Starting phenix.real_space_refine on Fri Mar 15 04:22:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aso_11902/03_2024/7aso_11902.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aso_11902/03_2024/7aso_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_11902/03_2024/7aso_11902.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aso_11902/03_2024/7aso_11902.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aso_11902/03_2024/7aso_11902.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aso_11902/03_2024/7aso_11902.pdb" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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-dev-5265/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: 27 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: 46.45, 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: 43.15 Conformation dependent library (CDL) restraints added in 5.9 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: 32.61 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: 110.70 Time building geometry restraints manager: 47.35 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: 73763 35.98 - 71.96: 11723 71.96 - 107.94: 1458 107.94 - 143.92: 142 143.92 - 179.90: 68 Dihedral angle restraints: 87154 sinusoidal: 73628 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 87151 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: 3.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 18.670 Check model and map are aligned: 1.330 Set scattering table: 0.830 Process input model: 313.130 Find NCS groups from input model: 2.120 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 342.100 ------------------------------------------------------------------------------- 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 : 27.009 179.898 78410 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 % Allowed : 13.28 % Favored : 73.21 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP 2 44 HIS 0.024 0.002 HIS B 33 PHE 0.056 0.002 PHE 2 27 TYR 0.050 0.003 TYR 4 63 ARG 0.020 0.001 ARG E 88 *********************** 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 : 4.960 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. REVERT: B 151 GLN cc_start: 0.1032 (OUTLIER) cc_final: 0.0677 (pm20) REVERT: E 13 ASN cc_start: 0.2839 (OUTLIER) cc_final: 0.2081 (m-40) REVERT: E 90 MET cc_start: 0.1805 (mpp) cc_final: 0.0533 (mmt) REVERT: G 4 LYS cc_start: 0.0113 (OUTLIER) cc_final: -0.0258 (ptpp) REVERT: G 30 ILE cc_start: 0.1708 (OUTLIER) cc_final: 0.1036 (pt) REVERT: G 84 ASN cc_start: 0.4658 (OUTLIER) cc_final: 0.4258 (m110) REVERT: G 117 GLU cc_start: 0.2191 (OUTLIER) cc_final: 0.1411 (tm-30) REVERT: G 126 ASP cc_start: 0.2845 (OUTLIER) cc_final: 0.1826 (p0) REVERT: F 19 MET cc_start: -0.0460 (OUTLIER) cc_final: -0.1412 (mtm) REVERT: F 108 THR cc_start: -0.0965 (OUTLIER) cc_final: -0.1198 (t) REVERT: H 121 LYS cc_start: 0.1966 (OUTLIER) cc_final: 0.0891 (tttm) REVERT: 3 63 ARG cc_start: 0.3081 (ptt-90) cc_final: 0.2386 (ptp90) REVERT: 3 107 ARG cc_start: 0.3019 (mmt180) cc_final: 0.2537 (mtt90) REVERT: 4 90 ARG cc_start: 0.1737 (OUTLIER) cc_final: -0.0075 (tpt170) REVERT: 5 38 LYS cc_start: 0.1725 (OUTLIER) cc_final: 0.1385 (mmtt) REVERT: 6 59 MET cc_start: -0.0353 (ptt) cc_final: -0.1335 (ptp) REVERT: 9 34 LEU cc_start: 0.0895 (OUTLIER) cc_final: 0.0358 (mm) REVERT: 9 37 PHE cc_start: 0.0670 (OUTLIER) cc_final: -0.1508 (m-80) REVERT: 9 43 LYS cc_start: 0.1197 (OUTLIER) cc_final: 0.0406 (mtpt) REVERT: 9 44 ILE cc_start: -0.1274 (OUTLIER) cc_final: -0.1922 (mt) REVERT: 9 48 ARG cc_start: 0.3746 (OUTLIER) cc_final: 0.2903 (mtt180) REVERT: 9 59 MET cc_start: 0.1824 (ptp) cc_final: 0.0952 (mmp) REVERT: I 81 LYS cc_start: 0.1732 (OUTLIER) cc_final: -0.0786 (mttp) REVERT: A 16 LYS cc_start: 0.1117 (ptpt) cc_final: 0.0808 (mttt) REVERT: A 25 LYS cc_start: 0.4780 (mtpt) cc_final: 0.3818 (mtpp) REVERT: J 54 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7800 (ttt180) REVERT: J 137 LYS cc_start: 0.5771 (OUTLIER) cc_final: 0.4525 (tppt) REVERT: L 160 LYS cc_start: 0.0505 (pttt) cc_final: 0.0050 (pttt) REVERT: M 123 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6926 (tp) REVERT: N 71 ARG cc_start: 0.6792 (OUTLIER) cc_final: 0.6136 (mtt90) REVERT: V 51 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7708 (tp) REVERT: W 48 VAL cc_start: 0.5841 (OUTLIER) cc_final: 0.5624 (t) REVERT: W 83 LYS cc_start: 0.6126 (OUTLIER) cc_final: 0.5879 (pttm) REVERT: g 37 LYS cc_start: 0.0134 (OUTLIER) cc_final: -0.1082 (pttm) outliers start: 433 outliers final: 142 residues processed: 1059 average time/residue: 1.2047 time to fit residues: 2090.1592 Evaluate side-chains 769 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 601 time to evaluate : 4.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 151 GLN Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 203 ARG Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 71 LYS Chi-restraints excluded: chain G residue 4 LYS Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 67 ASN Chi-restraints excluded: chain G residue 84 ASN Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain F residue 19 MET Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 132 TRP Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 121 LYS Chi-restraints excluded: chain 1 residue 68 ARG Chi-restraints excluded: chain 2 residue 59 THR Chi-restraints excluded: chain 4 residue 90 ARG Chi-restraints excluded: chain 4 residue 92 ARG Chi-restraints excluded: chain 5 residue 24 CYS Chi-restraints excluded: chain 5 residue 38 LYS Chi-restraints excluded: chain 7 residue 3 VAL Chi-restraints excluded: chain 7 residue 10 LEU Chi-restraints excluded: chain 7 residue 32 ARG Chi-restraints excluded: chain 7 residue 80 ILE Chi-restraints excluded: chain 9 residue 34 LEU Chi-restraints excluded: chain 9 residue 37 PHE Chi-restraints excluded: chain 9 residue 43 LYS Chi-restraints excluded: chain 9 residue 44 ILE Chi-restraints excluded: chain 9 residue 45 LEU Chi-restraints excluded: chain 9 residue 48 ARG Chi-restraints excluded: chain 9 residue 49 VAL Chi-restraints excluded: chain 9 residue 53 SER Chi-restraints excluded: chain 9 residue 64 ILE Chi-restraints excluded: chain I residue 81 LYS Chi-restraints excluded: chain e residue 2 THR Chi-restraints excluded: chain e residue 55 ASP Chi-restraints excluded: chain e residue 70 ASN Chi-restraints excluded: chain e residue 93 ASN Chi-restraints excluded: chain e residue 176 ASN Chi-restraints excluded: chain e residue 177 THR Chi-restraints excluded: chain e residue 180 VAL Chi-restraints excluded: chain e residue 183 LEU Chi-restraints excluded: chain e residue 216 LYS Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 21 ASP Chi-restraints excluded: chain J residue 41 ARG Chi-restraints excluded: chain J residue 54 ARG Chi-restraints excluded: chain J residue 58 SER Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 192 LEU Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 55 GLU Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain L residue 175 LYS Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 19 ILE Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 45 TYR Chi-restraints excluded: chain M residue 54 TYR Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 65 PHE Chi-restraints excluded: chain M residue 85 ILE Chi-restraints excluded: chain M residue 93 LEU Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain M residue 130 GLU Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 71 ARG Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain O residue 17 ASN Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 33 ARG Chi-restraints excluded: chain O residue 38 GLN Chi-restraints excluded: chain O residue 60 ARG Chi-restraints excluded: chain O residue 95 LEU Chi-restraints excluded: chain O residue 121 LEU Chi-restraints excluded: chain O residue 128 PHE Chi-restraints excluded: chain P residue 3 LEU Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain Q residue 4 ARG Chi-restraints excluded: chain Q residue 8 ARG Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 112 ASP Chi-restraints excluded: chain Q residue 116 SER Chi-restraints excluded: chain Q residue 118 ILE Chi-restraints excluded: chain Q residue 122 VAL Chi-restraints excluded: chain R residue 89 ILE Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 25 PHE Chi-restraints excluded: chain S residue 33 LYS Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 41 LYS Chi-restraints excluded: chain S residue 93 LYS Chi-restraints excluded: chain S residue 97 GLU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain U residue 6 GLU Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain U residue 77 LYS Chi-restraints excluded: chain U residue 80 LYS Chi-restraints excluded: chain U residue 99 LYS Chi-restraints excluded: chain V residue 9 THR Chi-restraints excluded: chain V residue 33 ILE Chi-restraints excluded: chain V residue 37 LYS Chi-restraints excluded: chain V residue 41 LYS Chi-restraints excluded: chain V residue 51 LEU Chi-restraints excluded: chain V residue 99 ARG Chi-restraints excluded: chain V residue 107 VAL Chi-restraints excluded: chain W residue 5 ASP Chi-restraints excluded: chain W residue 26 THR Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain W residue 45 ILE Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 65 MET Chi-restraints excluded: chain W residue 68 TYR Chi-restraints excluded: chain W residue 73 ASN Chi-restraints excluded: chain W residue 75 ARG Chi-restraints excluded: chain W residue 82 LEU Chi-restraints excluded: chain W residue 83 LYS Chi-restraints excluded: chain b residue 44 ILE Chi-restraints excluded: chain c residue 60 THR Chi-restraints excluded: chain d residue 66 LYS Chi-restraints excluded: chain f residue 6 ILE Chi-restraints excluded: chain f residue 11 SER Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 15 ARG Chi-restraints excluded: chain f residue 51 LYS Chi-restraints excluded: chain