Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 23:50:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aso_11902/04_2023/7aso_11902.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aso_11902/04_2023/7aso_11902.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aso_11902/04_2023/7aso_11902.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aso_11902/04_2023/7aso_11902.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aso_11902/04_2023/7aso_11902.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aso_11902/04_2023/7aso_11902.pdb" } resolution = 3.11 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4247 5.49 5 S 78 5.16 5 C 62165 2.51 5 N 23310 2.21 5 O 35730 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 19": "OE1" <-> "OE2" Residue "B GLU 45": "OE1" <-> "OE2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B GLU 82": "OE1" <-> "OE2" Residue "B GLU 84": "OE1" <-> "OE2" Residue "B ARG 87": "NH1" <-> "NH2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B ARG 121": "NH1" <-> "NH2" Residue "B GLU 124": "OE1" <-> "OE2" Residue "B ARG 126": "NH1" <-> "NH2" Residue "B ARG 139": "NH1" <-> "NH2" Residue "B ARG 163": "NH1" <-> "NH2" Residue "B GLU 165": "OE1" <-> "OE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "l ARG 58": "NH1" <-> "NH2" Residue "D GLU 10": "OE1" <-> "OE2" Residue "D GLU 13": "OE1" <-> "OE2" Residue "D ARG 29": "NH1" <-> "NH2" Residue "D ARG 30": "NH1" <-> "NH2" Residue "D ARG 32": "NH1" <-> "NH2" Residue "D GLU 65": "OE1" <-> "OE2" Residue "D GLU 163": "OE1" <-> "OE2" Residue "E ARG 11": "NH1" <-> "NH2" Residue "E GLU 16": "OE1" <-> "OE2" Residue "E GLU 24": "OE1" <-> "OE2" Residue "E ARG 46": "NH1" <-> "NH2" Residue "E ARG 64": "NH1" <-> "NH2" Residue "E ARG 78": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G ARG 10": "NH1" <-> "NH2" Residue "G ARG 36": "NH1" <-> "NH2" Residue "G ARG 41": "NH1" <-> "NH2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "G GLU 74": "OE1" <-> "OE2" Residue "G GLU 90": "OE1" <-> "OE2" Residue "G ARG 92": "NH1" <-> "NH2" Residue "G ARG 96": "NH1" <-> "NH2" Residue "G ARG 111": "NH1" <-> "NH2" Residue "F GLU 23": "OE1" <-> "OE2" Residue "F GLU 26": "OE1" <-> "OE2" Residue "F GLU 38": "OE1" <-> "OE2" Residue "F ARG 61": "NH1" <-> "NH2" Residue "F ARG 72": "NH1" <-> "NH2" Residue "F GLU 93": "OE1" <-> "OE2" Residue "F ARG 119": "NH1" <-> "NH2" Residue "F GLU 126": "OE1" <-> "OE2" Residue "H ARG 38": "NH1" <-> "NH2" Residue "H GLU 39": "OE1" <-> "OE2" Residue "H GLU 44": "OE1" <-> "OE2" Residue "H ARG 82": "NH1" <-> "NH2" Residue "H ARG 115": "NH1" <-> "NH2" Residue "H ARG 125": "NH1" <-> "NH2" Residue "1 ARG 16": "NH1" <-> "NH2" Residue "1 GLU 63": "OE1" <-> "OE2" Residue "2 GLU 83": "OE1" <-> "OE2" Residue "2 GLU 94": "OE1" <-> "OE2" Residue "2 GLU 106": "OE1" <-> "OE2" Residue "2 ARG 111": "NH1" <-> "NH2" Residue "3 ARG 9": "NH1" <-> "NH2" Residue "3 ARG 12": "NH1" <-> "NH2" Residue "3 ARG 63": "NH1" <-> "NH2" Residue "3 ARG 69": "NH1" <-> "NH2" Residue "4 ARG 11": "NH1" <-> "NH2" Residue "4 ARG 14": "NH1" <-> "NH2" Residue "4 ARG 70": "NH1" <-> "NH2" Residue "4 ARG 71": "NH1" <-> "NH2" Residue "4 ARG 79": "NH1" <-> "NH2" Residue "4 ARG 98": "NH1" <-> "NH2" Residue "5 GLU 20": "OE1" <-> "OE2" Residue "5 GLU 25": "OE1" <-> "OE2" Residue "5 ARG 26": "NH1" <-> "NH2" Residue "5 ARG 29": "NH1" <-> "NH2" Residue "5 ARG 41": "NH1" <-> "NH2" Residue "5 ARG 57": "NH1" <-> "NH2" Residue "6 ARG 7": "NH1" <-> "NH2" Residue "6 GLU 14": "OE1" <-> "OE2" Residue "6 ARG 16": "NH1" <-> "NH2" Residue "6 GLU 26": "OE1" <-> "OE2" Residue "6 GLU 41": "OE1" <-> "OE2" Residue "6 ARG 54": "NH1" <-> "NH2" Residue "6 ARG 63": "NH1" <-> "NH2" Residue "6 ARG 71": "NH1" <-> "NH2" Residue "6 GLU 80": "OE1" <-> "OE2" Residue "6 ARG 88": "NH1" <-> "NH2" Residue "7 ARG 26": "NH1" <-> "NH2" Residue "7 ARG 29": "NH1" <-> "NH2" Residue "7 GLU 78": "OE1" <-> "OE2" Residue "8 ARG 39": "NH1" <-> "NH2" Residue "9 GLU 32": "OE1" <-> "OE2" Residue "9 ARG 47": "NH1" <-> "NH2" Residue "I PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 13": "OE1" <-> "OE2" Residue "I ARG 37": "NH1" <-> "NH2" Residue "I ARG 55": "NH1" <-> "NH2" Residue "A ARG 10": "NH1" <-> "NH2" Residue "e GLU 18": "OE1" <-> "OE2" Residue "e GLU 29": "OE1" <-> "OE2" Residue "e GLU 54": "OE1" <-> "OE2" Residue "e ARG 89": "NH1" <-> "NH2" Residue "e GLU 90": "OE1" <-> "OE2" Residue "J GLU 35": "OE1" <-> "OE2" Residue "J ARG 45": "NH1" <-> "NH2" Residue "J ARG 54": "NH1" <-> "NH2" Residue "J ARG 107": "NH1" <-> "NH2" Residue "J GLU 157": "OE1" <-> "OE2" Residue "J GLU 159": "OE1" <-> "OE2" Residue "J GLU 164": "OE1" <-> "OE2" Residue "J ARG 168": "NH1" <-> "NH2" Residue "J GLU 203": "OE1" <-> "OE2" Residue "K GLU 55": "OE1" <-> "OE2" Residue "K GLU 81": "OE1" <-> "OE2" Residue "K ARG 112": "NH1" <-> "NH2" Residue "L ARG 69": "NH1" <-> "NH2" Residue "L ARG 163": "NH1" <-> "NH2" Residue "M GLU 9": "OE1" <-> "OE2" Residue "M GLU 32": "OE1" <-> "OE2" Residue "M ARG 95": "NH1" <-> "NH2" Residue "M ARG 100": "NH1" <-> "NH2" Residue "M GLU 117": "OE1" <-> "OE2" Residue "M GLU 130": "OE1" <-> "OE2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N GLU 18": "OE1" <-> "OE2" Residue "N ARG 88": "NH1" <-> "NH2" Residue "O ARG 21": "NH1" <-> "NH2" Residue "O ARG 64": "NH1" <-> "NH2" Residue "P ARG 10": "NH1" <-> "NH2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P ARG 45": "NH1" <-> "NH2" Residue "P ARG 51": "NH1" <-> "NH2" Residue "P ARG 56": "NH1" <-> "NH2" Residue "P ARG 115": "NH1" <-> "NH2" Residue "Q GLU 28": "OE1" <-> "OE2" Residue "Q GLU 74": "OE1" <-> "OE2" Residue "Q GLU 76": "OE1" <-> "OE2" Residue "Q GLU 95": "OE1" <-> "OE2" Residue "Q ARG 110": "NH1" <-> "NH2" Residue "R ARG 14": "NH1" <-> "NH2" Residue "R ARG 35": "NH1" <-> "NH2" Residue "R GLU 91": "OE1" <-> "OE2" Residue "S ARG 48": "NH1" <-> "NH2" Residue "S GLU 73": "OE1" <-> "OE2" Residue "U GLU 6": "OE1" <-> "OE2" Residue "U GLU 16": "OE1" <-> "OE2" Residue "U GLU 29": "OE1" <-> "OE2" Residue "U ARG 84": "NH1" <-> "NH2" Residue "V GLU 2": "OE1" <-> "OE2" Residue "V ARG 8": "NH1" <-> "NH2" Residue "V ARG 11": "NH1" <-> "NH2" Residue "V GLU 59": "OE1" <-> "OE2" Residue "V ARG 88": "NH1" <-> "NH2" Residue "V GLU 112": "OE1" <-> "OE2" Residue "W GLU 44": "OE1" <-> "OE2" Residue "W ARG 64": "NH1" <-> "NH2" Residue "W ARG 76": "NH1" <-> "NH2" Residue "Z ARG 32": "NH1" <-> "NH2" Residue "Z ARG 80": "NH1" <-> "NH2" Residue "a ARG 22": "NH1" <-> "NH2" Residue "a GLU 45": "OE1" <-> "OE2" Residue "a GLU 47": "OE1" <-> "OE2" Residue "a ARG 57": "NH1" <-> "NH2" Residue "b ARG 22": "NH1" <-> "NH2" Residue "b ARG 28": "NH1" <-> "NH2" Residue "b ARG 49": "NH1" <-> "NH2" Residue "b ARG 61": "NH1" <-> "NH2" Residue "b GLU 78": "OE1" <-> "OE2" Residue "b ARG 79": "NH1" <-> "NH2" Residue "b ARG 82": "NH1" <-> "NH2" Residue "c ARG 28": "NH1" <-> "NH2" Residue "c ARG 37": "NH1" <-> "NH2" Residue "d GLU 5": "OE1" <-> "OE2" Residue "d ARG 7": "NH1" <-> "NH2" Residue "d GLU 23": "OE1" <-> "OE2" Residue "d GLU 24": "OE1" <-> "OE2" Residue "d PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 44": "NH1" <-> "NH2" Residue "d ARG 47": "NH1" <-> "NH2" Residue "d ARG 52": "NH1" <-> "NH2" Residue "d ARG 58": "NH1" <-> "NH2" Residue "d ARG 60": "NH1" <-> "NH2" Residue "d GLU 63": "OE1" <-> "OE2" Residue "f ARG 10": "NH1" <-> "NH2" Residue "f GLU 38": "OE1" <-> "OE2" Residue "g ARG 7": "NH1" <-> "NH2" Residue "T ARG 38": "NH1" <-> "NH2" Residue "i ARG 20": "NH1" <-> "NH2" Residue "i ARG 22": "NH1" <-> "NH2" Residue "i ARG 37": "NH1" <-> "NH2" Residue "i ARG 40": "NH1" <-> "NH2" Residue "j ARG 48": "NH1" <-> "NH2" Residue "k ARG 19": "NH1" <-> "NH2" Residue "h GLU 38": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 125530 Number of models: 1 Model: "" Number of chains: 47 Chain: "C" Number of atoms: 2430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 2430 Classifications: {'RNA': 114} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 54, 'rna3p_pyr': 48} Link IDs: {'rna2p': 12, 'rna3p': 101} Chain: "B" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1551 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 3, 'TRANS': 198} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "l" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1058 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 8, 'TRANS': 189} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 579 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 480 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 5, 'TYR:plan': 7, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 14, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 326 Chain: "D" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1153 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 148} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 785 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 93} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1164 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 6, 'TRANS': 148} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 57 Chain: "F" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1007 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 125} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 975 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 119} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "1" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 626 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 74} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "2" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 826 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 106} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "3" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 976 Classifications: {'peptide': 136} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 8, 'TRANS': 127} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 