Starting phenix.real_space_refine on Fri Apr 12 05:19:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcq_18332/04_2024/8qcq_18332_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcq_18332/04_2024/8qcq_18332.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcq_18332/04_2024/8qcq_18332_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcq_18332/04_2024/8qcq_18332_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcq_18332/04_2024/8qcq_18332_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcq_18332/04_2024/8qcq_18332.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcq_18332/04_2024/8qcq_18332.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcq_18332/04_2024/8qcq_18332_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcq_18332/04_2024/8qcq_18332_neut_updated.pdb" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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: 8 Type Number sf(0) Gaussians K 43 8.98 5 Zn 5 6.06 5 P 4547 5.49 5 Mg 199 5.21 5 S 122 5.16 5 C 67139 2.51 5 N 25200 2.21 5 O 39409 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 GLU 29": "OE1" <-> "OE2" Residue "0 GLU 35": "OE1" <-> "OE2" Residue "0 ARG 41": "NH1" <-> "NH2" Residue "1 GLU 11": "OE1" <-> "OE2" Residue "1 GLU 14": "OE1" <-> "OE2" Residue "1 GLU 31": "OE1" <-> "OE2" Residue "1 GLU 47": "OE1" <-> "OE2" Residue "4 GLU 12": "OE1" <-> "OE2" Residue "6 PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 21": "OE1" <-> "OE2" Residue "6 GLU 23": "OE1" <-> "OE2" Residue "6 GLU 29": "OE1" <-> "OE2" Residue "6 GLU 30": "OE1" <-> "OE2" Residue "6 GLU 34": "OE1" <-> "OE2" Residue "6 PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 23": "OE1" <-> "OE2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C GLU 100": "OE1" <-> "OE2" Residue "C GLU 121": "OE1" <-> "OE2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C GLU 168": "OE1" <-> "OE2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C GLU 198": "OE1" <-> "OE2" Residue "C GLU 201": "OE1" <-> "OE2" Residue "C GLU 236": "OE1" <-> "OE2" Residue "D GLU 18": "OE1" <-> "OE2" Residue "D GLU 29": "OE1" <-> "OE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "D GLU 65": "OE1" <-> "OE2" Residue "D GLU 87": "OE1" <-> "OE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 92": "OE1" <-> "OE2" Residue "D GLU 96": "OE1" <-> "OE2" Residue "D GLU 167": "OE1" <-> "OE2" Residue "D GLU 175": "OE1" <-> "OE2" Residue "D GLU 182": "OE1" <-> "OE2" Residue "E GLU 18": "OE1" <-> "OE2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E GLU 30": "OE1" <-> "OE2" Residue "E GLU 127": "OE1" <-> "OE2" Residue "E GLU 138": "OE1" <-> "OE2" Residue "E GLU 161": "OE1" <-> "OE2" Residue "E GLU 177": "OE1" <-> "OE2" Residue "E GLU 200": "OE1" <-> "OE2" Residue "E GLU 203": "OE1" <-> "OE2" Residue "F GLU 6": "OE1" <-> "OE2" Residue "F GLU 11": "OE1" <-> "OE2" Residue "F GLU 32": "OE1" <-> "OE2" Residue "F GLU 55": "OE1" <-> "OE2" Residue "F GLU 56": "OE1" <-> "OE2" Residue "F GLU 81": "OE1" <-> "OE2" Residue "F GLU 94": "OE1" <-> "OE2" Residue "F GLU 134": "OE1" <-> "OE2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "F TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 164": "OE1" <-> "OE2" Residue "F GLU 165": "OE1" <-> "OE2" Residue "F GLU 168": "OE1" <-> "OE2" Residue "G GLU 10": "OE1" <-> "OE2" Residue "G GLU 33": "OE1" <-> "OE2" Residue "G PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G GLU 78": "OE1" <-> "OE2" Residue "G GLU 85": "OE1" <-> "OE2" Residue "G GLU 89": "OE1" <-> "OE2" Residue "G GLU 115": "OE1" <-> "OE2" Residue "G GLU 119": "OE1" <-> "OE2" Residue "G GLU 120": "OE1" <-> "OE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "G GLU 125": "OE1" <-> "OE2" Residue "G GLU 156": "OE1" <-> "OE2" Residue "G GLU 168": "OE1" <-> "OE2" Residue "G GLU 174": "OE1" <-> "OE2" Residue "J GLU 13": "OE1" <-> "OE2" Residue "J GLU 32": "OE1" <-> "OE2" Residue "J GLU 64": "OE1" <-> "OE2" Residue "J GLU 92": "OE1" <-> "OE2" Residue "J GLU 99": "OE1" <-> "OE2" Residue "J GLU 103": "OE1" <-> "OE2" Residue "J GLU 130": "OE1" <-> "OE2" Residue "J GLU 134": "OE1" <-> "OE2" Residue "K GLU 5": "OE1" <-> "OE2" Residue "K GLU 18": "OE1" <-> "OE2" Residue "K GLU 81": "OE1" <-> "OE2" Residue "K GLU 105": "OE1" <-> "OE2" Residue "K GLU 108": "OE1" <-> "OE2" Residue "K PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 120": "OE1" <-> "OE2" Residue "L GLU 51": "OE1" <-> "OE2" Residue "L GLU 73": "OE1" <-> "OE2" Residue "L GLU 98": "OE1" <-> "OE2" Residue "L GLU 118": "OE1" <-> "OE2" Residue "M GLU 26": "OE1" <-> "OE2" Residue "M GLU 38": "OE1" <-> "OE2" Residue "M GLU 48": "OE1" <-> "OE2" Residue "M GLU 80": "OE1" <-> "OE2" Residue "M GLU 91": "OE1" <-> "OE2" Residue "M PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 105": "OE1" <-> "OE2" Residue "M GLU 111": "OE1" <-> "OE2" Residue "M GLU 112": "OE1" <-> "OE2" Residue "M GLU 116": "OE1" <-> "OE2" Residue "M PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 135": "OE1" <-> "OE2" Residue "N GLU 28": "OE1" <-> "OE2" Residue "N ARG 29": "NH1" <-> "NH2" Residue "N GLU 31": "OE1" <-> "OE2" Residue "N GLU 34": "OE1" <-> "OE2" Residue "N GLU 39": "OE1" <-> "OE2" Residue "N GLU 69": "OE1" <-> "OE2" Residue "N GLU 73": "OE1" <-> "OE2" Residue "N GLU 74": "OE1" <-> "OE2" Residue "N GLU 92": "OE1" <-> "OE2" Residue "N GLU 93": "OE1" <-> "OE2" Residue "N GLU 118": "OE1" <-> "OE2" Residue "O GLU 27": "OE1" <-> "OE2" Residue "O GLU 87": "OE1" <-> "OE2" Residue "O GLU 115": "OE1" <-> "OE2" Residue "P GLU 6": "OE1" <-> "OE2" Residue "P GLU 11": "OE1" <-> "OE2" Residue "P PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 44": "OE1" <-> "OE2" Residue "P ARG 51": "NH1" <-> "NH2" Residue "P GLU 57": "OE1" <-> "OE2" Residue "P GLU 71": "OE1" <-> "OE2" Residue "P GLU 85": "OE1" <-> "OE2" Residue "P GLU 112": "OE1" <-> "OE2" Residue "Q ARG 11": "NH1" <-> "NH2" Residue "Q GLU 89": "OE1" <-> "OE2" Residue "R GLU 15": "OE1" <-> "OE2" Residue "R GLU 16": "OE1" <-> "OE2" Residue "R GLU 23": "OE1" <-> "OE2" Residue "R GLU 28": "OE1" <-> "OE2" Residue "R GLU 31": "OE1" <-> "OE2" Residue "R GLU 36": "OE1" <-> "OE2" Residue "R GLU 63": "OE1" <-> "OE2" Residue "R GLU 98": "OE1" <-> "OE2" Residue "S GLU 31": "OE1" <-> "OE2" Residue "S GLU 48": "OE1" <-> "OE2" Residue "S GLU 59": "OE1" <-> "OE2" Residue "S GLU 63": "OE1" <-> "OE2" Residue "S PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 78": "OE1" <-> "OE2" Residue "S GLU 109": "OE1" <-> "OE2" Residue "T GLU 15": "OE1" <-> "OE2" Residue "T GLU 23": "OE1" <-> "OE2" Residue "T GLU 29": "OE1" <-> "OE2" Residue "T GLU 44": "OE1" <-> "OE2" Residue "T ASP 52": "OD1" <-> "OD2" Residue "T ARG 65": "NH1" <-> "NH2" Residue "T GLU 89": "OE1" <-> "OE2" Residue "U TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 86": "OE1" <-> "OE2" Residue "W GLU 25": "OE1" <-> "OE2" Residue "W GLU 57": "OE1" <-> "OE2" Residue "W GLU 78": "OE1" <-> "OE2" Residue "Y GLU 5": "OE1" <-> "OE2" Residue "Y GLU 13": "OE1" <-> "OE2" Residue "Y GLU 15": "OE1" <-> "OE2" Residue "Y GLU 24": "OE1" <-> "OE2" Residue "Y PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 38": "OE1" <-> "OE2" Residue "Y GLU 45": "OE1" <-> "OE2" Residue "Y GLU 59": "OE1" <-> "OE2" Residue "Z GLU 38": "OE1" <-> "OE2" Residue "e GLU 13": "OE1" <-> "OE2" Residue "e GLU 55": "OE1" <-> "OE2" Residue "e GLU 65": "OE1" <-> "OE2" Residue "e GLU 73": "OE1" <-> "OE2" Residue "e GLU 84": "OE1" <-> "OE2" Residue "e PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 101": "OE1" <-> "OE2" Residue "e GLU 116": "OE1" <-> "OE2" Residue "e GLU 146": "OE1" <-> "OE2" Residue "e ARG 149": "NH1" <-> "NH2" Residue "e GLU 162": "OE1" <-> "OE2" Residue "e GLU 163": "OE1" <-> "OE2" Residue "k GLU 19": "OE1" <-> "OE2" Residue "k PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 96": "OE1" <-> "OE2" Residue "l GLU 34": "OE1" <-> "OE2" Residue "l ASP 116": "OD1" <-> "OD2" Residue "o GLU 6": "OE1" <-> "OE2" Residue "o GLU 14": "OE1" <-> "OE2" Residue "o GLU 26": "OE1" <-> "OE2" Residue "o GLU 41": "OE1" <-> "OE2" Residue "o ARG 54": "NH1" <-> "NH2" Residue "o ARG 71": "NH1" <-> "NH2" Residue "o TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 3": "OE1" <-> "OE2" Residue "q GLU 79": "OE1" <-> "OE2" Residue "q GLU 82": "OE1" <-> "OE2" Residue "t GLU 36": "OE1" <-> "OE2" Residue "t GLU 43": "OE1" <-> "OE2" Residue "c GLU 19": "OE1" <-> "OE2" Residue "c GLU 34": "OE1" <-> "OE2" Residue "c GLU 40": "OE1" <-> "OE2" Residue "c GLU 55": "OE1" <-> "OE2" Residue "c GLU 82": "OE1" <-> "OE2" Residue "c GLU 104": "OE1" <-> "OE2" Residue "c GLU 124": "OE1" <-> "OE2" Residue "c ARG 139": "NH1" <-> "NH2" Residue "c GLU 165": "OE1" <-> "OE2" Residue "c TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 169": "OE1" <-> "OE2" Residue "c GLU 187": "OE1" <-> "OE2" Residue "g GLU 74": "OE1" <-> "OE2" Residue "g GLU 90": "OE1" <-> "OE2" Residue "g GLU 94": "OE1" <-> "OE2" Residue "g GLU 113": "OE1" <-> "OE2" Residue "g GLU 118": "OE1" <-> "OE2" Residue "g GLU 123": "OE1" <-> "OE2" Residue "g GLU 139": "OE1" <-> "OE2" Residue "g GLU 146": "OE1" <-> "OE2" Residue "i GLU 34": "OE1" <-> "OE2" Residue "i GLU 37": "OE1" <-> "OE2" Residue "i GLU 46": "OE1" <-> "OE2" Residue "i GLU 56": "OE1" <-> "OE2" Residue "i GLU 89": "OE1" <-> "OE2" Residue "i GLU 93": "OE1" <-> "OE2" Residue "i GLU 112": "OE1" <-> "OE2" Residue "i PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 14": "OD1" <-> "OD2" Residue "j GLU 23": "OE1" <-> "OE2" Residue "j GLU 27": "OE1" <-> "OE2" Residue "j GLU 45": "OE1" <-> "OE2" Residue "j GLU 63": "OE1" <-> "OE2" Residue "j GLU 66": "OE1" <-> "OE2" Residue "j GLU 99": "OE1" <-> "OE2" Residue "m GLU 36": "OE1" <-> "OE2" Residue "m GLU 41": "OE1" <-> "OE2" Residue "m GLU 51": "OE1" <-> "OE2" Residue "m GLU 52": "OE1" <-> "OE2" Residue "m GLU 66": "OE1" <-> "OE2" Residue "m GLU 72": "OE1" <-> "OE2" Residue "m GLU 82": "OE1" <-> "OE2" Residue "n GLU 20": "OE1" <-> "OE2" Residue "n GLU 46": "OE1" <-> "OE2" Residue "s ARG 3": "NH1" <-> "NH2" Residue "s GLU 20": "OE1" <-> "OE2" Residue "s GLU 24": "OE1" <-> "OE2" Residue "s GLU 64": "OE1" <-> "OE2" Residue "s GLU 73": "OE1" <-> "OE2" Residue "h GLU 26": "OE1" <-> "OE2" Residue "h ASP 48": "OD1" <-> "OD2" Residue "h PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 53": "OE1" <-> "OE2" Residue "h ASP 54": "OD1" <-> "OD2" Residue "h PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 72": "NH1" <-> "NH2" Residue "h ASP 115": "OD1" <-> "OD2" Residue "h GLU 117": "OE1" <-> "OE2" Residue "r GLU 40": "OE1" <-> "OE2" Residue "r ARG 68": "NH1" <-> "NH2" Residue "f GLU 5": "OE1" <-> "OE2" Residue "f ARG 11": "NH1" <-> "NH2" Residue "f ARG 46": "NH1" <-> "NH2" Residue "f TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 74": "OE1" <-> "OE2" Residue "f PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 77": "NH1" <-> "NH2" Residue "7 ARG 120": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 136664 Number of models: 1 Model: "" Number of chains: 81 Chain: "0" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 433 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 3, 'TRANS': 51} Chain: "1" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 403 Classifications: {'peptide': 48} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "2" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 368 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "3" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 522 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'TRANS': 64} Chain: "4" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 297 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "6" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 356 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "A" Number of atoms: 58964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2745, 58964 Inner-chain residues flagged as termini: ['pdbres=" G A 328 "', 'pdbres=" G A1220 "'] Classifications: {'RNA': 2745} Modifications used: {'5*END': 2, 'rna2p': 2, 'rna2p_pur': 277, 'rna2p_pyr': 132, 'rna3p': 1, 'rna3p_pur': 1321, 'rna3p_pyr': 1011} Link IDs: {'rna2p': 411, 'rna3p': 2333} Chain breaks: 6 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 2392 Classifications: {'RNA': 112} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 8, 'rna3p_pur': 54, 'rna3p_pyr': 44} Link IDs: {'rna2p': 14, 'rna3p': 97} Chain: "C" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2094 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 17, 'TRANS': 255} Chain: "D" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1575 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 10, 'TRANS': 196} Chain: "E" Number of atoms: 1567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1567 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "F" Number of atoms: 1405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1405 Classifications: {'peptide': 178} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain: "G" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1342 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 9, 'TRANS': 165} Chain: "J" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1142 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 135} Chain: "K" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 921 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1082 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain: "M" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1076 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain: "N" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 954 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "O" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 913 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain: "P" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 945 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "Q" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 950 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'TRANS': 117} Chain: "R" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 795 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 98} Chain: "S" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 850 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "T" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 716 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "U" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 770 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 6, 'TRANS': 95} Chain: "W" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 650 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "X" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 468 Classifications: {'peptide': 61} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "Y" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'TRANS': 64} Chain: "Z" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 456 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "a" Number of atoms: 32891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1533, 32891 Classifications: {'RNA': 1533} Modifications used: {'rna2p_pur': 119, 'rna2p_pyr': 85, 'rna3p_pur': 751, 'rna3p_pyr': 578} Link IDs: {'rna2p': 204, 'rna3p': 1328} Chain: "e" Number of atoms: 1170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1170 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 151} Chain: "k" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 847 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "l" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1047 Classifications: {'peptide': 135} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 127} Chain: "o" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 730 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "q" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 699 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "t" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 658 Classifications: {'peptide': 86} Link IDs: {'TRANS': 85} Chain: "y" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1645 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 35, 'rna3p_pyr': 33} Link IDs: {'rna2p': 9, 'rna3p': 67} Chain: "w" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1645 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 34, 'rna3p_pyr': 33} Link IDs: {'rna2p': 9, 'rna3p': 67} Chain: "8" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'RNA': 6} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "c" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1607 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 3, 'TRANS': 200} Chain: "g" Number of atoms: 1199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1199 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "i" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 994 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "j" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 788 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 91} Chain: "m" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 942 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "n" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 498 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "s" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 668 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "h" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 958 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "r" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 522 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "f" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 755 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain: "7" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Classifications: {'peptide': 9} Link IDs: {'PTRANS': 1, 'TRANS': 7} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 195 Unusual residues: {' K': 40, ' MG': 155} Classifications: {'undetermined': 195} Link IDs: {None: 194} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 2, ' MG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Unusual residues: {' MG': 40} Classifications: {'undetermined': 40} Link IDs: {None: 39} Chain: "y" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Chain: "w" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 811, 811 Classifications: {'water': 811} Link IDs: {None: 810} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "L" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "N" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 132 Classifications: {'water': 132} Link IDs: {None: 131} Chain: "k" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "y" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "w" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "7" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 242 SG CYS 0 30 133.250 246.123 128.229 1.00 55.10 S ATOM 261 SG CYS 0 33 130.639 247.778 125.997 1.00 68.78 S ATOM 339 SG CYS 0 43 132.069 244.330 125.251 1.00 57.04 S ATOM 359 SG CYS 0 46 134.282 247.315 124.746 1.00 57.34 S ATOM 493 SG CYS 1 9 42.938 130.418 93.899 1.00 70.46 S ATOM 515 SG CYS 1 12 42.280 133.545 92.139 1.00 70.61 S ATOM 724 SG CYS 1 36 41.734 133.638 95.621 1.00 65.70 S ATOM 1811 SG CYS 4 11 122.056 143.754 176.000 1.00 59.62 S ATOM 1835 SG CYS 4 14 120.167 147.014 174.644 1.00 60.21 S ATOM 1939 SG CYS 4 27 123.555 147.033 176.567 1.00 53.07 S ATOM 2145 SG CYS 6 16 63.083 64.845 127.952 1.00148.76 S ATOM 2156 SG CYS 6 18 63.121 63.355 129.394 1.00161.53 S ATOM 2296 SG CYS 6 36 61.876 67.604 130.462 1.00138.52 S ATOM 2317 SG CYS 6 39 64.759 64.683 129.344 1.00132.31 S ATOM A0OS0 SG CYS n 24 142.024 55.726 120.356 1.00 73.36 S ATOM A0OSQ SG CYS n 27 143.304 59.333 120.829 1.00 72.67 S ATOM A0OVP SG CYS n 40 141.276 58.388 117.686 1.00 73.58 S ATOM A0OWE SG CYS n 43 144.675 57.165 118.077 1.00 73.28 S Time building chain proxies: 52.38, per 1000 atoms: 0.38 Number of scatterers: 136664 At special positions: 0 Unit cell: (266.5, 272.24, 226.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 5 29.99 K 43 19.00 S 122 16.00 P 4547 15.00 Mg 199 11.99 O 39409 8.00 N 25200 7.00 C 67139 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 55.60 Conformation dependent library (CDL) restraints added in 5.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 05001 " pdb="ZN ZN 05001 " - pdb=" SG CYS 0 30 " pdb="ZN ZN 05001 " - pdb=" SG CYS 0 33 " pdb="ZN ZN 05001 " - pdb=" SG CYS 0 46 " pdb="ZN ZN 05001 " - pdb=" SG CYS 0 43 " pdb=" ZN 1 101 " pdb="ZN ZN 1 101 " - pdb=" SG CYS 1 12 " pdb="ZN ZN 1 101 " - pdb=" SG CYS 1 9 " pdb="ZN ZN 1 101 " - pdb=" SG CYS 1 36 " pdb=" ZN 4 101 " pdb="ZN ZN 4 101 " - pdb=" ND1 HIS 4 32 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 14 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 27 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 11 " pdb=" ZN 65001 " pdb="ZN ZN 65001 " - pdb=" SG CYS 6 39 " pdb="ZN ZN 65001 " - pdb=" SG CYS 6 36 " pdb="ZN ZN 65001 " - pdb=" SG CYS 6 18 " pdb="ZN ZN 65001 " - pdb=" SG CYS 6 16 " pdb=" ZN n5001 " pdb="ZN ZN n5001 " - pdb=" SG CYS n 27 " pdb="ZN ZN n5001 " - pdb=" SG CYS n 24 " pdb="ZN ZN n5001 " - pdb=" SG CYS n 43 " pdb="ZN ZN n5001 " - pdb=" SG CYS n 40 " Number of angles added : 21 9466 Ramachandran restraints generated. 4733 Oldfield, 0 Emsley, 4733 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8814 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 141 helices and 68 sheets defined 36.1% alpha, 20.3% beta 1532 base pairs and 2449 stacking pairs defined. Time for finding SS restraints: 68.27 Creating SS restraints... Processing helix chain '0' and resid 9 through 19 removed outlier: 4.935A pdb=" N HIS 0 19 " --> pdb=" O LEU 0 15 " (cutoff:3.500A) Processing helix chain '1' and resid 22 through 27 Proline residue: 1 27 - end of helix Processing helix chain '2' and resid 8 through 16 Processing helix chain '2' and resid 17 through 25 removed outlier: 4.090A pdb=" N SER 2 24 " --> pdb=" O SER 2 20 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LYS 2 25 " --> pdb=" O ARG 2 21 " (cutoff:3.500A) Processing helix chain '2' and resid 26 through 38 Processing helix chain '3' and resid 7 through 14 removed outlier: 3.531A pdb=" N ARG 3 13 " --> pdb=" O GLY 3 9 " (cutoff:3.500A) Processing helix chain '3' and resid 32 through 37 removed outlier: 3.932A pdb=" N LYS 3 36 " --> pdb=" O LEU 3 32 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N SER 3 37 " --> pdb=" O PHE 3 33 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 32 through 37' Processing helix chain '3' and resid 38 through 47 removed outlier: 3.988A pdb=" N LYS 3 46 " --> pdb=" O ARG 3 42 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N SER 3 47 " --> pdb=" O LYS 3 43 " (cutoff:3.500A) Processing helix chain '3' and resid 51 through 63 removed outlier: 3.525A pdb=" N ARG 3 57 " --> pdb=" O GLY 3 53 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N GLN 3 60 " --> pdb=" O LYS 3 56 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N MET 3 61 " --> pdb=" O ARG 3 57 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU 3 62 " --> pdb=" O ILE 3 58 " (cutoff:3.500A) Processing helix chain '6' and resid 40 through 45 Processing helix chain 'C' and resid 30 through 35 removed outlier: 3.650A pdb=" N LEU C 34 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ALA C 35 " --> pdb=" O LYS C 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 30 through 35' Processing helix chain 'C' and resid 131 through 136 removed outlier: 3.695A pdb=" N ILE C 135 " --> pdb=" O PRO C 131 " (cutoff:3.500A) Proline residue: C 136 - end of helix No H-bonds generated for 'chain 'C' and resid 131 through 136' Processing helix chain 'C' and resid 207 through 215 removed outlier: 3.738A pdb=" N SER C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 3.901A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ASN C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 226' Processing helix chain 'C' and resid 266 through 271 removed outlier: 5.442A pdb=" N VAL C 271 " --> pdb=" O ASP C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 202 removed outlier: 4.384A pdb=" N GLU C 201 " --> pdb=" O GLU C 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 62 removed outlier: 5.016A pdb=" N ASN D 62 " --> pdb=" O GLU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 71 removed outlier: 4.570A pdb=" N LYS D 71 " --> pdb=" O GLY D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 92 removed outlier: 3.942A pdb=" N TYR D 91 " --> pdb=" O GLU D 87 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N GLU D 92 " --> pdb=" O MET D 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 87 through 92' Processing helix chain 'D' and resid 98 through 103 removed outlier: 4.903A pdb=" N PHE D 102 " --> pdb=" O LYS D 98 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N SER D 103 " --> pdb=" O VAL D 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 98 through 103' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 121 through 127 removed outlier: 4.406A pdb=" N HIS D 126 " --> pdb=" O GLY D 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 45 removed outlier: 3.682A pdb=" N ARG E 45 " --> pdb=" O ARG E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 58 removed outlier: 6.287A pdb=" N ARG E 58 " --> pdb=" O ARG E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 121 Processing helix chain 'E' and resid 135 through 147 Processing helix chain 'E' and resid 160 through 168 Processing helix chain 'E' and resid 182 through 190 removed outlier: 3.508A pdb=" N HIS E 189 " --> pdb=" O ASP E 185 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLU E 190 " --> pdb=" O VAL E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 207 removed outlier: 3.508A pdb=" N VAL E 205 " --> pdb=" O LYS E 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 11 Processing helix chain 'F' and resid 12 through 21 Processing helix chain 'F' and resid 40 through 46 removed outlier: 4.737A pdb=" N VAL F 44 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLN F 45 " --> pdb=" O GLY F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 62 removed outlier: 4.573A pdb=" N ASP F 51 " --> pdb=" O ALA F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 112 removed outlier: 4.749A pdb=" N LEU F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Proline residue: F 109 - end of helix removed outlier: 6.042A pdb=" N ARG F 112 " --> pdb=" O LEU F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 147 removed outlier: 3.696A pdb=" N VAL F 146 " --> pdb=" O ASP F 142 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N THR F 147 " --> pdb=" O TYR F 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 142 through 147' Processing helix chain 'F' and resid 162 through 174 removed outlier: 4.450A pdb=" N GLY F 174 " --> pdb=" O LEU F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 139 removed outlier: 3.870A pdb=" N ILE F 137 " --> pdb=" O GLU F 134 " (cutoff:3.500A) Proline residue: F 139 - end of helix Processing helix chain 'G' and resid 2 through 8 removed outlier: 5.687A pdb=" N LEU G 8 " --> pdb=" O VAL G 4 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 82 removed outlier: 3.840A pdb=" N GLY G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 154 removed outlier: 3.695A pdb=" N VAL G 152 " --> pdb=" O ASN G 148 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ARG G 153 " --> pdb=" O ILE G 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 39 Processing helix chain 'J' and resid 89 through 96 Processing helix chain 'J' and resid 97 through 111 Proline residue: J 111 - end of helix Processing helix chain 'J' and resid 113 through 124 removed outlier: 3.636A pdb=" N LYS J 121 " --> pdb=" O ARG J 117 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS J 122 " --> pdb=" O GLN J 118 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU J 123 " --> pdb=" O MET J 119 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASN J 124 " --> pdb=" O PHE J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 73 removed outlier: 4.452A pdb=" N LYS J 73 " --> pdb=" O LYS J 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 68 through 73' Processing helix chain 'K' and resid 103 through 110 removed outlier: 4.766A pdb=" N ARG K 107 " --> pdb=" O ALA K 103 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU K 108 " --> pdb=" O ARG K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 118 Processing helix chain 'L' and