Starting phenix.real_space_refine (version: dev) on Tue May 17 09:52:50 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz4_20588/05_2022/6tz4_20588.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz4_20588/05_2022/6tz4_20588.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz4_20588/05_2022/6tz4_20588.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz4_20588/05_2022/6tz4_20588.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz4_20588/05_2022/6tz4_20588.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz4_20588/05_2022/6tz4_20588.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.22s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 99216 Number of models: 1 Model: "" Number of chains: 72 Chain: "JB" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1366 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "MB" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1390 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "A" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1366 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1390 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1366 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1390 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "E" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1366 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1390 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "G" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1366 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1390 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "I" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1366 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "J" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1390 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "K" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1366 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "L" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1390 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "M" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1366 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "N" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1390 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "O" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1366 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "P" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1390 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "Q" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1366 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "R" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1390 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "S" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1366 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "T" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1390 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "V" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1366 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "W" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1390 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "X" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1366 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "Y" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1390 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "Z" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1366 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "AA" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1390 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "BA" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1366 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "CA" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1390 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "DA" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1366 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "EA" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1390 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "FA" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1366 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "GA" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1390 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "HA" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1366 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "IA" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1390 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "JA" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1366 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "KA" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1390 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "LA" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1366 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "MA" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1390 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "NA" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1366 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "OA" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1390 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "PA" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1366 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "QA" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1390 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "RA" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1366 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "SA" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1390 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "TA" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1366 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "UA" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1390 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "VA" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1366 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "WA" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1390 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "XA" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1366 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "YA" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1390 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "ZA" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1366 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "AB" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1390 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "BB" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1366 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "CB" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1390 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "DB" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1366 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "EB" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1390 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "FB" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1366 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "GB" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1390 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "HB" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1366 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "IB" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1390 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "LB" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1366 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "KB" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1390 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "NB" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1366 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "OB" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1390 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "PB" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1366 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "QB" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1390 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "RB" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1366 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "SB" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1390 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "02" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1366 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "01" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1390 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Time building chain proxies: 41.01, per 1000 atoms: 0.41 Number of scatterers: 99216 At special positions: 0 Unit cell: (264.74, 265.96, 175.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 648 16.00 O 18756 8.00 N 17748 7.00 C 62064 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 34.31 Conformation dependent library (CDL) restraints added in 11.3 seconds 25272 Ramachandran restraints generated. 12636 Oldfield, 0 Emsley, 12636 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 25056 Finding SS restraints... Secondary structure from input PDB file: 504 helices and 0 sheets defined 88.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.25 Creating SS restraints... Processing helix chain 'JB' and resid 2 through 41 removed outlier: 3.607A pdb=" N GLNJB 41 " --> pdb=" O GLUJB 37 " (cutoff:3.500A) Processing helix chain 'JB' and resid 44 through 106 removed outlier: 3.697A pdb=" N ALAJB 48 " --> pdb=" O ASNJB 44 " (cutoff:3.500A) Processing helix chain 'JB' and resid 107 through 140 Processing helix chain 'JB' and resid 145 through 161 removed outlier: 4.085A pdb=" N VALJB 149 " --> pdb=" O PROJB 145 " (cutoff:3.500A) Processing helix chain 'JB' and resid 187 through 198 Processing helix chain 'MB' and resid 7 through 45 removed outlier: 3.781A pdb=" N LEUMB 11 " --> pdb=" O LYSMB 7 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYSMB 38 " --> pdb=" O GLNMB 34 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLUMB 39 " --> pdb=" O LYSMB 35 " (cutoff:3.500A) Processing helix chain 'MB' and resid 49 through 82 Processing helix chain 'MB' and resid 82 through 87 Processing helix chain 'MB' and resid 93 through 111 removed outlier: 4.406A pdb=" N GLUMB 98 " --> pdb=" O SERMB 94 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SERMB 99 " --> pdb=" O GLYMB 95 " (cutoff:3.500A) Proline residue: MB 108 - end of helix Processing helix chain 'MB' and resid 115 through 128 removed outlier: 3.555A pdb=" N ILEMB 119 " --> pdb=" O ALAMB 115 " (cutoff:3.500A) Processing helix chain 'MB' and resid 135 through 141 removed outlier: 3.602A pdb=" N ASNMB 139 " --> pdb=" O LEUMB 135 " (cutoff:3.500A) Processing helix chain 'MB' and resid 145 through 152 Processing helix chain 'MB' and resid 158 through 173 Processing helix chain 'MB' and resid 180 through 186 removed outlier: 3.762A pdb=" N GLUMB 186 " --> pdb=" O VALMB 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 41 removed outlier: 3.606A pdb=" N GLN A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 106 removed outlier: 3.696A pdb=" N ALA A 48 " --> pdb=" O ASN A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 140 Processing helix chain 'A' and resid 145 through 161 removed outlier: 4.085A pdb=" N VAL A 149 " --> pdb=" O PRO A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 198 Processing helix chain 'B' and resid 7 through 45 removed outlier: 3.780A pdb=" N LEU B 11 " --> pdb=" O LYS B 7 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS B 38 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU B 39 " --> pdb=" O LYS B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 82 Processing helix chain 'B' and resid 82 through 87 Processing helix chain 'B' and resid 93 through 111 removed outlier: 4.405A pdb=" N GLU B 98 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SER B 99 " --> pdb=" O GLY B 95 " (cutoff:3.500A) Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 115 through 128 removed outlier: 3.555A pdb=" N ILE B 119 " --> pdb=" O ALA B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 141 removed outlier: 3.602A pdb=" N ASN B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 152 Processing helix chain 'B' and resid 158 through 173 Processing helix chain 'B' and resid 180 through 186 removed outlier: 3.762A pdb=" N GLU B 186 " --> pdb=" O VAL B 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 41 removed outlier: 3.607A pdb=" N GLN C 41 " --> pdb=" O GLU C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 106 removed outlier: 3.696A pdb=" N ALA C 48 " --> pdb=" O ASN C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 140 Processing helix chain 'C' and resid 145 through 161 removed outlier: 4.085A pdb=" N VAL C 149 " --> pdb=" O PRO C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 198 Processing helix chain 'D' and resid 7 through 45 removed outlier: 3.781A pdb=" N LEU D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS D 38 " --> pdb=" O GLN D 34 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU D 39 " --> pdb=" O LYS D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 82 Processing helix chain 'D' and resid 82 through 87 Processing helix chain 'D' and resid 93 through 111 removed outlier: 4.405A pdb=" N GLU D 98 " --> pdb=" O SER D 94 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SER D 99 " --> pdb=" O GLY D 95 " (cutoff:3.500A) Proline residue: D 108 - end of helix Processing helix chain 'D' and resid 115 through 128 removed outlier: 3.555A pdb=" N ILE D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 141 removed outlier: 3.602A pdb=" N ASN D 139 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 152 Processing helix chain 'D' and resid 158 through 173 Processing helix chain 'D' and resid 180 through 186 removed outlier: 3.762A pdb=" N GLU D 186 " --> pdb=" O VAL D 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 41 removed outlier: 3.606A pdb=" N GLN E 41 " --> pdb=" O GLU E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 106 removed outlier: 3.696A pdb=" N ALA E 48 " --> pdb=" O ASN E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 140 Processing helix chain 'E' and resid 145 through 161 removed outlier: 4.085A pdb=" N VAL E 149 " --> pdb=" O PRO E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 198 Processing helix chain 'F' and resid 7 through 45 removed outlier: 3.781A pdb=" N LEU F 11 " --> pdb=" O LYS F 7 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS F 38 " --> pdb=" O GLN F 34 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU F 39 " --> pdb=" O LYS F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 82 Processing helix chain 'F' and resid 82 through 87 Processing helix chain 'F' and resid 93 through 111 removed outlier: 4.405A pdb=" N GLU F 98 " --> pdb=" O SER F 94 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SER F 99 " --> pdb=" O GLY F 95 " (cutoff:3.500A) Proline residue: F 108 - end of helix Processing helix chain 'F' and resid 115 through 128 removed outlier: 3.555A pdb=" N ILE F 119 " --> pdb=" O ALA F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 141 removed outlier: 3.602A pdb=" N ASN F 139 " --> pdb=" O LEU F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 152 Processing helix chain 'F' and resid 158 through 173 Processing helix chain 'F' and resid 180 through 186 removed outlier: 3.762A pdb=" N GLU F 186 " --> pdb=" O VAL F 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 41 removed outlier: 3.606A pdb=" N GLN G 41 " --> pdb=" O GLU G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 106 removed outlier: 3.696A pdb=" N ALA G 48 " --> pdb=" O ASN G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 140 Processing helix