual 119.60 100.07 19.53 3.00e+00 1.11e-01 4.24e+01 angle pdb=" OP1 G7M C1003 " pdb=" P G7M C1003 " pdb=" OP2 G7M C1003 " ideal model delta sigma weight residual 119.60 100.07 19.53 3.00e+00 1.11e-01 4.24e+01 angle pdb=" OP1 G7M G1003 " pdb=" P G7M G1003 " pdb=" OP2 G7M G1003 " ideal model delta sigma weight residual 119.60 100.08 19.52 3.00e+00 1.11e-01 4.23e+01 angle pdb=" OP1 G7M A1003 " pdb=" P G7M A1003 " pdb=" OP2 G7M A1003 " ideal model delta sigma weight residual 119.60 100.08 19.52 3.00e+00 1.11e-01 4.23e+01 ... (remaining 59767 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 23209 17.68 - 35.35: 2442 35.35 - 53.03: 509 53.03 - 70.70: 156 70.70 - 88.38: 60 Dihedral angle restraints: 26376 sinusoidal: 10428 harmonic: 15948 Sorted by residual: dihedral pdb=" CA GLU E 26 " pdb=" C GLU E 26 " pdb=" N VAL E 27 " pdb=" CA VAL E 27 " ideal model delta harmonic sigma weight residual -180.00 -160.42 -19.58 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA GLU C 26 " pdb=" C GLU C 26 " pdb=" N VAL C 27 " pdb=" CA VAL C 27 " ideal model delta harmonic sigma weight residual -180.00 -160.43 -19.57 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA GLU I 26 " pdb=" C GLU I 26 " pdb=" N VAL I 27 " pdb=" CA VAL I 27 " ideal model delta harmonic sigma weight residual -180.00 -160.44 -19.56 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 26373 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 3641 0.040 - 0.081: 2022 0.081 - 0.121: 800 0.121 - 0.161: 260 0.161 - 0.202: 21 Chirality restraints: 6744 Sorted by residual: chirality pdb=" C1' G7M F1003 " pdb=" O4' G7M F1003 " pdb=" C2' G7M F1003 " pdb=" N9 G7M F1003 " both_signs ideal model delta sigma weight residual False 2.46 2.26 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" C1' G7M C1003 " pdb=" O4' G7M C1003 " pdb=" C2' G7M C1003 " pdb=" N9 G7M C1003 " both_signs ideal model delta sigma weight residual False 2.46 2.26 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" C1' G7M L1003 " pdb=" O4' G7M L1003 " pdb=" C2' G7M L1003 " pdb=" N9 G7M L1003 " both_signs ideal model delta sigma weight residual False 2.46 2.26 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 6741 not shown) Planarity restraints: 7512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 183 " 0.021 2.00e-02 2.50e+03 1.37e-02 3.30e+00 pdb=" CG PHE C 183 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE C 183 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE C 183 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE C 183 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE C 183 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 183 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 183 " 0.021 2.00e-02 2.50e+03 1.37e-02 3.28e+00 pdb=" CG PHE B 183 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE B 183 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE B 183 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 183 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 183 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 183 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 183 " -0.020 2.00e-02 2.50e+03 1.37e-02 3.27e+00 pdb=" CG PHE K 183 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE K 183 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE K 183 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE K 183 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE K 183 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE K 183 " -0.010 2.00e-02 2.50e+03 ... (remaining 7509 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 581 2.67 - 3.23: 39176 3.23 - 3.79: 66057 3.79 - 4.34: 97534 4.34 - 4.90: 152286 Nonbonded interactions: 355634 Sorted by model distance: nonbonded pdb=" OE1 GLU C 129 " pdb="ZN ZN C1001 " model vdw 2.118 2.230 nonbonded pdb=" OE1 GLU I 129 " pdb="ZN ZN I1001 " model vdw 2.118 2.230 nonbonded pdb=" OE1 GLU J 129 " pdb="ZN ZN J1001 " model vdw 2.118 2.230 nonbonded pdb=" OE1 GLU D 129 " pdb="ZN ZN D1001 " model vdw 2.118 2.230 nonbonded pdb=" OE1 GLU A 129 " pdb="ZN ZN A1001 " model vdw 2.118 2.230 ... (remaining 355629 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 12 6.06 5 P 12 5.49 5 S 336 5.16 5 C 27180 2.51 5 N 7512 2.21 5 O 9480 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 5.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 28.850 Check model and map are aligned: 0.680 Convert atoms to be neutral: 0.370 Process input model: 118.310 Find NCS groups from input model: 3.630 Set up NCS constraints: 0.400 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 171.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 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 : 0.009 0.232 44064 Z= 0.586 Angle : 1.033 19.530 59772 Z= 0.556 Chirality : 0.057 0.202 6744 Planarity : 0.006 0.045 7512 Dihedral : 16.146 88.378 16032 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer Outliers : 1.31 % 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: -0.25 (0.11), residues: 5340 helix: 1.58 (0.13), residues: 1644 sheet: 0.60 (0.15), residues: 1020 loop : -1.69 (0.10), residues: 2676 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10680 Ramachandran restraints generated. 5340 Oldfield, 0 Emsley, 5340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10680 Ramachandran restraints generated. 