Starting phenix.real_space_refine on Sat Mar 2 22:34:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q9a_4478/03_2024/6q9a_4478_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q9a_4478/03_2024/6q9a_4478.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q9a_4478/03_2024/6q9a_4478_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/6q9a_4478/03_2024/6q9a_4478_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q9a_4478/03_2024/6q9a_4478_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q9a_4478/03_2024/6q9a_4478.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q9a_4478/03_2024/6q9a_4478.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q9a_4478/03_2024/6q9a_4478_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q9a_4478/03_2024/6q9a_4478_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= 0.002 sd= 0.018 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4996 5.49 5 Mg 437 5.21 5 S 159 5.16 5 C 77626 2.51 5 N 28787 2.21 5 O 43162 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 35": "OE1" <-> "OE2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B ARG 63": "NH1" <-> "NH2" Residue "B ARG 80": "NH1" <-> "NH2" Residue "B GLU 100": "OE1" <-> "OE2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B GLU 194": "OE1" <-> "OE2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B ARG 212": "NH1" <-> "NH2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C GLU 28": "OE1" <-> "OE2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C ARG 83": "NH1" <-> "NH2" Residue "C GLU 86": "OE1" <-> "OE2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C GLU 183": "OE1" <-> "OE2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "D GLU 16": "OE1" <-> "OE2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 44": "NH1" <-> "NH2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D ARG 102": "NH1" <-> "NH2" Residue "D GLU 127": "OE1" <-> "OE2" Residue "D ARG 162": "NH1" <-> "NH2" Residue "D ARG 170": "NH1" <-> "NH2" Residue "E ARG 30": "NH1" <-> "NH2" Residue "E ARG 71": "NH1" <-> "NH2" Residue "E ARG 92": "NH1" <-> "NH2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 98": "OE1" <-> "OE2" Residue "E GLU 101": "OE1" <-> "OE2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 110": "NH1" <-> "NH2" Residue "E ARG 112": "NH1" <-> "NH2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E GLU 164": "OE1" <-> "OE2" Residue "E GLU 165": "OE1" <-> "OE2" Residue "F ARG 3": "NH1" <-> "NH2" Residue "F ARG 152": "NH1" <-> "NH2" Residue "F ARG 153": "NH1" <-> "NH2" Residue "F ARG 163": "NH1" <-> "NH2" Residue "F GLU 167": "OE1" <-> "OE2" Residue "F ARG 170": "NH1" <-> "NH2" Residue "G GLU 45": "OE1" <-> "OE2" Residue "G ARG 50": "NH1" <-> "NH2" Residue "G ARG 51": "NH1" <-> "NH2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G ARG 68": "NH1" <-> "NH2" Residue "G GLU 109": "OE1" <-> "OE2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 49": "OE1" <-> "OE2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 34": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J GLU 91": "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 ARG 17": "NH1" <-> "NH2" Residue "K ARG 18": "NH1" <-> "NH2" Residue "K GLU 92": "OE1" <-> "OE2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L GLU 51": "OE1" <-> "OE2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L GLU 86": "OE1" <-> "OE2" Residue "L ARG 123": "NH1" <-> "NH2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 114": "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 GLU 49": "OE1" <-> "OE2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 13": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O ARG 25": "NH1" <-> "NH2" Residue "O GLU 55": "OE1" <-> "OE2" 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 GLU 11": "OE1" <-> "OE2" Residue "P PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 21": "NH1" <-> "NH2" Residue "P ARG 62": "NH1" <-> "NH2" Residue "P GLU 68": "OE1" <-> "OE2" Residue "P GLU 71": "OE1" <-> "OE2" Residue "P ARG 89": "NH1" <-> "NH2" Residue "P TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 101": "NH1" <-> "NH2" Residue "P GLU 102": "OE1" <-> "OE2" Residue "P ARG 109": "NH1" <-> "NH2" Residue "Q ARG 3": "NH1" <-> "NH2" Residue "Q ARG 6": "NH1" <-> "NH2" Residue "Q ARG 13": "NH1" <-> "NH2" Residue "Q ARG 33": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q ARG 70": "NH1" <-> "NH2" Residue "Q GLU 111": "OE1" <-> "OE2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R GLU 37": "OE1" <-> "OE2" Residue "R GLU 62": "OE1" <-> "OE2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "S GLU 59": "OE1" <-> "OE2" Residue "S PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 78": "OE1" <-> "OE2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 92": "NH1" <-> "NH2" Residue "T ARG 3": "NH1" <-> "NH2" Residue "T ARG 6": "NH1" <-> "NH2" Residue "T GLU 18": "OE1" <-> "OE2" Residue "T GLU 56": "OE1" <-> "OE2" Residue "T GLU 89": "OE1" <-> "OE2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U GLU 37": "OE1" <-> "OE2" Residue "U ARG 82": "NH1" <-> "NH2" Residue "U ARG 86": "NH1" <-> "NH2" Residue "U ARG 94": "NH1" <-> "NH2" Residue "V GLU 11": "OE1" <-> "OE2" Residue "V ARG 19": "NH1" <-> "NH2" Residue "W GLU 17": "OE1" <-> "OE2" Residue "W PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 3": "NH1" <-> "NH2" Residue "X ARG 18": "NH1" <-> "NH2" Residue "X ARG 37": "NH1" <-> "NH2" Residue "X ARG 45": "NH1" <-> "NH2" Residue "X ARG 50": "NH1" <-> "NH2" Residue "X ARG 57": "NH1" <-> "NH2" Residue "X ARG 74": "NH1" <-> "NH2" Residue "Y GLU 5": "OE1" <-> "OE2" 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 11": "NH1" <-> "NH2" Residue "Z ARG 30": "NH1" <-> "NH2" Residue "Z ARG 45": "NH1" <-> "NH2" Residue "a ARG 56": "NH1" <-> "NH2" Residue "a PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 63": "NH1" <-> "NH2" Residue "b ARG 10": "NH1" <-> "NH2" Residue "b ARG 16": "NH1" <-> "NH2" Residue "b ARG 52": "NH1" <-> "NH2" Residue "c ARG 28": "NH1" <-> "NH2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "d ARG 3": "NH1" <-> "NH2" Residue "d ARG 14": "NH1" <-> "NH2" Residue "d ARG 19": "NH1" <-> "NH2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "d ARG 41": "NH1" <-> "NH2" Residue "e ARG 13": "NH1" <-> "NH2" Residue "e ARG 30": "NH1" <-> "NH2" Residue "e ARG 40": "NH1" <-> "NH2" Residue "e ARG 42": "NH1" <-> "NH2" Residue "f ARG 24": "NH1" <-> "NH2" Residue "g GLU 52": "OE1" <-> "OE2" Residue "g GLU 56": "OE1" <-> "OE2" Residue "g ARG 63": "NH1" <-> "NH2" Residue "g ARG 74": "NH1" <-> "NH2" Residue "g GLU 133": "OE1" <-> "OE2" Residue "g GLU 142": "OE1" <-> "OE2" Residue "g GLU 175": "OE1" <-> "OE2" Residue "g ARG 208": "NH1" <-> "NH2" Residue "g ARG 225": "NH1" <-> "NH2" Residue "h ARG 54": "NH1" <-> "NH2" Residue "h ARG 72": "NH1" <-> "NH2" Residue "h ARG 88": "NH1" <-> "NH2" Residue "h ARG 127": "NH1" <-> "NH2" Residue "h ARG 131": "NH1" <-> "NH2" Residue "h ARG 132": "NH1" <-> "NH2" Residue "h GLU 152": "OE1" <-> "OE2" Residue "h GLU 161": "OE1" <-> "OE2" Residue "h ARG 164": "NH1" <-> "NH2" Residue "h GLU 188": "OE1" <-> "OE2" Residue "i GLU 15": "OE1" <-> "OE2" Residue "i ASP 29": "OD1" <-> "OD2" Residue "i GLU 69": "OE1" <-> "OE2" Residue "i ARG 73": "NH1" <-> "NH2" Residue "i ARG 81": "NH1" <-> "NH2" Residue "i GLU 88": "OE1" <-> "OE2" Residue "i GLU 147": "OE1" <-> "OE2" Residue "i GLU 160": "OE1" <-> "OE2" Residue "i GLU 172": "OE1" <-> "OE2" Residue "i GLU 202": "OE1" <-> "OE2" Residue "j ARG 45": "NH1" <-> "NH2" Residue "j ARG 68": "NH1" <-> "NH2" Residue "j ARG 69": "NH1" <-> "NH2" Residue "j ARG 93": "NH1" <-> "NH2" Residue "j ARG 157": "NH1" <-> "NH2" Residue "j GLU 163": "OE1" <-> "OE2" Residue "k GLU 23": "OE1" <-> "OE2" Residue "k GLU 33": "OE1" <-> "OE2" Residue "k ARG 45": "NH1" <-> "NH2" Residue "k ARG 79": "NH1" <-> "NH2" Residue "l ARG 4": "NH1" <-> "NH2" Residue "l ARG 53": "NH1" <-> "NH2" Residue "l GLU 60": "OE1" <-> "OE2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l ARG 79": "NH1" <-> "NH2" Residue "l ARG 92": "NH1" <-> "NH2" Residue "m GLU 42": "OE1" <-> "OE2" Residue "m GLU 43": "OE1" <-> "OE2" Residue "m GLU 58": "OE1" <-> "OE2" Residue "m GLU 124": "OE1" <-> "OE2" Residue "n ARG 11": "NH1" <-> "NH2" Residue "n ARG 41": "NH1" <-> "NH2" Residue "n GLU 89": "OE1" <-> "OE2" Residue "n ARG 130": "NH1" <-> "NH2" Residue "o ARG 5": "NH1" <-> "NH2" Residue "o GLU 27": "OE1" <-> "OE2" Residue "o ARG 45": "NH1" <-> "NH2" Residue "o GLU 66": "OE1" <-> "OE2" Residue "o ARG 89": "NH1" <-> "NH2" Residue "p ARG 37": "NH1" <-> "NH2" Residue "p GLU 68": "OE1" <-> "OE2" Residue "p ARG 69": "NH1" <-> "NH2" Residue "p ARG 93": "NH1" <-> "NH2" Residue "p ARG 106": "NH1" <-> "NH2" Residue "q ARG 9": "NH1" <-> "NH2" Residue "q ARG 14": "NH1" <-> "NH2" Residue "q GLU 25": "OE1" <-> "OE2" Residue "q ARG 50": "NH1" <-> "NH2" Residue "q ARG 83": "NH1" <-> "NH2" Residue "r ARG 29": "NH1" <-> "NH2" Residue "r GLU 50": "OE1" <-> "OE2" Residue "r ARG 70": "NH1" <-> "NH2" Residue "r ARG 87": "NH1" <-> "NH2" Residue "r ARG 109": "NH1" <-> "NH2" Residue "s GLU 26": "OE1" <-> "OE2" Residue "s ARG 59": "NH1" <-> "NH2" Residue "s ARG 63": "NH1" <-> "NH2" Residue "s ARG 65": "NH1" <-> "NH2" Residue "s ARG 69": "NH1" <-> "NH2" Residue "s ARG 85": "NH1" <-> "NH2" Residue "t GLU 6": "OE1" <-> "OE2" Residue "t ARG 72": "NH1" <-> "NH2" Residue "t ARG 89": "NH1" <-> "NH2" Residue "u PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 28": "NH1" <-> "NH2" Residue "u ARG 51": "NH1" <-> "NH2" Residue "v ARG 11": "NH1" <-> "NH2" Residue "v ARG 27": "NH1" <-> "NH2" Residue "v GLU 60": "OE1" <-> "OE2" Residue "v ARG 65": "NH1" <-> "NH2" Residue "v ARG 77": "NH1" <-> "NH2" Residue "v GLU 80": "OE1" <-> "OE2" Residue "w ARG 61": "NH1" <-> "NH2" Residue "x ARG 32": "NH1" <-> "NH2" Residue "y GLU 15": "OE1" <-> "OE2" Residue "y GLU 53": "OE1" <-> "OE2" Residue "y ARG 60": "NH1" <-> "NH2" Residue "y ARG 74": "NH1" <-> "NH2" Residue "z ARG 33": "NH1" <-> "NH2" Residue "z GLU 36": "OE1" <-> "OE2" Residue "z GLU 44": "OE1" <-> "OE2" Residue "z ARG 45": "NH1" <-> "NH2" Residue "z ARG 55": "NH1" <-> "NH2" Residue "z ARG 62": "NH1" <-> "NH2" Residue "z ARG 67": "NH1" <-> "NH2" Residue "z ARG 69": "NH1" <-> "NH2" Residue "5 ARG 45": "NH1" <-> "NH2" Residue "5 ARG 59": "NH1" <-> "NH2" Residue "5 ARG 86": "NH1" <-> "NH2" Residue "5 ARG 88": "NH1" <-> "NH2" Residue "5 GLU 107": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 155169 Number of models: 1 Model: "" Number of chains: 70 Chain: "1" Number of atoms: 62336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62336 Classifications: {'RNA': 2903} Modifications used: {'rna2p': 6, 'rna2p_pur': 288, 'rna2p_pyr': 169, 'rna3p': 16, 'rna3p_pur': 1379, 'rna3p_pyr': 1045} Link IDs: {'rna2p': 462, 'rna3p': 2440} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 9 Chain: "2" Number of atoms: 32929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1534, 32929 Classifications: {'RNA': 1534} Modifications used: {'rna2p': 2, 'rna2p_pur': 117, 'rna2p_pyr': 89, 'rna3p': 9, 'rna3p_pur': 752, 'rna3p_pyr': 564} Link IDs: {'rna2p': 207, 'rna3p': 1326} Chain breaks: 3 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2569 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 8, 'rna3p_pur': 56, 'rna3p_pyr': 48} Link IDs: {'rna2p': 15, 'rna3p': 104} Chain: "6" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 115 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "7" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1621 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 32, 'rna3p_pyr': 31} Link IDs: {'rna2p': 13, 'rna3p': 62} Chain: "B" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "C" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1551 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 200} Chain: "D" 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: "E" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1411 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "F" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1313 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain: "G" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1101 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 3, 'TRANS': 144} Chain: "H" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 980 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "I" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 984 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 9, 'TRANS': 125} 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: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "L" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1043 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "M" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1065 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain: "N" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 951 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "O" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 884 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "P" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 908 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} 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: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 810 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'TRANS': 100} Chain: "S" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 845 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 2, 'TRANS': 106} Chain: "T" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 746 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain: "U" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 774 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "V" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 747 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain: "W" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 572 Classifications: {'peptide': 75} 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: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "Z" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 434 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "a" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "b" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 434 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "c" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 417 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "d" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 367 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "e" 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: "f" 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: "g" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1760 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "h" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1636 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "i" 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: "j" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "k" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 848 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "l" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1191 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 5, 'TRANS': 146} Chain: "m" 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: "n" 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: "o" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 790 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "p" 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: "q" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 951 Classifications: {'peptide': 122} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 114} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'0TD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 900 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "s" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "t" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 708 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'TRANS': 86} Chain: "u" 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: "v" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 649 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "w" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 544 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "x" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 663 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "y" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 664 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "z" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "5" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 940 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "4" Number of atoms: 7758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 7758 Classifications: {'RNA': 363} Modifications used: {'rna2p_pur': 36, 'rna2p_pyr': 17, 'rna3p_pur': 162, 'rna3p_pyr': 148} Link IDs: {'rna2p': 52, 'rna3p': 310} Chain: "1" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 292 Unusual residues: {' MG': 292} Classifications: {'undetermined': 292} Link IDs: {None: 291} Chain: "2" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 127 Unusual residues: {' MG': 127} Classifications: {'undetermined': 127} Link IDs: {None: 126} Chain: "3" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' MG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "7" 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} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Q" 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "s" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0J49 SG CYS a 40 148.174 199.634 45.716 1.00 68.35 S ATOM A0KOH SG CYS f 11 200.132 132.984 114.065 1.00 46.15 S ATOM A0KP6 SG CYS f 14 198.358 129.878 114.216 1.00 43.70 S ATOM A0KS1 SG CYS f 27 200.140 130.644 118.100 1.00 47.64 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="MG MG 13145 " occ=0.50 Time building chain proxies: 59.52, per 1000 atoms: 0.38 Number of scatterers: 155169 At special positions: 0 Unit cell: (263.35, 308.2, 272.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 159 16.00 P 4996 15.00 Mg 437 11.99 O 43162 8.00 N 28787 7.00 C 77626 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS a 18 " - pdb=" SG CYS a 37 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 64.56 Conformation dependent library (CDL) restraints added in 8.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN a 101 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 40 " pdb=" ZN f 102 " pdb="ZN ZN f 102 " - pdb=" ND1 HIS f 33 " pdb="ZN ZN f 102 " - pdb=" SG CYS f 14 " pdb="ZN ZN f 102 " - pdb=" SG CYS f 27 " pdb="ZN ZN f 102 " - pdb=" SG CYS f 11 " Number of angles added : 3 11966 Ramachandran restraints generated. 5983 Oldfield, 0 Emsley, 5983 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11198 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 38.3% alpha, 18.5% beta 1572 base pairs and 2635 stacking pairs defined. Time for finding SS restraints: 75.11 Creating SS restraints... Processing helix chain 'B' and resid 11 through 16 removed outlier: 7.386A pdb=" N HIS B 15 " --> pdb=" O PRO B 11 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL B 16 " --> pdb=" O GLY B 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 11 through 16' Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.663A pdb=" N LEU B 34 " --> pdb=" O PHE B 30 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLU B 35 " --> pdb=" O ALA B 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 30 through 35' Processing helix chain 'B' and resid 207 through 215 removed outlier: 3.867A pdb=" N ALA B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 226 removed outlier: 4.490A pdb=" N MET B 225 " --> pdb=" O ARG B 221 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ASN B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 221 through 226' Processing helix chain 'B' and resid 260 through 268 removed outlier: 4.132A pdb=" N ASP B 264 " --> pdb=" O ASN B 260 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N LYS B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N PHE B 266 " --> pdb=" O ARG B 262 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL B 268 " --> pdb=" O ASP B 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 260 through 268' Processing helix chain 'C' and resid 56 through 61 removed outlier: 5.695A pdb=" N THR C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 72 Processing helix chain 'C' and resid 97 through 102 removed outlier: 4.431A pdb=" N LEU C 100 " --> pdb=" O SER C 97 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE C 101 " --> pdb=" O VAL C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 126 removed outlier: 4.429A pdb=" N TRP C 125 " --> pdb=" O GLY C 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 41 removed outlier: 6.207A pdb=" N GLN D 41 " --> pdb=" O ALA D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 116 Processing helix chain 'D' and resid 130 through 142 Processing helix chain 'D' and resid 154 through 163 removed outlier: 4.922A pdb=" N ASN D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 183 Processing helix chain 'D' and resid 189 through 201 Processing helix chain 'D' and resid 16 through 21 Processing helix chain 'E' and resid 2 through 21 removed outlier: 3.713A pdb=" N VAL E 12 " --> pdb=" O TYR E 8 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N VAL E 13 " --> pdb=" O LYS E 9 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LYS E 14 " --> pdb=" O ASP E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 62 removed outlier: 3.957A pdb=" N ASP E 51 " --> pdb=" O LYS E 47 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 111 removed outlier: 5.702A pdb=" N VAL E 108 " --> pdb=" O ILE E 104 " (cutoff:3.500A) Proline residue: E 109 - end of helix Processing helix chain 'E' and resid 142 through 147 removed outlier: 6.202A pdb=" N ASP E 147 " --> pdb=" O TYR E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 174 removed outlier: 3.784A pdb=" N GLY E 166 " --> pdb=" O SER E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 45 removed outlier: 4.275A pdb=" N ALA E 43 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE E 44 " --> pdb=" O GLY E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 139 removed outlier: 3.820A pdb=" N ILE