chain 'G' and resid 145 through 161 removed outlier: 4.084A pdb=" N VAL G 149 " --> pdb=" O PRO G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 198 Processing helix chain 'H' and resid 7 through 45 removed outlier: 3.780A pdb=" N LEU H 11 " --> pdb=" O LYS H 7 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS H 38 " --> pdb=" O GLN H 34 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU H 39 " --> pdb=" O LYS H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 82 Processing helix chain 'H' and resid 82 through 87 Processing helix chain 'H' and resid 93 through 111 removed outlier: 4.405A pdb=" N GLU H 98 " --> pdb=" O SER H 94 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SER H 99 " --> pdb=" O GLY H 95 " (cutoff:3.500A) Proline residue: H 108 - end of helix Processing helix chain 'H' and resid 115 through 128 removed outlier: 3.555A pdb=" N ILE H 119 " --> pdb=" O ALA H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 141 removed outlier: 3.602A pdb=" N ASN H 139 " --> pdb=" O LEU H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 152 Processing helix chain 'H' and resid 158 through 173 Processing helix chain 'H' and resid 180 through 186 removed outlier: 3.763A pdb=" N GLU H 186 " --> pdb=" O VAL H 182 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 41 removed outlier: 3.606A pdb=" N GLN I 41 " --> pdb=" O GLU I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 106 removed outlier: 3.696A pdb=" N ALA I 48 " --> pdb=" O ASN I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 140 Processing helix chain 'I' and resid 145 through 161 removed outlier: 4.085A pdb=" N VAL I 149 " --> pdb=" O PRO I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 187 through 198 Processing helix chain 'J' and resid 7 through 45 removed outlier: 3.781A pdb=" N LEU J 11 " --> pdb=" O LYS J 7 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS J 38 " --> pdb=" O GLN J 34 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU J 39 " --> pdb=" O LYS J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 82 Processing helix chain 'J' and resid 82 through 87 Processing helix chain 'J' and resid 93 through 111 removed outlier: 4.405A pdb=" N GLU J 98 " --> pdb=" O SER J 94 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N SER J 99 " --> pdb=" O GLY J 95 " (cutoff:3.500A) Proline residue: J 108 - end of helix Processing helix chain 'J' and resid 115 through 128 removed outlier: 3.555A pdb=" N ILE J 119 " --> pdb=" O ALA J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 135 through 141 removed outlier: 3.602A pdb=" N ASN J 139 " --> pdb=" O LEU J 135 " (cutoff:3.500A) Processing helix chain 'J' and resid 145 through 152 Processing helix chain 'J' and resid 158 through 173 Processing helix chain 'J' and resid 180 through 186 removed outlier: 3.762A pdb=" N GLU J 186 " --> pdb=" O VAL J 182 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 41 removed outlier: 3.606A pdb=" N GLN K 41 " --> pdb=" O GLU K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 106 removed outlier: 3.696A pdb=" N ALA K 48 " --> pdb=" O ASN K 44 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 140 Processing helix chain 'K' and resid 145 through 161 removed outlier: 4.084A pdb=" N VAL K 149 " --> pdb=" O PRO K 145 " (cutoff:3.500A) Processing helix chain 'K' and resid 187 through 198 Processing helix chain 'L' and resid 7 through 45 removed outlier: 3.781A pdb=" N LEU L 11 " --> pdb=" O LYS L 7 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS L 38 " --> pdb=" O GLN L 34 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU L 39 " --> pdb=" O LYS L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 82 Processing helix chain 'L' and resid 82 through 87 Processing helix chain 'L' and resid 93 through 111 removed outlier: 4.405A pdb=" N GLU L 98 " --> pdb=" O SER L 94 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SER L 99 " --> pdb=" O GLY L 95 " (cutoff:3.500A) Proline residue: L 108 - end of helix Processing helix chain 'L' and resid 115 through 128 removed outlier: 3.556A pdb=" N ILE L 119 " --> pdb=" O ALA L 115 " (cutoff:3.500A) Processing helix chain 'L' and resid 135 through 141 removed outlier: 3.602A pdb=" N ASN L 139 " --> pdb=" O LEU L 135 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 152 Processing helix chain 'L' and resid 158 through 173 Processing helix chain 'L' and resid 180 through 186 removed outlier: 3.762A pdb=" N GLU L 186 " --> pdb=" O VAL L 182 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 41 removed outlier: 3.607A pdb=" N GLN M 41 " --> pdb=" O GLU M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 106 removed outlier: 3.696A pdb=" N ALA M 48 " --> pdb=" O ASN M 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 140 Processing helix chain 'M' and resid 145 through 161 removed outlier: 4.085A pdb=" N VAL M 149 " --> pdb=" O PRO M 145 " (cutoff:3.500A) Processing helix chain 'M' and resid 187 through 198 Processing helix chain 'N' and resid 7 through 45 removed outlier: 3.781A pdb=" N LEU N 11 " --> pdb=" O LYS N 7 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS N 38 " --> pdb=" O GLN N 34 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU N 39 " --> pdb=" O LYS N 35 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 82 Processing helix chain 'N' and resid 82 through 87 Processing helix chain 'N' and resid 93 through 111 removed outlier: 4.405A pdb=" N GLU N 98 " --> pdb=" O SER N 94 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SER N 99 " --> pdb=" O GLY N 95 " (cutoff:3.500A) Proline residue: N 108 - end of helix Processing helix chain 'N' and resid 115 through 128 removed outlier: 3.556A pdb=" N ILE N 119 " --> pdb=" O ALA N 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 135 through 141 removed outlier: 3.602A pdb=" N ASN N 139 " --> pdb=" O LEU N 135 " (cutoff:3.500A) Processing helix chain 'N' and resid 145 through 152 Processing helix chain 'N' and resid 158 through 173 Processing helix chain 'N' and resid 180 through 186 removed outlier: 3.761A pdb=" N GLU N 186 " --> pdb=" O VAL N 182 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 41 removed outlier: 3.607A pdb=" N GLN O 41 " --> pdb=" O GLU O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 106 removed outlier: 3.696A pdb=" N ALA O 48 " --> pdb=" O ASN O 44 " (cutoff:3.500A) Processing helix chain 'O' and resid 107 through 140 Processing helix chain 'O' and resid 145 through 161 removed outlier: 4.084A pdb=" N VAL O 149 " --> pdb=" O PRO O 145 " (cutoff:3.500A) Processing helix chain 'O' and resid 187 through 198 Processing helix chain 'P' and resid 7 through 45 removed outlier: 3.781A pdb=" N LEU P 11 " --> pdb=" O LYS P 7 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS P 38 " --> pdb=" O GLN P 34 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU P 39 " --> pdb=" O LYS P 35 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 82 Processing helix chain 'P' and resid 82 through 87 Processing helix chain 'P' and resid 93 through 111 removed outlier: 4.406A pdb=" N GLU P 98 " --> pdb=" O SER P 94 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N SER P 99 " --> pdb=" O GLY P 95 " (cutoff:3.500A) Proline residue: P 108 - end of helix Processing helix chain 'P' and resid 115 through 128 removed outlier: 3.556A pdb=" N ILE P 119 " --> pdb=" O ALA P 115 " (cutoff:3.500A) Processing helix chain 'P' and resid 135 through 141 removed outlier: 3.602A pdb=" N ASN P 139 " --> pdb=" O LEU P 135 " (cutoff:3.500A) Processing helix chain 'P' and resid 145 through 152 Processing helix chain 'P' and resid 158 through 173 Processing helix chain 'P' and resid 180 through 186 removed outlier: 3.762A pdb=" N GLU P 186 " --> pdb=" O VAL P 182 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 41 removed outlier: 3.607A pdb=" N GLN Q 41 " --> pdb=" O GLU Q 37 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 106 removed outlier: 3.697A pdb=" N ALA Q 48 " --> pdb=" O ASN Q 44 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 140 Processing helix chain 'Q' and resid 145 through 161 removed outlier: 4.085A pdb=" N VAL Q 149 " --> pdb=" O PRO Q 145 " (cutoff:3.500A) Processing helix chain 'Q' and resid 187 through 198 Processing helix chain 'R' and resid 7 through 45 removed outlier: 3.781A pdb=" N LEU R 11 " --> pdb=" O LYS R 7 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS R 38 " --> pdb=" O GLN R 34 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU R 39 " --> pdb=" O LYS R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 82 Processing helix chain 'R' and resid 82 through 87 Processing helix chain 'R' and resid 93 through 111 removed outlier: 4.406A pdb=" N GLU R 98 " --> pdb=" O SER R 94 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SER R 99 " --> pdb=" O GLY R 95 " (cutoff:3.500A) Proline residue: R 108 - end of helix Processing helix chain 'R' and resid 115 through 128 removed outlier: 3.556A pdb=" N ILE R 119 " --> pdb=" O ALA R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 135 through 141 removed outlier: 3.601A pdb=" N ASN R 139 " --> pdb=" O LEU R 135 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 152 Processing helix chain 'R' and resid 158 through 173 Processing helix chain 'R' and resid 180 through 186 removed outlier: 3.762A pdb=" N GLU R 186 " --> pdb=" O VAL R 182 " (cutoff:3.500A) Processing helix chain 'S' and resid 3 through 41 removed outlier: 3.607A pdb=" N GLN S 41 " --> pdb=" O GLU S 37 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 106 removed outlier: 3.696A pdb=" N ALA S 48 " --> pdb=" O ASN S 44 " (cutoff:3.500A) Processing helix chain 'S' and resid 107 through 140 Processing helix chain 'S' and resid 145 through 161 removed outlier: 4.085A pdb=" N VAL S 149 " --> pdb=" O PRO S 145 " (cutoff:3.500A) Processing helix chain 'S' and resid 187 through 198 Processing helix chain 'T' and resid 7 through 45 removed outlier: 3.781A pdb=" N LEU T 11 " --> pdb=" O LYS T 7 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS T 38 " --> pdb=" O GLN T 34 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU T 39 " --> pdb=" O LYS T 35 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 82 Processing helix chain 'T' and resid 82 through 87 Processing helix chain 'T' and resid 93 through 111 removed outlier: 4.405A pdb=" N GLU T 98 " --> pdb=" O SER T 94 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SER T 99 " --> pdb=" O GLY T 95 " (cutoff:3.500A) Proline residue: T 108 - end of helix Processing helix chain 'T' and resid 115 through 128 removed outlier: 3.556A pdb=" N ILE T 119 " --> pdb=" O ALA T 115 " (cutoff:3.500A) Processing helix chain 'T' and resid 135 through 141 removed outlier: 3.602A pdb=" N ASN T 139 " --> pdb=" O LEU T 135 " (cutoff:3.500A) Processing helix chain 'T' and resid 145 through 152 Processing helix chain 'T' and resid 158 through 173 Processing helix chain 'T' and resid 180 through 186 removed outlier: 3.762A pdb=" N GLU T 186 " --> pdb=" O VAL T 182 " (cutoff:3.500A) Processing helix chain 'V' and resid 3 through 41 removed outlier: 3.607A pdb=" N GLN V 41 " --> pdb=" O GLU V 37 " (cutoff:3.500A) Processing helix chain 'V' and resid 44 through 106 removed outlier: 3.696A pdb=" N ALA V 48 " --> pdb=" O ASN V 44 " (cutoff:3.500A) Processing helix chain 'V' and resid 107 through 140 Processing helix chain 'V' and resid 145 through 161 removed outlier: 4.085A pdb=" N VAL V 149 " --> pdb=" O PRO V 145 " (cutoff:3.500A) Processing helix chain 'V' and resid 187 through 198 Processing helix chain 'W' and resid 7 through 45 removed outlier: 3.781A pdb=" N LEU W 11 " --> pdb=" O LYS W 7 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS W 38 " --> pdb=" O GLN W 34 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU W 39 " --> pdb=" O LYS W 35 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 82 Processing helix chain 'W' and resid 82 through 87 Processing helix chain 'W' and resid 93 through 111 removed outlier: 4.405A pdb=" N GLU W 98 " --> pdb=" O SER W 94 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SER W 99 " --> pdb=" O GLY W 95 " (cutoff:3.500A) Proline residue: W 108 - end of helix Processing helix chain 'W' and resid 115 through 128 removed outlier: 3.556A pdb=" N ILE W 119 " --> pdb=" O ALA W 115 " (cutoff:3.500A) Processing helix chain 'W' and resid 135 through 141 removed outlier: 3.602A pdb=" N ASN W 139 " --> pdb=" O LEU W 135 " (cutoff:3.500A) Processing helix chain 'W' and resid 145 through 152 Processing helix chain 'W' and resid 158 through 173 Processing helix chain 'W' and resid 180 through 186 removed outlier: 3.762A pdb=" N GLU W 186 " --> pdb=" O VAL W 182 " (cutoff:3.500A) Processing helix chain 'X' and resid 3 through 41 removed outlier: 3.607A pdb=" N GLN X 41 " --> pdb=" O GLU X 37 " (cutoff:3.500A) Processing helix chain 'X' and resid 44 through 106 removed outlier: 3.696A pdb=" N ALA X 48 " --> pdb=" O ASN X 44 " (cutoff:3.500A) Processing helix chain 'X' and resid 107 through 140 Processing helix chain 'X' and resid 145 through 161 removed outlier: 4.084A pdb=" N VAL X 149 " --> pdb=" O PRO X 145 " (cutoff:3.500A) Processing helix chain 'X' and resid 187 through 198 Processing helix chain 'Y' and resid 7 through 45 removed outlier: 3.780A pdb=" N LEU Y 11 " --> pdb=" O LYS Y 7 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS Y 38 " --> pdb=" O GLN Y 34 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU Y 39 " --> pdb=" O LYS Y 35 " (cutoff:3.500A) Processing helix chain 'Y' and resid 49 through 82 Processing helix chain 'Y' and resid 82 through 87 Processing helix chain 'Y' and resid 93 through 111 removed outlier: 4.405A pdb=" N GLU Y 98 " --> pdb=" O SER Y 94 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SER Y 99 " --> pdb=" O GLY Y 95 " (cutoff:3.500A) Proline residue: Y 108 - end of helix Processing helix chain 'Y' and resid 115 through 128 removed outlier: 3.555A pdb=" N ILE Y 119 " --> pdb=" O ALA Y 115 " (cutoff:3.500A) Processing helix chain 'Y' and resid 135 through 141 removed outlier: 3.601A pdb=" N ASN Y 139 " --> pdb=" O LEU Y 135 " (cutoff:3.500A) Processing helix chain 'Y' and resid 145 through 152 Processing helix chain 'Y' and resid 158 through 173 Processing helix chain 'Y' and resid 180 through 186 removed outlier: 3.762A pdb=" N GLU Y 186 " --> pdb=" O VAL Y 182 " (cutoff:3.500A) Processing helix chain 'Z' and resid 3 through 41 removed outlier: 3.607A pdb=" N GLN Z 41 " --> pdb=" O GLU Z 37 " (cutoff:3.500A) Processing helix chain 'Z' and resid 44 through 106 removed outlier: 3.696A pdb=" N ALA Z 48 " --> pdb=" O ASN Z 44 " (cutoff:3.500A) Processing helix chain 'Z' and resid 107 through 140 Processing helix chain 'Z' and resid 145 through 161 removed outlier: 4.085A pdb=" N VAL Z 149 " --> pdb=" O PRO Z 145 " (cutoff:3.500A) Processing helix chain 'Z' and resid 187 through 198 Processing helix chain 'AA' and resid 7 through 45 removed outlier: 3.780A pdb=" N LEUAA 11 " --> pdb=" O LYSAA 7 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYSAA 38 " --> pdb=" O GLNAA 34 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLUAA 39 " --> pdb=" O LYSAA 35 " (cutoff:3.500A) Processing helix chain 'AA' and resid 49 through 82 Processing helix chain 'AA' and resid 82 through 87 Processing helix chain 'AA' and resid 93 through 111 removed outlier: 4.406A pdb=" N GLUAA 98 " --> pdb=" O SERAA 94 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SERAA 99 " --> pdb=" O GLYAA 95 " (cutoff:3.500A) Proline residue: AA 108 - end of helix Processing helix chain 'AA' and resid 115 through 128 removed outlier: 3.555A pdb=" N ILEAA 119 " --> pdb=" O ALAAA 115 " (cutoff:3.500A) Processing helix chain 'AA' and resid 135 through 141 removed outlier: 3.601A pdb=" N ASNAA 139 " --> pdb=" O LEUAA 135 " (cutoff:3.500A) Processing helix chain 'AA' and resid 145 through 152 