Starting phenix.real_space_refine on Sat Feb 24 15:06:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgh_31581/02_2024/7fgh_31581_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgh_31581/02_2024/7fgh_31581.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgh_31581/02_2024/7fgh_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_31581/02_2024/7fgh_31581_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgh_31581/02_2024/7fgh_31581_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgh_31581/02_2024/7fgh_31581.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgh_31581/02_2024/7fgh_31581.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgh_31581/02_2024/7fgh_31581_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgh_31581/02_2024/7fgh_31581_updated.pdb" } resolution = 2.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.053 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 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. 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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 26.25, per 1000 atoms: 0.59 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: 18.14 Conformation dependent library (CDL) restraints added in 7.5 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: 9.36 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: 18.69 Time building geometry restraints manager: 18.70 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=" C1' G7M I1003 " pdb=" N9 G7M I1003 " pdb=" C8 G7M I1003 " ideal model delta sigma weight residual 94.96 115.54 -20.58 3.00e+00 1.11e-01 4.70e+01 angle pdb=" C1' G7M H1003 " pdb=" N9 G7M H1003 " pdb=" C8 G7M H1003 " ideal model delta sigma weight residual 94.96 115.53 -20.57 3.00e+00 1.11e-01 4.70e+01 angle pdb=" C1' G7M K1003 " pdb=" N9 G7M K1003 " pdb=" C8 G7M K1003 " ideal model delta sigma weight residual 94.96 115.53 -20.57 3.00e+00 1.11e-01 4.70e+01 angle pdb=" C1' G7M E1003 " pdb=" N9 G7M E1003 " pdb=" C8 G7M E1003 " ideal model delta sigma weight residual 94.96 115.53 -20.57 3.00e+00 1.11e-01 4.70e+01 angle pdb=" C1' G7M B1003 " pdb=" N9 G7M B1003 " pdb=" C8 G7M B1003 " ideal model delta sigma weight residual 94.96 115.53 -20.57 3.00e+00 1.11e-01 4.70e+01 ... (remaining 59767 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 23221 17.68 - 35.35: 2478 35.35 - 53.03: 533 53.03 - 70.70: 144 70.70 - 88.38: 72 Dihedral angle restraints: 26448 sinusoidal: 10500 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 26445 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 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: 15.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 28.970 Check model and map are aligned: 0.660 Set scattering table: 0.440 Process input model: 127.680 Find NCS groups from input model: 3.570 Set up NCS constraints: 0.420 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 189.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 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 : 1.058 20.578 59772 Z= 0.561 Chirality : 0.057 0.202 6744 Planarity : 0.006 0.045 7512 Dihedral : 16.266 88.378 16104 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.31 % Allowed : 12.82 % Favored : 85.88 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 175 HIS 0.006 0.002 HIS H 259 PHE 0.028 0.003 PHE L 183 TYR 0.017 0.002 TYR C 150 ARG 0.007 0.001 ARG K 238 *********************** 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 : 5.413 Fit side-chains outliers start: 60 outliers final: 12 residues processed: 465 average time/residue: 1.8908 time to fit residues: 1051.4062 Evaluate side-chains 403 residues out of total 4692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 391 time to evaluate : 5.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain F residue 410 VAL Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain I residue 410 VAL Chi-restraints excluded: chain J residue 410 VAL Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain L residue 410 VAL 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: 0.7583 moved from start: 0.0922 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= 0.185 Angle : 0.595 10.126 59772 Z= 0.319 Chirality : 0.045 0.146 6744 Planarity : 0.005 0.039 7512 Dihedral : 7.005 69.940 6036 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.96 % Allowed : 12.23 % Favored : 84.81 % 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: 2.05 (0.14), residues: 1644 sheet: 0.29 (0.14), residues: 1248 loop : -1.61 (0.11), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 175 HIS 0.006 0.001 HIS C 37 PHE 0.016 0.002 PHE K 183 TYR 0.011 0.001 TYR B 150 ARG 0.005 0.000 ARG F 238 *********************** 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 538 residues out of total 4692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 402 time to evaluate : 5.