resid 37 through 42 removed outlier: 3.745A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N SER L 42 " --> pdb=" O GLN L 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 37 through 42' Processing helix chain 'L' and resid 56 through 62 Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 78 through 85 removed outlier: 3.639A pdb=" N LEU L 82 " --> pdb=" O ASN L 78 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY L 84 " --> pdb=" O ASP L 80 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE L 85 " --> pdb=" O LYS L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 100 Processing helix chain 'L' and resid 129 through 140 removed outlier: 3.597A pdb=" N GLY L 140 " --> pdb=" O VAL L 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 59 Processing helix chain 'M' and resid 110 through 126 removed outlier: 3.963A pdb=" N LYS M 124 " --> pdb=" O LEU M 120 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU M 125 " --> pdb=" O ALA M 121 " (cutoff:3.500A) Proline residue: M 126 - end of helix Processing helix chain 'N' and resid 9 through 28 Processing helix chain 'N' and resid 34 through 54 removed outlier: 4.460A pdb=" N SER N 42 " --> pdb=" O LYS N 38 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL N 43 " --> pdb=" O GLU N 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 66 removed outlier: 3.804A pdb=" N TYR N 65 " --> pdb=" O GLN N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 78 through 92 removed outlier: 3.890A pdb=" N ILE N 87 " --> pdb=" O LEU N 83 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ALA N 88 " --> pdb=" O PHE N 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 6 through 22 removed outlier: 4.309A pdb=" N LYS O 21 " --> pdb=" O ARG O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 89 removed outlier: 3.528A pdb=" N ALA O 74 " --> pdb=" O ASP O 70 " (cutoff:3.500A) Processing helix chain 'O' and resid 104 through 117 Processing helix chain 'P' and resid 2 through 14 removed outlier: 4.926A pdb=" N GLU P 11 " --> pdb=" O ASP P 7 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N GLN P 12 " --> pdb=" O ILE P 8 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU P 13 " --> pdb=" O THR P 9 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ARG P 14 " --> pdb=" O LYS P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 104 removed outlier: 4.418A pdb=" N ARG P 101 " --> pdb=" O LEU P 97 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLU P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU P 103 " --> pdb=" O TYR P 99 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ARG P 104 " --> pdb=" O LEU P 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 97 through 104' Processing helix chain 'P' and resid 105 through 110 removed outlier: 3.738A pdb=" N ARG P 109 " --> pdb=" O GLY P 105 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ILE P 110 " --> pdb=" O LYS P 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 105 through 110' Processing helix chain 'Q' and resid 8 through 22 removed outlier: 3.563A pdb=" N VAL Q 17 " --> pdb=" O ARG Q 13 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 3.847A pdb=" N THR Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 32 through 37 Processing helix chain 'Q' and resid 40 through 54 removed outlier: 4.109A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 56 through 73 Processing helix chain 'Q' and resid 75 through 87 Processing helix chain 'Q' and resid 91 through 101 Processing helix chain 'Q' and resid 102 through 119 Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.966A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 Processing helix chain 'S' and resid 41 through 61 Proline residue: S 45 - end of helix Processing helix chain 'T' and resid 3 through 9 removed outlier: 3.848A pdb=" N VAL T 7 " --> pdb=" O ASP T 3 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU T 8 " --> pdb=" O PRO T 4 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N LYS T 9 " --> pdb=" O ARG T 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 3 through 9' Processing helix chain 'T' and resid 14 through 24 removed outlier: 3.654A pdb=" N THR T 22 " --> pdb=" O ALA T 18 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU T 23 " --> pdb=" O ASP T 19 " (cutoff:3.500A) Processing helix chain 'T' and resid 35 through 47 Processing helix chain 'U' and resid 64 through 69 removed outlier: 4.228A pdb=" N VAL U 68 " --> pdb=" O HIS U 64 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N MET U 69 " --> pdb=" O VAL U 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 64 through 69' Processing helix chain 'X' and resid 50 through 56 removed outlier: 4.474A pdb=" N SER X 56 " --> pdb=" O ARG X 52 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 10 removed outlier: 3.868A pdb=" N ASP Y 8 " --> pdb=" O ASN Y 4 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU Y 9 " --> pdb=" O GLU Y 5 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N THR Y 10 " --> pdb=" O ILE Y 6 " (cutoff:3.500A) Processing helix chain 'Y' and resid 11 through 35 Processing helix chain 'Y' and resid 39 through 66 removed outlier: 4.645A pdb=" N ILE Y 43 " --> pdb=" O ASN Y 39 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG Y 44 " --> pdb=" O THR Y 40 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LYS Y 66 " --> pdb=" O ILE Y 62 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 removed outlier: 3.668A pdb=" N GLY Z 27 " --> pdb=" O VAL Z 23 " (cutoff:3.500A) Processing helix chain 'Z' and resid 40 through 51 Processing helix chain 'e' and resid 55 through 70 removed outlier: 4.192A pdb=" N LYS e 68 " --> pdb=" O VAL e 64 " (cutoff:3.500A) Processing helix chain 'e' and resid 109 through 119 removed outlier: 3.516A pdb=" N VAL e 114 " --> pdb=" O PRO e 110 " (cutoff:3.500A) Processing helix chain 'e' and resid 133 through 148 removed outlier: 3.943A pdb=" N ILE e 137 " --> pdb=" O PRO e 133 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER e 145 " --> pdb=" O LEU e 141 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU e 147 " --> pdb=" O GLY e 143 " (cutoff:3.500A) Processing helix chain 'e' and resid 150 through 158 Processing helix chain 'e' and resid 160 through 166 Processing helix chain 'k' and resid 56 through 62 removed outlier: 4.216A pdb=" N SER k 60 " --> pdb=" O GLY k 56 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR k 61 " --> pdb=" O SER k 57 " (cutoff:3.500A) Proline residue: k 62 - end of helix No H-bonds generated for 'chain 'k' and resid 56 through 62' Processing helix chain 'k' and resid 63 through 80 removed outlier: 3.987A pdb=" N GLU k 78 " --> pdb=" O LYS k 74 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N HIS k 79 " --> pdb=" O GLY k 75 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY k 80 " --> pdb=" O SER k 76 " (cutoff:3.500A) Processing helix chain 'k' and resid 94 through 105 removed outlier: 3.896A pdb=" N ALA k 98 " --> pdb=" O GLY k 94 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA k 104 " --> pdb=" O ARG k 100 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ALA k 105 " --> pdb=" O ALA k 101 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 11 Processing helix chain 'l' and resid 21 through 26 removed outlier: 4.033A pdb=" N ASN l 25 " --> pdb=" O SER l 21 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS l 26 " --> pdb=" O PRO l 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 21 through 26' Processing helix chain 'o' and resid 4 through 16 removed outlier: 4.427A pdb=" N LYS o 8 " --> pdb=" O THR o 4 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN o 13 " --> pdb=" O ASN o 9 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU o 14 " --> pdb=" O GLN o 10 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N PHE o 15 " --> pdb=" O LEU o 11 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 47 removed outlier: 3.761A pdb=" N THR o 45 " --> pdb=" O GLU o 41 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS o 47 " --> pdb=" O LEU o 43 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.556A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 Processing helix chain 't' and resid 4 through 42 removed outlier: 3.629A pdb=" N GLU t 16 " --> pdb=" O LYS t 12 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS t 20 " --> pdb=" O GLU t 16 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE t 24 " --> pdb=" O HIS t 20 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL t 35 " --> pdb=" O ALA t 31 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA t 40 " --> pdb=" O GLU t 36 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN t 41 " --> pdb=" O ALA t 37 " (cutoff:3.500A) Processing helix chain 't' and resid 44 through 65 removed outlier: 3.642A pdb=" N THR t 49 " --> pdb=" O ASP t 45 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU t 53 " --> pdb=" O THR t 49 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA t 61 " --> pdb=" O ARG t 57 " (cutoff:3.500A) Processing helix chain 't' and resid 68 through 87 removed outlier: 3.818A pdb=" N SER t 87 " --> pdb=" O VAL t 83 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 removed outlier: 3.559A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 47 removed outlier: 3.554A pdb=" N SER c 47 " --> pdb=" O SER c 43 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 77 Processing helix chain 'c' and resid 80 through 95 removed outlier: 3.970A pdb=" N GLU c 84 " --> pdb=" O GLY c 80 " (cutoff:3.500A) Processing helix chain 'c' and resid 107 through 112 removed outlier: 3.956A pdb=" N ASP c 111 " --> pdb=" O ARG c 107 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ALA c 112 " --> pdb=" O ALA c 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 107 through 112' Processing helix chain 'c' and resid 113 through 126 Processing helix chain 'c' and resid 128 through 144 removed outlier: 3.559A pdb=" N GLN c 136 " --> pdb=" O ALA c 132 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 removed outlier: 4.310A pdb=" N LEU g 26 " --> pdb=" O LEU g 22 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 55 removed outlier: 3.693A pdb=" N SER g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 removed outlier: 3.565A pdb=" N ASN g 68 " --> pdb=" O GLN g 64 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 111 removed outlier: 3.812A pdb=" N THR g 97 " --> pdb=" O PRO g 93 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR g 98 " --> pdb=" O GLU g 94 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG g 111 " --> pdb=" O TYR g 107 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 Processing helix chain 'g' and resid 132 through 149 Processing helix chain 'i' and resid 34 through 39 Processing helix chain 'i' and resid 41 through 56 removed outlier: 3.517A pdb=" N ILE i 45 " --> pdb=" O SER i 41 " (cutoff:3.500A) Proline residue: i 51 - end of helix Processing helix chain 'i' and resid 71 through 91 removed outlier: 3.538A pdb=" N LEU i 88 " --> pdb=" O ALA i 84 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU i 89 " --> pdb=" O ARG i 85 " (cutoff:3.500A) Processing helix chain 'i' and resid 92 through 102 removed outlier: 4.866A pdb=" N THR i 96 " --> pdb=" O PRO i 92 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N THR i 97 " --> pdb=" O GLU i 93 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 removed outlier: 3.538A pdb=" N LEU j 18 " --> pdb=" O ASP j 14 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 91 removed outlier: 3.696A pdb=" N VAL j 84 " --> pdb=" O THR j 80 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP j 85 " --> pdb=" O PRO j 81 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N MET j 88 " --> pdb=" O VAL j 84 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG j 89 " --> pdb=" O ASP j 85 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU j 90 " --> pdb=" O ALA j 86 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ASP j 91 " --> pdb=" O LEU j 87 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 22 removed outlier: 3.925A pdb=" N THR m 20 " --> pdb=" O VAL m 16 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE m 22 " --> pdb=" O SER m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 Processing helix chain 'm' and resid 49 through 64 removed outlier: 3.757A pdb=" N LYS m 62 " --> pdb=" O ASP m 58 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU m 63 " --> pdb=" O ILE m 59 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N LYS m 64 " --> pdb=" O ILE m 60 " (cutoff:3.500A) Processing helix chain 'm' and resid 66 through 84 Processing helix chain 'm' and resid 85 through 94 Processing helix chain 'm' and resid 106 through 111 Processing helix chain 'n' and resid 3 through 13 removed outlier: 5.333A pdb=" N THR n 13 " --> pdb=" O LYS n 9 " (cutoff:3.500A) Processing helix chain 'n' and resid 16 through 21 removed outlier: 3.876A pdb=" N GLU n 20 " --> pdb=" O PHE n 16 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N TYR n 21 " --> pdb=" O LYS n 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 16 through 21' Processing helix chain 'n' and resid 40 through 51 Processing helix chain 's' and resid 12 through 26 removed outlier: 4.322A pdb=" N THR s 25 " --> pdb=" O LYS s 21 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASP s 26 " --> pdb=" O LEU s 22 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 76 removed outlier: 4.418A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA s 75 " --> pdb=" O LEU s 71 " (cutoff:3.500A) Proline residue: s 76 - end of helix No H-bonds generated for 'chain 's' and resid 70 through 76' Processing helix chain 'h' and resid 9 through 21 removed outlier: 3.912A pdb=" N ARG h 13 " --> pdb=" O ASP h 9 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 43 removed outlier: 3.637A pdb=" N ILE h 39 " --> pdb=" O GLU h 35 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLU h 43 " --> pdb=" O ILE h 39 " (cutoff:3.500A) Processing helix chain 'h' and resid 114 through 121 removed outlier: 3.740A pdb=" N ALA h 118 " --> pdb=" O THR h 114 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG h 119 " --> pdb=" O ASP h 115 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LYS h 121 " --> pdb=" O GLU h 117 " (cutoff:3.500A) Processing helix chain 'r' and resid 16 through 22 Processing helix chain 'r' and resid 30 through 39 removed outlier: 3.913A pdb=" N LYS r 36 " --> pdb=" O ASP r 32 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE r 37 " --> pdb=" O LEU r 33 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL r 38 " --> pdb=" O LEU r 34 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N SER r 39 " --> pdb=" O LYS r 35 " (cutoff:3.500A) Processing helix chain 'r' and resid 46 through 51 Processing helix chain 'r' and resid 53 through 71 removed outlier: 3.568A pdb=" N MET r 70 " --> pdb=" O ARG r 66 " (cutoff:3.500A) Processing helix chain 'f' and resid 15 through 32 Processing helix chain 'f' and resid 68 through 83 removed outlier: 6.069A pdb=" N VAL f 72 " --> pdb=" O ASP f 68 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N ASP f 83 " --> pdb=" O ALA f 79 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '1' and resid 3 through 8 Processing sheet with id= 2, first strand: chain '1' and resid 30 through 34 removed outlier: 5.810A pdb=" N VAL 1 30 " --> pdb=" O GLU 1 47 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '4' and resid 14 through 19 Processing sheet with id= 4, first strand: chain '6' and resid 20 through 25 removed outlier: 4.066A pdb=" N ASN 6 20 " --> pdb=" O CYS 6 16 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N THR 6 24 " --> pdb=" O ALA 6 12 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N GLU 6 29 " --> pdb=" O LYS 6 11 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N THR 6 13 " --> pdb=" O GLU 6 29 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'C' and resid 2 through 6 removed outlier: 6.479A pdb=" N ALA C 2 " --> pdb=" O ASP C 20 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N MET C 16 " --> pdb=" O TYR C 6 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 75 through 78 removed outlier: 4.637A pdb=" N THR C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N GLY C 127 " --> pdb=" O GLU C 115 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N MET C 117 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 80 through 83 removed outlier: 3.524A pdb=" N THR C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ASN C 90 " --> pdb=" O ALA C 106 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'C' and resid 138 through 142 removed outlier: 4.375A pdb=" N THR C 139 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU C 173 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'D' and resid 3 through 7 removed outlier: 5.532A pdb=" N LYS D 3 " --> pdb=" O SER D 204 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU D 167 " --> pdb=" O SER D 114 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'D' and resid 11 through 17 removed outlier: 3.699A pdb=" N GLY D 11 " --> pdb=" O VAL D 27 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASP D 21 " --> pdb=" O ALA D 17 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'D' and resid 33 through 36 removed outlier: 6.617A pdb=" N GLN D 50 " --> pdb=" O LEU D 36 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'E' and resid 2 through 6 removed outlier: 4.287A pdb=" N GLY E 15 " --> pdb=" O LEU E 6 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'E' and resid 122 through 125 Processing sheet with id= 14, first strand: chain 'F' and resid 65 through 69 removed outlier: 3.655A pdb=" N GLY F 86 " --> pdb=" O THR F 68 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS F 33 " --> pdb=" O VAL F 157 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N GLY F 39 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLY F 151 " --> pdb=" O GLY F 39 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'F' and resid 72 through 75 removed outlier: 7.042A pdb=" N LYS F 72 " --> pdb=" O GLU F 81 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU F 81 " --> pdb=" O LYS F 72 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'G' and resid 16 through 20 removed outlier: 3.819A pdb=" N THR G 24 " --> pdb=" O ASN G 20 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'G' and resid 43 through 46 Processing sheet with id= 18, first strand: chain 'G' and resid 95 through 100 Processing sheet with id= 19, first strand: chain 'G' and resid 122 through 126 removed outlier: 5.896A pdb=" N THR G 130 " --> pdb=" O LEU G 90 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'J' and resid 53 through 58 removed outlier: 5.093A pdb=" N ASP J 20 " --> pdb=" O TYR J 141 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'J' and resid 75 through 79 removed outlier: 7.247A pdb=" N GLY J 84 " --> pdb=" O THR J 79 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'K' and resid 6 through 10 removed outlier: 4.662A pdb=" N THR K 6 " --> pdb=" O THR K 21 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ARG K 17 " --> pdb=" O VAL K 10 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'K' and resid 38 through 41 Processing sheet with id= 24, first strand: chain 'K' and resid 63 through 66 removed outlier: 3.611A pdb=" N LYS K 66 " --> pdb=" O GLU K 81 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLU K 81 " --> pdb=" O LYS K 66 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'K' and resid 68 through 71 removed outlier: 3.777A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'M' and resid 38 through 41 No H-bonds generated for sheet with id= 26 Processing sheet with id= 27, first strand: chain 'M' and resid 63 through 66 removed outlier: 3.876A pdb=" N PHE M 104 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N GLU M 31 " --> pdb=" O ARG M 134 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LYS M 128 " --> pdb=" O LEU M 37 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'M' and resid 73 through 77 removed outlier: 6.745A pdb=" N TYR M 74 " --> pdb=" O GLU M 91 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'N' and resid 29 through 33 Processing sheet with id= 30, first strand: chain 'O' and resid 53 through 57 removed outlier: 3.592A pdb=" N ALA O 54 " --> pdb=" O ILE O 44 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'P' and resid 38 through 45 removed outlier: 6.687A pdb=" N THR P 25 " --> pdb=" O VAL P 87 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS P 83 " --> pdb=" O HIS P 29 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'P' and resid 49 through 53 removed outlier: 3.578A pdb=" N LYS P 49 " --> pdb=" O THR P 60 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLY P 53 " --> pdb=" O SER P 56 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'R' and resid 11 through 15 removed outlier: 4.056A pdb=" N TYR R 2 " --> pdb=" O GLY R 42 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE R 40 " --> pdb=" O ILE R 4 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'R' and resid 18 through 23 removed outlier: 4.161A pdb=" N GLN R 18 " --> pdb=" O ILE R 97 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LYS R 94 " --> pdb=" O GLU R 63 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR R 59 " --> pdb=" O GLU R 98 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLU R 31 " --> pdb=" O VAL R 62 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'R' and resid 56 through 59 Processing sheet with id= 36, first strand: chain 'R' and resid 64 through 67 Processing sheet with id= 37, first strand: chain 'R' and resid 70 through 77 removed outlier: 4.180A pdb=" N VAL R 82 " --> pdb=" O LYS R 77 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'S' and resid 2 through 8 removed outlier: 6.664A pdb=" N VAL S 106 " --> pdb=" O SER S 72 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'S' and resid 73 through 79 removed outlier: 4.731A pdb=" N THR S 100 " --> pdb=" O GLY S 79 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'S' and resid 81 through 88 removed outlier: 4.050A pdb=" N ARG S 92 " --> pdb=" O ARG S 88 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'T' and resid 25 through 29 removed outlier: 4.316A pdb=" N LYS T 62 " --> pdb=" O THR T 73 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N ARG T 75 " --> pdb=" O LYS T 60 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LYS T 60 " --> pdb=" O ARG T 75 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ARG T 77 " --> pdb=" O ASN T 58 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASN T 58 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ALA T 79 " --> pdb=" O ILE T 56 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE T 56 " --> pdb=" O ALA T 79 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL T 81 " --> pdb=" O VAL T 54 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL T 54 " --> pdb=" O VAL T 81 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'U' and resid 25 through 28 Processing sheet with id= 43, first strand: chain 'U' and resid 39 through 46 removed outlier: 5.025A pdb=" N ASN U 39 " --> pdb=" O ALA U 61 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'U' and resid 80 through 84 removed outlier: 6.735A pdb=" N ARG U 80 " --> pdb=" O LYS U 95 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ARG U 92 " --> pdb=" O LEU U 101 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN U 99 " --> pdb=" O ALA U 94 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'W' and resid 45 through 48 removed outlier: 4.613A pdb=" N GLN W 48 " --> pdb=" O ASP W 65 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ASP W 65 " --> pdb=" O GLN W 48 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR W 66 " --> pdb=" O GLY W 62 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'W' and resid 73 through 79 Processing sheet with id= 47, first strand: chain 'X' and resid 11 through 19 No H-bonds generated for sheet with id= 47 Processing sheet with id= 48, first strand: chain 'Z' and resid 32 through 38 removed outlier: 4.332A pdb=" N GLN Z 33 " --> pdb=" O LEU Z 8 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LYS Z 3 " --> pdb=" O GLN Z 59 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N LEU Z 53 " --> pdb=" O LYS Z 9 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'e' and resid 11 through 16 removed outlier: 6.795A pdb=" N LEU e 36 " --> pdb=" O VAL e 16 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'e' and resid 83 through 88 removed outlier: 7.519A pdb=" N HIS e 83 " --> pdb=" O PRO e 98 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ASN e 93 " --> pdb=" O LEU e 128 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA e 99 " --> pdb=" O ASP e 122 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASP e 122 " --> pdb=" O ALA e 99 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'e' and resid 35 through 41 removed outlier: 4.331A pdb=" N ALA e 35 " --> pdb=" O GLY e 51 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY e 51 " --> pdb=" O ALA e 35 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N VAL e 37 " --> pdb=" O GLY e 49 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY e 49 " --> pdb=" O VAL e 37 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N HIS e 45 " --> pdb=" O ASP e 41 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'k' and resid 45 through 48 removed outlier: 3.560A pdb=" N SER k 45 " --> pdb=" O ILE k 36 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER k 47 " --> pdb=" O VAL k 34 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR k 83 " --> pdb=" O GLU k 19 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE k 25 " --> pdb=" O THR k 87 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LYS k 89 " --> pdb=" O ILE k 25 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER k 27 " --> pdb=" O LYS k 89 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'l' and resid 27 through 30 removed outlier: 3.720A pdb=" N THR l 36 " --> pdb=" O GLY l 27 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU l 34 " --> pdb=" O ASN l 29 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'l' and resid 42 through 45 removed outlier: 4.923A pdb=" N LEU l 94 " --> pdb=" O VAL l 111 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY l 98 " --> pdb=" O ARG l 107 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ARG l 107 " --> pdb=" O GLY l 98 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'l' and resid 49 through 54 removed outlier: 5.156A pdb=" N LYS l 64 " --> pdb=" O ILE l 80 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'q' and resid 9 through 13 Processing sheet with id= 57, first strand: chain 'q' and resid 21 through 32 No H-bonds generated for sheet with id= 57 Processing sheet with id= 58, first strand: chain 'q' and resid 58 through 61 No H-bonds generated for sheet with id= 58 Processing sheet with id= 59, first strand: chain 'c' and resid 53 through 58 removed outlier: 4.022A pdb=" N LYS c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'c' and resid 163 through 168 Processing sheet with id= 61, first strand: chain 'g' and resid 72 through 79 removed outlier: 6.529A pdb=" N VAL g 72 " --> pdb=" O VAL g 91 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG g 78 " --> pdb=" O TYR g 85 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'i' and resid 5 through 11 removed outlier: 3.810A pdb=" N THR i 60 " --> pdb=" O GLY i 24 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ARG i 27 " --> pdb=" O TYR i 61 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'j' and resid 39 through 42 removed outlier: 4.405A pdb=" N LYS j 71 " --> pdb=" O LEU j 42 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'j' and resid 44 through 52 Processing sheet with id= 65, first strand: chain 's' and resid 30 through 34 removed outlier: 5.039A pdb=" N HIS s 47 " --> pdb=" O ILE s 62 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'h' and resid 103 through 107 removed outlier: 5.283A pdb=" N ILE h 103 " --> pdb=" O ALA h 129 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA h 129 " --> pdb=" O ILE h 103 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE h 105 " --> pdb=" O VAL h 127 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL h 127 " --> pdb=" O ILE h 105 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N SER h 107 " --> pdb=" O GLY h 125 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'f' and resid 39 through 43 removed outlier: 4.053A pdb=" N GLY f 39 " --> pdb=" O ASN f 64 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TRP f 43 " --> pdb=" O TYR f 60 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N TYR f 60 " --> pdb=" O TRP f 43 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LYS f 3 " --> pdb=" O GLU f 93 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET f 7 " --> pdb=" O ILE f 89 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG f 87 " --> pdb=" O ILE f 9 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'f' and resid 44 through 47 removed outlier: 3.594A pdb=" N GLY f 44 " --> pdb=" O TYR f 60 " (cutoff:3.500A) 1490 hydrogen bonds defined for protein. 