E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE E 138 " --> pdb=" O GLN E 135 " (cutoff:3.500A) Proline residue: E 139 - end of helix No H-bonds generated for 'chain 'E' and resid 134 through 139' Processing helix chain 'F' and resid 2 through 8 removed outlier: 4.421A pdb=" N ALA F 7 " --> pdb=" O ARG F 3 " (cutoff:3.500A) Proline residue: F 8 - end of helix Processing helix chain 'F' and resid 60 through 81 removed outlier: 4.183A pdb=" N GLN F 64 " --> pdb=" O ASP F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 153 removed outlier: 3.866A pdb=" N ARG F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 29 Processing helix chain 'G' and resid 40 through 50 Processing helix chain 'G' and resid 51 through 74 removed outlier: 4.215A pdb=" N ALA G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LYS G 57 " --> pdb=" O GLU G 53 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ALA G 74 " --> pdb=" O GLU G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 107 Processing helix chain 'H' and resid 3 through 21 Processing helix chain 'H' and resid 33 through 48 removed outlier: 3.629A pdb=" N ALA H 44 " --> pdb=" O GLU H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 68 removed outlier: 4.522A pdb=" N VAL H 64 " --> pdb=" O LEU H 60 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU H 65 " --> pdb=" O ARG H 61 " (cutoff:3.500A) Proline residue: H 68 - end of helix Processing helix chain 'H' and resid 74 through 79 removed outlier: 4.413A pdb=" N GLY H 78 " --> pdb=" O ASP H 74 " (cutoff:3.500A) Proline residue: H 79 - end of helix No H-bonds generated for 'chain 'H' and resid 74 through 79' Processing helix chain 'H' and resid 93 through 105 removed outlier: 4.300A pdb=" N LYS H 97 " --> pdb=" O ALA H 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 28 removed outlier: 4.659A pdb=" N LEU I 27 " --> pdb=" O VAL I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 49 removed outlier: 4.554A pdb=" N SER I 47 " --> pdb=" O ALA I 43 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE I 48 " --> pdb=" O LYS I 44 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N GLU I 49 " --> pdb=" O THR I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 84 Processing helix chain 'I' and resid 101 through 110 Processing helix chain 'I' and resid 120 through 136 removed outlier: 3.563A pdb=" N MET I 124 " --> pdb=" O ASP I 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 97 through 109 removed outlier: 4.960A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 123 removed outlier: 4.017A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N LYS J 123 " --> pdb=" O PHE J 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 119 Processing helix chain 'L' and resid 37 through 42 removed outlier: 4.085A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N SER L 42 " --> pdb=" O GLN L 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 37 through 42' Processing helix chain 'L' and resid 56 through 62 Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 4.581A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 68 through 75' Processing helix chain 'L' and resid 78 through 86 removed outlier: 3.956A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLU L 86 " --> pdb=" O LEU L 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 86' Processing helix chain 'L' and resid 91 through 99 Processing helix chain 'L' and resid 128 through 139 Processing helix chain 'M' and resid 42 through 58 Processing helix chain 'M' and resid 109 through 125 removed outlier: 4.537A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU M 124 " --> pdb=" O ALA M 120 " (cutoff:3.500A) Proline residue: M 125 - end of helix Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 38 through 57 removed outlier: 4.522A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 4.467A 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: 5.046A 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 3 through 22 removed outlier: 5.265A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG O 15 " --> pdb=" O ALA O 11 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 60 Processing helix chain 'O' and resid 67 through 86 Processing helix chain 'O' and resid 101 through 114 Processing helix chain 'P' and resid 2 through 13 removed outlier: 4.232A pdb=" N GLN P 12 " --> pdb=" O LEU P 8 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 104 removed outlier: 5.316A pdb=" N ARG P 101 " --> pdb=" O LEU P 97 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLU P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG P 103 " --> pdb=" O TYR P 99 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N THR P 104 " --> pdb=" O LEU P 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 97 through 104' Processing helix chain 'Q' and resid 6 through 22 removed outlier: 4.030A pdb=" N ALA Q 10 " --> pdb=" O ARG Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 4.534A pdb=" N ARG Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 32 through 37 removed outlier: 4.287A pdb=" N GLN Q 37 " --> pdb=" O ARG Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 39 through 73 removed outlier: 4.120A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 87 Processing helix chain 'Q' and resid 91 through 102 Processing helix chain 'Q' and resid 103 through 118 Processing helix chain 'S' and resid 13 through 25 removed outlier: 4.147A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 Processing helix chain 'S' and resid 41 through 61 removed outlier: 3.555A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 11 removed outlier: 4.472A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 27 removed outlier: 3.573A pdb=" N SER T 27 " --> pdb=" O ALA T 23 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 51 removed outlier: 3.858A pdb=" N PHE T 51 " --> pdb=" O VAL T 47 " (cutoff:3.500A) Processing helix chain 'U' and resid 66 through 71 removed outlier: 4.104A pdb=" N VAL U 70 " --> pdb=" O GLN U 66 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ALA U 71 " --> pdb=" O VAL U 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 66 through 71' Processing helix chain 'V' and resid 13 through 24 removed outlier: 3.797A pdb=" N SER V 17 " --> pdb=" O GLY V 13 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 54 removed outlier: 3.965A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LYS V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ALA V 54 " --> pdb=" O MET V 50 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 63 Processing helix chain 'X' and resid 64 through 75 Processing helix chain 'Y' and resid 2 through 9 removed outlier: 3.799A pdb=" N GLU Y 8 " --> pdb=" O LYS Y 4 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS Y 9 " --> pdb=" O GLU Y 5 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 35 removed outlier: 3.839A pdb=" N SER Y 34 " --> pdb=" O MET Y 30 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY Y 35 " --> pdb=" O GLN Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 63 removed outlier: 4.472A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N GLY Y 62 " --> pdb=" O ASN Y 58 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA Y 63 " --> pdb=" O GLU Y 59 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 28 Processing helix chain 'Z' and resid 41 through 52 Processing helix chain 'a' and resid 55 through 64 Processing helix chain 'b' and resid 9 through 21 removed outlier: 4.764A pdb=" N HIS b 19 " --> pdb=" O MET b 15 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASP b 20 " --> pdb=" O ARG b 16 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA b 21 " --> pdb=" O ARG b 17 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 16 Processing helix chain 'd' and resid 17 through 24 removed outlier: 4.709A pdb=" N THR d 24 " --> pdb=" O ALA d 20 " (cutoff:3.500A) Processing helix chain 'd' and resid 25 through 38 removed outlier: 3.796A pdb=" N GLN d 29 " --> pdb=" O LYS d 25 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL d 30 " --> pdb=" O ASN d 26 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA d 36 " --> pdb=" O ALA d 32 " (cutoff:3.500A) Processing helix chain 'e' and resid 7 through 14 Processing helix chain 'e' and resid 32 through 37 removed outlier: 4.988A pdb=" N LYS e 36 " --> pdb=" O ILE e 32 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ALA e 37 " --> pdb=" O LEU e 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 32 through 37' Processing helix chain 'e' and resid 38 through 46 Proline residue: e 46 - end of helix Processing helix chain 'e' and resid 52 through 63 removed outlier: 4.642A pdb=" N GLY e 56 " --> pdb=" O LYS e 52 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU e 57 " --> pdb=" O GLY e 53 " (cutoff:3.500A) Proline residue: e 63 - end of helix Processing helix chain 'g' and resid 5 through 13 Processing helix chain 'g' and resid 43 through 64 Proline residue: g 48 - end of helix removed outlier: 3.856A pdb=" N LYS g 64 " --> pdb=" O ILE g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 76 through 88 removed outlier: 3.867A pdb=" N CYS g 87 " --> pdb=" O ALA g 83 " (cutoff:3.500A) Processing helix chain 'g' and resid 103 through 122 removed outlier: 3.779A pdb=" N VAL g 107 " --> pdb=" O ASN g 103 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLN g 109 " --> pdb=" O LYS g 105 " (cutoff:3.500A) Processing helix chain 'g' and resid 130 through 148 Processing helix chain 'g' and resid 165 through 170 Processing helix chain 'g' and resid 171 through 180 Processing helix chain 'g' and resid 192 through 197 removed outlier: 4.640A pdb=" N VAL g 196 " --> pdb=" O ASP g 192 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ASP g 197 " --> pdb=" O PRO g 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 192 through 197' Processing helix chain 'g' and resid 206 through 227 Processing helix chain 'h' and resid 6 through 12 removed outlier: 4.182A pdb=" N ARG h 11 " --> pdb=" O PRO h 7 " (cutoff:3.500A) Processing helix chain 'h' and resid 25 through 48 removed outlier: 3.973A pdb=" N PHE h 29 " --> pdb=" O ASN h 25 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ALA h 30 " --> pdb=" O THR h 26 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ASP h 31 " --> pdb=" O LYS h 27 " (cutoff:3.500A) Processing helix chain 'h' and resid 72 through 78 removed outlier: 4.220A pdb=" N VAL h 76 " --> pdb=" O ARG h 72 " (cutoff:3.500A) Processing helix chain 'h' and resid 81 through 96 removed outlier: 4.319A pdb=" N GLU h 85 " --> pdb=" O GLY h 81 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL h 90 " --> pdb=" O LYS h 86 " (cutoff:3.500A) Processing helix chain 'h' and resid 112 through 127 removed outlier: 3.652A pdb=" N VAL h 116 " --> pdb=" O ASP h 112 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA h 117 " --> pdb=" O ALA h 113 " (cutoff:3.500A) Processing helix chain 'h' and resid 129 through 145 Processing helix chain 'i' and resid 7 through 16 removed outlier: 3.929A pdb=" N LEU i 11 " --> pdb=" O PRO i 7 " (cutoff:3.500A) Processing helix chain 'i' and resid 27 through 33 removed outlier: 5.017A pdb=" N LYS i 33 " --> pdb=" O ASP i 29 " (cutoff:3.500A) Processing helix chain 'i' and resid 49 through 66 Processing helix chain 'i' and resid 68 through 83 removed outlier: 5.462A pdb=" N LYS i 83 " --> pdb=" O ALA i 79 " (cutoff:3.500A) Processing helix chain 'i' and resid 85 through 97 Processing helix chain 'i' and resid 98 through 106 Processing helix chain 'i' and resid 110 through 121 removed outlier: 4.021A pdb=" N LYS i 121 " --> pdb=" O LEU i 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 146 through 151 removed outlier: 4.574A pdb=" N LYS i 151 " --> pdb=" O GLU i 147 " (cutoff:3.500A) Processing helix chain 'i' and resid 152 through 166 removed outlier: 3.859A pdb=" N LYS i 156 " --> pdb=" O GLN i 152 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLU i 166 " --> pdb=" O ALA i 162 " (cutoff:3.500A) Processing helix chain 'i' and resid 187 through 192 removed outlier: 4.336A pdb=" N LEU i 191 " --> pdb=" O GLU i 187 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N SER i 192 " --> pdb=" O ARG i 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 187 through 192' Processing helix chain 'i' and resid 196 through 206 removed outlier: 4.895A pdb=" N ILE i 200 " --> pdb=" O ASN i 196 " (cutoff:3.500A) Processing helix chain 'j' and resid 55 through 71 removed outlier: 4.698A pdb=" N ASN j 70 " --> pdb=" O LYS j 66 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N MET j 71 " --> pdb=" O ALA j 67 " (cutoff:3.500A) Processing helix chain 'j' and resid 109 through 119 removed outlier: 4.296A pdb=" N ALA j 113 " --> pdb=" O GLY j 109 " (cutoff:3.500A) Processing helix chain 'j' and resid 132 through 148 removed outlier: 5.846A pdb=" N ASN j 148 " --> pdb=" O LEU j 144 " (cutoff:3.500A) Processing helix chain 'j' and resid 149 through 158 Processing helix chain 'j' and resid 160 through 165 Processing helix chain 'k' and resid 14 through 33 removed outlier: 3.798A pdb=" N VAL k 18 " --> pdb=" O GLN k 14 " (cutoff:3.500A) Proline residue: k 19 - end of helix removed outlier: 4.565A pdb=" N ALA k 32 " --> pdb=" O ALA k 28 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLU k 33 " --> pdb=" O ILE k 29 " (cutoff:3.500A) Processing helix chain 'k' and resid 67 through 81 Processing helix chain 'l' and resid 20 through 32 removed outlier: 5.391A pdb=" N VAL l 32 " --> pdb=" O ASN l 28 " (cutoff:3.500A) Processing helix chain 'l' and resid 35 through 55 removed outlier: 3.975A pdb=" N ALA l 39 " --> pdb=" O LYS l 35 " (cutoff:3.500A) Processing helix chain 'l' and resid 57 through 70 removed outlier: 3.961A pdb=" N VAL l 69 " --> pdb=" O ALA l 65 " (cutoff:3.500A) Processing helix chain 'l' and resid 92 through 111 removed outlier: 4.919A pdb=" N ASN l 97 " --> pdb=" O PRO l 93 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA l 98 " --> pdb=" O VAL l 94 " (cutoff:3.500A) Processing helix chain 'l' and resid 115 through 130 Processing helix chain 'l' and resid 132 through 149 Processing helix chain 'm' and resid 5 through 21 Processing helix chain 'm' and resid 30 through 44 Processing helix chain 'm' and resid 112 through 120 Processing helix chain 'n' and resid 34 through 40 removed outlier: 5.320A pdb=" N GLY n 40 " --> pdb=" O GLU n 36 " (cutoff:3.500A) Processing helix chain 'n' and resid 41 through 50 Processing helix chain 'n' and resid 51 through 56 removed outlier: 4.750A pdb=" N ASP n 56 " --> pdb=" O LEU n 52 " (cutoff:3.500A) Processing helix chain 'n' and resid 71 through 92 removed outlier: 3.553A pdb=" N GLU n 92 " --> pdb=" O MET n 88 " (cutoff:3.500A) Processing helix chain 'n' and resid 94 through 102 Processing helix chain 'o' and resid 14 through 33 removed outlier: 3.604A pdb=" N THR o 32 " --> pdb=" O THR o 28 " (cutoff:3.500A) Processing helix chain 'o' and resid 82 through 90 Processing helix chain 'p' and resid 46 through 51 removed outlier: 4.702A pdb=" N GLY p 51 " --> pdb=" O ALA p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 59 through 75 removed outlier: 3.564A pdb=" N ALA p 63 " --> pdb=" O THR p 59 " (cutoff:3.500A) Processing helix chain 'p' and resid 93 through 104 removed outlier: 4.749A pdb=" N ILE p 97 " --> pdb=" O ARG p 93 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 10 Processing helix chain 'q' and resid 113 through 118 removed outlier: 3.795A pdb=" N TYR q 117 " --> pdb=" O ALA q 113 " (cutoff:3.500A) Processing helix chain 'r' and resid 14 through 22 removed outlier: 4.076A pdb=" N SER r 21 " --> pdb=" O ILE r 17 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ILE r 22 " --> pdb=" O ALA r 18 " (cutoff:3.500A) Processing helix chain 'r' and resid 26 through 38 Processing helix chain 'r' and resid 49 through 64 removed outlier: 3.842A pdb=" N PHE r 63 " --> pdb=" O GLU r 59 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N VAL r 64 " --> pdb=" O VAL r 60 " (cutoff:3.500A) Processing helix chain 'r' and resid 66 through 84 Processing helix chain 'r' and resid 85 through 94 Processing helix chain 'r' and resid 106 through 111 Processing helix chain 's' and resid 3 through 21 Processing helix chain 's' and resid 22 through 33 Processing helix chain 's' and resid 37 through 52 Proline residue: s 52 - end of helix Processing helix chain 's' and resid 80 through 91 Processing helix chain 't' and resid 4 through 16 Processing helix chain 't' and resid 24 through 47 removed outlier: 4.973A pdb=" N GLY t 41 " --> pdb=" O ASN t 37 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N HIS t 42 " --> pdb=" O HIS t 38 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU t 45 " --> pdb=" O GLY t 41 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N LYS t 47 " --> pdb=" O PHE t 43 " (cutoff:3.500A) Processing helix chain 't' and resid 50 through 74 removed outlier: 4.303A pdb=" N GLY t 55 " --> pdb=" O HIS t 51 " (cutoff:3.500A) Processing helix chain 't' and resid 75 through 86 Processing helix chain 'u' and resid 53 through 64 Processing helix chain 'u' and resid 68 through 82 Processing helix chain 'w' and resid 11 through 17 Processing helix chain 'w' and resid 25 through 34 removed outlier: 4.077A pdb=" N TYR w 32 " --> pdb=" O THR w 28 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N THR w 34 " --> pdb=" O LYS w 30 " (cutoff:3.500A) Processing helix chain 'w' and resid 41 through 46 Processing helix chain 'w' and resid 48 through 66 Processing helix chain 'x' and resid 12 through 26 Processing helix chain 'x' and resid 41 through 46 removed outlier: 3.862A pdb=" N ILE x 45 " --> pdb=" O PHE x 41 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLY x 46 " --> pdb=" O PRO x 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 41 through 46' Processing helix chain 'x' and resid 71 through 76 removed outlier: 4.624A pdb=" N ALA x 75 " --> pdb=" O LEU x 71 " (cutoff:3.500A) Proline residue: x 76 - end of helix No H-bonds generated for 'chain 'x' and resid 71 through 76' Processing helix chain 'y' and resid 4 through 41 removed outlier: 3.681A pdb=" N VAL y 35 " --> pdb=" O PHE y 31 " (cutoff:3.500A) Processing helix chain 'y' and resid 43 through 65 Proline residue: y 56 - end of helix Processing helix chain 'y' and resid 68 through 86 Processing helix chain 'z' and resid 11 through 27 Processing helix chain 'z' and resid 28 through 36 Processing helix chain 'z' and resid 40 through 65 removed outlier: 5.084A pdb=" N GLU z 63 " --> pdb=" O LYS z 59 " (cutoff:3.500A) Processing helix chain '5' and resid 17 through 22 removed outlier: 4.379A pdb=" N ARG 5 21 " --> pdb=" O ASN 5 17 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N HIS 5 22 " --> pdb=" O LYS 5 18 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 17 through 22' Processing helix chain '5' and resid 40 through 47 removed outlier: 4.617A pdb=" N ALA 5 46 " --> pdb=" O LYS 5 42 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLY 5 47 " --> pdb=" O SER 5 43 " (cutoff:3.500A) Processing helix chain '5' and resid 93 through 105 removed outlier: 3.897A pdb=" N ASP 5 98 " --> pdb=" O GLN 5 94 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TYR 5 101 " --> pdb=" O LEU 5 97 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'B' and resid 2 through 5 removed outlier: 4.058A pdb=" N VAL B 20 " --> pdb=" O ALA B 2 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B 4 " --> pdb=" O LYS B 18 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'B' and resid 80 through 83 removed outlier: 6.632A pdb=" N LEU B 93 " --> pdb=" O GLU B 79 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ILE B 74 " --> pdb=" O SER B 118 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N SER B 118 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ASP B 114 " --> pdb=" O VAL B 78 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'B' and resid 138 through 142 removed outlier: 4.187A pdb=" N SER B 139 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR B 173 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLU B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'B' and resid 91 through 97 removed outlier: 3.981A pdb=" N TYR B 96 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLU B 100 " --> pdb=" O TYR B 96 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'C' and resid 3 through 8 removed outlier: 4.299A pdb=" N SER C 199 " --> pdb=" O LYS C 8 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 10 through 16 removed outlier: 4.023A pdb=" N GLY C 10 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR C 16 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 32 through 35 removed outlier: 6.787A pdb=" N GLN C 49 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N TYR C 45 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU C 40 " --> pdb=" O TYR C 45 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN C 36 " --> pdb=" O GLN C 49 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'C' and resid 46 through 51 removed outlier: 5.727A pdb=" N ARG C 46 " --> pdb=" O LEU C 84 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'C' and resid 105 through 108 removed outlier: 6.345A pdb=" N LYS C 105 " --> pdb=" O VAL C 177 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'D' and resid 1 through 6 removed outlier: 5.275A pdb=" N SER D 10 " --> pdb=" O LEU D 5 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'D' and resid 117 through 120 removed outlier: 5.998A pdb=" N ARG D 117 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL D 146 " --> pdb=" O LYS D 166 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'E' and resid 65 through 69 removed outlier: 5.453A pdb=" N GLY E 39 " --> pdb=" O GLY E 151 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLY E 151 " --> pdb=" O GLY E 39 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'F' and resid 16 through 19 Processing sheet with id= 14, first strand: chain 'F' and resid 41 through 45 Processing sheet with id= 15, first strand: chain 'F' and resid 94 through 98 removed outlier: 4.340A pdb=" N VAL F 113 " --> pdb=" O LEU F 105 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'F' and resid 121 through 125 removed outlier: 5.943A pdb=" N THR F 129 " --> pdb=" O LEU F 89 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL F 90 " --> pdb=" O GLY F 161 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'G' and resid 17 through 21 removed outlier: 