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.6630 (OUTLIER) cc_final: 0.6378 (tm-30) REVERT: A 54 GLU cc_start: 0.5774 (OUTLIER) cc_final: 0.5556 (mp0) REVERT: A 402 MET cc_start: 0.7433 (mtm) cc_final: 0.7154 (ttm) REVERT: B 30 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.6842 (ttm-80) REVERT: B 54 GLU cc_start: 0.5717 (OUTLIER) cc_final: 0.5345 (mp0) REVERT: C 26 GLU cc_start: 0.6620 (OUTLIER) cc_final: 0.6322 (tm-30) REVERT: C 30 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.6702 (ttm-80) REVERT: C 54 GLU cc_start: 0.5702 (OUTLIER) cc_final: 0.5316 (mp0) REVERT: C 364 GLN cc_start: 0.6439 (OUTLIER) cc_final: 0.5752 (mt0) REVERT: D 26 GLU cc_start: 0.6664 (OUTLIER) cc_final: 0.6398 (tm-30) REVERT: D 54 GLU cc_start: 0.5765 (OUTLIER) cc_final: 0.5521 (mp0) REVERT: D 402 MET cc_start: 0.7479 (mtm) cc_final: 0.7165 (ttm) REVERT: E 30 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.6820 (ttm-80) REVERT: E 54 GLU cc_start: 0.5690 (OUTLIER) cc_final: 0.5316 (mp0) REVERT: F 30 ARG cc_start: 0.7255 (OUTLIER) cc_final: 0.6698 (ttm-80) REVERT: F 54 GLU cc_start: 0.5689 (OUTLIER) cc_final: 0.5314 (mp0) REVERT: F 364 GLN cc_start: 0.6471 (OUTLIER) cc_final: 0.5757 (mt0) REVERT: G 26 GLU cc_start: 0.6646 (OUTLIER) cc_final: 0.6381 (tm-30) REVERT: G 54 GLU cc_start: 0.5756 (OUTLIER) cc_final: 0.5517 (mp0) REVERT: G 353 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7101 (mp0) REVERT: G 402 MET cc_start: 0.7439 (mtm) cc_final: 0.7123 (ttm) REVERT: H 30 ARG cc_start: 0.7278 (OUTLIER) cc_final: 0.6836 (ttm-80) REVERT: H 54 GLU cc_start: 0.5683 (OUTLIER) cc_final: 0.5344 (mp0) REVERT: H 123 MET cc_start: 0.6384 (mmp) cc_final: 0.5949 (mmp) REVERT: I 30 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6671 (ttm-80) REVERT: I 54 GLU cc_start: 0.5716 (OUTLIER) cc_final: 0.5342 (mp0) REVERT: I 364 GLN cc_start: 0.6455 (OUTLIER) cc_final: 0.5751 (mt0) REVERT: J 26 GLU cc_start: 0.6661 (OUTLIER) cc_final: 0.6398 (tm-30) REVERT: J 54 GLU cc_start: 0.5767 (OUTLIER) cc_final: 0.5530 (mp0) REVERT: J 353 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7074 (mp0) REVERT: J 402 MET cc_start: 0.7432 (mtm) cc_final: 0.7166 (ttm) REVERT: K 30 ARG cc_start: 0.7278 (OUTLIER) cc_final: 0.6838 (ttm-80) REVERT: K 54 GLU cc_start: 0.5704 (OUTLIER) cc_final: 0.5321 (mp0) REVERT: K 123 MET cc_start: 0.6374 (mmp) cc_final: 0.5949 (mmp) REVERT: L 26 GLU cc_start: 0.6618 (OUTLIER) cc_final: 0.6316 (tm-30) REVERT: L 30 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.6682 (ttm-80) REVERT: L 54 GLU cc_start: 0.5736 (OUTLIER) cc_final: 0.5353 (mp0) REVERT: L 364 GLN cc_start: 0.6450 (OUTLIER) cc_final: 0.5735 (mt0) outliers start: 136 outliers final: 28 residues processed: 485 average time/residue: 1.9188 time to fit residues: 1108.8305 Evaluate side-chains 456 residues out of total 4692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 396 time to evaluate : 5.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 364 GLN Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 99 LYS Chi-restraints excluded: chain F residue 364 GLN Chi-restraints excluded: chain F residue 410 VAL Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain G residue 353 GLU Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain G residue 471 LEU Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 54 GLU Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain I residue 364 GLN Chi-restraints excluded: chain I residue 410 VAL Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 54 GLU Chi-restraints excluded: chain J residue 353 GLU Chi-restraints excluded: chain J residue 410 VAL Chi-restraints excluded: chain J residue 471 LEU Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 30 ARG Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 54 GLU Chi-restraints excluded: chain L residue 99 LYS Chi-restraints excluded: chain L residue 364 GLN Chi-restraints excluded: chain L residue 410 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 272 optimal weight: 0.5980 chunk 152 optimal weight: 5.9990 chunk 408 optimal weight: 0.0870 chunk 333 optimal weight: 0.9990 chunk 135 optimal weight: 10.0000 chunk 491 optimal weight: 4.9990 chunk 530 optimal weight: 5.9990 chunk 437 optimal weight: 2.9990 chunk 487 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 394 optimal weight: 4.9990 overall best weight: 1.5364 ------------------------------------------------------------------------------- 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: 0.7597 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 44064 Z= 0.195 Angle : 0.615 11.450 59772 Z= 0.330 Chirality : 0.045 0.148 6744 Planarity : 0.005 0.039 7512 Dihedral : 6.590 66.156 6036 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.39 % Allowed : 12.14 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.11), residues: 5340 helix: 2.03 (0.14), residues: 1656 sheet: 0.30 (0.14), residues: 1248 loop : -1.57 (0.11), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 175 HIS 0.006 0.001 HIS B 37 PHE 0.018 0.002 PHE D 183 TYR 0.014 0.001 TYR H 150 ARG 0.003 0.000 ARG G 238 *********************** 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 512 residues out of total 4692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 402 time to evaluate : 5.