Starting phenix.real_space_refine on Sat Mar 23 02:22:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysu_10908/03_2024/6ysu_10908_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysu_10908/03_2024/6ysu_10908.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysu_10908/03_2024/6ysu_10908_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysu_10908/03_2024/6ysu_10908_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysu_10908/03_2024/6ysu_10908_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysu_10908/03_2024/6ysu_10908.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysu_10908/03_2024/6ysu_10908.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysu_10908/03_2024/6ysu_10908_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysu_10908/03_2024/6ysu_10908_updated.pdb" } resolution = 3.7 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: 8 Type Number sf(0) Gaussians Zn 1 6.06 5 P 4645 5.49 5 Mg 356 5.21 5 S 142 5.16 5 Na 1 4.78 5 C 73457 2.51 5 N 27254 2.21 5 O 40543 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 GLU 35": "OE1" <-> "OE2" Residue "0 ARG 39": "NH1" <-> "NH2" Residue "0 ARG 51": "NH1" <-> "NH2" 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 "C ARG 132": "NH1" <-> "NH2" Residue "C GLU 193": "OE1" <-> "OE2" Residue "C ARG 211": "NH1" <-> "NH2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ARG 21": "NH1" <-> "NH2" 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 GLU 122": "OE1" <-> "OE2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" 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 "G ARG 2": "NH1" <-> "NH2" Residue "G GLU 129": "OE1" <-> "OE2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 162": "NH1" <-> "NH2" Residue "G ARG 169": "NH1" <-> "NH2" Residue "H ARG 51": "NH1" <-> "NH2" Residue "H GLU 55": "OE1" <-> "OE2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J GLU 90": "OE1" <-> "OE2" Residue "J ARG 95": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J GLU 102": "OE1" <-> "OE2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "K GLU 106": "OE1" <-> "OE2" Residue "K GLU 121": "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 76": "OE1" <-> "OE2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L GLU 106": "OE1" <-> "OE2" 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 GLU 47": "OE1" <-> "OE2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 59": "NH1" <-> "NH2" Residue "M GLU 104": "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 70": "OE1" <-> "OE2" Residue "P ARG 88": "NH1" <-> "NH2" Residue "P ARG 100": "NH1" <-> "NH2" Residue "P GLU 101": "OE1" <-> "OE2" Residue "P ARG 108": "NH1" <-> "NH2" 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 ARG 68": "NH1" <-> "NH2" Residue "R GLU 70": "OE1" <-> "OE2" 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 GLU 52": "OE1" <-> "OE2" 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 56": "OE1" <-> "OE2" Residue "T ARG 73": "NH1" <-> "NH2" Residue "T GLU 89": "OE1" <-> "OE2" 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 ARG 93": "NH1" <-> "NH2" Residue "Y GLU 12": "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 55": "OE1" <-> "OE2" Residue "b ASP 87": "OD1" <-> "OD2" Residue "b ARG 107": "NH1" <-> "NH2" Residue "b GLU 132": "OE1" <-> "OE2" Residue "b GLU 168": "OE1" <-> "OE2" Residue "b ARG 224": "NH1" <-> "NH2" 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 151": "OE1" <-> "OE2" Residue "c GLU 160": "OE1" <-> "OE2" Residue "c GLU 169": "OE1" <-> "OE2" Residue "d ARG 25": "NH1" <-> "NH2" Residue "d ARG 69": "NH1" <-> "NH2" Residue "d GLU 77": "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 178": "OE1" <-> "OE2" Residue "d ARG 183": "NH1" <-> "NH2" Residue "e ARG 156": "NH1" <-> "NH2" Residue "f ARG 2": "NH1" <-> "NH2" Residue "f GLU 16": "OE1" <-> "OE2" Residue "g GLU 105": "OE1" <-> "OE2" Residue "h GLU 46": "OE1" <-> "OE2" Residue "h GLU 90": "OE1" <-> "OE2" Residue "i ARG 40": "NH1" <-> "NH2" Residue "i ARG 44": "NH1" <-> "NH2" Residue "i GLU 96": "OE1" <-> "OE2" Residue "i ARG 123": "NH1" <-> "NH2" Residue "j GLU 24": "OE1" <-> "OE2" Residue "j GLU 47": "OE1" <-> "OE2" Residue "k GLU 75": "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 "m GLU 46": "OE1" <-> "OE2" Residue "n ARG 23": "NH1" <-> "NH2" Residue "n GLU 86": "OE1" <-> "OE2" Residue "o GLU 82": "OE1" <-> "OE2" Residue "p ARG 28": "NH1" <-> "NH2" Residue "p GLU 47": "OE1" <-> "OE2" Residue "q GLU 79": "OE1" <-> "OE2" Residue "r GLU 19": "OE1" <-> "OE2" Residue "s ARG 2": "NH1" <-> "NH2" Residue "s ARG 80": "NH1" <-> "NH2" Residue "u GLU 7": "OE1" <-> "OE2" Residue "u ARG 16": "NH1" <-> "NH2" Residue "u ARG 20": "NH1" <-> "NH2" Residue "u ARG 34": "NH1" <-> "NH2" Residue "u GLU 38": "OE1" <-> "OE2" Residue "u GLU 43": "OE1" <-> "OE2" Residue "u ARG 46": "NH1" <-> "NH2" Residue "v ARG 12": "NH1" <-> "NH2" Residue "y ARG 21": "NH1" <-> "NH2" Residue "y ARG 55": "NH1" <-> "NH2" Residue "y GLU 76": "OE1" <-> "OE2" Residue "y ARG 78": "NH1" <-> "NH2" Residue "y ARG 90": "NH1" <-> "NH2" Residue "y ARG 105": "NH1" <-> "NH2" Residue "y ARG 109": "NH1" <-> "NH2" Residue "y ARG 117": "NH1" <-> "NH2" Residue "y ARG 118": "NH1" <-> "NH2" Residue "y ARG 132": "NH1" <-> "NH2" Residue "y ARG 136": "NH1" <-> "NH2" 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: 146399 Number of models: 1 Model: "" Number of chains: 69 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: "A" Number of atoms: 62336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62336 Classifications: {'RNA': 2903} Modifications used: {'p5*END': 1, 'rna2p': 6, 'rna2p_pur': 241, 'rna2p_pyr': 121, 'rna3p': 17, 'rna3p_pur': 1425, 'rna3p_pyr': 1093} Link IDs: {'rna2p': 368, 'rna3p': 2534} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 42 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: 33051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1540, 33051 Inner-chain residues flagged as termini: ['pdbres=" A a 2 "'] Classifications: {'RNA': 1540} Modifications used: {'p5*END': 1, 'rna2p': 2, 'rna2p_pur': 102, 'rna2p_pyr': 66, 'rna3p': 9, 'rna3p_pur': 767, 'rna3p_pyr': 594} Link IDs: {'rna2p': 170, 'rna3p': 1369} 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: 464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 464 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} 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: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 121 Classifications: {'peptide': 14} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 8} Chain: "w" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1631 Classifications: {'RNA': 76} Modifications used: {'rna2p': 2, 'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p': 5, 'rna3p_pur': 31, 'rna3p_pyr': 28} 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: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 125 Classifications: {'RNA': 6} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 2, 'rna3p_pyr': 3} Link IDs: {'rna3p': 5} Chain: "y" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1078 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 134} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "0" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 245 Unusual residues: {' MG': 244, ' NA': 1} Classifications: {'undetermined': 245} Link IDs: {None: 244} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Unusual residues: {' MG': 93} Classifications: {'undetermined': 93} Link IDs: {None: 92} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "w" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1819 SG CYS 4 11 177.340 101.840 126.451 1.00 76.79 S ATOM 1844 SG CYS 4 14 176.919 103.428 125.984 1.00 73.95 S ATOM 1947 SG CYS 4 27 177.033 101.763 123.938 1.00 74.63 S Time building chain proxies: 55.91, per 1000 atoms: 0.38 Number of scatterers: 146399 At special positions: 0 Unit cell: (234.768, 263.712, 244.416, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 S 142 16.00 P 4645 15.00 Mg 356 11.99 Na 1 11.00 O 40543 8.00 N 27254 7.00 C 73457 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 70.89 Conformation dependent library (CDL) restraints added in 6.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 4 101 " pdb="ZN ZN 4 101 " - pdb=" ND1 HIS 4 33 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 11 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 27 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 14 " Number of angles added : 3 11852 Ramachandran restraints generated. 5926 Oldfield, 0 Emsley, 5926 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11090 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: 181 helices and 72 sheets defined 38.5% alpha, 18.2% beta 1551 base pairs and 2243 stacking pairs defined. Time for finding SS restraints: 73.30 Creating SS restraints... Processing helix chain '0' and resid 8 through 20 removed outlier: 4.020A pdb=" N ARG 0 16 " --> pdb=" O ARG 0 12 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N HIS 0 18 " --> pdb=" O MET 0 14 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ASP 0 19 " --> pdb=" O ARG 0 15 " (cutoff:3.500A) removed outlier: 3.776A 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 24 removed outlier: 5.223A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) Processing helix chain '2' and resid 25 through 38 removed outlier: 3.685A pdb=" N ALA 2 36 " --> pdb=" O ALA 2 32 " (cutoff:3.500A) Processing helix chain '3' and resid 6 through 13 removed outlier: 3.739A pdb=" N ALA 3 10 " --> pdb=" O VAL 3 6 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS 3 11 " --> pdb=" O ARG 3 7 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ARG 3 12 " --> pdb=" O GLY 3 8 " (cutoff:3.500A) Processing helix chain '3' and resid 36 through 45 removed outlier: 3.642A pdb=" N ARG 3 44 " --> pdb=" O LYS 3 40 " (cutoff:3.500A) Proline residue: 3 45 - end of helix Processing helix chain '3' and resid 53 through 62 removed outlier: 3.703A pdb=" N VAL 3 57 " --> pdb=" O ASP 3 53 " (cutoff:3.500A) Proline residue: 3 62 - end of helix Processing helix chain '5' and resid 3 through 21 removed outlier: 4.051A pdb=" N ILE 5 11 " --> pdb=" O ASP 5 7 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU 5 17 " --> pdb=" O ALA 5 13 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS 5 20 " --> pdb=" O SER 5 16 " (cutoff:3.500A) Processing helix chain '5' and resid 33 through 47 removed outlier: 3.973A pdb=" N MET 5 38 " --> pdb=" O THR 5 34 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS 5 43 " --> pdb=" O THR 5 39 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA 5 44 " --> pdb=" O GLU 5 40 " (cutoff:3.500A) Processing helix chain '5' and resid 59 through 68 removed outlier: 4.364A pdb=" N VAL 5 64 " --> pdb=" O LEU 5 60 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU 5 65 " --> pdb=" O ARG 5 61 " (cutoff:3.500A) Proline residue: 5 68 - end of helix Processing helix chain '5' and resid 93 through 105 removed outlier: 4.391A pdb=" N ALA 5 100 " --> pdb=" O PHE 5 96 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA 5 104 " --> pdb=" O ALA 5 100 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYS 5 105 " --> pdb=" O LYS 5 101 " (cutoff:3.500A) Processing helix chain '5' and resid 71 through 79 removed outlier: 4.240A pdb=" N PHE 5 76 " --> pdb=" O LYS 5 73 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL 5 77 " --> pdb=" O ASP 5 74 " (cutoff:3.500A) Proline residue: 5 79 - end of helix Processing helix chain 'C' and resid 10 through 16 removed outlier: 7.089A pdb=" N HIS C 14 " --> pdb=" O PRO C 10 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL C 15 " --> pdb=" O GLY C 11 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL C 16 " --> pdb=" O ARG C 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 10 through 16' Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.783A pdb=" N LEU C 33 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 5.563A 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 removed outlier: 3.933A pdb=" N ILE C 134 " --> pdb=" O PRO C 130 " (cutoff:3.500A) Proline residue: C 135 - end of helix No H-bonds generated for 'chain 'C' and resid 130 through 135' Processing helix chain 'C' and resid 206 through 214 removed outlier: 3.759A pdb=" N ALA C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 225 removed outlier: 3.596A pdb=" N MET C 224 " --> pdb=" O ARG C 220 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ASN C 225 " --> pdb=" O GLY C 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 220 through 225' Processing helix chain 'C' and resid 259 through 267 removed outlier: 6.322A pdb=" N ASP C 263 " --> pdb=" O ASN C 259 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LYS C 264 " --> pdb=" O LYS C 260 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N PHE C 265 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N VAL C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 201 removed outlier: 4.444A pdb=" N MET C 200 " --> pdb=" O ALA C 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 61 removed outlier: 3.629A pdb=" N VAL D 60 " --> pdb=" O LYS D 56 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N THR D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 56 through 61' Processing helix chain 'D' and resid 62 through 72 removed outlier: 3.815A pdb=" N HIS D 67 " --> pdb=" O PRO D 63 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 103 removed outlier: 4.484A pdb=" N ALA D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ASP D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 98 through 103' Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 41 removed outlier: 6.055A pdb=" N GLN E 41 " --> pdb=" O ALA E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 116 removed outlier: 3.621A pdb=" N SER E 107 " --> pdb=" O GLY E 103 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER E 110 " --> pdb=" O LYS E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 142 Processing helix chain 'E' and resid 154 through 163 removed outlier: 4.701A 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: 3.732A pdb=" N GLU F 10 " --> pdb=" O TYR F 6 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N VAL F 12 " --> pdb=" O LYS F 8 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N LYS F 13 " --> pdb=" O ASP F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 61 removed outlier: 4.574A pdb=" N LEU F 49 " --> pdb=" O ASP F 45 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASN F 51 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA F 54 " --> pdb=" O ASP F 50 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA F 57 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 110 removed outlier: 3.632A pdb=" N GLU F 97 " --> pdb=" O GLU F 93 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE F 103 " --> pdb=" O PHE F 99 " (cutoff:3.500A) removed outlier: 5.281A 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 removed outlier: 4.732A pdb=" N ILE F 136 " --> pdb=" O GLU F 133 " (cutoff:3.500A) Proline residue: F 138 - end of helix Processing helix chain 'G' and resid 1 through 7 Proline residue: G 7 - end of helix Processing helix chain 'G' and resid 59 through 80 removed outlier: 3.501A pdb=" N ILE G 76 " --> pdb=" O ASN G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 152 removed outlier: 3.633A pdb=" N ALA G 144 " --> pdb=" O ILE G 140 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N TYR G 150 " --> pdb=" O ASP G 146 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 29 Processing helix chain 'H' and resid 40 through 49 removed outlier: 6.621A pdb=" N ILE H 44 " --> pdb=" O THR H 40 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU H 45 " --> pdb=" O LYS H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 69 removed outlier: 3.787A pdb=" N GLU H 55 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ALA H 56 " --> pdb=" O ALA H 52 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ALA H 65 " --> pdb=" O VAL H 61 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASN H 66 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ARG H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA H 69 " --> pdb=" O ALA H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 105 removed outlier: 4.563A pdb=" N ALA H 102 " --> pdb=" O ASP H 98 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N THR H 104 " --> pdb=" O ALA H 100 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA H 105 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 24 Processing helix chain 'I' and resid 33 through 38 removed outlier: 4.586A pdb=" N PHE I 37 " --> pdb=" O ASN I 33 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N CYS I 38 " --> pdb=" O ILE I 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 33 through 38' Processing helix chain 'I' and resid 74 through 79 Processing helix chain 'I' and resid 101 through 113 removed outlier: 4.289A pdb=" N GLU I 107 " --> pdb=" O ALA I 103 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 135 removed outlier: 3.559A pdb=" N MET I 124 " --> pdb=" O ASP I 120 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N MET I 135 " --> pdb=" O THR I 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 4.463A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 97 through 110 removed outlier: 3.863A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N MET J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 123 removed outlier: 3.949A pdb=" N ARG J 120 " --> pdb=" O ARG J 116 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LYS J 123 " --> pdb=" O PHE J 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 109 removed outlier: 4.108A pdb=" N ARG K 108 " --> pdb=" O THR K 104 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N SER K 109 " --> pdb=" O ARG K 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 104 through 109' Processing helix chain 'K' and resid 112 through 119 removed outlier: 4.111A pdb=" N LEU K 118 " --> pdb=" O LYS K 114 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 62 removed outlier: 3.622A pdb=" N LEU L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 4.092A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 83 removed outlier: 4.119A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.462A 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: 3.627A pdb=" N LEU L 95 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ALA L 97 " --> pdb=" O ASN L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 139 removed outlier: 5.338A pdb=" N ARG L 132 " --> pdb=" O THR L 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 58 removed outlier: 4.780A pdb=" N LYS M 58 " --> pdb=" O THR M 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 125 removed outlier: 4.011A pdb=" N ALA M 116 " --> pdb=" O LEU M 112 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU M 119 " --> pdb=" O GLU M 115 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) removed outlier: 4.209A 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 removed outlier: 4.003A pdb=" N ALA N 19 " --> pdb=" O SER N 15 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG N 22 " --> pdb=" O GLN N 18 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 57 removed outlier: 3.928A pdb=" N GLU N 43 " --> pdb=" O PRO N 39 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 4.047A pdb=" N LYS N 56 " --> pdb=" O ILE N 52 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 Processing helix chain 'N' and resid 72 through 88 removed outlier: 4.385A pdb=" N PHE N 80 " --> pdb=" O VAL N 76 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASN N 81 " --> pdb=" O ALA N 77 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LEU N 83 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 5.636A 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: 5.117A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 6.263A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 5.150A 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: 3.565A pdb=" N LYS P 5 " --> pdb=" O SER P 1 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU P 10 " --> pdb=" O GLN P 6 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLN P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET P 12 " --> pdb=" O GLU P 8 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 103 removed outlier: 4.751A pdb=" N ARG P 100 " --> pdb=" O LEU P 96 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N GLU P 101 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N THR P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 96 through 103' Processing helix chain 'Q' and resid 5 through 21 removed outlier: 4.409A pdb=" N ALA Q 9 " --> pdb=" O ARG Q 5 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ARG Q 10 " --> pdb=" O GLY Q 6 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS Q 15 " --> pdb=" O ALA Q 11 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN Q 19 " --> pdb=" O LYS Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 removed outlier: 3.906A pdb=" N ARG Q 29 " --> pdb=" O GLY Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 31 through 36 removed outlier: 4.564A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 72 removed outlier: 4.600A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG Q 57 " --> pdb=" O LYS Q 53 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA Q 62 " --> pdb=" O GLN Q 58 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN Q 71 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 86 Processing helix chain 'Q' and resid 90 through 101 Processing helix chain 'Q' and resid 102 through 117 Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.886A pdb=" N VAL S 17 " --> pdb=" O SER S 13 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ARG S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 removed outlier: 4.015A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 61 removed outlier: 4.347A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 11 removed outlier: 4.354A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 27 removed outlier: 3.924A pdb=" N SER T 21 " --> pdb=" O SER T 17 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 51 removed outlier: 3.820A pdb=" N LYS T 44 " --> pdb=" O LYS T 40 " (cutoff:3.500A) Processing helix chain 'U' and resid 65 through 70 removed outlier: 3.990A pdb=" N VAL U 69 " --> pdb=" O GLN U 65 " (cutoff:3.500A) removed outlier: 5.453A 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 removed outlier: 3.823A pdb=" N ARG V 21 " --> pdb=" O SER V 17 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASN V 24 " --> pdb=" O LEU V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 54 