5.049A pdb=" N ASP G 17 " --> pdb=" O LEU G 5 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLN G 2 " --> pdb=" O ALA G 39 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LYS G 35 " --> pdb=" O LEU G 6 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'G' and resid 76 through 82 removed outlier: 5.769A pdb=" N GLU G 76 " --> pdb=" O LYS G 141 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE G 143 " --> pdb=" O GLU G 76 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA G 140 " --> pdb=" O PHE G 132 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL G 130 " --> pdb=" O VAL G 142 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER G 131 " --> pdb=" O ARG G 116 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG G 116 " --> pdb=" O SER G 131 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLU G 114 " --> pdb=" O GLN G 133 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'H' and resid 23 through 28 removed outlier: 3.754A pdb=" N LEU H 23 " --> pdb=" O GLU H 87 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'I' and resid 54 through 58 Processing sheet with id= 21, first strand: chain 'J' and resid 14 through 19 removed outlier: 3.545A pdb=" N TYR J 53 " --> pdb=" O ASP J 14 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'K' and resid 57 through 60 removed outlier: 6.826A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS K 84 " --> pdb=" O ASN K 9 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'L' and resid 120 through 123 removed outlier: 3.855A pdb=" N LYS L 141 " --> pdb=" O VAL L 120 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL L 122 " --> pdb=" O LYS L 141 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'M' and resid 62 through 65 removed outlier: 4.004A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS M 100 " --> pdb=" O ALA M 35 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'M' and resid 30 through 36 removed outlier: 8.215A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'N' and resid 33 through 37 removed outlier: 6.352A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS N 100 " --> pdb=" O MET N 110 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU N 114 " --> pdb=" O ARG N 96 " (cutoff:3.500A) removed outlier: 9.070A pdb=" N TYR N 94 " --> pdb=" O VAL N 116 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'O' and resid 49 through 53 removed outlier: 3.715A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE O 35 " --> pdb=" O THR O 53 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'P' and resid 38 through 45 removed outlier: 7.068A pdb=" N THR P 25 " --> pdb=" O LYS P 87 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'P' and resid 49 through 53 removed outlier: 4.015A pdb=" N ALA P 49 " --> pdb=" O THR P 60 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ARG P 53 " --> pdb=" O HIS P 56 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS P 56 " --> pdb=" O ARG P 53 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N SER P 57 " --> pdb=" O THR P 76 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'R' and resid 11 through 15 removed outlier: 7.114A pdb=" N LEU R 39 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE R 41 " --> pdb=" O LYS R 48 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASN R 43 " --> pdb=" O GLU R 46 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU R 46 " --> pdb=" O ASN R 43 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'R' and resid 18 through 23 removed outlier: 3.862A pdb=" N GLN R 18 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLU R 31 " --> pdb=" O VAL R 63 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'R' and resid 65 through 68 removed outlier: 3.619A pdb=" N ALA R 65 " --> pdb=" O ASP R 95 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'R' and resid 71 through 78 removed outlier: 4.228A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'S' and resid 2 through 8 removed outlier: 4.783A pdb=" N THR S 100 " --> pdb=" O GLY S 79 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS S 73 " --> pdb=" O VAL S 106 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'S' and resid 80 through 88 removed outlier: 4.655A pdb=" N THR S 100 " --> pdb=" O PRO S 80 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG S 92 " --> pdb=" O ARG S 88 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'T' and resid 12 through 15 removed outlier: 5.823A pdb=" N VAL T 31 " --> pdb=" O HIS T 15 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASN T 28 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'U' and resid 41 through 45 No H-bonds generated for sheet with id= 37 Processing sheet with id= 38, first strand: chain 'U' and resid 83 through 87 Processing sheet with id= 39, first strand: chain 'V' and resid 39 through 42 removed outlier: 6.112A pdb=" N ALA V 39 " --> pdb=" O ARG V 9 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE V 2 " --> pdb=" O VAL V 60 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'W' and resid 50 through 54 removed outlier: 8.067A pdb=" N ASN W 50 " --> pdb=" O LYS W 62 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS W 62 " --> pdb=" O ASN W 50 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N THR W 58 " --> pdb=" O GLY W 54 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'W' and resid 65 through 71 removed outlier: 3.757A pdb=" N LYS W 66 " --> pdb=" O GLU W 83 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'X' and resid 12 through 19 removed outlier: 4.967A pdb=" N ASN X 23 " --> pdb=" O SER X 19 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'X' and resid 35 through 41 removed outlier: 3.791A pdb=" N ARG X 45 " --> pdb=" O VAL X 40 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'Z' and resid 34 through 39 removed outlier: 4.639A pdb=" N HIS Z 34 " --> pdb=" O GLN Z 9 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N MET Z 54 " --> pdb=" O THR Z 10 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'a' and resid 20 through 25 removed outlier: 4.345A pdb=" N ASN a 20 " --> pdb=" O CYS a 16 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'c' and resid 19 through 24 removed outlier: 6.985A pdb=" N HIS c 19 " --> pdb=" O SER c 13 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE c 48 " --> pdb=" O SER c 14 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N LEU c 34 " --> pdb=" O GLU c 51 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'e' and resid 22 through 25 removed outlier: 5.883A pdb=" N PHE e 22 " --> pdb=" O VAL e 50 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'f' and resid 14 through 19 removed outlier: 4.705A pdb=" N ILE f 23 " --> pdb=" O GLN f 37 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'g' and resid 89 through 92 Processing sheet with id= 50, first strand: chain 'h' and resid 54 through 59 Processing sheet with id= 51, first strand: chain 'h' and resid 164 through 170 removed outlier: 6.355A pdb=" N ARG h 164 " --> pdb=" O GLY h 155 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ASP h 181 " --> pdb=" O LYS h 204 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'i' and resid 141 through 145 removed outlier: 3.686A pdb=" N ASP i 141 " --> pdb=" O PHE i 182 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N MET i 178 " --> pdb=" O ILE i 145 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU i 179 " --> pdb=" O ASP i 174 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'j' and resid 11 through 16 removed outlier: 6.862A pdb=" N LEU j 36 " --> pdb=" O ILE j 16 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'j' and resid 84 through 88 removed outlier: 3.561A pdb=" N ALA j 99 " --> pdb=" O ASN j 122 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASN j 122 " --> pdb=" O ALA j 99 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'j' and resid 32 through 41 removed outlier: 7.386A pdb=" N ARG j 45 " --> pdb=" O ASP j 41 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'k' and resid 38 through 42 removed outlier: 3.527A pdb=" N ARG k 38 " --> pdb=" O ASN k 63 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N TYR k 59 " --> pdb=" O TRP k 42 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N HIS k 3 " --> pdb=" O THR k 92 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG k 86 " --> pdb=" O MET k 9 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'k' and resid 43 through 47 removed outlier: 3.716A pdb=" N GLY k 43 " --> pdb=" O TYR k 59 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N HIS k 55 " --> pdb=" O LEU k 47 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'l' and resid 73 through 79 removed outlier: 5.861A pdb=" N TYR l 85 " --> pdb=" O ARG l 78 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'm' and resid 23 through 29 removed outlier: 6.448A pdb=" N ALA m 23 " --> pdb=" O LEU m 63 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP m 48 " --> pdb=" O THR m 62 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'm' and resid 74 through 77 removed outlier: 3.684A pdb=" N SER m 74 " --> pdb=" O ALA m 130 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN m 76 " --> pdb=" O TYR m 128 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N CYS m 127 " --> pdb=" O VAL m 103 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL m 103 " --> pdb=" O ILE m 126 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'n' and resid 5 through 11 removed outlier: 5.212A pdb=" N LYS n 27 " --> pdb=" O LEU n 61 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N VAL n 29 " --> pdb=" O LEU n 63 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'o' and resid 39 through 42 removed outlier: 5.067A pdb=" N LEU o 71 " --> pdb=" O LEU o 42 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG o 5 " --> pdb=" O GLY o 103 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'o' and resid 44 through 52 Processing sheet with id= 64, first strand: chain 'p' and resid 42 through 45 removed outlier: 3.707A pdb=" N ILE p 31 " --> pdb=" O HIS p 24 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'q' and resid 29 through 33 removed outlier: 5.486A pdb=" N LEU q 81 " --> pdb=" O VAL q 98 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N HIS q 96 " --> pdb=" O ARG q 83 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ARG q 94 " --> pdb=" O GLY q 85 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'q' and resid 36 through 41 removed outlier: 5.193A pdb=" N LYS q 51 " --> pdb=" O ILE q 67 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'u' and resid 1 through 11 removed outlier: 4.135A pdb=" N GLY u 37 " --> pdb=" O VAL u 19 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'v' and resid 7 through 11 removed outlier: 7.223A pdb=" N GLU v 60 " --> pdb=" O VAL v 76 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'v' and resid 19 through 26 No H-bonds generated for sheet with id= 69 Processing sheet with id= 70, first strand: chain 'x' and resid 30 through 33 removed outlier: 4.242A pdb=" N LEU x 47 " --> pdb=" O VAL x 62 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N GLN x 56 " --> pdb=" O ASN x 53 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain '5' and resid 56 through 59 removed outlier: 5.987A pdb=" N ARG 5 59 " --> pdb=" O GLU 5 62 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain '5' and resid 110 through 114 removed outlier: 5.005A pdb=" N THR 5 110 " --> pdb=" O ALA 5 130 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LYS 5 126 " --> pdb=" O LEU 5 114 " (cutoff:3.500A) 2014 hydrogen bonds defined for protein. 5985 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3973 hydrogen bonds 6340 hydrogen bond angles 0 basepair planarities 1572 basepair parallelities 2635 stacking parallelities Total time for adding SS restraints: 268.48 Time building geometry restraints manager: 69.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 12550 1.29 - 1.42: 75648 1.42 - 1.56: 69752 1.56 - 1.69: 9994 1.69 - 1.82: 282 Bond restraints: 168226 Sorted by residual: bond pdb=" C4 5MU 1 747 " pdb=" C5 5MU 1 747 " ideal model delta sigma weight residual 1.802 1.402 0.400 2.00e-02 2.50e+03 3.99e+02 bond pdb=" C4 5MU 11939 " pdb=" C5 5MU 11939 " ideal model delta sigma weight residual 1.802 1.414 0.388 2.00e-02 2.50e+03 3.77e+02 bond pdb=" N1 5MU 11939 " pdb=" C6 5MU 11939 " ideal model delta sigma weight residual 1.635 1.307 0.328 2.00e-02 2.50e+03 2.68e+02 bond pdb=" N1 5MU 1 747 " pdb=" C6 5MU 1 747 " ideal model delta sigma weight residual 1.635 1.311 0.324 2.00e-02 2.50e+03 2.62e+02 bond pdb=" C6 G7M 12069 " pdb=" O6 G7M 12069 " ideal model delta sigma weight residual 1.185 1.431 -0.246 2.00e-02 2.50e+03 1.52e+02 ... (remaining 168221 not shown) Histogram of bond angle deviations from ideal: 88.75 - 99.18: 31 99.18 - 109.62: 72024 109.62 - 120.05: 114882 120.05 - 130.48: 62734 130.48 - 140.91: 2204 Bond angle restraints: 251875 Sorted by residual: angle pdb=" O3' C 4 48 " pdb=" P C 4 49 " pdb=" O5' C 4 49 " ideal model delta sigma weight residual 104.00 120.14 -16.14 1.50e+00 4.44e-01 1.16e+02 angle pdb=" C4' U 4 9 " pdb=" C3' U 4 9 " pdb=" O3' U 4 9 " ideal model delta sigma weight residual 113.00 128.84 -15.84 1.50e+00 4.44e-01 1.11e+02 angle pdb=" C1' G7M 12069 " pdb=" N9 G7M 12069 " pdb=" C8 G7M 12069 " ideal model delta sigma weight residual 94.96 125.11 -30.15 3.00e+00 1.11e-01 1.01e+02 angle pdb=" C1' OMG 12251 " pdb=" N9 OMG 12251 " pdb=" C4 OMG 12251 " ideal model delta sigma weight residual 108.29 137.30 -29.01 3.00e+00 1.11e-01 9.35e+01 angle pdb=" O3' C 4 266 " pdb=" P G 4 267 " pdb=" O5' G 4 267 " ideal model delta sigma weight residual 104.00 118.44 -14.44 1.50e+00 4.44e-01 9.27e+01 ... (remaining 251870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 94196 36.00 - 72.00: 12054 72.00 - 107.99: 1289 107.99 - 143.99: 39 143.99 - 179.99: 71 Dihedral angle restraints: 107649 sinusoidal: 90293 harmonic: 17356 Sorted by residual: dihedral pdb=" C5* PSU 11911 " pdb=" C4* PSU 11911 " pdb=" C3* PSU 11911 " pdb=" O3* PSU 11911 " ideal model delta sinusoidal sigma weight residual 82.00 -86.98 168.98 1 8.00e+00 1.56e-02 2.97e+02 dihedral pdb=" C5* PSU 1 746 " pdb=" C4* PSU 1 746 " pdb=" C3* PSU 1 746 " pdb=" O3* PSU 1 746 " ideal model delta sinusoidal sigma weight residual 82.00 -110.42 -167.58 1 8.00e+00 1.56e-02 2.96e+02 dihedral pdb=" C5* PSU 11917 " pdb=" C4* PSU 11917 " pdb=" C3* PSU 11917 " pdb=" O3* PSU 11917 " ideal model delta sinusoidal sigma weight residual 82.00 -81.64 163.64 1 8.00e+00 1.56e-02 2.94e+02 ... (remaining 107646 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.085: 32124 1.085 - 2.170: 0 2.170 - 3.254: 0 3.254 - 4.339: 3 4.339 - 5.424: 32 Chirality restraints: 32159 Sorted by residual: chirality pdb=" C3' 6MZ 12030 " pdb=" C4' 6MZ 12030 " pdb=" O3' 6MZ 12030 " pdb=" C2' 6MZ 12030 " both_signs ideal model delta sigma weight residual False -2.74 2.68 -5.42 2.00e-01 2.50e+01 7.36e+02 chirality pdb=" C2' G7M 12069 " pdb=" C3' G7M 12069 " pdb=" O2' G7M 12069 " pdb=" C1' G7M 12069 " both_signs ideal model delta sigma weight residual False -2.75 2.67 -5.42 2.00e-01 2.50e+01 7.34e+02 chirality pdb=" C2' OMU 12552 " pdb=" C3' OMU 12552 " pdb=" O2' OMU 12552 " pdb=" C1' OMU 12552 " both_signs ideal model delta sigma weight residual False -2.75 2.66 -5.42 2.00e-01 2.50e+01 7.34e+02 ... (remaining 32156 not shown) Planarity restraints: 13346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC 12498 " 0.480 2.00e-02 2.50e+03 6.45e-01 9.36e+03 pdb=" C4' OMC 12498 " -0.231 2.00e-02 2.50e+03 pdb=" O4' OMC 12498 " 0.581 2.00e-02 2.50e+03 pdb=" C3' OMC 12498 " -0.785 2.00e-02 2.50e+03 pdb=" O3' OMC 12498 " -0.699 2.00e-02 2.50e+03 pdb=" C2' OMC 12498 " -0.042 2.00e-02 2.50e+03 pdb=" O2' OMC 12498 " 1.155 2.00e-02 2.50e+03 pdb=" C1' OMC 12498 " 0.307 2.00e-02 2.50e+03 pdb=" N1 OMC 12498 " -0.766 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MU 11939 " 0.504 2.00e-02 2.50e+03 6.21e-01 8.67e+03 pdb=" C4' 5MU 11939 " 0.629 2.00e-02 2.50e+03 pdb=" O4' 5MU 11939 " -0.164 2.00e-02 2.50e+03 pdb=" C3' 5MU 11939 " 0.128 2.00e-02 2.50e+03 pdb=" O3' 5MU 11939 " -1.109 2.00e-02 2.50e+03 pdb=" C2' 5MU 11939 " -0.117 2.00e-02 2.50e+03 pdb=" O2' 5MU 11939 " 1.023 2.00e-02 2.50e+03 pdb=" C1' 5MU 11939 " -0.652 2.00e-02 2.50e+03 pdb=" N1 5MU 11939 " -0.242 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 7MG 2 527 " 0.262 2.00e-02 2.50e+03 6.10e-01 8.37e+03 pdb=" C4' 7MG 2 527 " 0.650 2.00e-02 2.50e+03 pdb=" O4' 7MG 2 527 " 0.213 2.00e-02 2.50e+03 pdb=" C3' 7MG 2 527 " 0.002 2.00e-02 2.50e+03 pdb=" O3' 7MG 2 527 " -1.175 2.00e-02 2.50e+03 pdb=" C2' 7MG 2 527 " -0.149 2.00e-02 2.50e+03 pdb=" O2' 7MG 2 527 " 0.840 2.00e-02 2.50e+03 pdb=" C1' 7MG 2 527 " 0.177 2.00e-02 2.50e+03 pdb=" N9 7MG 2 527 " -0.820 2.00e-02 2.50e+03 ... (remaining 13343 not shown) Histogram of nonbonded interaction distances: 1.28 - 2.00: 8 2.00 - 2.73: 20199 2.73 - 3.45: 195963 3.45 - 4.18: 487911 4.18 - 4.90: 678454 Nonbonded interactions: 1382535 Sorted by model distance: nonbonded pdb="MG MG 21714 " pdb="MG MG 21715 " model vdw 1.280 1.300 nonbonded pdb="MG MG 13133 " pdb="MG MG 13150 " model vdw 1.295 1.300 nonbonded pdb="MG MG 13265 " pdb="MG MG 13272 " model vdw 1.335 1.300 nonbonded pdb="MG MG 21614 " pdb="MG MG 21632 " model vdw 1.643 1.300 nonbonded pdb="MG MG 13138 " pdb="MG MG 13281 " model vdw 1.926 1.300 ... (remaining 1382530 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=0.50 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: 3.700 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: 17.440 Check model and map are aligned: 1.670 Set scattering table: 1.120 Process input model: 601.060 Find NCS groups from input model: 3.160 Set up NCS constraints: 0.350 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 631.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 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 : 0.009 0.400 168226 Z= 0.559 Angle : 1.125 30.147 251875 Z= 0.563 Chirality : 0.170 5.424 32159 Planarity : 0.019 0.645 13346 Dihedral : 24.211 179.988 96448 Min Nonbonded Distance : 1.280 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.06 % Favored : 90.89 % Rotamer: Outliers : 0.79 % Allowed : 11.59 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.09 % 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: -4.18 (0.09), residues: 5983 helix: -2.52 (0.08), residues: 1999 sheet: -2.46 (0.14), residues: 1058 loop : -3.07 (0.09), residues: 2926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP g 23 HIS 0.011 0.002 HIS i 198 PHE 0.045 0.003 PHE H 106 TYR 0.024 0.003 TYR k 49 ARG 0.011 0.001 ARG Q 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11966 Ramachandran restraints generated. 5983 Oldfield, 0 Emsley, 5983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11966 Ramachandran restraints generated. 5983 Oldfield, 0 Emsley, 5983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1454 residues out of total 4954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 1415 time to evaluate : 6.591 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: B 146 MET cc_start: 0.7771 (ptm) cc_final: 0.7327 (ptm) REVERT: B 225 MET cc_start: 0.8927 (mtm) cc_final: 0.8713 (mtm) REVERT: D 77 ILE cc_start: 0.9390 (pt) cc_final: 0.9047 (pt) REVERT: E 18 THR cc_start: 0.8486 (m) cc_final: 0.7974 (p) REVERT: E 81 GLN cc_start: 0.8471 (tm-30) cc_final: 0.8104 (tm-30) REVERT: E 165 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7565 (mt-10) REVERT: I 16 MET cc_start: 0.4485 (ptm) cc_final: 0.4220 (ptm) REVERT: I 116 MET cc_start: 0.2081 (tpt) cc_final: 0.0602 (tpt) REVERT: J 2 LYS cc_start: 0.8200 (mtmt) cc_final: 0.7888 (pttp) REVERT: J 60 ASP cc_start: 0.8203 (p0) cc_final: 0.7853 (p0) REVERT: J 86 GLN cc_start: 0.8923 (tm-30) cc_final: 0.8530 (tm-30) REVERT: J 106 LYS cc_start: 0.8544 (tttm) cc_final: 0.8050 (ttmm) REVERT: J 108 MET cc_start: 0.8979 (mtt) cc_final: 0.8668 (mtt) REVERT: J 118 MET cc_start: 0.8552 (mtt) cc_final: 0.8324 (mtt) REVERT: J 128 ASN cc_start: 0.8158 (t0) cc_final: 0.7943 (t0) REVERT: K 12 ASP cc_start: 0.8379 (p0) cc_final: 0.8105 (p0) REVERT: K 73 ASP cc_start: 0.7965 (t0) cc_final: 0.7688 (t0) REVERT: L 123 ARG cc_start: 0.7512 (mtt-85) cc_final: 0.6689 (mtt-85) REVERT: M 82 MET cc_start: 0.8725 (mmp) cc_final: 0.8523 (mmt) REVERT: N 1 MET cc_start: 0.8585 (pmm) cc_final: 0.8271 (pmm) REVERT: N 35 LYS cc_start: 0.8417 (tttt) cc_final: 0.8183 (tttp) REVERT: Q 49 ASP cc_start: 0.7436 (m-30) cc_final: 0.7201 (m-30) REVERT: Q 89 GLU cc_start: 0.6182 (tp30) cc_final: 0.5768 (tp30) REVERT: R 43 ASN cc_start: 0.7215 (t0) cc_final: 0.6974 (m-40) REVERT: S 11 ARG cc_start: 0.8487 (tpt90) cc_final: 0.8090 (tpt-90) REVERT: S 52 GLU cc_start: 0.7447 (mt-10) cc_final: 0.6890 (mt-10) REVERT: U 17 LYS cc_start: 0.7981 (pttt) cc_final: 0.7656 (ttpt) REVERT: U 18 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.7521 (p0) REVERT: U 83 VAL cc_start: 0.9246 (OUTLIER) cc_final: 0.8970 (m) REVERT: U 87 PHE cc_start: 0.8132 (m-80) cc_final: 0.7723 (m-80) REVERT: V 1 MET cc_start: 0.5815 (ptt) cc_final: 0.5443 (ptp) REVERT: V 24 ASN cc_start: 0.7807 (t0) cc_final: 0.7555 (t0) REVERT: V 29 ILE cc_start: 0.9253 (tp) cc_final: 0.8967 (tp) REVERT: V 40 ILE cc_start: 0.9369 (pt) cc_final: 0.8969 (pt) REVERT: V 57 TYR cc_start: 0.7879 (m-80) cc_final: 0.7549 (m-80) REVERT: V 72 VAL cc_start: 0.9211 (p) cc_final: 0.9003 (t) REVERT: W 68 LYS cc_start: 0.8726 (ttpp) cc_final: 0.8089 (tptp) REVERT: c 32 GLU cc_start: 0.7851 (pm20) cc_final: 0.7543 (mm-30) REVERT: f 9 LYS cc_start: 0.8355 (mtpt) cc_final: 0.8155 (mtpt) REVERT: f 37 GLN cc_start: 0.8847 (tt0) cc_final: 0.8428 (tt0) REVERT: g 174 LYS cc_start: 0.7998 (tttm) cc_final: 0.7797 (ttpp) REVERT: h 25 ASN cc_start: 0.8255 (m-40) cc_final: 0.7946 (m-40) REVERT: h 37 PHE cc_start: 0.8137 (t80) cc_final: 0.7751 (t80) REVERT: h 86 LYS cc_start: 0.8392 (ttpt) cc_final: 0.7983 (tttm) REVERT: i 64 ILE cc_start: 0.9085 (mt) cc_final: 0.8760 (mt) REVERT: i 103 TYR cc_start: 0.8531 (t80) cc_final: 0.8299 (t80) REVERT: j 50 TYR cc_start: 0.8693 (t80) cc_final: 0.8395 (t80) REVERT: j 86 LYS cc_start: 0.8644 (mttt) cc_final: 0.8375 (mtpp) REVERT: j 106 ILE cc_start: 0.9192 (mm) cc_final: 0.8951 (mm) REVERT: k 1 MET cc_start: 0.6935 (mtm) cc_final: 0.6672 (mtt) REVERT: k 82 ASP cc_start: 0.8066 (t0) cc_final: 0.7770 (t0) REVERT: l 116 MET cc_start: 0.7771 (tpt) cc_final: 0.7560 (tpt) REVERT: m 30 SER cc_start: 0.9041 (p) cc_final: 0.8629 (p) REVERT: m 48 ASP cc_start: 0.6671 (t70) cc_final: 0.6347 (t0) REVERT: m 96 MET cc_start: 0.7428 (mmm) cc_final: 0.7144 (mmm) REVERT: n 58 VAL cc_start: 0.7635 (t) cc_final: 0.7329 (m) REVERT: n 92 GLU cc_start: 0.7152 (mp0) cc_final: 0.6882 (mp0) REVERT: n 115 LYS cc_start: 0.8988 (mppt) cc_final: 0.8738 (mptt) REVERT: o 87 LEU cc_start: 0.8539 (pp) cc_final: 0.8208 (pp) REVERT: p 64 GLN cc_start: 0.8306 (pt0) cc_final: 0.7979 (pt0) REVERT: p 109 ASN cc_start: 0.8323 (m110) cc_final: 0.8050 (m-40) REVERT: q 56 ARG cc_start: 0.8075 (ttm-80) cc_final: 0.7816 (ttp-110) REVERT: r 8 ASN cc_start: 0.8552 (t0) cc_final: 0.8335 (t0) REVERT: s 66 GLN cc_start: 0.7658 (mt0) cc_final: 0.7163 (mt0) REVERT: s 79 LEU cc_start: 0.9342 (mt) cc_final: 0.8791 (mt) REVERT: s 90 ARG cc_start: 0.7557 (ttt180) cc_final: 0.7218 (ttm110) REVERT: t 48 LYS cc_start: 0.7720 (mmtm) cc_final: 0.6887 (tttt) REVERT: u 40 ASN cc_start: 0.8642 (t0) cc_final: 0.8439 (t0) REVERT: u 56 ARG cc_start: 0.8069 (mmm160) cc_final: 0.7621 (mmp-170) REVERT: v 17 MET cc_start: 0.7575 (ptt) cc_final: 0.7295 (ptm) REVERT: w 66 SER cc_start: 0.9075 (t) cc_final: 0.8834 (t) REVERT: y 49 LYS cc_start: 0.7088 (tppt) cc_final: 0.6760 (mmtt) REVERT: y 54 MET cc_start: 0.8417 (tmm) cc_final: 0.8132 (tmm) REVERT: y 61 GLN cc_start: 0.8733 (mm-40) cc_final: 0.8358 (mp10) REVERT: y 78 ASN cc_start: 0.8364 (m-40) cc_final: 0.8162 (m-40) REVERT: y 84 ASN cc_start: 0.7173 (m-40) cc_final: 0.6824 (m110) REVERT: z 5 LYS cc_start: 0.7683 (mtpp) cc_final: 0.7338 (mtmt) outliers start: 39 outliers final: 16 residues processed: 1446 average time/residue: 1.4958 time to fit residues: 3701.1370 Evaluate side-chains 1093 residues out of total 4954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 1075 time to evaluate : 5.