4380 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3853 hydrogen bonds 6114 hydrogen bond angles 0 basepair planarities 1532 basepair parallelities 2449 stacking parallelities Total time for adding SS restraints: 310.71 Time building geometry restraints manager: 60.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 17064 1.33 - 1.46: 70291 1.46 - 1.58: 50962 1.58 - 1.71: 9044 1.71 - 1.84: 219 Bond restraints: 147580 Sorted by residual: bond pdb=" C5 2MA A2532 " pdb=" C6 2MA A2532 " ideal model delta sigma weight residual 1.540 1.376 0.164 2.00e-02 2.50e+03 6.73e+01 bond pdb=" N3 OMG A2280 " pdb=" C4 OMG A2280 " ideal model delta sigma weight residual 1.492 1.348 0.144 2.00e-02 2.50e+03 5.16e+01 bond pdb=" N3 2MA A2532 " pdb=" C4 2MA A2532 " ideal model delta sigma weight residual 1.488 1.347 0.141 2.00e-02 2.50e+03 4.98e+01 bond pdb=" C2 OMG A2280 " pdb=" N3 OMG A2280 " ideal model delta sigma weight residual 1.466 1.336 0.130 2.00e-02 2.50e+03 4.26e+01 bond pdb=" C5 OMG A2280 " pdb=" C6 OMG A2280 " ideal model delta sigma weight residual 1.548 1.418 0.130 2.00e-02 2.50e+03 4.21e+01 ... (remaining 147575 not shown) Histogram of bond angle deviations from ideal: 78.95 - 90.32: 19 90.32 - 101.70: 10038 101.70 - 113.08: 97742 113.08 - 124.46: 94067 124.46 - 135.84: 19914 Bond angle restraints: 221780 Sorted by residual: angle pdb=" O3' A A 732 " pdb=" P U A 733 " pdb=" O5' U A 733 " ideal model delta sigma weight residual 104.00 79.28 24.72 1.50e+00 4.44e-01 2.72e+02 angle pdb=" O3' A A 225 " pdb=" P A A 226 " pdb=" O5' A A 226 " ideal model delta sigma weight residual 104.00 81.38 22.62 1.50e+00 4.44e-01 2.27e+02 angle pdb=" O3' A A1375 " pdb=" P G A1376 " pdb=" O5' G A1376 " ideal model delta sigma weight residual 104.00 82.00 22.00 1.50e+00 4.44e-01 2.15e+02 angle pdb=" O3' A A 490 " pdb=" P C A 491 " pdb=" O5' C A 491 " ideal model delta sigma weight residual 104.00 84.35 19.65 1.50e+00 4.44e-01 1.72e+02 angle pdb=" O3' G a1313 " pdb=" P G a1314 " pdb=" O5' G a1314 " ideal model delta sigma weight residual 104.00 87.06 16.94 1.50e+00 4.44e-01 1.27e+02 ... (remaining 221775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.77: 84321 35.77 - 71.55: 9440 71.55 - 107.32: 1021 107.32 - 143.09: 22 143.09 - 178.87: 34 Dihedral angle restraints: 94838 sinusoidal: 81134 harmonic: 13704 Sorted by residual: dihedral pdb=" C5' G a 641 " pdb=" C4' G a 641 " pdb=" C3' G a 641 " pdb=" O3' G a 641 " ideal model delta sinusoidal sigma weight residual 147.00 81.50 65.50 1 8.00e+00 1.56e-02 8.78e+01 dihedral pdb=" O4' U A2334 " pdb=" C1' U A2334 " pdb=" N1 U A2334 " pdb=" C2 U A2334 " ideal model delta sinusoidal sigma weight residual -160.00 18.87 -178.87 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U a 16 " pdb=" C1' U a 16 " pdb=" N1 U a 16 " pdb=" C2 U a 16 " ideal model delta sinusoidal sigma weight residual 200.00 23.21 176.79 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 94835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.186: 26151 0.186 - 0.372: 2284 0.372 - 0.559: 44 0.559 - 0.745: 8 0.745 - 0.931: 2 Chirality restraints: 28489 Sorted by residual: chirality pdb=" P C A 491 " pdb=" OP1 C A 491 " pdb=" OP2 C A 491 " pdb=" O5' C A 491 " both_signs ideal model delta sigma weight residual True 2.41 -1.48 0.93 2.00e-01 2.50e+01 2.17e+01 chirality pdb=" P U A 733 " pdb=" OP1 U A 733 " pdb=" OP2 U A 733 " pdb=" O5' U A 733 " both_signs ideal model delta sigma weight residual True 2.41 -1.52 0.89 2.00e-01 2.50e+01 2.00e+01 chirality pdb=" P C 8 16 " pdb=" OP1 C 8 16 " pdb=" OP2 C 8 16 " pdb=" O5' C 8 16 " both_signs ideal model delta sigma weight residual True 2.41 -3.09 -0.68 2.00e-01 2.50e+01 1.14e+01 ... (remaining 28486 not shown) Planarity restraints: 11146 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMG A2280 " 0.066 2.00e-02 2.50e+03 5.79e-01 7.53e+03 pdb=" C4' OMG A2280 " 0.425 2.00e-02 2.50e+03 pdb=" O4' OMG A2280 " 0.635 2.00e-02 2.50e+03 pdb=" C3' OMG A2280 " -0.633 2.00e-02 2.50e+03 pdb=" O3' OMG A2280 " -0.603 2.00e-02 2.50e+03 pdb=" C2' OMG A2280 " -0.170 2.00e-02 2.50e+03 pdb=" O2' OMG A2280 " 0.914 2.00e-02 2.50e+03 pdb=" C1' OMG A2280 " 0.228 2.00e-02 2.50e+03 pdb=" N9 OMG A2280 " -0.863 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A1071 " -0.118 2.00e-02 2.50e+03 6.15e-02 1.13e+02 pdb=" N9 G A1071 " 0.070 2.00e-02 2.50e+03 pdb=" C8 G A1071 " 0.040 2.00e-02 2.50e+03 pdb=" N7 G A1071 " 0.042 2.00e-02 2.50e+03 pdb=" C5 G A1071 " 0.023 2.00e-02 2.50e+03 pdb=" C6 G A1071 " -0.051 2.00e-02 2.50e+03 pdb=" O6 G A1071 " -0.033 2.00e-02 2.50e+03 pdb=" N1 G A1071 " -0.038 2.00e-02 2.50e+03 pdb=" C2 G A1071 " -0.043 2.00e-02 2.50e+03 pdb=" N2 G A1071 " 0.112 2.00e-02 2.50e+03 pdb=" N3 G A1071 " -0.041 2.00e-02 2.50e+03 pdb=" C4 G A1071 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 558 " 0.140 2.00e-02 2.50e+03 5.63e-02 9.49e+01 pdb=" N9 G A 558 " -0.063 2.00e-02 2.50e+03 pdb=" C8 G A 558 " -0.017 2.00e-02 2.50e+03 pdb=" N7 G A 558 " -0.038 2.00e-02 2.50e+03 pdb=" C5 G A 558 " -0.024 2.00e-02 2.50e+03 pdb=" C6 G A 558 " 0.058 2.00e-02 2.50e+03 pdb=" O6 G A 558 " 0.032 2.00e-02 2.50e+03 pdb=" N1 G A 558 " 0.046 2.00e-02 2.50e+03 pdb=" C2 G A 558 " -0.012 2.00e-02 2.50e+03 pdb=" N2 G A 558 " -0.020 2.00e-02 2.50e+03 pdb=" N3 G A 558 " -0.048 2.00e-02 2.50e+03 pdb=" C4 G A 558 " -0.054 2.00e-02 2.50e+03 ... (remaining 11143 not shown) Histogram of nonbonded interaction distances: 1.28 - 2.05: 405 2.05 - 2.82: 34514 2.82 - 3.59: 254235 3.59 - 4.37: 534640 4.37 - 5.14: 721626 Nonbonded interactions: 1545420 Sorted by model distance: nonbonded pdb=" O3' A w 77 " pdb=" C PRO 7 122 " model vdw 1.275 3.270 nonbonded pdb=" O3' A y 77 " pdb=" C PRO y 101 " model vdw 1.283 3.270 nonbonded pdb="MG MG A3096 " pdb=" O HOH A3237 " model vdw 1.722 2.170 nonbonded pdb="MG MG A3051 " pdb=" O HOH A3995 " model vdw 1.753 2.170 nonbonded pdb="MG MG A3090 " pdb=" O HOH A3971 " model vdw 1.777 2.170 ... (remaining 1545415 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'w' and resid 1 through 77) selection = (chain 'y' and resid 1 through 77) } 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: 4.320 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: 0.130 Extract box with map and model: 19.780 Check model and map are aligned: 1.450 Set scattering table: 0.930 Process input model: 601.640 Find NCS groups from input model: 2.540 Set up NCS constraints: 0.360 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:11.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 642.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 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 : 0.008 0.164 147580 Z= 0.505 Angle : 1.701 29.054 221780 Z= 1.048 Chirality : 0.111 0.931 28489 Planarity : 0.017 0.579 11146 Dihedral : 22.832 178.867 86024 Min Nonbonded Distance : 1.275 Molprobity Statistics. All-atom Clashscore : 0.82 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.63 % Favored : 95.14 % Rotamer: Outliers : 1.07 % Allowed : 5.47 % Favored : 93.46 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.18 % 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: -2.32 (0.10), residues: 4733 helix: -1.64 (0.10), residues: 1448 sheet: -1.48 (0.15), residues: 923 loop : -1.39 (0.11), residues: 2362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.007 TRP k 46 HIS 0.020 0.004 HIS C 230 PHE 0.058 0.006 PHE R 74 TYR 0.050 0.006 TYR Q 32 ARG 0.052 0.004 ARG l 123 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9466 Ramachandran restraints generated. 4733 Oldfield, 0 Emsley, 4733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9466 Ramachandran restraints generated. 4733 Oldfield, 0 Emsley, 4733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1012 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 969 time to evaluate : 5.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 29 GLU cc_start: 0.7044 (tt0) cc_final: 0.6661 (tm-30) REVERT: 0 35 GLU cc_start: 0.7232 (mm-30) cc_final: 0.6848 (mm-30) REVERT: 0 53 ASP cc_start: 0.6044 (t0) cc_final: 0.5750 (t70) REVERT: 1 33 LYS cc_start: 0.6192 (ttmt) cc_final: 0.5526 (mmmt) REVERT: 1 47 GLU cc_start: 0.6209 (tt0) cc_final: 0.5963 (tt0) REVERT: 3 15 LYS cc_start: 0.7368 (ttmm) cc_final: 0.6822 (mtmm) REVERT: 3 56 LYS cc_start: 0.6945 (ptpt) cc_final: 0.6246 (pptt) REVERT: 3 59 LYS cc_start: 0.6433 (ptmm) cc_final: 0.6170 (pttm) REVERT: 4 1 MET cc_start: 0.7843 (tpp) cc_final: 0.7577 (tpp) REVERT: 4 12 GLU cc_start: 0.5937 (mt-10) cc_final: 0.5246 (pm20) REVERT: 4 13 LYS cc_start: 0.6243 (mttt) cc_final: 0.5666 (mmtt) REVERT: 4 15 LYS cc_start: 0.6550 (mtpt) cc_final: 0.5945 (mttt) REVERT: 4 18 ARG cc_start: 0.7153 (ttt90) cc_final: 0.6469 (tpp80) REVERT: 4 24 MET cc_start: 0.8085 (mtp) cc_final: 0.7797 (mtp) REVERT: 4 28 GLU cc_start: 0.5648 (pt0) cc_final: 0.5340 (pp20) REVERT: 4 35 LYS cc_start: 0.7488 (ttmt) cc_final: 0.6823 (ttmp) REVERT: 6 1 MET cc_start: 0.5250 (mmm) cc_final: 0.5037 (mmm) REVERT: C 23 GLU cc_start: 0.6498 (mp0) cc_final: 0.5968 (pm20) REVERT: C 28 LYS cc_start: 0.6164 (mttt) cc_final: 0.5685 (mmpt) REVERT: C 30 GLU cc_start: 0.7008 (tp30) cc_final: 0.6776 (tp30) REVERT: C 61 GLN cc_start: 0.8487 (mm110) cc_final: 0.8220 (mm-40) REVERT: C 72 ASP cc_start: 0.6656 (m-30) cc_final: 0.6412 (m-30) REVERT: C 77 ARG cc_start: 0.6881 (ttp80) cc_final: 0.6599 (tmm160) REVERT: C 82 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7811 (mt-10) REVERT: C 100 GLU cc_start: 0.7452 (tt0) cc_final: 0.7211 (tt0) REVERT: C 111 GLN cc_start: 0.6874 (mm-40) cc_final: 0.6653 (mm-40) REVERT: C 117 MET cc_start: 0.7431 (tpp) cc_final: 0.6942 (tpp) REVERT: C 163 GLN cc_start: 0.7393 (tt0) cc_final: 0.7018 (mt0) REVERT: C 172 VAL cc_start: 0.7804 (t) cc_final: 0.7270 (p) REVERT: C 175 ARG cc_start: 0.7697 (ttm110) cc_final: 0.7396 (ttp-110) REVERT: C 183 MET cc_start: 0.7943 (mtp) cc_final: 0.7666 (mtt) REVERT: C 189 ARG cc_start: 0.7609 (mtt-85) cc_final: 0.7331 (mmm160) REVERT: C 198 GLU cc_start: 0.7133 (tt0) cc_final: 0.6549 (pm20) REVERT: C 199 GLN cc_start: 0.6448 (mt0) cc_final: 0.5840 (pt0) REVERT: C 201 GLU cc_start: 0.7099 (pt0) cc_final: 0.6487 (tt0) REVERT: C 244 LYS cc_start: 0.7037 (mttm) cc_final: 0.6837 (mtmt) REVERT: C 245 SER cc_start: 0.7569 (t) cc_final: 0.7256 (p) REVERT: C 261 LYS cc_start: 0.6358 (tttm) cc_final: 0.5397 (mmtt) REVERT: C 262 LYS cc_start: 0.5547 (OUTLIER) cc_final: 0.4895 (mtpp) REVERT: C 272 ARG cc_start: 0.5852 (ttp-170) cc_final: 0.5284 (ttp-110) REVERT: C 273 ARG cc_start: 0.5790 (mmt90) cc_final: 0.5470 (mtp180) REVERT: D 18 GLU cc_start: 0.5763 (mt-10) cc_final: 0.5337 (tm-30) REVERT: D 29 GLU cc_start: 0.7596 (tt0) cc_final: 0.7344 (tt0) REVERT: D 55 ASP cc_start: 0.7288 (m-30) cc_final: 0.7085 (m-30) REVERT: D 58 GLU cc_start: 0.6259 (tm-30) cc_final: 0.5804 (tm-30) REVERT: D 66 LYS cc_start: 0.7221 (mttp) cc_final: 0.6913 (mttp) REVERT: D 71 LYS cc_start: 0.6066 (mttt) cc_final: 0.5297 (ttpm) REVERT: D 73 GLU cc_start: 0.6393 (mt-10) cc_final: 0.6083 (mt-10) REVERT: D 92 GLU cc_start: 0.6890 (tt0) cc_final: 0.6250 (pt0) REVERT: D 103 SER cc_start: 0.7316 (p) cc_final: 0.7109 (m) REVERT: D 178 LYS cc_start: 0.7371 (ttmt) cc_final: 0.6778 (tptm) REVERT: D 180 ASP cc_start: 0.6965 (t0) cc_final: 0.6737 (t0) REVERT: D 182 GLU cc_start: 0.5748 (mt-10) cc_final: 0.5437 (mm-30) REVERT: D 183 ARG cc_start: 0.6457 (mtt90) cc_final: 0.5867 (mtt90) REVERT: E 20 ASN cc_start: 0.6758 (t0) cc_final: 0.6383 (t0) REVERT: E 27 GLU cc_start: 0.5795 (tt0) cc_final: 0.5387 (tm-30) REVERT: E 100 LYS cc_start: 0.7048 (mmtt) cc_final: 0.6608 (mmtt) REVERT: E 103 LYS cc_start: 0.6975 (ttmm) cc_final: 0.6221 (ttmt) REVERT: E 107 ARG cc_start: 0.6744 (mmt90) cc_final: 0.6103 (mtp85) REVERT: E 127 GLU cc_start: 0.5730 (tp30) cc_final: 0.5409 (tt0) REVERT: E 129 LEU cc_start: 0.6545 (tp) cc_final: 0.5837 (tp) REVERT: E 137 LYS cc_start: 0.6504 (tttt) cc_final: 0.6260 (ttpt) REVERT: E 139 MET cc_start: 0.7068 (tpt) cc_final: 0.6810 (tpp) REVERT: E 144 LYS cc_start: 0.5725 (mmtp) cc_final: 0.5520 (mmtm) REVERT: E 149 GLU cc_start: 0.5872 (tp30) cc_final: 0.5610 (mm-30) REVERT: E 161 GLU cc_start: 0.5509 (tt0) cc_final: 0.4979 (pt0) REVERT: E 166 SER cc_start: 0.7400 (m) cc_final: 0.7148 (p) REVERT: E 181 ILE cc_start: 0.6619 (tt) cc_final: 0.6414 (pp) REVERT: E 193 LEU cc_start: 0.7388 (mp) cc_final: 0.7184 (mp) REVERT: E 196 LYS cc_start: 0.6408 (ttpt) cc_final: 0.5935 (ttpp) REVERT: F 11 GLU cc_start: 0.4928 (mt-10) cc_final: 0.4672 (mm-30) REVERT: F 17 MET cc_start: 0.4644 (tpt) cc_final: 0.4436 (tpt) REVERT: F 32 GLU cc_start: 0.5508 (tp30) cc_final: 0.5206 (tp30) REVERT: F 38 MET cc_start: 0.6910 (mtp) cc_final: 0.6562 (mtt) REVERT: F 57 LEU cc_start: 0.5868 (tp) cc_final: 0.5638 (tp) REVERT: F 71 LYS cc_start: 0.5330 (mttt) cc_final: 0.5117 (mttm) REVERT: F 72 LYS cc_start: 0.4856 (mtpp) cc_final: 0.4510 (mmmt) REVERT: F 95 ARG cc_start: 0.5305 (mmt90) cc_final: 0.4997 (mmt90) REVERT: F 119 LYS cc_start: 0.5515 (mttp) cc_final: 0.5233 (pttt) REVERT: F 148 LYS cc_start: 0.4177 (tptt) cc_final: 0.3336 (mmpt) REVERT: F 150 ARG cc_start: 0.4876 (ptp-110) cc_final: 0.4592 (ptp-110) REVERT: F 168 GLU cc_start: 0.4892 (tp30) cc_final: 0.4521 (mm-30) REVERT: G 38 PHE cc_start: 0.5062 (m-80) cc_final: 0.4728 (m-80) REVERT: G 42 MET cc_start: 0.3814 (mmp) cc_final: 0.3500 (mmp) REVERT: G 60 LYS cc_start: 0.4115 (ptmt) cc_final: 0.3890 (ttpp) REVERT: G 65 LEU cc_start: 0.6023 (mt) cc_final: 0.5735 (tp) REVERT: G 82 LYS cc_start: 0.4704 (mtpt) cc_final: 0.4349 (mptt) REVERT: G 86 ARG cc_start: 0.5251 (mmm-85) cc_final: 0.4577 (tpt-90) REVERT: G 89 GLU cc_start: 0.5925 (mt-10) cc_final: 0.5173 (tt0) REVERT: G 95 TYR cc_start: 0.6190 (m-10) cc_final: 0.5965 (m-10) REVERT: G 140 GLU cc_start: 0.6086 (tt0) cc_final: 0.5573 (tt0) REVERT: G 166 GLU cc_start: 0.5213 (tt0) cc_final: 0.4738 (tp30) REVERT: G 174 GLU cc_start: 0.5494 (mt-10) cc_final: 0.4864 (pt0) REVERT: J 15 LYS cc_start: 0.6951 (mttm) cc_final: 0.6702 (mmtm) REVERT: J 20 ASP cc_start: 0.8029 (t0) cc_final: 0.7776 (t0) REVERT: J 32 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7220 (tt0) REVERT: J 47 PRO cc_start: 0.7725 (Cg_endo) cc_final: 0.7438 (Cg_exo) REVERT: J 62 LYS cc_start: 0.6882 (mmtp) cc_final: 0.6315 (mtmt) REVERT: J 64 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6458 (tp30) REVERT: J 68 LYS cc_start: 0.6821 (mttt) cc_final: 0.6094 (mmmt) REVERT: J 92 GLU cc_start: 0.6928 (tt0) cc_final: 0.6454 (mt-10) REVERT: J 93 MET cc_start: 0.7563 (mmm) cc_final: 0.7099 (mmm) REVERT: J 100 LYS cc_start: 0.6766 (mttp) cc_final: 0.6531 (mttp) REVERT: J 101 MET cc_start: 0.7881 (ttt) cc_final: 0.7581 (ttp) REVERT: J 103 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7629 (mt-10) REVERT: J 107 LYS cc_start: 0.7035 (tttm) cc_final: 0.6720 (ttmt) REVERT: J 127 ARG cc_start: 0.6241 (ttm110) cc_final: 0.5835 (ttm-80) REVERT: J 139 GLU cc_start: 0.7462 (mt-10) cc_final: 0.6575 (mm-30) REVERT: K 1 MET cc_start: 0.7527 (mtp) cc_final: 0.7190 (mtm) REVERT: K 9 LYS cc_start: 0.7765 (mttt) cc_final: 0.7038 (ttmt) REVERT: K 17 ARG cc_start: 0.7294 (mtt90) cc_final: 0.6743 (mtp180) REVERT: K 34 ASN cc_start: 0.7111 (p0) cc_final: 0.6545 (m-40) REVERT: K 45 GLN cc_start: 0.7173 (mt0) cc_final: 0.6600 (mm110) REVERT: K 48 PRO cc_start: 0.6391 (Cg_exo) cc_final: 0.6005 (Cg_endo) REVERT: K 70 ARG cc_start: 0.7606 (ttt90) cc_final: 0.6839 (ttp-110) REVERT: K 80 ASP cc_start: 0.7462 (m-30) cc_final: 0.7240 (m-30) REVERT: K 94 ARG cc_start: 0.6840 (mtp180) cc_final: 0.6500 (mtp180) REVERT: K 105 GLU cc_start: 0.7412 (mp0) cc_final: 0.7098 (mp0) REVERT: K 107 ARG cc_start: 0.6382 (mtp-110) cc_final: 0.5642 (mtt-85) REVERT: K 110 ASN cc_start: 0.5953 (m110) cc_final: 0.5679 (t0) REVERT: K 112 MET cc_start: 0.7040 (mmm) cc_final: 0.6552 (mmm) REVERT: K 113 LYS cc_start: 0.6493 (mttt) cc_final: 0.5739 (tptt) REVERT: L 7 LYS cc_start: 0.6930 (tptt) cc_final: 0.6650 (mmmt) REVERT: L 10 GLU cc_start: 0.6096 (tt0) cc_final: 0.5863 (mm-30) REVERT: L 14 LYS cc_start: 0.7488 (mtpt) cc_final: 0.7241 (mtpp) REVERT: L 72 LYS cc_start: 0.6856 (mttm) cc_final: 0.6548 (mttt) REVERT: L 92 THR cc_start: 0.6106 (p) cc_final: 0.5786 (m) REVERT: L 98 GLU cc_start: 0.5308 (tp30) cc_final: 0.5079 (tp30) REVERT: L 126 ASN cc_start: 0.7760 (m-40) cc_final: 0.7547 (m110) REVERT: L 131 SER cc_start: 0.7000 (t) cc_final: 0.6614 (p) REVERT: L 133 LYS cc_start: 0.6605 (tttm) cc_final: 0.6247 (ttpt) REVERT: M 5 LYS cc_start: 0.7001 (tttt) cc_final: 0.6576 (mtmp) REVERT: M 6 ARG cc_start: 0.6864 (ptm-80) cc_final: 0.6295 (ptm-80) REVERT: M 18 ARG cc_start: 0.7412 (mtt90) cc_final: 0.6191 (mtp180) REVERT: M 22 LYS cc_start: 0.7391 (mtpt) cc_final: 0.7171 (mtmt) REVERT: M 45 ARG cc_start: 0.7122 (mtp85) cc_final: 0.6866 (mtt-85) REVERT: M 54 MET cc_start: 0.8038 (ptp) cc_final: 0.7616 (ptt) REVERT: M 58 MET cc_start: 0.7393 (mtp) cc_final: 0.7094 (mtp) REVERT: M 71 SER cc_start: 0.7752 (p) cc_final: 0.7358 (m) REVERT: M 80 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6740 (mt-10) REVERT: M 112 GLU cc_start: 0.6615 (tt0) cc_final: 0.5798 (mp0) REVERT: M 130 LYS cc_start: 0.7016 (ptmt) cc_final: 0.6638 (ttpt) REVERT: M 134 ARG cc_start: 0.5995 (ptm160) cc_final: 0.5586 (ptp-110) REVERT: N 34 GLU cc_start: 0.7398 (tt0) cc_final: 0.6828 (tp30) REVERT: N 68 ASN cc_start: 0.6783 (m-40) cc_final: 0.6580 (m-40) REVERT: N 69 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6848 (mt-10) REVERT: N 72 ASN cc_start: 0.6776 (t0) cc_final: 0.6293 (t0) REVERT: N 90 ARG cc_start: 0.6396 (ttm170) cc_final: 0.6141 (ttp-170) REVERT: O 12 LEU cc_start: 0.7074 (mt) cc_final: 0.6845 (mp) REVERT: O 28 ARG cc_start: 0.5880 (tmm-80) cc_final: 0.5232 (ttt180) REVERT: O 51 VAL cc_start: 0.6266 (t) cc_final: 0.6021 (m) REVERT: O 102 TYR cc_start: 0.7298 (t80) cc_final: 0.6618 (t80) REVERT: O 107 LYS cc_start: 0.6652 (tttt) cc_final: 0.6318 (tttt) REVERT: P 1 MET cc_start: 0.3389 (ttm) cc_final: 0.2869 (ptt) REVERT: P 10 LYS cc_start: 0.6581 (mtmt) cc_final: 0.6059 (ttpt) REVERT: P 11 GLU cc_start: 0.6687 (pt0) cc_final: 0.6153 (pm20) REVERT: P 27 ARG cc_start: 0.7236 (mtt-85) cc_final: 0.6807 (mtt180) REVERT: P 83 LYS cc_start: 0.7473 (pttt) cc_final: 0.7218 (pttm) REVERT: P 88 ARG cc_start: 0.7464 (ptm-80) cc_final: 0.6553 (ptt-90) REVERT: P 89 TYR cc_start: 0.7990 (m-80) cc_final: 0.7628 (m-80) REVERT: P 104 ARG cc_start: 0.6224 (mmm-85) cc_final: 0.5995 (mmm-85) REVERT: P 109 ARG cc_start: 0.6280 (mtm180) cc_final: 0.5875 (mtm180) REVERT: P 111 LYS cc_start: 0.6554 (mttt) cc_final: 0.5708 (pttm) REVERT: Q 11 ARG cc_start: 0.6761 (ptm-80) cc_final: 0.6510 (ttp-110) REVERT: Q 15 LYS cc_start: 0.7110 (mmtt) cc_final: 0.6791 (mttp) REVERT: Q 19 LYS cc_start: 0.7304 (tmtp) cc_final: 0.6549 (mmtt) REVERT: Q 78 ARG cc_start: 0.7027 (mtp180) cc_final: 0.5931 (mtp-110) REVERT: Q 89 GLU cc_start: 0.6801 (mt-10) cc_final: 0.6412 (mm-30) REVERT: Q 97 ASP cc_start: 0.7275 (t70) cc_final: 0.6754 (t0) REVERT: Q 108 GLN cc_start: 0.6750 (mt0) cc_final: 0.6484 (tt0) REVERT: Q 116 GLN cc_start: 0.7064 (mm-40) cc_final: 0.6508 (mm-40) REVERT: R 1 MET cc_start: 0.6160 (ttt) cc_final: 0.5695 (ttm) REVERT: R 6 LYS cc_start: 0.6942 (tttp) cc_final: 0.6343 (ttpt) REVERT: R 12 ILE cc_start: 0.7988 (pt) cc_final: 0.7698 (mp) REVERT: R 13 LYS cc_start: 0.7524 (tttm) cc_final: 0.7296 (ttpp) REVERT: R 15 GLU cc_start: 0.6824 (mt-10) cc_final: 0.6530 (mt-10) REVERT: R 28 GLU cc_start: 0.6712 (mt-10) cc_final: 0.6312 (mp0) REVERT: R 33 VAL cc_start: 0.7164 (p) cc_final: 0.6902 (m) REVERT: R 37 ASP cc_start: 0.6518 (m-30) cc_final: 0.6287 (m-30) REVERT: R 47 LYS cc_start: 0.6701 (mmtp) cc_final: 0.6023 (mtpt) REVERT: R 48 VAL cc_start: 0.7510 (t) cc_final: 0.6893 (m) REVERT: R 61 LYS cc_start: 0.6399 (tttt) cc_final: 0.5943 (ttmm) REVERT: R 63 GLU cc_start: 0.7129 (mm-30) cc_final: 0.6634 (mm-30) REVERT: R 98 GLU cc_start: 0.6022 (mt-10) cc_final: 0.5764 (mm-30) REVERT: S 1 MET cc_start: 0.4575 (tpt) cc_final: 0.4271 (tpp) REVERT: S 2 GLN cc_start: 0.6994 (mt0) cc_final: 0.6686 (mt0) REVERT: S 31 GLU cc_start: 0.6977 (tt0) cc_final: 0.6185 (tp30) REVERT: S 48 GLU cc_start: 0.7647 (tt0) cc_final: 0.7126 (tp30) REVERT: S 63 GLU cc_start: 0.6304 (mt-10) cc_final: 0.5988 (mm-30) REVERT: S 64 MET cc_start: 0.6951 (mtp) cc_final: 0.6034 (mtp) REVERT: S 65 ASP cc_start: 0.5728 (t70) cc_final: 0.5446 (t0) REVERT: S 68 ASN cc_start: 0.6506 (m-40) cc_final: 0.6086 (m110) REVERT: S 92 ARG cc_start: 0.6381 (mtt180) cc_final: 0.5578 (mmp-170) REVERT: T 10 ARG cc_start: 0.7022 (ptm160) cc_final: 0.6507 (ptp90) REVERT: T 20 LEU cc_start: 0.5558 (mt) cc_final: 0.4983 (mt) REVERT: T 21 MET cc_start: 0.6233 (mtt) cc_final: 0.5908 (ttm) REVERT: T 23 GLU cc_start: 0.5789 (mt-10) cc_final: 0.5480 (tt0) REVERT: T 33 ARG cc_start: 0.6717 (mmt90) cc_final: 0.6322 (mpp-170) REVERT: T 41 ASP cc_start: 0.6990 (m-30) cc_final: 0.6763 (m-30) REVERT: T 44 GLU cc_start: 0.5934 (mt-10) cc_final: 0.5708 (mt-10) REVERT: T 50 LYS cc_start: 0.6114 (mttt) cc_final: 0.5637 (mmtm) REVERT: T 68 ARG cc_start: 0.4957 (ptm-80) cc_final: 0.4254 (pmt170) REVERT: T 69 TYR cc_start: 0.6088 (m-80) cc_final: 0.5311 (m-80) REVERT: T 88 LYS cc_start: 0.5414 (ttpt) cc_final: 0.4410 (mmtp) REVERT: U 1 MET cc_start: 0.6568 (mtm) cc_final: 0.6361 (mtm) REVERT: U 20 GLN cc_start: 0.7073 (mt0) cc_final: 0.6685 (mt0) REVERT: U 22 THR cc_start: 0.7270 (m) cc_final: 0.6797 (t) REVERT: U 30 LYS cc_start: 0.5897 (mttt) cc_final: 0.5569 (mtmt) REVERT: U 32 ARG cc_start: 0.7151 (mtt-85) cc_final: 0.6901 (mtp85) REVERT: U 40 MET cc_start: 0.6792 (mmm) cc_final: 0.6447 (mmm) REVERT: U 43 LYS cc_start: 0.6100 (tptp) cc_final: 0.5747 (tptp) REVERT: U 71 LEU cc_start: 0.6862 (mt) cc_final: 0.6402 (mm) REVERT: U 77 GLU cc_start: 0.5925 (mt-10) cc_final: 0.4869 (tp30) REVERT: U 84 LYS cc_start: 0.6186 (pttt) cc_final: 0.5725 (ptpt) REVERT: W 19 LYS cc_start: 0.7397 (mtmp) cc_final: 0.7119 (mttm) REVERT: W 25 GLU cc_start: 0.6597 (mt-10) cc_final: 0.5861 (mm-30) REVERT: W 57 GLU cc_start: 0.6550 (mt-10) cc_final: 0.6072 (mm-30) REVERT: W 76 LYS cc_start: 0.7966 (mmtt) cc_final: 0.7694 (mmmt) REVERT: X 13 THR cc_start: 0.5800 (m) cc_final: 0.5526 (p) REVERT: X 35 LYS cc_start: 0.5527 (mmtt) cc_final: 0.5299 (tptt) REVERT: X 38 ILE cc_start: 0.5538 (pt) cc_final: 0.5331 (pp) REVERT: X 45 LYS cc_start: 0.4896 (tttt) cc_final: 0.4681 (tptm) REVERT: Y 17 LYS cc_start: 0.4641 (mtpt) cc_final: 0.4394 (mttp) REVERT: Y 23 GLU cc_start: 0.6500 (mt-10) cc_final: 0.5795 (tt0) REVERT: Y 29 ARG cc_start: 0.6364 (mtt180) cc_final: 0.5948 (mmt180) REVERT: Y 32 LEU cc_start: 0.7052 (tp) cc_final: 0.6783 (tp) REVERT: Y 34 THR cc_start: 0.5827 (p) cc_final: 0.5613 (p) REVERT: Y 45 GLU cc_start: 0.6617 (mt-10) cc_final: 0.6299 (tt0) REVERT: Y 48 LYS cc_start: 0.6856 (mttt) cc_final: 0.6049 (mptt) REVERT: Y 53 MET cc_start: 0.7374 (mtt) cc_final: 0.6727 (mtm) REVERT: Z 9 LYS cc_start: 0.7046 (mmtt) cc_final: 0.6768 (mmtp) REVERT: Z 10 ARG cc_start: 0.7184 (mmt90) cc_final: 0.6471 (mmm160) REVERT: Z 17 GLU cc_start: 0.6779 (tp30) cc_final: 0.6259 (tm-30) REVERT: Z 29 LYS cc_start: 0.7634 (mtmt) cc_final: 0.7387 (mtmp) REVERT: Z 38 GLU cc_start: 0.6552 (mm-30) cc_final: 0.6112 (mm-30) REVERT: Z 49 LYS cc_start: 0.6955 (tttp) cc_final: 0.6713 (tttp) REVERT: Z 55 SER cc_start: 0.7477 (t) cc_final: 0.7083 (p) REVERT: e 10 GLU cc_start: 0.4291 (mm-30) cc_final: 0.3423 (tm-30) REVERT: e 12 GLU cc_start: 0.4880 (tt0) cc_final: 0.4098 (mp0) REVERT: e 20 ARG cc_start: 0.6267 (ttp-170) cc_final: 0.5689 (ttp-170) REVERT: e 30 ARG cc_start: 0.6187 (mmm160) cc_final: 0.5884 (mpt180) REVERT: e 39 VAL cc_start: 0.5887 (p) cc_final: 0.5567 (t) REVERT: e 52 LYS cc_start: 0.4197 (OUTLIER) cc_final: 0.3861 (ttpp) REVERT: e 61 ARG cc_start: 0.5394 (ttm170) cc_final: 0.5177 (mpt-90) REVERT: e 62 LYS cc_start: 0.5190 (mmtm) cc_final: 0.4811 (tmmm) REVERT: e 76 MET cc_start: 0.4955 (mtp) cc_final: 0.4728 (mmm) REVERT: e 84 GLU cc_start: 0.5119 (tt0) cc_final: 0.4413 (pp20) REVERT: e 98 PRO cc_start: 0.5872 (Cg_endo) cc_final: 0.5520 (Cg_exo) REVERT: e 101 GLU cc_start: 0.4421 (mm-30) cc_final: 0.4118 (mm-30) REVERT: l 3 THR cc_start: 0.6761 (m) cc_final: 0.6359 (p) REVERT: l 20 LYS cc_start: 0.5068 (mtmt) cc_final: 0.4698 (mptp) REVERT: l 26 LYS cc_start: 0.5160 (mmtm) cc_final: 0.4934 (mmpt) REVERT: l 33 LYS cc_start: 0.4696 (mtmt) cc_final: 0.4211 (tppt) REVERT: l 43 LYS cc_start: 0.5279 (mmtp) cc_final: 0.5048 (mmtp) REVERT: l 50 VAL cc_start: 0.5496 (OUTLIER) cc_final: 0.4836 (p) REVERT: l 57 LYS cc_start: 0.5549 (mtmt) cc_final: 0.5052 (mttm) REVERT: l 64 LYS cc_start: 0.5014 (pttp) cc_final: 0.4665 (mmtm) REVERT: l 99 ARG cc_start: 0.5022 (ptm160) cc_final: 0.4717 (ptm160) REVERT: l 101 LYS cc_start: 0.5769 (tppp) cc_final: 0.4892 (mptt) REVERT: l 134 LYS cc_start: 0.2598 (OUTLIER) cc_final: 0.1798 (tptm) REVERT: o 37 ASN cc_start: 0.6314 (m-40) cc_final: 0.6067 (m110) REVERT: o 44 ARG cc_start: 0.5566 (mmt90) cc_final: 0.5308 (mpt180) REVERT: o 47 LYS cc_start: 0.6292 (mmtt) cc_final: 0.5931 (mttt) REVERT: o 63 ARG cc_start: 0.6859 (ttp-170) cc_final: 0.6443 (ttm170) REVERT: o 71 ARG cc_start: 0.5547 (ttp-110) cc_final: 0.5320 (ttp-110) REVERT: q 40 VAL cc_start: 0.4571 (t) cc_final: 0.4318 (m) REVERT: t 9 LYS cc_start: 0.4855 (tttt) cc_final: 0.4605 (ttpp) REVERT: t 76 LYS cc_start: 0.3298 (mtmt) cc_final: 0.3047 (mttp) REVERT: c 16 ARG cc_start: 0.5216 (mmt180) cc_final: 0.4772 (ttt180) REVERT: c 26 LYS cc_start: 0.4413 (tptm) cc_final: 0.3944 (mmmt) REVERT: c 45 ARG cc_start: 0.4416 (ttt90) cc_final: 0.4098 (ttm170) REVERT: c 53 LYS cc_start: 0.5510 (ttmt) cc_final: 0.5300 (ttpp) REVERT: c 114 LEU cc_start: 0.4834 (mt) cc_final: 0.4576 (mp) REVERT: c 121 ARG cc_start: 0.4664 (mtm110) cc_final: 0.3729 (mmt-90) REVERT: c 130 ARG cc_start: 0.4875 (mtt90) cc_final: 0.4576 (mpp80) REVERT: c 131 ARG cc_start: 0.4102 (ttm170) cc_final: 0.3713 (tpp80) REVERT: c 134 LYS cc_start: 0.5362 (mttt) cc_final: 0.5007 (mmmm) REVERT: c 149 LYS cc_start: 0.6301 (tttt) cc_final: 0.5965 (ttpt) REVERT: c 175 HIS cc_start: 0.7246 (m170) cc_final: 0.6834 (m170) REVERT: c 186 SER cc_start: 0.7269 (t) cc_final: 0.7015 (p) REVERT: g 21 LYS cc_start: 0.4580 (mttt) cc_final: 0.3975 (mmtt) REVERT: g 29 LYS cc_start: 0.5261 (mmtt) cc_final: 0.4631 (mmtm) REVERT: g 31 MET cc_start: 0.6847 (ttp) cc_final: 0.6568 (ttp) REVERT: g 67 LYS cc_start: 0.4897 (ttpt) cc_final: 0.4631 (mttt) REVERT: g 70 MET cc_start: 0.4810 (mtm) cc_final: 0.4038 (mmm) REVERT: g 109 ARG cc_start: 0.5521 (mtt180) cc_final: 0.5261 (mtt180) REVERT: g 111 ARG cc_start: 0.4297 (mtp85) cc_final: 0.3956 (mtt-85) REVERT: g 116 MET cc_start: 0.4820 (tpt) cc_final: 0.4480 (tpp) REVERT: g 144 MET cc_start: 0.4649 (mtm) cc_final: 0.4429 (mmm) REVERT: i 20 ARG cc_start: 0.3859 (mtm110) cc_final: 0.3273 (mtm180) REVERT: i 85 ARG cc_start: 0.5079 (mtt180) cc_final: 0.4319 (mtt90) REVERT: i 97 THR cc_start: 0.4540 (t) cc_final: 0.4332 (m) REVERT: i 104 LEU cc_start: 0.5049 (mt) cc_final: 0.4683 (tp) REVERT: i 122 ARG cc_start: 0.7118 (mmt90) cc_final: 0.6902 (mmt180) REVERT: i 123 ARG cc_start: 0.5839 (tmt170) cc_final: 0.5404 (mmm160) REVERT: j 66 GLU cc_start: 0.6968 (pt0) cc_final: 0.6647 (pt0) REVERT: j 68 ARG cc_start: 0.5505 (mtt180) cc_final: 0.5160 (mtt180) REVERT: m 3 ARG cc_start: 0.4672 (ttm-80) cc_final: 0.4442 (ttt180) REVERT: m 27 ARG cc_start: 0.4825 (ptm160) cc_final: 0.4560 (ttm170) REVERT: m 32 GLN cc_start: 0.4724 (pt0) cc_final: 0.4009 (mm-40) REVERT: m 89 ILE cc_start: 0.5943 (mt) cc_final: 0.5491 (mp) REVERT: m 92 ARG cc_start: 0.3531 (ptm160) cc_final: 0.3175 (ptt90) REVERT: m 93 ARG cc_start: 0.5468 (mtt180) cc_final: 0.4764 (mtp180) REVERT: m 103 LYS cc_start: 0.6537 (tttt) cc_final: 0.6304 (tttm) REVERT: m 104 ASN cc_start: 0.6874 (m110) cc_final: 0.6662 (m110) REVERT: n 3 LYS cc_start: 0.6183 (mtmt) cc_final: 0.5872 (mtpt) REVERT: n 6 MET cc_start: 0.6531 (mmm) cc_final: 0.6062 (mmt) REVERT: s 66 MET cc_start: 0.5359 (mtt) cc_final: 0.5054 (mtm) REVERT: h 19 MET cc_start: 0.5174 (ttm) cc_final: 0.4925 (ttm) REVERT: h 21 ARG cc_start: 0.4423 (mtt180) cc_final: 0.3996 (mtt90) REVERT: h 42 ARG cc_start: 0.3161 (mmt-90) cc_final: 0.2890 (mpt180) REVERT: h 86 ARG cc_start: 0.6172 (mmt180) cc_final: 0.5815 (mmt180) REVERT: h 128 LEU cc_start: 0.4938 (OUTLIER) cc_final: 0.4619 (tp) REVERT: r 36 LYS cc_start: 0.4622 (mttt) cc_final: 0.4255 (mtpt) REVERT: r 57 GLN cc_start: 0.5693 (tp40) cc_final: 0.5476 (tp-100) REVERT: f 7 MET cc_start: 0.6371 (ttm) cc_final: 0.6008 (ttm) REVERT: f 28 ASN cc_start: 0.4272 (m-40) cc_final: 0.4055 (t0) REVERT: f 31 THR cc_start: 0.4888 (p) cc_final: 0.4639 (t) REVERT: f 50 TYR cc_start: 0.5563 (p90) cc_final: 0.5238 (p90) REVERT: f 52 ILE cc_start: 0.4079 (OUTLIER) cc_final: 0.3527 (mp) REVERT: f 73 GLN cc_start: 0.4655 (mt0) cc_final: 0.4384 (mt0) REVERT: f 74 GLU cc_start: 0.4990 (tp30) cc_final: 0.4364 (mp0) outliers start: 43 outliers final: 7 residues processed: 1004 average time/residue: 2.4849 time to fit residues: 3373.6725 Evaluate side-chains 766 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 753 time to evaluate : 5.