Starting phenix.real_space_refine on Thu Mar 28 01:20:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pjw_13462/03_2024/7pjw_13462_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pjw_13462/03_2024/7pjw_13462.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pjw_13462/03_2024/7pjw_13462_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pjw_13462/03_2024/7pjw_13462_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pjw_13462/03_2024/7pjw_13462_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pjw_13462/03_2024/7pjw_13462.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pjw_13462/03_2024/7pjw_13462.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pjw_13462/03_2024/7pjw_13462_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pjw_13462/03_2024/7pjw_13462_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4730 5.49 5 S 174 5.16 5 C 77336 2.51 5 N 28395 2.21 5 O 42084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 ARG 9": "NH1" <-> "NH2" Residue "0 ARG 15": "NH1" <-> "NH2" Residue "0 ARG 39": "NH1" <-> "NH2" Residue "0 ARG 51": "NH1" <-> "NH2" Residue "1 GLU 6": "OE1" <-> "OE2" Residue "1 GLU 34": "OE1" <-> "OE2" Residue "1 ARG 43": "NH1" <-> "NH2" Residue "2 ARG 12": "NH1" <-> "NH2" Residue "2 ARG 14": "NH1" <-> "NH2" Residue "2 ARG 19": "NH1" <-> "NH2" Residue "2 ARG 21": "NH1" <-> "NH2" Residue "2 ARG 33": "NH1" <-> "NH2" Residue "2 ARG 41": "NH1" <-> "NH2" Residue "3 ARG 12": "NH1" <-> "NH2" Residue "3 ARG 29": "NH1" <-> "NH2" Residue "3 ARG 39": "NH1" <-> "NH2" Residue "3 ARG 41": "NH1" <-> "NH2" Residue "4 ARG 12": "NH1" <-> "NH2" Residue "4 ARG 24": "NH1" <-> "NH2" Residue "6 ARG 49": "NH1" <-> "NH2" Residue "6 ARG 56": "NH1" <-> "NH2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C ARG 211": "NH1" <-> "NH2" Residue "C GLU 235": "OE1" <-> "OE2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "D GLU 74": "OE1" <-> "OE2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D GLU 99": "OE1" <-> "OE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E GLU 25": "OE1" <-> "OE2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "E GLU 198": "OE1" <-> "OE2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 111": "NH1" <-> "NH2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "F GLU 133": "OE1" <-> "OE2" Residue "F GLU 139": "OE1" <-> "OE2" Residue "G ARG 2": "NH1" <-> "NH2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G GLU 80": "OE1" <-> "OE2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G GLU 154": "OE1" <-> "OE2" Residue "G ARG 162": "NH1" <-> "NH2" Residue "G ARG 169": "NH1" <-> "NH2" Residue "G GLU 172": "OE1" <-> "OE2" Residue "H GLU 48": "OE1" <-> "OE2" Residue "H ARG 51": "NH1" <-> "NH2" Residue "H GLU 53": "OE1" <-> "OE2" Residue "H GLU 76": "OE1" <-> "OE2" Residue "H GLU 127": "OE1" <-> "OE2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J ARG 95": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "K GLU 106": "OE1" <-> "OE2" Residue "K GLU 110": "OE1" <-> "OE2" Residue "L ARG 2": "NH1" <-> "NH2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L GLU 51": "OE1" <-> "OE2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 59": "NH1" <-> "NH2" Residue "M GLU 75": "OE1" <-> "OE2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "N ARG 4": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N GLU 43": "OE1" <-> "OE2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ARG 71": "NH1" <-> "NH2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O ARG 25": "NH1" <-> "NH2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P ARG 61": "NH1" <-> "NH2" Residue "P GLU 67": "OE1" <-> "OE2" Residue "P ARG 88": "NH1" <-> "NH2" Residue "P ARG 100": "NH1" <-> "NH2" Residue "P ARG 108": "NH1" <-> "NH2" Residue "P GLU 111": "OE1" <-> "OE2" Residue "Q ARG 2": "NH1" <-> "NH2" Residue "Q ARG 5": "NH1" <-> "NH2" Residue "Q ARG 12": "NH1" <-> "NH2" Residue "Q ARG 32": "NH1" <-> "NH2" Residue "Q ARG 47": "NH1" <-> "NH2" Residue "Q ARG 69": "NH1" <-> "NH2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R GLU 46": "OE1" <-> "OE2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 80": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 95": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T ARG 3": "NH1" <-> "NH2" Residue "T GLU 42": "OE1" <-> "OE2" Residue "T ARG 73": "NH1" <-> "NH2" Residue "U ARG 5": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 81": "NH1" <-> "NH2" Residue "U ARG 85": "NH1" <-> "NH2" Residue "U GLU 87": "OE1" <-> "OE2" Residue "U ARG 93": "NH1" <-> "NH2" Residue "Y ARG 7": "NH1" <-> "NH2" Residue "Y GLU 24": "OE1" <-> "OE2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 10": "NH1" <-> "NH2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "Z ARG 44": "NH1" <-> "NH2" Residue "b ARG 20": "NH1" <-> "NH2" Residue "b GLU 51": "OE1" <-> "OE2" Residue "b GLU 55": "OE1" <-> "OE2" Residue "b ARG 107": "NH1" <-> "NH2" Residue "b GLU 117": "OE1" <-> "OE2" Residue "b GLU 132": "OE1" <-> "OE2" Residue "b ARG 224": "NH1" <-> "NH2" Residue "c GLU 45": "OE1" <-> "OE2" Residue "c ARG 58": "NH1" <-> "NH2" Residue "c GLU 84": "OE1" <-> "OE2" Residue "c GLU 104": "OE1" <-> "OE2" Residue "c ARG 106": "NH1" <-> "NH2" Residue "c ARG 130": "NH1" <-> "NH2" Residue "c GLU 160": "OE1" <-> "OE2" Residue "c GLU 169": "OE1" <-> "OE2" Residue "d ARG 25": "NH1" <-> "NH2" Residue "d GLU 34": "OE1" <-> "OE2" Residue "d ARG 46": "NH1" <-> "NH2" Residue "d GLU 56": "OE1" <-> "OE2" Residue "d ARG 69": "NH1" <-> "NH2" Residue "d GLU 94": "OE1" <-> "OE2" Residue "d ARG 103": "NH1" <-> "NH2" Residue "d ARG 110": "NH1" <-> "NH2" Residue "d ARG 127": "NH1" <-> "NH2" Residue "d ARG 153": "NH1" <-> "NH2" Residue "d GLU 159": "OE1" <-> "OE2" Residue "d GLU 165": "OE1" <-> "OE2" Residue "d GLU 178": "OE1" <-> "OE2" Residue "d ARG 183": "NH1" <-> "NH2" Residue "e GLU 12": "OE1" <-> "OE2" Residue "e GLU 64": "OE1" <-> "OE2" Residue "e ARG 156": "NH1" <-> "NH2" Residue "f ARG 2": "NH1" <-> "NH2" Residue "f GLU 16": "OE1" <-> "OE2" Residue "f GLU 23": "OE1" <-> "OE2" Residue "f GLU 40": "OE1" <-> "OE2" Residue "g GLU 57": "OE1" <-> "OE2" Residue "g GLU 73": "OE1" <-> "OE2" Residue "g GLU 128": "OE1" <-> "OE2" Residue "h GLU 46": "OE1" <-> "OE2" Residue "h GLU 57": "OE1" <-> "OE2" Residue "i ARG 40": "NH1" <-> "NH2" Residue "i ARG 44": "NH1" <-> "NH2" Residue "i ARG 123": "NH1" <-> "NH2" Residue "j GLU 24": "OE1" <-> "OE2" Residue "k ARG 121": "NH1" <-> "NH2" Residue "k ARG 126": "NH1" <-> "NH2" Residue "l GLU 24": "OE1" <-> "OE2" Residue "l ARG 55": "NH1" <-> "NH2" Residue "l GLU 61": "OE1" <-> "OE2" Residue "l GLU 75": "OE1" <-> "OE2" Residue "m GLU 71": "OE1" <-> "OE2" Residue "n ARG 23": "NH1" <-> "NH2" Residue "n GLU 86": "OE1" <-> "OE2" Residue "o GLU 44": "OE1" <-> "OE2" Residue "p ARG 28": "NH1" <-> "NH2" Residue "p GLU 48": "OE1" <-> "OE2" Residue "q GLU 48": "OE1" <-> "OE2" Residue "s ARG 2": "NH1" <-> "NH2" Residue "s GLU 19": "OE1" <-> "OE2" Residue "s ARG 80": "NH1" <-> "NH2" Residue "u ARG 16": "NH1" <-> "NH2" Residue "u ARG 20": "NH1" <-> "NH2" Residue "u ARG 34": "NH1" <-> "NH2" Residue "u ARG 46": "NH1" <-> "NH2" Residue "x TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 57": "OE1" <-> "OE2" Residue "x GLU 123": "OE1" <-> "OE2" Residue "x GLU 202": "OE1" <-> "OE2" Residue "x GLU 204": "OE1" <-> "OE2" Residue "x GLU 212": "OE1" <-> "OE2" Residue "x GLU 241": "OE1" <-> "OE2" Residue "x GLU 440": "OE1" <-> "OE2" Residue "x GLU 547": "OE1" <-> "OE2" Residue "x GLU 558": "OE1" <-> "OE2" Residue "x PHE 600": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 602": "OE1" <-> "OE2" Residue "x GLU 621": "OE1" <-> "OE2" Residue "x GLU 656": "OE1" <-> "OE2" Residue "x GLU 688": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 152719 Number of models: 1 Model: "" Number of chains: 61 Chain: "0" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "1" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "2" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "3" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "4" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "5" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 647 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 5, 'TRANS': 125} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 355 Unresolved non-hydrogen angles: 447 Unresolved non-hydrogen dihedrals: 288 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 6, 'GLU:plan': 11, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 180 Chain: "6" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "A" Number of atoms: 62339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62339 Classifications: {'RNA': 2903} Modifications used: {'p5*END': 1, 'rna2p': 6, 'rna2p_pur': 246, 'rna2p_pyr': 127, 'rna3p': 17, 'rna3p_pur': 1421, 'rna3p_pyr': 1086} Link IDs: {'rna2p': 379, 'rna3p': 2523} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 9 Chain: "B" Number of atoms: 2570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2570 Classifications: {'RNA': 120} Modifications used: {'p5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 59, 'rna3p_pyr': 51} Link IDs: {'rna2p': 10, 'rna3p': 109} Chain: "C" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "F" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "H" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "I" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 693 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'PTRANS': 9, 'TRANS': 131} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 353 Unresolved non-hydrogen angles: 441 Unresolved non-hydrogen dihedrals: 288 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 140 Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "a" Number of atoms: 33050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1540, 33050 Classifications: {'RNA': 1540} Modifications used: {'rna2p': 1, 'rna2p_pur': 107, 'rna2p_pyr': 69, 'rna3p': 10, 'rna3p_pur': 762, 'rna3p_pyr': 591} Link IDs: {'rna2p': 177, 'rna3p': 1362} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 7 Chain: "b" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1704 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "c" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "d" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "e" Number of atoms: 1141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1141 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 151} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "f" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 817 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "g" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "h" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "i" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "j" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "k" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 869 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "l" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "m" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "n" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 799 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "o" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "p" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "r" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "s" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 658 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "t" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "u" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 506 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 62} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "v" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1642 Classifications: {'RNA': 77} Modifications used: {'p5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 7, 'rna3p': 4, 'rna3p_pur': 31, 'rna3p_pyr': 26} Link IDs: {'rna2p': 14, 'rna3p': 62} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "w" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1631 Classifications: {'RNA': 76} Modifications used: {'rna2p': 1, 'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p': 6, 'rna3p_pur': 32, 'rna3p_pyr': 27} Link IDs: {'rna2p': 11, 'rna3p': 64} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 1 Chain: "x" Number of atoms: 5444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 703, 5444 Classifications: {'peptide': 703} Link IDs: {'PTRANS': 33, 'TRANS': 669} Chain: "y" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "z" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 230 Classifications: {'RNA': 11} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 6} Link IDs: {'rna3p': 10} Chain: "a" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'AM2': 1} Classifications: {'undetermined': 1} Chain: "x" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'GDP': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 57.35, per 1000 atoms: 0.38 Number of scatterers: 152719 At special positions: 0 Unit cell: (238.96, 262.16, 241.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 174 16.00 P 4730 15.00 O 42084 8.00 N 28395 7.00 C 77336 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS 4 11 " - pdb=" SG CYS 4 14 " distance=1.81 Simple disulfide: pdb=" SG CYS 4 11 " - pdb=" SG CYS 4 27 " distance=2.90 Simple disulfide: pdb=" SG CYS 4 14 " - pdb=" SG CYS 4 27 " distance=2.15 Simple disulfide: pdb=" SG CYS 6 16 " - pdb=" SG CYS 6 37 " distance=1.93 Simple disulfide: pdb=" SG CYS 6 16 " - pdb=" SG CYS 6 40 " distance=2.79 Simple disulfide: pdb=" SG CYS 6 37 " - pdb=" SG CYS 6 40 " distance=2.46 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: 71.13 Conformation dependent library (CDL) restraints added in 8.3 seconds 13102 Ramachandran restraints generated. 6551 Oldfield, 0 Emsley, 6551 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12228 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: 199 helices and 81 sheets defined 37.7% alpha, 17.7% beta 1570 base pairs and 2308 stacking pairs defined. Time for finding SS restraints: 79.67 Creating SS restraints... Processing helix chain '0' and resid 8 through 20 removed outlier: 5.408A pdb=" N HIS 0 18 " --> pdb=" O MET 0 14 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ASP 0 19 " --> pdb=" O ARG 0 15 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ALA 0 20 " --> pdb=" O ARG 0 16 " (cutoff:3.500A) Processing helix chain '2' and resid 8 through 16 Processing helix chain '2' and resid 17 through 25 removed outlier: 5.103A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N LYS 2 25 " --> pdb=" O ARG 2 21 " (cutoff:3.500A) Processing helix chain '2' and resid 26 through 38 removed outlier: 4.338A pdb=" N VAL 2 30 " --> pdb=" O ASN 2 26 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA 2 32 " --> pdb=" O ARG 2 28 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG 2 33 " --> pdb=" O GLN 2 29 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG 2 34 " --> pdb=" O VAL 2 30 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA 2 36 " --> pdb=" O ALA 2 32 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LYS 2 37 " --> pdb=" O ARG 2 33 " (cutoff:3.500A) Processing helix chain '3' and resid 6 through 13 removed outlier: 4.338A pdb=" N ARG 3 12 " --> pdb=" O GLY 3 8 " (cutoff:3.500A) Processing helix chain '3' and resid 36 through 45 removed outlier: 3.601A pdb=" N LYS 3 40 " --> pdb=" O ALA 3 36 " (cutoff:3.500A) Proline residue: 3 45 - end of helix Processing helix chain '3' and resid 50 through 62 removed outlier: 4.612A pdb=" N GLY 3 55 " --> pdb=" O LYS 3 51 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LEU 3 56 " --> pdb=" O GLY 3 52 " (cutoff:3.500A) Proline residue: 3 62 - end of helix Processing helix chain '3' and resid 25 through 30 removed outlier: 4.986A pdb=" N LEU 3 28 " --> pdb=" O HIS 3 25 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ARG 3 29 " --> pdb=" O ALA 3 26 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N HIS 3 30 " --> pdb=" O ASN 3 27 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 25 through 30' Processing helix chain '5' and resid 3 through 21 removed outlier: 3.851A pdb=" N VAL 5 12 " --> pdb=" O LYS 5 8 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU 5 17 " --> pdb=" O ALA 5 13 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL 5 18 " --> pdb=" O GLU 5 14 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY 5 21 " --> pdb=" O GLU 5 17 " (cutoff:3.500A) Processing helix chain '5' and resid 34 through 48 Processing helix chain '5' and resid 59 through 67 removed outlier: 4.516A pdb=" N VAL 5 64 " --> pdb=" O LEU 5 60 " (cutoff:3.500A) Processing helix chain '5' and resid 93 through 105 removed outlier: 4.529A pdb=" N ALA 5 104 " --> pdb=" O ALA 5 100 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS 5 105 " --> pdb=" O LYS 5 101 " (cutoff:3.500A) Processing helix chain '5' and resid 75 through 80 Proline residue: 5 79 - end of helix Processing helix chain '5' and resid 109 through 114 removed outlier: 6.219A pdb=" N ALA 5 112 " --> pdb=" O LYS 5 109 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE 5 113 " --> pdb=" O ALA 5 110 " (cutoff:3.500A) Processing helix chain '6' and resid 41 through 46 Processing helix chain '6' and resid 56 through 63 removed outlier: 4.731A pdb=" N ARG 6 63 " --> pdb=" O ARG 6 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 15 removed outlier: 3.642A pdb=" N ARG C 13 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N HIS C 14 " --> pdb=" O PRO C 10 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N VAL C 15 " --> pdb=" O GLY C 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 9 through 15' Processing helix chain 'C' and resid 29 through 34 removed outlier: 4.325A pdb=" N LEU C 33 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLU C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 29 through 34' Processing helix chain 'C' and resid 130 through 135 Proline residue: C 135 - end of helix Processing helix chain 'C' and resid 206 through 214 removed outlier: 3.812A pdb=" N ALA C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ARG C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 225 removed outlier: 5.371A pdb=" N ASN C 225 " --> pdb=" O GLY C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 267 removed outlier: 6.119A pdb=" N ASP C 263 " --> pdb=" O ASN C 259 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LYS C 264 " --> pdb=" O LYS C 260 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N PHE C 265 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE C 266 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N VAL C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 259 through 267' Processing helix chain 'D' and resid 61 through 72 Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'D' and resid 97 through 102 removed outlier: 3.575A pdb=" N LEU D 100 " --> pdb=" O SER D 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 41 removed outlier: 5.489A pdb=" N GLN E 41 " --> pdb=" O ALA E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 116 Processing helix chain 'E' and resid 130 through 142 Processing helix chain 'E' and resid 154 through 163 removed outlier: 5.103A pdb=" N ASN E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 Processing helix chain 'E' and resid 189 through 201 Processing helix chain 'F' and resid 1 through 20 removed outlier: 5.030A pdb=" N VAL F 12 " --> pdb=" O LYS F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 46 Processing helix chain 'F' and resid 47 through 61 removed outlier: 3.892A pdb=" N ASN F 51 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA F 52 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLY F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 110 removed outlier: 5.285A pdb=" N VAL F 107 " --> pdb=" O ILE F 103 " (cutoff:3.500A) Proline residue: F 108 - end of helix Processing helix chain 'F' and resid 161 through 173 Processing helix chain 'F' and resid 133 through 138 Proline residue: F 138 - end of helix Processing helix chain 'G' and resid 1 through 6 removed outlier: 4.140A pdb=" N ALA G 6 " --> pdb=" O ARG G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 80 Processing helix chain 'G' and resid 136 through 152 removed outlier: 3.618A pdb=" N TYR G 150 " --> pdb=" O ASP G 146 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ARG G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 28 Processing helix chain 'H' and resid 40 through 50 removed outlier: 3.528A pdb=" N ARG H 50 " --> pdb=" O PHE H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 67 removed outlier: 4.439A pdb=" N ALA H 56 " --> pdb=" O ALA H 52 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ALA H 65 " --> pdb=" O VAL H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 105 Processing helix chain 'I' and resid 19 through 24 Processing helix chain 'I' and resid 39 through 44 removed outlier: 4.864A pdb=" N ALA I 43 " --> pdb=" O LYS I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 84 removed outlier: 4.308A pdb=" N LYS I 80 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA I 83 " --> pdb=" O LEU I 79 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY I 84 " --> pdb=" O LYS I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 113 Processing helix chain 'I' and resid 120 through 134 Processing helix chain 'J' and resid 24 through 38 Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.617A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 123 removed outlier: 4.542A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LYS J 123 " --> pdb=" O PHE J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 135 removed outlier: 3.952A pdb=" N ALA J 133 " --> pdb=" O HIS J 130 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ALA J 134 " --> pdb=" O ASN J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 removed outlier: 4.070A pdb=" N LYS J 72 " --> pdb=" O ASN J 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 67 through 72' Processing helix chain 'K' and resid 112 through 119 Processing helix chain 'L' and resid 56 through 62 Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 3.750A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 83 removed outlier: 4.080A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 83' Processing helix chain 'L' and resid 91 through 99 removed outlier: 4.610A pdb=" N ALA L 97 " --> pdb=" O ASN L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 139 Processing helix chain 'M' and resid 42 through 58 removed outlier: 4.709A pdb=" N LYS M 58 " --> pdb=" O THR M 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 125 removed outlier: 4.620A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU M 124 " --> pdb=" O ALA M 120 " (cutoff:3.500A) Proline residue: M 125 - end of helix Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 38 through 56 removed outlier: 4.209A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 59 through 71 Processing helix chain 'N' and resid 72 through 88 removed