Processing helix chain 'AA' and resid 158 through 173 Processing helix chain 'AA' and resid 180 through 186 removed outlier: 3.762A pdb=" N GLUAA 186 " --> pdb=" O VALAA 182 " (cutoff:3.500A) Processing helix chain 'BA' and resid 3 through 41 removed outlier: 3.607A pdb=" N GLNBA 41 " --> pdb=" O GLUBA 37 " (cutoff:3.500A) Processing helix chain 'BA' and resid 44 through 106 removed outlier: 3.696A pdb=" N ALABA 48 " --> pdb=" O ASNBA 44 " (cutoff:3.500A) Processing helix chain 'BA' and resid 107 through 140 Processing helix chain 'BA' and resid 145 through 161 removed outlier: 4.085A pdb=" N VALBA 149 " --> pdb=" O PROBA 145 " (cutoff:3.500A) Processing helix chain 'BA' and resid 187 through 198 Processing helix chain 'CA' and resid 7 through 45 removed outlier: 3.781A pdb=" N LEUCA 11 " --> pdb=" O LYSCA 7 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYSCA 38 " --> pdb=" O GLNCA 34 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLUCA 39 " --> pdb=" O LYSCA 35 " (cutoff:3.500A) Processing helix chain 'CA' and resid 49 through 82 Processing helix chain 'CA' and resid 82 through 87 Processing helix chain 'CA' and resid 93 through 111 removed outlier: 4.406A pdb=" N GLUCA 98 " --> pdb=" O SERCA 94 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SERCA 99 " --> pdb=" O GLYCA 95 " (cutoff:3.500A) Proline residue: CA 108 - end of helix Processing helix chain 'CA' and resid 115 through 128 removed outlier: 3.555A pdb=" N ILECA 119 " --> pdb=" O ALACA 115 " (cutoff:3.500A) Processing helix chain 'CA' and resid 135 through 141 removed outlier: 3.603A pdb=" N ASNCA 139 " --> pdb=" O LEUCA 135 " (cutoff:3.500A) Processing helix chain 'CA' and resid 145 through 152 Processing helix chain 'CA' and resid 158 through 173 Processing helix chain 'CA' and resid 180 through 186 removed outlier: 3.761A pdb=" N GLUCA 186 " --> pdb=" O VALCA 182 " (cutoff:3.500A) Processing helix chain 'DA' and resid 3 through 41 removed outlier: 3.607A pdb=" N GLNDA 41 " --> pdb=" O GLUDA 37 " (cutoff:3.500A) Processing helix chain 'DA' and resid 44 through 106 removed outlier: 3.696A pdb=" N ALADA 48 " --> pdb=" O ASNDA 44 " (cutoff:3.500A) Processing helix chain 'DA' and resid 107 through 140 Processing helix chain 'DA' and resid 145 through 161 removed outlier: 4.085A pdb=" N VALDA 149 " --> pdb=" O PRODA 145 " (cutoff:3.500A) Processing helix chain 'DA' and resid 187 through 198 Processing helix chain 'EA' and resid 7 through 45 removed outlier: 3.781A pdb=" N LEUEA 11 " --> pdb=" O LYSEA 7 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYSEA 38 " --> pdb=" O GLNEA 34 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLUEA 39 " --> pdb=" O LYSEA 35 " (cutoff:3.500A) Processing helix chain 'EA' and resid 49 through 82 Processing helix chain 'EA' and resid 82 through 87 Processing helix chain 'EA' and resid 93 through 111 removed outlier: 4.405A pdb=" N GLUEA 98 " --> pdb=" O SEREA 94 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N SEREA 99 " --> pdb=" O GLYEA 95 " (cutoff:3.500A) Proline residue: EA 108 - end of helix Processing helix chain 'EA' and resid 115 through 128 removed outlier: 3.556A pdb=" N ILEEA 119 " --> pdb=" O ALAEA 115 " (cutoff:3.500A) Processing helix chain 'EA' and resid 135 through 141 removed outlier: 3.601A pdb=" N ASNEA 139 " --> pdb=" O LEUEA 135 " (cutoff:3.500A) Processing helix chain 'EA' and resid 145 through 152 Processing helix chain 'EA' and resid 158 through 173 Processing helix chain 'EA' and resid 180 through 186 removed outlier: 3.763A pdb=" N GLUEA 186 " --> pdb=" O VALEA 182 " (cutoff:3.500A) Processing helix chain 'FA' and resid 3 through 41 removed outlier: 3.607A pdb=" N GLNFA 41 " --> pdb=" O GLUFA 37 " (cutoff:3.500A) Processing helix chain 'FA' and resid 44 through 106 removed outlier: 3.695A pdb=" N ALAFA 48 " --> pdb=" O ASNFA 44 " (cutoff:3.500A) Processing helix chain 'FA' and resid 107 through 140 Processing helix chain 'FA' and resid 145 through 161 removed outlier: 4.085A pdb=" N VALFA 149 " --> pdb=" O PROFA 145 " (cutoff:3.500A) Processing helix chain 'FA' and resid 187 through 198 Processing helix chain 'GA' and resid 7 through 45 removed outlier: 3.781A pdb=" N LEUGA 11 " --> pdb=" O LYSGA 7 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYSGA 38 " --> pdb=" O GLNGA 34 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLUGA 39 " --> pdb=" O LYSGA 35 " (cutoff:3.500A) Processing helix chain 'GA' and resid 49 through 82 Processing helix chain 'GA' and resid 82 through 87 Processing helix chain 'GA' and resid 93 through 111 removed outlier: 4.405A pdb=" N GLUGA 98 " --> pdb=" O SERGA 94 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SERGA 99 " --> pdb=" O GLYGA 95 " (cutoff:3.500A) Proline residue: GA 108 - end of helix Processing helix chain 'GA' and resid 115 through 128 removed outlier: 3.556A pdb=" N ILEGA 119 " --> pdb=" O ALAGA 115 " (cutoff:3.500A) Processing helix chain 'GA' and resid 135 through 141 removed outlier: 3.602A pdb=" N ASNGA 139 " --> pdb=" O LEUGA 135 " (cutoff:3.500A) Processing helix chain 'GA' and resid 145 through 152 Processing helix chain 'GA' and resid 158 through 173 Processing helix chain 'GA' and resid 180 through 186 removed outlier: 3.763A pdb=" N GLUGA 186 " --> pdb=" O VALGA 182 " (cutoff:3.500A) Processing helix chain 'HA' and resid 3 through 41 removed outlier: 3.607A pdb=" N GLNHA 41 " --> pdb=" O GLUHA 37 " (cutoff:3.500A) Processing helix chain 'HA' and resid 44 through 106 removed outlier: 3.696A pdb=" N ALAHA 48 " --> pdb=" O ASNHA 44 " (cutoff:3.500A) Processing helix chain 'HA' and resid 107 through 140 Processing helix chain 'HA' and resid 145 through 161 removed outlier: 4.085A pdb=" N VALHA 149 " --> pdb=" O PROHA 145 " (cutoff:3.500A) Processing helix chain 'HA' and resid 187 through 198 Processing helix chain 'IA' and resid 7 through 45 removed outlier: 3.781A pdb=" N LEUIA 11 " --> pdb=" O LYSIA 7 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYSIA 38 " --> pdb=" O GLNIA 34 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLUIA 39 " --> pdb=" O LYSIA 35 " (cutoff:3.500A) Processing helix chain 'IA' and resid 49 through 82 Processing helix chain 'IA' and resid 82 through 87 Processing helix chain 'IA' and resid 93 through 111 removed outlier: 4.405A pdb=" N GLUIA 98 " --> pdb=" O SERIA 94 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SERIA 99 " --> pdb=" O GLYIA 95 " (cutoff:3.500A) Proline residue: IA 108 - end of helix Processing helix chain 'IA' and resid 115 through 128 removed outlier: 3.556A pdb=" N ILEIA 119 " --> pdb=" O ALAIA 115 " (cutoff:3.500A) Processing helix chain 'IA' and resid 135 through 141 removed outlier: 3.602A pdb=" N ASNIA 139 " --> pdb=" O LEUIA 135 " (cutoff:3.500A) Processing helix chain 'IA' and resid 145 through 152 Processing helix chain 'IA' and resid 158 through 173 Processing helix chain 'IA' and resid 180 through 186 removed outlier: 3.762A pdb=" N GLUIA 186 " --> pdb=" O VALIA 182 " (cutoff:3.500A) Processing helix chain 'JA' and resid 3 through 41 removed outlier: 3.607A pdb=" N GLNJA 41 " --> pdb=" O GLUJA 37 " (cutoff:3.500A) Processing helix chain 'JA' and resid 44 through 106 removed outlier: 3.696A pdb=" N ALAJA 48 " --> pdb=" O ASNJA 44 " (cutoff:3.500A) Processing helix chain 'JA' and resid 107 through 140 Processing helix chain 'JA' and resid 145 through 161 removed outlier: 4.085A pdb=" N VALJA 149 " --> pdb=" O PROJA 145 " (cutoff:3.500A) Processing helix chain 'JA' and resid 187 through 198 Processing helix chain 'KA' and resid 7 through 45 removed outlier: 3.781A pdb=" N LEUKA 11 " --> pdb=" O LYSKA 7 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYSKA 38 " --> pdb=" O GLNKA 34 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLUKA 39 " --> pdb=" O LYSKA 35 " (cutoff:3.500A) Processing helix chain 'KA' and resid 49 through 82 Processing helix chain 'KA' and resid 82 through 87 Processing helix chain 'KA' and resid 93 through 111 removed outlier: 4.406A pdb=" N GLUKA 98 " --> pdb=" O SERKA 94 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N SERKA 99 " --> pdb=" O GLYKA 95 " (cutoff:3.500A) Proline residue: KA 108 - end of helix Processing helix chain 'KA' and resid 115 through 128 removed outlier: 3.556A pdb=" N ILEKA 119 " --> pdb=" O ALAKA 115 " (cutoff:3.500A) Processing helix chain 'KA' and resid 135 through 141 removed outlier: 3.601A pdb=" N ASNKA 139 " --> pdb=" O LEUKA 135 " (cutoff:3.500A) Processing helix chain 'KA' and resid 145 through 152 Processing helix chain 'KA' and resid 158 through 173 Processing helix chain 'KA' and resid 180 through 186 removed outlier: 3.762A pdb=" N GLUKA 186 " --> pdb=" O VALKA 182 " (cutoff:3.500A) Processing helix chain 'LA' and resid 3 through 41 removed outlier: 3.606A pdb=" N GLNLA 41 " --> pdb=" O GLULA 37 " (cutoff:3.500A) Processing helix chain 'LA' and resid 44 through 106 removed outlier: 3.696A pdb=" N ALALA 48 " --> pdb=" O ASNLA 44 " (cutoff:3.500A) Processing helix chain 'LA' and resid 107 through 140 Processing helix chain 'LA' and resid 145 through 161 removed outlier: 4.085A pdb=" N VALLA 149 " --> pdb=" O PROLA 145 " (cutoff:3.500A) Processing helix chain 'LA' and resid 187 through 198 Processing helix chain 'MA' and resid 7 through 45 removed outlier: 3.781A pdb=" N LEUMA 11 " --> pdb=" O LYSMA 7 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYSMA 38 " --> pdb=" O GLNMA 34 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLUMA 39 " --> pdb=" O LYSMA 35 " (cutoff:3.500A) Processing helix chain 'MA' and resid 49 through 82 Processing helix chain 'MA' and resid 82 through 87 Processing helix chain 'MA' and resid 93 through 111 removed outlier: 4.405A pdb=" N GLUMA 98 " --> pdb=" O SERMA 94 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SERMA 99 " --> pdb=" O GLYMA 95 " (cutoff:3.500A) Proline residue: MA 108 - end of helix Processing helix chain 'MA' and resid 115 through 128 removed outlier: 3.556A pdb=" N ILEMA 119 " --> pdb=" O ALAMA 115 " (cutoff:3.500A) Processing helix chain 'MA' and resid 135 through 141 removed outlier: 3.601A pdb=" N ASNMA 139 " --> pdb=" O LEUMA 135 " (cutoff:3.500A) Processing helix chain 'MA' and resid 145 through 152 Processing helix chain 'MA' and resid 158 through 173 Processing helix chain 'MA' and resid 180 through 186 removed outlier: 3.762A pdb=" N GLUMA 186 " --> pdb=" O VALMA 182 " (cutoff:3.500A) Processing helix chain 'NA' and resid 3 through 41 removed outlier: 3.606A pdb=" N GLNNA 41 " --> pdb=" O GLUNA 37 " (cutoff:3.500A) Processing helix chain 'NA' and resid 44 through 106 removed outlier: 3.696A pdb=" N ALANA 48 " --> pdb=" O ASNNA 44 " (cutoff:3.500A) Processing helix chain 'NA' and resid 107 through 140 Processing helix chain 'NA' and resid 145 through 161 removed outlier: 4.085A pdb=" N VALNA 149 " --> pdb=" O PRONA 145 " (cutoff:3.500A) Processing helix chain 'NA' and resid 187 through 198 Processing helix chain 'OA' and resid 7 through 45 removed outlier: 3.780A pdb=" N LEUOA 11 " --> pdb=" O LYSOA 7 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYSOA 38 " --> pdb=" O GLNOA 34 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLUOA 39 " --> pdb=" O LYSOA 35 " (cutoff:3.500A) Processing helix chain 'OA' and resid 49 through 82 Processing helix chain 'OA' and resid 82 through 87 Processing helix chain 'OA' and resid 93 through 111 removed outlier: 4.405A pdb=" N GLUOA 98 " --> pdb=" O SEROA 94 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SEROA 99 " --> pdb=" O GLYOA 95 " (cutoff:3.500A) Proline residue: OA 108 - end of helix Processing helix chain 'OA' and resid 115 through 128 removed outlier: 3.555A pdb=" N ILEOA 119 " --> pdb=" O ALAOA 115 " (cutoff:3.500A) Processing helix chain 'OA' and resid 135 through 141 removed outlier: 3.602A pdb=" N ASNOA 139 " --> pdb=" O LEUOA 135 " (cutoff:3.500A) Processing helix chain 'OA' and resid 145 through 152 Processing helix chain 'OA' and resid 158 through 173 Processing helix chain 'OA' and resid 180 through 186 removed outlier: 3.763A pdb=" N GLUOA 186 " --> pdb=" O VALOA 182 " (cutoff:3.500A) Processing helix chain 'PA' and resid 3 through 41 removed outlier: 3.606A pdb=" N GLNPA 41 " --> pdb=" O GLUPA 37 " (cutoff:3.500A) Processing helix chain 'PA' and resid 44 through 106 removed outlier: 3.696A pdb=" N ALAPA 48 " --> pdb=" O ASNPA 44 " (cutoff:3.500A) Processing helix chain 'PA' and resid 107 through 140 Processing helix chain 'PA' and resid 145 through 161 removed outlier: 4.086A pdb=" N VALPA 149 " --> pdb=" O PROPA 145 " (cutoff:3.500A) Processing helix chain 'PA' and resid 187 through 198 Processing helix chain 'QA' and resid 7 through 45 removed outlier: 3.780A pdb=" N LEUQA 11 " --> pdb=" O LYSQA 7 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYSQA 38 " --> pdb=" O GLNQA 34 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLUQA 39 " --> pdb=" O LYSQA 35 " (cutoff:3.500A) Processing helix chain 'QA' and resid 49 through 82 Processing helix chain 'QA' and resid 82 through 87 Processing helix chain 'QA' and resid 93 through 111 removed outlier: 4.405A pdb=" N GLUQA 98 " --> pdb=" O SERQA 94 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N SERQA 99 " --> pdb=" O GLYQA 95 " (cutoff:3.500A) Proline residue: QA 108 - end of helix Processing helix chain 'QA' and resid 115 through 128 removed outlier: 3.555A pdb=" N ILEQA 119 " --> pdb=" O ALAQA 115 " (cutoff:3.500A) Processing helix chain 'QA' and resid 135 through 141 removed outlier: 3.602A pdb=" N ASNQA 139 " --> pdb=" O LEUQA 135 " (cutoff:3.500A) Processing helix chain 'QA' and resid 145 through 152 Processing helix chain 'QA' and resid 158 through 173 Processing helix chain 'QA' and resid 180 through 186 removed outlier: 3.762A pdb=" N GLUQA 186 " --> pdb=" O VALQA 182 " (cutoff:3.500A) Processing helix chain 'RA' and resid 3 through 41 removed outlier: 3.607A pdb=" N GLNRA 41 " --> pdb=" O GLURA 37 " (cutoff:3.500A) Processing helix chain 'RA' and resid 44 through 106 removed outlier: 3.697A pdb=" N ALARA 48 " --> pdb=" O ASNRA 44 " (cutoff:3.500A) Processing helix chain 'RA' and resid 107 through 140 Processing helix chain 'RA' and resid 145 through 161 removed outlier: 4.085A pdb=" N VALRA 149 " --> pdb=" O PRORA 145 " (cutoff:3.500A) Processing helix chain 'RA' and resid 187 through 198 Processing helix chain 'SA' and resid 7 through 45 removed outlier: 3.781A pdb=" N LEUSA 11 " --> pdb=" O LYSSA 7 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYSSA 38 " --> pdb=" O GLNSA 34 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLUSA 39 " --> pdb=" O LYSSA 35 " (cutoff:3.500A) Processing helix chain 'SA' and resid 49 through 82 Processing helix chain 'SA' and resid 82 through 87 Processing helix chain 'SA' and resid 93 through 111 removed outlier: 4.406A pdb=" N GLUSA 98 " --> pdb=" O SERSA 94 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SERSA 99 " --> pdb=" O GLYSA 95 " (cutoff:3.500A) Proline residue: SA 108 - end of helix Processing helix chain 'SA' and resid 115 through 128 removed outlier: 3.556A pdb=" N ILESA 119 " --> pdb=" O ALASA 115 " (cutoff:3.500A) Processing helix chain 'SA' and resid 135 through 141 removed outlier: 3.602A pdb=" N ASNSA 139 " --> pdb=" O LEUSA 135 " (cutoff:3.500A) Processing helix chain 'SA' and resid 145 through 152 Processing helix chain 'SA' and resid 158 through 173 Processing helix chain 'SA' and resid 180 through 186 removed outlier: 3.762A pdb=" N GLUSA 186 " --> pdb=" O VALSA 182 " (cutoff:3.500A) Processing helix chain 'TA' and resid 3 through 41 removed outlier: 3.606A pdb=" N GLNTA 41 " --> pdb=" O GLUTA 37 " (cutoff:3.500A) Processing helix chain 'TA' and resid 44 through 106 removed outlier: 3.696A pdb=" N ALATA 48 " --> pdb=" O ASNTA 44 " (cutoff:3.500A) Processing helix chain 'TA' and resid 107 through 140 Processing helix chain 'TA' and resid 145 through 161 removed outlier: 4.085A pdb=" N