Starting phenix.real_space_refine on Mon Apr 15 02:52:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7h_33665/04_2024/7y7h_33665_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7h_33665/04_2024/7y7h_33665.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7h_33665/04_2024/7y7h_33665_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7h_33665/04_2024/7y7h_33665_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7h_33665/04_2024/7y7h_33665_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7h_33665/04_2024/7y7h_33665.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7h_33665/04_2024/7y7h_33665.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7h_33665/04_2024/7y7h_33665_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7h_33665/04_2024/7y7h_33665_updated.pdb" } resolution = 2.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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: 6 Type Number sf(0) Gaussians P 4557 5.49 5 Mg 263 5.21 5 S 150 5.16 5 C 71128 2.51 5 N 26436 2.21 5 O 39431 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 175": "OE1" <-> "OE2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "C GLU 85": "OE1" <-> "OE2" Residue "C GLU 110": "OE1" <-> "OE2" Residue "C ASP 118": "OD1" <-> "OD2" Residue "C GLU 125": "OE1" <-> "OE2" Residue "C ARG 131": "NH1" <-> "NH2" Residue "C TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D GLU 78": "OE1" <-> "OE2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D GLU 147": "OE1" <-> "OE2" Residue "D GLU 163": "OE1" <-> "OE2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "D GLU 197": "OE1" <-> "OE2" Residue "E ASP 41": "OD1" <-> "OD2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E GLU 101": "OE1" <-> "OE2" Residue "E GLU 116": "OE1" <-> "OE2" Residue "E GLU 151": "OE1" <-> "OE2" Residue "F ASP 41": "OD1" <-> "OD2" Residue "F TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 73": "OE1" <-> "OE2" Residue "G GLU 21": "OE1" <-> "OE2" Residue "G GLU 48": "OE1" <-> "OE2" Residue "G GLU 63": "OE1" <-> "OE2" Residue "G GLU 67": "OE1" <-> "OE2" Residue "G GLU 74": "OE1" <-> "OE2" Residue "G GLU 90": "OE1" <-> "OE2" Residue "G GLU 106": "OE1" <-> "OE2" Residue "H ASP 5": "OD1" <-> "OD2" Residue "H GLU 52": "OE1" <-> "OE2" Residue "I TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 53": "OE1" <-> "OE2" Residue "I ARG 95": "NH1" <-> "NH2" Residue "I GLU 112": "OE1" <-> "OE2" Residue "I ARG 124": "NH1" <-> "NH2" Residue "J GLU 24": "OE1" <-> "OE2" Residue "K GLU 68": "OE1" <-> "OE2" Residue "L ARG 14": "NH1" <-> "NH2" Residue "L ARG 56": "NH1" <-> "NH2" Residue "M ASP 11": "OD1" <-> "OD2" Residue "M TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 41": "OE1" <-> "OE2" Residue "M GLU 59": "OE1" <-> "OE2" Residue "M ASP 82": "OD1" <-> "OD2" Residue "N TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 39": "OE1" <-> "OE2" Residue "N ARG 65": "NH1" <-> "NH2" Residue "N GLU 86": "OE1" <-> "OE2" Residue "N GLU 92": "OE1" <-> "OE2" Residue "O GLU 14": "OE1" <-> "OE2" Residue "O PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 26": "OE1" <-> "OE2" Residue "O GLU 45": "OE1" <-> "OE2" Residue "P ARG 28": "NH1" <-> "NH2" Residue "P GLU 34": "OE1" <-> "OE2" Residue "P PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 15": "OD1" <-> "OD2" Residue "Q GLU 63": "OE1" <-> "OE2" Residue "R ASP 25": "OD1" <-> "OD2" Residue "S ARG 3": "NH1" <-> "NH2" Residue "S ARG 32": "NH1" <-> "NH2" Residue "S GLU 65": "OE1" <-> "OE2" Residue "S ARG 81": "NH1" <-> "NH2" Residue "T TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 40": "OE1" <-> "OE2" Residue "U ARG 35": "NH1" <-> "NH2" Residue "U ARG 66": "NH1" <-> "NH2" Residue "c GLU 35": "OE1" <-> "OE2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "c ARG 63": "NH1" <-> "NH2" Residue "c ARG 80": "NH1" <-> "NH2" Residue "c ARG 133": "NH1" <-> "NH2" Residue "c GLU 145": "OE1" <-> "OE2" Residue "c ARG 167": "NH1" <-> "NH2" Residue "c ARG 177": "NH1" <-> "NH2" Residue "c GLU 180": "OE1" <-> "OE2" Residue "c ARG 182": "NH1" <-> "NH2" Residue "c ARG 189": "NH1" <-> "NH2" Residue "c ARG 203": "NH1" <-> "NH2" Residue "c ARG 212": "NH1" <-> "NH2" Residue "c GLU 236": "OE1" <-> "OE2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d GLU 17": "OE1" <-> "OE2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "d ARG 59": "NH1" <-> "NH2" Residue "d GLU 64": "OE1" <-> "OE2" Residue "d ARG 83": "NH1" <-> "NH2" Residue "d GLU 88": "OE1" <-> "OE2" Residue "d GLU 89": "OE1" <-> "OE2" Residue "d ARG 169": "NH1" <-> "NH2" Residue "d GLU 183": "OE1" <-> "OE2" Residue "e GLU 16": "OE1" <-> "OE2" Residue "e PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 44": "NH1" <-> "NH2" Residue "e ARG 49": "NH1" <-> "NH2" Residue "e ARG 61": "NH1" <-> "NH2" Residue "e ARG 88": "NH1" <-> "NH2" Residue "e TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 102": "NH1" <-> "NH2" Residue "e GLU 155": "OE1" <-> "OE2" Residue "e ARG 162": "NH1" <-> "NH2" Residue "e ARG 170": "NH1" <-> "NH2" Residue "f TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 32": "OE1" <-> "OE2" Residue "f GLU 42": "OE1" <-> "OE2" Residue "f ARG 71": "NH1" <-> "NH2" Residue "f ARG 80": "NH1" <-> "NH2" Residue "f TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 92": "NH1" <-> "NH2" Residue "f GLU 101": "OE1" <-> "OE2" Residue "f ARG 102": "NH1" <-> "NH2" Residue "f ARG 110": "NH1" <-> "NH2" Residue "f ARG 112": "NH1" <-> "NH2" Residue "f ARG 115": "NH1" <-> "NH2" Residue "f ARG 133": "NH1" <-> "NH2" Residue "f GLU 134": "OE1" <-> "OE2" Residue "g ARG 3": "NH1" <-> "NH2" Residue "g GLU 42": "OE1" <-> "OE2" Residue "g TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 81": "OE1" <-> "OE2" Residue "g ASP 114": "OD1" <-> "OD2" Residue "g ARG 153": "NH1" <-> "NH2" Residue "g GLU 155": "OE1" <-> "OE2" Residue "g ARG 163": "NH1" <-> "NH2" Residue "g GLU 167": "OE1" <-> "OE2" Residue "g ARG 170": "NH1" <-> "NH2" Residue "h ARG 27": "NH1" <-> "NH2" Residue "i ARG 13": "NH1" <-> "NH2" Residue "i ARG 37": "NH1" <-> "NH2" Residue "i GLU 43": "OE1" <-> "OE2" Residue "i GLU 91": "OE1" <-> "OE2" Residue "i ARG 96": "NH1" <-> "NH2" Residue "i ARG 120": "NH1" <-> "NH2" Residue "j GLU 45": "OE1" <-> "OE2" Residue "j GLU 92": "OE1" <-> "OE2" Residue "k ARG 21": "NH1" <-> "NH2" Residue "k ARG 33": "NH1" <-> "NH2" Residue "k ARG 41": "NH1" <-> "NH2" Residue "k ARG 47": "NH1" <-> "NH2" Residue "k GLU 51": "OE1" <-> "OE2" Residue "k TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 60": "NH1" <-> "NH2" Residue "k PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 78": "NH1" <-> "NH2" Residue "k ASP 91": "OD1" <-> "OD2" Residue "k ARG 126": "NH1" <-> "NH2" Residue "k GLU 136": "OE1" <-> "OE2" Residue "l ARG 10": "NH1" <-> "NH2" Residue "l ARG 18": "NH1" <-> "NH2" Residue "l ARG 40": "NH1" <-> "NH2" Residue "l ARG 44": "NH1" <-> "NH2" Residue "l GLU 47": "OE1" <-> "OE2" Residue "l ARG 50": "NH1" <-> "NH2" Residue "l ARG 55": "NH1" <-> "NH2" Residue "l ASP 70": "OD1" <-> "OD2" Residue "l GLU 75": "OE1" <-> "OE2" Residue "l ARG 114": "NH1" <-> "NH2" Residue "m ARG 12": "NH1" <-> "NH2" Residue "m ARG 17": "NH1" <-> "NH2" Residue "m ARG 22": "NH1" <-> "NH2" Residue "m GLU 32": "OE1" <-> "OE2" Residue "m GLU 43": "OE1" <-> "OE2" Residue "m ARG 46": "NH1" <-> "NH2" Residue "m GLU 49": "OE1" <-> "OE2" Residue "m ARG 63": "NH1" <-> "NH2" Residue "m ARG 64": "NH1" <-> "NH2" Residue "m ARG 69": "NH1" <-> "NH2" Residue "m ARG 71": "NH1" <-> "NH2" Residue "m GLU 74": "OE1" <-> "OE2" Residue "m ARG 96": "NH1" <-> "NH2" Residue "m ARG 118": "NH1" <-> "NH2" Residue "n ARG 10": "NH1" <-> "NH2" Residue "n ARG 16": "NH1" <-> "NH2" Residue "n ARG 25": "NH1" <-> "NH2" Residue "n GLU 46": "OE1" <-> "OE2" Residue "n GLU 80": "OE1" <-> "OE2" Residue "n ARG 81": "NH1" <-> "NH2" Residue "n ARG 94": "NH1" <-> "NH2" Residue "n ARG 102": "NH1" <-> "NH2" Residue "n ARG 111": "NH1" <-> "NH2" Residue "n GLU 112": "OE1" <-> "OE2" Residue "o ARG 21": "NH1" <-> "NH2" Residue "o GLU 27": "OE1" <-> "OE2" Residue "o ARG 39": "NH1" <-> "NH2" Residue "o PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 44": "OE1" <-> "OE2" Residue "o ASP 82": "OD1" <-> "OD2" Residue "o ARG 89": "NH1" <-> "NH2" Residue "o ARG 101": "NH1" <-> "NH2" Residue "o ARG 109": "NH1" <-> "NH2" Residue "o GLU 112": "OE1" <-> "OE2" Residue "p ARG 3": "NH1" <-> "NH2" Residue "p ARG 6": "NH1" <-> "NH2" Residue "p ARG 13": "NH1" <-> "NH2" Residue "p ARG 33": "NH1" <-> "NH2" Residue "p ARG 48": "NH1" <-> "NH2" Residue "p ASP 91": "OD1" <-> "OD2" Residue "p ASP 102": "OD1" <-> "OD2" Residue "p PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 21": "NH1" <-> "NH2" Residue "q GLU 23": "OE1" <-> "OE2" Residue "q GLU 46": "OE1" <-> "OE2" Residue "q GLU 62": "OE1" <-> "OE2" Residue "q ARG 68": "NH1" <-> "NH2" Residue "q ARG 79": "NH1" <-> "NH2" Residue "q ARG 84": "NH1" <-> "NH2" Residue "r GLU 2": "OE1" <-> "OE2" Residue "r ARG 84": "NH1" <-> "NH2" Residue "r ARG 88": "NH1" <-> "NH2" Residue "r ARG 95": "NH1" <-> "NH2" Residue "r ARG 110": "NH1" <-> "NH2" Residue "s GLU 5": "OE1" <-> "OE2" Residue "s ARG 73": "NH1" <-> "NH2" Residue "t ARG 6": "NH1" <-> "NH2" Residue "t ARG 7": "NH1" <-> "NH2" Residue "t ASP 18": "OD1" <-> "OD2" Residue "t GLU 62": "OE1" <-> "OE2" Residue "t ASP 81": "OD1" <-> "OD2" Residue "t ARG 82": "NH1" <-> "NH2" Residue "t ARG 86": "NH1" <-> "NH2" Residue "t GLU 88": "OE1" <-> "OE2" Residue "t ARG 94": "NH1" <-> "NH2" Residue "u GLU 11": "OE1" <-> "OE2" Residue "u GLU 41": "OE1" <-> "OE2" Residue "u TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 17": "OE1" <-> "OE2" Residue "v GLU 83": "OE1" <-> "OE2" Residue "w ARG 3": "NH1" <-> "NH2" Residue "w ARG 11": "NH1" <-> "NH2" Residue "w PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ARG 37": "NH1" <-> "NH2" Residue "w GLU 41": "OE1" <-> "OE2" Residue "w GLU 43": "OE1" <-> "OE2" Residue "w ARG 50": "NH1" <-> "NH2" Residue "w ARG 57": "NH1" <-> "NH2" Residue "w ARG 74": "NH1" <-> "NH2" Residue "x GLU 8": "OE1" <-> "OE2" Residue "x ARG 29": "NH1" <-> "NH2" Residue "x ARG 47": "NH1" <-> "NH2" Residue "x ARG 52": "NH1" <-> "NH2" Residue "y ARG 11": "NH1" <-> "NH2" Residue "y ARG 30": "NH1" <-> "NH2" Residue "y GLU 39": "OE1" <-> "OE2" Residue "y ARG 45": "NH1" <-> "NH2" Residue "z ARG 10": "NH1" <-> "NH2" Residue "z ARG 16": "NH1" <-> "NH2" Residue "z GLU 36": "OE1" <-> "OE2" Residue "z ARG 52": "NH1" <-> "NH2" Residue "0 GLU 7": "OE1" <-> "OE2" Residue "0 ARG 44": "NH1" <-> "NH2" Residue "1 ARG 3": "NH1" <-> "NH2" Residue "1 ARG 12": "NH1" <-> "NH2" Residue "1 ARG 14": "NH1" <-> "NH2" Residue "1 ARG 21": "NH1" <-> "NH2" Residue "1 ARG 33": "NH1" <-> "NH2" Residue "1 ARG 41": "NH1" <-> "NH2" Residue "2 ARG 13": "NH1" <-> "NH2" Residue "2 ARG 30": "NH1" <-> "NH2" Residue "2 ARG 40": "NH1" <-> "NH2" Residue "2 ASP 54": "OD1" <-> "OD2" Residue "3 ARG 24": "NH1" <-> "NH2" Residue "4 GLU 11": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 141965 Number of models: 1 Model: "" Number of chains: 64 Chain: "A" Number of atoms: 32634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1520, 32634 Classifications: {'RNA': 1520} Modifications used: {'rna2p': 1, 'rna2p_pur': 120, 'rna2p_pyr': 82, 'rna3p': 10, 'rna3p_pur': 743, 'rna3p_pyr': 564} Link IDs: {'rna2p': 203, 'rna3p': 1316} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 7 Chain: "B" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "C" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "F" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 839 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "G" Number of atoms: 1203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1203 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 5, 'TRANS': 147} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 92} Chain: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'IAS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D2T:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "N" 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: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 643 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "Q" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 641 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" 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: "S" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 668 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "T" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "U" 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: "a" Number of atoms: 59130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2753, 59130 Classifications: {'RNA': 2753} Modifications used: {'rna2p': 7, 'rna2p_pur': 267, 'rna2p_pyr': 139, 'rna3p': 17, 'rna3p_pur': 1318, 'rna3p_pyr': 1005} Link IDs: {'rna2p': 412, 'rna3p': 2340} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 10 Chain: "b" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2549 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 49} Link IDs: {'rna2p': 13, 'rna3p': 105} Chain: "c" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "d" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1566 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEQ:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "f" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "g" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "h" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 303 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "i" 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: "j" 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: "k" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "l" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1075 Unusual residues: {'MS6': 1} Classifications: {'peptide': 135, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126, None: 2} Not linked: pdbres="4D4 l 81 " pdbres="MS6 l 82 " Not linked: pdbres="MS6 l 82 " pdbres="GLY l 83 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4D4:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "m" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 945 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "n" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "o" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "p" 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: "q" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'TRANS': 101} Chain: "r" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "s" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "t" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "u" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "v" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 628 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "w" 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: "x" 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: "y" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "z" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "0" 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: "1" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "2" 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: "3" 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: "4" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 480 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain breaks: 1 Chain: "X" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 276 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 5, 'rna3p_pyr': 6} Link IDs: {'rna2p': 2, 'rna3p': 10} Chain: "Z" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1645 Classifications: {'RNA': 77} Modifications used: {'p5*END': 1, 'rna2p': 1, 'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p': 4, 'rna3p_pur': 35, 'rna3p_pyr': 30} Link IDs: {'rna2p': 8, 'rna3p': 68} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 3 Chain: "V" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1647 Classifications: {'RNA': 76} Modifications used: {'5*END': 1, 'rna2p': 4, 'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p': 13, 'rna3p_pur': 27, 'rna3p_pyr': 25} Link IDs: {'rna2p': 11, 'rna3p': 64} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 11 Chain: "A" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Unusual residues: {' MG': 68} Classifications: {'undetermined': 68} Link IDs: {None: 67} Chain: "a" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 184 Unusual residues: {' MG': 184} Classifications: {'undetermined': 184} Link IDs: {None: 183} Chain: "b" 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: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "V" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'GAL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 55.65, per 1000 atoms: 0.39 Number of scatterers: 141965 At special positions: 0 Unit cell: (251.035, 239.436, 246.893, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 150 16.00 P 4557 15.00 Mg 263 11.99 O 39431 8.00 N 26436 7.00 C 71128 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 58.83 Conformation dependent library (CDL) restraints added in 7.0 seconds 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10270 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: 171 helices and 72 sheets defined 39.0% alpha, 19.9% beta 1582 base pairs and 2443 stacking pairs defined. Time for finding SS restraints: 74.61 Creating SS restraints... Processing helix chain 'B' and resid 5 through 13 removed outlier: 3.750A pdb=" N MET B 9 " --> pdb=" O SER B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 64 Proline residue: B 48 - end of helix Processing helix chain 'B' and resid 73 through 88 removed outlier: 3.504A pdb=" N SER B 77 " --> pdb=" O LYS B 73 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N GLU B 78 " --> pdb=" O ARG B 74 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ALA B 79 " --> pdb=" O ALA B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 124 removed outlier: 3.671A pdb=" N GLY B 124 " --> pdb=" O GLN B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 130 removed outlier: 4.580A pdb=" N LEU B 129 " --> pdb=" O THR B 125 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR B 130 " --> pdb=" O PHE B 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 125 through 130' Processing helix chain 'B' and resid 131 through 148 removed outlier: 4.579A pdb=" N LEU B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 170 removed outlier: 3.660A pdb=" N GLU B 169 " --> pdb=" O ASP B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 180 Processing helix chain 'B' and resid 206 through 227 removed outlier: 3.596A pdb=" N GLN B 227 " --> pdb=" O GLU B 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 12 removed outlier: 3.936A pdb=" N ARG C 11 " --> pdb=" O PRO C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 48 Processing helix chain 'C' and resid 72 through 78 Processing helix chain 'C' and resid 81 through 96 Processing helix chain 'C' and resid 108 through 113 removed outlier: 4.230A pdb=" N ASP C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ALA C 113 " --> pdb=" O PRO C 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 108 through 113' Processing helix chain 'C' and resid 114 through 127 removed outlier: 3.589A pdb=" N ARG C 127 " --> pdb=" O GLN C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 145 Processing helix chain 'D' and resid 7 through 16 removed outlier: 4.617A pdb=" N LEU D 11 " --> pdb=" O PRO D 7 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 32 removed outlier: 4.113A pdb=" N LYS D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 66 Processing helix chain 'D' and resid 68 through 83 removed outlier: 5.232A pdb=" N LYS D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 97 removed outlier: 3.919A pdb=" N ARG D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 106 Processing helix chain 'D' and resid 110 through 121 removed outlier: 3.753A pdb=" N LYS D 121 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 151 removed outlier: 4.438A pdb=" N LYS D 151 " --> pdb=" O GLU D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 166 removed outlier: 3.886A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLU D 166 " --> pdb=" O ALA D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 192 removed outlier: 3.691A pdb=" N LEU D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N SER D 192 " --> pdb=" O ARG D 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 187 through 192' Processing helix chain 'D' and resid 196 through 206 removed outlier: 3.564A pdb=" N ILE D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 71 removed outlier: 4.070A pdb=" N MET E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 119 Processing helix chain 'E' and resid 132 through 147 removed outlier: 3.527A pdb=" N MET E 147 " --> pdb=" O GLY E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 158 Processing helix chain 'E' and resid 160 through 165 Processing helix chain 'F' and resid 14 through 33 Proline residue: F 19 - end of helix removed outlier: 3.697A pdb=" N GLU F 33 " --> pdb=" O ILE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 82 removed outlier: 3.506A pdb=" N ILE F 71 " --> pdb=" O PRO F 67 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ASP F 82 " --> pdb=" O PHE F 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 31 Processing helix chain 'G' and resid 35 through 55 removed outlier: 3.505A pdb=" N ALA G 39 " --> pdb=" O LYS G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 70 removed outlier: 4.081A pdb=" N ALA G 61 " --> pdb=" O SER G 57 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN G 68 " --> pdb=" O VAL G 64 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 112 removed outlier: 3.518A pdb=" N ARG G 111 " --> pdb=" O ALA G 107 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLY G 112 " --> pdb=" O ALA G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 130 removed outlier: 3.601A pdb=" N GLU G 129 " --> pdb=" O SER G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 149 removed outlier: 3.517A pdb=" N ASN G 148 " --> pdb=" O MET G 144 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS G 149 " --> pdb=" O ALA G 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 21 Processing helix chain 'H' and resid 30 through 44 Processing helix chain 'H' and resid 112 through 120 Processing helix chain 'I' and resid 34 through 40 removed outlier: 4.796A pdb=" N GLY I 40 " --> pdb=" O GLU I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 56 Proline residue: I 51 - end of helix Processing helix chain 'I' and resid 71 through 92 removed outlier: 3.644A pdb=" N GLU I 92 " --> pdb=" O MET I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 102 removed outlier: 4.964A pdb=" N GLU I 97 " --> pdb=" O SER I 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 33 removed outlier: 3.579A pdb=" N ILE J 18 " --> pdb=" O ASP J 14 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY J 33 " --> pdb=" O ALA J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 91 removed outlier: 3.721A pdb=" N VAL J 84 " --> pdb=" O THR J 80 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASP J 85 " --> pdb=" O GLU J 81 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU J 90 " --> pdb=" O ALA J 86 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ASP J 91 " --> pdb=" O LEU J 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 51 removed outlier: 4.367A pdb=" N GLY K 51 " --> pdb=" O ALA K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 59 removed outlier: 3.945A pdb=" N SER K 58 " --> pdb=" O GLY K 54 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N THR K 59 " --> pdb=" O SER K 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 54 through 59' Processing helix chain 'K' and resid 60 through 75 Processing helix chain 'K' and resid 92 through 104 removed outlier: 4.841A pdb=" N THR K 96 " --> pdb=" O GLY K 92 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE K 97 " --> pdb=" O ARG K 93 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY K 104 " --> pdb=" O LEU K 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 11 Proline residue: L 11 - end of helix Processing helix chain 'L' and resid 113 through 118 removed outlier: 3.746A pdb=" N TYR L 117 " --> pdb=" O ALA L 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 22 removed outlier: 3.913A pdb=" N SER M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ILE M 22 " --> pdb=" O ALA M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 44 through 49 removed outlier: 5.758A pdb=" N SER M 49 " --> pdb=" O ILE M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 50 through 64 removed outlier: 3.919A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N PHE M 63 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N VAL M 64 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 84 removed outlier: 3.580A pdb=" N GLY M 84 " --> pdb=" O LEU M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 94 Processing helix chain 'M' and resid 106 through 111 removed outlier: 3.856A pdb=" N LYS M 110 " --> pdb=" O ALA M 106 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 21 removed outlier: 3.549A pdb=" N LYS N 7 " --> pdb=" O LYS N 3 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 33 Processing helix chain 'N' and resid 37 through 51 removed outlier: 3.520A pdb=" N LEU N 51 " --> pdb=" O LYS N 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 91 Processing helix chain 'N' and resid 52 through 57 Proline residue: N 57 - end of helix Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 24 through 44 removed outlier: 4.313A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 removed outlier: 3.911A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 86 Processing helix chain 'P' and resid 53 through 64 Processing helix chain 'P' and resid 68 through 80 removed outlier: 3.870A pdb=" N LYS P 80 " --> pdb=" O LYS P 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 11 through 17 removed outlier: 3.544A pdb=" N ALA R 15 " --> pdb=" O CYS R 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 34 removed outlier: 4.191A pdb=" N ASN R 31 " --> pdb=" O ALA R 27 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N TYR R 32 " --> pdb=" O THR R 28 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE R 33 " --> pdb=" O LEU R 29 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N THR R 34 " --> pdb=" O LYS R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 46 removed outlier: 3.579A pdb=" N THR R 45 " --> pdb=" O PRO R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 66 Processing helix chain 'S' and resid 12 through 26 Processing helix chain 'S' and resid 70 through 76 removed outlier: 