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain U residue 18 ASP Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain m residue 12 THR Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain u residue 19 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1083 random chunks: chunk 914 optimal weight: 4.9990 chunk 820 optimal weight: 5.9990 chunk 455 optimal weight: 20.0000 chunk 280 optimal weight: 10.0000 chunk 553 optimal weight: 0.5980 chunk 438 optimal weight: 10.0000 chunk 848 optimal weight: 6.9990 chunk 328 optimal weight: 10.0000 chunk 516 optimal weight: 1.9990 chunk 631 optimal weight: 3.9990 chunk 983 optimal weight: 9.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 ASN B 53 HIS B 58 HIS B 86 ASN C 32 ASN C 36 GLN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 GLN D 41 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN D 156 ASN D 163 ASN E 63 GLN ** F 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 88 GLN F 128 GLN G 33 GLN ** G 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 47 HIS J 128 ASN K 29 HIS K 90 ASN L 54 GLN M 13 HIS N 107 ASN O 29 HIS P 56 HIS Q 37 GLN R 6 GLN R 87 GLN R 91 GLN S 60 HIS S 102 HIS U 54 GLN U 69 ASN W 46 HIS W 57 HIS ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 9 GLN b 5 GLN d 6 GLN ** d 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 26 HIS f 37 GLN ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 94 HIS g 109 GLN h 32 ASN ** i 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 140 ASN j 70 ASN j 121 HIS ** j 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 11 HIS k 17 GLN m 67 GLN n 25 ASN n 75 GLN p 29 ASN ** p 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 109 ASN ** q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 75 GLN r 12 HIS r 105 ASN s 4 GLN u 79 ASN v 9 GLN v 45 HIS w 31 ASN ** w 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 64 ASN ** 5 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 168226 Z= 0.258 Angle : 0.726 14.122 251875 Z= 0.379 Chirality : 0.039 0.473 32159 Planarity : 0.006 0.128 13346 Dihedral : 24.258 179.905 84579 Min Nonbonded Distance : 1.045 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.52 % Favored : 93.46 % Rotamer: Outliers : 3.33 % Allowed : 19.90 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -2.88 (0.10), residues: 5983 helix: -0.69 (0.11), residues: 2024 sheet: -2.23 (0.14), residues: 1099 loop : -2.70 (0.10), residues: 2860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP h 201 HIS 0.009 0.001 HIS k 11 PHE 0.023 0.002 PHE g 90 TYR 0.023 0.002 TYR E 7 ARG 0.006 0.000 ARG v 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11966 Ramachandran restraints generated. 5983 Oldfield, 0 Emsley, 5983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11966 Ramachandran restraints generated. 5983 Oldfield, 0 Emsley, 5983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1314 residues out of total 4954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1149 time to evaluate : 6.740 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: B 79 GLU cc_start: 0.6733 (mt-10) cc_final: 0.6464 (tt0) REVERT: D 77 ILE cc_start: 0.9337 (pt) cc_final: 0.8971 (pt) REVERT: D 200 LEU cc_start: 0.6935 (OUTLIER) cc_final: 0.6405 (mt) REVERT: E 18 THR cc_start: 0.8235 (m) cc_final: 0.7853 (p) REVERT: E 81 GLN cc_start: 0.8484 (tm-30) cc_final: 0.8075 (tm-30) REVERT: E 85 ILE cc_start: 0.8389 (mt) cc_final: 0.8188 (mm) REVERT: E 96 MET cc_start: 0.8488 (tmm) cc_final: 0.8288 (tmm) REVERT: E 128 TYR cc_start: 0.8376 (t80) cc_final: 0.7949 (t80) REVERT: E 130 MET cc_start: 0.6772 (ptt) cc_final: 0.6425 (ptt) REVERT: F 73 ASN cc_start: 0.8998 (t0) cc_final: 0.8794 (t0) REVERT: G 2 GLN cc_start: 0.7310 (mm110) cc_final: 0.6325 (mt0) REVERT: I 16 MET cc_start: 0.4532 (ptm) cc_final: 0.4278 (ptm) REVERT: I 35 MET cc_start: 0.5970 (pmm) cc_final: 0.5259 (ptp) REVERT: I 116 MET cc_start: 0.1777 (tpt) cc_final: 0.0423 (tpt) REVERT: J 2 LYS cc_start: 0.8209 (mtmt) cc_final: 0.7847 (pttp) REVERT: J 60 ASP cc_start: 0.8238 (p0) cc_final: 0.7599 (p0) REVERT: J 106 LYS cc_start: 0.8557 (tttm) cc_final: 0.8010 (ttmm) REVERT: K 12 ASP cc_start: 0.8271 (p0) cc_final: 0.8012 (p0) REVERT: K 92 GLU cc_start: 0.7462 (tm-30) cc_final: 0.7256 (tm-30) REVERT: L 106 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7399 (mm-30) REVERT: L 123 ARG cc_start: 0.7097 (mtt-85) cc_final: 0.6808 (mtt-85) REVERT: M 13 HIS cc_start: 0.8964 (OUTLIER) cc_final: 0.8561 (m170) REVERT: M 82 MET cc_start: 0.8581 (mmp) cc_final: 0.8332 (mmt) REVERT: N 1 MET cc_start: 0.8522 (pmm) cc_final: 0.8261 (pmm) REVERT: O 64 TYR cc_start: 0.6261 (t80) cc_final: 0.5958 (t80) REVERT: Q 89 GLU cc_start: 0.6231 (tp30) cc_final: 0.5663 (tp30) REVERT: R 43 ASN cc_start: 0.7178 (t0) cc_final: 0.6833 (m-40) REVERT: S 11 ARG cc_start: 0.8397 (tpt90) cc_final: 0.7951 (tpt-90) REVERT: T 1 MET cc_start: 0.6904 (tpt) cc_final: 0.6565 (tpt) REVERT: U 17 LYS cc_start: 0.8070 (pttt) cc_final: 0.7827 (ttpt) REVERT: U 37 GLU cc_start: 0.7485 (tm-30) cc_final: 0.7268 (tm-30) REVERT: U 83 VAL cc_start: 0.9267 (OUTLIER) cc_final: 0.8980 (m) REVERT: V 1 MET cc_start: 0.6056 (ptt) cc_final: 0.5681 (ptp) REVERT: V 24 ASN cc_start: 0.7843 (t0) cc_final: 0.7623 (t0) REVERT: V 40 ILE cc_start: 0.9144 (pt) cc_final: 0.8814 (pt) REVERT: W 68 LYS cc_start: 0.8883 (ttpp) cc_final: 0.8544 (tttt) REVERT: X 54 LYS cc_start: 0.8428 (ttpt) cc_final: 0.8132 (ttpt) REVERT: Y 59 GLU cc_start: 0.6451 (OUTLIER) cc_final: 0.6135 (mt-10) REVERT: c 32 GLU cc_start: 0.7743 (pm20) cc_final: 0.7462 (mm-30) REVERT: f 8 LYS cc_start: 0.8214 (tppp) cc_final: 0.8013 (tttp) REVERT: g 9 MET cc_start: 0.7675 (mtt) cc_final: 0.7468 (mtp) REVERT: h 42 TYR cc_start: 0.8385 (t80) cc_final: 0.8123 (t80) REVERT: h 86 LYS cc_start: 0.8376 (ttpt) cc_final: 0.7947 (tttm) REVERT: i 64 ILE cc_start: 0.9084 (mt) cc_final: 0.8751 (mt) REVERT: j 50 TYR cc_start: 0.8651 (t80) cc_final: 0.8298 (t80) REVERT: j 86 LYS cc_start: 0.8663 (mttt) cc_final: 0.8305 (mtpp) REVERT: j 106 ILE cc_start: 0.9126 (mm) cc_final: 0.8893 (mm) REVERT: k 1 MET cc_start: 0.7025 (mtm) cc_final: 0.6180 (mtt) REVERT: k 14 GLN cc_start: 0.8162 (mm-40) cc_final: 0.7820 (mp10) REVERT: k 54 LEU cc_start: 0.8038 (tp) cc_final: 0.7733 (mt) REVERT: k 82 ASP cc_start: 0.7750 (t0) cc_final: 0.7452 (t0) REVERT: l 101 MET cc_start: 0.8521 (mtm) cc_final: 0.8157 (mtm) REVERT: l 116 MET cc_start: 0.7801 (tpt) cc_final: 0.7535 (tpt) REVERT: m 30 SER cc_start: 0.8977 (p) cc_final: 0.8545 (p) REVERT: m 48 ASP cc_start: 0.6759 (t70) cc_final: 0.6444 (t0) REVERT: m 96 MET cc_start: 0.7400 (mmm) cc_final: 0.7132 (mmm) REVERT: n 58 VAL cc_start: 0.7995 (t) cc_final: 0.7771 (m) REVERT: n 94 LEU cc_start: 0.8440 (mt) cc_final: 0.7973 (mt) REVERT: p 56 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.7246 (mtm180) REVERT: p 61 PHE cc_start: 0.8501 (t80) cc_final: 0.8253 (t80) REVERT: p 64 GLN cc_start: 0.8342 (pt0) cc_final: 0.7987 (pt0) REVERT: q 29 GLN cc_start: 0.9195 (mp10) cc_final: 0.8991 (mp10) REVERT: r 8 ASN cc_start: 0.8558 (t0) cc_final: 0.8326 (t0) REVERT: s 31 ILE cc_start: 0.8358 (mt) cc_final: 0.8120 (tt) REVERT: s 90 ARG cc_start: 0.7414 (ttt180) cc_final: 0.7062 (ttm110) REVERT: s 92 GLU cc_start: 0.8119 (tt0) cc_final: 0.7636 (tt0) REVERT: t 11 ILE cc_start: 0.8313 (mm) cc_final: 0.8021 (mm) REVERT: t 45 GLU cc_start: 0.7525 (tm-30) cc_final: 0.7317 (tm-30) REVERT: t 48 LYS cc_start: 0.7640 (mmtm) cc_final: 0.6785 (tttt) REVERT: u 40 ASN cc_start: 0.8529 (t0) cc_final: 0.8299 (t0) REVERT: v 17 MET cc_start: 0.7490 (ptt) cc_final: 0.7232 (ptm) REVERT: w 66 SER cc_start: 0.9000 (t) cc_final: 0.8748 (t) REVERT: y 84 ASN cc_start: 0.7258 (m-40) cc_final: 0.6998 (m110) REVERT: z 5 LYS cc_start: 0.7544 (mtpp) cc_final: 0.7182 (mtmt) outliers start: 165 outliers final: 114 residues processed: 1246 average time/residue: 1.3529 time to fit residues: 2930.5337 Evaluate side-chains 1166 residues out of total 4954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 1047 time to evaluate : 5.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 84 TYR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain P residue 7 GLN Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 110 VAL Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 92 ASN Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain W residue 35 SER Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 59 GLU Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain b residue 6 ASN Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain c residue 29 THR Chi-restraints excluded: chain c residue 35 GLU Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain g residue 82 ASP Chi-restraints excluded: chain g residue 168 HIS Chi-restraints excluded: chain h residue 10 ILE Chi-restraints excluded: chain h residue 20 SER Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 44 THR Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain k residue 13 ASP Chi-restraints excluded: chain k residue 70 VAL Chi-restraints excluded: chain k residue 71 ILE Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain m residue 12 THR Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 80 ARG Chi-restraints excluded: chain m residue 106 THR Chi-restraints excluded: chain m residue 111 MET Chi-restraints excluded: chain m residue 125 ILE Chi-restraints excluded: chain n residue 105 THR Chi-restraints excluded: chain o residue 26 VAL Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 31 ILE Chi-restraints excluded: chain p residue 56 ARG Chi-restraints excluded: chain p residue 96 THR Chi-restraints excluded: chain p residue 111 THR Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 107 VAL Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 20 THR Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain s residue 67 THR Chi-restraints excluded: chain s residue 80 SER Chi-restraints excluded: chain s residue 82 ILE Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain v residue 22 VAL Chi-restraints excluded: chain v residue 53 CYS Chi-restraints excluded: chain w residue 11 CYS Chi-restraints excluded: chain w residue 25 ASP Chi-restraints excluded: chain w residue 70 TYR Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 11 ILE Chi-restraints excluded: chain x residue 12 ASP Chi-restraints excluded: chain x residue 47 LEU Chi-restraints excluded: chain y residue 35 VAL Chi-restraints excluded: chain y residue 86 LEU Chi-restraints excluded: chain z residue 53 VAL Chi-restraints excluded: chain 5 residue 111 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1083 random chunks: chunk 546 optimal weight: 10.0000 chunk 305 optimal weight: 10.0000 chunk 818 optimal weight: 9.9990 chunk 669 optimal weight: 10.0000 chunk 271 optimal weight: 8.9990 chunk 985 optimal weight: 10.0000 chunk 1064 optimal weight: 30.0000 chunk 877 optimal weight: 3.9990 chunk 977 optimal weight: 0.9990 chunk 335 optimal weight: 10.0000 chunk 790 optimal weight: 2.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 HIS C 130 GLN C 164 GLN D 136 GLN D 156 ASN ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN ** G 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 10 GLN P 41 GLN T 15 HIS ** T 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 5 ASN V 75 GLN Y 15 ASN Y 20 ASN ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 37 GLN ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 58 ASN ** g 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 109 GLN h 32 ASN ** i 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 131 ASN ** j 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 11 HIS k 17 GLN n 75 GLN p 38 GLN ** p 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 29 ASN u 79 ASN ** v 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 168226 Z= 0.365 Angle : 0.771 14.066 251875 Z= 0.397 Chirality : 0.041 0.478 32159 Planarity : 0.007 0.134 13346 Dihedral : 24.172 179.961 84576 Min Nonbonded Distance : 1.058 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.77 % Favored : 91.21 % Rotamer: Outliers : 5.17 % Allowed : 23.29 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -2.43 (0.10), residues: 5983 helix: -0.13 (0.11), residues: 2022 sheet: -2.07 (0.15), residues: 1086 loop : -2.56 (0.11), residues: 2875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 64 HIS 0.014 0.001 HIS M 13 PHE 0.026 0.002 PHE z 12 TYR 0.024 0.002 TYR E 7 ARG 0.007 0.001 ARG n 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11966 Ramachandran restraints generated. 5983 Oldfield, 0 Emsley, 5983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11966 Ramachandran restraints generated. 5983 Oldfield, 0 Emsley, 5983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1369 residues out of total 4954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 256 poor density : 1113 time to evaluate : 6.609 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: B 79 GLU cc_start: 0.6762 (mt-10) cc_final: 0.6550 (tt0) REVERT: B 130 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8151 (pp) REVERT: B 205 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8603 (mt) REVERT: D 163 ASN cc_start: 0.8518 (t0) cc_final: 0.8261 (m-40) REVERT: E 16 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8199 (mm) REVERT: E 17 MET cc_start: 0.7960 (ttm) cc_final: 0.7755 (tpp) REVERT: E 18 THR cc_start: 0.8133 (m) cc_final: 0.7823 (p) REVERT: E 81 GLN cc_start: 0.8477 (tm-30) cc_final: 0.8115 (tm-30) REVERT: E 96 MET cc_start: 0.8552 (tmm) cc_final: 0.7912 (tmm) REVERT: E 98 GLU cc_start: 0.6875 (tm-30) cc_final: 0.6552 (tm-30) REVERT: E 128 TYR cc_start: 0.8419 (t80) cc_final: 0.7735 (t80) REVERT: E 130 MET cc_start: 0.6917 (ptt) cc_final: 0.6614 (ptt) REVERT: G 2 GLN cc_start: 0.7496 (mm110) cc_final: 0.6294 (mt0) REVERT: G 91 PHE cc_start: 0.6620 (OUTLIER) cc_final: 0.6399 (m-80) REVERT: H 73 LYS cc_start: 0.6495 (mptt) cc_final: 0.6196 (mptt) REVERT: H 122 GLN cc_start: 0.2192 (OUTLIER) cc_final: 0.1433 (pt0) REVERT: I 35 MET cc_start: 0.6031 (pmm) cc_final: 0.5407 (ptp) REVERT: I 116 MET cc_start: 0.2128 (tpt) cc_final: 0.0534 (tpt) REVERT: J 2 LYS cc_start: 0.8202 (mtmt) cc_final: 0.7851 (pttp) REVERT: J 60 ASP cc_start: 0.8251 (p0) cc_final: 0.7693 (p0) REVERT: J 106 LYS cc_start: 0.8603 (tttm) cc_final: 0.8051 (ttmm) REVERT: J 136 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7718 (mt0) REVERT: K 12 ASP cc_start: 0.8218 (p0) cc_final: 0.7983 (p0) REVERT: K 92 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7169 (tm-30) REVERT: M 82 MET cc_start: 0.8425 (mmp) cc_final: 0.8129 (mmt) REVERT: N 1 MET cc_start: 0.8568 (pmm) cc_final: 0.8288 (pmm) REVERT: O 64 TYR cc_start: 0.6544 (t80) cc_final: 0.6306 (t80) REVERT: O 115 LEU cc_start: 0.8828 (mt) cc_final: 0.8561 (tt) REVERT: P 9 GLU cc_start: 0.6908 (tm-30) cc_final: 0.6648 (tt0) REVERT: Q 49 ASP cc_start: 0.7493 (m-30) cc_final: 0.7217 (m-30) REVERT: Q 89 GLU cc_start: 0.6473 (tp30) cc_final: 0.6063 (tp30) REVERT: R 43 ASN cc_start: 0.7361 (t0) cc_final: 0.7007 (m-40) REVERT: S 11 ARG cc_start: 0.8534 (tpt90) cc_final: 0.8133 (tpt-90) REVERT: T 69 ARG cc_start: 0.7540 (ttp-110) cc_final: 0.7317 (ttm110) REVERT: U 5 ILE cc_start: 0.9347 (mm) cc_final: 0.9145 (mm) REVERT: U 17 LYS cc_start: 0.8193 (pttt) cc_final: 0.7646 (ttpt) REVERT: U 18 ASP cc_start: 0.8301 (p0) cc_final: 0.7352 (p0) REVERT: V 1 MET cc_start: 0.6222 (ptt) cc_final: 0.5960 (ptp) REVERT: V 24 ASN cc_start: 0.7714 (t0) cc_final: 0.7294 (t0) REVERT: V 29 ILE cc_start: 0.9300 (tp) cc_final: 0.9026 (tp) REVERT: V 40 ILE cc_start: 0.9125 (pt) cc_final: 0.8810 (pt) REVERT: W 56 ASP cc_start: 0.8624 (p0) cc_final: 0.8369 (p0) REVERT: W 68 LYS cc_start: 0.8981 (ttpp) cc_final: 0.8606 (tttt) REVERT: X 54 LYS cc_start: 0.8515 (ttpt) cc_final: 0.8214 (ttpt) REVERT: Y 24 GLU cc_start: 0.7347 (mm-30) cc_final: 0.7119 (mm-30) REVERT: Y 59 GLU cc_start: 0.6535 (OUTLIER) cc_final: 0.6181 (mt-10) REVERT: c 32 GLU cc_start: 0.7817 (pm20) cc_final: 0.7532 (mm-30) REVERT: h 42 TYR cc_start: 0.8412 (t80) cc_final: 0.8154 (t80) REVERT: h 86 LYS cc_start: 0.8404 (ttpt) cc_final: 0.7819 (tmtt) REVERT: i 64 ILE cc_start: 0.9092 (mt) cc_final: 0.8888 (mt) REVERT: i 103 TYR cc_start: 0.8612 (t80) cc_final: 0.8382 (t80) REVERT: i 131 ASN cc_start: 0.7724 (OUTLIER) cc_final: 0.7444 (t0) REVERT: j 86 LYS cc_start: 0.8714 (mttt) cc_final: 0.8459 (mtpp) REVERT: j 106 ILE cc_start: 0.9203 (mm) cc_final: 0.8979 (mm) REVERT: k 54 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7662 (mt) REVERT: k 102 MET cc_start: 0.7433 (ppp) cc_final: 0.6905 (ppp) REVERT: l 101 MET cc_start: 0.8645 (mtm) cc_final: 0.8274 (mtm) REVERT: l 116 MET cc_start: 0.7848 (tpt) cc_final: 0.7574 (tpt) REVERT: m 30 SER cc_start: 0.9203 (p) cc_final: 0.8772 (p) REVERT: m 118 GLN cc_start: 0.7629 (mt0) cc_final: 0.7425 (mt0) REVERT: n 58 VAL cc_start: 0.7936 (t) cc_final: 0.7658 (m) REVERT: n 64 TYR cc_start: 0.7592 (t80) cc_final: 0.7175 (t80) REVERT: n 94 LEU cc_start: 0.8131 (mt) cc_final: 0.7688 (mt) REVERT: n 95 ARG cc_start: 0.7944 (tpp80) cc_final: 0.7276 (tpp80) REVERT: n 115 LYS cc_start: 0.8945 (mppt) cc_final: 0.8527 (mptt) REVERT: o 87 LEU cc_start: 0.8342 (pp) cc_final: 0.8057 (pp) REVERT: p 56 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.7135 (mtm180) REVERT: p 64 GLN cc_start: 0.8352 (pt0) cc_final: 0.8114 (pt0) REVERT: r 8 ASN cc_start: 0.8587 (t0) cc_final: 0.8303 (t0) REVERT: r 102 THR cc_start: 0.9266 (p) cc_final: 0.8797 (m) REVERT: s 31 ILE cc_start: 0.8432 (mt) cc_final: 0.8208 (tt) REVERT: s 92 GLU cc_start: 0.8122 (tt0) cc_final: 0.7291 (tt0) REVERT: t 11 ILE cc_start: 0.8362 (mm) cc_final: 0.8060 (mm) REVERT: u 40 ASN cc_start: 0.8503 (t0) cc_final: 0.8248 (t0) REVERT: v 17 MET cc_start: 0.7507 (ptt) cc_final: 0.7210 (ptm) REVERT: w 66 SER cc_start: 0.8996 (t) cc_final: 0.8771 (t) REVERT: y 84 ASN cc_start: 0.7446 (m-40) cc_final: 0.7155 (m110) REVERT: z 5 LYS cc_start: 0.7585 (mtpp) cc_final: 0.7255 (mtmt) outliers start: 256 outliers final: 179 residues processed: 1272 average time/residue: 1.3400 time to fit residues: 3000.3706 Evaluate side-chains 1238 residues out of total 4954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 1049 time to evaluate : 6.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 22 ASP Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 58 TYR Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 91 PHE Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 84 TYR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 122 GLN Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 136 GLN Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 89 ASN Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain P residue 7 GLN Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain Q residue 110 VAL Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 95 ASP Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 106 VAL Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 75 GLN Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain W residue 35 SER Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 59 GLU Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 39 GLU Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain b residue 6 ASN Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain c residue 29 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 9 VAL Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain f residue 36 ARG Chi-restraints excluded: chain g residue 82 ASP Chi-restraints excluded: chain g residue 168 HIS Chi-restraints excluded: chain g residue 179 LEU Chi-restraints excluded: chain g residue 196 VAL Chi-restraints excluded: chain h residue 10 ILE Chi-restraints excluded: chain h residue 20 SER Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 44 THR Chi-restraints excluded: chain h residue 56 VAL Chi-restraints excluded: chain h residue 191 THR Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain i residue 131 ASN Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 63 ASN Chi-restraints excluded: chain k residue 70 VAL Chi-restraints excluded: chain k residue 71 ILE Chi-restraints excluded: chain l residue 72 THR Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 120 LEU Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain m residue 12 THR Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 106 THR Chi-restraints excluded: chain m residue 111 MET Chi-restraints excluded: chain m residue 112 THR Chi-restraints excluded: chain m residue 125 ILE Chi-restraints excluded: chain n residue 28 ILE Chi-restraints excluded: chain n residue 48 VAL Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 104 VAL Chi-restraints excluded: chain n residue 105 THR Chi-restraints excluded: chain o residue 18 ILE Chi-restraints excluded: chain o residue 26 VAL Chi-restraints excluded: chain o residue 73 LEU Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 31 ILE Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 56 ARG Chi-restraints excluded: chain p residue 111 THR Chi-restraints excluded: chain q residue 39 THR Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 102 LEU Chi-restraints excluded: chain q residue 107 VAL Chi-restraints excluded: chain r residue 12 HIS Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 19 LEU Chi-restraints excluded: chain r residue 20 THR Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 69 LEU Chi-restraints excluded: chain r residue 89 LEU Chi-restraints excluded: chain s residue 67 THR Chi-restraints excluded: chain s residue 80 SER Chi-restraints excluded: chain s residue 82 ILE Chi-restraints excluded: chain u residue 9 HIS Chi-restraints excluded: chain u residue 12 LYS Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 20 VAL Chi-restraints excluded: chain v residue 22 VAL Chi-restraints excluded: chain v residue 53 CYS Chi-restraints excluded: chain w residue 11 CYS Chi-restraints excluded: chain w residue 33 ILE Chi-restraints excluded: chain w residue 70 TYR Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 12 ASP Chi-restraints excluded: chain x residue 39 THR Chi-restraints excluded: chain y residue 35 VAL Chi-restraints excluded: chain y residue 39 ILE Chi-restraints excluded: chain y residue 57 ILE Chi-restraints excluded: chain y residue 86 LEU Chi-restraints excluded: chain z residue 53 VAL Chi-restraints excluded: chain z residue 70 LEU Chi-restraints excluded: chain 5 residue 111 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1083 random chunks: chunk 973 optimal weight: 2.9990 chunk 740 optimal weight: 5.9990 chunk 511 optimal weight: 0.9990 chunk 109 optimal weight: 30.0000 chunk 470 optimal weight: 0.9980 chunk 661 optimal weight: 4.9990 chunk 988 optimal weight: 0.9980 chunk 1046 optimal weight: 5.9990 chunk 516 optimal weight: 6.9990 chunk 937 optimal weight: 1.9990 chunk 282 optimal weight: 7.