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 262 LYS Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain e residue 52 LYS Chi-restraints excluded: chain e residue 133 PRO Chi-restraints excluded: chain e residue 137 ILE Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 134 LYS Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain h residue 66 TYR Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 128 LEU Chi-restraints excluded: chain f residue 52 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 770 optimal weight: 8.9990 chunk 691 optimal weight: 20.0000 chunk 383 optimal weight: 4.9990 chunk 236 optimal weight: 5.9990 chunk 466 optimal weight: 9.9990 chunk 369 optimal weight: 5.9990 chunk 714 optimal weight: 9.9990 chunk 276 optimal weight: 10.0000 chunk 434 optimal weight: 5.9990 chunk 532 optimal weight: 7.9990 chunk 828 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 40 HIS 0 50 ASN 0 55 ASN 3 26 HIS 3 35 ASN 3 38 GLN 3 60 GLN D 43 ASN E 9 GLN E 10 ASN E 46 GLN F 63 GLN F 127 ASN F 172 GLN G 129 GLN J 136 GLN K 3 GLN L 70 ASN L 106 ASN N 76 ASN O 32 ASN O 39 HIS Q 37 GLN R 18 GLN R 83 HIS S 67 ASN S 68 ASN S 95 GLN T 58 ASN U 53 GLN W 94 GLN X 17 ASN X 23 ASN Y 27 ASN Z 59 GLN e 83 HIS e 131 ASN k 17 ASN k 40 HIS k 42 ASN l 5 ASN l 59 ASN o 18 HIS o 51 HIS t 20 HIS c 3 GLN c 133 GLN g 148 ASN i 5 GLN i 31 ASN j 78 ASN m 118 ASN s 14 HIS s 43 GLN s 47 HIS h 18 ASN r 21 ASN r 69 GLN f 33 ASN Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 147580 Z= 0.316 Angle : 0.847 18.769 221780 Z= 0.429 Chirality : 0.046 0.367 28489 Planarity : 0.007 0.150 11146 Dihedral : 23.775 176.929 76348 Min Nonbonded Distance : 1.678 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.36 % Favored : 96.53 % Rotamer: Outliers : 2.98 % Allowed : 9.54 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.11), residues: 4733 helix: 0.10 (0.12), residues: 1463 sheet: -1.13 (0.15), residues: 956 loop : -0.91 (0.12), residues: 2314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP k 46 HIS 0.011 0.002 HIS s 14 PHE 0.031 0.003 PHE R 74 TYR 0.025 0.003 TYR o 78 ARG 0.011 0.001 ARG k 26 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9466 Ramachandran restraints generated. 4733 Oldfield, 0 Emsley, 4733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9466 Ramachandran restraints generated. 4733 Oldfield, 0 Emsley, 4733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 883 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 763 time to evaluate : 5.457 Fit side-chains revert: symmetry clash REVERT: 0 35 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7068 (mm-30) REVERT: 0 44 LYS cc_start: 0.6945 (mtmt) cc_final: 0.6241 (mmtm) REVERT: 1 23 LYS cc_start: 0.5149 (mtmt) cc_final: 0.4901 (tttp) REVERT: 1 33 LYS cc_start: 0.6288 (ttmt) cc_final: 0.5809 (mmmt) REVERT: 1 46 ARG cc_start: 0.6596 (ttm110) cc_final: 0.6329 (ttp-110) REVERT: 1 47 GLU cc_start: 0.6326 (tt0) cc_final: 0.6068 (tt0) REVERT: 3 15 LYS cc_start: 0.7322 (ttmm) cc_final: 0.6610 (ptpt) REVERT: 3 59 LYS cc_start: 0.6327 (ptmm) cc_final: 0.6064 (pttm) REVERT: 4 12 GLU cc_start: 0.5947 (mt-10) cc_final: 0.5118 (pm20) REVERT: 4 13 LYS cc_start: 0.5979 (mttt) cc_final: 0.5435 (mmtt) REVERT: 4 15 LYS cc_start: 0.6426 (mtpt) cc_final: 0.5822 (mtmt) REVERT: 4 18 ARG cc_start: 0.6897 (ttt90) cc_final: 0.6240 (tpp80) REVERT: 4 24 MET cc_start: 0.8132 (mtp) cc_final: 0.7837 (mtp) REVERT: 4 28 GLU cc_start: 0.5799 (pt0) cc_final: 0.5418 (pm20) REVERT: C 23 GLU cc_start: 0.6384 (mp0) cc_final: 0.5886 (pm20) REVERT: C 28 LYS cc_start: 0.6268 (mttt) cc_final: 0.5793 (tppt) REVERT: C 77 ARG cc_start: 0.6646 (ttp80) cc_final: 0.5740 (mtt-85) REVERT: C 100 GLU cc_start: 0.7473 (tt0) cc_final: 0.7139 (tt0) REVERT: C 183 MET cc_start: 0.7935 (mtp) cc_final: 0.7618 (mtt) REVERT: C 189 ARG cc_start: 0.7452 (mtt-85) cc_final: 0.7237 (mmm160) REVERT: C 198 GLU cc_start: 0.7002 (tt0) cc_final: 0.6408 (pm20) REVERT: C 199 GLN cc_start: 0.6577 (mt0) cc_final: 0.5992 (pm20) REVERT: C 244 LYS cc_start: 0.7159 (mttm) cc_final: 0.6942 (mtmt) REVERT: C 245 SER cc_start: 0.7492 (t) cc_final: 0.7240 (p) REVERT: C 261 LYS cc_start: 0.6303 (tttm) cc_final: 0.5356 (mmtt) REVERT: C 267 ASP cc_start: 0.6716 (m-30) cc_final: 0.6445 (m-30) REVERT: C 272 ARG cc_start: 0.5610 (ttp-170) cc_final: 0.4939 (ttp-110) REVERT: C 273 ARG cc_start: 0.6027 (mmt90) cc_final: 0.5612 (mtp180) REVERT: D 29 GLU cc_start: 0.7620 (tt0) cc_final: 0.7413 (tt0) REVERT: D 71 LYS cc_start: 0.6206 (mttt) cc_final: 0.5687 (ttpp) REVERT: D 73 GLU cc_start: 0.6380 (mt-10) cc_final: 0.6123 (mt-10) REVERT: D 92 GLU cc_start: 0.7075 (tt0) cc_final: 0.6405 (pt0) REVERT: D 106 GLU cc_start: 0.7071 (tt0) cc_final: 0.6568 (mt-10) REVERT: D 178 LYS cc_start: 0.7148 (ttmt) cc_final: 0.6509 (tttt) REVERT: D 180 ASP cc_start: 0.7055 (t0) cc_final: 0.6769 (t0) REVERT: D 182 GLU cc_start: 0.5872 (mt-10) cc_final: 0.5523 (mm-30) REVERT: D 183 ARG cc_start: 0.6274 (mtt90) cc_final: 0.6057 (mtt90) REVERT: E 27 GLU cc_start: 0.5702 (tt0) cc_final: 0.5256 (tm-30) REVERT: E 100 LYS cc_start: 0.7021 (mmtt) cc_final: 0.6629 (mmtt) REVERT: E 103 LYS cc_start: 0.7051 (ttmm) cc_final: 0.6385 (ttmt) REVERT: E 127 GLU cc_start: 0.5986 (tp30) cc_final: 0.5467 (tt0) REVERT: E 129 LEU cc_start: 0.6910 (tp) cc_final: 0.6639 (tp) REVERT: E 161 GLU cc_start: 0.5344 (tt0) cc_final: 0.4815 (pt0) REVERT: E 181 ILE cc_start: 0.6588 (tt) cc_final: 0.6314 (pp) REVERT: E 196 LYS cc_start: 0.6468 (ttpt) cc_final: 0.6019 (ttpp) REVERT: E 201 LYS cc_start: 0.6542 (ttmm) cc_final: 0.6184 (ttmm) REVERT: F 17 MET cc_start: 0.4459 (tpt) cc_final: 0.4223 (tpt) REVERT: F 56 GLU cc_start: 0.4714 (mt-10) cc_final: 0.3984 (tt0) REVERT: F 69 ARG cc_start: 0.5733 (mtt-85) cc_final: 0.4856 (mpp80) REVERT: F 72 LYS cc_start: 0.4923 (mtpp) cc_final: 0.4526 (tptt) REVERT: F 136 LEU cc_start: 0.4186 (mt) cc_final: 0.3831 (pp) REVERT: F 168 GLU cc_start: 0.4989 (tp30) cc_final: 0.4758 (mm-30) REVERT: G 70 ARG cc_start: 0.5020 (tpt90) cc_final: 0.4762 (tpt170) REVERT: G 86 ARG cc_start: 0.4955 (mmm-85) cc_final: 0.4544 (tpt-90) REVERT: G 131 LYS cc_start: 0.5536 (OUTLIER) cc_final: 0.5017 (tppp) REVERT: J 13 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6184 (tp30) REVERT: J 20 ASP cc_start: 0.7724 (t0) cc_final: 0.7523 (t0) REVERT: J 32 GLU cc_start: 0.7409 (mt-10) cc_final: 0.7140 (tt0) REVERT: J 62 LYS cc_start: 0.6962 (mmtp) cc_final: 0.6502 (mtmt) REVERT: J 64 GLU cc_start: 0.7332 (mt-10) cc_final: 0.6571 (tp30) REVERT: J 92 GLU cc_start: 0.6802 (tt0) cc_final: 0.6459 (mt-10) REVERT: J 107 LYS cc_start: 0.6872 (tttm) cc_final: 0.6582 (ttmt) REVERT: J 127 ARG cc_start: 0.6408 (ttm110) cc_final: 0.6055 (ttm-80) REVERT: J 130 GLU cc_start: 0.6507 (mt-10) cc_final: 0.6127 (mp0) REVERT: J 139 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6647 (mm-30) REVERT: K 9 LYS cc_start: 0.7796 (mttt) cc_final: 0.7080 (ttmt) REVERT: K 34 ASN cc_start: 0.7069 (p0) cc_final: 0.6594 (m110) REVERT: K 45 GLN cc_start: 0.7280 (mt0) cc_final: 0.6793 (mm110) REVERT: K 48 PRO cc_start: 0.6333 (Cg_exo) cc_final: 0.6064 (Cg_endo) REVERT: K 70 ARG cc_start: 0.7522 (ttt180) cc_final: 0.6816 (ttt-90) REVERT: K 94 ARG cc_start: 0.6744 (mtp180) cc_final: 0.6463 (mtp180) REVERT: K 105 GLU cc_start: 0.7104 (mp0) cc_final: 0.6882 (mp0) REVERT: K 107 ARG cc_start: 0.6263 (mtp-110) cc_final: 0.5803 (mtm-85) REVERT: K 110 ASN cc_start: 0.5908 (m110) cc_final: 0.5645 (t0) REVERT: K 112 MET cc_start: 0.6852 (mmm) cc_final: 0.6501 (mmm) REVERT: K 113 LYS cc_start: 0.6292 (mttt) cc_final: 0.5553 (tppt) REVERT: L 10 GLU cc_start: 0.6118 (tt0) cc_final: 0.5828 (mm-30) REVERT: L 14 LYS cc_start: 0.7452 (mtpt) cc_final: 0.7179 (mtpp) REVERT: L 90 GLU cc_start: 0.5681 (tt0) cc_final: 0.5097 (tm-30) REVERT: L 94 GLU cc_start: 0.5449 (mp0) cc_final: 0.5213 (mp0) REVERT: L 124 LYS cc_start: 0.5909 (mtpm) cc_final: 0.5531 (mttm) REVERT: L 133 LYS cc_start: 0.6567 (tttm) cc_final: 0.6215 (ttpt) REVERT: M 5 LYS cc_start: 0.6918 (tttt) cc_final: 0.6526 (mtmp) REVERT: M 18 ARG cc_start: 0.7305 (mtt90) cc_final: 0.6187 (mtp180) REVERT: M 45 ARG cc_start: 0.7016 (mtp85) cc_final: 0.6796 (mtt-85) REVERT: M 130 LYS cc_start: 0.7001 (ptmt) cc_final: 0.6783 (ttpt) REVERT: M 133 LYS cc_start: 0.7190 (mtmp) cc_final: 0.6706 (mttp) REVERT: M 134 ARG cc_start: 0.5993 (ptm160) cc_final: 0.5357 (ttm170) REVERT: N 34 GLU cc_start: 0.7164 (tt0) cc_final: 0.6609 (tp30) REVERT: N 69 GLU cc_start: 0.7003 (mt-10) cc_final: 0.6755 (mt-10) REVERT: N 72 ASN cc_start: 0.6793 (t0) cc_final: 0.6299 (t0) REVERT: N 75 ASN cc_start: 0.5789 (m-40) cc_final: 0.5413 (m110) REVERT: O 8 ASN cc_start: 0.7477 (t0) cc_final: 0.6979 (t0) REVERT: O 38 LYS cc_start: 0.5596 (mttt) cc_final: 0.5144 (mtmm) REVERT: O 94 VAL cc_start: 0.6956 (m) cc_final: 0.6583 (p) REVERT: O 102 TYR cc_start: 0.7175 (t80) cc_final: 0.6570 (t80) REVERT: O 107 LYS cc_start: 0.6673 (tttt) cc_final: 0.6303 (tttt) REVERT: P 1 MET cc_start: 0.3497 (ttm) cc_final: 0.3243 (ptm) REVERT: P 6 GLU cc_start: 0.6558 (mt-10) cc_final: 0.5621 (tm-30) REVERT: P 11 GLU cc_start: 0.6532 (pt0) cc_final: 0.6209 (tt0) REVERT: P 27 ARG cc_start: 0.7174 (mtt-85) cc_final: 0.6830 (mtt180) REVERT: P 39 ARG cc_start: 0.6574 (ptm-80) cc_final: 0.6196 (ptt90) REVERT: P 83 LYS cc_start: 0.7411 (pttt) cc_final: 0.7150 (pttm) REVERT: P 88 ARG cc_start: 0.7431 (ptm-80) cc_final: 0.6458 (ptt-90) REVERT: P 109 ARG cc_start: 0.6191 (mtm180) cc_final: 0.5792 (mtm180) REVERT: P 111 LYS cc_start: 0.6859 (mttt) cc_final: 0.6582 (mtmt) REVERT: P 113 ILE cc_start: 0.6399 (OUTLIER) cc_final: 0.6132 (pt) REVERT: Q 15 LYS cc_start: 0.7055 (mmtt) cc_final: 0.6792 (mtpm) REVERT: Q 19 LYS cc_start: 0.7252 (tmtp) cc_final: 0.6494 (mmtt) REVERT: Q 89 GLU cc_start: 0.6820 (mt-10) cc_final: 0.6400 (mm-30) REVERT: Q 97 ASP cc_start: 0.7255 (t70) cc_final: 0.6775 (t0) REVERT: Q 116 GLN cc_start: 0.6987 (mm-40) cc_final: 0.6519 (mm-40) REVERT: R 1 MET cc_start: 0.6462 (ttm) cc_final: 0.6035 (ttm) REVERT: R 6 LYS cc_start: 0.6930 (tttp) cc_final: 0.6559 (mtpp) REVERT: R 12 ILE cc_start: 0.8019 (pt) cc_final: 0.7798 (mp) REVERT: R 15 GLU cc_start: 0.6558 (mt-10) cc_final: 0.6245 (mt-10) REVERT: R 36 GLU cc_start: 0.6144 (mt-10) cc_final: 0.5320 (pm20) REVERT: R 47 LYS cc_start: 0.6783 (mmtp) cc_final: 0.6173 (mtpt) REVERT: R 63 GLU cc_start: 0.6628 (mm-30) cc_final: 0.6306 (mm-30) REVERT: R 98 GLU cc_start: 0.6103 (mt-10) cc_final: 0.5474 (mp0) REVERT: R 99 LYS cc_start: 0.6545 (tttt) cc_final: 0.6193 (mmmt) REVERT: S 1 MET cc_start: 0.4419 (tpt) cc_final: 0.4091 (tpp) REVERT: S 2 GLN cc_start: 0.7015 (mt0) cc_final: 0.6695 (mt0) REVERT: S 11 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.5116 (tmm160) REVERT: S 21 MET cc_start: 0.7577 (mmt) cc_final: 0.7327 (tpp) REVERT: S 31 GLU cc_start: 0.6800 (tt0) cc_final: 0.6139 (tp30) REVERT: S 48 GLU cc_start: 0.7714 (tt0) cc_final: 0.7106 (tp30) REVERT: S 52 LYS cc_start: 0.7755 (mttm) cc_final: 0.7467 (mttp) REVERT: S 63 GLU cc_start: 0.6328 (mt-10) cc_final: 0.6080 (mm-30) REVERT: S 65 ASP cc_start: 0.5459 (t0) cc_final: 0.4943 (t0) REVERT: S 68 ASN cc_start: 0.6328 (m110) cc_final: 0.5974 (m110) REVERT: S 85 PHE cc_start: 0.7248 (m-80) cc_final: 0.7013 (m-80) REVERT: S 92 ARG cc_start: 0.6045 (mtt180) cc_final: 0.5196 (mmp-170) REVERT: S 109 GLU cc_start: 0.5932 (mt-10) cc_final: 0.5392 (mm-30) REVERT: T 10 ARG cc_start: 0.7116 (ptm160) cc_final: 0.6631 (ptp90) REVERT: T 19 ASP cc_start: 0.4844 (m-30) cc_final: 0.4602 (t70) REVERT: T 20 LEU cc_start: 0.5244 (mt) cc_final: 0.4972 (mt) REVERT: T 21 MET cc_start: 0.5904 (mtt) cc_final: 0.5520 (mtm) REVERT: T 23 GLU cc_start: 0.5609 (mt-10) cc_final: 0.5336 (tt0) REVERT: T 33 ARG cc_start: 0.6733 (mmt90) cc_final: 0.6349 (mpp-170) REVERT: T 41 ASP cc_start: 0.6781 (m-30) cc_final: 0.6566 (m-30) REVERT: T 50 LYS cc_start: 0.6224 (mttt) cc_final: 0.5693 (mmtm) REVERT: T 68 ARG cc_start: 0.5039 (ptm-80) cc_final: 0.4382 (pmt170) REVERT: T 72 MET cc_start: 0.7286 (OUTLIER) cc_final: 0.6888 (mmt) REVERT: U 4 LYS cc_start: 0.7206 (OUTLIER) cc_final: 0.6631 (ptpp) REVERT: U 22 THR cc_start: 0.7147 (m) cc_final: 0.6810 (t) REVERT: U 30 LYS cc_start: 0.6250 (mttt) cc_final: 0.5840 (mtmt) REVERT: U 40 MET cc_start: 0.6905 (mmm) cc_final: 0.6654 (mmm) REVERT: U 71 LEU cc_start: 0.6765 (mt) cc_final: 0.6350 (mm) REVERT: U 77 GLU cc_start: 0.6062 (mt-10) cc_final: 0.4827 (mm-30) REVERT: U 84 LYS cc_start: 0.6151 (pttt) cc_final: 0.5738 (pttp) REVERT: W 19 LYS cc_start: 0.7495 (mtmp) cc_final: 0.6999 (mmtt) REVERT: W 25 GLU cc_start: 0.6887 (mt-10) cc_final: 0.6089 (pt0) REVERT: W 57 GLU cc_start: 0.6404 (mt-10) cc_final: 0.6048 (tp30) REVERT: W 76 LYS cc_start: 0.7832 (mmtt) cc_final: 0.7622 (mmmt) REVERT: X 60 GLU cc_start: 0.4598 (pt0) cc_final: 0.4031 (tp30) REVERT: Y 23 GLU cc_start: 0.6394 (mt-10) cc_final: 0.5643 (tm-30) REVERT: Y 29 ARG cc_start: 0.6188 (mtt180) cc_final: 0.5926 (mtt-85) REVERT: Y 45 GLU cc_start: 0.6500 (mt-10) cc_final: 0.6081 (tm-30) REVERT: Y 48 LYS cc_start: 0.6663 (mttt) cc_final: 0.5927 (mptt) REVERT: Y 50 ILE cc_start: 0.7116 (OUTLIER) cc_final: 0.6860 (mp) REVERT: Y 53 MET cc_start: 0.7211 (mtt) cc_final: 0.6290 (mtm) REVERT: Z 9 LYS cc_start: 0.7144 (mmtt) cc_final: 0.6908 (mmtp) REVERT: Z 10 ARG cc_start: 0.7163 (mmt90) cc_final: 0.6622 (mmt180) REVERT: Z 17 GLU cc_start: 0.6889 (tp30) cc_final: 0.6210 (tm-30) REVERT: Z 29 LYS cc_start: 0.7590 (mtmt) cc_final: 0.7316 (mtmm) REVERT: Z 38 GLU cc_start: 0.6680 (mm-30) cc_final: 0.6089 (mm-30) REVERT: Z 46 MET cc_start: 0.7973 (mtp) cc_final: 0.7618 (mtp) REVERT: Z 55 SER cc_start: 0.7553 (t) cc_final: 0.7266 (m) REVERT: Z 57 LYS cc_start: 0.6179 (mptt) cc_final: 0.5742 (ttpp) REVERT: e 10 GLU cc_start: 0.3950 (mm-30) cc_final: 0.3121 (tm-30) REVERT: e 12 GLU cc_start: 0.4851 (tt0) cc_final: 0.4309 (mt-10) REVERT: e 30 ARG cc_start: 0.5850 (mmm160) cc_final: 0.5607 (mmt90) REVERT: e 52 LYS cc_start: 0.3961 (OUTLIER) cc_final: 0.3659 (ttpp) REVERT: e 61 ARG cc_start: 0.5109 (ttm170) cc_final: 0.4825 (mtt-85) REVERT: e 62 LYS cc_start: 0.5080 (mmtm) cc_final: 0.4779 (tmmm) REVERT: e 84 GLU cc_start: 0.5453 (tt0) cc_final: 0.4608 (pp20) REVERT: e 101 GLU cc_start: 0.4558 (mm-30) cc_final: 0.4236 (tm-30) REVERT: e 122 ASP cc_start: 0.5589 (m-30) cc_final: 0.5341 (m-30) REVERT: e 138 ARG cc_start: 0.5963 (mmt90) cc_final: 0.5117 (mtp180) REVERT: l 3 THR cc_start: 0.7013 (m) cc_final: 0.6705 (p) REVERT: l 26 LYS cc_start: 0.5089 (mmtm) cc_final: 0.4741 (mmmt) REVERT: l 33 LYS cc_start: 0.4579 (mtmt) cc_final: 0.4134 (tppt) REVERT: l 64 LYS cc_start: 0.4911 (pttp) cc_final: 0.4551 (mmtt) REVERT: l 99 ARG cc_start: 0.4898 (ptm160) cc_final: 0.4372 (ptp-110) REVERT: l 101 LYS cc_start: 0.5239 (tppp) cc_final: 0.4693 (mptt) REVERT: l 133 LYS cc_start: 0.2884 (ttmm) cc_final: 0.2412 (tttm) REVERT: o 7 ARG cc_start: 0.3712 (OUTLIER) cc_final: 0.3388 (ttm110) REVERT: o 34 ASP cc_start: 0.5459 (t70) cc_final: 0.5147 (t70) REVERT: o 44 ARG cc_start: 0.5918 (mmt90) cc_final: 0.5660 (mmt90) REVERT: o 47 LYS cc_start: 0.6074 (mmtt) cc_final: 0.5731 (mttt) REVERT: o 57 LEU cc_start: 0.6678 (mt) cc_final: 0.6381 (mt) REVERT: o 63 ARG cc_start: 0.6829 (ttp-170) cc_final: 0.6530 (ttp80) REVERT: o 80 GLU cc_start: 0.4552 (OUTLIER) cc_final: 0.4094 (mt-10) REVERT: q 35 LEU cc_start: 0.5187 (tp) cc_final: 0.4857 (tm) REVERT: q 40 VAL cc_start: 0.4916 (OUTLIER) cc_final: 0.4678 (m) REVERT: q 64 MET cc_start: 0.3387 (tpt) cc_final: 0.2360 (tmt) REVERT: c 10 LEU cc_start: 0.6820 (tp) cc_final: 0.6612 (tp) REVERT: c 67 ILE cc_start: 0.5437 (mt) cc_final: 0.5147 (mt) REVERT: c 107 ARG cc_start: 0.3743 (tpp80) cc_final: 0.3402 (ptp-170) REVERT: c 130 ARG cc_start: 0.4768 (mtt90) cc_final: 0.4478 (mpp80) REVERT: c 131 ARG cc_start: 0.4080 (ttm170) cc_final: 0.3832 (tpt170) REVERT: c 134 LYS cc_start: 0.5181 (mttt) cc_final: 0.4865 (mmmm) REVERT: c 186 SER cc_start: 0.7277 (t) cc_final: 0.6801 (p) REVERT: c 189 ASP cc_start: 0.5367 (t0) cc_final: 0.5154 (t0) REVERT: g 25 ARG cc_start: 0.5250 (mmt180) cc_final: 0.4430 (mtt90) REVERT: g 31 MET cc_start: 0.6724 (ttp) cc_final: 0.6233 (ttp) REVERT: g 67 LYS cc_start: 0.4937 (ttpt) cc_final: 0.4650 (mttt) REVERT: g 70 MET cc_start: 0.4919 (mtm) cc_final: 0.4484 (mtm) REVERT: g 74 GLU cc_start: 0.5174 (pt0) cc_final: 0.4706 (pm20) REVERT: g 107 TYR cc_start: 0.4769 (m-80) cc_final: 0.3808 (m-80) REVERT: g 111 ARG cc_start: 0.4320 (mtp85) cc_final: 0.4056 (mtt-85) REVERT: g 117 GLU cc_start: 0.5035 (pm20) cc_final: 0.4772 (mp0) REVERT: g 144 MET cc_start: 0.4775 (mtm) cc_final: 0.4431 (tpp) REVERT: g 146 GLU cc_start: 0.4641 (tt0) cc_final: 0.4427 (mm-30) REVERT: i 20 ARG cc_start: 0.3668 (mtm110) cc_final: 0.3072 (mtm180) REVERT: i 123 ARG cc_start: 0.5867 (tmt170) cc_final: 0.5313 (tpp-160) REVERT: j 71 LYS cc_start: 0.5167 (OUTLIER) cc_final: 0.4726 (mttp) REVERT: m 11 ARG cc_start: 0.3246 (mtp-110) cc_final: 0.2990 (ttp-170) REVERT: m 27 ARG cc_start: 0.5086 (ptm160) cc_final: 0.4812 (mtm110) REVERT: m 32 GLN cc_start: 0.4427 (pt0) cc_final: 0.3845 (mm-40) REVERT: m 57 ARG cc_start: 0.4141 (mtt-85) cc_final: 0.3903 (mtt90) REVERT: m 89 ILE cc_start: 0.5926 (mt) cc_final: 0.5669 (mp) REVERT: m 93 ARG cc_start: 0.5327 (mtt180) cc_final: 0.4688 (mtp180) REVERT: m 109 ARG cc_start: 0.5134 (mmm160) cc_final: 0.4496 (mmm160) REVERT: n 6 MET cc_start: 0.6212 (mmm) cc_final: 0.5800 (mmm) REVERT: n 26 ARG cc_start: 0.6251 (ttt-90) cc_final: 0.5886 (ttp80) REVERT: n 35 ARG cc_start: 0.6148 (mtt180) cc_final: 0.5946 (mtt180) REVERT: n 50 LYS cc_start: 0.6077 (mttt) cc_final: 0.5869 (mttt) REVERT: n 57 LYS cc_start: 0.6121 (ptpp) cc_final: 0.5236 (pttp) REVERT: h 9 ASP cc_start: 0.4145 (OUTLIER) cc_final: 0.2944 (t70) REVERT: h 15 ARG cc_start: 0.6426 (ttm110) cc_final: 0.5490 (ttm110) REVERT: h 42 ARG cc_start: 0.3411 (mmt-90) cc_final: 0.3077 (mmp80) REVERT: r 36 LYS cc_start: 0.4523 (mttt) cc_final: 0.4215 (mtpt) REVERT: r 55 LYS cc_start: 0.4836 (ttpt) cc_final: 0.4557 (tttt) REVERT: r 56 TYR cc_start: 0.4769 (m-80) cc_final: 0.4491 (m-80) REVERT: r 66 ARG cc_start: 0.5342 (mtt180) cc_final: 0.5033 (mtt180) REVERT: f 7 MET cc_start: 0.6572 (ttm) cc_final: 0.6189 (ttm) REVERT: f 74 GLU cc_start: 0.4811 (tp30) cc_final: 0.4422 (mp0) outliers start: 120 outliers final: 50 residues processed: 842 average time/residue: 2.4777 time to fit residues: 2847.5012 Evaluate side-chains 750 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 687 time to evaluate : 5.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 41 LYS Chi-restraints excluded: chain 3 residue 4 MET Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 131 LYS Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 11 THR Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain O residue 23 SER Chi-restraints excluded: chain P residue 113 ILE Chi-restraints excluded: chain S residue 11 ARG Chi-restraints excluded: chain T residue 72 MET Chi-restraints excluded: chain T residue 73 THR Chi-restraints excluded: chain U residue 4 LYS Chi-restraints excluded: chain U residue 85 VAL Chi-restraints excluded: chain W residue 78 GLU Chi-restraints excluded: chain Y residue 20 SER Chi-restraints excluded: chain Y residue 44 ARG Chi-restraints excluded: chain Y residue 50 ILE Chi-restraints excluded: chain e residue 52 LYS Chi-restraints excluded: chain e residue 93 ASN Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 137 ILE Chi-restraints excluded: chain e residue 157 ARG Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 44 ILE Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain l residue 13 VAL Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 38 VAL Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 128 SER Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain o residue 68 THR Chi-restraints excluded: chain o residue 80 GLU Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain c residue 6 ASN Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain g residue 32 ILE Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 135 VAL Chi-restraints excluded: chain j residue 71 LYS Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain n residue 9 LYS Chi-restraints excluded: chain n residue 32 SER Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain h residue 9 ASP Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 45 PHE Chi-restraints excluded: chain h residue 46 ILE Chi-restraints excluded: chain h residue 66 TYR Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 85 LEU Chi-restraints excluded: chain h residue 110 GLN Chi-restraints excluded: chain f residue 36 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 460 optimal weight: 3.9990 chunk 257 optimal weight: 10.0000 chunk 689 optimal weight: 20.0000 chunk 563 optimal weight: 9.9990 chunk 228 optimal weight: 10.0000 chunk 829 optimal weight: 20.0000 chunk 896 optimal weight: 20.0000 chunk 738 optimal weight: 30.0000 chunk 822 optimal weight: 0.9990 chunk 282 optimal weight: 10.0000 chunk 665 optimal weight: 10.0000 overall best weight: 6.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 188 ASN F 127 ASN G 148 ASN L 17 ASN N 61 GLN O 37 ASN Q 108 GLN e 45 HIS k 31 ASN k 121 ASN o 37 ASN ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 68 HIS i 81 HIS r 53 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 147580 Z= 0.366 Angle : 0.924 22.307 221780 Z= 0.462 Chirality : 0.048 0.423 28489 Planarity : 0.008 0.155 11146 Dihedral : 23.935 178.922 76332 Min Nonbonded Distance : 1.618 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.65 % Favored : 95.25 % Rotamer: Outliers : 3.83 % Allowed : 12.00 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -1.13 (0.11), residues: 4733 helix: -0.14 (0.12), residues: 1467 sheet: -0.99 (0.16), residues: 926 loop : -0.95 (0.12), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP k 46 HIS 0.011 0.003 HIS t 20 PHE 0.029 0.004 PHE R 74 TYR 0.031 0.004 TYR G 158 ARG 0.011 0.001 ARG f 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9466 Ramachandran restraints generated. 4733 Oldfield, 0 Emsley, 4733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9466 Ramachandran restraints generated. 4733 Oldfield, 0 Emsley, 4733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 711 time to evaluate : 4.907 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 44 LYS cc_start: 0.7162 (mtmt) cc_final: 0.6543 (mmtm) REVERT: 1 23 LYS cc_start: 0.5260 (mtmt) cc_final: 0.5036 (mmtt) REVERT: 1 33 LYS cc_start: 0.6283 (ttmt) cc_final: 0.5813 (mmmt) REVERT: 1 46 ARG cc_start: 0.6726 (ttm110) cc_final: 0.6464 (ttm110) REVERT: 1 47 GLU cc_start: 0.6187 (tt0) cc_final: 0.5901 (tt0) REVERT: 3 15 LYS cc_start: 0.7301 (ttmm) cc_final: 0.6614 (ptpt) REVERT: 4 13 LYS cc_start: 0.5994 (mttt) cc_final: 0.5372 (mmtt) REVERT: 4 15 LYS cc_start: 0.6425 (mtpt) cc_final: 0.5717 (tttp) REVERT: 4 18 ARG cc_start: 0.6723 (ttt90) cc_final: 0.6048 (tpp80) REVERT: 4 20 LYS cc_start: 0.6498 (mmtt) cc_final: 0.6253 (mttm) REVERT: 4 24 MET cc_start: 0.8089 (mtp) cc_final: 0.7758 (mtp) REVERT: 4 28 GLU cc_start: 0.5676 (pt0) cc_final: 0.5373 (pm20) REVERT: 6 1 MET cc_start: 0.4434 (OUTLIER) cc_final: 0.3733 (mtp) REVERT: C 23 GLU cc_start: 0.6335 (OUTLIER) cc_final: 0.5884 (pm20) REVERT: C 28 LYS cc_start: 0.6353 (mttt) cc_final: 0.5928 (pttm) REVERT: C 77 ARG cc_start: 0.6655 (ttp80) cc_final: 0.5805 (mtt-85) REVERT: C 100 GLU cc_start: 0.7477 (tt0) cc_final: 0.7196 (tt0) REVERT: C 183 MET cc_start: 0.8047 (mtp) cc_final: 0.7754 (mtt) REVERT: C 198 GLU cc_start: 0.6985 (tt0) cc_final: 0.6391 (pm20) REVERT: C 199 GLN cc_start: 0.6527 (mt0) cc_final: 0.5982 (pm20) REVERT: C 245 SER cc_start: 0.7330 (t) cc_final: 0.7054 (p) REVERT: C 261 LYS cc_start: 0.6246 (tttm) cc_final: 0.5319 (mmtt) REVERT: C 262 LYS cc_start: 0.5085 (mmtp) cc_final: 0.4558 (mtpp) REVERT: C 267 ASP cc_start: 0.6838 (m-30) cc_final: 0.6607 (m-30) REVERT: C 273 ARG cc_start: 0.5789 (mmt90) cc_final: 0.5379 (mmp-170) REVERT: D 71 LYS cc_start: 0.6178 (mttt) cc_final: 0.5667 (ttpp) REVERT: D 73 GLU cc_start: 0.6284 (mt-10) cc_final: 0.6032 (mt-10) REVERT: D 92 GLU cc_start: 0.7037 (tt0) cc_final: 0.6363 (pt0) REVERT: D 103 SER cc_start: 0.7213 (p) cc_final: 0.6896 (m) REVERT: D 178 LYS cc_start: 0.7286 (ttmt) cc_final: 0.6804 (tttm) REVERT: D 180 ASP cc_start: 0.7177 (t0) cc_final: 0.6901 (t0) REVERT: D 182 GLU cc_start: 0.5807 (mt-10) cc_final: 0.5423 (tp30) REVERT: E 10 ASN cc_start: 0.5913 (OUTLIER) cc_final: 0.5660 (p0) REVERT: E 27 GLU cc_start: 0.5607 (tt0) cc_final: 0.5174 (tm-30) REVERT: E 103 LYS cc_start: 0.7065 (ttmm) cc_final: 0.6339 (ttmt) REVERT: E 127 GLU cc_start: 0.6017 (tp30) cc_final: 0.5512 (tt0) REVERT: E 161 GLU cc_start: 0.5327 (tt0) cc_final: 0.4861 (mp0) REVERT: E 181 ILE cc_start: 0.6588 (tt) cc_final: 0.6262 (pp) REVERT: E 196 LYS cc_start: 0.6390 (ttpt) cc_final: 0.5920 (ttpp) REVERT: E 201 LYS cc_start: 0.6567 (ttmm) cc_final: 0.6205 (ttmm) REVERT: F 27 GLN cc_start: 0.6202 (OUTLIER) cc_final: 0.5946 (mt0) REVERT: F 69 ARG cc_start: 0.5629 (mtt-85) cc_final: 0.4809 (mpp80) REVERT: F 94 GLU cc_start: 0.4916 (OUTLIER) cc_final: 0.4601 (tt0) REVERT: F 95 ARG cc_start: 0.5224 (mmt90) cc_final: 0.4987 (mmt90) REVERT: F 152 MET cc_start: 0.6310 (OUTLIER) cc_final: 0.5932 (ptp) REVERT: F 165 GLU cc_start: 0.5409 (OUTLIER) cc_final: 0.5189 (mt-10) REVERT: G 166 GLU cc_start: 0.5559 (tt0) cc_final: 0.5158 (tp30) REVERT: J 13 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.6189 (tp30) REVERT: J 15 LYS cc_start: 0.6967 (mttp) cc_final: 0.6700 (mtmt) REVERT: J 32 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7225 (tt0) REVERT: J 62 LYS cc_start: 0.6904 (mmtp) cc_final: 0.6499 (mtmt) REVERT: J 92 GLU cc_start: 0.6707 (tt0) cc_final: 0.6434 (mt-10) REVERT: J 107 LYS cc_start: 0.6939 (tttm) cc_final: 0.6594 (ttpt) REVERT: J 130 GLU cc_start: 0.6531 (mt-10) cc_final: 0.5938 (mm-30) REVERT: J 139 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6341 (mm-30) REVERT: K 9 LYS cc_start: 0.7727 (mttt) cc_final: 0.7059 (ttmt) REVERT: K 34 ASN cc_start: 0.7008 (p0) cc_final: 0.6774 (m-40) REVERT: K 45 GLN cc_start: 0.7271 (mt0) cc_final: 0.6873 (mm110) REVERT: K 48 PRO cc_start: 0.6315 (Cg_exo) cc_final: 0.6027 (Cg_endo) REVERT: K 51 VAL cc_start: 0.6581 (t) cc_final: 0.6267 (p) REVERT: K 70 ARG cc_start: 0.7563 (ttt180) cc_final: 0.6841 (ttt-90) REVERT: K 107 ARG cc_start: 0.6281 (mtp-110) cc_final: 0.5802 (mtm-85) REVERT: K 110 ASN cc_start: 0.5749 (m110) cc_final: 0.5530 (t0) REVERT: K 112 MET cc_start: 0.6918 (mmm) cc_final: 0.6609 (mmm) REVERT: K 113 LYS cc_start: 0.6374 (mttt) cc_final: 0.5584 (tppt) REVERT: L 10 GLU cc_start: 0.6337 (tt0) cc_final: 0.5977 (mm-30) REVERT: L 14 LYS cc_start: 0.7486 (mtpt) cc_final: 0.7208 (mtpp) REVERT: L 90 GLU cc_start: 0.5634 (tt0) cc_final: 0.5089 (tm-30) REVERT: L 133 LYS cc_start: 0.6560 (tttm) cc_final: 0.6214 (ttpt) REVERT: L 137 GLU cc_start: 0.5130 (mt-10) cc_final: 0.4794 (mm-30) REVERT: M 5 LYS cc_start: 0.6862 (tttt) cc_final: 0.6542 (mtmp) REVERT: M 18 