VALTA 149 " --> pdb=" O PROTA 145 " (cutoff:3.500A) Processing helix chain 'TA' and resid 187 through 198 Processing helix chain 'UA' and resid 7 through 45 removed outlier: 3.781A pdb=" N LEUUA 11 " --> pdb=" O LYSUA 7 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYSUA 38 " --> pdb=" O GLNUA 34 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLUUA 39 " --> pdb=" O LYSUA 35 " (cutoff:3.500A) Processing helix chain 'UA' and resid 49 through 82 Processing helix chain 'UA' and resid 82 through 87 Processing helix chain 'UA' and resid 93 through 111 removed outlier: 4.405A pdb=" N GLUUA 98 " --> pdb=" O SERUA 94 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SERUA 99 " --> pdb=" O GLYUA 95 " (cutoff:3.500A) Proline residue: UA 108 - end of helix Processing helix chain 'UA' and resid 115 through 128 removed outlier: 3.556A pdb=" N ILEUA 119 " --> pdb=" O ALAUA 115 " (cutoff:3.500A) Processing helix chain 'UA' and resid 135 through 141 removed outlier: 3.602A pdb=" N ASNUA 139 " --> pdb=" O LEUUA 135 " (cutoff:3.500A) Processing helix chain 'UA' and resid 145 through 152 Processing helix chain 'UA' and resid 158 through 173 Processing helix chain 'UA' and resid 180 through 186 removed outlier: 3.762A pdb=" N GLUUA 186 " --> pdb=" O VALUA 182 " (cutoff:3.500A) Processing helix chain 'VA' and resid 3 through 41 removed outlier: 3.607A pdb=" N GLNVA 41 " --> pdb=" O GLUVA 37 " (cutoff:3.500A) Processing helix chain 'VA' and resid 44 through 106 removed outlier: 3.696A pdb=" N ALAVA 48 " --> pdb=" O ASNVA 44 " (cutoff:3.500A) Processing helix chain 'VA' and resid 107 through 140 Processing helix chain 'VA' and resid 145 through 161 removed outlier: 4.085A pdb=" N VALVA 149 " --> pdb=" O PROVA 145 " (cutoff:3.500A) Processing helix chain 'VA' and resid 187 through 198 Processing helix chain 'WA' and resid 7 through 45 removed outlier: 3.780A pdb=" N LEUWA 11 " --> pdb=" O LYSWA 7 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYSWA 38 " --> pdb=" O GLNWA 34 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLUWA 39 " --> pdb=" O LYSWA 35 " (cutoff:3.500A) Processing helix chain 'WA' and resid 49 through 82 Processing helix chain 'WA' and resid 82 through 87 Processing helix chain 'WA' and resid 93 through 111 removed outlier: 4.405A pdb=" N GLUWA 98 " --> pdb=" O SERWA 94 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SERWA 99 " --> pdb=" O GLYWA 95 " (cutoff:3.500A) Proline residue: WA 108 - end of helix Processing helix chain 'WA' and resid 115 through 128 removed outlier: 3.555A pdb=" N ILEWA 119 " --> pdb=" O ALAWA 115 " (cutoff:3.500A) Processing helix chain 'WA' and resid 135 through 141 removed outlier: 3.602A pdb=" N ASNWA 139 " --> pdb=" O LEUWA 135 " (cutoff:3.500A) Processing helix chain 'WA' and resid 145 through 152 Processing helix chain 'WA' and resid 158 through 173 Processing helix chain 'WA' and resid 180 through 186 removed outlier: 3.762A pdb=" N GLUWA 186 " --> pdb=" O VALWA 182 " (cutoff:3.500A) Processing helix chain 'XA' and resid 3 through 41 removed outlier: 3.607A pdb=" N GLNXA 41 " --> pdb=" O GLUXA 37 " (cutoff:3.500A) Processing helix chain 'XA' and resid 44 through 106 removed outlier: 3.696A pdb=" N ALAXA 48 " --> pdb=" O ASNXA 44 " (cutoff:3.500A) Processing helix chain 'XA' and resid 107 through 140 Processing helix chain 'XA' and resid 145 through 161 removed outlier: 4.085A pdb=" N VALXA 149 " --> pdb=" O PROXA 145 " (cutoff:3.500A) Processing helix chain 'XA' and resid 187 through 198 Processing helix chain 'YA' and resid 7 through 45 removed outlier: 3.780A pdb=" N LEUYA 11 " --> pdb=" O LYSYA 7 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYSYA 38 " --> pdb=" O GLNYA 34 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLUYA 39 " --> pdb=" O LYSYA 35 " (cutoff:3.500A) Processing helix chain 'YA' and resid 49 through 82 Processing helix chain 'YA' and resid 82 through 87 Processing helix chain 'YA' and resid 93 through 111 removed outlier: 4.405A pdb=" N GLUYA 98 " --> pdb=" O SERYA 94 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SERYA 99 " --> pdb=" O GLYYA 95 " (cutoff:3.500A) Proline residue: YA 108 - end of helix Processing helix chain 'YA' and resid 115 through 128 removed outlier: 3.555A pdb=" N ILEYA 119 " --> pdb=" O ALAYA 115 " (cutoff:3.500A) Processing helix chain 'YA' and resid 135 through 141 removed outlier: 3.602A pdb=" N ASNYA 139 " --> pdb=" O LEUYA 135 " (cutoff:3.500A) Processing helix chain 'YA' and resid 145 through 152 Processing helix chain 'YA' and resid 158 through 173 Processing helix chain 'YA' and resid 180 through 186 removed outlier: 3.762A pdb=" N GLUYA 186 " --> pdb=" O VALYA 182 " (cutoff:3.500A) Processing helix chain 'ZA' and resid 3 through 41 removed outlier: 3.607A pdb=" N GLNZA 41 " --> pdb=" O GLUZA 37 " (cutoff:3.500A) Processing helix chain 'ZA' and resid 44 through 106 removed outlier: 3.696A pdb=" N ALAZA 48 " --> pdb=" O ASNZA 44 " (cutoff:3.500A) Processing helix chain 'ZA' and resid 107 through 140 Processing helix chain 'ZA' and resid 145 through 161 removed outlier: 4.085A pdb=" N VALZA 149 " --> pdb=" O PROZA 145 " (cutoff:3.500A) Processing helix chain 'ZA' and resid 187 through 198 Processing helix chain 'AB' and resid 7 through 45 removed outlier: 3.781A pdb=" N LEUAB 11 " --> pdb=" O LYSAB 7 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYSAB 38 " --> pdb=" O GLNAB 34 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLUAB 39 " --> pdb=" O LYSAB 35 " (cutoff:3.500A) Processing helix chain 'AB' and resid 49 through 82 Processing helix chain 'AB' and resid 82 through 87 Processing helix chain 'AB' and resid 93 through 111 removed outlier: 4.406A pdb=" N GLUAB 98 " --> pdb=" O SERAB 94 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SERAB 99 " --> pdb=" O GLYAB 95 " (cutoff:3.500A) Proline residue: AB 108 - end of helix Processing helix chain 'AB' and resid 115 through 128 removed outlier: 3.555A pdb=" N ILEAB 119 " --> pdb=" O ALAAB 115 " (cutoff:3.500A) Processing helix chain 'AB' and resid 135 through 141 removed outlier: 3.601A pdb=" N ASNAB 139 " --> pdb=" O LEUAB 135 " (cutoff:3.500A) Processing helix chain 'AB' and resid 145 through 152 Processing helix chain 'AB' and resid 158 through 173 Processing helix chain 'AB' and resid 180 through 186 removed outlier: 3.762A pdb=" N GLUAB 186 " --> pdb=" O VALAB 182 " (cutoff:3.500A) Processing helix chain 'BB' and resid 3 through 41 removed outlier: 3.606A pdb=" N GLNBB 41 " --> pdb=" O GLUBB 37 " (cutoff:3.500A) Processing helix chain 'BB' and resid 44 through 106 removed outlier: 3.696A pdb=" N ALABB 48 " --> pdb=" O ASNBB 44 " (cutoff:3.500A) Processing helix chain 'BB' and resid 107 through 140 Processing helix chain 'BB' and resid 145 through 161 removed outlier: 4.085A pdb=" N VALBB 149 " --> pdb=" O PROBB 145 " (cutoff:3.500A) Processing helix chain 'BB' and resid 187 through 198 Processing helix chain 'CB' and resid 7 through 45 removed outlier: 3.781A pdb=" N LEUCB 11 " --> pdb=" O LYSCB 7 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYSCB 38 " --> pdb=" O GLNCB 34 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLUCB 39 " --> pdb=" O LYSCB 35 " (cutoff:3.500A) Processing helix chain 'CB' and resid 49 through 82 Processing helix chain 'CB' and resid 82 through 87 Processing helix chain 'CB' and resid 93 through 111 removed outlier: 4.405A pdb=" N GLUCB 98 " --> pdb=" O SERCB 94 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SERCB 99 " --> pdb=" O GLYCB 95 " (cutoff:3.500A) Proline residue: CB 108 - end of helix Processing helix chain 'CB' and resid 115 through 128 removed outlier: 3.555A pdb=" N ILECB 119 " --> pdb=" O ALACB 115 " (cutoff:3.500A) Processing helix chain 'CB' and resid 135 through 141 removed outlier: 3.601A pdb=" N ASNCB 139 " --> pdb=" O LEUCB 135 " (cutoff:3.500A) Processing helix chain 'CB' and resid 145 through 152 Processing helix chain 'CB' and resid 158 through 173 Processing helix chain 'CB' and resid 180 through 186 removed outlier: 3.762A pdb=" N GLUCB 186 " --> pdb=" O VALCB 182 " (cutoff:3.500A) Processing helix chain 'DB' and resid 3 through 41 removed outlier: 3.607A pdb=" N GLNDB 41 " --> pdb=" O GLUDB 37 " (cutoff:3.500A) Processing helix chain 'DB' and resid 44 through 106 removed outlier: 3.696A pdb=" N ALADB 48 " --> pdb=" O ASNDB 44 " (cutoff:3.500A) Processing helix chain 'DB' and resid 107 through 140 Processing helix chain 'DB' and resid 145 through 161 removed outlier: 4.085A pdb=" N VALDB 149 " --> pdb=" O PRODB 145 " (cutoff:3.500A) Processing helix chain 'DB' and resid 187 through 198 Processing helix chain 'EB' and resid 7 through 45 removed outlier: 3.781A pdb=" N LEUEB 11 " --> pdb=" O LYSEB 7 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYSEB 38 " --> pdb=" O GLNEB 34 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLUEB 39 " --> pdb=" O LYSEB 35 " (cutoff:3.500A) Processing helix chain 'EB' and resid 49 through 82 Processing helix chain 'EB' and resid 82 through 87 Processing helix chain 'EB' and resid 93 through 111 removed outlier: 4.405A pdb=" N GLUEB 98 " --> pdb=" O SEREB 94 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SEREB 99 " --> pdb=" O GLYEB 95 " (cutoff:3.500A) Proline residue: EB 108 - end of helix Processing helix chain 'EB' and resid 115 through 128 removed outlier: 3.555A pdb=" N ILEEB 119 " --> pdb=" O ALAEB 115 " (cutoff:3.500A) Processing helix chain 'EB' and resid 135 through 141 removed outlier: 3.602A pdb=" N ASNEB 139 " --> pdb=" O LEUEB 135 " (cutoff:3.500A) Processing helix chain 'EB' and resid 145 through 152 Processing helix chain 'EB' and resid 158 through 173 Processing helix chain 'EB' and resid 180 through 186 removed outlier: 3.762A pdb=" N GLUEB 186 " --> pdb=" O VALEB 182 " (cutoff:3.500A) Processing helix chain 'FB' and resid 3 through 41 removed outlier: 3.607A pdb=" N GLNFB 41 " --> pdb=" O GLUFB 37 " (cutoff:3.500A) Processing helix chain 'FB' and resid 44 through 106 removed outlier: 3.696A pdb=" N ALAFB 48 " --> pdb=" O ASNFB 44 " (cutoff:3.500A) Processing helix chain 'FB' and resid 107 through 140 Processing helix chain 'FB' and resid 145 through 161 removed outlier: 4.085A pdb=" N VALFB 149 " --> pdb=" O PROFB 145 " (cutoff:3.500A) Processing helix chain 'FB' and resid 187 through 198 Processing helix chain 'GB' and resid 7 through 45 removed outlier: 3.781A pdb=" N LEUGB 11 " --> pdb=" O LYSGB 7 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYSGB 38 " --> pdb=" O GLNGB 34 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLUGB 39 " --> pdb=" O LYSGB 35 " (cutoff:3.500A) Processing helix chain 'GB' and resid 49 through 82 Processing helix chain 'GB' and resid 82 through 87 Processing helix chain 'GB' and resid 93 through 111 removed outlier: 4.405A pdb=" N GLUGB 98 " --> pdb=" O SERGB 94 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N SERGB 99 " --> pdb=" O GLYGB 95 " (cutoff:3.500A) Proline residue: GB 108 - end of helix Processing helix chain 'GB' and resid 115 through 128 removed outlier: 3.555A pdb=" N ILEGB 119 " --> pdb=" O ALAGB 115 " (cutoff:3.500A) Processing helix chain 'GB' and resid 135 through 141 removed outlier: 3.602A pdb=" N ASNGB 139 " --> pdb=" O LEUGB 135 " (cutoff:3.500A) Processing helix chain 'GB' and resid 145 through 152 Processing helix chain 'GB' and resid 158 through 173 Processing helix chain 'GB' and resid 180 through 186 removed outlier: 3.762A pdb=" N GLUGB 186 " --> pdb=" O VALGB 182 " (cutoff:3.500A) Processing helix chain 'HB' and resid 3 through 41 removed outlier: 3.606A pdb=" N GLNHB 41 " --> pdb=" O GLUHB 37 " (cutoff:3.500A) Processing helix chain 'HB' and resid 44 through 106 removed outlier: 3.696A pdb=" N ALAHB 48 " --> pdb=" O ASNHB 44 " (cutoff:3.500A) Processing helix chain 'HB' and resid 107 through 140 Processing helix chain 'HB' and resid 145 through 161 removed outlier: 4.084A pdb=" N VALHB 149 " --> pdb=" O PROHB 145 " (cutoff:3.500A) Processing helix chain 'HB' and resid 187 through 198 Processing helix chain 'IB' and resid 7 through 45 removed outlier: 3.781A pdb=" N LEUIB 11 " --> pdb=" O LYSIB 7 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYSIB 38 " --> pdb=" O GLNIB 34 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLUIB 39 " --> pdb=" O LYSIB 35 " (cutoff:3.500A) Processing helix chain 'IB' and resid 49 through 82 Processing helix chain 'IB' and resid 82 through 87 Processing helix chain 'IB' and resid 93 through 111 removed outlier: 4.405A pdb=" N GLUIB 98 " --> pdb=" O SERIB 94 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SERIB 99 " --> pdb=" O GLYIB 95 " (cutoff:3.500A) Proline residue: IB 108 - end of helix Processing helix chain 'IB' and resid 115 through 128 removed outlier: 3.555A pdb=" N ILEIB 119 " --> pdb=" O ALAIB 115 " (cutoff:3.500A) Processing helix chain 'IB' and resid 135 through 141 removed outlier: 3.602A pdb=" N ASNIB 139 " --> pdb=" O LEUIB 135 " (cutoff:3.500A) Processing helix chain 'IB' and resid 145 through 152 Processing helix chain 'IB' and resid 158 through 173 Processing helix chain 'IB' and resid 180 through 186 removed outlier: 3.762A pdb=" N GLUIB 186 " --> pdb=" O VALIB 182 " (cutoff:3.500A) Processing helix chain 'LB' and resid 3 through 41 removed outlier: 3.607A pdb=" N GLNLB 41 " --> pdb=" O GLULB 37 " (cutoff:3.500A) Processing helix chain 'LB' and resid 44 through 106 removed outlier: 3.696A pdb=" N ALALB 48 " --> pdb=" O ASNLB 44 " (cutoff:3.500A) Processing helix chain 'LB' and resid 107 through 140 Processing helix chain 'LB' and resid 145 through 161 removed outlier: 4.084A pdb=" N VALLB 149 " --> pdb=" O PROLB 145 " (cutoff:3.500A) Processing helix chain 'LB' and resid 187 through 198 Processing helix chain 'KB' and resid 7 through 45 removed outlier: 3.781A pdb=" N LEUKB 11 " --> pdb=" O LYSKB 7 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYSKB 38 " --> pdb=" O GLNKB 34 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLUKB 39 " --> pdb=" O LYSKB 35 " (cutoff:3.500A) Processing helix chain 'KB' and resid 49 through 82 Processing helix chain 'KB' and resid 82 through 87 Processing helix chain 'KB' and resid 93 through 111 removed outlier: 4.405A pdb=" N GLUKB 98 " --> pdb=" O SERKB 94 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SERKB 99 " --> pdb=" O GLYKB 95 " (cutoff:3.500A) Proline residue: KB 108 - end of helix Processing helix chain 'KB' and resid 115 through 128 removed outlier: 3.556A pdb=" N ILEKB 119 " --> pdb=" O ALAKB 115 " (cutoff:3.500A) Processing helix chain 'KB' and resid 135 through 141 removed outlier: 3.601A pdb=" N ASNKB 139 " --> pdb=" O LEUKB 135 " (cutoff:3.500A) Processing helix chain 'KB' and resid 145 through 152 Processing helix chain 'KB' and resid 158 through 173 Processing helix chain 'KB' and resid 180 through 186 removed outlier: 3.762A pdb=" N GLUKB 186 " --> pdb=" O VALKB 182 " (cutoff:3.500A) Processing helix chain 'NB' and resid 3 through 41 removed outlier: 3.607A pdb=" N GLNNB 41 " --> pdb=" O GLUNB 37 " (cutoff:3.500A) Processing helix chain 'NB' and resid 44 through 106 removed outlier: 3.696A pdb=" N ALANB 48 " --> pdb=" O ASNNB 44 " (cutoff:3.500A) Processing helix chain 'NB' and resid 107 through 140 Processing helix chain 'NB' and resid 145 through 161 removed outlier: 4.085A pdb=" N VALNB 149 " --> pdb=" O PRONB 145 " (cutoff:3.500A) Processing helix chain 'NB' and resid 187 through 198 Processing helix chain 'OB' and resid 7 through 45 removed outlier: 3.781A pdb=" N LEUOB 11 " --> pdb=" O LYSOB 7 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYSOB 38 " --> pdb=" O GLNOB 34 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLUOB 39 " --> pdb=" O LYSOB 35 " (cutoff:3.500A) Processing helix chain 'OB' and resid 49 through 82 Processing helix chain 'OB' and resid 82 through 87 Processing helix chain 'OB' and resid 93 through 111 removed outlier: 4.406A pdb=" N