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 GLN D 156 ASN ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 6 ASN ** d 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 109 GLN h 32 ASN ** i 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 131 ASN ** j 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 11 HIS k 37 HIS n 75 GLN ** q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 79 ASN v 9 GLN ** w 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 78 ASN 5 69 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 168226 Z= 0.158 Angle : 0.619 14.497 251875 Z= 0.332 Chirality : 0.034 0.457 32159 Planarity : 0.006 0.123 13346 Dihedral : 24.049 179.997 84575 Min Nonbonded Distance : 1.155 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.20 % Favored : 94.79 % Rotamer: Outliers : 3.45 % Allowed : 26.18 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.11), residues: 5983 helix: 0.50 (0.12), residues: 2026 sheet: -1.90 (0.15), residues: 1106 loop : -2.30 (0.11), residues: 2851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP h 201 HIS 0.014 0.001 HIS M 13 PHE 0.029 0.001 PHE j 31 TYR 0.025 0.002 TYR a 9 ARG 0.006 0.000 ARG y 60 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11966 Ramachandran restraints generated. 5983 Oldfield, 0 Emsley, 5983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11966 Ramachandran restraints generated. 5983 Oldfield, 0 Emsley, 5983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1343 residues out of total 4954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 1172 time to evaluate : 6.568 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: B 35 GLU cc_start: 0.6943 (mm-30) cc_final: 0.6737 (mt-10) REVERT: E 18 THR cc_start: 0.8094 (m) cc_final: 0.7753 (p) REVERT: E 20 PHE cc_start: 0.7525 (OUTLIER) cc_final: 0.7251 (m-10) REVERT: E 81 GLN cc_start: 0.8370 (tm-30) cc_final: 0.8029 (tm-30) REVERT: E 96 MET cc_start: 0.8428 (tmm) cc_final: 0.7655 (tmm) REVERT: E 98 GLU cc_start: 0.6543 (tm-30) cc_final: 0.6333 (tm-30) REVERT: E 128 TYR cc_start: 0.8241 (t80) cc_final: 0.7567 (t80) REVERT: G 2 GLN cc_start: 0.7323 (mm110) cc_final: 0.6308 (mt0) REVERT: G 91 PHE cc_start: 0.6830 (OUTLIER) cc_final: 0.6348 (m-80) REVERT: I 135 MET cc_start: 0.2226 (mtp) cc_final: 0.1206 (mmt) REVERT: J 2 LYS cc_start: 0.8117 (mtmt) cc_final: 0.7842 (pttp) REVERT: J 60 ASP cc_start: 0.8131 (p0) cc_final: 0.7543 (p0) REVERT: J 106 LYS cc_start: 0.8526 (tttm) cc_final: 0.7967 (ttmm) REVERT: J 108 MET cc_start: 0.8501 (mtt) cc_final: 0.8118 (mtt) REVERT: K 9 ASN cc_start: 0.7853 (p0) cc_final: 0.7650 (p0) REVERT: K 12 ASP cc_start: 0.8216 (p0) cc_final: 0.7934 (p0) REVERT: K 92 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7361 (tm-30) REVERT: L 58 TYR cc_start: 0.8468 (p90) cc_final: 0.7977 (p90) REVERT: L 76 GLU cc_start: 0.7188 (pt0) cc_final: 0.6856 (pt0) REVERT: L 106 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7284 (mm-30) REVERT: M 44 ARG cc_start: 0.7814 (mtt-85) cc_final: 0.7476 (mtp85) REVERT: M 59 ARG cc_start: 0.7872 (mpt180) cc_final: 0.7550 (mpp-170) REVERT: N 1 MET cc_start: 0.8531 (pmm) cc_final: 0.8215 (pmm) REVERT: N 44 LEU cc_start: 0.9512 (tp) cc_final: 0.9255 (tt) REVERT: N 51 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8692 (mm) REVERT: N 107 ASN cc_start: 0.9117 (t0) cc_final: 0.8467 (t0) REVERT: Q 49 ASP cc_start: 0.7280 (m-30) cc_final: 0.7007 (m-30) REVERT: Q 89 GLU cc_start: 0.6109 (tp30) cc_final: 0.5583 (tp30) REVERT: S 11 ARG cc_start: 0.8396 (tpt90) cc_final: 0.7850 (tpt-90) REVERT: T 69 ARG cc_start: 0.7545 (ttp-110) cc_final: 0.7315 (ttm110) REVERT: U 5 ILE cc_start: 0.9270 (mm) cc_final: 0.9031 (mm) REVERT: U 17 LYS cc_start: 0.8068 (pttt) cc_final: 0.7618 (ttpt) REVERT: U 18 ASP cc_start: 0.8109 (p0) cc_final: 0.7245 (p0) REVERT: U 62 GLU cc_start: 0.8124 (tp30) cc_final: 0.7856 (tp30) REVERT: V 1 MET cc_start: 0.6097 (ptt) cc_final: 0.5772 (ptp) REVERT: V 24 ASN cc_start: 0.7937 (t0) cc_final: 0.7447 (t0) REVERT: V 29 ILE cc_start: 0.9256 (tp) cc_final: 0.8961 (tp) REVERT: V 40 ILE cc_start: 0.8972 (pt) cc_final: 0.8587 (pt) REVERT: W 68 LYS cc_start: 0.8876 (ttpp) cc_final: 0.8046 (tptp) REVERT: X 54 LYS cc_start: 0.8435 (ttpt) cc_final: 0.8191 (ttmt) REVERT: Y 24 GLU cc_start: 0.7271 (mm-30) cc_final: 0.6986 (mm-30) REVERT: Y 30 MET cc_start: 0.8204 (mmt) cc_final: 0.7858 (mmp) REVERT: Y 59 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6221 (mt-10) REVERT: a 23 LYS cc_start: 0.7801 (tptt) cc_final: 0.7256 (mmtp) REVERT: a 25 ARG cc_start: 0.7510 (mtp-110) cc_final: 0.7190 (mtp-110) REVERT: g 40 ILE cc_start: 0.7824 (pt) cc_final: 0.7553 (mt) REVERT: h 86 LYS cc_start: 0.8348 (ttpt) cc_final: 0.7782 (tmtt) REVERT: i 64 ILE cc_start: 0.9021 (mt) cc_final: 0.8812 (mt) REVERT: j 86 LYS cc_start: 0.8857 (mttt) cc_final: 0.8525 (mtpp) REVERT: j 106 ILE cc_start: 0.9105 (mm) cc_final: 0.8828 (mm) REVERT: k 54 LEU cc_start: 0.7976 (tp) cc_final: 0.7716 (mt) REVERT: k 102 MET cc_start: 0.7364 (ppp) cc_final: 0.6906 (ppp) REVERT: l 101 MET cc_start: 0.8431 (mtm) cc_final: 0.8161 (mtm) REVERT: l 116 MET cc_start: 0.7636 (tpt) cc_final: 0.7408 (tpt) REVERT: m 30 SER cc_start: 0.9185 (p) cc_final: 0.8696 (p) REVERT: m 118 GLN cc_start: 0.7499 (mt0) cc_final: 0.7283 (mm-40) REVERT: n 57 MET cc_start: 0.6272 (mtp) cc_final: 0.5938 (mtp) REVERT: n 58 VAL cc_start: 0.8105 (t) cc_final: 0.7876 (m) REVERT: n 107 ASP cc_start: 0.8292 (OUTLIER) cc_final: 0.7941 (m-30) REVERT: n 115 LYS cc_start: 0.8902 (mppt) cc_final: 0.8531 (mptt) REVERT: o 87 LEU cc_start: 0.8407 (pp) cc_final: 0.8187 (pp) REVERT: p 64 GLN cc_start: 0.8188 (pt0) cc_final: 0.7964 (pt0) REVERT: p 70 CYS cc_start: 0.8761 (t) cc_final: 0.8455 (t) REVERT: r 47 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6887 (pm20) REVERT: r 102 THR cc_start: 0.9054 (p) cc_final: 0.8792 (m) REVERT: t 11 ILE cc_start: 0.8310 (mm) cc_final: 0.8024 (mm) REVERT: u 40 ASN cc_start: 0.8531 (t0) cc_final: 0.8314 (t0) REVERT: w 66 SER cc_start: 0.8930 (t) cc_final: 0.8724 (t) REVERT: x 69 HIS cc_start: 0.7598 (m90) cc_final: 0.7280 (m-70) outliers start: 171 outliers final: 115 residues processed: 1280 average time/residue: 1.4218 time to fit residues: 3189.6368 Evaluate side-chains 1195 residues out of total 4954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 1074 time to evaluate : 6.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 91 PHE Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 84 TYR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain Q residue 110 VAL Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 95 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 106 VAL Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain U residue 101 GLU Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 59 GLU Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain a residue 33 ASN Chi-restraints excluded: chain b residue 6 ASN Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain c residue 29 THR Chi-restraints excluded: chain d residue 9 VAL Chi-restraints excluded: chain g residue 82 ASP Chi-restraints excluded: chain g residue 168 HIS Chi-restraints excluded: chain g residue 179 LEU Chi-restraints excluded: chain h residue 10 ILE Chi-restraints excluded: chain h residue 20 SER Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain i residue 129 VAL Chi-restraints excluded: chain i residue 137 VAL Chi-restraints excluded: chain j residue 45 ARG Chi-restraints excluded: chain j residue 46 VAL Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 96 MET Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain l residue 22 LEU Chi-restraints excluded: chain l residue 72 THR Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 80 ARG Chi-restraints excluded: chain m residue 111 MET Chi-restraints excluded: chain m residue 125 ILE Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 28 ILE Chi-restraints excluded: chain n residue 107 ASP Chi-restraints excluded: chain p residue 31 ILE Chi-restraints excluded: chain q residue 20 ASN Chi-restraints excluded: chain q residue 39 THR Chi-restraints excluded: chain q residue 102 LEU Chi-restraints excluded: chain q residue 105 SER Chi-restraints excluded: chain q residue 107 VAL Chi-restraints excluded: chain r residue 20 THR Chi-restraints excluded: chain r residue 47 GLU Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 89 LEU Chi-restraints excluded: chain s residue 80 SER Chi-restraints excluded: chain u residue 9 HIS Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 20 VAL Chi-restraints excluded: chain v residue 22 VAL Chi-restraints excluded: chain v residue 53 CYS Chi-restraints excluded: chain w residue 11 CYS Chi-restraints excluded: chain w residue 25 ASP Chi-restraints excluded: chain w residue 70 TYR Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 11 ILE Chi-restraints excluded: chain x residue 12 ASP Chi-restraints excluded: chain x residue 60 VAL Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain y residue 30 THR Chi-restraints excluded: chain y residue 35 VAL Chi-restraints excluded: chain y residue 86 LEU Chi-restraints excluded: chain z residue 70 LEU Chi-restraints excluded: chain 5 residue 34 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1083 random chunks: chunk 871 optimal weight: 5.9990 chunk 594 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 779 optimal weight: 6.9990 chunk 431 optimal weight: 10.0000 chunk 893 optimal weight: 4.9990 chunk 723 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 534 optimal weight: 0.9990 chunk 939 optimal weight: 20.0000 chunk 264 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 GLN ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 ASN R 43 ASN Y 15 ASN ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 109 GLN h 32 ASN ** i 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 131 ASN ** j 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 11 HIS ** k 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 75 GLN p 101 ASN ** q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 8 ASN u 79 ASN v 9 GLN ** w 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 168226 Z= 0.315 Angle : 0.706 14.100 251875 Z= 0.368 Chirality : 0.038 0.468 32159 Planarity : 0.006 0.129 13346 Dihedral : 24.025 179.784 84574 Min Nonbonded Distance : 1.065 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.79 % Favored : 92.19 % Rotamer: Outliers : 5.31 % Allowed : 26.48 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.11), residues: 5983 helix: 0.47 (0.11), residues: 2034 sheet: -1.82 (0.15), residues: 1102 loop : -2.32 (0.11), residues: 2847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 97 HIS 0.006 0.001 HIS k 11 PHE 0.025 0.002 PHE j 31 TYR 0.024 0.002 TYR E 7 ARG 0.009 0.001 ARG j 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11966 Ramachandran restraints generated. 5983 Oldfield, 0 Emsley, 5983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11966 Ramachandran restraints generated. 5983 Oldfield, 0 Emsley, 5983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1345 residues out of total 4954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 1082 time to evaluate : 6.685 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: B 171 TYR cc_start: 0.7899 (m-80) cc_final: 0.7676 (m-80) REVERT: B 205 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8384 (mm) REVERT: C 30 GLU cc_start: 0.5509 (OUTLIER) cc_final: 0.5067 (tt0) REVERT: C 202 ILE cc_start: 0.9222 (OUTLIER) cc_final: 0.9001 (mp) REVERT: D 156 ASN cc_start: 0.7107 (t0) cc_final: 0.6859 (m-40) REVERT: E 16 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8309 (mm) REVERT: E 18 THR cc_start: 0.8041 (m) cc_final: 0.7769 (p) REVERT: E 20 PHE cc_start: 0.7356 (OUTLIER) cc_final: 0.7144 (m-10) REVERT: E 81 GLN cc_start: 0.8446 (tm-30) cc_final: 0.8108 (tm-30) REVERT: E 96 MET cc_start: 0.8522 (tmm) cc_final: 0.7905 (tmm) REVERT: F 49 THR cc_start: 0.6629 (OUTLIER) cc_final: 0.6355 (t) REVERT: G 2 GLN cc_start: 0.7462 (mm110) cc_final: 0.6278 (mt0) REVERT: G 87 GLU cc_start: 0.7132 (pp20) cc_final: 0.6229 (pt0) REVERT: G 91 PHE cc_start: 0.6843 (OUTLIER) cc_final: 0.6439 (m-80) REVERT: H 122 GLN cc_start: 0.2131 (OUTLIER) cc_final: 0.1353 (pt0) REVERT: I 116 MET cc_start: 0.1855 (tpt) cc_final: 0.0386 (tpt) REVERT: J 2 LYS cc_start: 0.8157 (mtmt) cc_final: 0.7846 (pttp) REVERT: J 60 ASP cc_start: 0.8088 (p0) cc_final: 0.7555 (p0) REVERT: J 106 LYS cc_start: 0.8637 (tttm) cc_final: 0.8063 (ttmm) REVERT: K 12 ASP cc_start: 0.8139 (p0) cc_final: 0.7903 (p0) REVERT: K 92 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7258 (tm-30) REVERT: L 76 GLU cc_start: 0.7256 (pt0) cc_final: 0.7008 (pt0) REVERT: L 100 ILE cc_start: 0.8735 (mm) cc_final: 0.8530 (mm) REVERT: M 82 MET cc_start: 0.8394 (mmp) cc_final: 0.8076 (mmt) REVERT: N 1 MET cc_start: 0.8564 (pmm) cc_final: 0.8287 (pmm) REVERT: N 51 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8800 (mt) REVERT: N 72 ASP cc_start: 0.6481 (OUTLIER) cc_final: 0.6212 (m-30) REVERT: N 107 ASN cc_start: 0.9110 (t0) cc_final: 0.8905 (t0) REVERT: O 115 LEU cc_start: 0.8770 (mt) cc_final: 0.8469 (tt) REVERT: O 117 PHE cc_start: 0.7225 (p90) cc_final: 0.6795 (p90) REVERT: P 9 GLU cc_start: 0.6769 (tm-30) cc_final: 0.6478 (tt0) REVERT: Q 49 ASP cc_start: 0.7433 (m-30) cc_final: 0.7153 (m-30) REVERT: Q 89 GLU cc_start: 0.6356 (tp30) cc_final: 0.5957 (tp30) REVERT: S 11 ARG cc_start: 0.8371 (tpt90) cc_final: 0.7839 (tpt-90) REVERT: T 69 ARG cc_start: 0.7733 (ttp-110) cc_final: 0.7440 (ttm110) REVERT: U 5 ILE cc_start: 0.9350 (mm) cc_final: 0.9105 (mm) REVERT: U 17 LYS cc_start: 0.8089 (pttt) cc_final: 0.7625 (ttpt) REVERT: U 18 ASP cc_start: 0.8190 (p0) cc_final: 0.7201 (p0) REVERT: V 1 MET cc_start: 0.6288 (ptt) cc_final: 0.5975 (ptp) REVERT: V 24 ASN cc_start: 0.8052 (t0) cc_final: 0.7474 (t0) REVERT: V 29 ILE cc_start: 0.9264 (tp) cc_final: 0.8970 (tp) REVERT: V 40 ILE cc_start: 0.8891 (pt) cc_final: 0.8565 (pt) REVERT: V 43 ASP cc_start: 0.7629 (m-30) cc_final: 0.7320 (m-30) REVERT: W 68 LYS cc_start: 0.8933 (ttpp) cc_final: 0.8068 (tptp) REVERT: X 33 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8778 (mp) REVERT: X 54 LYS cc_start: 0.8491 (ttpt) cc_final: 0.8166 (ttpt) REVERT: Y 24 GLU cc_start: 0.7341 (mm-30) cc_final: 0.7138 (mm-30) REVERT: Y 30 MET cc_start: 0.8197 (mmt) cc_final: 0.7899 (mmp) REVERT: Y 59 GLU cc_start: 0.6571 (OUTLIER) cc_final: 0.6214 (mt-10) REVERT: a 9 TYR cc_start: 0.6556 (t80) cc_final: 0.6187 (t80) REVERT: g 9 MET cc_start: 0.7600 (mtt) cc_final: 0.7355 (mtp) REVERT: h 42 TYR cc_start: 0.8441 (t80) cc_final: 0.8213 (t80) REVERT: h 86 LYS cc_start: 0.8355 (ttpt) cc_final: 0.7868 (tmtt) REVERT: h 143 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7501 (ptp90) REVERT: i 64 ILE cc_start: 0.9053 (mt) cc_final: 0.8835 (mt) REVERT: i 103 TYR cc_start: 0.8479 (t80) cc_final: 0.8193 (t80) REVERT: j 31 PHE cc_start: 0.8399 (m-80) cc_final: 0.8030 (m-80) REVERT: j 68 ARG cc_start: 0.8044 (ttp80) cc_final: 0.7770 (ttp80) REVERT: j 86 LYS cc_start: 0.8769 (mttt) cc_final: 0.8462 (mtpp) REVERT: j 106 ILE cc_start: 0.9160 (mm) cc_final: 0.8875 (mm) REVERT: k 54 LEU cc_start: 0.8004 (tp) cc_final: 0.7688 (mt) REVERT: k 102 MET cc_start: 0.7431 (ppp) cc_final: 0.6961 (ppp) REVERT: l 101 MET cc_start: 0.8576 (mtm) cc_final: 0.8318 (mtm) REVERT: m 30 SER cc_start: 0.9247 (p) cc_final: 0.8759 (p) REVERT: n 64 TYR cc_start: 0.7578 (t80) cc_final: 0.6942 (t80) REVERT: n 115 LYS cc_start: 0.8935 (mppt) cc_final: 0.8532 (mptt) REVERT: o 87 LEU cc_start: 0.8516 (pp) cc_final: 0.8254 (pp) REVERT: p 56 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.7142 (mtm180) REVERT: p 64 GLN cc_start: 0.8280 (pt0) cc_final: 0.8067 (pt0) REVERT: p 70 CYS cc_start: 0.8741 (t) cc_final: 0.8431 (t) REVERT: r 102 THR cc_start: 0.9173 (p) cc_final: 0.8719 (m) REVERT: t 11 ILE cc_start: 0.8311 (mm) cc_final: 0.8013 (mm) REVERT: u 31 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.7481 (ptm160) REVERT: u 40 ASN cc_start: 0.8432 (t0) cc_final: 0.8129 (t0) outliers start: 263 outliers final: 198 residues processed: 1255 average time/residue: 1.3312 time to fit residues: 2922.5656 Evaluate side-chains 1254 residues out of total 4954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 1041 time to evaluate : 6.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 22 ASP Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 92 HIS Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 58 TYR Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 91 PHE Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 84 TYR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 122 GLN Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain Q residue 110 VAL Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain R residue 95 ASP Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 106 VAL Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 60 GLU Chi-restraints excluded: chain U residue 65 ILE Chi-restraints excluded: chain U residue 101 GLU Chi-restraints excluded: chain U residue 103 ILE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain W residue 35 SER Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 59 GLU Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain a residue 33 ASN Chi-restraints excluded: chain a residue 38 SER Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain c residue 29 THR Chi-restraints excluded: chain d residue 9 VAL Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain f residue 16 ILE Chi-restraints excluded: chain g residue 14 VAL Chi-restraints excluded: chain g residue 82 ASP Chi-restraints excluded: chain g residue 93 ASN Chi-restraints excluded: chain g residue 100 MET Chi-restraints excluded: chain g residue 125 THR Chi-restraints excluded: chain g residue 168 HIS Chi-restraints excluded: chain g residue 179 LEU Chi-restraints excluded: chain h residue 10 ILE Chi-restraints excluded: chain h residue 20 SER Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 56 VAL Chi-restraints excluded: chain h residue 129 MET Chi-restraints excluded: chain h residue 143 ARG Chi-restraints excluded: chain h residue 191 THR Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain i residue 129 VAL Chi-restraints excluded: chain i residue 137 VAL Chi-restraints excluded: chain j residue 45 ARG Chi-restraints excluded: chain j residue 46 VAL Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 96 MET Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 70 VAL Chi-restraints excluded: chain k residue 71 ILE Chi-restraints excluded: chain l residue 72 THR Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain m residue 12 THR Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 92 LEU Chi-restraints excluded: chain m residue 106 THR Chi-restraints excluded: chain m residue 111 MET Chi-restraints excluded: chain m residue 125 ILE Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 28 ILE Chi-restraints excluded: chain n residue 104 VAL Chi-restraints excluded: chain n residue 105 THR Chi-restraints excluded: chain o residue 26 VAL Chi-restraints excluded: chain o residue 73 LEU Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 31 ILE Chi-restraints excluded: chain p residue 56 ARG Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain p residue 96 THR Chi-restraints excluded: chain p residue 111 THR Chi-restraints excluded: chain q residue 20 ASN Chi-restraints excluded: chain q residue 39 THR Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 102 LEU Chi-restraints excluded: chain q residue 105 SER Chi-restraints excluded: chain q residue 107 VAL Chi-restraints excluded: chain r residue 12 HIS Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 20 THR Chi-restraints excluded: chain r residue 47 GLU Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 69 LEU Chi-restraints excluded: chain r residue 89 LEU Chi-restraints excluded: chain s residue 67 THR Chi-restraints excluded: chain s residue 80 SER Chi-restraints excluded: chain s residue 82 ILE Chi-restraints excluded: chain s residue 84 VAL Chi-restraints excluded: chain u residue 9 HIS Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 20 VAL Chi-restraints excluded: chain u residue 31 ARG Chi-restraints excluded: chain v residue 22 VAL Chi-restraints excluded: chain v residue 53 CYS Chi-restraints excluded: chain v residue 61 ILE Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain w residue 11 CYS Chi-restraints excluded: chain w residue 25 ASP Chi-restraints excluded: chain w residue 55 LEU Chi-restraints excluded: chain w residue 70 TYR Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 11 ILE Chi-restraints excluded: chain x residue 12 ASP Chi-restraints excluded: chain x residue 39 THR Chi-restraints excluded: chain y residue 30 THR Chi-restraints excluded: chain y residue 35 VAL Chi-restraints excluded: chain y residue 39 ILE Chi-restraints excluded: chain y residue 57 ILE Chi-restraints excluded: chain y residue 86 LEU Chi-restraints excluded: chain z residue 5 LYS Chi-restraints excluded: chain z residue 53 VAL Chi-restraints excluded: chain z residue 70 LEU Chi-restraints excluded: chain 5 residue 34 LEU Chi-restraints excluded: chain 5 residue 111 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1083 random chunks: chunk 352 optimal weight: 10.0000 chunk 942 optimal weight: 6.9990 chunk 206 optimal weight: 7.9990 chunk 614 optimal weight: 0.6980 chunk 258 optimal weight: 7.9990 chunk 1047 optimal weight: 50.0000 chunk 869 optimal weight: 8.9990 chunk 485 optimal weight: 0.3980 chunk 87 optimal weight: 10.0000 chunk 346 optimal weight: 10.0000 chunk 550 optimal weight: 10.0000 overall best weight: 4.