ARG cc_start: 0.7306 (mtt90) cc_final: 0.6221 (mtp180) REVERT: M 54 MET cc_start: 0.7810 (ptp) cc_final: 0.7529 (ptt) REVERT: M 130 LYS cc_start: 0.7199 (ptmt) cc_final: 0.6910 (ttpt) REVERT: M 134 ARG cc_start: 0.5957 (ptm160) cc_final: 0.5488 (ttm170) REVERT: N 34 GLU cc_start: 0.7123 (tt0) cc_final: 0.6580 (tp30) REVERT: N 46 LYS cc_start: 0.7403 (mttt) cc_final: 0.7166 (mttm) REVERT: N 72 ASN cc_start: 0.6845 (t0) cc_final: 0.6394 (t0) REVERT: O 7 LYS cc_start: 0.6347 (mttt) cc_final: 0.5933 (mtmm) REVERT: O 8 ASN cc_start: 0.7473 (t0) cc_final: 0.6848 (t0) REVERT: O 12 LEU cc_start: 0.7245 (mp) cc_final: 0.6741 (mm) REVERT: O 28 ARG cc_start: 0.5819 (OUTLIER) cc_final: 0.4972 (ttp-110) REVERT: O 38 LYS cc_start: 0.5131 (mttt) cc_final: 0.4855 (mtmm) REVERT: O 94 VAL cc_start: 0.6928 (m) cc_final: 0.6608 (p) REVERT: P 6 GLU cc_start: 0.6586 (mt-10) cc_final: 0.5552 (tm-30) REVERT: P 11 GLU cc_start: 0.6652 (pt0) cc_final: 0.6346 (tt0) REVERT: P 27 ARG cc_start: 0.7157 (mtt-85) cc_final: 0.6848 (mtt180) REVERT: P 85 GLU cc_start: 0.6843 (pt0) cc_final: 0.5909 (mt-10) REVERT: P 88 ARG cc_start: 0.7404 (ptm-80) cc_final: 0.6437 (ptt-90) REVERT: P 111 LYS cc_start: 0.6842 (mttt) cc_final: 0.6231 (tptt) REVERT: P 113 ILE cc_start: 0.6456 (OUTLIER) cc_final: 0.6125 (pt) REVERT: Q 15 LYS cc_start: 0.7045 (mmtt) cc_final: 0.6828 (mtpm) REVERT: Q 19 LYS cc_start: 0.7243 (tmtp) cc_final: 0.6546 (mptt) REVERT: Q 97 ASP cc_start: 0.7280 (t70) cc_final: 0.6861 (t0) REVERT: Q 116 GLN cc_start: 0.6790 (mm-40) cc_final: 0.6512 (mm-40) REVERT: R 1 MET cc_start: 0.6417 (ttm) cc_final: 0.6100 (ttm) REVERT: R 6 LYS cc_start: 0.6888 (tttp) cc_final: 0.6505 (mtpp) REVERT: R 15 GLU cc_start: 0.6582 (mt-10) cc_final: 0.6268 (mt-10) REVERT: R 47 LYS cc_start: 0.6697 (mmtp) cc_final: 0.6341 (mtpt) REVERT: R 50 ASN cc_start: 0.6032 (p0) cc_final: 0.5621 (p0) REVERT: R 99 LYS cc_start: 0.6545 (tttt) cc_final: 0.6312 (mmtt) REVERT: S 11 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.5135 (tmm160) REVERT: S 21 MET cc_start: 0.7521 (mmt) cc_final: 0.7202 (tpp) REVERT: S 31 GLU cc_start: 0.6818 (tt0) cc_final: 0.6137 (tp30) REVERT: S 48 GLU cc_start: 0.7718 (tt0) cc_final: 0.7146 (tp30) REVERT: S 63 GLU cc_start: 0.6318 (mt-10) cc_final: 0.6080 (mm-30) REVERT: S 65 ASP cc_start: 0.5397 (t0) cc_final: 0.5164 (t0) REVERT: S 85 PHE cc_start: 0.7255 (m-80) cc_final: 0.7021 (m-80) REVERT: T 2 LYS cc_start: 0.3333 (OUTLIER) cc_final: 0.3127 (ptpt) REVERT: T 10 ARG cc_start: 0.7172 (ptm160) cc_final: 0.6657 (ptp90) REVERT: T 20 LEU cc_start: 0.5333 (mt) cc_final: 0.5059 (mt) REVERT: T 21 MET cc_start: 0.5785 (mtt) cc_final: 0.5485 (mtm) REVERT: T 23 GLU cc_start: 0.5779 (mt-10) cc_final: 0.5383 (mp0) REVERT: T 33 ARG cc_start: 0.6673 (mmt90) cc_final: 0.6332 (mpp-170) REVERT: T 41 ASP cc_start: 0.6669 (m-30) cc_final: 0.6447 (m-30) REVERT: T 50 LYS cc_start: 0.6153 (mttt) cc_final: 0.5622 (mmtm) REVERT: T 68 ARG cc_start: 0.5095 (ptm-80) cc_final: 0.4345 (ptm160) REVERT: T 72 MET cc_start: 0.7326 (OUTLIER) cc_final: 0.6861 (mmt) REVERT: U 4 LYS cc_start: 0.7121 (OUTLIER) cc_final: 0.6548 (ptpp) REVERT: U 22 THR cc_start: 0.7073 (m) cc_final: 0.6716 (t) REVERT: U 30 LYS cc_start: 0.6260 (mttt) cc_final: 0.5867 (mtmt) REVERT: U 40 MET cc_start: 0.6823 (mmm) cc_final: 0.6528 (mmm) REVERT: U 84 LYS cc_start: 0.6196 (pttt) cc_final: 0.5767 (pttp) REVERT: W 19 LYS cc_start: 0.7464 (mtmp) cc_final: 0.7169 (mmtt) REVERT: W 25 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6612 (mm-30) REVERT: W 57 GLU cc_start: 0.6530 (mt-10) cc_final: 0.6040 (mm-30) REVERT: X 60 GLU cc_start: 0.4563 (pt0) cc_final: 0.4056 (tp30) REVERT: Y 23 GLU cc_start: 0.6384 (mt-10) cc_final: 0.5654 (tm-30) REVERT: Y 29 ARG cc_start: 0.6203 (mtt180) cc_final: 0.5925 (mtt-85) REVERT: Y 45 GLU cc_start: 0.6380 (mt-10) cc_final: 0.6018 (tm-30) REVERT: Y 48 LYS cc_start: 0.6740 (mttt) cc_final: 0.6114 (mptt) REVERT: Y 50 ILE cc_start: 0.7046 (OUTLIER) cc_final: 0.6566 (mp) REVERT: Y 53 MET cc_start: 0.7130 (mtt) cc_final: 0.6368 (mtm) REVERT: Z 9 LYS cc_start: 0.7107 (mmtt) cc_final: 0.6887 (mmtp) REVERT: Z 10 ARG cc_start: 0.7307 (mmt90) cc_final: 0.6483 (mmm160) REVERT: Z 29 LYS cc_start: 0.7550 (mtmt) cc_final: 0.7302 (mtmm) REVERT: Z 38 GLU cc_start: 0.6682 (mm-30) cc_final: 0.5996 (mm-30) REVERT: Z 46 MET cc_start: 0.8005 (mtp) cc_final: 0.7611 (mtp) REVERT: Z 55 SER cc_start: 0.7632 (t) cc_final: 0.7359 (m) REVERT: Z 57 LYS cc_start: 0.6068 (mptt) cc_final: 0.5745 (ttpp) REVERT: e 10 GLU cc_start: 0.3835 (mm-30) cc_final: 0.3552 (pm20) REVERT: e 12 GLU cc_start: 0.4881 (tt0) cc_final: 0.4221 (mp0) REVERT: e 61 ARG cc_start: 0.5178 (ttm170) cc_final: 0.4934 (mpt-90) REVERT: e 62 LYS cc_start: 0.4817 (mmtm) cc_final: 0.4565 (tmmm) REVERT: e 84 GLU cc_start: 0.5303 (tt0) cc_final: 0.4894 (mm-30) REVERT: e 101 GLU cc_start: 0.4546 (mm-30) cc_final: 0.3981 (pm20) REVERT: e 138 ARG cc_start: 0.6231 (mmt90) cc_final: 0.5176 (mtp85) REVERT: k 44 ILE cc_start: 0.5131 (OUTLIER) cc_final: 0.4716 (mp) REVERT: l 3 THR cc_start: 0.7047 (m) cc_final: 0.6777 (p) REVERT: l 26 LYS cc_start: 0.5112 (mmtm) cc_final: 0.4804 (mmmt) REVERT: l 33 LYS cc_start: 0.4693 (mtmt) cc_final: 0.4396 (tptt) REVERT: l 64 LYS cc_start: 0.5086 (pttp) cc_final: 0.4683 (mmtt) REVERT: l 90 HIS cc_start: 0.3873 (OUTLIER) cc_final: 0.3060 (t70) REVERT: l 99 ARG cc_start: 0.4944 (ptm160) cc_final: 0.4369 (ptp-110) REVERT: l 101 LYS cc_start: 0.5249 (tppp) cc_final: 0.4666 (mptt) REVERT: l 133 LYS cc_start: 0.3166 (ttmm) cc_final: 0.2784 (ttpt) REVERT: o 7 ARG cc_start: 0.3818 (OUTLIER) cc_final: 0.3436 (ttm110) REVERT: o 34 ASP cc_start: 0.5608 (t70) cc_final: 0.5341 (t70) REVERT: o 44 ARG cc_start: 0.5877 (mmt90) cc_final: 0.5663 (mmt90) REVERT: q 35 LEU cc_start: 0.5034 (tp) cc_final: 0.4700 (pt) REVERT: q 40 VAL cc_start: 0.5368 (OUTLIER) cc_final: 0.5162 (m) REVERT: c 48 ASP cc_start: 0.4372 (m-30) cc_final: 0.3907 (p0) REVERT: c 86 LEU cc_start: 0.3861 (tp) cc_final: 0.3657 (tm) REVERT: c 107 ARG cc_start: 0.3592 (tpp80) cc_final: 0.3314 (ptp-170) REVERT: c 134 LYS cc_start: 0.5094 (mttt) cc_final: 0.4855 (mmmm) REVERT: c 186 SER cc_start: 0.7271 (t) cc_final: 0.6862 (p) REVERT: g 31 MET cc_start: 0.6638 (ttp) cc_final: 0.6184 (ttp) REVERT: g 67 LYS cc_start: 0.5042 (ttpt) cc_final: 0.4779 (mmtm) REVERT: g 70 MET cc_start: 0.5125 (mtm) cc_final: 0.4601 (mtm) REVERT: g 90 GLU cc_start: 0.5114 (tt0) cc_final: 0.4709 (pt0) REVERT: g 107 TYR cc_start: 0.4999 (m-80) cc_final: 0.4708 (m-80) REVERT: g 111 ARG cc_start: 0.4239 (mtp85) cc_final: 0.3908 (mtt-85) REVERT: g 144 MET cc_start: 0.4884 (mtm) cc_final: 0.4453 (mmm) REVERT: i 20 ARG cc_start: 0.3815 (mtm110) cc_final: 0.3411 (mtm180) REVERT: i 123 ARG cc_start: 0.5837 (tmt170) cc_final: 0.5370 (tpp-160) REVERT: j 46 LYS cc_start: 0.5909 (ttpt) cc_final: 0.4991 (ttpp) REVERT: j 71 LYS cc_start: 0.5188 (OUTLIER) cc_final: 0.4734 (mttp) REVERT: m 11 ARG cc_start: 0.3340 (mtp-110) cc_final: 0.2812 (mtp180) REVERT: m 27 ARG cc_start: 0.5012 (ptm160) cc_final: 0.4762 (mtm110) REVERT: m 89 ILE cc_start: 0.6083 (mt) cc_final: 0.5781 (mm) REVERT: n 11 GLN cc_start: 0.5466 (OUTLIER) cc_final: 0.5017 (mt0) REVERT: n 26 ARG cc_start: 0.6262 (ttt-90) cc_final: 0.5816 (ttp80) REVERT: n 50 LYS cc_start: 0.6123 (mttt) cc_final: 0.5753 (mttp) REVERT: n 57 LYS cc_start: 0.6184 (ptpp) cc_final: 0.5307 (pttp) REVERT: h 9 ASP cc_start: 0.4116 (OUTLIER) cc_final: 0.2855 (t70) REVERT: h 23 GLU cc_start: 0.4769 (OUTLIER) cc_final: 0.4553 (mm-30) REVERT: h 85 LEU cc_start: 0.3330 (OUTLIER) cc_final: 0.3096 (tp) REVERT: r 66 ARG cc_start: 0.5219 (mtt180) cc_final: 0.4934 (mtt180) REVERT: f 7 MET cc_start: 0.6607 (ttm) cc_final: 0.6035 (ttm) REVERT: f 74 GLU cc_start: 0.5268 (tp30) cc_final: 0.4679 (mp0) outliers start: 154 outliers final: 68 residues processed: 815 average time/residue: 2.3849 time to fit residues: 2653.1079 Evaluate side-chains 754 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 661 time to evaluate : 5.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 41 LYS Chi-restraints excluded: chain 3 residue 4 MET Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain E residue 10 ASN Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 175 MET Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 161 LYS Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 11 THR Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 139 GLU Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 23 SER Chi-restraints excluded: chain O residue 28 ARG Chi-restraints excluded: chain O residue 72 SER Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 113 ILE Chi-restraints excluded: chain S residue 11 ARG Chi-restraints excluded: chain T residue 2 LYS Chi-restraints excluded: chain T residue 72 MET Chi-restraints excluded: chain T residue 73 THR Chi-restraints excluded: chain U residue 4 LYS Chi-restraints excluded: chain U residue 85 VAL Chi-restraints excluded: chain W residue 78 GLU Chi-restraints excluded: chain Y residue 17 LYS Chi-restraints excluded: chain Y residue 20 SER Chi-restraints excluded: chain Y residue 44 ARG Chi-restraints excluded: chain Y residue 50 ILE Chi-restraints excluded: chain e residue 37 VAL Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain e residue 157 ARG Chi-restraints excluded: chain k residue 28 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 44 ILE Chi-restraints excluded: chain k residue 118 VAL Chi-restraints excluded: chain l residue 13 VAL Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 38 VAL Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 90 HIS Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 128 SER Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain o residue 11 LEU Chi-restraints excluded: chain o residue 68 THR Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain t residue 86 LEU Chi-restraints excluded: chain c residue 6 ASN Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 32 ILE Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 135 VAL Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain i residue 87 LEU Chi-restraints excluded: chain j residue 71 LYS Chi-restraints excluded: chain n residue 5 SER Chi-restraints excluded: chain n residue 9 LYS Chi-restraints excluded: chain n residue 11 GLN Chi-restraints excluded: chain n residue 32 SER Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain s residue 16 MET Chi-restraints excluded: chain s residue 19 ILE Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain h residue 9 ASP Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 23 GLU Chi-restraints excluded: chain h residue 45 PHE Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 66 TYR Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 85 LEU Chi-restraints excluded: chain h residue 109 SER Chi-restraints excluded: chain h residue 110 GLN Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain f residue 81 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 819 optimal weight: 20.0000 chunk 623 optimal weight: 20.0000 chunk 430 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 395 optimal weight: 2.9990 chunk 557 optimal weight: 0.9990 chunk 832 optimal weight: 5.9990 chunk 881 optimal weight: 7.9990 chunk 435 optimal weight: 5.9990 chunk 789 optimal weight: 10.0000 chunk 237 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 75 ASN G 148 ASN O 37 ASN Q 52 GLN Q 108 GLN e 45 HIS e 135 ASN l 5 ASN o 37 ASN t 42 ASN c 113 GLN m 32 GLN m 100 GLN m 104 ASN r 53 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 147580 Z= 0.260 Angle : 0.749 18.055 221780 Z= 0.384 Chirality : 0.042 0.342 28489 Planarity : 0.006 0.146 11146 Dihedral : 23.767 178.598 76326 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.72 % Favored : 96.18 % Rotamer: Outliers : 3.55 % Allowed : 14.29 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.11), residues: 4733 helix: 0.17 (0.12), residues: 1481 sheet: -0.86 (0.16), residues: 940 loop : -0.84 (0.12), residues: 2312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP k 46 HIS 0.008 0.002 HIS t 20 PHE 0.022 0.003 PHE R 74 TYR 0.023 0.003 TYR Q 32 ARG 0.008 0.001 ARG f 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9466 Ramachandran restraints generated. 4733 Oldfield, 0 Emsley, 4733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9466 Ramachandran restraints generated. 4733 Oldfield, 0 Emsley, 4733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 675 time to evaluate : 5.423 Fit side-chains revert: symmetry clash REVERT: 0 44 LYS cc_start: 0.7168 (mtmt) cc_final: 0.6532 (mmtm) REVERT: 1 23 LYS cc_start: 0.5276 (mtmt) cc_final: 0.4967 (mmtp) REVERT: 1 33 LYS cc_start: 0.6275 (ttmt) cc_final: 0.5834 (mmmt) REVERT: 1 46 ARG cc_start: 0.6770 (ttm110) cc_final: 0.6561 (ttm110) REVERT: 1 47 GLU cc_start: 0.6178 (tt0) cc_final: 0.5955 (tt0) REVERT: 3 15 LYS cc_start: 0.7238 (ttmm) cc_final: 0.6569 (ptpt) REVERT: 4 13 LYS cc_start: 0.5939 (mttt) cc_final: 0.5315 (mmtt) REVERT: 4 15 LYS cc_start: 0.6484 (mtpt) cc_final: 0.5822 (tttp) REVERT: 4 18 ARG cc_start: 0.6791 (ttt90) cc_final: 0.5996 (tpp80) REVERT: 4 20 LYS cc_start: 0.6465 (mmtt) cc_final: 0.6228 (mttm) REVERT: 4 24 MET cc_start: 0.8112 (mtp) cc_final: 0.7819 (mtp) REVERT: 4 28 GLU cc_start: 0.5634 (pt0) cc_final: 0.5326 (pm20) REVERT: 6 1 MET cc_start: 0.4468 (OUTLIER) cc_final: 0.3839 (mtp) REVERT: C 23 GLU cc_start: 0.6417 (OUTLIER) cc_final: 0.5950 (pm20) REVERT: C 28 LYS cc_start: 0.6299 (mttt) cc_final: 0.5873 (pttm) REVERT: C 77 ARG cc_start: 0.6514 (ttp80) cc_final: 0.5693 (mtt-85) REVERT: C 100 GLU cc_start: 0.7462 (tt0) cc_final: 0.7133 (tt0) REVERT: C 183 MET cc_start: 0.8104 (mtp) cc_final: 0.7824 (mtt) REVERT: C 198 GLU cc_start: 0.6948 (tt0) cc_final: 0.6378 (pm20) REVERT: C 199 GLN cc_start: 0.6514 (mt0) cc_final: 0.5983 (pm20) REVERT: C 245 SER cc_start: 0.7387 (t) cc_final: 0.7123 (p) REVERT: C 261 LYS cc_start: 0.6264 (tttm) cc_final: 0.5289 (mmtt) REVERT: C 267 ASP cc_start: 0.6808 (m-30) cc_final: 0.6518 (m-30) REVERT: C 273 ARG cc_start: 0.5799 (mmt90) cc_final: 0.5352 (mmp-170) REVERT: D 71 LYS cc_start: 0.6222 (mttt) cc_final: 0.5711 (ttpp) REVERT: D 73 GLU cc_start: 0.6366 (mt-10) cc_final: 0.6096 (mt-10) REVERT: D 92 GLU cc_start: 0.7044 (tt0) cc_final: 0.6357 (pt0) REVERT: D 103 SER cc_start: 0.7223 (p) cc_final: 0.6937 (m) REVERT: D 178 LYS cc_start: 0.7272 (ttmt) cc_final: 0.6763 (tttm) REVERT: D 180 ASP cc_start: 0.7080 (t0) cc_final: 0.6876 (t0) REVERT: D 182 GLU cc_start: 0.5836 (mt-10) cc_final: 0.5552 (mm-30) REVERT: E 27 GLU cc_start: 0.5680 (tt0) cc_final: 0.5236 (tm-30) REVERT: E 103 LYS cc_start: 0.7034 (ttmm) cc_final: 0.6317 (ttmt) REVERT: E 127 GLU cc_start: 0.5963 (tp30) cc_final: 0.5446 (tt0) REVERT: E 129 LEU cc_start: 0.6774 (tp) cc_final: 0.6454 (tp) REVERT: E 161 GLU cc_start: 0.5307 (tt0) cc_final: 0.4827 (mp0) REVERT: E 181 ILE cc_start: 0.6557 (tt) cc_final: 0.6279 (pp) REVERT: E 196 LYS cc_start: 0.6393 (ttpt) cc_final: 0.5864 (ttpt) REVERT: F 30 LYS cc_start: 0.5940 (pttt) cc_final: 0.5468 (ptpp) REVERT: F 63 GLN cc_start: 0.6184 (mt0) cc_final: 0.5974 (mt0) REVERT: F 69 ARG cc_start: 0.5626 (mtt-85) cc_final: 0.4930 (mpp80) REVERT: F 72 LYS cc_start: 0.5111 (mtpp) cc_final: 0.4679 (mtmm) REVERT: F 95 ARG cc_start: 0.5159 (mmt90) cc_final: 0.4941 (mmt90) REVERT: F 136 LEU cc_start: 0.4157 (OUTLIER) cc_final: 0.3895 (pp) REVERT: F 165 GLU cc_start: 0.5394 (OUTLIER) cc_final: 0.5147 (mt-10) REVERT: G 131 LYS cc_start: 0.5554 (OUTLIER) cc_final: 0.5034 (tppp) REVERT: G 166 GLU cc_start: 0.5558 (tt0) cc_final: 0.5118 (tp30) REVERT: J 13 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6214 (tp30) REVERT: J 15 LYS cc_start: 0.6901 (mttp) cc_final: 0.6639 (mtmt) REVERT: J 62 LYS cc_start: 0.6979 (mmtp) cc_final: 0.6491 (mtmt) REVERT: J 92 GLU cc_start: 0.6758 (tt0) cc_final: 0.6461 (mt-10) REVERT: J 107 LYS cc_start: 0.6866 (tttm) cc_final: 0.6533 (ttpt) REVERT: J 130 GLU cc_start: 0.6554 (mt-10) cc_final: 0.6015 (mm-30) REVERT: J 139 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6460 (mm-30) REVERT: K 9 LYS cc_start: 0.7772 (mttt) cc_final: 0.7050 (ttmt) REVERT: K 34 ASN cc_start: 0.6989 (p0) cc_final: 0.6742 (m-40) REVERT: K 45 GLN cc_start: 0.7253 (mt0) cc_final: 0.6856 (mm110) REVERT: K 48 PRO cc_start: 0.6253 (Cg_exo) cc_final: 0.5935 (Cg_endo) REVERT: K 70 ARG cc_start: 0.7505 (ttt180) cc_final: 0.6805 (ttt-90) REVERT: K 107 ARG cc_start: 0.6211 (mtp-110) cc_final: 0.5737 (mtm-85) REVERT: K 110 ASN cc_start: 0.5637 (m110) cc_final: 0.5388 (t0) REVERT: K 112 MET cc_start: 0.6905 (mmm) cc_final: 0.6654 (mmm) REVERT: K 113 LYS cc_start: 0.6312 (mttt) cc_final: 0.5552 (tppt) REVERT: L 14 LYS cc_start: 0.7507 (mtpt) cc_final: 0.7228 (mtpp) REVERT: L 124 LYS cc_start: 0.6101 (mtpt) cc_final: 0.5897 (mttm) REVERT: L 133 LYS cc_start: 0.6579 (tttm) cc_final: 0.6150 (ttpt) REVERT: L 137 GLU cc_start: 0.5498 (mt-10) cc_final: 0.5012 (mm-30) REVERT: M 5 LYS cc_start: 0.6778 (tttt) cc_final: 0.6137 (mmtm) REVERT: M 18 ARG cc_start: 0.7270 (mtt90) cc_final: 0.6245 (mtp180) REVERT: M 130 LYS cc_start: 0.7128 (ptmt) cc_final: 0.6838 (ttpt) REVERT: M 134 ARG cc_start: 0.5923 (ptm160) cc_final: 0.5507 (ttm170) REVERT: N 34 GLU cc_start: 0.7099 (tt0) cc_final: 0.6567 (tp30) REVERT: N 72 ASN cc_start: 0.6875 (t0) cc_final: 0.6305 (t0) REVERT: O 7 LYS cc_start: 0.6340 (mttt) cc_final: 0.5992 (mtmm) REVERT: O 8 ASN cc_start: 0.7417 (t0) cc_final: 0.6673 (t0) REVERT: O 12 LEU cc_start: 0.7275 (mp) cc_final: 0.6960 (mm) REVERT: O 28 ARG cc_start: 0.5765 (OUTLIER) cc_final: 0.5042 (ttp-110) REVERT: O 94 VAL cc_start: 0.6989 (OUTLIER) cc_final: 0.6709 (p) REVERT: P 11 GLU cc_start: 0.6640 (pt0) cc_final: 0.5984 (pm20) REVERT: P 27 ARG cc_start: 0.7139 (mtt-85) cc_final: 0.6820 (mtt180) REVERT: P 83 LYS cc_start: 0.7381 (pttt) cc_final: 0.7111 (pttm) REVERT: P 85 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.5861 (mt-10) REVERT: P 88 ARG cc_start: 0.7395 (ptm-80) cc_final: 0.6432 (ptt-90) REVERT: P 109 ARG cc_start: 0.6148 (mtm180) cc_final: 0.5664 (mtm180) REVERT: P 111 LYS cc_start: 0.6884 (mttt) cc_final: 0.6329 (tptt) REVERT: Q 19 LYS cc_start: 0.7245 (tmtp) cc_final: 0.6505 (mmtt) REVERT: Q 97 ASP cc_start: 0.7281 (t70) cc_final: 0.6832 (t0) REVERT: Q 116 GLN cc_start: 0.6769 (mm-40) cc_final: 0.6471 (mm-40) REVERT: R 1 MET cc_start: 0.6426 (ttm) cc_final: 0.6203 (ttm) REVERT: R 47 LYS cc_start: 0.6675 (mmtp) cc_final: 0.6286 (mtpt) REVERT: R 98 GLU cc_start: 0.6240 (mt-10) cc_final: 0.5589 (mp0) REVERT: R 99 LYS cc_start: 0.6534 (tttt) cc_final: 0.6282 (mmtt) REVERT: S 11 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.5477 (tmm160) REVERT: S 31 GLU cc_start: 0.6799 (tt0) cc_final: 0.6121 (tp30) REVERT: S 48 GLU cc_start: 0.7709 (tt0) cc_final: 0.7173 (tp30) REVERT: S 65 ASP cc_start: 0.5338 (t0) cc_final: 0.5079 (t0) REVERT: S 85 PHE cc_start: 0.7191 (m-80) cc_final: 0.6976 (m-80) REVERT: S 92 ARG cc_start: 0.5926 (mtt-85) cc_final: 0.5543 (mtt90) REVERT: T 10 ARG cc_start: 0.7221 (ptm160) cc_final: 0.6688 (ptp90) REVERT: T 21 MET cc_start: 0.5949 (mtt) cc_final: 0.5666 (mtm) REVERT: T 29 GLU cc_start: 0.7125 (mt-10) cc_final: 0.6616 (tt0) REVERT: T 33 ARG cc_start: 0.6629 (mmt90) cc_final: 0.6283 (mpp-170) REVERT: T 50 LYS cc_start: 0.6180 (mttt) cc_final: 0.5645 (mmtm) REVERT: T 68 ARG cc_start: 0.5131 (ptm-80) cc_final: 0.4436 (tmt-80) REVERT: U 4 LYS cc_start: 0.7131 (OUTLIER) cc_final: 0.6566 (ptpp) REVERT: U 22 THR cc_start: 0.6991 (m) cc_final: 0.6626 (t) REVERT: U 30 LYS cc_start: 0.6169 (mttt) cc_final: 0.5797 (mtmt) REVERT: U 40 MET cc_start: 0.6789 (mmm) cc_final: 0.6526 (mmm) REVERT: U 84 LYS cc_start: 0.6181 (pttt) cc_final: 0.5749 (pttp) REVERT: W 19 LYS cc_start: 0.7532 (mtmp) cc_final: 0.7184 (mmtt) REVERT: W 57 GLU cc_start: 0.6539 (mt-10) cc_final: 0.6013 (mm-30) REVERT: X 60 GLU cc_start: 0.4554 (pt0) cc_final: 0.4105 (mp0) REVERT: Y 23 GLU cc_start: 0.6364 (mt-10) cc_final: 0.5582 (tm-30) REVERT: Y 29 ARG cc_start: 0.6174 (mtt180) cc_final: 0.5931 (mtt-85) REVERT: Y 45 GLU cc_start: 0.6547 (mt-10) cc_final: 0.6341 (tt0) REVERT: Y 48 LYS cc_start: 0.6710 (mttt) cc_final: 0.6140 (mptt) REVERT: Y 50 ILE cc_start: 0.7143 (OUTLIER) cc_final: 0.6876 (mp) REVERT: Y 53 MET cc_start: 0.7103 (mtt) cc_final: 0.6319 (mtm) REVERT: Z 9 LYS cc_start: 0.7089 (mmtt) cc_final: 0.6875 (mmtp) REVERT: Z 10 ARG cc_start: 0.7251 (mmt90) cc_final: 0.6455 (mmm160) REVERT: Z 29 LYS cc_start: 0.7574 (mtmt) cc_final: 0.7336 (mtmm) REVERT: Z 30 LYS cc_start: 0.7526 (OUTLIER) cc_final: 0.7318 (mtmt) REVERT: Z 38 GLU cc_start: 0.6741 (mm-30) cc_final: 0.6028 (mm-30) REVERT: Z 55 SER cc_start: 0.7566 (t) cc_final: 0.7262 (m) REVERT: Z 57 LYS cc_start: 0.5982 (mptt) cc_final: 0.5686 (ttpp) REVERT: e 10 GLU cc_start: 0.3797 (mm-30) cc_final: 0.3583 (pm20) REVERT: e 12 GLU cc_start: 0.4942 (tt0) cc_final: 0.4470 (mt-10) REVERT: e 61 ARG cc_start: 0.5117 (ttm170) cc_final: 0.4899 (mpt-90) REVERT: e 62 LYS cc_start: 0.5102 (mmtm) cc_final: 0.4827 (tmmm) REVERT: e 76 MET cc_start: 0.4724 (mtm) cc_final: 0.4494 (mmm) REVERT: e 84 GLU cc_start: 0.5413 (tt0) cc_final: 0.4786 (mt-10) REVERT: e 98 PRO cc_start: 0.5478 (Cg_endo) cc_final: 0.5205 (Cg_exo) REVERT: e 101 GLU cc_start: 0.4582 (mm-30) cc_final: 0.4342 (mm-30) REVERT: e 138 ARG cc_start: 0.6316 (mmt90) cc_final: 0.5229 (mtp180) REVERT: k 37 THR cc_start: 0.4290 (OUTLIER) cc_final: 0.4064 (p) REVERT: k 44 ILE cc_start: 0.5205 (OUTLIER) cc_final: 0.4660 (mp) REVERT: l 3 THR cc_start: 0.7087 (m) cc_final: 0.6780 (p) REVERT: l 26 LYS cc_start: 0.5115 (mmtm) cc_final: 0.4806 (mmmt) REVERT: l 33 LYS cc_start: 0.4649 (mtmt) cc_final: 0.4391 (tptt) REVERT: l 64 LYS cc_start: 0.5096 (pttp) cc_final: 0.4674 (mmtm) REVERT: l 123 ARG cc_start: 0.3556 (ttm110) cc_final: 0.3324 (ttm110) REVERT: l 133 LYS cc_start: 0.3025 (ttmm) cc_final: 0.2638 (ttpt) REVERT: o 44 ARG cc_start: 0.5846 (mmt90) cc_final: 0.5619 (mmt90) REVERT: o 63 ARG cc_start: 0.6889 (ttp-170) cc_final: 0.6581 (ttp80) REVERT: q 40 VAL cc_start: 0.5110 (t) cc_final: 0.4869 (m) REVERT: c 134 LYS cc_start: 0.5087 (mttt) cc_final: 0.4857 (mmmm) REVERT: c 186 SER cc_start: 0.7332 (t) cc_final: 0.6849 (p) REVERT: c 189 ASP cc_start: 0.5385 (t0) cc_final: 0.4931 (p0) REVERT: g 31 MET cc_start: 0.6687 (ttp) cc_final: 0.6128 (ttp) REVERT: g 67 LYS cc_start: 0.5028 (ttpt) cc_final: 0.4772 (mmtm) REVERT: g 70 MET cc_start: 0.5088 (mtm) cc_final: 0.4795 (mtm) REVERT: g 107 TYR cc_start: 0.4996 (m-80) cc_final: 0.4746 (m-80) REVERT: g 111 ARG cc_start: 0.4258 (mtp85) cc_final: 0.4016 (mtt-85) REVERT: g 144 MET cc_start: 0.4936 (mtm) cc_final: 0.4500 (mmm) REVERT: i 123 ARG cc_start: 0.5809 (tmt170) cc_final: 0.5368 (tpp-160) REVERT: j 71 LYS cc_start: 0.5210 (OUTLIER) cc_final: 0.4971 (mttt) REVERT: m 27 ARG cc_start: 0.4996 (ptm160) cc_final: 0.4763 (mtm110) REVERT: n 11 GLN cc_start: 0.5348 (mt0) cc_final: 0.4879 (mt0) REVERT: n 26 ARG cc_start: 0.6229 (ttt-90) cc_final: 0.5998 (ttp80) REVERT: n 57 LYS cc_start: 0.6162 (ptpp) cc_final: 0.5335 (pttp) REVERT: s 16 MET cc_start: 0.5187 (OUTLIER) cc_final: 0.4873 (ttm) REVERT: s 35 SER cc_start: 0.7095 (OUTLIER) cc_final: 0.6845 (p) REVERT: h 42 ARG cc_start: 0.3163 (mmt-90) cc_final: 0.2766 (mpt180) REVERT: f 7 MET cc_start: 0.6079 (ttm) cc_final: 0.5838 (ttm) REVERT: f 74 GLU cc_start: 0.5184 (tp30) cc_final: 0.4528 (mp0) REVERT: f 91 VAL cc_start: 0.5548 (t) cc_final: 0.5173 (m) outliers start: 143 outliers final: 71 residues processed: 765 average time/residue: 2.3897 time to fit residues: 2499.8239 Evaluate side-chains 734 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 644 time to evaluate : 5.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 4 MET Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 64 LYS Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain G residue 131 LYS Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain J residue 11 THR Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 139 GLU Chi-restraints excluded: chain L residue 7 LYS Chi-restraints excluded: chain L residue 69 ILE Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 23 SER Chi-restraints excluded: chain O residue 28 ARG Chi-restraints excluded: chain O residue 72 SER Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 63 GLU Chi-restraints excluded: chain S residue 11 ARG Chi-restraints excluded: chain S residue 94 SER Chi-restraints excluded: chain U residue 4 LYS Chi-restraints excluded: chain U residue 85 VAL Chi-restraints excluded: chain W residue 78 GLU Chi-restraints excluded: chain Y residue 20 SER Chi-restraints excluded: chain Y residue 44 ARG Chi-restraints excluded: chain Y residue 50 ILE Chi-restraints excluded: chain Z residue 30 LYS Chi-restraints excluded: chain e residue 37 VAL Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain e residue 157 ARG Chi-restraints excluded: chain k residue 28 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 44 ILE Chi-restraints excluded: chain k residue 118 VAL Chi-restraints excluded: chain l residue 13 VAL Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 128 SER Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 68 THR Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain c residue 6 ASN Chi-restraints excluded: chain c residue 101 ASN Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 32 ILE Chi-restraints excluded: chain g residue 135 VAL Chi-restraints excluded: chain i residue 87 LEU Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain j residue 71 LYS Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain m residue 92 ARG Chi-restraints excluded: chain n residue 5 SER Chi-restraints excluded: chain n residue 9 LYS Chi-restraints excluded: chain n residue 32 SER Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain s residue 16 MET Chi-restraints excluded: chain s residue 19 ILE Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 45 PHE Chi-restraints excluded: chain h residue 66 TYR Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 109 SER Chi-restraints excluded: chain h residue 110 GLN Chi-restraints excluded: chain f residue 63 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 734 optimal weight: 8.9990 chunk 500 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 656 optimal weight: 10.0000 chunk 363 optimal weight: 0.9980 chunk 752 optimal weight: 7.9990 chunk 609 optimal weight: 20.0000 chunk 1 optimal weight: 0.8980 chunk 450 optimal weight: 7.9990 chunk 791 optimal weight: 20.0000 chunk 222 optimal weight: 10.0000 overall best weight: 4.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 61 GLN G 148 ASN O 37 ASN Q 108 GLN l 5 ASN l 90 HIS o 37 ASN t 3 ASN c 113 GLN i 38 HIS m 32 GLN f 27 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 147580 Z= 0.260 Angle : 0.760 18.179 221780 Z= 0.389 Chirality : 0.042 0.341 28489 Planarity : 0.006 0.148 11146 Dihedral : 23.804 179.268 76324 Min Nonbonded Distance : 1.690 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.29 % Favored : 95.63 % Rotamer: Outliers : 4.00 % Allowed : 15.06 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.11), residues: 4733 helix: 0.24 (0.12), residues: 1479 sheet: -0.73 (0.16), residues: 916 loop : -0.83 (0.12), residues: 2338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP k 46 HIS 0.008 0.002 HIS t 20 PHE 0.022 0.003 PHE R 74 TYR 0.022 0.003 TYR Q 32 ARG 0.009 0.001 ARG 2 3 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9466 Ramachandran restraints generated. 4733 Oldfield, 0 Emsley, 4733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9466 Ramachandran restraints generated. 