outlier: 4.538A pdb=" N PHE N 80 " --> pdb=" O VAL N 76 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LEU N 83 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N GLY N 84 " --> pdb=" O PHE N 80 " (cutoff:3.500A) Proline residue: N 85 - end of helix Processing helix chain 'O' and resid 2 through 22 removed outlier: 4.672A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 5.203A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 Processing helix chain 'O' and resid 101 through 114 Processing helix chain 'P' and resid 1 through 12 removed outlier: 4.171A pdb=" N GLU P 10 " --> pdb=" O GLN P 6 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 103 removed outlier: 4.306A pdb=" N ARG P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N THR P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 98 through 103' Processing helix chain 'Q' and resid 5 through 21 removed outlier: 4.476A pdb=" N ALA Q 9 " --> pdb=" O ARG Q 5 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE Q 16 " --> pdb=" O ARG Q 12 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN Q 19 " --> pdb=" O LYS Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 Processing helix chain 'Q' and resid 42 through 60 removed outlier: 4.154A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 62 through 72 Processing helix chain 'Q' and resid 74 through 86 Processing helix chain 'Q' and resid 90 through 100 Processing helix chain 'Q' and resid 101 through 117 Processing helix chain 'S' and resid 13 through 25 removed outlier: 4.900A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 Processing helix chain 'S' and resid 41 through 61 Processing helix chain 'T' and resid 3 through 11 removed outlier: 4.148A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 27 Processing helix chain 'T' and resid 39 through 51 Processing helix chain 'U' and resid 65 through 70 removed outlier: 3.686A pdb=" N VAL U 69 " --> pdb=" O GLN U 65 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ALA U 70 " --> pdb=" O VAL U 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 65 through 70' Processing helix chain 'V' and resid 13 through 24 Processing helix chain 'V' and resid 43 through 53 removed outlier: 4.258A pdb=" N LYS V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 59 removed outlier: 4.254A pdb=" N SER V 58 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 62 removed outlier: 4.509A pdb=" N GLY X 62 " --> pdb=" O ILE X 58 " (cutoff:3.500A) Processing helix chain 'X' and resid 63 through 74 Processing helix chain 'Y' and resid 2 through 9 Processing helix chain 'Y' and resid 10 through 35 removed outlier: 4.546A pdb=" N LEU Y 18 " --> pdb=" O LEU Y 14 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEU Y 19 " --> pdb=" O ASN Y 15 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N LEU Y 21 " --> pdb=" O GLU Y 17 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N LEU Y 22 " --> pdb=" O LEU Y 18 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 63 removed outlier: 4.693A pdb=" N LEU Y 43 " --> pdb=" O GLN Y 39 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLY Y 62 " --> pdb=" O ASN Y 58 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA Y 63 " --> pdb=" O GLU Y 59 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 51 Processing helix chain 'b' and resid 23 through 28 removed outlier: 4.424A pdb=" N LYS b 27 " --> pdb=" O ASN b 23 " (cutoff:3.500A) Proline residue: b 28 - end of helix No H-bonds generated for 'chain 'b' and resid 23 through 28' Processing helix chain 'b' and resid 41 through 63 Proline residue: b 47 - end of helix Processing helix chain 'b' and resid 72 through 87 removed outlier: 5.062A pdb=" N GLU b 77 " --> pdb=" O ARG b 73 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ALA b 78 " --> pdb=" O ALA b 74 " (cutoff:3.500A) Processing helix chain 'b' and resid 102 through 122 removed outlier: 4.892A pdb=" N GLN b 108 " --> pdb=" O LYS b 104 " (cutoff:3.500A) Processing helix chain 'b' and resid 124 through 129 removed outlier: 3.788A pdb=" N LEU b 128 " --> pdb=" O THR b 124 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N THR b 129 " --> pdb=" O PHE b 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 124 through 129' Processing helix chain 'b' and resid 130 through 147 Processing helix chain 'b' and resid 164 through 169 Processing helix chain 'b' and resid 170 through 179 removed outlier: 4.412A pdb=" N ASN b 177 " --> pdb=" O LYS b 173 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU b 178 " --> pdb=" O GLU b 174 " (cutoff:3.500A) Processing helix chain 'b' and resid 205 through 225 removed outlier: 4.807A pdb=" N SER b 225 " --> pdb=" O ARG b 221 " (cutoff:3.500A) Processing helix chain 'c' and resid 5 through 11 Processing helix chain 'c' and resid 27 through 47 Processing helix chain 'c' and resid 71 through 77 Processing helix chain 'c' and resid 80 through 95 removed outlier: 4.090A pdb=" N ILE c 93 " --> pdb=" O VAL c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 126 Processing helix chain 'c' and resid 128 through 144 Processing helix chain 'd' and resid 6 through 15 removed outlier: 4.461A pdb=" N LEU d 10 " --> pdb=" O PRO d 6 " (cutoff:3.500A) Processing helix chain 'd' and resid 26 through 31 removed outlier: 4.924A pdb=" N LYS d 30 " --> pdb=" O ALA d 26 " (cutoff:3.500A) Processing helix chain 'd' and resid 48 through 65 Processing helix chain 'd' and resid 68 through 82 removed outlier: 6.346A pdb=" N ASN d 73 " --> pdb=" O ARG d 69 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ALA d 78 " --> pdb=" O TYR d 74 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU d 81 " --> pdb=" O GLU d 77 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LYS d 82 " --> pdb=" O ALA d 78 " (cutoff:3.500A) Processing helix chain 'd' and resid 84 through 96 removed outlier: 3.582A pdb=" N ARG d 96 " --> pdb=" O LEU d 92 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 105 Processing helix chain 'd' and resid 109 through 120 removed outlier: 3.886A pdb=" N LYS d 120 " --> pdb=" O LEU d 116 " (cutoff:3.500A) Processing helix chain 'd' and resid 145 through 150 removed outlier: 4.629A pdb=" N LYS d 149 " --> pdb=" O ARG d 145 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N LYS d 150 " --> pdb=" O GLU d 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 145 through 150' Processing helix chain 'd' and resid 151 through 162 removed outlier: 6.186A pdb=" N LYS d 155 " --> pdb=" O GLN d 151 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLU d 162 " --> pdb=" O LEU d 158 " (cutoff:3.500A) Processing helix chain 'd' and resid 186 through 191 removed outlier: 4.246A pdb=" N LEU d 190 " --> pdb=" O GLU d 186 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N SER d 191 " --> pdb=" O ARG d 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 186 through 191' Processing helix chain 'd' and resid 195 through 205 removed outlier: 3.571A pdb=" N ILE d 199 " --> pdb=" O ASN d 195 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 70 removed outlier: 4.062A pdb=" N ARG e 68 " --> pdb=" O GLU e 64 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 118 removed outlier: 6.212A pdb=" N ALA e 112 " --> pdb=" O GLY e 108 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N VAL e 113 " --> pdb=" O ALA e 109 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 146 Processing helix chain 'e' and resid 148 through 157 removed outlier: 4.279A pdb=" N GLY e 157 " --> pdb=" O ALA e 153 " (cutoff:3.500A) Processing helix chain 'e' and resid 159 through 165 Processing helix chain 'f' and resid 11 through 19 removed outlier: 6.494A pdb=" N GLU f 16 " --> pdb=" O PRO f 12 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLN f 17 " --> pdb=" O ASP f 13 " (cutoff:3.500A) Proline residue: f 19 - end of helix Processing helix chain 'f' and resid 20 through 33 Processing helix chain 'f' and resid 67 through 81 Processing helix chain 'g' and resid 19 through 30 Processing helix chain 'g' and resid 34 through 54 Processing helix chain 'g' and resid 56 through 69 Processing helix chain 'g' and resid 91 through 111 removed outlier: 4.158A pdb=" N ARG g 110 " --> pdb=" O ALA g 106 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N GLY g 111 " --> pdb=" O ALA g 107 " (cutoff:3.500A) Processing helix chain 'g' and resid 114 through 129 Processing helix chain 'g' and resid 131 through 148 removed outlier: 4.642A pdb=" N GLU g 145 " --> pdb=" O HIS g 141 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LYS g 148 " --> pdb=" O ALA g 144 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 20 Processing helix chain 'h' and resid 29 through 43 Processing helix chain 'h' and resid 111 through 119 Processing helix chain 'i' and resid 33 through 38 Processing helix chain 'i' and resid 40 through 55 Proline residue: i 50 - end of helix Processing helix chain 'i' and resid 70 through 90 removed outlier: 4.655A pdb=" N ASP i 90 " --> pdb=" O LEU i 86 " (cutoff:3.500A) Processing helix chain 'i' and resid 93 through 101 removed outlier: 4.261A pdb=" N LYS i 99 " --> pdb=" O SER i 95 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ALA i 100 " --> pdb=" O GLU i 96 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 32 removed outlier: 3.977A pdb=" N LYS j 30 " --> pdb=" O VAL j 26 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ARG j 31 " --> pdb=" O GLU j 27 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N THR j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 removed outlier: 6.583A pdb=" N VAL j 84 " --> pdb=" O THR j 80 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ASP j 85 " --> pdb=" O GLU j 81 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA j 86 " --> pdb=" O LYS j 82 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG j 89 " --> pdb=" O ASP j 85 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LEU j 90 " --> pdb=" O ALA j 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 50 removed outlier: 3.862A pdb=" N GLY k 50 " --> pdb=" O ALA k 46 " (cutoff:3.500A) Processing helix chain 'k' and resid 58 through 74 removed outlier: 4.740A pdb=" N ALA k 72 " --> pdb=" O ARG k 68 " (cutoff:3.500A) Processing helix chain 'k' and resid 91 through 103 removed outlier: 4.901A pdb=" N THR k 95 " --> pdb=" O GLY k 91 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ILE k 96 " --> pdb=" O ARG k 92 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY k 103 " --> pdb=" O LEU k 99 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 10 Proline residue: l 10 - end of helix Processing helix chain 'l' and resid 112 through 117 removed outlier: 4.840A pdb=" N TYR l 116 " --> pdb=" O ALA l 112 " (cutoff:3.500A) Processing helix chain 'm' and resid 13 through 21 removed outlier: 4.229A pdb=" N SER m 20 " --> pdb=" O ILE m 16 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ILE m 21 " --> pdb=" O ALA m 17 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 37 Processing helix chain 'm' and resid 48 through 63 removed outlier: 3.817A pdb=" N LYS m 61 " --> pdb=" O ASP m 57 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL m 63 " --> pdb=" O VAL m 59 " (cutoff:3.500A) Processing helix chain 'm' and resid 65 through 83 Processing helix chain 'm' and resid 84 through 93 Processing helix chain 'm' and resid 105 through 110 Processing helix chain 'n' and resid 2 through 20 Processing helix chain 'n' and resid 21 through 32 removed outlier: 4.205A pdb=" N GLU n 25 " --> pdb=" O ALA n 21 " (cutoff:3.500A) Processing helix chain 'n' and resid 38 through 52 removed outlier: 4.389A pdb=" N TRP n 42 " --> pdb=" O ASP n 38 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU n 46 " --> pdb=" O TRP n 42 " (cutoff:3.500A) Proline residue: n 52 - end of helix Processing helix chain 'n' and resid 80 through 91 Processing helix chain 'o' and resid 3 through 15 Processing helix chain 'o' and resid 23 through 43 removed outlier: 4.724A pdb=" N GLY o 40 " --> pdb=" O ASN o 36 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N HIS o 41 " --> pdb=" O HIS o 37 " (cutoff:3.500A) Processing helix chain 'o' and resid 48 through 73 removed outlier: 4.822A pdb=" N GLY o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) Processing helix chain 'o' and resid 74 through 85 Processing helix chain 'p' and resid 46 through 51 removed outlier: 5.737A pdb=" N THR p 50 " --> pdb=" O LYS p 46 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ARG p 51 " --> pdb=" O GLU p 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 46 through 51' Processing helix chain 'p' and resid 53 through 64 Processing helix chain 'p' and resid 68 through 80 removed outlier: 4.813A pdb=" N LYS p 80 " --> pdb=" O LYS p 76 " (cutoff:3.500A) Processing helix chain 'r' and resid 10 through 16 removed outlier: 4.895A pdb=" N GLU r 15 " --> pdb=" O ARG r 11 " (cutoff:3.500A) Processing helix chain 'r' and resid 24 through 33 removed outlier: 4.075A pdb=" N ASN r 30 " --> pdb=" O ALA r 26 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N TYR r 31 " --> pdb=" O THR r 27 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE r 32 " --> pdb=" O LEU r 28 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N THR r 33 " --> pdb=" O LYS r 29 " (cutoff:3.500A) Processing helix chain 'r' and resid 40 through 45 Processing helix chain 'r' and resid 47 through 65 Processing helix chain 's' and resid 11 through 24 Processing helix chain 't' and resid 5 through 41 removed outlier: 3.850A pdb=" N ARG t 9 " --> pdb=" O SER t 5 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY t 41 " --> pdb=" O ALA t 37 " (cutoff:3.500A) Processing helix chain 't' and resid 43 through 62 Proline residue: t 55 - end of helix Processing helix chain 't' and resid 67 through 86 removed outlier: 3.975A pdb=" N ALA t 86 " --> pdb=" O ILE t 82 " (cutoff:3.500A) Processing helix chain 'u' and resid 10 through 26 removed outlier: 5.821A pdb=" N ALA u 14 " --> pdb=" O PRO u 10 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU u 15 " --> pdb=" O PHE u 11 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU u 23 " --> pdb=" O LYS u 19 " (cutoff:3.500A) Processing helix chain 'u' and resid 27 through 35 Processing helix chain 'u' and resid 39 through 56 removed outlier: 4.984A pdb=" N ALA u 56 " --> pdb=" O VAL u 52 " (cutoff:3.500A) Processing helix chain 'u' and resid 57 through 62 removed outlier: 3.749A pdb=" N ARG u 61 " --> pdb=" O LYS u 58 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU u 62 " --> pdb=" O LEU u 59 " (cutoff:3.500A) Processing helix chain 'x' and resid 21 through 34 Processing helix chain 'x' and resid 52 through 59 removed outlier: 6.081A pdb=" N GLN x 56 " --> pdb=" O MET x 52 " (cutoff:3.500A) Processing helix chain 'x' and resid 94 through 106 removed outlier: 3.629A pdb=" N VAL x 98 " --> pdb=" O PHE x 94 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ASP x 106 " --> pdb=" O MET x 102 " (cutoff:3.500A) Processing helix chain 'x' and resid 119 through 133 removed outlier: 4.603A pdb=" N TYR x 132 " --> pdb=" O GLN x 128 " (cutoff:3.500A) Processing helix chain 'x' and resid 149 through 160 removed outlier: 4.439A pdb=" N VAL x 153 " --> pdb=" O ASN x 149 " (cutoff:3.500A) Processing helix chain 'x' and resid 207 through 230 removed outlier: 4.821A pdb=" N GLU x 212 " --> pdb=" O ALA x 208 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU x 213 " --> pdb=" O ASP x 209 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA x 228 " --> pdb=" O SER x 224 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N SER x 229 " --> pdb=" O ALA x 225 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLU x 230 " --> pdb=" O ALA x 226 " (cutoff:3.500A) Processing helix chain 'x' and resid 231 through 239 removed outlier: 4.137A pdb=" N LYS x 235 " --> pdb=" O GLU x 231 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR x 236 " --> pdb=" O LEU x 232 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY x 239 " --> pdb=" O LYS x 235 " (cutoff:3.500A) Processing helix chain 'x' and resid 243 through 258 Processing helix chain 'x' and resid 273 through 284 Processing helix chain 'x' and resid 287 through 292 Proline residue: x 292 - end of helix Processing helix chain 'x' and resid 426 through 442 removed outlier: 4.004A pdb=" N ALA x 433 " --> pdb=" O LYS x 429 " (cutoff:3.500A) Proline residue: x 442 - end of helix Processing helix chain 'x' and resid 461 through 475 Processing helix chain 'x' and resid 547 through 563 removed outlier: 5.154A pdb=" N ALA x 551 " --> pdb=" O GLU x 547 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU x 558 " --> pdb=" O LYS x 554 " (cutoff:3.500A) Processing helix chain 'x' and resid 588 through 608 removed outlier: 3.755A pdb=" N LYS x 605 " --> pdb=" O LYS x 601 " (cutoff:3.500A) Processing helix chain 'x' and resid 623 through 638 removed outlier: 3.787A pdb=" N THR x 627 " --> pdb=" O PRO x 623 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLY x 628 " --> pdb=" O GLU x 624 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ASP x 629 " --> pdb=" O GLU x 625 " (cutoff:3.500A) Processing helix chain 'x' and resid 658 through 663 removed outlier: 4.590A pdb=" N PHE x 663 " --> pdb=" O LEU x 659 " (cutoff:3.500A) Processing helix chain 'x' and resid 664 through 674 removed outlier: 3.938A pdb=" N GLN x 668 " --> pdb=" O GLY x 664 " (cutoff:3.500A) Processing helix chain 'x' and resid 695 through 701 Processing sheet with id= 1, first strand: chain '0' and resid 28 through 31 removed outlier: 4.239A pdb=" N GLU 0 35 " --> pdb=" O ASP 0 30 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '1' and resid 7 through 11 Processing sheet with id= 3, first strand: chain '1' and resid 33 through 38 removed outlier: 6.505A pdb=" N LEU 1 33 " --> pdb=" O GLU 1 50 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU 1 50 " --> pdb=" O LEU 1 33 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU 1 35 " --> pdb=" O TYR 1 48 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '3' and resid 21 through 24 removed outlier: 5.520A pdb=" N PHE 3 21 " --> pdb=" O VAL 3 49 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '5' and resid 24 through 28 removed outlier: 3.594A pdb=" N SER 5 85 " --> pdb=" O ALA 5 25 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL 5 27 " --> pdb=" O ALA 5 83 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 1 through 4 removed outlier: 4.335A pdb=" N ALA C 1 " --> pdb=" O VAL C 19 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL C 3 " --> pdb=" O LYS C 17 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 74 through 77 removed outlier: 3.667A pdb=" N VAL C 77 " --> pdb=" O ASP C 113 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ASP C 113 " --> pdb=" O VAL C 77 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'C' and resid 89 through 94 removed outlier: 5.281A pdb=" N ASN C 89 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE C 103 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL C 93 " --> pdb=" O ARG C 101 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'C' and resid 161 through 164 removed outlier: 6.991A pdb=" N THR C 172 " --> pdb=" O VAL C 164 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.587A pdb=" N LEU D 201 " --> pdb=" O GLY D 6 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL D 172 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N GLU D 168 " --> pdb=" O SER D 113 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'D' and resid 10 through 16 removed outlier: 4.152A pdb=" N GLY D 10 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE D 22 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'D' and resid 36 through 40 removed outlier: 3.748A pdb=" N GLN D 36 " --> pdb=" O GLN D 49 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA D 47 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU D 40 " --> pdb=" O TYR D 45 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TYR D 45 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN D 94 " --> pdb=" O VAL D 34 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'D' and resid 46 through 51 removed outlier: 5.938A pdb=" N ARG D 46 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'D' and resid 105 through 108 removed outlier: 6.038A pdb=" N LYS D 105 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'E' and resid 2 through 5 removed outlier: 5.122A pdb=" N SER E 10 " --> pdb=" O LEU E 5 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'E' and resid 117 through 120 removed outlier: 5.869A pdb=" N ARG E 117 " --> pdb=" O ASP E 184 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N MET E 188 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS E 185 " --> pdb=" O ASP E 145 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL E 146 " --> pdb=" O LYS E 166 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP E 168 " --> pdb=" O VAL E 146 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'F' and resid 64 through 68 removed outlier: 5.848A pdb=" N GLY F 38 " --> pdb=" O GLY F 150 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N GLY F 150 " --> pdb=" O GLY F 38 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'G' and resid 15 through 18 Processing sheet with id= 19, first strand: chain 'G' and resid 40 through 44 Processing sheet with id= 20, first strand: chain 'G' and resid 81 through 88 removed outlier: 3.691A pdb=" N PHE G 82 " --> pdb=" O GLY G 134 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N THR G 128 " --> pdb=" O LEU G 88 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU G 123 " --> pdb=" O VAL G 131 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.709A pdb=" N LEU H 6 " --> pdb=" O LYS H 35 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LYS H 35 " --> pdb=" O LEU H 6 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'H' and resid 77 through 82 removed outlier: 4.055A pdb=" N VAL H 147 " --> pdb=" O ILE H 80 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N SER H 82 " --> pdb=" O VAL H 147 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'H' and resid 114 through 117 removed outlier: 4.739A pdb=" N GLU H 114 " --> pdb=" O GLN H 133 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'K' and resid 5 through 9 removed outlier: 4.148A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'K' and resid 39 through 42 Processing sheet with id= 26, first strand: chain 'K' and resid 68 through 71 removed outlier: 4.123A pdb=" N VAL K 69 " --> pdb=" O ILE K 77 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'M' and resid 37 through 40 removed outlier: 3.584A pdb=" N TYR M 91 " --> pdb=" O ILE M 73 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'M' and resid 62 through 65 removed outlier: 3.557A pdb=" N GLU M 104 " --> pdb=" O TRP M 64 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE M 31 " --> pdb=" O MET M 105 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LYS M 100 " --> pdb=" O ALA M 35 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'M' and resid 