57 Chain: "4" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 828 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 3, 'TRANS': 109} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 39 Chain: "5" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 497 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 57} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "6" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 713 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 86} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "7" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 537 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 5, 'TRANS': 77} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 65 Chain: "8" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 520 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 1, 'TRANS': 78} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 67 Chain: "9" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 458 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 53} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 541 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 4, 'TRANS': 73} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 61 Chain: "A" Number of atoms: 503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 503 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'TRANS': 77} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "X" Number of atoms: 30328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1415, 30328 Inner-chain residues flagged as termini: ['pdbres=" U X 494 "', 'pdbres=" G X 855 "'] Classifications: {'RNA': 1415} Modifications used: {'5*END': 2, 'rna2p_pur': 170, 'rna2p_pyr': 108, 'rna3p_pur': 637, 'rna3p_pyr': 500} Link IDs: {'rna2p': 278, 'rna3p': 1136} Chain breaks: 11 Chain: "e" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1570 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 8, 'TRANS': 206} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 45 Chain: "J" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1514 Classifications: {'peptide': 205} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 14} Link IDs: {'PTRANS': 9, 'TRANS': 195} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 44 Chain: "K" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1021 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 5, 'TRANS': 159} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 292 Unresolved non-hydrogen angles: 364 Unresolved non-hydrogen dihedrals: 237 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 150 Chain: "L" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1062 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 7, 'TRANS': 166} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 305 Unresolved non-hydrogen angles: 385 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 169 Chain: "M" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1124 Classifications: {'peptide': 145} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 138} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "N" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 918 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "O" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1020 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 5, 'TRANS': 139} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 32 Chain: "P" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1043 Classifications: {'peptide': 136} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 128} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "Q" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 898 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "R" Number of atoms: 765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 765 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 1, 'TRANS': 111} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 5, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 61 Chain: "S" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 942 Classifications: {'peptide': 116} Link IDs: {'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "U" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 749 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 99} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "V" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 837 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 107} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "W" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 694 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 86} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "Z" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 734 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 97} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "a" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 648 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 36 Chain: "b" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 615 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "c" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 47} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 493 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 61} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "f" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 54} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "g" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 356 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 3, 'TRANS': 43} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "T" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 380 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 44} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "i" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 367 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "j" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 446 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 59} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 24 Chain: "k" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 272 Classifications: {'peptide': 37} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 33} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "h" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 447 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 3, 'TRANS': 70} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 6, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 98 Chain: "Y" Number of atoms: 58326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2720, 58326 Classifications: {'RNA': 2720} Modifications used: {'rna2p_pur': 300, 'rna2p_pyr': 163, 'rna3p_pur': 1267, 'rna3p_pyr': 989} Link IDs: {'rna2p': 463, 'rna3p': 2256} Chain breaks: 16 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' G%rna3p_pur:plan2': 1, ' G%rna3p_pur:plan': 1, ' U%rna3p_pyr:plan': 1} Unresolved non-hydrogen planarities: 21 Time building chain proxies: 46.00, per 1000 atoms: 0.37 Number of scatterers: 125530 At special positions: 0 Unit cell: (268.32, 219.3, 257.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 78 16.00 P 4247 15.00 O 35730 8.00 N 23310 7.00 C 62165 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS 5 24 " - pdb=" SG CYS 5 40 " distance=2.04 Simple disulfide: pdb=" SG CYS 5 27 " - pdb=" SG CYS 5 43 " distance=2.03 Simple disulfide: pdb=" SG CYS T 9 " - pdb=" SG CYS T 12 " distance=2.03 Simple disulfide: pdb=" SG CYS T 9 " - pdb=" SG CYS T 36 " distance=2.03 Simple disulfide: pdb=" SG CYS T 12 " - pdb=" SG CYS T 36 " distance=2.03 Simple disulfide: pdb=" SG CYS k 14 " - pdb=" SG CYS k 27 " distance=2.05 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: 45.87 Conformation dependent library (CDL) restraints added in 5.0 seconds 9306 Ramachandran restraints generated. 4653 Oldfield, 0 Emsley, 4653 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8726 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 50 sheets defined 19.6% alpha, 7.7% beta 524 base pairs and 1752 stacking pairs defined. Time for finding SS restraints: 28.79 Creating SS restraints... Processing helix chain 'B' and resid 35 through 40 Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.809A pdb=" N ALA B 92 " --> pdb=" O ASN B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 119 removed outlier: 4.152A pdb=" N VAL B 115 " --> pdb=" O ASP B 111 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU B 117 " --> pdb=" O ARG B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 142 removed outlier: 3.750A pdb=" N VAL B 132 " --> pdb=" O SER B 128 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN B 135 " --> pdb=" O ARG B 131 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA B 140 " --> pdb=" O ALA B 136 " (cutoff:3.500A) Processing helix chain 'l' and resid 46 through 59 removed outlier: 3.695A pdb=" N TYR l 59 " --> pdb=" O GLN l 55 " (cutoff:3.500A) Processing helix chain 'l' and resid 68 through 75 removed outlier: 4.457A pdb=" N PHE l 72 " --> pdb=" O PHE l 68 " (cutoff:3.500A) Processing helix chain 'l' and resid 76 through 78 No H-bonds generated for 'chain 'l' and resid 76 through 78' Processing helix chain 'l' and resid 81 through 88 removed outlier: 4.449A pdb=" N ASN l 85 " --> pdb=" O VAL l 81 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N MET l 87 " --> pdb=" O GLY l 83 " (cutoff:3.500A) Processing helix chain 'l' and resid 106 through 110 removed outlier: 3.885A pdb=" N ALA l 110 " --> pdb=" O ARG l 107 " (cutoff:3.500A) Processing helix chain 'l' and resid 151 through 155 removed outlier: 3.681A pdb=" N VAL l 155 " --> pdb=" O VAL l 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 67 removed outlier: 4.082A pdb=" N ALA D 66 " --> pdb=" O LYS D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 70 No H-bonds generated for 'chain 'D' and resid 68 through 70' Processing helix chain 