4733 Oldfield, 0 Emsley, 4733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 656 time to evaluate : 5.416 Fit side-chains revert: symmetry clash REVERT: 0 44 LYS cc_start: 0.7123 (mtmt) cc_final: 0.6506 (mmtm) REVERT: 1 23 LYS cc_start: 0.5164 (mtmt) cc_final: 0.4870 (mmtp) REVERT: 1 33 LYS cc_start: 0.6278 (ttmt) cc_final: 0.5828 (mmmt) REVERT: 1 47 GLU cc_start: 0.6235 (tt0) cc_final: 0.6034 (tt0) REVERT: 3 15 LYS cc_start: 0.7291 (ttmm) cc_final: 0.6650 (ptpt) REVERT: 4 13 LYS cc_start: 0.6007 (mttt) cc_final: 0.5389 (mmtt) REVERT: 4 15 LYS cc_start: 0.6460 (mtpt) cc_final: 0.5802 (tttp) REVERT: 4 18 ARG cc_start: 0.6773 (ttt90) cc_final: 0.6026 (tpp80) REVERT: 4 20 LYS cc_start: 0.6493 (mmtt) cc_final: 0.6269 (mttm) REVERT: 4 24 MET cc_start: 0.8114 (mtp) cc_final: 0.7771 (mtp) REVERT: 4 28 GLU cc_start: 0.5622 (pt0) cc_final: 0.5329 (pm20) REVERT: 6 1 MET cc_start: 0.4425 (OUTLIER) cc_final: 0.3758 (mtp) REVERT: C 23 GLU cc_start: 0.6426 (OUTLIER) cc_final: 0.5960 (pm20) REVERT: C 28 LYS cc_start: 0.6336 (mttt) cc_final: 0.5901 (pttm) REVERT: C 77 ARG cc_start: 0.6575 (ttp80) cc_final: 0.5724 (mtt-85) REVERT: C 100 GLU cc_start: 0.7461 (tt0) cc_final: 0.7138 (tt0) REVERT: C 172 VAL cc_start: 0.7651 (t) cc_final: 0.7373 (m) REVERT: C 183 MET cc_start: 0.8109 (mtp) cc_final: 0.7802 (mtt) REVERT: C 198 GLU cc_start: 0.6959 (tt0) cc_final: 0.6379 (pm20) REVERT: C 199 GLN cc_start: 0.6495 (mt0) cc_final: 0.5975 (pm20) REVERT: C 245 SER cc_start: 0.7459 (t) cc_final: 0.7204 (p) REVERT: C 261 LYS cc_start: 0.6277 (tttm) cc_final: 0.5293 (mmtt) REVERT: C 267 ASP cc_start: 0.6867 (m-30) cc_final: 0.6634 (m-30) REVERT: C 273 ARG cc_start: 0.5773 (mmt90) cc_final: 0.5349 (mmp-170) REVERT: D 71 LYS cc_start: 0.6181 (mttt) cc_final: 0.5683 (ttpp) REVERT: D 73 GLU cc_start: 0.6354 (mt-10) cc_final: 0.6099 (mt-10) REVERT: D 92 GLU cc_start: 0.7055 (tt0) cc_final: 0.6360 (pt0) REVERT: D 103 SER cc_start: 0.7226 (p) cc_final: 0.6927 (m) REVERT: D 178 LYS cc_start: 0.7203 (ttmt) cc_final: 0.6726 (tttm) REVERT: D 182 GLU cc_start: 0.5784 (mt-10) cc_final: 0.5489 (mm-30) REVERT: E 27 GLU cc_start: 0.5620 (tt0) cc_final: 0.5345 (mt-10) REVERT: E 103 LYS cc_start: 0.7017 (ttmm) cc_final: 0.6301 (ttmt) REVERT: E 127 GLU cc_start: 0.5946 (tp30) cc_final: 0.5467 (tt0) REVERT: E 161 GLU cc_start: 0.5346 (tt0) cc_final: 0.4842 (mp0) REVERT: E 181 ILE cc_start: 0.6562 (tt) cc_final: 0.6285 (pp) REVERT: E 196 LYS cc_start: 0.6457 (ttpt) cc_final: 0.5947 (ttpt) REVERT: F 63 GLN cc_start: 0.6143 (mt0) cc_final: 0.5904 (mt0) REVERT: F 69 ARG cc_start: 0.5502 (mtt-85) cc_final: 0.4743 (mpp80) REVERT: F 94 GLU cc_start: 0.4913 (tp30) cc_final: 0.4618 (tt0) REVERT: F 95 ARG cc_start: 0.5179 (mmt90) cc_final: 0.4940 (mmt90) REVERT: F 136 LEU cc_start: 0.4236 (OUTLIER) cc_final: 0.3967 (pp) REVERT: F 152 MET cc_start: 0.6373 (OUTLIER) cc_final: 0.5968 (ptp) REVERT: F 165 GLU cc_start: 0.5374 (OUTLIER) cc_final: 0.5127 (mt-10) REVERT: G 61 GLU cc_start: 0.4734 (mp0) cc_final: 0.4486 (tt0) REVERT: G 131 LYS cc_start: 0.5508 (OUTLIER) cc_final: 0.5016 (tppp) REVERT: G 166 GLU cc_start: 0.5538 (tt0) cc_final: 0.5115 (tp30) REVERT: J 13 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6210 (tp30) REVERT: J 15 LYS cc_start: 0.6910 (mttp) cc_final: 0.6639 (mtmt) REVERT: J 62 LYS cc_start: 0.6956 (mmtp) cc_final: 0.6470 (mtmt) REVERT: J 107 LYS cc_start: 0.6897 (tttm) cc_final: 0.6541 (ttpt) REVERT: J 130 GLU cc_start: 0.6581 (mt-10) cc_final: 0.6067 (mm-30) REVERT: J 139 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6436 (mm-30) REVERT: K 9 LYS cc_start: 0.7771 (mttt) cc_final: 0.7052 (ttmt) REVERT: K 34 ASN cc_start: 0.6984 (p0) cc_final: 0.6739 (m-40) REVERT: K 45 GLN cc_start: 0.7336 (mt0) cc_final: 0.6922 (mm110) REVERT: K 48 PRO cc_start: 0.6151 (Cg_exo) cc_final: 0.5824 (Cg_endo) REVERT: K 70 ARG cc_start: 0.7573 (ttt180) cc_final: 0.6823 (ttt-90) REVERT: K 107 ARG cc_start: 0.6174 (mtp-110) cc_final: 0.5712 (mtm-85) REVERT: K 110 ASN cc_start: 0.5560 (m110) cc_final: 0.5349 (t0) REVERT: K 112 MET cc_start: 0.6895 (mmm) cc_final: 0.6634 (mmm) REVERT: K 113 LYS cc_start: 0.6326 (mttt) cc_final: 0.5583 (tppt) REVERT: L 14 LYS cc_start: 0.7542 (mtpt) cc_final: 0.7295 (mtpp) REVERT: L 90 GLU cc_start: 0.4927 (tt0) cc_final: 0.4495 (tm-30) REVERT: L 133 LYS cc_start: 0.6663 (tttm) cc_final: 0.6285 (ttpt) REVERT: L 137 GLU cc_start: 0.5503 (mt-10) cc_final: 0.5071 (mt-10) REVERT: M 5 LYS cc_start: 0.6684 (tttt) cc_final: 0.6079 (mmtm) REVERT: M 18 ARG cc_start: 0.7259 (mtt90) cc_final: 0.6212 (mtp180) REVERT: M 54 MET cc_start: 0.7840 (ptp) cc_final: 0.7616 (ptt) REVERT: M 130 LYS cc_start: 0.7158 (ptmt) cc_final: 0.6843 (ttpt) REVERT: N 34 GLU cc_start: 0.7148 (tt0) cc_final: 0.6605 (tp30) REVERT: N 72 ASN cc_start: 0.6815 (t0) cc_final: 0.6257 (t0) REVERT: N 75 ASN cc_start: 0.5553 (m110) cc_final: 0.4849 (m110) REVERT: O 8 ASN cc_start: 0.7422 (t0) cc_final: 0.6663 (t0) REVERT: O 12 LEU cc_start: 0.7214 (mp) cc_final: 0.6921 (mm) REVERT: O 28 ARG cc_start: 0.5774 (OUTLIER) cc_final: 0.5051 (ttp-110) REVERT: O 94 VAL cc_start: 0.6992 (OUTLIER) cc_final: 0.6711 (p) REVERT: P 6 GLU cc_start: 0.6473 (mt-10) cc_final: 0.5470 (tm-30) REVERT: P 11 GLU cc_start: 0.6651 (pt0) cc_final: 0.6039 (pm20) REVERT: P 27 ARG cc_start: 0.7121 (mtt-85) cc_final: 0.6783 (mtt180) REVERT: P 85 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.5901 (mt-10) REVERT: P 88 ARG cc_start: 0.7362 (ptm-80) cc_final: 0.6435 (ptt-90) REVERT: P 111 LYS cc_start: 0.6900 (mttt) cc_final: 0.6339 (tptt) REVERT: Q 19 LYS cc_start: 0.7247 (tmtp) cc_final: 0.6539 (mptt) REVERT: Q 97 ASP cc_start: 0.7298 (t70) cc_final: 0.6863 (t0) REVERT: Q 116 GLN cc_start: 0.6767 (mm-40) cc_final: 0.6472 (mm-40) REVERT: R 1 MET cc_start: 0.6319 (ttm) cc_final: 0.6061 (ttm) REVERT: R 6 LYS cc_start: 0.7026 (tttm) cc_final: 0.6217 (pttt) REVERT: R 47 LYS cc_start: 0.6608 (mmtp) cc_final: 0.6284 (mtpt) REVERT: R 50 ASN cc_start: 0.5869 (p0) cc_final: 0.5427 (p0) REVERT: R 98 GLU cc_start: 0.6286 (mt-10) cc_final: 0.5618 (mp0) REVERT: R 99 LYS cc_start: 0.6511 (tttt) cc_final: 0.6298 (mmtt) REVERT: S 11 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.5423 (tmm160) REVERT: S 31 GLU cc_start: 0.6800 (tt0) cc_final: 0.6123 (tp30) REVERT: S 48 GLU cc_start: 0.7687 (tt0) cc_final: 0.7151 (tp30) REVERT: S 85 PHE cc_start: 0.7188 (m-80) cc_final: 0.6954 (m-80) REVERT: S 92 ARG cc_start: 0.5916 (mtt-85) cc_final: 0.5533 (mtt90) REVERT: S 110 LYS cc_start: 0.5000 (tptm) cc_final: 0.4781 (tttm) REVERT: T 10 ARG cc_start: 0.7171 (ptm160) cc_final: 0.6648 (ptp90) REVERT: T 21 MET cc_start: 0.5906 (mtt) cc_final: 0.5610 (mtm) REVERT: T 29 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6629 (tt0) REVERT: T 33 ARG cc_start: 0.6612 (mmt90) cc_final: 0.6296 (mpp-170) REVERT: T 50 LYS cc_start: 0.6157 (mttt) cc_final: 0.5636 (mmtm) REVERT: T 68 ARG cc_start: 0.5141 (ptm-80) cc_final: 0.4444 (tmt-80) REVERT: T 72 MET cc_start: 0.7301 (OUTLIER) cc_final: 0.7065 (mmm) REVERT: U 4 LYS cc_start: 0.7119 (OUTLIER) cc_final: 0.6553 (ptpp) REVERT: U 22 THR cc_start: 0.6985 (m) cc_final: 0.6616 (t) REVERT: U 30 LYS cc_start: 0.6199 (mttt) cc_final: 0.5830 (mtmt) REVERT: U 40 MET cc_start: 0.6747 (mmm) cc_final: 0.6478 (mmm) REVERT: U 84 LYS cc_start: 0.6202 (pttt) cc_final: 0.5783 (pttp) REVERT: W 19 LYS cc_start: 0.7547 (mtmp) cc_final: 0.7185 (mmtt) REVERT: W 57 GLU cc_start: 0.6512 (mt-10) cc_final: 0.5974 (mm-30) REVERT: X 60 GLU cc_start: 0.4526 (pt0) cc_final: 0.4077 (mp0) REVERT: Y 23 GLU cc_start: 0.6369 (mt-10) cc_final: 0.5599 (tm-30) REVERT: Y 29 ARG cc_start: 0.6122 (mtt180) cc_final: 0.5862 (mtt-85) REVERT: Y 45 GLU cc_start: 0.6606 (mt-10) cc_final: 0.6382 (tt0) REVERT: Y 48 LYS cc_start: 0.6617 (mttt) cc_final: 0.6130 (mptt) REVERT: Y 50 ILE cc_start: 0.7150 (OUTLIER) cc_final: 0.6886 (mp) REVERT: Y 53 MET cc_start: 0.7109 (mtt) cc_final: 0.6335 (mtm) REVERT: Z 10 ARG cc_start: 0.7330 (mmt90) cc_final: 0.6488 (mmm160) REVERT: Z 29 LYS cc_start: 0.7559 (mtmt) cc_final: 0.7271 (mtmm) REVERT: Z 55 SER cc_start: 0.7605 (t) cc_final: 0.7305 (m) REVERT: Z 57 LYS cc_start: 0.5969 (mptt) cc_final: 0.5691 (ttpp) REVERT: e 10 GLU cc_start: 0.3744 (mm-30) cc_final: 0.3531 (pm20) REVERT: e 12 GLU cc_start: 0.4906 (tt0) cc_final: 0.4378 (mt-10) REVERT: e 61 ARG cc_start: 0.5133 (ttm170) cc_final: 0.4892 (mpt-90) REVERT: e 62 LYS cc_start: 0.5101 (mmtm) cc_final: 0.4799 (tmmm) REVERT: e 76 MET cc_start: 0.4749 (mtm) cc_final: 0.4511 (mmm) REVERT: e 84 GLU cc_start: 0.5251 (tt0) cc_final: 0.4815 (mm-30) REVERT: e 98 PRO cc_start: 0.5387 (Cg_endo) cc_final: 0.4956 (Cg_exo) REVERT: e 101 GLU cc_start: 0.4643 (mm-30) cc_final: 0.4410 (mm-30) REVERT: l 3 THR cc_start: 0.7105 (m) cc_final: 0.6803 (p) REVERT: l 26 LYS cc_start: 0.5128 (mmtm) cc_final: 0.4836 (mmmt) REVERT: l 33 LYS cc_start: 0.4649 (mtmt) cc_final: 0.4423 (tptt) REVERT: l 54 THR cc_start: 0.5753 (OUTLIER) cc_final: 0.5425 (p) REVERT: l 64 LYS cc_start: 0.5019 (pttp) cc_final: 0.4581 (mmtm) REVERT: l 123 ARG cc_start: 0.3628 (OUTLIER) cc_final: 0.3418 (ttm110) REVERT: l 133 LYS cc_start: 0.3181 (ttmm) cc_final: 0.2769 (ttpt) REVERT: o 44 ARG cc_start: 0.5901 (mmt90) cc_final: 0.5646 (mmt90) REVERT: q 40 VAL cc_start: 0.4893 (OUTLIER) cc_final: 0.4655 (m) REVERT: c 97 ARG cc_start: 0.3965 (OUTLIER) cc_final: 0.3744 (mtm-85) REVERT: c 134 LYS cc_start: 0.5097 (mttt) cc_final: 0.4858 (mmmm) REVERT: c 186 SER cc_start: 0.7367 (t) cc_final: 0.6892 (p) REVERT: c 189 ASP cc_start: 0.5405 (t0) cc_final: 0.4949 (p0) REVERT: g 31 MET cc_start: 0.6632 (ttp) cc_final: 0.6137 (ttp) REVERT: g 67 LYS cc_start: 0.5185 (ttpt) cc_final: 0.4940 (mmtm) REVERT: g 70 MET cc_start: 0.5121 (mtm) cc_final: 0.4793 (mtp) REVERT: g 107 TYR cc_start: 0.4988 (m-80) cc_final: 0.4717 (m-80) REVERT: g 111 ARG cc_start: 0.4239 (mtp85) cc_final: 0.4010 (mtt-85) REVERT: g 144 MET cc_start: 0.4803 (mtm) cc_final: 0.4447 (mmm) REVERT: i 123 ARG cc_start: 0.5857 (tmt170) cc_final: 0.5390 (tpp-160) REVERT: j 71 LYS cc_start: 0.5193 (OUTLIER) cc_final: 0.4935 (mttt) REVERT: m 27 ARG cc_start: 0.5038 (ptm160) cc_final: 0.4768 (mtm110) REVERT: n 57 LYS cc_start: 0.6195 (ptpp) cc_final: 0.5313 (pttp) REVERT: s 16 MET cc_start: 0.5121 (OUTLIER) cc_final: 0.4828 (ttm) REVERT: s 35 SER cc_start: 0.7047 (OUTLIER) cc_final: 0.6804 (p) REVERT: h 23 GLU cc_start: 0.4795 (OUTLIER) cc_final: 0.4567 (mm-30) REVERT: h 42 ARG cc_start: 0.3303 (mmt-90) cc_final: 0.3035 (mmp80) REVERT: h 85 LEU cc_start: 0.3231 (OUTLIER) cc_final: 0.2969 (tp) REVERT: h 109 SER cc_start: 0.3077 (OUTLIER) cc_final: 0.2668 (t) REVERT: r 43 LYS cc_start: 0.5000 (mttp) cc_final: 0.4751 (mttt) REVERT: f 7 MET cc_start: 0.6008 (ttm) cc_final: 0.5744 (ttm) REVERT: f 74 GLU cc_start: 0.5240 (tp30) cc_final: 0.4592 (mp0) REVERT: f 91 VAL cc_start: 0.5482 (t) cc_final: 0.5211 (m) outliers start: 161 outliers final: 78 residues processed: 764 average time/residue: 2.3027 time to fit residues: 2421.3332 Evaluate side-chains 745 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 642 time to evaluate : 5.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 41 LYS Chi-restraints excluded: chain 3 residue 4 MET Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 71 LYS Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 131 LYS Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain J residue 11 THR Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 139 GLU Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 23 SER Chi-restraints excluded: chain O residue 28 ARG Chi-restraints excluded: chain O residue 72 SER Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 113 ILE Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain S residue 11 ARG Chi-restraints excluded: chain S residue 94 SER Chi-restraints excluded: chain T residue 72 MET Chi-restraints excluded: chain U residue 4 LYS Chi-restraints excluded: chain U residue 85 VAL Chi-restraints excluded: chain U residue 102 ASP Chi-restraints excluded: chain W residue 78 GLU Chi-restraints excluded: chain X residue 4 LYS Chi-restraints excluded: chain Y residue 17 LYS Chi-restraints excluded: chain Y residue 20 SER Chi-restraints excluded: chain Y residue 44 ARG Chi-restraints excluded: chain Y residue 50 ILE Chi-restraints excluded: chain e residue 37 VAL Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 83 THR Chi-restraints excluded: chain k residue 118 VAL Chi-restraints excluded: chain k residue 123 CYS Chi-restraints excluded: chain l residue 13 VAL Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 123 ARG Chi-restraints excluded: chain l residue 128 SER Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain o residue 11 LEU Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 68 THR Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain c residue 6 ASN Chi-restraints excluded: chain c residue 97 ARG Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 32 ILE Chi-restraints excluded: chain g residue 135 VAL Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain i residue 87 LEU Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain j residue 71 LYS Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain m residue 92 ARG Chi-restraints excluded: chain n residue 9 LYS Chi-restraints excluded: chain n residue 32 SER Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain s residue 16 MET Chi-restraints excluded: chain s residue 19 ILE Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 23 GLU Chi-restraints excluded: chain h residue 45 PHE Chi-restraints excluded: chain h residue 66 TYR Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 85 LEU Chi-restraints excluded: chain h residue 109 SER Chi-restraints excluded: chain h residue 110 GLN Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain f residue 81 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 296 optimal weight: 10.0000 chunk 793 optimal weight: 20.0000 chunk 174 optimal weight: 10.0000 chunk 517 optimal weight: 2.9990 chunk 217 optimal weight: 9.9990 chunk 882 optimal weight: 0.9980 chunk 732 optimal weight: 10.0000 chunk 408 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 291 optimal weight: 10.0000 chunk 463 optimal weight: 2.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 148 ASN O 37 ASN Q 108 GLN l 5 ASN l 90 HIS o 37 ASN c 113 GLN m 32 GLN ** h 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 27 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 147580 Z= 0.294 Angle : 0.805 19.899 221780 Z= 0.408 Chirality : 0.044 0.360 28489 Planarity : 0.007 0.150 11146 Dihedral : 23.836 179.833 76324 Min Nonbonded Distance : 1.677 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.12 % Favored : 95.80 % Rotamer: Outliers : 4.47 % Allowed : 15.33 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.11), residues: 4733 helix: 0.12 (0.12), residues: 1473 sheet: -0.75 (0.16), residues: 908 loop : -0.87 (0.12), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP k 46 HIS 0.009 0.002 HIS t 20 PHE 0.023 0.003 PHE R 74 TYR 0.023 0.003 TYR Q 32 ARG 0.009 0.001 ARG f 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9466 Ramachandran restraints generated. 4733 Oldfield, 0 Emsley, 4733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9466 Ramachandran restraints generated. 4733 Oldfield, 0 Emsley, 4733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 653 time to evaluate : 5.589 Fit side-chains revert: symmetry clash REVERT: 0 44 LYS cc_start: 0.7151 (mtmt) cc_final: 0.6512 (mmtm) REVERT: 1 23 LYS cc_start: 0.5162 (mtmt) cc_final: 0.4871 (mmtp) REVERT: 1 33 LYS cc_start: 0.6291 (ttmt) cc_final: 0.5824 (mmmt) REVERT: 3 15 LYS cc_start: 0.7330 (ttmm) cc_final: 0.6685 (ptpt) REVERT: 4 13 LYS cc_start: 0.6020 (mttt) cc_final: 0.5408 (mmtt) REVERT: 4 15 LYS cc_start: 0.6463 (mtpt) cc_final: 0.5807 (tttp) REVERT: 4 18 ARG cc_start: 0.6799 (ttt90) cc_final: 0.6060 (tpp80) REVERT: 4 20 LYS cc_start: 0.6553 (mmtt) cc_final: 0.6342 (mttm) REVERT: 4 24 MET cc_start: 0.8131 (mtp) cc_final: 0.7781 (mtp) REVERT: 4 28 GLU cc_start: 0.5619 (pt0) cc_final: 0.5325 (pm20) REVERT: 6 1 MET cc_start: 0.4367 (OUTLIER) cc_final: 0.3628 (mtp) REVERT: C 23 GLU cc_start: 0.6353 (OUTLIER) cc_final: 0.5925 (pm20) REVERT: C 28 LYS cc_start: 0.6364 (mttt) cc_final: 0.5934 (pttm) REVERT: C 77 ARG cc_start: 0.6600 (ttp80) cc_final: 0.5746 (mtt-85) REVERT: C 100 GLU cc_start: 0.7457 (tt0) cc_final: 0.7184 (tt0) REVERT: C 183 MET cc_start: 0.8110 (mtp) cc_final: 0.7811 (mtt) REVERT: C 198 GLU cc_start: 0.6936 (tt0) cc_final: 0.6365 (pm20) REVERT: C 199 GLN cc_start: 0.6492 (mt0) cc_final: 0.5962 (pm20) REVERT: C 245 SER cc_start: 0.7410 (t) cc_final: 0.7137 (p) REVERT: C 261 LYS cc_start: 0.6269 (tttm) cc_final: 0.5320 (mmtt) REVERT: C 262 LYS cc_start: 0.5078 (mmtp) cc_final: 0.4578 (mtpp) REVERT: C 267 ASP cc_start: 0.6881 (m-30) cc_final: 0.6637 (m-30) REVERT: C 273 ARG cc_start: 0.5802 (mmt90) cc_final: 0.5399 (mtp180) REVERT: D 71 LYS cc_start: 0.6178 (mttt) cc_final: 0.5674 (ttpp) REVERT: D 73 GLU cc_start: 0.6316 (mt-10) cc_final: 0.6081 (mt-10) REVERT: D 92 GLU cc_start: 0.7000 (tt0) cc_final: 0.6316 (pt0) REVERT: D 103 SER cc_start: 0.7183 (p) cc_final: 0.6885 (m) REVERT: D 178 LYS cc_start: 0.7221 (ttmt) cc_final: 0.6651 (tttt) REVERT: D 182 GLU cc_start: 0.5810 (mt-10) cc_final: 0.5507 (mm-30) REVERT: E 27 GLU cc_start: 0.5720 (tt0) cc_final: 0.5450 (mt-10) REVERT: E 103 LYS cc_start: 0.7028 (ttmm) cc_final: 0.6308 (ttmt) REVERT: E 127 GLU cc_start: 0.5909 (tp30) cc_final: 0.5431 (tt0) REVERT: E 161 GLU cc_start: 0.5339 (tt0) cc_final: 0.4840 (mp0) REVERT: E 181 ILE cc_start: 0.6560 (tt) cc_final: 0.6278 (pp) REVERT: E 196 LYS cc_start: 0.6507 (ttpt) cc_final: 0.6019 (ttpt) REVERT: F 30 LYS cc_start: 0.6007 (pttt) cc_final: 0.5537 (ptpp) REVERT: F 63 GLN cc_start: 0.6145 (mt0) cc_final: 0.5924 (mt0) REVERT: F 69 ARG cc_start: 0.5541 (mtt-85) cc_final: 0.4801 (mpp80) REVERT: F 95 ARG cc_start: 0.5164 (mmt90) cc_final: 0.4941 (mmt90) REVERT: F 152 MET cc_start: 0.6306 (OUTLIER) cc_final: 0.5888 (ptp) REVERT: F 165 GLU cc_start: 0.5459 (OUTLIER) cc_final: 0.5184 (mt-10) REVERT: G 14 ASP cc_start: 0.2098 (OUTLIER) cc_final: 0.1797 (p0) REVERT: G 131 LYS cc_start: 0.5413 (OUTLIER) cc_final: 0.4937 (tppp) REVERT: G 166 GLU cc_start: 0.5557 (tt0) cc_final: 0.5121 (tp30) REVERT: J 13 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.6220 (tp30) REVERT: J 62 LYS cc_start: 0.6928 (mmtp) cc_final: 0.6464 (mtmt) REVERT: J 92 GLU cc_start: 0.6734 (tt0) cc_final: 0.6447 (mt-10) REVERT: J 107 LYS cc_start: 0.6897 (tttm) cc_final: 0.6543 (ttpt) REVERT: J 130 GLU cc_start: 0.6573 (mt-10) cc_final: 0.6024 (mm-30) REVERT: J 139 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6417 (mm-30) REVERT: K 9 LYS cc_start: 0.7723 (mttt) cc_final: 0.6984 (ttmt) REVERT: K 34 ASN cc_start: 0.6987 (p0) cc_final: 0.6426 (t0) REVERT: K 45 GLN cc_start: 0.7338 (mt0) cc_final: 0.6907 (mm110) REVERT: K 48 PRO cc_start: 0.6191 (Cg_exo) cc_final: 0.5869 (Cg_endo) REVERT: K 70 ARG cc_start: 0.7554 (ttt180) cc_final: 0.6815 (ttt-90) REVERT: K 107 ARG cc_start: 0.6190 (mtp-110) cc_final: 0.5734 (mtm-85) REVERT: K 110 ASN cc_start: 0.5563 (m110) cc_final: 0.5347 (t0) REVERT: K 112 MET cc_start: 0.6905 (mmm) cc_final: 0.6655 (mmm) REVERT: K 113 LYS cc_start: 0.6312 (mttt) cc_final: 0.5578 (tppt) REVERT: L 14 LYS cc_start: 0.7484 (mtpt) cc_final: 0.7246 (mtpp) REVERT: L 90 GLU cc_start: 0.4938 (tt0) cc_final: 0.4468 (tm-30) REVERT: L 133 LYS cc_start: 0.6664 (tttm) cc_final: 0.6297 (ttpt) REVERT: L 137 GLU cc_start: 0.5377 (mt-10) cc_final: 0.4904 (mt-10) REVERT: M 5 LYS cc_start: 0.6650 (tttt) cc_final: 0.6015 (mmtm) REVERT: M 18 ARG cc_start: 0.7252 (mtt90) cc_final: 0.6223 (mtp180) REVERT: M 54 MET cc_start: 0.7832 (ptp) cc_final: 0.7587 (ptt) REVERT: M 130 LYS cc_start: 0.7157 (ptmt) cc_final: 0.6838 (ttpt) REVERT: N 34 GLU cc_start: 0.7146 (tt0) cc_final: 0.6584 (tp30) REVERT: N 72 ASN cc_start: 0.6800 (t0) cc_final: 0.6247 (t0) REVERT: N 75 ASN cc_start: 0.5580 (m110) cc_final: 0.4889 (m110) REVERT: O 8 ASN cc_start: 0.7467 (t0) cc_final: 0.6870 (t0) REVERT: O 12 LEU cc_start: 0.7241 (mp) cc_final: 0.6829 (mm) REVERT: O 28 ARG cc_start: 0.5795 (OUTLIER) cc_final: 0.5193 (ttp-110) REVERT: O 94 VAL cc_start: 0.6952 (OUTLIER) cc_final: 0.6670 (p) REVERT: P 6 GLU cc_start: 0.6503 (mt-10) cc_final: 0.5544 (tm-30) REVERT: P 11 GLU cc_start: 0.6605 (pt0) cc_final: 0.6040 (pm20) REVERT: P 27 ARG cc_start: 0.7118 (mtt-85) cc_final: 0.6782 (mtt180) REVERT: P 85 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.5885 (mt-10) REVERT: P 88 ARG cc_start: 0.7349 (ptm-80) cc_final: 0.6416 (ptt-90) REVERT: P 111 LYS cc_start: 0.6934 (mttt) cc_final: 0.6362 (tptt) REVERT: Q 19 LYS cc_start: 0.7248 (tmtp) cc_final: 0.6469 (mmtt) REVERT: Q 97 ASP cc_start: 0.7286 (t70) cc_final: 0.6862 (t0) REVERT: Q 116 GLN cc_start: 0.6720 (mm-40) cc_final: 0.6426 (mm-40) REVERT: R 1 MET cc_start: 0.6303 (ttm) cc_final: 0.6055 (ttm) REVERT: R 36 GLU cc_start: 0.6429 (mt-10) cc_final: 0.5392 (pm20) REVERT: R 47 LYS cc_start: 0.6510 (mmtp) cc_final: 0.6178 (mtpt) REVERT: R 50 ASN cc_start: 0.5946 (p0) cc_final: 0.5457 (p0) REVERT: R 63 GLU cc_start: 0.7024 (mm-30) cc_final: 0.6468 (mm-30) REVERT: R 98 GLU cc_start: 0.6211 (mt-10) cc_final: 0.5547 (mp0) REVERT: S 11 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.5555 (tmm160) REVERT: S 31 GLU cc_start: 0.6813 (tt0) cc_final: 0.6132 (tp30) REVERT: S 48 GLU cc_start: 0.7709 (tt0) cc_final: 0.7165 (tp30) REVERT: S 85 PHE cc_start: 0.7207 (m-80) cc_final: 0.6969 (m-80) REVERT: S 92 ARG cc_start: 0.5873 (mtt-85) cc_final: 0.5503 (mtt90) REVERT: T 10 ARG cc_start: 0.7148 (ptm160) cc_final: 0.6704 (ptp90) REVERT: T 21 MET cc_start: 0.5941 (mtt) cc_final: 0.5637 (mtm) REVERT: T 29 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6619 (tt0) REVERT: T 33 ARG cc_start: 0.6618 (mmt90) cc_final: 0.6303 (mpp-170) REVERT: T 50 LYS cc_start: 0.6181 (mttt) cc_final: 0.5659 (mmtm) REVERT: T 68 ARG cc_start: 0.5144 (ptm-80) cc_final: 0.4481 (tmt-80) REVERT: T 72 MET cc_start: 0.7313 (OUTLIER) cc_final: 0.6854 (mmt) REVERT: U 4 LYS cc_start: 0.7077 (OUTLIER) cc_final: 0.6513 (ptpp) REVERT: U 22 THR cc_start: 0.6959 (m) cc_final: 0.6598 (t) REVERT: U 30 LYS cc_start: 0.6254 (mttt) cc_final: 0.5847 (mtmt) REVERT: U 40 MET cc_start: 0.6823 (mmm) cc_final: 0.6540 (mmm) REVERT: U 84 LYS cc_start: 0.6190 (pttt) cc_final: 0.5772 (pttp) REVERT: W 19 LYS cc_start: 0.7568 (mtmp) cc_final: 0.7205 (mmtt) REVERT: W 57 GLU cc_start: 0.6523 (mt-10) cc_final: 0.5990 (mm-30) REVERT: X 60 GLU cc_start: 0.4551 (pt0) cc_final: 0.4045 (tp30) REVERT: Y 23 GLU cc_start: 0.6380 (mt-10) cc_final: 0.5620 (tm-30) REVERT: Y 29 ARG cc_start: 0.6159 (mtt180) cc_final: 0.5910 (mtt-85) REVERT: Y 45 GLU cc_start: 0.6613 (mt-10) cc_final: 0.6398 (tt0) REVERT: Y 48 LYS cc_start: 0.6546 (mttt) cc_final: 0.6106 (mptt) REVERT: Y 50 ILE cc_start: 0.7098 (OUTLIER) cc_final: 0.6833 (mp) REVERT: Y 53 MET cc_start: 0.7059 (mtt) cc_final: 0.6255 (mtm) REVERT: Z 10 ARG cc_start: 0.7352 (mmt90) cc_final: 0.6494 (mmm160) REVERT: Z 29 LYS cc_start: 0.7555 (mtmt) cc_final: 0.7270 (mtmm) REVERT: Z 46 MET cc_start: 0.8001 (mtp) cc_final: 0.7615 (mtp) REVERT: Z 55 SER cc_start: 0.7424 (t) cc_final: 0.7129 (m) REVERT: e 10 GLU cc_start: 0.3847 (mm-30) cc_final: 0.2969 (tm-30) REVERT: e 12 GLU cc_start: 0.4910 (tt0) cc_final: 0.4254 (mp0) REVERT: e 61 ARG cc_start: 0.5141 (ttm170) cc_final: 0.4914 (mpt-90) REVERT: e 62 LYS cc_start: 0.5084 (mmtm) cc_final: 0.4800 (tmmm) REVERT: e 76 MET cc_start: 0.4774 (mtm) cc_final: 0.4543 (mmm) REVERT: e 84 GLU cc_start: 0.5279 (tt0) cc_final: 0.4865 (mm-30) REVERT: e 98 PRO cc_start: 0.5278 (Cg_endo) cc_final: 0.4833 (Cg_exo) REVERT: e 101 GLU cc_start: 0.4706 (mm-30) cc_final: 0.4447 (mm-30) REVERT: l 3 THR cc_start: 0.7085 (m) cc_final: 0.6800 (p) REVERT: l 26 LYS cc_start: 0.5114 (mmtm) cc_final: 0.4829 (mmmt) REVERT: l 33 LYS cc_start: 0.4657 (mtmt) cc_final: 0.4418 (tptt) REVERT: l 50 VAL cc_start: 0.5589 (OUTLIER) cc_final: 0.5106 (p) REVERT: l 54 THR cc_start: 0.5718 (OUTLIER) cc_final: 0.5383 (p) REVERT: l 64 LYS cc_start: 0.5076 (pttp) cc_final: 0.4649 (mmtt) REVERT: l 133 LYS cc_start: 0.3298 (ttmm) cc_final: 0.2883 (ttpt) REVERT: o 44 ARG cc_start: 0.5920 (mmt90) cc_final: 0.5667 (mmt90) REVERT: q 35 LEU cc_start: 0.4916 (tp) cc_final: 0.4701 (pt) REVERT: q 40 VAL cc_start: 0.4863 (OUTLIER) cc_final: 0.4632 (m) REVERT: c 97 ARG cc_start: 0.4084 (OUTLIER) cc_final: 0.3825 (mtp-110) REVERT: c 134 LYS cc_start: 0.5074 (mttt) cc_final: 0.4832 (mmmm) REVERT: c 186 SER cc_start: 0.7369 (t) cc_final: 0.6952 (p) REVERT: c 189 ASP cc_start: 0.5406 (t0) cc_final: 0.4946 (p0) REVERT: g 7 VAL cc_start: 0.3150 (p) cc_final: 0.2863 (m) REVERT: g 31 MET cc_start: 0.6671 (ttp) cc_final: 0.6160 (ttp) REVERT: g 67 LYS cc_start: 0.5159 (ttpt) cc_final: 0.4920 (mmtm) REVERT: g 70 MET cc_start: 0.5256 (mtm) cc_final: 0.4991 (mtm) REVERT: g 90 GLU cc_start: 0.5079 (tt0) cc_final: 0.4846 (pt0) REVERT: g 107 TYR cc_start: 0.5002 (m-80) cc_final: 0.4750 (m-80) REVERT: g 111 ARG cc_start: 0.4227 (mtp85) cc_final: 0.3999 (mtt-85) REVERT: g 144 MET cc_start: 0.4838 (mtm) cc_final: 0.4467 (mmm) REVERT: i 123 ARG cc_start: 0.5842 (OUTLIER) cc_final: 0.5300 (tpp-160) REVERT: j 46 LYS cc_start: 0.6014 (ttpt) cc_final: 0.5059 (ttpp) REVERT: j 71 LYS cc_start: 0.5191 (OUTLIER) cc_final: 0.4923 (mttt) REVERT: m 27 ARG cc_start: 0.4949 (ptm160) cc_final: 0.4688 (mtm110) REVERT: m 70 ARG cc_start: 0.5588 (mtt-85) cc_final: 0.5353 (mmt90) REVERT: n 57 LYS cc_start: 0.6197 (ptpp) cc_final: 0.5321 (pttp) REVERT: s 35 SER cc_start: 0.7192 (OUTLIER) cc_final: 0.6914 (p) REVERT: s 70 LYS cc_start: 0.6263 (mmtt) cc_final: 0.5880 (mttt) REVERT: h 9 ASP cc_start: 0.4174 (OUTLIER) cc_final: 0.3082 (t70) REVERT: h 23 GLU cc_start: 0.4778 (OUTLIER) cc_final: 0.4505 (mm-30) REVERT: h 65 LYS cc_start: 0.4703 (OUTLIER) cc_final: 0.4060 (ptpt) REVERT: h 85 LEU cc_start: 0.3264 (OUTLIER) cc_final: 0.3033 (tp) REVERT: h 109 SER cc_start: 0.3049 (OUTLIER) cc_final: 0.2635 (t) REVERT: f 7 MET cc_start: 0.6135 (ttm) cc_final: 0.5892 (ttm) REVERT: f 74 GLU cc_start: 0.5278 (tp30) cc_final: 0.4632 (mp0) REVERT: f 91 VAL cc_start: 0.5545 (t) cc_final: 0.5270 (m) outliers start: 180 outliers final: 95 residues processed: 778 average time/residue: 2.4244 time to fit residues: 2612.2379 Evaluate side-chains 764 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 642 time to evaluate : 5.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 41 LYS Chi-restraints excluded: chain 3 residue 4 MET Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain E residue 201 LYS Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 71 LYS Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 131 LYS Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain J residue 11 THR Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 100 LYS Chi-restraints excluded: chain J residue 139 GLU Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain O residue 4 LYS Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 23 SER Chi-restraints excluded: chain O residue 28 ARG Chi-restraints excluded: chain O residue 72 SER Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain P residue 113 ILE Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain S residue 11 ARG Chi-restraints excluded: chain S residue 94 SER Chi-restraints excluded: chain T residue 72 MET Chi-restraints excluded: chain T residue 73 THR Chi-restraints excluded: chain U residue 4 LYS Chi-restraints excluded: chain U residue 85 VAL Chi-restraints excluded: chain U residue 102 ASP Chi-restraints excluded: chain W residue 78 GLU Chi-restraints excluded: chain X residue 4 LYS Chi-restraints excluded: chain Y residue 17 LYS Chi-restraints excluded: chain Y residue 20 SER Chi-restraints excluded: chain Y residue 44 ARG Chi-restraints excluded: chain Y residue 50 ILE Chi-restraints excluded: chain e residue 37 VAL Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 120 VAL Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 44 ILE Chi-restraints excluded: chain k residue 83 THR Chi-restraints excluded: chain k residue 118 VAL Chi-restraints excluded: chain k residue 123 CYS Chi-restraints excluded: chain l residue 13 VAL Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 38 VAL Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 128 SER Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain o residue 11 LEU Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 68 THR Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain t residue 45 ASP Chi-restraints excluded: chain t residue 64 THR Chi-restraints excluded: chain c residue 6 ASN Chi-restraints excluded: chain c residue 97 ARG Chi-restraints excluded: chain c residue 101 ASN Chi-restraints excluded: chain c residue 106 LYS Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 32 ILE Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 135 VAL Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain i residue 87 LEU Chi-restraints excluded: chain i residue 123 ARG Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain j residue 71 LYS Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain m residue 92 ARG Chi-restraints excluded: chain n residue 9 LYS Chi-restraints excluded: chain n residue 32 SER Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain s residue 19 ILE Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain h residue 9 ASP Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 23 GLU Chi-restraints excluded: chain h residue 45 PHE Chi-restraints excluded: chain h residue 65 LYS Chi-restraints excluded: chain h residue 66 TYR Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 85 LEU Chi-restraints excluded: chain h residue 109 SER Chi-restraints excluded: chain h residue 110 GLN Chi-restraints excluded: chain f residue 36 GLU Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain f residue 81 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 850 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 502 optimal weight: 1.9990 chunk 644 optimal weight: 20.0000 chunk 499 optimal weight: 0.8980 chunk 742 optimal weight: 0.9990 chunk 492 optimal weight: 6.9990 chunk 879 optimal weight: 0.1980 chunk 550 optimal weight: 0.0980 chunk 535 optimal weight: 1.9990 chunk 405 optimal weight: 5.