Starting phenix.real_space_refine on Sat Feb 24 15:15:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cpj_30431/02_2024/7cpj_30431_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cpj_30431/02_2024/7cpj_30431.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cpj_30431/02_2024/7cpj_30431_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cpj_30431/02_2024/7cpj_30431_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cpj_30431/02_2024/7cpj_30431_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cpj_30431/02_2024/7cpj_30431.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cpj_30431/02_2024/7cpj_30431.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cpj_30431/02_2024/7cpj_30431_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cpj_30431/02_2024/7cpj_30431_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4639 5.49 5 S 155 5.16 5 C 73469 2.51 5 N 27181 2.21 5 O 40497 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 77": "OE1" <-> "OE2" Residue "b PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 107": "NH1" <-> "NH2" Residue "b ASP 126": "OD1" <-> "OD2" Residue "b ASP 152": "OD1" <-> "OD2" Residue "b ASP 158": "OD1" <-> "OD2" Residue "b ASP 164": "OD1" <-> "OD2" Residue "b ASP 196": "OD1" <-> "OD2" Residue "b ASP 203": "OD1" <-> "OD2" Residue "b ASP 204": "OD1" <-> "OD2" Residue "b ARG 224": "NH1" <-> "NH2" Residue "c PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 82": "OD1" <-> "OD2" Residue "c ARG 106": "NH1" <-> "NH2" Residue "c PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 130": "NH1" <-> "NH2" Residue "c GLU 165": "OE1" <-> "OE2" Residue "c ASP 182": "OD1" <-> "OD2" Residue "d TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 14": "OE1" <-> "OE2" Residue "d ASP 17": "OD1" <-> "OD2" Residue "d TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 98": "OD1" <-> "OD2" Residue "d TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 173": "OD1" <-> "OD2" Residue "d GLU 186": "OE1" <-> "OE2" Residue "e PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 141": "OD1" <-> "OD2" Residue "e GLU 150": "OE1" <-> "OE2" Residue "e ARG 156": "NH1" <-> "NH2" Residue "f GLU 5": "OE1" <-> "OE2" Residue "f TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 69": "OE1" <-> "OE2" Residue "f PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 82": "OD1" <-> "OD2" Residue "g ASP 32": "OD1" <-> "OD2" Residue "g TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 145": "OE1" <-> "OE2" Residue "h ASP 8": "OD1" <-> "OD2" Residue "h ASP 47": "OD1" <-> "OD2" Residue "h TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 35": "OE1" <-> "OE2" Residue "i PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 123": "NH1" <-> "NH2" Residue "j ASP 75": "OD1" <-> "OD2" Residue "j GLU 81": "OE1" <-> "OE2" Residue "j ASP 91": "OD1" <-> "OD2" Residue "k TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 93": "OE1" <-> "OE2" Residue "l GLU 24": "OE1" <-> "OE2" Residue "l ARG 55": "NH1" <-> "NH2" Residue "l ASP 102": "OD1" <-> "OD2" Residue "m TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 53": "OD1" <-> "OD2" Residue "n GLU 25": "OE1" <-> "OE2" Residue "n GLU 86": "OE1" <-> "OE2" Residue "o GLU 13": "OE1" <-> "OE2" Residue "o PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 28": "NH1" <-> "NH2" Residue "p ASP 53": "OD1" <-> "OD2" Residue "q PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 19": "OE1" <-> "OE2" Residue "r TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 71": "OD1" <-> "OD2" Residue "s ASP 11": "OD1" <-> "OD2" Residue "t GLU 39": "OE1" <-> "OE2" Residue "t PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 7": "OE1" <-> "OE2" Residue "u PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 120": "OD1" <-> "OD2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 186": "OD1" <-> "OD2" Residue "C GLU 193": "OE1" <-> "OE2" Residue "C PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D GLU 89": "OE1" <-> "OE2" Residue "D PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E TYR 35": "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 69": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ASP 116": "OD1" <-> "OD2" Residue "E GLU 122": "OE1" <-> "OE2" Residue "E PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 140": "OD1" <-> "OD2" Residue "E GLU 155": "OE1" <-> "OE2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "E ASP 191": "OD1" <-> "OD2" Residue "F TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 45": "OD1" <-> "OD2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 111": "NH1" <-> "NH2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "F ASP 143": "OD1" <-> "OD2" Residue "F PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 2": "NH1" <-> "NH2" Residue "G ASP 46": "OD1" <-> "OD2" Residue "G TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 59": "OD1" <-> "OD2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 162": "NH1" <-> "NH2" Residue "G ARG 169": "NH1" <-> "NH2" Residue "H GLU 87": "OE1" <-> "OE2" Residue "H ASP 98": "OD1" <-> "OD2" Residue "H PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 46": "OD1" <-> "OD2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ASP 19": "OD1" <-> "OD2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "K PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 80": "OD1" <-> "OD2" Residue "K GLU 121": "OE1" <-> "OE2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ASP 91": "OD1" <-> "OD2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 59": "NH1" <-> "NH2" Residue "M TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 106": "OD1" <-> "OD2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "M GLU 115": "OE1" <-> "OE2" Residue "M PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N ASP 58": "OD1" <-> "OD2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ARG 71": "NH1" <-> "NH2" Residue "N PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 117": "OD1" <-> "OD2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O ARG 25": "NH1" <-> "NH2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "O GLU 112": "OE1" <-> "OE2" Residue "P GLU 10": "OE1" <-> "OE2" Residue "P PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P ASP 23": "OD1" <-> "OD2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 61": "NH1" <-> "NH2" Residue "P ARG 88": "NH1" <-> "NH2" Residue "P ARG 100": "NH1" <-> "NH2" Residue "P ARG 108": "NH1" <-> "NH2" Residue "Q ARG 2": "NH1" <-> "NH2" Residue "Q ARG 5": "NH1" <-> "NH2" Residue "Q ARG 12": "NH1" <-> "NH2" Residue "Q TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 32": "NH1" <-> "NH2" Residue "Q ARG 47": "NH1" <-> "NH2" Residue "Q ARG 69": "NH1" <-> "NH2" Residue "Q ASP 101": "OD1" <-> "OD2" Residue "R PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 37": "OE1" <-> "OE2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "R PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 95": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T GLU 18": "OE1" <-> "OE2" Residue "T ARG 73": "NH1" <-> "NH2" Residue "T TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 5": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 81": "NH1" <-> "NH2" Residue "U ARG 85": "NH1" <-> "NH2" Residue "U ARG 93": "NH1" <-> "NH2" Residue "U PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 45": "OD1" <-> "OD2" Residue "W PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 64": "OD1" <-> "OD2" Residue "X TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 10": "NH1" <-> "NH2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "Z ARG 44": "NH1" <-> "NH2" Residue "0 ARG 9": "NH1" <-> "NH2" Residue "0 ARG 15": "NH1" <-> "NH2" Residue "0 ARG 39": "NH1" <-> "NH2" Residue "0 ARG 51": "NH1" <-> "NH2" Residue "1 PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 43": "NH1" <-> "NH2" Residue "1 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 3": "NH1" <-> "NH2" Residue "2 ARG 12": "NH1" <-> "NH2" Residue "2 ARG 14": "NH1" <-> "NH2" Residue "2 ARG 19": "NH1" <-> "NH2" Residue "2 ARG 21": "NH1" <-> "NH2" Residue "2 ARG 33": "NH1" <-> "NH2" Residue "2 ARG 41": "NH1" <-> "NH2" Residue "3 ARG 12": "NH1" <-> "NH2" Residue "3 PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 29": "NH1" <-> "NH2" Residue "3 ARG 39": "NH1" <-> "NH2" Residue "3 ARG 41": "NH1" <-> "NH2" Residue "4 ARG 12": "NH1" <-> "NH2" Residue "4 ARG 24": "NH1" <-> "NH2" Residue "5 TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 70": "OE1" <-> "OE2" Residue "5 PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 98": "OE1" <-> "OE2" Residue "5 PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 10": "OE1" <-> "OE2" Residue "6 GLU 11": "OE1" <-> "OE2" Residue "6 ARG 49": "NH1" <-> "NH2" Residue "6 ARG 56": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 145941 Number of models: 1 Model: "" Number of chains: 58 Chain: "a" Number of atoms: 33030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33030 Classifications: {'RNA': 1539} Modifications used: {'p5*END': 1, 'rna2p': 1, 'rna2p_pur': 94, 'rna2p_pyr': 52, 'rna3p': 11, 'rna3p_pur': 773, 'rna3p_pyr': 608} Link IDs: {'rna2p': 147, 'rna3p': 1391} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 7 Chain: "b" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1704 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "c" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 198} Chain: "d" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "e" Number of atoms: 1141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1141 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 151} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "f" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 817 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "g" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "h" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "i" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "j" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "k" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 869 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "l" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "m" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "n" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 799 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "o" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "p" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "r" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 504 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 62} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "s" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "t" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "u" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 495 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 62} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "A" Number of atoms: 62276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2900, 62276 Classifications: {'RNA': 2900} Modifications used: {'p5*END': 1, 'rna2p': 7, 'rna2p_pur': 228, 'rna2p_pyr': 107, 'rna3p': 17, 'rna3p_pur': 1438, 'rna3p_pyr': 1103} Link IDs: {'rna2p': 342, 'rna3p': 2557} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 10 Chain: "B" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2572 Classifications: {'RNA': 120} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 62, 'rna3p_pyr': 51} Link IDs: {'rna2p': 7, 'rna3p': 112} Chain: "C" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "F" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "H" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "I" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1032 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "0" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "1" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "2" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "3" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "4" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "5" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 988 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "6" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "9" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1646 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 33, 'rna3p_pyr': 31} Link IDs: {'rna2p': 13, 'rna3p': 63} Chain: "x" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna3p': 2} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Classifications: {'peptide': 1} Chain: "9" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Time building chain proxies: 55.39, per 1000 atoms: 0.38 Number of scatterers: 145941 At special positions: 0 Unit cell: (248.43, 235.2, 249.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 155 16.00 P 4639 15.00 O 40497 8.00 N 27181 7.00 C 73469 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 63.68 Conformation dependent library (CDL) restraints added in 6.9 seconds 11694 Ramachandran restraints generated. 5847 Oldfield, 0 Emsley, 5847 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10936 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: 184 helices and 69 sheets defined 39.2% alpha, 17.4% beta 1543 base pairs and 2401 stacking pairs defined. Time for finding SS restraints: 73.82 Creating SS restraints... Processing helix chain 'b' and resid 41 through 63 Proline residue: b 47 - end of helix Processing helix chain 'b' and resid 72 through 87 removed outlier: 6.468A pdb=" N SER b 76 " --> pdb=" O LYS b 72 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLU b 77 " --> pdb=" O ARG b 73 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ALA b 78 " --> pdb=" O ALA b 74 " (cutoff:3.500A) Processing helix chain 'b' and resid 102 through 122 removed outlier: 3.525A pdb=" N VAL b 106 " --> pdb=" O ASN b 102 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N GLN b 108 " --> pdb=" O LYS b 104 " (cutoff:3.500A) Processing helix chain 'b' and resid 129 through 147 Processing helix chain 'b' and resid 164 through 169 removed outlier: 4.113A pdb=" N HIS b 169 " --> pdb=" O ALA b 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 170 through 179 removed outlier: 3.725A pdb=" N LEU b 178 " --> pdb=" O GLU b 174 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLY b 179 " --> pdb=" O ALA b 175 " (cutoff:3.500A) Processing helix chain 'b' and resid 205 through 225 Processing helix chain 'c' and resid 5 through 11 removed outlier: 4.195A pdb=" N ARG c 10 " --> pdb=" O PRO c 6 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 47 Processing helix chain 'c' and resid 71 through 77 Processing helix chain 'c' and resid 80 through 95 Processing helix chain 'c' and resid 111 through 126 removed outlier: 3.643A pdb=" N ARG c 125 " --> pdb=" O SER c 121 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG c 126 " --> pdb=" O GLN c 122 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 144 Processing helix chain 'd' and resid 6 through 15 removed outlier: 4.248A pdb=" N LEU d 10 " --> pdb=" O PRO d 6 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N SER d 11 " --> pdb=" O LYS d 7 " (cutoff:3.500A) Processing helix chain 'd' and resid 48 through 65 Processing helix chain 'd' and resid 67 through 82 removed outlier: 5.076A pdb=" N LYS d 82 " --> pdb=" O ALA d 78 " (cutoff:3.500A) Processing helix chain 'd' and resid 84 through 96 Processing helix chain 'd' and resid 97 through 105 removed outlier: 3.865A pdb=" N GLY d 105 " --> pdb=" O VAL d 101 " (cutoff:3.500A) Processing helix chain 'd' and resid 109 through 120 removed outlier: 5.320A pdb=" N LYS d 120 " --> pdb=" O LEU d 116 " (cutoff:3.500A) Processing helix chain 'd' and resid 152 through 163 removed outlier: 5.244A pdb=" N ALA d 156 " --> pdb=" O SER d 152 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLN d 163 " --> pdb=" O GLU d 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 186 through 191 removed outlier: 4.073A pdb=" N LEU d 190 " --> pdb=" O GLU d 186 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N SER d 191 " --> pdb=" O ARG d 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 186 through 191' Processing helix chain 'd' and resid 195 through 205 Processing helix chain 'e' and resid 54 through 70 removed