4.660A pdb=" N PHE S 74 " --> pdb=" O LYS S 70 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA S 75 " --> pdb=" O LEU S 71 " (cutoff:3.500A) Proline residue: S 76 - end of helix No H-bonds generated for 'chain 'S' and resid 70 through 76' Processing helix chain 'T' and resid 4 through 41 Processing helix chain 'T' and resid 44 through 65 Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 68 through 87 removed outlier: 3.911A pdb=" N ALA T 87 " --> pdb=" O ILE T 83 " (cutoff:3.500A) Processing helix chain 'U' and resid 11 through 27 Processing helix chain 'U' and resid 28 through 37 removed outlier: 4.771A pdb=" N PHE U 37 " --> pdb=" O ARG U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 69 removed outlier: 3.668A pdb=" N THR U 68 " --> pdb=" O ASN U 64 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ARG U 69 " --> pdb=" O ALA U 65 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 15 removed outlier: 5.203A pdb=" N HIS c 15 " --> pdb=" O PRO c 11 " (cutoff:3.500A) Processing helix chain 'c' and resid 30 through 35 removed outlier: 4.129A pdb=" N LEU c 34 " --> pdb=" O PHE c 30 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N GLU c 35 " --> pdb=" O ALA c 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 30 through 35' Processing helix chain 'c' and resid 131 through 136 removed outlier: 3.779A pdb=" N ILE c 135 " --> pdb=" O PRO c 131 " (cutoff:3.500A) Proline residue: c 136 - end of helix No H-bonds generated for 'chain 'c' and resid 131 through 136' Processing helix chain 'c' and resid 207 through 215 removed outlier: 3.740A pdb=" N ALA c 211 " --> pdb=" O LYS c 207 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG c 214 " --> pdb=" O ALA c 210 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY c 215 " --> pdb=" O ALA c 211 " (cutoff:3.500A) Processing helix chain 'c' and resid 221 through 226 removed outlier: 4.055A pdb=" N MET c 225 " --> pdb=" O ARG c 221 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ASN c 226 " --> pdb=" O GLY c 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 221 through 226' Processing helix chain 'c' and resid 260 through 268 removed outlier: 3.734A pdb=" N ASP c 264 " --> pdb=" O ASN c 260 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LYS c 265 " --> pdb=" O LYS c 261 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N PHE c 266 " --> pdb=" O ARG c 262 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE c 267 " --> pdb=" O THR c 263 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N VAL c 268 " --> pdb=" O ASP c 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 260 through 268' Processing helix chain 'c' and resid 197 through 202 removed outlier: 4.269A pdb=" N MET c 201 " --> pdb=" O ALA c 198 " (cutoff:3.500A) Processing helix chain 'd' and resid 56 through 61 removed outlier: 3.556A pdb=" N VAL d 60 " --> pdb=" O LYS d 56 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N THR d 61 " --> pdb=" O ALA d 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 56 through 61' Processing helix chain 'd' and resid 62 through 72 Processing helix chain 'd' and resid 98 through 103 removed outlier: 4.115A pdb=" N ALA d 102 " --> pdb=" O VAL d 98 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ASP d 103 " --> pdb=" O GLU d 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 98 through 103' Processing helix chain 'd' and resid 120 through 125 Processing helix chain 'e' and resid 15 through 20 Processing helix chain 'e' and resid 24 through 40 removed outlier: 3.511A pdb=" N ALA e 39 " --> pdb=" O TYR e 35 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG e 40 " --> pdb=" O ALA e 36 " (cutoff:3.500A) Processing helix chain 'e' and resid 97 through 116 removed outlier: 3.717A pdb=" N ASP e 116 " --> pdb=" O LEU e 112 " (cutoff:3.500A) Processing helix chain 'e' and resid 130 through 142 Processing helix chain 'e' and resid 154 through 163 removed outlier: 4.754A pdb=" N ASN e 163 " --> pdb=" O LEU e 159 " (cutoff:3.500A) Processing helix chain 'e' and resid 176 through 183 removed outlier: 3.563A pdb=" N PHE e 183 " --> pdb=" O SER e 179 " (cutoff:3.500A) Processing helix chain 'e' and resid 189 through 201 Processing helix chain 'f' and resid 2 through 21 removed outlier: 5.243A pdb=" N VAL f 13 " --> pdb=" O LYS f 9 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LYS f 14 " --> pdb=" O ASP f 10 " (cutoff:3.500A) Processing helix chain 'f' and resid 42 through 47 removed outlier: 3.997A pdb=" N ASP f 46 " --> pdb=" O GLU f 42 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS f 47 " --> pdb=" O ALA f 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 42 through 47' Processing helix chain 'f' and resid 48 through 62 Processing helix chain 'f' and resid 93 through 111 removed outlier: 4.665A pdb=" N VAL f 108 " --> pdb=" O ILE f 104 " (cutoff:3.500A) Proline residue: f 109 - end of helix Processing helix chain 'f' and resid 162 through 174 removed outlier: 3.830A pdb=" N PHE f 173 " --> pdb=" O LEU f 169 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP f 174 " --> pdb=" O LEU f 170 " (cutoff:3.500A) Processing helix chain 'f' and resid 134 through 139 removed outlier: 4.030A pdb=" N ILE f 137 " --> pdb=" O GLU f 134 " (cutoff:3.500A) Proline residue: f 139 - end of helix Processing helix chain 'g' and resid 2 through 8 removed outlier: 3.704A pdb=" N ALA g 7 " --> pdb=" O ARG g 3 " (cutoff:3.500A) Proline residue: g 8 - end of helix Processing helix chain 'g' and resid 60 through 81 removed outlier: 4.879A pdb=" N GLN g 64 " --> pdb=" O ASP g 60 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL g 79 " --> pdb=" O MET g 75 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR g 80 " --> pdb=" O VAL g 76 " (cutoff:3.500A) Processing helix chain 'g' and resid 137 through 153 removed outlier: 4.205A pdb=" N ARG g 152 " --> pdb=" O LEU g 148 " (cutoff:3.500A) Processing helix chain 'h' and resid 22 through 28 Processing helix chain 'h' and resid 29 through 34 removed outlier: 3.556A pdb=" N GLY h 34 " --> pdb=" O LEU h 30 " (cutoff:3.500A) Processing helix chain 'i' and resid 24 through 38 removed outlier: 4.068A pdb=" N GLU i 31 " --> pdb=" O ARG i 27 " (cutoff:3.500A) Processing helix chain 'i' and resid 88 through 96 Processing helix chain 'i' and resid 97 through 110 removed outlier: 4.322A pdb=" N ILE i 101 " --> pdb=" O PRO i 97 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET i 108 " --> pdb=" O ALA i 104 " (cutoff:3.500A) Proline residue: i 110 - end of helix Processing helix chain 'i' and resid 112 through 122 removed outlier: 3.993A pdb=" N LYS i 121 " --> pdb=" O ALA i 117 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU i 122 " --> pdb=" O MET i 118 " (cutoff:3.500A) Processing helix chain 'j' and resid 104 through 109 removed outlier: 4.675A pdb=" N ARG j 108 " --> pdb=" O THR j 104 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N SER j 109 " --> pdb=" O ARG j 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 104 through 109' Processing helix chain 'j' and resid 112 through 119 Processing helix chain 'k' and resid 37 through 42 removed outlier: 3.787A pdb=" N ARG k 41 " --> pdb=" O GLY k 37 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N SER k 42 " --> pdb=" O GLN k 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 37 through 42' Processing helix chain 'k' and resid 56 through 62 removed outlier: 3.681A pdb=" N LEU k 61 " --> pdb=" O LEU k 57 " (cutoff:3.500A) Proline residue: k 62 - end of helix Processing helix chain 'k' and resid 68 through 75 removed outlier: 4.078A pdb=" N ALA k 72 " --> pdb=" O SER k 68 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE k 73 " --> pdb=" O ARG k 69 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR k 74 " --> pdb=" O LYS k 70 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ALA k 75 " --> pdb=" O ALA k 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 68 through 75' Processing helix chain 'k' and resid 78 through 85 removed outlier: 3.732A pdb=" N LEU k 82 " --> pdb=" O ARG k 78 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA k 83 " --> pdb=" O LEU k 79 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LYS k 84 " --> pdb=" O SER k 80 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL k 85 " --> pdb=" O ASP k 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 78 through 85' Processing helix chain 'k' and resid 91 through 99 Processing helix chain 'k' and resid 128 through 139 Processing helix chain 'l' and resid 42 through 58 Processing helix chain 'l' and resid 109 through 125 removed outlier: 3.623A pdb=" N ALA l 122 " --> pdb=" O LYS l 118 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS l 123 " --> pdb=" O LEU l 119 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU l 124 " --> pdb=" O ALA l 120 " (cutoff:3.500A) Proline residue: l 125 - end of helix Processing helix chain 'm' and resid 13 through 32 Processing helix chain 'm' and resid 38 through 57 removed outlier: 4.226A pdb=" N ARG m 46 " --> pdb=" O LYS m 42 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL m 47 " --> pdb=" O GLU m 43 " (cutoff:3.500A) Proline residue: m 50 - end of helix removed outlier: 3.591A pdb=" N LYS m 56 " --> pdb=" O ILE m 52 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N THR m 57 " --> pdb=" O THR m 53 " (cutoff:3.500A) Processing helix chain 'm' and resid 59 through 71 removed outlier: 4.450A pdb=" N THR m 70 " --> pdb=" O ALA m 66 " (cutoff:3.500A) Processing helix chain 'm' and resid 72 through 88 removed outlier: 4.910A pdb=" N GLY m 84 " --> pdb=" O PHE m 80 " (cutoff:3.500A) Proline residue: m 85 - end of helix Processing helix chain 'n' and resid 2 through 22 removed outlier: 4.656A pdb=" N ARG n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ALA n 14 " --> pdb=" O ARG n 10 " (cutoff:3.500A) Processing helix chain 'n' and resid 55 through 63 removed outlier: 5.206A pdb=" N GLN n 61 " --> pdb=" O ALA n 57 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N LEU n 62 " --> pdb=" O ILE n 58 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N LYS n 63 " --> pdb=" O ALA n 59 " (cutoff:3.500A) Processing helix chain 'n' and resid 67 through 86 Processing helix chain 'n' and resid 101 through 114 removed outlier: 3.529A pdb=" N GLY n 114 " --> pdb=" O ALA n 110 " (cutoff:3.500A) Processing helix chain 'o' and resid 2 through 13 removed outlier: 3.619A pdb=" N GLU o 11 " --> pdb=" O GLN o 7 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLN o 12 " --> pdb=" O LEU o 8 " (cutoff:3.500A) Processing helix chain 'o' and resid 97 through 104 removed outlier: 4.669A pdb=" N ARG o 101 " --> pdb=" O LEU o 97 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLU o 102 " --> pdb=" O TYR o 98 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARG o 103 " --> pdb=" O TYR o 99 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N THR o 104 " --> pdb=" O LEU o 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 97 through 104' Processing helix chain 'p' and resid 6 through 22 removed outlier: 3.924A pdb=" N LYS p 22 " --> pdb=" O LEU p 18 " (cutoff:3.500A) Processing helix chain 'p' and resid 26 through 31 removed outlier: 3.708A pdb=" N ARG p 30 " --> pdb=" O GLY p 26 " (cutoff:3.500A) Processing helix chain 'p' and resid 32 through 37 removed outlier: 4.075A pdb=" N GLN p 37 " --> pdb=" O ARG p 33 " (cutoff:3.500A) Processing helix chain 'p' and resid 39 through 73 removed outlier: 3.911A pdb=" N ARG p 51 " --> pdb=" O TYR p 47 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LYS p 54 " --> pdb=" O ARG p 50 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG p 55 " --> pdb=" O ARG p 51 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN p 72 " --> pdb=" O ALA p 68 " (cutoff:3.500A) Processing helix chain 'p' and resid 75 through 87 Processing helix chain 'p' and resid 91 through 102 Processing helix chain 'p' and resid 103 through 118 Processing helix chain 'r' and resid 13 through 25 removed outlier: 3.745A pdb=" N VAL r 20 " --> pdb=" O LYS r 16 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU r 23 " --> pdb=" O LEU r 19 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE r 24 " --> pdb=" O VAL r 20 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG r 25 " --> pdb=" O ALA r 21 " (cutoff:3.500A) Processing helix chain 'r' and resid 28 through 39 Processing helix chain 'r' and resid 41 through 61 removed outlier: 3.625A pdb=" N VAL r 45 " --> pdb=" O LYS r 41 " (cutoff:3.500A) Processing helix chain 's' and resid 3 through 11 removed outlier: 4.268A pdb=" N LEU s 11 " --> pdb=" O LEU s 7 " (cutoff:3.500A) Processing helix chain 's' and resid 17 through 27 Processing helix chain 's' and resid 39 through 50 Processing helix chain 't' and resid 66 through 71 removed outlier: 3.879A pdb=" N VAL t 70 " --> pdb=" O GLN t 66 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ALA t 71 " --> pdb=" O VAL t 67 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 66 through 71' Processing helix chain 'u' and resid 13 through 24 removed outlier: 3.534A pdb=" N ASN u 24 " --> pdb=" O LEU u 20 " (cutoff:3.500A) Processing helix chain 'u' and resid 43 through 53 removed outlier: 3.643A pdb=" N ALA u 52 " --> pdb=" O MET u 48 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LYS u 53 " --> pdb=" O ASN u 49 " (cutoff:3.500A) Processing helix chain 'u' and resid 54 through 59 removed outlier: 4.214A pdb=" N SER u 58 " --> pdb=" O ALA u 54 " (cutoff:3.500A) Processing helix chain 'w' and resid 52 through 63 Processing helix chain 'w' and resid 64 through 75 Processing helix chain 'x' and resid 2 through 10 removed outlier: 3.980A pdb=" N LYS x 9 " --> pdb=" O GLU x 5 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N SER x 10 " --> pdb=" O LEU x 6 " (cutoff:3.500A) Processing helix chain 'x' and resid 11 through 35 Processing helix chain 'x' and resid 40 through 62 removed outlier: 4.437A pdb=" N LYS x 44 " --> pdb=" O SER x 40 " (cutoff:3.500A) Processing helix chain 'y' and resid 17 through 28 Processing helix chain 'y' and resid 41 through 52 Processing helix chain 'z' and resid 9 through 19 removed outlier: 4.805A pdb=" N HIS z 19 " --> pdb=" O MET z 15 " (cutoff:3.500A) Processing helix chain '1' and resid 8 through 16 Processing helix chain '1' and resid 17 through 24 removed outlier: 4.429A pdb=" N THR 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) Processing helix chain '1' and resid 25 through 38 Processing helix chain '2' and resid 7 through 14 removed outlier: 4.079A pdb=" N ARG 2 13 " --> pdb=" O GLY 2 9 " (cutoff:3.500A) Processing helix chain '2' and resid 37 through 46 Proline residue: 2 46 - end of helix Processing helix chain '2' and resid 51 through 63 removed outlier: 4.777A pdb=" N GLY 2 56 " --> pdb=" O LYS 2 52 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LEU 2 57 " --> pdb=" O GLY 2 53 " (cutoff:3.500A) Proline residue: 2 63 - end of helix Processing helix chain '4' and resid 41 through 46 Processing helix chain '4' and resid 55 through 65 removed outlier: 3.603A pdb=" N ARG 4 59 " --> pdb=" O GLY 4 55 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN 4 65 " --> pdb=" O ASN 4 61 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'B' and resid 15 through 18 removed outlier: 6.065A pdb=" N HIS B 15 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY B 17 " --> pdb=" O HIS B 39 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N HIS B 39 " --> pdb=" O GLY B 17 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'B' and resid 90 through 93 removed outlier: 3.623A pdb=" N ILE B 164 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 53 through 59 Processing sheet with id= 4, first strand: chain 'C' and resid 164 through 169 removed outlier: 3.619A pdb=" N GLY C 194 " --> pdb=" O THR C 191 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASP C 181 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'D' and resid 141 through 144 removed outlier: 4.075A pdb=" N ASP D 141 " --> pdb=" O PHE D 182 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'E' and resid 11 through 16 removed outlier: 6.777A pdb=" N LEU E 36 " --> pdb=" O ILE E 16 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'E' and resid 84 through 88 removed outlier: 3.681A pdb=" N ALA E 99 " --> pdb=" O ASN E 122 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ASN E 122 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'E' and resid 32 through 41 removed outlier: 3.577A pdb=" N ASP E 41 " --> pdb=" O ARG E 45 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ARG E 45 " --> pdb=" O ASP E 41 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'F' and resid 38 through 42 removed outlier: 5.457A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG F 86 " --> pdb=" O MET F 9 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'F' and resid 43 through 47 removed outlier: 3.754A pdb=" N GLY F 43 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N HIS F 55 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'G' and resid 72 through 79 removed outlier: 6.344A pdb=" N THR G 72 " --> pdb=" O VAL G 91 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'H' and resid 23 through 29 removed outlier: 6.622A pdb=" N ALA H 23 " --> pdb=" O LEU H 63 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP H 48 " --> pdb=" O THR H 62 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'H' and resid 74 through 77 removed outlier: 3.589A pdb=" N CYS H 127 " --> pdb=" O VAL H 103 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'I' and resid 5 through 11 removed outlier: 4.291A pdb=" N LYS I 60 " --> pdb=" O GLY I 24 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS I 27 " --> pdb=" O LEU I 61 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'J' and resid 39 through 42 removed outlier: 4.559A pdb=" N LEU J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE J 76 " --> pdb=" O ILE J 6 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'J' and resid 44 through 52 Processing sheet with id= 17, first strand: chain 'K' and resid 30 through 35 removed outlier: 6.838A pdb=" N VAL K 84 " --> pdb=" O THR K 108 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'K' and resid 83 through 88 removed outlier: 6.085A pdb=" N GLY K 88 " --> pdb=" O VAL K 113 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'L' and resid 29 through 32 removed outlier: 5.268A pdb=" N LEU L 81 " --> pdb=" O VAL L 98 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'L' and resid 36 through 41 removed outlier: 3.725A pdb=" N ARG L 36 " --> pdb=" O ARG L 54 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LYS L 51 " --> pdb=" O ILE L 67 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'P' and resid 4 through 10 Processing sheet with id= 22, first strand: chain 'Q' and resid 7 through 11 removed outlier: 6.882A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'Q' and resid 19 through 30 No H-bonds generated for sheet with id= 23 Processing sheet with id= 24, first strand: chain 'S' and resid 30 through 34 removed outlier: 4.701A pdb=" N LEU S 47 " --> pdb=" O VAL S 62 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'c' and resid 2 through 6 removed outlier: 5.709A pdb=" N VAL c 16 " --> pdb=" O CYS c 6 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'c' and resid 73 through 78 removed outlier: 5.250A pdb=" N ILE c 74 " --> pdb=" O SER c 118 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N SER c 118 " --> pdb=" O ILE c 74 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASP c 114 " --> pdb=" O VAL c 78 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLY c 127 " --> pdb=" O GLN c 115 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N GLN c 117 " --> pdb=" O GLY c 127 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'c' and resid 80 through 83 removed outlier: 3.579A pdb=" N ARG c 80 " --> pdb=" O LEU c 93 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ASN c 90 " --> pdb=" O ALA c 106 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'c' and resid 138 through 142 removed outlier: 4.196A pdb=" N SER c 139 " --> pdb=" O ILE c 164 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR c 173 " --> pdb=" O VAL c 165 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU c 180 " --> pdb=" O LEU c 176 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'd' and resid 11 through 16 removed outlier: 3.788A pdb=" N VAL d 20 " --> pdb=" O THR d 16 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL d 26 " --> pdb=" O VAL d 9 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N SER d 199 " --> pdb=" O LYS d 8 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ASP d 200 " --> pdb=" O THR d 112 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N THR d 112 " --> pdb=" O ASP d 200 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLU d 168 " --> pdb=" O SER d 113 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'd' and resid 36 through 40 removed outlier: 3.797A pdb=" N LEU d 40 " --> pdb=" O TYR d 45 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TYR d 45 " --> pdb=" O LEU d 40 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLN d 49 " --> pdb=" O THR d 35 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLN d 94 " --> pdb=" O VAL d 34 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'd' and resid 179 through 182 Processing sheet with id= 32, first strand: chain 'd' and resid 24 through 28 No H-bonds generated for sheet with id= 32 Processing sheet with id= 33, first strand: chain 'd' and resid 46 through 51 removed outlier: 5.939A pdb=" N ARG d 46 " --> pdb=" O LEU d 84 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'd' and resid 105 through 108 removed outlier: 6.815A pdb=" N LYS d 105 " --> pdb=" O VAL d 177 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'e' and resid 1 through 6 removed outlier: 4.782A pdb=" N SER e 10 " --> pdb=" O LEU e 5 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'e' and resid 117 through 120 removed outlier: 5.623A pdb=" N ARG e 117 " --> pdb=" O ASP e 184 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'f' and resid 65 through 69 removed outlier: 5.025A pdb=" N ILE f 85 " --> pdb=" O VAL f 40 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N GLY f 39 " --> pdb=" O GLY f 151 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N GLY f 151 " --> pdb=" O GLY f 39 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'f' and resid 72 through 75 removed outlier: 6.931A pdb=" N LYS f 72 " --> pdb=" O GLN f 81 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLN f 81 " --> pdb=" O LYS f 72 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'g' and resid 16 through 19 Processing sheet with id= 40, first strand: chain 'g' and resid 41 through 44 removed outlier: 3.710A pdb=" N LYS g 44 " --> pdb=" O THR g 51 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N THR g 51 " --> pdb=" O LYS g 44 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'g' and resid 94 through 99 removed outlier: 3.625A pdb=" N VAL g 102 " --> pdb=" O LYS g 99 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ASN g 101 " --> pdb=" O LEU g 117 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL g 113 " --> pdb=" O LEU g 105 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'g' and resid 121 through 125 removed outlier: 5.921A pdb=" N THR g 129 " --> pdb=" O LEU g 89 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL g 90 " --> pdb=" O GLY g 161 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'h' and resid 17 through 20 removed outlier: 4.323A pdb=" N ASP h 17 " --> pdb=" O LEU h 5 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLN h 2 " --> pdb=" O ALA h 39 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LYS h 35 " --> pdb=" O LEU h 6 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'i' and resid 52 through 57 removed outlier: 4.954A pdb=" N ASP i 19 " --> pdb=" O LEU i 140 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'i' and resid 74 through 78 removed outlier: 7.600A pdb=" N GLY i 83 " --> pdb=" O THR i 78 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'j' and resid 56 through 60 removed outlier: 4.700A pdb=" N ASP j 56 " --> pdb=" O ILE j 43 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LYS j 40 " --> pdb=" O ILE j 22 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N THR j 6 " --> pdb=" O CYS j 21 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ASN j 82 " --> pdb=" O MET j 7 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'l' and resid 37 through 40 No H-bonds generated for sheet with id= 47 Processing sheet with id= 48, first strand: chain 'l' and resid 62 through 65 removed outlier: 3.527A pdb=" N TYR l 103 " --> pdb=" O LEU l 33 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU l 33 " --> pdb=" O LEU l 102 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS l 100 " --> pdb=" O ALA l 35 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'l' and resid 30 through 36 removed outlier: 7.665A pdb=" N SER l 30 " --> pdb=" O LYS l 133 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS l 127 " --> pdb=" O VAL l 36 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'm' and resid 33 through 37 removed outlier: 5.476A pdb=" N MET m 110 " --> pdb=" O CYS m 100 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N TYR m 94 " --> pdb=" O VAL m 116 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'n' and resid 49 through 53 removed outlier: 3.709A pdb=" N VAL n 49 " --> pdb=" O VAL n 39 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE n 35 " --> pdb=" O THR n 53 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'o' and resid 38 through 45 removed outlier: 6.308A pdb=" N THR o 25 " --> pdb=" O LYS o 87 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER o 83 " --> pdb=" O LYS o 29 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'o' and resid 49 through 52 removed outlier: 3.803A pdb=" N ALA o 49 " --> pdb=" O THR o 60 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N SER o 57 " --> pdb=" O THR o 76 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'q' and resid 11 through 15 removed outlier: 3.581A pdb=" N MET q 40 " --> pdb=" O VAL q 4 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU q 39 " --> pdb=" O GLY q 50 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLU q 46 " --> pdb=" O ASN q 43 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'q' and resid 17 through 23 removed outlier: 4.082A pdb=" N GLN q 18 " --> pdb=" O ILE q 98 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASP q 95 " --> pdb=" O VAL q 64 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LYS q 60 " --> pdb=" O THR q 99 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLU q 31 " --> pdb=" O VAL q 63 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'q' and resid 57 through 60 Processing sheet with id= 57, first strand: chain 'q' and resid 65 through 68 Processing sheet with id= 58, first strand: chain 'q' and resid 71 through 78 removed outlier: 4.126A pdb=" N TYR q 83 " --> pdb=" O ARG q 78 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'r' and resid 2 through 8 removed outlier: 6.877A pdb=" N VAL r 106 " --> pdb=" O THR r 72 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 's' and resid 28 through 33 removed outlier: 6.543A pdb=" N ASN s 28 " --> pdb=" O LEU s 87 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LYS s 66 " --> pdb=" O ARG s 77 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ASP s 79 " --> pdb=" O LYS s 64 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LYS s 64 " --> pdb=" O ASP s 79 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LYS s 81 " --> pdb=" O VAL s 62 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL s 62 " --> pdb=" O LYS s 81 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ALA s 83 " --> pdb=" O THR s 60 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR s 60 " --> pdb=" O ALA s 83 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL s 85 " --> pdb=" O VAL s 58 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL s 58 " --> pdb=" O VAL s 85 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 't' and resid 83 through 87 Processing sheet with id= 62, first strand: chain 'u' and resid 69 through 72 removed outlier: 6.563A pdb=" N ALA u 39 " --> pdb=" O ARG u 9 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE u 89 " --> pdb=" O PRO u 27 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'v' and resid 51 through 54 removed outlier: 4.168A pdb=" N THR v 58 " --> pdb=" O GLY v 54 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'v' and resid 66 through 72 Processing sheet with id= 65, first strand: chain 'w' and resid 12 through 19 removed outlier: 4.555A pdb=" N ASN w 23 " --> pdb=" O SER w 19 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'w' and resid 35 through 41 removed outlier: 3.726A pdb=" N ARG w 45 " --> pdb=" O VAL w 40 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'y' and resid 33 through 39 removed outlier: 4.393A pdb=" N HIS y 34 " --> pdb=" O GLN y 9 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N MET y 54 " --> pdb=" O THR y 10 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'z' and resid 28 through 31 removed outlier: 6.459A pdb=" N SER z 29 " --> pdb=" O LYS z 37 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS z 37 " --> pdb=" O SER z 29 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ASP z 31 " --> pdb=" O GLY z 35 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain '0' and resid 19 through 25 removed outlier: 5.976A pdb=" N HIS 0 19 " --> pdb=" O SER 0 13 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE 0 48 " --> pdb=" O SER 0 14 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU 0 34 " --> pdb=" O GLU 0 51 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain '2' and resid 22 through 25 removed outlier: 5.598A pdb=" N PHE 2 22 " --> pdb=" O VAL 2 50 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain '3' and resid 1 through 5 removed outlier: 6.676A pdb=" N HIS 3 33 " --> pdb=" O CYS 3 27 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N CYS 3 27 " --> pdb=" O HIS 3 33 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ILE 3 23 " --> pdb=" O GLN 3 37 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain '4' and resid 20 through 25 removed outlier: 4.245A pdb=" N ASN 4 20 " --> pdb=" O CYS 4 16 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU 4 32 " --> pdb=" O THR 4 13 " (cutoff:3.500A) 1916 hydrogen bonds defined for protein. 