removed outlier: 4.089A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ALA V 54 " --> pdb=" O MET V 50 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 62 removed outlier: 4.259A 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 1 through 9 removed outlier: 3.918A pdb=" N GLU Y 5 " --> pdb=" O MET Y 1 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ARG Y 7 " --> pdb=" O ALA Y 3 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU Y 8 " --> pdb=" O LYS Y 4 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N LYS Y 9 " --> pdb=" O GLU Y 5 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 35 removed outlier: 3.981A pdb=" N LEU Y 14 " --> pdb=" O SER Y 10 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU Y 18 " --> pdb=" O LEU Y 14 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN Y 20 " --> pdb=" O THR Y 16 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU Y 21 " --> pdb=" O GLU Y 17 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ARG Y 23 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU Y 24 " --> pdb=" O ASN Y 20 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N PHE Y 26 " --> pdb=" O LEU Y 22 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASN Y 27 " --> pdb=" O ARG Y 23 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU Y 28 " --> pdb=" O GLU Y 24 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 62 removed outlier: 4.481A pdb=" N LEU Y 43 " --> pdb=" O GLN Y 39 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLY Y 62 " --> pdb=" O ASN Y 58 " (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: 4.116A 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 removed outlier: 3.656A pdb=" N ALA b 54 " --> pdb=" O ASN b 50 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS b 63 " --> pdb=" O ILE b 59 " (cutoff:3.500A) Processing helix chain 'b' and resid 72 through 87 removed outlier: 5.854A pdb=" N GLU b 77 " --> pdb=" O ARG b 73 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ALA b 78 " --> pdb=" O ALA b 74 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU b 84 " --> pdb=" O LYS b 80 " (cutoff:3.500A) Processing helix chain 'b' and resid 102 through 122 removed outlier: 4.185A pdb=" N GLN b 108 " --> pdb=" O LYS b 104 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER b 109 " --> pdb=" O THR b 105 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR b 118 " --> pdb=" O LYS b 114 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN b 121 " --> pdb=" O GLU b 117 " (cutoff:3.500A) Processing helix chain 'b' and resid 129 through 147 removed outlier: 3.559A pdb=" N SER b 146 " --> pdb=" O LYS b 142 " (cutoff:3.500A) Processing helix chain 'b' and resid 164 through 169 removed outlier: 4.241A pdb=" N HIS b 169 " --> pdb=" O ALA b 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 170 through 179 removed outlier: 3.882A pdb=" N ASN b 177 " --> pdb=" O LYS b 173 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU b 178 " --> pdb=" O GLU b 174 " (cutoff:3.500A) Processing helix chain 'b' and resid 205 through 225 removed outlier: 3.761A pdb=" N ALA b 218 " --> pdb=" O GLY b 214 " (cutoff:3.500A) removed outlier: 5.077A 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: 3.929A pdb=" N ILE c 93 " --> pdb=" O VAL c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 107 through 112 removed outlier: 4.022A pdb=" N ASP c 111 " --> pdb=" O LYS c 107 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ALA c 112 " --> pdb=" O PRO c 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 107 through 112' Processing helix chain 'c' and resid 113 through 126 Processing helix chain 'c' and resid 128 through 144 removed outlier: 3.782A pdb=" N ARG c 135 " --> pdb=" O ARG c 131 " (cutoff:3.500A) Processing helix chain 'd' and resid 6 through 15 removed outlier: 4.676A pdb=" N LEU d 10 " --> pdb=" O PRO d 6 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N SER d 11 " --> pdb=" O LYS d 7 " (cutoff:3.500A) Processing helix chain 'd' and resid 26 through 31 removed outlier: 4.767A pdb=" N LYS d 30 " --> pdb=" O ALA d 26 " (cutoff:3.500A) Processing helix chain 'd' and resid 48 through 65 removed outlier: 3.815A pdb=" N TYR d 64 " --> pdb=" O VAL d 60 " (cutoff:3.500A) Processing helix chain 'd' and resid 67 through 82 removed outlier: 3.805A pdb=" N PHE d 71 " --> pdb=" O LEU d 67 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ASN d 73 " --> pdb=" O ARG d 69 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N TYR d 74 " --> pdb=" O GLN d 70 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA d 78 " --> pdb=" O TYR d 74 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LEU d 81 " --> pdb=" O GLU d 77 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LYS d 82 " --> pdb=" O ALA d 78 " (cutoff:3.500A) Processing helix chain 'd' and resid 84 through 96 removed outlier: 3.900A pdb=" N LEU d 90 " --> pdb=" O GLY d 86 " (cutoff:3.500A) removed outlier: 3.581A 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: 3.739A pdb=" N LYS d 120 " --> pdb=" O LEU d 116 " (cutoff:3.500A) Processing helix chain 'd' and resid 145 through 150 removed outlier: 3.963A pdb=" N LYS d 149 " --> pdb=" O ARG d 145 " (cutoff:3.500A) removed outlier: 8.400A 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 165 removed outlier: 6.191A pdb=" N LYS d 155 " --> pdb=" O GLN d 151 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLU d 162 " --> pdb=" O LEU d 158 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N GLN d 163 " --> pdb=" O GLU d 159 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG d 164 " --> pdb=" O LEU d 160 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU d 165 " --> pdb=" O ALA d 161 " (cutoff:3.500A) Processing helix chain 'd' and resid 186 through 191 removed outlier: 3.803A pdb=" N LEU d 190 " --> pdb=" O GLU d 186 " (cutoff:3.500A) removed outlier: 5.262A 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: 4.237A pdb=" N ILE d 199 " --> pdb=" O ASN d 195 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 70 removed outlier: 3.781A pdb=" N MET e 70 " --> pdb=" O ALA e 66 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 118 removed outlier: 6.767A pdb=" N ALA e 112 " --> pdb=" O GLY e 108 " (cutoff:3.500A) removed outlier: 4.570A 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: 4.269A pdb=" N GLY e 157 " --> pdb=" O ALA e 153 " (cutoff:3.500A) Processing helix chain 'e' and resid 159 through 165 removed outlier: 3.815A pdb=" N GLY e 165 " --> pdb=" O GLU e 161 " (cutoff:3.500A) Processing helix chain 'f' and resid 11 through 19 removed outlier: 6.315A pdb=" N GLU f 16 " --> pdb=" O PRO f 12 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N GLN f 17 " --> pdb=" O ASP f 13 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL f 18 " --> pdb=" O GLN f 14 " (cutoff:3.500A) Proline residue: f 19 - end of helix Processing helix chain 'f' and resid 20 through 33 removed outlier: 3.558A pdb=" N ALA f 32 " --> pdb=" O ALA f 28 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 82 removed outlier: 5.225A pdb=" N ASP f 82 " --> pdb=" O PHE f 78 " (cutoff:3.500A) Processing helix chain 'g' and resid 19 through 30 Processing helix chain 'g' and resid 34 through 53 removed outlier: 3.650A pdb=" N ALA g 45 " --> pdb=" O ILE g 41 " (cutoff:3.500A) Processing helix chain 'g' and resid 56 through 69 Processing helix chain 'g' and resid 91 through 111 removed outlier: 3.732A pdb=" N LYS g 109 " --> pdb=" O GLU g 105 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ARG g 110 " --> pdb=" O ALA g 106 " (cutoff:3.500A) removed outlier: 5.258A 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: 4.408A pdb=" N GLU g 145 " --> pdb=" O HIS g 141 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA g 146 " --> pdb=" O ARG g 142 " (cutoff:3.500A) removed outlier: 5.653A 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 removed outlier: 3.586A pdb=" N VAL i 54 " --> pdb=" O PRO i 50 " (cutoff:3.500A) Processing helix chain 'i' and resid 70 through 90 removed outlier: 4.563A pdb=" N GLU i 88 " --> pdb=" O ARG i 84 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR i 89 " --> pdb=" O ALA i 85 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ASP i 90 " --> pdb=" O LEU i 86 " (cutoff:3.500A) Processing helix chain 'i' and resid 91 through 101 removed outlier: 5.014A pdb=" N SER i 95 " --> pdb=" O GLU i 91 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLU i 96 " --> pdb=" O SER i 92 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 31 removed outlier: 4.412A pdb=" N LYS j 30 " --> pdb=" O VAL j 26 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ARG j 31 " --> pdb=" O GLU j 27 " (cutoff:3.500A) Processing helix chain 'j' and resid 82 through 90 removed outlier: 4.409A pdb=" N ALA j 86 " --> pdb=" O LYS j 82 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ARG j 89 " --> pdb=" O ASP j 85 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N LEU j 90 " --> pdb=" O ALA j 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 50 removed outlier: 3.865A pdb=" N GLY k 50 " --> pdb=" O ALA k 46 " (cutoff:3.500A) Processing helix chain 'k' and resid 53 through 58 removed outlier: 4.462A pdb=" N SER k 57 " --> pdb=" O GLY k 53 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR k 58 " --> pdb=" O SER k 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 53 through 58' Processing helix chain 'k' and resid 59 through 74 removed outlier: 4.460A pdb=" N ALA k 72 " --> pdb=" O ARG k 68 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL k 73 " --> pdb=" O CYS k 69 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LYS k 74 " --> pdb=" O ALA k 70 " (cutoff:3.500A) Processing helix chain 'k' and resid 91 through 103 removed outlier: 4.335A pdb=" N THR k 95 " --> pdb=" O GLY k 91 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ILE k 96 " --> pdb=" O ARG k 92 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY k 103 " --> pdb=" O LEU k 99 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 10 removed outlier: 3.521A pdb=" N LEU l 6 " --> pdb=" O THR l 2 " (cutoff:3.500A) Proline residue: l 10 - end of helix Processing helix chain 'l' and resid 112 through 117 removed outlier: 4.912A pdb=" N TYR l 116 " --> pdb=" O ALA l 112 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY l 117 " --> pdb=" O ARG l 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 112 through 117' Processing helix chain 'm' and resid 13 through 21 removed outlier: 3.596A pdb=" N THR m 19 " --> pdb=" O VAL m 15 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER m 20 " --> pdb=" O ILE m 16 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ILE m 21 " --> pdb=" O ALA m 17 " (cutoff:3.500A) Processing helix chain 'm' and resid 25 through 37 Processing helix chain 'm' and resid 43 through 48 removed outlier: 3.749A pdb=" N LEU m 47 " --> pdb=" O LYS m 43 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N SER m 48 " --> pdb=" O ILE m 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 43 through 48' Processing helix chain 'm' and resid 49 through 63 removed outlier: 3.664A pdb=" N THR m 54 " --> pdb=" O GLY m 50 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N LYS m 61 " --> pdb=" O ASP m 57 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N PHE m 62 " --> pdb=" O GLU m 58 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N VAL m 63 " --> pdb=" O VAL m 59 " (cutoff:3.500A) Processing helix chain 'm' and resid 65 through 83 removed outlier: 3.872A pdb=" N ARG m 70 " --> pdb=" O GLY m 66 " (cutoff:3.500A) 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 removed outlier: 4.198A pdb=" N GLU n 9 " --> pdb=" O MET n 5 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL n 10 " --> pdb=" O LYS n 6 " (cutoff:3.500A) Processing helix chain 'n' and resid 21 through 32 removed outlier: 4.536A pdb=" N GLU n 25 " --> pdb=" O ALA n 21 " (cutoff:3.500A) Processing helix chain 'n' and resid 41 through 51 removed outlier: 5.410A pdb=" N VAL n 45 " --> pdb=" O ARG n 41 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU n 46 " --> pdb=" O TRP n 42 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU n 51 " --> pdb=" O LYS n 47 " (cutoff:3.500A) Processing helix chain 'n' and resid 80 through 91 removed outlier: 4.092A pdb=" N ARG n 85 " --> pdb=" O ARG n 81 " (cutoff:3.500A) Processing helix chain 'o' and resid 3 through 15 Processing helix chain 'o' and resid 23 through 43 removed outlier: 3.813A pdb=" N GLY o 40 " --> pdb=" O ASN o 36 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N HIS o 41 " --> pdb=" O HIS o 37 " (cutoff:3.500A) Processing helix chain 'o' and resid 48 through 73 removed outlier: 4.572A pdb=" N GLY o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) Processing helix chain 'o' and resid 74 through 85 removed outlier: 3.520A pdb=" N GLN o 79 " --> pdb=" O ALA o 75 " (cutoff:3.500A) Processing helix chain 'p' and resid 53 through 64 Processing helix chain 'p' and resid 68 through 80 removed outlier: 4.461A pdb=" N LYS p 80 " --> pdb=" O LYS p 76 " (cutoff:3.500A) Processing helix chain 'r' and resid 24 through 33 removed outlier: 4.645A pdb=" N ASN r 30 " --> pdb=" O ALA r 26 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N THR r 33 " --> pdb=" O LYS r 29 " (cutoff:3.500A) Processing helix chain 'r' and resid 40 through 45 removed outlier: 3.601A pdb=" N THR r 44 " --> pdb=" O PRO r 40 " (cutoff:3.500A) Processing helix chain 'r' and resid 47 through 65 Processing helix chain 's' and resid 11 through 24 Processing helix chain 's' and resid 69 through 75 removed outlier: 4.333A pdb=" N PHE s 73 " --> pdb=" O LYS s 69 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA s 74 " --> pdb=" O LEU s 70 " (cutoff:3.500A) Proline residue: s 75 - end of helix No H-bonds generated for 'chain 's' and resid 69 through 75' Processing helix chain 't' and resid 5 through 40 removed outlier: 3.996A pdb=" N ARG t 9 " --> pdb=" O SER t 5 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N HIS t 19 " --> pdb=" O LYS t 15 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER t 25 " --> pdb=" O ALA t 21 " (cutoff:3.500A) Processing helix chain 't' and resid 43 through 64 Proline residue: t 55 - end of helix removed outlier: 4.310A pdb=" N GLY t 64 " --> pdb=" O GLN t 60 " (cutoff:3.500A) Processing helix chain 't' and resid 67 through 86 removed outlier: 3.684A pdb=" N GLN t 81 " --> pdb=" O ASN t 77 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA t 86 " --> pdb=" O ILE t 82 " (cutoff:3.500A) Processing helix chain 'u' and resid 12 through 26 removed outlier: 3.810A pdb=" N ARG u 16 " --> pdb=" O ASP u 12 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N GLU u 23 " --> pdb=" O LYS u 19 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA u 25 " --> pdb=" O SER u 21 " (cutoff:3.500A) Processing helix chain 'u' and resid 27 through 36 removed outlier: 3.577A pdb=" N ARG u 34 " --> pdb=" O GLU u 30 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N PHE u 36 " --> pdb=" O ARG u 32 " (cutoff:3.500A) Processing helix chain 'u' and resid 39 through 56 removed outlier: 4.472A pdb=" N ALA u 56 " --> pdb=" O VAL u 52 " (cutoff:3.500A) Processing helix chain 'y' and resid 27 through 33 removed outlier: 4.511A pdb=" N ASN y 31 " --> pdb=" O GLY y 27 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS y 32 " --> pdb=" O GLN y 28 " (cutoff:3.500A) Processing helix chain 'y' and resid 49 through 60 removed outlier: 3.772A pdb=" N LYS y 53 " --> pdb=" O PRO y 49 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLU y 54 " --> pdb=" O GLU y 50 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ARG y 55 " --> pdb=" O TYR y 51 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA y 58 " --> pdb=" O GLU y 54 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N SER y 60 " --> pdb=" O LEU y 56 " (cutoff:3.500A) Processing helix chain 'y' and resid 79 through 100 Processing helix chain 'y' and resid 111 through 133 removed outlier: 3.836A pdb=" N MET y 131 " --> pdb=" O SER y 127 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N GLY y 133 " --> pdb=" O LYS y 129 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '1' and resid 18 through 23 removed outlier: 6.706A pdb=" N HIS 1 18 " --> pdb=" O SER 1 12 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE 1 47 " --> pdb=" O SER 1 13 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU 1 33 " --> pdb=" O GLU 1 50 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '3' and resid 21 through 24 removed outlier: 5.463A pdb=" N PHE 3 21 " --> pdb=" O VAL 3 49 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '4' and resid 14 through 18 removed outlier: 6.187A pdb=" N ILE 4 23 " --> pdb=" O GLN 4 37 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN 4 37 " --> pdb=" O ILE 4 23 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N CYS 4 27 " --> pdb=" O HIS 4 33 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N HIS 4 33 " --> pdb=" O CYS 4 27 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '5' and resid 24 through 28 removed outlier: 3.669A pdb=" N ALA 5 25 " --> pdb=" O SER 5 85 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'C' and resid 79 through 82 removed outlier: 6.612A pdb=" N LEU C 92 " --> pdb=" O GLU C 78 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP C 113 " --> pdb=" O VAL C 77 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 137 through 141 removed outlier: 4.458A pdb=" N SER C 138 " --> pdb=" O ILE C 163 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 142 through 145 removed outlier: 4.963A pdb=" N ASN C 142 " --> pdb=" O THR C 190 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N THR C 190 " --> pdb=" O ASN C 142 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ARG C 188 " --> pdb=" O GLU C 144 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'C' and resid 171 through 174 Processing sheet with id= 9, first strand: chain 'C' and resid 90 through 95 removed outlier: 3.575A pdb=" N GLU C 99 " --> pdb=" O TYR C 95 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.756A pdb=" N VAL D 170 " --> pdb=" O GLY D 111 " (cutoff:3.500A) removed outlier: 4.567A 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: 4.628A pdb=" N GLY D 10 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 3.787A 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 39 removed outlier: 3.763A pdb=" N GLN D 36 " --> pdb=" O GLN D 49 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 4.618A 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: 6.995A pdb=" N ARG D 46 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'E' and resid 1 through 6 removed outlier: 4.245A pdb=" N SER E 10 " --> pdb=" O LEU E 5 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'E' and resid 117 through 120 removed outlier: 5.948A pdb=" N ARG E 117 " --> pdb=" O ASP E 184 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'F' and resid 64 through 68 removed outlier: 4.023A pdb=" N VAL F 88 " --> pdb=" O LEU F 35 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N GLY F 38 " --> pdb=" O GLY F 150 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N GLY F 150 " --> pdb=" O GLY F 38 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'G' and resid 14 through 18 removed outlier: 3.524A pdb=" N GLY G 30 " --> pdb=" O GLY G 27 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'G' and resid 40 through 44 Processing sheet with id= 19, first strand: chain 'G' and resid 81 through 88 removed outlier: 5.944A pdb=" N THR G 128 " --> pdb=" O LEU G 88 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'G' and resid 93 through 97 removed outlier: 3.924A pdb=" N ALA G 96 " --> pdb=" O ASN G 103 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'H' and resid 17 through 21 removed outlier: 5.166A pdb=" N ASP H 17 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 5.503A 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 81 removed outlier: 4.299A pdb=" N ALA H 140 " --> pdb=" O PHE H 132 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE H 132 " --> pdb=" O ALA H 140 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N GLU H 114 " --> pdb=" O GLN H 133 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'I' and resid 53 through 57 removed outlier: 3.779A pdb=" N VAL I 57 " --> pdb=" O VAL I 69 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL I 69 " --> pdb=" O VAL I 57 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'J' and resid 52 through 57 removed outlier: 3.796A pdb=" N GLN J 138 " --> pdb=" O TRP J 15 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASP J 19 " --> pdb=" O LEU J 140 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'J' and resid 74 through 77 Processing sheet with id= 26, first strand: chain 'K' and resid 5 through 9 removed outlier: 4.167A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'K' and resid 37 through 41 removed outlier: 4.540A pdb=" N ASP K 37 " --> pdb=" O VAL K 62 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS K 59 " --> pdb=" O LEU K 87 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'M' and resid 62 through 65 removed outlier: 4.016A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS M 100 " --> pdb=" O ALA M 35 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'M' and resid 71 through 74 removed outlier: 3.593A pdb=" N LYS M 71 " --> pdb=" O VAL M 93 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'M' and resid 30 through 36 removed outlier: 7.836A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'N' and resid 33 through 36 removed outlier: 4.868A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'O' and resid 49 through 52 removed outlier: 3.670A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL O 28 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'P' and resid 37 through 44 removed outlier: 6.019A pdb=" N THR P 24 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER P 82 " --> pdb=" O LYS P 28 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'P' and resid 48 through 51 removed outlier: 3.885A pdb=" N ALA P 48 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N SER P 56 " --> pdb=" O THR P 75 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'R' and resid 11 through 14 removed outlier: 6.284A pdb=" N TYR R 2 " --> pdb=" O ILE R 41 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE R 41 " --> pdb=" O TYR R 2 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL R 4 " --> pdb=" O LEU R 39 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'R' and resid 19 through 22 removed outlier: 3.580A pdb=" N VAL R 96 " --> pdb=" O VAL R 20 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'R' and