30 through 36 removed outlier: 7.657A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'O' and resid 35 through 41 removed outlier: 3.563A pdb=" N VAL O 28 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'P' and resid 48 through 52 removed outlier: 3.976A pdb=" N ALA P 48 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ARG P 52 " --> pdb=" O HIS P 55 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS P 55 " --> pdb=" O ARG P 52 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N THR P 59 " --> pdb=" O ILE P 47 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL P 45 " --> pdb=" O ARG P 61 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER P 82 " --> pdb=" O LYS P 28 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'P' and resid 57 through 64 removed outlier: 4.045A pdb=" N GLU P 67 " --> pdb=" O SER P 64 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'R' and resid 11 through 15 removed outlier: 6.167A pdb=" N TYR R 2 " --> pdb=" O ALA R 42 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE R 41 " --> pdb=" O LYS R 48 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ASN R 43 " --> pdb=" O GLU R 46 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'R' and resid 18 through 23 removed outlier: 4.138A pdb=" N GLN R 18 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL R 20 " --> pdb=" O VAL R 96 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL R 96 " --> pdb=" O VAL R 20 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU R 22 " --> pdb=" O THR R 94 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU R 62 " --> pdb=" O LYS R 97 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N GLU R 31 " --> pdb=" O VAL R 63 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'R' and resid 57 through 60 Processing sheet with id= 36, first strand: chain 'R' and resid 65 through 68 removed outlier: 3.978A pdb=" N ALA R 65 " --> pdb=" O ASP R 95 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'R' and resid 71 through 78 removed outlier: 3.540A pdb=" N LYS R 76 " --> pdb=" O LYS R 85 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'S' and resid 2 through 8 Processing sheet with id= 39, first strand: chain 'T' and resid 12 through 15 removed outlier: 3.518A pdb=" N ALA T 13 " --> pdb=" O LYS T 33 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS T 15 " --> pdb=" O VAL T 31 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL T 31 " --> pdb=" O HIS T 15 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ASN T 28 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU T 32 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA T 83 " --> pdb=" O LEU T 32 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS T 70 " --> pdb=" O ARG T 73 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS T 68 " --> pdb=" O GLY T 75 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'U' and resid 39 through 43 removed outlier: 4.926A pdb=" N ASN U 39 " --> pdb=" O ALA U 62 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL U 41 " --> pdb=" O LYS U 60 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL U 58 " --> pdb=" O LYS U 43 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'V' and resid 69 through 72 removed outlier: 3.802A pdb=" N THR V 62 " --> pdb=" O PHE V 2 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA V 6 " --> pdb=" O VAL V 64 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE V 29 " --> pdb=" O ILE V 89 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'W' and resid 30 through 33 removed outlier: 4.070A pdb=" N SER W 31 " --> pdb=" O ALA W 57 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU W 55 " --> pdb=" O ILE W 33 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N THR W 54 " --> pdb=" O GLY W 50 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N PHE W 56 " --> pdb=" O GLY W 48 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'W' and resid 62 through 67 removed outlier: 3.700A pdb=" N LYS W 62 " --> pdb=" O GLU W 79 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'X' and resid 11 through 18 removed outlier: 3.849A pdb=" N VAL X 12 " --> pdb=" O PHE X 28 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY X 14 " --> pdb=" O ARG X 26 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR X 24 " --> pdb=" O ASN X 16 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER X 18 " --> pdb=" O ASN X 22 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ASN X 22 " --> pdb=" O SER X 18 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'X' and resid 34 through 40 removed outlier: 3.643A pdb=" N ARG X 44 " --> pdb=" O VAL X 39 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'Z' and resid 33 through 38 removed outlier: 5.080A pdb=" N HIS Z 33 " --> pdb=" O GLN Z 8 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N MET Z 53 " --> pdb=" O THR Z 9 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'b' and resid 89 through 92 removed outlier: 4.183A pdb=" N LEU b 67 " --> pdb=" O ALA b 159 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU b 160 " --> pdb=" O PRO b 181 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'c' and resid 18 through 21 removed outlier: 6.010A pdb=" N ASN c 18 " --> pdb=" O ILE c 54 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE c 56 " --> pdb=" O ASN c 18 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG c 58 " --> pdb=" O THR c 20 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE c 67 " --> pdb=" O ASN c 101 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA c 103 " --> pdb=" O ILE c 67 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'c' and resid 163 through 169 removed outlier: 3.873A pdb=" N GLY c 147 " --> pdb=" O PHE c 202 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS c 149 " --> pdb=" O TRP c 200 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'd' and resid 140 through 144 removed outlier: 4.242A pdb=" N ASP d 140 " --> pdb=" O PHE d 181 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLY d 179 " --> pdb=" O VAL d 142 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N MET d 177 " --> pdb=" O ILE d 144 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'e' and resid 10 through 15 removed outlier: 6.533A pdb=" N LEU e 35 " --> pdb=" O ILE e 15 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'e' and resid 82 through 87 removed outlier: 7.552A pdb=" N HIS e 82 " --> pdb=" O PRO e 97 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N VAL e 93 " --> pdb=" O GLY e 86 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA e 98 " --> pdb=" O ASN e 121 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASN e 121 " --> pdb=" O ALA e 98 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'e' and resid 32 through 39 removed outlier: 3.831A pdb=" N ALA e 34 " --> pdb=" O GLY e 50 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLY e 50 " --> pdb=" O ALA e 34 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'f' and resid 38 through 43 removed outlier: 4.947A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N HIS f 58 " --> pdb=" O VAL f 10 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET f 9 " --> pdb=" O ARG f 86 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ARG f 86 " --> pdb=" O MET f 9 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'f' and resid 44 through 47 removed outlier: 5.904A pdb=" N LEU f 47 " --> pdb=" O HIS f 55 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N HIS f 55 " --> pdb=" O LEU f 47 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'g' and resid 72 through 76 Processing sheet with id= 57, first strand: chain 'h' and resid 22 through 27 removed outlier: 6.495A pdb=" N ALA h 22 " --> pdb=" O LEU h 62 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU h 60 " --> pdb=" O VAL h 24 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'h' and resid 73 through 76 removed outlier: 5.541A pdb=" N SER h 73 " --> pdb=" O ALA h 129 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS h 126 " --> pdb=" O VAL h 102 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL h 102 " --> pdb=" O ILE h 125 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'i' and resid 4 through 10 removed outlier: 4.459A pdb=" N GLY i 9 " --> pdb=" O ALA i 16 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'j' and resid 39 through 42 removed outlier: 4.822A pdb=" N LEU j 42 " --> pdb=" O LEU j 71 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LEU j 71 " --> pdb=" O LEU j 42 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE j 8 " --> pdb=" O VAL j 74 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS j 11 " --> pdb=" O ASP j 97 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'j' and resid 44 through 52 removed outlier: 3.534A pdb=" N ARG j 45 " --> pdb=" O THR j 69 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU j 47 " --> pdb=" O ILE j 67 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL j 51 " --> pdb=" O ASP j 63 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'k' and resid 13 through 16 No H-bonds generated for sheet with id= 62 Processing sheet with id= 63, first strand: chain 'k' and resid 29 through 34 removed outlier: 4.049A pdb=" N THR k 32 " --> pdb=" O HIS k 21 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU k 82 " --> pdb=" O GLY k 18 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET k 84 " --> pdb=" O ALA k 20 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE k 22 " --> pdb=" O MET k 84 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASN k 108 " --> pdb=" O LEU k 81 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N GLY k 87 " --> pdb=" O VAL k 112 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'l' and resid 28 through 32 removed outlier: 3.624A pdb=" N ILE l 79 " --> pdb=" O GLY l 31 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'l' and resid 34 through 40 removed outlier: 3.823A pdb=" N ARG l 35 " --> pdb=" O ARG l 53 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG l 53 " --> pdb=" O ARG l 35 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N LYS l 50 " --> pdb=" O ILE l 66 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE l 66 " --> pdb=" O LYS l 50 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N PHE l 60 " --> pdb=" O LEU l 56 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'p' and resid 4 through 11 removed outlier: 5.748A pdb=" N GLN p 18 " --> pdb=" O ALA p 7 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLY p 37 " --> pdb=" O VAL p 19 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'q' and resid 6 through 10 removed outlier: 6.670A pdb=" N GLU q 59 " --> pdb=" O VAL q 75 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'q' and resid 18 through 29 No H-bonds generated for sheet with id= 68 Processing sheet with id= 69, first strand: chain 'q' and resid 55 through 58 No H-bonds generated for sheet with id= 69 Processing sheet with id= 70, first strand: chain 's' and resid 29 through 32 removed outlier: 4.138A pdb=" N LEU s 30 " --> pdb=" O THR s 47 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU s 46 " --> pdb=" O VAL s 61 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'x' and resid 63 through 70 removed outlier: 7.170A pdb=" N THR x 63 " --> pdb=" O PRO x 89 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA x 65 " --> pdb=" O ASP x 87 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASP x 87 " --> pdb=" O ALA x 65 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE x 83 " --> pdb=" O ALA x 69 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ALA x 16 " --> pdb=" O THR x 88 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER x 15 " --> pdb=" O VAL x 109 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ARG x 136 " --> pdb=" O ILE x 260 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU x 262 " --> pdb=" O ARG x 136 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N CYS x 265 " --> pdb=" O LEU x 168 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'x' and resid 169 through 172 removed outlier: 3.841A pdb=" N GLY x 180 " --> pdb=" O ILE x 172 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LYS x 188 " --> pdb=" O ASP x 183 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASN x 191 " --> pdb=" O GLU x 202 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLU x 202 " --> pdb=" O ASN x 191 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'x' and resid 293 through 297 removed outlier: 3.616A pdb=" N ILE x 294 " --> pdb=" O ARG x 308 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG x 308 " --> pdb=" O ILE x 294 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'x' and resid 316 through 321 removed outlier: 7.267A pdb=" N PHE x 316 " --> pdb=" O ASP x 398 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'x' and resid 322 through 326 removed outlier: 3.867A pdb=" N LYS x 322 " --> pdb=" O PHE x 334 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP x 326 " --> pdb=" O GLY x 330 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL x 337 " --> pdb=" O ASP x 380 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASP x 380 " --> pdb=" O VAL x 337 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG x 361 " --> pdb=" O ILE x 385 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'x' and resid 340 through 343 removed outlier: 6.863A pdb=" N GLY x 340 " --> pdb=" O ALA x 378 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'x' and resid 347 through 350 Processing sheet with id= 78, first strand: chain 'x' and resid 444 through 449 removed outlier: 5.097A pdb=" N GLN x 454 " --> pdb=" O ASP x 449 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N THR x 455 " --> pdb=" O VAL x 419 " (cutoff:3.500A) removed outlier: 9.854A pdb=" N SER x 416 " --> pdb=" O PRO x 485 " (cutoff:3.500A) removed outlier: 37.174A pdb=" N ALA x 480 " --> pdb=" O THR x 622 " (cutoff:3.500A) removed outlier: 32.573A pdb=" N THR x 622 " --> pdb=" O ALA x 480 " (cutoff:3.500A) removed outlier: 30.734A pdb=" N VAL x 482 " --> pdb=" O VAL x 620 " (cutoff:3.500A) removed outlier: 27.653A pdb=" N VAL x 620 " --> pdb=" O VAL x 482 " (cutoff:3.500A) removed outlier: 23.250A pdb=" N LYS x 484 " --> pdb=" O VAL x 618 " (cutoff:3.500A) removed outlier: 20.589A pdb=" N VAL x 618 " --> pdb=" O LYS x 484 " (cutoff:3.500A) removed outlier: 16.812A pdb=" N GLN x 486 " --> pdb=" O MET x 616 " (cutoff:3.500A) removed outlier: 12.287A pdb=" N MET x 616 " --> pdb=" O GLN x 486 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ALA x 488 " --> pdb=" O PRO x 614 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR x 622 " --> pdb=" O VAL x 651 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LYS x 652 " --> pdb=" O GLN x 644 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN x 644 " --> pdb=" O LYS x 652 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N HIS x 654 " --> pdb=" O LYS x 642 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'x' and resid 497 through 501 removed outlier: 3.674A pdb=" N THR x 498 " --> pdb=" O MET x 521 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N HIS x 516 " --> pdb=" O GLY x 580 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY x 580 " --> pdb=" O HIS x 516 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL x 518 " --> pdb=" O HIS x 578 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR x 522 " --> pdb=" O GLY x 574 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU x 524 " --> pdb=" O ASP x 572 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ASP x 572 " --> pdb=" O LEU x 524 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'x' and resid 616 through 622 Processing sheet with id= 81, first strand: chain 'x' and resid 612 through 616 No H-bonds generated for sheet with id= 81 2010 hydrogen bonds defined for protein. 5928 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3955 hydrogen bonds 6222 hydrogen bond angles 0 basepair planarities 1570 basepair parallelities 2308 stacking parallelities Total time for adding SS restraints: 248.47 Time building geometry restraints manager: 76.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 13048 1.30 - 1.43: 73570 1.43 - 1.56: 69212 1.56 - 1.69: 9448 1.69 - 1.83: 308 Bond restraints: 165586 Sorted by residual: bond pdb=" C2' 3TD A1915 " pdb=" C1' 3TD A1915 " ideal model delta sigma weight residual 1.529 1.284 0.245 1.50e-02 4.44e+03 2.67e+02 bond pdb=" C4 5MU w 54 " pdb=" C5 5MU w 54 " ideal model delta sigma weight residual 1.802 1.482 0.320 2.00e-02 2.50e+03 2.57e+02 bond pdb=" O4' 3TD A1915 " pdb=" C1' 3TD A1915 " ideal model delta sigma weight residual 1.412 1.644 -0.232 1.50e-02 4.44e+03 2.38e+02 bond pdb=" N1 5MU w 54 " pdb=" C6 5MU w 54 " ideal model delta sigma weight residual 1.635 1.333 0.302 2.00e-02 2.50e+03 2.28e+02 bond pdb=" C5 5MU v 54 " pdb=" C6 5MU v 54 " ideal model delta sigma weight residual 1.155 1.441 -0.286 2.00e-02 2.50e+03 2.05e+02 ... (remaining 165581 not shown) Histogram of bond angle deviations from ideal: 67.16 - 81.94: 4 81.94 - 96.72: 14 96.72 - 111.49: 106458 111.49 - 126.27: 125902 126.27 - 141.05: 14677 Bond angle restraints: 247055 Sorted by residual: angle pdb=" O3' G A2029 " pdb=" P 6MZ A2030 " pdb=" O5' 6MZ A2030 " ideal model delta sigma weight residual 104.00 135.16 -31.16 1.50e+00 4.44e-01 4.32e+02 angle pdb=" OP1 3TD A1915 " pdb=" P 3TD A1915 " pdb=" O9 3TD A1915 " ideal model delta sigma weight residual 109.46 67.16 42.30 3.00e+00 1.11e-01 1.99e+02 angle pdb=" C3' G A2029 " pdb=" O3' G A2029 " pdb=" P 6MZ A2030 " ideal model delta sigma weight residual 120.20 141.05 -20.85 1.50e+00 4.44e-01 1.93e+02 angle pdb=" O3' MIA w 37 " pdb=" C3' MIA w 37 " pdb=" C2' MIA w 37 " ideal model delta sigma weight residual 113.70 92.88 20.82 1.50e+00 4.44e-01 1.93e+02 angle pdb=" O3' 6MZ A2030 " pdb=" P A A2031 " pdb=" OP1 A A2031 " ideal model delta sigma weight residual 108.00 68.87 39.13 3.00e+00 1.11e-01 1.70e+02 ... (remaining 247050 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 92528 35.78 - 71.56: 11744 71.56 - 107.34: 1396 107.34 - 143.12: 34 143.12 - 178.90: 49 Dihedral angle restraints: 105751 sinusoidal: 86791 harmonic: 18960 Sorted by residual: dihedral pdb=" C5' G A 481 " pdb=" C4' G A 481 " pdb=" C3' G A 481 " pdb=" O3' G A 481 " ideal model delta sinusoidal sigma weight residual 147.00 72.83 74.17 1 8.00e+00 1.56e-02 1.09e+02 dihedral pdb=" C5' U z 2 " pdb=" C4' U z 2 " pdb=" C3' U z 2 " pdb=" O3' U z 2 " ideal model delta sinusoidal sigma weight residual 82.00 152.09 -70.09 1 8.00e+00 1.56e-02 9.89e+01 dihedral pdb=" C5' C A1730 " pdb=" C4' C A1730 " pdb=" C3' C A1730 " pdb=" O3' C A1730 " ideal model delta sinusoidal sigma weight residual 147.00 80.63 66.37 1 8.00e+00 1.56e-02 8.99e+01 ... (remaining 105748 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.178: 31190 0.178 - 0.355: 195 0.355 - 0.533: 13 0.533 - 0.710: 1 0.710 - 0.888: 1 Chirality restraints: 31400 Sorted by residual: chirality pdb=" C3' C A1914 " pdb=" C4' C A1914 " pdb=" O3' C A1914 " pdb=" C2' C A1914 " both_signs ideal model delta sigma weight residual False -2.48 -1.59 -0.89 2.00e-01 2.50e+01 1.97e+01 chirality pdb=" C2' 3TD A1915 " pdb=" C3' 3TD A1915 " pdb=" O2' 3TD A1915 " pdb=" C1' 3TD A1915 " both_signs ideal model delta sigma weight residual False -2.75 -2.11 -0.64 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" C3' G z 3 " pdb=" C4' G z 3 " pdb=" O3' G z 3 " pdb=" C2' G z 3 " both_signs ideal model delta sigma weight residual False -2.48 -2.99 0.52 2.00e-01 2.50e+01 6.63e+00 ... (remaining 31397 not shown) Planarity restraints: 13806 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a1516 " 0.068 2.00e-02 2.50e+03 6.31e-01 8.96e+03 pdb=" C4' 2MG a1516 " 0.464 2.00e-02 2.50e+03 pdb=" O4' 2MG a1516 " 0.742 2.00e-02 2.50e+03 pdb=" C3' 2MG a1516 " -0.596 2.00e-02 2.50e+03 pdb=" O3' 2MG a1516 " -0.656 2.00e-02 2.50e+03 pdb=" C2' 2MG a1516 " -0.191 2.00e-02 2.50e+03 pdb=" O2' 2MG a1516 " 0.978 2.00e-02 2.50e+03 pdb=" C1' 2MG a1516 " 0.190 2.00e-02 2.50e+03 pdb=" N9 2MG a1516 " -1.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MU A1939 " -0.951 2.00e-02 2.50e+03 6.14e-01 8.49e+03 pdb=" C4' 5MU A1939 " 0.179 2.00e-02 2.50e+03 pdb=" O4' 5MU A1939 " 0.861 2.00e-02 2.50e+03 pdb=" C3' 5MU A1939 " -0.258 2.00e-02 2.50e+03 pdb=" O3' 5MU A1939 " 0.853 2.00e-02 2.50e+03 pdb=" C2' 5MU A1939 " -0.612 2.00e-02 2.50e+03 pdb=" O2' 5MU A1939 " -0.574 2.00e-02 2.50e+03 pdb=" C1' 5MU A1939 " 0.467 2.00e-02 2.50e+03 pdb=" N1 5MU A1939 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC A2498 " -0.057 2.00e-02 2.50e+03 5.99e-01 8.07e+03 pdb=" C4' OMC A2498 " 0.469 2.00e-02 2.50e+03 pdb=" O4' OMC A2498 " 0.726 2.00e-02 2.50e+03 pdb=" C3' OMC A2498 " -0.587 2.00e-02 2.50e+03 pdb=" O3' OMC A2498 " -0.565 2.00e-02 2.50e+03 pdb=" C2' OMC A2498 " -0.209 2.00e-02 2.50e+03 pdb=" O2' OMC A2498 " 0.916 2.00e-02 2.50e+03 pdb=" C1' OMC A2498 " 0.242 2.00e-02 2.50e+03 pdb=" N1 OMC A2498 " -0.934 2.00e-02 2.50e+03 ... (remaining 13803 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.06: 25 2.06 - 2.77: 32212 2.77 - 3.48: 225723 3.48 - 4.19: 483255 4.19 - 4.90: 663003 Nonbonded interactions: 1404218 Sorted by model distance: nonbonded pdb=" O3' A w 76 " pdb=" C PHE y 102 " model vdw 1.344 3.270 nonbonded pdb=" C5' U z 2 " pdb=" C6 U z 2 " model vdw 1.478 3.740 nonbonded pdb=" OP1 A a1500 " pdb=" OP1 A a1508 " model vdw 1.708 3.040 nonbonded pdb=" OP1 C A 948 " pdb=" OP1 G A 962 " model vdw 1.715 3.040 nonbonded pdb=" OP2 C a1054 " pdb=" OP1 A a1197 " model vdw 1.736 3.040 ... (remaining 1404213 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 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: 0.150 Extract box with map and model: 11.320 Check model and map are aligned: 1.660 Set scattering table: 1.000 Process input model: 567.140 Find NCS groups from input model: 3.120 Set up NCS constraints: 0.410 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: 0.030 Load rotamer database and sin/cos tables:2.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 589.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.320 165586 Z= 0.463 Angle : 0.938 42.295 247055 Z= 0.502 Chirality : 0.048 0.888 31400 Planarity : 0.019 0.631 13806 Dihedral : 24.061 178.904 93505 Min Nonbonded Distance : 1.344 Molprobity Statistics. All-atom Clashscore : 23.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.54 % Favored : 86.29 % Rotamer: Outliers : 0.46 % Allowed : 9.36 % Favored : 90.18 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.51 (0.08), residues: 6551 helix: -2.27 (0.09), residues: 2170 sheet: -3.13 (0.14), residues: 1021 loop : -3.51 (0.08), residues: 3360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP C 212 HIS 0.012 0.002 HIS b 169 PHE 0.042 0.002 PHE y 102 TYR 0.020 0.002 TYR H 25 ARG 0.011 0.001 ARG i 123 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13102 Ramachandran restraints generated. 6551 Oldfield, 0 Emsley, 6551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13102 Ramachandran restraints generated. 