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 86 ASN G 148 ASN O 37 ASN Q 108 GLN ** k 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 5 ASN l 90 HIS o 37 ASN m 32 GLN f 27 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 147580 Z= 0.113 Angle : 0.533 12.949 221780 Z= 0.283 Chirality : 0.033 0.330 28489 Planarity : 0.004 0.127 11146 Dihedral : 23.537 179.218 76324 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.47 % Favored : 97.46 % Rotamer: Outliers : 2.24 % Allowed : 17.89 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.12), residues: 4733 helix: 1.11 (0.13), residues: 1478 sheet: -0.56 (0.16), residues: 925 loop : -0.57 (0.12), residues: 2330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP c 200 HIS 0.006 0.001 HIS O 103 PHE 0.014 0.001 PHE g 62 TYR 0.017 0.001 TYR M 57 ARG 0.007 0.000 ARG l 123 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9466 Ramachandran restraints generated. 4733 Oldfield, 0 Emsley, 4733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9466 Ramachandran restraints generated. 4733 Oldfield, 0 Emsley, 4733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 691 time to evaluate : 5.605 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 55 ASN cc_start: 0.4281 (OUTLIER) cc_final: 0.3621 (p0) REVERT: 1 23 LYS cc_start: 0.5113 (mtmt) cc_final: 0.4846 (mmtp) REVERT: 1 33 LYS cc_start: 0.6289 (ttmt) cc_final: 0.5810 (mmmt) REVERT: 3 56 LYS cc_start: 0.6826 (ptpt) cc_final: 0.6154 (pptt) REVERT: 4 13 LYS cc_start: 0.6056 (mttt) cc_final: 0.5450 (mmtt) REVERT: 4 15 LYS cc_start: 0.6553 (mtpt) cc_final: 0.5900 (tttp) REVERT: 4 18 ARG cc_start: 0.6805 (ttt90) cc_final: 0.6601 (mtp180) REVERT: 4 24 MET cc_start: 0.7915 (mtp) cc_final: 0.7690 (mtp) REVERT: 4 28 GLU cc_start: 0.5569 (pt0) cc_final: 0.5276 (pm20) REVERT: 6 1 MET cc_start: 0.4645 (mmm) cc_final: 0.3877 (mtp) REVERT: 6 23 GLU cc_start: 0.4000 (pt0) cc_final: 0.3366 (pp20) REVERT: C 23 GLU cc_start: 0.6349 (OUTLIER) cc_final: 0.5880 (pm20) REVERT: C 28 LYS cc_start: 0.6311 (mttt) cc_final: 0.5909 (pttm) REVERT: C 77 ARG cc_start: 0.6532 (ttp80) cc_final: 0.5718 (mtm-85) REVERT: C 100 GLU cc_start: 0.7403 (tt0) cc_final: 0.7144 (tt0) REVERT: C 172 VAL cc_start: 0.7551 (t) cc_final: 0.7204 (m) REVERT: C 198 GLU cc_start: 0.6930 (tt0) cc_final: 0.6317 (pm20) REVERT: C 199 GLN cc_start: 0.6473 (mt0) cc_final: 0.5925 (pm20) REVERT: C 261 LYS cc_start: 0.6277 (tttm) cc_final: 0.5281 (mmtt) REVERT: C 267 ASP cc_start: 0.6598 (m-30) cc_final: 0.6333 (m-30) REVERT: C 273 ARG cc_start: 0.5890 (mmt90) cc_final: 0.5472 (mtp180) REVERT: D 71 LYS cc_start: 0.6288 (mttt) cc_final: 0.5750 (ttpp) REVERT: D 73 GLU cc_start: 0.6271 (mt-10) cc_final: 0.6028 (mt-10) REVERT: D 92 GLU cc_start: 0.7059 (tt0) cc_final: 0.6378 (pt0) REVERT: D 178 LYS cc_start: 0.7221 (ttmt) cc_final: 0.6738 (tttt) REVERT: D 182 GLU cc_start: 0.5865 (mt-10) cc_final: 0.5559 (mm-30) REVERT: E 27 GLU cc_start: 0.5752 (tt0) cc_final: 0.5518 (mt-10) REVERT: E 103 LYS cc_start: 0.6989 (ttmm) cc_final: 0.6177 (tttt) REVERT: E 127 GLU cc_start: 0.5876 (tp30) cc_final: 0.5458 (tt0) REVERT: E 161 GLU cc_start: 0.5327 (tt0) cc_final: 0.4765 (mp0) REVERT: E 196 LYS cc_start: 0.6471 (ttpt) cc_final: 0.5913 (ttpt) REVERT: F 17 MET cc_start: 0.4574 (tpt) cc_final: 0.4255 (tpt) REVERT: F 32 GLU cc_start: 0.5665 (tp30) cc_final: 0.5420 (tp30) REVERT: F 56 GLU cc_start: 0.4645 (mt-10) cc_final: 0.4079 (tt0) REVERT: F 69 ARG cc_start: 0.5575 (mtt-85) cc_final: 0.4837 (mpp80) REVERT: F 94 GLU cc_start: 0.4898 (tp30) cc_final: 0.4613 (tt0) REVERT: F 95 ARG cc_start: 0.5125 (mmt90) cc_final: 0.4906 (mmt90) REVERT: F 119 LYS cc_start: 0.5414 (mttt) cc_final: 0.5121 (mppt) REVERT: F 165 GLU cc_start: 0.5066 (mt-10) cc_final: 0.4817 (mt-10) REVERT: G 61 GLU cc_start: 0.4634 (mp0) cc_final: 0.4401 (tt0) REVERT: G 131 LYS cc_start: 0.5590 (OUTLIER) cc_final: 0.5042 (tppt) REVERT: G 166 GLU cc_start: 0.5513 (tt0) cc_final: 0.5103 (tp30) REVERT: J 13 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.6162 (tp30) REVERT: J 62 LYS cc_start: 0.6936 (mmtp) cc_final: 0.6486 (mtmt) REVERT: J 92 GLU cc_start: 0.6713 (tt0) cc_final: 0.6348 (mt-10) REVERT: J 99 GLU cc_start: 0.6978 (mp0) cc_final: 0.6753 (mt-10) REVERT: J 103 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7432 (mt-10) REVERT: J 107 LYS cc_start: 0.6826 (tttm) cc_final: 0.6472 (ttpt) REVERT: J 130 GLU cc_start: 0.6454 (mt-10) cc_final: 0.5924 (mm-30) REVERT: J 139 GLU cc_start: 0.7257 (mt-10) cc_final: 0.6356 (mm-30) REVERT: K 9 LYS cc_start: 0.7755 (mttt) cc_final: 0.7053 (ttmt) REVERT: K 34 ASN cc_start: 0.7019 (p0) cc_final: 0.6431 (t0) REVERT: K 45 GLN cc_start: 0.7290 (mt0) cc_final: 0.6873 (mm110) REVERT: K 48 PRO cc_start: 0.6250 (Cg_exo) cc_final: 0.5879 (Cg_endo) REVERT: K 51 VAL cc_start: 0.6609 (t) cc_final: 0.6335 (p) REVERT: K 70 ARG cc_start: 0.7544 (ttt180) cc_final: 0.6808 (ttt-90) REVERT: K 107 ARG cc_start: 0.6198 (mtp-110) cc_final: 0.5658 (mtm-85) REVERT: K 110 ASN cc_start: 0.5673 (m110) cc_final: 0.5423 (t0) REVERT: K 112 MET cc_start: 0.6927 (mmm) cc_final: 0.6706 (mmm) REVERT: K 113 LYS cc_start: 0.6375 (mttt) cc_final: 0.5612 (tppt) REVERT: L 14 LYS cc_start: 0.7366 (mtpt) cc_final: 0.7127 (mtpp) REVERT: L 90 GLU cc_start: 0.4831 (tt0) cc_final: 0.4367 (tm-30) REVERT: L 98 GLU cc_start: 0.5211 (tp30) cc_final: 0.4939 (tt0) REVERT: L 133 LYS cc_start: 0.6599 (tttm) cc_final: 0.6255 (ttpt) REVERT: M 5 LYS cc_start: 0.6691 (tttt) cc_final: 0.6455 (mtmp) REVERT: M 18 ARG cc_start: 0.7159 (mtt90) cc_final: 0.6149 (mtp180) REVERT: M 130 LYS cc_start: 0.7024 (ptmt) cc_final: 0.6654 (ttpt) REVERT: N 34 GLU cc_start: 0.7181 (tt0) cc_final: 0.6631 (tp30) REVERT: N 46 LYS cc_start: 0.7494 (mttt) cc_final: 0.7292 (mttm) REVERT: N 72 ASN cc_start: 0.6827 (t0) cc_final: 0.6235 (t0) REVERT: N 75 ASN cc_start: 0.5661 (m110) cc_final: 0.4907 (m110) REVERT: O 8 ASN cc_start: 0.7344 (t0) cc_final: 0.6970 (t0) REVERT: O 12 LEU cc_start: 0.7154 (mp) cc_final: 0.6902 (mm) REVERT: O 28 ARG cc_start: 0.5770 (tmm-80) cc_final: 0.5150 (ttp-110) REVERT: O 94 VAL cc_start: 0.6912 (OUTLIER) cc_final: 0.6648 (p) REVERT: P 6 GLU cc_start: 0.6275 (mt-10) cc_final: 0.5222 (tm-30) REVERT: P 11 GLU cc_start: 0.6656 (pt0) cc_final: 0.6101 (pm20) REVERT: P 27 ARG cc_start: 0.7030 (mtt-85) cc_final: 0.6750 (mtt180) REVERT: P 83 LYS cc_start: 0.7356 (pttt) cc_final: 0.7120 (pttm) REVERT: P 85 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.5850 (mt-10) REVERT: P 88 ARG cc_start: 0.7347 (ptm-80) cc_final: 0.6477 (ptt-90) REVERT: P 109 ARG cc_start: 0.6203 (mtm180) cc_final: 0.5638 (mtm180) REVERT: P 111 LYS cc_start: 0.6816 (mttt) cc_final: 0.6237 (tptt) REVERT: Q 19 LYS cc_start: 0.7218 (tmtp) cc_final: 0.6426 (mmtt) REVERT: Q 97 ASP cc_start: 0.7292 (t70) cc_final: 0.6855 (t0) REVERT: Q 103 LEU cc_start: 0.6431 (tp) cc_final: 0.6001 (tp) REVERT: Q 116 GLN cc_start: 0.6861 (mm-40) cc_final: 0.6561 (mm-40) REVERT: R 1 MET cc_start: 0.6121 (ttm) cc_final: 0.5891 (ttm) REVERT: R 6 LYS cc_start: 0.6969 (tttm) cc_final: 0.6534 (ttpp) REVERT: R 47 LYS cc_start: 0.6561 (mmtp) cc_final: 0.6228 (mtpt) REVERT: R 54 GLU cc_start: 0.5816 (tt0) cc_final: 0.5527 (tp30) REVERT: R 63 GLU cc_start: 0.6942 (mm-30) cc_final: 0.6431 (mm-30) REVERT: R 98 GLU cc_start: 0.6216 (mt-10) cc_final: 0.5632 (mp0) REVERT: S 1 MET cc_start: 0.4804 (tpp) cc_final: 0.4567 (tpp) REVERT: S 31 GLU cc_start: 0.6708 (tt0) cc_final: 0.6022 (tp30) REVERT: S 48 GLU cc_start: 0.7662 (tt0) cc_final: 0.6743 (tm-30) REVERT: S 92 ARG cc_start: 0.5839 (mtt-85) cc_final: 0.5337 (mtt90) REVERT: T 10 ARG cc_start: 0.7229 (ptm160) cc_final: 0.6685 (ptp90) REVERT: T 21 MET cc_start: 0.5996 (mtt) cc_final: 0.5692 (mtm) REVERT: T 29 GLU cc_start: 0.7048 (mt-10) cc_final: 0.6569 (tt0) REVERT: T 33 ARG cc_start: 0.6725 (mmt90) cc_final: 0.6441 (mpp-170) REVERT: T 50 LYS cc_start: 0.6164 (mttt) cc_final: 0.5636 (mmtm) REVERT: T 68 ARG cc_start: 0.5182 (ptm-80) cc_final: 0.4495 (tmt-80) REVERT: U 4 LYS cc_start: 0.7154 (OUTLIER) cc_final: 0.6647 (ptpp) REVERT: U 22 THR cc_start: 0.7019 (m) cc_final: 0.6650 (t) REVERT: U 30 LYS cc_start: 0.6119 (mttt) cc_final: 0.5726 (mtmt) REVERT: U 58 ASN cc_start: 0.6424 (m110) cc_final: 0.5818 (m110) REVERT: U 84 LYS cc_start: 0.6171 (pttt) cc_final: 0.5743 (pttp) REVERT: W 19 LYS cc_start: 0.7583 (mtmp) cc_final: 0.7218 (mmtt) REVERT: W 57 GLU cc_start: 0.6543 (mt-10) cc_final: 0.6006 (mm-30) REVERT: W 78 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7528 (pm20) REVERT: X 48 TYR cc_start: 0.6713 (m-80) cc_final: 0.6188 (m-80) REVERT: X 60 GLU cc_start: 0.4496 (pt0) cc_final: 0.3943 (tp30) REVERT: Y 23 GLU cc_start: 0.6385 (mt-10) cc_final: 0.5521 (tm-30) REVERT: Y 29 ARG cc_start: 0.6132 (mtt180) cc_final: 0.5894 (mtt-85) REVERT: Y 44 ARG cc_start: 0.6317 (ttp80) cc_final: 0.5725 (ttm170) REVERT: Y 45 GLU cc_start: 0.6624 (mt-10) cc_final: 0.6390 (tt0) REVERT: Y 48 LYS cc_start: 0.6576 (mttt) cc_final: 0.6057 (mppt) REVERT: Y 53 MET cc_start: 0.7088 (mtt) cc_final: 0.6389 (mtm) REVERT: Z 10 ARG cc_start: 0.7182 (mmt90) cc_final: 0.6400 (mmm160) REVERT: Z 17 GLU cc_start: 0.6815 (tp30) cc_final: 0.6119 (tm-30) REVERT: Z 38 GLU cc_start: 0.6673 (mm-30) cc_final: 0.5975 (mm-30) REVERT: Z 55 SER cc_start: 0.7558 (t) cc_final: 0.7240 (p) REVERT: Z 57 LYS cc_start: 0.6374 (ttmp) cc_final: 0.5791 (ttpp) REVERT: e 10 GLU cc_start: 0.4031 (mm-30) cc_final: 0.3202 (tm-30) REVERT: e 12 GLU cc_start: 0.5022 (tt0) cc_final: 0.4568 (mt-10) REVERT: e 84 GLU cc_start: 0.5127 (tt0) cc_final: 0.4652 (mm-30) REVERT: e 101 GLU cc_start: 0.4485 (mm-30) cc_final: 0.4208 (mm-30) REVERT: e 138 ARG cc_start: 0.6273 (mmt90) cc_final: 0.4958 (mtt90) REVERT: k 66 GLN cc_start: 0.4057 (OUTLIER) cc_final: 0.3852 (tt0) REVERT: k 67 MET cc_start: 0.4976 (mmp) cc_final: 0.4614 (tpp) REVERT: l 3 THR cc_start: 0.7114 (m) cc_final: 0.6811 (p) REVERT: l 26 LYS cc_start: 0.5242 (mmtm) cc_final: 0.4944 (mmmt) REVERT: l 33 LYS cc_start: 0.4632 (mtmt) cc_final: 0.4374 (tptt) REVERT: l 64 LYS cc_start: 0.5049 (pttp) cc_final: 0.4671 (mmtm) REVERT: l 133 LYS cc_start: 0.3084 (ttmm) cc_final: 0.2583 (tttm) REVERT: o 7 ARG cc_start: 0.3716 (OUTLIER) cc_final: 0.3451 (ttm110) REVERT: o 44 ARG cc_start: 0.5738 (mmt90) cc_final: 0.5390 (mmt90) REVERT: o 47 LYS cc_start: 0.6260 (tppp) cc_final: 0.6041 (mttt) REVERT: o 59 MET cc_start: 0.6977 (mtt) cc_final: 0.6574 (mtp) REVERT: o 63 ARG cc_start: 0.6916 (ttp-170) cc_final: 0.6592 (ttm170) REVERT: q 40 VAL cc_start: 0.4903 (t) cc_final: 0.4697 (m) REVERT: t 17 ARG cc_start: 0.3619 (mtp-110) cc_final: 0.3276 (mtt-85) REVERT: c 186 SER cc_start: 0.7407 (t) cc_final: 0.6936 (p) REVERT: c 189 ASP cc_start: 0.5455 (t0) cc_final: 0.4979 (p0) REVERT: g 25 ARG cc_start: 0.5049 (mtt-85) cc_final: 0.4678 (mtt90) REVERT: g 31 MET cc_start: 0.6755 (ttp) cc_final: 0.6200 (ttp) REVERT: g 67 LYS cc_start: 0.5051 (ttpt) cc_final: 0.4782 (mttt) REVERT: g 120 LEU cc_start: 0.5644 (tp) cc_final: 0.5440 (tt) REVERT: i 87 LEU cc_start: 0.5360 (OUTLIER) cc_final: 0.5159 (mt) REVERT: i 123 ARG cc_start: 0.5780 (tmt170) cc_final: 0.5388 (tpp-160) REVERT: j 72 ARG cc_start: 0.5622 (mmt-90) cc_final: 0.5366 (tpp-160) REVERT: m 27 ARG cc_start: 0.5076 (ptm160) cc_final: 0.4782 (mtm110) REVERT: n 9 LYS cc_start: 0.6710 (OUTLIER) cc_final: 0.6482 (ttpt) REVERT: n 11 GLN cc_start: 0.4961 (mt0) cc_final: 0.4743 (mt0) REVERT: n 57 LYS cc_start: 0.6183 (ptpp) cc_final: 0.5321 (pttp) REVERT: s 16 MET cc_start: 0.5013 (OUTLIER) cc_final: 0.4770 (ttm) REVERT: s 70 LYS cc_start: 0.6315 (mmtt) cc_final: 0.5934 (mttt) REVERT: h 42 ARG cc_start: 0.3430 (mmt-90) cc_final: 0.3100 (mmp80) REVERT: h 85 LEU cc_start: 0.3182 (OUTLIER) cc_final: 0.2886 (tp) REVERT: h 87 VAL cc_start: 0.4977 (t) cc_final: 0.4479 (m) REVERT: h 109 SER cc_start: 0.2642 (p) cc_final: 0.2304 (t) REVERT: f 74 GLU cc_start: 0.5102 (tp30) cc_final: 0.4497 (mp0) REVERT: f 91 VAL cc_start: 0.5509 (t) cc_final: 0.5225 (m) outliers start: 90 outliers final: 34 residues processed: 754 average time/residue: 2.5104 time to fit residues: 2587.8543 Evaluate side-chains 678 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 630 time to evaluate : 5.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 55 ASN Chi-restraints excluded: chain 3 residue 4 MET Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 131 LYS Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain O residue 4 LYS Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain U residue 4 LYS Chi-restraints excluded: chain W residue 78 GLU Chi-restraints excluded: chain X residue 4 LYS Chi-restraints excluded: chain Y residue 20 SER Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 42 LYS Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain k residue 34 VAL Chi-restraints excluded: chain k residue 66 GLN Chi-restraints excluded: chain k residue 123 CYS Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 38 VAL Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain t residue 86 LEU Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain i residue 87 LEU Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 92 ARG Chi-restraints excluded: chain n residue 9 LYS Chi-restraints excluded: chain s residue 16 MET Chi-restraints excluded: chain s residue 19 ILE Chi-restraints excluded: chain h residue 66 TYR Chi-restraints excluded: chain h residue 85 LEU Chi-restraints excluded: chain f residue 23 ILE Chi-restraints excluded: chain f residue 63 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 543 optimal weight: 8.9990 chunk 351 optimal weight: 0.7980 chunk 524 optimal weight: 6.9990 chunk 264 optimal weight: 10.0000 chunk 172 optimal weight: 20.0000 chunk 170 optimal weight: 10.0000 chunk 558 optimal weight: 0.3980 chunk 598 optimal weight: 20.0000 chunk 434 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 690 optimal weight: 30.0000 overall best weight: 4.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 GLN G 148 ASN O 37 ASN S 28 GLN ** k 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 5 ASN l 90 HIS o 37 ASN m 32 GLN f 27 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 147580 Z= 0.262 Angle : 0.747 17.507 221780 Z= 0.379 Chirality : 0.041 0.343 28489 Planarity : 0.006 0.147 11146 Dihedral : 23.731 179.407 76322 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.91 % Favored : 96.03 % Rotamer: Outliers : 2.73 % Allowed : 18.04 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.12), residues: 4733 helix: 0.58 (0.13), residues: 1485 sheet: -0.60 (0.16), residues: 935 loop : -0.68 (0.12), residues: 2313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP k 46 HIS 0.008 0.002 HIS t 20 PHE 0.021 0.003 PHE Q 57 TYR 0.022 0.002 TYR Q 32 ARG 0.009 0.001 ARG F 150 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9466 Ramachandran restraints generated. 4733 Oldfield, 0 Emsley, 4733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9466 Ramachandran restraints generated. 4733 Oldfield, 0 Emsley, 4733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 628 time to evaluate : 5.530 Fit side-chains REVERT: 0 44 LYS cc_start: 0.7191 (mtmt) cc_final: 0.6546 (mtpp) REVERT: 1 23 LYS cc_start: 0.5091 (mtmt) cc_final: 0.4803 (mmtp) REVERT: 1 33 LYS cc_start: 0.6305 (ttmt) cc_final: 0.5824 (mmmt) REVERT: 4 13 LYS cc_start: 0.6068 (mttt) cc_final: 0.5426 (mmtt) REVERT: 4 15 LYS cc_start: 0.6511 (mtpt) cc_final: 0.5852 (tttp) REVERT: 4 18 ARG cc_start: 0.6789 (ttt90) cc_final: 0.6029 (tpp80) REVERT: 4 20 LYS cc_start: 0.6541 (mmtt) cc_final: 0.6326 (mttm) REVERT: 4 24 MET cc_start: 0.8107 (mtp) cc_final: 0.7829 (mtp) REVERT: 4 28 GLU cc_start: 0.5620 (pt0) cc_final: 0.5323 (pm20) REVERT: 6 1 MET cc_start: 0.4519 (OUTLIER) cc_final: 0.3854 (mtp) REVERT: C 23 GLU cc_start: 0.6407 (OUTLIER) cc_final: 0.5936 (pm20) REVERT: C 28 LYS cc_start: 0.6366 (mttt) cc_final: 0.5944 (pttm) REVERT: C 77 ARG cc_start: 0.6496 (ttp80) cc_final: 0.5664 (mtt-85) REVERT: C 100 GLU cc_start: 0.7464 (tt0) cc_final: 0.7161 (tt0) REVERT: C 198 GLU cc_start: 0.6958 (tt0) cc_final: 0.6374 (pm20) REVERT: C 199 GLN cc_start: 0.6487 (mt0) cc_final: 0.5968 (pm20) REVERT: C 261 LYS cc_start: 0.6244 (tttm) cc_final: 0.5281 (mmtt) REVERT: C 267 ASP cc_start: 0.6749 (m-30) cc_final: 0.6443 (m-30) REVERT: C 273 ARG cc_start: 0.5824 (mmt90) cc_final: 0.5421 (mtp180) REVERT: D 71 LYS cc_start: 0.6154 (mttt) cc_final: 0.5677 (ttpp) REVERT: D 73 GLU cc_start: 0.6329 (mt-10) cc_final: 0.6079 (mt-10) REVERT: D 92 GLU cc_start: 0.7057 (tt0) cc_final: 0.6354 (pt0) REVERT: D 178 LYS cc_start: 0.7214 (ttmt) cc_final: 0.6748 (tttm) REVERT: D 182 GLU cc_start: 0.5865 (mt-10) cc_final: 0.5537 (mm-30) REVERT: E 27 GLU cc_start: 0.5601 (tt0) cc_final: 0.5167 (tm-30) REVERT: E 103 LYS cc_start: 0.7027 (ttmm) cc_final: 0.6308 (ttmt) REVERT: E 127 GLU cc_start: 0.5868 (tp30) cc_final: 0.5566 (mt-10) REVERT: E 144 LYS cc_start: 0.6120 (tppt) cc_final: 0.5666 (tttt) REVERT: E 161 GLU cc_start: 0.5368 (tt0) cc_final: 0.4848 (mp0) REVERT: E 196 LYS cc_start: 0.6523 (ttpt) cc_final: 0.6023 (ttpt) REVERT: F 50 ILE cc_start: 0.5286 (OUTLIER) cc_final: 0.4914 (mp) REVERT: F 69 ARG cc_start: 0.5557 (mtt-85) cc_final: 0.4804 (mpp80) REVERT: F 95 ARG cc_start: 0.5181 (mmt90) cc_final: 0.4943 (mmt90) REVERT: F 152 MET cc_start: 0.6541 (ptp) cc_final: 0.6300 (ptp) REVERT: F 165 GLU cc_start: 0.5263 (mt-10) cc_final: 0.5027 (mt-10) REVERT: G 14 ASP cc_start: 0.2018 (OUTLIER) cc_final: 0.1722 (p0) REVERT: G 131 LYS cc_start: 0.5529 (OUTLIER) cc_final: 0.5064 (tppp) REVERT: G 166 GLU cc_start: 0.5579 (tt0) cc_final: 0.5170 (tp30) REVERT: J 13 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.6208 (tp30) REVERT: J 15 LYS cc_start: 0.6873 (mttp) cc_final: 0.6603 (mtmt) REVERT: J 62 LYS cc_start: 0.6951 (mmtp) cc_final: 0.6541 (mtmt) REVERT: J 92 GLU cc_start: 0.6776 (tt0) cc_final: 0.6441 (mt-10) REVERT: J 107 LYS cc_start: 0.6890 (tttm) cc_final: 0.6598 (ttmt) REVERT: J 130 GLU cc_start: 0.6643 (mt-10) cc_final: 0.6097 (mm-30) REVERT: J 139 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6387 (mm-30) REVERT: K 9 LYS cc_start: 0.7711 (mttt) cc_final: 0.6976 (ttmt) REVERT: K 34 ASN cc_start: 0.6978 (p0) cc_final: 0.6429 (t0) REVERT: K 45 GLN cc_start: 0.7337 (mt0) cc_final: 0.6924 (mm110) REVERT: K 48 PRO cc_start: 0.6222 (Cg_exo) cc_final: 0.5837 (Cg_endo) REVERT: K 70 ARG cc_start: 0.7581 (ttt180) cc_final: 0.6850 (ttt-90) REVERT: K 107 ARG cc_start: 0.6179 (mtp-110) cc_final: 0.5750 (mtm-85) REVERT: K 112 MET cc_start: 0.6894 (mmm) cc_final: 0.6639 (mmm) REVERT: K 113 LYS cc_start: 0.6363 (mttt) cc_final: 0.5597 (tppt) REVERT: L 14 LYS cc_start: 0.7448 (mtpt) cc_final: 0.7220 (mtpp) REVERT: L 90 GLU cc_start: 0.4817 (tt0) cc_final: 0.4398 (tm-30) REVERT: L 133 LYS cc_start: 0.6660 (tttm) cc_final: 0.6347 (ttpp) REVERT: L 137 GLU cc_start: 0.5448 (mt-10) cc_final: 0.4999 (mt-10) REVERT: M 5 LYS cc_start: 0.6698 (tttt) cc_final: 0.6083 (mmtm) REVERT: M 18 ARG cc_start: 0.7224 (mtt90) cc_final: 0.6197 (mtp180) REVERT: M 26 GLU cc_start: 0.6819 (mm-30) cc_final: 0.6539 (mm-30) REVERT: M 54 MET cc_start: 0.7832 (ptp) cc_final: 0.7537 (ptt) REVERT: N 34 GLU cc_start: 0.7183 (tt0) cc_final: 0.6641 (tp30) REVERT: N 72 ASN cc_start: 0.6814 (t0) cc_final: 0.6242 (t0) REVERT: N 75 ASN cc_start: 0.5274 (m110) cc_final: 0.4463 (m110) REVERT: O 8 ASN cc_start: 0.7421 (t0) cc_final: 0.6700 (t0) REVERT: O 12 LEU cc_start: 0.7199 (mp) cc_final: 0.6955 (mm) REVERT: O 28 ARG cc_start: 0.5812 (OUTLIER) cc_final: 0.5195 (ttp-110) REVERT: O 94 VAL cc_start: 0.6927 (OUTLIER) cc_final: 0.6638 (p) REVERT: P 6 GLU cc_start: 0.6511 (mt-10) cc_final: 0.5551 (tm-30) REVERT: P 11 GLU cc_start: 0.6566 (pt0) cc_final: 0.6088 (pm20) REVERT: P 27 ARG cc_start: 0.7123 (mtt-85) cc_final: 0.6837 (mtt180) REVERT: P 85 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.5861 (mt-10) REVERT: P 88 ARG cc_start: 0.7336 (ptm-80) cc_final: 0.6427 (ptt-90) REVERT: P 111 LYS cc_start: 0.6867 (mttt) cc_final: 0.6326 (tptt) REVERT: Q 19 LYS cc_start: 0.7231 (tmtp) cc_final: 0.6489 (mmtt) REVERT: Q 97 ASP cc_start: 0.7311 (t70) cc_final: 0.6872 (t0) REVERT: Q 116 GLN cc_start: 0.6723 (mm-40) cc_final: 0.6436 (mm-40) REVERT: R 1 MET cc_start: 0.6307 (ttm) cc_final: 0.6047 (ttm) REVERT: R 36 GLU cc_start: 0.6339 (mt-10) cc_final: 0.5333 (pm20) REVERT: R 47 LYS cc_start: 0.6541 (mmtp) cc_final: 0.6218 (mtpt) REVERT: R 50 ASN cc_start: 0.5870 (p0) cc_final: 0.5405 (p0) REVERT: R 54 GLU cc_start: 0.5776 (tt0) cc_final: 0.5445 (tp30) REVERT: R 63 GLU cc_start: 0.6958 (mm-30) cc_final: 0.6372 (mm-30) REVERT: R 98 GLU cc_start: 0.6253 (mt-10) cc_final: 0.5581 (mp0) REVERT: S 31 GLU cc_start: 0.6800 (tt0) cc_final: 0.6111 (tp30) REVERT: S 48 GLU cc_start: 0.7663 (tt0) cc_final: 0.6755 (tm-30) REVERT: S 92 ARG cc_start: 0.5816 (mtt-85) cc_final: 0.5446 (mtt90) REVERT: T 10 ARG cc_start: 0.7153 (ptm160) cc_final: 0.6648 (ptp90) REVERT: T 21 MET cc_start: 0.5982 (mtt) cc_final: 0.5671 (mtm) REVERT: T 29 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6606 (tt0) REVERT: T 33 ARG cc_start: 0.6639 (mmt90) cc_final: 0.6314 (mpp-170) REVERT: T 50 LYS cc_start: 0.6062 (mttt) cc_final: 0.5563 (mmtm) REVERT: T 68 ARG cc_start: 0.5131 (ptm-80) cc_final: 0.4470 (tmt-80) REVERT: U 4 LYS cc_start: 0.7052 (OUTLIER) cc_final: 0.6514 (ptpp) REVERT: U 22 THR cc_start: 0.6999 (m) cc_final: 0.6637 (t) REVERT: U 30 LYS cc_start: 0.6233 (mttt) cc_final: 0.5677 (mptt) REVERT: U 84 LYS cc_start: 0.6212 (pttt) cc_final: 0.5792 (pttp) REVERT: W 19 LYS cc_start: 0.7563 (mtmp) cc_final: 0.7199 (mmtt) REVERT: W 57 GLU cc_start: 0.6509 (mt-10) cc_final: 0.5988 (mm-30) REVERT: X 35 LYS cc_start: 0.5728 (tptt) cc_final: 0.5469 (tptt) REVERT: X 48 TYR cc_start: 0.6706 (m-80) cc_final: 0.6395 (m-80) REVERT: X 60 GLU cc_start: 0.4480 (pt0) cc_final: 0.3910 (tp30) REVERT: Y 23 GLU cc_start: 0.6386 (mt-10) cc_final: 0.5574 (tm-30) REVERT: Y 29 ARG cc_start: 0.6163 (mtt180) cc_final: 0.5928 (mtt-85) REVERT: Y 45 GLU cc_start: 0.6554 (mt-10) cc_final: 0.6352 (tt0) REVERT: Y 48 LYS cc_start: 0.6546 (mttt) cc_final: 0.6118 (mptt) REVERT: Y 53 MET cc_start: 0.7095 (mtt) cc_final: 0.6306 (mtm) REVERT: Z 10 ARG cc_start: 0.7325 (mmt90) cc_final: 0.6507 (mmm160) REVERT: Z 38 GLU cc_start: 0.6710 (mm-30) cc_final: 0.6002 (mm-30) REVERT: Z 55 SER cc_start: 0.7360 (t) cc_final: 0.7034 (p) REVERT: Z 57 LYS cc_start: 0.6416 (ttmp) cc_final: 0.5856 (ttpp) REVERT: e 10 GLU cc_start: 0.3927 (mm-30) cc_final: 0.2980 (tm-30) REVERT: e 12 GLU cc_start: 0.4878 (tt0) cc_final: 0.4339 (mp0) REVERT: e 61 ARG cc_start: 0.5108 (ttm170) cc_final: 0.4906 (mpt-90) REVERT: e 62 LYS cc_start: 0.5120 (mmtm) cc_final: 0.4828 (tmmm) REVERT: e 76 MET cc_start: 0.4479 (mmm) cc_final: 0.4142 (mmm) REVERT: e 84 GLU cc_start: 0.5312 (tt0) cc_final: 0.4826 (mm-30) REVERT: e 98 PRO cc_start: 0.5381 (Cg_endo) cc_final: 0.4997 (Cg_exo) REVERT: e 101 GLU cc_start: 0.4608 (mm-30) cc_final: 0.4365 (mm-30) REVERT: k 67 MET cc_start: 0.4885 (mmp) cc_final: 0.4368 (tpp) REVERT: l 3 THR cc_start: 0.6994 (m) cc_final: 0.6722 (p) REVERT: l 26 LYS cc_start: 0.5072 (mmtm) cc_final: 0.4761 (mmmt) REVERT: l 33 LYS cc_start: 0.4698 (mtmt) cc_final: 0.4464 (tptt) REVERT: l 64 LYS cc_start: 0.5026 (pttp) cc_final: 0.4610 (mmtm) REVERT: l 133 LYS cc_start: 0.3274 (ttmm) cc_final: 0.2731 (tttm) REVERT: o 44 ARG cc_start: 0.5953 (mmt90) cc_final: 0.5619 (mpt180) REVERT: o 63 ARG cc_start: 0.6988 (ttp-170) cc_final: 0.6711 (ttp80) REVERT: q 40 VAL cc_start: 0.4937 (OUTLIER) cc_final: 0.4711 (m) REVERT: c 97 ARG cc_start: 0.4057 (OUTLIER) cc_final: 0.3799 (mtp-110) REVERT: c 186 SER cc_start: 0.7342 (t) cc_final: 0.6860 (p) REVERT: c 189 ASP cc_start: 0.5509 (t0) cc_final: 0.5026 (p0) REVERT: g 7 VAL cc_start: 0.3061 (p) cc_final: 0.2801 (m) REVERT: g 31 MET cc_start: 0.6686 (ttp) cc_final: 0.6158 (ttp) REVERT: g 70 MET cc_start: 0.5328 (mtm) cc_final: 0.4787 (mmm) REVERT: g 107 TYR cc_start: 0.4955 (m-80) cc_final: 0.4666 (m-80) REVERT: m 27 ARG cc_start: 0.4996 (ptm160) cc_final: 0.4747 (mtm110) REVERT: m 70 ARG cc_start: 0.5665 (mtt-85) cc_final: 0.5424 (mmt90) REVERT: n 11 GLN cc_start: 0.4964 (mt0) cc_final: 0.4731 (mt0) REVERT: n 57 LYS cc_start: 0.6194 (ptpp) cc_final: 0.5311 (pttp) REVERT: s 16 MET cc_start: 0.5108 (OUTLIER) cc_final: 0.4891 (ttm) REVERT: h 23 GLU cc_start: 0.4770 (OUTLIER) cc_final: 0.4533 (mm-30) REVERT: h 42 ARG cc_start: 0.3415 (mmt-90) cc_final: 0.3017 (mmm-85) REVERT: h 85 LEU cc_start: 0.3247 (OUTLIER) cc_final: 0.2992 (tp) REVERT: h 109 SER cc_start: 0.3011 (OUTLIER) cc_final: 0.2612 (t) REVERT: r 43 LYS cc_start: 0.4988 (mttp) cc_final: 0.4770 (mttt) REVERT: f 74 GLU cc_start: 0.5112 (tp30) cc_final: 0.4573 (mp0) REVERT: f 91 VAL cc_start: 0.5569 (t) cc_final: 0.5273 (m) outliers start: 110 outliers final: 55 residues processed: 705 average time/residue: 2.2788 time to fit residues: 2211.7171 Evaluate side-chains 699 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 627 time to evaluate : 5.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 4 MET Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain E residue 10 ASN Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 131 LYS Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 139 GLU Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain O residue 4 LYS Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 28 ARG Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain U residue 4 LYS Chi-restraints excluded: chain U residue 31 ASP Chi-restraints excluded: chain U residue 85 VAL Chi-restraints excluded: chain W residue 78 GLU Chi-restraints excluded: chain Y residue 17 LYS Chi-restraints excluded: chain Y residue 20 SER Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 123 CYS Chi-restraints excluded: chain l residue 13 VAL Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain o residue 11 LEU Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain c residue 6 ASN Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 97 ARG Chi-restraints excluded: chain c residue 101 ASN Chi-restraints excluded: chain c residue 106 LYS Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 98 THR Chi-restraints excluded: chain i residue 87 LEU Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 92 ARG Chi-restraints excluded: chain n residue 9 LYS Chi-restraints excluded: chain n residue 32 SER Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain s residue 16 MET Chi-restraints excluded: chain s residue 19 ILE Chi-restraints excluded: chain h residue 23 GLU Chi-restraints excluded: chain h residue 66 TYR Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 85 LEU Chi-restraints excluded: chain h residue 109 SER Chi-restraints excluded: chain f residue 63 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 799 optimal weight: 20.0000 chunk 842 optimal weight: 0.4980 chunk 768 optimal weight: 9.9990 chunk 819 optimal weight: 7.9990 chunk 841 optimal weight: 0.9990 chunk 493 optimal weight: 3.9990 chunk 356 optimal weight: 8.9990 chunk 643 optimal weight: 20.0000 chunk 251 optimal weight: 10.0000 chunk 740 optimal weight: 2.9990 chunk 774 optimal weight: 10.0000 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 148 ASN O 37 ASN Q 108 GLN S 28 GLN ** k 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 66 GLN l 5 ASN l 90 HIS o 37 ASN m 32 GLN r 53 ASN f 27 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 147580 Z= 0.203 Angle : 0.665 14.953 221780 Z= 0.344 Chirality : 0.038 0.330 28489 Planarity : 0.005 0.142 11146 Dihedral : 23.686 179.288 76322 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.40 % Favored : 96.53 % Rotamer: Outliers : 2.24 % Allowed : 18.56 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.12), residues: 4733 helix: 0.64 (0.13), residues: 1486 sheet: -0.59 (0.16), residues: 929 loop : -0.66 (0.12), residues: 2318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP k 46 HIS 0.006 0.001 HIS t 20 PHE 0.018 0.002 PHE Q 57 TYR 0.020 0.002 TYR Q 32 ARG 0.008 0.001 ARG l 123 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9466 Ramachandran restraints generated. 