resid 30 through 36 removed outlier: 4.264A pdb=" N GLU R 31 " --> pdb=" O VAL R 63 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'R' and resid 71 through 78 removed outlier: 4.230A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'S' and resid 2 through 8 removed outlier: 5.066A pdb=" N THR S 100 " --> pdb=" O GLY S 79 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'S' and resid 80 through 88 removed outlier: 4.496A pdb=" N THR S 100 " --> pdb=" O PRO S 80 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG S 92 " --> pdb=" O ARG S 88 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'T' and resid 28 through 33 removed outlier: 6.060A pdb=" N ASN T 28 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY T 75 " --> pdb=" O LYS T 68 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS T 68 " --> pdb=" O GLY T 75 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'U' and resid 39 through 44 removed outlier: 4.863A pdb=" N ASN U 39 " --> pdb=" O ALA U 62 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'U' and resid 82 through 86 Processing sheet with id= 44, first strand: chain 'V' and resid 69 through 72 removed outlier: 3.889A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'W' and resid 47 through 50 removed outlier: 4.371A pdb=" N PHE W 56 " --> pdb=" O GLY W 48 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR W 54 " --> pdb=" O GLY W 50 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'W' and resid 61 through 67 Processing sheet with id= 47, first strand: chain 'X' and resid 11 through 16 removed outlier: 4.279A pdb=" N THR X 24 " --> pdb=" O ASN X 16 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'X' and resid 34 through 40 Processing sheet with id= 49, first strand: chain 'Z' and resid 32 through 38 removed outlier: 4.423A pdb=" N HIS Z 33 " --> pdb=" O GLN Z 8 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N MET Z 53 " --> pdb=" O THR Z 9 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'b' and resid 88 through 92 Processing sheet with id= 51, first strand: chain 'c' and resid 53 through 58 Processing sheet with id= 52, first strand: chain 'c' and resid 163 through 168 removed outlier: 5.914A pdb=" N ASP c 180 " --> pdb=" O LYS c 203 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'd' and resid 140 through 143 removed outlier: 4.052A pdb=" N ASP d 140 " --> pdb=" O PHE d 181 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N GLY d 179 " --> pdb=" O VAL d 142 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLU d 178 " --> pdb=" O ASP d 173 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLU d 171 " --> pdb=" O THR d 180 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'e' and resid 11 through 15 removed outlier: 6.786A pdb=" N LEU e 35 " --> pdb=" O ILE e 15 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'e' and resid 82 through 87 removed outlier: 7.175A pdb=" N HIS e 82 " --> pdb=" O PRO e 97 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL e 93 " --> pdb=" O GLY e 86 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG e 92 " --> pdb=" O TYR e 127 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA e 98 " --> pdb=" O ASN e 121 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ASN e 121 " --> pdb=" O ALA e 98 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'e' and resid 31 through 39 removed outlier: 4.567A pdb=" N GLY e 50 " --> pdb=" O ALA e 34 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'f' and resid 38 through 42 removed outlier: 5.339A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N HIS f 3 " --> pdb=" O THR f 92 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N MET f 90 " --> pdb=" O GLU f 5 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N MET f 9 " --> pdb=" O ARG f 86 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ARG f 86 " --> pdb=" O MET f 9 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'f' and resid 43 through 46 removed outlier: 3.821A pdb=" N GLY f 43 " --> pdb=" O TYR f 59 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'g' and resid 72 through 77 Processing sheet with id= 60, first strand: chain 'h' and resid 22 through 28 removed outlier: 7.229A pdb=" N ALA h 22 " --> pdb=" O LEU h 62 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU h 51 " --> pdb=" O GLU h 57 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASP h 47 " --> pdb=" O THR h 61 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'h' and resid 73 through 76 removed outlier: 5.975A pdb=" N SER h 73 " --> pdb=" O ALA h 129 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS h 126 " --> pdb=" O VAL h 102 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL h 102 " --> pdb=" O ILE h 125 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'i' and resid 4 through 10 removed outlier: 4.285A pdb=" N GLY i 9 " --> pdb=" O ALA i 16 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LYS i 26 " --> pdb=" O LEU i 60 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'j' and resid 39 through 42 removed outlier: 3.956A pdb=" N LEU j 42 " --> pdb=" O LEU j 71 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU j 71 " --> pdb=" O LEU j 42 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ILE j 8 " --> pdb=" O VAL j 74 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'j' and resid 44 through 52 Processing sheet with id= 65, first strand: chain 'k' and resid 41 through 44 removed outlier: 4.025A pdb=" N VAL k 31 " --> pdb=" O ALA k 44 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA k 20 " --> pdb=" O GLU k 82 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL k 83 " --> pdb=" O THR k 107 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'l' and resid 28 through 31 Processing sheet with id= 67, first strand: chain 'l' and resid 35 through 40 removed outlier: 5.000A pdb=" N LYS l 50 " --> pdb=" O ILE l 66 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'p' and resid 1 through 10 removed outlier: 7.422A pdb=" N MET p 1 " --> pdb=" O SER p 24 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLN p 18 " --> pdb=" O ALA p 7 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY p 37 " --> pdb=" O VAL p 19 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY p 49 " --> pdb=" O ASN p 40 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'q' and resid 6 through 10 removed outlier: 7.111A pdb=" N GLU q 59 " --> pdb=" O VAL q 75 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'q' and resid 18 through 29 No H-bonds generated for sheet with id= 70 Processing sheet with id= 71, first strand: chain 's' and resid 29 through 32 removed outlier: 4.134A pdb=" N LEU s 30 " --> pdb=" O THR s 47 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU s 46 " --> pdb=" O VAL s 61 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'y' and resid 15 through 21 1867 hydrogen bonds defined for protein. 5505 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3902 hydrogen bonds 6098 hydrogen bond angles 0 basepair planarities 1551 basepair parallelities 2243 stacking parallelities Total time for adding SS restraints: 267.64 Time building geometry restraints manager: 75.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 12001 1.27 - 1.41: 51734 1.41 - 1.54: 85243 1.54 - 1.68: 9371 1.68 - 1.81: 256 Bond restraints: 158605 Sorted by residual: bond pdb=" C5 5MU w 54 " pdb=" C6 5MU w 54 " ideal model delta sigma weight residual 1.155 1.435 -0.280 2.00e-02 2.50e+03 1.96e+02 bond pdb=" C5 5MU A1939 " pdb=" C6 5MU A1939 " ideal model delta sigma weight residual 1.155 1.432 -0.277 2.00e-02 2.50e+03 1.92e+02 bond pdb=" C13 MIA w 37 " pdb=" C14 MIA w 37 " ideal model delta sigma weight residual 1.317 1.529 -0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C4 5MU A1939 " pdb=" C5 5MU A1939 " ideal model delta sigma weight residual 1.802 1.601 0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" C4 5MU w 54 " pdb=" C5 5MU w 54 " ideal model delta sigma weight residual 1.802 1.611 0.191 2.00e-02 2.50e+03 9.10e+01 ... (remaining 158600 not shown) Histogram of bond angle deviations from ideal: 79.27 - 94.07: 4 94.07 - 108.88: 58864 108.88 - 123.68: 156041 123.68 - 138.49: 22289 138.49 - 153.29: 3 Bond angle restraints: 237201 Sorted by residual: angle pdb=" C1' OMG A2251 " pdb=" N9 OMG A2251 " pdb=" C4 OMG A2251 " ideal model delta sigma weight residual 108.29 153.29 -45.00 3.00e+00 1.11e-01 2.25e+02 angle pdb=" C1' OMG A2251 " pdb=" N9 OMG A2251 " pdb=" C8 OMG A2251 " ideal model delta sigma weight residual 142.82 98.57 44.25 3.00e+00 1.11e-01 2.18e+02 angle pdb=" N PHE d 71 " pdb=" CA PHE d 71 " pdb=" C PHE d 71 " ideal model delta sigma weight residual 110.80 86.68 24.12 2.13e+00 2.20e-01 1.28e+02 angle pdb=" CA GLN d 70 " pdb=" C GLN d 70 " pdb=" N PHE d 71 " ideal model delta sigma weight residual 116.21 101.78 14.43 1.29e+00 6.01e-01 1.25e+02 angle pdb=" OP2 A a 2 " pdb=" P A a 2 " pdb=" OP3 A a 2 " ideal model delta sigma weight residual 109.47 79.27 30.20 3.00e+00 1.11e-01 1.01e+02 ... (remaining 237196 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 88301 35.85 - 71.70: 11725 71.70 - 107.54: 1348 107.54 - 143.39: 39 143.39 - 179.24: 43 Dihedral angle restraints: 101456 sinusoidal: 84276 harmonic: 17180 Sorted by residual: dihedral pdb=" C4' U a 85 " pdb=" C3' U a 85 " pdb=" C2' U a 85 " pdb=" C1' U a 85 " ideal model delta sinusoidal sigma weight residual -35.00 32.58 -67.58 1 8.00e+00 1.56e-02 9.28e+01 dihedral pdb=" C5' U a 85 " pdb=" C4' U a 85 " pdb=" C3' U a 85 " pdb=" O3' U a 85 " ideal model delta sinusoidal sigma weight residual 147.00 81.21 65.79 1 8.00e+00 1.56e-02 8.85e+01 dihedral pdb=" O4' U a 603 " pdb=" C1' U a 603 " pdb=" N1 U a 603 " pdb=" C2 U a 603 " ideal model delta sinusoidal sigma weight residual -160.00 17.16 -177.16 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 101453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.225: 30213 0.225 - 0.450: 29 0.450 - 0.675: 2 0.675 - 0.900: 0 0.900 - 1.125: 1 Chirality restraints: 30245 Sorted by residual: chirality pdb=" P A a 2 " pdb=" OP1 A a 2 " pdb=" OP2 A a 2 " pdb=" O5' A a 2 " both_signs ideal model delta sigma weight residual True 2.41 -1.29 1.12 2.00e-01 2.50e+01 3.16e+01 chirality pdb=" C1' G A1171 " pdb=" O4' G A1171 " pdb=" C2' G A1171 " pdb=" N9 G A1171 " both_signs ideal model delta sigma weight residual False 2.46 1.98 0.48 2.00e-01 2.50e+01 5.69e+00 chirality pdb=" C3' C A1052 " pdb=" C4' C A1052 " pdb=" O3' C A1052 " pdb=" C2' C A1052 " both_signs ideal model delta sigma weight residual False -2.48 -2.00 -0.47 2.00e-01 2.50e+01 5.63e+00 ... (remaining 30242 not shown) Planarity restraints: 12834 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MC a1407 " 0.078 2.00e-02 2.50e+03 6.07e-01 8.28e+03 pdb=" C4' 5MC a1407 " 0.432 2.00e-02 2.50e+03 pdb=" O4' 5MC a1407 " 0.594 2.00e-02 2.50e+03 pdb=" C3' 5MC a1407 " -0.604 2.00e-02 2.50e+03 pdb=" O3' 5MC a1407 " -0.672 2.00e-02 2.50e+03 pdb=" C2' 5MC a1407 " -0.157 2.00e-02 2.50e+03 pdb=" O2' 5MC a1407 " 1.018 2.00e-02 2.50e+03 pdb=" C1' 5MC a1407 " 0.226 2.00e-02 2.50e+03 pdb=" N1 5MC a1407 " -0.915 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a 966 " -0.895 2.00e-02 2.50e+03 5.92e-01 7.89e+03 pdb=" C4' 2MG a 966 " 0.196 2.00e-02 2.50e+03 pdb=" O4' 2MG a 966 " 0.774 2.00e-02 2.50e+03 pdb=" C3' 2MG a 966 " -0.241 2.00e-02 2.50e+03 pdb=" O3' 2MG a 966 " 0.868 2.00e-02 2.50e+03 pdb=" C2' 2MG a 966 " -0.595 2.00e-02 2.50e+03 pdb=" O2' 2MG a 966 " -0.576 2.00e-02 2.50e+03 pdb=" C1' 2MG a 966 " 0.467 2.00e-02 2.50e+03 pdb=" N9 2MG a 966 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a1207 " -0.057 2.00e-02 2.50e+03 5.86e-01 7.73e+03 pdb=" C4' 2MG a1207 " -0.435 2.00e-02 2.50e+03 pdb=" O4' 2MG a1207 " -0.613 2.00e-02 2.50e+03 pdb=" C3' 2MG a1207 " 0.599 2.00e-02 2.50e+03 pdb=" O3' 2MG a1207 " 0.616 2.00e-02 2.50e+03 pdb=" C2' 2MG a1207 " 0.190 2.00e-02 2.50e+03 pdb=" O2' 2MG a1207 " -0.959 2.00e-02 2.50e+03 pdb=" C1' 2MG a1207 " -0.224 2.00e-02 2.50e+03 pdb=" N9 2MG a1207 " 0.883 2.00e-02 2.50e+03 ... (remaining 12831 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.07: 266 2.07 - 2.78: 35418 2.78 - 3.49: 217524 3.49 - 4.19: 478599 4.19 - 4.90: 648424 Nonbonded interactions: 1380231 Sorted by model distance: nonbonded pdb=" O5' G a 108 " pdb="MG MG a1657 " model vdw 1.368 2.170 nonbonded pdb=" OP2 G A1271 " pdb=" OP1 U A1648 " model vdw 1.405 3.040 nonbonded pdb=" OP1 A a 174 " pdb=" OP2 C a 175 " model vdw 1.448 3.040 nonbonded pdb=" OP2 C a1069 " pdb="MG MG a1638 " model vdw 1.472 2.170 nonbonded pdb=" OP2 A a 964 " pdb="MG MG a1677 " model vdw 1.482 2.170 ... (remaining 1380226 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: 1.550 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: 0.110 Extract box with map and model: 12.910 Check model and map are aligned: 1.560 Set scattering table: 0.980 Process input model: 588.010 Find NCS groups from input model: 3.060 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 611.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 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 0.280 158605 Z= 0.427 Angle : 0.795 45.003 237201 Z= 0.408 Chirality : 0.042 1.125 30245 Planarity : 0.018 0.607 12834 Dihedral : 24.258 179.239 90366 Min Nonbonded Distance : 1.368 Molprobity Statistics. All-atom Clashscore : 20.57 Ramachandran Plot: Outliers : 0.19 % Allowed : 12.10 % Favored : 87.72 % Rotamer: Outliers : 0.17 % Allowed : 7.92 % Favored : 91.91 % Cbeta Deviations : 0.04 % 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: -4.65 (0.09), residues: 5926 helix: -2.49 (0.09), residues: 1915 sheet: -3.14 (0.13), residues: 1065 loop : -3.50 (0.09), residues: 2946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP C 212 HIS 0.009 0.002 HIS k 117 PHE 0.076 0.002 PHE d 71 TYR 0.019 0.002 TYR S 38 ARG 0.013 0.001 ARG h 14 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11852 Ramachandran restraints generated. 5926 Oldfield, 0 Emsley, 5926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11852 Ramachandran restraints generated. 5926 Oldfield, 0 Emsley, 5926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1810 residues out of total 4915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1802 time to evaluate : 6.203 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: 0 45 ASP cc_start: 0.8298 (m-30) cc_final: 0.8096 (m-30) REVERT: 1 7 LYS cc_start: 0.8930 (ptpt) cc_final: 0.8472 (ptpp) REVERT: 2 11 LYS cc_start: 0.9210 (mttt) cc_final: 0.8810 (mttm) REVERT: 3 63 TYR cc_start: 0.7379 (m-80) cc_final: 0.6814 (m-80) REVERT: C 83 ASP cc_start: 0.7401 (t0) cc_final: 0.6268 (t0) REVERT: C 120 ASP cc_start: 0.7726 (p0) cc_final: 0.7505 (p0) REVERT: C 145 MET cc_start: 0.8771 (mmm) cc_final: 0.8561 (mmt) REVERT: D 7 LYS cc_start: 0.8726 (ttmt) cc_final: 0.8354 (ttmm) REVERT: D 64 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7972 (mt-10) REVERT: D 96 ILE cc_start: 0.9560 (mt) cc_final: 0.9357 (mt) REVERT: D 141 ARG cc_start: 0.8652 (mtp85) cc_final: 0.8377 (mtp-110) REVERT: D 183 GLU cc_start: 0.7759 (pm20) cc_final: 0.7485 (mp0) REVERT: D 186 LEU cc_start: 0.9073 (mt) cc_final: 0.8782 (mt) REVERT: E 1 MET cc_start: 0.6972 (mmm) cc_final: 0.6678 (mmm) REVERT: E 168 ASP cc_start: 0.7387 (t0) cc_final: 0.7166 (t0) REVERT: F 25 MET cc_start: 0.8836 (mmp) cc_final: 0.8472 (mmt) REVERT: F 70 ARG cc_start: 0.7818 (ttp80) cc_final: 0.7596 (ptt180) REVERT: F 76 PHE cc_start: 0.7569 (m-80) cc_final: 0.7357 (m-80) REVERT: F 156 THR cc_start: 0.8830 (m) cc_final: 0.8516 (p) REVERT: G 31 GLU cc_start: 0.6873 (tt0) cc_final: 0.6422 (tt0) REVERT: G 51 PHE cc_start: 0.8629 (m-80) cc_final: 0.8415 (m-80) REVERT: G 74 MET cc_start: 0.7226 (ttm) cc_final: 0.6825 (ttm) REVERT: G 76 ILE cc_start: 0.9029 (mm) cc_final: 0.8648 (mt) REVERT: H 17 ASP cc_start: 0.7257 (m-30) cc_final: 0.6962 (m-30) REVERT: H 97 ARG cc_start: 0.7962 (tpm170) cc_final: 0.7600 (tpm170) REVERT: H 114 GLU cc_start: 0.8282 (mp0) cc_final: 0.7815 (tt0) REVERT: J 67 ASN cc_start: 0.7754 (t0) cc_final: 0.7442 (t0) REVERT: J 71 ASP cc_start: 0.8594 (m-30) cc_final: 0.7717 (m-30) REVERT: K 12 ASP cc_start: 0.8598 (p0) cc_final: 0.8283 (p0) REVERT: K 51 LYS cc_start: 0.8178 (mtmm) cc_final: 0.7620 (mttm) REVERT: K 95 ILE cc_start: 0.9059 (mt) cc_final: 0.8855 (mt) REVERT: M 18 ARG cc_start: 0.8468 (mtp-110) cc_final: 0.8266 (mtm110) REVERT: M 119 LEU cc_start: 0.9083 (tp) cc_final: 0.8865 (tp) REVERT: N 27 SER cc_start: 0.9114 (m) cc_final: 0.8759 (t) REVERT: N 75 ILE cc_start: 0.9346 (mm) cc_final: 0.9141 (mm) REVERT: O 54 VAL cc_start: 0.8808 (t) cc_final: 0.8042 (t) REVERT: O 85 LYS cc_start: 0.8591 (mmtm) cc_final: 0.8373 (tppt) REVERT: P 7 LEU cc_start: 0.9133 (mm) cc_final: 0.8855 (mm) REVERT: P 70 GLU cc_start: 0.7595 (mp0) cc_final: 0.7130 (mp0) REVERT: R 1 MET cc_start: 0.6479 (tpt) cc_final: 0.6258 (tpp) REVERT: R 21 ARG cc_start: 0.8725 (ttm-80) cc_final: 0.8350 (ttm-80) REVERT: S 59 GLU cc_start: 0.7779 (pp20) cc_final: 0.7487 (pp20) REVERT: U 17 ASP cc_start: 0.7880 (m-30) cc_final: 0.7634 (m-30) REVERT: U 21 ARG cc_start: 0.8575 (ttp-170) cc_final: 0.8096 (mtp-110) REVERT: V 25 LYS cc_start: 0.8895 (mtmm) cc_final: 0.8668 (mtmm) REVERT: V 29 ILE cc_start: 0.9200 (tp) cc_final: 0.8720 (tp) REVERT: V 51 GLN cc_start: 0.8571 (pp30) cc_final: 0.8165 (pp30) REVERT: V 53 LYS cc_start: 0.8581 (mppt) cc_final: 0.8264 (mtmt) REVERT: W 37 ARG cc_start: 0.8650 (mmt-90) cc_final: 0.8351 (mmt-90) REVERT: W 64 LYS cc_start: 0.9023 (tptm) cc_final: 0.8710 (tttp) REVERT: X 71 ARG cc_start: 0.8843 (ttm110) cc_final: 0.8579 (mtm-85) REVERT: Y 5 GLU cc_start: 0.8747 (mp0) cc_final: 0.8273 (mp0) REVERT: Z 55 LYS cc_start: 0.7785 (tttm) cc_final: 0.7530 (tttp) REVERT: b 138 ARG cc_start: 0.7686 (ttt180) cc_final: 0.7353 (ttp-170) REVERT: b 160 LEU cc_start: 0.9231 (tp) cc_final: 0.8939 (tp) REVERT: c 33 ASP cc_start: 0.8328 (t0) cc_final: 0.7968 (p0) REVERT: c 122 GLN cc_start: 0.8821 (mt0) cc_final: 0.8422 (mt0) REVERT: c 151 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7016 (tm-30) REVERT: c 184 ASN cc_start: 0.8847 (t0) cc_final: 0.8622 (t0) REVERT: d 99 ASN cc_start: 0.8600 (t0) cc_final: 0.8373 (t0) REVERT: e 40 ASP cc_start: 0.8719 (p0) cc_final: 0.7955 (p0) REVERT: e 104 ILE cc_start: 0.8804 (mt) cc_final: 0.8535 (mm) REVERT: f 5 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7629 (tm-30) REVERT: g 96 ASN cc_start: 0.8845 (m-40) cc_final: 0.7659 (m110) REVERT: g 100 MET cc_start: 0.8329 (mtm) cc_final: 0.7955 (mpp) REVERT: g 102 TRP cc_start: 0.8990 (m-10) cc_final: 0.8219 (m-10) REVERT: h 17 GLN cc_start: 0.9149 (mm-40) cc_final: 0.8867 (mm-40) REVERT: h 62 LEU cc_start: 0.9120 (mt) cc_final: 0.8703 (mt) REVERT: h 65 PHE cc_start: 0.8413 (t80) cc_final: 0.7988 (t80) REVERT: h 78 SER cc_start: 0.9073 (t) cc_final: 0.8627 (t) REVERT: h 112 ASP cc_start: 0.8923 (p0) cc_final: 0.8622 (p0) REVERT: h 123 GLU cc_start: 0.7907 (tt0) cc_final: 0.7565 (tt0) REVERT: i 21 LYS cc_start: 0.8220 (mtpt) cc_final: 0.7994 (ttmm) REVERT: i 93 LEU cc_start: 0.8125 (mt) cc_final: 0.7727 (pp) REVERT: i 123 ARG cc_start: 0.8274 (mtt-85) cc_final: 0.7856 (ttm110) REVERT: j 20 GLN cc_start: 0.8659 (mt0) cc_final: 0.8445 (pp30) REVERT: j 58 ASN cc_start: 0.9209 (m110) cc_final: 0.8993 (m110) REVERT: j 65 TYR cc_start: 0.8676 (m-80) cc_final: 0.8448 (m-80) REVERT: k 69 CYS cc_start: 0.8550 (t) cc_final: 0.7442 (t) REVERT: k 76 TYR cc_start: 0.8597 (m-80) cc_final: 0.8296 (m-80) REVERT: k 86 LYS cc_start: 0.8248 (ttmm) cc_final: 0.7874 (ttmm) REVERT: k 106 ILE cc_start: 0.9194 (mm) cc_final: 0.8959 (mt) REVERT: l 37 TYR cc_start: 0.8052 (p90) cc_final: 0.7376 (p90) REVERT: l 77 SER cc_start: 0.9291 (m) cc_final: 0.8998 (t) REVERT: l 88 ASP cc_start: 0.7638 (t0) cc_final: 0.7189 (t0) REVERT: l 102 ASP cc_start: 0.8543 (t0) cc_final: 0.8306 (t0) REVERT: m 30 LYS cc_start: 0.8999 (pttt) cc_final: 0.8706 (tttt) REVERT: m 102 LYS cc_start: 0.9041 (tttt) cc_final: 0.8556 (tttp) REVERT: n 29 ILE cc_start: 0.8821 (mt) cc_final: 0.8585 (mt) REVERT: n 62 ASN cc_start: 0.9154 (t0) cc_final: 0.8888 (t0) REVERT: o 20 ASP cc_start: 0.7256 (t0) cc_final: 0.6456 (t70) REVERT: o 23 SER cc_start: 0.8650 (p) cc_final: 0.8449 (p) REVERT: o 37 HIS cc_start: 0.8658 (t70) cc_final: 0.8121 (t70) REVERT: p 42 ILE cc_start: 0.8272 (pt) cc_final: 0.7897 (pt) REVERT: q 14 ASP cc_start: 0.8204 (p0) cc_final: 0.6728 (t0) REVERT: q 48 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7371 (pt0) REVERT: q 64 ARG cc_start: 0.8338 (ttp-110) cc_final: 0.7937 (ttp80) REVERT: s 2 ARG cc_start: 0.8098 (tpt-90) cc_final: 0.7053 (ttt90) REVERT: s 6 LYS cc_start: 0.8682 (mttt) cc_final: 0.8433 (mttm) REVERT: s 76 THR cc_start: 0.7527 (p) cc_final: 0.6958 (t) REVERT: t 50 PHE cc_start: 0.8966 (t80) cc_final: 0.8431 (t80) REVERT: t 54 GLN cc_start: 0.8375 (tt0) cc_final: 0.7719 (tt0) REVERT: t 67 HIS cc_start: 0.8181 (t-90) cc_final: 0.7428 (t70) REVERT: t 69 ASN cc_start: 0.8935 (m-40) cc_final: 0.8585 (m110) REVERT: u 30 GLU cc_start: 0.8358 (tm-30) cc_final: 0.7955 (tm-30) REVERT: u 39 LYS cc_start: 0.8655 (ttmt) cc_final: 0.8264 (mtpt) REVERT: u 44 ARG cc_start: 0.8151 (mtm-85) cc_final: 0.7869 (mtm-85) REVERT: y 97 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7946 (tm-30) outliers start: 8 outliers final: 3 residues processed: 1806 average time/residue: 1.4779 time to fit residues: 4585.1769 Evaluate side-chains 1477 residues out of total 4915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1474 time to evaluate : 6.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain j residue 32 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 880 optimal weight: 40.0000 chunk 790 optimal weight: 9.9990 chunk 438 optimal weight: 10.0000 chunk 270 optimal weight: 10.0000 chunk 533 optimal weight: 8.9990 chunk 422 optimal weight: 50.0000 chunk 817 optimal weight: 8.9990 chunk 316 optimal weight: 20.0000 chunk 497 optimal weight: 6.9990 chunk 608 optimal weight: 8.9990 chunk 947 optimal weight: 7.