6551 Oldfield, 0 Emsley, 6551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2113 residues out of total 5431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 2089 time to evaluate : 5.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 22 MET cc_start: 0.7824 (mmm) cc_final: 0.7333 (tpt) REVERT: C 131 MET cc_start: 0.6931 (mtm) cc_final: 0.6333 (mtm) REVERT: C 212 TRP cc_start: 0.7864 (p90) cc_final: 0.6939 (p90) REVERT: C 250 GLN cc_start: 0.8822 (tm-30) cc_final: 0.8604 (tm-30) REVERT: D 112 THR cc_start: 0.9022 (m) cc_final: 0.8701 (p) REVERT: E 90 GLN cc_start: 0.6945 (mt0) cc_final: 0.6669 (mt0) REVERT: E 185 LYS cc_start: 0.8037 (mmtp) cc_final: 0.7664 (mttt) REVERT: F 15 LEU cc_start: 0.8337 (mt) cc_final: 0.8101 (mt) REVERT: F 32 LYS cc_start: 0.8765 (pttt) cc_final: 0.8087 (ptpt) REVERT: F 95 MET cc_start: 0.6357 (ttp) cc_final: 0.5159 (tmm) REVERT: G 121 THR cc_start: 0.6349 (m) cc_final: 0.5935 (m) REVERT: J 119 PHE cc_start: 0.7808 (t80) cc_final: 0.7540 (t80) REVERT: K 32 TYR cc_start: 0.7808 (m-10) cc_final: 0.7581 (m-10) REVERT: L 128 THR cc_start: 0.8490 (p) cc_final: 0.8114 (p) REVERT: M 9 PHE cc_start: 0.5978 (m-80) cc_final: 0.5312 (m-80) REVERT: O 19 GLN cc_start: 0.7877 (tt0) cc_final: 0.7583 (tm-30) REVERT: P 9 GLN cc_start: 0.7098 (mm110) cc_final: 0.6581 (mm110) REVERT: P 39 LEU cc_start: 0.7501 (tt) cc_final: 0.7292 (tt) REVERT: P 81 ASP cc_start: 0.7951 (t70) cc_final: 0.7718 (t0) REVERT: P 112 ARG cc_start: 0.6768 (ttp-110) cc_final: 0.6173 (ttp-170) REVERT: Q 64 ILE cc_start: 0.9037 (mt) cc_final: 0.8813 (tt) REVERT: R 74 ILE cc_start: 0.8605 (mt) cc_final: 0.8403 (mt) REVERT: R 93 PHE cc_start: 0.8405 (p90) cc_final: 0.8019 (p90) REVERT: S 40 ASN cc_start: 0.6666 (p0) cc_final: 0.6414 (p0) REVERT: S 75 PHE cc_start: 0.8352 (p90) cc_final: 0.8042 (p90) REVERT: T 29 THR cc_start: 0.8913 (m) cc_final: 0.8500 (p) REVERT: W 13 GLU cc_start: 0.6085 (mm-30) cc_final: 0.5737 (mm-30) REVERT: X 25 LYS cc_start: 0.8668 (mmtt) cc_final: 0.8251 (mttm) REVERT: Y 14 LEU cc_start: 0.8525 (pp) cc_final: 0.8220 (pp) REVERT: Z 48 ASN cc_start: 0.7812 (t0) cc_final: 0.7402 (t0) REVERT: Z 50 VAL cc_start: 0.8890 (m) cc_final: 0.8635 (p) REVERT: b 158 ASP cc_start: 0.6341 (m-30) cc_final: 0.5420 (t0) REVERT: c 67 ILE cc_start: 0.8448 (mp) cc_final: 0.8246 (mt) REVERT: c 183 TYR cc_start: 0.7335 (t80) cc_final: 0.7130 (t80) REVERT: c 206 ILE cc_start: 0.3775 (mm) cc_final: 0.3498 (mm) REVERT: d 40 HIS cc_start: 0.7622 (m-70) cc_final: 0.7074 (m-70) REVERT: d 92 LEU cc_start: 0.8110 (mt) cc_final: 0.7164 (mt) REVERT: d 120 LYS cc_start: 0.8003 (mttt) cc_final: 0.7680 (pttt) REVERT: e 40 ASP cc_start: 0.7730 (p0) cc_final: 0.6689 (t0) REVERT: e 146 MET cc_start: 0.8135 (ttp) cc_final: 0.7783 (ttt) REVERT: f 6 ILE cc_start: 0.8887 (mp) cc_final: 0.8678 (mm) REVERT: g 104 VAL cc_start: 0.8230 (t) cc_final: 0.7953 (t) REVERT: g 108 ARG cc_start: 0.7396 (mtt180) cc_final: 0.6626 (ttt-90) REVERT: g 125 ASP cc_start: 0.4597 (m-30) cc_final: 0.3677 (m-30) REVERT: k 12 ARG cc_start: 0.3445 (ptp-170) cc_final: 0.2423 (mpt180) REVERT: k 14 GLN cc_start: 0.6618 (mm110) cc_final: 0.6258 (pp30) REVERT: m 16 ILE cc_start: 0.6620 (mm) cc_final: 0.6384 (mm) REVERT: o 42 PHE cc_start: 0.7700 (m-80) cc_final: 0.7215 (m-80) REVERT: o 86 LEU cc_start: 0.8225 (mt) cc_final: 0.7898 (tp) REVERT: p 16 PHE cc_start: 0.6775 (t80) cc_final: 0.6509 (t80) REVERT: p 42 ILE cc_start: 0.8110 (pt) cc_final: 0.7811 (mt) REVERT: r 63 TYR cc_start: 0.8264 (t80) cc_final: 0.8048 (t80) REVERT: s 2 ARG cc_start: 0.6737 (tpt-90) cc_final: 0.6447 (ttm-80) REVERT: u 53 LYS cc_start: 0.7901 (mmmm) cc_final: 0.7428 (ttpt) REVERT: x 101 SER cc_start: 0.8768 (m) cc_final: 0.8515 (p) REVERT: x 181 VAL cc_start: 0.7525 (t) cc_final: 0.6445 (t) REVERT: x 323 ILE cc_start: 0.8542 (mm) cc_final: 0.8328 (mt) REVERT: x 460 MET cc_start: 0.5909 (mtp) cc_final: 0.5501 (ttt) REVERT: x 463 LEU cc_start: 0.8949 (tt) cc_final: 0.8688 (tp) REVERT: x 681 MET cc_start: 0.7157 (tmm) cc_final: 0.6740 (tmm) outliers start: 24 outliers final: 4 residues processed: 2105 average time/residue: 1.5573 time to fit residues: 5564.6814 Evaluate side-chains 1298 residues out of total 5431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1294 time to evaluate : 6.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain x residue 98 VAL Chi-restraints excluded: chain x residue 294 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1114 random chunks: chunk 940 optimal weight: 4.9990 chunk 844 optimal weight: 20.0000 chunk 468 optimal weight: 8.9990 chunk 288 optimal weight: 20.0000 chunk 569 optimal weight: 8.9990 chunk 451 optimal weight: 40.0000 chunk 873 optimal weight: 10.0000 chunk 337 optimal weight: 20.0000 chunk 530 optimal weight: 5.9990 chunk 649 optimal weight: 20.0000 chunk 1011 optimal weight: 30.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 5 ASN 0 41 HIS 2 13 ASN 3 23 HIS C 44 ASN ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 ASN C 133 ASN C 225 ASN ** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN D 185 ASN E 24 ASN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN G 103 ASN H 28 ASN ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS J 128 ASN ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN K 90 ASN K 93 GLN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 HIS N 23 ASN N 107 ASN O 38 GLN ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN Q 36 GLN Q 55 GLN Q 71 ASN R 43 ASN S 7 HIS S 15 GLN T 59 ASN U 73 ASN W 42 HIS X 15 ASN Y 27 ASN Y 36 GLN Y 58 ASN Z 33 HIS b 108 GLN b 145 ASN b 167 HIS ** d 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 73 ASN d 88 ASN d 135 GLN d 197 HIS e 11 GLN ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 94 HIS g 85 GLN ** g 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 3 GLN ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 56 HIS j 58 ASN k 100 ASN l 71 HIS l 111 GLN m 13 HIS n 66 GLN p 18 GLN q 8 GLN r 51 GLN ** s 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 56 HIS t 12 GLN t 19 HIS t 47 GLN t 77 ASN x 36 ASN x 81 HIS ** x 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 271 ASN ** x 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 454 GLN x 516 HIS x 583 HIS x 626 ASN Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 165586 Z= 0.282 Angle : 0.806 23.304 247055 Z= 0.418 Chirality : 0.041 0.763 31400 Planarity : 0.007 0.128 13806 Dihedral : 24.469 178.963 81041 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 21.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.07 % Favored : 89.85 % Rotamer: Outliers : 4.52 % Allowed : 19.22 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.09), residues: 6551 helix: -0.98 (0.10), residues: 2168 sheet: -2.67 (0.14), residues: 1064 loop : -2.93 (0.09), residues: 3319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP x 192 HIS 0.011 0.002 HIS O 100 PHE 0.029 0.002 PHE u 11 TYR 0.034 0.002 TYR G 156 ARG 0.010 0.001 ARG F 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13102 Ramachandran restraints generated. 6551 Oldfield, 0 Emsley, 6551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13102 Ramachandran restraints generated. 6551 Oldfield, 0 Emsley, 6551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1610 residues out of total 5431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 1375 time to evaluate : 6.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 16 THR cc_start: 0.7566 (p) cc_final: 0.7348 (p) REVERT: 2 22 MET cc_start: 0.7762 (mmm) cc_final: 0.7369 (tpt) REVERT: 3 21 PHE cc_start: 0.8031 (m-80) cc_final: 0.7661 (m-10) REVERT: 3 28 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8222 (tt) REVERT: 3 37 THR cc_start: 0.8171 (p) cc_final: 0.7861 (t) REVERT: C 14 HIS cc_start: 0.7829 (m-70) cc_final: 0.7585 (m170) REVERT: C 155 ARG cc_start: 0.8577 (ttp-110) cc_final: 0.8054 (ttp-110) REVERT: C 180 MET cc_start: 0.8819 (mtt) cc_final: 0.8546 (mtt) REVERT: C 212 TRP cc_start: 0.7879 (p90) cc_final: 0.6563 (p90) REVERT: C 250 GLN cc_start: 0.9019 (tm-30) cc_final: 0.8488 (tm-30) REVERT: D 149 ASN cc_start: 0.8511 (t0) cc_final: 0.8305 (t0) REVERT: D 200 ASP cc_start: 0.8295 (t70) cc_final: 0.7837 (m-30) REVERT: D 204 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8543 (ttpt) REVERT: E 184 ASP cc_start: 0.7883 (m-30) cc_final: 0.7678 (m-30) REVERT: E 185 LYS cc_start: 0.8298 (mmtp) cc_final: 0.8003 (mtmt) REVERT: F 95 MET cc_start: 0.6299 (ttp) cc_final: 0.5109 (tmm) REVERT: G 49 LEU cc_start: 0.8080 (mt) cc_final: 0.7778 (mt) REVERT: G 166 GLU cc_start: 0.7544 (pt0) cc_final: 0.7291 (mm-30) REVERT: J 119 PHE cc_start: 0.7901 (t80) cc_final: 0.7537 (t80) REVERT: K 7 MET cc_start: 0.7983 (mmt) cc_final: 0.7548 (mmt) REVERT: K 32 TYR cc_start: 0.8221 (m-10) cc_final: 0.7976 (m-10) REVERT: L 128 THR cc_start: 0.8568 (p) cc_final: 0.8284 (p) REVERT: M 106 ASP cc_start: 0.6972 (t0) cc_final: 0.6452 (t0) REVERT: N 20 MET cc_start: 0.8283 (tmm) cc_final: 0.7959 (tmm) REVERT: O 19 GLN cc_start: 0.7934 (tt0) cc_final: 0.7715 (tm-30) REVERT: P 9 GLN cc_start: 0.7342 (mm110) cc_final: 0.6806 (mm110) REVERT: P 112 ARG cc_start: 0.7125 (ttp-110) cc_final: 0.6191 (ttt180) REVERT: S 25 ARG cc_start: 0.8453 (ttm-80) cc_final: 0.7785 (ttm-80) REVERT: S 75 PHE cc_start: 0.8462 (p90) cc_final: 0.8017 (p90) REVERT: T 24 MET cc_start: 0.7958 (tpt) cc_final: 0.7642 (tpt) REVERT: T 29 THR cc_start: 0.8788 (m) cc_final: 0.8577 (p) REVERT: U 13 LEU cc_start: 0.6612 (mp) cc_final: 0.6157 (tp) REVERT: W 7 ARG cc_start: 0.6684 (tpp-160) cc_final: 0.6361 (tpt90) REVERT: W 13 GLU cc_start: 0.6229 (mm-30) cc_final: 0.5853 (mm-30) REVERT: X 10 ARG cc_start: 0.7115 (OUTLIER) cc_final: 0.6167 (ttp-110) REVERT: X 69 GLU cc_start: 0.7568 (tt0) cc_final: 0.7207 (tt0) REVERT: X 70 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8294 (mm) REVERT: Z 48 ASN cc_start: 0.7692 (t0) cc_final: 0.7340 (t0) REVERT: Z 50 VAL cc_start: 0.8926 (m) cc_final: 0.8680 (p) REVERT: b 108 GLN cc_start: 0.7816 (mm-40) cc_final: 0.7537 (mm-40) REVERT: b 110 ILE cc_start: 0.7350 (mm) cc_final: 0.6918 (mt) REVERT: d 22 SER cc_start: 0.7851 (t) cc_final: 0.7438 (p) REVERT: d 30 LYS cc_start: 0.1546 (mttt) cc_final: 0.1235 (mttp) REVERT: d 59 LYS cc_start: 0.7378 (tttt) cc_final: 0.7063 (tttt) REVERT: d 114 ARG cc_start: 0.7779 (ttt180) cc_final: 0.7300 (tpp80) REVERT: d 177 MET cc_start: 0.8252 (mtt) cc_final: 0.7989 (mtt) REVERT: d 199 ILE cc_start: 0.8728 (mm) cc_final: 0.8388 (mm) REVERT: e 40 ASP cc_start: 0.7685 (p0) cc_final: 0.6941 (t0) REVERT: e 63 MET cc_start: 0.7894 (mmt) cc_final: 0.7479 (mmm) REVERT: e 110 MET cc_start: 0.8622 (mmm) cc_final: 0.8405 (tpp) REVERT: f 62 MET cc_start: 0.6864 (ptp) cc_final: 0.6566 (ptp) REVERT: g 104 VAL cc_start: 0.8202 (t) cc_final: 0.7818 (t) REVERT: g 108 ARG cc_start: 0.7463 (mtt180) cc_final: 0.6679 (ttt-90) REVERT: g 115 MET cc_start: 0.8080 (mmm) cc_final: 0.7308 (mmm) REVERT: g 125 ASP cc_start: 0.4993 (m-30) cc_final: 0.4622 (m-30) REVERT: g 138 GLU cc_start: 0.7699 (tm-30) cc_final: 0.7312 (tm-30) REVERT: h 55 LYS cc_start: 0.6912 (mtpp) cc_final: 0.6640 (mtmm) REVERT: h 110 MET cc_start: 0.8308 (ptp) cc_final: 0.8085 (ptp) REVERT: i 6 TYR cc_start: 0.7406 (t80) cc_final: 0.6433 (t80) REVERT: k 14 GLN cc_start: 0.6883 (mm110) cc_final: 0.5969 (pp30) REVERT: k 78 ILE cc_start: 0.8042 (mt) cc_final: 0.7724 (mt) REVERT: l 32 VAL cc_start: 0.8342 (m) cc_final: 0.8087 (m) REVERT: l 55 ARG cc_start: 0.7393 (tmm-80) cc_final: 0.6890 (ttp-110) REVERT: m 65 GLU cc_start: 0.8121 (mp0) cc_final: 0.7549 (mt-10) REVERT: m 68 LEU cc_start: 0.8582 (tp) cc_final: 0.8157 (tp) REVERT: n 29 ILE cc_start: 0.5356 (pt) cc_final: 0.5146 (mm) REVERT: o 42 PHE cc_start: 0.7534 (m-80) cc_final: 0.7193 (m-80) REVERT: o 86 LEU cc_start: 0.8336 (mt) cc_final: 0.8104 (tp) REVERT: q 47 ASP cc_start: 0.6848 (t70) cc_final: 0.6311 (p0) REVERT: r 46 THR cc_start: 0.6028 (p) cc_final: 0.5365 (t) REVERT: u 4 LYS cc_start: 0.6416 (pttt) cc_final: 0.6186 (pttt) REVERT: u 53 LYS cc_start: 0.7926 (mmmm) cc_final: 0.7354 (ttpt) REVERT: x 101 SER cc_start: 0.8477 (m) cc_final: 0.8219 (p) REVERT: x 112 TYR cc_start: 0.7985 (m-80) cc_final: 0.7510 (m-80) REVERT: x 192 TRP cc_start: 0.8427 (m-90) cc_final: 0.7885 (m-10) REVERT: x 463 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8648 (tp) REVERT: x 573 MET cc_start: 0.2560 (tmm) cc_final: 0.1562 (ttp) REVERT: x 616 MET cc_start: 0.6175 (mmm) cc_final: 0.5725 (mmm) REVERT: x 681 MET cc_start: 0.7123 (tmm) cc_final: 0.6702 (ppp) outliers start: 235 outliers final: 142 residues processed: 1514 average time/residue: 1.3312 time to fit residues: 3526.0946 Evaluate side-chains 1340 residues out of total 5431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1193 time to evaluate : 6.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 4 residue 10 LEU Chi-restraints excluded: chain 4 residue 16 ILE Chi-restraints excluded: chain 4 residue 35 GLN Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain K residue 29 HIS Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain O residue 2 ASP Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 65 ASN Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 24 LYS Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 43 ASP Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 8 ASN Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain X residue 10 ARG Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 61 LYS Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Z residue 53 MET Chi-restraints excluded: chain b residue 101 THR Chi-restraints excluded: chain b residue 105 THR Chi-restraints excluded: chain b residue 146 SER Chi-restraints excluded: chain b residue 186 VAL Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 119 ILE Chi-restraints excluded: chain c residue 185 THR Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 172 VAL Chi-restraints excluded: chain d residue 180 THR Chi-restraints excluded: chain d residue 188 SER Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 139 THR Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain h residue 13 ILE Chi-restraints excluded: chain h residue 78 SER Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 83 THR Chi-restraints excluded: chain i residue 89 TYR Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 83 THR Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 51 PHE Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain k residue 96 ILE Chi-restraints excluded: chain k residue 107 THR Chi-restraints excluded: chain m residue 19 THR Chi-restraints excluded: chain m residue 40 GLU Chi-restraints excluded: chain n residue 55 SER Chi-restraints excluded: chain o residue 23 SER Chi-restraints excluded: chain o residue 26 VAL Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 78 THR Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 78 VAL Chi-restraints excluded: chain q residue 6 THR Chi-restraints excluded: chain q residue 46 HIS Chi-restraints excluded: chain q residue 49 ASN Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 65 MET Chi-restraints excluded: chain t residue 25 SER Chi-restraints excluded: chain t residue 67 HIS Chi-restraints excluded: chain t residue 82 ILE Chi-restraints excluded: chain x residue 118 VAL Chi-restraints excluded: chain x residue 122 SER Chi-restraints excluded: chain x residue 264 THR Chi-restraints excluded: chain x residue 274 VAL Chi-restraints excluded: chain x residue 294 ILE Chi-restraints excluded: chain x residue 457 ILE Chi-restraints excluded: chain x residue 463 LEU Chi-restraints excluded: chain x residue 493 ILE Chi-restraints excluded: chain x residue 635 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1114 random chunks: chunk 562 optimal weight: 20.0000 chunk 313 optimal weight: 20.0000 chunk 841 optimal weight: 10.0000 chunk 688 optimal weight: 40.0000 chunk 279 optimal weight: 20.0000 chunk 1013 optimal weight: 30.0000 chunk 1094 optimal weight: 9.9990 chunk 902 optimal weight: 8.9990 chunk 1005 optimal weight: 9.9990 chunk 345 optimal weight: 0.9990 chunk 813 optimal weight: 9.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 45 HIS 3 23 HIS ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS G 103 ASN ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 15 GLN T 59 ASN W 72 ASN ** b 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 24 ASN ** d 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 135 GLN ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 147 ASN h 3 GLN ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 118 ASN l 5 GLN ** o 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 8 GLN r 51 GLN ** s 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 69 ASN x 37 HIS x 121 GLN x 149 ASN ** x 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 427 GLN ** x 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 583 HIS x 668 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.123 165586 Z= 0.283 Angle : 0.776 23.331 247055 Z= 0.404 Chirality : 0.039 0.424 31400 Planarity : 0.007 0.133 13806 Dihedral : 24.349 179.839 81040 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 21.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.18 % Favored : 89.80 % Rotamer: Outliers : 5.53 % Allowed : 22.14 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.82 (0.10), residues: 6551 helix: -0.60 (0.10), residues: 2167 sheet: -2.35 (0.15), residues: 1112 loop : -2.62 (0.10), residues: 3272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP b 103 HIS 0.011 0.002 HIS C 141 PHE 0.042 0.003 PHE b 49 TYR 0.043 0.002 TYR O 99 ARG 0.014 0.001 ARG l 55 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13102 Ramachandran restraints generated. 6551 Oldfield, 0 Emsley, 6551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13102 Ramachandran restraints generated. 6551 Oldfield, 0 Emsley, 6551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1562 residues out of total 5431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 1274 time to evaluate : 6.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 22 MET cc_start: 0.7752 (mmm) cc_final: 0.7159 (tpt) REVERT: 3 28 LEU cc_start: 0.8752 (mp) cc_final: 0.8434 (tt) REVERT: 3 37 THR cc_start: 0.8359 (p) cc_final: 0.8119 (t) REVERT: C 14 HIS cc_start: 0.7709 (m-70) cc_final: 0.7461 (m170) REVERT: C 144 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6701 (mt-10) REVERT: C 155 ARG cc_start: 0.8624 (ttp-110) cc_final: 0.8234 (ttp-110) REVERT: C 250 GLN cc_start: 0.9068 (tm-30) cc_final: 0.8691 (tm-30) REVERT: D 27 ILE cc_start: 0.9017 (mm) cc_final: 0.8808 (mm) REVERT: E 140 ASP cc_start: 0.7624 (m-30) cc_final: 0.7424 (m-30) REVERT: E 185 LYS cc_start: 0.8444 (mmtp) cc_final: 0.8108 (mtmt) REVERT: F 16 MET cc_start: 0.7720 (mmt) cc_final: 0.7494 (mmt) REVERT: F 27 VAL cc_start: 0.8915 (t) cc_final: 0.8691 (m) REVERT: F 95 MET cc_start: 0.6178 (ttp) cc_final: 0.5022 (tmm) REVERT: F 172 PHE cc_start: 0.7815 (OUTLIER) cc_final: 0.7466 (t80) REVERT: J 119 PHE cc_start: 0.7839 (t80) cc_final: 0.7542 (t80) REVERT: K 22 ILE cc_start: 0.8668 (pt) cc_final: 0.8466 (pt) REVERT: K 32 TYR cc_start: 0.8413 (m-10) cc_final: 0.8060 (m-10) REVERT: L 128 THR cc_start: 0.8622 (p) cc_final: 0.8340 (p) REVERT: L 143 GLU cc_start: 0.7704 (pt0) cc_final: 0.7401 (pt0) REVERT: M 106 ASP cc_start: 0.7105 (t0) cc_final: 0.6435 (t0) REVERT: N 20 MET cc_start: 0.8290 (tmm) cc_final: 0.8014 (tmm) REVERT: O 56 LYS cc_start: 0.7125 (OUTLIER) cc_final: 0.5764 (mtpp) REVERT: P 9 GLN cc_start: 0.6941 (mm110) cc_final: 0.6709 (mm110) REVERT: P 18 SER cc_start: 0.8565 (t) cc_final: 0.8177 (t) REVERT: P 99 LEU cc_start: 0.8660 (mp) cc_final: 0.8406 (tp) REVERT: P 112 ARG cc_start: 0.7581 (ttp-110) cc_final: 0.6543 (ttp-170) REVERT: Q 46 TYR cc_start: 0.8528 (t80) cc_final: 0.7966 (t80) REVERT: Q 101 ASP cc_start: 0.7989 (t70) cc_final: 0.7688 (t70) REVERT: S 1 MET cc_start: 0.5901 (OUTLIER) cc_final: 0.5679 (ptt) REVERT: T 24 MET cc_start: 0.8118 (tpt) cc_final: 0.7657 (tpt) REVERT: T 29 THR cc_start: 0.8989 (m) cc_final: 0.8626 (p) REVERT: U 25 LYS cc_start: 0.8140 (mmmt) cc_final: 0.7541 (tptp) REVERT: V 7 GLU cc_start: 0.6818 (tp30) cc_final: 0.6533 (mm-30) REVERT: V 21 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.6857 (mpt-90) REVERT: V 44 HIS cc_start: 0.8056 (OUTLIER) cc_final: 0.7796 (t70) REVERT: W 13 GLU cc_start: 0.6215 (mm-30) cc_final: 0.5925 (mm-30) REVERT: X 53 LYS cc_start: 0.8150 (ttmt) cc_final: 0.7879 (tppt) REVERT: Z 9 THR cc_start: 0.8517 (p) cc_final: 0.8154 (m) REVERT: Z 48 ASN cc_start: 0.7732 (t0) cc_final: 0.7367 (t0) REVERT: Z 50 VAL cc_start: 0.9003 (m) cc_final: 0.8744 (p) REVERT: b 108 GLN cc_start: 0.7590 (mm-40) cc_final: 0.7389 (mm-40) REVERT: d 22 SER cc_start: 0.7880 (t) cc_final: 0.7612 (p) REVERT: d 59 LYS cc_start: 0.7220 (tttt) cc_final: 0.6968 (tttt) REVERT: d 114 ARG cc_start: 0.7653 (ttt180) cc_final: 0.7351 (tpp80) REVERT: d 120 LYS cc_start: 0.8051 (mttt) cc_final: 0.7686 (pttt) REVERT: d 177 MET cc_start: 0.8072 (mtt) cc_final: 0.7727 (mtt) REVERT: e 40 ASP cc_start: 0.7692 (p0) cc_final: 0.6974 (t0) REVERT: f 1 MET cc_start: 0.6590 (mmm) cc_final: 0.6302 (mmm) REVERT: g 21 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7498 (pp) REVERT: g 104 VAL cc_start: 0.8330 (t) cc_final: 0.7937 (t) REVERT: g 108 ARG cc_start: 0.7511 (mtt180) cc_final: 0.6600 (ttt-90) REVERT: g 115 MET cc_start: 0.8105 (mmm) cc_final: 0.7321 (mmm) REVERT: g 125 ASP cc_start: 0.5432 (m-30) cc_final: 0.5224 (m-30) REVERT: h 26 MET cc_start: 0.6377 (ptm) cc_final: 0.5850 (ptp) REVERT: h 42 GLU cc_start: 0.6663 (mm-30) cc_final: 0.6388 (mm-30) REVERT: h 84 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8672 (tt) REVERT: i 6 TYR cc_start: 0.7385 (t80) cc_final: 0.6567 (t80) REVERT: k 14 GLN cc_start: 0.6833 (mm110) cc_final: 0.5806 (pp30) REVERT: k 78 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7805 (mt) REVERT: k 81 LEU cc_start: 0.8969 (tp) cc_final: 0.8754 (tt) REVERT: l 76 HIS cc_start: 0.8114 (m-70) cc_final: 0.7856 (m90) REVERT: l 114 SER cc_start: 0.7442 (m) cc_final: 0.6984 (p) REVERT: m 68 LEU cc_start: 0.8479 (tp) cc_final: 0.8043 (tp) REVERT: n 29 ILE cc_start: 0.5077 (pt) cc_final: 0.4789 (mm) REVERT: n 89 MET cc_start: 0.7527 (mmt) cc_final: 0.7118 (mmp) REVERT: o 42 PHE cc_start: 0.7734 (m-10) cc_final: 0.7146 (m-80) REVERT: q 47 ASP cc_start: 0.7063 (t70) cc_final: 0.6638 (p0) REVERT: s 66 VAL cc_start: 0.7689 (OUTLIER) cc_final: 0.7446 (m) REVERT: t 32 LYS cc_start: 0.8057 (mmtp) cc_final: 0.7824 (mtmt) REVERT: t 59 ARG cc_start: 0.7725 (ttm110) cc_final: 0.7312 (ttp-110) REVERT: u 53 LYS cc_start: 0.8017 (mmmm) cc_final: 0.7350 (ttpt) REVERT: x 416 SER cc_start: 0.8626 (m) cc_final: 0.8421 (p) REVERT: x 573 MET cc_start: 0.2190 (tmm) cc_final: 0.1729 (ttp) REVERT: x 681 MET cc_start: 0.7285 (OUTLIER) cc_final: 0.6801 (ppp) outliers start: 288 outliers final: 180 residues processed: 1460 average time/residue: 1.2643 time to fit residues: 3225.9179 Evaluate side-chains 1315 residues out of total 5431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 1125 time to evaluate : 5.