g residue 23 SER Chi-restraints excluded: chain g residue 37 LYS Chi-restraints excluded: chain T residue 9 CYS Chi-restraints excluded: chain T residue 15 ARG Chi-restraints excluded: chain T residue 21 LYS Chi-restraints excluded: chain T residue 33 LYS Chi-restraints excluded: chain T residue 36 CYS Chi-restraints excluded: chain T residue 41 LYS Chi-restraints excluded: chain i residue 2 VAL Chi-restraints excluded: chain i residue 15 LYS Chi-restraints excluded: chain i residue 31 VAL Chi-restraints excluded: chain j residue 61 LEU Chi-restraints excluded: chain h residue 5 ILE Chi-restraints excluded: chain h residue 6 HIS 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: 20.0000 chunk 227 optimal weight: 50.0000 chunk 448 optimal weight: 8.9990 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: 7.7994 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 ASN G 122 ASN F 99 ASN 1 15 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 ** k 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4445 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 136844 Z= 0.308 Angle : 0.737 10.770 205973 Z= 0.383 Chirality : 0.041 0.356 26701 Planarity : 0.005 0.075 10352 Dihedral : 26.459 179.184 71215 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.32 % Allowed : 15.13 % Favored : 84.55 % Rotamer: Outliers : 5.58 % Allowed : 23.32 % Favored : 71.09 % 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: -5.16 (0.10), residues: 4653 helix: -3.08 (0.13), residues: 1021 sheet: -2.90 (0.19), residues: 572 loop : -3.93 (0.09), residues: 3060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP c 48 HIS 0.015 0.002 HIS 1 15 PHE 0.017 0.002 PHE a 79 TYR 0.030 0.002 TYR 3 108 ARG 0.009 0.001 ARG j 24 *********************** 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 792 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 613 time to evaluate : 4.759 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: "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 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 REVERT: E 62 ILE cc_start: 0.5384 (mp) cc_final: 0.5149 (mp) REVERT: E 90 MET cc_start: 0.1922 (mpp) cc_final: 0.0470 (mmt) REVERT: F 19 MET cc_start: -0.0427 (OUTLIER) cc_final: -0.3107 (ptt) REVERT: F 23 GLU cc_start: 0.3407 (tp30) cc_final: 0.2996 (mm-30) REVERT: H 121 LYS cc_start: 0.2455 (mmtt) cc_final: 0.1549 (tttp) REVERT: 3 63 ARG cc_start: 0.2924 (ptt-90) cc_final: 0.2028 (ttm110) REVERT: 3 107 ARG cc_start: 0.2674 (mmt180) cc_final: 0.2270 (mtt90) REVERT: 5 38 LYS cc_start: 0.1539 (OUTLIER) cc_final: 0.1263 (mmtt) REVERT: 7 81 MET cc_start: 0.2361 (mtm) cc_final: 0.2104 (mtm) REVERT: 9 37 PHE cc_start: -0.0013 (OUTLIER) cc_final: -0.0759 (m-80) REVERT: 9 59 MET cc_start: 0.1922 (ptp) cc_final: 0.1162 (mmp) REVERT: A 16 LYS cc_start: 0.0955 (ptpt) cc_final: 0.0592 (mttt) REVERT: A 25 LYS cc_start: 0.4692 (mtpt) cc_final: 0.3754 (mtpp) REVERT: L 163 ARG cc_start: 0.4960 (ptm-80) cc_final: 0.4648 (ptt90) REVERT: L 172 LYS cc_start: 0.3144 (mmmt) cc_final: 0.2821 (mmmt) REVERT: W 48 VAL cc_start: 0.5810 (OUTLIER) cc_final: 0.5392 (m) REVERT: a 46 VAL cc_start: 0.3373 (t) cc_final: 0.3021 (m) REVERT: g 36 TYR cc_start: 0.2603 (OUTLIER) cc_final: 0.2348 (t80) REVERT: g 37 LYS cc_start: -0.0014 (OUTLIER) cc_final: -0.3064 (pttt) outliers start: 179 outliers final: 119 residues processed: 736 average time/residue: 1.1501 time to fit residues: 1447.3303 Evaluate side-chains 676 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 551 time to evaluate : 4.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain l residue 100 SER Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 67 ASN Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 148 ASN Chi-restraints excluded: chain F residue 19 MET Chi-restraints excluded: chain F residue 132 TRP Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 49 ASP Chi-restraints excluded: chain 4 residue 92 ARG Chi-restraints excluded: chain 5 residue 24 CYS Chi-restraints excluded: chain 5 residue 38 LYS Chi-restraints excluded: chain 7 residue 3 VAL Chi-restraints excluded: chain 7 residue 10 LEU Chi-restraints excluded: chain 7 residue 33 ILE Chi-restraints excluded: chain 7 residue 34 ILE Chi-restraints excluded: chain 9 residue 37 PHE Chi-restraints excluded: chain 9 residue 38 ILE Chi-restraints excluded: chain 9 residue 45 LEU Chi-restraints excluded: chain 9 residue 49 VAL Chi-restraints excluded: chain e residue 41 VAL Chi-restraints excluded: chain e residue 55 ASP Chi-restraints excluded: chain e residue 176 ASN Chi-restraints excluded: chain e residue 180 VAL Chi-restraints excluded: chain e residue 215 ILE Chi-restraints excluded: chain e residue 216 LYS Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 21 ASP Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 185 ASP Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 194 ILE Chi-restraints excluded: chain K residue 55 GLU Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 158 LYS Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 65 PHE Chi-restraints excluded: chain M residue 80 ASN Chi-restraints excluded: chain M residue 93 LEU Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain N residue 5 GLU Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 60 ARG Chi-restraints excluded: chain O residue 116 SER Chi-restraints excluded: chain O residue 121 LEU Chi-restraints excluded: chain O residue 128 PHE Chi-restraints excluded: chain P residue 3 LEU Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 40 SER Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain Q residue 32 THR Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 112 ASP Chi-restraints excluded: chain Q residue 122 VAL Chi-restraints excluded: chain R residue 21 ASN Chi-restraints excluded: chain R residue 32 ASN Chi-restraints excluded: chain R residue 89 ILE Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 33 LYS Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain U residue 14 VAL Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain V residue 9 THR Chi-restraints excluded: chain V residue 39 THR Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain V residue 106 VAL Chi-restraints excluded: chain W residue 5 ASP Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 72 THR Chi-restraints excluded: chain W residue 73 ASN Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 82 LEU Chi-restraints excluded: chain Z residue 31 ASP Chi-restraints excluded: chain Z residue 39 ASN Chi-restraints excluded: chain Z residue 93 ILE Chi-restraints excluded: chain a residue 55 VAL Chi-restraints excluded: chain a residue 90 ASP Chi-restraints excluded: chain b residue 51 THR Chi-restraints excluded: chain c residue 45 LYS Chi-restraints excluded: chain c residue 60 THR Chi-restraints excluded: chain d residue 66 LYS Chi-restraints excluded: chain f residue 5 GLN Chi-restraints excluded: chain f residue 6 ILE Chi-restraints excluded: chain f residue 11 SER Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 15 ARG Chi-restraints excluded: chain f residue 18 THR Chi-restraints excluded: chain f residue 56 VAL Chi-restraints excluded: chain g residue 36 TYR Chi-restraints excluded: chain g residue 37 LYS Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain T residue 9 CYS Chi-restraints excluded: chain T residue 21 LYS Chi-restraints excluded: chain T residue 41 LYS Chi-restraints excluded: chain i residue 26 LYS Chi-restraints excluded: chain i residue 31 VAL Chi-restraints excluded: chain j residue 41 LYS Chi-restraints excluded: chain j residue 61 LEU Chi-restraints excluded: chain h residue 5 ILE Chi-restraints excluded: chain h residue 6 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 443 optimal weight: 7.9990 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: 13.5998 ------------------------------------------------------------------------------- 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** D 135 ASN D 145 GLN ** F 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** L 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 70 ASN Q 73 ASN S 44 GLN ** 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 c 23 ASN f 5 GLN ** 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4567 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.120 136844 Z= 0.473 Angle : 0.816 10.499 205973 Z= 0.413 Chirality : 0.046 0.361 26701 Planarity : 0.006 0.064 10352 Dihedral : 26.458 178.049 70954 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.24 % Allowed : 15.58 % Favored : 84.18 % Rotamer: Outliers : 7.64 % Allowed : 24.82 % Favored : 67.54 % 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: -4.72 (0.10), residues: 4653 helix: -2.55 (0.14), residues: 1036 sheet: -2.64 (0.18), residues: 600 loop : -3.70 (0.09), residues: 3017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP 2 44 HIS 0.013 0.002 HIS L 111 PHE 0.028 0.002 PHE d 26 TYR 0.026 0.002 TYR 4 63 ARG 0.015 0.001 ARG 9 68 *********************** 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 799 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 554 time to evaluate : 4.820 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 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: "LEU N 122 " (corrupted residue). Skipping it. revert: symmetry clash 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 TARDY: cannot create tardy model for: "LEU j 61 " (corrupted residue). Skipping it. REVERT: E 7 MET cc_start: 0.1190 (tmm) cc_final: 0.0579 (tmm) REVERT: E 62 ILE cc_start: 0.5200 (OUTLIER) cc_final: 0.4895 (mp) REVERT: G 63 GLU cc_start: 0.3631 (tp30) cc_final: 0.1981 (mm-30) REVERT: F 23 GLU cc_start: 0.3279 (tp30) cc_final: 0.2899 (mm-30) REVERT: 3 63 ARG cc_start: 0.2860 (ptt-90) cc_final: 0.2126 (ttm110) REVERT: 3 107 ARG cc_start: 0.2628 (mmt180) cc_final: 0.2092 (mtt90) REVERT: 5 45 ARG cc_start: -0.0953 (OUTLIER) cc_final: -0.2028 (ttm110) REVERT: 6 59 MET cc_start: -0.0641 (ptt) cc_final: -0.0926 (mtp) REVERT: 9 59 MET cc_start: 0.1696 (ptp) cc_final: 0.1111 (mmp) REVERT: A 16 LYS cc_start: 0.0915 (ptpt) cc_final: 0.0541 (mttt) REVERT: A 25 LYS cc_start: 0.4634 (mtpt) cc_final: 0.3281 (mmtt) REVERT: A 33 LYS cc_start: -0.0212 (ttmt) cc_final: -0.1417 (tttm) REVERT: L 163 ARG cc_start: 0.5153 (ptm-80) cc_final: 0.4909 (ptt90) REVERT: M 50 ASP cc_start: 0.6758 (t70) cc_final: 0.6429 (t0) REVERT: M 123 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6993 (tp) REVERT: P 22 LYS cc_start: 0.5415 (OUTLIER) cc_final: 0.4277 (mttt) REVERT: b 49 ARG cc_start: 0.7477 (mmp80) cc_final: 0.7271 (mmp80) REVERT: k 1 MET cc_start: 0.2498 (pmm) cc_final: 0.2075 (mmt) outliers start: 245 outliers final: 165 residues processed: 732 average time/residue: 1.1195 time to fit residues: 1405.1208 Evaluate side-chains 683 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 514 time to evaluate : 4.