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 4 GLN ** 0 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 25 HIS 3 27 ASN ** 4 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 HIS ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN D 49 GLN D 136 ASN ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 GLN H 28 ASN L 104 GLN M 13 HIS M 45 GLN N 9 GLN P 2 ASN Q 36 GLN R 86 GLN R 89 HIS T 59 ASN U 44 HIS V 44 HIS X 22 ASN b 108 GLN b 167 HIS c 2 GLN c 122 GLN d 130 ASN d 135 GLN d 139 ASN ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 66 GLN i 4 GLN i 24 ASN i 30 ASN i 74 GLN j 15 HIS j 20 GLN j 58 ASN j 64 GLN k 80 ASN ** n 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 27 GLN o 34 GLN o 39 GLN o 61 GLN q 8 GLN t 51 ASN ** t 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 28 GLN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 158605 Z= 0.355 Angle : 0.764 30.214 237201 Z= 0.396 Chirality : 0.040 1.130 30245 Planarity : 0.007 0.132 12834 Dihedral : 24.705 179.919 79064 Min Nonbonded Distance : 1.706 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.26 % Favored : 88.64 % Rotamer: Outliers : 3.50 % Allowed : 19.44 % Favored : 77.06 % 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: -3.56 (0.10), residues: 5926 helix: -1.34 (0.11), residues: 1931 sheet: -2.71 (0.14), residues: 1051 loop : -2.96 (0.10), residues: 2944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP s 33 HIS 0.007 0.001 HIS k 117 PHE 0.032 0.002 PHE F 99 TYR 0.025 0.002 TYR P 98 ARG 0.008 0.001 ARG k 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11852 Ramachandran restraints generated. 5926 Oldfield, 0 Emsley, 5926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11852 Ramachandran restraints generated. 5926 Oldfield, 0 Emsley, 5926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1734 residues out of total 4915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 1570 time to evaluate : 6.255 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: 0 16 ARG cc_start: 0.8535 (mtt180) cc_final: 0.8285 (mtt90) REVERT: 0 35 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7264 (mt-10) REVERT: 1 26 LYS cc_start: 0.8711 (mmtt) cc_final: 0.8340 (mmtp) REVERT: 2 11 LYS cc_start: 0.9156 (mttt) cc_final: 0.8833 (mttm) REVERT: 3 63 TYR cc_start: 0.7365 (m-80) cc_final: 0.6922 (m-80) REVERT: 4 2 LYS cc_start: 0.8498 (mttp) cc_final: 0.8058 (mtpp) REVERT: C 120 ASP cc_start: 0.7687 (p0) cc_final: 0.7482 (p0) REVERT: D 7 LYS cc_start: 0.8763 (ttmt) cc_final: 0.8419 (ttmm) REVERT: D 64 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7887 (mt-10) REVERT: D 96 ILE cc_start: 0.9533 (mt) cc_final: 0.9311 (mt) REVERT: D 186 LEU cc_start: 0.8959 (mt) cc_final: 0.8711 (mt) REVERT: E 1 MET cc_start: 0.6888 (mmm) cc_final: 0.6687 (mmm) REVERT: E 168 ASP cc_start: 0.7681 (t0) cc_final: 0.7420 (t0) REVERT: F 70 ARG cc_start: 0.7835 (ttp80) cc_final: 0.7611 (ptt180) REVERT: F 156 THR cc_start: 0.8817 (m) cc_final: 0.8521 (p) REVERT: F 174 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.7235 (m-80) REVERT: G 25 ILE cc_start: 0.9167 (mm) cc_final: 0.8794 (mp) REVERT: G 51 PHE cc_start: 0.8621 (m-80) cc_final: 0.8414 (m-80) REVERT: G 138 GLN cc_start: 0.8844 (tm-30) cc_final: 0.8326 (tm-30) REVERT: G 142 GLN cc_start: 0.8654 (tp40) cc_final: 0.7492 (tp40) REVERT: G 146 ASP cc_start: 0.8095 (m-30) cc_final: 0.6973 (m-30) REVERT: H 17 ASP cc_start: 0.7048 (m-30) cc_final: 0.6747 (m-30) REVERT: H 37 VAL cc_start: 0.9079 (OUTLIER) cc_final: 0.8814 (m) REVERT: H 97 ARG cc_start: 0.8048 (tpm170) cc_final: 0.7578 (tpm170) REVERT: J 67 ASN cc_start: 0.7553 (t0) cc_final: 0.6874 (t0) REVERT: J 71 ASP cc_start: 0.8627 (m-30) cc_final: 0.7688 (m-30) REVERT: K 12 ASP cc_start: 0.8726 (p0) cc_final: 0.8454 (p0) REVERT: K 51 LYS cc_start: 0.8207 (mtmm) cc_final: 0.7636 (mttm) REVERT: K 58 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8933 (pp) REVERT: M 47 GLU cc_start: 0.7456 (tm-30) cc_final: 0.6941 (tm-30) REVERT: M 51 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7663 (mtp-110) REVERT: M 119 LEU cc_start: 0.8994 (tp) cc_final: 0.8746 (tp) REVERT: O 38 GLN cc_start: 0.7907 (mt0) cc_final: 0.7689 (mt0) REVERT: O 54 VAL cc_start: 0.8834 (t) cc_final: 0.8495 (t) REVERT: P 7 LEU cc_start: 0.9195 (mm) cc_final: 0.8933 (mm) REVERT: P 67 GLU cc_start: 0.8674 (tp30) cc_final: 0.8118 (tp30) REVERT: R 21 ARG cc_start: 0.8846 (ttm-80) cc_final: 0.8582 (ttm110) REVERT: S 15 GLN cc_start: 0.7754 (tt0) cc_final: 0.7048 (tt0) REVERT: S 59 GLU cc_start: 0.7631 (pp20) cc_final: 0.7376 (pp20) REVERT: T 42 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8266 (tt0) REVERT: U 21 ARG cc_start: 0.8494 (ttp-170) cc_final: 0.8117 (mtp-110) REVERT: V 51 GLN cc_start: 0.8479 (pp30) cc_final: 0.7987 (pp30) REVERT: V 53 LYS cc_start: 0.8545 (mppt) cc_final: 0.8211 (mtpt) REVERT: V 78 GLN cc_start: 0.8324 (mt0) cc_final: 0.7677 (tt0) REVERT: W 37 ARG cc_start: 0.8569 (mmt-90) cc_final: 0.8311 (mmt-90) REVERT: W 56 PHE cc_start: 0.9278 (p90) cc_final: 0.8945 (p90) REVERT: W 60 ASP cc_start: 0.7421 (m-30) cc_final: 0.6849 (p0) REVERT: Y 5 GLU cc_start: 0.8648 (mp0) cc_final: 0.8345 (mp0) REVERT: Y 37 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8210 (tp) REVERT: b 8 MET cc_start: 0.7865 (tmm) cc_final: 0.7497 (tmm) REVERT: b 51 GLU cc_start: 0.8234 (tp30) cc_final: 0.8029 (tp30) REVERT: b 138 ARG cc_start: 0.7654 (ttt180) cc_final: 0.7383 (ttp80) REVERT: b 160 LEU cc_start: 0.9205 (tp) cc_final: 0.8889 (tp) REVERT: c 36 PHE cc_start: 0.8187 (t80) cc_final: 0.7824 (t80) REVERT: c 151 GLU cc_start: 0.7471 (tm-30) cc_final: 0.7197 (tm-30) REVERT: d 99 ASN cc_start: 0.8479 (t0) cc_final: 0.8200 (t0) REVERT: d 151 GLN cc_start: 0.7405 (mm-40) cc_final: 0.7138 (tp-100) REVERT: e 40 ASP cc_start: 0.8584 (p0) cc_final: 0.8054 (p0) REVERT: e 67 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.8198 (mpp80) REVERT: f 5 GLU cc_start: 0.8367 (tm-30) cc_final: 0.7895 (tm-30) REVERT: f 24 ARG cc_start: 0.8518 (ttm110) cc_final: 0.8078 (mmm160) REVERT: f 91 ARG cc_start: 0.9083 (mmm-85) cc_final: 0.8839 (mmm160) REVERT: g 96 ASN cc_start: 0.8872 (m-40) cc_final: 0.8527 (m110) REVERT: g 102 TRP cc_start: 0.8947 (m-10) cc_final: 0.7945 (m-10) REVERT: h 11 THR cc_start: 0.9182 (m) cc_final: 0.8867 (p) REVERT: h 17 GLN cc_start: 0.9183 (mm-40) cc_final: 0.8958 (mm-40) REVERT: h 42 GLU cc_start: 0.6701 (mm-30) cc_final: 0.6448 (mm-30) REVERT: h 62 LEU cc_start: 0.9013 (mt) cc_final: 0.8722 (mt) REVERT: h 78 SER cc_start: 0.9021 (t) cc_final: 0.8652 (t) REVERT: h 112 ASP cc_start: 0.8913 (p0) cc_final: 0.8569 (p0) REVERT: h 123 GLU cc_start: 0.7769 (tt0) cc_final: 0.7510 (tt0) REVERT: i 61 ASP cc_start: 0.6797 (OUTLIER) cc_final: 0.6479 (m-30) REVERT: i 93 LEU cc_start: 0.8100 (mt) cc_final: 0.7707 (pp) REVERT: i 119 LYS cc_start: 0.8264 (ptmt) cc_final: 0.7960 (ptmt) REVERT: j 20 GLN cc_start: 0.8601 (mt0) cc_final: 0.8399 (pp30) REVERT: j 65 TYR cc_start: 0.8687 (m-80) cc_final: 0.8450 (m-80) REVERT: l 88 ASP cc_start: 0.7596 (t0) cc_final: 0.7181 (t0) REVERT: l 102 ASP cc_start: 0.8515 (t0) cc_final: 0.8269 (t0) REVERT: m 58 GLU cc_start: 0.8374 (tt0) cc_final: 0.8035 (tt0) REVERT: m 82 LEU cc_start: 0.8172 (mt) cc_final: 0.7956 (mt) REVERT: m 102 LYS cc_start: 0.8985 (tttt) cc_final: 0.8613 (tttp) REVERT: n 29 ILE cc_start: 0.8686 (mt) cc_final: 0.8449 (mt) REVERT: n 62 ASN cc_start: 0.9195 (t0) cc_final: 0.8954 (t0) REVERT: n 66 GLN cc_start: 0.8481 (mt0) cc_final: 0.8131 (mm-40) REVERT: o 20 ASP cc_start: 0.7246 (t0) cc_final: 0.6505 (t70) REVERT: o 23 SER cc_start: 0.8762 (p) cc_final: 0.8523 (p) REVERT: o 27 GLN cc_start: 0.8779 (mt0) cc_final: 0.8539 (mt0) REVERT: o 37 HIS cc_start: 0.8672 (t70) cc_final: 0.8110 (t70) REVERT: p 31 ARG cc_start: 0.8551 (ptm160) cc_final: 0.8299 (ptp-170) REVERT: q 18 LYS cc_start: 0.8874 (ttpt) cc_final: 0.8633 (ttpt) REVERT: q 48 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7368 (pt0) REVERT: q 64 ARG cc_start: 0.8320 (ttp-110) cc_final: 0.7909 (ttp80) REVERT: r 21 ASP cc_start: 0.8265 (t0) cc_final: 0.7954 (t0) REVERT: r 37 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8178 (mtpp) REVERT: r 63 TYR cc_start: 0.9153 (t80) cc_final: 0.8794 (t80) REVERT: s 2 ARG cc_start: 0.8077 (tpt-90) cc_final: 0.7100 (ttt90) REVERT: s 76 THR cc_start: 0.7495 (p) cc_final: 0.6926 (t) REVERT: t 50 PHE cc_start: 0.8899 (t80) cc_final: 0.8325 (t80) REVERT: t 69 ASN cc_start: 0.8909 (m-40) cc_final: 0.8665 (m110) REVERT: u 19 LYS cc_start: 0.8013 (ttmm) cc_final: 0.7751 (mttm) REVERT: y 14 GLU cc_start: 0.7203 (pt0) cc_final: 0.6927 (pt0) outliers start: 164 outliers final: 114 residues processed: 1622 average time/residue: 1.2886 time to fit residues: 3615.1823 Evaluate side-chains 1576 residues out of total 4915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 1453 time to evaluate : 6.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 19 ASP Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 29 VAL Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 9 VAL Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 174 PHE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 100 PHE Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 5 LYS Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 51 ARG Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 45 SER Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 61 GLN Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 42 GLU Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain V residue 17 SER Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 22 ASN Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 58 ILE Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 40 GLN Chi-restraints excluded: chain d residue 20 LEU Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 172 VAL Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain e residue 23 THR Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 67 ARG Chi-restraints excluded: chain e residue 95 MET Chi-restraints excluded: chain e residue 139 THR Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain g residue 86 VAL Chi-restraints excluded: chain g residue 139 ASP Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 38 VAL Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 84 ILE Chi-restraints excluded: chain h residue 125 ILE Chi-restraints excluded: chain i residue 20 ILE Chi-restraints excluded: chain i residue 29 ILE Chi-restraints excluded: chain i residue 61 ASP Chi-restraints excluded: chain i residue 83 THR Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain k residue 64 VAL Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain m residue 10 ASP Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 19 THR Chi-restraints excluded: chain m residue 42 VAL Chi-restraints excluded: chain n residue 50 THR Chi-restraints excluded: chain n residue 54 ASP Chi-restraints excluded: chain n residue 97 LYS Chi-restraints excluded: chain o residue 60 SER Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 26 ASN Chi-restraints excluded: chain p residue 69 ASP Chi-restraints excluded: chain r residue 37 LYS Chi-restraints excluded: chain s residue 26 ASP Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain t residue 19 HIS Chi-restraints excluded: chain t residue 56 ILE Chi-restraints excluded: chain u residue 52 VAL Chi-restraints excluded: chain y residue 51 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 526 optimal weight: 10.0000 chunk 293 optimal weight: 10.0000 chunk 788 optimal weight: 10.0000 chunk 644 optimal weight: 20.0000 chunk 261 optimal weight: 10.0000 chunk 948 optimal weight: 9.9990 chunk 1025 optimal weight: 30.0000 chunk 845 optimal weight: 20.0000 chunk 940 optimal weight: 4.9990 chunk 323 optimal weight: 10.0000 chunk 761 optimal weight: 20.0000 overall best weight: 8.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 HIS E 115 GLN ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 28 ASN L 104 GLN M 45 GLN P 2 ASN Q 80 ASN R 18 GLN R 86 GLN W 42 HIS X 22 ASN Y 38 GLN d 139 ASN ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 35 GLN j 58 ASN k 27 ASN ** k 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 39 GLN ** p 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 46 HIS t 54 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 158605 Z= 0.374 Angle : 0.762 30.240 237201 Z= 0.395 Chirality : 0.040 1.133 30245 Planarity : 0.007 0.130 12834 Dihedral : 24.611 179.866 79062 Min Nonbonded Distance : 0.911 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.02 % Favored : 88.86 % Rotamer: Outliers : 4.93 % Allowed : 21.49 % Favored : 73.58 % 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: -3.05 (0.10), residues: 5926 helix: -0.85 (0.11), residues: 1924 sheet: -2.41 (0.14), residues: 1045 loop : -2.71 (0.10), residues: 2957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 212 HIS 0.006 0.001 HIS k 117 PHE 0.029 0.002 PHE F 99 TYR 0.028 0.002 TYR F 127 ARG 0.006 0.001 ARG C 269 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11852 Ramachandran restraints generated. 5926 Oldfield, 0 Emsley, 5926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11852 Ramachandran restraints generated. 5926 Oldfield, 0 Emsley, 5926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1735 residues out of total 4915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 1504 time to evaluate : 6.167 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: 0 9 ARG cc_start: 0.8735 (ptp90) cc_final: 0.8509 (ptp90) REVERT: 0 16 ARG cc_start: 0.8514 (mtt180) cc_final: 0.8216 (mtt90) REVERT: 1 35 LEU cc_start: 0.8964 (mt) cc_final: 0.8756 (mp) REVERT: 2 11 LYS cc_start: 0.9151 (mttt) cc_final: 0.8827 (mttm) REVERT: 3 63 TYR cc_start: 0.7418 (m-80) cc_final: 0.6924 (m-80) REVERT: 4 2 LYS cc_start: 0.8527 (mttp) cc_final: 0.8268 (mmmm) REVERT: D 7 LYS cc_start: 0.8724 (ttmt) cc_final: 0.8399 (ttmm) REVERT: D 64 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7872 (mt-10) REVERT: D 96 ILE cc_start: 0.9513 (mt) cc_final: 0.9291 (mt) REVERT: D 186 LEU cc_start: 0.8956 (mt) cc_final: 0.8729 (mt) REVERT: E 1 MET cc_start: 0.6905 (mmm) cc_final: 0.6428 (mmm) REVERT: F 70 ARG cc_start: 0.7824 (ttp80) cc_final: 0.7610 (ptt180) REVERT: F 156 THR cc_start: 0.8811 (m) cc_final: 0.8505 (p) REVERT: F 174 PHE cc_start: 0.7739 (OUTLIER) cc_final: 0.7325 (m-80) REVERT: G 138 GLN cc_start: 0.8787 (tm-30) cc_final: 0.8273 (tm-30) REVERT: G 142 GLN cc_start: 0.8598 (tp40) cc_final: 0.7423 (tp40) REVERT: G 146 ASP cc_start: 0.8071 (m-30) cc_final: 0.7000 (m-30) REVERT: H 17 ASP cc_start: 0.7014 (m-30) cc_final: 0.6563 (m-30) REVERT: H 97 ARG cc_start: 0.8075 (tpm170) cc_final: 0.7634 (tpm170) REVERT: J 52 ASP cc_start: 0.8506 (m-30) cc_final: 0.8259 (m-30) REVERT: J 67 ASN cc_start: 0.7524 (t0) cc_final: 0.6847 (t0) REVERT: J 71 ASP cc_start: 0.8671 (m-30) cc_final: 0.7674 (m-30) REVERT: J 81 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8562 (tp) REVERT: K 12 ASP cc_start: 0.8698 (p0) cc_final: 0.8420 (p0) REVERT: M 47 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7263 (tm-30) REVERT: M 51 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7676 (mtp-110) REVERT: M 119 LEU cc_start: 0.8988 (tp) cc_final: 0.8763 (tp) REVERT: O 54 VAL cc_start: 0.8801 (t) cc_final: 0.8565 (t) REVERT: O 85 LYS cc_start: 0.8934 (ttmm) cc_final: 0.8366 (tppt) REVERT: P 7 LEU cc_start: 0.9229 (mm) cc_final: 0.8971 (mm) REVERT: P 67 GLU cc_start: 0.8726 (tp30) cc_final: 0.8183 (tp30) REVERT: P 93 LYS cc_start: 0.9353 (ttmm) cc_final: 0.9059 (mtpp) REVERT: Q 80 ASN cc_start: 0.8521 (OUTLIER) cc_final: 0.8011 (m110) REVERT: R 21 ARG cc_start: 0.8863 (ttm-80) cc_final: 0.8402 (ttm-80) REVERT: S 15 GLN cc_start: 0.7704 (tt0) cc_final: 0.6911 (tt0) REVERT: S 65 ASP cc_start: 0.7614 (t0) cc_final: 0.7097 (t0) REVERT: T 42 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8282 (tt0) REVERT: U 21 ARG cc_start: 0.8529 (ttp-170) cc_final: 0.8165 (mtp-110) REVERT: V 11 GLU cc_start: 0.8261 (pm20) cc_final: 0.7658 (pm20) REVERT: V 48 MET cc_start: 0.8975 (tpt) cc_final: 0.8458 (tpt) REVERT: V 51 GLN cc_start: 0.8418 (pp30) cc_final: 0.7956 (pp30) REVERT: W 37 ARG cc_start: 0.8569 (mmt-90) cc_final: 0.8263 (mmt-90) REVERT: W 60 ASP cc_start: 0.7467 (m-30) cc_final: 0.6968 (p0) REVERT: Y 1 MET cc_start: 0.7550 (ptt) cc_final: 0.7287 (ptt) REVERT: Y 5 GLU cc_start: 0.8686 (mp0) cc_final: 0.8470 (mp0) REVERT: Z 55 LYS cc_start: 0.7818 (tttp) cc_final: 0.7536 (tttp) REVERT: b 8 MET cc_start: 0.7880 (tmm) cc_final: 0.7552 (tmm) REVERT: b 99 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.8024 (tpp) REVERT: b 138 ARG cc_start: 0.7635 (ttt180) cc_final: 0.7383 (ttp80) REVERT: c 36 PHE cc_start: 0.8214 (t80) cc_final: 0.7738 (t80) REVERT: c 151 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7354 (tm-30) REVERT: d 99 ASN cc_start: 0.8341 (t0) cc_final: 0.8084 (t0) REVERT: d 140 ASP cc_start: 0.8116 (m-30) cc_final: 0.7821 (m-30) REVERT: d 151 GLN cc_start: 0.7517 (mm-40) cc_final: 0.7254 (tp40) REVERT: e 40 ASP cc_start: 0.8638 (p0) cc_final: 0.8117 (p0) REVERT: e 67 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.8178 (mpp80) REVERT: f 5 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7548 (tm-30) REVERT: f 24 ARG cc_start: 0.8578 (ttm110) cc_final: 0.8000 (mmm160) REVERT: f 36 ILE cc_start: 0.9330 (mp) cc_final: 0.9080 (mt) REVERT: f 90 MET cc_start: 0.8240 (mtm) cc_final: 0.7571 (mtm) REVERT: h 11 THR cc_start: 0.9189 (m) cc_final: 0.8864 (p) REVERT: h 17 GLN cc_start: 0.9171 (mm-40) cc_final: 0.8969 (mm-40) REVERT: h 62 LEU cc_start: 0.8986 (mt) cc_final: 0.8743 (mt) REVERT: h 65 PHE cc_start: 0.8421 (t80) cc_final: 0.7972 (t80) REVERT: h 78 SER cc_start: 0.8929 (t) cc_final: 0.8560 (t) REVERT: h 112 ASP cc_start: 0.8901 (p0) cc_final: 0.8564 (p0) REVERT: h 123 GLU cc_start: 0.7813 (tt0) cc_final: 0.7518 (tt0) REVERT: i 61 ASP cc_start: 0.6829 (OUTLIER) cc_final: 0.6542 (m-30) REVERT: i 93 LEU cc_start: 0.8073 (mt) cc_final: 0.7705 (pp) REVERT: i 119 LYS cc_start: 0.8324 (ptmt) cc_final: 0.7944 (ptmt) REVERT: j 20 GLN cc_start: 0.8633 (mt0) cc_final: 0.8381 (pp30) REVERT: j 65 TYR cc_start: 0.8706 (m-80) cc_final: 0.8477 (m-80) REVERT: k 76 TYR cc_start: 0.8376 (m-80) cc_final: 0.7884 (m-10) REVERT: k 86 LYS cc_start: 0.7863 (ttmm) cc_final: 0.7547 (ttmm) REVERT: l 37 TYR cc_start: 0.7969 (p90) cc_final: 0.7428 (p90) REVERT: l 88 ASP cc_start: 0.7610 (t0) cc_final: 0.7205 (t0) REVERT: m 58 GLU cc_start: 0.8394 (tt0) cc_final: 0.8158 (tt0) REVERT: n 62 ASN cc_start: 0.9217 (t0) cc_final: 0.8967 (t0) REVERT: n 66 GLN cc_start: 0.8384 (mt0) cc_final: 0.8039 (mm-40) REVERT: o 20 ASP cc_start: 0.7390 (t0) cc_final: 0.6543 (t70) REVERT: o 23 SER cc_start: 0.8774 (p) cc_final: 0.8400 (p) REVERT: o 27 GLN cc_start: 0.8964 (mt0) cc_final: 0.8680 (mt0) REVERT: o 37 HIS cc_start: 0.8680 (t70) cc_final: 0.8122 (t70) REVERT: p 12 LYS cc_start: 0.7985 (ttpt) cc_final: 0.7704 (ttpt) REVERT: p 31 ARG cc_start: 0.8589 (ptm160) cc_final: 0.8327 (ptp-170) REVERT: q 14 ASP cc_start: 0.8129 (p0) cc_final: 0.6766 (t0) REVERT: q 64 ARG cc_start: 0.8331 (ttp-110) cc_final: 0.7936 (ttp80) REVERT: r 24 ASP cc_start: 0.8166 (t0) cc_final: 0.7700 (t70) REVERT: r 37 LYS cc_start: 0.8488 (mtpp) cc_final: 0.8137 (mtpp) REVERT: r 63 TYR cc_start: 0.9159 (t80) cc_final: 0.8746 (t80) REVERT: s 2 ARG cc_start: 0.8111 (tpt-90) cc_final: 0.7262 (ttt90) REVERT: s 76 THR cc_start: 0.7684 (p) cc_final: 0.7109 (t) REVERT: t 50 PHE cc_start: 0.8873 (t80) cc_final: 0.8378 (t80) REVERT: u 19 LYS cc_start: 0.7907 (ttmm) cc_final: 0.7640 (mttm) REVERT: y 14 GLU cc_start: 0.7011 (pt0) cc_final: 0.6286 (pt0) REVERT: y 108 THR cc_start: 0.6735 (OUTLIER) cc_final: 0.6371 (m) outliers start: 231 outliers final: 166 residues processed: 1601 average time/residue: 1.2687 time to fit residues: 3509.4680 Evaluate side-chains 1599 residues out of total 4915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 1424 time to evaluate : 6.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 3 GLN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 19 ASP Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 29 VAL Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 9 VAL Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 174 PHE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 43 ASN Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 135 HIS Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 100 PHE Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 51 ARG Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain O residue 45 SER Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 80 ASN Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 42 GLU Chi-restraints excluded: chain T residue 76 ARG Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 17 SER Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 58 ILE Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain b residue 99 MET Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 150 ILE Chi-restraints excluded: chain c residue 2 GLN Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 40 GLN Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain d residue 11 SER Chi-restraints excluded: chain d residue 20 LEU Chi-restraints excluded: chain d residue 24 VAL Chi-restraints excluded: chain d residue 33 ILE Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 172 VAL Chi-restraints excluded: chain e residue 23 THR Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 59 ILE Chi-restraints excluded: chain e residue 67 ARG Chi-restraints excluded: chain e residue 76 ASN Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain g residue 26 VAL Chi-restraints excluded: chain g residue 86 VAL Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain g residue 139 ASP Chi-restraints excluded: chain h residue 38 VAL Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 84 ILE Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 125 ILE Chi-restraints excluded: chain i residue 20 ILE Chi-restraints excluded: chain i residue 29 ILE Chi-restraints excluded: chain i residue 61 ASP Chi-restraints excluded: chain i residue 83 THR Chi-restraints excluded: chain j residue 22 THR Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 31 VAL Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 64 VAL Chi-restraints excluded: chain k residue 69 CYS Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 96 ILE Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain m residue 10 ASP Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 42 VAL Chi-restraints excluded: chain n residue 50 THR Chi-restraints excluded: chain n residue 54 ASP Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain n residue 97 LYS Chi-restraints excluded: chain o residue 11 VAL Chi-restraints excluded: chain o residue 60 SER Chi-restraints excluded: chain o residue 78 THR Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 69 ASP Chi-restraints excluded: chain q residue 67 SER Chi-restraints excluded: chain s residue 13 HIS Chi-restraints excluded: chain s residue 26 ASP Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain t residue 19 HIS Chi-restraints excluded: chain t residue 42 ASP Chi-restraints excluded: chain t residue 54 GLN Chi-restraints excluded: chain t residue 56 ILE Chi-restraints excluded: chain u residue 52 VAL Chi-restraints excluded: chain y residue 51 TYR Chi-restraints excluded: chain y residue 81 GLU Chi-restraints excluded: chain y residue 108 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 937 optimal weight: 20.0000 chunk 713 optimal weight: 20.0000 chunk 492 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 452 optimal weight: 0.9990 chunk 637 optimal weight: 5.9990 chunk 952 optimal weight: 10.0000 chunk 1008 optimal weight: 0.2980 chunk 497 optimal weight: 8.9990 chunk 902 optimal weight: 4.9990 chunk 271 optimal weight: 10.0000 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 5 ASN ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN H 28 ASN ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 GLN P 2 ASN R 18 GLN R 86 GLN U 39 ASN U 73 ASN W 42 HIS X 22 ASN d 139 ASN d 197 HIS ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 35 GLN k 100 ASN n 66 GLN n 71 HIS o 39 GLN ** p 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 29 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 158605 Z= 0.198 Angle : 0.661 30.250 237201 Z= 0.349 Chirality : 0.035 1.142 30245 Planarity : 0.006 0.124 12834 Dihedral : 24.467 179.754 79062 Min Nonbonded Distance : 1.097 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.83 % Favored : 91.11 % Rotamer: Outliers : 4.55 % Allowed : 23.77 % Favored : 71.68 % 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: -2.45 (0.10), residues: 5926 helix: -0.33 (0.12), residues: 1929 sheet: -2.11 (0.15), residues: 1001 loop : -2.36 (0.11), residues: 2996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP b 103 HIS 0.007 0.001 HIS O 34 PHE 0.026 0.002 PHE F 98 TYR 0.028 0.002 TYR F 127 ARG 0.006 0.000 ARG C 269 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11852 Ramachandran restraints generated. 