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 4 residue 35 GLN Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 165 HIS Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 172 PHE Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 29 HIS Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 131 VAL Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 56 LYS Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain P residue 65 ASN Chi-restraints excluded: chain P residue 83 ILE Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 21 ARG Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 43 ASP Chi-restraints excluded: chain V residue 44 HIS Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 8 ASN Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain X residue 4 CYS Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Z residue 53 MET Chi-restraints excluded: chain b residue 101 THR Chi-restraints excluded: chain b residue 129 THR Chi-restraints excluded: chain b residue 146 SER Chi-restraints excluded: chain b residue 186 VAL Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 110 LEU Chi-restraints excluded: chain c residue 119 ILE Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 185 THR Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 172 VAL Chi-restraints excluded: chain d residue 180 THR Chi-restraints excluded: chain d residue 188 SER Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain e residue 37 VAL Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain h residue 13 ILE Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 78 SER Chi-restraints excluded: chain h residue 84 ILE Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 62 LEU Chi-restraints excluded: chain i residue 89 TYR Chi-restraints excluded: chain i residue 103 VAL Chi-restraints excluded: chain i residue 126 PHE Chi-restraints excluded: chain j residue 22 THR Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 51 PHE Chi-restraints excluded: chain k residue 69 CYS Chi-restraints excluded: chain k residue 78 ILE Chi-restraints excluded: chain k residue 115 ILE Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 101 LEU Chi-restraints excluded: chain l residue 118 VAL Chi-restraints excluded: chain m residue 32 ILE Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain n residue 55 SER Chi-restraints excluded: chain o residue 23 SER Chi-restraints excluded: chain o residue 78 THR Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 66 THR Chi-restraints excluded: chain p residue 78 VAL Chi-restraints excluded: chain q residue 6 THR Chi-restraints excluded: chain q residue 46 HIS Chi-restraints excluded: chain q residue 49 ASN Chi-restraints excluded: chain q residue 60 ILE Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 65 MET Chi-restraints excluded: chain s residue 66 VAL Chi-restraints excluded: chain t residue 25 SER Chi-restraints excluded: chain t residue 67 HIS Chi-restraints excluded: chain t residue 74 HIS Chi-restraints excluded: chain t residue 82 ILE Chi-restraints excluded: chain x residue 39 ILE Chi-restraints excluded: chain x residue 42 VAL Chi-restraints excluded: chain x residue 105 LEU Chi-restraints excluded: chain x residue 122 SER Chi-restraints excluded: chain x residue 151 LEU Chi-restraints excluded: chain x residue 153 VAL Chi-restraints excluded: chain x residue 243 THR Chi-restraints excluded: chain x residue 294 ILE Chi-restraints excluded: chain x residue 417 ILE Chi-restraints excluded: chain x residue 519 ILE Chi-restraints excluded: chain x residue 622 THR Chi-restraints excluded: chain x residue 635 SER Chi-restraints excluded: chain x residue 657 VAL Chi-restraints excluded: chain x residue 668 GLN Chi-restraints excluded: chain x residue 672 LEU Chi-restraints excluded: chain x residue 681 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1114 random chunks: chunk 1001 optimal weight: 0.9980 chunk 761 optimal weight: 30.0000 chunk 525 optimal weight: 9.9990 chunk 112 optimal weight: 20.0000 chunk 483 optimal weight: 7.9990 chunk 680 optimal weight: 20.0000 chunk 1017 optimal weight: 7.9990 chunk 1076 optimal weight: 20.0000 chunk 531 optimal weight: 5.9990 chunk 963 optimal weight: 20.0000 chunk 290 optimal weight: 20.0000 overall best weight: 6.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 HIS G 103 ASN ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 35 HIS ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 59 ASN ** T 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 68 ASN U 73 ASN V 44 HIS b 88 GLN ** b 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 138 GLN ** d 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 115 GLN ** e 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 3 HIS g 85 GLN ** i 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 58 ASN k 118 ASN l 5 GLN l 111 GLN m 99 GLN ** p 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 8 GLN s 13 HIS t 19 HIS t 60 GLN ** x 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 309 HIS ** x 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 165586 Z= 0.240 Angle : 0.727 23.095 247055 Z= 0.381 Chirality : 0.037 0.470 31400 Planarity : 0.006 0.124 13806 Dihedral : 24.269 179.746 81040 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.74 % Favored : 90.20 % Rotamer: Outliers : 5.42 % Allowed : 24.04 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.46 (0.10), residues: 6551 helix: -0.30 (0.11), residues: 2185 sheet: -2.00 (0.15), residues: 1085 loop : -2.46 (0.10), residues: 3281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP b 22 HIS 0.010 0.001 HIS J 77 PHE 0.026 0.002 PHE M 130 TYR 0.045 0.002 TYR O 99 ARG 0.009 0.001 ARG G 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13102 Ramachandran restraints generated. 6551 Oldfield, 0 Emsley, 6551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13102 Ramachandran restraints generated. 6551 Oldfield, 0 Emsley, 6551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1491 residues out of total 5431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 282 poor density : 1209 time to evaluate : 5.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 22 MET cc_start: 0.7549 (mmm) cc_final: 0.6990 (tpt) REVERT: 2 26 ASN cc_start: 0.7333 (t0) cc_final: 0.7081 (t0) REVERT: 3 28 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8357 (tt) REVERT: 3 37 THR cc_start: 0.8362 (p) cc_final: 0.8096 (t) REVERT: 3 63 TYR cc_start: 0.7483 (m-80) cc_final: 0.7191 (m-80) REVERT: C 14 HIS cc_start: 0.7579 (m-70) cc_final: 0.7356 (m170) REVERT: C 144 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6811 (mt-10) REVERT: C 155 ARG cc_start: 0.8595 (ttp-110) cc_final: 0.8279 (ttp-110) REVERT: C 250 GLN cc_start: 0.9099 (tm-30) cc_final: 0.8706 (tm-30) REVERT: D 148 GLN cc_start: 0.8243 (mp10) cc_final: 0.7571 (mt0) REVERT: E 185 LYS cc_start: 0.8532 (mmtp) cc_final: 0.8061 (mtmt) REVERT: F 95 MET cc_start: 0.6348 (ttp) cc_final: 0.5167 (tmm) REVERT: F 172 PHE cc_start: 0.7731 (OUTLIER) cc_final: 0.7441 (t80) REVERT: J 1 MET cc_start: 0.7637 (pmm) cc_final: 0.7276 (pmm) REVERT: J 119 PHE cc_start: 0.7817 (t80) cc_final: 0.7540 (t80) REVERT: J 128 ASN cc_start: 0.8825 (t0) cc_final: 0.8564 (t0) REVERT: K 118 LEU cc_start: 0.7997 (tp) cc_final: 0.7737 (mt) REVERT: L 128 THR cc_start: 0.8582 (p) cc_final: 0.8308 (p) REVERT: M 106 ASP cc_start: 0.6806 (t0) cc_final: 0.5888 (t0) REVERT: N 20 MET cc_start: 0.8346 (tmm) cc_final: 0.7959 (tmm) REVERT: N 107 ASN cc_start: 0.8804 (t0) cc_final: 0.8594 (t0) REVERT: O 56 LYS cc_start: 0.7036 (OUTLIER) cc_final: 0.5937 (mtpp) REVERT: P 18 SER cc_start: 0.8533 (t) cc_final: 0.8165 (t) REVERT: P 99 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8386 (tp) REVERT: P 112 ARG cc_start: 0.7558 (ttp-110) cc_final: 0.6410 (ttp-170) REVERT: Q 46 TYR cc_start: 0.8495 (t80) cc_final: 0.7872 (t80) REVERT: Q 101 ASP cc_start: 0.8030 (t70) cc_final: 0.7809 (t70) REVERT: R 76 LYS cc_start: 0.8256 (mttt) cc_final: 0.7670 (mttp) REVERT: T 24 MET cc_start: 0.8052 (tpt) cc_final: 0.7513 (tpt) REVERT: U 13 LEU cc_start: 0.6764 (mp) cc_final: 0.6300 (tp) REVERT: X 7 THR cc_start: 0.8442 (t) cc_final: 0.8175 (t) REVERT: X 25 LYS cc_start: 0.8275 (mmtm) cc_final: 0.7958 (mttm) REVERT: X 70 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8194 (mm) REVERT: Z 9 THR cc_start: 0.8556 (p) cc_final: 0.8209 (m) REVERT: Z 48 ASN cc_start: 0.7607 (t0) cc_final: 0.7282 (t0) REVERT: b 23 ASN cc_start: 0.7479 (t0) cc_final: 0.7219 (t0) REVERT: c 126 ARG cc_start: 0.6161 (mtt180) cc_final: 0.5697 (mtm-85) REVERT: d 22 SER cc_start: 0.7928 (t) cc_final: 0.7632 (p) REVERT: d 35 GLN cc_start: 0.7840 (pm20) cc_final: 0.7556 (pm20) REVERT: d 59 LYS cc_start: 0.7224 (tttt) cc_final: 0.7006 (tttt) REVERT: d 114 ARG cc_start: 0.7617 (ttt180) cc_final: 0.7333 (tpp80) REVERT: d 120 LYS cc_start: 0.8031 (mttt) cc_final: 0.7745 (pttt) REVERT: e 40 ASP cc_start: 0.7532 (p0) cc_final: 0.6886 (t0) REVERT: e 42 ASN cc_start: 0.7808 (t0) cc_final: 0.7452 (t0) REVERT: g 24 LYS cc_start: 0.7663 (tptt) cc_final: 0.7456 (tptt) REVERT: g 104 VAL cc_start: 0.8079 (t) cc_final: 0.7731 (t) REVERT: g 108 ARG cc_start: 0.7423 (mtt180) cc_final: 0.6637 (ttt-90) REVERT: g 115 MET cc_start: 0.8015 (mmm) cc_final: 0.7393 (mmm) REVERT: g 125 ASP cc_start: 0.5383 (m-30) cc_final: 0.4776 (m-30) REVERT: h 14 ARG cc_start: 0.7362 (ttm110) cc_final: 0.7051 (ttt180) REVERT: j 56 HIS cc_start: 0.7155 (OUTLIER) cc_final: 0.6684 (t-90) REVERT: k 14 GLN cc_start: 0.6921 (mm110) cc_final: 0.5910 (pp30) REVERT: k 68 ARG cc_start: 0.7672 (ttp-170) cc_final: 0.7429 (ttp80) REVERT: k 78 ILE cc_start: 0.8262 (mt) cc_final: 0.7967 (mt) REVERT: l 14 LYS cc_start: 0.4977 (OUTLIER) cc_final: 0.4540 (tttp) REVERT: l 114 SER cc_start: 0.7426 (m) cc_final: 0.6990 (p) REVERT: n 29 ILE cc_start: 0.5256 (pt) cc_final: 0.5008 (mm) REVERT: o 42 PHE cc_start: 0.7625 (m-10) cc_final: 0.7102 (m-80) REVERT: q 47 ASP cc_start: 0.7119 (OUTLIER) cc_final: 0.6915 (p0) REVERT: s 66 VAL cc_start: 0.7753 (OUTLIER) cc_final: 0.7421 (m) REVERT: t 59 ARG cc_start: 0.7709 (ttm110) cc_final: 0.7265 (ttp-110) REVERT: u 12 ASP cc_start: 0.3783 (OUTLIER) cc_final: 0.3454 (m-30) REVERT: u 53 LYS cc_start: 0.8016 (mmmm) cc_final: 0.7502 (ttpt) REVERT: x 157 ILE cc_start: 0.7262 (mt) cc_final: 0.6976 (mt) REVERT: x 267 SER cc_start: 0.8144 (p) cc_final: 0.7747 (m) REVERT: x 361 ARG cc_start: 0.8316 (mtt90) cc_final: 0.8054 (mpt-90) REVERT: x 365 MET cc_start: 0.6874 (mmt) cc_final: 0.6630 (mmt) REVERT: x 573 MET cc_start: 0.2248 (tmm) cc_final: 0.1904 (ttp) REVERT: x 577 LEU cc_start: 0.6243 (pt) cc_final: 0.4804 (tp) outliers start: 282 outliers final: 183 residues processed: 1377 average time/residue: 1.3009 time to fit residues: 3163.0930 Evaluate side-chains 1290 residues out of total 5431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 1097 time to evaluate : 5.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 2 residue 3 ARG Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 4 residue 35 GLN Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain C residue 24 HIS Chi-restraints excluded: chain C residue 52 HIS Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 165 HIS Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 172 PHE Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain H residue 11 ASN Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain K residue 29 HIS Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 131 VAL Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 56 LYS Chi-restraints excluded: chain O residue 67 ASN Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain P residue 65 ASN Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 94 ASP Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 8 ASN Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain X residue 4 CYS Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain b residue 101 THR Chi-restraints excluded: chain b residue 146 SER Chi-restraints excluded: chain b residue 186 VAL Chi-restraints excluded: chain b residue 189 ASN Chi-restraints excluded: chain c residue 110 LEU Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 185 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 131 ILE Chi-restraints excluded: chain d residue 172 VAL Chi-restraints excluded: chain d residue 188 SER Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain e residue 37 VAL Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 139 THR Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain h residue 13 ILE Chi-restraints excluded: chain h residue 78 SER Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 28 VAL Chi-restraints excluded: chain i residue 46 VAL Chi-restraints excluded: chain j residue 56 HIS Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain j residue 83 THR Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 51 PHE Chi-restraints excluded: chain k residue 107 THR Chi-restraints excluded: chain l residue 7 VAL Chi-restraints excluded: chain l residue 14 LYS Chi-restraints excluded: chain l residue 101 LEU Chi-restraints excluded: chain l residue 118 VAL Chi-restraints excluded: chain m residue 32 ILE Chi-restraints excluded: chain m residue 82 LEU Chi-restraints excluded: chain n residue 55 SER Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 23 SER Chi-restraints excluded: chain o residue 26 VAL Chi-restraints excluded: chain o residue 78 THR Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 57 ILE Chi-restraints excluded: chain p residue 66 THR Chi-restraints excluded: chain p residue 78 VAL Chi-restraints excluded: chain q residue 6 THR Chi-restraints excluded: chain q residue 16 MET Chi-restraints excluded: chain q residue 46 HIS Chi-restraints excluded: chain q residue 47 ASP Chi-restraints excluded: chain q residue 49 ASN Chi-restraints excluded: chain q residue 60 ILE Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 65 MET Chi-restraints excluded: chain s residue 66 VAL Chi-restraints excluded: chain s residue 76 THR Chi-restraints excluded: chain t residue 19 HIS Chi-restraints excluded: chain t residue 25 SER Chi-restraints excluded: chain t residue 67 HIS Chi-restraints excluded: chain t residue 74 HIS Chi-restraints excluded: chain u residue 12 ASP Chi-restraints excluded: chain x residue 39 ILE Chi-restraints excluded: chain x residue 42 VAL Chi-restraints excluded: chain x residue 67 THR Chi-restraints excluded: chain x residue 98 VAL Chi-restraints excluded: chain x residue 105 LEU Chi-restraints excluded: chain x residue 118 VAL Chi-restraints excluded: chain x residue 137 ILE Chi-restraints excluded: chain x residue 153 VAL Chi-restraints excluded: chain x residue 243 THR Chi-restraints excluded: chain x residue 264 THR Chi-restraints excluded: chain x residue 282 ILE Chi-restraints excluded: chain x residue 417 ILE Chi-restraints excluded: chain x residue 490 ARG Chi-restraints excluded: chain x residue 493 ILE Chi-restraints excluded: chain x residue 519 ILE Chi-restraints excluded: chain x residue 635 SER Chi-restraints excluded: chain x residue 668 GLN Chi-restraints excluded: chain x residue 681 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1114 random chunks: chunk 896 optimal weight: 0.0050 chunk 611 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 801 optimal weight: 10.0000 chunk 444 optimal weight: 0.0470 chunk 918 optimal weight: 7.9990 chunk 744 optimal weight: 40.0000 chunk 1 optimal weight: 20.0000 chunk 549 optimal weight: 8.9990 chunk 966 optimal weight: 3.9990 chunk 271 optimal weight: 20.0000 overall best weight: 3.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 23 HIS C 14 HIS ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN E 29 HIS E 90 GLN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 ASN ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 47 HIS ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 ASN ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 GLN ** T 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 73 ASN ** X 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 70 GLN ** d 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 115 GLN ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 85 GLN h 66 GLN ** i 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 5 GLN ** p 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 8 GLN x 128 GLN ** x 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 516 HIS ** x 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 165586 Z= 0.170 Angle : 0.672 23.176 247055 Z= 0.356 Chirality : 0.035 0.452 31400 Planarity : 0.006 0.125 13806 Dihedral : 24.188 179.333 81038 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.76 % Favored : 91.22 % Rotamer: Outliers : 5.00 % Allowed : 25.56 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.16 (0.10), residues: 6551 helix: -0.05 (0.11), residues: 2183 sheet: -1.80 (0.15), residues: 1084 loop : -2.30 (0.10), residues: 3284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP b 22 HIS 0.023 0.001 HIS t 19 PHE 0.027 0.002 PHE g 25 TYR 0.024 0.002 TYR x 284 ARG 0.008 0.001 ARG 2 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13102 Ramachandran restraints generated. 6551 Oldfield, 0 Emsley, 6551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13102 Ramachandran restraints generated. 6551 Oldfield, 0 Emsley, 6551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1447 residues out of total 5431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 1187 time to evaluate : 5.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 22 MET cc_start: 0.7468 (mmm) cc_final: 0.6911 (tpt) REVERT: 2 26 ASN cc_start: 0.7280 (t0) cc_final: 0.6957 (t0) REVERT: 3 28 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8338 (tt) REVERT: 3 37 THR cc_start: 0.8369 (p) cc_final: 0.8074 (t) REVERT: 3 63 TYR cc_start: 0.7373 (m-80) cc_final: 0.7072 (m-80) REVERT: C 144 GLU cc_start: 0.7214 (mt-10) cc_final: 0.6570 (mt-10) REVERT: C 155 ARG cc_start: 0.8538 (ttp-110) cc_final: 0.8030 (ttp-110) REVERT: C 250 GLN cc_start: 0.9059 (tm-30) cc_final: 0.8850 (tm-30) REVERT: E 185 LYS cc_start: 0.8454 (mmtp) cc_final: 0.7976 (mtmt) REVERT: F 16 MET cc_start: 0.7702 (mmt) cc_final: 0.6498 (mtt) REVERT: F 49 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7544 (tp) REVERT: F 95 MET cc_start: 0.6265 (ttp) cc_final: 0.5136 (tmm) REVERT: J 1 MET cc_start: 0.7583 (pmm) cc_final: 0.7220 (pmm) REVERT: J 119 PHE cc_start: 0.7765 (t80) cc_final: 0.7485 (t80) REVERT: J 128 ASN cc_start: 0.8868 (t0) cc_final: 0.8557 (t0) REVERT: L 55 MET cc_start: 0.7792 (tpp) cc_final: 0.7586 (mmt) REVERT: L 128 THR cc_start: 0.8532 (p) cc_final: 0.8261 (p) REVERT: M 18 ARG cc_start: 0.7627 (mmm-85) cc_final: 0.7357 (tpp80) REVERT: M 106 ASP cc_start: 0.6876 (t0) cc_final: 0.5982 (t0) REVERT: N 20 MET cc_start: 0.8308 (tmm) cc_final: 0.7993 (tmm) REVERT: P 99 LEU cc_start: 0.8644 (mp) cc_final: 0.8356 (tp) REVERT: P 112 ARG cc_start: 0.7521 (ttp-110) cc_final: 0.6396 (ttp-170) REVERT: Q 64 ILE cc_start: 0.9316 (mt) cc_final: 0.8825 (tt) REVERT: R 76 LYS cc_start: 0.8100 (mttt) cc_final: 0.7542 (mttp) REVERT: R 81 LYS cc_start: 0.8490 (mmtm) cc_final: 0.8217 (mmtp) REVERT: T 4 GLU cc_start: 0.7137 (tp30) cc_final: 0.6768 (tp30) REVERT: U 13 LEU cc_start: 0.6913 (mp) cc_final: 0.6417 (tp) REVERT: V 88 HIS cc_start: 0.7348 (t-170) cc_final: 0.7137 (t-170) REVERT: W 25 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7531 (mm-30) REVERT: X 7 THR cc_start: 0.8314 (t) cc_final: 0.8074 (t) REVERT: X 70 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8205 (mm) REVERT: Z 9 THR cc_start: 0.8580 (p) cc_final: 0.8160 (m) REVERT: Z 48 ASN cc_start: 0.7866 (t0) cc_final: 0.7524 (t0) REVERT: Z 53 MET cc_start: 0.8618 (ptp) cc_final: 0.8368 (ptp) REVERT: Z 57 GLU cc_start: 0.6825 (pm20) cc_final: 0.5985 (tp30) REVERT: b 23 ASN cc_start: 0.7098 (t0) cc_final: 0.6896 (t0) REVERT: b 158 ASP cc_start: 0.7017 (m-30) cc_final: 0.5773 (t0) REVERT: c 126 ARG cc_start: 0.6132 (mtt180) cc_final: 0.5476 (mtm-85) REVERT: c 133 MET cc_start: 0.7195 (ptm) cc_final: 0.6781 (ptp) REVERT: d 22 SER cc_start: 0.7813 (t) cc_final: 0.7434 (p) REVERT: d 59 LYS cc_start: 0.7131 (tttt) cc_final: 0.6766 (tttt) REVERT: d 118 SER cc_start: 0.8535 (t) cc_final: 0.8228 (m) REVERT: d 120 LYS cc_start: 0.8005 (mttt) cc_final: 0.7729 (pttt) REVERT: d 199 ILE cc_start: 0.8512 (mm) cc_final: 0.8309 (mm) REVERT: e 40 ASP cc_start: 0.7419 (p0) cc_final: 0.7018 (t0) REVERT: e 42 ASN cc_start: 0.7886 (t0) cc_final: 0.7677 (t0) REVERT: g 58 LEU cc_start: 0.7221 (tp) cc_final: 0.6994 (mp) REVERT: g 104 VAL cc_start: 0.7933 (t) cc_final: 0.7728 (t) REVERT: g 108 ARG cc_start: 0.7356 (mtt180) cc_final: 0.6755 (ttt-90) REVERT: g 125 ASP cc_start: 0.5076 (m-30) cc_final: 0.4786 (m-30) REVERT: h 14 ARG cc_start: 0.7286 (ttm110) cc_final: 0.6958 (ttt180) REVERT: h 78 SER cc_start: 0.7886 (m) cc_final: 0.7247 (p) REVERT: i 37 TYR cc_start: 0.7342 (t80) cc_final: 0.7125 (t80) REVERT: j 6 ILE cc_start: 0.7457 (mm) cc_final: 0.6762 (pt) REVERT: j 56 HIS cc_start: 0.7007 (OUTLIER) cc_final: 0.6558 (t-90) REVERT: k 14 GLN cc_start: 0.6819 (mm110) cc_final: 0.5774 (pp30) REVERT: l 13 ARG cc_start: 0.7111 (OUTLIER) cc_final: 0.6626 (tpp80) REVERT: m 68 LEU cc_start: 0.8311 (tp) cc_final: 0.7898 (tt) REVERT: n 75 ARG cc_start: 0.6579 (mtm180) cc_final: 0.6205 (mtm-85) REVERT: n 89 MET cc_start: 0.7250 (mmt) cc_final: 0.6966 (mmp) REVERT: o 13 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.7113 (tp30) REVERT: q 47 ASP cc_start: 0.7052 (OUTLIER) cc_final: 0.6838 (p0) REVERT: s 66 VAL cc_start: 0.7411 (OUTLIER) cc_final: 0.7117 (m) REVERT: u 11 PHE cc_start: 0.2756 (t80) cc_final: 0.2488 (t80) REVERT: u 53 LYS cc_start: 0.7912 (mmmm) cc_final: 0.7422 (ttpt) REVERT: x 14 ILE cc_start: 0.8069 (mm) cc_final: 0.7823 (mm) REVERT: x 267 SER cc_start: 0.8091 (p) cc_final: 0.7698 (m) REVERT: x 357 GLU cc_start: 0.6039 (mp0) cc_final: 0.5720 (mp0) REVERT: x 400 ASP cc_start: 0.7077 (OUTLIER) cc_final: 0.6849 (p0) REVERT: x 577 LEU cc_start: 0.5859 (pt) cc_final: 0.4618 (tp) REVERT: x 593 LYS cc_start: 0.5855 (tptt) cc_final: 0.4603 (mtmt) outliers start: 260 outliers final: 174 residues processed: 1352 average time/residue: 1.1433 time to fit residues: 2718.6168 Evaluate side-chains 1281 residues out of total 5431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 1098 time to evaluate : 5.