5340 Oldfield, 0 Emsley, 5340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 4692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 441 time to evaluate : 5.431 Fit side-chains outliers start: 60 outliers final: 12 residues processed: 465 average time/residue: 1.7673 time to fit residues: 994.5575 Evaluate side-chains 403 residues out of total 4692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 391 time to evaluate : 5.083 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 0 time to fit residues: 7.4343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 455 optimal weight: 5.9990 chunk 409 optimal weight: 0.9990 chunk 227 optimal weight: 4.9990 chunk 139 optimal weight: 0.9980 chunk 276 optimal weight: 2.9990 chunk 218 optimal weight: 0.8980 chunk 423 optimal weight: 0.2980 chunk 163 optimal weight: 3.9990 chunk 257 optimal weight: 2.9990 chunk 315 optimal weight: 10.0000 chunk 490 optimal weight: 7.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 389 GLN D 95 ASN G 95 ASN J 95 ASN J 389 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 44064 Z= 0.181 Angle : 0.575 4.767 59772 Z= 0.314 Chirality : 0.044 0.145 6744 Planarity : 0.005 0.039 7512 Dihedral : 5.147 47.140 5952 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer Outliers : 2.92 % 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: 0.04 (0.11), residues: 5340 helix: 2.05 (0.14), residues: 1644 sheet: 0.29 (0.14), residues: 1248 loop : -1.61 (0.11), residues: 2448 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10680 Ramachandran restraints generated. 5340 Oldfield, 0 Emsley, 5340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10680 Ramachandran restraints generated. 5340 Oldfield, 0 Emsley, 5340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 4692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 402 time to evaluate : 5.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 134 outliers final: 28 residues processed: 484 average time/residue: 1.7887 time to fit residues: 1042.4911 Evaluate side-chains 439 residues out of total 4692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 411 time to evaluate : 4.967 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 16 residues processed: 12 average time/residue: 0.4753 time to fit residues: 16.3268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 272 optimal weight: 0.1980 chunk 152 optimal weight: 5.9990 chunk 408 optimal weight: 0.0980 chunk 333 optimal weight: 0.9980 chunk 135 optimal weight: 10.0000 chunk 491 optimal weight: 4.9990 chunk 530 optimal weight: 0.0770 chunk 437 optimal weight: 3.9990 chunk 487 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 394 optimal weight: 4.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- 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: 0.7888 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 44064 Z= 0.159 Angle : 0.533 4.991 59772 Z= 0.288 Chirality : 0.043 0.139 6744 Planarity : 0.005 0.037 7512 Dihedral : 4.929 46.852 5952 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer Outliers : 2.09 % 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: 0.09 (0.11), residues: 5340 helix: 1.99 (0.14), residues: 1668 sheet: 0.39 (0.14), residues: 1248 loop : -1.58 (0.11), residues: 2424 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10680 Ramachandran restraints generated. 5340 Oldfield, 0 Emsley, 5340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10680 Ramachandran restraints generated. 5340 Oldfield, 0 Emsley, 5340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 4692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 420 time to evaluate : 5.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 96 outliers final: 36 residues processed: 472 average time/residue: 1.8417 time to fit residues: 1050.0852 Evaluate side-chains 453 residues out of total 4692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 417 time to evaluate : 5.390 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 23 residues processed: 13 average time/residue: 0.7674 time to fit residues: 22.3317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 485 optimal weight: 6.9990 chunk 369 optimal weight: 9.9990 chunk 254 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 234 optimal weight: 9.9990 chunk 329 optimal weight: 2.9990 chunk 493 optimal weight: 9.9990 chunk 521 optimal weight: 8.9990 chunk 257 optimal weight: 0.7980 chunk 467 optimal weight: 9.9990 chunk 140 optimal weight: 0.0670 overall best weight: 2.9724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 389 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 44064 Z= 0.283 Angle : 0.693 5.947 59772 Z= 0.385 Chirality : 0.049 0.161 6744 Planarity : 0.006 0.046 7512 Dihedral : 5.479 57.206 5952 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer Outliers : 2.59 % 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: -0.01 (0.11), residues: 5340 helix: 1.94 (0.14), residues: 1656 sheet: 0.76 (0.16), residues: 900 loop : -1.58 (0.10), residues: 2784 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10680 Ramachandran restraints generated. 5340 Oldfield, 0 Emsley, 5340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10680 Ramachandran restraints generated. 5340 Oldfield, 0 Emsley, 5340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 4692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 408 time to evaluate : 5.