5926 Oldfield, 0 Emsley, 5926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11852 Ramachandran restraints generated. 5926 Oldfield, 0 Emsley, 5926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1762 residues out of total 4915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 1549 time to evaluate : 6.209 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: 0 9 ARG cc_start: 0.8599 (ptp90) cc_final: 0.8395 (ptp90) REVERT: 0 35 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7198 (mt-10) REVERT: 1 7 LYS cc_start: 0.8744 (ptpt) cc_final: 0.8435 (ptpp) REVERT: 2 11 LYS cc_start: 0.9120 (mttt) cc_final: 0.8745 (mttm) REVERT: 3 63 TYR cc_start: 0.7253 (m-80) cc_final: 0.6800 (m-80) REVERT: 4 2 LYS cc_start: 0.8520 (mttp) cc_final: 0.8227 (mmmm) REVERT: 4 23 ILE cc_start: 0.9477 (mm) cc_final: 0.9222 (mm) REVERT: C 20 ASN cc_start: 0.8230 (t0) cc_final: 0.7997 (t0) REVERT: C 186 ASP cc_start: 0.7770 (t0) cc_final: 0.7554 (t0) REVERT: C 212 TRP cc_start: 0.8532 (p90) cc_final: 0.8309 (p-90) REVERT: D 7 LYS cc_start: 0.8727 (ttmt) cc_final: 0.8382 (ttmm) REVERT: D 96 ILE cc_start: 0.9421 (mt) cc_final: 0.9155 (mt) REVERT: E 1 MET cc_start: 0.6772 (mmm) cc_final: 0.6378 (mmm) REVERT: E 7 ASP cc_start: 0.6942 (OUTLIER) cc_final: 0.6270 (p0) REVERT: F 25 MET cc_start: 0.8439 (mmm) cc_final: 0.8103 (mmt) REVERT: F 156 THR cc_start: 0.8751 (m) cc_final: 0.8502 (p) REVERT: F 174 PHE cc_start: 0.7675 (OUTLIER) cc_final: 0.7262 (m-80) REVERT: G 138 GLN cc_start: 0.8706 (tm-30) cc_final: 0.8189 (tm-30) REVERT: G 142 GLN cc_start: 0.8555 (tp40) cc_final: 0.7411 (tp40) REVERT: G 146 ASP cc_start: 0.8080 (m-30) cc_final: 0.6952 (m-30) REVERT: H 1 MET cc_start: 0.6734 (ptm) cc_final: 0.6510 (ptm) REVERT: H 17 ASP cc_start: 0.6872 (m-30) cc_final: 0.6501 (m-30) REVERT: H 37 VAL cc_start: 0.9132 (OUTLIER) cc_final: 0.8894 (m) REVERT: H 97 ARG cc_start: 0.8041 (tpm170) cc_final: 0.7552 (tpm170) REVERT: J 52 ASP cc_start: 0.8469 (m-30) cc_final: 0.8224 (m-30) REVERT: J 67 ASN cc_start: 0.7463 (t0) cc_final: 0.7073 (t0) REVERT: J 81 ILE cc_start: 0.8809 (tp) cc_final: 0.8561 (tp) REVERT: K 12 ASP cc_start: 0.8652 (p0) cc_final: 0.8322 (p0) REVERT: M 47 GLU cc_start: 0.7526 (tm-30) cc_final: 0.7137 (tm-30) REVERT: M 51 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7643 (mtp-110) REVERT: M 119 LEU cc_start: 0.8813 (tp) cc_final: 0.8560 (tp) REVERT: N 49 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7919 (mt-10) REVERT: N 82 GLU cc_start: 0.7567 (mp0) cc_final: 0.7240 (mp0) REVERT: O 106 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8202 (tp) REVERT: P 7 LEU cc_start: 0.9264 (mm) cc_final: 0.9022 (mm) REVERT: P 93 LYS cc_start: 0.9278 (ttmm) cc_final: 0.9012 (mtpp) REVERT: Q 80 ASN cc_start: 0.8758 (m-40) cc_final: 0.8497 (m-40) REVERT: R 21 ARG cc_start: 0.8783 (ttm-80) cc_final: 0.8392 (ttm-80) REVERT: R 31 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7798 (tp30) REVERT: S 4 ILE cc_start: 0.9140 (mp) cc_final: 0.8867 (mp) REVERT: S 15 GLN cc_start: 0.7470 (tt0) cc_final: 0.7239 (tt0) REVERT: S 65 ASP cc_start: 0.7495 (t0) cc_final: 0.7107 (t0) REVERT: V 29 ILE cc_start: 0.9212 (tp) cc_final: 0.8913 (tp) REVERT: W 37 ARG cc_start: 0.8405 (mmt-90) cc_final: 0.8161 (mmt-90) REVERT: W 60 ASP cc_start: 0.7353 (m-30) cc_final: 0.6967 (p0) REVERT: Y 1 MET cc_start: 0.7491 (ptt) cc_final: 0.7290 (ptt) REVERT: Y 5 GLU cc_start: 0.8648 (mp0) cc_final: 0.8382 (mp0) REVERT: Y 20 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.8074 (p0) REVERT: b 8 MET cc_start: 0.7825 (tmm) cc_final: 0.7585 (tmm) REVERT: b 138 ARG cc_start: 0.7665 (ttt180) cc_final: 0.7170 (ttp80) REVERT: b 156 LEU cc_start: 0.8678 (mm) cc_final: 0.8449 (mt) REVERT: d 68 GLU cc_start: 0.8373 (tp30) cc_final: 0.8158 (tp30) REVERT: d 151 GLN cc_start: 0.7204 (mm-40) cc_final: 0.6912 (tp-100) REVERT: e 40 ASP cc_start: 0.8517 (p0) cc_final: 0.7974 (p0) REVERT: e 67 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.8150 (mpp80) REVERT: e 111 ARG cc_start: 0.8230 (ttm-80) cc_final: 0.7822 (ttm-80) REVERT: f 5 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7280 (tm-30) REVERT: f 24 ARG cc_start: 0.8504 (ttm110) cc_final: 0.7966 (mmm160) REVERT: f 36 ILE cc_start: 0.9315 (mp) cc_final: 0.9093 (mt) REVERT: f 53 LYS cc_start: 0.8736 (mmtt) cc_final: 0.8516 (mmtm) REVERT: f 90 MET cc_start: 0.8029 (mtm) cc_final: 0.6752 (mtp) REVERT: g 14 ASP cc_start: 0.8139 (t70) cc_final: 0.7923 (t0) REVERT: g 27 ASN cc_start: 0.7481 (m-40) cc_final: 0.7250 (t0) REVERT: h 11 THR cc_start: 0.9126 (m) cc_final: 0.8839 (p) REVERT: h 62 LEU cc_start: 0.8987 (mt) cc_final: 0.8753 (mt) REVERT: h 65 PHE cc_start: 0.8243 (t80) cc_final: 0.7890 (t80) REVERT: h 78 SER cc_start: 0.8750 (t) cc_final: 0.8357 (t) REVERT: h 112 ASP cc_start: 0.8846 (p0) cc_final: 0.8497 (p0) REVERT: h 123 GLU cc_start: 0.7690 (tt0) cc_final: 0.7425 (tt0) REVERT: i 49 GLN cc_start: 0.8670 (tm-30) cc_final: 0.8400 (tm-30) REVERT: i 93 LEU cc_start: 0.8112 (mt) cc_final: 0.7794 (pp) REVERT: j 20 GLN cc_start: 0.8585 (mt0) cc_final: 0.8350 (pp30) REVERT: j 56 HIS cc_start: 0.8248 (OUTLIER) cc_final: 0.8015 (t-90) REVERT: k 28 ASN cc_start: 0.8548 (t0) cc_final: 0.8245 (t0) REVERT: k 76 TYR cc_start: 0.8299 (m-80) cc_final: 0.7924 (m-80) REVERT: l 13 ARG cc_start: 0.7874 (ttm110) cc_final: 0.7649 (ttm110) REVERT: l 65 TYR cc_start: 0.8343 (t80) cc_final: 0.8113 (t80) REVERT: l 85 ARG cc_start: 0.8242 (mtp85) cc_final: 0.7934 (ttm110) REVERT: l 88 ASP cc_start: 0.7485 (t0) cc_final: 0.7072 (t0) REVERT: m 58 GLU cc_start: 0.8297 (tt0) cc_final: 0.7936 (tt0) REVERT: n 62 ASN cc_start: 0.9137 (t0) cc_final: 0.8748 (t0) REVERT: n 66 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.8082 (mt0) REVERT: o 20 ASP cc_start: 0.7347 (t0) cc_final: 0.6536 (t70) REVERT: o 23 SER cc_start: 0.8693 (p) cc_final: 0.8234 (p) REVERT: o 27 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8568 (mt0) REVERT: o 37 HIS cc_start: 0.8640 (t70) cc_final: 0.8047 (t70) REVERT: p 12 LYS cc_start: 0.7874 (ttpt) cc_final: 0.7654 (ttpp) REVERT: q 15 LYS cc_start: 0.8340 (mtpt) cc_final: 0.7998 (ptpp) REVERT: r 37 LYS cc_start: 0.8177 (mtpp) cc_final: 0.7909 (mtpp) REVERT: r 63 TYR cc_start: 0.8964 (t80) cc_final: 0.8562 (t80) REVERT: s 2 ARG cc_start: 0.7967 (tpt-90) cc_final: 0.7025 (ttt90) REVERT: t 67 HIS cc_start: 0.7783 (t-90) cc_final: 0.7399 (t-90) REVERT: t 69 ASN cc_start: 0.8954 (m110) cc_final: 0.8610 (m110) REVERT: u 30 GLU cc_start: 0.8273 (tm-30) cc_final: 0.8065 (tm-30) REVERT: u 34 ARG cc_start: 0.8382 (ttm110) cc_final: 0.8151 (ttm110) REVERT: y 14 GLU cc_start: 0.6332 (pt0) cc_final: 0.6108 (pm20) outliers start: 213 outliers final: 126 residues processed: 1641 average time/residue: 1.2831 time to fit residues: 3638.6638 Evaluate side-chains 1557 residues out of total 4915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1421 time to evaluate : 6.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 19 ASP Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 174 PHE Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 100 PHE Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 5 LYS Chi-restraints excluded: chain M residue 51 ARG Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 61 GLN Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain P residue 62 LYS Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 2 ILE Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 39 ASN Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 17 SER Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 22 ASN Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain Y residue 20 ASN Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 188 THR Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 32 LEU Chi-restraints excluded: chain c residue 40 GLN Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain d residue 24 VAL Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain e residue 23 THR Chi-restraints excluded: chain e residue 67 ARG Chi-restraints excluded: chain e residue 76 ASN Chi-restraints excluded: chain e residue 95 MET Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain g residue 26 VAL Chi-restraints excluded: chain h residue 13 ILE Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain i residue 20 ILE Chi-restraints excluded: chain i residue 29 ILE Chi-restraints excluded: chain j residue 22 THR Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 56 HIS Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain k residue 31 VAL Chi-restraints excluded: chain k residue 69 CYS Chi-restraints excluded: chain k residue 96 ILE Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain m residue 10 ASP Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 42 VAL Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 50 THR Chi-restraints excluded: chain n residue 54 ASP Chi-restraints excluded: chain n residue 66 GLN Chi-restraints excluded: chain n residue 97 LYS Chi-restraints excluded: chain o residue 11 VAL Chi-restraints excluded: chain o residue 27 GLN Chi-restraints excluded: chain o residue 38 LEU Chi-restraints excluded: chain o residue 60 SER Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 37 ILE Chi-restraints excluded: chain s residue 13 HIS Chi-restraints excluded: chain s residue 18 VAL Chi-restraints excluded: chain s residue 26 ASP Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain t residue 19 HIS Chi-restraints excluded: chain u residue 52 VAL Chi-restraints excluded: chain y residue 51 TYR Chi-restraints excluded: chain y residue 81 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 839 optimal weight: 10.0000 chunk 572 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 750 optimal weight: 30.0000 chunk 415 optimal weight: 1.9990 chunk 860 optimal weight: 10.0000 chunk 696 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 514 optimal weight: 6.9990 chunk 904 optimal weight: 10.0000 chunk 254 optimal weight: 40.0000 overall best weight: 6.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 28 ASN J 80 HIS ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN Q 80 ASN X 35 HIS ** b 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 2 GLN d 115 GLN d 139 ASN ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 96 ASN i 3 ASN j 58 ASN n 66 GLN p 59 HIS p 63 GLN ** p 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 54 GLN ** t 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 29 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 158605 Z= 0.301 Angle : 0.705 30.230 237201 Z= 0.368 Chirality : 0.038 1.144 30245 Planarity : 0.006 0.128 12834 Dihedral : 24.431 179.836 79062 Min Nonbonded Distance : 1.048 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.11 % Favored : 89.81 % Rotamer: Outliers : 5.40 % Allowed : 24.48 % Favored : 70.12 % 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: -2.37 (0.11), residues: 5926 helix: -0.25 (0.12), residues: 1919 sheet: -2.05 (0.15), residues: 1038 loop : -2.31 (0.11), residues: 2969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP b 103 HIS 0.007 0.001 HIS k 117 PHE 0.029 0.002 PHE H 46 TYR 0.025 0.002 TYR y 52 ARG 0.010 0.000 ARG 2 41 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11852 Ramachandran restraints generated. 5926 Oldfield, 0 Emsley, 5926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11852 Ramachandran restraints generated. 5926 Oldfield, 0 Emsley, 5926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1725 residues out of total 4915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 1472 time to evaluate : 6.223 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: 1 7 LYS cc_start: 0.8803 (ptpt) cc_final: 0.8557 (ptpp) REVERT: 2 11 LYS cc_start: 0.9132 (mttt) cc_final: 0.8760 (mttm) REVERT: 3 31 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.7841 (tp) REVERT: 3 63 TYR cc_start: 0.7351 (m-80) cc_final: 0.6865 (m-80) REVERT: C 20 ASN cc_start: 0.8006 (t0) cc_final: 0.7760 (t0) REVERT: C 186 ASP cc_start: 0.7848 (t0) cc_final: 0.7646 (t0) REVERT: D 7 LYS cc_start: 0.8736 (ttmt) cc_final: 0.8384 (ttmm) REVERT: D 96 ILE cc_start: 0.9500 (mt) cc_final: 0.9236 (mt) REVERT: E 1 MET cc_start: 0.6823 (mmm) cc_final: 0.6451 (mmm) REVERT: E 7 ASP cc_start: 0.7072 (OUTLIER) cc_final: 0.6354 (p0) REVERT: F 70 ARG cc_start: 0.7587 (ptt180) cc_final: 0.7358 (ptp-170) REVERT: F 99 PHE cc_start: 0.7996 (t80) cc_final: 0.7728 (t80) REVERT: F 156 THR cc_start: 0.8785 (m) cc_final: 0.8523 (p) REVERT: F 169 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8568 (mm) REVERT: F 174 PHE cc_start: 0.7740 (OUTLIER) cc_final: 0.7280 (m-80) REVERT: G 138 GLN cc_start: 0.8773 (tm-30) cc_final: 0.8246 (tm-30) REVERT: G 142 GLN cc_start: 0.8577 (tp40) cc_final: 0.7367 (tp40) REVERT: G 146 ASP cc_start: 0.8009 (m-30) cc_final: 0.6919 (m-30) REVERT: H 17 ASP cc_start: 0.6981 (m-30) cc_final: 0.6580 (m-30) REVERT: H 37 VAL cc_start: 0.9201 (OUTLIER) cc_final: 0.8969 (m) REVERT: H 97 ARG cc_start: 0.8031 (tpm170) cc_final: 0.7596 (tpm170) REVERT: J 52 ASP cc_start: 0.8494 (m-30) cc_final: 0.8254 (m-30) REVERT: J 67 ASN cc_start: 0.7517 (t0) cc_final: 0.6838 (t0) REVERT: J 71 ASP cc_start: 0.8653 (m-30) cc_final: 0.7697 (m-30) REVERT: J 81 ILE cc_start: 0.8784 (tp) cc_final: 0.8535 (tp) REVERT: K 12 ASP cc_start: 0.8680 (p0) cc_final: 0.8360 (p0) REVERT: M 47 GLU cc_start: 0.7511 (tm-30) cc_final: 0.7126 (tm-30) REVERT: M 51 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7604 (mtp-110) REVERT: M 119 LEU cc_start: 0.8936 (tp) cc_final: 0.8691 (tp) REVERT: N 82 GLU cc_start: 0.7561 (mp0) cc_final: 0.7321 (mp0) REVERT: O 80 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7870 (tm-30) REVERT: P 7 LEU cc_start: 0.9260 (mm) cc_final: 0.8991 (mm) REVERT: P 70 GLU cc_start: 0.7458 (mp0) cc_final: 0.7056 (mp0) REVERT: P 93 LYS cc_start: 0.9311 (ttmm) cc_final: 0.9081 (mtpp) REVERT: Q 80 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.8401 (m110) REVERT: R 21 ARG cc_start: 0.8698 (ttm-80) cc_final: 0.8251 (ttm-80) REVERT: S 1 MET cc_start: 0.8361 (tmm) cc_final: 0.8060 (tmm) REVERT: S 4 ILE cc_start: 0.9153 (mp) cc_final: 0.8908 (mp) REVERT: S 65 ASP cc_start: 0.7506 (t0) cc_final: 0.7251 (t0) REVERT: V 11 GLU cc_start: 0.8249 (pm20) cc_final: 0.7701 (pm20) REVERT: V 29 ILE cc_start: 0.9223 (tp) cc_final: 0.8930 (tp) REVERT: V 48 MET cc_start: 0.8888 (tpt) cc_final: 0.8409 (tpt) REVERT: V 78 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.8312 (tt0) REVERT: W 37 ARG cc_start: 0.8404 (mmt-90) cc_final: 0.8134 (mmt-90) REVERT: W 60 ASP cc_start: 0.7494 (m-30) cc_final: 0.6991 (p0) REVERT: X 55 MET cc_start: 0.8907 (mmm) cc_final: 0.8645 (mmt) REVERT: Y 1 MET cc_start: 0.7620 (ptt) cc_final: 0.7401 (ptt) REVERT: Y 5 GLU cc_start: 0.8691 (mp0) cc_final: 0.8422 (mp0) REVERT: b 8 MET cc_start: 0.7858 (tmm) cc_final: 0.7531 (tmm) REVERT: b 55 GLU cc_start: 0.8353 (tp30) cc_final: 0.8085 (tp30) REVERT: b 119 GLN cc_start: 0.8423 (mt0) cc_final: 0.8131 (mt0) REVERT: b 125 PHE cc_start: 0.7592 (OUTLIER) cc_final: 0.6558 (m-10) REVERT: b 138 ARG cc_start: 0.7655 (ttt180) cc_final: 0.7386 (ttt-90) REVERT: c 151 GLU cc_start: 0.7262 (tm-30) cc_final: 0.6901 (tm-30) REVERT: d 151 GLN cc_start: 0.7364 (mm-40) cc_final: 0.7150 (tp-100) REVERT: e 40 ASP cc_start: 0.8532 (p0) cc_final: 0.8005 (p0) REVERT: e 77 ASN cc_start: 0.7324 (t0) cc_final: 0.7096 (t0) REVERT: f 5 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7957 (tm-30) REVERT: f 22 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8743 (mt) REVERT: f 24 ARG cc_start: 0.8527 (ttm110) cc_final: 0.8279 (ttm110) REVERT: f 36 ILE cc_start: 0.9331 (mp) cc_final: 0.9129 (mt) REVERT: f 90 MET cc_start: 0.7991 (mtm) cc_final: 0.7670 (mpp) REVERT: g 27 ASN cc_start: 0.7617 (m-40) cc_final: 0.7416 (t0) REVERT: h 11 THR cc_start: 0.9117 (m) cc_final: 0.8800 (p) REVERT: h 17 GLN cc_start: 0.9232 (mm-40) cc_final: 0.8794 (mm-40) REVERT: h 62 LEU cc_start: 0.9034 (mt) cc_final: 0.8746 (mt) REVERT: h 65 PHE cc_start: 0.8308 (t80) cc_final: 0.7902 (t80) REVERT: h 78 SER cc_start: 0.8827 (t) cc_final: 0.8419 (t) REVERT: h 112 ASP cc_start: 0.8912 (p0) cc_final: 0.8584 (p0) REVERT: h 120 LEU cc_start: 0.9161 (pp) cc_final: 0.8919 (pt) REVERT: h 123 GLU cc_start: 0.7626 (tt0) cc_final: 0.7341 (tt0) REVERT: i 93 LEU cc_start: 0.8112 (mt) cc_final: 0.7806 (pp) REVERT: i 109 GLN cc_start: 0.8385 (pt0) cc_final: 0.8128 (pt0) REVERT: i 119 LYS cc_start: 0.8482 (ptmt) cc_final: 0.8174 (ptpt) REVERT: j 20 GLN cc_start: 0.8610 (mt0) cc_final: 0.8380 (pp30) REVERT: j 56 HIS cc_start: 0.8393 (OUTLIER) cc_final: 0.8185 (t-90) REVERT: k 28 ASN cc_start: 0.8681 (t0) cc_final: 0.8381 (t0) REVERT: k 76 TYR cc_start: 0.8327 (m-80) cc_final: 0.7955 (m-80) REVERT: l 65 TYR cc_start: 0.8369 (t80) cc_final: 0.8137 (t80) REVERT: l 88 ASP cc_start: 0.7588 (t0) cc_final: 0.7160 (t0) REVERT: n 62 ASN cc_start: 0.9180 (t0) cc_final: 0.8728 (t0) REVERT: o 20 ASP cc_start: 0.7234 (t0) cc_final: 0.6667 (t70) REVERT: o 27 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8548 (mt0) REVERT: o 37 HIS cc_start: 0.8660 (t70) cc_final: 0.7973 (t70) REVERT: p 12 LYS cc_start: 0.7910 (ttpt) cc_final: 0.7633 (tttp) REVERT: r 37 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7971 (mtpp) REVERT: r 63 TYR cc_start: 0.8997 (t80) cc_final: 0.8582 (t80) REVERT: s 2 ARG cc_start: 0.8009 (tpt-90) cc_final: 0.7094 (ttt90) REVERT: s 76 THR cc_start: 0.7706 (p) cc_final: 0.7265 (t) REVERT: t 67 HIS cc_start: 0.7939 (t-90) cc_final: 0.7486 (t70) REVERT: t 69 ASN cc_start: 0.8947 (m110) cc_final: 0.8511 (m110) REVERT: y 108 THR cc_start: 0.6474 (OUTLIER) cc_final: 0.6098 (m) outliers start: 253 outliers final: 189 residues processed: 1601 average time/residue: 1.2622 time to fit residues: 3501.7798 Evaluate side-chains 1626 residues out of total 4915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 1423 time to evaluate : 6.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 3 GLN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 19 ASP Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 29 VAL Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 9 VAL Chi-restraints excluded: chain 2 residue 24 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 C residue 18 VAL Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 174 PHE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 100 PHE Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 51 ARG Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 45 SER Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 61 GLN Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain P residue 62 LYS Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 80 ASN Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 2 ILE Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 17 SER Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 55 GLU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 78 GLN Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 58 ILE Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 125 PHE Chi-restraints excluded: chain b residue 188 THR Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 32 LEU Chi-restraints excluded: chain c residue 40 GLN Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 110 LEU Chi-restraints excluded: chain d residue 11 SER Chi-restraints excluded: chain d residue 33 ILE Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain e residue 23 THR Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 71 ILE Chi-restraints excluded: chain e residue 76 ASN Chi-restraints excluded: chain e residue 95 MET Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 139 THR Chi-restraints excluded: chain f residue 22 ILE Chi-restraints excluded: chain f residue 61 LEU Chi-restraints excluded: chain g residue 26 VAL Chi-restraints excluded: chain g residue 86 VAL Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain g residue 139 ASP Chi-restraints excluded: chain h residue 9 MET Chi-restraints excluded: chain h residue 13 ILE Chi-restraints excluded: chain h residue 38 VAL Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 84 ILE Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain i residue 20 ILE Chi-restraints excluded: chain i residue 29 ILE Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain i residue 61 ASP Chi-restraints excluded: chain i residue 83 THR Chi-restraints excluded: chain j residue 22 THR Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 56 HIS Chi-restraints excluded: chain j residue 58 ASN Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain k residue 31 VAL Chi-restraints excluded: chain k residue 64 VAL Chi-restraints excluded: chain k residue 69 CYS Chi-restraints excluded: chain k residue 96 ILE Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 81 ILE Chi-restraints excluded: chain m residue 10 ASP Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 42 VAL Chi-restraints excluded: chain n residue 34 ASN Chi-restraints excluded: chain n residue 50 THR Chi-restraints excluded: chain n residue 54 ASP Chi-restraints excluded: chain n residue 97 LYS Chi-restraints excluded: chain o residue 11 VAL Chi-restraints excluded: chain o residue 27 GLN Chi-restraints excluded: chain o residue 38 LEU Chi-restraints excluded: chain o residue 60 SER Chi-restraints excluded: chain o residue 78 THR Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 69 ASP Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 28 VAL Chi-restraints excluded: chain q residue 37 ILE Chi-restraints excluded: chain q residue 67 SER Chi-restraints excluded: chain r residue 37 LYS Chi-restraints excluded: chain s residue 13 HIS Chi-restraints excluded: chain s residue 18 VAL Chi-restraints excluded: chain s residue 26 ASP Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain t residue 19 HIS Chi-restraints excluded: chain t residue 42 ASP Chi-restraints excluded: chain t residue 54 GLN Chi-restraints excluded: chain u residue 52 VAL Chi-restraints excluded: chain y residue 51 TYR Chi-restraints excluded: chain y residue 81 GLU Chi-restraints excluded: chain y residue 95 ILE Chi-restraints excluded: chain y residue 108 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 339 optimal weight: 2.9990 chunk 907 optimal weight: 9.9990 chunk 199 optimal weight: 10.0000 chunk 591 optimal weight: 6.9990 chunk 248 optimal weight: 50.0000 chunk 1009 optimal weight: 20.0000 chunk 837 optimal weight: 30.0000 chunk 467 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 333 optimal weight: 20.0000 chunk 529 optimal weight: 10.0000 overall best weight: 6.