outlier: 3.786A pdb=" N MET e 70 " --> pdb=" O ALA e 66 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 118 removed outlier: 6.552A pdb=" N ALA e 112 " --> pdb=" O GLY e 108 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 146 Processing helix chain 'e' and resid 148 through 156 Processing helix chain 'e' and resid 159 through 165 Processing helix chain 'f' and resid 11 through 18 Processing helix chain 'f' and resid 19 through 33 Processing helix chain 'f' and resid 67 through 81 Processing helix chain 'g' and resid 19 through 30 Processing helix chain 'g' and resid 34 through 54 Processing helix chain 'g' and resid 56 through 69 removed outlier: 6.330A pdb=" N ASN g 67 " --> pdb=" O VAL g 63 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N VAL g 68 " --> pdb=" O ALA g 64 " (cutoff:3.500A) Processing helix chain 'g' and resid 91 through 111 removed outlier: 3.919A pdb=" N ARG g 110 " --> pdb=" O ALA g 106 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N GLY g 111 " --> pdb=" O ALA g 107 " (cutoff:3.500A) Processing helix chain 'g' and resid 114 through 129 Processing helix chain 'g' and resid 131 through 149 removed outlier: 3.958A pdb=" N GLU g 145 " --> pdb=" O HIS g 141 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ALA g 146 " --> pdb=" O ARG g 142 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASN g 147 " --> pdb=" O MET g 143 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LYS g 148 " --> pdb=" O ALA g 144 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ALA g 149 " --> pdb=" O GLU g 145 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 20 Processing helix chain 'h' and resid 29 through 43 Processing helix chain 'h' and resid 111 through 119 Processing helix chain 'i' and resid 33 through 38 Processing helix chain 'i' and resid 43 through 55 removed outlier: 5.168A pdb=" N VAL i 47 " --> pdb=" O ALA i 43 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG i 48 " --> pdb=" O ARG i 44 " (cutoff:3.500A) Proline residue: i 50 - end of helix removed outlier: 4.329A pdb=" N LEU i 53 " --> pdb=" O GLN i 49 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL i 54 " --> pdb=" O PRO i 50 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP i 55 " --> pdb=" O LEU i 51 " (cutoff:3.500A) Processing helix chain 'i' and resid 70 through 87 removed outlier: 4.460A pdb=" N MET i 87 " --> pdb=" O THR i 83 " (cutoff:3.500A) Processing helix chain 'i' and resid 90 through 101 removed outlier: 3.582A pdb=" N ARG i 94 " --> pdb=" O ASP i 90 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N GLU i 96 " --> pdb=" O SER i 92 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS i 99 " --> pdb=" O SER i 95 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 removed outlier: 4.122A pdb=" N ALA j 29 " --> pdb=" O ILE j 25 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N THR j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 removed outlier: 3.708A pdb=" N MET j 88 " --> pdb=" O VAL j 84 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ARG j 89 " --> pdb=" O ASP j 85 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU j 90 " --> pdb=" O ALA j 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 50 removed outlier: 4.516A pdb=" N GLY k 50 " --> pdb=" O ALA k 46 " (cutoff:3.500A) Processing helix chain 'k' and resid 53 through 59 removed outlier: 3.972A pdb=" N SER k 57 " --> pdb=" O GLY k 53 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N THR k 58 " --> pdb=" O SER k 54 " (cutoff:3.500A) Proline residue: k 59 - end of helix No H-bonds generated for 'chain 'k' and resid 53 through 59' Processing helix chain 'k' and resid 60 through 77 removed outlier: 4.832A pdb=" N ALA k 72 " --> pdb=" O ARG k 68 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL k 73 " --> pdb=" O CYS k 69 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS k 74 " --> pdb=" O ALA k 70 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLU k 75 " --> pdb=" O ASP k 71 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N TYR k 76 " --> pdb=" O ALA k 72 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY k 77 " --> pdb=" O VAL k 73 " (cutoff:3.500A) Processing helix chain 'k' and resid 91 through 103 removed outlier: 5.674A pdb=" N THR k 95 " --> pdb=" O GLY k 91 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ILE k 96 " --> pdb=" O ARG k 92 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLY k 103 " --> pdb=" O LEU k 99 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 10 Proline residue: l 10 - end of helix Processing helix chain 'l' and resid 112 through 117 removed outlier: 4.638A pdb=" N TYR l 116 " --> pdb=" O ALA l 112 " (cutoff:3.500A) Processing helix chain 'm' and resid 13 through 21 removed outlier: 4.720A pdb=" N ILE m 21 " --> pdb=" O ALA m 17 " (cutoff:3.500A) Processing helix chain 'm' and resid 25 through 37 Processing helix chain 'm' and resid 48 through 63 removed outlier: 3.584A pdb=" N ILE m 52 " --> pdb=" O SER m 48 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR m 54 " --> pdb=" O GLY m 50 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LYS m 61 " --> pdb=" O ASP m 57 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE m 62 " --> pdb=" O GLU m 58 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N VAL m 63 " --> pdb=" O VAL m 59 " (cutoff:3.500A) Processing helix chain 'm' and resid 65 through 83 Processing helix chain 'm' and resid 84 through 93 Processing helix chain 'm' and resid 105 through 110 Processing helix chain 'n' and resid 2 through 23 removed outlier: 5.515A pdb=" N ALA n 21 " --> pdb=" O ASP n 17 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LYS n 22 " --> pdb=" O LYS n 18 " (cutoff:3.500A) Processing helix chain 'n' and resid 24 through 32 removed outlier: 4.393A pdb=" N ILE n 30 " --> pdb=" O LEU n 26 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER n 31 " --> pdb=" O LYS n 27 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASP n 32 " --> pdb=" O ALA n 28 " (cutoff:3.500A) Processing helix chain 'n' and resid 38 through 51 removed outlier: 4.001A pdb=" N TRP n 42 " --> pdb=" O ASP n 38 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU n 51 " --> pdb=" O LYS n 47 " (cutoff:3.500A) Processing helix chain 'n' and resid 80 through 91 removed outlier: 4.013A pdb=" N ARG n 90 " --> pdb=" O GLU n 86 " (cutoff:3.500A) Processing helix chain 'o' and resid 3 through 15 Processing helix chain 'o' and resid 23 through 46 removed outlier: 4.422A pdb=" N GLY o 40 " --> pdb=" O ASN o 36 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N HIS o 41 " --> pdb=" O HIS o 37 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N HIS o 45 " --> pdb=" O HIS o 41 " (cutoff:3.500A) Processing helix chain 'o' and resid 48 through 73 Processing helix chain 'o' and resid 74 through 85 Processing helix chain 'p' and resid 53 through 64 Processing helix chain 'p' and resid 68 through 79 Processing helix chain 'r' and resid 11 through 16 removed outlier: 4.679A pdb=" N GLU r 15 " --> pdb=" O ARG r 11 " (cutoff:3.500A) Processing helix chain 'r' and resid 24 through 33 removed outlier: 5.241A pdb=" N ASN r 30 " --> pdb=" O ALA r 26 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TYR r 31 " --> pdb=" O THR r 27 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE r 32 " --> pdb=" O LEU r 28 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N THR r 33 " --> pdb=" O LYS r 29 " (cutoff:3.500A) Processing helix chain 'r' and resid 40 through 45 Processing helix chain 'r' and resid 47 through 65 Processing helix chain 's' and resid 11 through 25 Processing helix chain 's' and resid 69 through 75 removed outlier: 4.280A pdb=" N PHE s 73 " --> pdb=" O LYS s 69 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ALA s 74 " --> pdb=" O LEU s 70 " (cutoff:3.500A) Proline residue: s 75 - end of helix No H-bonds generated for 'chain 's' and resid 69 through 75' Processing helix chain 't' and resid 6 through 41 removed outlier: 4.875A pdb=" N ALA t 10 " --> pdb=" O ALA t 6 " (cutoff:3.500A) Processing helix chain 't' and resid 43 through 64 Proline residue: t 55 - end of helix Processing helix chain 't' and resid 67 through 86 removed outlier: 5.748A pdb=" N ALA t 71 " --> pdb=" O HIS t 67 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA t 72 " --> pdb=" O LYS t 68 " (cutoff:3.500A) Processing helix chain 'u' and resid 16 through 22 removed outlier: 3.823A pdb=" N ARG u 20 " --> pdb=" O ARG u 16 " (cutoff:3.500A) Processing helix chain 'u' and resid 26 through 31 removed outlier: 5.364A pdb=" N GLU u 30 " --> pdb=" O GLY u 26 " (cutoff:3.500A) Processing helix chain 'u' and resid 38 through 61 removed outlier: 3.695A pdb=" N THR u 42 " --> pdb=" O GLU u 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 15 removed outlier: 7.137A pdb=" N HIS C 14 " --> pdb=" O PRO C 10 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL C 15 " --> pdb=" O GLY C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 removed outlier: 4.147A pdb=" N LEU C 33 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N GLU C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 29 through 34' Processing helix chain 'C' and resid 130 through 135 removed outlier: 3.612A pdb=" N ILE C 134 " --> pdb=" O PRO C 130 " (cutoff:3.500A) Proline residue: C 135 - end of helix No H-bonds generated for 'chain 'C' and resid 130 through 135' Processing helix chain 'C' and resid 206 through 214 removed outlier: 4.222A pdb=" N ALA C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 225 removed outlier: 4.104A pdb=" N MET C 224 " --> pdb=" O ARG C 220 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ASN C 225 " --> pdb=" O GLY C 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 220 through 225' Processing helix chain 'C' and resid 259 through 267 removed outlier: 6.258A pdb=" N ASP C 263 " --> pdb=" O ASN C 259 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LYS C 264 " --> pdb=" O LYS C 260 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N PHE C 265 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE C 266 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N VAL C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 259 through 267' Processing helix chain 'C' and resid 196 through 201 removed outlier: 4.391A pdb=" N MET C 200 " --> pdb=" O ALA C 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 72 Processing helix chain 'D' and resid 98 through 105 removed outlier: 4.412A pdb=" N ALA D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ASP D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VAL D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LYS D 105 " --> pdb=" O PHE D 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 98 through 105' Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 120 through 126 removed outlier: 4.159A pdb=" N TRP D 125 " --> pdb=" O GLY D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 41 removed outlier: 5.513A pdb=" N GLN E 41 " --> pdb=" O ALA E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 53 removed outlier: 7.048A pdb=" N THR E 53 " --> pdb=" O ARG E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 116 Processing helix chain 'E' and resid 130 through 142 Processing helix chain 'E' and resid 154 through 165 removed outlier: 4.877A pdb=" N ASN E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LEU E 164 " --> pdb=" O ALA E 160 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N HIS E 165 " --> pdb=" O ALA E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 Processing helix chain 'E' and resid 189 through 201 Processing helix chain 'F' and resid 1 through 20 removed outlier: 5.020A pdb=" N VAL F 12 " --> pdb=" O LYS F 8 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLU F 18 " --> pdb=" O LYS F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 46 removed outlier: 3.809A pdb=" N LYS F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 61 removed outlier: 4.274A pdb=" N ASN F 51 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA F 57 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLY F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 110 removed outlier: 3.780A pdb=" N ILE F 105 " --> pdb=" O ARG F 101 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N VAL F 107 " --> pdb=" O ILE F 103 " (cutoff:3.500A) Proline residue: F 108 - end of helix Processing helix chain 'F' and resid 161 through 173 removed outlier: 3.590A pdb=" N LEU F 168 " --> pdb=" O GLU F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 138 Proline residue: F 138 - end of helix Processing helix chain 'G' and resid 1 through 7 removed outlier: 4.392A pdb=" N ALA G 6 " --> pdb=" O ARG G 2 " (cutoff:3.500A) Proline residue: G 7 - end of helix Processing helix chain 'G' and resid 59 through 80 Processing helix chain 'G' and resid 136 through 152 removed outlier: 4.766A pdb=" N ARG G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 28 Processing helix chain 'H' and resid 29 through 34 Processing helix chain 'H' and resid 40 through 49 removed outlier: 5.624A pdb=" N ILE H 44 " --> pdb=" O THR H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 72 removed outlier: 3.868A pdb=" N ALA H 56 " --> pdb=" O ALA H 52 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LYS H 57 " --> pdb=" O GLU H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 107 removed outlier: 4.132A pdb=" N ILE H 99 " --> pdb=" O GLY H 95 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 29 removed outlier: 4.531A pdb=" N LEU I 27 " --> pdb=" O VAL I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 49 removed outlier: 4.964A pdb=" N CYS I 38 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS I 39 " --> pdb=" O MET I 35 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N PHE I 41 " --> pdb=" O PHE I 37 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ASN I 42 " --> pdb=" O CYS I 38 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ALA I 43 " --> pdb=" O LYS I 39 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LYS I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N THR I 45 " --> pdb=" O PHE I 41 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER I 47 " --> pdb=" O ALA I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 83 removed outlier: 4.335A pdb=" N LYS I 80 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LYS I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ALA I 83 " --> pdb=" O LEU I 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 113 removed outlier: 4.269A pdb=" N THR I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LYS I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ALA I 113 " --> pdb=" O ALA I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 136 removed outlier: 4.050A pdb=" N MET I 124 " --> pdb=" O ASP I 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.320A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 122 removed outlier: 3.560A pdb=" N ARG J 120 " --> pdb=" O ARG J 116 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 109 removed outlier: 4.290A pdb=" N ARG K 108 " --> pdb=" O THR K 104 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N SER K 109 " --> pdb=" O ARG K 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 104 through 109' Processing helix chain 'K' and resid 112 through 119 Processing helix chain 'L' and resid 37 through 42 removed outlier: 3.620A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N SER L 42 " --> pdb=" O GLN L 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 37 through 42' Processing helix chain 'L' and resid 56 through 62 Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 4.260A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 68 through 75' Processing helix chain 'L' and resid 78 through 86 removed outlier: 4.318A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N GLU L 86 " --> pdb=" O LEU L 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 86' Processing helix chain 'L' and resid 91 through 99 removed outlier: 4.227A pdb=" N LEU L 95 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS L 96 " --> pdb=" O LEU L 92 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ALA L 97 " --> pdb=" O ASN L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 139 removed outlier: 5.474A