'D' and resid 109 through 113 Processing helix chain 'D' and resid 135 through 145 Processing helix chain 'D' and resid 152 through 158 removed outlier: 4.150A pdb=" N LEU D 156 " --> pdb=" O ASP D 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 29 removed outlier: 3.625A pdb=" N LYS E 19 " --> pdb=" O GLU E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 79 removed outlier: 3.856A pdb=" N GLU E 75 " --> pdb=" O LYS E 71 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE E 76 " --> pdb=" O ALA E 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 43 Processing helix chain 'G' and resid 49 through 54 Processing helix chain 'G' and resid 92 through 96 removed outlier: 4.018A pdb=" N ARG G 96 " --> pdb=" O PRO G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 121 Processing helix chain 'F' and resid 7 through 13 removed outlier: 4.295A pdb=" N THR F 12 " --> pdb=" O ALA F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 44 Processing helix chain 'F' and resid 117 through 121 removed outlier: 3.825A pdb=" N ARG F 121 " --> pdb=" O ALA F 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 55 Proline residue: H 53 - end of helix Processing helix chain 'H' and resid 85 through 93 Processing helix chain '1' and resid 18 through 31 Processing helix chain '2' and resid 67 through 72 removed outlier: 3.690A pdb=" N LYS 2 72 " --> pdb=" O GLU 2 68 " (cutoff:3.500A) Processing helix chain '2' and resid 93 through 97 Processing helix chain '3' and resid 4 through 10 removed outlier: 3.755A pdb=" N VAL 3 8 " --> pdb=" O ILE 3 4 " (cutoff:3.500A) Processing helix chain '4' and resid 51 through 63 removed outlier: 4.221A pdb=" N VAL 4 60 " --> pdb=" O ILE 4 56 " (cutoff:3.500A) Processing helix chain '4' and resid 68 through 70 No H-bonds generated for 'chain '4' and resid 68 through 70' Processing helix chain '4' and resid 71 through 82 removed outlier: 4.333A pdb=" N LEU 4 75 " --> pdb=" O ARG 4 71 " (cutoff:3.500A) Processing helix chain '5' and resid 7 through 12 Processing helix chain '5' and resid 44 through 48 removed outlier: 3.682A pdb=" N LEU 5 47 " --> pdb=" O PHE 5 44 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA 5 48 " --> pdb=" O ARG 5 45 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 44 through 48' Processing helix chain '6' and resid 4 through 13 removed outlier: 3.660A pdb=" N LYS 6 8 " --> pdb=" O SER 6 4 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS 6 13 " --> pdb=" O ASN 6 9 " (cutoff:3.500A) Processing helix chain '6' and resid 26 through 40 Processing helix chain '6' and resid 51 through 68 removed outlier: 3.873A pdb=" N GLY 6 55 " --> pdb=" O HIS 6 51 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU 6 57 " --> pdb=" O ARG 6 53 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET 6 59 " --> pdb=" O GLY 6 55 " (cutoff:3.500A) Processing helix chain '6' and resid 74 through 85 removed outlier: 4.161A pdb=" N TYR 6 78 " --> pdb=" O ASP 6 74 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS 6 83 " --> pdb=" O ARG 6 79 " (cutoff:3.500A) Processing helix chain '7' and resid 71 through 77 removed outlier: 3.912A pdb=" N LEU 7 75 " --> pdb=" O VAL 7 71 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS 7 77 " --> pdb=" O ASN 7 73 " (cutoff:3.500A) Processing helix chain '9' and resid 46 through 51 Processing helix chain '9' and resid 53 through 71 removed outlier: 3.656A pdb=" N ILE 9 64 " --> pdb=" O LEU 9 60 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N MET 9 70 " --> pdb=" O ARG 9 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 23 Processing helix chain 'A' and resid 6 through 11 removed outlier: 3.594A pdb=" N ARG A 10 " --> pdb=" O SER A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 30 removed outlier: 4.894A pdb=" N GLN A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 61 removed outlier: 4.373A pdb=" N LYS A 55 " --> pdb=" O SER A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'e' and resid 70 through 78 Processing helix chain 'e' and resid 129 through 134 removed outlier: 3.643A pdb=" N ARG e 133 " --> pdb=" O GLY e 129 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 39 removed outlier: 3.800A pdb=" N GLU J 35 " --> pdb=" O SER J 31 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA J 36 " --> pdb=" O VAL J 32 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE J 37 " --> pdb=" O LEU J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 119 removed outlier: 3.534A pdb=" N LEU J 114 " --> pdb=" O LEU J 110 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER J 115 " --> pdb=" O ARG J 111 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE J 116 " --> pdb=" O SER J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 135 through 146 Processing helix chain 'J' and resid 160 through 166 removed outlier: 3.597A pdb=" N SER J 166 " --> pdb=" O ASN J 162 " (cutoff:3.500A) Processing helix chain 'J' and resid 200 through 206 Processing helix chain 'K' and resid 4 through 11 removed outlier: 3.621A pdb=" N ASN K 9 " --> pdb=" O LYS K 5 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLU K 11 " --> pdb=" O LYS K 7 " (cutoff:3.500A) Processing helix chain 'K' and resid 11 through 16 removed outlier: 4.318A pdb=" N ASN K 15 " --> pdb=" O GLU K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 49 Processing helix chain 'K' and resid 52 through 58 Processing helix chain 'K' and resid 154 through 160 removed outlier: 4.093A pdb=" N THR K 158 " --> pdb=" O ILE K 154 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA K 160 " --> pdb=" O ILE K 156 " (cutoff:3.500A) Processing helix chain 'L' and resid 58 through 81 removed outlier: 3.507A pdb=" N ARG L 62 " --> pdb=" O SER L 58 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR L 63 " --> pdb=" O LYS L 59 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY L 66 " --> pdb=" O ARG L 62 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ALA L 70 " --> pdb=" O GLY L 66 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 148 removed outlier: 4.390A pdb=" N ALA L 143 " --> pdb=" O GLU L 139 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU L 144 " --> pdb=" O GLN L 140 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 39 removed outlier: 3.925A pdb=" N GLU M 32 " --> pdb=" O ARG M 28 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL M 33 " --> pdb=" O LEU M 29 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER M 35 " --> pdb=" O SER M 31 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE M 36 " --> pdb=" O GLU M 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 108 removed outlier: 4.273A pdb=" N LEU M 101 " --> pdb=" O ASN M 97 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE M 102 " --> pdb=" O PRO M 98 " (cutoff:3.500A) Processing helix chain 'M' and resid 118 through 121 removed outlier: 3.540A pdb=" N LYS M 121 " --> pdb=" O LYS M 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 118 through 121' Processing helix chain 'O' and resid 56 through 61 removed outlier: 3.874A pdb=" N ARG O 60 " --> pdb=" O PRO O 56 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU O 61 " --> pdb=" O LEU O 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 56 through 61' Processing helix chain 'O' and resid 78 through 82 removed outlier: 3.675A pdb=" N GLN O 81 " --> pdb=" O ASN O 78 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU O 82 " --> pdb=" O LEU O 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 78 through 82' Processing helix chain 'O' and resid 92 through 98 removed outlier: 3.585A pdb=" N GLU O 98 " --> pdb=" O ALA O 94 " (cutoff:3.500A) Processing helix chain 'O' and resid 131 through 140 Processing helix chain 'P' and resid 44 through 49 Processing helix chain 'P' and resid 51 through 59 Processing helix chain 'P' and resid 110 through 123 removed outlier: 4.436A pdb=" N LEU P 120 " --> pdb=" O GLU P 116 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N HIS P 123 " --> pdb=" O ARG P 119 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 24 Processing helix chain 'Q' and resid 33 through 38 Processing helix chain 'Q' and resid 44 through 54 removed outlier: 3.813A pdb=" N LYS Q 53 " --> pdb=" O THR Q 49 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY Q 54 " --> pdb=" O LEU Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 55 through 63 Processing helix chain 'Q' and resid 81 through 86 Processing helix chain 'Q' and resid 89 through 93 removed outlier: 3.804A pdb=" N TYR Q 93 " --> pdb=" O ALA Q 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 7 through 19 removed outlier: 3.576A pdb=" N ARG R 17 " --> pdb=" O LYS R 13 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 108 removed outlier: 4.231A pdb=" N ALA R 107 " --> pdb=" O GLY R 103 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU R 108 " --> pdb=" O ARG R 104 " (cutoff:3.500A) Processing helix chain 'S' and resid 10 through 15 Processing helix chain 'S' and resid 31 through 49 removed outlier: 3.505A pdb=" N ALA S 35 " --> pdb=" O LEU S 31 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLN S 37 " --> pdb=" O LYS S 33 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY S 43 " --> pdb=" O VAL S 39 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN S 44 " --> pdb=" O MET S 40 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG S 48 " --> pdb=" O GLN S 44 " (cutoff:3.500A) Processing helix chain 'S' and resid 52 through 68 removed outlier: 3.787A pdb=" N PHE S 57 " --> pdb=" O ARG S 53 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG S 58 " --> pdb=" O LYS S 54 " (cutoff:3.500A) Processing helix chain 'S' and resid 75 through 86 Processing helix chain 'S' and resid 91 through 101 Processing helix chain 'S' and resid 102 through 113 removed outlier: 3.755A pdb=" N PHE S 106 " --> pdb=" O ASP S 102 " (cutoff:3.500A) Processing helix chain 'V' and resid 28 through 37 removed outlier: 3.538A pdb=" N