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 GLN ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 ASN ** G 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 15 ASN ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 6 ASN ** d 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 109 GLN h 32 ASN ** i 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 131 ASN ** j 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 11 HIS ** k 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 75 GLN p 101 ASN ** q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 79 ASN v 9 GLN ** w 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 69 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 168226 Z= 0.326 Angle : 0.720 14.094 251875 Z= 0.374 Chirality : 0.039 0.455 32159 Planarity : 0.006 0.129 13346 Dihedral : 24.030 179.842 84574 Min Nonbonded Distance : 1.069 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.42 % Favored : 92.56 % Rotamer: Outliers : 6.06 % Allowed : 26.91 % Favored : 67.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.11), residues: 5983 helix: 0.51 (0.11), residues: 2017 sheet: -1.84 (0.15), residues: 1112 loop : -2.28 (0.11), residues: 2854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 64 HIS 0.006 0.001 HIS k 11 PHE 0.023 0.002 PHE z 12 TYR 0.025 0.002 TYR E 7 ARG 0.009 0.001 ARG j 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11966 Ramachandran restraints generated. 5983 Oldfield, 0 Emsley, 5983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11966 Ramachandran restraints generated. 5983 Oldfield, 0 Emsley, 5983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1367 residues out of total 4954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 300 poor density : 1067 time to evaluate : 6.797 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: B 205 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8388 (mm) REVERT: E 16 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8292 (mm) REVERT: E 18 THR cc_start: 0.7960 (m) cc_final: 0.7652 (p) REVERT: E 20 PHE cc_start: 0.7437 (OUTLIER) cc_final: 0.7191 (m-10) REVERT: E 81 GLN cc_start: 0.8482 (tm-30) cc_final: 0.8187 (tm-30) REVERT: E 96 MET cc_start: 0.8560 (tmm) cc_final: 0.7958 (tmm) REVERT: E 98 GLU cc_start: 0.6854 (tm-30) cc_final: 0.6599 (tm-30) REVERT: E 128 TYR cc_start: 0.8536 (t80) cc_final: 0.8319 (t80) REVERT: E 175 PHE cc_start: 0.7182 (OUTLIER) cc_final: 0.5261 (m-80) REVERT: F 49 THR cc_start: 0.6732 (OUTLIER) cc_final: 0.6438 (t) REVERT: G 2 GLN cc_start: 0.7354 (mm110) cc_final: 0.5852 (mt0) REVERT: G 91 PHE cc_start: 0.6929 (OUTLIER) cc_final: 0.6593 (m-80) REVERT: I 116 MET cc_start: 0.1866 (tpt) cc_final: 0.0377 (tpt) REVERT: J 2 LYS cc_start: 0.8139 (mtmt) cc_final: 0.7872 (pttp) REVERT: J 60 ASP cc_start: 0.8059 (p0) cc_final: 0.7595 (p0) REVERT: J 106 LYS cc_start: 0.8638 (tttm) cc_final: 0.8093 (ttmm) REVERT: K 12 ASP cc_start: 0.8161 (p0) cc_final: 0.7946 (p0) REVERT: K 92 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7222 (tm-30) REVERT: L 76 GLU cc_start: 0.7287 (pt0) cc_final: 0.7037 (pt0) REVERT: M 82 MET cc_start: 0.8394 (mmp) cc_final: 0.8091 (mmt) REVERT: N 1 MET cc_start: 0.8508 (pmm) cc_final: 0.8238 (pmm) REVERT: N 51 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8799 (mt) REVERT: N 72 ASP cc_start: 0.6512 (OUTLIER) cc_final: 0.6202 (m-30) REVERT: O 115 LEU cc_start: 0.8817 (mt) cc_final: 0.8541 (tt) REVERT: O 117 PHE cc_start: 0.7301 (p90) cc_final: 0.6802 (p90) REVERT: P 9 GLU cc_start: 0.6854 (tm-30) cc_final: 0.6624 (tt0) REVERT: Q 49 ASP cc_start: 0.7500 (m-30) cc_final: 0.7199 (m-30) REVERT: Q 89 GLU cc_start: 0.6512 (tp30) cc_final: 0.6087 (tp30) REVERT: S 11 ARG cc_start: 0.8463 (tpt90) cc_final: 0.8001 (tpt-90) REVERT: T 69 ARG cc_start: 0.7762 (ttp-110) cc_final: 0.7445 (ttm110) REVERT: U 5 ILE cc_start: 0.9348 (mm) cc_final: 0.9140 (mm) REVERT: U 17 LYS cc_start: 0.8126 (pttt) cc_final: 0.7681 (ttpt) REVERT: U 18 ASP cc_start: 0.8191 (p0) cc_final: 0.7229 (p0) REVERT: V 1 MET cc_start: 0.6299 (ptt) cc_final: 0.5954 (ptp) REVERT: V 24 ASN cc_start: 0.8049 (t0) cc_final: 0.7503 (t0) REVERT: V 29 ILE cc_start: 0.9265 (tp) cc_final: 0.8984 (tp) REVERT: V 43 ASP cc_start: 0.7676 (m-30) cc_final: 0.7350 (m-30) REVERT: W 68 LYS cc_start: 0.8938 (ttpp) cc_final: 0.8054 (tptp) REVERT: X 33 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8795 (mp) REVERT: X 54 LYS cc_start: 0.8512 (ttpt) cc_final: 0.8160 (ttmt) REVERT: Y 30 MET cc_start: 0.8273 (mmt) cc_final: 0.8001 (mmp) REVERT: Y 59 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.6314 (mt-10) REVERT: g 126 PHE cc_start: 0.6923 (t80) cc_final: 0.6301 (t80) REVERT: h 33 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8966 (mm) REVERT: h 86 LYS cc_start: 0.8550 (ttpt) cc_final: 0.7964 (tmtt) REVERT: i 64 ILE cc_start: 0.9040 (mt) cc_final: 0.8825 (mt) REVERT: i 103 TYR cc_start: 0.8502 (t80) cc_final: 0.8184 (t80) REVERT: i 131 ASN cc_start: 0.7535 (OUTLIER) cc_final: 0.7320 (t0) REVERT: j 68 ARG cc_start: 0.8054 (ttp80) cc_final: 0.7810 (ttp80) REVERT: j 86 LYS cc_start: 0.8751 (mttt) cc_final: 0.8448 (mtpp) REVERT: j 106 ILE cc_start: 0.9154 (mm) cc_final: 0.8871 (mm) REVERT: k 17 GLN cc_start: 0.6546 (pt0) cc_final: 0.6335 (pt0) REVERT: k 54 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7711 (mt) REVERT: k 102 MET cc_start: 0.7215 (ppp) cc_final: 0.6788 (ppp) REVERT: l 28 ASN cc_start: 0.8956 (m110) cc_final: 0.8722 (m-40) REVERT: l 101 MET cc_start: 0.8581 (mtm) cc_final: 0.8327 (mtm) REVERT: n 64 TYR cc_start: 0.7708 (t80) cc_final: 0.7058 (t80) REVERT: n 95 ARG cc_start: 0.7773 (tpp80) cc_final: 0.7410 (tpp80) REVERT: n 115 LYS cc_start: 0.8930 (mppt) cc_final: 0.8590 (mptt) REVERT: o 87 LEU cc_start: 0.8476 (pp) cc_final: 0.8266 (pp) REVERT: p 56 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.7093 (mtm180) REVERT: p 70 CYS cc_start: 0.8742 (t) cc_final: 0.8414 (t) REVERT: r 102 THR cc_start: 0.9172 (p) cc_final: 0.8702 (m) REVERT: s 90 ARG cc_start: 0.7283 (ttm110) cc_final: 0.6978 (ttp-110) REVERT: t 11 ILE cc_start: 0.8321 (mm) cc_final: 0.8031 (mm) REVERT: u 31 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.7492 (ptm160) REVERT: u 40 ASN cc_start: 0.8436 (t0) cc_final: 0.8172 (t0) REVERT: z 62 ARG cc_start: 0.5962 (OUTLIER) cc_final: 0.5093 (ttp80) outliers start: 300 outliers final: 236 residues processed: 1268 average time/residue: 1.3098 time to fit residues: 2923.3033 Evaluate side-chains 1283 residues out of total 4954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 1031 time to evaluate : 6.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 22 ASP Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 92 HIS Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 58 TYR Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 91 PHE Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 84 TYR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 37 ASP Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 89 ASN Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 100 CYS Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain Q residue 110 VAL Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 95 ASP Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 55 ILE Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 106 VAL Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 60 GLU Chi-restraints excluded: chain U residue 65 ILE Chi-restraints excluded: chain U residue 101 GLU Chi-restraints excluded: chain U residue 103 ILE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 59 GLU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain W residue 35 SER Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 59 GLU Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 52 SER Chi-restraints excluded: chain a residue 12 ILE Chi-restraints excluded: chain a residue 33 ASN Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 36 GLU Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain c residue 29 THR Chi-restraints excluded: chain d residue 9 VAL Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain e residue 59 ILE Chi-restraints excluded: chain f residue 16 ILE Chi-restraints excluded: chain g residue 82 ASP Chi-restraints excluded: chain g residue 93 ASN Chi-restraints excluded: chain g residue 100 MET Chi-restraints excluded: chain g residue 125 THR Chi-restraints excluded: chain g residue 168 HIS Chi-restraints excluded: chain g residue 179 LEU Chi-restraints excluded: chain g residue 183 VAL Chi-restraints excluded: chain g residue 191 SER Chi-restraints excluded: chain g residue 196 VAL Chi-restraints excluded: chain h residue 10 ILE Chi-restraints excluded: chain h residue 20 SER Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 33 LEU Chi-restraints excluded: chain h residue 44 THR Chi-restraints excluded: chain h residue 56 VAL Chi-restraints excluded: chain h residue 129 MET Chi-restraints excluded: chain h residue 143 ARG Chi-restraints excluded: chain h residue 177 THR Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain i residue 131 ASN Chi-restraints excluded: chain i residue 137 VAL Chi-restraints excluded: chain j residue 45 ARG Chi-restraints excluded: chain j residue 46 VAL Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 96 MET Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 70 VAL Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 72 THR Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain m residue 12 THR Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 79 SER Chi-restraints excluded: chain m residue 80 ARG Chi-restraints excluded: chain m residue 92 LEU Chi-restraints excluded: chain m residue 106 THR Chi-restraints excluded: chain m residue 111 MET Chi-restraints excluded: chain m residue 125 ILE Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 28 ILE Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 104 VAL Chi-restraints excluded: chain n residue 105 THR Chi-restraints excluded: chain o residue 26 VAL Chi-restraints excluded: chain o residue 73 LEU Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 31 ILE Chi-restraints excluded: chain p residue 56 ARG Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain p residue 96 THR Chi-restraints excluded: chain p residue 111 THR Chi-restraints excluded: chain q residue 20 ASN Chi-restraints excluded: chain q residue 24 LEU Chi-restraints excluded: chain q residue 39 THR Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 102 LEU Chi-restraints excluded: chain q residue 105 SER Chi-restraints excluded: chain q residue 107 VAL Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 20 THR Chi-restraints excluded: chain r residue 43 VAL Chi-restraints excluded: chain r residue 47 GLU Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 69 LEU Chi-restraints excluded: chain r residue 89 LEU Chi-restraints excluded: chain s residue 67 THR Chi-restraints excluded: chain s residue 80 SER Chi-restraints excluded: chain s residue 82 ILE Chi-restraints excluded: chain s residue 84 VAL Chi-restraints excluded: chain u residue 9 HIS Chi-restraints excluded: chain u residue 12 LYS Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 20 VAL Chi-restraints excluded: chain u residue 24 SER Chi-restraints excluded: chain u residue 31 ARG Chi-restraints excluded: chain v residue 22 VAL Chi-restraints excluded: chain v residue 53 CYS Chi-restraints excluded: chain v residue 61 ILE Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 75 LEU Chi-restraints excluded: chain w residue 11 CYS Chi-restraints excluded: chain w residue 25 ASP Chi-restraints excluded: chain w residue 55 LEU Chi-restraints excluded: chain w residue 70 TYR Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 11 ILE Chi-restraints excluded: chain x residue 12 ASP Chi-restraints excluded: chain x residue 16 LEU Chi-restraints excluded: chain x residue 39 THR Chi-restraints excluded: chain y residue 30 THR Chi-restraints excluded: chain y residue 35 VAL Chi-restraints excluded: chain y residue 39 ILE Chi-restraints excluded: chain y residue 57 ILE Chi-restraints excluded: chain y residue 86 LEU Chi-restraints excluded: chain z residue 14 VAL Chi-restraints excluded: chain z residue 53 VAL Chi-restraints excluded: chain z residue 62 ARG Chi-restraints excluded: chain z residue 70 LEU Chi-restraints excluded: chain 5 residue 34 LEU Chi-restraints excluded: chain 5 residue 111 VAL Chi-restraints excluded: chain 5 residue 112 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1083 random chunks: chunk 1010 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 597 optimal weight: 9.9990 chunk 765 optimal weight: 9.9990 chunk 592 optimal weight: 10.0000 chunk 882 optimal weight: 6.9990 chunk 585 optimal weight: 0.0370 chunk 1043 optimal weight: 9.9990 chunk 653 optimal weight: 6.9990 chunk 636 optimal weight: 2.9990 chunk 481 optimal weight: 5.9990 overall best weight: 3.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 GLN ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 HIS E 127 ASN ** G 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 11 GLN ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN ** d 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 109 GLN h 32 ASN i 59 GLN i 131 ASN ** j 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 11 HIS k 17 GLN n 75 GLN p 101 ASN ** q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 79 ASN ** w 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 168226 Z= 0.256 Angle : 0.672 14.082 251875 Z= 0.354 Chirality : 0.037 0.443 32159 Planarity : 0.006 0.128 13346 Dihedral : 24.003 179.772 84574 Min Nonbonded Distance : 1.091 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.29 % Favored : 92.70 % Rotamer: Outliers : 5.67 % Allowed : 28.02 % Favored : 66.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.11), residues: 5983 helix: 0.66 (0.12), residues: 2023 sheet: -1.75 (0.15), residues: 1107 loop : -2.22 (0.11), residues: 2853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP h 201 HIS 0.008 0.001 HIS M 13 PHE 0.020 0.002 PHE a 60 TYR 0.035 0.002 TYR O 99 ARG 0.012 0.000 ARG W 25 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11966 Ramachandran restraints generated. 5983 Oldfield, 0 Emsley, 5983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11966 Ramachandran restraints generated. 5983 Oldfield, 0 Emsley, 5983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1357 residues out of total 4954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 1076 time to evaluate : 7.292 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: B 205 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8446 (mm) REVERT: C 30 GLU cc_start: 0.5272 (OUTLIER) cc_final: 0.4858 (tt0) REVERT: E 17 MET cc_start: 0.7561 (ttm) cc_final: 0.7359 (ttm) REVERT: E 20 PHE cc_start: 0.7402 (OUTLIER) cc_final: 0.7184 (m-10) REVERT: E 81 GLN cc_start: 0.8463 (tm-30) cc_final: 0.8169 (tm-30) REVERT: E 85 ILE cc_start: 0.8433 (mt) cc_final: 0.8200 (mt) REVERT: E 98 GLU cc_start: 0.6800 (tm-30) cc_final: 0.6557 (tm-30) REVERT: E 128 TYR cc_start: 0.8626 (t80) cc_final: 0.8111 (t80) REVERT: F 49 THR cc_start: 0.6664 (OUTLIER) cc_final: 0.6400 (t) REVERT: F 153 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7595 (mtp180) REVERT: G 2 GLN cc_start: 0.7216 (mm110) cc_final: 0.5838 (mt0) REVERT: G 87 GLU cc_start: 0.7408 (pp20) cc_final: 0.6630 (pp20) REVERT: G 91 PHE cc_start: 0.6868 (OUTLIER) cc_final: 0.6515 (m-80) REVERT: H 122 GLN cc_start: 0.2220 (OUTLIER) cc_final: 0.1345 (pt0) REVERT: I 116 MET cc_start: 0.2030 (tpt) cc_final: 0.0583 (tpt) REVERT: J 2 LYS cc_start: 0.8121 (mtmt) cc_final: 0.7882 (pttp) REVERT: J 60 ASP cc_start: 0.8033 (p0) cc_final: 0.7597 (p0) REVERT: J 106 LYS cc_start: 0.8565 (tttm) cc_final: 0.8014 (ttmm) REVERT: K 12 ASP cc_start: 0.8168 (p0) cc_final: 0.7967 (p0) REVERT: K 92 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7315 (tm-30) REVERT: K 107 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7882 (mp) REVERT: L 76 GLU cc_start: 0.7252 (pt0) cc_final: 0.7007 (pt0) REVERT: M 13 HIS cc_start: 0.9051 (OUTLIER) cc_final: 0.8512 (m170) REVERT: M 82 MET cc_start: 0.8361 (mmp) cc_final: 0.8020 (mmt) REVERT: N 51 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8773 (mt) REVERT: N 72 ASP cc_start: 0.6414 (OUTLIER) cc_final: 0.6086 (m-30) REVERT: O 115 LEU cc_start: 0.8802 (mt) cc_final: 0.8590 (tp) REVERT: O 117 PHE cc_start: 0.7226 (p90) cc_final: 0.6815 (p90) REVERT: P 9 GLU cc_start: 0.6785 (tm-30) cc_final: 0.6478 (tt0) REVERT: Q 49 ASP cc_start: 0.7443 (m-30) cc_final: 0.7200 (m-30) REVERT: Q 89 GLU cc_start: 0.6370 (tp30) cc_final: 0.5956 (tp30) REVERT: S 11 ARG cc_start: 0.8466 (tpt90) cc_final: 0.7999 (tpt-90) REVERT: T 69 ARG cc_start: 0.7836 (ttp-110) cc_final: 0.7623 (ttm110) REVERT: U 5 ILE cc_start: 0.9329 (mm) cc_final: 0.9117 (mm) REVERT: U 17 LYS cc_start: 0.8140 (pttt) cc_final: 0.7731 (ttpt) REVERT: U 18 ASP cc_start: 0.7992 (p0) cc_final: 0.7007 (p0) REVERT: V 1 MET cc_start: 0.6164 (ptt) cc_final: 0.5868 (ptp) REVERT: V 24 ASN cc_start: 0.8073 (t0) cc_final: 0.7538 (t0) REVERT: V 29 ILE cc_start: 0.9250 (tp) cc_final: 0.8963 (tp) REVERT: V 40 ILE cc_start: 0.8830 (pt) cc_final: 0.8539 (pt) REVERT: W 68 LYS cc_start: 0.8919 (ttpp) cc_final: 0.8064 (tptp) REVERT: X 54 LYS cc_start: 0.8470 (ttpt) cc_final: 0.8113 (ttmt) REVERT: Y 30 MET cc_start: 0.8246 (mmt) cc_final: 0.7952 (mmp) REVERT: Y 59 GLU cc_start: 0.6702 (OUTLIER) cc_final: 0.6344 (mt-10) REVERT: a 9 TYR cc_start: 0.6912 (t80) cc_final: 0.6599 (t80) REVERT: g 126 PHE cc_start: 0.6789 (t80) cc_final: 0.6206 (t80) REVERT: g 175 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7766 (mp0) REVERT: h 33 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8991 (mm) REVERT: h 40 ARG cc_start: 0.8460 (tpp80) cc_final: 0.7604 (tpp80) REVERT: h 86 LYS cc_start: 0.8536 (ttpt) cc_final: 0.7956 (tmtt) REVERT: i 64 ILE cc_start: 0.9038 (mt) cc_final: 0.8821 (mt) REVERT: i 103 TYR cc_start: 0.8539 (t80) cc_final: 0.8188 (t80) REVERT: i 131 ASN cc_start: 0.7139 (OUTLIER) cc_final: 0.6778 (t0) REVERT: j 86 LYS cc_start: 0.8897 (mttt) cc_final: 0.8553 (mtpp) REVERT: j 106 ILE cc_start: 0.9165 (mm) cc_final: 0.8883 (mm) REVERT: k 54 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7689 (mt) REVERT: k 102 MET cc_start: 0.7290 (ppp) cc_final: 0.6911 (ppp) REVERT: l 101 MET cc_start: 0.8539 (mtm) cc_final: 0.8276 (mtm) REVERT: n 64 TYR cc_start: 0.7713 (t80) cc_final: 0.7054 (t80) REVERT: n 115 LYS cc_start: 0.8935 (mppt) cc_final: 0.8655 (mptt) REVERT: o 87 LEU cc_start: 0.8503 (pp) cc_final: 0.8171 (pp) REVERT: p 56 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.7065 (mtm180) REVERT: p 70 CYS cc_start: 0.8742 (t) cc_final: 0.8436 (t) REVERT: q 43 LYS cc_start: 0.8036 (pttm) cc_final: 0.7604 (mtpp) REVERT: r 102 THR cc_start: 0.9134 (p) cc_final: 0.8634 (m) REVERT: s 90 ARG cc_start: 0.7346 (ttm110) cc_final: 0.6834 (ttp-110) REVERT: t 11 ILE cc_start: 0.8369 (mm) cc_final: 0.8084 (mm) REVERT: u 31 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.7448 (ptm160) REVERT: u 40 ASN cc_start: 0.8419 (t0) cc_final: 0.8125 (t0) REVERT: z 62 ARG cc_start: 0.5988 (OUTLIER) cc_final: 0.5159 (ttp80) outliers start: 281 outliers final: 234 residues processed: 1262 average time/residue: 1.3142 time to fit residues: 2909.7540 Evaluate side-chains 1290 residues out of total 4954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 1037 time to evaluate : 6.