5655 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3981 hydrogen bonds 6242 hydrogen bond angles 0 basepair planarities 1582 basepair parallelities 2443 stacking parallelities Total time for adding SS restraints: 252.33 Time building geometry restraints manager: 63.79 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: 11584 1.29 - 1.43: 69665 1.43 - 1.56: 63404 1.56 - 1.69: 9115 1.69 - 1.83: 264 Bond restraints: 154032 Sorted by residual: bond pdb=" C5 5MU Z 55 " pdb=" C6 5MU Z 55 " ideal model delta sigma weight residual 1.155 1.445 -0.290 2.00e-02 2.50e+03 2.10e+02 bond pdb=" C5 5MU V 54 " pdb=" C6 5MU V 54 " ideal model delta sigma weight residual 1.155 1.444 -0.289 2.00e-02 2.50e+03 2.09e+02 bond pdb=" C5 5MU a 747 " pdb=" C6 5MU a 747 " ideal model delta sigma weight residual 1.155 1.440 -0.285 2.00e-02 2.50e+03 2.03e+02 bond pdb=" C5 5MU a1939 " pdb=" C6 5MU a1939 " ideal model delta sigma weight residual 1.155 1.439 -0.284 2.00e-02 2.50e+03 2.02e+02 bond pdb=" C MS6 l 82 " pdb=" S MS6 l 82 " ideal model delta sigma weight residual 1.829 1.571 0.258 2.00e-02 2.50e+03 1.66e+02 ... (remaining 154027 not shown) Histogram of bond angle deviations from ideal: 98.01 - 106.91: 29286 106.91 - 115.81: 103585 115.81 - 124.72: 79083 124.72 - 133.62: 18518 133.62 - 142.53: 41 Bond angle restraints: 230513 Sorted by residual: angle pdb=" C1' 2MA a2503 " pdb=" N9 2MA a2503 " pdb=" C8 2MA a2503 " ideal model delta sigma weight residual 106.32 142.53 -36.21 3.00e+00 1.11e-01 1.46e+02 angle pdb=" C1' 2MA a2503 " pdb=" N9 2MA a2503 " pdb=" C4 2MA a2503 " ideal model delta sigma weight residual 138.88 109.90 28.98 3.00e+00 1.11e-01 9.33e+01 angle pdb=" C1' 1MA V 58 " pdb=" N9 1MA V 58 " pdb=" C8 1MA V 58 " ideal model delta sigma weight residual 100.68 128.34 -27.66 3.00e+00 1.11e-01 8.50e+01 angle pdb=" C ASN g 48 " pdb=" N THR g 49 " pdb=" CA THR g 49 " ideal model delta sigma weight residual 121.54 136.65 -15.11 1.91e+00 2.74e-01 6.26e+01 angle pdb=" C1' 56B V 34 " pdb=" N9 56B V 34 " pdb=" C4 56B V 34 " ideal model delta sigma weight residual 105.37 127.99 -22.62 3.00e+00 1.11e-01 5.68e+01 ... (remaining 230508 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 87447 35.92 - 71.83: 9859 71.83 - 107.75: 1163 107.75 - 143.66: 19 143.66 - 179.58: 10 Dihedral angle restraints: 98498 sinusoidal: 82577 harmonic: 15921 Sorted by residual: dihedral pdb=" CA ASP g 47 " pdb=" C ASP g 47 " pdb=" N ASN g 48 " pdb=" CA ASN g 48 " ideal model delta harmonic sigma weight residual 180.00 -119.68 -60.32 0 5.00e+00 4.00e-02 1.46e+02 dihedral pdb=" CA HIS 2 31 " pdb=" C HIS 2 31 " pdb=" N ILE 2 32 " pdb=" CA ILE 2 32 " ideal model delta harmonic sigma weight residual 180.00 -132.90 -47.10 0 5.00e+00 4.00e-02 8.87e+01 dihedral pdb=" O4' U A 365 " pdb=" C1' U A 365 " pdb=" N1 U A 365 " pdb=" C2 U A 365 " ideal model delta sinusoidal sigma weight residual 200.00 46.16 153.84 1 1.50e+01 4.44e-03 8.10e+01 ... (remaining 98495 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 27042 0.081 - 0.162: 2089 0.162 - 0.244: 147 0.244 - 0.325: 14 0.325 - 0.406: 4 Chirality restraints: 29296 Sorted by residual: chirality pdb=" C11 56B V 34 " pdb=" C10 56B V 34 " pdb=" C12 56B V 34 " pdb=" O11 56B V 34 " both_signs ideal model delta sigma weight residual False 2.63 3.03 -0.41 2.00e-01 2.50e+01 4.12e+00 chirality pdb=" C3 GAL V 101 " pdb=" C2 GAL V 101 " pdb=" C4 GAL V 101 " pdb=" O3 GAL V 101 " both_signs ideal model delta sigma weight residual False 2.41 2.79 -0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" C1* PSU a2580 " pdb=" O4* PSU a2580 " pdb=" C2* PSU a2580 " pdb=" C5 PSU a2580 " both_signs ideal model delta sigma weight residual False 2.55 2.19 0.36 2.00e-01 2.50e+01 3.19e+00 ... (remaining 29293 not shown) Planarity restraints: 12270 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG V 10 " 0.123 2.00e-02 2.50e+03 6.67e-01 1.00e+04 pdb=" C4' 2MG V 10 " 0.503 2.00e-02 2.50e+03 pdb=" O4' 2MG V 10 " 0.740 2.00e-02 2.50e+03 pdb=" C3' 2MG V 10 " -0.560 2.00e-02 2.50e+03 pdb=" O3' 2MG V 10 " -0.739 2.00e-02 2.50e+03 pdb=" C2' 2MG V 10 " -0.164 2.00e-02 2.50e+03 pdb=" O2' 2MG V 10 " 1.044 2.00e-02 2.50e+03 pdb=" C1' 2MG V 10 " 0.146 2.00e-02 2.50e+03 pdb=" N9 2MG V 10 " -1.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1516 " -0.069 2.00e-02 2.50e+03 6.06e-01 8.27e+03 pdb=" C4' 2MG A1516 " -0.435 2.00e-02 2.50e+03 pdb=" O4' 2MG A1516 " -0.624 2.00e-02 2.50e+03 pdb=" C3' 2MG A1516 " 0.601 2.00e-02 2.50e+03 pdb=" O3' 2MG A1516 " 0.656 2.00e-02 2.50e+03 pdb=" C2' 2MG A1516 " 0.166 2.00e-02 2.50e+03 pdb=" O2' 2MG A1516 " -1.000 2.00e-02 2.50e+03 pdb=" C1' 2MG A1516 " -0.220 2.00e-02 2.50e+03 pdb=" N9 2MG A1516 " 0.926 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1207 " -0.053 2.00e-02 2.50e+03 5.93e-01 7.91e+03 pdb=" C4' 2MG A1207 " -0.446 2.00e-02 2.50e+03 pdb=" O4' 2MG A1207 " -0.647 2.00e-02 2.50e+03 pdb=" C3' 2MG A1207 " 0.594 2.00e-02 2.50e+03 pdb=" O3' 2MG A1207 " 0.618 2.00e-02 2.50e+03 pdb=" C2' 2MG A1207 " 0.195 2.00e-02 2.50e+03 pdb=" O2' 2MG A1207 " -0.952 2.00e-02 2.50e+03 pdb=" C1' 2MG A1207 " -0.215 2.00e-02 2.50e+03 pdb=" N9 2MG A1207 " 0.905 2.00e-02 2.50e+03 ... (remaining 12267 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 698 2.47 - 3.08: 88428 3.08 - 3.68: 263117 3.68 - 4.29: 413341 4.29 - 4.90: 551104 Nonbonded interactions: 1316688 Sorted by model distance: nonbonded pdb=" OP1 C a2385 " pdb="MG MG a6112 " model vdw 1.859 2.170 nonbonded pdb=" OP2 A a2821 " pdb="MG MG a6111 " model vdw 1.863 2.170 nonbonded pdb=" OP1 G a1026 " pdb="MG MG a6120 " model vdw 1.874 2.170 nonbonded pdb=" OP1 U A1224 " pdb="MG MG A1624 " model vdw 1.886 2.170 nonbonded pdb=" OP1 C a 948 " pdb="MG MG a6030 " model vdw 1.892 2.170 ... (remaining 1316683 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.150 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: 35.430 Check model and map are aligned: 1.570 Set scattering table: 1.000 Process input model: 548.600 Find NCS groups from input model: 2.810 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 608.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 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 : 0.010 0.290 154032 Z= 0.599 Angle : 0.737 36.205 230513 Z= 0.377 Chirality : 0.046 0.406 29296 Planarity : 0.026 0.667 12270 Dihedral : 22.523 179.577 88228 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.96 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.11), residues: 5480 helix: 1.08 (0.12), residues: 1851 sheet: -0.08 (0.15), residues: 1094 loop : -0.57 (0.12), residues: 2535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP B 96 HIS 0.039 0.002 HIS K 118 PHE 0.023 0.002 PHE S 61 TYR 0.015 0.002 TYR L 38 ARG 0.016 0.001 ARG S 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1035 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1035 time to evaluate : 6.189 Fit side-chains revert: symmetry clash REVERT: B 43 LEU cc_start: 0.3260 (mt) cc_final: 0.2925 (mm) REVERT: B 100 MET cc_start: 0.5359 (ttm) cc_final: 0.4589 (mtp) REVERT: B 103 ASN cc_start: 0.5153 (t0) cc_final: 0.4868 (t0) REVERT: B 112 LYS cc_start: 0.4693 (ttpt) cc_final: 0.4372 (mttt) REVERT: B 135 LEU cc_start: 0.2337 (mp) cc_final: 0.2109 (tt) REVERT: B 143 LYS cc_start: 0.4218 (tppp) cc_final: 0.3761 (ttmm) REVERT: C 31 ASP cc_start: 0.7519 (m-30) cc_final: 0.7295 (m-30) REVERT: C 34 ASP cc_start: 0.7445 (t0) cc_final: 0.7143 (t0) REVERT: C 45 LYS cc_start: 0.7233 (tttm) cc_final: 0.6704 (tmmt) REVERT: C 49 LYS cc_start: 0.7352 (mptt) cc_final: 0.6867 (mmmt) REVERT: C 88 ARG cc_start: 0.5875 (tmm-80) cc_final: 0.5358 (ttt-90) REVERT: C 98 PRO cc_start: 0.6427 (Cg_endo) cc_final: 0.6170 (Cg_exo) REVERT: C 100 GLN cc_start: 0.5922 (tt0) cc_final: 0.5669 (tm-30) REVERT: C 134 MET cc_start: 0.7357 (mtp) cc_final: 0.6841 (mtm) REVERT: C 142 MET cc_start: 0.7085 (mmm) cc_final: 0.6451 (mmm) REVERT: C 170 GLU cc_start: 0.6916 (tt0) cc_final: 0.6504 (tp30) REVERT: C 188 GLU cc_start: 0.6979 (mt-10) cc_final: 0.6563 (mp0) REVERT: C 193 TYR cc_start: 0.7095 (m-80) cc_final: 0.6834 (m-80) REVERT: D 53 VAL cc_start: 0.5754 (t) cc_final: 0.5554 (m) REVERT: D 54 GLN cc_start: 0.7090 (mt0) cc_final: 0.6809 (mt0) REVERT: D 74 ASN cc_start: 0.7106 (m-40) cc_final: 0.6876 (m110) REVERT: D 81 ARG cc_start: 0.6365 (ttp80) cc_final: 0.5999 (ttt-90) REVERT: D 91 LEU cc_start: 0.6024 (mt) cc_final: 0.5502 (mt) REVERT: D 151 LYS cc_start: 0.4661 (pttp) cc_final: 0.4328 (mmtm) REVERT: D 156 LYS cc_start: 0.4889 (mmtm) cc_final: 0.4477 (mtmt) REVERT: E 62 LYS cc_start: 0.7667 (mttt) cc_final: 0.7452 (mtpt) REVERT: E 68 ARG cc_start: 0.7047 (ttm110) cc_final: 0.6836 (mtm-85) REVERT: E 78 ASN cc_start: 0.6438 (m-40) cc_final: 0.6194 (t0) REVERT: E 97 GLN cc_start: 0.7543 (mt0) cc_final: 0.7108 (mt0) REVERT: F 21 MET cc_start: 0.4930 (mtm) cc_final: 0.3816 (mmt) REVERT: F 40 GLU cc_start: 0.7291 (mt-10) cc_final: 0.6956 (mt-10) REVERT: F 42 TRP cc_start: 0.6913 (m-10) cc_final: 0.6338 (m-10) REVERT: F 79 ARG cc_start: 0.6660 (ttm-80) cc_final: 0.6244 (ttm-80) REVERT: F 102 MET cc_start: 0.5083 (ptp) cc_final: 0.4462 (ptt) REVERT: G 47 LEU cc_start: 0.6767 (mt) cc_final: 0.6544 (mt) REVERT: G 68 ASN cc_start: 0.6264 (m-40) cc_final: 0.5674 (m-40) REVERT: G 76 LYS cc_start: 0.5874 (mtmt) cc_final: 0.5392 (mtpp) REVERT: G 106 GLU cc_start: 0.6330 (tt0) cc_final: 0.6013 (mm-30) REVERT: G 110 LYS cc_start: 0.6537 (mtmm) cc_final: 0.5973 (mttp) REVERT: G 137 LYS cc_start: 0.6636 (tptm) cc_final: 0.6286 (tmtt) REVERT: G 148 ASN cc_start: 0.7819 (m-40) cc_final: 0.7025 (m-40) REVERT: H 31 LYS cc_start: 0.6756 (ptmt) cc_final: 0.6392 (mmtp) REVERT: H 38 ASN cc_start: 0.6657 (t0) cc_final: 0.6453 (t0) REVERT: H 50 LYS cc_start: 0.7350 (ptmm) cc_final: 0.7110 (pttt) REVERT: H 76 GLN cc_start: 0.7446 (pt0) cc_final: 0.6691 (mm110) REVERT: H 88 ARG cc_start: 0.7196 (mtp85) cc_final: 0.6949 (mtp180) REVERT: H 89 LYS cc_start: 0.6798 (pttp) cc_final: 0.6553 (pttm) REVERT: H 108 LYS cc_start: 0.7120 (mmtp) cc_final: 0.6840 (mmtp) REVERT: I 42 GLU cc_start: 0.5849 (mm-30) cc_final: 0.5556 (tp30) REVERT: I 46 MET cc_start: 0.6653 (ttp) cc_final: 0.5972 (ttt) REVERT: I 50 GLN cc_start: 0.8272 (mt0) cc_final: 0.7757 (mt0) REVERT: I 64 TYR cc_start: 0.7739 (t80) cc_final: 0.7536 (t80) REVERT: I 66 THR cc_start: 0.7727 (m) cc_final: 0.7192 (p) REVERT: I 68 LYS cc_start: 0.7413 (mtpt) cc_final: 0.6981 (mtpp) REVERT: I 119 ARG cc_start: 0.6908 (mtm-85) cc_final: 0.6533 (mtp180) REVERT: J 16 ARG cc_start: 0.5322 (mtm-85) cc_final: 0.5102 (mtm-85) REVERT: J 73 LEU cc_start: 0.7514 (tp) cc_final: 0.7064 (tm) REVERT: J 74 VAL cc_start: 0.7270 (t) cc_final: 0.7020 (t) REVERT: J 88 MET cc_start: 0.4317 (mmm) cc_final: 0.3621 (mpt) REVERT: K 27 PHE cc_start: 0.7883 (m-80) cc_final: 0.7447 (m-80) REVERT: K 61 PHE cc_start: 0.7260 (t80) cc_final: 0.6893 (t80) REVERT: K 69 ARG cc_start: 0.6677 (mmm-85) cc_final: 0.6255 (mpt180) REVERT: K 97 ILE cc_start: 0.6251 (mt) cc_final: 0.5664 (tp) REVERT: K 107 ILE cc_start: 0.5882 (mm) cc_final: 0.5509 (mt) REVERT: L 10 LYS cc_start: 0.7262 (ttpt) cc_final: 0.6955 (ttmm) REVERT: L 30 LYS cc_start: 0.7513 (mmtp) cc_final: 0.7190 (mmtm) REVERT: L 39 THR cc_start: 0.7736 (m) cc_final: 0.7497 (t) REVERT: L 56 ARG cc_start: 0.6116 (ttp80) cc_final: 0.5476 (tmm160) REVERT: L 77 HIS cc_start: 0.7237 (m-70) cc_final: 0.6832 (m-70) REVERT: L 117 TYR cc_start: 0.7397 (m-80) cc_final: 0.7058 (m-80) REVERT: M 3 ARG cc_start: 0.6543 (mtp85) cc_final: 0.6094 (mmm-85) REVERT: M 34 LEU cc_start: 0.7160 (mt) cc_final: 0.6942 (mm) REVERT: M 39 ILE cc_start: 0.6395 (mt) cc_final: 0.6062 (mp) REVERT: M 43 VAL cc_start: 0.7322 (p) cc_final: 0.7086 (t) REVERT: M 93 ARG cc_start: 0.6377 (mmt90) cc_final: 0.5768 (mmt90) REVERT: N 90 ARG cc_start: 0.7011 (mtm-85) cc_final: 0.6498 (mtm110) REVERT: N 100 SER cc_start: 0.7715 (p) cc_final: 0.7445 (p) REVERT: O 58 ARG cc_start: 0.6848 (ttt180) cc_final: 0.6429 (ttm110) REVERT: O 71 LYS cc_start: 0.7906 (tttt) cc_final: 0.7618 (ttmt) REVERT: O 77 ARG cc_start: 0.5958 (ttp80) cc_final: 0.5688 (ttp80) REVERT: Q 17 MET cc_start: 0.5321 (ptm) cc_final: 0.5048 (ptm) REVERT: Q 19 LYS cc_start: 0.6401 (mttm) cc_final: 0.6197 (mttt) REVERT: Q 61 ILE cc_start: 0.7291 (pt) cc_final: 0.7083 (pt) REVERT: Q 65 ARG cc_start: 0.6249 (ptt-90) cc_final: 0.6035 (ptt-90) REVERT: Q 73 TRP cc_start: 0.7084 (m100) cc_final: 0.6842 (m100) REVERT: R 50 LYS cc_start: 0.7187 (ptmt) cc_final: 0.6896 (ptpt) REVERT: R 57 ARG cc_start: 0.7482 (ttm110) cc_final: 0.7233 (mtt90) REVERT: T 29 ARG cc_start: 0.6945 (mtm-85) cc_final: 0.6633 (mtm180) REVERT: T 60 ARG cc_start: 0.5977 (ttm110) cc_final: 0.5756 (ttm110) REVERT: T 69 LYS cc_start: 0.6420 (mtmt) cc_final: 0.5889 (mptt) REVERT: U 33 ARG cc_start: 0.4601 (mmm-85) cc_final: 0.4346 (ttm110) REVERT: U 47 ARG cc_start: 0.6250 (ttp-170) cc_final: 0.5864 (ttp-110) REVERT: c 5 LYS cc_start: 0.7562 (mtpp) cc_final: 0.7348 (tttt) REVERT: c 23 GLU cc_start: 0.6532 (pt0) cc_final: 0.6291 (pt0) REVERT: c 70 ASN cc_start: 0.7534 (p0) cc_final: 0.7322 (p0) REVERT: c 97 LYS cc_start: 0.7838 (mmmm) cc_final: 0.7618 (mmtm) REVERT: c 133 ARG cc_start: 0.7364 (ptp-110) cc_final: 0.6969 (ptp90) REVERT: c 183 LYS cc_start: 0.7898 (ttmm) cc_final: 0.7652 (tppp) REVERT: c 189 ARG cc_start: 0.7406 (mtt-85) cc_final: 0.7091 (mtt-85) REVERT: c 269 ARG cc_start: 0.6812 (mtp85) cc_final: 0.6581 (ttm170) REVERT: d 62 LYS cc_start: 0.8401 (mtpp) cc_final: 0.8181 (mtpp) REVERT: d 88 GLU cc_start: 0.6162 (mt-10) cc_final: 0.5902 (mt-10) REVERT: d 103 ASP cc_start: 0.6985 (m-30) cc_final: 0.6710 (m-30) REVERT: d 105 LYS cc_start: 0.7928 (mmtm) cc_final: 0.7587 (mttp) REVERT: d 181 ASP cc_start: 0.6757 (t0) cc_final: 0.6442 (t0) REVERT: d 183 GLU cc_start: 0.6101 (pm20) cc_final: 0.5787 (pt0) REVERT: d 200 ASP cc_start: 0.7552 (m-30) cc_final: 0.7325 (m-30) REVERT: e 1 MET cc_start: 0.5638 (ptm) cc_final: 0.5242 (ptt) REVERT: e 106 LYS cc_start: 0.8001 (mtpt) cc_final: 0.7623 (mtpm) REVERT: e 123 LYS cc_start: 0.6037 (ptmm) cc_final: 0.5470 (ptpt) REVERT: e 141 MET cc_start: 0.6271 (mtp) cc_final: 0.5677 (mtp) REVERT: e 144 GLU cc_start: 0.5366 (pm20) cc_final: 0.4950 (tp30) REVERT: e 162 ARG cc_start: 0.7969 (ttp-170) cc_final: 0.7716 (ttp-170) REVERT: e 171 ASP cc_start: 0.6947 (t70) cc_final: 0.6433 (t0) REVERT: e 185 LYS cc_start: 0.7053 (mmtm) cc_final: 0.6805 (mmtp) REVERT: f 26 MET cc_start: 0.7866 (mmm) cc_final: 0.7538 (mmm) REVERT: f 56 ASP cc_start: 0.6766 (m-30) cc_final: 0.6364 (m-30) REVERT: f 101 GLU cc_start: 0.6140 (tt0) cc_final: 0.5854 (tt0) REVERT: f 128 TYR cc_start: 0.7848 (t80) cc_final: 0.7607 (t80) REVERT: f 130 MET cc_start: 0.7952 (ptm) cc_final: 0.7609 (ptm) REVERT: f 148 ARG cc_start: 0.5328 (ptm160) cc_final: 0.5105 (ptm160) REVERT: f 178 ARG cc_start: 0.5531 (mtm-85) cc_final: 0.4859 (mtt180) REVERT: g 69 ARG cc_start: 0.7094 (tmt170) cc_final: 0.5951 (tmt170) REVERT: g 89 LEU cc_start: 0.7583 (mt) cc_final: 0.7240 (mt) REVERT: g 104 ASN cc_start: 0.6688 (m110) cc_final: 0.6021 (t0) REVERT: g 134 LYS cc_start: 0.7555 (mmmm) cc_final: 0.6606 (mttp) REVERT: h 1 MET cc_start: 0.5238 (ptm) cc_final: 0.4754 (ptm) REVERT: h 3 VAL cc_start: 0.6188 (p) cc_final: 0.5915 (t) REVERT: i 12 LYS cc_start: 0.6234 (mmmm) cc_final: 0.5943 (mmmt) REVERT: i 43 GLU cc_start: 0.8247 (mp0) cc_final: 0.7736 (mp0) REVERT: i 49 ASP cc_start: 0.7691 (t0) cc_final: 0.7147 (t0) REVERT: i 106 LYS cc_start: 0.8166 (tttm) cc_final: 0.7545 (ttmt) REVERT: i 138 GLN cc_start: 0.7505 (pt0) cc_final: 0.7224 (pt0) REVERT: j 7 MET cc_start: 0.8328 (mmm) cc_final: 0.7998 (mmm) REVERT: j 17 ARG cc_start: 0.7103 (mmt-90) cc_final: 0.6879 (mpt180) REVERT: j 53 LYS cc_start: 0.7702 (pttp) cc_final: 0.7225 (ptmm) REVERT: j 93 GLN cc_start: 0.7110 (mm-40) cc_final: 0.6772 (mp10) REVERT: j 95 ILE cc_start: 0.8003 (mt) cc_final: 0.7768 (mt) REVERT: j 113 MET cc_start: 0.6378 (mmm) cc_final: 0.6013 (ttp) REVERT: j 114 LYS cc_start: 0.6555 (mtpp) cc_final: 0.5896 (tppt) REVERT: j 117 SER cc_start: 0.7882 (p) cc_final: 0.7623 (m) REVERT: k 2 ARG cc_start: 0.7309 (mmm-85) cc_final: 0.6885 (mmm-85) REVERT: k 80 SER cc_start: 0.7882 (p) cc_final: 0.7429 (m) REVERT: k 103 ILE cc_start: 0.7804 (mm) cc_final: 0.7561 (tp) REVERT: k 123 ARG cc_start: 0.6583 (ttm170) cc_final: 0.6240 (mtm110) REVERT: k 126 ARG cc_start: 0.7650 (mtm180) cc_final: 0.7209 (mtp180) REVERT: l 10 ARG cc_start: 0.7358 (mtm-85) cc_final: 0.7025 (mtm110) REVERT: l 28 PHE cc_start: 0.8129 (m-80) cc_final: 0.7924 (m-80) REVERT: l 47 GLU cc_start: 0.7636 (tp30) cc_final: 0.7237 (tp30) REVERT: l 60 GLN cc_start: 0.6222 (mm110) cc_final: 0.5565 (mp10) REVERT: l 75 GLU cc_start: 0.7147 (mm-30) cc_final: 0.6817 (mt-10) REVERT: l 88 ASN cc_start: 0.7902 (m110) cc_final: 0.7608 (m-40) REVERT: l 90 GLU cc_start: 0.7360 (mm-30) cc_final: 0.7057 (mm-30) REVERT: l 127 LYS cc_start: 0.7623 (ttmt) cc_final: 0.7360 (ttmt) REVERT: m 1 MET cc_start: 0.8395 (mtm) cc_final: 0.8088 (mtm) REVERT: m 20 MET cc_start: 0.8459 (ttp) cc_final: 0.8081 (ttp) REVERT: n 13 ARG cc_start: 0.6755 (ttm-80) cc_final: 0.6435 (ttp-170) REVERT: n 16 ARG cc_start: 0.6667 (mmp80) cc_final: 0.6462 (mmt-90) REVERT: n 89 ASP cc_start: 0.6681 (t0) cc_final: 0.6325 (m-30) REVERT: n 103 VAL cc_start: 0.7858 (m) cc_final: 0.7656 (t) REVERT: o 4 ILE cc_start: 0.7797 (mt) cc_final: 0.7215 (mm) REVERT: o 6 LYS cc_start: 0.6933 (ptpt) cc_final: 0.6450 (pptt) REVERT: o 7 GLN cc_start: 0.7463 (tm-30) cc_final: 0.6583 (tt0) REVERT: o 9 GLU cc_start: 0.7321 (mt-10) cc_final: 0.7099 (mt-10) REVERT: o 10 GLN cc_start: 0.7003 (mm-40) cc_final: 0.6402 (mt0) REVERT: o 38 LYS cc_start: 0.6433 (ptmt) cc_final: 0.6083 (pttt) REVERT: o 68 GLU cc_start: 0.6009 (mm-30) cc_final: 0.5649 (tm-30) REVERT: o 88 ARG cc_start: 0.7874 (ttp80) cc_final: 0.7421 (ttp80) REVERT: o 89 ARG cc_start: 0.7694 (mmt180) cc_final: 0.7379 (mmm160) REVERT: o 111 LYS cc_start: 0.7873 (ptmm) cc_final: 0.7088 (pttt) REVERT: p 22 LYS cc_start: 0.8207 (mttm) cc_final: 0.7971 (mmtt) REVERT: p 85 LYS cc_start: 0.7345 (mttt) cc_final: 0.7141 (mttt) REVERT: q 48 LYS cc_start: 0.7785 (mttm) cc_final: 0.7233 (mttt) REVERT: q 70 GLU cc_start: 0.7002 (mm-30) cc_final: 0.6727 (tp30) REVERT: q 97 LYS cc_start: 0.7772 (tttp) cc_final: 0.7536 (tttm) REVERT: r 31 GLN cc_start: 0.6918 (mt0) cc_final: 0.6675 (mt0) REVERT: r 82 MET cc_start: 0.7759 (mtt) cc_final: 0.7117 (mtt) REVERT: s 1 MET cc_start: 0.2969 (mpp) cc_final: 0.2764 (mmm) REVERT: s 3 ARG cc_start: 0.6718 (mtm-85) cc_final: 0.5424 (mmt-90) REVERT: s 5 GLU cc_start: 0.6717 (mt-10) cc_final: 0.6466 (tt0) REVERT: s 26 LYS cc_start: 0.6738 (mmtp) cc_final: 0.6480 (mmpt) REVERT: s 30 ILE cc_start: 0.7490 (mm) cc_final: 0.7107 (tt) REVERT: t 7 ARG cc_start: 0.6793 (ttm110) cc_final: 0.6437 (ttp-110) REVERT: t 27 ASN cc_start: 0.7417 (t0) cc_final: 0.7195 (t0) REVERT: u 1 MET cc_start: 0.3731 (tpt) cc_final: 0.3477 (mpm) REVERT: u 7 GLU cc_start: 0.5863 (mm-30) cc_final: 0.5438 (tp30) REVERT: u 24 ASN cc_start: 0.7459 (t0) cc_final: 0.7194 (m110) REVERT: u 53 LYS cc_start: 0.6269 (mttp) cc_final: 0.6045 (mttt) REVERT: u 57 TYR cc_start: 0.7333 (m-80) cc_final: 0.7012 (m-80) REVERT: u 85 LYS cc_start: 0.7234 (mtpp) cc_final: 0.6972 (mttm) REVERT: u 90 ASP cc_start: 0.7924 (m-30) cc_final: 0.7662 (m-30) REVERT: v 25 ARG cc_start: 0.7689 (mmt90) cc_final: 0.7482 (mmt90) REVERT: v 72 LYS cc_start: 0.7838 (mtpp) cc_final: 0.7265 (mtpt) REVERT: v 75 LYS cc_start: 0.7317 (mttt) cc_final: 0.6806 (mppt) REVERT: x 23 ARG cc_start: 0.6878 (mtt90) cc_final: 0.6564 (mtm-85) REVERT: x 45 GLN cc_start: 0.6669 (mt0) cc_final: 0.5942 (mm-40) REVERT: x 58 ASN cc_start: 0.7068 (t0) cc_final: 0.6431 (m110) REVERT: y 16 ARG cc_start: 0.8001 (mmt180) cc_final: 0.7497 (mmt180) REVERT: y 45 ARG cc_start: 0.8114 (mmt180) cc_final: 0.7844 (mpt90) REVERT: z 52 ARG cc_start: 0.6672 (ttt180) cc_final: 0.6047 (ttp-110) REVERT: 0 7 GLU cc_start: 0.7170 (pt0) cc_final: 0.6858 (pt0) REVERT: 0 12 VAL cc_start: 0.8588 (p) cc_final: 0.8337 (t) REVERT: 0 32 GLU cc_start: 0.6398 (pm20) cc_final: 0.5617 (tp30) REVERT: 0 35 GLU cc_start: 0.7156 (tt0) cc_final: 0.6810 (tt0) REVERT: 0 38 LYS cc_start: 0.8409 (mtpp) cc_final: 0.8181 (mtpm) REVERT: 0 40 ASP cc_start: 0.8447 (t0) cc_final: 0.8227 (t70) REVERT: 0 48 ILE cc_start: 0.8348 (mm) cc_final: 0.8079 (mm) REVERT: 2 15 LYS cc_start: 0.8213 (mmtm) cc_final: 0.7476 (mmmm) REVERT: 2 19 LYS cc_start: 0.8115 (mttm) cc_final: 0.7758 (mttp) REVERT: 3 15 LYS cc_start: 0.7739 (mttm) cc_final: 0.7300 (mtpp) REVERT: 3 30 GLU cc_start: 0.6759 (tp30) cc_final: 0.6448 (tp30) REVERT: 4 22 MET cc_start: 0.6339 (mtm) cc_final: 0.5902 (mpp) REVERT: 4 25 ARG cc_start: 0.6105 (mmm-85) cc_final: 0.5890 (mtt90) outliers start: 0 outliers final: 2 residues processed: 1035 average time/residue: 2.4529 time to fit residues: 3475.7269 Evaluate side-chains 845 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 843 time to evaluate : 6.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 40 ILE Chi-restraints excluded: chain 4 residue 5 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 835 optimal weight: 0.8980 chunk 750 optimal weight: 20.0000 chunk 416 optimal weight: 10.0000 chunk 256 optimal weight: 6.9990 chunk 506 optimal weight: 8.9990 chunk 400 optimal weight: 10.0000 chunk 775 optimal weight: 2.9990 chunk 300 optimal weight: 6.9990 chunk 471 optimal weight: 30.0000 chunk 577 optimal weight: 5.9990 chunk 899 optimal weight: 9.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN H 21 ASN I 4 ASN ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN N 35 ASN ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 59 HIS R 54 GLN T 3 ASN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 163 GLN e 156 ASN ** g 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 128 ASN i 136 GLN j 88 ASN n 98 GLN o 41 GLN p 71 GLN q 6 GLN x 20 ASN x 27 ASN x 45 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 154032 Z= 0.256 Angle : 0.766 16.888 230513 Z= 0.415 Chirality : 0.039 0.348 29296 Planarity : 0.008 0.141 12270 Dihedral : 23.070 177.752 77194 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.59 % Favored : 96.35 % Rotamer: Outliers : 2.34 % Allowed : 9.25 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.11), residues: 5480 helix: 1.29 (0.12), residues: 1874 sheet: 0.11 (0.16), residues: 1049 loop : -0.48 (0.12), residues: 2557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 96 HIS 0.024 0.002 HIS K 118 PHE 0.024 0.002 PHE m 21 TYR 0.019 0.002 TYR f 22 ARG 0.010 0.001 ARG p 51 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 976 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 869 time to evaluate : 6.