ALA V 34 " --> pdb=" O ALA V 30 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 58 removed outlier: 4.039A pdb=" N ILE V 47 " --> pdb=" O SER V 43 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA V 56 " --> pdb=" O MET V 52 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA V 58 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'W' and resid 41 through 46 removed outlier: 3.576A pdb=" N ILE W 45 " --> pdb=" O ALA W 41 " (cutoff:3.500A) Processing helix chain 'a' and resid 50 through 54 Processing helix chain 'c' and resid 52 through 54 No H-bonds generated for 'chain 'c' and resid 52 through 54' Processing helix chain 'd' and resid 14 through 33 removed outlier: 3.703A pdb=" N GLN d 31 " --> pdb=" O ASN d 27 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU d 32 " --> pdb=" O LEU d 28 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA d 33 " --> pdb=" O ARG d 29 " (cutoff:3.500A) Processing helix chain 'd' and resid 49 through 63 removed outlier: 3.594A pdb=" N VAL d 56 " --> pdb=" O ARG d 52 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLU d 61 " --> pdb=" O ALA d 57 " (cutoff:3.500A) Processing helix chain 'f' and resid 16 through 27 removed outlier: 3.698A pdb=" N GLY f 27 " --> pdb=" O VAL f 23 " (cutoff:3.500A) Processing helix chain 'f' and resid 40 through 50 removed outlier: 3.618A pdb=" N GLY f 45 " --> pdb=" O PRO f 41 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN f 46 " --> pdb=" O ALA f 42 " (cutoff:3.500A) Processing helix chain 'g' and resid 11 through 17 removed outlier: 3.623A pdb=" N ARG g 16 " --> pdb=" O ARG g 12 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG g 17 " --> pdb=" O LYS g 13 " (cutoff:3.500A) Processing helix chain 'i' and resid 9 through 17 removed outlier: 3.540A pdb=" N HIS i 17 " --> pdb=" O HIS i 13 " (cutoff:3.500A) Processing helix chain 'i' and resid 29 through 39 removed outlier: 3.746A pdb=" N ALA i 33 " --> pdb=" O ARG i 29 " (cutoff:3.500A) Processing helix chain 'j' and resid 34 through 39 removed outlier: 3.545A pdb=" N THR j 38 " --> pdb=" O ALA j 34 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS j 39 " --> pdb=" O ASN j 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 34 through 39' Processing sheet with id=AA1, first strand: chain 'B' and resid 151 through 152 Processing sheet with id=AA2, first strand: chain 'D' and resid 22 through 23 removed outlier: 3.619A pdb=" N ARG D 30 " --> pdb=" O LYS D 23 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 59 through 60 removed outlier: 3.739A pdb=" N ILE E 9 " --> pdb=" O ARG E 88 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ARG E 88 " --> pdb=" O ILE E 9 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 40 through 41 Processing sheet with id=AA5, first strand: chain 'F' and resid 26 through 28 Processing sheet with id=AA6, first strand: chain 'F' and resid 105 through 107 Processing sheet with id=AA7, first strand: chain 'H' and resid 19 through 20 removed outlier: 3.558A pdb=" N ARG H 20 " --> pdb=" O ASN H 68 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 24 through 25 Processing sheet with id=AA9, first strand: chain '1' and resid 47 through 48 Processing sheet with id=AB1, first strand: chain '2' and resid 20 through 21 Processing sheet with id=AB2, first strand: chain '2' and resid 24 through 25 Processing sheet with id=AB3, first strand: chain '3' and resid 95 through 97 Processing sheet with id=AB4, first strand: chain '7' and resid 18 through 19 Processing sheet with id=AB5, first strand: chain '8' and resid 11 through 12 Processing sheet with id=AB6, first strand: chain '8' and resid 26 through 29 removed outlier: 3.678A pdb=" N THR 8 29 " --> pdb=" O TYR 8 42 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYR 8 42 " --> pdb=" O THR 8 29 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'e' and resid 13 through 16 removed outlier: 6.765A pdb=" N VAL e 194 " --> pdb=" O VAL e 188 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL e 188 " --> pdb=" O VAL e 194 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU e 196 " --> pdb=" O VAL e 186 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLU e 184 " --> pdb=" O LYS e 198 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N THR e 179 " --> pdb=" O GLY e 120 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N GLY e 120 " --> pdb=" O THR e 179 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLN e 181 " --> pdb=" O VAL e 118 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL e 118 " --> pdb=" O GLN e 181 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY e 207 " --> pdb=" O LYS e 9 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE e 5 " --> pdb=" O ILE e 211 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'e' and resid 35 through 39 removed outlier: 4.976A pdb=" N GLN e 37 " --> pdb=" O GLN e 50 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 8 through 9 Processing sheet with id=AC1, first strand: chain 'J' and resid 123 through 126 Processing sheet with id=AC2, first strand: chain 'J' and resid 152 through 156 removed outlier: 3.586A pdb=" N GLN J 174 " --> pdb=" O VAL J 152 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 85 through 86 removed outlier: 4.406A pdb=" N VAL K 35 " --> pdb=" O SER K 147 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N SER K 147 " --> pdb=" O VAL K 35 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 97 through 98 removed outlier: 3.785A pdb=" N ILE L 104 " --> pdb=" O GLN L 97 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 123 through 124 removed outlier: 6.507A pdb=" N TRP M 16 " --> pdb=" O GLU M 139 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 7 through 10 removed outlier: 3.667A pdb=" N VAL N 10 " --> pdb=" O ARG N 17 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N ARG N 17 " --> pdb=" O VAL N 10 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA N 16 " --> pdb=" O ALA N 46 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ALA N 46 " --> pdb=" O ALA N 16 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLU N 18 " --> pdb=" O LYS N 44 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL N 40 " --> pdb=" O ILE N 22 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ASP N 37 " --> pdb=" O ILE N 62 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA N 83 " --> pdb=" O VAL N 63 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N CYS N 84 " --> pdb=" O ARG N 7 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LYS N 9 " --> pdb=" O CYS N 84 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N ILE N 86 " --> pdb=" O LYS N 9 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'O' and resid 75 through 77 removed outlier: 6.099A pdb=" N ILE O 109 " --> pdb=" O LYS O 127 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'O' and resid 89 through 91 removed outlier: 6.190A pdb=" N THR O 122 " --> pdb=" O THR O 89 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'P' and resid 64 through 66 removed outlier: 6.779A pdb=" N LEU P 34 " --> pdb=" O LEU P 103 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLU P 105 " --> pdb=" O PHE P 32 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N PHE P 32 " --> pdb=" O GLU P 105 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'P' and resid 40 through 42 removed outlier: 3.633A pdb=" N SER P 40 " --> pdb=" O VAL P 97 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Q' and resid 30 through 32 removed outlier: 4.764A pdb=" N SER Q 116 " --> pdb=" O GLN Q 106 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'U' and resid 3 through 5 removed outlier: 3.851A pdb=" N PHE U 40 " --> pdb=" O ILE U 4 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'U' and resid 19 through 22 removed outlier: 3.567A pdb=" N THR U 93 " --> pdb=" O VAL U 22 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR U 61 " --> pdb=" O THR U 96 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'U' and resid 71 through 76 Processing sheet with id=AD6, first strand: chain 'V' and resid 3 through 6 removed outlier: 5.550A pdb=" N HIS V 102 " --> pdb=" O ALA V 76 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ALA V 76 " --> pdb=" O HIS V 102 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR V 104 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ALA V 74 " --> pdb=" O THR V 104 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL V 106 " --> pdb=" O LYS V 72 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'V' and resid 82 through 87 removed outlier: 3.628A pdb=" N ARG V 86 " --> pdb=" O SER V 94 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'W' and resid 7 through 10 removed outlier: 6.506A pdb=" N ASP W 28 " --> pdb=" O LYS W 8 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N THR W 26 " --> pdb=" O PRO W 10 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ARG W 76 " --> pdb=" O VAL W 29 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG W 75 " --> pdb=" O TYR W 58 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Z' and resid 19 through 22 removed outlier: 3.736A pdb=" N LYS Z 19 " --> pdb=" O VAL Z 11 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL Z 9 " --> pdb=" O GLY Z 21 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Z' and resid 32 through 33 Processing sheet with id=AE2, first strand: chain 'Z' and resid 40 through 41 removed outlier: 4.108A pdb=" N MET Z 41 " --> pdb=" O THR Z 59 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N THR Z 59 " --> pdb=" O MET Z 41 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'Z' and resid 82 through 84 Processing sheet with id=AE4, first strand: chain 'a' and resid 8 through 9 Processing sheet with id=AE5, first strand: chain 'b' and resid 30 through 31 removed outlier: 6.617A pdb=" N LEU b 67 " --> pdb=" O LEU b 45 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'b' and resid 38 through 39 removed outlier: 4.260A