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain l residue 60 LEU Chi-restraints excluded: chain l residue 100 SER Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 129 ASN Chi-restraints excluded: chain G residue 148 ASN Chi-restraints excluded: chain F residue 132 TRP Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain 2 residue 59 THR Chi-restraints excluded: chain 4 residue 22 ILE Chi-restraints excluded: chain 5 residue 24 CYS Chi-restraints excluded: chain 5 residue 39 LEU Chi-restraints excluded: chain 5 residue 45 ARG Chi-restraints excluded: chain 7 residue 33 ILE Chi-restraints excluded: chain 7 residue 34 ILE Chi-restraints excluded: chain 8 residue 24 THR Chi-restraints excluded: chain 9 residue 38 ILE Chi-restraints excluded: chain 9 residue 45 LEU Chi-restraints excluded: chain 9 residue 49 VAL Chi-restraints excluded: chain 9 residue 53 SER Chi-restraints excluded: chain e residue 13 THR Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain e residue 55 ASP Chi-restraints excluded: chain e residue 65 SER Chi-restraints excluded: chain e residue 101 VAL Chi-restraints excluded: chain e residue 108 ASP Chi-restraints excluded: chain e residue 158 SER Chi-restraints excluded: chain e residue 176 ASN Chi-restraints excluded: chain e residue 177 THR Chi-restraints excluded: chain e residue 180 VAL Chi-restraints excluded: chain e residue 216 LYS Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 21 ASP Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain J residue 115 SER Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 182 ASN Chi-restraints excluded: chain J residue 185 ASP Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 194 ILE Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 55 GLU Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 158 LYS Chi-restraints excluded: chain L residue 169 VAL Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 80 ASN Chi-restraints excluded: chain M residue 85 ILE Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain M residue 105 SER Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain N residue 5 GLU Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain O residue 17 ASN Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 60 ARG Chi-restraints excluded: chain O residue 70 ASN Chi-restraints excluded: chain O residue 71 ARG Chi-restraints excluded: chain O residue 101 VAL Chi-restraints excluded: chain O residue 116 SER Chi-restraints excluded: chain O residue 121 LEU Chi-restraints excluded: chain O residue 128 PHE Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 22 LYS Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 39 THR Chi-restraints excluded: chain P residue 40 SER Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain Q residue 32 THR Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 112 ASP Chi-restraints excluded: chain R residue 21 ASN Chi-restraints excluded: chain R residue 32 ASN Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain R residue 89 ILE Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 10 THR Chi-restraints excluded: chain S residue 11 ARG Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain U residue 6 GLU Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain V residue 17 VAL Chi-restraints excluded: chain V residue 39 THR Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain W residue 12 ILE Chi-restraints excluded: chain W residue 26 THR Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain W residue 50 VAL Chi-restraints excluded: chain W residue 68 TYR Chi-restraints excluded: chain W residue 72 THR Chi-restraints excluded: chain W residue 73 ASN Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 82 LEU Chi-restraints excluded: chain Z residue 31 ASP Chi-restraints excluded: chain Z residue 33 VAL Chi-restraints excluded: chain Z residue 39 ASN Chi-restraints excluded: chain Z residue 67 ASN Chi-restraints excluded: chain Z residue 93 ILE Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 90 ASP Chi-restraints excluded: chain b residue 26 SER Chi-restraints excluded: chain b residue 51 THR Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain c residue 45 LYS Chi-restraints excluded: chain d residue 66 LYS Chi-restraints excluded: chain f residue 6 ILE Chi-restraints excluded: chain f residue 11 SER Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 15 ARG Chi-restraints excluded: chain f residue 18 THR Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 56 VAL Chi-restraints excluded: chain g residue 23 SER Chi-restraints excluded: chain g residue 24 VAL Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain T residue 9 CYS Chi-restraints excluded: chain T residue 10 THR Chi-restraints excluded: chain T residue 12 CYS Chi-restraints excluded: chain T residue 26 ASN Chi-restraints excluded: chain i residue 17 HIS Chi-restraints excluded: chain i residue 26 LYS Chi-restraints excluded: chain i residue 31 VAL Chi-restraints excluded: chain j residue 6 THR Chi-restraints excluded: chain j residue 25 SER Chi-restraints excluded: chain j residue 58 VAL Chi-restraints excluded: chain j residue 61 LEU Chi-restraints excluded: chain k residue 3 VAL Chi-restraints excluded: chain h residue 5 ILE Chi-restraints excluded: chain h residue 6 HIS 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: 50.0000 chunk 414 optimal weight: 0.5980 chunk 88 optimal weight: 30.0000 chunk 381 optimal weight: 9.9990 chunk 536 optimal weight: 20.0000 chunk 801 optimal weight: 0.8980 chunk 848 optimal weight: 10.0000 chunk 418 optimal weight: 30.0000 chunk 759 optimal weight: 8.9990 chunk 228 optimal weight: 50.0000 overall best weight: 6.0988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 56 HIS ** 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** ** L 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 73 ASN U 18 GLN ** Z 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 16 ASN g 32 ASN j 31 HIS ** k 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4484 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 136844 Z= 0.230 Angle : 0.663 9.510 205973 Z= 0.341 Chirality : 0.039 0.370 26701 Planarity : 0.004 0.062 10352 Dihedral : 26.262 179.906 70904 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.97 % Favored : 87.86 % Rotamer: Outliers : 5.77 % Allowed : 27.56 % Favored : 66.67 % 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: -4.30 (0.11), residues: 4653 helix: -2.04 (0.15), residues: 1041 sheet: -2.52 (0.18), residues: 653 loop : -3.46 (0.10), residues: 2959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP c 48 HIS 0.008 0.001 HIS 9 69 PHE 0.015 0.001 PHE J 139 TYR 0.021 0.001 TYR 4 63 ARG 0.008 0.001 ARG g 41 *********************** 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 753 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 568 time to evaluate : 4.792 Fit side-chains TARDY: cannot create tardy model for: "ARG B 203 " (corrupted residue). Skipping it. 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 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: "LEU N 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash 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 TARDY: cannot create tardy model for: "LEU j 61 " (corrupted residue). Skipping it. REVERT: E 7 MET cc_start: 0.1063 (tmm) cc_final: 0.0351 (tmm) REVERT: E 62 ILE cc_start: 0.5212 (mp) cc_final: 0.4931 (mp) REVERT: E 90 MET cc_start: 0.1281 (mmm) cc_final: 0.0979 (mmt) REVERT: G 139 GLU cc_start: 0.3289 (pt0) cc_final: 0.0336 (mm-30) REVERT: F 23 GLU cc_start: 0.3236 (tp30) cc_final: 0.2885 (mm-30) REVERT: F 80 ILE cc_start: 0.0638 (OUTLIER) cc_final: 0.0148 (pt) REVERT: 3 63 ARG cc_start: 0.2795 (ptt-90) cc_final: 0.2070 (ttm110) REVERT: 3 107 ARG cc_start: 0.2615 (mmt180) cc_final: 0.1953 (mtt90) REVERT: 9 59 MET cc_start: 0.1694 (ptp) cc_final: 0.1241 (mmp) REVERT: A 12 LYS cc_start: 0.0269 (ptpt) cc_final: -0.1719 (ptmt) REVERT: A 25 LYS cc_start: 0.4417 (mtpt) cc_final: 0.3096 (mmtt) REVERT: A 33 LYS cc_start: -0.0156 (ttmt) cc_final: -0.1413 (tttm) REVERT: A 36 LYS cc_start: 0.4740 (mmmt) cc_final: 0.2571 (pttm) REVERT: e 149 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.6709 (mtp85) REVERT: O 33 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7798 (mtt-85) REVERT: P 22 LYS cc_start: 0.5582 (OUTLIER) cc_final: 0.4429 (mttt) outliers start: 185 outliers final: 120 residues processed: 696 average time/residue: 1.1340 time to fit residues: 1356.4264 Evaluate side-chains 666 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 542 time to evaluate : 4.