pdb=" N ARG L 132 " --> pdb=" O THR L 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 58 removed outlier: 3.992A pdb=" N ALA M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 125 Proline residue: M 125 - end of helix Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 38 through 56 removed outlier: 4.383A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 59 through 71 removed outlier: 4.570A pdb=" N THR N 70 " --> pdb=" O ALA N 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 88 removed outlier: 4.717A pdb=" N PHE N 80 " --> pdb=" O VAL N 76 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LEU N 83 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLY N 84 " --> pdb=" O PHE N 80 " (cutoff:3.500A) Proline residue: N 85 - end of helix Processing helix chain 'O' and resid 2 through 22 removed outlier: 4.395A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 62 removed outlier: 4.031A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 Processing helix chain 'O' and resid 101 through 114 Processing helix chain 'P' and resid 1 through 12 removed outlier: 4.511A pdb=" N GLN P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 103 removed outlier: 4.599A pdb=" N ARG P 100 " --> pdb=" O LEU P 96 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N GLU P 101 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N THR P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 96 through 103' Processing helix chain 'Q' and resid 5 through 21 removed outlier: 4.169A pdb=" N LYS Q 21 " --> pdb=" O LEU Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 removed outlier: 4.174A pdb=" N ARG Q 29 " --> pdb=" O GLY Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 31 through 36 Processing helix chain 'Q' and resid 38 through 72 removed outlier: 4.457A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 86 Processing helix chain 'Q' and resid 90 through 101 Processing helix chain 'Q' and resid 102 through 117 Processing helix chain 'S' and resid 13 through 25 removed outlier: 4.669A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 Processing helix chain 'S' and resid 41 through 61 Processing helix chain 'S' and resid 65 through 70 removed outlier: 4.306A pdb=" N LEU S 69 " --> pdb=" O ASP S 65 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LYS S 70 " --> pdb=" O ILE S 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 65 through 70' Processing helix chain 'T' and resid 1 through 11 removed outlier: 4.419A pdb=" N GLU T 5 " --> pdb=" O MET T 1 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 27 Processing helix chain 'T' and resid 39 through 51 removed outlier: 4.227A pdb=" N PHE T 51 " --> pdb=" O VAL T 47 " (cutoff:3.500A) Processing helix chain 'U' and resid 65 through 70 removed outlier: 4.013A pdb=" N VAL U 69 " --> pdb=" O GLN U 65 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ALA U 70 " --> pdb=" O VAL U 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 65 through 70' Processing helix chain 'V' and resid 13 through 24 removed outlier: 3.725A pdb=" N ASN V 24 " --> pdb=" O LEU V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 53 removed outlier: 3.696A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LYS V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 59 Processing helix chain 'X' and resid 51 through 62 removed outlier: 3.947A pdb=" N GLY X 62 " --> pdb=" O ILE X 58 " (cutoff:3.500A) Processing helix chain 'X' and resid 63 through 74 Processing helix chain 'Y' and resid 1 through 7 removed outlier: 4.328A pdb=" N LEU Y 6 " --> pdb=" O LYS Y 2 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ARG Y 7 " --> pdb=" O ALA Y 3 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 23 Processing helix chain 'Y' and resid 25 through 35 Processing helix chain 'Y' and resid 39 through 62 removed outlier: 4.556A pdb=" N LEU Y 43 " --> pdb=" O GLN Y 39 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N GLY Y 62 " --> pdb=" O ASN Y 58 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 51 Processing helix chain '0' and resid 8 through 18 removed outlier: 4.926A pdb=" N HIS 0 18 " --> pdb=" O MET 0 14 " (cutoff:3.500A) Processing helix chain '1' and resid 25 through 30 Proline residue: 1 30 - end of helix Processing helix chain '2' and resid 8 through 16 Processing helix chain '2' and resid 17 through 24 removed outlier: 4.276A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) Processing helix chain '2' and resid 25 through 38 Processing helix chain '3' and resid 6 through 13 removed outlier: 3.808A pdb=" N LYS 3 11 " --> pdb=" O ARG 3 7 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG 3 12 " --> pdb=" O GLY 3 8 " (cutoff:3.500A) Processing helix chain '3' and resid 31 through 36 removed outlier: 4.611A pdb=" N LYS 3 35 " --> pdb=" O ILE 3 31 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ALA 3 36 " --> pdb=" O LEU 3 32 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 31 through 36' Processing helix chain '3' and resid 37 through 45 Proline residue: 3 45 - end of helix Processing helix chain '3' and resid 50 through 62 removed outlier: 5.021A pdb=" N GLY 3 55 " --> pdb=" O LYS 3 51 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LEU 3 56 " --> pdb=" O GLY 3 52 " (cutoff:3.500A) Proline residue: 3 62 - end of helix Processing helix chain '4' and resid 30 through 35 removed outlier: 4.393A pdb=" N LYS 4 34 " --> pdb=" O GLU 4 30 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N GLN 4 35 " --> pdb=" O PRO 4 31 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 30 through 35' Processing helix chain '5' and resid 3 through 21 removed outlier: 4.361A pdb=" N LYS 5 20 " --> pdb=" O SER 5 16 " (cutoff:3.500A) Processing helix chain '5' and resid 33 through 48 removed outlier: 3.615A pdb=" N ARG 5 42 " --> pdb=" O MET 5 38 " (cutoff:3.500A) Processing helix chain '5' and resid 59 through 69 removed outlier: 3.968A pdb=" N VAL 5 64 " --> pdb=" O LEU 5 60 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU 5 65 " --> pdb=" O ARG 5 61 " (cutoff:3.500A) Proline residue: 5 68 - end of helix Processing helix chain '5' and resid 94 through 106 removed outlier: 3.760A pdb=" N ALA 5 100 " --> pdb=" O PHE 5 96 " (cutoff:3.500A) Processing helix chain '5' and resid 71 through 78 removed outlier: 3.511A pdb=" N ASP 5 74 " --> pdb=" O CYS 5 71 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA 5 75 " --> pdb=" O LEU 5 72 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N PHE 5 76 " --> pdb=" O LYS 5 73 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY 5 78 " --> pdb=" O ALA 5 75 " (cutoff:3.500A) Processing helix chain '6' and resid 42 through 53 removed outlier: 4.986A pdb=" N GLN 6 48 " --> pdb=" O PHE 6 44 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR 6 53 " --> pdb=" O ARG 6 49 " (cutoff:3.500A) Processing helix chain '6' and resid 55 through 65 removed outlier: 4.696A pdb=" N ARG 6 59 " --> pdb=" O GLY 6 55 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'b' and resid 30 through 33 Processing sheet with id= 2, first strand: chain 'b' and resid 66 through 70 removed outlier: 4.174A pdb=" N PHE b 197 " --> pdb=" O VAL b 182 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'c' and resid 52 through 58 Processing sheet with id= 4, first strand: chain 'c' and resid 163 through 169 removed outlier: 3.584A pdb=" N GLY c 147 " --> pdb=" O PHE c 202 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ASP c 180 " --> pdb=" O LYS c 203 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'd' and resid 140 through 144 removed outlier: 3.884A pdb=" N ASP d 140 " --> pdb=" O PHE d 181 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL d 142 " --> pdb=" O GLY d 179 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N MET d 177 " --> pdb=" O ILE d 144 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLU d 178 " --> pdb=" O ASP d 173 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'e' and resid 12 through 15 removed outlier: 6.699A pdb=" N LEU e 35 " --> pdb=" O ILE e 15 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ILE e 29 " --> pdb=" O LYS e 22 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA e 16 " --> pdb=" O LEU e 35 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'e' and resid 82 through 87 removed outlier: 7.094A pdb=" N HIS e 82 " --> pdb=" O PRO e 97 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL e 93 " --> pdb=" O GLY e 86 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N TYR e 127 " --> pdb=" O ARG e 92 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU e 123 " --> pdb=" O GLN e 96 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'e' and resid 32 through 39 removed outlier: 4.549A pdb=" N GLY e 50 " --> pdb=" O ALA e 34 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'f' and resid 38 through 43 removed outlier: 5.882A pdb=" N ILE f 6 " --> pdb=" O MET f 62 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU f 5 " --> pdb=" O MET f 90 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ARG f 86 " --> pdb=" O MET f 9 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'g' and resid 71 through 76 No H-bonds generated for sheet with id= 10 Processing sheet with id= 11, first strand: chain 'h' and resid 22 through 28 removed outlier: 6.209A pdb=" N ALA h 22 " --> pdb=" O LEU h 62 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER h 28 " --> pdb=" O PRO h 56 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU h 51 " --> pdb=" O GLU h 57 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'h' and resid 73 through 76 removed outlier: 6.641A pdb=" N VAL h 102 " --> pdb=" O ILE h 125 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'i' and resid 4 through 10 removed outlier: 4.604A pdb=" N GLY i 9 " --> pdb=" O ALA i 16 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS i 26 " --> pdb=" O LEU i 60 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'j' and resid 39 through 42 removed outlier: 4.863A pdb=" N LEU j 42 " --> pdb=" O LEU j 71 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU j 71 " --> pdb=" O LEU j 42 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE j 8 " --> pdb=" O VAL j 74 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'j' and resid 44 through 52 Processing sheet with id= 16, first strand: chain 'k' and resid 30 through 34 Processing sheet with id= 17, first strand: chain 'l' and resid 28 through 31 removed outlier: 5.037A pdb=" N LEU l 80 " --> pdb=" O VAL l 97 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'l' and resid 35 through 40 removed outlier: 4.510A pdb=" N ARG l 35 " --> pdb=" O ARG l 53 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LYS l 50 " --> pdb=" O ILE l 66 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'p' and resid 4 through 10 removed outlier: 5.860A pdb=" N GLN p 18 " --> pdb=" O ALA p 7 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLY p 37 " --> pdb=" O VAL p 19 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'q' and resid 6 through 10 removed outlier: 6.897A pdb=" N GLU q 59 " --> pdb=" O VAL q 75 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'q' and resid 18 through 29 No H-bonds generated for sheet with id= 21 Processing sheet with id= 22, first strand: chain 's' and resid 29 through 33 removed outlier: 3.703A pdb=" N LEU s 30 " --> pdb=" O THR s 47 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU s 46 " --> pdb=" O VAL s 61 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'C' and resid 1 through 4 removed outlier: 3.943A pdb=" N ALA C 1 " --> pdb=" O VAL C 19 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'C' and resid 74 through 77 removed outlier: 4.560A pdb=" N ASP C 113 " --> pdb=" O VAL C 77 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'C' and resid 79 through 82 removed outlier: 5.513A pdb=" N ASN C 89 " --> pdb=" O ALA C 105 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'C' and resid 161 through 164 removed outlier: 6.902A pdb=" N THR C 172 " --> pdb=" O VAL C 164 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'D' and resid 3 through 6 Processing sheet with id= 28, first strand: chain 'D' and resid 11 through 16 removed outlier: 4.672A pdb=" N VAL D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'D' and resid 79 through 84 removed outlier: 5.867A pdb=" N ARG D 46 " --> pdb=" O LEU D 84 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLN D 94 " --> pdb=" O VAL D 34 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'E' and resid 1 through 6 removed outlier: 4.146A pdb=" N LEU E 5 " --> pdb=" O SER E 10 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N SER E 10 " --> pdb=" O LEU E 5 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'E' and resid 117 through 120 removed outlier: 5.423A pdb=" N ARG E 117 " --> pdb=" O ASP E 184 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP E 168 " --> pdb=" O VAL E 146 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'F' and resid 64 through 68 removed outlier: 3.730A pdb=" N GLY F 85 " --> pdb=" O THR F 67 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLY F 38 " --> pdb=" O GLY F 150 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N GLY F 150 " --> pdb=" O GLY F 38 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLY F 125 " --> pdb=" O THR F 157 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'G' and resid 21 through 26 removed outlier: 6.188A pdb=" N GLN G 21 " --> pdb=" O LEU G 36 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU G 36 " --> pdb=" O GLN G 21 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'G' and resid 40 through 45 removed outlier: 4.282A pdb=" N ALA G 45 " --> pdb=" O THR G 48 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'G' and resid 94 through 97 removed outlier: 7.237A pdb=" N ASN G 100 " --> pdb=" O LEU G 116 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'G' and resid 128 through 135 removed outlier: 5.912A pdb=" N THR G 128 " --> pdb=" O LEU G 88 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'H' and resid 3 through 6 removed outlier: 6.802A pdb=" N LYS H 35 " --> pdb=" O LEU H 6 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'H' and resid 76 through 81 Processing sheet with id= 39, first strand: chain 'H' and resid 114 through 117 removed outlier: 5.656A pdb=" N GLU H 114 " --> pdb=" O GLN H 133 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'J' and resid 52 through 57 removed outlier: 4.994A pdb=" N ASP J 19 " --> pdb=" O LEU J 140 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'J' and resid 74 through 78 removed outlier: 7.169A pdb=" N GLY J 83 " --> pdb=" O THR J 78 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'K' and resid 18 through 21 removed outlier: 4.264A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'K' and resid 38 through 41 Processing sheet with id= 44, first strand: chain 'M' and resid 62 through 65 removed outlier: 3.773A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LYS M 100 " --> pdb=" O ALA M 35 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'M' and resid 30 through 36 removed outlier: 7.366A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'N' and resid 33 through 37 removed outlier: 4.071A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'O' and resid 49 through 52 removed outlier: 4.024A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'P' and resid 48 through 52 removed outlier: 3.668A pdb=" N ALA P 48 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ARG P 52 " --> pdb=" O HIS P 55 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR P 59 " --> pdb=" O ILE P 47 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR P 24 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER P 82 " --> pdb=" O LYS P 28 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'P' and resid 57 through 63 Processing sheet with id= 50, first strand: chain 'R' and resid 11 through 15 Processing sheet with id= 51, first strand: chain 'R' and resid 18 through 23 removed outlier: 3.798A pdb=" N GLN R 18 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N GLU R 31 " --> pdb=" O VAL R 63 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'R' and resid 57 through 60 Processing sheet with id= 53, first strand: chain 'R' and resid 68 through 78 No H-bonds