GLUOB 98 " --> pdb=" O SEROB 94 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SEROB 99 " --> pdb=" O GLYOB 95 " (cutoff:3.500A) Proline residue: OB 108 - end of helix Processing helix chain 'OB' and resid 115 through 128 removed outlier: 3.556A pdb=" N ILEOB 119 " --> pdb=" O ALAOB 115 " (cutoff:3.500A) Processing helix chain 'OB' and resid 135 through 141 removed outlier: 3.602A pdb=" N ASNOB 139 " --> pdb=" O LEUOB 135 " (cutoff:3.500A) Processing helix chain 'OB' and resid 145 through 152 Processing helix chain 'OB' and resid 158 through 173 Processing helix chain 'OB' and resid 180 through 186 removed outlier: 3.762A pdb=" N GLUOB 186 " --> pdb=" O VALOB 182 " (cutoff:3.500A) Processing helix chain 'PB' and resid 3 through 41 removed outlier: 3.607A pdb=" N GLNPB 41 " --> pdb=" O GLUPB 37 " (cutoff:3.500A) Processing helix chain 'PB' and resid 44 through 106 removed outlier: 3.696A pdb=" N ALAPB 48 " --> pdb=" O ASNPB 44 " (cutoff:3.500A) Processing helix chain 'PB' and resid 107 through 140 Processing helix chain 'PB' and resid 145 through 161 removed outlier: 4.085A pdb=" N VALPB 149 " --> pdb=" O PROPB 145 " (cutoff:3.500A) Processing helix chain 'PB' and resid 187 through 198 Processing helix chain 'QB' and resid 7 through 45 removed outlier: 3.781A pdb=" N LEUQB 11 " --> pdb=" O LYSQB 7 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYSQB 38 " --> pdb=" O GLNQB 34 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLUQB 39 " --> pdb=" O LYSQB 35 " (cutoff:3.500A) Processing helix chain 'QB' and resid 49 through 82 Processing helix chain 'QB' and resid 82 through 87 Processing helix chain 'QB' and resid 93 through 111 removed outlier: 4.404A pdb=" N GLUQB 98 " --> pdb=" O SERQB 94 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SERQB 99 " --> pdb=" O GLYQB 95 " (cutoff:3.500A) Proline residue: QB 108 - end of helix Processing helix chain 'QB' and resid 115 through 128 removed outlier: 3.556A pdb=" N ILEQB 119 " --> pdb=" O ALAQB 115 " (cutoff:3.500A) Processing helix chain 'QB' and resid 135 through 141 removed outlier: 3.602A pdb=" N ASNQB 139 " --> pdb=" O LEUQB 135 " (cutoff:3.500A) Processing helix chain 'QB' and resid 145 through 152 Processing helix chain 'QB' and resid 158 through 173 Processing helix chain 'QB' and resid 180 through 186 removed outlier: 3.763A pdb=" N GLUQB 186 " --> pdb=" O VALQB 182 " (cutoff:3.500A) Processing helix chain 'RB' and resid 3 through 41 removed outlier: 3.607A pdb=" N GLNRB 41 " --> pdb=" O GLURB 37 " (cutoff:3.500A) Processing helix chain 'RB' and resid 44 through 106 removed outlier: 3.696A pdb=" N ALARB 48 " --> pdb=" O ASNRB 44 " (cutoff:3.500A) Processing helix chain 'RB' and resid 107 through 140 Processing helix chain 'RB' and resid 145 through 161 removed outlier: 4.086A pdb=" N VALRB 149 " --> pdb=" O PRORB 145 " (cutoff:3.500A) Processing helix chain 'RB' and resid 187 through 198 Processing helix chain 'SB' and resid 7 through 45 removed outlier: 3.781A pdb=" N LEUSB 11 " --> pdb=" O LYSSB 7 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYSSB 38 " --> pdb=" O GLNSB 34 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLUSB 39 " --> pdb=" O LYSSB 35 " (cutoff:3.500A) Processing helix chain 'SB' and resid 49 through 82 Processing helix chain 'SB' and resid 82 through 87 Processing helix chain 'SB' and resid 93 through 111 removed outlier: 4.405A pdb=" N GLUSB 98 " --> pdb=" O SERSB 94 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SERSB 99 " --> pdb=" O GLYSB 95 " (cutoff:3.500A) Proline residue: SB 108 - end of helix Processing helix chain 'SB' and resid 115 through 128 removed outlier: 3.555A pdb=" N ILESB 119 " --> pdb=" O ALASB 115 " (cutoff:3.500A) Processing helix chain 'SB' and resid 135 through 141 removed outlier: 3.602A pdb=" N ASNSB 139 " --> pdb=" O LEUSB 135 " (cutoff:3.500A) Processing helix chain 'SB' and resid 145 through 152 Processing helix chain 'SB' and resid 158 through 173 Processing helix chain 'SB' and resid 180 through 186 removed outlier: 3.763A pdb=" N GLUSB 186 " --> pdb=" O VALSB 182 " (cutoff:3.500A) Processing helix chain '02' and resid 3 through 41 removed outlier: 3.606A pdb=" N GLN02 41 " --> pdb=" O GLU02 37 " (cutoff:3.500A) Processing helix chain '02' and resid 44 through 106 removed outlier: 3.696A pdb=" N ALA02 48 " --> pdb=" O ASN02 44 " (cutoff:3.500A) Processing helix chain '02' and resid 107 through 140 Processing helix chain '02' and resid 145 through 161 removed outlier: 4.086A pdb=" N VAL02 149 " --> pdb=" O PRO02 145 " (cutoff:3.500A) Processing helix chain '02' and resid 187 through 198 Processing helix chain '01' and resid 7 through 45 removed outlier: 3.780A pdb=" N LEU01 11 " --> pdb=" O LYS01 7 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS01 38 " --> pdb=" O GLN01 34 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU01 39 " --> pdb=" O LYS01 35 " (cutoff:3.500A) Processing helix chain '01' and resid 49 through 82 Processing helix chain '01' and resid 82 through 87 Processing helix chain '01' and resid 93 through 111 removed outlier: 4.405A pdb=" N GLU01 98 " --> pdb=" O SER01 94 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N SER01 99 " --> pdb=" O GLY01 95 " (cutoff:3.500A) Proline residue: 01 108 - end of helix Processing helix chain '01' and resid 115 through 128 removed outlier: 3.555A pdb=" N ILE01 119 " --> pdb=" O ALA01 115 " (cutoff:3.500A) Processing helix chain '01' and resid 135 through 141 removed outlier: 3.601A pdb=" N ASN01 139 " --> pdb=" O LEU01 135 " (cutoff:3.500A) Processing helix chain '01' and resid 145 through 152 Processing helix chain '01' and resid 158 through 173 Processing helix chain '01' and resid 180 through 186 removed outlier: 3.761A pdb=" N GLU01 186 " --> pdb=" O VAL01 182 " (cutoff:3.500A) 8821 hydrogen bonds defined for protein. 26463 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: 41.39 Time building geometry restraints manager: 37.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 33876 1.34 - 1.46: 18127 1.46 - 1.57: 46889 1.57 - 1.69: 0 1.69 - 1.81: 1188 Bond restraints: 100080 Sorted by residual: bond pdb=" N GLNPB 131 " pdb=" CA GLNPB 131 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.19e-02 7.06e+03 5.19e+00 bond pdb=" N GLN V 131 " pdb=" CA GLN V 131 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.19e-02 7.06e+03 5.16e+00 bond pdb=" N GLNLB 131 " pdb=" CA GLNLB 131 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.19e-02 7.06e+03 5.15e+00 bond pdb=" N GLN G 131 " pdb=" CA GLN G 131 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.19e-02 7.06e+03 5.15e+00 bond pdb=" N GLNLA 131 " pdb=" CA GLNLA 131 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.19e-02 7.06e+03 5.14e+00 ... (remaining 100075 not shown) Histogram of bond angle deviations from ideal: 99.21 - 106.16: 1286 106.16 - 113.11: 57691 113.11 - 120.05: 34172 120.05 - 127.00: 40806 127.00 - 133.94: 469 Bond angle restraints: 134424 Sorted by residual: angle pdb=" N ILE Y 141 " pdb=" CA ILE Y 141 " pdb=" C ILE Y 141 " ideal model delta sigma weight residual 111.91 109.34 2.57 8.90e-01 1.26e+00 8.31e+00 angle pdb=" N ILESB 141 " pdb=" CA ILESB 141 " pdb=" C ILESB 141 " ideal model delta sigma weight residual 111.91 109.35 2.56 8.90e-01 1.26e+00 8.29e+00 angle pdb=" N ILEAA 141 " pdb=" CA ILEAA 141 " pdb=" C ILEAA 141 " ideal model delta sigma weight residual 111.91 109.35 2.56 8.90e-01 1.26e+00 8.28e+00 angle pdb=" N ILEGB 141 " pdb=" CA ILEGB 141 " pdb=" C ILEGB 141 " ideal model delta sigma weight residual 111.91 109.35 2.56 8.90e-01 1.26e+00 8.25e+00 angle pdb=" N ILEGA 141 " pdb=" CA ILEGA 141 " pdb=" C ILEGA 141 " ideal model delta sigma weight residual 111.91 109.36 2.55 8.90e-01 1.26e+00 8.22e+00 ... (remaining 134419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.18: 59941 13.18 - 26.37: 2807 26.37 - 39.55: 576 39.55 - 52.73: 144 52.73 - 65.92: 72 Dihedral angle restraints: 63540 sinusoidal: 25488 harmonic: 38052 Sorted by residual: dihedral pdb=" CA ARG02 49 " pdb=" CB ARG02 49 " pdb=" CG ARG02 49 " pdb=" CD ARG02 49 " ideal model delta sinusoidal sigma weight residual 180.00 131.38 48.62 3 1.50e+01 4.44e-03 8.66e+00 dihedral pdb=" CA ARGFB 49 " pdb=" CB ARGFB 49 " pdb=" CG ARGFB 49 " pdb=" CD ARGFB 49 " ideal model delta sinusoidal sigma weight residual 180.00 131.39 48.61 3 1.50e+01 4.44e-03 8.66e+00 dihedral pdb=" CA ARGBB 49 " pdb=" CB ARGBB 49 " pdb=" CG ARGBB 49 " pdb=" CD ARGBB 49 " ideal model delta sinusoidal sigma weight residual 180.00 131.39 48.61 3 1.50e+01 4.44e-03 8.66e+00 ... (remaining 63537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 10272 0.036 - 0.072: 4350 0.072 - 0.109: 1050 0.109 - 0.145: 204 0.145 - 0.181: 36 Chirality restraints: 15912 Sorted by residual: chirality pdb=" CA GLNHB 131 " pdb=" N GLNHB 131 " pdb=" C GLNHB 131 " pdb=" CB GLNHB 131 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.19e-01 chirality pdb=" CA GLNZA 131 " pdb=" N GLNZA 131 " pdb=" C GLNZA 131 " pdb=" CB GLNZA 131 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.13e-01 chirality pdb=" CA GLNBB 131 " pdb=" N GLNBB 131 " pdb=" C GLNBB 131 " pdb=" CB GLNBB 131 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.12e-01 ... (remaining 15909 not shown) Planarity restraints: 17244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYSNA 33 " -0.004 2.00e-02 2.50e+03 8.83e-03 7.80e-01 pdb=" C LYSNA 33 " 0.015 2.00e-02 2.50e+03 pdb=" O LYSNA 33 " -0.006 2.00e-02 2.50e+03 pdb=" N ALANA 34 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYSFB 33 " -0.004 2.00e-02 2.50e+03 8.81e-03 7.77e-01 pdb=" C LYSFB 33 " 0.015 2.00e-02 2.50e+03 pdb=" O LYSFB 33 " -0.006 2.00e-02 2.50e+03 pdb=" N ALAFB 34 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYSBB 33 " -0.004 2.00e-02 2.50e+03 8.81e-03 7.75e-01 pdb=" C LYSBB 33 " 0.015 2.00e-02 2.50e+03 pdb=" O LYSBB 33 " -0.006 2.00e-02 2.50e+03 pdb=" N ALABB 34 " -0.005 2.00e-02 2.50e+03 ... (remaining 17241 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 17779 2.75 - 3.29: 107928 3.29 - 3.82: 166013 3.82 - 4.36: 190432 4.36 - 4.90: 329342 Nonbonded interactions: 811494 Sorted by model distance: nonbonded pdb=" O MET B 149 " pdb=" OG SER B 153 " model vdw 2.212 2.440 nonbonded pdb=" O MET P 149 " pdb=" OG SER P 153 " model vdw 2.212 2.440 nonbonded pdb=" O MET J 149 " pdb=" OG SER J 153 " model vdw 2.212 2.440 nonbonded pdb=" O METWA 149 " pdb=" OG SERWA 153 " model vdw 2.212 2.440 nonbonded pdb=" O METMB 149 " pdb=" OG SERMB 153 " model vdw 2.212 2.440 ... (remaining 811489 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 '01' selection = chain 'AA' selection = chain 'AB' selection = chain 'B' selection = chain 'CA' selection = chain 'CB' selection = chain 'D' selection = chain 'EA' selection = chain 'EB' selection = chain 'F' selection = chain 'GA' selection = chain 'GB' selection = chain 'H' selection = chain 'IA' selection = chain 'IB' selection = chain 'J' selection = chain 'KA' selection = chain 'KB' selection = chain 'L' selection = chain 'MA' selection = chain 'MB' selection = chain 'N' selection = chain 'OA' selection = chain 'OB' selection = chain 'P' selection = chain 'QA' selection = chain 'QB' selection = chain 'R' selection = chain 'SA' selection = chain 'SB' selection = chain 'T' selection = chain 'UA' selection = chain 'W' selection = chain 'WA' selection = chain 'Y' selection = chain 'YA' } ncs_group { reference = chain '02' selection = chain 'A' selection = chain 'BA' selection = chain 'BB' selection = chain 'C' selection = chain 'DA' selection = chain 'DB' selection = chain 'E' selection = chain 'FA' selection = chain 'FB' selection = chain 'G' selection = chain 'HA' selection = chain 'HB' selection = chain 'I' selection = chain 'JA' selection = chain 'JB' selection = chain 'K' selection = chain 'LA' selection = chain 'LB' selection = chain 'M' selection = chain 'NA' selection = chain 'NB' selection = chain 'O' selection = chain 'PA' selection = chain 'PB' selection = chain 'Q' selection = chain 'RA' selection = chain 'RB' selection = chain 'S' selection = chain 'TA' selection = chain 'V' selection = chain 'VA' selection = chain 'X' selection = chain 'XA' selection = chain 'Z' selection = chain 'ZA' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 648 5.16 5 C 62064 2.51 5 N 17748 2.21 5 O 18756 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.520 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: 0.090 Extract box with map and model: 15.760 Check model and map are aligned: 1.090 Convert atoms to be neutral: 0.640 Process input model: 206.810 Find NCS groups from input model: 5.990 Set up NCS constraints: 1.500 Set refine NCS operators: 0.000 Set scattering table: 0.040 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 237.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5698 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 : 0.010 0.067 100080 Z= 0.681 Angle : 0.480 3.772 134424 Z= 0.317 Chirality : 0.042 0.181 15912 Planarity : 0.002 0.015 17244 Dihedral : 8.472 65.918 38484 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.07), residues: 12636 helix: 0.37 (0.04), residues: 11160 sheet: None (None), residues: 0 loop : -2.72 (0.13), residues: 1476 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25272 Ramachandran restraints generated. 12636 Oldfield, 0 Emsley, 12636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25272 Ramachandran restraints generated. 12636 Oldfield, 0 Emsley, 12636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5346 residues out of total 11124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5346 time to evaluate : 8.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 5346 average time/residue: 0.9314 time to fit residues: 8236.6617 Evaluate side-chains 3459 residues out of total 11124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3459 time to evaluate : 8.894 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 12.6282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1260 random chunks: chunk 1063 optimal weight: 6.9990 chunk 955 optimal weight: 2.9990 chunk 529 optimal weight: 0.9980 chunk 326 optimal weight: 0.9980 chunk 644 optimal weight: 5.9990 chunk 510 optimal weight: 2.9990 chunk 987 optimal weight: 1.9990 chunk 382 optimal weight: 9.9990 chunk 600 optimal weight: 5.9990 chunk 735 optimal weight: 0.7980 chunk 1144 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: JB 41 GLN ** JB 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** JB 148 GLN MB 87 GLN MB 150 HIS MB 172 ASN ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN B 150 HIS B 172 ASN ** C 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 GLN ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 HIS D 123 GLN E 7 HIS E 41 GLN E 121 GLN ** E 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 150 HIS ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 123 GLN H 150 HIS H 172 ASN ** I 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 131 GLN ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 123 GLN ** K 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 107 ASN ** K 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS L 150 HIS M 131 GLN M 154 GLN ** N 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 150 HIS N 172 ASN ** O 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 44 ASN P 123 GLN Q 7 HIS Q 41 GLN Q 146 GLN Q 148 GLN R 150 HIS ** R 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 150 HIS T 172 ASN ** W 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 123 GLN W 172 ASN ** X 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 154 GLN ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 41 GLN Z 154 GLN ** AA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 150 HIS AA 172 ASN ** CA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 123 GLN CA 172 ASN DA 7 HIS DA 130 GLN DA 131 GLN ** EA 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EA 58 HIS ** EA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FA 7 HIS FA 41 GLN GA 58 HIS GA 172 ASN HA 107 ASN ** HA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** IA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JA 131 GLN ** KA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** KA 123 GLN LA 7 HIS LA 41 GLN LA 190 GLN MA 150 HIS ** NA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OA 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** PA 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** PA 131 GLN QA 58 HIS QA 123 GLN QA 172 ASN RA 7 HIS RA 41 GLN ** RA 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SA 111 GLN SA 150 HIS ** TA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** TA 120 HIS ** UA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** UA 58 HIS VA 130 GLN VA 131 GLN WA 20 ASN WA 123 GLN XA 7 HIS XA 148 GLN XA 154 GLN YA 150 HIS ZA 44 ASN ** AB 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BB 131 GLN ** BB 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CB 123 GLN DB 7 HIS DB 41 GLN EB 20 ASN EB 150 HIS ** GB 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GB 111 GLN GB 172 ASN ** HB 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** HB 44 ASN IB 123 GLN IB 172 ASN ** KB 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** KB 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NB 3 ASN ** OB 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** OB 123 GLN PB 10 ASN PB 131 GLN QB 58 HIS QB 172 ASN ** SB 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SB 123 GLN SB 150 HIS SB 172 ASN ** 02 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 02 131 GLN ** 01 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 01 172 ASN Total number of N/Q/H flips: 101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6456 moved from start: 0.5192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.100 100080 Z= 0.253 Angle : 0.675 14.565 134424 Z= 0.339 Chirality : 0.037 0.462 15912 Planarity : 0.005 0.085 17244 Dihedral : 3.180 15.194 13788 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer Outliers : 3.