pdb=" N GLY b 73 " --> pdb=" O VAL b 39 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ILE b 53 " --> pdb=" O LYS b 85 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N VAL b 87 " --> pdb=" O ILE b 53 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N VAL b 89 " --> pdb=" O PRO b 55 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N GLU b 57 " --> pdb=" O VAL b 89 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'c' and resid 14 through 18 removed outlier: 3.714A pdb=" N GLY c 15 " --> pdb=" O ARG c 27 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG c 27 " --> pdb=" O GLY c 15 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'c' and resid 33 through 38 Processing sheet with id=AE9, first strand: chain 'f' and resid 3 through 7 removed outlier: 3.526A pdb=" N ILE f 6 " --> pdb=" O VAL f 35 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'g' and resid 28 through 29 removed outlier: 3.620A pdb=" N LYS g 37 " --> pdb=" O THR g 28 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'T' and resid 3 through 4 Processing sheet with id=AF3, first strand: chain 'T' and resid 31 through 34 removed outlier: 3.552A pdb=" N MET T 32 " --> pdb=" O HIS T 45 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'j' and resid 14 through 15 removed outlier: 4.279A pdb=" N LEU j 44 " --> pdb=" O LEU j 22 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'k' and resid 15 through 16 removed outlier: 3.599A pdb=" N LYS k 15 " --> pdb=" O ILE k 26 " (cutoff:3.500A) 640 hydrogen bonds defined for protein. 1767 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1214 hydrogen bonds 1870 hydrogen bond angles 0 basepair planarities 524 basepair parallelities 1752 stacking parallelities Total time for adding SS restraints: 133.42 Time building geometry restraints manager: 50.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 12265 1.32 - 1.46: 67118 1.46 - 1.60: 53118 1.60 - 1.74: 4203 1.74 - 1.87: 140 Bond restraints: 136844 Sorted by residual: bond pdb=" O3' U Y 765 " pdb=" P G Y 766 " ideal model delta sigma weight residual 1.607 1.698 -0.091 1.50e-02 4.44e+03 3.70e+01 bond pdb=" N LYS e 57 " pdb=" CA LYS e 57 " ideal model delta sigma weight residual 1.457 1.488 -0.031 6.40e-03 2.44e+04 2.41e+01 bond pdb=" N SER S 101 " pdb=" CA SER S 101 " ideal model delta sigma weight residual 1.457 1.487 -0.031 6.40e-03 2.44e+04 2.29e+01 bond pdb=" N ASN f 40 " pdb=" CA ASN f 40 " ideal model delta sigma weight residual 1.455 1.489 -0.033 7.00e-03 2.04e+04 2.29e+01 bond pdb=" N HIS e 148 " pdb=" CA HIS e 148 " ideal model delta sigma weight residual 1.458 1.487 -0.029 6.30e-03 2.52e+04 2.10e+01 ... (remaining 136839 not shown) Histogram of bond angle deviations from ideal: 96.84 - 104.34: 15843 104.34 - 111.84: 79652 111.84 - 119.34: 46431 119.34 - 126.84: 52877 126.84 - 134.34: 11170 Bond angle restraints: 205973 Sorted by residual: angle pdb=" O3' U Y1897 " pdb=" C3' U Y1897 " pdb=" C2' U Y1897 " ideal model delta sigma weight residual 109.50 124.00 -14.50 1.50e+00 4.44e-01 9.34e+01 angle pdb=" O3' G X 679 " pdb=" C3' G X 679 " pdb=" C2' G X 679 " ideal model delta sigma weight residual 109.50 123.61 -14.11 1.50e+00 4.44e-01 8.85e+01 angle pdb=" O3' A Y1463 " pdb=" C3' A Y1463 " pdb=" C2' A Y1463 " ideal model delta sigma weight residual 113.70 126.95 -13.25 1.50e+00 4.44e-01 7.80e+01 angle pdb=" C4' U X 970 " pdb=" C3' U X 970 " pdb=" O3' U X 970 " ideal model delta sigma weight residual 109.40 122.35 -12.95 1.50e+00 4.44e-01 7.46e+01 angle pdb=" C4' C Y1898 " pdb=" C3' C Y1898 " pdb=" O3' C Y1898 " ideal model delta sigma weight residual 109.40 122.07 -12.67 1.50e+00 4.44e-01 7.13e+01 ... (remaining 205968 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 65335 35.98 - 71.96: 6238 71.96 - 107.94: 565 107.94 - 143.92: 142 143.92 - 179.90: 68 Dihedral angle restraints: 72348 sinusoidal: 58822 harmonic: 13526 Sorted by residual: dihedral pdb=" C5' U Y 835 " pdb=" C4' U Y 835 " pdb=" C3' U Y 835 " pdb=" O3' U Y 835 " ideal model delta sinusoidal sigma weight residual 147.00 75.54 71.46 1 8.00e+00 1.56e-02 1.02e+02 dihedral pdb=" CB CYS T 9 " pdb=" SG CYS T 9 " pdb=" SG CYS T 36 " pdb=" CB CYS T 36 " ideal model delta sinusoidal sigma weight residual -86.00 2.93 -88.93 1 1.00e+01 1.00e-02 9.42e+01 dihedral pdb=" C4' A Y2338 " pdb=" C3' A Y2338 " pdb=" C2' A Y2338 " pdb=" C1' A Y2338 " ideal model delta sinusoidal sigma weight residual 36.34 60.41 -24.06 1 3.10e+00 1.04e-01 8.68e+01 ... (remaining 72345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.167: 23980 0.167 - 0.334: 2671 0.334 - 0.501: 23 0.501 - 0.668: 17 0.668 - 0.835: 10 Chirality restraints: 26701 Sorted by residual: chirality pdb=" C3' G X 679 " pdb=" C4' G X 679 " pdb=" O3' G X 679 " pdb=" C2' G X 679 " both_signs ideal model delta sigma weight residual False -2.74 -1.91 -0.84 2.00e-01 2.50e+01 1.74e+01 chirality pdb=" C3' A X 695 " pdb=" C4' A X 695 " pdb=" O3' A X 695 " pdb=" C2' A X 695 " both_signs ideal model delta sigma weight residual False -2.74 -1.98 -0.76 2.00e-01 2.50e+01 1.45e+01 chirality pdb=" C3' U X 880 " pdb=" C4' U X 880 " pdb=" O3' U X 880 " pdb=" C2' U X 880 " both_signs ideal model delta sigma weight residual False -2.74 -2.00 -0.74 2.00e-01 2.50e+01 1.37e+01 ... (remaining 26698 not shown) Planarity restraints: 10352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR 3 79 " -0.041 2.00e-02 2.50e+03 7.94e-02 6.31e+01 pdb=" C TYR 3 79 " 0.137 2.00e-02 2.50e+03 pdb=" O TYR 3 79 " -0.051 2.00e-02 2.50e+03 pdb=" N ILE 3 80 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE H 43 " 0.016 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C PHE H 43 " -0.057 2.00e-02 2.50e+03 pdb=" O PHE H 43 " 0.022 2.00e-02 2.50e+03 pdb=" N GLU H 44 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE 2 27 " -0.030 2.00e-02 2.50e+03 2.49e-02 1.09e+01 pdb=" CG PHE 2 27 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE 2 27 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE 2 27 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE 2 27 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE 2 27 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE 2 27 " -0.006 2.00e-02 2.50e+03 ... (remaining 10349 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 320 2.45 - 3.06: 73069 3.06 - 3.67: 221405 3.67 - 4.29: 325442 4.29 - 4.90: 466842 Nonbonded interactions: 1087078 Sorted by model distance: nonbonded pdb=" NH2 ARG H 115 " pdb=" OE1 GLN 1 64 " model vdw 1.837 2.520 nonbonded pdb=" NH2 ARG H 115 " pdb=" NE2 GLN 1 64 " model vdw 1.939 3.200 nonbonded pdb=" NZ LYS K 33 " pdb=" O LYS K 88 " model vdw 1.970 2.520 nonbonded pdb=" O2' G X1059 " pdb=" O2' G X1226 " model vdw 2.038 2.440 nonbonded pdb=" O2' U Y2370 " pdb=" O2' U Y2400 " model vdw 2.040 2.440 ... (remaining 1087073 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 22.300 Check model and map are aligned: 1.380 Set scattering table: 0.820 Process input model: 336.310 Find NCS groups from input model: 2.150 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 368.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4359 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 : 0.007 0.139 136844 Z= 0.469 Angle : 1.047 14.497 205973 Z= 0.717 Chirality : 0.100 0.835 26701 Planarity : 0.004 0.079 10352 Dihedral : 22.662 179.898 63604 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 24.01 Ramachandran Plot: Outliers : 1.87 % Allowed : 22.05 % Favored : 76.08 % Rotamer Outliers : 13.50 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.53 % 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: -5.91 (0.09), residues: 4653 helix: -4.02 (0.10), residues: 1040 sheet: -3.39 (0.19), residues: 500 loop : -4.29 (0.08), residues: 3113 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9306 Ramachandran restraints generated. 4653 Oldfield, 0 Emsley, 4653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9306 Ramachandran restraints generated. 4653 Oldfield, 0 Emsley, 4653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1191 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 433 poor density : 758 time to evaluate : 5.043 Fit side-chains TARDY: cannot create tardy model for: "ARG B 203 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TRP F 132 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS e 216 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 175 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU N 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL Q 122 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU S 117 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR c 60 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS d 66 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 61 " (corrupted residue). Skipping it. outliers start: 433 outliers final: 142 residues processed: 1059 average time/residue: 1.1618 time to fit residues: 2054.8631 Evaluate side-chains 739 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 597 time to evaluate : 5.014 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ARG B 203 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TRP F 132 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS e 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS L 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL Q 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU S 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR c 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS d 66 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 61 " (corrupted residue). Skipping it. outliers start: 142 outliers final: 11 residues processed: 142 average time/residue: 0.9805 time to fit residues: 249.6705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 741 optimal weight: 20.0000 chunk 665 optimal weight: 10.0000 chunk 369 optimal weight: 7.9990 chunk 227 optimal weight: 50.0000 chunk 448 optimal weight: 10.0000 chunk 355 optimal weight: 2.9990 chunk 688 optimal weight: 10.0000 chunk 266 optimal weight: 50.0000 chunk 418 optimal weight: 20.0000 chunk 512 optimal weight: 6.9990 chunk 797 optimal weight: 10.0000 overall best weight: 7.