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.6688 (OUTLIER) cc_final: 0.6421 (tm-30) REVERT: A 54 GLU cc_start: 0.5765 (OUTLIER) cc_final: 0.5532 (mp0) REVERT: B 30 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.6883 (ttm-80) REVERT: B 54 GLU cc_start: 0.5716 (OUTLIER) cc_final: 0.5402 (mp0) REVERT: C 30 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.6728 (ttm-80) REVERT: C 364 GLN cc_start: 0.6402 (OUTLIER) cc_final: 0.5673 (mt0) REVERT: D 26 GLU cc_start: 0.6723 (OUTLIER) cc_final: 0.6445 (tm-30) REVERT: D 54 GLU cc_start: 0.5742 (OUTLIER) cc_final: 0.5492 (mp0) REVERT: D 353 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7123 (mp0) REVERT: E 30 ARG cc_start: 0.7295 (OUTLIER) cc_final: 0.6840 (ttm-80) REVERT: E 54 GLU cc_start: 0.5719 (OUTLIER) cc_final: 0.5402 (mp0) REVERT: F 30 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.6712 (ttm-80) REVERT: F 364 GLN cc_start: 0.6430 (OUTLIER) cc_final: 0.5699 (mt0) REVERT: G 26 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.6420 (tm-30) REVERT: G 54 GLU cc_start: 0.5739 (OUTLIER) cc_final: 0.5494 (mp0) REVERT: G 402 MET cc_start: 0.7481 (mtm) cc_final: 0.7092 (ttm) REVERT: H 30 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.6879 (ttm-80) REVERT: H 54 GLU cc_start: 0.5727 (OUTLIER) cc_final: 0.5458 (mp0) REVERT: I 30 ARG cc_start: 0.7273 (OUTLIER) cc_final: 0.6703 (ttm-80) REVERT: I 364 GLN cc_start: 0.6512 (OUTLIER) cc_final: 0.5800 (mt0) REVERT: J 26 GLU cc_start: 0.6712 (OUTLIER) cc_final: 0.6438 (tm-30) REVERT: J 54 GLU cc_start: 0.5742 (OUTLIER) cc_final: 0.5508 (mp0) REVERT: J 353 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7167 (mp0) REVERT: K 30 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.6861 (ttm-80) REVERT: K 54 GLU cc_start: 0.5720 (OUTLIER) cc_final: 0.5417 (mp0) REVERT: K 123 MET cc_start: 0.6318 (mmp) cc_final: 0.5907 (mmp) REVERT: L 30 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.6710 (ttm-80) REVERT: L 54 GLU cc_start: 0.5773 (OUTLIER) cc_final: 0.5412 (mp0) REVERT: L 364 GLN cc_start: 0.6399 (OUTLIER) cc_final: 0.5658 (mt0) outliers start: 110 outliers final: 32 residues processed: 465 average time/residue: 1.9163 time to fit residues: 1058.7381 Evaluate side-chains 450 residues out of total 4692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 391 time to evaluate : 5.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 364 GLN Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 353 GLU Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 99 LYS Chi-restraints excluded: chain F residue 364 GLN Chi-restraints excluded: chain F residue 410 VAL Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain I residue 364 GLN Chi-restraints excluded: chain I residue 410 VAL Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 54 GLU Chi-restraints excluded: chain J residue 353 GLU Chi-restraints excluded: chain J residue 410 VAL Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 30 ARG Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain K residue 471 LEU Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 54 GLU Chi-restraints excluded: chain L residue 59 SER Chi-restraints excluded: chain L residue 99 LYS Chi-restraints excluded: chain L residue 364 GLN Chi-restraints excluded: chain L residue 410 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 485 optimal weight: 2.9990 chunk 369 optimal weight: 6.9990 chunk 254 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 234 optimal weight: 5.9990 chunk 329 optimal weight: 3.9990 chunk 493 optimal weight: 10.0000 chunk 521 optimal weight: 8.9990 chunk 257 optimal weight: 0.5980 chunk 467 optimal weight: 1.9990 chunk 140 optimal weight: 0.3980 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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: 0.7593 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 44064 Z= 0.194 Angle : 0.603 10.768 59772 Z= 0.325 Chirality : 0.045 0.150 6744 Planarity : 0.005 0.041 7512 Dihedral : 6.394 64.395 6036 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.31 % Allowed : 12.55 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.11), residues: 5340 helix: 2.05 (0.14), residues: 1656 sheet: 0.29 (0.14), residues: 1248 loop : -1.53 (0.11), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 175 HIS 0.006 0.001 HIS L 37 PHE 0.017 0.002 PHE J 183 TYR 0.013 0.001 TYR E 150 ARG 0.009 0.000 ARG F 238 *********************** 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 500 residues out of total 4692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 394 time to evaluate : 6.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.6699 (OUTLIER) cc_final: 0.6444 (tm-30) REVERT: A 402 MET cc_start: 0.7495 (mtp) cc_final: 0.7222 (ttm) REVERT: B 30 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.6846 (ttm-80) REVERT: B 54 GLU cc_start: 0.5768 (OUTLIER) cc_final: 0.5456 (mp0) REVERT: C 26 GLU cc_start: 0.6679 (OUTLIER) cc_final: 0.6400 (tm-30) REVERT: C 30 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.6687 (ttm-80) REVERT: C 364 GLN cc_start: 0.6473 (OUTLIER) cc_final: 0.6271 (mt0) REVERT: D 26 GLU cc_start: 0.6737 (OUTLIER) cc_final: 0.6485 (tm-30) REVERT: D 54 GLU cc_start: 0.5772 (OUTLIER) cc_final: 0.5561 (mp0) REVERT: D 353 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7136 (mp0) REVERT: D 402 MET cc_start: 0.7498 (mtp) cc_final: 0.7229 (ttm) REVERT: E 30 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.6826 (ttm-80) REVERT: E 54 GLU cc_start: 0.5780 (OUTLIER) cc_final: 0.5458 (mp0) REVERT: F 30 ARG cc_start: 0.7219 (OUTLIER) cc_final: 0.6680 (ttm-80) REVERT: F 364 GLN cc_start: 0.6495 (OUTLIER) cc_final: 0.5734 (mt0) REVERT: G 26 GLU cc_start: 0.6717 (OUTLIER) cc_final: 0.6466 (tm-30) REVERT: G 54 GLU cc_start: 0.5770 (OUTLIER) cc_final: 0.5562 (mp0) REVERT: G 353 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7171 (mp0) REVERT: G 402 MET cc_start: 0.7464 (mtm) cc_final: 0.7083 (ttm) REVERT: H 30 ARG cc_start: 0.7276 (OUTLIER) cc_final: 0.6846 (ttm-80) REVERT: H 54 GLU cc_start: 0.5794 (OUTLIER) cc_final: 0.5529 (mp0) REVERT: I 30 ARG cc_start: 0.7220 (OUTLIER) cc_final: 0.6672 (ttm-80) REVERT: I 364 GLN cc_start: 0.6492 (OUTLIER) cc_final: 0.5775 (mt0) REVERT: J 26 GLU cc_start: 0.6735 (OUTLIER) cc_final: 0.6491 (tm-30) REVERT: J 402 MET cc_start: 0.7506 (mtp) cc_final: 0.7239 (ttm) REVERT: K 30 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6840 (ttm-80) REVERT: K 54 GLU cc_start: 0.5775 (OUTLIER) cc_final: 0.5450 (mp0) REVERT: L 26 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.6388 (tm-30) REVERT: L 30 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.6672 (ttm-80) REVERT: L 54 GLU cc_start: 0.5766 (OUTLIER) cc_final: 0.5400 (mp0) outliers start: 106 outliers final: 35 residues processed: 469 average time/residue: 1.8562 time to fit residues: 1047.5261 Evaluate side-chains 455 residues out of total 4692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 394 time to evaluate : 5.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 364 GLN Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 353 GLU Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 99 LYS Chi-restraints excluded: chain F residue 364 GLN Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 353 GLU Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain I residue 364 GLN Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 30 ARG Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 471 LEU Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 54 GLU Chi-restraints excluded: chain L residue 59 SER Chi-restraints excluded: chain L residue 99 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 434 optimal weight: 2.9990 chunk 296 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 5.9990 chunk 445 optimal weight: 6.9990 chunk 360 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 266 optimal weight: 0.5980 chunk 468 optimal weight: 0.6980 chunk 131 optimal weight: 0.0870 overall best weight: 2.0762 ------------------------------------------------------------------------------- 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: 0.7611 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 44064 Z= 0.225 Angle : 0.646 11.514 59772 Z= 0.350 Chirality : 0.047 0.155 6744 Planarity : 0.005 0.038 7512 Dihedral : 6.383 64.690 6024 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.42 % Allowed : 12.88 % Favored : 84.70 % 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: 0.06 (0.11), residues: 5340 helix: 2.01 (0.14), residues: 1656 sheet: 0.37 (0.15), residues: 1128 loop : -1.53 (0.11), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 175 HIS 0.006 0.002 HIS B 37 PHE 0.020 0.002 PHE D 183 TYR 0.016 0.002 TYR H 150 ARG 0.006 0.000 ARG C 238 *********************** 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 510 residues out of total 4692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 399 time to evaluate : 5.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6510 (tm-30) REVERT: A 353 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7182 (mp0) REVERT: A 402 MET cc_start: 0.7479 (mtp) cc_final: 0.7222 (ttm) REVERT: B 30 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6891 (ttm-80) REVERT: B 54 GLU cc_start: 0.5836 (OUTLIER) cc_final: 0.5539 (mp0) REVERT: C 26 GLU cc_start: 0.6682 (OUTLIER) cc_final: 0.6413 (tm-30) REVERT: C 30 ARG cc_start: 0.7281 (OUTLIER) cc_final: 0.6740 (ttm-80) REVERT: C 364 GLN cc_start: 0.6472 (OUTLIER) cc_final: 0.5779 (mt0) REVERT: D 26 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.6544 (tm-30) REVERT: D 353 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7169 (mp0) REVERT: D 402 MET cc_start: 0.7487 (mtp) cc_final: 0.7223 (ttm) REVERT: E 30 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.6868 (ttm-80) REVERT: E 54 GLU cc_start: 0.5873 (OUTLIER) cc_final: 0.5567 (mp0) REVERT: F 30 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.6686 (ttm-80) REVERT: F 364 GLN cc_start: 0.6498 (OUTLIER) cc_final: 0.5783 (mt0) REVERT: G 26 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6534 (tm-30) REVERT: G 353 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7188 (mp0) REVERT: G 402 MET cc_start: 0.7440 (mtm) cc_final: 0.7150 (ttm) REVERT: H 30 ARG cc_start: 0.7328 (OUTLIER) cc_final: 0.6884 (ttm-80) REVERT: H 54 GLU cc_start: 0.5878 (OUTLIER) cc_final: 0.5625 (mp0) REVERT: I 30 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.6701 (ttm-80) REVERT: I 364 GLN cc_start: 0.6484 (OUTLIER) cc_final: 0.5770 (mt0) REVERT: J 26 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.6548 (tm-30) REVERT: J 353 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7168 (mp0) REVERT: J 402 MET cc_start: 0.7507 (mtp) cc_final: 0.7223 (ttm) REVERT: K 30 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.6888 (ttm-80) REVERT: K 54 GLU cc_start: 0.5847 (OUTLIER) cc_final: 0.5540 (mp0) REVERT: L 26 GLU cc_start: 0.6661 (OUTLIER) cc_final: 0.6392 (tm-30) REVERT: L 30 ARG cc_start: 0.7288 (OUTLIER) cc_final: 0.6720 (ttm-80) outliers start: 111 outliers final: 39 residues processed: 465 average time/residue: 1.8764 time to fit residues: 1043.9076 Evaluate side-chains 456 residues out of total 4692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 392 time to evaluate : 5.