generated for sheet with id= 53 Processing sheet with id= 54, first strand: chain 'S' and resid 3 through 8 removed outlier: 4.515A pdb=" N THR S 3 " --> pdb=" O VAL S 107 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N THR S 100 " --> pdb=" O GLY S 79 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'S' and resid 81 through 88 removed outlier: 3.844A pdb=" N ARG S 92 " --> pdb=" O ARG S 88 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'T' and resid 28 through 33 removed outlier: 6.502A pdb=" N ASN T 28 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'U' and resid 39 through 44 No H-bonds generated for sheet with id= 57 Processing sheet with id= 58, first strand: chain 'U' and resid 82 through 85 Processing sheet with id= 59, first strand: chain 'V' and resid 69 through 72 Processing sheet with id= 60, first strand: chain 'W' and resid 47 through 50 removed outlier: 4.387A pdb=" N THR W 54 " --> pdb=" O GLY W 50 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'W' and resid 63 through 67 Processing sheet with id= 62, first strand: chain 'X' and resid 10 through 18 No H-bonds generated for sheet with id= 62 Processing sheet with id= 63, first strand: chain 'X' and resid 34 through 40 Processing sheet with id= 64, first strand: chain 'Z' and resid 32 through 38 removed outlier: 4.278A pdb=" N HIS Z 33 " --> pdb=" O GLN Z 8 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS Z 5 " --> pdb=" O GLU Z 57 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N MET Z 53 " --> pdb=" O THR Z 9 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain '1' and resid 18 through 23 removed outlier: 6.228A pdb=" N HIS 1 18 " --> pdb=" O SER 1 12 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LEU 1 33 " --> pdb=" O GLU 1 50 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain '3' and resid 21 through 24 removed outlier: 5.304A pdb=" N PHE 3 21 " --> pdb=" O VAL 3 49 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain '4' and resid 13 through 19 removed outlier: 8.358A pdb=" N ASN 4 13 " --> pdb=" O SER 4 28 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain '5' and resid 22 through 28 removed outlier: 4.297A pdb=" N LEU 5 23 " --> pdb=" O GLU 5 87 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLU 5 87 " --> pdb=" O LEU 5 23 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain '6' and resid 20 through 25 removed outlier: 4.671A pdb=" N ASN 6 20 " --> pdb=" O CYS 6 16 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N CYS 6 16 " --> pdb=" O ASN 6 20 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N HIS 6 30 " --> pdb=" O GLU 6 11 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR 6 13 " --> pdb=" O HIS 6 30 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU 6 32 " --> pdb=" O THR 6 13 " (cutoff:3.500A) 1879 hydrogen bonds defined for protein. 5529 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3883 hydrogen bonds 6064 hydrogen bond angles 0 basepair planarities 1543 basepair parallelities 2401 stacking parallelities Total time for adding SS restraints: 227.03 Time building geometry restraints manager: 68.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 11974 1.28 - 1.42: 65213 1.42 - 1.55: 71759 1.55 - 1.68: 9284 1.68 - 1.81: 277 Bond restraints: 158507 Sorted by residual: bond pdb=" C5 5MU A1939 " pdb=" C6 5MU A1939 " ideal model delta sigma weight residual 1.155 1.443 -0.288 2.00e-02 2.50e+03 2.08e+02 bond pdb=" C4 5MU A1939 " pdb=" C5 5MU A1939 " ideal model delta sigma weight residual 1.802 1.604 0.198 2.00e-02 2.50e+03 9.80e+01 bond pdb=" N1 H2U A2449 " pdb=" C2 H2U A2449 " ideal model delta sigma weight residual 1.482 1.302 0.180 2.00e-02 2.50e+03 8.09e+01 bond pdb=" C8 G7M a 527 " pdb=" N7 G7M a 527 " ideal model delta sigma weight residual 1.348 1.515 -0.167 2.00e-02 2.50e+03 6.96e+01 bond pdb=" C2 H2U A2449 " pdb=" N3 H2U A2449 " ideal model delta sigma weight residual 1.483 1.317 0.166 2.00e-02 2.50e+03 6.90e+01 ... (remaining 158502 not shown) Histogram of bond angle deviations from ideal: 95.71 - 106.93: 31496 106.93 - 118.16: 119828 118.16 - 129.38: 81569 129.38 - 140.60: 4093 140.60 - 151.83: 4 Bond angle restraints: 236990 Sorted by residual: angle pdb=" C1' OMG A2251 " pdb=" N9 OMG A2251 " pdb=" C8 OMG A2251 " ideal model delta sigma weight residual 142.82 106.86 35.96 3.00e+00 1.11e-01 1.44e+02 angle pdb=" C1' OMG A2251 " pdb=" N9 OMG A2251 " pdb=" C4 OMG A2251 " ideal model delta sigma weight residual 108.29 143.41 -35.12 3.00e+00 1.11e-01 1.37e+02 angle pdb=" C1' G7M A2069 " pdb=" N9 G7M A2069 " pdb=" C8 G7M A2069 " ideal model delta sigma weight residual 94.96 128.27 -33.31 3.00e+00 1.11e-01 1.23e+02 angle pdb=" C1' G7M a 527 " pdb=" N9 G7M a 527 " pdb=" C8 G7M a 527 " ideal model delta sigma weight residual 94.96 127.51 -32.55 3.00e+00 1.11e-01 1.18e+02 angle pdb=" C1' G7M a1405 " pdb=" N9 G7M a1405 " pdb=" C8 G7M a1405 " ideal model delta sigma weight residual 94.96 125.81 -30.85 3.00e+00 1.11e-01 1.06e+02 ... (remaining 236985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 89224 35.80 - 71.60: 10913 71.60 - 107.40: 1242 107.40 - 143.19: 26 143.19 - 178.99: 27 Dihedral angle restraints: 101432 sinusoidal: 84485 harmonic: 16947 Sorted by residual: dihedral pdb=" CA THR q 69 " pdb=" C THR q 69 " pdb=" N LYS q 70 " pdb=" CA LYS q 70 " ideal model delta harmonic sigma weight residual -180.00 -125.62 -54.38 0 5.00e+00 4.00e-02 1.18e+02 dihedral pdb=" CA LEU l 101 " pdb=" C LEU l 101 " pdb=" N ASP l 102 " pdb=" CA ASP l 102 " ideal model delta harmonic sigma weight residual 180.00 -126.04 -53.96 0 5.00e+00 4.00e-02 1.16e+02 dihedral pdb=" CA HIS 3 30 " pdb=" C HIS 3 30 " pdb=" N ILE 3 31 " pdb=" CA ILE 3 31 " ideal model delta harmonic sigma weight residual 180.00 -129.80 -50.20 0 5.00e+00 4.00e-02 1.01e+02 ... (remaining 101429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 27035 0.079 - 0.158: 2887 0.158 - 0.236: 226 0.236 - 0.315: 33 0.315 - 0.394: 12 Chirality restraints: 30193 Sorted by residual: chirality pdb=" C3' G A2391 " pdb=" C4' G A2391 " pdb=" O3' G A2391 " pdb=" C2' G A2391 " both_signs ideal model delta sigma weight residual False -2.74 -2.35 -0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" C3' G a 380 " pdb=" C4' G a 380 " pdb=" O3' G a 380 " pdb=" C2' G a 380 " both_signs ideal model delta sigma weight residual False -2.48 -2.10 -0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" C3' C a1399 " pdb=" C4' C a1399 " pdb=" O3' C a1399 " pdb=" C2' C a1399 " both_signs ideal model delta sigma weight residual False -2.74 -2.38 -0.36 2.00e-01 2.50e+01 3.30e+00 ... (remaining 30190 not shown) Planarity restraints: 12798 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a1516 " -0.083 2.00e-02 2.50e+03 6.14e-01 8.49e+03 pdb=" C4' 2MG a1516 " -0.444 2.00e-02 2.50e+03 pdb=" O4' 2MG a1516 " -0.606 2.00e-02 2.50e+03 pdb=" C3' 2MG a1516 " 0.596 2.00e-02 2.50e+03 pdb=" O3' 2MG a1516 " 0.688 2.00e-02 2.50e+03 pdb=" C2' 2MG a1516 " 0.153 2.00e-02 2.50e+03 pdb=" O2' 2MG a1516 " -1.025 2.00e-02 2.50e+03 pdb=" C1' 2MG a1516 " -0.215 2.00e-02 2.50e+03 pdb=" N9 2MG a1516 " 0.936 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A2445 " -0.065 2.00e-02 2.50e+03 5.96e-01 7.99e+03 pdb=" C4' 2MG A2445 " -0.459 2.00e-02 2.50e+03 pdb=" O4' 2MG A2445 " -0.658 2.00e-02 2.50e+03 pdb=" C3' 2MG A2445 " 0.586 2.00e-02 2.50e+03 pdb=" O3' 2MG A2445 " 0.624 2.00e-02 2.50e+03 pdb=" C2' 2MG A2445 " 0.202 2.00e-02 2.50e+03 pdb=" O2' 2MG A2445 " -0.942 2.00e-02 2.50e+03 pdb=" C1' 2MG A2445 " -0.207 2.00e-02 2.50e+03 pdb=" N9 2MG A2445 " 0.919 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a1207 " -0.064 2.00e-02 2.50e+03 5.93e-01 7.92e+03 pdb=" C4' 2MG a1207 " -0.439 2.00e-02 2.50e+03 pdb=" O4' 2MG a1207 " -0.597 2.00e-02 2.50e+03 pdb=" C3' 2MG a1207 " 0.594 2.00e-02 2.50e+03 pdb=" O3' 2MG a1207 " 0.643 2.00e-02 2.50e+03 pdb=" C2' 2MG a1207 " 0.179 2.00e-02 2.50e+03 pdb=" O2' 2MG a1207 " -0.990 2.00e-02 2.50e+03 pdb=" C1' 2MG a1207 " -0.216 2.00e-02 2.50e+03 pdb=" N9 2MG a1207 " 0.889 2.00e-02 2.50e+03 ... (remaining 12795 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.07: 10 2.07 - 2.77: 32076 2.77 - 3.48: 196137 3.48 - 4.19: 473538 4.19 - 4.90: 651801 Nonbonded interactions: 1353562 Sorted by model distance: nonbonded pdb=" C ILE A3001 " pdb=" N PRO 9 101 " model vdw 1.356 3.350 nonbonded pdb=" O3' A 9 76 " pdb=" C PRO 9 101 " model vdw 1.397 3.270 nonbonded pdb=" O4 U a 409 " pdb=" O6 G a 433 " model vdw 1.944 2.432 nonbonded pdb=" N2 G A 883 " pdb=" O2 C A 893 " model vdw 1.971 2.496 nonbonded pdb=" O6 G 9 49 " pdb=" O4 U 9 65 " model vdw 1.997 2.432 ... (remaining 1353557 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: 2.070 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: 0.080 Extract box with map and model: 11.560 Check model and map are aligned: 1.560 Set scattering table: 0.940 Process input model: 522.450 Find NCS groups from input model: 2.900 Set up NCS constraints: 0.390 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 544.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 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 0.288 158507 Z= 0.586 Angle : 0.920 35.959 236990 Z= 0.463 Chirality : 0.050 0.394 30193 Planarity : 0.019 0.614 12798 Dihedral : 23.446 178.993 90496 Min Nonbonded Distance : 1.356 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.48 % Allowed : 13.82 % Favored : 85.70 % Rotamer: Outliers : 0.29 % Allowed : 8.44 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.55 (0.09), residues: 5847 helix: -2.51 (0.09), residues: 1928 sheet: -2.59 (0.15), residues: 974 loop : -3.58 (0.09), residues: 2945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP C 212 HIS 0.015 0.002 HIS 3 30 PHE 0.037 0.003 PHE F 174 TYR 0.024 0.003 TYR F 82 ARG 0.015 0.001 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11694 Ramachandran restraints generated. 5847 Oldfield, 0 Emsley, 5847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11694 Ramachandran restraints generated. 5847 Oldfield, 0 Emsley, 5847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1321 residues out of total 4853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1307 time to evaluate : 6.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 26 MET cc_start: 0.7282 (mmm) cc_final: 0.7061 (mmt) REVERT: b 115 ASP cc_start: 0.5757 (m-30) cc_final: 0.5556 (t0) REVERT: b 203 ASP cc_start: 0.6868 (p0) cc_final: 0.6621 (p0) REVERT: b 224 ARG cc_start: 0.6651 (tpp80) cc_final: 0.6415 (tpp80) REVERT: c 7 ASN cc_start: 0.8420 (t0) cc_final: 0.8047 (t0) REVERT: c 9 ILE cc_start: 0.9392 (tp) cc_final: 0.9170 (tp) REVERT: c 171 ARG cc_start: 0.7745 (ttp-110) cc_final: 0.7507 (ttp80) REVERT: d 122 ILE cc_start: 0.8689 (tt) cc_final: 0.8449 (tt) REVERT: e 25 LYS cc_start: 0.9054 (ttpt) cc_final: 0.8365 (tptt) REVERT: e 36 THR cc_start: 0.8983 (m) cc_final: 0.8553 (m) REVERT: e 60 GLN cc_start: 0.8320 (mm110) cc_final: 0.7904 (mm110) REVERT: e 96 GLN cc_start: 0.8271 (tt0) cc_final: 0.7996 (tt0) REVERT: f 39 LEU cc_start: 0.8818 (mt) cc_final: 0.8326 (mt) REVERT: f 56 LYS cc_start: 0.7845 (ttmt) cc_final: 0.7521 (ttmm) REVERT: g 12 LEU cc_start: 0.8765 (pt) cc_final: 0.8564 (pt) REVERT: g 41 ILE cc_start: 0.8444 (mm) cc_final: 0.8234 (mm) REVERT: h 26 MET cc_start: 0.8710 (ptp) cc_final: 0.8457 (ptp) REVERT: h 116 ARG cc_start: 0.7702 (mtt180) cc_final: 0.7270 (mtt180) REVERT: i 67 LYS cc_start: 0.8540 (ptpp) cc_final: 0.8179 (pttt) REVERT: i 74 GLN cc_start: 0.7624 (mt0) cc_final: 0.7048 (mt0) REVERT: i 114 LYS cc_start: 0.8084 (mttp) cc_final: 0.7830 (mttt) REVERT: i 118 ARG cc_start: 0.7488 (mtp180) cc_final: 0.7058 (mtp85) REVERT: j 63 ASP cc_start: 0.7820 (m-30) cc_final: 0.7444 (m-30) REVERT: k 28 ASN cc_start: 0.8511 (m-40) cc_final: 0.8266 (m-40) REVERT: k 52 ARG cc_start: 0.7774 (tpm170) cc_final: 0.7476 (mmm160) REVERT: k 74 LYS cc_start: 0.8003 (mtmm) cc_final: 0.7179 (mmtm) REVERT: k 81 LEU cc_start: 0.8462 (mt) cc_final: 0.8092 (mt) REVERT: m 40 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8158 (mt-10) REVERT: m 41 ASP cc_start: 0.6995 (m-30) cc_final: 0.6549 (t70) REVERT: m 80 MET cc_start: 0.7683 (ptp) cc_final: 0.7469 (ptm) REVERT: n 11 LYS cc_start: 0.8407 (ttpp) cc_final: 0.7753 (mtmt) REVERT: n 22 LYS cc_start: 0.6597 (mmtt) cc_final: 0.6371 (tmtt) REVERT: n 34 ASN cc_start: 0.7164 (m110) cc_final: 0.6420 (m110) REVERT: n 47 LYS cc_start: 0.7285 (ttpp) cc_final: 0.6816 (ttmt) REVERT: n 89 MET cc_start: 0.8677 (mmt) cc_final: 0.8461 (mmp) REVERT: o 70 LYS cc_start: 0.9272 (ttpt) cc_final: 0.8934 (tttt) REVERT: q 32 ILE cc_start: 0.9132 (mt) cc_final: 0.8809 (mt) REVERT: q 33 TYR cc_start: 0.8796 (m-80) cc_final: 0.8455 (m-80) REVERT: r 47 ARG cc_start: 0.7162 (mmt-90) cc_final: 0.6688 (ttt180) REVERT: s 6 LYS cc_start: 0.5937 (mmtp) cc_final: 0.5595 (pttm) REVERT: s 15 LEU cc_start: 0.7167 (pp) cc_final: 0.6722 (pp) REVERT: s 31 ARG cc_start: 0.6774 (mtp85) cc_final: 0.6361 (mtm110) REVERT: s 44 ILE cc_start: 0.8255 (mm) cc_final: 0.8007 (mm) REVERT: t 12 GLN cc_start: 0.8038 (mt0) cc_final: 0.7798 (mt0) REVERT: t 18 LYS cc_start: 0.8221 (mttt) cc_final: 0.8012 (mtpt) REVERT: C 2 VAL cc_start: 0.8653 (t) cc_final: 0.8357 (p) REVERT: C 65 ASP cc_start: 0.8388 (t0) cc_final: 0.8089 (t0) REVERT: C 184 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8058 (mm-30) REVERT: C 187 CYS cc_start: 0.8224 (m) cc_final: 0.7928 (m) REVERT: C 270 ARG cc_start: 0.8392 (ptt-90) cc_final: 0.8022 (ptt-90) REVERT: D 18 ASP cc_start: 0.8695 (p0) cc_final: 0.8406 (p0) REVERT: D 45 TYR cc_start: 0.8640 (p90) cc_final: 0.8400 (p90) REVERT: D 81 GLU cc_start: 0.7948 (tt0) cc_final: 0.7720 (tt0) REVERT: D 133 THR cc_start: 0.9114 (p) cc_final: 0.8866 (p) REVERT: D 181 ASP cc_start: 0.8122 (t0) cc_final: 0.7902 (t0) REVERT: E 2 GLU cc_start: 0.6427 (mp0) cc_final: 0.6100 (mp0) REVERT: E 16 GLU cc_start: 0.8391 (tt0) cc_final: 0.7949 (tt0) REVERT: E 115 GLN cc_start: 0.8324 (mt0) cc_final: 0.7855 (mt0) REVERT: E 156 ASN cc_start: 0.8502 (m-40) cc_final: 0.8120 (m-40) REVERT: F 111 ARG cc_start: 0.7755 (ptt90) cc_final: 0.6286 (ttp80) REVERT: G 17 LYS cc_start: 0.7323 (tttm) cc_final: 0.6920 (mmmt) REVERT: G 19 ASN cc_start: 0.7946 (t0) cc_final: 0.7648 (t0) REVERT: G 41 GLU cc_start: 0.7753 (pt0) cc_final: 0.7543 (tt0) REVERT: G 140 ILE cc_start: 0.8472 (pt) cc_final: 0.8127 (mt) REVERT: G 146 ASP cc_start: 0.7965 (m-30) cc_final: 0.7689 (m-30) REVERT: G 148 ARG cc_start: 0.9029 (ttt-90) cc_final: 0.8656 (ttt-90) REVERT: G 151 ARG cc_start: 0.8007 (ttm-80) cc_final: 0.7774 (ttm170) REVERT: J 128 ASN cc_start: 0.8838 (t0) cc_final: 0.8354 (t0) REVERT: K 45 GLU cc_start: 0.7277 (tm-30) cc_final: 0.6911 (tm-30) REVERT: K 59 LYS cc_start: 0.8707 (mttt) cc_final: 0.8506 (mtmt) REVERT: K 88 ASN cc_start: 0.7844 (t0) cc_final: 0.7474 (t0) REVERT: K 114 LYS cc_start: 0.8226 (tppt) cc_final: 0.7989 (mmtt) REVERT: L 129 LYS cc_start: 0.8568 (ttmm) cc_final: 0.8276 (mtmm) REVERT: L 136 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6775 (mm-30) REVERT: M 6 ARG cc_start: 0.7254 (ptm-80) cc_final: 0.6681 (ptp90) REVERT: M 9 PHE cc_start: 0.8841 (m-80) cc_final: 0.8413 (m-10) REVERT: M 53 MET cc_start: 0.8409 (ttp) cc_final: 0.8060 (ttp) REVERT: M 136 MET cc_start: 0.6384 (tmm) cc_final: 0.4772 (mpp) REVERT: Q 48 ASP cc_start: 0.8320 (m-30) cc_final: 0.8057 (m-30) REVERT: S 1 MET cc_start: 0.6153 (ttp) cc_final: 0.5754 (tmm) REVERT: S 40 ASN cc_start: 0.8097 (m-40) cc_final: 0.7872 (m-40) REVERT: U 13 LEU cc_start: 0.8515 (mt) cc_final: 0.8271 (mt) REVERT: U 45 GLN cc_start: 0.8228 (tt0) cc_final: 0.7975 (tp40) REVERT: U 87 GLU cc_start: 0.7273 (mp0) cc_final: 0.6856 (mp0) REVERT: V 5 ASN cc_start: 0.8571 (m-40) cc_final: 0.8298 (m-40) REVERT: V 12 GLN cc_start: 0.8459 (mp10) cc_final: 0.8228 (mt0) REVERT: V 59 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7721 (mt-10) REVERT: 0 48 TYR cc_start: 0.8694 (t80) cc_final: 0.8478 (t80) REVERT: 2 30 VAL cc_start: 0.8854 (t) cc_final: 0.8631 (t) REVERT: 3 58 ILE cc_start: 0.9142 (tp) cc_final: 0.8897 (mt) REVERT: 4 36 ARG cc_start: 0.8158 (ttt-90) cc_final: 0.7832 (ttt-90) REVERT: 5 86 MET cc_start: 0.4010 (tpp) cc_final: 0.3742 (tpp) REVERT: 6 2 LYS cc_start: 0.6857 (mttt) cc_final: 0.6620 (mttm) outliers start: 14 outliers final: 9 residues processed: 1318 average time/residue: 1.3636 time to fit residues: 3022.4729 Evaluate side-chains 1093 residues out of total 4853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1084 time to evaluate : 6.