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 21 LEU Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 38 LEU Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 31 LEU Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 4 residue 35 GLN Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 28 VAL Chi-restraints excluded: chain C residue 52 HIS Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 165 HIS Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain H residue 27 ARG Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 29 HIS Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 131 VAL Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 65 ASN Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain S residue 94 ASP Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 43 ASP Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 8 ASN Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain X residue 4 CYS Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Z residue 26 LEU Chi-restraints excluded: chain b residue 129 THR Chi-restraints excluded: chain b residue 146 SER Chi-restraints excluded: chain b residue 169 HIS Chi-restraints excluded: chain b residue 186 VAL Chi-restraints excluded: chain b residue 189 ASN Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 110 LEU Chi-restraints excluded: chain c residue 185 THR Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 58 GLN Chi-restraints excluded: chain d residue 70 GLN Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 131 ILE Chi-restraints excluded: chain d residue 172 VAL Chi-restraints excluded: chain d residue 180 THR Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain e residue 37 VAL Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 139 THR Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 27 ASN Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain h residue 13 ILE Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 28 VAL Chi-restraints excluded: chain i residue 126 PHE Chi-restraints excluded: chain j residue 22 THR Chi-restraints excluded: chain j residue 56 HIS Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 51 PHE Chi-restraints excluded: chain k residue 107 THR Chi-restraints excluded: chain l residue 7 VAL Chi-restraints excluded: chain l residue 13 ARG Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 101 LEU Chi-restraints excluded: chain m residue 32 ILE Chi-restraints excluded: chain m residue 40 GLU Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain n residue 55 SER Chi-restraints excluded: chain o residue 13 GLU Chi-restraints excluded: chain o residue 26 VAL Chi-restraints excluded: chain o residue 78 THR Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 57 ILE Chi-restraints excluded: chain q residue 16 MET Chi-restraints excluded: chain q residue 46 HIS Chi-restraints excluded: chain q residue 47 ASP Chi-restraints excluded: chain q residue 49 ASN Chi-restraints excluded: chain s residue 65 MET Chi-restraints excluded: chain s residue 66 VAL Chi-restraints excluded: chain t residue 67 HIS Chi-restraints excluded: chain x residue 39 ILE Chi-restraints excluded: chain x residue 42 VAL Chi-restraints excluded: chain x residue 67 THR Chi-restraints excluded: chain x residue 83 ILE Chi-restraints excluded: chain x residue 98 VAL Chi-restraints excluded: chain x residue 105 LEU Chi-restraints excluded: chain x residue 118 VAL Chi-restraints excluded: chain x residue 153 VAL Chi-restraints excluded: chain x residue 243 THR Chi-restraints excluded: chain x residue 264 THR Chi-restraints excluded: chain x residue 277 MET Chi-restraints excluded: chain x residue 400 ASP Chi-restraints excluded: chain x residue 417 ILE Chi-restraints excluded: chain x residue 448 THR Chi-restraints excluded: chain x residue 490 ARG Chi-restraints excluded: chain x residue 493 ILE Chi-restraints excluded: chain x residue 681 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1114 random chunks: chunk 362 optimal weight: 20.0000 chunk 969 optimal weight: 5.9990 chunk 212 optimal weight: 20.0000 chunk 632 optimal weight: 6.9990 chunk 265 optimal weight: 20.0000 chunk 1077 optimal weight: 50.0000 chunk 894 optimal weight: 50.0000 chunk 499 optimal weight: 0.0270 chunk 89 optimal weight: 20.0000 chunk 356 optimal weight: 7.9990 chunk 565 optimal weight: 20.0000 overall best weight: 8.2048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 GLN G 103 ASN H 2 GLN ** H 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 28 ASN ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 68 ASN U 73 ASN V 49 ASN ** b 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 70 GLN ** d 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 115 GLN d 151 GLN ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 85 GLN ** i 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 5 GLN ** o 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 36 ASN ** p 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 8 GLN ** x 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 668 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 165586 Z= 0.285 Angle : 0.751 23.353 247055 Z= 0.391 Chirality : 0.038 0.481 31400 Planarity : 0.006 0.127 13806 Dihedral : 24.179 179.743 81038 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 21.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.52 % Favored : 89.44 % Rotamer: Outliers : 6.30 % Allowed : 25.46 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.27 (0.10), residues: 6551 helix: -0.20 (0.11), residues: 2197 sheet: -1.91 (0.15), residues: 1111 loop : -2.31 (0.10), residues: 3243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP g 102 HIS 0.009 0.001 HIS J 77 PHE 0.035 0.002 PHE H 46 TYR 0.024 0.002 TYR x 284 ARG 0.018 0.001 ARG D 124 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13102 Ramachandran restraints generated. 6551 Oldfield, 0 Emsley, 6551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13102 Ramachandran restraints generated. 6551 Oldfield, 0 Emsley, 6551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1440 residues out of total 5431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 328 poor density : 1112 time to evaluate : 5.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 22 MET cc_start: 0.7543 (mmm) cc_final: 0.6757 (ttt) REVERT: 2 26 ASN cc_start: 0.7513 (t0) cc_final: 0.7245 (t0) REVERT: 3 28 LEU cc_start: 0.8755 (mp) cc_final: 0.8395 (tt) REVERT: 3 37 THR cc_start: 0.8410 (p) cc_final: 0.8152 (t) REVERT: 6 9 TYR cc_start: 0.7242 (t80) cc_final: 0.6945 (t80) REVERT: C 144 GLU cc_start: 0.7327 (mt-10) cc_final: 0.6585 (mt-10) REVERT: C 155 ARG cc_start: 0.8613 (ttp-110) cc_final: 0.8065 (ttp-110) REVERT: C 156 SER cc_start: 0.9156 (t) cc_final: 0.8951 (p) REVERT: D 148 GLN cc_start: 0.8376 (mp10) cc_final: 0.7643 (mt0) REVERT: E 155 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7042 (tm-30) REVERT: F 16 MET cc_start: 0.7703 (mmt) cc_final: 0.6540 (mtt) REVERT: F 95 MET cc_start: 0.6608 (ttp) cc_final: 0.5584 (tmm) REVERT: F 97 GLU cc_start: 0.7027 (tt0) cc_final: 0.6619 (tt0) REVERT: H 127 GLU cc_start: -0.0838 (OUTLIER) cc_final: -0.1128 (mt-10) REVERT: J 119 PHE cc_start: 0.7875 (t80) cc_final: 0.7602 (t80) REVERT: J 128 ASN cc_start: 0.8879 (t0) cc_final: 0.8621 (t0) REVERT: L 128 THR cc_start: 0.8596 (p) cc_final: 0.8263 (p) REVERT: N 20 MET cc_start: 0.8380 (tmm) cc_final: 0.7982 (tmm) REVERT: O 56 LYS cc_start: 0.7312 (OUTLIER) cc_final: 0.6180 (mtpp) REVERT: P 8 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7551 (tt0) REVERT: P 18 SER cc_start: 0.8564 (t) cc_final: 0.8144 (t) REVERT: P 99 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8451 (tp) REVERT: P 112 ARG cc_start: 0.7654 (ttp-110) cc_final: 0.6509 (ttt180) REVERT: Q 101 ASP cc_start: 0.7571 (t70) cc_final: 0.7267 (t70) REVERT: S 1 MET cc_start: 0.5879 (OUTLIER) cc_final: 0.5369 (ptt) REVERT: T 24 MET cc_start: 0.7947 (tpt) cc_final: 0.7578 (tpt) REVERT: U 13 LEU cc_start: 0.7042 (mp) cc_final: 0.6543 (tp) REVERT: V 21 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.6858 (mpt-90) REVERT: W 25 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7463 (mm-30) REVERT: X 7 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8231 (t) REVERT: X 25 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7713 (mttm) REVERT: X 70 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8284 (mm) REVERT: Z 9 THR cc_start: 0.8604 (p) cc_final: 0.8225 (m) REVERT: b 72 LYS cc_start: 0.5622 (mttp) cc_final: 0.5358 (tttm) REVERT: d 22 SER cc_start: 0.7927 (t) cc_final: 0.7623 (p) REVERT: d 59 LYS cc_start: 0.7086 (tttt) cc_final: 0.6741 (tttt) REVERT: d 120 LYS cc_start: 0.8017 (mttt) cc_final: 0.7814 (pttt) REVERT: d 205 LYS cc_start: 0.6308 (tptp) cc_final: 0.5932 (tppt) REVERT: e 40 ASP cc_start: 0.7479 (p0) cc_final: 0.6971 (t0) REVERT: e 42 ASN cc_start: 0.8041 (t0) cc_final: 0.7838 (t0) REVERT: g 58 LEU cc_start: 0.7165 (tp) cc_final: 0.6922 (mp) REVERT: g 104 VAL cc_start: 0.8116 (t) cc_final: 0.7733 (t) REVERT: g 108 ARG cc_start: 0.7481 (mtt180) cc_final: 0.6714 (ttt-90) REVERT: g 115 MET cc_start: 0.7979 (mmm) cc_final: 0.7394 (mmm) REVERT: g 122 GLU cc_start: 0.7417 (mm-30) cc_final: 0.7194 (mm-30) REVERT: g 125 ASP cc_start: 0.5277 (m-30) cc_final: 0.5024 (m-30) REVERT: h 14 ARG cc_start: 0.7223 (ttm110) cc_final: 0.6847 (ttt180) REVERT: j 6 ILE cc_start: 0.7429 (mm) cc_final: 0.6739 (pt) REVERT: j 48 ARG cc_start: 0.6685 (OUTLIER) cc_final: 0.6432 (mtt90) REVERT: j 56 HIS cc_start: 0.7342 (OUTLIER) cc_final: 0.6761 (t-90) REVERT: k 14 GLN cc_start: 0.6906 (mm110) cc_final: 0.5618 (pp30) REVERT: l 114 SER cc_start: 0.7202 (m) cc_final: 0.6780 (p) REVERT: m 68 LEU cc_start: 0.8355 (tp) cc_final: 0.7970 (tp) REVERT: n 8 ARG cc_start: 0.6654 (mtt180) cc_final: 0.6107 (mtt180) REVERT: n 75 ARG cc_start: 0.6693 (mtm180) cc_final: 0.6323 (mtm-85) REVERT: n 89 MET cc_start: 0.7388 (mmt) cc_final: 0.7040 (mmp) REVERT: q 47 ASP cc_start: 0.7144 (OUTLIER) cc_final: 0.6943 (p0) REVERT: s 56 HIS cc_start: 0.6694 (OUTLIER) cc_final: 0.5706 (m90) REVERT: s 66 VAL cc_start: 0.7765 (OUTLIER) cc_final: 0.7415 (m) REVERT: u 53 LYS cc_start: 0.7869 (mmmm) cc_final: 0.7470 (ttpt) REVERT: x 357 GLU cc_start: 0.6380 (mp0) cc_final: 0.5778 (mp0) REVERT: x 361 ARG cc_start: 0.8377 (mtt90) cc_final: 0.8127 (mpt-90) REVERT: x 400 ASP cc_start: 0.7228 (OUTLIER) cc_final: 0.6974 (p0) REVERT: x 577 LEU cc_start: 0.5387 (pt) cc_final: 0.4087 (tp) REVERT: x 593 LYS cc_start: 0.6015 (tptt) cc_final: 0.4818 (mtmt) outliers start: 328 outliers final: 230 residues processed: 1319 average time/residue: 1.1341 time to fit residues: 2643.8628 Evaluate side-chains 1304 residues out of total 5431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 1058 time to evaluate : 5.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 38 LEU Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 2 residue 3 ARG Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 31 LEU Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 4 residue 35 GLN Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 28 VAL Chi-restraints excluded: chain 6 residue 32 LEU Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain C residue 52 HIS Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain E residue 165 HIS Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain H residue 27 ARG Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain K residue 29 HIS Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 131 VAL Chi-restraints excluded: chain N residue 24 MET Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 56 LYS Chi-restraints excluded: chain O residue 67 ASN Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 8 GLU Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain P residue 65 ASN Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain Q residue 58 GLN Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 21 ARG Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 43 ASP Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain W residue 8 ASN Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain X residue 4 CYS Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 25 LYS Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Z residue 4 ILE Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 69 VAL Chi-restraints excluded: chain b residue 101 THR Chi-restraints excluded: chain b residue 129 THR Chi-restraints excluded: chain b residue 146 SER Chi-restraints excluded: chain b residue 186 VAL Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 110 LEU Chi-restraints excluded: chain c residue 117 ASP Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 185 THR Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 131 ILE Chi-restraints excluded: chain d residue 158 LEU Chi-restraints excluded: chain d residue 172 VAL Chi-restraints excluded: chain d residue 180 THR Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain e residue 37 VAL Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 139 THR Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 88 MET Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 27 ASN Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 32 ASP Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 89 GLU Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain h residue 8 ASP Chi-restraints excluded: chain h residue 13 ILE Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 112 ASP Chi-restraints excluded: chain i residue 28 VAL Chi-restraints excluded: chain i residue 46 VAL Chi-restraints excluded: chain i residue 66 VAL Chi-restraints excluded: chain j residue 22 THR Chi-restraints excluded: chain j residue 48 ARG Chi-restraints excluded: chain j residue 56 HIS Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 51 PHE Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain k residue 69 CYS Chi-restraints excluded: chain k residue 107 THR Chi-restraints excluded: chain l residue 7 VAL Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 118 VAL Chi-restraints excluded: chain m residue 40 GLU Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 82 LEU Chi-restraints excluded: chain n residue 55 SER Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 23 SER Chi-restraints excluded: chain o residue 78 THR Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 66 THR Chi-restraints excluded: chain p residue 78 VAL Chi-restraints excluded: chain q residue 6 THR Chi-restraints excluded: chain q residue 16 MET Chi-restraints excluded: chain q residue 46 HIS Chi-restraints excluded: chain q residue 47 ASP Chi-restraints excluded: chain q residue 49 ASN Chi-restraints excluded: chain q residue 60 ILE Chi-restraints excluded: chain r residue 39 VAL Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 56 HIS Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 65 MET Chi-restraints excluded: chain s residue 66 VAL Chi-restraints excluded: chain s residue 76 THR Chi-restraints excluded: chain t residue 3 ILE Chi-restraints excluded: chain t residue 67 HIS Chi-restraints excluded: chain t residue 74 HIS Chi-restraints excluded: chain x residue 39 ILE Chi-restraints excluded: chain x residue 42 VAL Chi-restraints excluded: chain x residue 67 THR Chi-restraints excluded: chain x residue 83 ILE Chi-restraints excluded: chain x residue 98 VAL Chi-restraints excluded: chain x residue 105 LEU Chi-restraints excluded: chain x residue 118 VAL Chi-restraints excluded: chain x residue 137 ILE Chi-restraints excluded: chain x residue 153 VAL Chi-restraints excluded: chain x residue 243 THR Chi-restraints excluded: chain x residue 264 THR Chi-restraints excluded: chain x residue 277 MET Chi-restraints excluded: chain x residue 282 ILE Chi-restraints excluded: chain x residue 400 ASP Chi-restraints excluded: chain x residue 417 ILE Chi-restraints excluded: chain x residue 448 THR Chi-restraints excluded: chain x residue 493 ILE Chi-restraints excluded: chain x residue 519 ILE Chi-restraints excluded: chain x residue 635 SER Chi-restraints excluded: chain x residue 668 GLN Chi-restraints excluded: chain x residue 672 LEU Chi-restraints excluded: chain x residue 681 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1114 random chunks: chunk 1039 optimal weight: 30.0000 chunk 121 optimal weight: 20.0000 chunk 614 optimal weight: 9.9990 chunk 787 optimal weight: 30.0000 chunk 609 optimal weight: 6.9990 chunk 907 optimal weight: 3.9990 chunk 601 optimal weight: 9.9990 chunk 1073 optimal weight: 5.9990 chunk 671 optimal weight: 20.0000 chunk 654 optimal weight: 40.0000 chunk 495 optimal weight: 1.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 HIS G 103 ASN ** H 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 ASN ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 70 GLN ** d 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 151 GLN e 76 ASN ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 85 GLN ** i 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 8 GLN r 51 GLN t 19 HIS ** x 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 165586 Z= 0.213 Angle : 0.698 23.237 247055 Z= 0.367 Chirality : 0.036 0.475 31400 Planarity : 0.006 0.125 13806 Dihedral : 24.158 179.026 81037 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 5.73 % Allowed : 26.58 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.13 (0.10), residues: 6551 helix: -0.11 (0.11), residues: 2205 sheet: -1.85 (0.15), residues: 1121 loop : -2.20 (0.10), residues: 3225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP b 22 HIS 0.007 0.001 HIS J 77 PHE 0.021 0.002 PHE b 15 TYR 0.034 0.002 TYR g 43 ARG 0.011 0.001 ARG R 84 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13102 Ramachandran restraints generated. 6551 Oldfield, 0 Emsley, 6551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13102 Ramachandran restraints generated. 6551 Oldfield, 0 Emsley, 6551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1393 residues out of total 5431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 298 poor density : 1095 time to evaluate : 5.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 22 MET cc_start: 0.7509 (mmm) cc_final: 0.6692 (ttt) REVERT: 2 26 ASN cc_start: 0.7446 (t0) cc_final: 0.7098 (t0) REVERT: 3 28 LEU cc_start: 0.8743 (mp) cc_final: 0.8336 (tt) REVERT: 3 37 THR cc_start: 0.8437 (p) cc_final: 0.8132 (t) REVERT: C 144 GLU cc_start: 0.7295 (mt-10) cc_final: 0.6524 (mt-10) REVERT: C 155 ARG cc_start: 0.8531 (ttp-110) cc_final: 0.8065 (ttp-110) REVERT: D 148 GLN cc_start: 0.8304 (mp10) cc_final: 0.7623 (mt0) REVERT: E 155 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6984 (tm-30) REVERT: E 185 LYS cc_start: 0.8448 (mmtp) cc_final: 0.7873 (mtmt) REVERT: F 16 MET cc_start: 0.7606 (mmt) cc_final: 0.6358 (mtt) REVERT: F 95 MET cc_start: 0.6533 (ttp) cc_final: 0.5446 (tmm) REVERT: F 97 GLU cc_start: 0.7040 (tt0) cc_final: 0.6834 (tt0) REVERT: F 172 PHE cc_start: 0.7764 (OUTLIER) cc_final: 0.6807 (t80) REVERT: H 127 GLU cc_start: -0.0440 (OUTLIER) cc_final: -0.0754 (mt-10) REVERT: J 1 MET cc_start: 0.7399 (pmm) cc_final: 0.7024 (pmm) REVERT: J 119 PHE cc_start: 0.7822 (t80) cc_final: 0.7545 (t80) REVERT: J 128 ASN cc_start: 0.8942 (t0) cc_final: 0.8692 (t0) REVERT: L 128 THR cc_start: 0.8574 (p) cc_final: 0.8308 (p) REVERT: M 18 ARG cc_start: 0.7718 (mmm-85) cc_final: 0.7449 (tpp80) REVERT: N 6 SER cc_start: 0.7637 (OUTLIER) cc_final: 0.6911 (p) REVERT: N 20 MET cc_start: 0.8311 (tmm) cc_final: 0.7991 (tmm) REVERT: O 56 LYS cc_start: 0.7393 (OUTLIER) cc_final: 0.6270 (mtpp) REVERT: P 18 SER cc_start: 0.8628 (t) cc_final: 0.8239 (t) REVERT: P 99 LEU cc_start: 0.8667 (mp) cc_final: 0.8418 (tp) REVERT: P 112 ARG cc_start: 0.7628 (ttp-110) cc_final: 0.6512 (ttp-170) REVERT: Q 64 ILE cc_start: 0.9342 (mt) cc_final: 0.8879 (tt) REVERT: Q 86 SER cc_start: 0.9064 (m) cc_final: 0.8758 (p) REVERT: Q 101 ASP cc_start: 0.7695 (t70) cc_final: 0.7303 (t70) REVERT: S 1 MET cc_start: 0.5958 (OUTLIER) cc_final: 0.5398 (ptt) REVERT: T 24 MET cc_start: 0.7952 (tpt) cc_final: 0.7521 (tpt) REVERT: U 13 LEU cc_start: 0.7022 (mp) cc_final: 0.6528 (tp) REVERT: U 72 PHE cc_start: 0.7808 (OUTLIER) cc_final: 0.7435 (t80) REVERT: V 21 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.7307 (mpt-90) REVERT: V 88 HIS cc_start: 0.7547 (t-170) cc_final: 0.7278 (t-170) REVERT: W 25 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7441 (mm-30) REVERT: X 25 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7736 (mttm) REVERT: X 70 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8354 (mm) REVERT: Z 9 THR cc_start: 0.8467 (p) cc_final: 0.8134 (m) REVERT: Z 53 MET cc_start: 0.8610 (ptp) cc_final: 0.8375 (ptp) REVERT: d 22 SER cc_start: 0.7845 (t) cc_final: 0.7621 (p) REVERT: d 118 SER cc_start: 0.8554 (t) cc_final: 0.8205 (m) REVERT: e 40 ASP cc_start: 0.7476 (p0) cc_final: 0.7040 (t0) REVERT: e 92 ARG cc_start: 0.7367 (mtt90) cc_final: 0.7122 (mtt90) REVERT: e 125 LYS cc_start: 0.6149 (tppt) cc_final: 0.5823 (tppt) REVERT: g 104 VAL cc_start: 0.8059 (t) cc_final: 0.7706 (t) REVERT: g 108 ARG cc_start: 0.7423 (mtt180) cc_final: 0.6705 (ttt-90) REVERT: g 115 MET cc_start: 0.7623 (mmm) cc_final: 0.7289 (mmm) REVERT: g 125 ASP cc_start: 0.5341 (m-30) cc_final: 0.5068 (m-30) REVERT: h 14 ARG cc_start: 0.7253 (ttm110) cc_final: 0.6905 (ttt180) REVERT: j 6 ILE cc_start: 0.7396 (mm) cc_final: 0.6583 (pt) REVERT: j 56 HIS cc_start: 0.7253 (OUTLIER) cc_final: 0.6594 (t-90) REVERT: k 14 GLN cc_start: 0.6914 (mm110) cc_final: 0.5656 (pp30) REVERT: k 17 ASP cc_start: 0.6753 (m-30) cc_final: 0.6553 (m-30) REVERT: l 114 SER cc_start: 0.7041 (m) cc_final: 0.6670 (p) REVERT: m 68 LEU cc_start: 0.8325 (tp) cc_final: 0.7951 (tp) REVERT: n 8 ARG cc_start: 0.6686 (mtt180) cc_final: 0.6183 (mtt180) REVERT: n 75 ARG cc_start: 0.6698 (mtm180) cc_final: 0.6310 (mtm-85) REVERT: n 89 MET cc_start: 0.7349 (mmt) cc_final: 0.6975 (mmp) REVERT: o 76 ARG cc_start: 0.6796 (ttm110) cc_final: 0.6573 (ttp-170) REVERT: s 56 HIS cc_start: 0.6572 (OUTLIER) cc_final: 0.5390 (m90) REVERT: s 66 VAL cc_start: 0.7699 (OUTLIER) cc_final: 0.7378 (m) REVERT: u 53 LYS cc_start: 0.7842 (mmmm) cc_final: 0.7473 (ttpt) REVERT: x 357 GLU cc_start: 0.6387 (mp0) cc_final: 0.6047 (mp0) REVERT: x 400 ASP cc_start: 0.7080 (OUTLIER) cc_final: 0.6871 (p0) REVERT: x 410 PHE cc_start: 0.7785 (p90) cc_final: 0.7458 (p90) REVERT: x 577 LEU cc_start: 0.5079 (pt) cc_final: 0.3773 (tp) REVERT: x 593 LYS cc_start: 0.5769 (tptt) cc_final: 0.4552 (mtmt) outliers start: 298 outliers final: 229 residues processed: 1291 average time/residue: 1.1114 time to fit residues: 2528.1065 Evaluate side-chains 1295 residues out of total 5431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 1052 time to evaluate : 5.