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 364 GLN Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 353 GLU Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 99 LYS Chi-restraints excluded: chain F residue 364 GLN Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 353 GLU Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain I residue 364 GLN Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 353 GLU Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 30 ARG Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 59 SER Chi-restraints excluded: chain L residue 99 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 175 optimal weight: 5.9990 chunk 470 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 306 optimal weight: 0.4980 chunk 128 optimal weight: 2.9990 chunk 522 optimal weight: 0.9990 chunk 433 optimal weight: 8.9990 chunk 241 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 172 optimal weight: 0.9980 chunk 274 optimal weight: 8.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 341 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 44064 Z= 0.212 Angle : 0.626 11.047 59772 Z= 0.339 Chirality : 0.046 0.152 6744 Planarity : 0.005 0.038 7512 Dihedral : 6.353 64.576 6024 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.98 % Allowed : 13.29 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.11), residues: 5340 helix: 2.04 (0.14), residues: 1656 sheet: 0.38 (0.15), residues: 1128 loop : -1.52 (0.11), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 175 HIS 0.006 0.001 HIS F 37 PHE 0.019 0.002 PHE G 183 TYR 0.014 0.002 TYR H 150 ARG 0.006 0.000 ARG I 238 *********************** 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 493 residues out of total 4692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 402 time to evaluate : 5.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.6520 (tm-30) REVERT: A 353 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7165 (mp0) REVERT: A 402 MET cc_start: 0.7463 (mtp) cc_final: 0.7230 (ttm) REVERT: B 30 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.6872 (ttm-80) REVERT: B 54 GLU cc_start: 0.5830 (OUTLIER) cc_final: 0.5540 (mp0) REVERT: C 26 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.6396 (tm-30) REVERT: C 30 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6695 (ttm-80) REVERT: C 364 GLN cc_start: 0.6477 (OUTLIER) cc_final: 0.5782 (mt0) REVERT: D 26 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6549 (tm-30) REVERT: D 353 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7148 (mp0) REVERT: D 402 MET cc_start: 0.7477 (mtp) cc_final: 0.7236 (ttm) REVERT: E 30 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.6848 (ttm-80) REVERT: E 54 GLU cc_start: 0.5831 (OUTLIER) cc_final: 0.5537 (mp0) REVERT: F 26 GLU cc_start: 0.6676 (OUTLIER) cc_final: 0.6393 (tm-30) REVERT: F 30 ARG cc_start: 0.7233 (OUTLIER) cc_final: 0.6655 (ttm-80) REVERT: F 364 GLN cc_start: 0.6495 (OUTLIER) cc_final: 0.5776 (mt0) REVERT: G 26 GLU cc_start: 0.6778 (OUTLIER) cc_final: 0.6539 (tm-30) REVERT: G 238 ARG cc_start: 0.7288 (OUTLIER) cc_final: 0.7010 (mtp85) REVERT: G 353 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7167 (mp0) REVERT: G 402 MET cc_start: 0.7436 (mtm) cc_final: 0.7127 (ttm) REVERT: H 30 ARG cc_start: 0.7303 (OUTLIER) cc_final: 0.6863 (ttm-80) REVERT: H 54 GLU cc_start: 0.5841 (OUTLIER) cc_final: 0.5632 (tp30) REVERT: I 26 GLU cc_start: 0.6684 (OUTLIER) cc_final: 0.6383 (tm-30) REVERT: I 30 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.6683 (ttm-80) REVERT: I 364 GLN cc_start: 0.6492 (OUTLIER) cc_final: 0.5778 (mt0) REVERT: J 26 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.6540 (tm-30) REVERT: J 238 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.7024 (mtp85) REVERT: J 353 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7165 (mp0) REVERT: J 402 MET cc_start: 0.7498 (mtp) cc_final: 0.7230 (ttm) REVERT: K 30 ARG cc_start: 0.7295 (OUTLIER) cc_final: 0.6857 (ttm-80) REVERT: K 54 GLU cc_start: 0.5830 (OUTLIER) cc_final: 0.5531 (mp0) REVERT: L 26 GLU cc_start: 0.6655 (OUTLIER) cc_final: 0.6409 (tm-30) REVERT: L 30 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6677 (ttm-80) outliers start: 91 outliers final: 38 residues processed: 462 average time/residue: 1.9280 time to fit residues: 1065.1275 Evaluate side-chains 469 residues out of total 4692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 402 time to evaluate : 5.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 364 GLN Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 353 GLU Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 99 LYS Chi-restraints excluded: chain F residue 364 GLN Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 238 ARG Chi-restraints excluded: chain G residue 353 GLU Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain I residue 26 GLU Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain I residue 364 GLN Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 238 ARG Chi-restraints excluded: chain J residue 353 GLU Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 30 ARG Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 59 SER Chi-restraints excluded: chain L residue 99 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 503 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 297 optimal weight: 10.0000 chunk 381 optimal weight: 1.9990 chunk 295 optimal weight: 0.0980 chunk 439 optimal weight: 0.9980 chunk 291 optimal weight: 0.0270 chunk 520 optimal weight: 