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 192 TYR Chi-restraints excluded: chain l residue 60 LEU Chi-restraints excluded: chain l residue 100 SER Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 129 ASN Chi-restraints excluded: chain G residue 148 ASN Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 132 TRP Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain 3 residue 8 VAL Chi-restraints excluded: chain 5 residue 24 CYS Chi-restraints excluded: chain 5 residue 39 LEU Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 7 residue 33 ILE Chi-restraints excluded: chain 7 residue 34 ILE Chi-restraints excluded: chain 8 residue 24 THR Chi-restraints excluded: chain 9 residue 49 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain e residue 55 ASP Chi-restraints excluded: chain e residue 65 SER Chi-restraints excluded: chain e residue 108 ASP Chi-restraints excluded: chain e residue 145 SER Chi-restraints excluded: chain e residue 149 ARG Chi-restraints excluded: chain e residue 176 ASN Chi-restraints excluded: chain e residue 180 VAL Chi-restraints excluded: chain e residue 200 ASN Chi-restraints excluded: chain e residue 216 LYS Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 182 ASN Chi-restraints excluded: chain J residue 185 ASP Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 55 GLU Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 158 LYS Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 65 PHE Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain M residue 93 LEU Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain M residue 105 SER Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 33 ARG Chi-restraints excluded: chain O residue 60 ARG Chi-restraints excluded: chain O residue 71 ARG Chi-restraints excluded: chain O residue 72 LYS Chi-restraints excluded: chain O residue 116 SER Chi-restraints excluded: chain O residue 121 LEU Chi-restraints excluded: chain O residue 128 PHE Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 22 LYS Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 40 SER Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain Q residue 32 THR Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain R residue 21 ASN Chi-restraints excluded: chain R residue 32 ASN Chi-restraints excluded: chain R residue 89 ILE Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain U residue 82 SER Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain W residue 26 THR Chi-restraints excluded: chain W residue 68 TYR Chi-restraints excluded: chain W residue 72 THR Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 82 LEU Chi-restraints excluded: chain Z residue 31 ASP Chi-restraints excluded: chain Z residue 93 ILE Chi-restraints excluded: chain a residue 55 VAL Chi-restraints excluded: chain b residue 51 THR Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain c residue 45 LYS Chi-restraints excluded: chain d residue 66 LYS Chi-restraints excluded: chain f residue 11 SER Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 15 ARG Chi-restraints excluded: chain f residue 18 THR Chi-restraints excluded: chain f residue 56 VAL Chi-restraints excluded: chain g residue 23 SER Chi-restraints excluded: chain g residue 24 VAL Chi-restraints excluded: chain g residue 36 TYR Chi-restraints excluded: chain T residue 9 CYS Chi-restraints excluded: chain T residue 43 THR Chi-restraints excluded: chain i residue 26 LYS Chi-restraints excluded: chain i residue 31 VAL Chi-restraints excluded: chain j residue 6 THR Chi-restraints excluded: chain j residue 25 SER Chi-restraints excluded: chain j residue 61 LEU Chi-restraints excluded: chain h residue 5 ILE Chi-restraints excluded: chain h residue 6 HIS 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: 5.9990 chunk 12 optimal weight: 20.0000 chunk 631 optimal weight: 10.0000 chunk 350 optimal weight: 7.9990 chunk 724 optimal weight: 10.0000 chunk 586 optimal weight: 10.0000 chunk 1 optimal weight: 50.0000 chunk 433 optimal weight: 10.0000 chunk 761 optimal weight: 10.0000 chunk 214 optimal weight: 50.0000 overall best weight: 8.7996 ------------------------------------------------------------------------------- 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 73 ASN e 128 GLN ** J 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 ASN ** 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 S 37 GLN S 52 GLN ** Z 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 38 ASN ** b 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4533 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 136844 Z= 0.326 Angle : 0.690 9.060 205973 Z= 0.352 Chirality : 0.040 0.400 26701 Planarity : 0.005 0.059 10352 Dihedral : 26.194 179.994 70889 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.54 % Favored : 86.29 % Rotamer: Outliers : 6.49 % Allowed : 27.19 % Favored : 66.32 % 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: -4.10 (0.11), residues: 4653 helix: -1.88 (0.15), residues: 1071 sheet: -2.33 (0.19), residues: 636 loop : -3.35 (0.10), residues: 2946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP c 48 HIS 0.006 0.001 HIS S 29 PHE 0.018 0.002 PHE J 139 TYR 0.020 0.001 TYR 4 63 ARG 0.009 0.001 ARG N 104 *********************** 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 741 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 533 time to evaluate : 4.884 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 TARDY: cannot create tardy model for: "LYS e 216 " (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 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 TARDY: cannot create tardy model for: "LEU j 61 " (corrupted residue). Skipping it. REVERT: E 7 MET cc_start: 0.1064 (tmm) cc_final: 0.0280 (tmm) REVERT: E 62 ILE cc_start: 0.5162 (OUTLIER) cc_final: 0.4889 (mp) REVERT: G 139 GLU cc_start: 0.3359 (pt0) cc_final: 0.0392 (mm-30) REVERT: G 144 MET cc_start: 0.0677 (ttt) cc_final: -0.0540 (ptt) REVERT: F 23 GLU cc_start: 0.3240 (tp30) cc_final: 0.2919 (mm-30) REVERT: F 80 ILE cc_start: 0.0895 (OUTLIER) cc_final: 0.0528 (pt) REVERT: 3 63 ARG cc_start: 0.2858 (ptt-90) cc_final: 0.1893 (ttm110) REVERT: 3 107 ARG cc_start: 0.2555 (mmt180) cc_final: 0.1806 (mtt90) REVERT: 5 45 ARG cc_start: -0.0844 (OUTLIER) cc_final: -0.3519 (mtt-85) REVERT: 9 59 MET cc_start: 0.1679 (ptp) cc_final: 0.1207 (mmp) REVERT: A 12 LYS cc_start: 0.0003 (ptpt) cc_final: -0.1548 (pttt) REVERT: A 25 LYS cc_start: 0.4377 (mtpt) cc_final: 0.3066 (mmtt) REVERT: A 36 LYS cc_start: 0.4748 (mmmt) cc_final: 0.2582 (pttm) REVERT: e 149 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.6780 (mtp85) REVERT: O 33 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7862 (mtt-85) REVERT: P 22 LYS cc_start: 0.5587 (OUTLIER) cc_final: 0.4392 (mttt) outliers start: 208 outliers final: 172 residues processed: 678 average time/residue: 1.1131 time to fit residues: 1297.6774 Evaluate side-chains 690 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 512 time to evaluate : 4.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 192 TYR Chi-restraints excluded: chain l residue 60 LEU Chi-restraints excluded: chain l residue 100 SER Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 129 ASN Chi-restraints excluded: chain G residue 148 ASN Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 132 TRP Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 83 HIS Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain 2 residue 81 THR Chi-restraints excluded: chain 3 residue 8 VAL Chi-restraints excluded: chain 3 residue 92 VAL Chi-restraints excluded: chain 5 residue 24 CYS Chi-restraints excluded: chain 5 residue 39 LEU Chi-restraints excluded: chain 5 residue 45 ARG Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 7 residue 33 ILE Chi-restraints excluded: chain 7 residue 34 ILE Chi-restraints excluded: chain 7 residue 73 ASN Chi-restraints excluded: chain 9 residue 49 VAL Chi-restraints excluded: chain 9 residue 53 SER Chi-restraints excluded: chain 9 residue 68 ARG Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain e residue 13 THR Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain e residue 55 ASP Chi-restraints excluded: chain e residue 65 SER Chi-restraints excluded: chain e residue 108 ASP Chi-restraints excluded: chain e residue 121 VAL Chi-restraints excluded: chain e residue 145 SER Chi-restraints excluded: chain e residue 149 ARG Chi-restraints excluded: chain e residue 176 ASN Chi-restraints excluded: chain e residue 177 THR Chi-restraints excluded: chain e residue 178 VAL Chi-restraints excluded: chain e residue 180 VAL Chi-restraints excluded: chain e residue 200 ASN Chi-restraints excluded: chain e residue 216 LYS Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 182 ASN Chi-restraints excluded: chain J residue 185 ASP Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 194 ILE Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 158 LYS Chi-restraints excluded: chain L residue 169 VAL Chi-restraints excluded: chain L residue 173 GLU Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 65 PHE Chi-restraints excluded: chain M residue 80 ASN Chi-restraints excluded: chain M residue 85 ILE Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain M residue 93 LEU Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain N residue 5 GLU Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 35 ILE Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 33 ARG Chi-restraints excluded: chain O residue 71 ARG Chi-restraints excluded: chain O residue 72 LYS Chi-restraints excluded: chain O residue 80 ASP Chi-restraints excluded: chain O residue 101 VAL Chi-restraints excluded: chain O residue 116 SER Chi-restraints excluded: chain O residue 119 LYS Chi-restraints excluded: chain O residue 121 LEU Chi-restraints excluded: chain O residue 128 PHE Chi-restraints excluded: chain P residue 7 VAL Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 22 LYS Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 39 THR Chi-restraints excluded: chain P residue 40 SER Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain Q residue 32 THR Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 112 ASP Chi-restraints excluded: chain R residue 21 ASN Chi-restraints excluded: chain R residue 32 ASN Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 89 ILE Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 10 THR Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain U residue 6 GLU Chi-restraints excluded: chain U residue 26 ASP Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain U residue 82 SER Chi-restraints excluded: chain V residue 17 VAL Chi-restraints excluded: chain V residue 33 ILE Chi-restraints excluded: chain V residue 39 THR Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain W residue 12 ILE Chi-restraints excluded: chain W residue 26 THR Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 68 TYR Chi-restraints excluded: chain W residue 72 THR Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 82 LEU Chi-restraints excluded: chain Z residue 27 LEU Chi-restraints excluded: chain Z residue 31 ASP Chi-restraints excluded: chain Z residue 34 VAL Chi-restraints excluded: chain Z residue 39 ASN Chi-restraints excluded: chain Z residue 93 ILE Chi-restraints excluded: chain a residue 24 SER Chi-restraints excluded: chain a residue 55 VAL Chi-restraints excluded: chain b residue 51 THR Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain c residue 28 ARG Chi-restraints excluded: chain c residue 45 LYS Chi-restraints excluded: chain d residue 49 THR Chi-restraints excluded: chain d residue 66 LYS Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 15 ARG Chi-restraints excluded: chain f residue 18 THR Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 56 VAL Chi-restraints excluded: chain g residue 23 SER Chi-restraints excluded: chain g residue 24 VAL Chi-restraints excluded: chain g residue 36 TYR Chi-restraints excluded: chain T residue 9 CYS Chi-restraints excluded: chain T residue 15 ARG Chi-restraints excluded: chain T residue 43 THR Chi-restraints excluded: chain T residue 44 LEU Chi-restraints excluded: chain i residue 26 LYS Chi-restraints excluded: chain i residue 31 VAL Chi-restraints excluded: chain j residue 6 THR Chi-restraints excluded: chain j residue 25 SER Chi-restraints excluded: chain j residue 61 LEU Chi-restraints excluded: chain k residue 3 VAL Chi-restraints excluded: chain k residue 24 MET Chi-restraints excluded: chain h residue 5 ILE Chi-restraints excluded: chain h residue 6 HIS 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: 2.9990 chunk 209 optimal weight: 70.0000 chunk 849 optimal weight: 10.0000 chunk 705 optimal weight: 10.0000 chunk 393 optimal weight: 20.0000 chunk 70 optimal weight: 0.0050 chunk 281 optimal weight: 50.0000 chunk 445 optimal weight: 7.9990 overall best weight: 6.2006 ------------------------------------------------------------------------------- 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 52 GLN ** 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** ** L 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 HIS 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** ** Z 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4489 moved from start: 0.3954 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= 0.230 Angle : 0.636 10.622 205973 Z= 0.326 Chirality : 0.038 0.349 26701 Planarity : 0.004 0.071 10352 Dihedral : 26.101 179.857 70881 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.28 % Favored : 88.55 % Rotamer: Outliers : 5.83 % Allowed : 28.91 % Favored : 65.26 % 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: -3.84 (0.11), residues: 4653 helix: -1.56 (0.16), residues: 1052 sheet: -2.21 (0.19), residues: 654 loop : -3.20 (0.10), residues: 2947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP c 48 HIS 0.006 0.001 HIS a 88 PHE 0.024 0.001 PHE a 48 TYR 0.022 0.001 TYR g 36 ARG 0.012 0.000 ARG g 41 *********************** 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 736 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 549 time to evaluate : 4.925 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 TARDY: cannot create tardy model for: "LYS e 216 " (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 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: B 141 MET cc_start: 0.1443 (mmm) cc_final: 0.1241 (mmp) REVERT: E 7 MET cc_start: 0.1001 (tmm) cc_final: 0.0370 (tmm) REVERT: E 62 ILE cc_start: 0.5046 (mp) cc_final: 0.4768 (mp) REVERT: E 90 MET cc_start: 0.0950 (mmp) cc_final: 0.0528 (tpp) REVERT: G 139 GLU cc_start: 0.3287 (pt0) cc_final: 0.0426 (mm-30) REVERT: G 144 MET cc_start: 0.0652 (ttt) cc_final: -0.0581 (ptt) REVERT: F 23 GLU cc_start: 0.3076 (tp30) cc_final: 0.2767 (mm-30) REVERT: F 80 ILE cc_start: 0.0817 (OUTLIER) cc_final: 0.0469 (pt) REVERT: 3 63 ARG cc_start: 0.2821 (ptt-90) cc_final: 0.1617 (ttm110) REVERT: 3 107 ARG cc_start: 0.2442 (mmt180) cc_final: 0.1678 (mtt90) REVERT: 4 101 LYS cc_start: 0.1364 (OUTLIER) cc_final: 0.0998 (mtpt) REVERT: 5 45 ARG cc_start: -0.0775 (OUTLIER) cc_final: -0.3436 (mtt-85) REVERT: 9 59 MET cc_start: 0.1584 (ptp) cc_final: 0.1254 (mmp) REVERT: A 25 LYS cc_start: 0.4306 (mtpt) cc_final: 0.3098 (mmtt) REVERT: A 36 LYS cc_start: 0.4667 (mmmt) cc_final: 0.2551 (pttm) REVERT: e 149 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.6693 (mtp85) REVERT: K 52 ASN cc_start: 0.3703 (OUTLIER) cc_final: 0.3473 (m110) REVERT: O 33 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7802 (mtt-85) REVERT: O 60 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.7362 (ptt180) REVERT: P 22 LYS cc_start: 0.5725 (OUTLIER) cc_final: 0.4527 (mttt) outliers start: 187 outliers final: 142 residues processed: 675 average time/residue: 1.1446 time to fit residues: 1321.6245 Evaluate side-chains 678 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 528 time to evaluate : 4.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 192 TYR Chi-restraints excluded: chain l residue 60 LEU Chi-restraints excluded: chain l residue 100 SER Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 148 ASN Chi-restraints excluded: chain F residue 22 HIS Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 132 TRP Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 20 ARG Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain 2 residue 59 THR Chi-restraints excluded: chain 2 residue 81 THR Chi-restraints excluded: chain 3 residue 8 VAL Chi-restraints excluded: chain 4 residue 101 LYS Chi-restraints excluded: chain 5 residue 24 CYS Chi-restraints excluded: chain 5 residue 45 ARG Chi-restraints excluded: chain 6 residue 26 GLU Chi-restraints excluded: chain 7 residue 33 ILE Chi-restraints excluded: chain 7 residue 34 ILE Chi-restraints excluded: chain 9 residue 53 SER Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain e residue 12 MET Chi-restraints excluded: chain e residue 43 VAL Chi-restraints excluded: chain e residue 55 ASP Chi-restraints excluded: chain e residue 65 SER Chi-restraints excluded: chain e residue 108 ASP Chi-restraints excluded: chain e residue 145 SER Chi-restraints excluded: chain e residue 149 ARG Chi-restraints excluded: chain e residue 176 ASN Chi-restraints excluded: chain e residue 180 VAL Chi-restraints excluded: chain e residue 200 ASN Chi-restraints excluded: chain e residue 211 ILE Chi-restraints excluded: chain e residue 216 LYS Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 58 SER Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 182 ASN Chi-restraints excluded: chain J residue 185 ASP Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 28 VAL Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 158 LYS Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 65 PHE Chi-restraints excluded: chain M residue 85 ILE Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain M residue 93 LEU Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain M residue 105 SER Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 33 ARG Chi-restraints excluded: chain O residue 60 ARG Chi-restraints excluded: chain O residue 72 LYS Chi-restraints excluded: chain O residue 116 SER Chi-restraints excluded: chain O residue 119 LYS Chi-restraints excluded: chain O residue 128 PHE Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 22 LYS Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 39 THR Chi-restraints excluded: chain P residue 40 SER Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 112 ASP Chi-restraints excluded: chain R residue 21 ASN Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 89 ILE Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 10 THR Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain U residue 6 GLU Chi-restraints excluded: chain U residue 26 ASP Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain U residue 82 SER Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain W residue 12 ILE Chi-restraints excluded: chain W residue 26 THR Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 68 TYR Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 82 LEU Chi-restraints excluded: chain Z residue 31 ASP Chi-restraints excluded: chain Z residue 93 ILE Chi-restraints excluded: chain a residue 31 VAL Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 55 VAL Chi-restraints excluded: chain b residue 51 THR Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain c residue 28 ARG Chi-restraints excluded: chain c residue 45 LYS Chi-restraints excluded: chain d residue 49 THR Chi-restraints excluded: chain d residue 66 LYS Chi-restraints excluded: chain f residue 11 SER Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 15 ARG Chi-restraints excluded: chain f residue 18 THR Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain g residue 23 SER Chi-restraints excluded: chain g residue 24 VAL Chi-restraints excluded: chain g residue 36 TYR Chi-restraints excluded: chain T residue 9 CYS Chi-restraints excluded: chain T residue 15 ARG Chi-restraints excluded: chain T residue 43 THR Chi-restraints excluded: chain i residue 26 LYS Chi-restraints excluded: chain i residue 31 VAL Chi-restraints excluded: chain j residue 6 THR Chi-restraints excluded: chain j residue 25 SER Chi-restraints excluded: chain j residue 61 LEU Chi-restraints excluded: chain k residue 3 VAL Chi-restraints excluded: chain k residue 24 MET Chi-restraints excluded: chain h residue 5 ILE 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: 9.9990 chunk 484 optimal weight: 2.9990 chunk 620 optimal weight: 20.0000 chunk 480 optimal weight: 9.9990 chunk 715 optimal weight: 10.0000 chunk 474 optimal weight: 6.9990 chunk 846 optimal weight: 10.0000 chunk 529 optimal weight: 10.0000 chunk 515 optimal weight: 8.9990 chunk 390 optimal weight: 20.