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.07), residues: 12636 helix: 1.70 (0.05), residues: 10980 sheet: None (None), residues: 0 loop : -1.70 (0.14), residues: 1656 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25272 Ramachandran restraints generated. 12636 Oldfield, 0 Emsley, 12636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25272 Ramachandran restraints generated. 12636 Oldfield, 0 Emsley, 12636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4585 residues out of total 11124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 400 poor density : 4185 time to evaluate : 8.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 400 outliers final: 174 residues processed: 4338 average time/residue: 0.9325 time to fit residues: 6823.5384 Evaluate side-chains 3707 residues out of total 11124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 3533 time to evaluate : 8.797 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 174 outliers final: 1 residues processed: 174 average time/residue: 0.7388 time to fit residues: 250.2922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1260 random chunks: chunk 635 optimal weight: 2.9990 chunk 355 optimal weight: 4.9990 chunk 952 optimal weight: 2.9990 chunk 779 optimal weight: 4.9990 chunk 315 optimal weight: 10.0000 chunk 1146 optimal weight: 6.9990 chunk 1238 optimal weight: 5.9990 chunk 1020 optimal weight: 6.9990 chunk 1136 optimal weight: 0.9980 chunk 390 optimal weight: 1.9990 chunk 919 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: JB 7 HIS ** MB 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** MB 87 GLN MB 111 GLN ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN C 10 ASN E 51 HIS E 148 GLN ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 GLN ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 154 GLN ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 ASN ** I 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 GLN K 51 HIS ** K 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 190 GLN M 44 ASN ** N 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 7 HIS ** P 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 172 ASN Q 121 GLN ** Q 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 58 HIS S 121 GLN ** W 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 172 ASN X 80 GLN X 148 GLN X 190 GLN ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EA 14 ASN EA 172 ASN FA 51 HIS ** HA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** IA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** IA 150 HIS IA 172 ASN ** KA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 51 HIS ** MA 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NA 44 ASN ** OA 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** OA 150 HIS OA 172 ASN ** PA 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** PA 80 GLN RA 190 GLN TA 130 GLN ** UA 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** UA 172 ASN VA 130 GLN VA 146 GLN WA 20 ASN WA 172 ASN XA 51 HIS XA 146 GLN YA 111 GLN ** YA 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ZA 120 HIS ZA 154 GLN AB 172 ASN EB 14 ASN EB 87 GLN FB 41 GLN FB 190 GLN HB 7 HIS ** HB 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 131 GLN LB 148 GLN ** KB 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** KB 20 ASN KB 174 ASN NB 3 ASN NB 60 ASN ** OB 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SB 172 ASN ** 02 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 02 60 ASN 02 80 GLN 01 14 ASN 01 20 ASN Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.8099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.102 100080 Z= 0.300 Angle : 0.714 13.289 134424 Z= 0.373 Chirality : 0.039 0.338 15912 Planarity : 0.005 0.092 17244 Dihedral : 3.497 18.529 13788 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer Outliers : 4.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.07), residues: 12636 helix: 1.76 (0.05), residues: 11016 sheet: None (None), residues: 0 loop : -1.88 (0.14), residues: 1620 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25272 Ramachandran restraints generated. 12636 Oldfield, 0 Emsley, 12636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25272 Ramachandran restraints generated. 12636 Oldfield, 0 Emsley, 12636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5032 residues out of total 11124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 413 poor density : 4619 time to evaluate : 8.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 413 outliers final: 158 residues processed: 4782 average time/residue: 0.9078 time to fit residues: 7253.9305 Evaluate side-chains 4111 residues out of total 11124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 3953 time to evaluate : 8.934 Switching outliers to nearest non-outliers outliers start: 158 outliers final: 0 residues processed: 158 average time/residue: 0.7800 time to fit residues: 239.6289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1260 random chunks: chunk 1132 optimal weight: 1.9990 chunk 861 optimal weight: 4.9990 chunk 594 optimal weight: 50.0000 chunk 126 optimal weight: 5.9990 chunk 547 optimal weight: 1.9990 chunk 769 optimal weight: 0.8980 chunk 1150 optimal weight: 30.0000 chunk 1217 optimal weight: 1.9990 chunk 601 optimal weight: 0.9980 chunk 1090 optimal weight: 6.9990 chunk 328 optimal weight: 8.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** JB 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** MB 14 ASN MB 123 GLN MB 172 ASN ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN C 10 ASN E 7 HIS E 121 GLN F 34 GLN ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 ASN G 64 ASN ** G 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 ASN ** I 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 7 HIS K 61 GLN K 131 GLN ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 150 HIS ** M 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 61 GLN N 150 HIS ** P 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 20 ASN R 111 GLN R 150 HIS ** R 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 121 GLN T 150 HIS V 44 ASN W 172 ASN X 3 ASN ** X 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 121 GLN BA 58 GLN BA 121 GLN CA 172 ASN ** DA 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DA 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DA 154 GLN ** EA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FA 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GA 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HA 121 GLN ** IA 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** IA 172 ASN JA 10 ASN KA 172 ASN ** LA 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LA 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MA 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NA 64 ASN OA 14 ASN ** OA 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** OA 172 ASN ** PA 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** RA 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** RA 131 GLN RA 146 GLN ** RA 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SA 150 HIS UA 172 ASN WA 20 ASN ** WA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** XA 80 GLN XA 131 GLN YA 14 ASN ** YA 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** YA 150 HIS ** ZA 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ZA 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ZA 41 GLN ** ZA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ZA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ZA 130 GLN ** ZA 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 7 HIS ** DB 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 131 GLN ** DB 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FB 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FB 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FB 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HB 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** IB 20 ASN LB 80 GLN ** LB 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** PB 10 ASN PB 154 GLN QB 20 ASN QB 87 GLN ** QB 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** RB 61 GLN ** SB 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 02 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 02 10 ASN Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.9204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.084 100080 Z= 0.236 Angle : 0.654 13.161 134424 Z= 0.336 Chirality : 0.036 0.427 15912 Planarity : 0.004 0.096 17244 Dihedral : 3.348 16.472 13788 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer Outliers : 3.29 % 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: 2.57 (0.07), residues: 12636 helix: 2.11 (0.05), residues: 11088 sheet: None (None), residues: 0 loop : -1.33 (0.14), residues: 1548 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25272 Ramachandran restraints generated. 12636 Oldfield, 0 Emsley, 12636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25272 Ramachandran restraints generated. 12636 Oldfield, 0 Emsley, 12636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4814 residues out of total 11124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 336 poor density : 4478 time to evaluate : 9.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 336 outliers final: 161 residues processed: 4594 average time/residue: 0.9309 time to fit residues: 7177.5397 Evaluate side-chains 4184 residues out of total 11124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 4023 time to evaluate : 8.958 Switching outliers to nearest non-outliers outliers start: 161 outliers final: 0 residues processed: 161 average time/residue: 0.7452 time to fit residues: 232.6864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1260 random chunks: chunk 1014 optimal weight: 0.0060 chunk 691 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 906 optimal weight: 0.4980 chunk 502 optimal weight: 2.9990 chunk 1039 optimal weight: 2.9990 chunk 841 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 621 optimal weight: 2.9990 chunk 1093 optimal weight: 4.9990 chunk 307 optimal weight: 1.9990 overall best weight: 1.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** JB 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** JB 121 GLN JB 130 GLN ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 GLN A 190 GLN ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN C 10 ASN C 44 ASN E 3 ASN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 GLN ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 58 GLN G 61 GLN G 64 ASN G 190 GLN H 172 ASN ** I 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 GLN K 3 ASN K 61 GLN ** K 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 130 GLN N 174 ASN ** O 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 172 ASN Q 80 GLN ** Q 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 121 GLN ** W 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 172 ASN ** X 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 10 ASN AA 111 GLN BA 58 GLN BA 128 GLN CA 172 ASN DA 41 GLN DA 148 GLN DA 154 GLN EA 20 ASN ** EA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FA 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GA 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HA 61 GLN IA 172 ASN JA 61 GLN KA 111 GLN LA 128 GLN LA 131 GLN LA 146 GLN ** LA 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** MA 111 GLN NA 64 ASN OA 34 GLN ** OA 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** PA 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** QA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** RA 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SA 20 ASN ** UA 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** XA 121 GLN XA 131 GLN ** XA 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** YA 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ZA 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** ZA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ZA 64 ASN ZA 130 GLN ** AB 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 80 GLN ** DB 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 131 GLN ** DB 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EB 20 ASN ** EB 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FB 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FB 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** FB 121 GLN HB 7 HIS IB 20 ASN IB 172 ASN ** LB 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NB 61 GLN PB 154 GLN ** QB 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SB 172 ASN ** 02 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 02 10 ASN 02 80 GLN Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.9782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.101 100080 Z= 0.228 Angle : 0.666 14.180 134424 Z= 0.342 Chirality : 0.036 0.345 15912 Planarity : 0.004 0.103 17244 Dihedral : 3.383 17.122 13788 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer Outliers : 2.67 % 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: 2.74 (0.07), residues: 12636 helix: 2.26 (0.05), residues: 11016 sheet: None (None), residues: 0 loop : -1.42 (0.14), residues: 1620 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25272 Ramachandran restraints generated. 12636 Oldfield, 0 Emsley, 12636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25272 Ramachandran restraints generated. 12636 Oldfield, 0 Emsley, 12636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4683 residues out of total 11124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 4410 time to evaluate : 8.