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 22 ASP Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 92 HIS Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 58 TYR Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 91 PHE Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 84 TYR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 122 GLN Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 104 GLU Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 100 CYS Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain Q residue 110 VAL Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain R residue 95 ASP Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 106 VAL Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 60 GLU Chi-restraints excluded: chain U residue 65 ILE Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain U residue 101 GLU Chi-restraints excluded: chain U residue 103 ILE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 59 GLU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain W residue 35 SER Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 59 GLU Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 52 SER Chi-restraints excluded: chain a residue 33 ASN Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 36 GLU Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain c residue 29 THR Chi-restraints excluded: chain d residue 9 VAL Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 59 ILE Chi-restraints excluded: chain f residue 16 ILE Chi-restraints excluded: chain g residue 6 MET Chi-restraints excluded: chain g residue 21 ARG Chi-restraints excluded: chain g residue 82 ASP Chi-restraints excluded: chain g residue 125 THR Chi-restraints excluded: chain g residue 168 HIS Chi-restraints excluded: chain g residue 175 GLU Chi-restraints excluded: chain g residue 179 LEU Chi-restraints excluded: chain g residue 183 VAL Chi-restraints excluded: chain g residue 196 VAL Chi-restraints excluded: chain h residue 10 ILE Chi-restraints excluded: chain h residue 20 SER Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 33 LEU Chi-restraints excluded: chain h residue 56 VAL Chi-restraints excluded: chain h residue 129 MET Chi-restraints excluded: chain h residue 143 ARG Chi-restraints excluded: chain h residue 149 ILE Chi-restraints excluded: chain h residue 191 THR Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain i residue 41 HIS Chi-restraints excluded: chain i residue 131 ASN Chi-restraints excluded: chain i residue 137 VAL Chi-restraints excluded: chain j residue 37 THR Chi-restraints excluded: chain j residue 45 ARG Chi-restraints excluded: chain j residue 46 VAL Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 96 MET Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 70 VAL Chi-restraints excluded: chain k residue 71 ILE Chi-restraints excluded: chain l residue 6 VAL Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 72 THR Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain m residue 12 THR Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 79 SER Chi-restraints excluded: chain m residue 80 ARG Chi-restraints excluded: chain m residue 92 LEU Chi-restraints excluded: chain m residue 106 THR Chi-restraints excluded: chain m residue 111 MET Chi-restraints excluded: chain m residue 112 THR Chi-restraints excluded: chain m residue 125 ILE Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 28 ILE Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 104 VAL Chi-restraints excluded: chain n residue 105 THR Chi-restraints excluded: chain o residue 26 VAL Chi-restraints excluded: chain o residue 73 LEU Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 31 ILE Chi-restraints excluded: chain p residue 56 ARG Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain p residue 96 THR Chi-restraints excluded: chain p residue 111 THR Chi-restraints excluded: chain q residue 20 ASN Chi-restraints excluded: chain q residue 39 THR Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 102 LEU Chi-restraints excluded: chain q residue 105 SER Chi-restraints excluded: chain q residue 107 VAL Chi-restraints excluded: chain r residue 12 HIS Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 20 THR Chi-restraints excluded: chain r residue 43 VAL Chi-restraints excluded: chain r residue 45 ILE Chi-restraints excluded: chain r residue 47 GLU Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 69 LEU Chi-restraints excluded: chain r residue 89 LEU Chi-restraints excluded: chain s residue 67 THR Chi-restraints excluded: chain s residue 80 SER Chi-restraints excluded: chain s residue 82 ILE Chi-restraints excluded: chain s residue 84 VAL Chi-restraints excluded: chain u residue 9 HIS Chi-restraints excluded: chain u residue 12 LYS Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 20 VAL Chi-restraints excluded: chain u residue 31 ARG Chi-restraints excluded: chain u residue 71 VAL Chi-restraints excluded: chain v residue 22 VAL Chi-restraints excluded: chain v residue 53 CYS Chi-restraints excluded: chain v residue 75 LEU Chi-restraints excluded: chain w residue 11 CYS Chi-restraints excluded: chain w residue 25 ASP Chi-restraints excluded: chain w residue 55 LEU Chi-restraints excluded: chain w residue 70 TYR Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 11 ILE Chi-restraints excluded: chain x residue 12 ASP Chi-restraints excluded: chain x residue 16 LEU Chi-restraints excluded: chain x residue 39 THR Chi-restraints excluded: chain y residue 30 THR Chi-restraints excluded: chain y residue 35 VAL Chi-restraints excluded: chain y residue 39 ILE Chi-restraints excluded: chain y residue 86 LEU Chi-restraints excluded: chain z residue 53 VAL Chi-restraints excluded: chain z residue 62 ARG Chi-restraints excluded: chain z residue 70 LEU Chi-restraints excluded: chain 5 residue 34 LEU Chi-restraints excluded: chain 5 residue 111 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1083 random chunks: chunk 645 optimal weight: 5.9990 chunk 416 optimal weight: 10.0000 chunk 623 optimal weight: 0.9980 chunk 314 optimal weight: 10.0000 chunk 205 optimal weight: 7.9990 chunk 202 optimal weight: 7.9990 chunk 663 optimal weight: 2.9990 chunk 711 optimal weight: 4.9990 chunk 516 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 820 optimal weight: 4.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 GLN ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 ASN ** G 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 32 ASN i 131 ASN ** j 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 11 HIS n 75 GLN p 101 ASN ** q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 91 HIS u 79 ASN w 54 GLN ** w 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 168226 Z= 0.267 Angle : 0.678 13.988 251875 Z= 0.356 Chirality : 0.037 0.441 32159 Planarity : 0.006 0.128 13346 Dihedral : 23.981 179.749 84574 Min Nonbonded Distance : 1.084 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.32 % Favored : 92.66 % Rotamer: Outliers : 6.10 % Allowed : 28.10 % Favored : 65.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.11), residues: 5983 helix: 0.66 (0.12), residues: 2022 sheet: -1.73 (0.15), residues: 1111 loop : -2.19 (0.11), residues: 2850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP h 201 HIS 0.007 0.001 HIS k 11 PHE 0.027 0.002 PHE j 31 TYR 0.035 0.002 TYR O 99 ARG 0.009 0.000 ARG a 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11966 Ramachandran restraints generated. 5983 Oldfield, 0 Emsley, 5983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11966 Ramachandran restraints generated. 5983 Oldfield, 0 Emsley, 5983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1360 residues out of total 4954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 302 poor density : 1058 time to evaluate : 6.708 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: B 205 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8478 (mm) REVERT: C 30 GLU cc_start: 0.5165 (OUTLIER) cc_final: 0.4736 (tt0) REVERT: D 163 ASN cc_start: 0.8314 (OUTLIER) cc_final: 0.8091 (m-40) REVERT: E 17 MET cc_start: 0.7570 (ttm) cc_final: 0.7348 (ttm) REVERT: E 20 PHE cc_start: 0.7396 (OUTLIER) cc_final: 0.7167 (m-10) REVERT: E 81 GLN cc_start: 0.8451 (tm-30) cc_final: 0.8167 (tm-30) REVERT: E 85 ILE cc_start: 0.8441 (mt) cc_final: 0.8217 (mt) REVERT: E 96 MET cc_start: 0.8693 (tmm) cc_final: 0.7927 (tmm) REVERT: E 128 TYR cc_start: 0.8652 (t80) cc_final: 0.8367 (t80) REVERT: E 175 PHE cc_start: 0.7152 (OUTLIER) cc_final: 0.5431 (m-80) REVERT: F 49 THR cc_start: 0.6670 (OUTLIER) cc_final: 0.6413 (t) REVERT: F 153 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7579 (mtp180) REVERT: G 2 GLN cc_start: 0.7128 (mm110) cc_final: 0.5948 (mt0) REVERT: G 91 PHE cc_start: 0.6805 (OUTLIER) cc_final: 0.6605 (m-80) REVERT: H 122 GLN cc_start: 0.2188 (OUTLIER) cc_final: 0.1305 (pt0) REVERT: I 116 MET cc_start: 0.1991 (tpt) cc_final: 0.0519 (tpt) REVERT: J 2 LYS cc_start: 0.8096 (mtmt) cc_final: 0.7873 (pttp) REVERT: J 60 ASP cc_start: 0.8013 (p0) cc_final: 0.7604 (p0) REVERT: J 106 LYS cc_start: 0.8568 (tttm) cc_final: 0.8017 (ttmm) REVERT: K 92 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7330 (tm-30) REVERT: K 107 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7923 (mp) REVERT: L 76 GLU cc_start: 0.7267 (pt0) cc_final: 0.7032 (pt0) REVERT: M 13 HIS cc_start: 0.9064 (OUTLIER) cc_final: 0.8520 (m170) REVERT: M 82 MET cc_start: 0.8357 (mmp) cc_final: 0.8048 (mmt) REVERT: N 51 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8778 (mt) REVERT: N 72 ASP cc_start: 0.6430 (OUTLIER) cc_final: 0.6094 (m-30) REVERT: O 115 LEU cc_start: 0.8787 (mt) cc_final: 0.8575 (tp) REVERT: O 117 PHE cc_start: 0.7221 (p90) cc_final: 0.6813 (p90) REVERT: P 9 GLU cc_start: 0.6905 (tm-30) cc_final: 0.6660 (tt0) REVERT: Q 5 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8253 (ttmt) REVERT: Q 49 ASP cc_start: 0.7511 (m-30) cc_final: 0.7251 (m-30) REVERT: Q 89 GLU cc_start: 0.6410 (tp30) cc_final: 0.5991 (tp30) REVERT: S 11 ARG cc_start: 0.8479 (tpt90) cc_final: 0.8009 (tpt-90) REVERT: T 69 ARG cc_start: 0.7840 (ttp-110) cc_final: 0.7621 (ttm110) REVERT: U 5 ILE cc_start: 0.9324 (mm) cc_final: 0.9097 (mm) REVERT: U 17 LYS cc_start: 0.8124 (pttt) cc_final: 0.7751 (ttpt) REVERT: U 18 ASP cc_start: 0.8037 (p0) cc_final: 0.7112 (p0) REVERT: V 1 MET cc_start: 0.6263 (ptt) cc_final: 0.5966 (ptp) REVERT: V 29 ILE cc_start: 0.9246 (tp) cc_final: 0.8948 (tp) REVERT: V 40 ILE cc_start: 0.8830 (pt) cc_final: 0.8533 (pt) REVERT: W 68 LYS cc_start: 0.8884 (ttpp) cc_final: 0.8055 (tptp) REVERT: X 33 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8797 (mp) REVERT: X 54 LYS cc_start: 0.8527 (ttpt) cc_final: 0.8166 (ttmt) REVERT: Y 30 MET cc_start: 0.8250 (mmt) cc_final: 0.7958 (mmp) REVERT: Y 59 GLU cc_start: 0.6607 (OUTLIER) cc_final: 0.6238 (mt-10) REVERT: g 126 PHE cc_start: 0.6734 (t80) cc_final: 0.6265 (t80) REVERT: g 175 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7815 (mp0) REVERT: h 33 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8965 (mm) REVERT: h 86 LYS cc_start: 0.8537 (ttpt) cc_final: 0.7948 (tmtt) REVERT: i 9 LEU cc_start: 0.8949 (mt) cc_final: 0.8691 (mt) REVERT: i 64 ILE cc_start: 0.9034 (mt) cc_final: 0.8816 (mt) REVERT: i 103 TYR cc_start: 0.8541 (t80) cc_final: 0.8261 (t80) REVERT: j 64 MET cc_start: 0.7922 (tpp) cc_final: 0.7699 (tpp) REVERT: j 86 LYS cc_start: 0.8899 (mttt) cc_final: 0.8551 (mtpp) REVERT: j 106 ILE cc_start: 0.9171 (mm) cc_final: 0.8884 (mm) REVERT: k 5 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7608 (tm-30) REVERT: k 54 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7693 (mt) REVERT: k 102 MET cc_start: 0.7247 (ppp) cc_final: 0.6855 (ppp) REVERT: l 28 ASN cc_start: 0.8955 (m110) cc_final: 0.8694 (m-40) REVERT: l 101 MET cc_start: 0.8519 (mtm) cc_final: 0.8307 (mtm) REVERT: n 64 TYR cc_start: 0.7719 (t80) cc_final: 0.7057 (t80) REVERT: n 95 ARG cc_start: 0.7612 (tpp80) cc_final: 0.7269 (tpp80) REVERT: n 115 LYS cc_start: 0.8934 (mppt) cc_final: 0.8627 (mptt) REVERT: p 56 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.7056 (mtm180) REVERT: p 70 CYS cc_start: 0.8686 (t) cc_final: 0.8316 (t) REVERT: q 43 LYS cc_start: 0.8042 (pttm) cc_final: 0.7598 (mtpp) REVERT: r 102 THR cc_start: 0.9129 (p) cc_final: 0.8598 (m) REVERT: s 90 ARG cc_start: 0.7289 (ttm110) cc_final: 0.6950 (ttp-110) REVERT: t 11 ILE cc_start: 0.8332 (mm) cc_final: 0.8030 (mm) REVERT: u 31 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.7453 (ptm160) REVERT: u 40 ASN cc_start: 0.8429 (t0) cc_final: 0.8135 (t0) REVERT: v 17 MET cc_start: 0.7707 (ptt) cc_final: 0.7299 (ptt) REVERT: z 62 ARG cc_start: 0.5865 (OUTLIER) cc_final: 0.5411 (pmt-80) outliers start: 302 outliers final: 257 residues processed: 1260 average time/residue: 1.3807 time to fit residues: 3068.0875 Evaluate side-chains 1317 residues out of total 4954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 279 poor density : 1038 time to evaluate : 6.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 22 ASP Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 92 HIS Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 58 TYR Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 91 PHE Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 84 TYR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 122 GLN Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 37 ASP Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 89 ASN Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 100 CYS Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain Q residue 5 LYS Chi-restraints excluded: chain Q residue 110 VAL Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain R residue 95 ASP Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 106 VAL Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 60 GLU Chi-restraints excluded: chain U residue 65 ILE Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain U residue 101 GLU Chi-restraints excluded: chain U residue 103 ILE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 59 GLU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain W residue 35 SER Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 59 GLU Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 52 SER Chi-restraints excluded: chain a residue 33 ASN Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 36 GLU Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain c residue 29 THR Chi-restraints excluded: chain d residue 9 VAL Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 59 ILE Chi-restraints excluded: chain f residue 16 ILE Chi-restraints excluded: chain g residue 6 MET Chi-restraints excluded: chain g residue 14 VAL Chi-restraints excluded: chain g residue 21 ARG Chi-restraints excluded: chain g residue 82 ASP Chi-restraints excluded: chain g residue 125 THR Chi-restraints excluded: chain g residue 168 HIS Chi-restraints excluded: chain g residue 175 GLU Chi-restraints excluded: chain g residue 179 LEU Chi-restraints excluded: chain g residue 183 VAL Chi-restraints excluded: chain g residue 191 SER Chi-restraints excluded: chain g residue 196 VAL Chi-restraints excluded: chain h residue 10 ILE Chi-restraints excluded: chain h residue 20 SER Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 33 LEU Chi-restraints excluded: chain h residue 56 VAL Chi-restraints excluded: chain h residue 129 MET Chi-restraints excluded: chain h residue 143 ARG Chi-restraints excluded: chain h residue 149 ILE Chi-restraints excluded: chain h residue 177 THR Chi-restraints excluded: chain h residue 191 THR Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain i residue 41 HIS Chi-restraints excluded: chain i residue 116 GLN Chi-restraints excluded: chain i residue 137 VAL Chi-restraints excluded: chain j residue 37 THR Chi-restraints excluded: chain j residue 45 ARG Chi-restraints excluded: chain j residue 46 VAL Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 96 MET Chi-restraints excluded: chain j residue 122 ASN Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 70 VAL Chi-restraints excluded: chain k residue 71 ILE Chi-restraints excluded: chain l residue 6 VAL Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 72 THR Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain m residue 12 THR Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 79 SER Chi-restraints excluded: chain m residue 80 ARG Chi-restraints excluded: chain m residue 92 LEU Chi-restraints excluded: chain m residue 106 THR Chi-restraints excluded: chain m residue 111 MET Chi-restraints excluded: chain m residue 112 THR Chi-restraints excluded: chain m residue 125 ILE Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 28 ILE Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 104 VAL Chi-restraints excluded: chain n residue 105 THR Chi-restraints excluded: chain o residue 26 VAL Chi-restraints excluded: chain o residue 73 LEU Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 31 ILE Chi-restraints excluded: chain p residue 56 ARG Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 64 GLN Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain p residue 111 THR Chi-restraints excluded: chain q residue 20 ASN Chi-restraints excluded: chain q residue 39 THR Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 102 LEU Chi-restraints excluded: chain q residue 105 SER Chi-restraints excluded: chain q residue 107 VAL Chi-restraints excluded: chain r residue 12 HIS Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 20 THR Chi-restraints excluded: chain r residue 43 VAL Chi-restraints excluded: chain r residue 45 ILE Chi-restraints excluded: chain r residue 47 GLU Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 69 LEU Chi-restraints excluded: chain r residue 89 LEU Chi-restraints excluded: chain s residue 67 THR Chi-restraints excluded: chain s residue 80 SER Chi-restraints excluded: chain s residue 82 ILE Chi-restraints excluded: chain s residue 84 VAL Chi-restraints excluded: chain u residue 9 HIS Chi-restraints excluded: chain u residue 12 LYS Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 20 VAL Chi-restraints excluded: chain u residue 31 ARG Chi-restraints excluded: chain u residue 71 VAL Chi-restraints excluded: chain v residue 22 VAL Chi-restraints excluded: chain v residue 28 PHE Chi-restraints excluded: chain v residue 53 CYS Chi-restraints excluded: chain v residue 75 LEU Chi-restraints excluded: chain w residue 11 CYS Chi-restraints excluded: chain w residue 25 ASP Chi-restraints excluded: chain w residue 55 LEU Chi-restraints excluded: chain w residue 70 TYR Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 11 ILE Chi-restraints excluded: chain x residue 12 ASP Chi-restraints excluded: chain x residue 16 LEU Chi-restraints excluded: chain x residue 39 THR Chi-restraints excluded: chain y residue 30 THR Chi-restraints excluded: chain y residue 35 VAL Chi-restraints excluded: chain y residue 39 ILE Chi-restraints excluded: chain y residue 57 ILE Chi-restraints excluded: chain y residue 86 LEU Chi-restraints excluded: chain z residue 14 VAL Chi-restraints excluded: chain z residue 53 VAL Chi-restraints excluded: chain z residue 62 ARG Chi-restraints excluded: chain z residue 70 LEU Chi-restraints excluded: chain 5 residue 34 LEU Chi-restraints excluded: chain 5 residue 111 VAL Chi-restraints excluded: chain 5 residue 112 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1083 random chunks: chunk 949 optimal weight: 3.9990 chunk 1000 optimal weight: 0.0270 chunk 912 optimal weight: 7.9990 chunk 972 optimal weight: 5.9990 chunk 999 optimal weight: 9.9990 chunk 585 optimal weight: 6.9990 chunk 423 optimal weight: 10.0000 chunk 763 optimal weight: 3.9990 chunk 298 optimal weight: 30.0000 chunk 878 optimal weight: 0.9990 chunk 919 optimal weight: 10.0000 overall best weight: 3.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 GLN ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 ASN ** G 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 32 ASN i 131 ASN ** j 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 11 HIS n 75 GLN p 101 ASN ** q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 71 HIS u 79 ASN w 54 GLN ** w 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 168226 Z= 0.222 Angle : 0.646 14.026 251875 Z= 0.342 Chirality : 0.035 0.427 32159 Planarity : 0.006 0.126 13346 Dihedral : 23.948 179.198 84574 Min Nonbonded Distance : 1.106 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.80 % Favored : 93.18 % Rotamer: Outliers : 5.47 % Allowed : 29.27 % Favored : 65.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.11), residues: 5983 helix: 0.79 (0.12), residues: 2019 sheet: -1.67 (0.15), residues: 1106 loop : -2.12 (0.11), residues: 2858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP h 201 HIS 0.010 0.001 HIS M 13 PHE 0.020 0.002 PHE a 60 TYR 0.035 0.002 TYR O 99 ARG 0.009 0.000 ARG a 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11966 Ramachandran restraints generated. 5983 Oldfield, 0 Emsley, 5983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11966 Ramachandran restraints generated. 5983 Oldfield, 0 Emsley, 5983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1345 residues out of total 4954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 1074 time to evaluate : 5.964 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: B 205 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8420 (mm) REVERT: C 30 GLU cc_start: 0.5078 (OUTLIER) cc_final: 0.4660 (tt0) REVERT: D 163 ASN cc_start: 0.8278 (OUTLIER) cc_final: 0.8043 (m-40) REVERT: E 20 PHE cc_start: 0.7396 (OUTLIER) cc_final: 0.7166 (m-10) REVERT: E 81 GLN cc_start: 0.8452 (tm-30) cc_final: 0.8153 (tm-30) REVERT: E 85 ILE cc_start: 0.8460 (mt) cc_final: 0.8248 (mt) REVERT: E 96 MET cc_start: 0.8694 (tmm) cc_final: 0.8406 (tmm) REVERT: E 175 PHE cc_start: 0.7081 (OUTLIER) cc_final: 0.5375 (m-80) REVERT: F 49 THR cc_start: 0.6685 (OUTLIER) cc_final: 0.6438 (t) REVERT: F 153 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7571 (mtp180) REVERT: G 2 GLN cc_start: 0.7126 (mm110) cc_final: 0.6195 (mt0) REVERT: H 122 GLN cc_start: 0.2289 (OUTLIER) cc_final: 0.1280 (pt0) REVERT: I 116 MET cc_start: 0.1986 (tpt) cc_final: 0.0555 (tpt) REVERT: J 60 ASP cc_start: 0.7993 (p0) cc_final: 0.7602 (p0) REVERT: J 106 LYS cc_start: 0.8561 (tttm) cc_final: 0.7946 (ttmm) REVERT: K 92 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7347 (tm-30) REVERT: K 107 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7914 (mp) REVERT: L 58 TYR cc_start: 0.8492 (p90) cc_final: 0.7963 (p90) REVERT: L 76 GLU cc_start: 0.7195 (pt0) cc_final: 0.6992 (pt0) REVERT: M 13 HIS cc_start: 0.9057 (OUTLIER) cc_final: 0.8476 (m170) REVERT: M 44 ARG cc_start: 0.7973 (mtt-85) cc_final: 0.7546 (mtp85) REVERT: M 82 MET cc_start: 0.8386 (mmp) cc_final: 0.8049 (mmt) REVERT: N 51 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8787 (mt) REVERT: O 117 PHE cc_start: 0.7176 (p90) cc_final: 0.6816 (p90) REVERT: P 9 GLU cc_start: 0.6836 (tm-30) cc_final: 0.6525 (tt0) REVERT: Q 5 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8217 (ttmt) REVERT: Q 49 ASP cc_start: 0.7461 (m-30) cc_final: 0.7191 (m-30) REVERT: Q 89 GLU cc_start: 0.6349 (tp30) cc_final: 0.6059 (tp30) REVERT: S 11 ARG cc_start: 0.8470 (tpt90) cc_final: 0.7949 (tpt-90) REVERT: T 69 ARG cc_start: 0.7840 (ttp-110) cc_final: 0.7619 (ttm110) REVERT: U 5 ILE cc_start: 0.9286 (mm) cc_final: 0.9040 (mm) REVERT: U 17 LYS cc_start: 0.8119 (pttt) cc_final: 0.7732 (ttpt) REVERT: U 18 ASP cc_start: 0.7994 (p0) cc_final: 0.7095 (p0) REVERT: V 1 MET cc_start: 0.6232 (ptt) cc_final: 0.5967 (ptp) REVERT: V 40 ILE cc_start: 0.8744 (pt) cc_final: 0.8473 (pt) REVERT: W 68 LYS cc_start: 0.8887 (ttpp) cc_final: 0.8082 (tptp) REVERT: X 33 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8788 (mp) REVERT: X 54 LYS cc_start: 0.8497 (ttpt) cc_final: 0.8133 (ttmt) REVERT: Y 20 ASN cc_start: 0.7683 (m110) cc_final: 0.7441 (m-40) REVERT: Y 30 MET cc_start: 0.8181 (mmt) cc_final: 0.7895 (mmp) REVERT: Y 59 GLU cc_start: 0.6552 (OUTLIER) cc_final: 0.6222 (mt-10) REVERT: d 26 ASN cc_start: 0.8146 (OUTLIER) cc_final: 0.7831 (m-40) REVERT: g 175 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7833 (mp0) REVERT: h 33 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8961 (mm) REVERT: h 86 LYS cc_start: 0.8525 (ttpt) cc_final: 0.7940 (tmtt) REVERT: i 9 LEU cc_start: 0.8892 (mt) cc_final: 0.8640 (mt) REVERT: i 64 ILE cc_start: 0.9020 (mt) cc_final: 0.8801 (mt) REVERT: i 103 TYR cc_start: 0.8521 (t80) cc_final: 0.8251 (t80) REVERT: j 20 ARG cc_start: 0.8191 (ttt-90) cc_final: 0.7933 (tmm-80) REVERT: j 86 LYS cc_start: 0.8898 (mttt) cc_final: 0.8539 (mtpp) REVERT: j 106 ILE cc_start: 0.9137 (mm) cc_final: 0.8878 (mm) REVERT: k 5 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7477 (tm-30) REVERT: k 54 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7696 (mt) REVERT: k 102 MET cc_start: 0.7199 (ppp) cc_final: 0.6846 (ppp) REVERT: l 101 MET cc_start: 0.8565 (mtm) cc_final: 0.8365 (mtm) REVERT: n 64 TYR cc_start: 0.7698 (t80) cc_final: 0.6967 (t80) REVERT: n 115 LYS cc_start: 0.8923 (mppt) cc_final: 0.8659 (mptt) REVERT: p 70 CYS cc_start: 0.8694 (t) cc_final: 0.8356 (t) REVERT: q 43 LYS cc_start: 0.8005 (pttm) cc_final: 0.7559 (mtpp) REVERT: r 102 THR cc_start: 0.9093 (p) cc_final: 0.8562 (m) REVERT: s 90 ARG cc_start: 0.7306 (ttm110) cc_final: 0.6981 (ttp-110) REVERT: t 11 ILE cc_start: 0.8348 (mm) cc_final: 0.8068 (mm) REVERT: u 40 ASN cc_start: 0.8436 (t0) cc_final: 0.8119 (t0) REVERT: z 9 ASN cc_start: 0.8148 (t0) cc_final: 0.7944 (t0) REVERT: z 62 ARG cc_start: 0.6005 (OUTLIER) cc_final: 0.5158 (ttp80) outliers start: 271 outliers final: 229 residues processed: 1252 average time/residue: 1.3082 time to fit residues: 2877.4293 Evaluate side-chains 1287 residues out of total 4954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 1039 time to evaluate : 6.