0.0020 chunk 325 optimal weight: 10.0000 chunk 317 optimal weight: 0.6980 chunk 240 optimal weight: 5.9990 overall best weight: 0.3646 ------------------------------------------------------------------------------- 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: 0.7510 moved from start: 0.1551 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= 0.134 Angle : 0.502 9.308 59772 Z= 0.260 Chirality : 0.042 0.127 6744 Planarity : 0.004 0.036 7512 Dihedral : 5.984 61.712 6024 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.85 % Allowed : 13.84 % Favored : 84.31 % 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: 0.46 (0.12), residues: 5340 helix: 2.25 (0.14), residues: 1644 sheet: 0.83 (0.14), residues: 1212 loop : -1.39 (0.11), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 394 HIS 0.004 0.001 HIS H 37 PHE 0.010 0.001 PHE E 264 TYR 0.008 0.001 TYR L 382 ARG 0.008 0.000 ARG C 221 *********************** 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 494 residues out of total 4692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 409 time to evaluate : 5.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.6701 (OUTLIER) cc_final: 0.6446 (tm-30) REVERT: A 402 MET cc_start: 0.7466 (mtp) cc_final: 0.7237 (ttm) REVERT: B 30 ARG cc_start: 0.7171 (OUTLIER) cc_final: 0.6773 (ttm-80) REVERT: C 26 GLU cc_start: 0.6645 (OUTLIER) cc_final: 0.6389 (tm-30) REVERT: C 30 ARG cc_start: 0.7112 (OUTLIER) cc_final: 0.6630 (ttm-80) REVERT: D 26 GLU cc_start: 0.6725 (OUTLIER) cc_final: 0.6483 (tm-30) REVERT: D 402 MET cc_start: 0.7466 (mtp) cc_final: 0.7238 (ttm) REVERT: E 30 ARG cc_start: 0.7136 (OUTLIER) cc_final: 0.6734 (ttm-80) REVERT: F 26 GLU cc_start: 0.6630 (OUTLIER) cc_final: 0.6342 (tm-30) REVERT: F 30 ARG cc_start: 0.7122 (OUTLIER) cc_final: 0.6591 (ttm-80) REVERT: G 26 GLU cc_start: 0.6701 (OUTLIER) cc_final: 0.6462 (tm-30) REVERT: G 402 MET cc_start: 0.7429 (mtm) cc_final: 0.7117 (ttm) REVERT: H 30 ARG cc_start: 0.7129 (OUTLIER) cc_final: 0.6717 (ttm-80) REVERT: I 26 GLU cc_start: 0.6634 (OUTLIER) cc_final: 0.6327 (tm-30) REVERT: I 30 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.6593 (ttm-80) REVERT: J 26 GLU cc_start: 0.6694 (OUTLIER) cc_final: 0.6466 (tm-30) REVERT: J 402 MET cc_start: 0.7489 (mtp) cc_final: 0.7239 (ttm) REVERT: K 30 ARG cc_start: 0.7157 (OUTLIER) cc_final: 0.6772 (ttm-80) REVERT: L 26 GLU cc_start: 0.6621 (OUTLIER) cc_final: 0.6379 (tm-30) REVERT: L 30 ARG cc_start: 0.7127 (OUTLIER) cc_final: 0.6615 (ttm-80) outliers start: 85 outliers final: 21 residues processed: 462 average time/residue: 1.7979 time to fit residues: 1000.0201 Evaluate side-chains 428 residues out of total 4692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 391 time to evaluate : 5.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain C residue 229 ARG Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 229 ARG Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain I residue 26 GLU Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 229 ARG Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 30 ARG Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 59 SER Chi-restraints excluded: chain L residue 229 ARG 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: 0.9990 chunk 310 optimal weight: 0.5980 chunk 156 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 330 optimal weight: 8.9990 chunk 354 optimal weight: 3.9990 chunk 257 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 409 optimal weight: 7.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 341 GLN F 341 GLN I 341 GLN L 341 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1327 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= 0.207 Angle : 0.613 10.975 59772 Z= 0.330 Chirality : 0.046 0.151 6744 Planarity : 0.005 0.036 7512 Dihedral : 6.195 63.041 6024 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.46 % Allowed : 14.49 % Favored : 84.05 % 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: 0.23 (0.11), residues: 5340 helix: 2.17 (0.14), residues: 1656 sheet: 0.51 (0.15), residues: 1128 loop : -1.46 (0.11), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 175 HIS 0.005 0.001 HIS H 37 PHE 0.019 0.002 PHE J 183 TYR 0.014 0.002 TYR E 150 ARG 0.006 0.000 ARG I 221 *********************** 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 470 residues out of total 4692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 403 time to evaluate : 5.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.6405 (tt0) REVERT: A 353 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7178 (mp0) REVERT: A 402 MET cc_start: 0.7466 (mtp) cc_final: 0.7216 (ttm) REVERT: B 30 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.6860 (ttm-80) REVERT: C 26 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.6422 (tm-30) REVERT: C 30 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.6691 (ttm-80) REVERT: D 26 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.6507 (tm-30) REVERT: D 353 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7152 (mp0) REVERT: D 402 MET cc_start: 0.7477 (mtp) cc_final: 0.7221 (ttm) REVERT: E 30 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.6827 (ttm-80) REVERT: F 26 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.6367 (tm-30) REVERT: F 30 ARG cc_start: 0.7224 (OUTLIER) cc_final: 0.6674 (ttm-80) REVERT: G 26 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.6502 (tm-30) REVERT: G 238 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.7027 (mtp85) REVERT: G 353 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7174 (mp0) REVERT: G 402 MET cc_start: 0.7414 (mtm) cc_final: 0.7126 (ttm) REVERT: H 30 ARG cc_start: 0.7278 (OUTLIER) cc_final: 0.6860 (ttm-80) REVERT: I 26 GLU cc_start: 0.6678 (OUTLIER) cc_final: 0.6403 (tm-30) REVERT: I 30 ARG cc_start: 0.7219 (OUTLIER) cc_final: 0.6661 (ttm-80) REVERT: J 26 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.6448 (tm-30) REVERT: J 238 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.7015 (mtp85) REVERT: J 353 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7187 (mp0) REVERT: J 402 MET cc_start: 0.7485 (mtp) cc_final: 0.7211 (ttm) REVERT: K 30 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.6857 (ttm-80) REVERT: L 26 GLU cc_start: 0.6635 (OUTLIER) cc_final: 0.6401 (tm-30) REVERT: L 30 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.6699 (ttm-80) outliers start: 67 outliers final: 23 residues processed: 448 average time/residue: 1.8586 time to fit residues: 996.8123 Evaluate side-chains 442 residues out of total 4692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 397 time to evaluate : 5.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 229 ARG Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 353 GLU Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 99 LYS Chi-restraints excluded: chain F residue 229 ARG Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 238 ARG Chi-restraints excluded: chain G residue 353 GLU Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain I residue 26 GLU Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 238 ARG Chi-restraints excluded: chain J residue 353 GLU Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 30 ARG Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 99 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 473 optimal weight: 0.0980 chunk 498 optimal weight: 0.9990 chunk 454 optimal weight: 7.9990 chunk 485 optimal weight: 3.9990 chunk 291 optimal weight: 10.0000 chunk 211 optimal weight: 4.9990 chunk 380 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 438 optimal weight: 6.9990 chunk 458 optimal weight: 2.9990 chunk 483 optimal weight: 0.6980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN C 341 GLN E 120 GLN F 341 GLN H 120 GLN K 120 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 44064 Z= 0.203 Angle : 0.611 10.891 59772 Z= 0.329 Chirality : 0.046 0.151 6744 Planarity : 0.005 0.037 7512 Dihedral : 6.245 63.338 6024 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.44 % Allowed : 14.58 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.11), residues: 5340 helix: 2.14 (0.14), residues: 1656 sheet: 0.46 (0.15), residues: 1128 loop : -1.45 (0.11), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 175 HIS 0.006 0.001 HIS E 37 PHE 0.019 0.002 PHE J 183 TYR 0.014 0.001 TYR H 150 ARG 0.006 0.000 ARG I 221 *********************** 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 469 residues out of total 4692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 403 time to evaluate : 6.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.6725 (OUTLIER) cc_final: 0.6484 (tm-30) REVERT: A 353 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7166 (mp0) REVERT: A 402 MET cc_start: 0.7464 (mtp) cc_final: 0.7235 (ttm) REVERT: B 30 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.6850 (ttm-80) REVERT: C 26 GLU cc_start: 0.6697 (OUTLIER) cc_final: 0.6459 (tm-30) REVERT: C 30 ARG cc_start: 0.7223 (OUTLIER) cc_final: 0.6708 (ttm-80) REVERT: D 26 GLU cc_start: 0.6736 (OUTLIER) cc_final: 0.6449 (tm-30) REVERT: D 353 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7158 (mp0) REVERT: D 402 MET cc_start: 0.7475 (mtp) cc_final: 0.7237 (ttm) REVERT: E 30 ARG cc_start: 0.7272 (OUTLIER) cc_final: 0.6824 (ttm-80) REVERT: F 26 GLU cc_start: 0.6668 (OUTLIER) cc_final: 0.6382 (tm-30) REVERT: F 30 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.6675 (ttm-80) REVERT: G 26 GLU cc_start: 0.6733 (OUTLIER) cc_final: 0.6509 (tm-30) REVERT: G 238 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.7031 (mtp85) REVERT: G 353 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7167 (mp0) REVERT: G 402 MET cc_start: 0.7407 (mtm) cc_final: 0.7129 (ttm) REVERT: H 30 ARG cc_start: 0.7274 (OUTLIER) cc_final: 0.6847 (ttm-80) REVERT: I 26 GLU cc_start: 0.6690 (OUTLIER) cc_final: 0.6388 (tm-30) REVERT: I 30 ARG cc_start: 0.7208 (OUTLIER) cc_final: 0.6664 (ttm-80) REVERT: J 26 GLU cc_start: 0.6744 (OUTLIER) cc_final: 0.6523 (tm-30) REVERT: J 238 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.7025 (mtp85) REVERT: J 353 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7171 (mp0) REVERT: J 402 MET cc_start: 0.7488 (mtp) cc_final: 0.7230 (ttm) REVERT: K 30 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.6849 (ttm-80) REVERT: L 26 GLU cc_start: 0.6651 (OUTLIER) cc_final: 0.6420 (tm-30) REVERT: L 30 ARG cc_start: 0.7232 (OUTLIER) cc_final: 0.6687 (ttm-80) outliers start: 66 outliers final: 29 residues processed: 449 average time/residue: 1.8891 time to fit residues: 1023.1575 Evaluate side-chains 450 residues out of total 4692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 399 time to evaluate : 5.