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 119 outliers final: 48 residues processed: 485 average time/residue: 1.6867 time to fit residues: 1002.0707 Evaluate side-chains 454 residues out of total 4692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 406 time to evaluate : 5.153 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 35 residues processed: 13 average time/residue: 0.4892 time to fit residues: 17.9272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 434 optimal weight: 4.9990 chunk 296 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 388 optimal weight: 0.8980 chunk 215 optimal weight: 5.9990 chunk 445 optimal weight: 9.9990 chunk 360 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 266 optimal weight: 0.0970 chunk 468 optimal weight: 0.0370 chunk 131 optimal weight: 0.0870 overall best weight: 1.2236 ------------------------------------------------------------------------------- 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: 0.7905 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 44064 Z= 0.176 Angle : 0.556 5.175 59772 Z= 0.304 Chirality : 0.044 0.143 6744 Planarity : 0.005 0.039 7512 Dihedral : 5.149 57.500 5952 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 1.94 % 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: 0.09 (0.11), residues: 5340 helix: 2.06 (0.14), residues: 1656 sheet: 0.41 (0.15), residues: 1128 loop : -1.53 (0.11), residues: 2556 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10680 Ramachandran restraints generated. 5340 Oldfield, 0 Emsley, 5340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10680 Ramachandran restraints generated. 5340 Oldfield, 0 Emsley, 5340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 4692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 416 time to evaluate : 5.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 89 outliers final: 42 residues processed: 468 average time/residue: 1.6798 time to fit residues: 959.1506 Evaluate side-chains 441 residues out of total 4692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 399 time to evaluate : 5.085 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 34 residues processed: 8 average time/residue: 0.4197 time to fit residues: 13.0467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 175 optimal weight: 0.5980 chunk 470 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 306 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 522 optimal weight: 10.0000 chunk 433 optimal weight: 0.7980 chunk 241 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 274 optimal weight: 10.0000 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 120 GLN F 341 GLN K 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 44064 Z= 0.247 Angle : 0.649 5.744 59772 Z= 0.359 Chirality : 0.047 0.159 6744 Planarity : 0.005 0.046 7512 Dihedral : 5.390 57.447 5952 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 1.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.11), residues: 5340 helix: 2.00 (0.14), residues: 1656 sheet: 0.77 (0.16), residues: 900 loop : -1.56 (0.10), residues: 2784 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10680 Ramachandran restraints generated. 5340 Oldfield, 0 Emsley, 5340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10680 Ramachandran restraints generated. 5340 Oldfield, 0 Emsley, 5340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 4692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 403 time to evaluate : 5.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 46 residues processed: 461 average time/residue: 1.7462 time to fit residues: 984.4795 Evaluate side-chains 454 residues out of total 4692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 408 time to evaluate : 4.995 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 33 residues processed: 13 average time/residue: 0.4882 time to fit residues: 17.6184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 503 optimal weight: 0.0000 chunk 58 optimal weight: 4.9990 chunk 297 optimal weight: 4.9990 chunk 381 optimal weight: 0.4980 chunk 295 optimal weight: 1.9990 chunk 439 optimal weight: 4.9990 chunk 291 optimal weight: 8.9990 chunk 520 optimal weight: 1.9990 chunk 325 optimal weight: 0.9990 chunk 317 optimal weight: 0.9980 chunk 240 optimal weight: 5.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- 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: 0.7889 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 44064 Z= 0.157 Angle : 0.527 4.735 59772 Z= 0.286 Chirality : 0.043 0.139 6744 Planarity : 0.005 0.036 7512 Dihedral : 5.015 54.425 5952 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.11), residues: 5340 helix: 2.18 (0.14), residues: 1644 sheet: 0.46 (0.15), residues: 1128 loop : -1.52 (0.11), residues: 2568 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10680 Ramachandran restraints generated. 5340 Oldfield, 0 Emsley, 5340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10680 Ramachandran restraints generated. 5340 Oldfield, 0 Emsley, 5340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 4692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 423 time to evaluate : 5.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 36 residues processed: 464 average time/residue: 1.6651 time to fit residues: 951.9581 Evaluate side-chains 440 residues out of total 4692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 404 time to evaluate : 5.033 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 30 residues processed: 6 average time/residue: 0.5000 time to fit residues: 12.3968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 321 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 310 optimal weight: 6.9990 chunk 156 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 100 optimal weight: 9.9990 chunk 330 optimal weight: 0.9980 chunk 354 optimal weight: 2.9990 chunk 257 optimal weight: 0.5980 chunk 48 optimal weight: 0.0270 chunk 409 optimal weight: 10.0000 overall best weight: 1.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 341 GLN I 341 GLN L 341 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 44064 Z= 0.166 Angle : 0.542 5.547 59772 Z= 0.294 Chirality : 0.044 0.144 6744 Planarity : 0.005 0.039 7512 Dihedral : 5.000 54.568 5952 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer Outliers : 1.68 % 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: 0.20 (0.11), residues: 5340 helix: 2.15 (0.14), residues: 1656 sheet: 0.48 (0.15), residues: 1128 loop : -1.48 (0.11), residues: 2556 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10680 Ramachandran restraints generated. 