4733 Oldfield, 0 Emsley, 4733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9466 Ramachandran restraints generated. 4733 Oldfield, 0 Emsley, 4733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 628 time to evaluate : 5.500 Fit side-chains revert: symmetry clash REVERT: 0 44 LYS cc_start: 0.7220 (mtmt) cc_final: 0.6563 (mmtm) REVERT: 1 23 LYS cc_start: 0.5021 (mtmt) cc_final: 0.4793 (mmtp) REVERT: 1 33 LYS cc_start: 0.6297 (ttmt) cc_final: 0.5824 (mmmt) REVERT: 4 13 LYS cc_start: 0.6046 (mttt) cc_final: 0.5408 (mmtt) REVERT: 4 15 LYS cc_start: 0.6516 (mtpt) cc_final: 0.5853 (tttp) REVERT: 4 18 ARG cc_start: 0.6783 (ttt90) cc_final: 0.6024 (tpp80) REVERT: 4 20 LYS cc_start: 0.6536 (mmtt) cc_final: 0.6318 (mttm) REVERT: 4 24 MET cc_start: 0.8110 (mtp) cc_final: 0.7778 (mtp) REVERT: 4 28 GLU cc_start: 0.5617 (pt0) cc_final: 0.5322 (pm20) REVERT: 6 1 MET cc_start: 0.4550 (OUTLIER) cc_final: 0.3882 (mtp) REVERT: C 23 GLU cc_start: 0.6433 (OUTLIER) cc_final: 0.5958 (pm20) REVERT: C 28 LYS cc_start: 0.6308 (mttt) cc_final: 0.5894 (pttm) REVERT: C 77 ARG cc_start: 0.6496 (ttp80) cc_final: 0.5677 (mtt-85) REVERT: C 100 GLU cc_start: 0.7444 (tt0) cc_final: 0.7157 (tt0) REVERT: C 172 VAL cc_start: 0.7639 (t) cc_final: 0.7357 (m) REVERT: C 183 MET cc_start: 0.7922 (mtp) cc_final: 0.7701 (mtt) REVERT: C 198 GLU cc_start: 0.6972 (tt0) cc_final: 0.6370 (pm20) REVERT: C 199 GLN cc_start: 0.6494 (mt0) cc_final: 0.5964 (pm20) REVERT: C 261 LYS cc_start: 0.6212 (tttm) cc_final: 0.5253 (mmtt) REVERT: C 267 ASP cc_start: 0.6738 (m-30) cc_final: 0.6444 (m-30) REVERT: C 273 ARG cc_start: 0.5844 (mmt90) cc_final: 0.5435 (mtp180) REVERT: D 71 LYS cc_start: 0.6161 (mttt) cc_final: 0.5687 (ttpp) REVERT: D 73 GLU cc_start: 0.6267 (mt-10) cc_final: 0.6028 (mt-10) REVERT: D 92 GLU cc_start: 0.7054 (tt0) cc_final: 0.6346 (pt0) REVERT: D 178 LYS cc_start: 0.7191 (ttmt) cc_final: 0.6731 (tttm) REVERT: D 182 GLU cc_start: 0.5867 (mt-10) cc_final: 0.5530 (mm-30) REVERT: E 27 GLU cc_start: 0.5679 (tt0) cc_final: 0.5427 (mt-10) REVERT: E 103 LYS cc_start: 0.6978 (ttmm) cc_final: 0.6261 (ttmt) REVERT: E 127 GLU cc_start: 0.5872 (tp30) cc_final: 0.5570 (mt-10) REVERT: E 161 GLU cc_start: 0.5373 (tt0) cc_final: 0.4853 (mp0) REVERT: E 196 LYS cc_start: 0.6493 (ttpt) cc_final: 0.6179 (ttpp) REVERT: F 32 GLU cc_start: 0.5681 (tp30) cc_final: 0.5468 (tp30) REVERT: F 50 ILE cc_start: 0.5172 (OUTLIER) cc_final: 0.4804 (mp) REVERT: F 69 ARG cc_start: 0.5538 (mtt-85) cc_final: 0.4806 (mpp80) REVERT: F 94 GLU cc_start: 0.4951 (tp30) cc_final: 0.4677 (tt0) REVERT: F 95 ARG cc_start: 0.5134 (mmt90) cc_final: 0.4889 (mmt90) REVERT: F 152 MET cc_start: 0.6560 (ptp) cc_final: 0.6314 (ptp) REVERT: F 165 GLU cc_start: 0.5189 (mt-10) cc_final: 0.4946 (mt-10) REVERT: G 131 LYS cc_start: 0.5615 (OUTLIER) cc_final: 0.5079 (tppp) REVERT: G 166 GLU cc_start: 0.5642 (tt0) cc_final: 0.5234 (tp30) REVERT: J 13 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6245 (tp30) REVERT: J 62 LYS cc_start: 0.6951 (mmtp) cc_final: 0.6544 (mtmt) REVERT: J 92 GLU cc_start: 0.6823 (tt0) cc_final: 0.6498 (mt-10) REVERT: J 107 LYS cc_start: 0.6847 (tttm) cc_final: 0.6499 (ttpt) REVERT: J 130 GLU cc_start: 0.6581 (mt-10) cc_final: 0.6018 (mm-30) REVERT: J 139 GLU cc_start: 0.7301 (mt-10) cc_final: 0.6413 (mm-30) REVERT: K 9 LYS cc_start: 0.7718 (mttt) cc_final: 0.6984 (ttmt) REVERT: K 34 ASN cc_start: 0.7002 (p0) cc_final: 0.6433 (t0) REVERT: K 45 GLN cc_start: 0.7314 (mt0) cc_final: 0.6881 (mm110) REVERT: K 48 PRO cc_start: 0.6276 (Cg_exo) cc_final: 0.5883 (Cg_endo) REVERT: K 70 ARG cc_start: 0.7630 (ttt180) cc_final: 0.6903 (ttt-90) REVERT: K 107 ARG cc_start: 0.6272 (mtp-110) cc_final: 0.5789 (mtm-85) REVERT: K 112 MET cc_start: 0.6935 (mmm) cc_final: 0.6661 (mmm) REVERT: K 113 LYS cc_start: 0.6321 (mttt) cc_final: 0.5589 (tppt) REVERT: L 14 LYS cc_start: 0.7447 (mtpt) cc_final: 0.7219 (mtpp) REVERT: L 90 GLU cc_start: 0.4827 (tt0) cc_final: 0.4422 (tm-30) REVERT: L 133 LYS cc_start: 0.6672 (tttm) cc_final: 0.6296 (ttpt) REVERT: L 137 GLU cc_start: 0.5456 (mt-10) cc_final: 0.4977 (mt-10) REVERT: M 5 LYS cc_start: 0.6707 (tttt) cc_final: 0.6459 (mtmp) REVERT: M 18 ARG cc_start: 0.7217 (mtt90) cc_final: 0.6163 (mtp180) REVERT: M 26 GLU cc_start: 0.6900 (mm-30) cc_final: 0.6625 (mm-30) REVERT: M 54 MET cc_start: 0.7825 (ptp) cc_final: 0.7590 (ptt) REVERT: N 34 GLU cc_start: 0.7202 (tt0) cc_final: 0.6652 (tp30) REVERT: N 72 ASN cc_start: 0.6828 (t0) cc_final: 0.6263 (t0) REVERT: N 75 ASN cc_start: 0.5305 (m110) cc_final: 0.4511 (m110) REVERT: O 8 ASN cc_start: 0.7343 (t0) cc_final: 0.7026 (t0) REVERT: O 12 LEU cc_start: 0.7163 (mp) cc_final: 0.6834 (mm) REVERT: O 28 ARG cc_start: 0.5802 (OUTLIER) cc_final: 0.5197 (ttp-110) REVERT: O 94 VAL cc_start: 0.6973 (OUTLIER) cc_final: 0.6678 (p) REVERT: P 6 GLU cc_start: 0.6483 (mt-10) cc_final: 0.5452 (tm-30) REVERT: P 11 GLU cc_start: 0.6530 (pt0) cc_final: 0.6076 (pm20) REVERT: P 27 ARG cc_start: 0.7104 (mtt-85) cc_final: 0.6824 (mtt180) REVERT: P 85 GLU cc_start: 0.6821 (OUTLIER) cc_final: 0.5870 (mt-10) REVERT: P 88 ARG cc_start: 0.7325 (ptm-80) cc_final: 0.6427 (ptt-90) REVERT: P 109 ARG cc_start: 0.6190 (mtm180) cc_final: 0.5752 (mtm180) REVERT: P 111 LYS cc_start: 0.6833 (mttt) cc_final: 0.6299 (tptt) REVERT: Q 19 LYS cc_start: 0.7223 (tmtp) cc_final: 0.6445 (mmtt) REVERT: Q 97 ASP cc_start: 0.7288 (t70) cc_final: 0.6857 (t0) REVERT: Q 116 GLN cc_start: 0.6723 (mm-40) cc_final: 0.6417 (mm-40) REVERT: R 1 MET cc_start: 0.6366 (ttm) cc_final: 0.6126 (ttm) REVERT: R 36 GLU cc_start: 0.6345 (mt-10) cc_final: 0.5280 (pm20) REVERT: R 47 LYS cc_start: 0.6517 (mmtp) cc_final: 0.6154 (mtpt) REVERT: R 50 ASN cc_start: 0.5973 (p0) cc_final: 0.5532 (p0) REVERT: R 54 GLU cc_start: 0.5772 (tt0) cc_final: 0.5465 (tp30) REVERT: R 63 GLU cc_start: 0.6980 (mm-30) cc_final: 0.6419 (mm-30) REVERT: R 98 GLU cc_start: 0.6245 (mt-10) cc_final: 0.5578 (mp0) REVERT: S 31 GLU cc_start: 0.6749 (tt0) cc_final: 0.6076 (tp30) REVERT: S 48 GLU cc_start: 0.7679 (tt0) cc_final: 0.6757 (tm-30) REVERT: S 92 ARG cc_start: 0.5797 (mtt-85) cc_final: 0.5410 (mtt90) REVERT: T 10 ARG cc_start: 0.7183 (ptm160) cc_final: 0.6671 (ptp90) REVERT: T 21 MET cc_start: 0.5983 (mtt) cc_final: 0.5679 (mtm) REVERT: T 29 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6577 (tt0) REVERT: T 33 ARG cc_start: 0.6604 (mmt90) cc_final: 0.6302 (mpp-170) REVERT: T 50 LYS cc_start: 0.6057 (mttt) cc_final: 0.5561 (mmtm) REVERT: T 68 ARG cc_start: 0.5135 (ptm-80) cc_final: 0.4462 (tmt-80) REVERT: U 4 LYS cc_start: 0.7075 (OUTLIER) cc_final: 0.6539 (ptpp) REVERT: U 22 THR cc_start: 0.6995 (m) cc_final: 0.6641 (t) REVERT: U 30 LYS cc_start: 0.6182 (mttt) cc_final: 0.5625 (mptt) REVERT: U 84 LYS cc_start: 0.6263 (pttt) cc_final: 0.5846 (pttp) REVERT: W 19 LYS cc_start: 0.7527 (mtmp) cc_final: 0.7179 (mmtt) REVERT: W 57 GLU cc_start: 0.6510 (mt-10) cc_final: 0.5980 (mm-30) REVERT: X 35 LYS cc_start: 0.5718 (tptt) cc_final: 0.5468 (tptt) REVERT: X 48 TYR cc_start: 0.6711 (m-80) cc_final: 0.6418 (m-80) REVERT: X 60 GLU cc_start: 0.4510 (pt0) cc_final: 0.4004 (mm-30) REVERT: Y 23 GLU cc_start: 0.6416 (mt-10) cc_final: 0.5574 (tm-30) REVERT: Y 29 ARG cc_start: 0.6169 (mtt180) cc_final: 0.5944 (mtt-85) REVERT: Y 45 GLU cc_start: 0.6548 (mt-10) cc_final: 0.6336 (tt0) REVERT: Y 48 LYS cc_start: 0.6598 (mttt) cc_final: 0.6197 (mptt) REVERT: Y 53 MET cc_start: 0.7094 (mtt) cc_final: 0.6359 (mtm) REVERT: Z 10 ARG cc_start: 0.7324 (mmt90) cc_final: 0.6515 (mmm160) REVERT: Z 38 GLU cc_start: 0.6701 (mm-30) cc_final: 0.5994 (mm-30) REVERT: Z 55 SER cc_start: 0.7405 (t) cc_final: 0.7059 (p) REVERT: Z 57 LYS cc_start: 0.6398 (ttmp) cc_final: 0.5842 (ttpp) REVERT: e 10 GLU cc_start: 0.4000 (mm-30) cc_final: 0.3048 (tm-30) REVERT: e 12 GLU cc_start: 0.4946 (tt0) cc_final: 0.4396 (mp0) REVERT: e 54 GLN cc_start: 0.4166 (OUTLIER) cc_final: 0.3936 (tp40) REVERT: e 62 LYS cc_start: 0.5206 (mmtm) cc_final: 0.4994 (tmmm) REVERT: e 76 MET cc_start: 0.4444 (mmm) cc_final: 0.4113 (mmm) REVERT: e 84 GLU cc_start: 0.5267 (tt0) cc_final: 0.4772 (mm-30) REVERT: e 101 GLU cc_start: 0.4600 (mm-30) cc_final: 0.4356 (mm-30) REVERT: k 67 MET cc_start: 0.4868 (mmp) cc_final: 0.4392 (tpp) REVERT: l 3 THR cc_start: 0.7064 (m) cc_final: 0.6785 (p) REVERT: l 26 LYS cc_start: 0.5139 (mmtm) cc_final: 0.4853 (mmmt) REVERT: l 33 LYS cc_start: 0.4705 (mtmt) cc_final: 0.4466 (tptt) REVERT: l 54 THR cc_start: 0.5524 (OUTLIER) cc_final: 0.5188 (p) REVERT: l 64 LYS cc_start: 0.5074 (pttp) cc_final: 0.4636 (mmtm) REVERT: l 133 LYS cc_start: 0.3185 (ttmm) cc_final: 0.2709 (tttm) REVERT: o 44 ARG cc_start: 0.5902 (mmt90) cc_final: 0.5570 (mpt180) REVERT: o 63 ARG cc_start: 0.6923 (ttp-170) cc_final: 0.6647 (ttp80) REVERT: c 97 ARG cc_start: 0.4074 (OUTLIER) cc_final: 0.3814 (mtp-110) REVERT: c 101 ASN cc_start: 0.4262 (OUTLIER) cc_final: 0.3800 (p0) REVERT: c 186 SER cc_start: 0.7312 (t) cc_final: 0.6837 (p) REVERT: c 189 ASP cc_start: 0.5540 (t0) cc_final: 0.5001 (p0) REVERT: g 7 VAL cc_start: 0.3079 (p) cc_final: 0.2823 (m) REVERT: g 31 MET cc_start: 0.6755 (ttp) cc_final: 0.6235 (ttp) REVERT: g 70 MET cc_start: 0.5281 (mtm) cc_final: 0.4955 (mtm) REVERT: g 107 TYR cc_start: 0.4948 (m-80) cc_final: 0.4594 (m-80) REVERT: j 72 ARG cc_start: 0.5613 (mmt-90) cc_final: 0.5348 (tpp-160) REVERT: m 27 ARG cc_start: 0.4997 (ptm160) cc_final: 0.4751 (mtm110) REVERT: n 11 GLN cc_start: 0.5015 (mt0) cc_final: 0.4779 (mt0) REVERT: n 57 LYS cc_start: 0.6185 (ptpp) cc_final: 0.5305 (pttp) REVERT: s 16 MET cc_start: 0.5103 (OUTLIER) cc_final: 0.4885 (ttm) REVERT: s 70 LYS cc_start: 0.6210 (mmtt) cc_final: 0.5865 (mttt) REVERT: h 23 GLU cc_start: 0.4819 (OUTLIER) cc_final: 0.4544 (mm-30) REVERT: h 42 ARG cc_start: 0.3434 (mmt-90) cc_final: 0.2994 (mmm-85) REVERT: h 85 LEU cc_start: 0.3337 (OUTLIER) cc_final: 0.3063 (tp) REVERT: r 43 LYS cc_start: 0.4866 (mttp) cc_final: 0.4651 (mttt) REVERT: f 74 GLU cc_start: 0.5128 (tp30) cc_final: 0.4605 (mp0) REVERT: f 91 VAL cc_start: 0.5550 (t) cc_final: 0.5268 (m) outliers start: 90 outliers final: 53 residues processed: 695 average time/residue: 2.4430 time to fit residues: 2324.6964 Evaluate side-chains 683 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 614 time to evaluate : 5.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 4 MET Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain E residue 10 ASN Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 131 LYS Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain K residue 94 ARG Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain O residue 4 LYS Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 28 ARG Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain S residue 94 SER Chi-restraints excluded: chain U residue 4 LYS Chi-restraints excluded: chain U residue 85 VAL Chi-restraints excluded: chain W residue 78 GLU Chi-restraints excluded: chain Y residue 20 SER Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 54 GLN Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain k residue 44 ILE Chi-restraints excluded: chain k residue 83 THR Chi-restraints excluded: chain k residue 123 CYS Chi-restraints excluded: chain l residue 13 VAL Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain o residue 11 LEU Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain t residue 86 LEU Chi-restraints excluded: chain c residue 6 ASN Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 97 ARG Chi-restraints excluded: chain c residue 101 ASN Chi-restraints excluded: chain c residue 106 LYS Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain i residue 87 LEU Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 92 ARG Chi-restraints excluded: chain n residue 9 LYS Chi-restraints excluded: chain n residue 32 SER Chi-restraints excluded: chain s residue 16 MET Chi-restraints excluded: chain s residue 19 ILE Chi-restraints excluded: chain h residue 23 GLU Chi-restraints excluded: chain h residue 66 TYR Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 85 LEU Chi-restraints excluded: chain f residue 23 ILE Chi-restraints excluded: chain f residue 63 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 816 optimal weight: 3.9990 chunk 537 optimal weight: 6.9990 chunk 866 optimal weight: 8.9990 chunk 528 optimal weight: 9.9990 chunk 410 optimal weight: 7.9990 chunk 602 optimal weight: 20.0000 chunk 908 optimal weight: 2.9990 chunk 836 optimal weight: 8.9990 chunk 723 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 558 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 148 ASN O 37 ASN Q 108 GLN S 28 GLN k 66 GLN l 5 ASN l 90 HIS o 37 ASN m 32 GLN ** h 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 27 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 147580 Z= 0.295 Angle : 0.802 19.090 221780 Z= 0.405 Chirality : 0.043 0.339 28489 Planarity : 0.006 0.150 11146 Dihedral : 23.830 178.408 76322 Min Nonbonded Distance : 1.658 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.42 % Favored : 95.52 % Rotamer: Outliers : 2.41 % Allowed : 18.49 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.11), residues: 4733 helix: 0.25 (0.12), residues: 1483 sheet: -0.65 (0.16), residues: 918 loop : -0.78 (0.12), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP k 46 HIS 0.009 0.002 HIS t 20 PHE 0.024 0.003 PHE Q 57 TYR 0.023 0.003 TYR Q 32 ARG 0.011 0.001 ARG F 150 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9466 Ramachandran restraints generated. 4733 Oldfield, 0 Emsley, 4733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9466 Ramachandran restraints generated. 4733 Oldfield, 0 Emsley, 4733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 632 time to evaluate : 5.542 Fit side-chains revert: symmetry clash REVERT: 0 44 LYS cc_start: 0.7180 (mtmt) cc_final: 0.6529 (mtpp) REVERT: 1 23 LYS cc_start: 0.5141 (mtmt) cc_final: 0.4866 (mmtp) REVERT: 1 33 LYS cc_start: 0.6351 (ttmt) cc_final: 0.5831 (mmmt) REVERT: 4 13 LYS cc_start: 0.6085 (mttt) cc_final: 0.5444 (mmtt) REVERT: 4 15 LYS cc_start: 0.6439 (mtpt) cc_final: 0.5773 (tttp) REVERT: 4 18 ARG cc_start: 0.6769 (ttt90) cc_final: 0.6032 (tpp80) REVERT: 4 20 LYS cc_start: 0.6550 (mmtt) cc_final: 0.6338 (mttm) REVERT: 4 24 MET cc_start: 0.8125 (mtp) cc_final: 0.7776 (mtp) REVERT: 4 28 GLU cc_start: 0.5617 (pt0) cc_final: 0.5327 (pm20) REVERT: 6 1 MET cc_start: 0.4370 (OUTLIER) cc_final: 0.3709 (mtp) REVERT: 6 40 HIS cc_start: 0.5926 (t-90) cc_final: 0.5720 (t70) REVERT: C 23 GLU cc_start: 0.6400 (OUTLIER) cc_final: 0.5942 (pm20) REVERT: C 28 LYS cc_start: 0.6346 (mttt) cc_final: 0.5904 (pttm) REVERT: C 77 ARG cc_start: 0.6479 (ttp80) cc_final: 0.5668 (mtt-85) REVERT: C 100 GLU cc_start: 0.7474 (tt0) cc_final: 0.7162 (tt0) REVERT: C 183 MET cc_start: 0.7982 (mtp) cc_final: 0.7753 (mtt) REVERT: C 198 GLU cc_start: 0.6923 (tt0) cc_final: 0.6352 (pm20) REVERT: C 199 GLN cc_start: 0.6494 (mt0) cc_final: 0.5970 (pm20) REVERT: C 261 LYS cc_start: 0.6269 (tttm) cc_final: 0.5345 (mmtt) REVERT: C 262 LYS cc_start: 0.5094 (mmtp) cc_final: 0.4414 (tttp) REVERT: C 267 ASP cc_start: 0.6844 (m-30) cc_final: 0.6578 (m-30) REVERT: C 273 ARG cc_start: 0.5739 (mmt90) cc_final: 0.5327 (mtp180) REVERT: D 71 LYS cc_start: 0.6180 (mttt) cc_final: 0.5676 (ttpp) REVERT: D 73 GLU cc_start: 0.6346 (mt-10) cc_final: 0.6095 (mt-10) REVERT: D 92 GLU cc_start: 0.7010 (tt0) cc_final: 0.6318 (pt0) REVERT: D 178 LYS cc_start: 0.7215 (ttmt) cc_final: 0.6404 (tttt) REVERT: D 182 GLU cc_start: 0.5882 (mt-10) cc_final: 0.5550 (mm-30) REVERT: E 18 GLU cc_start: 0.5780 (OUTLIER) cc_final: 0.5338 (tm-30) REVERT: E 27 GLU cc_start: 0.5615 (tt0) cc_final: 0.5186 (tm-30) REVERT: E 103 LYS cc_start: 0.7026 (ttmm) cc_final: 0.6307 (ttmt) REVERT: E 127 GLU cc_start: 0.5862 (tp30) cc_final: 0.5577 (mt-10) REVERT: E 144 LYS cc_start: 0.6246 (tppt) cc_final: 0.5809 (tttt) REVERT: E 161 GLU cc_start: 0.5357 (tt0) cc_final: 0.4860 (mp0) REVERT: E 196 LYS cc_start: 0.6503 (ttpt) cc_final: 0.6177 (ttpp) REVERT: F 69 ARG cc_start: 0.5584 (mtt-85) cc_final: 0.4852 (mpp80) REVERT: F 94 GLU cc_start: 0.4953 (tp30) cc_final: 0.4651 (tt0) REVERT: F 95 ARG cc_start: 0.5128 (mmt90) cc_final: 0.4871 (mmt90) REVERT: F 165 GLU cc_start: 0.5175 (OUTLIER) cc_final: 0.4942 (mt-10) REVERT: G 14 ASP cc_start: 0.2108 (OUTLIER) cc_final: 0.1812 (p0) REVERT: G 131 LYS cc_start: 0.5514 (OUTLIER) cc_final: 0.5068 (tppp) REVERT: G 166 GLU cc_start: 0.5583 (tt0) cc_final: 0.5159 (tp30) REVERT: J 13 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6209 (tp30) REVERT: J 62 LYS cc_start: 0.6971 (mmtp) cc_final: 0.6510 (mtmt) REVERT: J 92 GLU cc_start: 0.6717 (tt0) cc_final: 0.6435 (mt-10) REVERT: J 107 LYS cc_start: 0.6890 (tttm) cc_final: 0.6533 (ttpt) REVERT: J 130 GLU cc_start: 0.6599 (mt-10) cc_final: 0.6052 (mm-30) REVERT: J 139 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6413 (mm-30) REVERT: K 9 LYS cc_start: 0.7719 (mttt) cc_final: 0.6986 (ttmt) REVERT: K 34 ASN cc_start: 0.6981 (p0) cc_final: 0.6427 (t0) REVERT: K 45 GLN cc_start: 0.7308 (mt0) cc_final: 0.6885 (mm110) REVERT: K 48 PRO cc_start: 0.6151 (Cg_exo) cc_final: 0.5751 (Cg_endo) REVERT: K 70 ARG cc_start: 0.7554 (ttt180) cc_final: 0.6836 (ttt-90) REVERT: K 107 ARG cc_start: 0.6230 (mtp-110) cc_final: 0.5767 (mtm-85) REVERT: K 112 MET cc_start: 0.6896 (mmm) cc_final: 0.6620 (mmm) REVERT: K 113 LYS cc_start: 0.6338 (mttt) cc_final: 0.5582 (tppt) REVERT: L 14 LYS cc_start: 0.7459 (mtpt) cc_final: 0.7246 (mtpp) REVERT: L 90 GLU cc_start: 0.4845 (tt0) cc_final: 0.4436 (tm-30) REVERT: L 133 LYS cc_start: 0.6651 (tttm) cc_final: 0.6352 (ttpp) REVERT: L 137 GLU cc_start: 0.5260 (mt-10) cc_final: 0.4917 (mt-10) REVERT: M 5 LYS cc_start: 0.6702 (tttt) cc_final: 0.6057 (mmtm) REVERT: M 18 ARG cc_start: 0.7281 (mtt90) cc_final: 0.6229 (mtp180) REVERT: M 26 GLU cc_start: 0.6828 (mm-30) cc_final: 0.6564 (mm-30) REVERT: M 54 MET cc_start: 0.7823 (ptp) cc_final: 0.7554 (ptt) REVERT: N 34 GLU cc_start: 0.7145 (tt0) cc_final: 0.6595 (tp30) REVERT: N 72 ASN cc_start: 0.6820 (t0) cc_final: 0.6296 (t0) REVERT: N 75 ASN cc_start: 0.5263 (m110) cc_final: 0.4495 (m110) REVERT: O 8 ASN cc_start: 0.7471 (t0) cc_final: 0.6900 (t0) REVERT: O 12 LEU cc_start: 0.7202 (mp) cc_final: 0.6838 (mm) REVERT: O 28 ARG cc_start: 0.5758 (OUTLIER) cc_final: 0.5141 (ttp-110) REVERT: O 94 VAL cc_start: 0.6926 (OUTLIER) cc_final: 0.6636 (p) REVERT: P 6 GLU cc_start: 0.6564 (mt-10) cc_final: 0.5648 (tm-30) REVERT: P 11 GLU cc_start: 0.6638 (pt0) cc_final: 0.6174 (pm20) REVERT: P 27 ARG cc_start: 0.7137 (mtt-85) cc_final: 0.6847 (mtt180) REVERT: P 85 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.5906 (mt-10) REVERT: P 88 ARG cc_start: 0.7342 (ptm-80) cc_final: 0.6429 (ptt-90) REVERT: P 111 LYS cc_start: 0.6882 (mttt) cc_final: 0.6323 (tptt) REVERT: Q 19 LYS cc_start: 0.7232 (tmtp) cc_final: 0.6462 (mmtt) REVERT: Q 97 ASP cc_start: 0.7307 (t70) cc_final: 0.6887 (t0) REVERT: Q 116 GLN cc_start: 0.6724 (mm-40) cc_final: 0.6434 (mm-40) REVERT: R 1 MET cc_start: 0.6296 (ttm) cc_final: 0.6039 (ttm) REVERT: R 36 GLU cc_start: 0.6388 (mt-10) cc_final: 0.5366 (pm20) REVERT: R 47 LYS cc_start: 0.6509 (mmtp) cc_final: 0.6181 (mtpt) REVERT: R 50 ASN cc_start: 0.5901 (p0) cc_final: 0.5439 (p0) REVERT: R 54 GLU cc_start: 0.5786 (tt0) cc_final: 0.5477 (tp30) REVERT: R 63 GLU cc_start: 0.6950 (mm-30) cc_final: 0.6411 (mm-30) REVERT: R 98 GLU cc_start: 0.6267 (mt-10) cc_final: 0.5605 (mp0) REVERT: S 31 GLU cc_start: 0.6809 (tt0) cc_final: 0.6124 (tp30) REVERT: S 48 GLU cc_start: 0.7700 (tt0) cc_final: 0.6787 (tm-30) REVERT: S 92 ARG cc_start: 0.5833 (mtt-85) cc_final: 0.5457 (mtt90) REVERT: T 10 ARG cc_start: 0.7195 (ptm160) cc_final: 0.6682 (ptp90) REVERT: T 21 MET cc_start: 0.5960 (mtt) cc_final: 0.5644 (mtm) REVERT: T 29 GLU cc_start: 0.7094 (mt-10) cc_final: 0.6591 (tt0) REVERT: T 33 ARG cc_start: 0.6638 (mmt90) cc_final: 0.6295 (mpp-170) REVERT: T 50 LYS cc_start: 0.6084 (mttt) cc_final: 0.5572 (mmtm) REVERT: T 68 ARG cc_start: 0.5209 (ptm-80) cc_final: 0.4539 (tmt-80) REVERT: U 4 LYS cc_start: 0.7084 (OUTLIER) cc_final: 0.6534 (ptpp) REVERT: U 22 THR cc_start: 0.6961 (m) cc_final: 0.6613 (t) REVERT: U 30 LYS cc_start: 0.6270 (mttt) cc_final: 0.5700 (mptt) REVERT: U 84 LYS cc_start: 0.6191 (pttt) cc_final: 0.5778 (pttp) REVERT: W 19 LYS cc_start: 0.7558 (mtmp) cc_final: 0.7196 (mmtt) REVERT: W 57 GLU cc_start: 0.6479 (mt-10) cc_final: 0.5967 (mm-30) REVERT: X 35 LYS cc_start: 0.5726 (tptt) cc_final: 0.5477 (tptt) REVERT: X 60 GLU cc_start: 0.4516 (pt0) cc_final: 0.4010 (tp30) REVERT: Y 23 GLU cc_start: 0.6369 (mt-10) cc_final: 0.5600 (tm-30) REVERT: Y 29 ARG cc_start: 0.6138 (mtt180) cc_final: 0.5906 (mtt-85) REVERT: Y 48 LYS cc_start: 0.6580 (mttt) cc_final: 0.6162 (mptt) REVERT: Y 53 MET cc_start: 0.7066 (mtt) cc_final: 0.6250 (mtm) REVERT: Z 10 ARG cc_start: 0.7349 (mmt90) cc_final: 0.6503 (mmm160) REVERT: Z 38 GLU cc_start: 0.6742 (mm-30) cc_final: 0.6041 (mm-30) REVERT: Z 46 MET cc_start: 0.7989 (mtp) cc_final: 0.7619 (mtp) REVERT: Z 55 SER cc_start: 0.7399 (t) cc_final: 0.7057 (p) REVERT: Z 57 LYS cc_start: 0.6388 (ttmp) cc_final: 0.5839 (ttpp) REVERT: e 10 GLU cc_start: 0.3967 (mm-30) cc_final: 0.2999 (tm-30) REVERT: e 12 GLU cc_start: 0.4889 (tt0) cc_final: 0.4184 (mp0) REVERT: e 54 GLN cc_start: 0.4220 (OUTLIER) cc_final: 0.3953 (tp40) REVERT: e 61 ARG cc_start: 0.5122 (ttm170) cc_final: 0.4886 (mtt-85) REVERT: e 62 LYS cc_start: 0.5082 (mmtm) cc_final: 0.4793 (tmmm) REVERT: e 76 MET cc_start: 0.4465 (mmm) cc_final: 0.4140 (mmm) REVERT: e 84 GLU cc_start: 0.5284 (tt0) cc_final: 0.4831 (mm-30) REVERT: e 98 PRO cc_start: 0.5274 (Cg_endo) cc_final: 0.4785 (Cg_exo) REVERT: e 101 GLU cc_start: 0.4685 (mm-30) cc_final: 0.4443 (mm-30) REVERT: k 67 MET cc_start: 0.4855 (mmp) cc_final: 0.4359 (tpp) REVERT: l 3 THR cc_start: 0.7035 (m) cc_final: 0.6768 (p) REVERT: l 26 LYS cc_start: 0.5188 (mmtm) cc_final: 0.4875 (mmmt) REVERT: l 33 LYS cc_start: 0.4663 (mtmt) cc_final: 0.4432 (tptt) REVERT: l 50 VAL cc_start: 0.5606 (OUTLIER) cc_final: 0.5129 (p) REVERT: l 54 THR cc_start: 0.5728 (OUTLIER) cc_final: 0.5387 (p) REVERT: l 64 LYS cc_start: 0.5010 (pttp) cc_final: 0.4592 (mmtm) REVERT: l 133 LYS cc_start: 0.3204 (ttmm) cc_final: 0.2687 (tttm) REVERT: o 44 ARG cc_start: 0.5952 (mmt90) cc_final: 0.5676 (mmt90) REVERT: c 97 ARG cc_start: 0.4070 (OUTLIER) cc_final: 0.3821 (mtp-110) REVERT: c 101 ASN cc_start: 0.4352 (OUTLIER) cc_final: 0.3843 (p0) REVERT: c 186 SER cc_start: 0.7315 (t) cc_final: 0.6909 (p) REVERT: c 189 ASP cc_start: 0.5489 (t0) cc_final: 0.4917 (p0) REVERT: g 7 VAL cc_start: 0.2991 (p) cc_final: 0.2771 (m) REVERT: g 31 MET cc_start: 0.6645 (ttp) cc_final: 0.6180 (ttp) REVERT: g 70 MET cc_start: 0.5273 (mtm) cc_final: 0.4934 (mtm) REVERT: g 107 TYR cc_start: 0.4949 (m-80) cc_final: 0.4688 (m-80) REVERT: m 27 ARG cc_start: 0.5047 (ptm160) cc_final: 0.4757 (mtm110) REVERT: m 70 ARG cc_start: 0.5637 (mtt-85) cc_final: 0.5406 (mmt90) REVERT: n 11 GLN cc_start: 0.4982 (mt0) cc_final: 0.4755 (mt0) REVERT: n 57 LYS cc_start: 0.6166 (ptpp) cc_final: 0.5298 (pttp) REVERT: s 16 MET cc_start: 0.5064 (OUTLIER) cc_final: 0.4668 (ttm) REVERT: s 53 ASP cc_start: 0.6237 (p0) cc_final: 0.6002 (p0) REVERT: h 23 GLU cc_start: 0.4858 (OUTLIER) cc_final: 0.4630 (mm-30) REVERT: h 42 ARG cc_start: 0.3318 (mmt-90) cc_final: 0.2933 (mmm-85) REVERT: h 85 LEU cc_start: 0.3398 (OUTLIER) cc_final: 0.3097 (tp) REVERT: f 74 GLU cc_start: 0.5173 (tp30) cc_final: 0.4621 (mp0) REVERT: f 91 VAL cc_start: 0.5598 (t) cc_final: 0.5334 (m) outliers start: 97 outliers final: 60 residues processed: 699 average time/residue: 2.4305 time to fit residues: 2341.7040 Evaluate side-chains 709 residues out of total 4024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 629 time to evaluate : 5.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 4 MET Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain E residue 10 ASN Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 201 LYS Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 131 LYS Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 139 GLU Chi-restraints excluded: chain K residue 94 ARG Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain O residue 4 LYS Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 28 ARG Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain S residue 94 SER Chi-restraints excluded: chain U residue 4 LYS Chi-restraints excluded: chain U residue 31 ASP Chi-restraints excluded: chain U residue 85 VAL Chi-restraints excluded: chain W residue 78 GLU Chi-restraints excluded: chain Y residue 17 LYS Chi-restraints excluded: chain Y residue 20 SER Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 54 GLN Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 83 THR Chi-restraints excluded: chain k residue 123 CYS Chi-restraints excluded: chain l residue 13 VAL Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain o residue 11 LEU Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain t residue 86 LEU Chi-restraints excluded: chain c residue 6 ASN Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 97 ARG Chi-restraints excluded: chain c residue 101 ASN Chi-restraints excluded: chain c residue 106 LYS Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain c residue 171 THR Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain g residue 98 THR Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain i residue 87 LEU Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 92 ARG Chi-restraints excluded: chain n residue 9 LYS Chi-restraints excluded: chain n residue 32 SER Chi-restraints excluded: chain s residue 16 MET Chi-restraints excluded: chain s residue 19 ILE Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 23 GLU Chi-restraints excluded: chain h residue 66 TYR Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 85 LEU Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain f residue 81 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 443 optimal weight: 4.9990 chunk 574 optimal weight: 10.0000 chunk 770 optimal weight: 8.9990 chunk 221 optimal weight: 10.0000 chunk 667 optimal weight: 20.0000 chunk 106 optimal weight: 9.9990 chunk 201 optimal weight: 10.0000 chunk 724 optimal weight: 10.0000 chunk 303 optimal weight: 20.0000 chunk 744 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 148 ASN K 109 ASN O 37 ASN Q 108 GLN S 28 GLN k 66 GLN l 5 ASN l 90 HIS o 37 ASN ** q 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 32 GLN ** h 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 53 ASN f 27 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.174919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.151436 restraints weight = 117314.986| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 0.40 r_work: 0.3475 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 147580 Z= 0.417 Angle : 0.988 24.870 221780 Z= 0.486 Chirality : 0.051 0.420 28489 Planarity : 0.008 0.160 11146 Dihedral : 23.993 177.581 76322 Min Nonbonded Distance : 1.590 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.75 % Favored : 95.18 % Rotamer: Outliers : 2.71 % Allowed : 18.36 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -1.19 (0.11), residues: 4733 helix: -0.28 (0.12), residues: 1469 sheet: -0.83 (0.16), residues: 931 loop : -1.02 (0.12), residues: 2333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.004 TRP k 46 HIS 0.013 0.003 HIS t 20 PHE 0.027 0.004 PHE F 138 TYR 0.025 0.004 TYR Q 32 ARG 0.014 0.002 ARG F 150 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 38339.55 seconds wall clock time: 666 minutes 58.98 seconds (40018.98 seconds total)