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 21 LEU Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 38 LEU Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 31 LEU Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 4 residue 35 GLN Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 28 VAL Chi-restraints excluded: chain 6 residue 32 LEU Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain C residue 52 HIS Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 165 HIS Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 172 PHE Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain H residue 27 ARG Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain K residue 29 HIS Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 131 VAL Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 56 LYS Chi-restraints excluded: chain O residue 67 ASN Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain P residue 65 ASN Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 82 SER Chi-restraints excluded: chain Q residue 58 GLN Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain S residue 94 ASP Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain T residue 92 ASN Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain U residue 72 PHE Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 21 ARG Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 43 ASP Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain W residue 8 ASN Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain X residue 4 CYS Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 25 LYS Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Z residue 26 LEU Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 101 THR Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 129 THR Chi-restraints excluded: chain b residue 146 SER Chi-restraints excluded: chain b residue 169 HIS Chi-restraints excluded: chain b residue 186 VAL Chi-restraints excluded: chain b residue 189 ASN Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 110 LEU Chi-restraints excluded: chain c residue 128 MET Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain c residue 185 THR Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 70 GLN Chi-restraints excluded: chain d residue 131 ILE Chi-restraints excluded: chain d residue 172 VAL Chi-restraints excluded: chain d residue 180 THR Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain d residue 203 TYR Chi-restraints excluded: chain e residue 37 VAL Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 139 THR Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 27 ASN Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 89 GLU Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain h residue 13 ILE Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 112 ASP Chi-restraints excluded: chain i residue 28 VAL Chi-restraints excluded: chain i residue 46 VAL Chi-restraints excluded: chain i residue 66 VAL Chi-restraints excluded: chain i residue 103 VAL Chi-restraints excluded: chain i residue 126 PHE Chi-restraints excluded: chain j residue 22 THR Chi-restraints excluded: chain j residue 56 HIS Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 51 PHE Chi-restraints excluded: chain k residue 69 CYS Chi-restraints excluded: chain k residue 107 THR Chi-restraints excluded: chain l residue 7 VAL Chi-restraints excluded: chain l residue 13 ARG Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 101 LEU Chi-restraints excluded: chain m residue 40 GLU Chi-restraints excluded: chain m residue 44 ILE Chi-restraints excluded: chain m residue 48 SER Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 82 LEU Chi-restraints excluded: chain n residue 55 SER Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 23 SER Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain o residue 78 THR Chi-restraints excluded: chain p residue 52 LEU Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 66 THR Chi-restraints excluded: chain p residue 78 VAL Chi-restraints excluded: chain q residue 6 THR Chi-restraints excluded: chain q residue 16 MET Chi-restraints excluded: chain q residue 46 HIS Chi-restraints excluded: chain q residue 49 ASN Chi-restraints excluded: chain r residue 39 VAL Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 56 HIS Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 65 MET Chi-restraints excluded: chain s residue 66 VAL Chi-restraints excluded: chain s residue 76 THR Chi-restraints excluded: chain t residue 3 ILE Chi-restraints excluded: chain t residue 19 HIS Chi-restraints excluded: chain t residue 67 HIS Chi-restraints excluded: chain t residue 74 HIS Chi-restraints excluded: chain x residue 39 ILE Chi-restraints excluded: chain x residue 42 VAL Chi-restraints excluded: chain x residue 67 THR Chi-restraints excluded: chain x residue 83 ILE Chi-restraints excluded: chain x residue 98 VAL Chi-restraints excluded: chain x residue 105 LEU Chi-restraints excluded: chain x residue 118 VAL Chi-restraints excluded: chain x residue 153 VAL Chi-restraints excluded: chain x residue 264 THR Chi-restraints excluded: chain x residue 291 VAL Chi-restraints excluded: chain x residue 400 ASP Chi-restraints excluded: chain x residue 417 ILE Chi-restraints excluded: chain x residue 448 THR Chi-restraints excluded: chain x residue 465 LEU Chi-restraints excluded: chain x residue 493 ILE Chi-restraints excluded: chain x residue 519 ILE Chi-restraints excluded: chain x residue 635 SER Chi-restraints excluded: chain x residue 672 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1114 random chunks: chunk 664 optimal weight: 30.0000 chunk 428 optimal weight: 4.9990 chunk 641 optimal weight: 7.9990 chunk 323 optimal weight: 20.0000 chunk 210 optimal weight: 20.0000 chunk 208 optimal weight: 20.0000 chunk 682 optimal weight: 20.0000 chunk 731 optimal weight: 20.0000 chunk 530 optimal weight: 7.9990 chunk 100 optimal weight: 20.0000 chunk 843 optimal weight: 7.9990 overall best weight: 9.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 ASN ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 88 GLN ** b 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 85 GLN ** i 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 23 HIS ** o 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 8 GLN r 51 GLN ** x 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 165586 Z= 0.325 Angle : 0.783 23.449 247055 Z= 0.405 Chirality : 0.039 0.482 31400 Planarity : 0.007 0.128 13806 Dihedral : 24.172 179.461 81037 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 22.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.33 % Favored : 88.64 % Rotamer: Outliers : 6.03 % Allowed : 26.73 % Favored : 67.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.10), residues: 6551 helix: -0.25 (0.11), residues: 2187 sheet: -1.90 (0.15), residues: 1124 loop : -2.29 (0.10), residues: 3240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP x 126 HIS 0.074 0.002 HIS t 19 PHE 0.028 0.002 PHE P 73 TYR 0.075 0.002 TYR g 43 ARG 0.018 0.001 ARG x 490 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13102 Ramachandran restraints generated. 6551 Oldfield, 0 Emsley, 6551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13102 Ramachandran restraints generated. 6551 Oldfield, 0 Emsley, 6551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1398 residues out of total 5431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 314 poor density : 1084 time to evaluate : 5.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 3 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.8079 (tpp80) REVERT: 2 22 MET cc_start: 0.7575 (mmm) cc_final: 0.6773 (ttt) REVERT: 2 26 ASN cc_start: 0.7559 (t0) cc_final: 0.7201 (t0) REVERT: 3 28 LEU cc_start: 0.8825 (mp) cc_final: 0.8394 (tt) REVERT: 3 37 THR cc_start: 0.8453 (p) cc_final: 0.8180 (t) REVERT: 6 9 TYR cc_start: 0.7383 (t80) cc_final: 0.6919 (t80) REVERT: C 144 GLU cc_start: 0.7367 (mt-10) cc_final: 0.6578 (mt-10) REVERT: C 155 ARG cc_start: 0.8599 (ttp-110) cc_final: 0.8090 (ttp-110) REVERT: C 156 SER cc_start: 0.9161 (t) cc_final: 0.8930 (p) REVERT: D 148 GLN cc_start: 0.8381 (mp10) cc_final: 0.7662 (mt0) REVERT: E 155 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6993 (tm-30) REVERT: E 185 LYS cc_start: 0.8442 (mmtp) cc_final: 0.7858 (mtmt) REVERT: F 16 MET cc_start: 0.7667 (mmt) cc_final: 0.6460 (mtt) REVERT: F 95 MET cc_start: 0.6623 (ttp) cc_final: 0.5432 (tmm) REVERT: F 97 GLU cc_start: 0.6959 (tt0) cc_final: 0.6630 (tt0) REVERT: F 172 PHE cc_start: 0.7998 (OUTLIER) cc_final: 0.7352 (t80) REVERT: H 127 GLU cc_start: -0.0578 (OUTLIER) cc_final: -0.0850 (mt-10) REVERT: J 1 MET cc_start: 0.7522 (pmm) cc_final: 0.7211 (pmm) REVERT: J 119 PHE cc_start: 0.7907 (t80) cc_final: 0.7626 (t80) REVERT: J 128 ASN cc_start: 0.8884 (t0) cc_final: 0.8644 (t0) REVERT: L 128 THR cc_start: 0.8635 (p) cc_final: 0.8322 (p) REVERT: N 6 SER cc_start: 0.7640 (OUTLIER) cc_final: 0.6958 (p) REVERT: N 20 MET cc_start: 0.8344 (tmm) cc_final: 0.7970 (tmm) REVERT: N 35 LYS cc_start: 0.8712 (ttpp) cc_final: 0.8462 (mtpp) REVERT: O 2 ASP cc_start: 0.6333 (OUTLIER) cc_final: 0.5932 (p0) REVERT: O 56 LYS cc_start: 0.7276 (OUTLIER) cc_final: 0.6406 (mtpt) REVERT: O 60 GLU cc_start: 0.5113 (mp0) cc_final: 0.4860 (mp0) REVERT: P 18 SER cc_start: 0.8709 (t) cc_final: 0.8292 (t) REVERT: P 99 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8476 (tp) REVERT: P 112 ARG cc_start: 0.7748 (ttp-110) cc_final: 0.6625 (ttt180) REVERT: Q 86 SER cc_start: 0.9082 (m) cc_final: 0.8808 (p) REVERT: Q 101 ASP cc_start: 0.7877 (t70) cc_final: 0.7479 (t70) REVERT: S 1 MET cc_start: 0.5969 (OUTLIER) cc_final: 0.5451 (ptt) REVERT: S 25 ARG cc_start: 0.8453 (ttm-80) cc_final: 0.7974 (ttm-80) REVERT: S 86 MET cc_start: 0.8854 (tpt) cc_final: 0.8539 (tpt) REVERT: T 24 MET cc_start: 0.8009 (tpt) cc_final: 0.7589 (tpt) REVERT: U 13 LEU cc_start: 0.7193 (mp) cc_final: 0.6739 (tp) REVERT: U 72 PHE cc_start: 0.7801 (OUTLIER) cc_final: 0.7577 (t80) REVERT: V 21 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.7075 (mpt-90) REVERT: V 88 HIS cc_start: 0.7691 (t-170) cc_final: 0.7299 (t-170) REVERT: W 25 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7500 (mm-30) REVERT: X 25 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7727 (mttm) REVERT: X 70 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8400 (mm) REVERT: Z 9 THR cc_start: 0.8554 (p) cc_final: 0.8195 (m) REVERT: c 30 ASP cc_start: 0.7446 (t70) cc_final: 0.6970 (t70) REVERT: d 22 SER cc_start: 0.8081 (t) cc_final: 0.7756 (p) REVERT: d 59 LYS cc_start: 0.7237 (tttt) cc_final: 0.6945 (tttt) REVERT: d 118 SER cc_start: 0.8600 (t) cc_final: 0.8277 (m) REVERT: d 205 LYS cc_start: 0.6324 (tptp) cc_final: 0.5904 (tppt) REVERT: e 40 ASP cc_start: 0.7471 (p0) cc_final: 0.7006 (t0) REVERT: e 92 ARG cc_start: 0.7445 (mtt90) cc_final: 0.7144 (mtt90) REVERT: e 125 LYS cc_start: 0.6296 (tppt) cc_final: 0.5884 (tppt) REVERT: f 74 LEU cc_start: 0.8299 (mt) cc_final: 0.7957 (mt) REVERT: g 43 TYR cc_start: 0.7564 (m-80) cc_final: 0.7320 (m-80) REVERT: g 104 VAL cc_start: 0.8159 (t) cc_final: 0.7818 (t) REVERT: g 108 ARG cc_start: 0.7514 (mtt180) cc_final: 0.6788 (ttt-90) REVERT: g 115 MET cc_start: 0.8364 (mmm) cc_final: 0.7380 (mmm) REVERT: g 122 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7219 (mm-30) REVERT: g 125 ASP cc_start: 0.5664 (m-30) cc_final: 0.5397 (m-30) REVERT: h 14 ARG cc_start: 0.7222 (ttm110) cc_final: 0.6957 (ttt180) REVERT: i 6 TYR cc_start: 0.7296 (t80) cc_final: 0.6453 (t80) REVERT: j 6 ILE cc_start: 0.7404 (mm) cc_final: 0.6602 (pt) REVERT: j 56 HIS cc_start: 0.7294 (OUTLIER) cc_final: 0.6555 (t-90) REVERT: k 14 GLN cc_start: 0.6614 (mm110) cc_final: 0.5371 (pp30) REVERT: k 78 ILE cc_start: 0.8419 (mp) cc_final: 0.7793 (mt) REVERT: l 114 SER cc_start: 0.7224 (m) cc_final: 0.6715 (p) REVERT: m 68 LEU cc_start: 0.8400 (tp) cc_final: 0.8007 (tp) REVERT: n 75 ARG cc_start: 0.6757 (mtm180) cc_final: 0.6372 (mtm-85) REVERT: n 89 MET cc_start: 0.7449 (mmt) cc_final: 0.7062 (mmp) REVERT: q 39 ARG cc_start: 0.8137 (tpp-160) cc_final: 0.7795 (tpm170) REVERT: s 56 HIS cc_start: 0.6443 (OUTLIER) cc_final: 0.5369 (m90) REVERT: s 66 VAL cc_start: 0.7869 (OUTLIER) cc_final: 0.7602 (m) REVERT: t 59 ARG cc_start: 0.7964 (ttp-110) cc_final: 0.7464 (ttp-110) REVERT: u 53 LYS cc_start: 0.7881 (mmmm) cc_final: 0.7486 (ttpt) REVERT: x 357 GLU cc_start: 0.6542 (mp0) cc_final: 0.6195 (mp0) REVERT: x 361 ARG cc_start: 0.8406 (mtt90) cc_final: 0.8186 (mpt-90) REVERT: x 400 ASP cc_start: 0.7203 (OUTLIER) cc_final: 0.6975 (p0) REVERT: x 410 PHE cc_start: 0.7853 (p90) cc_final: 0.7522 (p90) REVERT: x 593 LYS cc_start: 0.5743 (tptt) cc_final: 0.4583 (mtmt) outliers start: 314 outliers final: 258 residues processed: 1287 average time/residue: 1.1094 time to fit residues: 2533.3431 Evaluate side-chains 1321 residues out of total 5431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 275 poor density : 1046 time to evaluate : 5.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 21 LEU Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 38 LEU Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 2 residue 3 ARG Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 31 LEU Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 4 residue 35 GLN Chi-restraints excluded: chain 6 residue 28 VAL Chi-restraints excluded: chain 6 residue 32 LEU Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain C residue 52 HIS Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 172 PHE Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain H residue 27 ARG Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain K residue 29 HIS Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain M residue 9 PHE Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 131 VAL Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 24 MET Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 2 ASP Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 56 LYS Chi-restraints excluded: chain O residue 67 ASN Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 58 GLN Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain T residue 92 ASN Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain U residue 72 PHE Chi-restraints excluded: chain U residue 87 GLU Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 21 ARG Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 43 ASP Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain W residue 8 ASN Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain W residue 19 VAL Chi-restraints excluded: chain W residue 27 VAL Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain X residue 4 CYS Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 25 LYS Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 101 THR Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 129 THR Chi-restraints excluded: chain b residue 146 SER Chi-restraints excluded: chain b residue 169 HIS Chi-restraints excluded: chain b residue 186 VAL Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain c residue 31 ASN Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 110 LEU Chi-restraints excluded: chain c residue 117 ASP Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 185 THR Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 131 ILE Chi-restraints excluded: chain d residue 172 VAL Chi-restraints excluded: chain d residue 180 THR Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain d residue 203 TYR Chi-restraints excluded: chain e residue 37 VAL Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 123 LEU Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 139 THR Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 51 ILE Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 27 ASN Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 32 ASP Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 89 GLU Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain h residue 13 ILE Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 78 SER Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 112 ASP Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 28 VAL Chi-restraints excluded: chain i residue 46 VAL Chi-restraints excluded: chain i residue 66 VAL Chi-restraints excluded: chain i residue 103 VAL Chi-restraints excluded: chain j residue 22 THR Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 56 HIS Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 51 PHE Chi-restraints excluded: chain k residue 69 CYS Chi-restraints excluded: chain k residue 107 THR Chi-restraints excluded: chain l residue 7 VAL Chi-restraints excluded: chain l residue 13 ARG Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 101 LEU Chi-restraints excluded: chain l residue 118 VAL Chi-restraints excluded: chain m residue 40 GLU Chi-restraints excluded: chain m residue 44 ILE Chi-restraints excluded: chain m residue 48 SER Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 82 LEU Chi-restraints excluded: chain n residue 55 SER Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 23 SER Chi-restraints excluded: chain o residue 37 HIS Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain o residue 78 THR Chi-restraints excluded: chain p residue 52 LEU Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 57 ILE Chi-restraints excluded: chain p residue 66 THR Chi-restraints excluded: chain p residue 78 VAL Chi-restraints excluded: chain q residue 6 THR Chi-restraints excluded: chain q residue 16 MET Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 46 HIS Chi-restraints excluded: chain q residue 49 ASN Chi-restraints excluded: chain q residue 60 ILE Chi-restraints excluded: chain r residue 39 VAL Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 56 HIS Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 65 MET Chi-restraints excluded: chain s residue 66 VAL Chi-restraints excluded: chain s residue 76 THR Chi-restraints excluded: chain t residue 65 LEU Chi-restraints excluded: chain t residue 67 HIS Chi-restraints excluded: chain t residue 74 HIS Chi-restraints excluded: chain x residue 25 THR Chi-restraints excluded: chain x residue 39 ILE Chi-restraints excluded: chain x residue 42 VAL Chi-restraints excluded: chain x residue 67 THR Chi-restraints excluded: chain x residue 83 ILE Chi-restraints excluded: chain x residue 98 VAL Chi-restraints excluded: chain x residue 105 LEU Chi-restraints excluded: chain x residue 137 ILE Chi-restraints excluded: chain x residue 151 LEU Chi-restraints excluded: chain x residue 153 VAL Chi-restraints excluded: chain x residue 264 THR Chi-restraints excluded: chain x residue 271 ASN Chi-restraints excluded: chain x residue 282 ILE Chi-restraints excluded: chain x residue 291 VAL Chi-restraints excluded: chain x residue 400 ASP Chi-restraints excluded: chain x residue 417 ILE Chi-restraints excluded: chain x residue 448 THR Chi-restraints excluded: chain x residue 457 ILE Chi-restraints excluded: chain x residue 465 LEU Chi-restraints excluded: chain x residue 493 ILE Chi-restraints excluded: chain x residue 519 ILE Chi-restraints excluded: chain x residue 635 SER Chi-restraints excluded: chain x residue 672 LEU Chi-restraints excluded: chain x residue 681 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1114 random chunks: chunk 976 optimal weight: 0.8980 chunk 1028 optimal weight: 4.9990 chunk 938 optimal weight: 7.9990 chunk 1000 optimal weight: 3.9990 chunk 602 optimal weight: 30.0000 chunk 435 optimal weight: 8.9990 chunk 785 optimal weight: 20.0000 chunk 307 optimal weight: 20.0000 chunk 904 optimal weight: 6.9990 chunk 946 optimal weight: 7.9990 chunk 997 optimal weight: 2.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 88 GLN b 102 ASN ** b 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 85 GLN ** i 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 8 GLN ** x 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 165586 Z= 0.181 Angle : 0.684 23.422 247055 Z= 0.360 Chirality : 0.035 0.472 31400 Planarity : 0.006 0.124 13806 Dihedral : 24.137 179.306 81037 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 4.82 % Allowed : 28.32 % Favored : 66.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.01 (0.10), residues: 6551 helix: -0.06 (0.11), residues: 2203 sheet: -1.75 (0.15), residues: 1097 loop : -2.10 (0.10), residues: 3251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP x 126 HIS 0.012 0.001 HIS E 165 PHE 0.021 0.002 PHE b 15 TYR 0.064 0.002 TYR g 43 ARG 0.014 0.001 ARG H 51 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13102 Ramachandran restraints generated. 6551 Oldfield, 0 Emsley, 6551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13102 Ramachandran restraints generated. 6551 Oldfield, 0 Emsley, 6551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1358 residues out of total 5431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 1107 time to evaluate : 5.