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 353 GLU Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 99 LYS Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 238 ARG Chi-restraints excluded: chain G residue 353 GLU Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain I residue 26 GLU Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 238 ARG Chi-restraints excluded: chain J residue 353 GLU Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 30 ARG Chi-restraints excluded: chain L residue 26 GLU Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 99 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 318 optimal weight: 0.0370 chunk 512 optimal weight: 3.9990 chunk 313 optimal weight: 0.1980 chunk 243 optimal weight: 2.9990 chunk 356 optimal weight: 0.6980 chunk 537 optimal weight: 0.9980 chunk 495 optimal weight: 10.0000 chunk 428 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 330 optimal weight: 0.8980 chunk 262 optimal weight: 2.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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: 0.7530 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 44064 Z= 0.140 Angle : 0.517 9.570 59772 Z= 0.270 Chirality : 0.042 0.133 6744 Planarity : 0.005 0.036 7512 Dihedral : 5.985 60.940 6024 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.87 % Allowed : 15.19 % Favored : 83.94 % 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: 0.52 (0.12), residues: 5340 helix: 2.31 (0.14), residues: 1644 sheet: 0.88 (0.14), residues: 1212 loop : -1.38 (0.11), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 394 HIS 0.004 0.001 HIS K 37 PHE 0.011 0.001 PHE E 264 TYR 0.008 0.001 TYR B 150 ARG 0.006 0.000 ARG I 238 ********************** 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 440 residues out of total 4692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 400 time to evaluate : 5.610 Fit side-chains REVERT: A 26 GLU cc_start: 0.6670 (OUTLIER) cc_final: 0.6434 (tm-30) REVERT: A 402 MET cc_start: 0.7466 (mtp) cc_final: 0.7242 (ttm) REVERT: B 30 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.6777 (ttm-80) REVERT: C 26 GLU cc_start: 0.6637 (OUTLIER) cc_final: 0.6392 (tm-30) REVERT: C 30 ARG cc_start: 0.7148 (OUTLIER) cc_final: 0.6670 (ttm-80) REVERT: D 26 GLU cc_start: 0.6690 (OUTLIER) cc_final: 0.6463 (tm-30) REVERT: D 402 MET cc_start: 0.7465 (mtp) cc_final: 0.7243 (ttm) REVERT: E 30 ARG cc_start: 0.7157 (OUTLIER) cc_final: 0.6754 (ttm-80) REVERT: F 26 GLU cc_start: 0.6637 (OUTLIER) cc_final: 0.6344 (tm-30) REVERT: F 30 ARG cc_start: 0.7166 (OUTLIER) cc_final: 0.6658 (ttm-80) REVERT: G 26 GLU cc_start: 0.6677 (OUTLIER) cc_final: 0.6450 (tm-30) REVERT: G 238 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.6988 (mtp85) REVERT: G 402 MET cc_start: 0.7383 (mtm) cc_final: 0.7094 (ttm) REVERT: H 30 ARG cc_start: 0.7159 (OUTLIER) cc_final: 0.6771 (ttm-80) REVERT: I 26 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.6415 (tm-30) REVERT: I 30 ARG cc_start: 0.7123 (OUTLIER) cc_final: 0.6625 (ttm-80) REVERT: J 26 GLU cc_start: 0.6677 (OUTLIER) cc_final: 0.6472 (tm-30) REVERT: J 238 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.6972 (mtp85) REVERT: J 402 MET cc_start: 0.7481 (mtp) cc_final: 0.7242 (ttm) REVERT: K 30 ARG cc_start: 0.7172 (OUTLIER) cc_final: 0.6784 (ttm-80) REVERT: L 30 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.6649 (ttm-80) outliers start: 40 outliers final: 16 residues processed: 428 average time/residue: 1.8108 time to fit residues: 934.5997 Evaluate side-chains 425 residues out of total 4692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 392 time to evaluate : 5.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 396 LYS Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 238 ARG Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain I residue 26 GLU Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 238 ARG Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 30 ARG Chi-restraints excluded: chain L residue 30 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 340 optimal weight: 0.0030 chunk 456 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 395 optimal weight: 3.9990 chunk 63 optimal weight: 0.2980 chunk 119 optimal weight: 7.9990 chunk 429 optimal weight: 6.9990 chunk 179 optimal weight: 4.9990 chunk 440 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 79 optimal weight: 0.5980 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 341 GLN F 341 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.136748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.104249 restraints weight = 44483.593| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.46 r_work: 0.3147 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 44064 Z= 0.179 Angle : 0.577 10.428 59772 Z= 0.308 Chirality : 0.044 0.146 6744 Planarity : 0.005 0.035 7512 Dihedral : 6.092 61.747 6024 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.15 % Allowed : 15.19 % Favored : 83.66 % 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: 0.32 (0.11), residues: 5340 helix: 2.24 (0.14), residues: 1656 sheet: 0.56 (0.15), residues: 1128 loop : -1.39 (0.11), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 175 HIS 0.006 0.001 HIS E 37 PHE 0.016 0.002 PHE J 183 TYR 0.013 0.001 TYR E 150 ARG 0.005 0.000 ARG C 238 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16575.83 seconds wall clock time: 297 minutes 14.75 seconds (17834.75 seconds total)