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 93 HIS Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain V residue 66 ASP Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 9 residue 101 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 873 optimal weight: 7.9990 chunk 783 optimal weight: 10.0000 chunk 434 optimal weight: 4.9990 chunk 267 optimal weight: 9.9990 chunk 528 optimal weight: 10.0000 chunk 418 optimal weight: 30.0000 chunk 810 optimal weight: 10.0000 chunk 313 optimal weight: 8.9990 chunk 492 optimal weight: 20.0000 chunk 603 optimal weight: 10.0000 chunk 938 optimal weight: 6.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 101 ASN c 189 HIS ** d 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 58 GLN d 88 ASN d 195 ASN e 76 ASN e 88 HIS ** f 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 30 ASN ** i 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 58 ASN j 64 GLN k 23 HIS k 27 ASN k 39 ASN m 13 HIS ** n 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 62 ASN o 27 GLN o 36 ASN o 45 HIS p 26 ASN q 8 GLN q 30 HIS r 51 GLN s 51 HIS ** t 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 ASN C 45 ASN C 89 ASN C 127 ASN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 HIS ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN E 41 GLN F 51 ASN ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN I 18 ASN ** I 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN K 3 GLN ** K 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 ASN M 17 ASN M 22 GLN O 29 HIS O 38 GLN O 61 GLN P 11 GLN P 40 GLN P 65 ASN Q 71 ASN R 82 HIS S 7 HIS S 31 GLN T 15 HIS U 65 GLN U 68 ASN W 8 ASN W 72 ASN Y 58 ASN 0 41 HIS 1 25 ASN 5 88 HIS ** 6 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.0736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 158507 Z= 0.439 Angle : 0.814 14.756 236990 Z= 0.425 Chirality : 0.045 0.373 30193 Planarity : 0.007 0.138 12798 Dihedral : 23.899 178.463 78905 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.07 % Favored : 87.60 % Rotamer: Outliers : 4.17 % Allowed : 17.08 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.09), residues: 5847 helix: -1.43 (0.10), residues: 1945 sheet: -2.35 (0.15), residues: 992 loop : -3.15 (0.10), residues: 2910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 212 HIS 0.013 0.002 HIS 3 30 PHE 0.022 0.002 PHE F 174 TYR 0.020 0.002 TYR I 7 ARG 0.007 0.001 ARG t 9 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11694 Ramachandran restraints generated. 5847 Oldfield, 0 Emsley, 5847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11694 Ramachandran restraints generated. 5847 Oldfield, 0 Emsley, 5847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1301 residues out of total 4853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 1100 time to evaluate : 6.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 26 MET cc_start: 0.7263 (mmm) cc_final: 0.7023 (mmt) REVERT: b 62 ARG cc_start: 0.5161 (ptp-170) cc_final: 0.4593 (mtm-85) REVERT: b 115 ASP cc_start: 0.5680 (m-30) cc_final: 0.5406 (t0) REVERT: c 9 ILE cc_start: 0.9357 (tp) cc_final: 0.9148 (tp) REVERT: c 48 LYS cc_start: 0.8765 (mmmm) cc_final: 0.7721 (tptp) REVERT: c 171 ARG cc_start: 0.7707 (ttp-110) cc_final: 0.7490 (mtp-110) REVERT: d 13 ARG cc_start: 0.8522 (tpt170) cc_final: 0.8027 (tpp-160) REVERT: d 54 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8297 (tp) REVERT: d 122 ILE cc_start: 0.8505 (tt) cc_final: 0.8147 (tt) REVERT: d 135 GLN cc_start: 0.8620 (tp40) cc_final: 0.8411 (tp40) REVERT: d 196 GLU cc_start: 0.7558 (pm20) cc_final: 0.6730 (pm20) REVERT: e 25 LYS cc_start: 0.9061 (ttpt) cc_final: 0.8388 (tptt) REVERT: e 67 ARG cc_start: 0.8349 (mtm110) cc_final: 0.8067 (mtm-85) REVERT: e 96 GLN cc_start: 0.8268 (tt0) cc_final: 0.7944 (tt0) REVERT: e 145 ASN cc_start: 0.8102 (p0) cc_final: 0.7878 (p0) REVERT: f 39 LEU cc_start: 0.8506 (mt) cc_final: 0.8102 (mt) REVERT: f 56 LYS cc_start: 0.7480 (ttmt) cc_final: 0.7104 (ttmm) REVERT: f 62 MET cc_start: 0.7350 (mmm) cc_final: 0.7096 (mmm) REVERT: g 137 ARG cc_start: 0.7873 (tmm160) cc_final: 0.7201 (ttp80) REVERT: h 26 MET cc_start: 0.8779 (ptp) cc_final: 0.8551 (ptp) REVERT: h 103 VAL cc_start: 0.8984 (OUTLIER) cc_final: 0.8743 (p) REVERT: h 116 ARG cc_start: 0.7706 (mtt180) cc_final: 0.7252 (mtt180) REVERT: i 61 ASP cc_start: 0.6726 (p0) cc_final: 0.6505 (p0) REVERT: i 67 LYS cc_start: 0.8539 (ptpp) cc_final: 0.8165 (pttt) REVERT: i 74 GLN cc_start: 0.7637 (mt0) cc_final: 0.7062 (mt0) REVERT: i 114 LYS cc_start: 0.8016 (mttp) cc_final: 0.7736 (mttt) REVERT: i 118 ARG cc_start: 0.7404 (mtp180) cc_final: 0.6906 (mtp85) REVERT: j 18 ILE cc_start: 0.7951 (OUTLIER) cc_final: 0.7608 (tt) REVERT: j 63 ASP cc_start: 0.7663 (m-30) cc_final: 0.7265 (m-30) REVERT: j 88 MET cc_start: 0.6075 (tpp) cc_final: 0.5836 (tpp) REVERT: k 12 ARG cc_start: 0.5518 (mtm180) cc_final: 0.5136 (mtt180) REVERT: k 28 ASN cc_start: 0.8606 (m-40) cc_final: 0.8224 (m-40) REVERT: k 74 LYS cc_start: 0.7971 (mtmm) cc_final: 0.7257 (mmtm) REVERT: l 101 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7999 (pp) REVERT: m 12 LYS cc_start: 0.7968 (ptpt) cc_final: 0.7507 (mtpt) REVERT: m 40 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8150 (mt-10) REVERT: m 41 ASP cc_start: 0.7156 (m-30) cc_final: 0.6692 (t70) REVERT: m 80 MET cc_start: 0.7664 (ptp) cc_final: 0.7347 (ptm) REVERT: n 11 LYS cc_start: 0.8430 (ttpp) cc_final: 0.7671 (mtmt) REVERT: n 47 LYS cc_start: 0.7508 (ttpp) cc_final: 0.7022 (ttmt) REVERT: o 70 LYS cc_start: 0.9269 (ttpt) cc_final: 0.8950 (tttt) REVERT: p 53 ASP cc_start: 0.7792 (p0) cc_final: 0.7588 (p0) REVERT: p 56 ARG cc_start: 0.8094 (mmm160) cc_final: 0.7551 (mtp85) REVERT: q 32 ILE cc_start: 0.9200 (mt) cc_final: 0.8851 (mt) REVERT: q 33 TYR cc_start: 0.8794 (m-80) cc_final: 0.8461 (m-80) REVERT: r 47 ARG cc_start: 0.7082 (mmt-90) cc_final: 0.6594 (ttt180) REVERT: s 6 LYS cc_start: 0.5965 (mmtp) cc_final: 0.5564 (pttm) REVERT: s 15 LEU cc_start: 0.7380 (pp) cc_final: 0.6770 (pp) REVERT: s 31 ARG cc_start: 0.6800 (mtp85) cc_final: 0.6265 (mtm110) REVERT: s 44 ILE cc_start: 0.8262 (mm) cc_final: 0.8024 (mm) REVERT: t 12 GLN cc_start: 0.8043 (mt0) cc_final: 0.7787 (mt0) REVERT: t 18 LYS cc_start: 0.8315 (mttt) cc_final: 0.8063 (mtpt) REVERT: t 29 THR cc_start: 0.9062 (p) cc_final: 0.8795 (p) REVERT: t 83 ASN cc_start: 0.8436 (m-40) cc_final: 0.8158 (m-40) REVERT: C 2 VAL cc_start: 0.8644 (t) cc_final: 0.8326 (p) REVERT: C 65 ASP cc_start: 0.8370 (t0) cc_final: 0.8127 (t0) REVERT: C 173 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8583 (mt) REVERT: C 187 CYS cc_start: 0.8206 (m) cc_final: 0.7961 (m) REVERT: C 235 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7520 (mm-30) REVERT: D 45 TYR cc_start: 0.8576 (p90) cc_final: 0.8361 (p90) REVERT: D 81 GLU cc_start: 0.7914 (tt0) cc_final: 0.7672 (tt0) REVERT: D 133 THR cc_start: 0.9105 (p) cc_final: 0.8834 (p) REVERT: D 181 ASP cc_start: 0.8079 (t0) cc_final: 0.7602 (t0) REVERT: E 46 GLN cc_start: 0.8969 (mp10) cc_final: 0.8635 (mt0) REVERT: E 115 GLN cc_start: 0.8241 (mt0) cc_final: 0.7913 (mt0) REVERT: E 156 ASN cc_start: 0.8495 (m-40) cc_final: 0.8115 (m-40) REVERT: F 71 LYS cc_start: 0.6932 (tmmt) cc_final: 0.6223 (pttm) REVERT: G 17 LYS cc_start: 0.7333 (tttm) cc_final: 0.6922 (mmmt) REVERT: G 19 ASN cc_start: 0.7937 (t0) cc_final: 0.7612 (t0) REVERT: G 25 ILE cc_start: 0.6674 (OUTLIER) cc_final: 0.6336 (mt) REVERT: G 41 GLU cc_start: 0.7886 (pt0) cc_final: 0.7518 (tt0) REVERT: G 146 ASP cc_start: 0.7797 (m-30) cc_final: 0.7415 (m-30) REVERT: G 148 ARG cc_start: 0.8939 (ttt-90) cc_final: 0.8387 (ttt-90) REVERT: G 150 TYR cc_start: 0.7718 (m-10) cc_final: 0.7488 (m-80) REVERT: G 163 TYR cc_start: 0.8790 (m-10) cc_final: 0.8521 (m-10) REVERT: I 12 VAL cc_start: 0.0081 (OUTLIER) cc_final: -0.0169 (m) REVERT: J 31 GLU cc_start: 0.7425 (tp30) cc_final: 0.7216 (tp30) REVERT: J 128 ASN cc_start: 0.8786 (t0) cc_final: 0.8286 (t0) REVERT: K 45 GLU cc_start: 0.7152 (tm-30) cc_final: 0.6948 (tm-30) REVERT: K 88 ASN cc_start: 0.7803 (t0) cc_final: 0.7453 (t0) REVERT: K 114 LYS cc_start: 0.8407 (tppt) cc_final: 0.8079 (mmtt) REVERT: L 129 LYS cc_start: 0.8582 (ttmm) cc_final: 0.8316 (mtmm) REVERT: M 6 ARG cc_start: 0.7288 (ptm-80) cc_final: 0.6678 (ptp90) REVERT: M 9 PHE cc_start: 0.8886 (m-80) cc_final: 0.8469 (m-10) REVERT: M 44 ARG cc_start: 0.8602 (mmt90) cc_final: 0.8305 (mtt180) REVERT: N 23 ASN cc_start: 0.8758 (m-40) cc_final: 0.8386 (m-40) REVERT: N 35 LYS cc_start: 0.8507 (tttp) cc_final: 0.8307 (tptp) REVERT: O 12 THR cc_start: 0.9333 (m) cc_final: 0.8775 (p) REVERT: Q 48 ASP cc_start: 0.8294 (m-30) cc_final: 0.8015 (m-30) REVERT: Q 110 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7780 (mm-30) REVERT: S 1 MET cc_start: 0.5928 (ttp) cc_final: 0.5467 (tmm) REVERT: U 13 LEU cc_start: 0.8459 (mt) cc_final: 0.8131 (mt) REVERT: U 87 GLU cc_start: 0.7275 (mp0) cc_final: 0.6833 (mp0) REVERT: V 12 GLN cc_start: 0.8447 (mp10) cc_final: 0.8217 (mt0) REVERT: W 25 GLU cc_start: 0.8109 (tt0) cc_final: 0.7908 (tt0) REVERT: 3 58 ILE cc_start: 0.9125 (tp) cc_final: 0.8836 (mt) REVERT: 4 20 ASP cc_start: 0.7859 (t0) cc_final: 0.7552 (t0) REVERT: 6 2 LYS cc_start: 0.6859 (mttt) cc_final: 0.6514 (mttm) outliers start: 201 outliers final: 149 residues processed: 1213 average time/residue: 1.2652 time to fit residues: 2652.0058 Evaluate side-chains 1203 residues out of total 4853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1047 time to evaluate : 6.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 20 ARG Chi-restraints excluded: chain b residue 66 ILE Chi-restraints excluded: chain b residue 93 HIS Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 153 MET Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 54 LEU Chi-restraints excluded: chain d residue 77 GLU Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain d residue 104 MET Chi-restraints excluded: chain d residue 123 MET Chi-restraints excluded: chain d residue 144 ILE Chi-restraints excluded: chain d residue 172 VAL Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain e residue 79 THR Chi-restraints excluded: chain e residue 85 LYS Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 135 VAL Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 13 ASP Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 83 THR Chi-restraints excluded: chain g residue 105 GLU Chi-restraints excluded: chain g residue 123 LEU Chi-restraints excluded: chain g residue 147 ASN Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 70 VAL Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain h residue 100 ILE Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain i residue 62 LEU Chi-restraints excluded: chain i residue 71 ILE Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain k residue 63 GLN Chi-restraints excluded: chain k residue 78 ILE Chi-restraints excluded: chain l residue 54 VAL Chi-restraints excluded: chain l residue 69 GLU Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain l residue 96 THR Chi-restraints excluded: chain l residue 101 LEU Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain l residue 118 VAL Chi-restraints excluded: chain m residue 19 THR Chi-restraints excluded: chain m residue 47 LEU Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain o residue 1 SER Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 57 ILE Chi-restraints excluded: chain p residue 63 GLN Chi-restraints excluded: chain q residue 20 ILE Chi-restraints excluded: chain q residue 37 ILE Chi-restraints excluded: chain r residue 27 THR Chi-restraints excluded: chain r residue 33 THR Chi-restraints excluded: chain r residue 65 SER Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 194 LYS Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 17 ASN Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 82 SER Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 74 SER Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 31 GLN Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 66 ASP Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain Z residue 18 LYS Chi-restraints excluded: chain 0 residue 10 SER Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 37 GLN Chi-restraints excluded: chain 5 residue 33 VAL Chi-restraints excluded: chain 6 residue 13 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 521 optimal weight: 10.0000 chunk 291 optimal weight: 9.9990 chunk 781 optimal weight: 7.9990 chunk 639 optimal weight: 7.9990 chunk 259 optimal weight: 0.0010 chunk 940 optimal weight: 4.9990 chunk 1016 optimal weight: 7.9990 chunk 837 optimal weight: 3.9990 chunk 932 optimal weight: 0.5980 chunk 320 optimal weight: 6.9990 chunk 754 optimal weight: 4.9990 overall best weight: 2.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 189 ASN ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 GLN g 67 ASN g 129 ASN ** i 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 125 GLN j 20 GLN j 64 GLN j 99 GLN ** n 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 62 ASN q 8 GLN ** t 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN D 136 ASN D 150 GLN G 63 GLN ** I 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 61 GLN P 40 GLN S 31 GLN W 72 ASN Y 27 ASN ** 6 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 158507 Z= 0.204 Angle : 0.655 14.748 236990 Z= 0.353 Chirality : 0.037 0.384 30193 Planarity : 0.006 0.126 12798 Dihedral : 23.732 179.761 78902 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.21 % Favored : 89.50 % Rotamer: Outliers : 4.21 % Allowed : 19.05 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.10), residues: 5847 helix: -0.56 (0.11), residues: 1929 sheet: -2.01 (0.16), residues: 1001 loop : -2.73 (0.10), residues: 2917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP c 200 HIS 0.008 0.001 HIS 3 30 PHE 0.018 0.001 PHE u 36 TYR 0.037 0.002 TYR F 6 ARG 0.010 0.000 ARG h 113 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11694 Ramachandran restraints generated. 5847 Oldfield, 0 Emsley, 5847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11694 Ramachandran restraints generated. 5847 Oldfield, 0 Emsley, 5847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1350 residues out of total 4853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 1147 time to evaluate : 6.