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 50 GLN D 54 GLN ** D 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 GLN G 122 ASN F 99 ASN 1 15 HIS 1 56 HIS ** 1 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 52 GLN ** 6 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 73 ASN e 167 GLN ** J 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 179 GLN ** J 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN O 143 HIS P 35 GLN Q 73 ASN U 18 GLN V 102 HIS ** Z 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 85 GLN d 64 GLN f 5 GLN g 14 ASN ** g 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 7 HIS ** j 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4448 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 136844 Z= 0.302 Angle : 0.776 10.538 205973 Z= 0.395 Chirality : 0.043 0.390 26701 Planarity : 0.006 0.070 10352 Dihedral : 21.041 178.898 56021 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.28 % Allowed : 13.93 % Favored : 85.79 % Rotamer Outliers : 4.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -5.08 (0.10), residues: 4653 helix: -3.01 (0.13), residues: 1025 sheet: -2.92 (0.18), residues: 602 loop : -3.86 (0.09), residues: 3026 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9306 Ramachandran restraints generated. 4653 Oldfield, 0 Emsley, 4653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9306 Ramachandran restraints generated. 4653 Oldfield, 0 Emsley, 4653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 623 time to evaluate : 5.083 Fit side-chains TARDY: cannot create tardy model for: "ARG B 203 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TRP F 132 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS e 216 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU N 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL Q 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU S 117 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR c 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS d 66 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 61 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 133 outliers final: 74 residues processed: 708 average time/residue: 1.1263 time to fit residues: 1357.7704 Evaluate side-chains 626 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 552 time to evaluate : 5.016 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ARG B 203 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TRP F 132 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYS e 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS L 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL Q 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU S 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR c 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS d 66 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 61 " (corrupted residue). Skipping it. outliers start: 74 outliers final: 10 residues processed: 74 average time/residue: 0.9103 time to fit residues: 130.1895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 443 optimal weight: 10.0000 chunk 247 optimal weight: 70.0000 chunk 663 optimal weight: 10.0000 chunk 542 optimal weight: 20.0000 chunk 219 optimal weight: 50.0000 chunk 798 optimal weight: 10.0000 chunk 862 optimal weight: 20.0000 chunk 711 optimal weight: 40.0000 chunk 792 optimal weight: 30.0000 chunk 272 optimal weight: 50.0000 chunk 640 optimal weight: 20.0000 overall best weight: 14.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 133 GLN l 50 GLN ** D 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 ASN 1 56 HIS ** 1 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 13 GLN ** 6 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 128 GLN e 148 HIS ** J 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 ASN ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 73 ASN S 44 GLN ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 23 ASN ** g 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4567 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.117 136844 Z= 0.484 Angle : 0.813 10.834 205973 Z= 0.411 Chirality : 0.046 0.360 26701 Planarity : 0.006 0.105 10352 Dihedral : 21.058 178.811 56021 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 20.29 Ramachandran Plot: Outliers : 0.24 % Allowed : 16.27 % Favored : 83.49 % Rotamer Outliers : 5.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -4.73 (0.10), residues: 4653 helix: -2.49 (0.14), residues: 1035 sheet: -2.65 (0.18), residues: 611 loop : -3.73 (0.09), residues: 3007 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9306 Ramachandran restraints generated. 4653 Oldfield, 0 Emsley, 4653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9306 Ramachandran restraints generated. 4653 Oldfield, 0 Emsley, 4653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 544 time to evaluate : 5.065 Fit side-chains TARDY: cannot create tardy model for: "ARG B 203 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TRP F 132 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS e 216 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU N 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL Q 122 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU S 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR c 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS d 66 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 61 " (corrupted residue). Skipping it. outliers start: 184 outliers final: 110 residues processed: 681 average time/residue: 1.0957 time to fit residues: 1274.1353 Evaluate side-chains 613 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 503 time to evaluate : 5.029 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ARG B 203 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TRP F 132 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYS e 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS L 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL Q 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU S 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR c 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS d 66 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 61 " (corrupted residue). Skipping it. outliers start: 110 outliers final: 10 residues processed: 110 average time/residue: 0.8567 time to fit residues: 183.8108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 789 optimal weight: 30.0000 chunk 600 optimal weight: 30.0000 chunk 414 optimal weight: 30.0000 chunk 88 optimal weight: 10.0000 chunk 381 optimal weight: 8.9990 chunk 536 optimal weight: 20.0000 chunk 801 optimal weight: 0.8980 chunk 848 optimal weight: 10.0000 chunk 418 optimal weight: 0.7980 chunk 759 optimal weight: 7.9990 chunk 228 optimal weight: 50.0000 overall best weight: 5.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 50 GLN ** D 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 15 ASN ** J 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 182 ASN ** L 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 ASN ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 70 ASN Q 73 ASN U 18 GLN ** Z 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 38 ASN f 5 GLN g 32 ASN j 31 HIS ** k 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4477 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 136844 Z= 0.223 Angle : 0.662 9.870 205973 Z= 0.340 Chirality : 0.039 0.369 26701 Planarity : 0.005 0.073 10352 Dihedral : 20.687 179.275 56021 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.39 % Favored : 88.42 % Rotamer Outliers : 3.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -4.24 (0.11), residues: 4653 helix: -1.95 (0.15), residues: 1029 sheet: -2.44 (0.18), residues: 652 loop : -3.44 (0.10), residues: 2972 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9306 Ramachandran restraints generated. 4653 Oldfield, 0 Emsley, 4653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9306 Ramachandran restraints generated. 4653 Oldfield, 0 Emsley, 4653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 573 time to evaluate : 5.136 Fit side-chains TARDY: cannot create tardy model for: "ARG B 203 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TRP F 132 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS e 216 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 175 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU N 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL Q 122 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU S 117 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR c 60 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYS d 66 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 61 " (corrupted residue). Skipping it. outliers start: 99 outliers final: 49 residues processed: 641 average time/residue: 1.2175 time to fit residues: 1333.9909 Evaluate side-chains 587 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 538 time to evaluate : 4.983 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ARG B 203 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TRP F 132 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYS e 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS L 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL Q 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU S 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR c 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS d 66 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 61 " (corrupted residue). Skipping it. outliers start: 49 outliers final: 10 residues processed: 49 average time/residue: 1.0108 time to fit residues: 95.8283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 706 optimal weight: 10.0000 chunk 481 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 631 optimal weight: 10.0000 chunk 350 optimal weight: 8.9990 chunk 724 optimal weight: 10.0000 chunk 586 optimal weight: 5.9990 chunk 1 optimal weight: 50.0000 chunk 433 optimal weight: 9.9990 chunk 761 optimal weight: 10.0000 chunk 214 optimal weight: 50.0000 overall best weight: 6.