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 28 ASN J 80 HIS ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 2 ASN Q 43 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN W 42 HIS ** X 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 GLN ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 139 ASN f 52 ASN ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 58 ASN ** n 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 39 GLN ** p 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 29 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 158605 Z= 0.281 Angle : 0.697 30.246 237201 Z= 0.364 Chirality : 0.037 1.149 30245 Planarity : 0.006 0.126 12834 Dihedral : 24.418 179.828 79062 Min Nonbonded Distance : 1.043 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.69 % Favored : 90.23 % Rotamer: Outliers : 5.87 % Allowed : 25.71 % Favored : 68.42 % 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: -2.25 (0.11), residues: 5926 helix: -0.22 (0.12), residues: 1928 sheet: -1.83 (0.16), residues: 1033 loop : -2.26 (0.11), residues: 2965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP s 33 HIS 0.007 0.001 HIS m 11 PHE 0.024 0.002 PHE H 47 TYR 0.033 0.002 TYR y 52 ARG 0.012 0.000 ARG C 213 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11852 Ramachandran restraints generated. 5926 Oldfield, 0 Emsley, 5926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11852 Ramachandran restraints generated. 5926 Oldfield, 0 Emsley, 5926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1752 residues out of total 4915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 275 poor density : 1477 time to evaluate : 5.654 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: 0 47 TYR cc_start: 0.8353 (m-80) cc_final: 0.7976 (m-10) REVERT: 1 7 LYS cc_start: 0.8756 (ptpt) cc_final: 0.8497 (ptpp) REVERT: 2 11 LYS cc_start: 0.9109 (mttt) cc_final: 0.8759 (mttm) REVERT: 3 31 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.7815 (tp) REVERT: 3 63 TYR cc_start: 0.7339 (m-80) cc_final: 0.6845 (m-80) REVERT: C 51 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8497 (ptt180) REVERT: C 212 TRP cc_start: 0.8668 (p90) cc_final: 0.8190 (p-90) REVERT: D 7 LYS cc_start: 0.8753 (ttmt) cc_final: 0.8384 (ttmm) REVERT: D 96 ILE cc_start: 0.9509 (mt) cc_final: 0.9237 (mt) REVERT: E 7 ASP cc_start: 0.7134 (OUTLIER) cc_final: 0.6420 (p0) REVERT: F 156 THR cc_start: 0.8804 (m) cc_final: 0.8584 (p) REVERT: F 169 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.8615 (mm) REVERT: F 174 PHE cc_start: 0.7638 (OUTLIER) cc_final: 0.7240 (m-80) REVERT: G 138 GLN cc_start: 0.8757 (tm-30) cc_final: 0.8235 (tm-30) REVERT: G 142 GLN cc_start: 0.8563 (tp40) cc_final: 0.7382 (tp40) REVERT: G 146 ASP cc_start: 0.8027 (m-30) cc_final: 0.6958 (m-30) REVERT: H 1 MET cc_start: 0.6857 (ptm) cc_final: 0.6443 (ptm) REVERT: H 17 ASP cc_start: 0.6983 (m-30) cc_final: 0.6486 (m-30) REVERT: H 37 VAL cc_start: 0.9203 (OUTLIER) cc_final: 0.8952 (m) REVERT: H 97 ARG cc_start: 0.8026 (tpm170) cc_final: 0.7534 (tpm170) REVERT: J 67 ASN cc_start: 0.7552 (t0) cc_final: 0.6846 (t0) REVERT: J 71 ASP cc_start: 0.8645 (m-30) cc_final: 0.7651 (m-30) REVERT: J 81 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8550 (tp) REVERT: K 12 ASP cc_start: 0.8687 (p0) cc_final: 0.8364 (p0) REVERT: M 47 GLU cc_start: 0.7473 (tm-30) cc_final: 0.7048 (tm-30) REVERT: M 51 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7618 (mtp-110) REVERT: M 119 LEU cc_start: 0.8976 (tp) cc_final: 0.8751 (tp) REVERT: N 82 GLU cc_start: 0.7573 (mp0) cc_final: 0.7317 (mp0) REVERT: P 7 LEU cc_start: 0.9248 (mm) cc_final: 0.8943 (mm) REVERT: P 10 GLU cc_start: 0.7786 (pt0) cc_final: 0.7585 (tp30) REVERT: P 70 GLU cc_start: 0.7464 (mp0) cc_final: 0.7100 (mp0) REVERT: P 93 LYS cc_start: 0.9278 (ttmm) cc_final: 0.9072 (mtpp) REVERT: Q 80 ASN cc_start: 0.8685 (m-40) cc_final: 0.8467 (m-40) REVERT: R 21 ARG cc_start: 0.8711 (ttm-80) cc_final: 0.8290 (ttm-80) REVERT: S 4 ILE cc_start: 0.9122 (mp) cc_final: 0.8863 (mp) REVERT: S 62 ASP cc_start: 0.7736 (t0) cc_final: 0.7145 (t0) REVERT: S 65 ASP cc_start: 0.7491 (t0) cc_final: 0.7248 (t0) REVERT: V 11 GLU cc_start: 0.8254 (pm20) cc_final: 0.7781 (pm20) REVERT: V 29 ILE cc_start: 0.9179 (tp) cc_final: 0.8904 (tp) REVERT: V 89 ILE cc_start: 0.9223 (mp) cc_final: 0.8898 (mm) REVERT: W 37 ARG cc_start: 0.8325 (mmt-90) cc_final: 0.8009 (mmt-90) REVERT: W 60 ASP cc_start: 0.7494 (m-30) cc_final: 0.6972 (p0) REVERT: X 55 MET cc_start: 0.8922 (mmm) cc_final: 0.8703 (mmt) REVERT: Y 1 MET cc_start: 0.7658 (ptt) cc_final: 0.7363 (ptt) REVERT: Y 5 GLU cc_start: 0.8695 (mp0) cc_final: 0.8408 (mp0) REVERT: Y 30 MET cc_start: 0.6643 (OUTLIER) cc_final: 0.6321 (ttt) REVERT: b 8 MET cc_start: 0.7832 (tmm) cc_final: 0.7510 (tmm) REVERT: b 119 GLN cc_start: 0.8360 (mt0) cc_final: 0.8049 (mt0) REVERT: b 125 PHE cc_start: 0.7482 (OUTLIER) cc_final: 0.6392 (m-10) REVERT: b 138 ARG cc_start: 0.7676 (ttt180) cc_final: 0.7394 (ttt-90) REVERT: b 158 ASP cc_start: 0.8140 (t0) cc_final: 0.7708 (m-30) REVERT: e 40 ASP cc_start: 0.8507 (p0) cc_final: 0.7969 (p0) REVERT: e 77 ASN cc_start: 0.7500 (t0) cc_final: 0.7212 (t0) REVERT: f 5 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7930 (tm-30) REVERT: f 24 ARG cc_start: 0.8078 (ttm110) cc_final: 0.7613 (mmm160) REVERT: f 25 TYR cc_start: 0.8840 (m-10) cc_final: 0.8501 (m-80) REVERT: f 88 MET cc_start: 0.8729 (ttt) cc_final: 0.8303 (ttt) REVERT: h 11 THR cc_start: 0.9123 (m) cc_final: 0.8840 (p) REVERT: h 17 GLN cc_start: 0.9216 (mm-40) cc_final: 0.8882 (mm-40) REVERT: h 62 LEU cc_start: 0.9033 (mt) cc_final: 0.8656 (mt) REVERT: h 65 PHE cc_start: 0.8307 (t80) cc_final: 0.7886 (t80) REVERT: h 78 SER cc_start: 0.8818 (t) cc_final: 0.8436 (t) REVERT: h 112 ASP cc_start: 0.8911 (p0) cc_final: 0.8583 (p0) REVERT: h 120 LEU cc_start: 0.9175 (pp) cc_final: 0.8967 (pt) REVERT: h 123 GLU cc_start: 0.7607 (tt0) cc_final: 0.7332 (tt0) REVERT: i 93 LEU cc_start: 0.8171 (mt) cc_final: 0.7870 (pp) REVERT: i 119 LYS cc_start: 0.8521 (ptmt) cc_final: 0.8080 (ptpt) REVERT: k 56 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8535 (mtpp) REVERT: k 76 TYR cc_start: 0.8370 (m-80) cc_final: 0.7993 (m-80) REVERT: k 99 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8904 (mp) REVERT: l 37 TYR cc_start: 0.7967 (p90) cc_final: 0.7396 (p90) REVERT: l 65 TYR cc_start: 0.8398 (t80) cc_final: 0.8171 (t80) REVERT: l 85 ARG cc_start: 0.8265 (mtp85) cc_final: 0.7975 (ttm110) REVERT: l 88 ASP cc_start: 0.7577 (t0) cc_final: 0.7153 (t0) REVERT: m 109 LYS cc_start: 0.8739 (mttt) cc_final: 0.8398 (mttt) REVERT: n 62 ASN cc_start: 0.9171 (t0) cc_final: 0.8718 (t0) REVERT: o 20 ASP cc_start: 0.7378 (t0) cc_final: 0.6675 (t70) REVERT: o 27 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8554 (mt0) REVERT: o 37 HIS cc_start: 0.8635 (t70) cc_final: 0.8069 (t70) REVERT: p 12 LYS cc_start: 0.7866 (ttpt) cc_final: 0.7602 (tttp) REVERT: p 31 ARG cc_start: 0.8604 (ptm160) cc_final: 0.8403 (ptp-170) REVERT: r 37 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7990 (mtpp) REVERT: r 63 TYR cc_start: 0.9022 (t80) cc_final: 0.8575 (t80) REVERT: s 2 ARG cc_start: 0.7963 (tpt-90) cc_final: 0.7066 (ttt90) REVERT: s 80 ARG cc_start: 0.7978 (mtm-85) cc_final: 0.7597 (mtm-85) REVERT: t 50 PHE cc_start: 0.8640 (t80) cc_final: 0.8433 (t80) REVERT: t 67 HIS cc_start: 0.7922 (t-90) cc_final: 0.7428 (t70) REVERT: t 69 ASN cc_start: 0.8925 (m110) cc_final: 0.8459 (m110) REVERT: y 108 THR cc_start: 0.6507 (OUTLIER) cc_final: 0.6120 (m) outliers start: 275 outliers final: 218 residues processed: 1615 average time/residue: 1.2770 time to fit residues: 3579.3980 Evaluate side-chains 1656 residues out of total 4915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 1423 time to evaluate : 6.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 3 GLN 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 26 SER Chi-restraints excluded: chain 0 residue 35 GLU Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 9 VAL Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 15 LYS Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 4 residue 13 ASN Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 51 ARG Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 174 PHE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 43 ASN Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 100 PHE Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 51 ARG Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 45 SER Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain P residue 62 LYS Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 2 ILE Chi-restraints excluded: chain T residue 48 GLN Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 17 SER Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 66 ASP Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 26 SER Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 40 GLU Chi-restraints excluded: chain X residue 58 ILE Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain Y residue 30 MET Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 125 PHE Chi-restraints excluded: chain b residue 188 THR Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain c residue 2 GLN Chi-restraints excluded: chain c residue 13 ILE Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 40 GLN Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 110 LEU Chi-restraints excluded: chain d residue 11 SER Chi-restraints excluded: chain d residue 24 VAL Chi-restraints excluded: chain d residue 33 ILE Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain e residue 23 THR Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 71 ILE Chi-restraints excluded: chain e residue 76 ASN Chi-restraints excluded: chain e residue 95 MET Chi-restraints excluded: chain e residue 123 LEU Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain f residue 61 LEU Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain g residue 26 VAL Chi-restraints excluded: chain g residue 86 VAL Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain g residue 139 ASP Chi-restraints excluded: chain h residue 9 MET Chi-restraints excluded: chain h residue 13 ILE Chi-restraints excluded: chain h residue 38 VAL Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 84 ILE Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain i residue 20 ILE Chi-restraints excluded: chain i residue 29 ILE Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain i residue 61 ASP Chi-restraints excluded: chain i residue 83 THR Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain j residue 22 THR Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 58 ASN Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain k residue 31 VAL Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 56 LYS Chi-restraints excluded: chain k residue 69 CYS Chi-restraints excluded: chain k residue 96 ILE Chi-restraints excluded: chain k residue 99 LEU Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 81 ILE Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain m residue 10 ASP Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 42 VAL Chi-restraints excluded: chain m residue 44 ILE Chi-restraints excluded: chain m residue 75 SER Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 34 ASN Chi-restraints excluded: chain n residue 50 THR Chi-restraints excluded: chain n residue 54 ASP Chi-restraints excluded: chain n residue 97 LYS Chi-restraints excluded: chain o residue 11 VAL Chi-restraints excluded: chain o residue 27 GLN Chi-restraints excluded: chain o residue 60 SER Chi-restraints excluded: chain o residue 78 THR Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 69 ASP Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 28 VAL Chi-restraints excluded: chain q residue 37 ILE Chi-restraints excluded: chain q residue 67 SER Chi-restraints excluded: chain r residue 32 ILE Chi-restraints excluded: chain r residue 37 LYS Chi-restraints excluded: chain s residue 13 HIS Chi-restraints excluded: chain s residue 18 VAL Chi-restraints excluded: chain s residue 26 ASP Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain t residue 3 ILE Chi-restraints excluded: chain t residue 19 HIS Chi-restraints excluded: chain t residue 42 ASP Chi-restraints excluded: chain t residue 54 GLN Chi-restraints excluded: chain u residue 52 VAL Chi-restraints excluded: chain y residue 51 TYR Chi-restraints excluded: chain y residue 52 TYR Chi-restraints excluded: chain y residue 81 GLU Chi-restraints excluded: chain y residue 95 ILE Chi-restraints excluded: chain y residue 97 GLU Chi-restraints excluded: chain y residue 108 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 972 optimal weight: 7.9990 chunk 113 optimal weight: 10.0000 chunk 574 optimal weight: 5.9990 chunk 736 optimal weight: 30.0000 chunk 570 optimal weight: 6.9990 chunk 849 optimal weight: 2.9990 chunk 563 optimal weight: 1.9990 chunk 1005 optimal weight: 9.9990 chunk 629 optimal weight: 2.9990 chunk 612 optimal weight: 9.9990 chunk 464 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 28 ASN J 80 HIS M 45 GLN N 3 HIS O 116 GLN P 2 ASN Q 43 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN W 42 HIS ** X 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 GLN b 50 ASN ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 139 ASN ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 58 ASN ** n 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 66 GLN o 39 GLN ** s 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 158605 Z= 0.201 Angle : 0.656 30.208 237201 Z= 0.346 Chirality : 0.035 1.154 30245 Planarity : 0.006 0.123 12834 Dihedral : 24.350 179.525 79062 Min Nonbonded Distance : 1.079 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.11 % Favored : 90.80 % Rotamer: Outliers : 5.44 % Allowed : 27.02 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.11), residues: 5926 helix: -0.04 (0.12), residues: 1923 sheet: -1.68 (0.16), residues: 1023 loop : -2.12 (0.11), residues: 2980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP s 33 HIS 0.006 0.001 HIS m 11 PHE 0.026 0.001 PHE F 99 TYR 0.026 0.002 TYR y 52 ARG 0.012 0.000 ARG 2 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11852 Ramachandran restraints generated. 5926 Oldfield, 0 Emsley, 5926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11852 Ramachandran restraints generated. 5926 Oldfield, 0 Emsley, 5926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1743 residues out of total 4915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 1488 time to evaluate : 8.397 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: 0 47 TYR cc_start: 0.8256 (m-80) cc_final: 0.7954 (m-10) REVERT: 1 7 LYS cc_start: 0.8696 (ptpt) cc_final: 0.8446 (ptpp) REVERT: 2 11 LYS cc_start: 0.9110 (mttt) cc_final: 0.8723 (mttm) REVERT: 3 31 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.7544 (tp) REVERT: 3 63 TYR cc_start: 0.7251 (m-80) cc_final: 0.6797 (m-80) REVERT: 4 23 ILE cc_start: 0.9491 (mm) cc_final: 0.9211 (mm) REVERT: C 212 TRP cc_start: 0.8515 (p90) cc_final: 0.8099 (p-90) REVERT: D 7 LYS cc_start: 0.8743 (ttmt) cc_final: 0.8375 (ttmm) REVERT: D 96 ILE cc_start: 0.9460 (mt) cc_final: 0.9164 (mt) REVERT: E 7 ASP cc_start: 0.7179 (OUTLIER) cc_final: 0.6463 (p0) REVERT: F 34 THR cc_start: 0.8896 (m) cc_final: 0.7919 (p) REVERT: F 156 THR cc_start: 0.8748 (m) cc_final: 0.8538 (p) REVERT: F 169 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8533 (mm) REVERT: F 174 PHE cc_start: 0.7568 (OUTLIER) cc_final: 0.7156 (m-80) REVERT: G 138 GLN cc_start: 0.8690 (tm-30) cc_final: 0.8201 (tm-30) REVERT: G 142 GLN cc_start: 0.8534 (tp40) cc_final: 0.7416 (tp40) REVERT: G 146 ASP cc_start: 0.7982 (m-30) cc_final: 0.6920 (m-30) REVERT: H 1 MET cc_start: 0.6517 (ptm) cc_final: 0.6101 (ptm) REVERT: H 37 VAL cc_start: 0.9104 (OUTLIER) cc_final: 0.8896 (m) REVERT: H 75 LEU cc_start: 0.5742 (OUTLIER) cc_final: 0.5182 (pp) REVERT: H 97 ARG cc_start: 0.8051 (tpm170) cc_final: 0.7546 (tpm170) REVERT: J 67 ASN cc_start: 0.7506 (t0) cc_final: 0.6771 (t0) REVERT: J 71 ASP cc_start: 0.8588 (m-30) cc_final: 0.7538 (m-30) REVERT: J 81 ILE cc_start: 0.8785 (tp) cc_final: 0.8538 (tp) REVERT: K 12 ASP cc_start: 0.8644 (p0) cc_final: 0.8318 (p0) REVERT: M 47 GLU cc_start: 0.7471 (tm-30) cc_final: 0.7095 (tm-30) REVERT: M 51 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7593 (mtp-110) REVERT: M 103 TYR cc_start: 0.8889 (m-80) cc_final: 0.8632 (m-10) REVERT: M 119 LEU cc_start: 0.8878 (tp) cc_final: 0.8639 (tp) REVERT: N 49 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7885 (mt-10) REVERT: N 82 GLU cc_start: 0.7527 (mp0) cc_final: 0.7273 (mp0) REVERT: O 106 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8221 (tp) REVERT: P 7 LEU cc_start: 0.9258 (mm) cc_final: 0.8951 (mm) REVERT: P 70 GLU cc_start: 0.7426 (mp0) cc_final: 0.7035 (mp0) REVERT: Q 80 ASN cc_start: 0.8639 (m-40) cc_final: 0.8320 (m-40) REVERT: R 21 ARG cc_start: 0.8672 (ttm-80) cc_final: 0.8364 (ttm110) REVERT: S 4 ILE cc_start: 0.9131 (mp) cc_final: 0.8884 (mp) REVERT: V 9 ARG cc_start: 0.8443 (mmm-85) cc_final: 0.8051 (mmm-85) REVERT: V 11 GLU cc_start: 0.8285 (pm20) cc_final: 0.7671 (pm20) REVERT: V 51 GLN cc_start: 0.8309 (pp30) cc_final: 0.7522 (pp30) REVERT: W 37 ARG cc_start: 0.8278 (mmt-90) cc_final: 0.8076 (mmt-90) REVERT: W 60 ASP cc_start: 0.7469 (m-30) cc_final: 0.6997 (p0) REVERT: Y 1 MET cc_start: 0.7616 (ptt) cc_final: 0.7375 (ptt) REVERT: Y 5 GLU cc_start: 0.8638 (mp0) cc_final: 0.8374 (mp0) REVERT: b 8 MET cc_start: 0.7780 (tmm) cc_final: 0.7517 (tmm) REVERT: b 119 GLN cc_start: 0.8319 (mt0) cc_final: 0.8055 (mt0) REVERT: b 125 PHE cc_start: 0.7413 (OUTLIER) cc_final: 0.6335 (m-10) REVERT: b 138 ARG cc_start: 0.7649 (ttt180) cc_final: 0.7339 (ttt-90) REVERT: b 158 ASP cc_start: 0.8101 (t0) cc_final: 0.7734 (m-30) REVERT: c 36 PHE cc_start: 0.8181 (t80) cc_final: 0.7726 (t80) REVERT: c 138 GLN cc_start: 0.7656 (pp30) cc_final: 0.7323 (pp30) REVERT: c 151 GLU cc_start: 0.7218 (tm-30) cc_final: 0.6895 (tm-30) REVERT: d 123 MET cc_start: 0.7670 (ttm) cc_final: 0.7436 (ttp) REVERT: e 40 ASP cc_start: 0.8490 (p0) cc_final: 0.7929 (p0) REVERT: e 67 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.8038 (mpp80) REVERT: f 5 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7714 (tm-30) REVERT: f 24 ARG cc_start: 0.8065 (ttm110) cc_final: 0.7690 (mmm160) REVERT: f 25 TYR cc_start: 0.8765 (m-10) cc_final: 0.8459 (m-80) REVERT: f 88 MET cc_start: 0.8618 (ttt) cc_final: 0.8354 (ttt) REVERT: f 90 MET cc_start: 0.7962 (mtm) cc_final: 0.7527 (mtm) REVERT: g 129 ASN cc_start: 0.7551 (m-40) cc_final: 0.7174 (t0) REVERT: h 17 GLN cc_start: 0.9215 (mm-40) cc_final: 0.8754 (mm-40) REVERT: h 62 LEU cc_start: 0.8962 (mt) cc_final: 0.8696 (mt) REVERT: h 65 PHE cc_start: 0.8217 (t80) cc_final: 0.7833 (t80) REVERT: h 112 ASP cc_start: 0.8887 (p0) cc_final: 0.8539 (p0) REVERT: h 123 GLU cc_start: 0.7628 (tt0) cc_final: 0.7394 (tt0) REVERT: i 49 GLN cc_start: 0.8633 (tm-30) cc_final: 0.8401 (tm-30) REVERT: i 93 LEU cc_start: 0.8066 (mt) cc_final: 0.7814 (pp) REVERT: i 119 LYS cc_start: 0.8522 (ptmt) cc_final: 0.8161 (ptmt) REVERT: j 20 GLN cc_start: 0.8689 (pp30) cc_final: 0.8450 (pp30) REVERT: k 52 ARG cc_start: 0.8188 (mmm-85) cc_final: 0.7911 (tpp-160) REVERT: k 99 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8856 (mp) REVERT: l 65 TYR cc_start: 0.8288 (t80) cc_final: 0.8051 (t80) REVERT: l 85 ARG cc_start: 0.8246 (mtp85) cc_final: 0.7966 (ttm110) REVERT: l 88 ASP cc_start: 0.7479 (t0) cc_final: 0.7085 (t0) REVERT: m 80 MET cc_start: 0.8276 (mmm) cc_final: 0.7990 (mmm) REVERT: n 62 ASN cc_start: 0.9127 (t0) cc_final: 0.8898 (t0) REVERT: n 66 GLN cc_start: 0.8254 (mt0) cc_final: 0.7973 (mm-40) REVERT: o 20 ASP cc_start: 0.7386 (t0) cc_final: 0.6728 (t70) REVERT: o 37 HIS cc_start: 0.8584 (t70) cc_final: 0.8021 (t70) REVERT: p 12 LYS cc_start: 0.7827 (ttpt) cc_final: 0.7572 (tttp) REVERT: p 31 ARG cc_start: 0.8553 (ptm160) cc_final: 0.8352 (ptp-170) REVERT: r 37 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7776 (mtpp) REVERT: r 63 TYR cc_start: 0.8948 (t80) cc_final: 0.8557 (t80) REVERT: s 2 ARG cc_start: 0.7941 (tpt-90) cc_final: 0.7074 (ttt90) REVERT: s 76 THR cc_start: 0.7846 (p) cc_final: 0.7454 (t) REVERT: t 67 HIS cc_start: 0.7895 (t-90) cc_final: 0.7363 (t70) REVERT: t 69 ASN cc_start: 0.8883 (m110) cc_final: 0.8434 (m110) REVERT: u 16 ARG cc_start: 0.7308 (ttt180) cc_final: 0.7011 (ttm170) REVERT: y 108 THR cc_start: 0.6324 (OUTLIER) cc_final: 0.5953 (m) outliers start: 255 outliers final: 195 residues processed: 1623 average time/residue: 1.2838 time to fit residues: 3614.0540 Evaluate side-chains 1629 residues out of total 4915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 1421 time to evaluate : 5.