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 8 MET cc_start: 0.6129 (mmt) cc_final: 0.5688 (mmt) REVERT: c 168 ARG cc_start: 0.8214 (ptp90) cc_final: 0.7631 (ttp80) REVERT: c 171 ARG cc_start: 0.7536 (ttp-110) cc_final: 0.7329 (mtp85) REVERT: d 13 ARG cc_start: 0.8401 (tpt170) cc_final: 0.8076 (tpp-160) REVERT: d 46 ARG cc_start: 0.7165 (mtm180) cc_final: 0.6623 (mmt180) REVERT: d 53 GLN cc_start: 0.8046 (mt0) cc_final: 0.7781 (mt0) REVERT: d 90 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7698 (mm) REVERT: d 122 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8069 (tt) REVERT: d 196 GLU cc_start: 0.7396 (pm20) cc_final: 0.6722 (pm20) REVERT: e 25 LYS cc_start: 0.9047 (ttpt) cc_final: 0.8390 (tptt) REVERT: e 96 GLN cc_start: 0.8138 (tt0) cc_final: 0.7810 (tt0) REVERT: e 110 MET cc_start: 0.8537 (mtm) cc_final: 0.8273 (ttm) REVERT: e 145 ASN cc_start: 0.7922 (p0) cc_final: 0.7627 (p0) REVERT: f 56 LYS cc_start: 0.7370 (ttmt) cc_final: 0.6957 (ttmm) REVERT: f 74 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.6923 (mm) REVERT: g 135 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8446 (ttmt) REVERT: g 137 ARG cc_start: 0.7765 (tmm160) cc_final: 0.7108 (ttp80) REVERT: h 116 ARG cc_start: 0.7629 (mtt180) cc_final: 0.7182 (mtt180) REVERT: i 12 LYS cc_start: 0.8081 (ttpt) cc_final: 0.7771 (ttpt) REVERT: i 67 LYS cc_start: 0.8543 (ptpp) cc_final: 0.8133 (pttt) REVERT: i 114 LYS cc_start: 0.7968 (mttp) cc_final: 0.7715 (mttt) REVERT: j 16 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.6889 (mmm-85) REVERT: j 56 HIS cc_start: 0.7692 (OUTLIER) cc_final: 0.7182 (t-170) REVERT: j 63 ASP cc_start: 0.7332 (m-30) cc_final: 0.7120 (m-30) REVERT: j 67 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.8095 (mp) REVERT: j 88 MET cc_start: 0.6109 (tpp) cc_final: 0.5809 (tpp) REVERT: k 28 ASN cc_start: 0.8452 (m-40) cc_final: 0.8116 (m-40) REVERT: k 74 LYS cc_start: 0.7988 (mtmm) cc_final: 0.7237 (mmtm) REVERT: l 106 VAL cc_start: 0.7113 (OUTLIER) cc_final: 0.6874 (p) REVERT: m 12 LYS cc_start: 0.8039 (ptpt) cc_final: 0.7559 (mtpt) REVERT: m 40 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8137 (mt-10) REVERT: m 41 ASP cc_start: 0.7197 (m-30) cc_final: 0.6707 (t70) REVERT: m 67 ASP cc_start: 0.7500 (OUTLIER) cc_final: 0.5787 (t70) REVERT: m 71 GLU cc_start: 0.5885 (mm-30) cc_final: 0.5677 (mm-30) REVERT: m 80 MET cc_start: 0.7594 (ptp) cc_final: 0.7238 (ptm) REVERT: n 11 LYS cc_start: 0.8264 (ttpp) cc_final: 0.7778 (ptmt) REVERT: o 44 GLU cc_start: 0.7164 (tt0) cc_final: 0.6957 (tt0) REVERT: o 70 LYS cc_start: 0.9257 (ttpt) cc_final: 0.8929 (tttt) REVERT: q 10 ARG cc_start: 0.7394 (ptm-80) cc_final: 0.6931 (mtp85) REVERT: q 32 ILE cc_start: 0.9175 (mt) cc_final: 0.8793 (mt) REVERT: q 33 TYR cc_start: 0.8771 (m-80) cc_final: 0.8370 (m-80) REVERT: q 79 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7297 (tm-30) REVERT: r 47 ARG cc_start: 0.6854 (mmt-90) cc_final: 0.6409 (ttt180) REVERT: r 49 LYS cc_start: 0.8798 (tttp) cc_final: 0.8476 (ttpt) REVERT: r 56 ARG cc_start: 0.7352 (ttm110) cc_final: 0.7131 (ttm110) REVERT: s 6 LYS cc_start: 0.5833 (mmtp) cc_final: 0.5521 (pttm) REVERT: s 15 LEU cc_start: 0.7368 (pp) cc_final: 0.6755 (pp) REVERT: s 31 ARG cc_start: 0.7035 (mtp85) cc_final: 0.6735 (mtm110) REVERT: s 33 TRP cc_start: 0.8599 (m-90) cc_final: 0.7525 (m-90) REVERT: s 77 ARG cc_start: 0.7294 (mtm-85) cc_final: 0.6977 (ptp-170) REVERT: C 2 VAL cc_start: 0.8627 (t) cc_final: 0.8344 (p) REVERT: C 43 ASN cc_start: 0.8439 (p0) cc_final: 0.8176 (p0) REVERT: C 170 TYR cc_start: 0.8501 (m-80) cc_final: 0.6824 (m-80) REVERT: C 250 GLN cc_start: 0.8539 (tm-30) cc_final: 0.8233 (tm-30) REVERT: C 270 ARG cc_start: 0.8348 (ptt-90) cc_final: 0.8145 (ptt-90) REVERT: D 40 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8323 (mp) REVERT: E 2 GLU cc_start: 0.6358 (mp0) cc_final: 0.6103 (mp0) REVERT: E 46 GLN cc_start: 0.8855 (mp10) cc_final: 0.8569 (mt0) REVERT: E 115 GLN cc_start: 0.8291 (mt0) cc_final: 0.8013 (mt0) REVERT: F 16 MET cc_start: 0.6192 (ttt) cc_final: 0.5953 (ttm) REVERT: F 76 PHE cc_start: 0.7823 (m-10) cc_final: 0.7346 (m-10) REVERT: F 168 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7765 (tt) REVERT: G 146 ASP cc_start: 0.7712 (m-30) cc_final: 0.7353 (m-30) REVERT: G 150 TYR cc_start: 0.7503 (m-10) cc_final: 0.7268 (m-80) REVERT: G 163 TYR cc_start: 0.8680 (m-10) cc_final: 0.8314 (m-10) REVERT: I 12 VAL cc_start: 0.0312 (OUTLIER) cc_final: 0.0066 (m) REVERT: I 116 MET cc_start: 0.1110 (tpt) cc_final: 0.0418 (mmm) REVERT: J 31 GLU cc_start: 0.7281 (tp30) cc_final: 0.7076 (tp30) REVERT: J 128 ASN cc_start: 0.8679 (t0) cc_final: 0.8188 (t0) REVERT: K 14 SER cc_start: 0.8649 (t) cc_final: 0.8281 (p) REVERT: K 88 ASN cc_start: 0.7776 (t0) cc_final: 0.7496 (t0) REVERT: K 114 LYS cc_start: 0.8294 (tppt) cc_final: 0.8038 (mmtt) REVERT: L 129 LYS cc_start: 0.8453 (ttmm) cc_final: 0.8197 (mtmm) REVERT: L 136 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6767 (mm-30) REVERT: M 6 ARG cc_start: 0.7205 (ptm-80) cc_final: 0.6571 (ptp90) REVERT: M 9 PHE cc_start: 0.8802 (m-80) cc_final: 0.8445 (m-10) REVERT: M 12 MET cc_start: 0.7624 (ttm) cc_final: 0.7127 (mtp) REVERT: N 18 GLN cc_start: 0.8416 (tt0) cc_final: 0.8206 (mt0) REVERT: O 12 THR cc_start: 0.9126 (m) cc_final: 0.8828 (p) REVERT: P 71 ARG cc_start: 0.7951 (ttt180) cc_final: 0.7606 (ttt-90) REVERT: Q 48 ASP cc_start: 0.8212 (m-30) cc_final: 0.7945 (m-30) REVERT: U 5 ARG cc_start: 0.8027 (ptp-170) cc_final: 0.7707 (mtt180) REVERT: U 13 LEU cc_start: 0.8455 (mt) cc_final: 0.8173 (mt) REVERT: U 87 GLU cc_start: 0.7193 (mp0) cc_final: 0.6870 (mp0) REVERT: U 100 GLU cc_start: 0.7698 (pt0) cc_final: 0.7423 (pt0) REVERT: V 12 GLN cc_start: 0.8394 (mp10) cc_final: 0.8124 (mt0) REVERT: V 68 LYS cc_start: 0.7803 (ptpt) cc_final: 0.7588 (mtmt) REVERT: V 76 ASP cc_start: 0.6682 (m-30) cc_final: 0.6340 (m-30) REVERT: W 7 ARG cc_start: 0.7324 (ttm110) cc_final: 0.7086 (mtm110) REVERT: Y 6 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.7027 (mt) REVERT: Y 39 GLN cc_start: 0.7426 (mt0) cc_final: 0.6960 (mp10) REVERT: 3 14 LYS cc_start: 0.8368 (mptt) cc_final: 0.8051 (mttp) REVERT: 4 20 ASP cc_start: 0.7786 (t0) cc_final: 0.7526 (t0) REVERT: 5 23 LEU cc_start: 0.3687 (mm) cc_final: 0.3207 (mt) REVERT: 6 2 LYS cc_start: 0.6740 (mttt) cc_final: 0.6416 (mttm) outliers start: 203 outliers final: 121 residues processed: 1260 average time/residue: 1.2774 time to fit residues: 2785.0245 Evaluate side-chains 1206 residues out of total 4853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1072 time to evaluate : 6.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 66 ILE Chi-restraints excluded: chain b residue 93 HIS Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 152 VAL Chi-restraints excluded: chain c residue 183 TYR Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 77 GLU Chi-restraints excluded: chain d residue 90 LEU Chi-restraints excluded: chain d residue 122 ILE Chi-restraints excluded: chain d residue 170 LEU Chi-restraints excluded: chain d residue 172 VAL Chi-restraints excluded: chain e residue 36 THR Chi-restraints excluded: chain e residue 79 THR Chi-restraints excluded: chain e residue 85 LYS Chi-restraints excluded: chain e residue 119 VAL Chi-restraints excluded: chain f residue 13 ASP Chi-restraints excluded: chain f residue 68 GLN Chi-restraints excluded: chain f residue 74 LEU Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 83 THR Chi-restraints excluded: chain g residue 105 GLU Chi-restraints excluded: chain g residue 135 LYS Chi-restraints excluded: chain h residue 10 LEU Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain i residue 20 ILE Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain i residue 62 LEU Chi-restraints excluded: chain i residue 71 ILE Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain i residue 106 ASP Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 16 ARG Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 56 HIS Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain j residue 102 LEU Chi-restraints excluded: chain k residue 63 GLN Chi-restraints excluded: chain k residue 78 ILE Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain k residue 95 THR Chi-restraints excluded: chain l residue 54 VAL Chi-restraints excluded: chain l residue 69 GLU Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 96 THR Chi-restraints excluded: chain l residue 97 VAL Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain l residue 118 VAL Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 19 THR Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain n residue 58 SER Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain o residue 1 SER Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 57 ILE Chi-restraints excluded: chain p residue 63 GLN Chi-restraints excluded: chain q residue 20 ILE Chi-restraints excluded: chain q residue 37 ILE Chi-restraints excluded: chain r residue 27 THR Chi-restraints excluded: chain r residue 33 THR Chi-restraints excluded: chain r residue 65 SER Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain N residue 45 ARG Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 82 SER Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 39 ASN Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 66 ASP Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 10 SER Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 4 residue 37 GLN Chi-restraints excluded: chain 5 residue 17 GLU Chi-restraints excluded: chain 6 residue 4 ASP Chi-restraints excluded: chain 6 residue 13 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 929 optimal weight: 6.9990 chunk 707 optimal weight: 9.9990 chunk 488 optimal weight: 50.0000 chunk 104 optimal weight: 20.0000 chunk 448 optimal weight: 10.0000 chunk 631 optimal weight: 10.0000 chunk 944 optimal weight: 4.9990 chunk 999 optimal weight: 9.9990 chunk 493 optimal weight: 20.0000 chunk 894 optimal weight: 0.4980 chunk 269 optimal weight: 2.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 67 ASN g 129 ASN ** n 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 62 ASN q 8 GLN ** t 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 GLN ** I 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 61 GLN R 86 GLN W 72 ASN ** 6 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 158507 Z= 0.305 Angle : 0.696 14.852 236990 Z= 0.370 Chirality : 0.039 0.377 30193 Planarity : 0.006 0.135 12798 Dihedral : 23.656 179.812 78902 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.79 % Favored : 88.90 % Rotamer: Outliers : 5.93 % Allowed : 20.68 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.10), residues: 5847 helix: -0.37 (0.11), residues: 1927 sheet: -1.91 (0.16), residues: 1024 loop : -2.60 (0.10), residues: 2896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP c 200 HIS 0.009 0.001 HIS 3 30 PHE 0.017 0.002 PHE u 36 TYR 0.020 0.002 TYR N 112 ARG 0.008 0.000 ARG j 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11694 Ramachandran restraints generated. 5847 Oldfield, 0 Emsley, 5847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11694 Ramachandran restraints generated. 5847 Oldfield, 0 Emsley, 5847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1348 residues out of total 4853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 1062 time to evaluate : 6.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 166 ASP cc_start: 0.5614 (OUTLIER) cc_final: 0.5346 (m-30) REVERT: c 168 ARG cc_start: 0.8274 (ptp90) cc_final: 0.7686 (ttp80) REVERT: c 171 ARG cc_start: 0.7540 (ttp-110) cc_final: 0.7259 (mtp180) REVERT: d 13 ARG cc_start: 0.8452 (tpt170) cc_final: 0.8055 (tpp-160) REVERT: d 122 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8295 (tt) REVERT: d 196 GLU cc_start: 0.7525 (pm20) cc_final: 0.6768 (pm20) REVERT: e 25 LYS cc_start: 0.9060 (ttpt) cc_final: 0.8383 (tptt) REVERT: e 145 ASN cc_start: 0.7856 (p0) cc_final: 0.7530 (p0) REVERT: f 33 GLU cc_start: 0.5910 (OUTLIER) cc_final: 0.5486 (tp30) REVERT: f 56 LYS cc_start: 0.7356 (ttmt) cc_final: 0.6918 (ttmm) REVERT: f 74 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.6951 (mm) REVERT: f 86 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8472 (ttp-110) REVERT: g 135 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8396 (ttmt) REVERT: g 137 ARG cc_start: 0.7833 (tmm160) cc_final: 0.7153 (ttp80) REVERT: h 103 VAL cc_start: 0.8884 (OUTLIER) cc_final: 0.8529 (p) REVERT: h 116 ARG cc_start: 0.7654 (mtt180) cc_final: 0.7205 (mtt180) REVERT: i 67 LYS cc_start: 0.8478 (ptpp) cc_final: 0.8059 (pttt) REVERT: i 114 LYS cc_start: 0.7989 (mttp) cc_final: 0.7731 (mttt) REVERT: j 14 ASP cc_start: 0.7927 (t0) cc_final: 0.7724 (t0) REVERT: j 18 ILE cc_start: 0.7927 (OUTLIER) cc_final: 0.7635 (tt) REVERT: j 56 HIS cc_start: 0.7692 (OUTLIER) cc_final: 0.7164 (t-170) REVERT: j 67 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8139 (mp) REVERT: k 28 ASN cc_start: 0.8590 (m-40) cc_final: 0.8098 (m-40) REVERT: k 68 ARG cc_start: 0.8020 (mtp-110) cc_final: 0.7551 (mtp-110) REVERT: k 74 LYS cc_start: 0.8003 (mtmm) cc_final: 0.7241 (mmtm) REVERT: l 74 GLN cc_start: 0.6759 (OUTLIER) cc_final: 0.6435 (pm20) REVERT: m 12 LYS cc_start: 0.7940 (ptpt) cc_final: 0.7467 (mtpt) REVERT: m 40 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8134 (mt-10) REVERT: m 41 ASP cc_start: 0.7221 (m-30) cc_final: 0.6708 (t70) REVERT: m 80 MET cc_start: 0.7707 (ptp) cc_final: 0.7373 (ptm) REVERT: n 11 LYS cc_start: 0.8290 (ttpp) cc_final: 0.7615 (mtmt) REVERT: n 22 LYS cc_start: 0.6740 (mmtt) cc_final: 0.6307 (tmtt) REVERT: o 44 GLU cc_start: 0.7182 (tt0) cc_final: 0.6980 (tt0) REVERT: o 70 LYS cc_start: 0.9254 (ttpt) cc_final: 0.8916 (tttt) REVERT: q 32 ILE cc_start: 0.9249 (mt) cc_final: 0.8838 (mt) REVERT: q 33 TYR cc_start: 0.8784 (m-80) cc_final: 0.8362 (m-80) REVERT: q 79 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7364 (tm-30) REVERT: r 47 ARG cc_start: 0.6977 (mmt-90) cc_final: 0.6531 (ttt180) REVERT: r 49 LYS cc_start: 0.8693 (tttp) cc_final: 0.8449 (ttpp) REVERT: r 56 ARG cc_start: 0.7413 (ttm110) cc_final: 0.6737 (ttm110) REVERT: s 6 LYS cc_start: 0.5954 (mmtp) cc_final: 0.5605 (pttm) REVERT: s 10 ILE cc_start: 0.8551 (tp) cc_final: 0.8347 (tp) REVERT: s 15 LEU cc_start: 0.7475 (pp) cc_final: 0.6900 (pp) REVERT: s 28 LYS cc_start: 0.6809 (OUTLIER) cc_final: 0.6059 (mtmt) REVERT: t 29 THR cc_start: 0.9191 (p) cc_final: 0.8955 (p) REVERT: C 2 VAL cc_start: 0.8585 (t) cc_final: 0.8374 (p) REVERT: C 43 ASN cc_start: 0.8608 (p0) cc_final: 0.8333 (p0) REVERT: C 170 TYR cc_start: 0.8573 (m-80) cc_final: 0.6882 (m-80) REVERT: C 173 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8660 (mt) REVERT: C 250 GLN cc_start: 0.8635 (tm-30) cc_final: 0.8324 (tm-30) REVERT: D 14 ILE cc_start: 0.9090 (mm) cc_final: 0.8876 (mm) REVERT: D 45 TYR cc_start: 0.8721 (p90) cc_final: 0.8473 (p90) REVERT: E 46 GLN cc_start: 0.8941 (mp10) cc_final: 0.8626 (mt0) REVERT: E 115 GLN cc_start: 0.8307 (mt0) cc_final: 0.8033 (mt0) REVERT: F 30 VAL cc_start: 0.8476 (t) cc_final: 0.8251 (p) REVERT: F 76 PHE cc_start: 0.7909 (m-10) cc_final: 0.7476 (m-10) REVERT: F 100 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7840 (tm-30) REVERT: F 168 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7896 (tt) REVERT: G 25 ILE cc_start: 0.6626 (OUTLIER) cc_final: 0.6330 (mt) REVERT: G 146 ASP cc_start: 0.7713 (m-30) cc_final: 0.7371 (m-30) REVERT: G 150 TYR cc_start: 0.7596 (m-10) cc_final: 0.7394 (m-80) REVERT: H 41 LYS cc_start: 0.4702 (OUTLIER) cc_final: 0.4285 (mtpt) REVERT: I 12 VAL cc_start: 0.0350 (OUTLIER) cc_final: 0.0137 (m) REVERT: I 116 MET cc_start: 0.0809 (tpt) cc_final: 0.0166 (mmm) REVERT: J 31 GLU cc_start: 0.7368 (tp30) cc_final: 0.7147 (tp30) REVERT: J 128 ASN cc_start: 0.8734 (t0) cc_final: 0.8209 (t0) REVERT: K 88 ASN cc_start: 0.7780 (t0) cc_final: 0.7515 (t0) REVERT: K 114 LYS cc_start: 0.8359 (tppt) cc_final: 0.8100 (mmtt) REVERT: L 129 LYS cc_start: 0.8518 (ttmm) cc_final: 0.8270 (mtmm) REVERT: L 136 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6778 (mm-30) REVERT: M 6 ARG cc_start: 0.7154 (ptm-80) cc_final: 0.6675 (ptp90) REVERT: M 9 PHE cc_start: 0.8825 (m-80) cc_final: 0.8506 (m-10) REVERT: M 53 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.7931 (mtm) REVERT: O 12 THR cc_start: 0.9296 (m) cc_final: 0.8791 (p) REVERT: P 71 ARG cc_start: 0.8083 (ttt180) cc_final: 0.7676 (ttt-90) REVERT: Q 48 ASP cc_start: 0.8252 (m-30) cc_final: 0.7966 (m-30) REVERT: U 5 ARG cc_start: 0.8056 (ptp-170) cc_final: 0.7758 (mtt180) REVERT: U 13 LEU cc_start: 0.8431 (mt) cc_final: 0.8153 (mt) REVERT: U 87 GLU cc_start: 0.7300 (mp0) cc_final: 0.6904 (mp0) REVERT: U 100 GLU cc_start: 0.7722 (pt0) cc_final: 0.7441 (pt0) REVERT: V 12 GLN cc_start: 0.8427 (mp10) cc_final: 0.8172 (mt0) REVERT: W 7 ARG cc_start: 0.7314 (ttm110) cc_final: 0.7064 (mtm110) REVERT: Y 6 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.6968 (mt) REVERT: Y 39 GLN cc_start: 0.7548 (mt0) cc_final: 0.6935 (mp10) REVERT: 3 14 LYS cc_start: 0.8365 (mptt) cc_final: 0.8114 (mptp) REVERT: 4 20 ASP cc_start: 0.7818 (t0) cc_final: 0.7287 (t0) REVERT: 6 2 LYS cc_start: 0.6724 (mttt) cc_final: 0.6295 (mttm) outliers start: 286 outliers final: 211 residues processed: 1232 average time/residue: 1.2577 time to fit residues: 2705.9859 Evaluate side-chains 1259 residues out of total 4853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 1029 time to evaluate : 6.