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 LYS cc_start: 0.4708 (ttpt) cc_final: 0.4335 (mttt) REVERT: B 135 LEU cc_start: 0.2868 (mp) cc_final: 0.2502 (tt) REVERT: B 187 VAL cc_start: 0.5176 (t) cc_final: 0.4648 (p) REVERT: C 28 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6395 (pt0) REVERT: C 34 ASP cc_start: 0.7501 (t0) cc_final: 0.7196 (t0) REVERT: C 41 GLN cc_start: 0.7045 (OUTLIER) cc_final: 0.6709 (pt0) REVERT: C 45 LYS cc_start: 0.7358 (tttm) cc_final: 0.6650 (tmmt) REVERT: C 88 ARG cc_start: 0.5899 (tmm-80) cc_final: 0.5284 (ttt-90) REVERT: C 98 PRO cc_start: 0.6557 (Cg_endo) cc_final: 0.6349 (Cg_exo) REVERT: C 110 GLU cc_start: 0.6823 (OUTLIER) cc_final: 0.5649 (mp0) REVERT: C 127 ARG cc_start: 0.6165 (mtm-85) cc_final: 0.5885 (mpp80) REVERT: C 142 MET cc_start: 0.7156 (mmm) cc_final: 0.6390 (mmm) REVERT: C 170 GLU cc_start: 0.6984 (tt0) cc_final: 0.6567 (tp30) REVERT: C 188 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6568 (mp0) REVERT: C 193 TYR cc_start: 0.7086 (m-80) cc_final: 0.6819 (m-80) REVERT: D 54 GLN cc_start: 0.7009 (mt0) cc_final: 0.6718 (mt0) REVERT: D 78 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6295 (tm-30) REVERT: D 151 LYS cc_start: 0.4682 (pttp) cc_final: 0.4336 (mmtm) REVERT: E 68 ARG cc_start: 0.7019 (ttm110) cc_final: 0.6643 (mtm180) REVERT: E 78 ASN cc_start: 0.6383 (m-40) cc_final: 0.6105 (t0) REVERT: E 86 LYS cc_start: 0.7413 (mmtm) cc_final: 0.6755 (mmmt) REVERT: F 42 TRP cc_start: 0.7033 (m-10) cc_final: 0.6486 (m-10) REVERT: F 79 ARG cc_start: 0.6667 (ttm-80) cc_final: 0.6208 (ttm-80) REVERT: F 102 MET cc_start: 0.5083 (ptp) cc_final: 0.4716 (ptp) REVERT: G 4 ARG cc_start: 0.5766 (tpp80) cc_final: 0.5211 (ptt180) REVERT: G 53 ARG cc_start: 0.6010 (ttm170) cc_final: 0.5456 (ttm170) REVERT: G 68 ASN cc_start: 0.6319 (m-40) cc_final: 0.5754 (m-40) REVERT: G 76 LYS cc_start: 0.5935 (mtmt) cc_final: 0.5547 (mtpp) REVERT: G 83 SER cc_start: 0.5736 (m) cc_final: 0.5361 (t) REVERT: G 90 GLU cc_start: 0.6155 (OUTLIER) cc_final: 0.5722 (mt-10) REVERT: G 110 LYS cc_start: 0.6082 (mtmm) cc_final: 0.5828 (mttm) REVERT: G 137 LYS cc_start: 0.6439 (tptm) cc_final: 0.6188 (tmtt) REVERT: G 148 ASN cc_start: 0.7857 (m-40) cc_final: 0.7545 (m110) REVERT: H 31 LYS cc_start: 0.6681 (ptmt) cc_final: 0.6434 (mmtp) REVERT: H 74 SER cc_start: 0.7788 (p) cc_final: 0.7374 (t) REVERT: H 76 GLN cc_start: 0.7460 (pt0) cc_final: 0.6735 (mm110) REVERT: H 88 ARG cc_start: 0.7077 (mtp85) cc_final: 0.6413 (mtm180) REVERT: H 108 LYS cc_start: 0.7209 (mmtp) cc_final: 0.6893 (mmtp) REVERT: I 42 GLU cc_start: 0.5903 (mm-30) cc_final: 0.5430 (tp30) REVERT: I 46 MET cc_start: 0.6573 (ttp) cc_final: 0.5938 (ttt) REVERT: I 50 GLN cc_start: 0.8283 (mt0) cc_final: 0.7799 (mt0) REVERT: I 68 LYS cc_start: 0.7270 (mtpt) cc_final: 0.6698 (mtpp) REVERT: J 16 ARG cc_start: 0.5540 (mtm-85) cc_final: 0.5286 (mtm-85) REVERT: J 73 LEU cc_start: 0.7521 (tp) cc_final: 0.7107 (tm) REVERT: J 88 MET cc_start: 0.4400 (mmm) cc_final: 0.3655 (mpt) REVERT: K 27 PHE cc_start: 0.7991 (m-80) cc_final: 0.7679 (m-80) REVERT: K 61 PHE cc_start: 0.7265 (t80) cc_final: 0.7056 (t80) REVERT: K 69 ARG cc_start: 0.6679 (mmm-85) cc_final: 0.6220 (mpt180) REVERT: K 97 ILE cc_start: 0.6246 (mt) cc_final: 0.5646 (tp) REVERT: K 107 ILE cc_start: 0.5830 (mm) cc_final: 0.5561 (mt) REVERT: L 39 THR cc_start: 0.7899 (m) cc_final: 0.7591 (t) REVERT: L 56 ARG cc_start: 0.6164 (ttp80) cc_final: 0.5338 (tmm160) REVERT: L 117 TYR cc_start: 0.7405 (m-80) cc_final: 0.7009 (m-80) REVERT: M 3 ARG cc_start: 0.6543 (mtp85) cc_final: 0.6116 (mmm-85) REVERT: M 43 VAL cc_start: 0.7414 (p) cc_final: 0.7214 (t) REVERT: M 93 ARG cc_start: 0.6398 (mmt90) cc_final: 0.5566 (mmm-85) REVERT: N 47 LYS cc_start: 0.7149 (tttt) cc_final: 0.6493 (ttmm) REVERT: N 90 ARG cc_start: 0.7087 (mtm-85) cc_final: 0.6701 (mtt90) REVERT: N 92 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7298 (mt-10) REVERT: N 100 SER cc_start: 0.7809 (p) cc_final: 0.7518 (p) REVERT: O 17 ARG cc_start: 0.3648 (mtm110) cc_final: 0.3188 (tmt170) REVERT: O 58 ARG cc_start: 0.6846 (ttt180) cc_final: 0.6385 (ttm110) REVERT: P 32 PHE cc_start: 0.7810 (p90) cc_final: 0.7372 (p90) REVERT: Q 17 MET cc_start: 0.5756 (ptm) cc_final: 0.5333 (ptm) REVERT: Q 19 LYS cc_start: 0.6491 (mttm) cc_final: 0.6268 (mttt) REVERT: Q 44 LEU cc_start: 0.7515 (mt) cc_final: 0.7314 (mt) REVERT: Q 75 LEU cc_start: 0.6973 (OUTLIER) cc_final: 0.6728 (tt) REVERT: R 57 ARG cc_start: 0.7470 (ttm110) cc_final: 0.7185 (mtt90) REVERT: T 21 ASN cc_start: 0.6332 (m110) cc_final: 0.6043 (m-40) REVERT: T 32 ILE cc_start: 0.6504 (OUTLIER) cc_final: 0.6303 (mp) REVERT: T 33 LYS cc_start: 0.6025 (tppt) cc_final: 0.5719 (pttp) REVERT: T 69 LYS cc_start: 0.6378 (mtmt) cc_final: 0.5923 (mptt) REVERT: T 85 LYS cc_start: 0.5343 (mtmm) cc_final: 0.5098 (mtpt) REVERT: U 33 ARG cc_start: 0.4693 (mmm-85) cc_final: 0.4464 (ttm110) REVERT: U 36 GLU cc_start: 0.5803 (tt0) cc_final: 0.5511 (tt0) REVERT: c 5 LYS cc_start: 0.7620 (mtpp) cc_final: 0.7381 (tttt) REVERT: c 18 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.8077 (ptmt) REVERT: c 66 ASP cc_start: 0.7784 (t0) cc_final: 0.7582 (t0) REVERT: c 100 GLU cc_start: 0.7846 (tt0) cc_final: 0.7351 (tt0) REVERT: c 133 ARG cc_start: 0.7403 (ptp-110) cc_final: 0.7065 (ptp-110) REVERT: c 183 LYS cc_start: 0.7884 (ttmm) cc_final: 0.7609 (tppp) REVERT: c 189 ARG cc_start: 0.7332 (mtt-85) cc_final: 0.7007 (mtt-85) REVERT: d 35 THR cc_start: 0.8542 (m) cc_final: 0.8222 (t) REVERT: d 74 GLU cc_start: 0.6654 (OUTLIER) cc_final: 0.6394 (mt-10) REVERT: d 103 ASP cc_start: 0.6955 (m-30) cc_final: 0.6717 (m-30) REVERT: d 105 LYS cc_start: 0.7870 (mmtm) cc_final: 0.7619 (mttp) REVERT: d 157 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8360 (ttpt) REVERT: d 181 ASP cc_start: 0.6853 (t0) cc_final: 0.6526 (t0) REVERT: d 183 GLU cc_start: 0.6085 (pm20) cc_final: 0.5812 (pt0) REVERT: d 200 ASP cc_start: 0.7637 (m-30) cc_final: 0.7368 (m-30) REVERT: e 1 MET cc_start: 0.5534 (ptm) cc_final: 0.5151 (ptt) REVERT: e 25 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7272 (tt0) REVERT: e 123 LYS cc_start: 0.6162 (ptmm) cc_final: 0.5534 (ptpt) REVERT: e 141 MET cc_start: 0.6285 (mtp) cc_final: 0.5924 (mtm) REVERT: e 144 GLU cc_start: 0.5428 (pm20) cc_final: 0.4991 (tp30) REVERT: e 171 ASP cc_start: 0.6883 (t70) cc_final: 0.6193 (t0) REVERT: e 194 LYS cc_start: 0.6856 (tttp) cc_final: 0.6540 (ttmt) REVERT: f 24 SER cc_start: 0.6784 (p) cc_final: 0.6520 (t) REVERT: f 26 MET cc_start: 0.7900 (mmm) cc_final: 0.7550 (mmm) REVERT: f 115 ARG cc_start: 0.5340 (tpt90) cc_final: 0.5015 (mmm160) REVERT: f 128 TYR cc_start: 0.7924 (t80) cc_final: 0.7226 (t80) REVERT: f 130 MET cc_start: 0.8074 (ptm) cc_final: 0.7302 (ppp) REVERT: f 178 ARG cc_start: 0.5790 (mtm-85) cc_final: 0.5020 (mtt180) REVERT: g 29 LYS cc_start: 0.5059 (ttpt) cc_final: 0.4855 (tmtm) REVERT: g 69 ARG cc_start: 0.7213 (tmt170) cc_final: 0.6134 (tmt170) REVERT: g 88 GLN cc_start: 0.7108 (tt0) cc_final: 0.6708 (tt0) REVERT: g 104 ASN cc_start: 0.6803 (m110) cc_final: 0.6378 (t0) REVERT: g 176 LYS cc_start: 0.3054 (mmmt) cc_final: 0.2798 (tppt) REVERT: h 1 MET cc_start: 0.5353 (ptm) cc_final: 0.4860 (ptm) REVERT: i 12 LYS cc_start: 0.6210 (mmmm) cc_final: 0.5944 (mmmt) REVERT: i 43 GLU cc_start: 0.8165 (mp0) cc_final: 0.7714 (mp0) REVERT: i 49 ASP cc_start: 0.7677 (t0) cc_final: 0.7080 (t0) REVERT: i 96 ARG cc_start: 0.6655 (mmm160) cc_final: 0.6374 (mmm-85) REVERT: i 106 LYS cc_start: 0.8082 (tttm) cc_final: 0.7502 (ttmm) REVERT: i 136 GLN cc_start: 0.7396 (mt0) cc_final: 0.7157 (mt0) REVERT: i 138 GLN cc_start: 0.7396 (pt0) cc_final: 0.7168 (pt0) REVERT: j 7 MET cc_start: 0.8254 (mmm) cc_final: 0.7906 (mmm) REVERT: j 17 ARG cc_start: 0.7184 (mmt-90) cc_final: 0.6873 (mpt180) REVERT: j 53 LYS cc_start: 0.7659 (pttp) cc_final: 0.7357 (ptmm) REVERT: j 93 GLN cc_start: 0.7447 (mm-40) cc_final: 0.6980 (mp10) REVERT: j 113 MET cc_start: 0.6414 (mmm) cc_final: 0.6097 (ttp) REVERT: j 114 LYS cc_start: 0.6847 (mtpp) cc_final: 0.6295 (mttp) REVERT: k 1 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.6777 (ptt) REVERT: k 80 SER cc_start: 0.7720 (p) cc_final: 0.7482 (m) REVERT: k 91 ASP cc_start: 0.6897 (p0) cc_final: 0.6679 (p0) REVERT: k 103 ILE cc_start: 0.7787 (mm) cc_final: 0.7535 (tp) REVERT: k 123 ARG cc_start: 0.6546 (ttm110) cc_final: 0.6188 (mtm110) REVERT: k 126 ARG cc_start: 0.7612 (mtm180) cc_final: 0.7244 (mtp180) REVERT: l 10 ARG cc_start: 0.7327 (mtm-85) cc_final: 0.6966 (mtm110) REVERT: l 22 GLN cc_start: 0.7276 (OUTLIER) cc_final: 0.6522 (mt0) REVERT: l 47 GLU cc_start: 0.7610 (tp30) cc_final: 0.7227 (tp30) REVERT: l 75 GLU cc_start: 0.6975 (mm-30) cc_final: 0.6537 (mm-30) REVERT: l 88 ASN cc_start: 0.7910 (m110) cc_final: 0.7128 (m-40) REVERT: l 90 GLU cc_start: 0.7504 (mm-30) cc_final: 0.6525 (mp0) REVERT: l 127 LYS cc_start: 0.7644 (ttmt) cc_final: 0.7355 (ttmt) REVERT: m 1 MET cc_start: 0.8349 (mtm) cc_final: 0.7984 (mtm) REVERT: m 117 ASP cc_start: 0.6974 (p0) cc_final: 0.6740 (m-30) REVERT: n 16 ARG cc_start: 0.6732 (mmp80) cc_final: 0.6483 (mmt-90) REVERT: n 46 GLU cc_start: 0.6165 (tm-30) cc_final: 0.5926 (tt0) REVERT: n 62 LEU cc_start: 0.7358 (mt) cc_final: 0.7046 (mt) REVERT: n 89 ASP cc_start: 0.6706 (t0) cc_final: 0.6336 (m-30) REVERT: n 98 GLN cc_start: 0.7796 (mm-40) cc_final: 0.7299 (mm-40) REVERT: n 116 GLN cc_start: 0.6502 (mm-40) cc_final: 0.6198 (mm110) REVERT: o 6 LYS cc_start: 0.6913 (ptpt) cc_final: 0.6302 (pptt) REVERT: o 9 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6974 (mt-10) REVERT: o 10 GLN cc_start: 0.6888 (mm-40) cc_final: 0.6409 (mt0) REVERT: o 38 LYS cc_start: 0.6516 (ptmt) cc_final: 0.6203 (pttt) REVERT: o 68 GLU cc_start: 0.6164 (mm-30) cc_final: 0.5750 (tm-30) REVERT: o 88 ARG cc_start: 0.7969 (ttp80) cc_final: 0.7277 (ttp80) REVERT: o 89 ARG cc_start: 0.7674 (mmt180) cc_final: 0.7333 (mmm160) REVERT: o 102 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6844 (mp0) REVERT: o 111 LYS cc_start: 0.7933 (ptmm) cc_final: 0.7102 (pttt) REVERT: q 40 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8172 (ttt) REVERT: q 48 LYS cc_start: 0.7666 (mttm) cc_final: 0.7054 (mttt) REVERT: q 73 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7598 (mmtm) REVERT: q 95 ASP cc_start: 0.7678 (m-30) cc_final: 0.7471 (m-30) REVERT: q 97 LYS cc_start: 0.7877 (tttp) cc_final: 0.7582 (tttm) REVERT: r 31 GLN cc_start: 0.6873 (mt0) cc_final: 0.6594 (mt0) REVERT: r 82 MET cc_start: 0.7942 (mtt) cc_final: 0.7247 (mtt) REVERT: s 3 ARG cc_start: 0.6336 (mtm-85) cc_final: 0.5548 (mtp85) REVERT: s 5 GLU cc_start: 0.6817 (mt-10) cc_final: 0.6616 (mt-10) REVERT: s 18 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.6569 (mp0) REVERT: s 42 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6519 (mp0) REVERT: s 49 LYS cc_start: 0.7308 (ttmt) cc_final: 0.6957 (tttp) REVERT: t 7 ARG cc_start: 0.6675 (ttm110) cc_final: 0.6113 (tpt-90) REVERT: u 24 ASN cc_start: 0.7348 (t0) cc_final: 0.7051 (m110) REVERT: u 53 LYS cc_start: 0.6270 (mttp) cc_final: 0.5950 (mttt) REVERT: u 57 TYR cc_start: 0.7336 (m-80) cc_final: 0.7060 (m-80) REVERT: u 85 LYS cc_start: 0.7195 (mtpp) cc_final: 0.6655 (mtmm) REVERT: u 90 ASP cc_start: 0.7972 (m-30) cc_final: 0.7752 (m-30) REVERT: v 72 LYS cc_start: 0.7805 (mtpp) cc_final: 0.7152 (mttt) REVERT: v 75 LYS cc_start: 0.7387 (mttt) cc_final: 0.6888 (mppt) REVERT: w 71 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7486 (mp) REVERT: x 24 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6591 (tm-30) REVERT: x 45 GLN cc_start: 0.6726 (mt0) cc_final: 0.6000 (mm-40) REVERT: x 58 ASN cc_start: 0.6966 (t0) cc_final: 0.6673 (m110) REVERT: y 16 ARG cc_start: 0.8025 (mmt180) cc_final: 0.7690 (mmt180) REVERT: y 45 ARG cc_start: 0.8071 (mmt180) cc_final: 0.7569 (mmt90) REVERT: 0 7 GLU cc_start: 0.7199 (pt0) cc_final: 0.6961 (pt0) REVERT: 0 32 GLU cc_start: 0.6413 (pm20) cc_final: 0.6010 (pm20) REVERT: 2 19 LYS cc_start: 0.8072 (mttm) cc_final: 0.7807 (mttp) REVERT: 3 1 MET cc_start: 0.8229 (tpp) cc_final: 0.8019 (tpp) REVERT: 3 15 LYS cc_start: 0.7691 (mttm) cc_final: 0.7406 (mtpp) REVERT: 3 30 GLU cc_start: 0.6766 (tp30) cc_final: 0.6384 (tp30) REVERT: 4 25 ARG cc_start: 0.6095 (mmm-85) cc_final: 0.5709 (mmt90) outliers start: 107 outliers final: 44 residues processed: 921 average time/residue: 2.3996 time to fit residues: 3056.5990 Evaluate side-chains 880 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 815 time to evaluate : 6.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain G residue 131 LYS Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain P residue 68 SER Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain c residue 18 LYS Chi-restraints excluded: chain c residue 19 VAL Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 74 GLU Chi-restraints excluded: chain d residue 99 GLU Chi-restraints excluded: chain d residue 157 LYS Chi-restraints excluded: chain e residue 25 GLU Chi-restraints excluded: chain e residue 88 ARG Chi-restraints excluded: chain e residue 175 ILE Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 44 ILE Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain g residue 11 VAL Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain i residue 7 LYS Chi-restraints excluded: chain j residue 105 ARG Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 7 SER Chi-restraints excluded: chain k residue 121 THR Chi-restraints excluded: chain l residue 22 GLN Chi-restraints excluded: chain m residue 65 LEU Chi-restraints excluded: chain n residue 91 SER Chi-restraints excluded: chain o residue 102 GLU Chi-restraints excluded: chain q residue 40 MET Chi-restraints excluded: chain q residue 73 LYS Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain r residue 27 LYS Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 72 THR Chi-restraints excluded: chain s residue 18 GLU Chi-restraints excluded: chain s residue 28 ASN Chi-restraints excluded: chain s residue 42 GLU Chi-restraints excluded: chain w residue 40 VAL Chi-restraints excluded: chain w residue 66 THR Chi-restraints excluded: chain w residue 71 LEU Chi-restraints excluded: chain x residue 24 GLU Chi-restraints excluded: chain 4 residue 5 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 499 optimal weight: 10.0000 chunk 279 optimal weight: 10.0000 chunk 748 optimal weight: 20.0000 chunk 612 optimal weight: 8.9990 chunk 248 optimal weight: 4.9990 chunk 900 optimal weight: 7.9990 chunk 972 optimal weight: 7.9990 chunk 802 optimal weight: 0.9980 chunk 893 optimal weight: 8.9990 chunk 307 optimal weight: 20.0000 chunk 722 optimal weight: 10.0000 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN D 74 ASN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 ASN F 52 ASN F 55 HIS I 4 ASN I 32 GLN ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 GLN c 163 GLN e 136 GLN ** g 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 88 ASN n 61 GLN p 71 GLN q 6 GLN s 28 ASN x 27 ASN 0 45 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 154032 Z= 0.309 Angle : 0.797 17.330 230513 Z= 0.429 Chirality : 0.042 0.370 29296 Planarity : 0.008 0.149 12270 Dihedral : 23.112 178.531 77192 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.83 % Favored : 96.11 % Rotamer: Outliers : 3.10 % Allowed : 12.37 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.11), residues: 5480 helix: 1.08 (0.12), residues: 1875 sheet: -0.07 (0.16), residues: 1075 loop : -0.60 (0.12), residues: 2530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP c 248 HIS 0.015 0.002 HIS K 118 PHE 0.022 0.002 PHE m 21 TYR 0.021 0.002 TYR r 38 ARG 0.014 0.001 ARG p 51 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 999 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 857 time to evaluate : 6.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 ASN cc_start: 0.3237 (OUTLIER) cc_final: 0.2552 (m110) REVERT: B 135 LEU cc_start: 0.2902 (mp) cc_final: 0.2534 (tt) REVERT: B 167 ASP cc_start: 0.3136 (p0) cc_final: 0.2682 (m-30) REVERT: B 187 VAL cc_start: 0.4905 (t) cc_final: 0.4293 (p) REVERT: C 28 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.6314 (pt0) REVERT: C 31 ASP cc_start: 0.7824 (m-30) cc_final: 0.7328 (m-30) REVERT: C 41 GLN cc_start: 0.7123 (OUTLIER) cc_final: 0.6782 (pt0) REVERT: C 88 ARG cc_start: 0.5984 (tmm-80) cc_final: 0.5281 (ttt-90) REVERT: C 127 ARG cc_start: 0.6279 (mtm-85) cc_final: 0.6007 (mpp-170) REVERT: C 170 GLU cc_start: 0.6910 (tt0) cc_final: 0.6628 (tp30) REVERT: C 188 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6678 (mp0) REVERT: D 54 GLN cc_start: 0.7077 (mt0) cc_final: 0.6775 (mt0) REVERT: D 78 GLU cc_start: 0.6581 (OUTLIER) cc_final: 0.6284 (tm-30) REVERT: D 151 LYS cc_start: 0.4691 (pttp) cc_final: 0.4299 (mmtm) REVERT: E 13 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6494 (mt-10) REVERT: E 68 ARG cc_start: 0.7058 (ttm110) cc_final: 0.6704 (mtm-85) REVERT: E 78 ASN cc_start: 0.6367 (m-40) cc_final: 0.6058 (t0) REVERT: E 86 LYS cc_start: 0.7520 (mmtm) cc_final: 0.6861 (mmmt) REVERT: F 79 ARG cc_start: 0.6678 (ttm-80) cc_final: 0.6239 (ttm-80) REVERT: F 90 MET cc_start: 0.7431 (mtt) cc_final: 0.7114 (mtt) REVERT: F 102 MET cc_start: 0.5275 (ptp) cc_final: 0.4439 (mpp) REVERT: G 4 ARG cc_start: 0.5806 (tpp80) cc_final: 0.5195 (ptt180) REVERT: G 68 ASN cc_start: 0.6313 (m-40) cc_final: 0.5740 (m110) REVERT: G 76 LYS cc_start: 0.6016 (mtmt) cc_final: 0.5621 (mtpp) REVERT: G 83 SER cc_start: 0.5475 (m) cc_final: 0.5200 (t) REVERT: G 137 LYS cc_start: 0.6494 (tptm) cc_final: 0.6165 (tmtt) REVERT: H 74 SER cc_start: 0.7796 (p) cc_final: 0.7424 (t) REVERT: H 76 GLN cc_start: 0.7434 (pt0) cc_final: 0.6309 (mm-40) REVERT: H 83 LEU cc_start: 0.8281 (tp) cc_final: 0.8059 (tt) REVERT: H 88 ARG cc_start: 0.7086 (mtp85) cc_final: 0.6733 (mtm180) REVERT: H 90 ASP cc_start: 0.5887 (p0) cc_final: 0.5404 (p0) REVERT: I 42 GLU cc_start: 0.6029 (mm-30) cc_final: 0.5521 (tp30) REVERT: I 46 MET cc_start: 0.6479 (ttp) cc_final: 0.5808 (ttt) REVERT: I 50 GLN cc_start: 0.8266 (mt0) cc_final: 0.7796 (mt0) REVERT: J 73 LEU cc_start: 0.7529 (tp) cc_final: 0.7118 (tm) REVERT: J 88 MET cc_start: 0.4132 (mmm) cc_final: 0.3457 (mpt) REVERT: J 89 ARG cc_start: 0.3074 (mtm110) cc_final: 0.2739 (ttm110) REVERT: K 27 PHE cc_start: 0.8047 (m-80) cc_final: 0.7840 (m-80) REVERT: K 69 ARG cc_start: 0.6713 (mmm-85) cc_final: 0.6265 (mpt180) REVERT: K 97 ILE cc_start: 0.6217 (mt) cc_final: 0.5452 (tp) REVERT: K 107 ILE cc_start: 0.5867 (mm) cc_final: 0.5637 (mt) REVERT: L 20 ASN cc_start: 0.6901 (m-40) cc_final: 0.6651 (m110) REVERT: L 39 THR cc_start: 0.7943 (m) cc_final: 0.7727 (t) REVERT: L 56 ARG cc_start: 0.6154 (ttp80) cc_final: 0.5316 (tmm160) REVERT: L 117 TYR cc_start: 0.7360 (m-80) cc_final: 0.6890 (m-80) REVERT: M 43 VAL cc_start: 0.7465 (p) cc_final: 0.7225 (t) REVERT: M 78 LYS cc_start: 0.5922 (tppt) cc_final: 0.5216 (mtmm) REVERT: M 93 ARG cc_start: 0.6385 (mmt90) cc_final: 0.5564 (mmm-85) REVERT: N 27 LEU cc_start: 0.7022 (mp) cc_final: 0.6762 (mm) REVERT: N 47 LYS cc_start: 0.7150 (tttt) cc_final: 0.6437 (ttmm) REVERT: N 90 ARG cc_start: 0.6914 (mtm-85) cc_final: 0.6423 (mtm110) REVERT: O 17 ARG cc_start: 0.3643 (mtm110) cc_final: 0.3162 (tmt170) REVERT: O 58 ARG cc_start: 0.6877 (ttt180) cc_final: 0.6427 (ttm110) REVERT: O 77 ARG cc_start: 0.6195 (ttp80) cc_final: 0.5815 (ttp80) REVERT: Q 11 ARG cc_start: 0.6435 (OUTLIER) cc_final: 0.5709 (mtp-110) REVERT: Q 17 MET cc_start: 0.5920 (ptm) cc_final: 0.5579 (ptm) REVERT: Q 19 LYS cc_start: 0.6619 (mttm) cc_final: 0.6204 (mttt) REVERT: Q 75 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6847 (tt) REVERT: T 21 ASN cc_start: 0.6409 (m110) cc_final: 0.6013 (m-40) REVERT: T 24 ARG cc_start: 0.6101 (mmm160) cc_final: 0.5589 (mpt180) REVERT: T 33 LYS cc_start: 0.6136 (tppt) cc_final: 0.5683 (pttp) REVERT: T 69 LYS cc_start: 0.6512 (mtmt) cc_final: 0.5962 (mptt) REVERT: U 17 ARG cc_start: 0.4426 (ttm-80) cc_final: 0.3728 (mtt-85) REVERT: U 34 ARG cc_start: 0.6480 (OUTLIER) cc_final: 0.5534 (ttm170) REVERT: U 36 GLU cc_start: 0.6213 (tt0) cc_final: 0.6011 (tt0) REVERT: c 5 LYS cc_start: 0.7584 (mtpp) cc_final: 0.7382 (tttt) REVERT: c 183 LYS cc_start: 0.7909 (ttmm) cc_final: 0.7627 (tppp) REVERT: c 189 ARG cc_start: 0.7326 (mtt-85) cc_final: 0.6958 (mtt-85) REVERT: d 74 GLU cc_start: 0.6622 (OUTLIER) cc_final: 0.6357 (mt-10) REVERT: d 105 LYS cc_start: 0.7858 (mmtm) cc_final: 0.7578 (mttp) REVERT: d 157 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8370 (ttpt) REVERT: d 181 ASP cc_start: 0.6749 (t0) cc_final: 0.6448 (t0) REVERT: d 183 GLU cc_start: 0.6104 (pm20) cc_final: 0.5747 (pt0) REVERT: d 200 ASP cc_start: 0.7543 (m-30) cc_final: 0.7297 (m-30) REVERT: e 1 MET cc_start: 0.5344 (ptm) cc_final: 0.4866 (ptt) REVERT: e 123 LYS cc_start: 0.6176 (ptmm) cc_final: 0.5614 (ptpt) REVERT: e 141 MET cc_start: 0.5937 (mtp) cc_final: 0.5675 (mtm) REVERT: e 171 ASP cc_start: 0.6943 (t70) cc_final: 0.6171 (t0) REVERT: f 24 SER cc_start: 0.6622 (p) cc_final: 0.6417 (t) REVERT: f 26 MET cc_start: 0.7852 (mmm) cc_final: 0.7591 (mmm) REVERT: f 128 TYR cc_start: 0.7877 (t80) cc_final: 0.7273 (t80) REVERT: f 130 MET cc_start: 0.7969 (ptm) cc_final: 0.7397 (ppp) REVERT: f 167 ARG cc_start: 0.6845 (ttm-80) cc_final: 0.6574 (ttp-110) REVERT: g 29 LYS cc_start: 0.5182 (ttpt) cc_final: 0.4925 (tmtm) REVERT: g 69 ARG cc_start: 0.7103 (tmt170) cc_final: 0.6107 (tmt170) REVERT: g 86 LYS cc_start: 0.6757 (mtpp) cc_final: 0.6133 (mptp) REVERT: g 88 GLN cc_start: 0.7089 (tt0) cc_final: 0.6715 (tt0) REVERT: g 104 ASN cc_start: 0.6774 (m110) cc_final: 0.6472 (t0) REVERT: g 176 LYS cc_start: 0.3266 (mmmt) cc_final: 0.2493 (tppt) REVERT: h 1 MET cc_start: 0.5442 (ptm) cc_final: 0.4918 (ptm) REVERT: i 12 LYS cc_start: 0.6251 (mmmm) cc_final: 0.5889 (mmmt) REVERT: i 43 GLU cc_start: 0.8197 (mp0) cc_final: 0.7770 (mp0) REVERT: i 49 ASP cc_start: 0.7663 (t0) cc_final: 0.7235 (t0) REVERT: i 60 ASP cc_start: 0.7889 (p0) cc_final: 0.7459 (p0) REVERT: i 96 ARG cc_start: 0.6640 (mmm160) cc_final: 0.6435 (mmm-85) REVERT: i 106 LYS cc_start: 0.8091 (tttm) cc_final: 0.7493 (ttmm) REVERT: i 138 GLN cc_start: 0.7528 (pt0) cc_final: 0.7233 (pt0) REVERT: j 7 MET cc_start: 0.8299 (mmm) cc_final: 0.7944 (mmm) REVERT: j 17 ARG cc_start: 0.7140 (mmt-90) cc_final: 0.6835 (mpt180) REVERT: j 53 LYS cc_start: 0.7619 (pttp) cc_final: 0.7250 (ptmm) REVERT: j 111 LYS cc_start: 0.6390 (mtpp) cc_final: 0.5839 (mtpt) REVERT: j 113 MET cc_start: 0.6198 (mmm) cc_final: 0.5981 (ttp) REVERT: j 114 LYS cc_start: 0.6922 (mtpp) cc_final: 0.6123 (mppt) REVERT: k 91 ASP cc_start: 0.7038 (p0) cc_final: 0.6808 (p0) REVERT: k 103 ILE cc_start: 0.7790 (mm) cc_final: 0.7547 (tp) REVERT: k 104 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7718 (mt0) REVERT: k 115 GLU cc_start: 0.6454 (tm-30) cc_final: 0.6110 (tp30) REVERT: k 123 ARG cc_start: 0.6689 (ttm170) cc_final: 0.6397 (ttm170) REVERT: k 126 ARG cc_start: 0.7590 (mtm180) cc_final: 0.7229 (mtp180) REVERT: l 10 ARG cc_start: 0.7374 (mtm-85) cc_final: 0.7000 (mtm110) REVERT: l 22 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.6762 (mt0) REVERT: l 47 GLU cc_start: 0.7762 (tp30) cc_final: 0.7521 (tp30) REVERT: l 75 GLU cc_start: 0.6937 (mm-30) cc_final: 0.6573 (mm-30) REVERT: l 88 ASN cc_start: 0.7950 (m110) cc_final: 0.7244 (m-40) REVERT: l 90 GLU cc_start: 0.7587 (mm-30) cc_final: 0.6718 (mp0) REVERT: n 16 ARG cc_start: 0.6712 (mmp80) cc_final: 0.6473 (mmt-90) REVERT: n 89 ASP cc_start: 0.6888 (t0) cc_final: 0.6608 (m-30) REVERT: n 98 GLN cc_start: 0.7794 (mm-40) cc_final: 0.7355 (mm-40) REVERT: n 116 GLN cc_start: 0.6625 (mm-40) cc_final: 0.6239 (mm110) REVERT: o 6 LYS cc_start: 0.6916 (ptpt) cc_final: 0.6310 (pptt) REVERT: o 9 GLU cc_start: 0.7243 (mt-10) cc_final: 0.6965 (mt-10) REVERT: o 10 GLN cc_start: 0.6948 (mm-40) cc_final: 0.6597 (mt0) REVERT: o 38 LYS cc_start: 0.6515 (ptmt) cc_final: 0.6197 (pttt) REVERT: o 68 GLU cc_start: 0.6095 (mm-30) cc_final: 0.5790 (tm-30) REVERT: o 88 ARG cc_start: 0.7924 (ttp80) cc_final: 0.7547 (ttp80) REVERT: o 89 ARG cc_start: 0.7496 (mmt180) cc_final: 0.7290 (mmm160) REVERT: o 111 LYS cc_start: 0.7998 (ptmm) cc_final: 0.7196 (pttm) REVERT: q 6 GLN cc_start: 0.7911 (pt0) cc_final: 0.6730 (tm130) REVERT: q 40 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8270 (ttt) REVERT: q 48 LYS cc_start: 0.7667 (mttm) cc_final: 0.7032 (mttt) REVERT: q 55 ASP cc_start: 0.6062 (m-30) cc_final: 0.5479 (t0) REVERT: q 95 ASP cc_start: 0.7842 (m-30) cc_final: 0.7602 (m-30) REVERT: q 97 LYS cc_start: 0.7867 (tttp) cc_final: 0.7659 (tttm) REVERT: r 31 GLN cc_start: 0.6758 (mt0) cc_final: 0.6481 (mt0) REVERT: r 82 MET cc_start: 0.7696 (mtt) cc_final: 0.7119 (mtt) REVERT: r 92 ARG cc_start: 0.7441 (ttm-80) cc_final: 0.6597 (ttm110) REVERT: s 3 ARG cc_start: 0.6408 (mtm-85) cc_final: 0.5569 (mtp85) REVERT: s 18 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.6574 (mp0) REVERT: s 42 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6460 (mp0) REVERT: s 52 GLU cc_start: 0.5567 (mp0) cc_final: 0.5090 (tm-30) REVERT: t 7 ARG cc_start: 0.6526 (ttm110) cc_final: 0.6148 (tpt-90) REVERT: u 1 MET cc_start: 0.4287 (tpp) cc_final: 0.3964 (mpp) REVERT: u 11 GLU cc_start: 0.7079 (pt0) cc_final: 0.6734 (pm20) REVERT: u 12 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.6961 (mm-40) REVERT: u 24 ASN cc_start: 0.7303 (t0) cc_final: 0.7052 (m110) REVERT: u 38 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7645 (pt) REVERT: u 53 LYS cc_start: 0.6343 (mttp) cc_final: 0.6097 (mttt) REVERT: u 85 LYS cc_start: 0.7169 (mtpp) cc_final: 0.6588 (mtmm) REVERT: u 90 ASP cc_start: 0.7977 (m-30) cc_final: 0.7727 (m-30) REVERT: v 68 LYS cc_start: 0.8293 (tttm) cc_final: 0.7886 (ttpt) REVERT: v 72 LYS cc_start: 0.7818 (mtpp) cc_final: 0.7157 (mtpt) REVERT: v 75 LYS cc_start: 0.7314 (mttt) cc_final: 0.6915 (mppt) REVERT: w 43 GLU cc_start: 0.6337 (OUTLIER) cc_final: 0.6116 (mt-10) REVERT: w 71 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7563 (mp) REVERT: x 9 LYS cc_start: 0.6115 (mttp) cc_final: 0.5885 (mtpt) REVERT: x 24 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6568 (tm-30) REVERT: x 45 GLN cc_start: 0.6809 (mt0) cc_final: 0.6058 (mm-40) REVERT: x 58 ASN cc_start: 0.7162 (t0) cc_final: 0.6411 (m110) REVERT: y 11 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7834 (mtt90) REVERT: 1 29 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7791 (mt0) REVERT: 2 19 LYS cc_start: 0.8095 (mttm) cc_final: 0.7765 (mttp) REVERT: 3 15 LYS cc_start: 0.7708 (mttm) cc_final: 0.7414 (mtpp) REVERT: 3 30 GLU cc_start: 0.6865 (tp30) cc_final: 0.6487 (mt-10) REVERT: 4 2 LYS cc_start: 0.7144 (mttt) cc_final: 0.6748 (mtmm) REVERT: 4 3 LYS cc_start: 0.6093 (mttp) cc_final: 0.5887 (ptpp) REVERT: 4 25 ARG cc_start: 0.6133 (mmm-85) cc_final: 0.5800 (mmt90) outliers start: 142 outliers final: 68 residues processed: 926 average time/residue: 2.3591 time to fit residues: 3036.5086 Evaluate side-chains 912 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 822 time to evaluate : 6.