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 19 ASP Chi-restraints excluded: chain 0 residue 21 LEU Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 26 SER Chi-restraints excluded: chain 0 residue 29 VAL Chi-restraints excluded: chain 0 residue 35 GLU Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 15 LYS Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 174 PHE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 100 PHE Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 51 ARG Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 61 GLN Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain P residue 62 LYS Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 2 ILE Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 48 GLN Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 17 SER Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 66 ASP Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 26 SER Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 40 GLU Chi-restraints excluded: chain X residue 58 ILE Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 59 GLU Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 125 PHE Chi-restraints excluded: chain b residue 156 LEU Chi-restraints excluded: chain b residue 188 THR Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain c residue 2 GLN Chi-restraints excluded: chain c residue 13 ILE Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 32 LEU Chi-restraints excluded: chain c residue 40 GLN Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain d residue 11 SER Chi-restraints excluded: chain d residue 24 VAL Chi-restraints excluded: chain d residue 35 GLN Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain e residue 23 THR Chi-restraints excluded: chain e residue 42 ASN Chi-restraints excluded: chain e residue 67 ARG Chi-restraints excluded: chain e residue 71 ILE Chi-restraints excluded: chain e residue 76 ASN Chi-restraints excluded: chain e residue 95 MET Chi-restraints excluded: chain e residue 123 LEU Chi-restraints excluded: chain f residue 61 LEU Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 86 VAL Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain g residue 139 ASP Chi-restraints excluded: chain h residue 13 ILE Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 84 ILE Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 125 ILE Chi-restraints excluded: chain i residue 20 ILE Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain i residue 83 THR Chi-restraints excluded: chain j residue 22 THR Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 58 ASN Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain k residue 31 VAL Chi-restraints excluded: chain k residue 69 CYS Chi-restraints excluded: chain k residue 96 ILE Chi-restraints excluded: chain k residue 99 LEU Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 81 ILE Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 42 VAL Chi-restraints excluded: chain m residue 75 SER Chi-restraints excluded: chain n residue 29 ILE Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 34 ASN Chi-restraints excluded: chain n residue 50 THR Chi-restraints excluded: chain n residue 54 ASP Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain o residue 11 VAL Chi-restraints excluded: chain o residue 23 SER Chi-restraints excluded: chain o residue 60 SER Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 69 ASP Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 28 VAL Chi-restraints excluded: chain q residue 37 ILE Chi-restraints excluded: chain q residue 67 SER Chi-restraints excluded: chain r residue 32 ILE Chi-restraints excluded: chain r residue 37 LYS Chi-restraints excluded: chain s residue 13 HIS Chi-restraints excluded: chain s residue 18 VAL Chi-restraints excluded: chain s residue 26 ASP Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain t residue 3 ILE Chi-restraints excluded: chain t residue 19 HIS Chi-restraints excluded: chain t residue 22 SER Chi-restraints excluded: chain u residue 52 VAL Chi-restraints excluded: chain y residue 51 TYR Chi-restraints excluded: chain y residue 52 TYR Chi-restraints excluded: chain y residue 81 GLU Chi-restraints excluded: chain y residue 95 ILE Chi-restraints excluded: chain y residue 108 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 621 optimal weight: 4.9990 chunk 401 optimal weight: 9.9990 chunk 600 optimal weight: 8.9990 chunk 302 optimal weight: 20.0000 chunk 197 optimal weight: 10.0000 chunk 194 optimal weight: 30.0000 chunk 639 optimal weight: 20.0000 chunk 684 optimal weight: 30.0000 chunk 497 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 790 optimal weight: 10.0000 overall best weight: 8.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 25 ASN 2 29 GLN ** 4 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 28 ASN J 128 ASN P 2 ASN Q 43 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN S 7 HIS ** X 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 GLN c 31 ASN ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 139 ASN e 81 GLN ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 58 ASN j 64 GLN m 13 HIS o 27 GLN o 39 GLN p 63 GLN ** p 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 54 GLN ** t 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 158605 Z= 0.367 Angle : 0.750 30.236 237201 Z= 0.388 Chirality : 0.039 1.157 30245 Planarity : 0.007 0.129 12834 Dihedral : 24.384 179.647 79062 Min Nonbonded Distance : 1.032 Molprobity Statistics. All-atom Clashscore : 19.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.53 % Favored : 89.37 % Rotamer: Outliers : 6.21 % Allowed : 26.85 % Favored : 66.94 % 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: -2.15 (0.11), residues: 5926 helix: -0.22 (0.12), residues: 1934 sheet: -1.74 (0.16), residues: 1043 loop : -2.15 (0.11), residues: 2949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP s 33 HIS 0.010 0.001 HIS 4 33 PHE 0.027 0.002 PHE c 22 TYR 0.031 0.002 TYR C 61 ARG 0.012 0.001 ARG 2 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11852 Ramachandran restraints generated. 5926 Oldfield, 0 Emsley, 5926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11852 Ramachandran restraints generated. 5926 Oldfield, 0 Emsley, 5926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1716 residues out of total 4915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 291 poor density : 1425 time to evaluate : 6.121 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: 0 47 TYR cc_start: 0.8322 (m-80) cc_final: 0.7992 (m-10) REVERT: 2 11 LYS cc_start: 0.9114 (mttt) cc_final: 0.8777 (mttm) REVERT: 3 31 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.7869 (tp) REVERT: 3 63 TYR cc_start: 0.7355 (m-80) cc_final: 0.6846 (m-80) REVERT: 4 2 LYS cc_start: 0.8820 (tttp) cc_final: 0.8544 (tptt) REVERT: C 51 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8521 (ptt90) REVERT: C 212 TRP cc_start: 0.8658 (p90) cc_final: 0.8117 (p-90) REVERT: D 7 LYS cc_start: 0.8792 (ttmt) cc_final: 0.8414 (ttmm) REVERT: D 96 ILE cc_start: 0.9531 (mt) cc_final: 0.9270 (mt) REVERT: E 7 ASP cc_start: 0.7288 (OUTLIER) cc_final: 0.6595 (p0) REVERT: F 98 PHE cc_start: 0.8670 (t80) cc_final: 0.8443 (t80) REVERT: F 156 THR cc_start: 0.8799 (m) cc_final: 0.8500 (p) REVERT: F 169 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.8777 (mm) REVERT: F 174 PHE cc_start: 0.7845 (OUTLIER) cc_final: 0.7404 (m-80) REVERT: G 138 GLN cc_start: 0.8750 (tm-30) cc_final: 0.8275 (tm-30) REVERT: G 142 GLN cc_start: 0.8567 (tp40) cc_final: 0.7414 (tp40) REVERT: G 146 ASP cc_start: 0.8027 (m-30) cc_final: 0.6943 (m-30) REVERT: H 1 MET cc_start: 0.6652 (ptm) cc_final: 0.6190 (ptm) REVERT: H 18 GLN cc_start: 0.8214 (mm-40) cc_final: 0.7945 (mm-40) REVERT: H 37 VAL cc_start: 0.9185 (OUTLIER) cc_final: 0.8955 (m) REVERT: H 75 LEU cc_start: 0.5972 (OUTLIER) cc_final: 0.5414 (pp) REVERT: J 67 ASN cc_start: 0.7633 (t0) cc_final: 0.6929 (t0) REVERT: J 71 ASP cc_start: 0.8680 (m-30) cc_final: 0.7612 (m-30) REVERT: J 81 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8541 (tp) REVERT: K 12 ASP cc_start: 0.8711 (p0) cc_final: 0.8367 (p0) REVERT: M 9 PHE cc_start: 0.8750 (m-10) cc_final: 0.8511 (m-10) REVERT: M 47 GLU cc_start: 0.7544 (tm-30) cc_final: 0.7267 (tm-30) REVERT: M 51 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7651 (ttp80) REVERT: M 119 LEU cc_start: 0.9013 (tp) cc_final: 0.8767 (tp) REVERT: N 82 GLU cc_start: 0.7611 (mp0) cc_final: 0.7379 (mp0) REVERT: P 7 LEU cc_start: 0.9150 (mm) cc_final: 0.8932 (mm) REVERT: P 70 GLU cc_start: 0.7479 (mp0) cc_final: 0.7169 (mp0) REVERT: Q 70 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7534 (mp10) REVERT: Q 80 ASN cc_start: 0.8628 (m-40) cc_final: 0.8257 (m-40) REVERT: R 21 ARG cc_start: 0.8717 (ttm-80) cc_final: 0.8339 (ttm110) REVERT: R 74 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8561 (mt) REVERT: V 9 ARG cc_start: 0.8574 (mmm-85) cc_final: 0.8197 (mmm-85) REVERT: V 11 GLU cc_start: 0.8235 (pm20) cc_final: 0.7738 (pm20) REVERT: V 29 ILE cc_start: 0.9179 (tp) cc_final: 0.8805 (tp) REVERT: V 78 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8381 (tt0) REVERT: W 60 ASP cc_start: 0.7607 (m-30) cc_final: 0.7025 (p0) REVERT: Y 1 MET cc_start: 0.7623 (ptt) cc_final: 0.7404 (ptt) REVERT: Y 5 GLU cc_start: 0.8660 (mp0) cc_final: 0.8456 (mp0) REVERT: b 51 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7218 (mp0) REVERT: b 119 GLN cc_start: 0.8373 (mt0) cc_final: 0.8099 (mt0) REVERT: b 125 PHE cc_start: 0.7509 (OUTLIER) cc_final: 0.6355 (m-10) REVERT: b 138 ARG cc_start: 0.7704 (ttt180) cc_final: 0.7367 (ttt-90) REVERT: b 158 ASP cc_start: 0.8204 (t0) cc_final: 0.7778 (m-30) REVERT: c 151 GLU cc_start: 0.7308 (tm-30) cc_final: 0.7007 (tm-30) REVERT: d 140 ASP cc_start: 0.8095 (m-30) cc_final: 0.7799 (m-30) REVERT: e 40 ASP cc_start: 0.8570 (p0) cc_final: 0.8022 (p0) REVERT: f 5 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7898 (tm-30) REVERT: f 24 ARG cc_start: 0.7985 (ttm110) cc_final: 0.7610 (mmm160) REVERT: f 25 TYR cc_start: 0.8826 (m-10) cc_final: 0.8599 (m-80) REVERT: f 90 MET cc_start: 0.8126 (mtm) cc_final: 0.7675 (mtm) REVERT: g 102 TRP cc_start: 0.8978 (m-10) cc_final: 0.7837 (m-10) REVERT: h 11 THR cc_start: 0.9065 (p) cc_final: 0.8467 (t) REVERT: h 17 GLN cc_start: 0.9236 (mm-40) cc_final: 0.8805 (mm-40) REVERT: h 62 LEU cc_start: 0.9013 (mt) cc_final: 0.8748 (mt) REVERT: h 65 PHE cc_start: 0.8314 (t80) cc_final: 0.7806 (t80) REVERT: h 112 ASP cc_start: 0.8945 (p0) cc_final: 0.8620 (p0) REVERT: h 123 GLU cc_start: 0.7799 (tt0) cc_final: 0.7557 (tt0) REVERT: i 93 LEU cc_start: 0.8091 (mt) cc_final: 0.7830 (pp) REVERT: i 119 LYS cc_start: 0.8527 (ptmt) cc_final: 0.8052 (ptpt) REVERT: j 20 GLN cc_start: 0.8740 (pp30) cc_final: 0.8529 (pp30) REVERT: k 17 ASP cc_start: 0.7529 (t0) cc_final: 0.6912 (t70) REVERT: k 99 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8926 (mp) REVERT: l 37 TYR cc_start: 0.7993 (p90) cc_final: 0.7368 (p90) REVERT: l 65 TYR cc_start: 0.8446 (t80) cc_final: 0.8201 (t80) REVERT: l 88 ASP cc_start: 0.7667 (t0) cc_final: 0.7237 (t0) REVERT: n 42 TRP cc_start: 0.8244 (t-100) cc_final: 0.7769 (t-100) REVERT: n 62 ASN cc_start: 0.9236 (t0) cc_final: 0.8964 (t0) REVERT: o 20 ASP cc_start: 0.7749 (t0) cc_final: 0.6846 (t0) REVERT: o 37 HIS cc_start: 0.8639 (t70) cc_final: 0.8070 (t70) REVERT: p 12 LYS cc_start: 0.7886 (ttpt) cc_final: 0.7622 (tttp) REVERT: r 37 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8105 (mtpp) REVERT: s 2 ARG cc_start: 0.8035 (tpt-90) cc_final: 0.7224 (ttt90) REVERT: s 80 ARG cc_start: 0.8016 (mtm-85) cc_final: 0.7575 (mtm-85) REVERT: t 67 HIS cc_start: 0.7981 (t-90) cc_final: 0.7396 (t70) REVERT: t 69 ASN cc_start: 0.8896 (m110) cc_final: 0.8414 (m110) REVERT: y 108 THR cc_start: 0.6570 (OUTLIER) cc_final: 0.6198 (m) outliers start: 291 outliers final: 234 residues processed: 1581 average time/residue: 1.2728 time to fit residues: 3495.4897 Evaluate side-chains 1638 residues out of total 4915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 1388 time to evaluate : 6.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 3 GLN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 19 ASP Chi-restraints excluded: chain 0 residue 21 LEU Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 26 SER Chi-restraints excluded: chain 0 residue 29 VAL Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 15 LYS Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 51 ARG Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 174 PHE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 100 PHE Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 51 ARG Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 45 SER Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 61 GLN Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain P residue 62 LYS Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 70 GLN Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 2 ILE Chi-restraints excluded: chain T residue 48 GLN Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 101 THR Chi-restraints excluded: chain V residue 17 SER Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 55 GLU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 66 ASP Chi-restraints excluded: chain V residue 78 GLN Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 26 SER Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain X residue 9 LYS Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 40 GLU Chi-restraints excluded: chain X residue 58 ILE Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 125 PHE Chi-restraints excluded: chain b residue 188 THR Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain c residue 2 GLN Chi-restraints excluded: chain c residue 13 ILE Chi-restraints excluded: chain c residue 25 THR Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 32 LEU Chi-restraints excluded: chain c residue 33 ASP Chi-restraints excluded: chain c residue 40 GLN Chi-restraints excluded: chain c residue 86 LEU Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain d residue 11 SER Chi-restraints excluded: chain d residue 24 VAL Chi-restraints excluded: chain d residue 33 ILE Chi-restraints excluded: chain d residue 35 GLN Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain e residue 23 THR Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 61 LYS Chi-restraints excluded: chain e residue 71 ILE Chi-restraints excluded: chain e residue 76 ASN Chi-restraints excluded: chain e residue 95 MET Chi-restraints excluded: chain e residue 123 LEU Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 22 ILE Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 51 ILE Chi-restraints excluded: chain f residue 61 LEU Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain g residue 86 VAL Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain g residue 124 SER Chi-restraints excluded: chain g residue 139 ASP Chi-restraints excluded: chain h residue 9 MET Chi-restraints excluded: chain h residue 13 ILE Chi-restraints excluded: chain h residue 38 VAL Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 84 ILE Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 125 ILE Chi-restraints excluded: chain i residue 20 ILE Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain i residue 61 ASP Chi-restraints excluded: chain i residue 83 THR Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain j residue 22 THR Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 58 ASN Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain k residue 31 VAL Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 69 CYS Chi-restraints excluded: chain k residue 96 ILE Chi-restraints excluded: chain k residue 99 LEU Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 74 GLN Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 81 ILE Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 42 VAL Chi-restraints excluded: chain m residue 44 ILE Chi-restraints excluded: chain m residue 75 SER Chi-restraints excluded: chain m residue 103 THR Chi-restraints excluded: chain n residue 29 ILE Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 34 ASN Chi-restraints excluded: chain n residue 50 THR Chi-restraints excluded: chain n residue 54 ASP Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain o residue 11 VAL Chi-restraints excluded: chain o residue 23 SER Chi-restraints excluded: chain o residue 60 SER Chi-restraints excluded: chain o residue 78 THR Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 69 ASP Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 28 VAL Chi-restraints excluded: chain q residue 37 ILE Chi-restraints excluded: chain q residue 67 SER Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain r residue 32 ILE Chi-restraints excluded: chain r residue 37 LYS Chi-restraints excluded: chain s residue 13 HIS Chi-restraints excluded: chain s residue 18 VAL Chi-restraints excluded: chain s residue 26 ASP Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain t residue 19 HIS Chi-restraints excluded: chain t residue 22 SER Chi-restraints excluded: chain t residue 42 ASP Chi-restraints excluded: chain t residue 54 GLN Chi-restraints excluded: chain u residue 52 VAL Chi-restraints excluded: chain y residue 51 TYR Chi-restraints excluded: chain y residue 52 TYR Chi-restraints excluded: chain y residue 81 GLU Chi-restraints excluded: chain y residue 108 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 914 optimal weight: 6.9990 chunk 963 optimal weight: 10.0000 chunk 878 optimal weight: 10.0000 chunk 936 optimal weight: 8.9990 chunk 962 optimal weight: 6.9990 chunk 563 optimal weight: 10.0000 chunk 408 optimal weight: 20.0000 chunk 735 optimal weight: 20.0000 chunk 287 optimal weight: 10.0000 chunk 846 optimal weight: 7.9990 chunk 886 optimal weight: 20.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 29 GLN ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 28 ASN ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 2 ASN Q 43 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN ** X 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 GLN ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 139 ASN e 81 GLN ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 58 ASN j 64 GLN ** n 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 39 GLN ** p 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 54 GLN ** t 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 15 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 158605 Z= 0.344 Angle : 0.738 30.201 237201 Z= 0.383 Chirality : 0.039 1.159 30245 Planarity : 0.006 0.128 12834 Dihedral : 24.391 179.759 79062 Min Nonbonded Distance : 1.021 Molprobity Statistics. All-atom Clashscore : 19.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.18 % Favored : 89.72 % Rotamer: Outliers : 5.85 % Allowed : 27.34 % Favored : 66.82 % 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: -2.18 (0.11), residues: 5926 helix: -0.26 (0.12), residues: 1936 sheet: -1.78 (0.16), residues: 1028 loop : -2.16 (0.11), residues: 2962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP b 103 HIS 0.008 0.001 HIS 4 33 PHE 0.026 0.002 PHE H 47 TYR 0.031 0.002 TYR C 61 ARG 0.012 0.001 ARG 2 41 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11852 Ramachandran restraints generated. 5926 Oldfield, 0 Emsley, 5926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11852 Ramachandran restraints generated. 5926 Oldfield, 0 Emsley, 5926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1669 residues out of total 4915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 1395 time to evaluate : 6.347 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: 0 11 LYS cc_start: 0.9143 (mptt) cc_final: 0.8887 (mptt) REVERT: 0 47 TYR cc_start: 0.8304 (m-80) cc_final: 0.7952 (m-10) REVERT: 2 11 LYS cc_start: 0.9124 (mttt) cc_final: 0.8790 (mttm) REVERT: 3 63 TYR cc_start: 0.7339 (m-80) cc_final: 0.6824 (m-80) REVERT: C 51 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8489 (ptt90) REVERT: C 212 TRP cc_start: 0.8669 (p90) cc_final: 0.8177 (p-90) REVERT: D 7 LYS cc_start: 0.8813 (ttmt) cc_final: 0.8412 (ttmm) REVERT: D 96 ILE cc_start: 0.9529 (mt) cc_final: 0.9252 (mt) REVERT: E 7 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.6656 (p0) REVERT: F 98 PHE cc_start: 0.8674 (t80) cc_final: 0.8432 (t80) REVERT: F 156 THR cc_start: 0.8802 (m) cc_final: 0.8505 (p) REVERT: F 169 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8774 (mm) REVERT: F 174 PHE cc_start: 0.7768 (OUTLIER) cc_final: 0.7394 (m-80) REVERT: G 138 GLN cc_start: 0.8760 (tm-30) cc_final: 0.8295 (tm-30) REVERT: G 142 GLN cc_start: 0.8566 (tp40) cc_final: 0.7444 (tp40) REVERT: G 146 ASP cc_start: 0.8022 (m-30) cc_final: 0.6959 (m-30) REVERT: H 1 MET cc_start: 0.6626 (ptm) cc_final: 0.6179 (ptm) REVERT: H 18 GLN cc_start: 0.8056 (mm-40) cc_final: 0.7831 (mm110) REVERT: H 75 LEU cc_start: 0.5986 (OUTLIER) cc_final: 0.5440 (pp) REVERT: J 67 ASN cc_start: 0.7612 (t0) cc_final: 0.6864 (t0) REVERT: J 71 ASP cc_start: 0.8691 (m-30) cc_final: 0.7576 (m-30) REVERT: J 81 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8540 (tp) REVERT: K 12 ASP cc_start: 0.8717 (p0) cc_final: 0.8374 (p0) REVERT: M 9 PHE cc_start: 0.8826 (m-10) cc_final: 0.8512 (m-10) REVERT: M 47 GLU cc_start: 0.7564 (tm-30) cc_final: 0.7270 (tm-30) REVERT: M 51 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7654 (ttp80) REVERT: M 119 LEU cc_start: 0.8963 (tp) cc_final: 0.8698 (tp) REVERT: N 82 GLU cc_start: 0.7631 (mp0) cc_final: 0.7360 (mp0) REVERT: P 7 LEU cc_start: 0.9145 (mm) cc_final: 0.8942 (mm) REVERT: P 70 GLU cc_start: 0.7462 (mp0) cc_final: 0.7185 (mp0) REVERT: Q 80 ASN cc_start: 0.8593 (m-40) cc_final: 0.8081 (m-40) REVERT: R 21 ARG cc_start: 0.8710 (ttm-80) cc_final: 0.8300 (ttm-80) REVERT: R 74 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8553 (mt) REVERT: V 9 ARG cc_start: 0.8582 (mmm-85) cc_final: 0.8243 (mmm-85) REVERT: V 29 ILE cc_start: 0.9236 (tp) cc_final: 0.8969 (tp) REVERT: V 78 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8396 (tt0) REVERT: W 37 ARG cc_start: 0.8300 (mmt-90) cc_final: 0.7928 (mmt-90) REVERT: W 60 ASP cc_start: 0.7579 (m-30) cc_final: 0.7029 (p0) REVERT: Y 24 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6857 (mt-10) REVERT: b 8 MET cc_start: 0.7641 (tmm) cc_final: 0.7408 (tmm) REVERT: b 51 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7154 (mp0) REVERT: b 119 GLN cc_start: 0.8341 (mt0) cc_final: 0.8060 (mt0) REVERT: b 125 PHE cc_start: 0.7542 (OUTLIER) cc_final: 0.6332 (m-10) REVERT: b 138 ARG cc_start: 0.7691 (ttt180) cc_final: 0.7333 (ttt-90) REVERT: b 158 ASP cc_start: 0.8249 (t0) cc_final: 0.7689 (m-30) REVERT: c 99 GLN cc_start: 0.7362 (pm20) cc_final: 0.7007 (pm20) REVERT: c 138 GLN cc_start: 0.7859 (pp30) cc_final: 0.7345 (pp30) REVERT: c 151 GLU cc_start: 0.7219 (tm-30) cc_final: 0.6897 (tm-30) REVERT: d 140 ASP cc_start: 0.8140 (m-30) cc_final: 0.7843 (m-30) REVERT: e 40 ASP cc_start: 0.8595 (p0) cc_final: 0.8034 (p0) REVERT: f 5 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7999 (tm-30) REVERT: f 25 TYR cc_start: 0.8833 (m-10) cc_final: 0.8600 (m-80) REVERT: f 36 ILE cc_start: 0.9427 (mp) cc_final: 0.9197 (mt) REVERT: g 27 ASN cc_start: 0.7722 (OUTLIER) cc_final: 0.7516 (t0) REVERT: g 89 GLU cc_start: 0.7842 (pp20) cc_final: 0.7015 (mp0) REVERT: g 102 TRP cc_start: 0.8929 (m-10) cc_final: 0.7784 (m-10) REVERT: h 11 THR cc_start: 0.9110 (p) cc_final: 0.8496 (t) REVERT: h 17 GLN cc_start: 0.9218 (mm-40) cc_final: 0.8832 (mm-40) REVERT: h 62 LEU cc_start: 0.9004 (mt) cc_final: 0.8603 (mt) REVERT: h 65 PHE cc_start: 0.8312 (t80) cc_final: 0.7872 (t80) REVERT: h 112 ASP cc_start: 0.8959 (p0) cc_final: 0.8635 (p0) REVERT: h 123 GLU cc_start: 0.7873 (tt0) cc_final: 0.7642 (tt0) REVERT: i 49 GLN cc_start: 0.8682 (tm-30) cc_final: 0.8463 (tm-30) REVERT: i 93 LEU cc_start: 0.8100 (mt) cc_final: 0.7826 (pp) REVERT: i 119 LYS cc_start: 0.8527 (ptmt) cc_final: 0.8215 (ptpt) REVERT: j 20 GLN cc_start: 0.8766 (pp30) cc_final: 0.8519 (pp30) REVERT: k 28 ASN cc_start: 0.8376 (t0) cc_final: 0.8079 (t0) REVERT: k 86 LYS cc_start: 0.7801 (ttmm) cc_final: 0.7506 (ttmm) REVERT: l 37 TYR cc_start: 0.7972 (p90) cc_final: 0.7383 (p90) REVERT: l 65 TYR cc_start: 0.8435 (t80) cc_final: 0.8203 (t80) REVERT: l 85 ARG cc_start: 0.8290 (mtp85) cc_final: 0.7997 (ttm110) REVERT: l 88 ASP cc_start: 0.7645 (t0) cc_final: 0.7211 (t0) REVERT: n 42 TRP cc_start: 0.8208 (t-100) cc_final: 0.7938 (t-100) REVERT: n 62 ASN cc_start: 0.9230 (t0) cc_final: 0.8907 (t0) REVERT: n 66 GLN cc_start: 0.8334 (mt0) cc_final: 0.8061 (mm-40) REVERT: o 20 ASP cc_start: 0.7712 (t0) cc_final: 0.6832 (t0) REVERT: o 37 HIS cc_start: 0.8620 (t70) cc_final: 0.8035 (t70) REVERT: p 12 LYS cc_start: 0.7859 (ttpt) cc_final: 0.7589 (tttp) REVERT: r 37 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8081 (mtpp) REVERT: s 2 ARG cc_start: 0.8040 (tpt-90) cc_final: 0.7179 (ttt90) REVERT: s 80 ARG cc_start: 0.8004 (mtm-85) cc_final: 0.7552 (mtm-85) REVERT: t 67 HIS cc_start: 0.7939 (t-90) cc_final: 0.7378 (t70) REVERT: t 69 ASN cc_start: 0.8887 (m110) cc_final: 0.8410 (m110) REVERT: y 108 THR cc_start: 0.6550 (OUTLIER) cc_final: 0.6182 (m) outliers start: 274 outliers final: 239 residues processed: 1544 average time/residue: 1.2817 time to fit residues: 3452.3656 Evaluate side-chains 1624 residues out of total 4915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 1372 time to evaluate : 6.