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 50 GLN ** D 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 GLN ** 1 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 128 GLN ** J 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 ASN ** L 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 119 GLN ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 70 ASN Q 73 ASN S 37 GLN ** Z 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 5 GLN ** k 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4501 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 136844 Z= 0.258 Angle : 0.648 8.990 205973 Z= 0.333 Chirality : 0.039 0.359 26701 Planarity : 0.004 0.058 10352 Dihedral : 20.571 178.949 56021 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.68 % Favored : 87.15 % Rotamer Outliers : 3.21 % 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: -4.02 (0.11), residues: 4653 helix: -1.71 (0.16), residues: 1057 sheet: -2.28 (0.19), residues: 650 loop : -3.33 (0.10), residues: 2946 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9306 Ramachandran restraints generated. 4653 Oldfield, 0 Emsley, 4653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9306 Ramachandran restraints generated. 4653 Oldfield, 0 Emsley, 4653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 550 time to evaluate : 5.231 Fit side-chains TARDY: cannot create tardy model for: "ARG B 203 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TRP F 132 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS e 216 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU N 122 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL Q 122 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU S 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR c 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS d 66 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 61 " (corrupted residue). Skipping it. outliers start: 103 outliers final: 64 residues processed: 614 average time/residue: 1.1592 time to fit residues: 1215.3640 Evaluate side-chains 589 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 525 time to evaluate : 6.649 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ARG B 203 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TRP F 132 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYS e 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS L 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL Q 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU S 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR c 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS d 66 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 61 " (corrupted residue). Skipping it. outliers start: 64 outliers final: 10 residues processed: 64 average time/residue: 0.9451 time to fit residues: 118.0085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 285 optimal weight: 50.0000 chunk 764 optimal weight: 10.0000 chunk 167 optimal weight: 50.0000 chunk 498 optimal weight: 0.9990 chunk 209 optimal weight: 80.0000 chunk 849 optimal weight: 10.0000 chunk 705 optimal weight: 10.0000 chunk 393 optimal weight: 8.9990 chunk 70 optimal weight: 30.0000 chunk 281 optimal weight: 50.0000 chunk 445 optimal weight: 4.9990 overall best weight: 6.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 50 GLN ** D 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 42 GLN ** 6 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 73 ASN ** R 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 5 GLN ** k 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4498 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 136844 Z= 0.253 Angle : 0.644 13.415 205973 Z= 0.330 Chirality : 0.038 0.345 26701 Planarity : 0.005 0.089 10352 Dihedral : 20.455 179.403 56021 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.22 % Favored : 88.61 % Rotamer Outliers : 3.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -3.80 (0.11), residues: 4653 helix: -1.51 (0.16), residues: 1063 sheet: -2.20 (0.19), residues: 629 loop : -3.18 (0.10), residues: 2961 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9306 Ramachandran restraints generated. 4653 Oldfield, 0 Emsley, 4653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9306 Ramachandran restraints generated. 4653 Oldfield, 0 Emsley, 4653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 538 time to evaluate : 5.076 Fit side-chains TARDY: cannot create tardy model for: "ARG B 203 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TRP F 132 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS e 216 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU N 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL Q 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU S 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR c 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS d 66 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 61 " (corrupted residue). Skipping it. outliers start: 107 outliers final: 60 residues processed: 605 average time/residue: 1.1457 time to fit residues: 1183.7504 Evaluate side-chains 573 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 513 time to evaluate : 5.070 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ARG B 203 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TRP F 132 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYS e 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS L 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL Q 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU S 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR c 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS d 66 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 61 " (corrupted residue). Skipping it. outliers start: 60 outliers final: 10 residues processed: 60 average time/residue: 0.9430 time to fit residues: 109.5061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 819 optimal weight: 50.0000 chunk 95 optimal weight: 50.0000 chunk 484 optimal weight: 7.9990 chunk 620 optimal weight: 20.0000 chunk 480 optimal weight: 9.9990 chunk 715 optimal weight: 10.0000 chunk 474 optimal weight: 3.9990 chunk 846 optimal weight: 10.0000 chunk 529 optimal weight: 5.9990 chunk 515 optimal weight: 9.9990 chunk 390 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 HIS F 31 ASN ** 1 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 ASN ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 73 ASN ** R 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 5 GLN ** k 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4500 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 136844 Z= 0.249 Angle : 0.633 10.299 205973 Z= 0.324 Chirality : 0.038 0.355 26701 Planarity : 0.004 0.057 10352 Dihedral : 20.375 179.773 56021 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.91 % Favored : 87.92 % Rotamer Outliers : 1.71 % 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: -3.66 (0.11), residues: 4653 helix: -1.34 (0.16), residues: 1068 sheet: -2.06 (0.19), residues: 641 loop : -3.13 (0.10), residues: 2944 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9306 Ramachandran restraints generated. 4653 Oldfield, 0 Emsley, 4653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9306 Ramachandran restraints generated. 4653 Oldfield, 0 Emsley, 4653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 533 time to evaluate : 5.162 Fit side-chains TARDY: cannot create tardy model for: "ARG B 203 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TRP F 132 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS e 216 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL Q 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU S 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR c 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS d 66 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 61 " (corrupted residue). Skipping it. outliers start: 55 outliers final: 39 residues processed: 569 average time/residue: 1.1469 time to fit residues: 1110.9697 Evaluate side-chains 552 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 513 time to evaluate : 5.002 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "TRP F 132 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYS e 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS L 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL Q 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU S 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR c 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS d 66 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 61 " (corrupted residue). Skipping it. outliers start: 39 outliers final: 9 residues processed: 39 average time/residue: 0.9259 time to fit residues: 72.6873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 523 optimal weight: 9.9990 chunk 337 optimal weight: 50.0000 chunk 505 optimal weight: 7.9990 chunk 254 optimal weight: 50.0000 chunk 166 optimal weight: 10.0000 chunk 163 optimal weight: 20.0000 chunk 538 optimal weight: 3.9990 chunk 576 optimal weight: 0.7980 chunk 418 optimal weight: 30.0000 chunk 78 optimal weight: 9.9990 chunk 665 optimal weight: 10.0000 overall best weight: 6.