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 22 ASP Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 92 HIS Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 58 TYR Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 84 TYR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 122 GLN Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 100 CYS Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain Q residue 5 LYS Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain R residue 95 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 106 VAL Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 60 GLU Chi-restraints excluded: chain U residue 65 ILE Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain U residue 103 ILE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain W residue 35 SER Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 59 GLU Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 52 SER Chi-restraints excluded: chain a residue 33 ASN Chi-restraints excluded: chain a residue 38 SER Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 36 GLU Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain c residue 29 THR Chi-restraints excluded: chain d residue 9 VAL Chi-restraints excluded: chain d residue 26 ASN Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 59 ILE Chi-restraints excluded: chain f residue 16 ILE Chi-restraints excluded: chain g residue 6 MET Chi-restraints excluded: chain g residue 14 VAL Chi-restraints excluded: chain g residue 21 ARG Chi-restraints excluded: chain g residue 82 ASP Chi-restraints excluded: chain g residue 168 HIS Chi-restraints excluded: chain g residue 175 GLU Chi-restraints excluded: chain g residue 179 LEU Chi-restraints excluded: chain g residue 183 VAL Chi-restraints excluded: chain g residue 191 SER Chi-restraints excluded: chain g residue 196 VAL Chi-restraints excluded: chain h residue 10 ILE Chi-restraints excluded: chain h residue 20 SER Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 33 LEU Chi-restraints excluded: chain h residue 56 VAL Chi-restraints excluded: chain h residue 129 MET Chi-restraints excluded: chain h residue 143 ARG Chi-restraints excluded: chain h residue 149 ILE Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain i residue 116 GLN Chi-restraints excluded: chain i residue 137 VAL Chi-restraints excluded: chain j residue 37 THR Chi-restraints excluded: chain j residue 45 ARG Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain j residue 96 MET Chi-restraints excluded: chain j residue 122 ASN Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 70 VAL Chi-restraints excluded: chain k residue 71 ILE Chi-restraints excluded: chain l residue 6 VAL Chi-restraints excluded: chain l residue 72 THR Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain m residue 12 THR Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 79 SER Chi-restraints excluded: chain m residue 80 ARG Chi-restraints excluded: chain m residue 106 THR Chi-restraints excluded: chain m residue 111 MET Chi-restraints excluded: chain m residue 125 ILE Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 28 ILE Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 104 VAL Chi-restraints excluded: chain n residue 105 THR Chi-restraints excluded: chain o residue 26 VAL Chi-restraints excluded: chain o residue 73 LEU Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 31 ILE Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 64 GLN Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain p residue 111 THR Chi-restraints excluded: chain q residue 20 ASN Chi-restraints excluded: chain q residue 39 THR Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 102 LEU Chi-restraints excluded: chain q residue 105 SER Chi-restraints excluded: chain q residue 107 VAL Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 20 THR Chi-restraints excluded: chain r residue 43 VAL Chi-restraints excluded: chain r residue 45 ILE Chi-restraints excluded: chain r residue 47 GLU Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 89 LEU Chi-restraints excluded: chain s residue 67 THR Chi-restraints excluded: chain s residue 80 SER Chi-restraints excluded: chain s residue 82 ILE Chi-restraints excluded: chain s residue 84 VAL Chi-restraints excluded: chain u residue 9 HIS Chi-restraints excluded: chain u residue 12 LYS Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 20 VAL Chi-restraints excluded: chain u residue 71 VAL Chi-restraints excluded: chain u residue 79 ASN Chi-restraints excluded: chain v residue 22 VAL Chi-restraints excluded: chain v residue 28 PHE Chi-restraints excluded: chain v residue 53 CYS Chi-restraints excluded: chain v residue 75 LEU Chi-restraints excluded: chain w residue 11 CYS Chi-restraints excluded: chain w residue 25 ASP Chi-restraints excluded: chain w residue 55 LEU Chi-restraints excluded: chain w residue 70 TYR Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 11 ILE Chi-restraints excluded: chain x residue 12 ASP Chi-restraints excluded: chain x residue 16 LEU Chi-restraints excluded: chain x residue 39 THR Chi-restraints excluded: chain y residue 30 THR Chi-restraints excluded: chain y residue 35 VAL Chi-restraints excluded: chain y residue 86 LEU Chi-restraints excluded: chain z residue 14 VAL Chi-restraints excluded: chain z residue 62 ARG Chi-restraints excluded: chain z residue 70 LEU Chi-restraints excluded: chain 5 residue 34 LEU Chi-restraints excluded: chain 5 residue 111 VAL Chi-restraints excluded: chain 5 residue 112 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1083 random chunks: chunk 969 optimal weight: 5.9990 chunk 638 optimal weight: 0.6980 chunk 1028 optimal weight: 5.9990 chunk 627 optimal weight: 5.9990 chunk 487 optimal weight: 8.9990 chunk 715 optimal weight: 2.9990 chunk 1078 optimal weight: 40.0000 chunk 993 optimal weight: 6.9990 chunk 859 optimal weight: 2.9990 chunk 89 optimal weight: 20.0000 chunk 663 optimal weight: 3.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 GLN ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 109 GLN h 32 ASN i 131 ASN ** j 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 11 HIS n 75 GLN p 101 ASN ** q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 54 GLN ** w 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.189 168226 Z= 0.250 Angle : 0.677 59.198 251875 Z= 0.365 Chirality : 0.036 0.803 32159 Planarity : 0.006 0.151 13346 Dihedral : 23.946 179.196 84574 Min Nonbonded Distance : 1.105 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.84 % Favored : 93.13 % Rotamer: Outliers : 5.31 % Allowed : 29.49 % Favored : 65.20 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.49 % 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: -1.53 (0.11), residues: 5983 helix: 0.79 (0.12), residues: 2018 sheet: -1.66 (0.15), residues: 1106 loop : -2.11 (0.11), residues: 2859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP h 201 HIS 0.010 0.001 HIS M 13 PHE 0.027 0.002 PHE G 91 TYR 0.033 0.002 TYR O 99 ARG 0.012 0.000 ARG n 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11966 Ramachandran restraints generated. 5983 Oldfield, 0 Emsley, 5983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11966 Ramachandran restraints generated. 5983 Oldfield, 0 Emsley, 5983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1302 residues out of total 4954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 1039 time to evaluate : 6.658 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: B 205 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8421 (mm) REVERT: C 30 GLU cc_start: 0.5077 (OUTLIER) cc_final: 0.4658 (tt0) REVERT: D 163 ASN cc_start: 0.8281 (OUTLIER) cc_final: 0.8046 (m-40) REVERT: E 20 PHE cc_start: 0.7381 (OUTLIER) cc_final: 0.7165 (m-10) REVERT: E 81 GLN cc_start: 0.8457 (tm-30) cc_final: 0.8156 (tm-30) REVERT: E 85 ILE cc_start: 0.8455 (mt) cc_final: 0.8250 (mt) REVERT: E 96 MET cc_start: 0.8689 (tmm) cc_final: 0.8405 (tmm) REVERT: E 175 PHE cc_start: 0.7061 (OUTLIER) cc_final: 0.5409 (m-80) REVERT: F 49 THR cc_start: 0.6684 (OUTLIER) cc_final: 0.6439 (t) REVERT: F 153 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7573 (mtp180) REVERT: G 2 GLN cc_start: 0.7079 (mm110) cc_final: 0.6189 (mt0) REVERT: H 122 GLN cc_start: 0.2287 (OUTLIER) cc_final: 0.1280 (pt0) REVERT: I 116 MET cc_start: 0.1988 (tpt) cc_final: 0.0551 (tpt) REVERT: J 60 ASP cc_start: 0.7993 (p0) cc_final: 0.7602 (p0) REVERT: J 106 LYS cc_start: 0.8570 (tttm) cc_final: 0.7947 (ttmm) REVERT: K 92 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7347 (tm-30) REVERT: K 107 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7916 (mp) REVERT: L 58 TYR cc_start: 0.8497 (p90) cc_final: 0.7965 (p90) REVERT: L 76 GLU cc_start: 0.7197 (pt0) cc_final: 0.6994 (pt0) REVERT: M 13 HIS cc_start: 0.9057 (OUTLIER) cc_final: 0.8478 (m170) REVERT: M 44 ARG cc_start: 0.7972 (mtt-85) cc_final: 0.7548 (mtp85) REVERT: M 82 MET cc_start: 0.8387 (mmp) cc_final: 0.8050 (mmt) REVERT: N 51 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8786 (mt) REVERT: O 117 PHE cc_start: 0.7134 (p90) cc_final: 0.6818 (p90) REVERT: P 9 GLU cc_start: 0.6837 (tm-30) cc_final: 0.6529 (tt0) REVERT: Q 5 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8219 (ttmt) REVERT: Q 49 ASP cc_start: 0.7473 (m-30) cc_final: 0.7197 (m-30) REVERT: Q 89 GLU cc_start: 0.6419 (tp30) cc_final: 0.6061 (tp30) REVERT: S 11 ARG cc_start: 0.8467 (tpt90) cc_final: 0.7949 (tpt-90) REVERT: T 69 ARG cc_start: 0.7841 (ttp-110) cc_final: 0.7620 (ttm110) REVERT: U 5 ILE cc_start: 0.9289 (mm) cc_final: 0.9040 (mm) REVERT: U 17 LYS cc_start: 0.8114 (pttt) cc_final: 0.7733 (ttpt) REVERT: U 18 ASP cc_start: 0.7995 (p0) cc_final: 0.7097 (p0) REVERT: V 1 MET cc_start: 0.6238 (ptt) cc_final: 0.5971 (ptp) REVERT: V 40 ILE cc_start: 0.8756 (pt) cc_final: 0.8475 (pt) REVERT: W 68 LYS cc_start: 0.8889 (ttpp) cc_final: 0.8078 (tptp) REVERT: X 33 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8788 (mp) REVERT: X 54 LYS cc_start: 0.8499 (ttpt) cc_final: 0.8132 (ttmt) REVERT: Y 20 ASN cc_start: 0.7686 (m110) cc_final: 0.7445 (m-40) REVERT: Y 30 MET cc_start: 0.8190 (mmt) cc_final: 0.7897 (mmp) REVERT: Y 59 GLU cc_start: 0.6551 (OUTLIER) cc_final: 0.6223 (mt-10) REVERT: d 26 ASN cc_start: 0.8091 (OUTLIER) cc_final: 0.7846 (m-40) REVERT: g 175 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7835 (mp0) REVERT: h 33 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8962 (mm) REVERT: h 86 LYS cc_start: 0.8525 (ttpt) cc_final: 0.7942 (tmtt) REVERT: i 9 LEU cc_start: 0.8892 (mt) cc_final: 0.8641 (mt) REVERT: i 64 ILE cc_start: 0.9023 (mt) cc_final: 0.8801 (mt) REVERT: i 103 TYR cc_start: 0.8540 (t80) cc_final: 0.8251 (t80) REVERT: j 86 LYS cc_start: 0.8893 (mttt) cc_final: 0.8538 (mtpp) REVERT: j 106 ILE cc_start: 0.9150 (mm) cc_final: 0.8879 (mm) REVERT: k 5 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7479 (tm-30) REVERT: k 54 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7698 (mt) REVERT: k 102 MET cc_start: 0.7221 (ppp) cc_final: 0.6852 (ppp) REVERT: l 101 MET cc_start: 0.8567 (mtm) cc_final: 0.8365 (mtm) REVERT: n 64 TYR cc_start: 0.7704 (t80) cc_final: 0.6968 (t80) REVERT: n 115 LYS cc_start: 0.8922 (mppt) cc_final: 0.8658 (mptt) REVERT: p 70 CYS cc_start: 0.8698 (t) cc_final: 0.8356 (t) REVERT: q 43 LYS cc_start: 0.8005 (pttm) cc_final: 0.7561 (mtpp) REVERT: r 102 THR cc_start: 0.9091 (p) cc_final: 0.8564 (m) REVERT: s 90 ARG cc_start: 0.7308 (ttm110) cc_final: 0.6975 (ttp-110) REVERT: t 11 ILE cc_start: 0.8348 (mm) cc_final: 0.8070 (mm) REVERT: u 40 ASN cc_start: 0.8437 (t0) cc_final: 0.8121 (t0) REVERT: u 79 ASN cc_start: 0.7931 (m110) cc_final: 0.6839 (t0) REVERT: z 9 ASN cc_start: 0.8148 (t0) cc_final: 0.7943 (t0) REVERT: z 62 ARG cc_start: 0.6010 (OUTLIER) cc_final: 0.5567 (pmt-80) outliers start: 263 outliers final: 235 residues processed: 1213 average time/residue: 1.3154 time to fit residues: 2796.0767 Evaluate side-chains 1292 residues out of total 4954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 1038 time to evaluate : 6.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 22 ASP Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 92 HIS Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 175 PHE Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 58 TYR Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 84 TYR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 122 GLN Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 37 ASP Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 100 CYS Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain Q residue 5 LYS Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain R residue 95 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 106 VAL Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 60 GLU Chi-restraints excluded: chain U residue 65 ILE Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain U residue 103 ILE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain W residue 35 SER Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 59 GLU Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 52 SER Chi-restraints excluded: chain a residue 33 ASN Chi-restraints excluded: chain a residue 38 SER Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 36 GLU Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain c residue 29 THR Chi-restraints excluded: chain d residue 9 VAL Chi-restraints excluded: chain d residue 26 ASN Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 59 ILE Chi-restraints excluded: chain f residue 16 ILE Chi-restraints excluded: chain g residue 6 MET Chi-restraints excluded: chain g residue 14 VAL Chi-restraints excluded: chain g residue 21 ARG Chi-restraints excluded: chain g residue 82 ASP Chi-restraints excluded: chain g residue 125 THR Chi-restraints excluded: chain g residue 168 HIS Chi-restraints excluded: chain g residue 175 GLU Chi-restraints excluded: chain g residue 179 LEU Chi-restraints excluded: chain g residue 183 VAL Chi-restraints excluded: chain g residue 191 SER Chi-restraints excluded: chain g residue 196 VAL Chi-restraints excluded: chain h residue 10 ILE Chi-restraints excluded: chain h residue 20 SER Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 33 LEU Chi-restraints excluded: chain h residue 56 VAL Chi-restraints excluded: chain h residue 129 MET Chi-restraints excluded: chain h residue 143 ARG Chi-restraints excluded: chain h residue 149 ILE Chi-restraints excluded: chain h residue 191 THR Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain i residue 116 GLN Chi-restraints excluded: chain i residue 137 VAL Chi-restraints excluded: chain j residue 37 THR Chi-restraints excluded: chain j residue 45 ARG Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain j residue 96 MET Chi-restraints excluded: chain j residue 122 ASN Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 70 VAL Chi-restraints excluded: chain k residue 71 ILE Chi-restraints excluded: chain l residue 6 VAL Chi-restraints excluded: chain l residue 22 LEU Chi-restraints excluded: chain l residue 72 THR Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain m residue 12 THR Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 79 SER Chi-restraints excluded: chain m residue 80 ARG Chi-restraints excluded: chain m residue 111 MET Chi-restraints excluded: chain m residue 125 ILE Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 28 ILE Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 61 LEU Chi-restraints excluded: chain n residue 104 VAL Chi-restraints excluded: chain n residue 105 THR Chi-restraints excluded: chain o residue 6 ILE Chi-restraints excluded: chain o residue 26 VAL Chi-restraints excluded: chain o residue 73 LEU Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 31 ILE Chi-restraints excluded: chain p residue 59 THR Chi-restraints excluded: chain p residue 64 GLN Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain p residue 111 THR Chi-restraints excluded: chain q residue 20 ASN Chi-restraints excluded: chain q residue 39 THR Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 102 LEU Chi-restraints excluded: chain q residue 105 SER Chi-restraints excluded: chain q residue 107 VAL Chi-restraints excluded: chain r residue 16 VAL Chi-restraints excluded: chain r residue 20 THR Chi-restraints excluded: chain r residue 43 VAL Chi-restraints excluded: chain r residue 45 ILE Chi-restraints excluded: chain r residue 47 GLU Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 69 LEU Chi-restraints excluded: chain r residue 89 LEU Chi-restraints excluded: chain s residue 67 THR Chi-restraints excluded: chain s residue 80 SER Chi-restraints excluded: chain s residue 82 ILE Chi-restraints excluded: chain s residue 84 VAL Chi-restraints excluded: chain u residue 9 HIS Chi-restraints excluded: chain u residue 12 LYS Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 20 VAL Chi-restraints excluded: chain u residue 71 VAL Chi-restraints excluded: chain v residue 22 VAL Chi-restraints excluded: chain v residue 28 PHE Chi-restraints excluded: chain v residue 53 CYS Chi-restraints excluded: chain v residue 75 LEU Chi-restraints excluded: chain w residue 11 CYS Chi-restraints excluded: chain w residue 25 ASP Chi-restraints excluded: chain w residue 55 LEU Chi-restraints excluded: chain w residue 70 TYR Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 11 ILE Chi-restraints excluded: chain x residue 12 ASP Chi-restraints excluded: chain x residue 16 LEU Chi-restraints excluded: chain x residue 39 THR Chi-restraints excluded: chain y residue 30 THR Chi-restraints excluded: chain y residue 35 VAL Chi-restraints excluded: chain y residue 86 LEU Chi-restraints excluded: chain z residue 14 VAL Chi-restraints excluded: chain z residue 62 ARG Chi-restraints excluded: chain z residue 70 LEU Chi-restraints excluded: chain 5 residue 34 LEU Chi-restraints excluded: chain 5 residue 111 VAL Chi-restraints excluded: chain 5 residue 112 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1083 random chunks: chunk 526 optimal weight: 6.9990 chunk 682 optimal weight: 0.7980 chunk 915 optimal weight: 5.9990 chunk 263 optimal weight: 10.0000 chunk 792 optimal weight: 8.9990 chunk 126 optimal weight: 8.9990 chunk 238 optimal weight: 10.0000 chunk 860 optimal weight: 2.9990 chunk 360 optimal weight: 10.0000 chunk 883 optimal weight: 4.9990 chunk 108 optimal weight: 30.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 GLN ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 109 GLN h 32 ASN i 131 ASN ** j 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 11 HIS ** k 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 25 ASN n 75 GLN p 101 ASN ** q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 54 GLN ** w 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.120816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.098774 restraints weight = 357718.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.099414 restraints weight = 211917.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.099464 restraints weight = 210969.291| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3312 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3312 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.189 168226 Z= 0.250 Angle : 0.677 59.155 251875 Z= 0.365 Chirality : 0.036 0.800 32159 Planarity : 0.006 0.151 13346 Dihedral : 23.946 179.196 84574 Min Nonbonded Distance : 1.105 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.84 % Favored : 93.13 % Rotamer: Outliers : 5.13 % Allowed : 29.65 % Favored : 65.22 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.49 % 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: -1.53 (0.11), residues: 5983 helix: 0.79 (0.12), residues: 2018 sheet: -1.66 (0.15), residues: 1106 loop : -2.11 (0.11), residues: 2859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP h 201 HIS 0.010 0.001 HIS M 13 PHE 0.027 0.002 PHE G 91 TYR 0.033 0.002 TYR O 99 ARG 0.012 0.000 ARG n 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 39879.85 seconds wall clock time: 698 minutes 6.89 seconds (41886.89 seconds total)