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 6 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** ** 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** ** Z 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4524 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 136844 Z= 0.283 Angle : 0.661 15.053 205973 Z= 0.337 Chirality : 0.039 0.360 26701 Planarity : 0.004 0.058 10352 Dihedral : 26.054 179.755 70873 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.36 % Favored : 87.47 % Rotamer: Outliers : 6.24 % Allowed : 28.91 % Favored : 64.86 % 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: -3.73 (0.11), residues: 4653 helix: -1.47 (0.16), residues: 1070 sheet: -2.03 (0.20), residues: 637 loop : -3.16 (0.10), residues: 2946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP c 48 HIS 0.006 0.001 HIS a 88 PHE 0.029 0.002 PHE E 55 TYR 0.018 0.001 TYR 4 63 ARG 0.009 0.001 ARG N 17 *********************** 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 727 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 527 time to evaluate : 5.077 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: B 141 MET cc_start: 0.1770 (mmm) cc_final: 0.1565 (mmp) REVERT: l 54 LYS cc_start: 0.1334 (mmtp) cc_final: 0.0987 (ptmt) REVERT: E 48 LEU cc_start: -0.3825 (OUTLIER) cc_final: -0.4516 (tp) REVERT: E 62 ILE cc_start: 0.5114 (OUTLIER) cc_final: 0.4892 (mp) REVERT: E 90 MET cc_start: 0.0830 (mmp) cc_final: 0.0029 (mmt) REVERT: G 49 LEU cc_start: 0.2110 (OUTLIER) cc_final: 0.1504 (pt) REVERT: G 139 GLU cc_start: 0.3330 (pt0) cc_final: 0.0424 (mm-30) REVERT: G 144 MET cc_start: 0.0404 (ttt) cc_final: -0.0620 (ptt) REVERT: F 23 GLU cc_start: 0.3018 (tp30) cc_final: 0.2633 (mm-30) REVERT: F 51 TYR cc_start: 0.3535 (OUTLIER) cc_final: 0.2714 (m-10) REVERT: F 80 ILE cc_start: 0.0787 (OUTLIER) cc_final: 0.0509 (pt) REVERT: 3 63 ARG cc_start: 0.2933 (ptt-90) cc_final: 0.2657 (ttm110) REVERT: 3 107 ARG cc_start: 0.2403 (mmt180) cc_final: 0.1566 (mtt90) REVERT: 5 45 ARG cc_start: -0.0746 (OUTLIER) cc_final: -0.3611 (mtt-85) REVERT: 9 59 MET cc_start: 0.1589 (ptp) cc_final: 0.1350 (mmp) REVERT: A 12 LYS cc_start: -0.0275 (ptpt) cc_final: -0.1766 (pttt) REVERT: A 25 LYS cc_start: 0.4215 (mtpt) cc_final: 0.3073 (mmtt) REVERT: A 36 LYS cc_start: 0.4715 (mmmt) cc_final: 0.2529 (pttm) REVERT: e 149 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.6736 (mtp85) REVERT: O 33 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7852 (mtt-85) outliers start: 200 outliers final: 154 residues processed: 668 average time/residue: 1.1623 time to fit residues: 1339.9754 Evaluate side-chains 678 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 516 time to evaluate : 4.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 192 TYR Chi-restraints excluded: chain l residue 60 LEU Chi-restraints excluded: chain l residue 100 SER Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 148 ASN Chi-restraints excluded: chain F residue 22 HIS Chi-restraints excluded: chain F residue 51 TYR Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 132 TRP Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 20 ARG Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 83 HIS Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain 2 residue 59 THR Chi-restraints excluded: chain 2 residue 81 THR Chi-restraints excluded: chain 3 residue 42 GLN Chi-restraints excluded: chain 4 residue 22 ILE Chi-restraints excluded: chain 5 residue 24 CYS Chi-restraints excluded: chain 5 residue 45 ARG Chi-restraints excluded: chain 7 residue 33 ILE Chi-restraints excluded: chain 7 residue 34 ILE Chi-restraints excluded: chain 9 residue 53 SER Chi-restraints excluded: chain 9 residue 68 ARG Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain e residue 12 MET Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain e residue 43 VAL Chi-restraints excluded: chain e residue 55 ASP Chi-restraints excluded: chain e residue 65 SER Chi-restraints excluded: chain e residue 108 ASP Chi-restraints excluded: chain e residue 115 VAL Chi-restraints excluded: chain e residue 145 SER Chi-restraints excluded: chain e residue 149 ARG Chi-restraints excluded: chain e residue 178 VAL Chi-restraints excluded: chain e residue 180 VAL Chi-restraints excluded: chain e residue 200 ASN Chi-restraints excluded: chain e residue 216 LYS Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 58 SER Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 182 ASN Chi-restraints excluded: chain J residue 185 ASP Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 194 ILE Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain K residue 28 VAL Chi-restraints excluded: chain K residue 38 MET Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 65 PHE Chi-restraints excluded: chain M residue 85 ILE Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain M residue 93 LEU Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain M residue 105 SER Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 33 ARG Chi-restraints excluded: chain O residue 71 ARG Chi-restraints excluded: chain O residue 116 SER Chi-restraints excluded: chain O residue 119 LYS Chi-restraints excluded: chain O residue 128 PHE Chi-restraints excluded: chain P residue 7 VAL Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 39 THR Chi-restraints excluded: chain P residue 40 SER Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 112 ASP Chi-restraints excluded: chain R residue 21 ASN Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 32 ASN Chi-restraints excluded: chain R residue 89 ILE Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 10 THR Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain U residue 6 GLU Chi-restraints excluded: chain U residue 26 ASP Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain U residue 82 SER Chi-restraints excluded: chain V residue 39 THR Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain W residue 12 ILE Chi-restraints excluded: chain W residue 26 THR Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain W residue 68 TYR Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 82 LEU Chi-restraints excluded: chain Z residue 26 THR Chi-restraints excluded: chain Z residue 31 ASP Chi-restraints excluded: chain Z residue 93 ILE Chi-restraints excluded: chain a residue 24 SER Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 55 VAL Chi-restraints excluded: chain b residue 51 THR Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain c residue 28 ARG Chi-restraints excluded: chain c residue 45 LYS Chi-restraints excluded: chain d residue 49 THR Chi-restraints excluded: chain d residue 66 LYS Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 15 ARG Chi-restraints excluded: chain f residue 18 THR Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain g residue 23 SER Chi-restraints excluded: chain g residue 24 VAL Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain T residue 9 CYS Chi-restraints excluded: chain T residue 12 CYS Chi-restraints excluded: chain T residue 15 ARG Chi-restraints excluded: chain T residue 26 ASN Chi-restraints excluded: chain T residue 43 THR Chi-restraints excluded: chain i residue 26 LYS Chi-restraints excluded: chain i residue 31 VAL Chi-restraints excluded: chain j residue 6 THR Chi-restraints excluded: chain j residue 25 SER Chi-restraints excluded: chain k residue 3 VAL Chi-restraints excluded: chain k residue 24 MET Chi-restraints excluded: chain h residue 5 ILE 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: 3.9990 chunk 254 optimal weight: 50.0000 chunk 166 optimal weight: 30.0000 chunk 163 optimal weight: 7.9990 chunk 538 optimal weight: 0.0070 chunk 576 optimal weight: 0.0670 chunk 418 optimal weight: 3.9990 chunk 78 optimal weight: 50.0000 chunk 665 optimal weight: 10.0000 overall best weight: 3.2142 ------------------------------------------------------------------------------- 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** F 31 ASN ** 1 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 40 ASN ** 3 6 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** M 41 ASN O 54 GLN Q 73 ASN ** R 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4450 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 136844 Z= 0.159 Angle : 0.600 11.379 205973 Z= 0.307 Chirality : 0.035 0.359 26701 Planarity : 0.004 0.057 10352 Dihedral : 25.944 179.968 70869 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.57 % Favored : 89.25 % Rotamer: Outliers : 4.74 % Allowed : 30.78 % Favored : 64.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.11), residues: 4653 helix: -1.23 (0.16), residues: 1052 sheet: -1.92 (0.20), residues: 635 loop : -2.99 (0.10), residues: 2966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 65 HIS 0.005 0.001 HIS f 52 PHE 0.019 0.001 PHE E 55 TYR 0.018 0.001 TYR P 9 ARG 0.007 0.000 ARG g 41 *********************** 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 707 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 555 time to evaluate : 4.805 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 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. REVERT: l 54 LYS cc_start: 0.1476 (mmtp) cc_final: 0.1048 (ptmt) REVERT: E 62 ILE cc_start: 0.5075 (OUTLIER) cc_final: 0.4821 (mp) REVERT: G 49 LEU cc_start: 0.2135 (OUTLIER) cc_final: 0.1639 (pt) REVERT: G 139 GLU cc_start: 0.3294 (pt0) cc_final: 0.0497 (mm-30) REVERT: G 144 MET cc_start: 0.0291 (ttt) cc_final: -0.0711 (ptt) REVERT: F 23 GLU cc_start: 0.2995 (tp30) cc_final: 0.2638 (mm-30) REVERT: F 51 TYR cc_start: 0.3376 (OUTLIER) cc_final: 0.2593 (m-10) REVERT: F 80 ILE cc_start: 0.0705 (OUTLIER) cc_final: 0.0494 (pt) REVERT: 3 63 ARG cc_start: 0.2870 (ptt-90) cc_final: 0.2496 (ttm110) REVERT: 3 107 ARG cc_start: 0.2231 (mmt180) cc_final: 0.1413 (mtt90) REVERT: 9 69 HIS cc_start: -0.1165 (OUTLIER) cc_final: -0.1910 (t-90) REVERT: A 25 LYS cc_start: 0.4056 (mtpt) cc_final: 0.3010 (mmtt) REVERT: A 36 LYS cc_start: 0.4669 (mmmt) cc_final: 0.2561 (pttm) REVERT: e 149 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.6670 (mtp85) REVERT: O 33 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7767 (mtt-85) REVERT: P 22 LYS cc_start: 0.5675 (OUTLIER) cc_final: 0.4559 (mttt) REVERT: U 18 GLN cc_start: 0.7106 (OUTLIER) cc_final: 0.6802 (pt0) outliers start: 152 outliers final: 117 residues processed: 660 average time/residue: 1.0971 time to fit residues: 1237.3275 Evaluate side-chains 661 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 535 time to evaluate : 4.