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 13 VAL Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 20 ARG Chi-restraints excluded: chain b residue 66 ILE Chi-restraints excluded: chain b residue 93 HIS Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 166 ASP Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 151 GLU Chi-restraints excluded: chain c residue 152 VAL Chi-restraints excluded: chain c residue 183 TYR Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 77 GLU Chi-restraints excluded: chain d residue 122 ILE Chi-restraints excluded: chain d residue 123 MET Chi-restraints excluded: chain d residue 144 ILE Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 172 VAL Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain e residue 14 LEU Chi-restraints excluded: chain e residue 36 THR Chi-restraints excluded: chain e residue 79 THR Chi-restraints excluded: chain e residue 85 LYS Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 119 VAL Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 13 ASP Chi-restraints excluded: chain f residue 33 GLU Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 74 LEU Chi-restraints excluded: chain f residue 86 ARG Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 83 THR Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 103 ILE Chi-restraints excluded: chain g residue 105 GLU Chi-restraints excluded: chain g residue 135 LYS Chi-restraints excluded: chain g residue 147 ASN Chi-restraints excluded: chain h residue 10 LEU Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 41 GLU Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain i residue 62 LEU Chi-restraints excluded: chain i residue 71 ILE Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain i residue 106 ASP Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 56 HIS Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain j residue 102 LEU Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain k residue 63 GLN Chi-restraints excluded: chain k residue 95 THR Chi-restraints excluded: chain k residue 113 THR Chi-restraints excluded: chain l residue 54 VAL Chi-restraints excluded: chain l residue 69 GLU Chi-restraints excluded: chain l residue 74 GLN Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain l residue 80 LEU Chi-restraints excluded: chain l residue 96 THR Chi-restraints excluded: chain l residue 97 VAL Chi-restraints excluded: chain l residue 101 LEU Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 19 THR Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain o residue 1 SER Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 57 ILE Chi-restraints excluded: chain p residue 63 GLN Chi-restraints excluded: chain q residue 20 ILE Chi-restraints excluded: chain q residue 37 ILE Chi-restraints excluded: chain q residue 68 LYS Chi-restraints excluded: chain r residue 25 ILE Chi-restraints excluded: chain r residue 27 THR Chi-restraints excluded: chain r residue 33 THR Chi-restraints excluded: chain r residue 65 SER Chi-restraints excluded: chain s residue 28 LYS Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 135 HIS Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 45 ARG Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 82 SER Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 39 ASN Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 66 ASP Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 66 GLU Chi-restraints excluded: chain W residue 74 LYS Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 22 LEU Chi-restraints excluded: chain Z residue 4 ILE Chi-restraints excluded: chain Z residue 36 GLU Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 55 LYS Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 10 SER Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 18 LYS Chi-restraints excluded: chain 4 residue 37 GLN Chi-restraints excluded: chain 5 residue 17 GLU Chi-restraints excluded: chain 5 residue 33 VAL Chi-restraints excluded: chain 5 residue 77 VAL Chi-restraints excluded: chain 6 residue 13 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 832 optimal weight: 3.9990 chunk 567 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 744 optimal weight: 7.9990 chunk 412 optimal weight: 10.0000 chunk 852 optimal weight: 5.9990 chunk 690 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 510 optimal weight: 10.0000 chunk 897 optimal weight: 6.9990 chunk 252 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 GLN ** g 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 36 GLN ** i 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 62 ASN ** p 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 8 GLN ** t 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 17 ASN O 61 GLN R 86 GLN W 72 ASN Y 27 ASN ** 6 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 158507 Z= 0.356 Angle : 0.729 15.065 236990 Z= 0.384 Chirality : 0.041 0.371 30193 Planarity : 0.007 0.137 12798 Dihedral : 23.645 179.010 78902 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.30 % Favored : 88.40 % Rotamer: Outliers : 6.96 % Allowed : 21.22 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.10), residues: 5847 helix: -0.33 (0.11), residues: 1926 sheet: -1.88 (0.16), residues: 1006 loop : -2.56 (0.10), residues: 2915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP c 200 HIS 0.010 0.001 HIS 3 30 PHE 0.023 0.002 PHE H 46 TYR 0.019 0.002 TYR F 6 ARG 0.008 0.001 ARG e 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11694 Ramachandran restraints generated. 5847 Oldfield, 0 Emsley, 5847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11694 Ramachandran restraints generated. 5847 Oldfield, 0 Emsley, 5847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1374 residues out of total 4853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 336 poor density : 1038 time to evaluate : 6.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 8 MET cc_start: 0.6235 (mmt) cc_final: 0.5747 (mmt) REVERT: b 141 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.6978 (tm-30) REVERT: b 166 ASP cc_start: 0.5645 (OUTLIER) cc_final: 0.5377 (m-30) REVERT: c 171 ARG cc_start: 0.7562 (ttp-110) cc_final: 0.7265 (mtp180) REVERT: d 13 ARG cc_start: 0.8477 (tpt170) cc_final: 0.8008 (tpp-160) REVERT: d 46 ARG cc_start: 0.7214 (mtm180) cc_final: 0.6652 (mmt180) REVERT: d 112 GLU cc_start: -0.0744 (OUTLIER) cc_final: -0.1842 (pt0) REVERT: d 122 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8247 (tt) REVERT: d 196 GLU cc_start: 0.7765 (pm20) cc_final: 0.6889 (pm20) REVERT: e 25 LYS cc_start: 0.9065 (ttpt) cc_final: 0.8386 (tptt) REVERT: e 64 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7432 (tt0) REVERT: e 75 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8191 (mt) REVERT: e 145 ASN cc_start: 0.7787 (p0) cc_final: 0.7393 (p0) REVERT: f 56 LYS cc_start: 0.7379 (ttmt) cc_final: 0.6752 (tttp) REVERT: f 74 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.6964 (mm) REVERT: f 86 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8362 (ttp-110) REVERT: f 87 SER cc_start: 0.9079 (p) cc_final: 0.8845 (t) REVERT: g 135 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8265 (ttmt) REVERT: g 137 ARG cc_start: 0.7856 (tmm160) cc_final: 0.7159 (ttp80) REVERT: h 103 VAL cc_start: 0.8906 (OUTLIER) cc_final: 0.8665 (p) REVERT: h 116 ARG cc_start: 0.7648 (mtt180) cc_final: 0.7195 (mtt180) REVERT: i 30 ASN cc_start: 0.8446 (m-40) cc_final: 0.8082 (m-40) REVERT: i 67 LYS cc_start: 0.8376 (ptpp) cc_final: 0.7986 (pttt) REVERT: j 14 ASP cc_start: 0.8018 (t0) cc_final: 0.7815 (t0) REVERT: j 16 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.7058 (mmt-90) REVERT: j 18 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7656 (tt) REVERT: j 56 HIS cc_start: 0.7696 (OUTLIER) cc_final: 0.7165 (t-170) REVERT: j 67 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8173 (mp) REVERT: k 68 ARG cc_start: 0.8018 (mtp-110) cc_final: 0.7595 (mtp-110) REVERT: k 74 LYS cc_start: 0.7998 (mtmm) cc_final: 0.7215 (mmtm) REVERT: l 74 GLN cc_start: 0.6692 (OUTLIER) cc_final: 0.6256 (pm20) REVERT: m 12 LYS cc_start: 0.7983 (ptpt) cc_final: 0.7481 (mtpt) REVERT: m 40 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8174 (mt-10) REVERT: m 41 ASP cc_start: 0.7232 (m-30) cc_final: 0.6711 (t70) REVERT: m 80 MET cc_start: 0.7656 (ptp) cc_final: 0.7347 (ptm) REVERT: n 22 LYS cc_start: 0.6513 (mmtt) cc_final: 0.6059 (tmtt) REVERT: o 70 LYS cc_start: 0.9279 (ttpt) cc_final: 0.8971 (tttt) REVERT: q 32 ILE cc_start: 0.9266 (mt) cc_final: 0.8871 (mt) REVERT: q 33 TYR cc_start: 0.8797 (m-80) cc_final: 0.8358 (m-80) REVERT: q 79 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7346 (tm-30) REVERT: r 20 ILE cc_start: 0.6971 (OUTLIER) cc_final: 0.6709 (mm) REVERT: r 47 ARG cc_start: 0.6724 (mmt-90) cc_final: 0.6380 (ttt180) REVERT: s 6 LYS cc_start: 0.6007 (mmtp) cc_final: 0.5699 (pttm) REVERT: s 15 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.6854 (pp) REVERT: t 23 ARG cc_start: 0.7892 (mmm160) cc_final: 0.7587 (mmt-90) REVERT: t 29 THR cc_start: 0.9207 (p) cc_final: 0.8983 (p) REVERT: C 2 VAL cc_start: 0.8589 (t) cc_final: 0.8342 (p) REVERT: C 43 ASN cc_start: 0.8758 (p0) cc_final: 0.8514 (p0) REVERT: C 173 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8604 (mt) REVERT: D 14 ILE cc_start: 0.9091 (mm) cc_final: 0.8886 (mm) REVERT: D 45 TYR cc_start: 0.8741 (p90) cc_final: 0.8501 (p90) REVERT: D 133 THR cc_start: 0.9068 (p) cc_final: 0.8807 (p) REVERT: E 46 GLN cc_start: 0.8963 (mp10) cc_final: 0.8639 (mt0) REVERT: E 115 GLN cc_start: 0.8312 (mt0) cc_final: 0.8040 (mt0) REVERT: F 30 VAL cc_start: 0.8500 (t) cc_final: 0.8286 (p) REVERT: F 76 PHE cc_start: 0.7959 (m-10) cc_final: 0.7581 (m-10) REVERT: G 25 ILE cc_start: 0.6651 (OUTLIER) cc_final: 0.6332 (mt) REVERT: G 146 ASP cc_start: 0.7757 (m-30) cc_final: 0.7426 (m-30) REVERT: H 41 LYS cc_start: 0.5374 (OUTLIER) cc_final: 0.4920 (mtpt) REVERT: I 48 ILE cc_start: 0.1271 (OUTLIER) cc_final: 0.0727 (tp) REVERT: I 116 MET cc_start: 0.0819 (tpt) cc_final: 0.0162 (mmm) REVERT: J 31 GLU cc_start: 0.7424 (tp30) cc_final: 0.7191 (tp30) REVERT: J 128 ASN cc_start: 0.8820 (t0) cc_final: 0.8329 (t0) REVERT: K 88 ASN cc_start: 0.7789 (t0) cc_final: 0.7424 (t0) REVERT: K 113 MET cc_start: 0.6809 (mmp) cc_final: 0.6509 (mmp) REVERT: L 129 LYS cc_start: 0.8564 (ttmm) cc_final: 0.8299 (mtmm) REVERT: L 136 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6777 (mm-30) REVERT: M 6 ARG cc_start: 0.7181 (ptm-80) cc_final: 0.6704 (ptp90) REVERT: M 9 PHE cc_start: 0.8852 (m-80) cc_final: 0.8529 (m-10) REVERT: M 53 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.7911 (mtm) REVERT: N 2 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.7884 (tmt170) REVERT: N 23 ASN cc_start: 0.8588 (m-40) cc_final: 0.8214 (m-40) REVERT: O 12 THR cc_start: 0.9299 (m) cc_final: 0.8732 (p) REVERT: P 71 ARG cc_start: 0.8129 (ttt180) cc_final: 0.7891 (ttt-90) REVERT: Q 48 ASP cc_start: 0.8274 (m-30) cc_final: 0.7986 (m-30) REVERT: T 50 LEU cc_start: 0.8788 (mm) cc_final: 0.8586 (mm) REVERT: U 5 ARG cc_start: 0.8070 (ptp-170) cc_final: 0.7730 (mtt180) REVERT: U 13 LEU cc_start: 0.8470 (mt) cc_final: 0.8214 (mt) REVERT: U 87 GLU cc_start: 0.7337 (mp0) cc_final: 0.6885 (mp0) REVERT: V 12 GLN cc_start: 0.8404 (mp10) cc_final: 0.8195 (mt0) REVERT: W 7 ARG cc_start: 0.7304 (ttm110) cc_final: 0.7064 (mtm110) REVERT: W 40 LYS cc_start: 0.8921 (mttt) cc_final: 0.8277 (mtpt) REVERT: Y 17 GLU cc_start: 0.8210 (tt0) cc_final: 0.7961 (tt0) REVERT: Y 39 GLN cc_start: 0.7611 (mt0) cc_final: 0.7003 (mp10) REVERT: 4 20 ASP cc_start: 0.7848 (t0) cc_final: 0.7329 (t0) REVERT: 5 23 LEU cc_start: 0.4004 (mm) cc_final: 0.3650 (mt) REVERT: 6 2 LYS cc_start: 0.6733 (mttt) cc_final: 0.6286 (mttm) outliers start: 336 outliers final: 262 residues processed: 1246 average time/residue: 1.2431 time to fit residues: 2709.9908 Evaluate side-chains 1299 residues out of total 4853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 1014 time to evaluate : 6.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 13 VAL Chi-restraints excluded: chain b residue 14 HIS Chi-restraints excluded: chain b residue 17 HIS Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 20 ARG Chi-restraints excluded: chain b residue 66 ILE Chi-restraints excluded: chain b residue 89 PHE Chi-restraints excluded: chain b residue 93 HIS Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 141 GLU Chi-restraints excluded: chain b residue 166 ASP Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 50 SER Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 151 GLU Chi-restraints excluded: chain c residue 152 VAL Chi-restraints excluded: chain c residue 183 TYR Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 63 ILE Chi-restraints excluded: chain d residue 77 GLU Chi-restraints excluded: chain d residue 112 GLU Chi-restraints excluded: chain d residue 122 ILE Chi-restraints excluded: chain d residue 123 MET Chi-restraints excluded: chain d residue 144 ILE Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain e residue 14 LEU Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 36 THR Chi-restraints excluded: chain e residue 64 GLU Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 79 THR Chi-restraints excluded: chain e residue 85 LYS Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 119 VAL Chi-restraints excluded: chain e residue 133 ILE Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 13 ASP Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 68 GLN Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 74 LEU Chi-restraints excluded: chain f residue 86 ARG Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 83 THR Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 105 GLU Chi-restraints excluded: chain g residue 135 LYS Chi-restraints excluded: chain g residue 147 ASN Chi-restraints excluded: chain h residue 10 LEU Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 41 GLU Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain i residue 36 GLN Chi-restraints excluded: chain i residue 46 VAL Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain i residue 59 LYS Chi-restraints excluded: chain i residue 62 LEU Chi-restraints excluded: chain i residue 71 ILE Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain i residue 106 ASP Chi-restraints excluded: chain i residue 126 PHE Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 16 ARG Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 56 HIS Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain j residue 102 LEU Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain k residue 63 GLN Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain k residue 95 THR Chi-restraints excluded: chain k residue 113 THR Chi-restraints excluded: chain l residue 54 VAL Chi-restraints excluded: chain l residue 69 GLU Chi-restraints excluded: chain l residue 74 GLN Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain l residue 80 LEU Chi-restraints excluded: chain l residue 96 THR Chi-restraints excluded: chain l residue 97 VAL Chi-restraints excluded: chain l residue 101 LEU Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 19 THR Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain o residue 1 SER Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 50 THR Chi-restraints excluded: chain p residue 57 ILE Chi-restraints excluded: chain p residue 63 GLN Chi-restraints excluded: chain q residue 20 ILE Chi-restraints excluded: chain q residue 37 ILE Chi-restraints excluded: chain q residue 64 ARG Chi-restraints excluded: chain q residue 68 LYS Chi-restraints excluded: chain r residue 20 ILE Chi-restraints excluded: chain r residue 25 ILE Chi-restraints excluded: chain r residue 27 THR Chi-restraints excluded: chain r residue 33 THR Chi-restraints excluded: chain r residue 65 SER Chi-restraints excluded: chain s residue 3 SER Chi-restraints excluded: chain s residue 15 LEU Chi-restraints excluded: chain s residue 28 LYS Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 48 ILE Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 17 ASN Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 35 LYS Chi-restraints excluded: chain N residue 45 ARG Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 82 SER Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 39 ASN Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 66 ASP Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 66 GLU Chi-restraints excluded: chain W residue 74 LYS Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 22 LEU Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain Z residue 18 LYS Chi-restraints excluded: chain Z residue 24 LEU Chi-restraints excluded: chain Z residue 36 GLU Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 55 LYS Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 10 SER Chi-restraints excluded: chain 0 residue 27 LEU Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 18 LYS Chi-restraints excluded: chain 4 residue 37 GLN Chi-restraints excluded: chain 5 residue 17 GLU Chi-restraints excluded: chain 5 residue 27 VAL Chi-restraints excluded: chain 5 residue 33 VAL Chi-restraints excluded: chain 5 residue 77 VAL Chi-restraints excluded: chain 6 residue 13 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 336 optimal weight: 4.9990 chunk 900 optimal weight: 9.9990 chunk 197 optimal weight: 9.9990 chunk 586 optimal weight: 7.9990 chunk 246 optimal weight: 8.9990 chunk 1000 optimal weight: 7.9990 chunk 830 optimal weight: 1.9990 chunk 463 optimal weight: 8.9990 chunk 83 optimal weight: 20.0000 chunk 330 optimal weight: 5.9990 chunk 525 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 41 ASN ** d 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 GLN ** g 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 62 ASN ** t 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 61 GLN R 86 GLN U 98 ASN W 72 ASN ** 6 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 158507 Z= 0.335 Angle : 0.715 15.019 236990 Z= 0.379 Chirality : 0.040 0.365 30193 Planarity : 0.007 0.135 12798 Dihedral : 23.632 178.968 78902 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.05 % Favored : 88.64 % Rotamer: Outliers : 7.67 % Allowed : 21.87 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.10), residues: 5847 helix: -0.25 (0.12), residues: 1924 sheet: -1.79 (0.16), residues: 1012 loop : -2.51 (0.11), residues: 2911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP c 200 HIS 0.010 0.001 HIS 3 30 PHE 0.025 0.002 PHE H 46 TYR 0.026 0.002 TYR S 38 ARG 0.010 0.000 ARG f 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11694 Ramachandran restraints generated. 