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 91 ARG Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 131 LYS Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain P residue 68 SER Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 34 ARG Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 74 GLU Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain d residue 99 GLU Chi-restraints excluded: chain d residue 157 LYS Chi-restraints excluded: chain e residue 88 ARG Chi-restraints excluded: chain e residue 175 ILE Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 44 ILE Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 11 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain h residue 3 VAL Chi-restraints excluded: chain i residue 7 LYS Chi-restraints excluded: chain j residue 105 ARG Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 5 THR Chi-restraints excluded: chain k residue 7 SER Chi-restraints excluded: chain k residue 104 GLN Chi-restraints excluded: chain k residue 121 THR Chi-restraints excluded: chain l residue 22 GLN Chi-restraints excluded: chain l residue 110 GLU Chi-restraints excluded: chain l residue 119 LEU Chi-restraints excluded: chain m residue 65 LEU Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain q residue 40 MET Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain r residue 27 LYS Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain s residue 18 GLU Chi-restraints excluded: chain s residue 42 GLU Chi-restraints excluded: chain s residue 55 VAL Chi-restraints excluded: chain u residue 12 GLN Chi-restraints excluded: chain u residue 38 LEU Chi-restraints excluded: chain w residue 40 VAL Chi-restraints excluded: chain w residue 43 GLU Chi-restraints excluded: chain w residue 66 THR Chi-restraints excluded: chain w residue 71 LEU Chi-restraints excluded: chain x residue 24 GLU Chi-restraints excluded: chain y residue 11 ARG Chi-restraints excluded: chain y residue 55 VAL Chi-restraints excluded: chain z residue 55 ILE Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 29 GLN Chi-restraints excluded: chain 2 residue 32 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 889 optimal weight: 20.0000 chunk 677 optimal weight: 5.9990 chunk 467 optimal weight: 10.0000 chunk 99 optimal weight: 30.0000 chunk 429 optimal weight: 10.0000 chunk 604 optimal weight: 10.0000 chunk 903 optimal weight: 6.9990 chunk 956 optimal weight: 3.9990 chunk 472 optimal weight: 40.0000 chunk 856 optimal weight: 7.9990 chunk 257 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 ASN F 52 ASN F 55 HIS G 142 HIS G 148 ASN I 4 ASN ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 163 GLN e 136 GLN f 37 ASN ** g 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 88 ASN p 71 GLN r 61 ASN s 28 ASN ** w 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 27 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 154032 Z= 0.314 Angle : 0.802 15.848 230513 Z= 0.431 Chirality : 0.042 0.360 29296 Planarity : 0.008 0.146 12270 Dihedral : 23.099 179.555 77190 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.09 % Favored : 95.86 % Rotamer: Outliers : 4.04 % Allowed : 13.97 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.11), residues: 5480 helix: 0.96 (0.12), residues: 1889 sheet: -0.11 (0.16), residues: 1054 loop : -0.69 (0.12), residues: 2537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP c 248 HIS 0.013 0.002 HIS B 39 PHE 0.021 0.002 PHE m 21 TYR 0.020 0.002 TYR r 38 ARG 0.014 0.001 ARG p 51 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1020 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 835 time to evaluate : 6.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 58 ASN cc_start: 0.3279 (OUTLIER) cc_final: 0.2609 (m110) REVERT: C 28 GLU cc_start: 0.6649 (OUTLIER) cc_final: 0.6342 (pt0) REVERT: C 31 ASP cc_start: 0.7847 (m-30) cc_final: 0.7368 (m-30) REVERT: C 36 ASP cc_start: 0.8109 (m-30) cc_final: 0.7465 (m-30) REVERT: C 41 GLN cc_start: 0.7041 (OUTLIER) cc_final: 0.6695 (pt0) REVERT: C 49 LYS cc_start: 0.7177 (mptt) cc_final: 0.6729 (mmmt) REVERT: C 88 ARG cc_start: 0.6039 (tmm-80) cc_final: 0.5303 (ttt-90) REVERT: C 127 ARG cc_start: 0.6276 (mtm-85) cc_final: 0.5946 (mpp80) REVERT: C 152 GLU cc_start: 0.7637 (tt0) cc_final: 0.7317 (tt0) REVERT: C 188 GLU cc_start: 0.7043 (mt-10) cc_final: 0.6694 (mp0) REVERT: D 54 GLN cc_start: 0.7070 (mt0) cc_final: 0.6771 (mt0) REVERT: D 78 GLU cc_start: 0.6554 (OUTLIER) cc_final: 0.6270 (tm-30) REVERT: D 81 ARG cc_start: 0.6632 (ttp80) cc_final: 0.6066 (ttt-90) REVERT: D 94 LEU cc_start: 0.5861 (OUTLIER) cc_final: 0.5604 (tp) REVERT: D 148 LYS cc_start: 0.5440 (ttpt) cc_final: 0.4598 (tmtp) REVERT: D 151 LYS cc_start: 0.4582 (pttp) cc_final: 0.4243 (mmtm) REVERT: E 68 ARG cc_start: 0.7053 (ttm110) cc_final: 0.6658 (mtm-85) REVERT: E 78 ASN cc_start: 0.6424 (m-40) cc_final: 0.6055 (t0) REVERT: E 86 LYS cc_start: 0.7541 (mmtm) cc_final: 0.6878 (mmmt) REVERT: F 56 LYS cc_start: 0.7585 (mtpt) cc_final: 0.7352 (mtpm) REVERT: F 79 ARG cc_start: 0.6674 (ttm-80) cc_final: 0.6357 (ttm-80) REVERT: F 102 MET cc_start: 0.5237 (ptp) cc_final: 0.4549 (mpp) REVERT: G 4 ARG cc_start: 0.5878 (tpp80) cc_final: 0.5304 (ptt180) REVERT: G 68 ASN cc_start: 0.6356 (m-40) cc_final: 0.5773 (m110) REVERT: G 76 LYS cc_start: 0.6005 (mtmt) cc_final: 0.5629 (mtpp) REVERT: G 79 ARG cc_start: 0.6110 (mtp-110) cc_final: 0.5591 (ttt-90) REVERT: G 83 SER cc_start: 0.5431 (m) cc_final: 0.5196 (t) REVERT: H 74 SER cc_start: 0.7788 (p) cc_final: 0.7412 (t) REVERT: H 76 GLN cc_start: 0.7470 (pt0) cc_final: 0.6683 (mm110) REVERT: H 88 ARG cc_start: 0.7084 (mtp85) cc_final: 0.6480 (mtm180) REVERT: H 90 ASP cc_start: 0.5785 (p0) cc_final: 0.5374 (p0) REVERT: I 42 GLU cc_start: 0.6036 (mm-30) cc_final: 0.5556 (tp30) REVERT: I 46 MET cc_start: 0.6566 (ttp) cc_final: 0.5984 (ttt) REVERT: J 16 ARG cc_start: 0.6297 (mmt90) cc_final: 0.5869 (mtt90) REVERT: J 73 LEU cc_start: 0.7544 (tp) cc_final: 0.7134 (tm) REVERT: J 88 MET cc_start: 0.4184 (mmm) cc_final: 0.3622 (mpt) REVERT: K 69 ARG cc_start: 0.6603 (mmm-85) cc_final: 0.6225 (mpt180) REVERT: K 97 ILE cc_start: 0.6168 (mt) cc_final: 0.5482 (tp) REVERT: K 107 ILE cc_start: 0.5880 (mm) cc_final: 0.5599 (mt) REVERT: L 20 ASN cc_start: 0.6909 (m-40) cc_final: 0.6644 (m110) REVERT: L 56 ARG cc_start: 0.6180 (OUTLIER) cc_final: 0.5371 (tmm160) REVERT: M 21 SER cc_start: 0.8343 (t) cc_final: 0.8050 (t) REVERT: M 43 VAL cc_start: 0.7426 (p) cc_final: 0.7167 (t) REVERT: M 58 ASP cc_start: 0.6177 (m-30) cc_final: 0.5884 (m-30) REVERT: M 78 LYS cc_start: 0.5883 (tppt) cc_final: 0.5222 (mtmm) REVERT: M 93 ARG cc_start: 0.6319 (mmt90) cc_final: 0.5635 (mmm-85) REVERT: N 27 LEU cc_start: 0.7016 (mp) cc_final: 0.6789 (mm) REVERT: N 90 ARG cc_start: 0.6864 (mtm-85) cc_final: 0.6535 (mtt90) REVERT: O 58 ARG cc_start: 0.6844 (ttt180) cc_final: 0.6415 (ttm110) REVERT: O 77 ARG cc_start: 0.6127 (ttp80) cc_final: 0.5887 (ttp80) REVERT: Q 11 ARG cc_start: 0.6394 (OUTLIER) cc_final: 0.5513 (mtp-110) REVERT: Q 17 MET cc_start: 0.5969 (ptm) cc_final: 0.5660 (ptm) REVERT: Q 19 LYS cc_start: 0.6609 (mttm) cc_final: 0.6216 (mttt) REVERT: Q 75 LEU cc_start: 0.7011 (OUTLIER) cc_final: 0.6775 (tt) REVERT: T 21 ASN cc_start: 0.6420 (m110) cc_final: 0.6033 (m-40) REVERT: T 24 ARG cc_start: 0.5950 (mmm160) cc_final: 0.5642 (mmp80) REVERT: T 33 LYS cc_start: 0.6247 (tppt) cc_final: 0.5794 (pttp) REVERT: T 64 LYS cc_start: 0.4769 (OUTLIER) cc_final: 0.3765 (mttp) REVERT: T 69 LYS cc_start: 0.6520 (mtmt) cc_final: 0.5977 (mptt) REVERT: U 3 VAL cc_start: 0.6382 (OUTLIER) cc_final: 0.5958 (t) REVERT: U 17 ARG cc_start: 0.4471 (ttm-80) cc_final: 0.3827 (mtt-85) REVERT: U 34 ARG cc_start: 0.6467 (OUTLIER) cc_final: 0.5509 (ttm170) REVERT: U 36 GLU cc_start: 0.6175 (tt0) cc_final: 0.5914 (tt0) REVERT: c 5 LYS cc_start: 0.7546 (mtpp) cc_final: 0.7262 (tttt) REVERT: c 117 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.7397 (tt0) REVERT: c 183 LYS cc_start: 0.7895 (ttmm) cc_final: 0.7651 (tppp) REVERT: c 189 ARG cc_start: 0.7327 (mtt-85) cc_final: 0.6954 (mtt-85) REVERT: d 157 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8364 (ttpt) REVERT: d 183 GLU cc_start: 0.6158 (pm20) cc_final: 0.5608 (pt0) REVERT: d 200 ASP cc_start: 0.7578 (m-30) cc_final: 0.7335 (m-30) REVERT: e 1 MET cc_start: 0.5254 (OUTLIER) cc_final: 0.4848 (ptt) REVERT: e 123 LYS cc_start: 0.6314 (ptmm) cc_final: 0.5721 (ptpt) REVERT: e 141 MET cc_start: 0.5935 (mtp) cc_final: 0.5700 (mtm) REVERT: e 171 ASP cc_start: 0.7043 (t70) cc_final: 0.6270 (t0) REVERT: f 48 LYS cc_start: 0.4853 (mtpp) cc_final: 0.4625 (mmmm) REVERT: f 128 TYR cc_start: 0.7851 (t80) cc_final: 0.7270 (t80) REVERT: f 130 MET cc_start: 0.7942 (ptm) cc_final: 0.7389 (ppp) REVERT: f 167 ARG cc_start: 0.6840 (ttm-80) cc_final: 0.6601 (ttp-110) REVERT: g 29 LYS cc_start: 0.5176 (ttpt) cc_final: 0.4857 (tmtm) REVERT: g 60 ASP cc_start: 0.5259 (OUTLIER) cc_final: 0.4955 (p0) REVERT: g 69 ARG cc_start: 0.7124 (tmt170) cc_final: 0.5998 (tmt170) REVERT: g 88 GLN cc_start: 0.7265 (tt0) cc_final: 0.6980 (tt0) REVERT: g 104 ASN cc_start: 0.6697 (m110) cc_final: 0.6467 (t0) REVERT: g 116 GLN cc_start: 0.6815 (tm-30) cc_final: 0.6229 (tm-30) REVERT: g 130 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.6578 (mm-30) REVERT: h 1 MET cc_start: 0.5372 (ptm) cc_final: 0.4849 (ptm) REVERT: h 6 LEU cc_start: 0.6066 (OUTLIER) cc_final: 0.5622 (tp) REVERT: i 12 LYS cc_start: 0.6222 (mmmm) cc_final: 0.5923 (mmmt) REVERT: i 43 GLU cc_start: 0.8194 (mp0) cc_final: 0.7761 (mp0) REVERT: i 60 ASP cc_start: 0.7887 (p0) cc_final: 0.7509 (p0) REVERT: i 106 LYS cc_start: 0.8117 (tttm) cc_final: 0.7502 (ttmm) REVERT: i 138 GLN cc_start: 0.7567 (pt0) cc_final: 0.7051 (mm-40) REVERT: j 7 MET cc_start: 0.8311 (mmm) cc_final: 0.7928 (mmm) REVERT: j 17 ARG cc_start: 0.7111 (mmt-90) cc_final: 0.6820 (mpt180) REVERT: j 53 LYS cc_start: 0.7631 (pttp) cc_final: 0.7263 (ptmm) REVERT: j 111 LYS cc_start: 0.6412 (mtpp) cc_final: 0.5942 (mtmt) REVERT: j 113 MET cc_start: 0.6181 (mmm) cc_final: 0.5953 (ttp) REVERT: j 114 LYS cc_start: 0.6891 (mtpp) cc_final: 0.6288 (mppt) REVERT: k 91 ASP cc_start: 0.7067 (p0) cc_final: 0.6829 (p0) REVERT: k 103 ILE cc_start: 0.7813 (mm) cc_final: 0.7564 (tp) REVERT: k 115 GLU cc_start: 0.6304 (tm-30) cc_final: 0.6065 (tp30) REVERT: k 126 ARG cc_start: 0.7612 (mtm180) cc_final: 0.7237 (mtp180) REVERT: k 143 GLU cc_start: 0.6262 (OUTLIER) cc_final: 0.6024 (mt-10) REVERT: l 10 ARG cc_start: 0.7387 (mtm-85) cc_final: 0.7036 (mtm110) REVERT: l 22 GLN cc_start: 0.7427 (OUTLIER) cc_final: 0.6793 (mt0) REVERT: l 47 GLU cc_start: 0.7770 (tp30) cc_final: 0.7535 (tp30) REVERT: l 53 MET cc_start: 0.7790 (ptm) cc_final: 0.7361 (ptp) REVERT: l 55 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.5861 (tmt170) REVERT: l 75 GLU cc_start: 0.6909 (mm-30) cc_final: 0.6558 (mm-30) REVERT: l 88 ASN cc_start: 0.8009 (m110) cc_final: 0.7316 (m-40) REVERT: l 90 GLU cc_start: 0.7599 (mm-30) cc_final: 0.6673 (mp0) REVERT: l 118 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7946 (tttm) REVERT: n 16 ARG cc_start: 0.6679 (mmp80) cc_final: 0.6453 (mmt-90) REVERT: n 46 GLU cc_start: 0.6078 (tm-30) cc_final: 0.5620 (tm-30) REVERT: n 98 GLN cc_start: 0.7781 (mm-40) cc_final: 0.7334 (mm-40) REVERT: n 116 GLN cc_start: 0.6681 (mm-40) cc_final: 0.6324 (mm110) REVERT: o 6 LYS cc_start: 0.6850 (ptpt) cc_final: 0.6298 (pptt) REVERT: o 9 GLU cc_start: 0.7261 (mt-10) cc_final: 0.7001 (mt-10) REVERT: o 10 GLN cc_start: 0.6922 (mm-40) cc_final: 0.6693 (mt0) REVERT: o 38 LYS cc_start: 0.6598 (ptmt) cc_final: 0.6256 (pttt) REVERT: o 68 GLU cc_start: 0.6139 (mm-30) cc_final: 0.5773 (tm-30) REVERT: o 111 LYS cc_start: 0.8014 (ptmm) cc_final: 0.7208 (pttm) REVERT: q 6 GLN cc_start: 0.7775 (pt0) cc_final: 0.6771 (tm130) REVERT: q 40 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8099 (ttt) REVERT: q 48 LYS cc_start: 0.7686 (mttm) cc_final: 0.7055 (mttt) REVERT: q 73 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7676 (mmtm) REVERT: r 31 GLN cc_start: 0.6800 (mt0) cc_final: 0.6589 (mt0) REVERT: r 72 THR cc_start: 0.8108 (p) cc_final: 0.7718 (t) REVERT: r 82 MET cc_start: 0.7626 (mtt) cc_final: 0.7205 (mtt) REVERT: r 92 ARG cc_start: 0.7472 (ttm-80) cc_final: 0.6654 (ttm110) REVERT: s 3 ARG cc_start: 0.6305 (mtm-85) cc_final: 0.5443 (mtp85) REVERT: s 18 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6574 (mp0) REVERT: s 42 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6522 (mp0) REVERT: s 52 GLU cc_start: 0.5573 (mp0) cc_final: 0.5114 (tm-30) REVERT: t 7 ARG cc_start: 0.6569 (ttm110) cc_final: 0.6157 (tpt-90) REVERT: u 11 GLU cc_start: 0.7075 (pt0) cc_final: 0.6702 (pm20) REVERT: u 12 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.6947 (mm-40) REVERT: u 38 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7644 (pt) REVERT: u 53 LYS cc_start: 0.6431 (mttp) cc_final: 0.6150 (mttt) REVERT: u 85 LYS cc_start: 0.7104 (mtpp) cc_final: 0.6660 (mtmm) REVERT: v 72 LYS cc_start: 0.7765 (mtpp) cc_final: 0.7145 (mttt) REVERT: w 71 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7559 (mp) REVERT: x 24 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6572 (tm-30) REVERT: x 45 GLN cc_start: 0.6898 (mt0) cc_final: 0.6100 (mm-40) REVERT: x 58 ASN cc_start: 0.7027 (t0) cc_final: 0.6385 (m110) REVERT: y 11 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7824 (mtt90) REVERT: 0 27 LYS cc_start: 0.7162 (mmtp) cc_final: 0.6927 (mttt) REVERT: 0 40 ASP cc_start: 0.8393 (t0) cc_final: 0.8138 (t70) REVERT: 1 29 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7721 (mt0) REVERT: 2 19 LYS cc_start: 0.8140 (mttm) cc_final: 0.7749 (mttp) REVERT: 2 57 LEU cc_start: 0.7786 (mt) cc_final: 0.7489 (mp) REVERT: 3 30 GLU cc_start: 0.6933 (tp30) cc_final: 0.6501 (mt-10) REVERT: 4 2 LYS cc_start: 0.7066 (mttt) cc_final: 0.6615 (mttp) REVERT: 4 3 LYS cc_start: 0.6019 (mttp) cc_final: 0.5770 (ptpp) REVERT: 4 25 ARG cc_start: 0.6017 (mmm-85) cc_final: 0.5799 (mmt90) outliers start: 185 outliers final: 96 residues processed: 930 average time/residue: 2.3860 time to fit residues: 3085.7616 Evaluate side-chains 946 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 819 time to evaluate : 6.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 131 LYS Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain L residue 36 ARG Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 56 ARG Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain N residue 23 LYS Chi-restraints excluded: chain N residue 80 SER Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain P residue 68 SER Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 64 LYS Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 34 ARG Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 117 GLN Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 74 GLU Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain d residue 99 GLU Chi-restraints excluded: chain d residue 157 LYS Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 51 GLU Chi-restraints excluded: chain e residue 139 LYS Chi-restraints excluded: chain e residue 175 ILE Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 44 ILE Chi-restraints excluded: chain f residue 72 LYS Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain g residue 4 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 11 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 130 GLU Chi-restraints excluded: chain h residue 3 VAL Chi-restraints excluded: chain h residue 6 LEU Chi-restraints excluded: chain i residue 7 LYS Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 90 GLU Chi-restraints excluded: chain j residue 105 ARG Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 5 THR Chi-restraints excluded: chain k residue 7 SER Chi-restraints excluded: chain k residue 121 THR Chi-restraints excluded: chain k residue 143 GLU Chi-restraints excluded: chain l residue 22 GLN Chi-restraints excluded: chain l residue 55 ARG Chi-restraints excluded: chain l residue 118 LYS Chi-restraints excluded: chain m residue 65 LEU Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain q residue 40 MET Chi-restraints excluded: chain q residue 73 LYS Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain r residue 27 LYS Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain s residue 18 GLU Chi-restraints excluded: chain s residue 42 GLU Chi-restraints excluded: chain s residue 55 VAL Chi-restraints excluded: chain u residue 12 GLN Chi-restraints excluded: chain u residue 38 LEU Chi-restraints excluded: chain w residue 40 VAL Chi-restraints excluded: chain w residue 66 THR Chi-restraints excluded: chain w residue 71 LEU Chi-restraints excluded: chain x residue 24 GLU Chi-restraints excluded: chain y residue 11 ARG Chi-restraints excluded: chain y residue 55 VAL Chi-restraints excluded: chain z residue 25 VAL Chi-restraints excluded: chain z residue 55 ILE Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 29 GLN Chi-restraints excluded: chain 2 residue 32 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 796 optimal weight: 6.9990 chunk 543 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 712 optimal weight: 0.3980 chunk 394 optimal weight: 10.0000 chunk 816 optimal weight: 5.9990 chunk 661 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 488 optimal weight: 30.0000 chunk 858 optimal weight: 1.9990 chunk 241 optimal weight: 6.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 HIS C 139 GLN D 74 ASN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN F 55 HIS G 142 HIS ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 GLN ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 163 GLN e 136 GLN ** g 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 88 ASN p 71 GLN s 28 ASN ** w 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 154032 Z= 0.239 Angle : 0.737 14.764 230513 Z= 0.406 Chirality : 0.039 0.375 29296 Planarity : 0.008 0.142 12270 Dihedral : 23.074 179.271 77190 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.00 % Favored : 95.95 % Rotamer: Outliers : 3.65 % Allowed : 15.80 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.11), residues: 5480 helix: 1.13 (0.12), residues: 1883 sheet: -0.09 (0.15), residues: 1074 loop : -0.67 (0.12), residues: 2523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP c 248 HIS 0.010 0.001 HIS B 39 PHE 0.020 0.002 PHE F 8 TYR 0.023 0.002 TYR L 38 ARG 0.011 0.001 ARG p 51 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 993 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 826 time to evaluate : 6.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 ASN cc_start: 0.3210 (OUTLIER) cc_final: 0.2544 (m110) REVERT: C 28 GLU cc_start: 0.6648 (OUTLIER) cc_final: 0.6303 (pt0) REVERT: C 31 ASP cc_start: 0.7842 (m-30) cc_final: 0.7369 (m-30) REVERT: C 41 GLN cc_start: 0.7019 (OUTLIER) cc_final: 0.6690 (pt0) REVERT: C 82 GLU cc_start: 0.4951 (OUTLIER) cc_final: 0.3900 (pm20) REVERT: C 88 ARG cc_start: 0.6026 (tmm-80) cc_final: 0.5293 (ttt-90) REVERT: C 110 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.5787 (mp0) REVERT: C 127 ARG cc_start: 0.6301 (mtm-85) cc_final: 0.5969 (mpp80) REVERT: C 152 GLU cc_start: 0.7687 (tt0) cc_final: 0.7394 (tt0) REVERT: C 188 GLU cc_start: 0.7022 (mt-10) cc_final: 0.6684 (mp0) REVERT: D 26 ARG cc_start: 0.4535 (OUTLIER) cc_final: 0.4303 (ptm160) REVERT: D 54 GLN cc_start: 0.7055 (mt0) cc_final: 0.6752 (mt0) REVERT: D 78 GLU cc_start: 0.6608 (OUTLIER) cc_final: 0.6239 (tm-30) REVERT: D 81 ARG cc_start: 0.6598 (ttp80) cc_final: 0.6031 (ttt-90) REVERT: D 124 MET cc_start: 0.6726 (ttt) cc_final: 0.6470 (mtt) REVERT: D 148 LYS cc_start: 0.5395 (ttpt) cc_final: 0.4561 (tmtp) REVERT: D 151 LYS cc_start: 0.4577 (pttp) cc_final: 0.4242 (mmtm) REVERT: D 202 GLU cc_start: 0.5465 (mm-30) cc_final: 0.4960 (mp0) REVERT: E 13 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6371 (mt-10) REVERT: E 68 ARG cc_start: 0.7033 (ttm110) cc_final: 0.6620 (mtm-85) REVERT: E 78 ASN cc_start: 0.6399 (m-40) cc_final: 0.6026 (t0) REVERT: E 86 LYS cc_start: 0.7516 (mmtm) cc_final: 0.6848 (mmmt) REVERT: F 56 LYS cc_start: 0.7581 (mtpt) cc_final: 0.7343 (mtpm) REVERT: F 79 ARG cc_start: 0.6670 (ttm-80) cc_final: 0.6350 (ttm-80) REVERT: F 102 MET cc_start: 0.5231 (ptp) cc_final: 0.4502 (mpp) REVERT: G 4 ARG cc_start: 0.5866 (tpp80) cc_final: 0.5305 (ptt180) REVERT: G 68 ASN cc_start: 0.6312 (m-40) cc_final: 0.5730 (m110) REVERT: G 76 LYS cc_start: 0.5986 (mtmt) cc_final: 0.5611 (mtpp) REVERT: G 79 ARG cc_start: 0.6110 (mtp-110) cc_final: 0.5578 (ttt-90) REVERT: G 83 SER cc_start: 0.5446 (m) cc_final: 0.5204 (t) REVERT: H 74 SER cc_start: 0.7740 (p) cc_final: 0.7374 (t) REVERT: H 76 GLN cc_start: 0.7426 (pt0) cc_final: 0.6641 (mm110) REVERT: H 88 ARG cc_start: 0.7089 (mtp85) cc_final: 0.6754 (mtm180) REVERT: H 90 ASP cc_start: 0.5793 (p0) cc_final: 0.5384 (p0) REVERT: I 42 GLU cc_start: 0.5906 (mm-30) cc_final: 0.5559 (tp30) REVERT: I 46 MET cc_start: 0.6546 (ttp) cc_final: 0.5959 (ttt) REVERT: J 16 ARG cc_start: 0.6352 (mmt90) cc_final: 0.5881 (mtt90) REVERT: J 73 LEU cc_start: 0.7538 (tp) cc_final: 0.7139 (tm) REVERT: J 88 MET cc_start: 0.4211 (mmm) cc_final: 0.3640 (mpt) REVERT: K 69 ARG cc_start: 0.6621 (mmm-85) cc_final: 0.6256 (mpt180) REVERT: K 107 ILE cc_start: 0.5870 (mm) cc_final: 0.5571 (mt) REVERT: L 20 ASN cc_start: 0.6910 (m-40) cc_final: 0.6639 (m110) REVERT: M 21 SER cc_start: 0.8337 (t) cc_final: 0.8056 (t) REVERT: M 43 VAL cc_start: 0.7448 (p) cc_final: 0.7189 (t) REVERT: M 78 LYS cc_start: 0.5923 (tppt) cc_final: 0.5222 (mtmm) REVERT: M 93 ARG cc_start: 0.6359 (mmt90) cc_final: 0.5642 (mmm-85) REVERT: N 27 LEU cc_start: 0.7010 (mp) cc_final: 0.6795 (mm) REVERT: N 90 ARG cc_start: 0.6821 (mtm-85) cc_final: 0.6500 (mtt90) REVERT: O 58 ARG cc_start: 0.6883 (ttt180) cc_final: 0.6452 (ttm110) REVERT: Q 17 MET cc_start: 0.5809 (ptm) cc_final: 0.5573 (ptm) REVERT: Q 19 LYS cc_start: 0.6595 (mttm) cc_final: 0.6198 (mttt) REVERT: Q 22 VAL cc_start: 0.6881 (OUTLIER) cc_final: 0.6498 (t) REVERT: Q 75 LEU cc_start: 0.6928 (OUTLIER) cc_final: 0.6704 (tt) REVERT: T 4 ILE cc_start: 0.5802 (OUTLIER) cc_final: 0.5321 (mp) REVERT: T 21 ASN cc_start: 0.6413 (m110) cc_final: 0.6024 (m-40) REVERT: T 24 ARG cc_start: 0.5911 (mmm160) cc_final: 0.5634 (mmp80) REVERT: T 69 LYS cc_start: 0.6616 (mtmt) cc_final: 0.5971 (mptt) REVERT: U 3 VAL cc_start: 0.6363 (OUTLIER) cc_final: 0.5948 (t) REVERT: U 17 ARG cc_start: 0.4378 (ttm-80) cc_final: 0.3732 (mtt-85) REVERT: U 34 ARG cc_start: 0.6514 (OUTLIER) cc_final: 0.5588 (ttm170) REVERT: U 36 GLU cc_start: 0.6152 (tt0) cc_final: 0.5938 (tt0) REVERT: c 5 LYS cc_start: 0.7571 (mtpp) cc_final: 0.7283 (tttt) REVERT: c 117 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.7382 (tt0) REVERT: c 182 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.6562 (ttt90) REVERT: c 183 LYS cc_start: 0.7875 (ttmm) cc_final: 0.7642 (tppp) REVERT: c 189 ARG cc_start: 0.7331 (mtt-85) cc_final: 0.6948 (mtt-85) REVERT: d 74 GLU cc_start: 0.6601 (OUTLIER) cc_final: 0.6334 (mt-10) REVERT: d 157 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8362 (ttpt) REVERT: d 183 GLU cc_start: 0.6079 (pm20) cc_final: 0.5554 (pt0) REVERT: d 200 ASP cc_start: 0.7535 (m-30) cc_final: 0.7300 (m-30) REVERT: e 1 MET cc_start: 0.5267 (OUTLIER) cc_final: 0.4798 (ptt) REVERT: e 132 LYS cc_start: 0.7156 (OUTLIER) cc_final: 0.6512 (pptt) REVERT: e 171 ASP cc_start: 0.7040 (t70) cc_final: 0.6267 (t0) REVERT: f 3 LYS cc_start: 0.5306 (tmmt) cc_final: 0.5008 (tmmt) REVERT: f 48 LYS cc_start: 0.4849 (mtpp) cc_final: 0.4626 (mmmm) REVERT: f 128 TYR cc_start: 0.7830 (t80) cc_final: 0.7213 (t80) REVERT: f 130 MET cc_start: 0.7945 (ptm) cc_final: 0.7480 (ppp) REVERT: f 167 ARG cc_start: 0.6819 (ttm-80) cc_final: 0.6587 (ttp-110) REVERT: g 29 LYS cc_start: 0.5158 (ttpt) cc_final: 0.4871 (tmtm) REVERT: g 60 ASP cc_start: 0.5180 (OUTLIER) cc_final: 0.4909 (p0) REVERT: g 69 ARG cc_start: 0.7107 (tmt170) cc_final: 0.5988 (tmt170) REVERT: g 88 GLN cc_start: 0.7270 (tt0) cc_final: 0.6976 (tt0) REVERT: g 104 ASN cc_start: 0.6881 (m110) cc_final: 0.6618 (t0) REVERT: g 116 GLN cc_start: 0.6791 (tm-30) cc_final: 0.6200 (tm-30) REVERT: g 130 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.6576 (mm-30) REVERT: h 1 MET cc_start: 0.5422 (ptm) cc_final: 0.4948 (ptm) REVERT: i 12 LYS cc_start: 0.6208 (mmmm) cc_final: 0.5910 (mmmt) REVERT: i 43 GLU cc_start: 0.8198 (mp0) cc_final: 0.7763 (mp0) REVERT: i 60 ASP cc_start: 0.7871 (p0) cc_final: 0.7509 (p0) REVERT: i 106 LYS cc_start: 0.8080 (tttm) cc_final: 0.7473 (ttmm) REVERT: i 138 GLN cc_start: 0.7542 (pt0) cc_final: 0.7055 (mm-40) REVERT: j 7 MET cc_start: 0.8324 (mmm) cc_final: 0.7955 (mmm) REVERT: j 17 ARG cc_start: 0.7104 (mmt-90) cc_final: 0.6821 (mpt180) REVERT: j 53 LYS cc_start: 0.7624 (pttp) cc_final: 0.7315 (ptmm) REVERT: j 111 LYS cc_start: 0.6427 (mtpp) cc_final: 0.5975 (mtmt) REVERT: j 113 MET cc_start: 0.6140 (mmm) cc_final: 0.5938 (ttp) REVERT: j 114 LYS cc_start: 0.6896 (mtpp) cc_final: 0.6462 (tptt) REVERT: k 1 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.6795 (ptt) REVERT: k 91 ASP cc_start: 0.7033 (p0) cc_final: 0.6797 (p0) REVERT: k 103 ILE cc_start: 0.7813 (mm) cc_final: 0.7557 (tp) REVERT: k 115 GLU cc_start: 0.6342 (OUTLIER) cc_final: 0.6105 (tp30) REVERT: k 126 ARG cc_start: 0.7540 (mtm180) cc_final: 0.7177 (mtp180) REVERT: k 143 GLU cc_start: 0.6235 (OUTLIER) cc_final: 0.6012 (mt-10) REVERT: l 10 ARG cc_start: 0.7382 (mtm-85) cc_final: 0.7028 (mtm110) REVERT: l 22 GLN cc_start: 0.7399 (OUTLIER) cc_final: 0.6804 (mt0) REVERT: l 47 GLU cc_start: 0.7741 (tp30) cc_final: 0.7495 (tp30) REVERT: l 53 MET cc_start: 0.7752 (ptm) cc_final: 0.7292 (ptp) REVERT: l 55 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.5832 (tmt170) REVERT: l 75 GLU cc_start: 0.6885 (mm-30) cc_final: 0.6539 (mm-30) REVERT: l 88 ASN cc_start: 0.7993 (m110) cc_final: 0.7317 (m-40) REVERT: l 90 GLU cc_start: 0.7578 (mm-30) cc_final: 0.6682 (mp0) REVERT: l 118 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7927 (tttm) REVERT: n 16 ARG cc_start: 0.6679 (mmp80) cc_final: 0.6449 (mmt-90) REVERT: n 46 GLU cc_start: 0.6068 (tm-30) cc_final: 0.5605 (tm-30) REVERT: n 98 GLN cc_start: 0.7774 (mm-40) cc_final: 0.7315 (mm-40) REVERT: n 116 GLN cc_start: 0.6672 (mm-40) cc_final: 0.6313 (mm110) REVERT: o 6 LYS cc_start: 0.6815 (ptpt) cc_final: 0.6325 (pptt) REVERT: o 9 GLU cc_start: 0.7250 (mt-10) cc_final: 0.6993 (mt-10) REVERT: o 10 GLN cc_start: 0.6896 (mm-40) cc_final: 0.6681 (mt0) REVERT: o 38 LYS cc_start: 0.6571 (ptmt) cc_final: 0.6216 (pttt) REVERT: o 68 GLU cc_start: 0.6135 (mm-30) cc_final: 0.5761 (tm-30) REVERT: o 111 LYS cc_start: 0.7998 (ptmm) cc_final: 0.7226 (pttm) REVERT: q 6 GLN cc_start: 0.7819 (pt0) cc_final: 0.6789 (tm130) REVERT: q 40 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8109 (ttt) REVERT: q 48 LYS cc_start: 0.7687 (mttm) cc_final: 0.7062 (mttt) REVERT: q 97 LYS cc_start: 0.7955 (ttmm) cc_final: 0.7746 (tttm) REVERT: r 31 GLN cc_start: 0.6780 (mt0) cc_final: 0.6548 (mt0) REVERT: r 72 THR cc_start: 0.8117 (p) cc_final: 0.7709 (t) REVERT: r 92 ARG cc_start: 0.7466 (ttm-80) cc_final: 0.6651 (ttm110) REVERT: s 3 ARG cc_start: 0.6367 (mtm-85) cc_final: 0.5517 (mtp85) REVERT: s 18 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6548 (mp0) REVERT: s 42 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6500 (mp0) REVERT: s 52 GLU cc_start: 0.5583 (mp0) cc_final: 0.5144 (tm-30) REVERT: t 7 ARG cc_start: 0.6553 (ttm110) cc_final: 0.6155 (tpt-90) REVERT: u 11 GLU cc_start: 0.7074 (pt0) cc_final: 0.6706 (pm20) REVERT: u 12 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.6935 (mm-40) REVERT: u 38 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7564 (pt) REVERT: u 53 LYS cc_start: 0.6412 (mttp) cc_final: 0.6123 (mttt) REVERT: w 71 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7571 (mp) REVERT: x 24 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6554 (tm-30) REVERT: x 45 GLN cc_start: 0.6860 (mt0) cc_final: 0.6045 (mm-40) REVERT: x 58 ASN cc_start: 0.7027 (t0) cc_final: 0.6367 (m110) REVERT: y 11 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7847 (mtt90) REVERT: 1 29 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7696 (mt0) REVERT: 2 15 LYS cc_start: 0.8183 (mmtm) cc_final: 0.7674 (mmmm) REVERT: 2 19 LYS cc_start: 0.8187 (mttm) cc_final: 0.7841 (mttp) REVERT: 2 57 LEU cc_start: 0.7759 (mt) cc_final: 0.7467 (mp) REVERT: 3 30 GLU cc_start: 0.6931 (tp30) cc_final: 0.6526 (mt-10) REVERT: 4 2 LYS cc_start: 0.7073 (mttt) cc_final: 0.6616 (mttp) REVERT: 4 3 LYS cc_start: 0.6093 (mttp) cc_final: 0.5810 (ptpp) REVERT: 4 25 ARG cc_start: 0.6025 (mmm-85) cc_final: 0.5800 (mmt90) outliers start: 167 outliers final: 97 residues processed: 917 average time/residue: 2.3565 time to fit residues: 3006.2495 Evaluate side-chains 946 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 813 time to evaluate : 6.