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 15 ASN ** 6 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 148 GLN ** L 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 HIS ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 73 ASN ** Z 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 38 ASN ** k 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4495 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 136844 Z= 0.239 Angle : 0.626 12.041 205973 Z= 0.320 Chirality : 0.037 0.438 26701 Planarity : 0.004 0.097 10352 Dihedral : 20.281 179.782 56021 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.81 % Favored : 89.02 % Rotamer Outliers : 1.65 % 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: -3.53 (0.11), residues: 4653 helix: -1.22 (0.16), residues: 1070 sheet: -2.08 (0.19), residues: 650 loop : -3.02 (0.10), residues: 2933 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9306 Ramachandran restraints generated. 4653 Oldfield, 0 Emsley, 4653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9306 Ramachandran restraints generated. 4653 Oldfield, 0 Emsley, 4653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 534 time to evaluate : 5.015 Fit side-chains TARDY: cannot create tardy model for: "ARG B 203 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TRP F 132 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS e 216 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 175 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL Q 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU S 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR c 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS d 66 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 61 " (corrupted residue). Skipping it. outliers start: 53 outliers final: 31 residues processed: 570 average time/residue: 1.1416 time to fit residues: 1106.5171 Evaluate side-chains 550 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 519 time to evaluate : 4.957 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "TRP F 132 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYS e 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS L 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL Q 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU S 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR c 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS d 66 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 61 " (corrupted residue). Skipping it. outliers start: 31 outliers final: 9 residues processed: 31 average time/residue: 0.8970 time to fit residues: 57.1472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 769 optimal weight: 20.0000 chunk 810 optimal weight: 30.0000 chunk 739 optimal weight: 10.0000 chunk 788 optimal weight: 50.0000 chunk 474 optimal weight: 4.9990 chunk 343 optimal weight: 50.0000 chunk 619 optimal weight: 30.0000 chunk 242 optimal weight: 50.0000 chunk 712 optimal weight: 50.0000 chunk 745 optimal weight: 50.0000 chunk 785 optimal weight: 50.0000 overall best weight: 18.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 40 ASN ** 5 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 GLN M 41 ASN M 136 GLN ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 73 ASN ** R 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4648 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.112 136844 Z= 0.642 Angle : 0.912 12.187 205973 Z= 0.447 Chirality : 0.051 0.388 26701 Planarity : 0.006 0.058 10352 Dihedral : 20.891 179.892 56021 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 25.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 14.46 % Favored : 85.36 % Rotamer Outliers : 1.65 % 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: -3.89 (0.11), residues: 4653 helix: -1.70 (0.15), residues: 1065 sheet: -2.33 (0.19), residues: 650 loop : -3.17 (0.10), residues: 2938 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9306 Ramachandran restraints generated. 4653 Oldfield, 0 Emsley, 4653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9306 Ramachandran restraints generated. 4653 Oldfield, 0 Emsley, 4653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 498 time to evaluate : 5.105 Fit side-chains TARDY: cannot create tardy model for: "ARG B 203 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TRP F 132 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS e 216 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 175 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL Q 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU S 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR c 60 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYS d 66 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 61 " (corrupted residue). Skipping it. outliers start: 53 outliers final: 36 residues processed: 529 average time/residue: 1.1475 time to fit residues: 1028.1406 Evaluate side-chains 518 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 482 time to evaluate : 4.977 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "TRP F 132 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYS e 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS L 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL Q 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU S 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR c 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS d 66 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 61 " (corrupted residue). Skipping it. outliers start: 36 outliers final: 9 residues processed: 36 average time/residue: 0.9228 time to fit residues: 66.7659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 517 optimal weight: 0.7980 chunk 833 optimal weight: 0.9980 chunk 508 optimal weight: 5.9990 chunk 395 optimal weight: 30.0000 chunk 579 optimal weight: 0.9990 chunk 874 optimal weight: 8.9990 chunk 805 optimal weight: 30.0000 chunk 696 optimal weight: 30.0000 chunk 72 optimal weight: 6.9990 chunk 538 optimal weight: 0.7980 chunk 427 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 54 GLN Q 73 ASN ** R 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 52 GLN W 54 ASN ** Z 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 38 ASN k 29 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4453 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.055 136844 Z= 0.150 Angle : 0.642 13.430 205973 Z= 0.326 Chirality : 0.036 0.295 26701 Planarity : 0.004 0.056 10352 Dihedral : 20.323 179.225 56021 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.25 % Favored : 89.58 % Rotamer Outliers : 0.72 % 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: -3.45 (0.11), residues: 4653 helix: -1.21 (0.16), residues: 1068 sheet: -1.90 (0.20), residues: 645 loop : -2.99 (0.10), residues: 2940 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9306 Ramachandran restraints generated. 4653 Oldfield, 0 Emsley, 4653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9306 Ramachandran restraints generated. 4653 Oldfield, 0 Emsley, 4653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 558 time to evaluate : 5.005 Fit side-chains TARDY: cannot create tardy model for: "ARG B 203 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TRP F 132 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS e 216 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 175 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL Q 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU S 117 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THR c 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS d 66 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 61 " (corrupted residue). Skipping it. outliers start: 23 outliers final: 15 residues processed: 573 average time/residue: 1.2774 time to fit residues: 1238.5721 Evaluate side-chains 542 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 527 time to evaluate : 4.969 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "TRP F 132 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYS e 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS L 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL Q 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU S 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR c 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS d 66 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 61 " (corrupted residue). Skipping it. outliers start: 15 outliers final: 9 residues processed: 15 average time/residue: 1.0288 time to fit residues: 31.9838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 553 optimal weight: 9.9990 chunk 741 optimal weight: 20.0000 chunk 213 optimal weight: 50.0000 chunk 642 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 chunk 193 optimal weight: 10.0000 chunk 697 optimal weight: 50.0000 chunk 291 optimal weight: 60.0000 chunk 716 optimal weight: 10.0000 chunk 88 optimal weight: 50.0000 chunk 128 optimal weight: 10.0000 overall best weight: 11.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 104 ASN ** P 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 73 ASN ** R 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 52 GLN W 54 ASN ** Z 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.118985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.072577 restraints weight = 543557.705| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 3.37 r_work: 0.2857 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.5097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.068 136844 Z= 0.409 Angle : 0.721 12.881 205973 Z= 0.363 Chirality : 0.042 0.335 26701 Planarity : 0.005 0.068 10352 Dihedral : 20.455 179.938 56021 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 13.00 % Favored : 86.89 % 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: -3.51 (0.11), residues: 4653 helix: -1.29 (0.16), residues: 1069 sheet: -2.02 (0.19), residues: 631 loop : -2.98 (0.10), residues: 2953 =============================================================================== Job complete usr+sys time: 26793.49 seconds wall clock time: 470 minutes 30.58 seconds (28230.58 seconds total)