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 3 GLN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 19 ASP Chi-restraints excluded: chain 0 residue 21 LEU Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 29 VAL Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 9 VAL Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 15 LYS Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 51 ARG Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 174 PHE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 31 ARG Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 100 PHE Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 5 LYS Chi-restraints excluded: chain M residue 51 ARG Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 45 SER Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 61 GLN Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain P residue 62 LYS Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 2 ILE Chi-restraints excluded: chain T residue 48 GLN Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 17 SER Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 55 GLU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 66 ASP Chi-restraints excluded: chain V residue 78 GLN Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 26 SER Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain X residue 9 LYS Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 40 GLU Chi-restraints excluded: chain X residue 58 ILE Chi-restraints excluded: chain Y residue 31 GLN Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 125 PHE Chi-restraints excluded: chain b residue 188 THR Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain c residue 2 GLN Chi-restraints excluded: chain c residue 13 ILE Chi-restraints excluded: chain c residue 25 THR Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 32 LEU Chi-restraints excluded: chain c residue 40 GLN Chi-restraints excluded: chain c residue 86 LEU Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain d residue 11 SER Chi-restraints excluded: chain d residue 24 VAL Chi-restraints excluded: chain d residue 33 ILE Chi-restraints excluded: chain d residue 35 GLN Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain e residue 23 THR Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 71 ILE Chi-restraints excluded: chain e residue 76 ASN Chi-restraints excluded: chain e residue 95 MET Chi-restraints excluded: chain e residue 123 LEU Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 51 ILE Chi-restraints excluded: chain f residue 61 LEU Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain g residue 27 ASN Chi-restraints excluded: chain g residue 86 VAL Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain h residue 13 ILE Chi-restraints excluded: chain h residue 38 VAL Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 84 ILE Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 125 ILE Chi-restraints excluded: chain i residue 20 ILE Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain i residue 61 ASP Chi-restraints excluded: chain i residue 83 THR Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain j residue 22 THR Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 58 ASN Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain k residue 31 VAL Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 69 CYS Chi-restraints excluded: chain k residue 96 ILE Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 74 GLN Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 81 ILE Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 42 VAL Chi-restraints excluded: chain m residue 44 ILE Chi-restraints excluded: chain m residue 75 SER Chi-restraints excluded: chain m residue 103 THR Chi-restraints excluded: chain n residue 29 ILE Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 34 ASN Chi-restraints excluded: chain n residue 50 THR Chi-restraints excluded: chain n residue 54 ASP Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain o residue 11 VAL Chi-restraints excluded: chain o residue 23 SER Chi-restraints excluded: chain o residue 60 SER Chi-restraints excluded: chain o residue 78 THR Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 69 ASP Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 28 VAL Chi-restraints excluded: chain q residue 67 SER Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain r residue 32 ILE Chi-restraints excluded: chain r residue 37 LYS Chi-restraints excluded: chain s residue 13 HIS Chi-restraints excluded: chain s residue 18 VAL Chi-restraints excluded: chain s residue 26 ASP Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 70 LEU Chi-restraints excluded: chain t residue 3 ILE Chi-restraints excluded: chain t residue 19 HIS Chi-restraints excluded: chain t residue 22 SER Chi-restraints excluded: chain t residue 42 ASP Chi-restraints excluded: chain t residue 54 GLN Chi-restraints excluded: chain u residue 52 VAL Chi-restraints excluded: chain y residue 51 TYR Chi-restraints excluded: chain y residue 52 TYR Chi-restraints excluded: chain y residue 81 GLU Chi-restraints excluded: chain y residue 97 GLU Chi-restraints excluded: chain y residue 108 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 933 optimal weight: 1.9990 chunk 615 optimal weight: 6.9990 chunk 990 optimal weight: 4.9990 chunk 604 optimal weight: 8.9990 chunk 469 optimal weight: 6.9990 chunk 688 optimal weight: 30.0000 chunk 1039 optimal weight: 20.0000 chunk 956 optimal weight: 7.9990 chunk 827 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 639 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 29 GLN ** 4 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN H 28 ASN Q 43 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN ** X 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 GLN ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 139 ASN ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 64 GLN ** n 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 27 GLN o 39 GLN ** p 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 54 GLN ** t 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 158605 Z= 0.245 Angle : 0.687 30.176 237201 Z= 0.360 Chirality : 0.036 1.163 30245 Planarity : 0.006 0.125 12834 Dihedral : 24.352 179.994 79062 Min Nonbonded Distance : 1.048 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.47 % Favored : 90.47 % Rotamer: Outliers : 5.48 % Allowed : 28.04 % Favored : 66.47 % 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: -2.02 (0.11), residues: 5926 helix: -0.11 (0.12), residues: 1932 sheet: -1.67 (0.16), residues: 1022 loop : -2.07 (0.11), residues: 2972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP b 103 HIS 0.006 0.001 HIS 4 33 PHE 0.024 0.002 PHE c 22 TYR 0.031 0.002 TYR C 61 ARG 0.014 0.000 ARG 2 41 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11852 Ramachandran restraints generated. 5926 Oldfield, 0 Emsley, 5926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11852 Ramachandran restraints generated. 5926 Oldfield, 0 Emsley, 5926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1665 residues out of total 4915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 1408 time to evaluate : 6.172 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: 0 47 TYR cc_start: 0.8299 (m-80) cc_final: 0.7980 (m-10) REVERT: 1 34 GLU cc_start: 0.6370 (tm-30) cc_final: 0.6045 (tm-30) REVERT: 2 11 LYS cc_start: 0.9096 (mttt) cc_final: 0.8751 (mttm) REVERT: 3 63 TYR cc_start: 0.7270 (m-80) cc_final: 0.6785 (m-80) REVERT: 4 23 ILE cc_start: 0.9447 (mm) cc_final: 0.9179 (mm) REVERT: C 51 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8472 (ptt90) REVERT: C 212 TRP cc_start: 0.8593 (p90) cc_final: 0.8200 (p-90) REVERT: D 7 LYS cc_start: 0.8854 (ttmt) cc_final: 0.8446 (ttmm) REVERT: D 96 ILE cc_start: 0.9490 (mt) cc_final: 0.9202 (mt) REVERT: E 7 ASP cc_start: 0.7313 (OUTLIER) cc_final: 0.6651 (p0) REVERT: F 34 THR cc_start: 0.8861 (m) cc_final: 0.7906 (p) REVERT: F 98 PHE cc_start: 0.8681 (t80) cc_final: 0.8436 (t80) REVERT: F 156 THR cc_start: 0.8802 (m) cc_final: 0.8532 (p) REVERT: F 169 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8494 (mm) REVERT: F 174 PHE cc_start: 0.7695 (OUTLIER) cc_final: 0.7217 (m-80) REVERT: G 138 GLN cc_start: 0.8715 (tm-30) cc_final: 0.8266 (tm-30) REVERT: G 142 GLN cc_start: 0.8550 (tp40) cc_final: 0.7470 (tp40) REVERT: G 146 ASP cc_start: 0.8007 (m-30) cc_final: 0.6957 (m-30) REVERT: H 75 LEU cc_start: 0.5804 (OUTLIER) cc_final: 0.5252 (pp) REVERT: J 67 ASN cc_start: 0.7523 (t0) cc_final: 0.6831 (t0) REVERT: J 71 ASP cc_start: 0.8611 (m-30) cc_final: 0.7603 (m-30) REVERT: J 81 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8499 (tp) REVERT: K 12 ASP cc_start: 0.8678 (p0) cc_final: 0.8342 (p0) REVERT: M 9 PHE cc_start: 0.8779 (m-10) cc_final: 0.8483 (m-10) REVERT: M 47 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7252 (tm-30) REVERT: M 51 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7580 (ttp80) REVERT: M 119 LEU cc_start: 0.8902 (tp) cc_final: 0.8624 (tp) REVERT: N 82 GLU cc_start: 0.7532 (mp0) cc_final: 0.7299 (mp0) REVERT: O 16 ARG cc_start: 0.8471 (tpp-160) cc_final: 0.8122 (mmt-90) REVERT: P 7 LEU cc_start: 0.9137 (mm) cc_final: 0.8918 (mm) REVERT: P 70 GLU cc_start: 0.7431 (mp0) cc_final: 0.7101 (mp0) REVERT: Q 80 ASN cc_start: 0.8587 (m-40) cc_final: 0.8169 (m-40) REVERT: Q 103 VAL cc_start: 0.8560 (m) cc_final: 0.8342 (t) REVERT: R 21 ARG cc_start: 0.8672 (ttm-80) cc_final: 0.8396 (ttm-80) REVERT: R 74 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8540 (mt) REVERT: S 4 ILE cc_start: 0.9105 (mp) cc_final: 0.8850 (mp) REVERT: V 9 ARG cc_start: 0.8617 (mmm-85) cc_final: 0.8283 (mmm-85) REVERT: V 29 ILE cc_start: 0.9165 (tp) cc_final: 0.8896 (tp) REVERT: W 60 ASP cc_start: 0.7481 (m-30) cc_final: 0.7039 (p0) REVERT: b 51 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7299 (mp0) REVERT: b 119 GLN cc_start: 0.8280 (mt0) cc_final: 0.8047 (mt0) REVERT: b 125 PHE cc_start: 0.7455 (OUTLIER) cc_final: 0.6299 (m-10) REVERT: b 138 ARG cc_start: 0.7636 (ttt180) cc_final: 0.7286 (ttt-90) REVERT: b 158 ASP cc_start: 0.8113 (t0) cc_final: 0.7619 (m-30) REVERT: c 99 GLN cc_start: 0.7463 (pm20) cc_final: 0.7164 (pm20) REVERT: c 138 GLN cc_start: 0.7813 (pp30) cc_final: 0.7271 (pp30) REVERT: c 151 GLU cc_start: 0.7257 (tm-30) cc_final: 0.6988 (tm-30) REVERT: d 140 ASP cc_start: 0.8075 (m-30) cc_final: 0.7784 (m-30) REVERT: e 40 ASP cc_start: 0.8506 (p0) cc_final: 0.7950 (p0) REVERT: f 25 TYR cc_start: 0.8809 (m-10) cc_final: 0.8599 (m-80) REVERT: f 36 ILE cc_start: 0.9414 (mp) cc_final: 0.9149 (mt) REVERT: g 89 GLU cc_start: 0.7719 (pp20) cc_final: 0.6962 (mp0) REVERT: g 102 TRP cc_start: 0.8920 (m-10) cc_final: 0.7778 (m-10) REVERT: g 129 ASN cc_start: 0.7565 (m-40) cc_final: 0.7335 (t0) REVERT: h 11 THR cc_start: 0.9119 (p) cc_final: 0.8513 (t) REVERT: h 17 GLN cc_start: 0.9207 (mm-40) cc_final: 0.8797 (mm-40) REVERT: h 62 LEU cc_start: 0.8948 (mt) cc_final: 0.8550 (mt) REVERT: h 65 PHE cc_start: 0.8220 (t80) cc_final: 0.7752 (t80) REVERT: h 112 ASP cc_start: 0.8933 (p0) cc_final: 0.8584 (p0) REVERT: h 123 GLU cc_start: 0.7841 (tt0) cc_final: 0.7560 (tt0) REVERT: i 49 GLN cc_start: 0.8618 (tm-30) cc_final: 0.8398 (tm-30) REVERT: i 93 LEU cc_start: 0.8096 (mt) cc_final: 0.7825 (pp) REVERT: i 119 LYS cc_start: 0.8395 (ptmt) cc_final: 0.8074 (ptpt) REVERT: j 20 GLN cc_start: 0.8712 (pp30) cc_final: 0.8480 (pp30) REVERT: j 65 TYR cc_start: 0.8645 (m-80) cc_final: 0.8412 (m-80) REVERT: k 28 ASN cc_start: 0.8339 (t0) cc_final: 0.8058 (t0) REVERT: k 86 LYS cc_start: 0.7748 (ttmm) cc_final: 0.7458 (ttmm) REVERT: l 37 TYR cc_start: 0.7953 (p90) cc_final: 0.7413 (p90) REVERT: l 65 TYR cc_start: 0.8326 (t80) cc_final: 0.8124 (t80) REVERT: l 85 ARG cc_start: 0.8220 (mtp85) cc_final: 0.7917 (ttm110) REVERT: l 88 ASP cc_start: 0.7655 (t0) cc_final: 0.7269 (t0) REVERT: n 42 TRP cc_start: 0.8010 (t-100) cc_final: 0.7656 (t-100) REVERT: n 62 ASN cc_start: 0.9177 (t0) cc_final: 0.8899 (t0) REVERT: n 66 GLN cc_start: 0.8246 (mt0) cc_final: 0.7987 (mm-40) REVERT: o 20 ASP cc_start: 0.7658 (t0) cc_final: 0.6850 (t0) REVERT: o 37 HIS cc_start: 0.8579 (t70) cc_final: 0.7997 (t70) REVERT: p 12 LYS cc_start: 0.7715 (ttpt) cc_final: 0.7452 (tttp) REVERT: p 70 ARG cc_start: 0.7865 (mmm-85) cc_final: 0.7027 (tpt-90) REVERT: s 2 ARG cc_start: 0.8001 (tpt-90) cc_final: 0.7131 (ttt90) REVERT: s 80 ARG cc_start: 0.8050 (mtm-85) cc_final: 0.7594 (mtm-85) REVERT: t 67 HIS cc_start: 0.7880 (t-90) cc_final: 0.7329 (t70) REVERT: t 69 ASN cc_start: 0.8888 (m110) cc_final: 0.8427 (m110) REVERT: y 108 THR cc_start: 0.6398 (OUTLIER) cc_final: 0.6017 (m) outliers start: 257 outliers final: 221 residues processed: 1549 average time/residue: 1.3217 time to fit residues: 3580.0209 Evaluate side-chains 1609 residues out of total 4915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 1378 time to evaluate : 6.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 19 ASP Chi-restraints excluded: chain 0 residue 21 LEU Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 26 SER Chi-restraints excluded: chain 0 residue 29 VAL Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 9 VAL Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 15 LYS Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 51 ARG Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 174 PHE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 100 PHE Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 51 ARG Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 45 SER Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 61 GLN Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain P residue 62 LYS Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain P residue 65 ASN Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 2 ILE Chi-restraints excluded: chain T residue 48 GLN Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 17 SER Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain V residue 66 ASP Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 26 SER Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain X residue 9 LYS Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 40 GLU Chi-restraints excluded: chain X residue 58 ILE Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 125 PHE Chi-restraints excluded: chain b residue 188 THR Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain c residue 2 GLN Chi-restraints excluded: chain c residue 13 ILE Chi-restraints excluded: chain c residue 25 THR Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 32 LEU Chi-restraints excluded: chain c residue 40 GLN Chi-restraints excluded: chain c residue 86 LEU Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain d residue 11 SER Chi-restraints excluded: chain d residue 24 VAL Chi-restraints excluded: chain d residue 35 GLN Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain e residue 23 THR Chi-restraints excluded: chain e residue 71 ILE Chi-restraints excluded: chain e residue 95 MET Chi-restraints excluded: chain e residue 123 LEU Chi-restraints excluded: chain f residue 61 LEU Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain g residue 86 VAL Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain g residue 124 SER Chi-restraints excluded: chain h residue 9 MET Chi-restraints excluded: chain h residue 13 ILE Chi-restraints excluded: chain h residue 38 VAL Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 84 ILE Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 125 ILE Chi-restraints excluded: chain i residue 20 ILE Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain i residue 61 ASP Chi-restraints excluded: chain i residue 83 THR Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain j residue 22 THR Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 58 ASN Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain k residue 31 VAL Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 69 CYS Chi-restraints excluded: chain k residue 96 ILE Chi-restraints excluded: chain l residue 24 GLU Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 74 GLN Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 81 ILE Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 42 VAL Chi-restraints excluded: chain m residue 44 ILE Chi-restraints excluded: chain m residue 75 SER Chi-restraints excluded: chain m residue 77 LYS Chi-restraints excluded: chain m residue 103 THR Chi-restraints excluded: chain n residue 29 ILE Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 34 ASN Chi-restraints excluded: chain n residue 50 THR Chi-restraints excluded: chain n residue 54 ASP Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain o residue 11 VAL Chi-restraints excluded: chain o residue 23 SER Chi-restraints excluded: chain o residue 60 SER Chi-restraints excluded: chain o residue 78 THR Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 69 ASP Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 28 VAL Chi-restraints excluded: chain q residue 67 SER Chi-restraints excluded: chain r residue 32 ILE Chi-restraints excluded: chain s residue 13 HIS Chi-restraints excluded: chain s residue 18 VAL Chi-restraints excluded: chain s residue 26 ASP Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 70 LEU Chi-restraints excluded: chain t residue 3 ILE Chi-restraints excluded: chain t residue 19 HIS Chi-restraints excluded: chain t residue 22 SER Chi-restraints excluded: chain t residue 42 ASP Chi-restraints excluded: chain t residue 54 GLN Chi-restraints excluded: chain u residue 52 VAL Chi-restraints excluded: chain y residue 51 TYR Chi-restraints excluded: chain y residue 52 TYR Chi-restraints excluded: chain y residue 81 GLU Chi-restraints excluded: chain y residue 97 GLU Chi-restraints excluded: chain y residue 108 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 507 optimal weight: 8.9990 chunk 657 optimal weight: 30.0000 chunk 881 optimal weight: 10.0000 chunk 253 optimal weight: 50.0000 chunk 762 optimal weight: 30.0000 chunk 122 optimal weight: 10.0000 chunk 229 optimal weight: 9.9990 chunk 828 optimal weight: 10.0000 chunk 346 optimal weight: 5.9990 chunk 850 optimal weight: 20.0000 chunk 104 optimal weight: 10.0000 overall best weight: 8.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 29 GLN ** 4 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 28 ASN P 2 ASN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 GLN ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 139 ASN ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 8 GLN ** g 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 4 ASN ** n 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 39 GLN ** p 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 54 GLN ** t 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.084040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.066474 restraints weight = 444332.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.067975 restraints weight = 199323.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.068020 restraints weight = 105788.479| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 158605 Z= 0.369 Angle : 0.751 30.144 237201 Z= 0.388 Chirality : 0.039 1.162 30245 Planarity : 0.007 0.154 12834 Dihedral : 24.324 179.858 79062 Min Nonbonded Distance : 1.000 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.63 % Favored : 89.28 % Rotamer: Outliers : 5.53 % Allowed : 28.30 % Favored : 66.18 % 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: -2.13 (0.11), residues: 5926 helix: -0.24 (0.12), residues: 1945 sheet: -1.71 (0.15), residues: 1059 loop : -2.13 (0.11), residues: 2922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.002 TRP s 33 HIS 0.011 0.001 HIS O 34 PHE 0.025 0.002 PHE c 129 TYR 0.031 0.002 TYR C 61 ARG 0.022 0.001 ARG C 213 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 45065.22 seconds wall clock time: 785 minutes 25.56 seconds (47125.56 seconds total)