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 273 outliers final: 117 residues processed: 4497 average time/residue: 0.9085 time to fit residues: 6838.0207 Evaluate side-chains 4178 residues out of total 11124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 4061 time to evaluate : 8.911 Switching outliers to nearest non-outliers outliers start: 117 outliers final: 0 residues processed: 117 average time/residue: 0.7364 time to fit residues: 170.2341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1260 random chunks: chunk 409 optimal weight: 0.9990 chunk 1096 optimal weight: 7.9990 chunk 240 optimal weight: 0.0010 chunk 715 optimal weight: 7.9990 chunk 300 optimal weight: 6.9990 chunk 1219 optimal weight: 10.0000 chunk 1012 optimal weight: 30.0000 chunk 564 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 403 optimal weight: 0.8980 chunk 640 optimal weight: 8.9990 overall best weight: 1.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** JB 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** JB 80 GLN ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 ASN C 60 ASN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 ASN E 7 HIS E 51 HIS E 148 GLN ** F 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 58 GLN G 61 GLN G 64 ASN ** I 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 ASN K 80 GLN ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 150 HIS N 150 HIS ** O 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 80 GLN ** Q 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 HIS ** R 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 154 GLN T 14 ASN T 150 HIS ** V 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 172 ASN X 148 GLN ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 58 HIS ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 58 GLN CA 14 ASN DA 41 GLN ** DA 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** FA 128 GLN ** FA 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** FA 190 GLN GA 111 GLN HA 61 GLN HA 121 GLN ** JA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** JA 121 GLN LA 3 ASN LA 60 ASN ** LA 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MA 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NA 61 GLN NA 64 ASN OA 34 GLN ** PA 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** PA 41 GLN ** QA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** RA 121 GLN ** RA 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SA 20 ASN SA 150 HIS UA 172 ASN VA 10 ASN VA 44 ASN ** VA 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** WA 58 HIS XA 80 GLN ** XA 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** YA 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** YA 150 HIS ** ZA 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** ZA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ZA 64 ASN ZA 154 GLN ** DB 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DB 154 GLN ** EB 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** FB 3 ASN ** FB 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FB 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GB 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GB 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LB 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 148 GLN NB 61 GLN ** OB 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** PB 60 ASN PB 154 GLN ** QB 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** QB 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** RB 61 GLN SB 20 ASN SB 172 ASN ** 02 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 02 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 02 10 ASN 02 41 GLN 02 130 GLN 01 20 ASN Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 1.0643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.122 100080 Z= 0.240 Angle : 0.703 14.795 134424 Z= 0.360 Chirality : 0.037 0.218 15912 Planarity : 0.004 0.085 17244 Dihedral : 3.455 18.610 13788 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer Outliers : 2.66 % 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: 2.78 (0.07), residues: 12636 helix: 2.24 (0.05), residues: 10944 sheet: None (None), residues: 0 loop : -0.88 (0.15), residues: 1692 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25272 Ramachandran restraints generated. 12636 Oldfield, 0 Emsley, 12636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25272 Ramachandran restraints generated. 12636 Oldfield, 0 Emsley, 12636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4788 residues out of total 11124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 4516 time to evaluate : 11.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 272 outliers final: 129 residues processed: 4609 average time/residue: 0.9149 time to fit residues: 7062.0134 Evaluate side-chains 4277 residues out of total 11124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 4148 time to evaluate : 8.949 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 129 outliers final: 1 residues processed: 129 average time/residue: 0.7163 time to fit residues: 183.2222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1260 random chunks: chunk 1175 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 chunk 694 optimal weight: 8.9990 chunk 890 optimal weight: 8.9990 chunk 689 optimal weight: 6.9990 chunk 1026 optimal weight: 0.9990 chunk 680 optimal weight: 9.9990 chunk 1214 optimal weight: 2.9990 chunk 760 optimal weight: 9.9990 chunk 740 optimal weight: 4.9990 chunk 560 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** JB 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** JB 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** JB 80 GLN ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 GLN ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 ASN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 GLN ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN E 61 GLN ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 58 GLN ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 ASN ** I 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 60 ASN ** I 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 148 GLN L 14 ASN M 121 GLN N 14 ASN ** N 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 80 GLN P 14 ASN P 58 HIS ** P 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 41 GLN Q 121 GLN ** Q 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 10 ASN ** S 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 60 ASN ** W 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 146 GLN AA 14 ASN ** AA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DA 41 GLN DA 51 HIS DA 61 GLN DA 80 GLN DA 148 GLN ** EA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FA 10 ASN ** FA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FA 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** FA 190 GLN HA 121 GLN JA 41 GLN ** JA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 148 GLN ** MA 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NA 61 GLN NA 64 ASN OA 34 GLN ** OA 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** PA 7 HIS PA 41 GLN PA 80 GLN PA 154 GLN ** QA 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** RA 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** RA 80 GLN ** RA 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SA 58 HIS ** UA 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** UA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** VA 10 ASN ** VA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** XA 121 GLN ** XA 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** YA 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ZA 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ZA 41 GLN ** ZA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ZA 64 ASN ** ZA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ZA 154 GLN ** ZA 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 150 HIS ** BB 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DB 61 GLN DB 80 GLN ** DB 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EB 58 HIS FB 41 GLN ** FB 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FB 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FB 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GB 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GB 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** KB 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NB 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OB 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OB 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** PB 41 GLN PB 61 GLN PB 148 GLN PB 154 GLN ** QB 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** RB 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** RB 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** RB 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 02 7 HIS 02 41 GLN ** 02 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 02 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 01 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 01 87 GLN Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 1.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.132 100080 Z= 0.362 Angle : 0.875 16.492 134424 Z= 0.452 Chirality : 0.043 0.259 15912 Planarity : 0.006 0.139 17244 Dihedral : 3.979 24.240 13788 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer Outliers : 3.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.07), residues: 12636 helix: 1.64 (0.05), residues: 10872 sheet: None (None), residues: 0 loop : -1.10 (0.15), residues: 1764 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25272 Ramachandran restraints generated. 12636 Oldfield, 0 Emsley, 12636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25272 Ramachandran restraints generated. 12636 Oldfield, 0 Emsley, 12636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5389 residues out of total 11124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 356 poor density : 5033 time to evaluate : 11.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 356 outliers final: 137 residues processed: 5165 average time/residue: 0.9182 time to fit residues: 7924.4609 Evaluate side-chains 4517 residues out of total 11124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 4380 time to evaluate : 9.078 Switching outliers to nearest non-outliers outliers start: 137 outliers final: 0 residues processed: 137 average time/residue: 0.7043 time to fit residues: 191.7613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1260 random chunks: chunk 751 optimal weight: 8.9990 chunk 484 optimal weight: 0.9980 chunk 725 optimal weight: 9.9990 chunk 365 optimal weight: 3.9990 chunk 238 optimal weight: 1.9990 chunk 235 optimal weight: 9.9990 chunk 772 optimal weight: 8.9990 chunk 827 optimal weight: 6.9990 chunk 600 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 954 optimal weight: 0.8980 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** JB 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** JB 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** JB 130 GLN JB 146 GLN ** MB 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 ASN C 41 GLN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 123 GLN ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 GLN G 61 GLN ** H 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 7 HIS I 10 ASN ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 154 GLN ** J 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 HIS K 3 ASN K 41 GLN K 148 GLN ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 58 GLN M 61 GLN ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 87 GLN O 10 ASN O 80 GLN O 121 GLN O 128 GLN P 14 ASN ** P 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 61 GLN ** Q 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 148 GLN ** R 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 10 ASN S 60 ASN S 64 ASN S 80 GLN T 20 ASN V 154 GLN ** W 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 64 ASN ** AA 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 60 ASN BA 154 GLN DA 64 ASN ** EA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FA 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FA 10 ASN ** FA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FA 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FA 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GA 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** IA 14 ASN ** IA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** IA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JA 61 GLN ** JA 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** JA 148 GLN LA 7 HIS LA 64 ASN ** LA 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 148 GLN NA 61 GLN OA 123 GLN PA 7 HIS PA 64 ASN PA 80 GLN PA 121 GLN PA 130 GLN ** QA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** QA 123 GLN ** RA 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** RA 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** RA 80 GLN RA 148 GLN ** SA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TA 61 GLN ** UA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** UA 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** UA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** VA 10 ASN ** VA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** VA 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** VA 154 GLN ** WA 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XA 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XA 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** XA 61 GLN XA 121 GLN XA 148 GLN ** YA 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ZA 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ZA 41 GLN ZA 64 ASN ** ZA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ZA 148 GLN ZA 154 GLN ** DB 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DB 121 GLN DB 148 GLN DB 190 GLN ** EB 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** FB 41 GLN FB 60 ASN ** GB 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GB 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 44 ASN LB 64 ASN ** LB 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NB 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NB 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OB 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OB 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** OB 58 HIS PB 10 ASN PB 154 GLN ** QB 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** QB 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** RB 58 GLN RB 61 GLN SB 123 GLN ** SB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 02 41 GLN 02 121 GLN Total number of N/Q/H flips: 76 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 1.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.159 100080 Z= 0.300 Angle : 0.820 13.554 134424 Z= 0.422 Chirality : 0.040 0.309 15912 Planarity : 0.005 0.095 17244 Dihedral : 3.794 21.257 13788 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer Outliers : 1.90 % 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: 2.35 (0.07), residues: 12636 helix: 1.98 (0.05), residues: 10872 sheet: None (None), residues: 0 loop : -1.08 (0.15), residues: 1764 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25272 Ramachandran restraints generated. 12636 Oldfield, 0 Emsley, 12636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25272 Ramachandran restraints generated. 12636 Oldfield, 0 Emsley, 12636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4904 residues out of total 11124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 4710 time to evaluate : 9.