5340 Oldfield, 0 Emsley, 5340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10680 Ramachandran restraints generated. 5340 Oldfield, 0 Emsley, 5340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 4692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 409 time to evaluate : 5.420 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 outliers start: 77 outliers final: 41 residues processed: 463 average time/residue: 1.7004 time to fit residues: 970.2454 Evaluate side-chains 444 residues out of total 4692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 403 time to evaluate : 5.374 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 35 residues processed: 6 average time/residue: 0.5260 time to fit residues: 12.8189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 473 optimal weight: 0.2980 chunk 498 optimal weight: 3.9990 chunk 454 optimal weight: 8.9990 chunk 485 optimal weight: 3.9990 chunk 291 optimal weight: 0.0870 chunk 211 optimal weight: 3.9990 chunk 380 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 438 optimal weight: 0.0670 chunk 458 optimal weight: 0.9980 chunk 483 optimal weight: 0.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 341 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 44064 Z= 0.134 Angle : 0.483 6.445 59772 Z= 0.255 Chirality : 0.041 0.130 6744 Planarity : 0.004 0.035 7512 Dihedral : 4.637 47.490 5952 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 1.22 % 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: 0.48 (0.12), residues: 5340 helix: 2.31 (0.14), residues: 1644 sheet: 0.84 (0.14), residues: 1212 loop : -1.42 (0.11), residues: 2484 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10680 Ramachandran restraints generated. 5340 Oldfield, 0 Emsley, 5340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10680 Ramachandran restraints generated. 5340 Oldfield, 0 Emsley, 5340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 4692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 401 time to evaluate : 5.510 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 outliers start: 56 outliers final: 43 residues processed: 451 average time/residue: 1.6720 time to fit residues: 937.7827 Evaluate side-chains 434 residues out of total 4692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 391 time to evaluate : 5.152 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 38 residues processed: 8 average time/residue: 0.5014 time to fit residues: 13.9690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 318 optimal weight: 2.9990 chunk 512 optimal weight: 4.9990 chunk 313 optimal weight: 10.0000 chunk 243 optimal weight: 0.2980 chunk 356 optimal weight: 0.9980 chunk 537 optimal weight: 8.9990 chunk 495 optimal weight: 10.0000 chunk 428 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 330 optimal weight: 6.9990 chunk 262 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 341 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 44064 Z= 0.183 Angle : 0.562 5.181 59772 Z= 0.306 Chirality : 0.044 0.146 6744 Planarity : 0.005 0.041 7512 Dihedral : 5.013 56.304 5952 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 1.35 % 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: 0.28 (0.11), residues: 5340 helix: 2.24 (0.14), residues: 1656 sheet: 0.55 (0.15), residues: 1128 loop : -1.45 (0.11), residues: 2556 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10680 Ramachandran restraints generated. 5340 Oldfield, 0 Emsley, 5340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10680 Ramachandran restraints generated. 5340 Oldfield, 0 Emsley, 5340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 4692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 404 time to evaluate : 5.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 39 residues processed: 445 average time/residue: 1.6727 time to fit residues: 913.6457 Evaluate side-chains 439 residues out of total 4692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 400 time to evaluate : 5.228 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 33 residues processed: 6 average time/residue: 0.5413 time to fit residues: 12.6238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 340 optimal weight: 1.9990 chunk 456 optimal weight: 5.9990 chunk 131 optimal weight: 0.5980 chunk 395 optimal weight: 1.9990 chunk 63 optimal weight: 0.0870 chunk 119 optimal weight: 0.9980 chunk 429 optimal weight: 6.9990 chunk 179 optimal weight: 4.9990 chunk 440 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 341 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.137854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.105650 restraints weight = 44736.477| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.48 r_work: 0.3180 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 44064 Z= 0.152 Angle : 0.516 5.114 59772 Z= 0.277 Chirality : 0.043 0.137 6744 Planarity : 0.005 0.036 7512 Dihedral : 4.848 52.238 5952 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer Outliers : 0.98 % 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: 0.33 (0.11), residues: 5340 helix: 2.31 (0.14), residues: 1644 sheet: 0.58 (0.14), residues: 1152 loop : -1.44 (0.11), residues: 2544 =============================================================================== Job complete usr+sys time: 15593.60 seconds wall clock time: 276 minutes 58.78 seconds (16618.78 seconds total)