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 131 LYS Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 36 ARG Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain M residue 62 LYS Chi-restraints excluded: chain N residue 23 LYS Chi-restraints excluded: chain N residue 80 SER Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain P residue 68 SER Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain T residue 4 ILE Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 34 ARG Chi-restraints excluded: chain c residue 19 VAL Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 117 GLN Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 182 ARG Chi-restraints excluded: chain c residue 203 ARG Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 11 MET Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 74 GLU Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain d residue 99 GLU Chi-restraints excluded: chain d residue 157 LYS Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 51 GLU Chi-restraints excluded: chain e residue 132 LYS Chi-restraints excluded: chain e residue 139 LYS Chi-restraints excluded: chain e residue 154 ASP Chi-restraints excluded: chain e residue 175 ILE Chi-restraints excluded: chain f residue 4 LEU Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 44 ILE Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain g residue 4 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 11 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 130 GLU Chi-restraints excluded: chain h residue 3 VAL Chi-restraints excluded: chain h residue 6 LEU Chi-restraints excluded: chain i residue 7 LYS Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 90 GLU Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 5 THR Chi-restraints excluded: chain k residue 7 SER Chi-restraints excluded: chain k residue 115 GLU Chi-restraints excluded: chain k residue 121 THR Chi-restraints excluded: chain k residue 143 GLU Chi-restraints excluded: chain l residue 22 GLN Chi-restraints excluded: chain l residue 55 ARG Chi-restraints excluded: chain l residue 118 LYS Chi-restraints excluded: chain m residue 65 LEU Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain q residue 40 MET Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain r residue 27 LYS Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain s residue 18 GLU Chi-restraints excluded: chain s residue 42 GLU Chi-restraints excluded: chain s residue 55 VAL Chi-restraints excluded: chain u residue 12 GLN Chi-restraints excluded: chain u residue 38 LEU Chi-restraints excluded: chain w residue 40 VAL Chi-restraints excluded: chain w residue 66 THR Chi-restraints excluded: chain w residue 71 LEU Chi-restraints excluded: chain x residue 24 GLU Chi-restraints excluded: chain y residue 11 ARG Chi-restraints excluded: chain z residue 25 VAL Chi-restraints excluded: chain 0 residue 7 GLU Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 29 GLN Chi-restraints excluded: chain 2 residue 32 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 321 optimal weight: 20.0000 chunk 861 optimal weight: 6.9990 chunk 189 optimal weight: 6.9990 chunk 561 optimal weight: 10.0000 chunk 236 optimal weight: 10.0000 chunk 957 optimal weight: 8.9990 chunk 795 optimal weight: 3.9990 chunk 443 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 316 optimal weight: 8.9990 chunk 502 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN F 55 HIS G 142 HIS ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 GLN c 163 GLN e 136 GLN ** e 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 88 ASN p 71 GLN r 61 ASN s 28 ASN ** w 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 13 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 154032 Z= 0.345 Angle : 0.841 17.550 230513 Z= 0.447 Chirality : 0.044 0.362 29296 Planarity : 0.009 0.150 12270 Dihedral : 23.145 179.429 77190 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.32 % Favored : 95.62 % Rotamer: Outliers : 4.39 % Allowed : 16.00 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.17 (0.11), residues: 5480 helix: 0.87 (0.12), residues: 1882 sheet: -0.25 (0.15), residues: 1091 loop : -0.74 (0.12), residues: 2507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP c 248 HIS 0.008 0.002 HIS B 39 PHE 0.023 0.003 PHE d 118 TYR 0.025 0.003 TYR L 38 ARG 0.010 0.001 ARG p 51 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1038 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 837 time to evaluate : 6.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 ASN cc_start: 0.3239 (OUTLIER) cc_final: 0.2559 (m110) REVERT: B 164 ILE cc_start: 0.4138 (OUTLIER) cc_final: 0.3605 (pp) REVERT: C 28 GLU cc_start: 0.6625 (OUTLIER) cc_final: 0.6301 (pt0) REVERT: C 31 ASP cc_start: 0.7825 (m-30) cc_final: 0.7357 (m-30) REVERT: C 41 GLN cc_start: 0.7054 (OUTLIER) cc_final: 0.6720 (pt0) REVERT: C 82 GLU cc_start: 0.5061 (OUTLIER) cc_final: 0.4192 (pm20) REVERT: C 88 ARG cc_start: 0.6031 (tmm-80) cc_final: 0.5394 (ttt-90) REVERT: C 127 ARG cc_start: 0.6331 (mtm-85) cc_final: 0.6012 (mpp80) REVERT: C 188 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6695 (mp0) REVERT: D 26 ARG cc_start: 0.4199 (OUTLIER) cc_final: 0.3933 (ptm160) REVERT: D 54 GLN cc_start: 0.7058 (mt0) cc_final: 0.6786 (mt0) REVERT: D 78 GLU cc_start: 0.6543 (OUTLIER) cc_final: 0.6239 (tm-30) REVERT: D 81 ARG cc_start: 0.6626 (ttp80) cc_final: 0.6116 (ttt-90) REVERT: D 94 LEU cc_start: 0.5818 (OUTLIER) cc_final: 0.5554 (tp) REVERT: D 124 MET cc_start: 0.6801 (ttt) cc_final: 0.6565 (mtt) REVERT: D 148 LYS cc_start: 0.5511 (ttpt) cc_final: 0.4636 (tmtp) REVERT: D 151 LYS cc_start: 0.4595 (pttp) cc_final: 0.4232 (mmtm) REVERT: D 202 GLU cc_start: 0.5563 (mm-30) cc_final: 0.5052 (mp0) REVERT: E 13 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6467 (mt-10) REVERT: E 68 ARG cc_start: 0.7074 (ttm110) cc_final: 0.6541 (mtm-85) REVERT: E 78 ASN cc_start: 0.6392 (m-40) cc_final: 0.6021 (t0) REVERT: E 86 LYS cc_start: 0.7528 (mmtm) cc_final: 0.6835 (mmmt) REVERT: F 56 LYS cc_start: 0.7574 (mtpt) cc_final: 0.7367 (mtpm) REVERT: F 102 MET cc_start: 0.5050 (ptp) cc_final: 0.4206 (mpp) REVERT: G 4 ARG cc_start: 0.5904 (tpp80) cc_final: 0.5341 (ptt180) REVERT: G 68 ASN cc_start: 0.6327 (m-40) cc_final: 0.5721 (m110) REVERT: G 76 LYS cc_start: 0.5964 (mtmt) cc_final: 0.5562 (mtpp) REVERT: G 83 SER cc_start: 0.5532 (m) cc_final: 0.5307 (t) REVERT: G 139 GLU cc_start: 0.6539 (OUTLIER) cc_final: 0.6221 (tp30) REVERT: H 3 MET cc_start: 0.7231 (OUTLIER) cc_final: 0.7007 (tpp) REVERT: H 67 GLN cc_start: 0.6254 (OUTLIER) cc_final: 0.5622 (mt0) REVERT: H 74 SER cc_start: 0.7771 (OUTLIER) cc_final: 0.7399 (t) REVERT: H 76 GLN cc_start: 0.7451 (pt0) cc_final: 0.6320 (mm-40) REVERT: H 88 ARG cc_start: 0.7092 (mtp85) cc_final: 0.6778 (mtm180) REVERT: H 90 ASP cc_start: 0.5737 (p0) cc_final: 0.5322 (p0) REVERT: I 42 GLU cc_start: 0.5920 (mm-30) cc_final: 0.5568 (tp30) REVERT: I 46 MET cc_start: 0.6528 (ttp) cc_final: 0.5992 (ttt) REVERT: J 16 ARG cc_start: 0.6319 (mmt90) cc_final: 0.5846 (mtt90) REVERT: J 73 LEU cc_start: 0.7507 (tp) cc_final: 0.7127 (tm) REVERT: J 88 MET cc_start: 0.4168 (mmm) cc_final: 0.3588 (mpt) REVERT: K 69 ARG cc_start: 0.6630 (mmm-85) cc_final: 0.6241 (mpt180) REVERT: K 107 ILE cc_start: 0.5855 (mm) cc_final: 0.5568 (mt) REVERT: L 20 ASN cc_start: 0.6914 (m-40) cc_final: 0.6639 (m110) REVERT: L 56 ARG cc_start: 0.6601 (ttm110) cc_final: 0.5798 (tmm160) REVERT: M 9 ILE cc_start: 0.6154 (pt) cc_final: 0.5819 (pt) REVERT: M 21 SER cc_start: 0.8410 (t) cc_final: 0.8109 (t) REVERT: M 43 VAL cc_start: 0.7391 (p) cc_final: 0.7105 (t) REVERT: M 58 ASP cc_start: 0.6167 (m-30) cc_final: 0.5905 (m-30) REVERT: M 78 LYS cc_start: 0.5888 (tppt) cc_final: 0.5206 (mtmm) REVERT: M 93 ARG cc_start: 0.6293 (mmt90) cc_final: 0.5645 (mmm-85) REVERT: N 27 LEU cc_start: 0.7040 (mp) cc_final: 0.6820 (mm) REVERT: N 90 ARG cc_start: 0.6858 (mtm-85) cc_final: 0.6426 (mtt90) REVERT: O 35 GLN cc_start: 0.7937 (tp40) cc_final: 0.7609 (tp40) REVERT: O 58 ARG cc_start: 0.6879 (ttt180) cc_final: 0.6538 (ttm110) REVERT: Q 11 ARG cc_start: 0.6413 (OUTLIER) cc_final: 0.5468 (mtp-110) REVERT: Q 17 MET cc_start: 0.5769 (ptm) cc_final: 0.5569 (ptm) REVERT: Q 19 LYS cc_start: 0.6596 (mttm) cc_final: 0.6216 (mttt) REVERT: Q 75 LEU cc_start: 0.6999 (OUTLIER) cc_final: 0.6749 (tt) REVERT: T 4 ILE cc_start: 0.5697 (OUTLIER) cc_final: 0.5300 (mp) REVERT: T 21 ASN cc_start: 0.6431 (m110) cc_final: 0.6037 (m-40) REVERT: T 24 ARG cc_start: 0.5960 (mmm160) cc_final: 0.5702 (mmp80) REVERT: T 33 LYS cc_start: 0.6276 (tppt) cc_final: 0.5835 (pttp) REVERT: T 64 LYS cc_start: 0.4695 (OUTLIER) cc_final: 0.4156 (mttp) REVERT: T 69 LYS cc_start: 0.6593 (mtmt) cc_final: 0.5893 (mptt) REVERT: U 3 VAL cc_start: 0.6340 (OUTLIER) cc_final: 0.6101 (m) REVERT: U 17 ARG cc_start: 0.4578 (ttm-80) cc_final: 0.3864 (mtt-85) REVERT: U 34 ARG cc_start: 0.6478 (OUTLIER) cc_final: 0.5475 (ttm170) REVERT: U 36 GLU cc_start: 0.6306 (tt0) cc_final: 0.6092 (tt0) REVERT: c 5 LYS cc_start: 0.7486 (mtpp) cc_final: 0.7162 (tttt) REVERT: c 117 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.7443 (tt0) REVERT: c 182 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.6544 (ttt90) REVERT: c 183 LYS cc_start: 0.7898 (ttmm) cc_final: 0.7655 (tppp) REVERT: c 189 ARG cc_start: 0.7381 (mtt-85) cc_final: 0.7001 (mtt-85) REVERT: d 157 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8380 (ttpt) REVERT: d 183 GLU cc_start: 0.6019 (pm20) cc_final: 0.5487 (pt0) REVERT: d 200 ASP cc_start: 0.7559 (m-30) cc_final: 0.7338 (m-30) REVERT: e 1 MET cc_start: 0.5321 (OUTLIER) cc_final: 0.4853 (ptt) REVERT: e 132 LYS cc_start: 0.7199 (OUTLIER) cc_final: 0.6562 (pptt) REVERT: e 139 LYS cc_start: 0.6862 (OUTLIER) cc_final: 0.6041 (mmtt) REVERT: e 171 ASP cc_start: 0.7098 (t70) cc_final: 0.6311 (t0) REVERT: f 11 GLU cc_start: 0.6125 (pm20) cc_final: 0.5822 (pm20) REVERT: f 128 TYR cc_start: 0.7909 (t80) cc_final: 0.7333 (t80) REVERT: f 130 MET cc_start: 0.7961 (ptm) cc_final: 0.7480 (ppp) REVERT: f 167 ARG cc_start: 0.6791 (ttm-80) cc_final: 0.6566 (ttp-110) REVERT: g 29 LYS cc_start: 0.5203 (ttpt) cc_final: 0.4887 (tmtm) REVERT: g 69 ARG cc_start: 0.7118 (tmt170) cc_final: 0.6060 (tmt170) REVERT: g 88 GLN cc_start: 0.7225 (tt0) cc_final: 0.6979 (tt0) REVERT: g 116 GLN cc_start: 0.6785 (tm-30) cc_final: 0.6191 (tm-30) REVERT: g 130 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6536 (mm-30) REVERT: h 1 MET cc_start: 0.5321 (ptm) cc_final: 0.4980 (ptm) REVERT: h 6 LEU cc_start: 0.6040 (OUTLIER) cc_final: 0.5621 (tp) REVERT: i 12 LYS cc_start: 0.6302 (mmmm) cc_final: 0.5975 (mmmt) REVERT: i 43 GLU cc_start: 0.8177 (mp0) cc_final: 0.7763 (mp0) REVERT: i 60 ASP cc_start: 0.7879 (p0) cc_final: 0.7554 (p0) REVERT: i 106 LYS cc_start: 0.8098 (tttm) cc_final: 0.7491 (ttmm) REVERT: i 138 GLN cc_start: 0.7589 (pt0) cc_final: 0.7074 (mm-40) REVERT: j 7 MET cc_start: 0.8305 (mmm) cc_final: 0.7930 (mmm) REVERT: j 17 ARG cc_start: 0.7135 (mmt-90) cc_final: 0.6833 (mpt180) REVERT: j 53 LYS cc_start: 0.7629 (pttp) cc_final: 0.7251 (ptmm) REVERT: j 111 LYS cc_start: 0.6393 (mtpp) cc_final: 0.6020 (mtmt) REVERT: j 114 LYS cc_start: 0.6955 (mtpp) cc_final: 0.6577 (tptt) REVERT: k 91 ASP cc_start: 0.7055 (p0) cc_final: 0.6814 (p0) REVERT: k 103 ILE cc_start: 0.7803 (mm) cc_final: 0.7551 (tp) REVERT: k 115 GLU cc_start: 0.6294 (OUTLIER) cc_final: 0.6062 (tp30) REVERT: k 126 ARG cc_start: 0.7547 (mtm180) cc_final: 0.7171 (mtp180) REVERT: l 10 ARG cc_start: 0.7393 (mtm-85) cc_final: 0.7055 (mtm110) REVERT: l 22 GLN cc_start: 0.7423 (OUTLIER) cc_final: 0.6806 (mt0) REVERT: l 47 GLU cc_start: 0.7812 (tp30) cc_final: 0.7462 (tp30) REVERT: l 53 MET cc_start: 0.7906 (ptm) cc_final: 0.7448 (ptp) REVERT: l 55 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.5819 (tmt170) REVERT: l 90 GLU cc_start: 0.7586 (mm-30) cc_final: 0.6711 (mp0) REVERT: l 118 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7958 (tttm) REVERT: n 46 GLU cc_start: 0.6103 (tm-30) cc_final: 0.5647 (tm-30) REVERT: n 62 LEU cc_start: 0.7256 (mt) cc_final: 0.6989 (mt) REVERT: n 116 GLN cc_start: 0.6637 (mm-40) cc_final: 0.6365 (mm110) REVERT: o 6 LYS cc_start: 0.6720 (ptpt) cc_final: 0.6162 (pptt) REVERT: o 9 GLU cc_start: 0.7268 (mt-10) cc_final: 0.7014 (mt-10) REVERT: o 10 GLN cc_start: 0.6901 (mm-40) cc_final: 0.6526 (mt0) REVERT: o 38 LYS cc_start: 0.6753 (ptmt) cc_final: 0.6338 (pttt) REVERT: o 68 GLU cc_start: 0.6168 (mm-30) cc_final: 0.5774 (tm-30) REVERT: o 89 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.6970 (mmt180) REVERT: o 111 LYS cc_start: 0.8001 (ptmm) cc_final: 0.7201 (pttm) REVERT: q 6 GLN cc_start: 0.7833 (pt0) cc_final: 0.6787 (tm130) REVERT: q 40 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8263 (ttt) REVERT: q 48 LYS cc_start: 0.7678 (mttm) cc_final: 0.7039 (mttt) REVERT: q 73 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7684 (mmtm) REVERT: r 72 THR cc_start: 0.8072 (p) cc_final: 0.7769 (t) REVERT: r 92 ARG cc_start: 0.7446 (ttm-80) cc_final: 0.6638 (ttm110) REVERT: s 3 ARG cc_start: 0.6369 (mtm-85) cc_final: 0.5494 (mtp85) REVERT: s 18 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6597 (mp0) REVERT: s 42 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6531 (mp0) REVERT: s 52 GLU cc_start: 0.5576 (mp0) cc_final: 0.5167 (tm-30) REVERT: t 8 ASP cc_start: 0.7306 (m-30) cc_final: 0.7093 (m-30) REVERT: u 1 MET cc_start: 0.4551 (ttt) cc_final: 0.3960 (mpp) REVERT: u 12 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.6940 (mm-40) REVERT: u 38 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7629 (pt) REVERT: v 72 LYS cc_start: 0.7760 (mtpp) cc_final: 0.7286 (mttt) REVERT: w 71 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7532 (mp) REVERT: x 24 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6536 (tm-30) REVERT: x 45 GLN cc_start: 0.6892 (mt0) cc_final: 0.6110 (mm-40) REVERT: x 58 ASN cc_start: 0.7063 (t0) cc_final: 0.6416 (m110) REVERT: y 11 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7850 (mtt90) REVERT: 0 32 GLU cc_start: 0.6272 (pm20) cc_final: 0.6009 (pm20) REVERT: 0 40 ASP cc_start: 0.8450 (t70) cc_final: 0.8211 (t70) REVERT: 1 29 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7767 (mt0) REVERT: 2 19 LYS cc_start: 0.8158 (mttm) cc_final: 0.7779 (mttp) REVERT: 2 57 LEU cc_start: 0.7777 (mt) cc_final: 0.7490 (mp) REVERT: 3 12 ARG cc_start: 0.6694 (ptm-80) cc_final: 0.6475 (ppt170) REVERT: 3 30 GLU cc_start: 0.6950 (tp30) cc_final: 0.6525 (mt-10) REVERT: 4 2 LYS cc_start: 0.7123 (mttt) cc_final: 0.6691 (mttp) REVERT: 4 3 LYS cc_start: 0.6070 (mttp) cc_final: 0.5791 (ptpp) REVERT: 4 25 ARG cc_start: 0.5983 (mmm-85) cc_final: 0.5752 (mmt90) outliers start: 201 outliers final: 114 residues processed: 948 average time/residue: 2.2977 time to fit residues: 3055.7018 Evaluate side-chains 983 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 827 time to evaluate : 5.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 131 LYS Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain H residue 3 MET Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 36 ARG Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain M residue 62 LYS Chi-restraints excluded: chain M residue 105 ASN Chi-restraints excluded: chain N residue 23 LYS Chi-restraints excluded: chain N residue 80 SER Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain P residue 68 SER Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain T residue 4 ILE Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 64 LYS Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 34 ARG Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 117 GLN Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 182 ARG Chi-restraints excluded: chain c residue 203 ARG Chi-restraints excluded: chain c residue 223 THR Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 11 MET Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 74 GLU Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain d residue 99 GLU Chi-restraints excluded: chain d residue 157 LYS Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 51 GLU Chi-restraints excluded: chain e residue 88 ARG Chi-restraints excluded: chain e residue 121 VAL Chi-restraints excluded: chain e residue 132 LYS Chi-restraints excluded: chain e residue 139 LYS Chi-restraints excluded: chain e residue 175 ILE Chi-restraints excluded: chain f residue 4 LEU Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 44 ILE Chi-restraints excluded: chain f residue 72 LYS Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain g residue 4 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 11 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 130 GLU Chi-restraints excluded: chain h residue 3 VAL Chi-restraints excluded: chain h residue 6 LEU Chi-restraints excluded: chain i residue 7 LYS Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 90 GLU Chi-restraints excluded: chain j residue 105 ARG Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 5 THR Chi-restraints excluded: chain k residue 7 SER Chi-restraints excluded: chain k residue 115 GLU Chi-restraints excluded: chain k residue 121 THR Chi-restraints excluded: chain l residue 22 GLN Chi-restraints excluded: chain l residue 55 ARG Chi-restraints excluded: chain l residue 118 LYS Chi-restraints excluded: chain l residue 119 LEU Chi-restraints excluded: chain m residue 65 LEU Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain q residue 40 MET Chi-restraints excluded: chain q residue 73 LYS Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain r residue 27 LYS Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 95 ARG Chi-restraints excluded: chain s residue 18 GLU Chi-restraints excluded: chain s residue 42 GLU Chi-restraints excluded: chain s residue 55 VAL Chi-restraints excluded: chain u residue 12 GLN Chi-restraints excluded: chain u residue 38 LEU Chi-restraints excluded: chain w residue 40 VAL Chi-restraints excluded: chain w residue 66 THR Chi-restraints excluded: chain w residue 71 LEU Chi-restraints excluded: chain x residue 16 THR Chi-restraints excluded: chain x residue 24 GLU Chi-restraints excluded: chain y residue 11 ARG Chi-restraints excluded: chain y residue 55 VAL Chi-restraints excluded: chain z residue 25 VAL Chi-restraints excluded: chain z residue 55 ILE Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 29 GLN Chi-restraints excluded: chain 2 residue 32 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 923 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 545 optimal weight: 10.0000 chunk 699 optimal weight: 10.0000 chunk 541 optimal weight: 10.0000 chunk 806 optimal weight: 8.9990 chunk 534 optimal weight: 10.0000 chunk 954 optimal weight: 9.9990 chunk 597 optimal weight: 10.0000 chunk 581 optimal weight: 10.0000 chunk 440 optimal weight: 9.9990 overall best weight: 9.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN F 55 HIS G 142 HIS H 67 GLN ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 56 HIS ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 13 GLN ** U 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 163 GLN e 136 GLN j 88 ASN p 71 GLN s 28 ASN s 48 GLN ** w 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 42 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.102 154032 Z= 0.455 Angle : 0.960 19.589 230513 Z= 0.497 Chirality : 0.049 0.363 29296 Planarity : 0.010 0.156 12270 Dihedral : 23.304 179.979 77190 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.78 % Favored : 95.16 % Rotamer: Outliers : 4.57 % Allowed : 16.72 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.52 (0.11), residues: 5480 helix: 0.46 (0.11), residues: 1883 sheet: -0.36 (0.15), residues: 1089 loop : -0.88 (0.12), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP c 248 HIS 0.009 0.002 HIS i 76 PHE 0.027 0.003 PHE m 21 TYR 0.029 0.003 TYR L 38 ARG 0.013 0.001 ARG p 51 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1043 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 834 time to evaluate : 6.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 MET cc_start: 0.4035 (OUTLIER) cc_final: 0.3042 (ttt) REVERT: B 58 ASN cc_start: 0.3058 (OUTLIER) cc_final: 0.2427 (m110) REVERT: B 135 LEU cc_start: 0.2998 (mp) cc_final: 0.2625 (tt) REVERT: B 164 ILE cc_start: 0.4087 (OUTLIER) cc_final: 0.3579 (pp) REVERT: B 199 VAL cc_start: 0.5799 (t) cc_final: 0.5452 (m) REVERT: C 28 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.6372 (pt0) REVERT: C 31 ASP cc_start: 0.7767 (m-30) cc_final: 0.7294 (m-30) REVERT: C 41 GLN cc_start: 0.7077 (OUTLIER) cc_final: 0.6744 (pt0) REVERT: C 88 ARG cc_start: 0.6025 (tmm-80) cc_final: 0.5424 (ttt-90) REVERT: C 127 ARG cc_start: 0.6324 (mtm-85) cc_final: 0.5964 (mpp80) REVERT: C 188 GLU cc_start: 0.7066 (mt-10) cc_final: 0.6719 (mp0) REVERT: D 54 GLN cc_start: 0.7069 (mt0) cc_final: 0.6828 (mt0) REVERT: D 78 GLU cc_start: 0.6659 (OUTLIER) cc_final: 0.6284 (tm-30) REVERT: D 94 LEU cc_start: 0.5866 (OUTLIER) cc_final: 0.5650 (tp) REVERT: D 124 MET cc_start: 0.6779 (OUTLIER) cc_final: 0.6456 (ttt) REVERT: D 148 LYS cc_start: 0.5372 (ttpt) cc_final: 0.4486 (tmtm) REVERT: D 151 LYS cc_start: 0.4626 (pttp) cc_final: 0.4175 (mmtm) REVERT: D 202 GLU cc_start: 0.5584 (mm-30) cc_final: 0.5078 (mp0) REVERT: E 68 ARG cc_start: 0.6983 (ttm110) cc_final: 0.6467 (mtm-85) REVERT: E 147 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.7369 (ptm) REVERT: F 5 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6240 (tp30) REVERT: F 56 LYS cc_start: 0.7583 (mtpt) cc_final: 0.7377 (mtpm) REVERT: F 102 MET cc_start: 0.5141 (ptp) cc_final: 0.4439 (mpp) REVERT: G 4 ARG cc_start: 0.5917 (tpp80) cc_final: 0.5361 (ptt180) REVERT: G 68 ASN cc_start: 0.6451 (m-40) cc_final: 0.5805 (m110) REVERT: G 76 LYS cc_start: 0.5987 (mtmt) cc_final: 0.5593 (mtpp) REVERT: G 83 SER cc_start: 0.5619 (m) cc_final: 0.5374 (t) REVERT: H 3 MET cc_start: 0.7226 (OUTLIER) cc_final: 0.7013 (tpp) REVERT: H 76 GLN cc_start: 0.7336 (pt0) cc_final: 0.6168 (mm-40) REVERT: H 88 ARG cc_start: 0.7081 (mtp85) cc_final: 0.6790 (mtm180) REVERT: H 90 ASP cc_start: 0.5734 (p0) cc_final: 0.5385 (p0) REVERT: I 42 GLU cc_start: 0.6117 (mm-30) cc_final: 0.5540 (tp30) REVERT: I 46 MET cc_start: 0.6501 (ttp) cc_final: 0.6036 (ttt) REVERT: J 16 ARG cc_start: 0.6355 (mmt90) cc_final: 0.5865 (mtt90) REVERT: J 73 LEU cc_start: 0.7529 (tp) cc_final: 0.7160 (tm) REVERT: K 69 ARG cc_start: 0.6678 (mmm-85) cc_final: 0.6252 (mpt180) REVERT: K 107 ILE cc_start: 0.5892 (mm) cc_final: 0.5634 (mt) REVERT: L 20 ASN cc_start: 0.6942 (m-40) cc_final: 0.6656 (m110) REVERT: L 56 ARG cc_start: 0.6539 (ttm110) cc_final: 0.5530 (tmm160) REVERT: M 9 ILE cc_start: 0.6255 (pt) cc_final: 0.5947 (pt) REVERT: M 43 VAL cc_start: 0.7386 (p) cc_final: 0.7081 (t) REVERT: M 58 ASP cc_start: 0.6212 (m-30) cc_final: 0.5917 (m-30) REVERT: M 78 LYS cc_start: 0.6137 (tppt) cc_final: 0.5382 (mtmm) REVERT: M 93 ARG cc_start: 0.6284 (mmt90) cc_final: 0.5643 (mmm-85) REVERT: N 27 LEU cc_start: 0.7075 (mp) cc_final: 0.6861 (mm) REVERT: N 90 ARG cc_start: 0.6897 (mtm-85) cc_final: 0.6529 (mtm180) REVERT: O 26 GLU cc_start: 0.6653 (mp0) cc_final: 0.6180 (mp0) REVERT: O 58 ARG cc_start: 0.6868 (ttt180) cc_final: 0.6550 (ttm110) REVERT: O 77 ARG cc_start: 0.6186 (ttp80) cc_final: 0.5660 (ttp80) REVERT: Q 75 LEU cc_start: 0.7024 (OUTLIER) cc_final: 0.6745 (tt) REVERT: T 21 ASN cc_start: 0.6408 (m110) cc_final: 0.6000 (m-40) REVERT: T 64 LYS cc_start: 0.4781 (OUTLIER) cc_final: 0.4510 (tttp) REVERT: T 69 LYS cc_start: 0.6610 (mtmt) cc_final: 0.5828 (mptt) REVERT: U 3 VAL cc_start: 0.6369 (OUTLIER) cc_final: 0.6118 (m) REVERT: U 17 ARG cc_start: 0.4564 (ttm-80) cc_final: 0.3792 (mtt-85) REVERT: U 21 ARG cc_start: 0.5874 (mmp-170) cc_final: 0.4572 (mmt-90) REVERT: U 34 ARG cc_start: 0.6424 (OUTLIER) cc_final: 0.5400 (ttm170) REVERT: c 5 LYS cc_start: 0.7561 (mtpp) cc_final: 0.7174 (tttt) REVERT: c 182 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.6399 (ttt90) REVERT: c 183 LYS cc_start: 0.7961 (ttmm) cc_final: 0.7676 (tppp) REVERT: c 189 ARG cc_start: 0.7639 (mtt-85) cc_final: 0.7279 (mtt-85) REVERT: d 74 GLU cc_start: 0.6648 (OUTLIER) cc_final: 0.6072 (mm-30) REVERT: d 183 GLU cc_start: 0.6021 (pm20) cc_final: 0.5417 (pt0) REVERT: e 1 MET cc_start: 0.5323 (OUTLIER) cc_final: 0.4891 (ptt) REVERT: e 132 LYS cc_start: 0.7203 (OUTLIER) cc_final: 0.6565 (pptt) REVERT: e 139 LYS cc_start: 0.6880 (OUTLIER) cc_final: 0.6041 (mmtt) REVERT: e 171 ASP cc_start: 0.7075 (t70) cc_final: 0.6270 (t0) REVERT: f 128 TYR cc_start: 0.7912 (t80) cc_final: 0.7393 (t80) REVERT: f 130 MET cc_start: 0.7911 (ptm) cc_final: 0.7622 (ptm) REVERT: f 167 ARG cc_start: 0.6771 (ttm-80) cc_final: 0.6383 (ttp-110) REVERT: g 29 LYS cc_start: 0.5233 (ttpt) cc_final: 0.4919 (tmtm) REVERT: g 69 ARG cc_start: 0.7123 (tmt170) cc_final: 0.6070 (tmt170) REVERT: g 116 GLN cc_start: 0.6858 (mm-40) cc_final: 0.6265 (tm-30) REVERT: g 130 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.6557 (mm-30) REVERT: h 1 MET cc_start: 0.5276 (ptm) cc_final: 0.3741 (ttp) REVERT: h 6 LEU cc_start: 0.6042 (OUTLIER) cc_final: 0.5718 (mt) REVERT: i 12 LYS cc_start: 0.6350 (mmmm) cc_final: 0.6019 (mmmt) REVERT: i 43 GLU cc_start: 0.8169 (mp0) cc_final: 0.7771 (mp0) REVERT: i 60 ASP cc_start: 0.7897 (p0) cc_final: 0.7567 (p0) REVERT: i 106 LYS cc_start: 0.8058 (tttm) cc_final: 0.7423 (ttmm) REVERT: i 138 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.7069 (mm-40) REVERT: j 7 MET cc_start: 0.8302 (mmm) cc_final: 0.7914 (mmm) REVERT: j 53 LYS cc_start: 0.7641 (pttp) cc_final: 0.7250 (ptmm) REVERT: j 111 LYS cc_start: 0.6412 (mtpp) cc_final: 0.6039 (mtmt) REVERT: j 114 LYS cc_start: 0.6990 (mtpp) cc_final: 0.6613 (tptt) REVERT: k 91 ASP cc_start: 0.7054 (p0) cc_final: 0.6813 (p0) REVERT: k 103 ILE cc_start: 0.7795 (mm) cc_final: 0.7435 (tp) REVERT: k 115 GLU cc_start: 0.6266 (OUTLIER) cc_final: 0.6031 (tp30) REVERT: k 126 ARG cc_start: 0.7511 (mtm180) cc_final: 0.7064 (mtp180) REVERT: l 10 ARG cc_start: 0.7395 (mtm-85) cc_final: 0.7061 (mtm110) REVERT: l 22 GLN cc_start: 0.7393 (OUTLIER) cc_final: 0.6739 (mt0) REVERT: l 47 GLU cc_start: 0.7844 (tp30) cc_final: 0.7455 (tp30) REVERT: l 53 MET cc_start: 0.7988 (ptm) cc_final: 0.7494 (ptp) REVERT: l 55 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.5855 (tmt170) REVERT: l 90 GLU cc_start: 0.7589 (mm-30) cc_final: 0.6645 (mp0) REVERT: l 118 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7950 (tttm) REVERT: n 46 GLU cc_start: 0.6128 (tm-30) cc_final: 0.5718 (tm-30) REVERT: n 62 LEU cc_start: 0.7254 (mt) cc_final: 0.6973 (mt) REVERT: n 89 ASP cc_start: 0.6963 (t0) cc_final: 0.6599 (OUTLIER) REVERT: n 116 GLN cc_start: 0.6745 (mm-40) cc_final: 0.6434 (mm110) REVERT: o 6 LYS cc_start: 0.6857 (ptpt) cc_final: 0.6224 (pptt) REVERT: o 9 GLU cc_start: 0.7292 (mt-10) cc_final: 0.6993 (mt-10) REVERT: o 10 GLN cc_start: 0.6890 (mm-40) cc_final: 0.6502 (mt0) REVERT: o 38 LYS cc_start: 0.6762 (ptmt) cc_final: 0.6335 (pttt) REVERT: o 68 GLU cc_start: 0.6230 (mm-30) cc_final: 0.5801 (tm-30) REVERT: o 89 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.6866 (mmt180) REVERT: o 111 LYS cc_start: 0.7989 (ptmm) cc_final: 0.7232 (pttm) REVERT: q 6 GLN cc_start: 0.7847 (pt0) cc_final: 0.6878 (tm130) REVERT: q 40 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8278 (ttt) REVERT: q 48 LYS cc_start: 0.7671 (mttm) cc_final: 0.7223 (mtpt) REVERT: q 73 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7702 (mmtm) REVERT: r 72 THR cc_start: 0.8126 (p) cc_final: 0.7869 (t) REVERT: r 92 ARG cc_start: 0.7424 (ttm-80) cc_final: 0.6630 (ttm110) REVERT: s 3 ARG cc_start: 0.6381 (mtm-85) cc_final: 0.5497 (mtp85) REVERT: s 18 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.6571 (mp0) REVERT: s 42 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6545 (mp0) REVERT: s 52 GLU cc_start: 0.5579 (mp0) cc_final: 0.5211 (tm-30) REVERT: t 8 ASP cc_start: 0.7334 (m-30) cc_final: 0.7099 (m-30) REVERT: t 60 GLU cc_start: 0.6171 (OUTLIER) cc_final: 0.5899 (mt-10) REVERT: u 1 MET cc_start: 0.4652 (ttt) cc_final: 0.3941 (mpp) REVERT: u 12 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.6929 (mm-40) REVERT: u 38 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7637 (pt) REVERT: w 62 LYS cc_start: 0.8233 (mtpt) cc_final: 0.7817 (mtpt) REVERT: w 71 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7575 (mp) REVERT: x 24 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6495 (tm-30) REVERT: x 58 ASN cc_start: 0.7085 (t0) cc_final: 0.6419 (m110) REVERT: y 11 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7882 (mtt90) REVERT: 0 32 GLU cc_start: 0.6267 (pm20) cc_final: 0.5977 (pm20) REVERT: 1 29 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7688 (mt0) REVERT: 1 42 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8285 (mp) REVERT: 2 15 LYS cc_start: 0.8334 (mmtm) cc_final: 0.7697 (mmmm) REVERT: 2 19 LYS cc_start: 0.8144 (mttm) cc_final: 0.7825 (mttp) REVERT: 2 57 LEU cc_start: 0.7835 (mt) cc_final: 0.7536 (mp) REVERT: 3 12 ARG cc_start: 0.6650 (ptm-80) cc_final: 0.6437 (ppt170) REVERT: 3 30 GLU cc_start: 0.6886 (tp30) cc_final: 0.6468 (mt-10) REVERT: 4 2 LYS cc_start: 0.7137 (mttt) cc_final: 0.6714 (mttp) REVERT: 4 3 LYS cc_start: 0.6062 (mttp) cc_final: 0.5769 (ptpp) REVERT: 4 25 ARG cc_start: 0.5998 (mmm-85) cc_final: 0.5682 (mmt90) outliers start: 209 outliers final: 120 residues processed: 945 average time/residue: 2.2825 time to fit residues: 3020.5499 Evaluate side-chains 975 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 816 time to evaluate : 6.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 147 MET Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain F residue 5 GLU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 131 LYS Chi-restraints excluded: chain H residue 3 MET Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain L residue 36 ARG Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain M residue 62 LYS Chi-restraints excluded: chain M residue 105 ASN Chi-restraints excluded: chain N residue 23 LYS Chi-restraints excluded: chain N residue 80 SER Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain P residue 68 SER Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 64 LYS Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 34 ARG Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 182 ARG Chi-restraints excluded: chain c residue 223 THR Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 74 GLU Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain d residue 99 GLU Chi-restraints excluded: chain d residue 157 LYS Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 13 THR Chi-restraints excluded: chain e residue 51 GLU Chi-restraints excluded: chain e residue 88 ARG Chi-restraints excluded: chain e residue 121 VAL Chi-restraints excluded: chain e residue 132 LYS Chi-restraints excluded: chain e residue 139 LYS Chi-restraints excluded: chain e residue 175 ILE Chi-restraints excluded: chain f residue 4 LEU Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 44 ILE Chi-restraints excluded: chain f residue 72 LYS Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain g residue 4 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 11 VAL Chi-restraints excluded: chain g residue 19 ILE Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 130 GLU Chi-restraints excluded: chain h residue 3 VAL Chi-restraints excluded: chain h residue 6 LEU Chi-restraints excluded: chain i residue 7 LYS Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 90 GLU Chi-restraints excluded: chain i residue 138 GLN Chi-restraints excluded: chain j residue 104 THR Chi-restraints excluded: chain j residue 105 ARG Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 5 THR Chi-restraints excluded: chain k residue 7 SER Chi-restraints excluded: chain k residue 46 VAL Chi-restraints excluded: chain k residue 115 GLU Chi-restraints excluded: chain k residue 121 THR Chi-restraints excluded: chain l residue 22 GLN Chi-restraints excluded: chain l residue 55 ARG Chi-restraints excluded: chain l residue 118 LYS Chi-restraints excluded: chain l residue 119 LEU Chi-restraints excluded: chain m residue 65 LEU Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain q residue 40 MET Chi-restraints excluded: chain q residue 73 LYS Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain r residue 27 LYS Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 95 ARG Chi-restraints excluded: chain s residue 18 GLU Chi-restraints excluded: chain s residue 42 GLU Chi-restraints excluded: chain s residue 55 VAL Chi-restraints excluded: chain t residue 60 GLU Chi-restraints excluded: chain u residue 12 GLN Chi-restraints excluded: chain u residue 38 LEU Chi-restraints excluded: chain w residue 17 ASN Chi-restraints excluded: chain w residue 40 VAL Chi-restraints excluded: chain w residue 66 THR Chi-restraints excluded: chain w residue 71 LEU Chi-restraints excluded: chain x residue 10 SER Chi-restraints excluded: chain x residue 11 VAL Chi-restraints excluded: chain x residue 16 THR Chi-restraints excluded: chain x residue 24 GLU Chi-restraints excluded: chain y residue 11 ARG Chi-restraints excluded: chain y residue 55 VAL Chi-restraints excluded: chain z residue 25 VAL Chi-restraints excluded: chain z residue 55 ILE Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 29 GLN Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain 2 residue 32 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 590 optimal weight: 10.0000 chunk 381 optimal weight: 0.0770 chunk 569 optimal weight: 9.9990 chunk 287 optimal weight: 9.9990 chunk 187 optimal weight: 5.9990 chunk 184 optimal weight: 9.9990 chunk 606 optimal weight: 10.0000 chunk 650 optimal weight: 10.0000 chunk 471 optimal weight: 30.0000 chunk 88 optimal weight: 10.0000 chunk 750 optimal weight: 9.9990 overall best weight: 7.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 139 GLN D 74 ASN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 ASN ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN F 55 HIS ** G 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 GLN ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 GLN P 40 ASN T 13 GLN U 64 ASN c 163 GLN e 136 GLN j 88 ASN p 71 GLN s 28 ASN ** w 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 154032 Z= 0.348 Angle : 0.846 16.941 230513 Z= 0.450 Chirality : 0.044 0.356 29296 Planarity : 0.009 0.149 12270 Dihedral : 23.186 179.766 77190 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.23 % Favored : 95.71 % Rotamer: Outliers : 4.20 % Allowed : 17.55 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.38 (0.11), residues: 5480 helix: 0.65 (0.11), residues: 1881 sheet: -0.32 (0.15), residues: 1075 loop : -0.84 (0.12), residues: 2524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP c 248 HIS 0.008 0.002 HIS i 76 PHE 0.023 0.003 PHE d 118 TYR 0.027 0.003 TYR L 38 ARG 0.010 0.001 ARG g 149 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1010 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 818 time to evaluate : 5.781 Fit side-chains revert: symmetry clash REVERT: B 9 MET cc_start: 0.4035 (OUTLIER) cc_final: 0.3047 (ttt) REVERT: B 58 ASN cc_start: 0.3083 (OUTLIER) cc_final: 0.2471 (m110) REVERT: B 135 LEU cc_start: 0.2958 (mp) cc_final: 0.2584 (tt) REVERT: B 164 ILE cc_start: 0.4031 (OUTLIER) cc_final: 0.3520 (pp) REVERT: C 28 GLU cc_start: 0.6631 (OUTLIER) cc_final: 0.6328 (pt0) REVERT: C 31 ASP cc_start: 0.7816 (m-30) cc_final: 0.7345 (m-30) REVERT: C 41 GLN cc_start: 0.7068 (OUTLIER) cc_final: 0.6747 (pt0) REVERT: C 88 ARG cc_start: 0.6003 (tmm-80) cc_final: 0.5413 (ttt-90) REVERT: C 127 ARG cc_start: 0.6270 (mtm-85) cc_final: 0.5931 (mpp80) REVERT: C 188 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6713 (mp0) REVERT: D 54 GLN cc_start: 0.7076 (mt0) cc_final: 0.6844 (mt0) REVERT: D 78 GLU cc_start: 0.6599 (OUTLIER) cc_final: 0.6342 (tm-30) REVERT: D 81 ARG cc_start: 0.6622 (ttp80) cc_final: 0.6128 (ttt-90) REVERT: D 94 LEU cc_start: 0.5822 (OUTLIER) cc_final: 0.5552 (tp) REVERT: D 124 MET cc_start: 0.6808 (OUTLIER) cc_final: 0.6532 (mtt) REVERT: D 135 TYR cc_start: 0.7170 (t80) cc_final: 0.6962 (t80) REVERT: D 148 LYS cc_start: 0.5364 (ttpt) cc_final: 0.4416 (tmtm) REVERT: D 202 GLU cc_start: 0.5644 (mm-30) cc_final: 0.5153 (mp0) REVERT: E 13 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6690 (mt-10) REVERT: E 68 ARG cc_start: 0.6978 (ttm110) cc_final: 0.6470 (mtm-85) REVERT: E 78 ASN cc_start: 0.6514 (m-40) cc_final: 0.6138 (t0) REVERT: E 86 LYS cc_start: 0.7527 (mmtm) cc_final: 0.6856 (mmmt) REVERT: F 56 LYS cc_start: 0.7610 (mtpt) cc_final: 0.7401 (mtpm) REVERT: F 102 MET cc_start: 0.5170 (ptp) cc_final: 0.4317 (mpp) REVERT: G 4 ARG cc_start: 0.5964 (tpp80) cc_final: 0.5387 (ptt180) REVERT: G 68 ASN cc_start: 0.6402 (m-40) cc_final: 0.5807 (m110) REVERT: G 76 LYS cc_start: 0.5955 (mtmt) cc_final: 0.5551 (mtpp) REVERT: G 83 SER cc_start: 0.5553 (m) cc_final: 0.5313 (t) REVERT: H 76 GLN cc_start: 0.7341 (pt0) cc_final: 0.6270 (mm-40) REVERT: H 83 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8162 (tp) REVERT: H 88 ARG cc_start: 0.7095 (mtp85) cc_final: 0.6525 (mtm180) REVERT: H 90 ASP cc_start: 0.5666 (OUTLIER) cc_final: 0.5326 (p0) REVERT: I 42 GLU cc_start: 0.5916 (mm-30) cc_final: 0.5416 (tp30) REVERT: I 46 MET cc_start: 0.6514 (ttp) cc_final: 0.6058 (ttt) REVERT: J 16 ARG cc_start: 0.6378 (mmt90) cc_final: 0.5810 (mtt90) REVERT: J 73 LEU cc_start: 0.7577 (tp) cc_final: 0.7216 (tm) REVERT: K 69 ARG cc_start: 0.6662 (mmm-85) cc_final: 0.6243 (mpt180) REVERT: K 107 ILE cc_start: 0.5936 (mm) cc_final: 0.5652 (mt) REVERT: L 20 ASN cc_start: 0.6922 (m-40) cc_final: 0.6655 (m110) REVERT: L 56 ARG cc_start: 0.6541 (ttm110) cc_final: 0.5445 (tmm160) REVERT: M 9 ILE cc_start: 0.6113 (pt) cc_final: 0.5773 (pt) REVERT: M 21 SER cc_start: 0.8421 (t) cc_final: 0.8116 (t) REVERT: M 43 VAL cc_start: 0.7365 (p) cc_final: 0.7053 (t) REVERT: M 78 LYS cc_start: 0.5840 (tppt) cc_final: 0.5170 (mtmm) REVERT: M 93 ARG cc_start: 0.6282 (mmt90) cc_final: 0.5628 (mmm-85) REVERT: N 27 LEU cc_start: 0.7039 (mp) cc_final: 0.6837 (mm) REVERT: N 90 ARG cc_start: 0.6760 (mtm-85) cc_final: 0.6405 (mtt90) REVERT: O 35 GLN cc_start: 0.7916 (tp40) cc_final: 0.7625 (tp40) REVERT: O 58 ARG cc_start: 0.6848 (ttt180) cc_final: 0.6539 (ttm110) REVERT: O 77 ARG cc_start: 0.6192 (ttp80) cc_final: 0.5810 (ttp80) REVERT: Q 11 ARG cc_start: 0.6413 (OUTLIER) cc_final: 0.5471 (mtp-110) REVERT: Q 75 LEU cc_start: 0.6957 (OUTLIER) cc_final: 0.6708 (tt) REVERT: T 21 ASN cc_start: 0.6426 (m110) cc_final: 0.6184 (m-40) REVERT: T 33 LYS cc_start: 0.6279 (tppt) cc_final: 0.5831 (pttp) REVERT: T 64 LYS cc_start: 0.4851 (OUTLIER) cc_final: 0.4357 (mttp) REVERT: T 69 LYS cc_start: 0.6651 (mtmt) cc_final: 0.5859 (mptt) REVERT: U 3 VAL cc_start: 0.6320 (OUTLIER) cc_final: 0.6103 (m) REVERT: U 17 ARG cc_start: 0.4597 (ttm-80) cc_final: 0.3799 (mtt-85) REVERT: U 34 ARG cc_start: 0.6453 (OUTLIER) cc_final: 0.5478 (ttm170) REVERT: c 5 LYS cc_start: 0.7533 (mtpp) cc_final: 0.7177 (tttt) REVERT: c 36 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7441 (ptmm) REVERT: c 182 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.6557 (ttt90) REVERT: c 183 LYS cc_start: 0.7936 (ttmm) cc_final: 0.7682 (tppp) REVERT: c 189 ARG cc_start: 0.7598 (mtt-85) cc_final: 0.7301 (mtt-85) REVERT: d 74 GLU cc_start: 0.6629 (OUTLIER) cc_final: 0.6053 (mm-30) REVERT: d 105 LYS cc_start: 0.7848 (mmtm) cc_final: 0.7624 (mttp) REVERT: d 157 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8381 (ttpt) REVERT: d 183 GLU cc_start: 0.5975 (pm20) cc_final: 0.5462 (pt0) REVERT: e 1 MET cc_start: 0.5271 (OUTLIER) cc_final: 0.4833 (ptt) REVERT: e 122 GLU cc_start: 0.6255 (tp30) cc_final: 0.5433 (tm-30) REVERT: e 132 LYS cc_start: 0.7202 (OUTLIER) cc_final: 0.6543 (pptt) REVERT: e 139 LYS cc_start: 0.6871 (OUTLIER) cc_final: 0.6038 (mmtt) REVERT: e 171 ASP cc_start: 0.7064 (t70) cc_final: 0.6259 (t0) REVERT: f 11 GLU cc_start: 0.5927 (OUTLIER) cc_final: 0.4757 (tm-30) REVERT: f 128 TYR cc_start: 0.7852 (t80) cc_final: 0.7385 (t80) REVERT: f 130 MET cc_start: 0.7938 (ptm) cc_final: 0.7601 (ptt) REVERT: f 167 ARG cc_start: 0.6761 (ttm-80) cc_final: 0.6536 (ttp-110) REVERT: g 29 LYS cc_start: 0.5259 (ttpt) cc_final: 0.4930 (tmtm) REVERT: g 69 ARG cc_start: 0.7111 (tmt170) cc_final: 0.5983 (tmt170) REVERT: g 130 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6532 (mm-30) REVERT: h 1 MET cc_start: 0.5344 (ptm) cc_final: 0.3585 (ttp) REVERT: h 6 LEU cc_start: 0.6023 (OUTLIER) cc_final: 0.5704 (mt) REVERT: i 12 LYS cc_start: 0.6343 (mmmm) cc_final: 0.6019 (mmmt) REVERT: i 43 GLU cc_start: 0.8179 (mp0) cc_final: 0.7774 (mp0) REVERT: i 60 ASP cc_start: 0.7892 (p0) cc_final: 0.7571 (p0) REVERT: i 106 LYS cc_start: 0.8078 (tttm) cc_final: 0.7433 (ttmm) REVERT: i 138 GLN cc_start: 0.7577 (OUTLIER) cc_final: 0.7087 (mm-40) REVERT: j 7 MET cc_start: 0.8300 (mmm) cc_final: 0.7934 (mmm) REVERT: j 53 LYS cc_start: 0.7634 (pttp) cc_final: 0.7320 (ptmm) REVERT: j 111 LYS cc_start: 0.6367 (mtpp) cc_final: 0.6019 (mtmt) REVERT: j 114 LYS cc_start: 0.6990 (mtpp) cc_final: 0.6600 (tptt) REVERT: k 91 ASP cc_start: 0.7060 (p0) cc_final: 0.6815 (p0) REVERT: k 103 ILE cc_start: 0.7805 (mm) cc_final: 0.7438 (tp) REVERT: k 115 GLU cc_start: 0.6317 (OUTLIER) cc_final: 0.6059 (tp30) REVERT: k 126 ARG cc_start: 0.7497 (mtm180) cc_final: 0.7085 (mtp180) REVERT: l 10 ARG cc_start: 0.7398 (mtm-85) cc_final: 0.7066 (mtm110) REVERT: l 22 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.6733 (mt0) REVERT: l 47 GLU cc_start: 0.7785 (tp30) cc_final: 0.7448 (tp30) REVERT: l 53 MET cc_start: 0.7915 (ptm) cc_final: 0.7456 (ptp) REVERT: l 55 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.5839 (tmt170) REVERT: l 90 GLU cc_start: 0.7597 (mm-30) cc_final: 0.6625 (mp0) REVERT: l 118 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7962 (tttm) REVERT: n 46 GLU cc_start: 0.6147 (tm-30) cc_final: 0.5730 (tm-30) REVERT: n 62 LEU cc_start: 0.7193 (mt) cc_final: 0.6907 (mt) REVERT: n 89 ASP cc_start: 0.6935 (t0) cc_final: 0.6592 (OUTLIER) REVERT: n 116 GLN cc_start: 0.6740 (mm-40) cc_final: 0.6440 (mm110) REVERT: o 6 LYS cc_start: 0.6686 (ptpt) cc_final: 0.6134 (pptt) REVERT: o 9 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6983 (mt-10) REVERT: o 10 GLN cc_start: 0.6878 (mm-40) cc_final: 0.6507 (mt0) REVERT: o 38 LYS cc_start: 0.6754 (ptmt) cc_final: 0.6327 (pttt) REVERT: o 68 GLU cc_start: 0.6179 (mm-30) cc_final: 0.5803 (tm-30) REVERT: o 89 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.6865 (mmt180) REVERT: o 111 LYS cc_start: 0.7980 (ptmm) cc_final: 0.7193 (pttm) REVERT: q 6 GLN cc_start: 0.7830 (pt0) cc_final: 0.6864 (tm130) REVERT: q 40 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8267 (ttt) REVERT: q 48 LYS cc_start: 0.7684 (mttm) cc_final: 0.7240 (mtpt) REVERT: q 73 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7704 (mmtm) REVERT: r 72 THR cc_start: 0.8098 (p) cc_final: 0.7806 (t) REVERT: r 92 ARG cc_start: 0.7457 (ttm-80) cc_final: 0.6651 (ttm110) REVERT: s 3 ARG cc_start: 0.6341 (mtm-85) cc_final: 0.5450 (mtp85) REVERT: s 18 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6576 (mp0) REVERT: s 42 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6537 (mp0) REVERT: s 52 GLU cc_start: 0.5529 (mp0) cc_final: 0.5115 (tm-30) REVERT: t 8 ASP cc_start: 0.7339 (m-30) cc_final: 0.7111 (m-30) REVERT: u 1 MET cc_start: 0.4571 (ttt) cc_final: 0.3910 (mpp) REVERT: u 12 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.6951 (mm-40) REVERT: u 38 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7619 (pt) REVERT: u 68 LYS cc_start: 0.6483 (ptmm) cc_final: 0.5630 (mppt) REVERT: w 71 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7539 (mp) REVERT: x 24 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6535 (tm-30) REVERT: x 58 ASN cc_start: 0.7076 (t0) cc_final: 0.6434 (m110) REVERT: y 11 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7857 (mtt90) REVERT: 0 32 GLU cc_start: 0.6304 (pm20) cc_final: 0.6018 (pm20) REVERT: 1 29 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7715 (mt0) REVERT: 1 42 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8255 (mp) REVERT: 2 15 LYS cc_start: 0.8282 (mmtm) cc_final: 0.7606 (mmmm) REVERT: 2 57 LEU cc_start: 0.7826 (mt) cc_final: 0.7549 (mp) REVERT: 3 12 ARG cc_start: 0.6685 (ptm-80) cc_final: 0.6484 (ppt170) REVERT: 3 30 GLU cc_start: 0.6891 (tp30) cc_final: 0.6472 (mt-10) REVERT: 4 2 LYS cc_start: 0.7122 (mttt) cc_final: 0.6710 (mttp) REVERT: 4 3 LYS cc_start: 0.6103 (mttp) cc_final: 0.5828 (ptpp) REVERT: 4 25 ARG cc_start: 0.5981 (mmm-85) cc_final: 0.5570 (tpp80) outliers start: 192 outliers final: 109 residues processed: 923 average time/residue: 2.3313 time to fit residues: 3002.9391 Evaluate side-chains 961 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 810 time to evaluate : 6.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 131 LYS Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain M residue 62 LYS Chi-restraints excluded: chain M residue 105 ASN Chi-restraints excluded: chain N residue 23 LYS Chi-restraints excluded: chain N residue 80 SER Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain P residue 68 SER Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 64 LYS Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 34 ARG Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 36 LYS Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 182 ARG Chi-restraints excluded: chain c residue 223 THR Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 74 GLU Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain d residue 99 GLU Chi-restraints excluded: chain d residue 157 LYS Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 13 THR Chi-restraints excluded: chain e residue 51 GLU Chi-restraints excluded: chain e residue 88 ARG Chi-restraints excluded: chain e residue 121 VAL Chi-restraints excluded: chain e residue 132 LYS Chi-restraints excluded: chain e residue 139 LYS Chi-restraints excluded: chain e residue 175 ILE Chi-restraints excluded: chain f residue 4 LEU Chi-restraints excluded: chain f residue 11 GLU Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 44 ILE Chi-restraints excluded: chain f residue 72 LYS Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain g residue 4 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 11 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 130 GLU Chi-restraints excluded: chain h residue 3 VAL Chi-restraints excluded: chain h residue 6 LEU Chi-restraints excluded: chain i residue 7 LYS Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 90 GLU Chi-restraints excluded: chain i residue 138 GLN Chi-restraints excluded: chain j residue 28 SER Chi-restraints excluded: chain j residue 104 THR Chi-restraints excluded: chain j residue 105 ARG Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 5 THR Chi-restraints excluded: chain k residue 7 SER Chi-restraints excluded: chain k residue 115 GLU Chi-restraints excluded: chain k residue 121 THR Chi-restraints excluded: chain l residue 22 GLN Chi-restraints excluded: chain l residue 55 ARG Chi-restraints excluded: chain l residue 118 LYS Chi-restraints excluded: chain m residue 65 LEU Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain q residue 40 MET Chi-restraints excluded: chain q residue 73 LYS Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain r residue 27 LYS Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 95 ARG Chi-restraints excluded: chain s residue 18 GLU Chi-restraints excluded: chain s residue 42 GLU Chi-restraints excluded: chain s residue 55 VAL Chi-restraints excluded: chain u residue 12 GLN Chi-restraints excluded: chain u residue 38 LEU Chi-restraints excluded: chain w residue 40 VAL Chi-restraints excluded: chain w residue 66 THR Chi-restraints excluded: chain w residue 71 LEU Chi-restraints excluded: chain x residue 10 SER Chi-restraints excluded: chain x residue 11 VAL Chi-restraints excluded: chain x residue 24 GLU Chi-restraints excluded: chain y residue 11 ARG Chi-restraints excluded: chain y residue 55 VAL Chi-restraints excluded: chain z residue 25 VAL Chi-restraints excluded: chain z residue 55 ILE Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 29 GLN Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 4 residue 28 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 868 optimal weight: 7.9990 chunk 914 optimal weight: 3.9990 chunk 834 optimal weight: 4.9990 chunk 889 optimal weight: 8.9990 chunk 913 optimal weight: 0.9990 chunk 535 optimal weight: 20.0000 chunk 387 optimal weight: 10.0000 chunk 698 optimal weight: 5.9990 chunk 272 optimal weight: 4.9990 chunk 803 optimal weight: 2.9990 chunk 840 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 139 GLN D 74 ASN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN F 55 HIS ** G 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN P 40 ASN U 64 ASN c 163 GLN e 115 GLN e 136 GLN ** g 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 88 ASN p 71 GLN r 61 ASN s 48 GLN ** w 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 45 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 154032 Z= 0.169 Angle : 0.675 13.904 230513 Z= 0.379 Chirality : 0.036 0.370 29296 Planarity : 0.007 0.133 12270 Dihedral : 22.994 179.698 77190 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.65 % Favored : 96.30 % Rotamer: Outliers : 2.97 % Allowed : 18.99 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.11), residues: 5480 helix: 1.20 (0.12), residues: 1893 sheet: -0.11 (0.16), residues: 1063 loop : -0.63 (0.12), residues: 2524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP c 248 HIS 0.007 0.001 HIS B 39 PHE 0.019 0.002 PHE F 8 TYR 0.023 0.002 TYR L 38 ARG 0.014 0.000 ARG g 149 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 983 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 847 time to evaluate : 6.310 Fit side-chains revert: symmetry clash REVERT: B 58 ASN cc_start: 0.3207 (OUTLIER) cc_final: 0.2427 (m110) REVERT: C 31 ASP cc_start: 0.7879 (m-30) cc_final: 0.7436 (m-30) REVERT: C 88 ARG cc_start: 0.5941 (tmm-80) cc_final: 0.5396 (ttt-90) REVERT: C 127 ARG cc_start: 0.6187 (mtm-85) cc_final: 0.5912 (mpp-170) REVERT: C 188 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6686 (mp0) REVERT: D 54 GLN cc_start: 0.7021 (mt0) cc_final: 0.6764 (mt0) REVERT: D 78 GLU cc_start: 0.6610 (OUTLIER) cc_final: 0.6199 (tm-30) REVERT: D 81 ARG cc_start: 0.6519 (ttp80) cc_final: 0.6170 (ttt-90) REVERT: D 94 LEU cc_start: 0.5754 (OUTLIER) cc_final: 0.5478 (tp) REVERT: D 124 MET cc_start: 0.6851 (ttt) cc_final: 0.6555 (mtt) REVERT: D 135 TYR cc_start: 0.7080 (t80) cc_final: 0.6852 (t80) REVERT: D 148 LYS cc_start: 0.5395 (ttpt) cc_final: 0.4464 (tmtm) REVERT: D 202 GLU cc_start: 0.5543 (mm-30) cc_final: 0.5049 (mp0) REVERT: E 68 ARG cc_start: 0.6960 (ttm110) cc_final: 0.6504 (mtm-85) REVERT: E 73 ASN cc_start: 0.6764 (m110) cc_final: 0.6405 (m-40) REVERT: E 78 ASN cc_start: 0.6405 (m-40) cc_final: 0.6046 (t0) REVERT: E 86 LYS cc_start: 0.7519 (mmtm) cc_final: 0.6841 (mmmt) REVERT: F 56 LYS cc_start: 0.7561 (mtpt) cc_final: 0.7347 (mtpm) REVERT: F 79 ARG cc_start: 0.6777 (ttm-80) cc_final: 0.6336 (ttm-80) REVERT: F 90 MET cc_start: 0.7401 (mtt) cc_final: 0.7130 (mtt) REVERT: F 102 MET cc_start: 0.5060 (ptp) cc_final: 0.4107 (mpp) REVERT: G 4 ARG cc_start: 0.5967 (tpp80) cc_final: 0.5389 (ptt180) REVERT: G 68 ASN cc_start: 0.6331 (m-40) cc_final: 0.5748 (m-40) REVERT: G 76 LYS cc_start: 0.5938 (mtmt) cc_final: 0.5508 (mtpp) REVERT: G 79 ARG cc_start: 0.6155 (mtp-110) cc_final: 0.5556 (ttt-90) REVERT: G 83 SER cc_start: 0.5486 (m) cc_final: 0.5246 (t) REVERT: H 3 MET cc_start: 0.7292 (OUTLIER) cc_final: 0.7030 (tpp) REVERT: H 74 SER cc_start: 0.7671 (p) cc_final: 0.7383 (t) REVERT: H 76 GLN cc_start: 0.7361 (pt0) cc_final: 0.6204 (mm-40) REVERT: H 88 ARG cc_start: 0.7138 (mtp85) cc_final: 0.6559 (mtm180) REVERT: H 90 ASP cc_start: 0.5682 (p0) cc_final: 0.5329 (p0) REVERT: I 42 GLU cc_start: 0.5895 (mm-30) cc_final: 0.5370 (tp30) REVERT: I 46 MET cc_start: 0.6461 (ttp) cc_final: 0.5964 (ttt) REVERT: J 73 LEU cc_start: 0.7532 (tp) cc_final: 0.7156 (tm) REVERT: K 69 ARG cc_start: 0.6677 (mmm-85) cc_final: 0.6260 (mpt180) REVERT: K 107 ILE cc_start: 0.5878 (mm) cc_final: 0.5561 (mt) REVERT: L 20 ASN cc_start: 0.6872 (m-40) cc_final: 0.6616 (m110) REVERT: L 56 ARG cc_start: 0.6533 (ttm110) cc_final: 0.5620 (tmm160) REVERT: M 21 SER cc_start: 0.8311 (t) cc_final: 0.8049 (t) REVERT: M 43 VAL cc_start: 0.7414 (p) cc_final: 0.7122 (t) REVERT: M 81 MET cc_start: 0.7462 (mtp) cc_final: 0.6863 (ttm) REVERT: M 93 ARG cc_start: 0.6282 (mmt90) cc_final: 0.5634 (mmm-85) REVERT: M 105 ASN cc_start: 0.6233 (OUTLIER) cc_final: 0.6016 (p0) REVERT: N 27 LEU cc_start: 0.7002 (mp) cc_final: 0.6789 (mm) REVERT: N 90 ARG cc_start: 0.6664 (mtm-85) cc_final: 0.6338 (mtt90) REVERT: O 58 ARG cc_start: 0.6824 (ttt180) cc_final: 0.6485 (ttm110) REVERT: O 77 ARG cc_start: 0.6156 (ttp80) cc_final: 0.5767 (ttp80) REVERT: S 32 ARG cc_start: 0.7030 (mtp-110) cc_final: 0.6829 (ptm160) REVERT: T 21 ASN cc_start: 0.6509 (m110) cc_final: 0.6206 (m-40) REVERT: T 33 LYS cc_start: 0.6052 (tppt) cc_final: 0.5696 (pttp) REVERT: T 64 LYS cc_start: 0.4740 (mtpp) cc_final: 0.3922 (tppt) REVERT: T 69 LYS cc_start: 0.6588 (mtmt) cc_final: 0.5910 (mptt) REVERT: U 3 VAL cc_start: 0.6265 (OUTLIER) cc_final: 0.5809 (t) REVERT: U 17 ARG cc_start: 0.4603 (ttm-80) cc_final: 0.3942 (mtt-85) REVERT: U 34 ARG cc_start: 0.6459 (OUTLIER) cc_final: 0.5589 (ttm170) REVERT: c 5 LYS cc_start: 0.7413 (mtpp) cc_final: 0.7107 (tttt) REVERT: c 167 ARG cc_start: 0.7633 (ttp-110) cc_final: 0.7252 (ttp-110) REVERT: c 182 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.6850 (ttt90) REVERT: c 183 LYS cc_start: 0.7863 (ttmm) cc_final: 0.7651 (tppp) REVERT: c 189 ARG cc_start: 0.7496 (mtt-85) cc_final: 0.7200 (mtt-85) REVERT: d 74 GLU cc_start: 0.6664 (OUTLIER) cc_final: 0.6115 (mm-30) REVERT: d 105 LYS cc_start: 0.7821 (mmtm) cc_final: 0.7564 (mttp) REVERT: d 157 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8287 (ttpt) REVERT: d 183 GLU cc_start: 0.6042 (pm20) cc_final: 0.5428 (pt0) REVERT: e 1 MET cc_start: 0.5313 (OUTLIER) cc_final: 0.4839 (ptt) REVERT: e 122 GLU cc_start: 0.6315 (tp30) cc_final: 0.5449 (tm-30) REVERT: e 139 LYS cc_start: 0.6829 (OUTLIER) cc_final: 0.6016 (mmtt) REVERT: e 171 ASP cc_start: 0.7066 (t70) cc_final: 0.6266 (t0) REVERT: f 11 GLU cc_start: 0.5841 (OUTLIER) cc_final: 0.4726 (tm-30) REVERT: f 128 TYR cc_start: 0.7785 (t80) cc_final: 0.7322 (t80) REVERT: f 130 MET cc_start: 0.7963 (ptm) cc_final: 0.7759 (ptm) REVERT: f 167 ARG cc_start: 0.6678 (ttm-80) cc_final: 0.6294 (ttp-110) REVERT: g 29 LYS cc_start: 0.5354 (ttpt) cc_final: 0.5038 (tmtm) REVERT: g 69 ARG cc_start: 0.7085 (tmt170) cc_final: 0.6014 (tmt170) REVERT: g 116 GLN cc_start: 0.6842 (tm-30) cc_final: 0.6321 (tm-30) REVERT: g 130 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.6566 (mm-30) REVERT: h 1 MET cc_start: 0.5289 (ptm) cc_final: 0.3523 (ttp) REVERT: i 12 LYS cc_start: 0.6309 (mmmm) cc_final: 0.5933 (mmmt) REVERT: i 43 GLU cc_start: 0.8178 (mp0) cc_final: 0.7777 (mp0) REVERT: i 60 ASP cc_start: 0.7865 (p0) cc_final: 0.7528 (p0) REVERT: i 106 LYS cc_start: 0.8082 (tttm) cc_final: 0.7478 (ttmm) REVERT: i 138 GLN cc_start: 0.7492 (pt0) cc_final: 0.7056 (mm-40) REVERT: j 7 MET cc_start: 0.8321 (mmm) cc_final: 0.8022 (mmm) REVERT: j 53 LYS cc_start: 0.7647 (pttp) cc_final: 0.7300 (ptmm) REVERT: j 111 LYS cc_start: 0.6371 (mtpp) cc_final: 0.5985 (mtmt) REVERT: j 114 LYS cc_start: 0.6996 (mtpp) cc_final: 0.6542 (tptt) REVERT: k 1 MET cc_start: 0.7557 (OUTLIER) cc_final: 0.6815 (ptt) REVERT: k 91 ASP cc_start: 0.7032 (p0) cc_final: 0.6762 (p0) REVERT: k 103 ILE cc_start: 0.7759 (mm) cc_final: 0.7505 (tp) REVERT: k 115 GLU cc_start: 0.6325 (OUTLIER) cc_final: 0.6099 (tp30) REVERT: k 123 ARG cc_start: 0.6735 (ttm170) cc_final: 0.6447 (mtm110) REVERT: k 126 ARG cc_start: 0.7549 (mtm180) cc_final: 0.7169 (mtp180) REVERT: l 10 ARG cc_start: 0.7337 (mtm-85) cc_final: 0.6940 (mtm110) REVERT: l 47 GLU cc_start: 0.7662 (tp30) cc_final: 0.7206 (tp30) REVERT: l 53 MET cc_start: 0.7771 (ptm) cc_final: 0.7302 (ptp) REVERT: l 90 GLU cc_start: 0.7524 (mm-30) cc_final: 0.6600 (mp0) REVERT: l 118 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7951 (tttm) REVERT: n 16 ARG cc_start: 0.6695 (mmp80) cc_final: 0.6460 (mmt-90) REVERT: n 46 GLU cc_start: 0.6171 (tm-30) cc_final: 0.5713 (tm-30) REVERT: n 62 LEU cc_start: 0.7218 (mt) cc_final: 0.6981 (mt) REVERT: n 89 ASP cc_start: 0.6764 (t0) cc_final: 0.6412 (OUTLIER) REVERT: n 98 GLN cc_start: 0.7738 (mm-40) cc_final: 0.7258 (mm-40) REVERT: n 116 GLN cc_start: 0.6704 (mm-40) cc_final: 0.6362 (mm110) REVERT: o 6 LYS cc_start: 0.6685 (ptpt) cc_final: 0.6212 (pptt) REVERT: o 9 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6976 (mt-10) REVERT: o 38 LYS cc_start: 0.6586 (ptmt) cc_final: 0.6192 (pttt) REVERT: o 68 GLU cc_start: 0.6220 (mm-30) cc_final: 0.5872 (tm-30) REVERT: o 89 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.6861 (mmt180) REVERT: o 111 LYS cc_start: 0.7992 (ptmm) cc_final: 0.7092 (pttt) REVERT: q 6 GLN cc_start: 0.7769 (pt0) cc_final: 0.6821 (tm-30) REVERT: q 40 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.8140 (ttt) REVERT: q 48 LYS cc_start: 0.7643 (mttm) cc_final: 0.7206 (mtpt) REVERT: r 72 THR cc_start: 0.8119 (p) cc_final: 0.7682 (t) REVERT: r 92 ARG cc_start: 0.7489 (ttm-80) cc_final: 0.6669 (ttm110) REVERT: s 3 ARG cc_start: 0.6356 (mtm-85) cc_final: 0.5427 (mtp85) REVERT: s 18 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6557 (mp0) REVERT: s 42 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6538 (mp0) REVERT: s 52 GLU cc_start: 0.5536 (mp0) cc_final: 0.5070 (tm-30) REVERT: t 7 ARG cc_start: 0.6522 (ttm110) cc_final: 0.6155 (tpt-90) REVERT: t 8 ASP cc_start: 0.7221 (m-30) cc_final: 0.7001 (m-30) REVERT: u 11 GLU cc_start: 0.6976 (pt0) cc_final: 0.6713 (pm20) REVERT: u 12 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.6916 (mm-40) REVERT: u 38 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7520 (pt) REVERT: u 53 LYS cc_start: 0.6417 (mttm) cc_final: 0.6124 (mttt) REVERT: u 90 ASP cc_start: 0.8032 (m-30) cc_final: 0.7798 (m-30) REVERT: v 72 LYS cc_start: 0.7712 (mtpp) cc_final: 0.7185 (mttt) REVERT: w 44 LYS cc_start: 0.5637 (mmpt) cc_final: 0.5423 (mmtm) REVERT: w 71 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7546 (mp) REVERT: x 24 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6516 (tm-30) REVERT: x 58 ASN cc_start: 0.7050 (t0) cc_final: 0.6391 (m110) REVERT: y 11 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7852 (mtt90) REVERT: 1 29 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7701 (mt0) REVERT: 1 42 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8287 (mp) REVERT: 2 15 LYS cc_start: 0.8285 (mmtm) cc_final: 0.7597 (mmmm) REVERT: 2 57 LEU cc_start: 0.7788 (mt) cc_final: 0.7539 (mp) REVERT: 3 30 GLU cc_start: 0.6940 (tp30) cc_final: 0.6530 (mt-10) REVERT: 4 2 LYS cc_start: 0.7005 (mttt) cc_final: 0.6605 (mttp) REVERT: 4 3 LYS cc_start: 0.6102 (mttp) cc_final: 0.5822 (ptpp) REVERT: 4 25 ARG cc_start: 0.5986 (mmm-85) cc_final: 0.5603 (tpp80) outliers start: 136 outliers final: 73 residues processed: 918 average time/residue: 2.3409 time to fit residues: 3002.8616 Evaluate side-chains 926 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 826 time to evaluate : 6.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 131 LYS Chi-restraints excluded: chain H residue 3 MET Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain M residue 62 LYS Chi-restraints excluded: chain M residue 105 ASN Chi-restraints excluded: chain N residue 80 SER Chi-restraints excluded: chain P residue 68 SER Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 34 ARG Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 182 ARG Chi-restraints excluded: chain c residue 223 THR Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 74 GLU Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain d residue 99 GLU Chi-restraints excluded: chain d residue 157 LYS Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 13 THR Chi-restraints excluded: chain e residue 51 GLU Chi-restraints excluded: chain e residue 88 ARG Chi-restraints excluded: chain e residue 139 LYS Chi-restraints excluded: chain e residue 175 ILE Chi-restraints excluded: chain f residue 4 LEU Chi-restraints excluded: chain f residue 11 GLU Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 130 GLU Chi-restraints excluded: chain h residue 3 VAL Chi-restraints excluded: chain i residue 7 LYS Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 90 GLU Chi-restraints excluded: chain j residue 28 SER Chi-restraints excluded: chain j residue 105 ARG Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 7 SER Chi-restraints excluded: chain k residue 46 VAL Chi-restraints excluded: chain k residue 115 GLU Chi-restraints excluded: chain k residue 121 THR Chi-restraints excluded: chain l residue 118 LYS Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain q residue 40 MET Chi-restraints excluded: chain r residue 27 LYS Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 95 ARG Chi-restraints excluded: chain s residue 18 GLU Chi-restraints excluded: chain s residue 42 GLU Chi-restraints excluded: chain s residue 55 VAL Chi-restraints excluded: chain u residue 12 GLN Chi-restraints excluded: chain u residue 38 LEU Chi-restraints excluded: chain w residue 40 VAL Chi-restraints excluded: chain w residue 71 LEU Chi-restraints excluded: chain x residue 24 GLU Chi-restraints excluded: chain y residue 11 ARG Chi-restraints excluded: chain y residue 55 VAL Chi-restraints excluded: chain z residue 25 VAL Chi-restraints excluded: chain z residue 55 ILE Chi-restraints excluded: chain 1 residue 29 GLN Chi-restraints excluded: chain 1 residue 42 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 886 optimal weight: 30.0000 chunk 583 optimal weight: 10.0000 chunk 940 optimal weight: 20.0000 chunk 573 optimal weight: 10.0000 chunk 446 optimal weight: 10.0000 chunk 653 optimal weight: 10.0000 chunk 986 optimal weight: 10.0000 chunk 907 optimal weight: 8.9990 chunk 785 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 606 optimal weight: 10.0000 overall best weight: 8.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 139 GLN D 74 ASN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN F 55 HIS G 142 HIS H 67 GLN ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN N 49 GLN O 35 GLN T 13 GLN T 21 ASN U 64 ASN c 163 GLN ** g 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 88 ASN p 71 GLN r 61 ASN s 28 ASN s 48 GLN ** w 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 154032 Z= 0.396 Angle : 0.885 18.344 230513 Z= 0.465 Chirality : 0.046 0.358 29296 Planarity : 0.009 0.152 12270 Dihedral : 23.175 179.370 77190 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.56 % Favored : 95.36 % Rotamer: Outliers : 2.91 % Allowed : 19.50 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.11), residues: 5480 helix: 0.76 (0.12), residues: 1888 sheet: -0.30 (0.15), residues: 1088 loop : -0.78 (0.12), residues: 2504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP G 103 HIS 0.008 0.002 HIS i 76 PHE 0.024 0.003 PHE d 118 TYR 0.033 0.003 TYR L 38 ARG 0.013 0.001 ARG g 149 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10960 Ramachandran restraints generated. 5480 Oldfield, 0 Emsley, 5480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 955 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 822 time to evaluate : 6.363 Fit side-chains revert: symmetry clash REVERT: B 58 ASN cc_start: 0.3186 (OUTLIER) cc_final: 0.2545 (m110) REVERT: B 135 LEU cc_start: 0.3005 (mp) cc_final: 0.2656 (tt) REVERT: B 164 ILE cc_start: 0.4013 (OUTLIER) cc_final: 0.3488 (pp) REVERT: C 31 ASP cc_start: 0.7830 (m-30) cc_final: 0.7365 (m-30) REVERT: C 88 ARG cc_start: 0.5966 (tmm-80) cc_final: 0.5379 (ttt-90) REVERT: C 127 ARG cc_start: 0.6273 (mtm-85) cc_final: 0.5969 (mpp80) REVERT: C 188 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6675 (mp0) REVERT: D 54 GLN cc_start: 0.7077 (mt0) cc_final: 0.6854 (mt0) REVERT: D 78 GLU cc_start: 0.6602 (OUTLIER) cc_final: 0.6276 (tm-30) REVERT: D 94 LEU cc_start: 0.5835 (OUTLIER) cc_final: 0.5564 (tp) REVERT: D 135 TYR cc_start: 0.7098 (t80) cc_final: 0.6829 (t80) REVERT: D 148 LYS cc_start: 0.5444 (ttpt) cc_final: 0.4505 (tmtm) REVERT: D 151 LYS cc_start: 0.4621 (pttp) cc_final: 0.4177 (mmtm) REVERT: D 202 GLU cc_start: 0.5711 (mm-30) cc_final: 0.5219 (mp0) REVERT: E 68 ARG cc_start: 0.7021 (ttm110) cc_final: 0.6518 (mtm-85) REVERT: E 78 ASN cc_start: 0.6516 (m-40) cc_final: 0.6141 (t0) REVERT: E 152 MET cc_start: 0.7245 (mtm) cc_final: 0.6971 (mtp) REVERT: F 35 LYS cc_start: 0.7420 (ptpp) cc_final: 0.6624 (mtpt) REVERT: F 56 LYS cc_start: 0.7612 (mtpt) cc_final: 0.7407 (mtpm) REVERT: F 102 MET cc_start: 0.5163 (ptp) cc_final: 0.4284 (mpp) REVERT: G 4 ARG cc_start: 0.5974 (tpp80) cc_final: 0.5399 (ptt180) REVERT: G 68 ASN cc_start: 0.6399 (m-40) cc_final: 0.5807 (m110) REVERT: G 76 LYS cc_start: 0.5942 (mtmt) cc_final: 0.5537 (mtpp) REVERT: G 83 SER cc_start: 0.5582 (m) cc_final: 0.5341 (t) REVERT: H 3 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.6943 (tpp) REVERT: H 76 GLN cc_start: 0.7360 (pt0) cc_final: 0.6284 (mm-40) REVERT: H 88 ARG cc_start: 0.7088 (mtp85) cc_final: 0.6513 (mtm180) REVERT: H 90 ASP cc_start: 0.5634 (OUTLIER) cc_final: 0.5345 (p0) REVERT: I 42 GLU cc_start: 0.5960 (mm-30) cc_final: 0.5447 (tp30) REVERT: I 46 MET cc_start: 0.6551 (ttp) cc_final: 0.6037 (ttt) REVERT: J 16 ARG cc_start: 0.6339 (mmt90) cc_final: 0.5819 (mtt90) REVERT: J 73 LEU cc_start: 0.7579 (tp) cc_final: 0.7214 (tm) REVERT: K 69 ARG cc_start: 0.6654 (mmm-85) cc_final: 0.6236 (mpt180) REVERT: K 107 ILE cc_start: 0.5894 (mm) cc_final: 0.5593 (mt) REVERT: L 20 ASN cc_start: 0.6922 (m-40) cc_final: 0.6636 (m110) REVERT: L 56 ARG cc_start: 0.6530 (ttm110) cc_final: 0.5533 (tmm160) REVERT: M 9 ILE cc_start: 0.6141 (pt) cc_final: 0.5809 (pt) REVERT: M 21 SER cc_start: 0.8429 (t) cc_final: 0.8131 (t) REVERT: M 43 VAL cc_start: 0.7370 (p) cc_final: 0.7062 (t) REVERT: M 78 LYS cc_start: 0.5945 (tppt) cc_final: 0.5255 (mtmm) REVERT: M 93 ARG cc_start: 0.6275 (mmt90) cc_final: 0.5591 (mmm-85) REVERT: N 27 LEU cc_start: 0.7044 (mp) cc_final: 0.6833 (mm) REVERT: O 26 GLU cc_start: 0.6634 (mp0) cc_final: 0.6153 (mp0) REVERT: O 35 GLN cc_start: 0.7949 (tp40) cc_final: 0.7695 (tp40) REVERT: O 58 ARG cc_start: 0.6878 (ttt180) cc_final: 0.6569 (ttm110) REVERT: O 77 ARG cc_start: 0.6188 (ttp80) cc_final: 0.5649 (ttp80) REVERT: T 21 ASN cc_start: 0.6453 (m-40) cc_final: 0.6177 (m-40) REVERT: T 69 LYS cc_start: 0.6691 (mtmt) cc_final: 0.5914 (mptt) REVERT: U 3 VAL cc_start: 0.6319 (OUTLIER) cc_final: 0.6111 (m) REVERT: U 17 ARG cc_start: 0.4638 (ttm-80) cc_final: 0.3827 (mtt-85) REVERT: U 34 ARG cc_start: 0.6475 (OUTLIER) cc_final: 0.5481 (ttm170) REVERT: c 5 LYS cc_start: 0.7515 (mtpp) cc_final: 0.7164 (tttt) REVERT: c 36 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7424 (ptmm) REVERT: c 182 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.6555 (ttt90) REVERT: c 183 LYS cc_start: 0.7948 (ttmm) cc_final: 0.7682 (tppp) REVERT: c 189 ARG cc_start: 0.7647 (mtt-85) cc_final: 0.7336 (mtt-85) REVERT: d 74 GLU cc_start: 0.6631 (OUTLIER) cc_final: 0.6043 (mm-30) REVERT: d 157 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8350 (ttpt) REVERT: d 183 GLU cc_start: 0.6007 (pm20) cc_final: 0.5412 (pt0) REVERT: e 1 MET cc_start: 0.5308 (OUTLIER) cc_final: 0.4839 (ptt) REVERT: e 122 GLU cc_start: 0.6310 (tp30) cc_final: 0.5473 (tm-30) REVERT: e 139 LYS cc_start: 0.6851 (OUTLIER) cc_final: 0.6027 (mmtt) REVERT: e 171 ASP cc_start: 0.7060 (t70) cc_final: 0.6252 (t0) REVERT: f 11 GLU cc_start: 0.5968 (OUTLIER) cc_final: 0.4859 (tm-30) REVERT: f 128 TYR cc_start: 0.7838 (t80) cc_final: 0.7383 (t80) REVERT: f 130 MET cc_start: 0.7926 (ptm) cc_final: 0.7631 (ptt) REVERT: f 167 ARG cc_start: 0.6784 (ttm-80) cc_final: 0.6547 (ttp-110) REVERT: g 29 LYS cc_start: 0.5263 (ttpt) cc_final: 0.4936 (tmtm) REVERT: g 69 ARG cc_start: 0.7115 (tmt170) cc_final: 0.6037 (tmt170) REVERT: g 130 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6583 (mm-30) REVERT: h 1 MET cc_start: 0.5342 (ptm) cc_final: 0.3542 (ttp) REVERT: i 12 LYS cc_start: 0.6334 (mmmm) cc_final: 0.6007 (mmmt) REVERT: i 43 GLU cc_start: 0.8172 (mp0) cc_final: 0.7775 (mp0) REVERT: i 60 ASP cc_start: 0.7899 (p0) cc_final: 0.7579 (p0) REVERT: i 106 LYS cc_start: 0.8066 (tttm) cc_final: 0.7472 (ttmm) REVERT: i 138 GLN cc_start: 0.7577 (pt0) cc_final: 0.7096 (mm-40) REVERT: j 7 MET cc_start: 0.8305 (mmm) cc_final: 0.7947 (mmm) REVERT: j 53 LYS cc_start: 0.7648 (pttp) cc_final: 0.7306 (ptmm) REVERT: j 111 LYS cc_start: 0.6513 (mtpp) cc_final: 0.6019 (mtmt) REVERT: j 114 LYS cc_start: 0.7002 (mtpp) cc_final: 0.6611 (tptt) REVERT: k 91 ASP cc_start: 0.7066 (p0) cc_final: 0.6820 (p0) REVERT: k 103 ILE cc_start: 0.7799 (mm) cc_final: 0.7545 (tp) REVERT: k 115 GLU cc_start: 0.6313 (OUTLIER) cc_final: 0.6068 (tp30) REVERT: k 126 ARG cc_start: 0.7484 (mtm180) cc_final: 0.7107 (mtp180) REVERT: l 10 ARG cc_start: 0.7391 (mtm-85) cc_final: 0.7057 (mtm110) REVERT: l 47 GLU cc_start: 0.7817 (tp30) cc_final: 0.7457 (tp30) REVERT: l 53 MET cc_start: 0.7948 (ptm) cc_final: 0.7470 (ptp) REVERT: l 78 LEU cc_start: 0.7822 (tp) cc_final: 0.7612 (tp) REVERT: l 90 GLU cc_start: 0.7545 (mm-30) cc_final: 0.6611 (mp0) REVERT: l 118 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7967 (tttm) REVERT: n 46 GLU cc_start: 0.6128 (tm-30) cc_final: 0.5712 (tm-30) REVERT: n 62 LEU cc_start: 0.7191 (mt) cc_final: 0.6905 (mt) REVERT: n 89 ASP cc_start: 0.7029 (t0) cc_final: 0.6677 (m-30) REVERT: n 116 GLN cc_start: 0.6596 (mm-40) cc_final: 0.6328 (mm110) REVERT: o 6 LYS cc_start: 0.6710 (ptpt) cc_final: 0.6123 (pptt) REVERT: o 9 GLU cc_start: 0.7283 (mt-10) cc_final: 0.6975 (mt-10) REVERT: o 10 GLN cc_start: 0.7071 (mt0) cc_final: 0.6437 (mt0) REVERT: o 38 LYS cc_start: 0.6607 (ptmt) cc_final: 0.6237 (pttt) REVERT: o 68 GLU cc_start: 0.6180 (mm-30) cc_final: 0.5784 (tm-30) REVERT: o 89 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.6853 (mmt180) REVERT: o 111 LYS cc_start: 0.7982 (ptmm) cc_final: 0.7199 (pttm) REVERT: q 6 GLN cc_start: 0.7834 (pt0) cc_final: 0.6866 (tm130) REVERT: q 40 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8255 (ttt) REVERT: q 48 LYS cc_start: 0.7684 (mttm) cc_final: 0.7251 (mtpt) REVERT: r 31 GLN cc_start: 0.6879 (mt0) cc_final: 0.6159 (pt0) REVERT: r 72 THR cc_start: 0.8088 (p) cc_final: 0.7802 (t) REVERT: r 92 ARG cc_start: 0.7445 (ttm-80) cc_final: 0.6632 (ttm110) REVERT: s 3 ARG cc_start: 0.6366 (mtm-85) cc_final: 0.5475 (mtp85) REVERT: s 18 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.6586 (mp0) REVERT: s 42 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6539 (mp0) REVERT: s 52 GLU cc_start: 0.5509 (mp0) cc_final: 0.5086 (tm-30) REVERT: t 8 ASP cc_start: 0.7325 (m-30) cc_final: 0.7100 (m-30) REVERT: u 12 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.6910 (mm-40) REVERT: u 38 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7638 (pt) REVERT: u 68 LYS cc_start: 0.6496 (ptmm) cc_final: 0.5611 (mppt) REVERT: w 62 LYS cc_start: 0.8245 (mtpt) cc_final: 0.7859 (mtpt) REVERT: w 71 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7561 (mp) REVERT: x 24 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6517 (tm-30) REVERT: x 58 ASN cc_start: 0.7095 (t0) cc_final: 0.6454 (m110) REVERT: y 11 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7867 (mtt90) REVERT: 0 32 GLU cc_start: 0.6305 (pm20) cc_final: 0.5990 (pm20) REVERT: 1 29 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7762 (mt0) REVERT: 1 42 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8219 (mp) REVERT: 2 15 LYS cc_start: 0.8284 (mmtm) cc_final: 0.7604 (mmmm) REVERT: 2 57 LEU cc_start: 0.7820 (mt) cc_final: 0.7544 (mp) REVERT: 3 30 GLU cc_start: 0.6896 (tp30) cc_final: 0.6470 (mt-10) REVERT: 4 2 LYS cc_start: 0.7112 (mttt) cc_final: 0.6705 (mttp) REVERT: 4 3 LYS cc_start: 0.6104 (mttp) cc_final: 0.5823 (ptpp) REVERT: 4 25 ARG cc_start: 0.6019 (mmm-85) cc_final: 0.5705 (mmt90) outliers start: 133 outliers final: 88 residues processed: 898 average time/residue: 2.3459 time to fit residues: 2935.0325 Evaluate side-chains 931 residues out of total 4576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 814 time to evaluate : 6.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 91 ARG Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 131 LYS Chi-restraints excluded: chain H residue 3 MET Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 88 LYS Chi-restraints excluded: chain M residue 62 LYS Chi-restraints excluded: chain M residue 105 ASN Chi-restraints excluded: chain N residue 80 SER Chi-restraints excluded: chain P residue 68 SER Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 72 SER Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 34 ARG Chi-restraints excluded: chain U residue 56 HIS Chi-restraints excluded: chain c residue 20 VAL Chi-restraints excluded: chain c residue 36 LYS Chi-restraints excluded: chain c residue 182 ARG Chi-restraints excluded: chain c residue 203 ARG Chi-restraints excluded: chain c residue 223 THR Chi-restraints excluded: chain d residue 7 LYS Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 74 GLU Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain d residue 99 GLU Chi-restraints excluded: chain d residue 157 LYS Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 13 THR Chi-restraints excluded: chain e residue 51 GLU Chi-restraints excluded: chain e residue 88 ARG Chi-restraints excluded: chain e residue 139 LYS Chi-restraints excluded: chain e residue 175 ILE Chi-restraints excluded: chain f residue 4 LEU Chi-restraints excluded: chain f residue 11 GLU Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 72 LYS Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain g residue 4 VAL Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 130 GLU Chi-restraints excluded: chain g residue 171 THR Chi-restraints excluded: chain h residue 3 VAL Chi-restraints excluded: chain i residue 7 LYS Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 90 GLU Chi-restraints excluded: chain j residue 28 SER Chi-restraints excluded: chain j residue 105 ARG Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 7 SER Chi-restraints excluded: chain k residue 46 VAL Chi-restraints excluded: chain k residue 115 GLU Chi-restraints excluded: chain k residue 121 THR Chi-restraints excluded: chain l residue 118 LYS Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain q residue 40 MET Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain r residue 27 LYS Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 95 ARG Chi-restraints excluded: chain s residue 18 GLU Chi-restraints excluded: chain s residue 42 GLU Chi-restraints excluded: chain s residue 55 VAL Chi-restraints excluded: chain u residue 12 GLN Chi-restraints excluded: chain u residue 38 LEU Chi-restraints excluded: chain w residue 40 VAL Chi-restraints excluded: chain w residue 71 LEU Chi-restraints excluded: chain x residue 16 THR Chi-restraints excluded: chain x residue 24 GLU Chi-restraints excluded: chain y residue 11 ARG Chi-restraints excluded: chain y residue 55 VAL Chi-restraints excluded: chain z residue 25 VAL Chi-restraints excluded: chain z residue 55 ILE Chi-restraints excluded: chain 1 residue 29 GLN Chi-restraints excluded: chain 1 residue 42 LEU Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 4 residue 1 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 481 optimal weight: 9.9990 chunk 623 optimal weight: 10.0000 chunk 836 optimal weight: 4.9990 chunk 240 optimal weight: 10.0000 chunk 724 optimal weight: 3.9990 chunk 115 optimal weight: 20.0000 chunk 218 optimal weight: 1.9990 chunk 786 optimal weight: 3.9990 chunk 329 optimal weight: 7.9990 chunk 807 optimal weight: 3.9990 chunk 99 optimal weight: 30.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 139 GLN D 74 ASN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN F 55 HIS G 142 HIS H 67 GLN ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN P 40 ASN c 163 GLN e 136 GLN ** g 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 88 ASN p 71 GLN r 61 ASN s 28 ASN s 48 GLN ** w 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 45 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.157608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.127215 restraints weight = 132003.869| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.31 r_work: 0.3068 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 154032 Z= 0.210 Angle : 0.713 14.420 230513 Z= 0.395 Chirality : 0.038 0.365 29296 Planarity : 0.007 0.138 12270 Dihedral : 23.034 179.970 77190 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.70 % Favored : 96.24 % Rotamer: Outliers : 2.82 % Allowed : 19.65 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.11), residues: 5480 helix: 1.10 (0.12), residues: 1891 sheet: -0.14 (0.15), residues: 1066 loop : -0.67 (0.12), residues: 2523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP c 248 HIS 0.006 0.001 HIS B 39 PHE 0.020 0.002 PHE F 8 TYR 0.031 0.002 TYR L 38 ARG 0.014 0.001 ARG g 149 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 43000.71 seconds wall clock time: 746 minutes 50.91 seconds (44810.91 seconds total)