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 194 outliers final: 93 residues processed: 4770 average time/residue: 0.9100 time to fit residues: 7280.7820 Evaluate side-chains 4464 residues out of total 11124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 4371 time to evaluate : 9.038 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 93 outliers final: 1 residues processed: 93 average time/residue: 0.7689 time to fit residues: 141.2522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1260 random chunks: chunk 1104 optimal weight: 5.9990 chunk 1163 optimal weight: 3.9990 chunk 1061 optimal weight: 0.7980 chunk 1131 optimal weight: 2.9990 chunk 681 optimal weight: 8.9990 chunk 493 optimal weight: 4.9990 chunk 888 optimal weight: 1.9990 chunk 347 optimal weight: 4.9990 chunk 1022 optimal weight: 5.9990 chunk 1070 optimal weight: 5.9990 chunk 1127 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: JB 51 HIS JB 60 ASN ** JB 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** JB 64 ASN ** JB 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 HIS ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 ASN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 ASN E 61 GLN ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 GLN G 121 GLN ** H 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 123 GLN H 174 ASN I 7 HIS I 10 ASN I 121 GLN ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 44 ASN M 58 GLN M 61 GLN M 190 GLN ** N 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 87 GLN ** O 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 61 GLN ** Q 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 121 GLN ** R 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 10 ASN S 64 ASN ** T 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 121 GLN X 148 GLN ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 58 GLN Z 61 GLN Z 64 ASN ** AA 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DA 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DA 64 ASN DA 80 GLN EA 20 ASN ** EA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FA 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** FA 64 ASN FA 121 GLN ** FA 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FA 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GA 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HA 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** IA 14 ASN ** IA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JA 61 GLN JA 154 GLN LA 107 ASN ** LA 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MA 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MA 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NA 58 GLN PA 7 HIS PA 41 GLN PA 64 ASN PA 80 GLN PA 148 GLN ** QA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** RA 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** RA 80 GLN ** SA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SA 150 HIS TA 58 GLN TA 61 GLN ** UA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** UA 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** UA 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** UA 150 HIS VA 10 ASN VA 61 GLN VA 80 GLN ** WA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XA 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** YA 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ZA 41 GLN ZA 64 ASN ** ZA 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 150 HIS BB 121 GLN CB 14 ASN CB 123 GLN ** DB 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DB 148 GLN DB 154 GLN DB 190 GLN EB 20 ASN ** EB 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FB 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GB 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GB 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GB 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GB 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HB 44 ASN HB 80 GLN LB 148 GLN ** KB 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OB 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OB 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** PB 10 ASN PB 147 ASN ** QB 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** QB 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 02 41 GLN 02 131 GLN 01 123 GLN ** 01 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 69 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 1.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.239 100080 Z= 0.322 Angle : 0.870 20.337 134424 Z= 0.445 Chirality : 0.041 0.372 15912 Planarity : 0.005 0.111 17244 Dihedral : 3.857 22.242 13788 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.07), residues: 12636 helix: 1.99 (0.05), residues: 10836 sheet: None (None), residues: 0 loop : -1.25 (0.14), residues: 1800 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25272 Ramachandran restraints generated. 12636 Oldfield, 0 Emsley, 12636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25272 Ramachandran restraints generated. 12636 Oldfield, 0 Emsley, 12636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4737 residues out of total 11124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 4599 time to evaluate : 9.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 138 outliers final: 63 residues processed: 4640 average time/residue: 0.9185 time to fit residues: 7149.4083 Evaluate side-chains 4425 residues out of total 11124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 4362 time to evaluate : 9.031 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 0 residues processed: 63 average time/residue: 0.7238 time to fit residues: 96.4736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1260 random chunks: chunk 743 optimal weight: 4.9990 chunk 1196 optimal weight: 10.0000 chunk 730 optimal weight: 8.9990 chunk 567 optimal weight: 6.9990 chunk 831 optimal weight: 6.9990 chunk 1255 optimal weight: 0.9990 chunk 1155 optimal weight: 10.0000 chunk 999 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 772 optimal weight: 5.9990 chunk 612 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: JB 60 ASN ** JB 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** JB 64 ASN JB 80 GLN ** JB 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** JB 146 GLN ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 ASN C 44 ASN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 GLN ** F 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 121 GLN ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 GLN ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 58 GLN M 61 GLN ** N 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 148 GLN ** R 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 14 ASN ** W 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 58 HIS X 7 HIS X 10 ASN X 148 GLN ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 64 ASN ** AA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DA 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DA 80 GLN ** EA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FA 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** FA 64 ASN FA 80 GLN FA 107 ASN ** FA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FA 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FA 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GA 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** IA 14 ASN JA 61 GLN JA 147 ASN ** KA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LA 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** MA 14 ASN ** MA 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OA 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** PA 64 ASN PA 80 GLN PA 121 GLN PA 148 GLN QA 20 ASN QA 111 GLN ** QA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** RA 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** RA 80 GLN RA 107 ASN RA 131 GLN ** SA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TA 61 GLN ** UA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** UA 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** UA 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** VA 10 ASN ** VA 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** VA 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** VA 154 GLN ** VA 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XA 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** YA 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** YA 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ZA 41 GLN ZA 64 ASN ** ZA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ZA 154 GLN ** AB 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CB 14 ASN CB 20 ASN DB 51 HIS DB 61 GLN EB 20 ASN ** GB 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GB 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GB 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HB 80 GLN IB 58 HIS LB 80 GLN NB 58 GLN ** NB 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OB 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OB 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** PB 147 ASN ** QB 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** RB 61 GLN RB 121 GLN ** SB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 02 10 ASN ** 02 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 02 80 GLN ** 01 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 01 111 GLN ** 01 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 01 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 1.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.299 100080 Z= 0.341 Angle : 0.913 20.549 134424 Z= 0.466 Chirality : 0.042 0.325 15912 Planarity : 0.005 0.112 17244 Dihedral : 3.943 24.321 13788 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer Outliers : 0.90 % 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: 2.23 (0.07), residues: 12636 helix: 1.85 (0.05), residues: 10944 sheet: None (None), residues: 0 loop : -0.85 (0.15), residues: 1692 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25272 Ramachandran restraints generated. 12636 Oldfield, 0 Emsley, 12636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25272 Ramachandran restraints generated. 12636 Oldfield, 0 Emsley, 12636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4599 residues out of total 11124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 4507 time to evaluate : 8.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 92 outliers final: 52 residues processed: 4533 average time/residue: 0.8716 time to fit residues: 6634.6232 Evaluate side-chains 4353 residues out of total 11124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 4301 time to evaluate : 8.842 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 0 residues processed: 52 average time/residue: 0.7133 time to fit residues: 80.6730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1260 random chunks: chunk 793 optimal weight: 5.9990 chunk 1064 optimal weight: 1.9990 chunk 306 optimal weight: 6.9990 chunk 921 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 277 optimal weight: 0.0670 chunk 1001 optimal weight: 20.0000 chunk 418 optimal weight: 9.9990 chunk 1028 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 184 optimal weight: 0.9980 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** JB 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** JB 64 ASN ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 ASN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 GLN ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 121 GLN ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 GLN ** J 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 10 ASN K 148 GLN ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 58 GLN M 61 GLN ** N 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 44 ASN O 80 GLN O 154 GLN ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 146 GLN Q 148 GLN ** R 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 111 GLN ** T 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 14 ASN ** W 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 64 ASN ** AA 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 121 GLN DA 10 ASN ** EA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FA 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FA 61 GLN FA 80 GLN ** FA 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** FA 148 GLN ** GA 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HA 58 GLN HA 121 GLN IA 14 ASN JA 61 GLN LA 107 ASN MA 14 ASN ** MA 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** MA 123 GLN ** OA 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** OA 123 GLN OA 150 HIS PA 64 ASN PA 80 GLN PA 131 GLN PA 148 GLN QA 20 ASN ** RA 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** RA 80 GLN ** SA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SA 150 HIS ** TA 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** UA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** UA 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** UA 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** UA 150 HIS VA 10 ASN ** VA 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** VA 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** WA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** XA 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** YA 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** YA 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ZA 41 GLN ZA 64 ASN ZA 154 GLN ** ZA 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 20 ASN ** AB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CB 14 ASN ** CB 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EB 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FB 41 GLN ** GB 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GB 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GB 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GB 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HB 80 GLN IB 123 GLN ** LB 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** KB 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** RB 61 GLN 02 10 ASN 02 41 GLN ** 02 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 02 80 GLN 01 20 ASN ** 01 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 01 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.106183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.090981 restraints weight = 242940.084| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 3.28 r_work: 0.3419 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work: 0.3399 rms_B_bonded: 3.03 restraints_weight: 0.1250 r_work: 0.3389 rms_B_bonded: 3.07 restraints_weight: 0.0625 r_work: 0.3378 rms_B_bonded: 3.13 restraints_weight: 0.0312 r_work: 0.3368 rms_B_bonded: 3.21 restraints_weight: 0.0156 r_work: 0.3357 rms_B_bonded: 3.31 restraints_weight: 0.0078 r_work: 0.3346 rms_B_bonded: 3.43 restraints_weight: 0.0039 r_work: 0.3335 rms_B_bonded: 3.56 restraints_weight: 0.0020 r_work: 0.3323 rms_B_bonded: 3.70 restraints_weight: 0.0010 r_work: 0.3311 rms_B_bonded: 3.87 restraints_weight: 0.0005 r_work: 0.3299 rms_B_bonded: 4.04 restraints_weight: 0.0002 r_work: 0.3287 rms_B_bonded: 4.24 restraints_weight: 0.0001 r_work: 0.3274 rms_B_bonded: 4.45 restraints_weight: 0.0001 r_work: 0.3260 rms_B_bonded: 4.67 restraints_weight: 0.0000 r_work: 0.3247 rms_B_bonded: 4.92 restraints_weight: 0.0000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 1.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.260 100080 Z= 0.309 Angle : 0.919 19.181 134424 Z= 0.467 Chirality : 0.041 0.398 15912 Planarity : 0.005 0.122 17244 Dihedral : 3.949 25.441 13788 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer Outliers : 0.64 % 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: 2.28 (0.07), residues: 12636 helix: 1.91 (0.05), residues: 10908 sheet: None (None), residues: 0 loop : -1.04 (0.14), residues: 1728 =============================================================================== Job complete usr+sys time: 79691.44 seconds wall clock time: 1364 minutes 18.14 seconds (81858.14 seconds total)