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 48 TYR cc_start: 0.8403 (m-80) cc_final: 0.7975 (m-80) REVERT: 2 22 MET cc_start: 0.7489 (mmm) cc_final: 0.6668 (ttt) REVERT: 3 28 LEU cc_start: 0.8777 (mp) cc_final: 0.8347 (tt) REVERT: 3 37 THR cc_start: 0.8453 (p) cc_final: 0.8199 (t) REVERT: 6 9 TYR cc_start: 0.7151 (t80) cc_final: 0.6682 (t80) REVERT: C 144 GLU cc_start: 0.7287 (mt-10) cc_final: 0.6541 (mt-10) REVERT: C 155 ARG cc_start: 0.8509 (ttp-110) cc_final: 0.8018 (ttp-110) REVERT: D 148 GLN cc_start: 0.8191 (mp10) cc_final: 0.7551 (mt0) REVERT: E 155 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6964 (tm-30) REVERT: E 185 LYS cc_start: 0.8386 (mmtp) cc_final: 0.7847 (mtmt) REVERT: F 16 MET cc_start: 0.7504 (mmt) cc_final: 0.6295 (mtt) REVERT: F 95 MET cc_start: 0.6654 (ttp) cc_final: 0.5609 (tmm) REVERT: F 97 GLU cc_start: 0.6946 (tt0) cc_final: 0.5947 (tt0) REVERT: F 137 PHE cc_start: 0.7983 (m-80) cc_final: 0.7757 (m-80) REVERT: F 172 PHE cc_start: 0.7756 (OUTLIER) cc_final: 0.6933 (t80) REVERT: J 1 MET cc_start: 0.7249 (pmm) cc_final: 0.6874 (pmm) REVERT: J 119 PHE cc_start: 0.7878 (t80) cc_final: 0.7583 (t80) REVERT: J 128 ASN cc_start: 0.8941 (t0) cc_final: 0.8716 (t0) REVERT: L 55 MET cc_start: 0.8253 (tpp) cc_final: 0.8024 (mmt) REVERT: L 128 THR cc_start: 0.8542 (p) cc_final: 0.8194 (p) REVERT: M 18 ARG cc_start: 0.7843 (mmm-85) cc_final: 0.7523 (tpp80) REVERT: N 6 SER cc_start: 0.7629 (OUTLIER) cc_final: 0.6959 (p) REVERT: N 20 MET cc_start: 0.8279 (tmm) cc_final: 0.7934 (tmm) REVERT: O 2 ASP cc_start: 0.6018 (OUTLIER) cc_final: 0.5653 (p0) REVERT: O 56 LYS cc_start: 0.7173 (OUTLIER) cc_final: 0.6232 (mtpt) REVERT: O 103 VAL cc_start: 0.8237 (m) cc_final: 0.7953 (t) REVERT: P 10 GLU cc_start: 0.8434 (mp0) cc_final: 0.8121 (mp0) REVERT: P 18 SER cc_start: 0.8598 (t) cc_final: 0.8220 (t) REVERT: P 99 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8416 (tp) REVERT: P 112 ARG cc_start: 0.7693 (ttp-110) cc_final: 0.6591 (ttt180) REVERT: Q 64 ILE cc_start: 0.9350 (mt) cc_final: 0.8907 (tt) REVERT: Q 86 SER cc_start: 0.9075 (m) cc_final: 0.8750 (p) REVERT: Q 101 ASP cc_start: 0.7862 (t70) cc_final: 0.7411 (t70) REVERT: S 1 MET cc_start: 0.6058 (OUTLIER) cc_final: 0.5462 (ptt) REVERT: S 25 ARG cc_start: 0.8222 (ttm-80) cc_final: 0.7864 (ttm-80) REVERT: S 86 MET cc_start: 0.8819 (tpt) cc_final: 0.8542 (tpt) REVERT: T 24 MET cc_start: 0.7975 (tpt) cc_final: 0.7509 (tpt) REVERT: U 13 LEU cc_start: 0.7023 (mp) cc_final: 0.6579 (tp) REVERT: U 72 PHE cc_start: 0.7770 (OUTLIER) cc_final: 0.7349 (t80) REVERT: V 21 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.7515 (mpt-90) REVERT: W 25 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7258 (mm-30) REVERT: X 25 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7772 (mttm) REVERT: X 32 LEU cc_start: 0.9181 (mt) cc_final: 0.8977 (mp) REVERT: X 70 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8398 (mm) REVERT: Z 9 THR cc_start: 0.8532 (p) cc_final: 0.8174 (m) REVERT: b 121 GLN cc_start: 0.6644 (tm-30) cc_final: 0.6134 (tm-30) REVERT: d 22 SER cc_start: 0.7862 (t) cc_final: 0.7604 (p) REVERT: d 59 LYS cc_start: 0.7215 (tttt) cc_final: 0.7006 (tttt) REVERT: d 118 SER cc_start: 0.8370 (t) cc_final: 0.8085 (m) REVERT: e 12 GLU cc_start: 0.6959 (tt0) cc_final: 0.6745 (tt0) REVERT: e 40 ASP cc_start: 0.7451 (p0) cc_final: 0.7176 (t70) REVERT: e 92 ARG cc_start: 0.7276 (mtt90) cc_final: 0.7024 (mtt90) REVERT: g 30 MET cc_start: 0.8515 (ttp) cc_final: 0.8291 (ttp) REVERT: g 43 TYR cc_start: 0.7530 (m-80) cc_final: 0.7236 (m-80) REVERT: g 104 VAL cc_start: 0.8110 (t) cc_final: 0.7738 (t) REVERT: g 108 ARG cc_start: 0.7353 (mtt180) cc_final: 0.6732 (ttt-90) REVERT: g 115 MET cc_start: 0.8163 (mmm) cc_final: 0.7373 (mmm) REVERT: i 6 TYR cc_start: 0.7262 (t80) cc_final: 0.6454 (t80) REVERT: j 6 ILE cc_start: 0.7367 (mm) cc_final: 0.6653 (pt) REVERT: j 56 HIS cc_start: 0.7243 (OUTLIER) cc_final: 0.6514 (t-90) REVERT: k 14 GLN cc_start: 0.6715 (mm110) cc_final: 0.5503 (pp30) REVERT: k 37 GLN cc_start: 0.7477 (pm20) cc_final: 0.7199 (pm20) REVERT: k 78 ILE cc_start: 0.8310 (mp) cc_final: 0.7561 (mt) REVERT: l 114 SER cc_start: 0.7033 (m) cc_final: 0.6695 (p) REVERT: m 68 LEU cc_start: 0.8385 (tp) cc_final: 0.8000 (tt) REVERT: n 8 ARG cc_start: 0.6664 (mtt180) cc_final: 0.6201 (mtt180) REVERT: n 65 ARG cc_start: 0.7088 (tmm160) cc_final: 0.6801 (ttt180) REVERT: n 75 ARG cc_start: 0.6695 (mtm180) cc_final: 0.6323 (mtm-85) REVERT: n 89 MET cc_start: 0.7386 (mmt) cc_final: 0.7064 (mmp) REVERT: q 39 ARG cc_start: 0.8123 (tpp-160) cc_final: 0.7824 (tpm170) REVERT: s 56 HIS cc_start: 0.6257 (OUTLIER) cc_final: 0.5174 (m90) REVERT: s 66 VAL cc_start: 0.7724 (OUTLIER) cc_final: 0.7444 (m) REVERT: t 59 ARG cc_start: 0.7867 (ttp-110) cc_final: 0.7359 (ttp-110) REVERT: t 70 LYS cc_start: 0.5912 (ttpt) cc_final: 0.5520 (tttt) REVERT: u 53 LYS cc_start: 0.7820 (mmmm) cc_final: 0.7483 (ttpt) REVERT: x 357 GLU cc_start: 0.6476 (mp0) cc_final: 0.6226 (mp0) REVERT: x 361 ARG cc_start: 0.8335 (mtt90) cc_final: 0.8057 (mpt-90) REVERT: x 400 ASP cc_start: 0.7044 (OUTLIER) cc_final: 0.6837 (p0) REVERT: x 410 PHE cc_start: 0.7643 (p90) cc_final: 0.7420 (p90) REVERT: x 593 LYS cc_start: 0.5426 (tptt) cc_final: 0.4368 (mtmt) outliers start: 251 outliers final: 204 residues processed: 1267 average time/residue: 1.1081 time to fit residues: 2475.6609 Evaluate side-chains 1274 residues out of total 5431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 1055 time to evaluate : 5.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 21 LEU Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 38 LEU Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 31 LEU Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 4 residue 35 GLN Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 28 VAL Chi-restraints excluded: chain 6 residue 32 LEU Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain C residue 52 HIS Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 172 PHE Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 137 LYS Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain K residue 29 HIS Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 131 VAL Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 2 ASP Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 56 LYS Chi-restraints excluded: chain O residue 67 ASN Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 65 ASN Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 82 SER Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain Q residue 58 GLN Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain S residue 94 ASP Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain T residue 92 ASN Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain U residue 72 PHE Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 21 ARG Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 43 ASP Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain W residue 8 ASN Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain X residue 4 CYS Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 25 LYS Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Z residue 26 LEU Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 101 THR Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 146 SER Chi-restraints excluded: chain b residue 169 HIS Chi-restraints excluded: chain b residue 186 VAL Chi-restraints excluded: chain b residue 189 ASN Chi-restraints excluded: chain c residue 31 ASN Chi-restraints excluded: chain c residue 43 THR Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 110 LEU Chi-restraints excluded: chain c residue 117 ASP Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain c residue 185 THR Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 131 ILE Chi-restraints excluded: chain d residue 172 VAL Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain d residue 203 TYR Chi-restraints excluded: chain e residue 37 VAL Chi-restraints excluded: chain e residue 123 LEU Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 139 THR Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 51 ILE Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 27 ASN Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 89 GLU Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain h residue 13 ILE Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 78 SER Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 112 ASP Chi-restraints excluded: chain i residue 28 VAL Chi-restraints excluded: chain i residue 46 VAL Chi-restraints excluded: chain i residue 57 VAL Chi-restraints excluded: chain i residue 66 VAL Chi-restraints excluded: chain i residue 103 VAL Chi-restraints excluded: chain i residue 126 PHE Chi-restraints excluded: chain j residue 22 THR Chi-restraints excluded: chain j residue 56 HIS Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 51 PHE Chi-restraints excluded: chain k residue 69 CYS Chi-restraints excluded: chain k residue 107 THR Chi-restraints excluded: chain l residue 7 VAL Chi-restraints excluded: chain l residue 13 ARG Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain m residue 40 GLU Chi-restraints excluded: chain n residue 55 SER Chi-restraints excluded: chain n residue 84 VAL Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 23 SER Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain o residue 78 THR Chi-restraints excluded: chain p residue 52 LEU Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 57 ILE Chi-restraints excluded: chain p residue 78 VAL Chi-restraints excluded: chain q residue 6 THR Chi-restraints excluded: chain q residue 46 HIS Chi-restraints excluded: chain q residue 49 ASN Chi-restraints excluded: chain s residue 56 HIS Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 65 MET Chi-restraints excluded: chain s residue 66 VAL Chi-restraints excluded: chain t residue 3 ILE Chi-restraints excluded: chain t residue 65 LEU Chi-restraints excluded: chain t residue 74 HIS Chi-restraints excluded: chain x residue 37 HIS Chi-restraints excluded: chain x residue 39 ILE Chi-restraints excluded: chain x residue 42 VAL Chi-restraints excluded: chain x residue 67 THR Chi-restraints excluded: chain x residue 83 ILE Chi-restraints excluded: chain x residue 98 VAL Chi-restraints excluded: chain x residue 105 LEU Chi-restraints excluded: chain x residue 264 THR Chi-restraints excluded: chain x residue 282 ILE Chi-restraints excluded: chain x residue 291 VAL Chi-restraints excluded: chain x residue 400 ASP Chi-restraints excluded: chain x residue 417 ILE Chi-restraints excluded: chain x residue 448 THR Chi-restraints excluded: chain x residue 457 ILE Chi-restraints excluded: chain x residue 465 LEU Chi-restraints excluded: chain x residue 493 ILE Chi-restraints excluded: chain x residue 519 ILE Chi-restraints excluded: chain x residue 672 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1114 random chunks: chunk 657 optimal weight: 30.0000 chunk 1058 optimal weight: 3.9990 chunk 645 optimal weight: 30.0000 chunk 501 optimal weight: 4.9990 chunk 735 optimal weight: 20.0000 chunk 1109 optimal weight: 20.0000 chunk 1021 optimal weight: 5.9990 chunk 883 optimal weight: 3.9990 chunk 91 optimal weight: 20.0000 chunk 682 optimal weight: 20.0000 chunk 541 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 86 GLN ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN K 93 GLN ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 ASN ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 88 GLN ** b 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 85 GLN ** i 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 58 ASN l 5 GLN ** o 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 51 GLN ** x 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 165586 Z= 0.217 Angle : 0.702 23.360 247055 Z= 0.368 Chirality : 0.036 0.478 31400 Planarity : 0.006 0.125 13806 Dihedral : 24.106 179.112 81037 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 19.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.83 % Favored : 90.15 % Rotamer: Outliers : 4.65 % Allowed : 28.65 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.00 (0.10), residues: 6551 helix: -0.06 (0.11), residues: 2200 sheet: -1.77 (0.15), residues: 1102 loop : -2.09 (0.10), residues: 3249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP x 126 HIS 0.012 0.001 HIS r 73 PHE 0.024 0.002 PHE V 2 TYR 0.059 0.002 TYR g 43 ARG 0.018 0.001 ARG Y 23 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13102 Ramachandran restraints generated. 6551 Oldfield, 0 Emsley, 6551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13102 Ramachandran restraints generated. 6551 Oldfield, 0 Emsley, 6551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1303 residues out of total 5431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 1061 time to evaluate : 5.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 48 TYR cc_start: 0.8433 (m-80) cc_final: 0.8090 (m-80) REVERT: 2 22 MET cc_start: 0.7493 (mmm) cc_final: 0.6719 (ttt) REVERT: 3 28 LEU cc_start: 0.8779 (mp) cc_final: 0.8371 (tt) REVERT: 3 37 THR cc_start: 0.8503 (p) cc_final: 0.8218 (t) REVERT: 6 9 TYR cc_start: 0.7207 (t80) cc_final: 0.6694 (t80) REVERT: C 144 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6415 (mt-10) REVERT: C 155 ARG cc_start: 0.8526 (ttp-110) cc_final: 0.8024 (ttp-110) REVERT: D 148 GLN cc_start: 0.8287 (mp10) cc_final: 0.7605 (mt0) REVERT: E 185 LYS cc_start: 0.8346 (mmtp) cc_final: 0.7782 (mtmt) REVERT: F 16 MET cc_start: 0.7537 (mmt) cc_final: 0.6318 (mtt) REVERT: F 95 MET cc_start: 0.6560 (ttp) cc_final: 0.5415 (tmm) REVERT: F 97 GLU cc_start: 0.6958 (tt0) cc_final: 0.5848 (tt0) REVERT: F 137 PHE cc_start: 0.7989 (m-80) cc_final: 0.7770 (m-80) REVERT: F 172 PHE cc_start: 0.7946 (OUTLIER) cc_final: 0.7343 (t80) REVERT: H 127 GLU cc_start: -0.0537 (OUTLIER) cc_final: -0.0807 (mt-10) REVERT: J 1 MET cc_start: 0.7263 (pmm) cc_final: 0.6887 (pmm) REVERT: J 119 PHE cc_start: 0.7887 (t80) cc_final: 0.7566 (t80) REVERT: J 128 ASN cc_start: 0.8929 (t0) cc_final: 0.8670 (t0) REVERT: L 128 THR cc_start: 0.8620 (p) cc_final: 0.8296 (p) REVERT: M 18 ARG cc_start: 0.7890 (mmm-85) cc_final: 0.7538 (tpp80) REVERT: N 6 SER cc_start: 0.7630 (OUTLIER) cc_final: 0.6958 (p) REVERT: N 20 MET cc_start: 0.8293 (tmm) cc_final: 0.7937 (tmm) REVERT: O 2 ASP cc_start: 0.5988 (OUTLIER) cc_final: 0.5615 (p0) REVERT: O 56 LYS cc_start: 0.7259 (OUTLIER) cc_final: 0.6244 (mtpp) REVERT: O 60 GLU cc_start: 0.5013 (mp0) cc_final: 0.4783 (mp0) REVERT: P 18 SER cc_start: 0.8615 (t) cc_final: 0.8235 (t) REVERT: P 99 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8456 (tp) REVERT: P 112 ARG cc_start: 0.7711 (ttp-110) cc_final: 0.6590 (ttp-170) REVERT: Q 58 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7195 (mt0) REVERT: Q 64 ILE cc_start: 0.9379 (mt) cc_final: 0.8910 (tt) REVERT: Q 86 SER cc_start: 0.9090 (m) cc_final: 0.8777 (p) REVERT: Q 101 ASP cc_start: 0.8048 (t70) cc_final: 0.7671 (t70) REVERT: S 1 MET cc_start: 0.6088 (OUTLIER) cc_final: 0.5530 (ptt) REVERT: S 25 ARG cc_start: 0.8260 (ttm-80) cc_final: 0.7874 (ttm-80) REVERT: S 86 MET cc_start: 0.8844 (tpt) cc_final: 0.8568 (tpt) REVERT: T 24 MET cc_start: 0.7933 (tpt) cc_final: 0.7455 (tpt) REVERT: U 13 LEU cc_start: 0.7073 (mp) cc_final: 0.6628 (tp) REVERT: U 72 PHE cc_start: 0.7789 (OUTLIER) cc_final: 0.7400 (t80) REVERT: V 21 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.7401 (mpt-90) REVERT: W 25 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7284 (mm-30) REVERT: X 25 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7680 (mttm) REVERT: X 32 LEU cc_start: 0.9206 (mt) cc_final: 0.8998 (mp) REVERT: X 70 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8470 (mm) REVERT: Z 9 THR cc_start: 0.8562 (p) cc_final: 0.8155 (m) REVERT: b 42 LEU cc_start: 0.5647 (OUTLIER) cc_final: 0.5082 (mp) REVERT: c 125 ARG cc_start: 0.6667 (mpp-170) cc_final: 0.6422 (mpp-170) REVERT: d 22 SER cc_start: 0.7934 (t) cc_final: 0.7633 (p) REVERT: d 118 SER cc_start: 0.8426 (t) cc_final: 0.8149 (m) REVERT: e 40 ASP cc_start: 0.7333 (p0) cc_final: 0.7060 (t70) REVERT: e 125 LYS cc_start: 0.6228 (tppt) cc_final: 0.5883 (tppt) REVERT: g 30 MET cc_start: 0.8533 (ttp) cc_final: 0.8311 (ttp) REVERT: g 43 TYR cc_start: 0.7508 (m-80) cc_final: 0.7192 (m-80) REVERT: g 104 VAL cc_start: 0.8225 (t) cc_final: 0.7883 (t) REVERT: g 108 ARG cc_start: 0.7377 (mtt180) cc_final: 0.6751 (ttt-90) REVERT: g 115 MET cc_start: 0.8086 (mmm) cc_final: 0.7379 (mmm) REVERT: h 110 MET cc_start: 0.8899 (pmm) cc_final: 0.8198 (pmm) REVERT: i 6 TYR cc_start: 0.7258 (t80) cc_final: 0.6450 (t80) REVERT: i 87 MET cc_start: 0.2482 (mmp) cc_final: 0.2214 (mmp) REVERT: j 6 ILE cc_start: 0.7328 (mm) cc_final: 0.6566 (pt) REVERT: j 56 HIS cc_start: 0.7257 (OUTLIER) cc_final: 0.6520 (t-90) REVERT: k 14 GLN cc_start: 0.6735 (mm110) cc_final: 0.5497 (pp30) REVERT: k 78 ILE cc_start: 0.8312 (mp) cc_final: 0.7570 (mt) REVERT: l 65 TYR cc_start: 0.8165 (t80) cc_final: 0.7889 (t80) REVERT: l 114 SER cc_start: 0.7148 (m) cc_final: 0.6748 (p) REVERT: m 68 LEU cc_start: 0.8392 (tp) cc_final: 0.8039 (tp) REVERT: n 8 ARG cc_start: 0.6692 (mtt180) cc_final: 0.6245 (mtt180) REVERT: n 75 ARG cc_start: 0.6724 (mtm180) cc_final: 0.6321 (mtm-85) REVERT: n 89 MET cc_start: 0.7426 (mmt) cc_final: 0.7080 (mmp) REVERT: q 39 ARG cc_start: 0.8099 (tpp-160) cc_final: 0.7781 (tpm170) REVERT: r 72 ARG cc_start: 0.5707 (mtm-85) cc_final: 0.5185 (mmt90) REVERT: s 56 HIS cc_start: 0.6260 (OUTLIER) cc_final: 0.5137 (m90) REVERT: s 66 VAL cc_start: 0.7753 (OUTLIER) cc_final: 0.7446 (m) REVERT: t 59 ARG cc_start: 0.7950 (ttp-110) cc_final: 0.7434 (ttp-110) REVERT: t 70 LYS cc_start: 0.5969 (ttpt) cc_final: 0.5553 (tttt) REVERT: u 53 LYS cc_start: 0.7838 (mmmm) cc_final: 0.7481 (ttpt) REVERT: x 357 GLU cc_start: 0.6570 (mp0) cc_final: 0.6282 (mp0) REVERT: x 361 ARG cc_start: 0.8367 (mtt90) cc_final: 0.8093 (mpt-90) REVERT: x 400 ASP cc_start: 0.7124 (OUTLIER) cc_final: 0.6894 (p0) REVERT: x 410 PHE cc_start: 0.7725 (p90) cc_final: 0.7493 (p90) REVERT: x 582 TYR cc_start: 0.5312 (OUTLIER) cc_final: 0.4332 (p90) REVERT: x 593 LYS cc_start: 0.5627 (tptt) cc_final: 0.4504 (mtmt) outliers start: 242 outliers final: 208 residues processed: 1222 average time/residue: 1.1095 time to fit residues: 2385.3438 Evaluate side-chains 1268 residues out of total 5431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 1042 time to evaluate : 5.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 21 LEU Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 38 LEU Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 31 LEU Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 4 residue 35 GLN Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 28 VAL Chi-restraints excluded: chain 6 residue 32 LEU Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain C residue 52 HIS Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 172 PHE Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 137 LYS Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 11 ASN Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain K residue 29 HIS Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 131 VAL Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 2 ASP Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 56 LYS Chi-restraints excluded: chain O residue 67 ASN Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain P residue 65 ASN Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 82 SER Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain Q residue 58 GLN Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain T residue 92 ASN Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain U residue 72 PHE Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 21 ARG Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 43 ASP Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain W residue 8 ASN Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain W residue 27 VAL Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain X residue 4 CYS Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 25 LYS Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 101 THR Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 146 SER Chi-restraints excluded: chain b residue 169 HIS Chi-restraints excluded: chain b residue 186 VAL Chi-restraints excluded: chain b residue 189 ASN Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain c residue 31 ASN Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 110 LEU Chi-restraints excluded: chain c residue 117 ASP Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 185 THR Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 131 ILE Chi-restraints excluded: chain d residue 172 VAL Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain d residue 203 TYR Chi-restraints excluded: chain e residue 37 VAL Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 88 MET Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 27 ASN Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 89 GLU Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain h residue 13 ILE Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 78 SER Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 112 ASP Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 28 VAL Chi-restraints excluded: chain i residue 46 VAL Chi-restraints excluded: chain i residue 57 VAL Chi-restraints excluded: chain i residue 66 VAL Chi-restraints excluded: chain i residue 103 VAL Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 22 THR Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 56 HIS Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 51 PHE Chi-restraints excluded: chain k residue 69 CYS Chi-restraints excluded: chain k residue 107 THR Chi-restraints excluded: chain l residue 7 VAL Chi-restraints excluded: chain l residue 13 ARG Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain m residue 40 GLU Chi-restraints excluded: chain m residue 44 ILE Chi-restraints excluded: chain n residue 55 SER Chi-restraints excluded: chain n residue 84 VAL Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 23 SER Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain o residue 78 THR Chi-restraints excluded: chain p residue 52 LEU Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 57 ILE Chi-restraints excluded: chain p residue 66 THR Chi-restraints excluded: chain p residue 78 VAL Chi-restraints excluded: chain q residue 6 THR Chi-restraints excluded: chain q residue 16 MET Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 46 HIS Chi-restraints excluded: chain q residue 49 ASN Chi-restraints excluded: chain r residue 39 VAL Chi-restraints excluded: chain s residue 56 HIS Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 65 MET Chi-restraints excluded: chain s residue 66 VAL Chi-restraints excluded: chain t residue 65 LEU Chi-restraints excluded: chain t residue 74 HIS Chi-restraints excluded: chain x residue 37 HIS Chi-restraints excluded: chain x residue 39 ILE Chi-restraints excluded: chain x residue 42 VAL Chi-restraints excluded: chain x residue 67 THR Chi-restraints excluded: chain x residue 83 ILE Chi-restraints excluded: chain x residue 98 VAL Chi-restraints excluded: chain x residue 105 LEU Chi-restraints excluded: chain x residue 264 THR Chi-restraints excluded: chain x residue 291 VAL Chi-restraints excluded: chain x residue 400 ASP Chi-restraints excluded: chain x residue 448 THR Chi-restraints excluded: chain x residue 457 ILE Chi-restraints excluded: chain x residue 465 LEU Chi-restraints excluded: chain x residue 493 ILE Chi-restraints excluded: chain x residue 519 ILE Chi-restraints excluded: chain x residue 582 TYR Chi-restraints excluded: chain x residue 672 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1114 random chunks: chunk 701 optimal weight: 20.0000 chunk 941 optimal weight: 6.9990 chunk 270 optimal weight: 20.0000 chunk 814 optimal weight: 5.9990 chunk 130 optimal weight: 40.0000 chunk 245 optimal weight: 20.0000 chunk 885 optimal weight: 30.0000 chunk 370 optimal weight: 20.0000 chunk 908 optimal weight: 10.0000 chunk 112 optimal weight: 20.0000 chunk 163 optimal weight: 20.0000 overall best weight: 12.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 68 ASN ** X 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 88 GLN ** b 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 121 ASN ** i 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 66 GLN ** o 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 8 GLN r 51 GLN ** x 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.114021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.099734 restraints weight = 427207.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.101291 restraints weight = 185605.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.102291 restraints weight = 106632.540| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.387 165586 Z= 0.324 Angle : 0.740 59.154 247055 Z= 0.390 Chirality : 0.038 1.229 31400 Planarity : 0.006 0.125 13806 Dihedral : 24.102 179.099 81037 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.91 % Favored : 90.08 % Rotamer: Outliers : 4.84 % Allowed : 28.55 % Favored : 66.60 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.04 (0.10), residues: 6551 helix: -0.09 (0.11), residues: 2205 sheet: -1.80 (0.15), residues: 1113 loop : -2.10 (0.10), residues: 3233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP x 126 HIS 0.010 0.001 HIS r 73 PHE 0.021 0.002 PHE M 130 TYR 0.088 0.002 TYR J 75 ARG 0.021 0.001 ARG F 147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 38968.82 seconds wall clock time: 681 minutes 40.22 seconds (40900.22 seconds total)