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 192 TYR Chi-restraints excluded: chain l residue 60 LEU Chi-restraints excluded: chain l residue 100 SER Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 148 ASN Chi-restraints excluded: chain F residue 22 HIS Chi-restraints excluded: chain F residue 51 TYR Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 132 TRP Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 20 ARG Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain 2 residue 59 THR Chi-restraints excluded: chain 2 residue 81 THR Chi-restraints excluded: chain 4 residue 22 ILE Chi-restraints excluded: chain 5 residue 24 CYS Chi-restraints excluded: chain 7 residue 33 ILE Chi-restraints excluded: chain 7 residue 34 ILE Chi-restraints excluded: chain 9 residue 53 SER Chi-restraints excluded: chain 9 residue 69 HIS Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain e residue 55 ASP Chi-restraints excluded: chain e residue 65 SER Chi-restraints excluded: chain e residue 115 VAL Chi-restraints excluded: chain e residue 145 SER Chi-restraints excluded: chain e residue 149 ARG Chi-restraints excluded: chain e residue 176 ASN Chi-restraints excluded: chain e residue 180 VAL Chi-restraints excluded: chain e residue 200 ASN Chi-restraints excluded: chain e residue 211 ILE Chi-restraints excluded: chain e residue 216 LYS Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 58 SER Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 182 ASN Chi-restraints excluded: chain J residue 185 ASP Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain K residue 28 VAL Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 65 PHE Chi-restraints excluded: chain M residue 85 ILE Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain M residue 93 LEU Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain M residue 105 SER Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain O residue 33 ARG Chi-restraints excluded: chain O residue 116 SER Chi-restraints excluded: chain O residue 119 LYS Chi-restraints excluded: chain O residue 128 PHE Chi-restraints excluded: chain P residue 7 VAL Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 22 LYS Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 39 THR Chi-restraints excluded: chain P residue 40 SER Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain Q residue 112 ASP Chi-restraints excluded: chain R residue 21 ASN Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 32 ASN Chi-restraints excluded: chain R residue 89 ILE Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 10 THR Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain U residue 6 GLU Chi-restraints excluded: chain U residue 18 GLN Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain W residue 12 ILE Chi-restraints excluded: chain W residue 26 THR Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 82 LEU Chi-restraints excluded: chain Z residue 31 ASP Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 55 VAL Chi-restraints excluded: chain b residue 51 THR Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain c residue 45 LYS Chi-restraints excluded: chain d residue 14 ILE Chi-restraints excluded: chain f residue 11 SER Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 15 ARG Chi-restraints excluded: chain f residue 18 THR Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain g residue 23 SER Chi-restraints excluded: chain g residue 24 VAL Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain T residue 9 CYS Chi-restraints excluded: chain i residue 26 LYS Chi-restraints excluded: chain j residue 25 SER Chi-restraints excluded: chain j residue 61 LEU Chi-restraints excluded: chain k residue 3 VAL Chi-restraints excluded: chain h residue 5 ILE 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: 60.0000 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: ** G 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 15 ASN ** 3 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 33 ASN ** 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 ** 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 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 16 ASN ** d 36 GLN ** 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: 0.4628 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.128 136844 Z= 0.619 Angle : 0.875 13.417 205973 Z= 0.428 Chirality : 0.048 0.391 26701 Planarity : 0.006 0.081 10352 Dihedral : 26.196 179.932 70863 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 23.88 Ramachandran Plot: Outliers : 0.17 % Allowed : 14.31 % Favored : 85.51 % Rotamer: Outliers : 5.46 % Allowed : 30.06 % Favored : 64.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.79 (0.11), residues: 4653 helix: -1.61 (0.15), residues: 1063 sheet: -2.24 (0.19), residues: 623 loop : -3.11 (0.10), residues: 2967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP c 48 HIS 0.009 0.002 HIS P 13 PHE 0.024 0.002 PHE E 55 TYR 0.023 0.002 TYR e 99 ARG 0.027 0.001 ARG F 121 *********************** 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 684 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 509 time to evaluate : 4.808 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 TARDY: cannot create tardy model for: "LYS e 216 " (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: "LEU j 61 " (corrupted residue). Skipping it. REVERT: l 54 LYS cc_start: 0.1540 (mmtp) cc_final: 0.1229 (ttpp) REVERT: G 49 LEU cc_start: 0.1963 (OUTLIER) cc_final: 0.1409 (pt) REVERT: G 139 GLU cc_start: 0.3315 (pt0) cc_final: 0.0287 (mm-30) REVERT: G 144 MET cc_start: 0.0344 (ttt) cc_final: -0.0527 (ptt) REVERT: F 23 GLU cc_start: 0.3227 (tp30) cc_final: 0.2945 (mm-30) REVERT: F 51 TYR cc_start: 0.3708 (OUTLIER) cc_final: 0.2966 (m-10) REVERT: F 80 ILE cc_start: 0.1034 (OUTLIER) cc_final: 0.0654 (pt) REVERT: 3 63 ARG cc_start: 0.2581 (ptt-90) cc_final: 0.2224 (ttm110) REVERT: 3 107 ARG cc_start: 0.2466 (mmt180) cc_final: 0.1575 (mtt90) REVERT: 5 45 ARG cc_start: -0.0675 (OUTLIER) cc_final: -0.3535 (mtt-85) REVERT: A 25 LYS cc_start: 0.3994 (mtpt) cc_final: 0.2887 (mmtt) REVERT: A 36 LYS cc_start: 0.4967 (mmmt) cc_final: 0.2852 (pttm) REVERT: e 161 SER cc_start: 0.7202 (t) cc_final: 0.6831 (m) REVERT: L 79 VAL cc_start: 0.1525 (p) cc_final: 0.1079 (t) REVERT: P 22 LYS cc_start: 0.5760 (OUTLIER) cc_final: 0.4696 (mttt) outliers start: 175 outliers final: 146 residues processed: 640 average time/residue: 1.0993 time to fit residues: 1195.9125 Evaluate side-chains 649 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 498 time to evaluate : 4.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain l residue 60 LEU Chi-restraints excluded: chain l residue 100 SER Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 148 ASN Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 22 HIS Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 51 TYR Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 132 TRP Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 20 ARG Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 83 HIS Chi-restraints excluded: chain 2 residue 59 THR Chi-restraints excluded: chain 2 residue 81 THR Chi-restraints excluded: chain 4 residue 22 ILE Chi-restraints excluded: chain 5 residue 24 CYS Chi-restraints excluded: chain 5 residue 45 ARG Chi-restraints excluded: chain 7 residue 33 ILE Chi-restraints excluded: chain 7 residue 34 ILE Chi-restraints excluded: chain 8 residue 24 THR Chi-restraints excluded: chain 9 residue 53 SER Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain e residue 55 ASP Chi-restraints excluded: chain e residue 65 SER Chi-restraints excluded: chain e residue 108 ASP Chi-restraints excluded: chain e residue 115 VAL Chi-restraints excluded: chain e residue 121 VAL Chi-restraints excluded: chain e residue 176 ASN Chi-restraints excluded: chain e residue 178 VAL Chi-restraints excluded: chain e residue 180 VAL Chi-restraints excluded: chain e residue 200 ASN Chi-restraints excluded: chain e residue 216 LYS Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 58 SER Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 182 ASN Chi-restraints excluded: chain J residue 185 ASP Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 194 ILE Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 65 PHE Chi-restraints excluded: chain M residue 85 ILE Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain M residue 93 LEU Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain M residue 105 SER Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain O residue 72 LYS Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 116 SER Chi-restraints excluded: chain O residue 119 LYS Chi-restraints excluded: chain O residue 128 PHE Chi-restraints excluded: chain P residue 7 VAL Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 22 LYS Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 40 SER Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain Q residue 32 THR Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 112 ASP Chi-restraints excluded: chain R residue 9 LYS Chi-restraints excluded: chain R residue 13 LYS Chi-restraints excluded: chain R residue 21 ASN Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 32 ASN Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 46 ASP Chi-restraints excluded: chain R residue 89 ILE Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 10 THR Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain U residue 6 GLU Chi-restraints excluded: chain U residue 14 VAL Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain V residue 17 VAL Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain W residue 12 ILE Chi-restraints excluded: chain W residue 26 THR Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain W residue 68 TYR Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 82 LEU Chi-restraints excluded: chain Z residue 31 ASP Chi-restraints excluded: chain Z residue 93 ILE Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 55 VAL Chi-restraints excluded: chain b residue 51 THR Chi-restraints excluded: chain b residue 59 VAL Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain c residue 45 LYS Chi-restraints excluded: chain d residue 14 ILE Chi-restraints excluded: chain f residue 11 SER Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 15 ARG Chi-restraints excluded: chain f residue 18 THR Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain g residue 23 SER Chi-restraints excluded: chain g residue 24 VAL Chi-restraints excluded: chain T residue 9 CYS Chi-restraints excluded: chain T residue 12 CYS Chi-restraints excluded: chain T residue 15 ARG Chi-restraints excluded: chain i residue 26 LYS Chi-restraints excluded: chain j residue 6 THR Chi-restraints excluded: chain j residue 25 SER Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 61 LEU Chi-restraints excluded: chain k residue 3 VAL Chi-restraints excluded: chain k residue 24 MET Chi-restraints excluded: chain h residue 5 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 517 optimal weight: 5.9990 chunk 833 optimal weight: 0.9980 chunk 508 optimal weight: 7.9990 chunk 395 optimal weight: 20.0000 chunk 579 optimal weight: 1.9990 chunk 874 optimal weight: 10.0000 chunk 805 optimal weight: 30.0000 chunk 696 optimal weight: 30.0000 chunk 72 optimal weight: 8.9990 chunk 538 optimal weight: 2.9990 chunk 427 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 33 ASN ** 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** M 136 GLN Q 73 ASN ** R 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4506 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 136844 Z= 0.183 Angle : 0.650 12.881 205973 Z= 0.331 Chirality : 0.037 0.318 26701 Planarity : 0.004 0.058 10352 Dihedral : 26.020 179.481 70863 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.01 % Favored : 87.81 % Rotamer: Outliers : 4.15 % Allowed : 31.59 % Favored : 64.27 % 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: -3.54 (0.11), residues: 4653 helix: -1.34 (0.16), residues: 1075 sheet: -2.03 (0.19), residues: 630 loop : -2.99 (0.10), residues: 2948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 65 HIS 0.006 0.001 HIS S 29 PHE 0.017 0.001 PHE E 55 TYR 0.045 0.002 TYR E 60 ARG 0.008 0.000 ARG P 115 ********************** 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 674 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 541 time to evaluate : 4.763 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 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: E 7 MET cc_start: 0.1103 (tmm) cc_final: 0.0653 (tmm) REVERT: G 49 LEU cc_start: 0.1893 (OUTLIER) cc_final: 0.1307 (pt) REVERT: G 139 GLU cc_start: 0.3175 (pt0) cc_final: 0.0284 (mm-30) REVERT: G 144 MET cc_start: 0.0278 (ttt) cc_final: -0.0597 (ptt) REVERT: F 23 GLU cc_start: 0.3123 (tp30) cc_final: 0.2754 (mm-30) REVERT: F 51 TYR cc_start: 0.3470 (OUTLIER) cc_final: 0.2741 (m-10) REVERT: F 80 ILE cc_start: 0.0915 (OUTLIER) cc_final: 0.0614 (pt) REVERT: 3 63 ARG cc_start: 0.2793 (ptt-90) cc_final: 0.2536 (ttm110) REVERT: 3 107 ARG cc_start: 0.2424 (mmt180) cc_final: 0.1512 (mtt90) REVERT: A 25 LYS cc_start: 0.3920 (mtpt) cc_final: 0.2880 (mmtt) REVERT: A 36 LYS cc_start: 0.4825 (mmmt) cc_final: 0.2626 (pttm) REVERT: e 161 SER cc_start: 0.7075 (t) cc_final: 0.6699 (m) REVERT: O 33 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7856 (mtt-85) REVERT: P 22 LYS cc_start: 0.5682 (OUTLIER) cc_final: 0.4592 (mttt) outliers start: 133 outliers final: 120 residues processed: 634 average time/residue: 1.0958 time to fit residues: 1185.6252 Evaluate side-chains 653 residues out of total 4021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 528 time to evaluate : 4.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 192 TYR Chi-restraints excluded: chain l residue 60 LEU Chi-restraints excluded: chain l residue 100 SER Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 148 ASN Chi-restraints excluded: chain F residue 22 HIS Chi-restraints excluded: chain F residue 51 TYR Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 132 TRP Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 20 ARG Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain 2 residue 59 THR Chi-restraints excluded: chain 2 residue 81 THR Chi-restraints excluded: chain 4 residue 22 ILE Chi-restraints excluded: chain 5 residue 24 CYS Chi-restraints excluded: chain 7 residue 33 ILE Chi-restraints excluded: chain 7 residue 34 ILE Chi-restraints excluded: chain 9 residue 53 SER Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain e residue 55 ASP Chi-restraints excluded: chain e residue 65 SER Chi-restraints excluded: chain e residue 176 ASN Chi-restraints excluded: chain e residue 180 VAL Chi-restraints excluded: chain e residue 200 ASN Chi-restraints excluded: chain e residue 216 LYS Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 58 SER Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 182 ASN Chi-restraints excluded: chain J residue 185 ASP Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 65 PHE Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain M residue 93 LEU Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain M residue 105 SER Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain O residue 33 ARG Chi-restraints excluded: chain O residue 72 LYS Chi-restraints excluded: chain O residue 116 SER Chi-restraints excluded: chain O residue 119 LYS Chi-restraints excluded: chain O residue 128 PHE Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 22 LYS Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 40 SER Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 112 ASP Chi-restraints excluded: chain R residue 21 ASN Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 32 ASN Chi-restraints excluded: chain R residue 46 ASP Chi-restraints excluded: chain R residue 89 ILE Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 10 THR Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain U residue 6 GLU Chi-restraints excluded: chain U residue 26 ASP Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain U residue 82 SER Chi-restraints excluded: chain V residue 17 VAL Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain W residue 12 ILE Chi-restraints excluded: chain W residue 26 THR Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 82 LEU Chi-restraints excluded: chain Z residue 31 ASP Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 55 VAL Chi-restraints excluded: chain b residue 51 THR Chi-restraints excluded: chain b residue 59 VAL Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain c residue 45 LYS Chi-restraints excluded: chain d residue 14 ILE Chi-restraints excluded: chain d residue 49 THR Chi-restraints excluded: chain d residue 66 LYS Chi-restraints excluded: chain f residue 11 SER Chi-restraints excluded: chain f residue 13 ILE Chi-restraints excluded: chain f residue 15 ARG Chi-restraints excluded: chain f residue 18 THR Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain g residue 23 SER Chi-restraints excluded: chain g residue 24 VAL Chi-restraints excluded: chain T residue 9 CYS Chi-restraints excluded: chain T residue 12 CYS Chi-restraints excluded: chain T residue 15 ARG Chi-restraints excluded: chain i residue 26 LYS Chi-restraints excluded: chain j residue 6 THR Chi-restraints excluded: chain j residue 25 SER Chi-restraints excluded: chain k residue 3 VAL Chi-restraints excluded: chain h residue 5 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 553 optimal weight: 50.0000 chunk 741 optimal weight: 20.0000 chunk 213 optimal weight: 50.0000 chunk 642 optimal weight: 20.0000 chunk 102 optimal weight: 50.0000 chunk 193 optimal weight: 30.0000 chunk 697 optimal weight: 40.0000 chunk 291 optimal weight: 60.0000 chunk 716 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 128 optimal weight: 0.3980 overall best weight: 12.0796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 50 GLN ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 6 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** ** 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** ** d 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.118823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.073160 restraints weight = 539492.751| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 3.51 r_work: 0.2840 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.5023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 136844 Z= 0.410 Angle : 0.741 11.230 205973 Z= 0.372 Chirality : 0.043 0.333 26701 Planarity : 0.005 0.058 10352 Dihedral : 26.085 179.733 70863 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 21.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 13.88 % Favored : 85.97 % Rotamer: Outliers : 4.74 % Allowed : 31.15 % Favored : 64.11 % 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: -3.61 (0.11), residues: 4653 helix: -1.40 (0.16), residues: 1061 sheet: -2.08 (0.19), residues: 629 loop : -3.04 (0.10), residues: 2963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 34 HIS 0.007 0.001 HIS P 13 PHE 0.026 0.002 PHE d 30 TYR 0.035 0.002 TYR P 57 ARG 0.024 0.001 ARG 2 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27512.17 seconds wall clock time: 482 minutes 21.13 seconds (28941.13 seconds total)