5847 Oldfield, 0 Emsley, 5847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11694 Ramachandran restraints generated. 5847 Oldfield, 0 Emsley, 5847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1401 residues out of total 4853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 370 poor density : 1031 time to evaluate : 6.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 141 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7144 (tm-30) REVERT: b 166 ASP cc_start: 0.5617 (OUTLIER) cc_final: 0.5355 (m-30) REVERT: c 74 ILE cc_start: 0.7459 (OUTLIER) cc_final: 0.7237 (mm) REVERT: c 168 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7612 (ptp90) REVERT: c 171 ARG cc_start: 0.7703 (ttp-110) cc_final: 0.7377 (ttp80) REVERT: d 13 ARG cc_start: 0.8471 (tpt170) cc_final: 0.8062 (tpp-160) REVERT: d 43 ARG cc_start: 0.5329 (OUTLIER) cc_final: 0.4089 (mtp-110) REVERT: d 112 GLU cc_start: -0.0794 (OUTLIER) cc_final: -0.1923 (pt0) REVERT: d 122 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8252 (tt) REVERT: d 196 GLU cc_start: 0.7734 (pm20) cc_final: 0.6815 (pm20) REVERT: e 25 LYS cc_start: 0.9069 (ttpt) cc_final: 0.8388 (tptt) REVERT: e 145 ASN cc_start: 0.7756 (p0) cc_final: 0.7339 (p0) REVERT: f 2 ARG cc_start: 0.6914 (mtt-85) cc_final: 0.6498 (mtt90) REVERT: f 54 LEU cc_start: 0.3386 (OUTLIER) cc_final: 0.2997 (mm) REVERT: f 56 LYS cc_start: 0.7360 (ttmt) cc_final: 0.6721 (tttp) REVERT: f 68 GLN cc_start: 0.6761 (OUTLIER) cc_final: 0.6428 (mt0) REVERT: f 74 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.6961 (mm) REVERT: f 86 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8329 (ttp-110) REVERT: f 87 SER cc_start: 0.9104 (p) cc_final: 0.8868 (t) REVERT: f 92 THR cc_start: 0.5573 (OUTLIER) cc_final: 0.5372 (t) REVERT: g 135 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8260 (ttmt) REVERT: g 137 ARG cc_start: 0.7851 (tmm160) cc_final: 0.7150 (ttp80) REVERT: h 103 VAL cc_start: 0.8895 (OUTLIER) cc_final: 0.8657 (p) REVERT: h 116 ARG cc_start: 0.7634 (mtt180) cc_final: 0.7177 (mtt180) REVERT: i 30 ASN cc_start: 0.8431 (m-40) cc_final: 0.8036 (m-40) REVERT: i 67 LYS cc_start: 0.8543 (ptpp) cc_final: 0.8122 (pttt) REVERT: j 16 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.7061 (mmt-90) REVERT: j 18 ILE cc_start: 0.7953 (OUTLIER) cc_final: 0.7633 (tt) REVERT: j 56 HIS cc_start: 0.7685 (OUTLIER) cc_final: 0.7154 (t-170) REVERT: j 67 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8177 (mp) REVERT: j 92 LEU cc_start: 0.3028 (OUTLIER) cc_final: 0.2774 (pp) REVERT: k 68 ARG cc_start: 0.8019 (mtp-110) cc_final: 0.7590 (mtp-110) REVERT: k 74 LYS cc_start: 0.8006 (mtmm) cc_final: 0.7218 (mmtm) REVERT: l 74 GLN cc_start: 0.6719 (OUTLIER) cc_final: 0.6285 (pm20) REVERT: l 76 HIS cc_start: 0.6566 (OUTLIER) cc_final: 0.6267 (m90) REVERT: m 12 LYS cc_start: 0.7935 (ptpt) cc_final: 0.7437 (mtpt) REVERT: m 40 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8178 (mt-10) REVERT: m 41 ASP cc_start: 0.7235 (m-30) cc_final: 0.6708 (t70) REVERT: m 80 MET cc_start: 0.7661 (ptp) cc_final: 0.7349 (ptm) REVERT: n 11 LYS cc_start: 0.8271 (ttpp) cc_final: 0.7780 (ptmt) REVERT: n 22 LYS cc_start: 0.6541 (mmtt) cc_final: 0.6094 (tmtt) REVERT: n 79 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8914 (pp) REVERT: o 44 GLU cc_start: 0.7049 (tt0) cc_final: 0.6829 (tm-30) REVERT: o 70 LYS cc_start: 0.9276 (ttpt) cc_final: 0.8968 (tttt) REVERT: q 32 ILE cc_start: 0.9276 (mt) cc_final: 0.8885 (mt) REVERT: q 33 TYR cc_start: 0.8795 (m-80) cc_final: 0.8347 (m-80) REVERT: q 79 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7336 (tm-30) REVERT: r 20 ILE cc_start: 0.6957 (OUTLIER) cc_final: 0.6712 (mm) REVERT: r 47 ARG cc_start: 0.6714 (mmt-90) cc_final: 0.6363 (ttt180) REVERT: s 6 LYS cc_start: 0.6032 (mmtp) cc_final: 0.5761 (pttm) REVERT: s 15 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.6830 (pp) REVERT: t 23 ARG cc_start: 0.7880 (mmm160) cc_final: 0.7587 (mmt-90) REVERT: t 29 THR cc_start: 0.8959 (p) cc_final: 0.8749 (p) REVERT: C 2 VAL cc_start: 0.8581 (t) cc_final: 0.8316 (p) REVERT: C 18 VAL cc_start: 0.8654 (t) cc_final: 0.8433 (m) REVERT: C 43 ASN cc_start: 0.8752 (p0) cc_final: 0.8501 (p0) REVERT: C 78 GLU cc_start: 0.7543 (tp30) cc_final: 0.7295 (tp30) REVERT: C 173 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8572 (mt) REVERT: D 45 TYR cc_start: 0.8716 (p90) cc_final: 0.8470 (p90) REVERT: D 126 ASN cc_start: 0.7741 (m-40) cc_final: 0.7496 (m110) REVERT: D 133 THR cc_start: 0.9063 (p) cc_final: 0.8808 (p) REVERT: E 46 GLN cc_start: 0.8957 (mp10) cc_final: 0.8638 (mt0) REVERT: E 115 GLN cc_start: 0.8311 (mt0) cc_final: 0.8037 (mt0) REVERT: F 30 VAL cc_start: 0.8521 (t) cc_final: 0.8260 (p) REVERT: F 76 PHE cc_start: 0.7969 (m-10) cc_final: 0.7638 (m-10) REVERT: F 100 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7871 (tm-30) REVERT: G 25 ILE cc_start: 0.6727 (OUTLIER) cc_final: 0.6433 (mt) REVERT: G 131 VAL cc_start: 0.8161 (t) cc_final: 0.7942 (p) REVERT: G 146 ASP cc_start: 0.7630 (m-30) cc_final: 0.7371 (m-30) REVERT: H 41 LYS cc_start: 0.5347 (OUTLIER) cc_final: 0.4897 (mtpt) REVERT: I 116 MET cc_start: 0.0805 (tpt) cc_final: 0.0129 (mmm) REVERT: J 31 GLU cc_start: 0.7412 (tp30) cc_final: 0.7185 (tp30) REVERT: J 128 ASN cc_start: 0.8822 (t0) cc_final: 0.8339 (t0) REVERT: K 88 ASN cc_start: 0.7784 (t0) cc_final: 0.7490 (t0) REVERT: K 113 MET cc_start: 0.6885 (mmp) cc_final: 0.6510 (mmp) REVERT: L 129 LYS cc_start: 0.8551 (ttmm) cc_final: 0.8288 (mtmm) REVERT: L 136 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6775 (mm-30) REVERT: M 6 ARG cc_start: 0.7180 (ptm-80) cc_final: 0.6700 (ptp90) REVERT: M 9 PHE cc_start: 0.8857 (m-80) cc_final: 0.8531 (m-10) REVERT: M 53 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.7825 (mtm) REVERT: N 23 ASN cc_start: 0.8683 (m-40) cc_final: 0.8296 (m-40) REVERT: O 12 THR cc_start: 0.9291 (m) cc_final: 0.8729 (p) REVERT: P 71 ARG cc_start: 0.8123 (ttt180) cc_final: 0.7705 (ttt-90) REVERT: Q 48 ASP cc_start: 0.8265 (m-30) cc_final: 0.7974 (m-30) REVERT: S 1 MET cc_start: 0.6479 (tmm) cc_final: 0.5992 (tmm) REVERT: T 7 LEU cc_start: 0.9011 (mp) cc_final: 0.8782 (mt) REVERT: T 26 LYS cc_start: 0.7876 (tmtt) cc_final: 0.7400 (tttp) REVERT: U 5 ARG cc_start: 0.8061 (ptp-170) cc_final: 0.7717 (mtt180) REVERT: U 13 LEU cc_start: 0.8460 (mt) cc_final: 0.8214 (mt) REVERT: U 87 GLU cc_start: 0.7293 (mp0) cc_final: 0.6886 (mp0) REVERT: V 12 GLN cc_start: 0.8408 (mp10) cc_final: 0.8193 (mt0) REVERT: W 7 ARG cc_start: 0.7305 (ttm110) cc_final: 0.7068 (mtm110) REVERT: W 40 LYS cc_start: 0.8917 (mttt) cc_final: 0.8275 (mtpt) REVERT: Y 6 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6928 (mt) REVERT: Y 17 GLU cc_start: 0.8207 (tt0) cc_final: 0.7991 (tt0) REVERT: Y 39 GLN cc_start: 0.7602 (mt0) cc_final: 0.7004 (mp10) REVERT: 4 20 ASP cc_start: 0.7840 (t0) cc_final: 0.7319 (t0) REVERT: 5 23 LEU cc_start: 0.3966 (mm) cc_final: 0.3571 (mt) REVERT: 6 2 LYS cc_start: 0.6714 (mttt) cc_final: 0.6414 (mttm) outliers start: 370 outliers final: 285 residues processed: 1261 average time/residue: 1.2194 time to fit residues: 2695.9714 Evaluate side-chains 1321 residues out of total 4853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 314 poor density : 1007 time to evaluate : 6.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 13 VAL Chi-restraints excluded: chain b residue 17 HIS Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 20 ARG Chi-restraints excluded: chain b residue 66 ILE Chi-restraints excluded: chain b residue 89 PHE Chi-restraints excluded: chain b residue 93 HIS Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 141 GLU Chi-restraints excluded: chain b residue 166 ASP Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 203 ASP Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 50 SER Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 74 ILE Chi-restraints excluded: chain c residue 151 GLU Chi-restraints excluded: chain c residue 168 ARG Chi-restraints excluded: chain c residue 183 TYR Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 43 ARG Chi-restraints excluded: chain d residue 63 ILE Chi-restraints excluded: chain d residue 66 VAL Chi-restraints excluded: chain d residue 77 GLU Chi-restraints excluded: chain d residue 112 GLU Chi-restraints excluded: chain d residue 122 ILE Chi-restraints excluded: chain d residue 123 MET Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 170 LEU Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain e residue 14 LEU Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 36 THR Chi-restraints excluded: chain e residue 79 THR Chi-restraints excluded: chain e residue 85 LYS Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 96 GLN Chi-restraints excluded: chain e residue 119 VAL Chi-restraints excluded: chain e residue 133 ILE Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 13 ASP Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 54 LEU Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 68 GLN Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 74 LEU Chi-restraints excluded: chain f residue 86 ARG Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 83 THR Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 103 ILE Chi-restraints excluded: chain g residue 105 GLU Chi-restraints excluded: chain g residue 135 LYS Chi-restraints excluded: chain g residue 147 ASN Chi-restraints excluded: chain h residue 10 LEU Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 41 GLU Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 57 GLU Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain h residue 100 ILE Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain i residue 46 VAL Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain i residue 59 LYS Chi-restraints excluded: chain i residue 62 LEU Chi-restraints excluded: chain i residue 71 ILE Chi-restraints excluded: chain i residue 93 LEU Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain i residue 106 ASP Chi-restraints excluded: chain i residue 126 PHE Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 16 ARG Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 56 HIS Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain k residue 63 GLN Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain k residue 95 THR Chi-restraints excluded: chain k residue 113 THR Chi-restraints excluded: chain l residue 54 VAL Chi-restraints excluded: chain l residue 69 GLU Chi-restraints excluded: chain l residue 74 GLN Chi-restraints excluded: chain l residue 76 HIS Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain l residue 80 LEU Chi-restraints excluded: chain l residue 89 LEU Chi-restraints excluded: chain l residue 96 THR Chi-restraints excluded: chain l residue 97 VAL Chi-restraints excluded: chain l residue 101 LEU Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain l residue 118 VAL Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 19 THR Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain m residue 76 ILE Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain n residue 79 LEU Chi-restraints excluded: chain o residue 1 SER Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 50 THR Chi-restraints excluded: chain p residue 57 ILE Chi-restraints excluded: chain p residue 63 GLN Chi-restraints excluded: chain q residue 20 ILE Chi-restraints excluded: chain q residue 37 ILE Chi-restraints excluded: chain q residue 64 ARG Chi-restraints excluded: chain q residue 68 LYS Chi-restraints excluded: chain r residue 20 ILE Chi-restraints excluded: chain r residue 25 ILE Chi-restraints excluded: chain r residue 27 THR Chi-restraints excluded: chain r residue 33 THR Chi-restraints excluded: chain r residue 65 SER Chi-restraints excluded: chain s residue 3 SER Chi-restraints excluded: chain s residue 15 LEU Chi-restraints excluded: chain s residue 28 LYS Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 48 ILE Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 31 VAL Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 123 LYS Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 135 HIS Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 45 ARG Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 82 SER Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 39 ASN Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 66 ASP Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 66 GLU Chi-restraints excluded: chain W residue 74 LYS Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 22 LEU Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain Z residue 4 ILE Chi-restraints excluded: chain Z residue 18 LYS Chi-restraints excluded: chain Z residue 36 GLU Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain Z residue 55 LYS Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 10 SER Chi-restraints excluded: chain 0 residue 42 ILE Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 18 LYS Chi-restraints excluded: chain 4 residue 37 GLN Chi-restraints excluded: chain 5 residue 17 GLU Chi-restraints excluded: chain 5 residue 27 VAL Chi-restraints excluded: chain 5 residue 33 VAL Chi-restraints excluded: chain 5 residue 77 VAL Chi-restraints excluded: chain 5 residue 114 GLU Chi-restraints excluded: chain 6 residue 4 ASP Chi-restraints excluded: chain 6 residue 13 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 964 optimal weight: 7.9990 chunk 112 optimal weight: 20.0000 chunk 570 optimal weight: 10.0000 chunk 730 optimal weight: 9.9990 chunk 566 optimal weight: 10.0000 chunk 842 optimal weight: 5.9990 chunk 558 optimal weight: 10.0000 chunk 996 optimal weight: 3.9990 chunk 623 optimal weight: 10.0000 chunk 607 optimal weight: 10.0000 chunk 460 optimal weight: 8.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 GLN ** g 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 62 ASN ** t 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN ** I 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 61 GLN R 86 GLN W 72 ASN ** 6 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 158507 Z= 0.418 Angle : 0.774 15.124 236990 Z= 0.405 Chirality : 0.043 0.361 30193 Planarity : 0.007 0.140 12798 Dihedral : 23.651 178.639 78902 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.85 % Favored : 87.86 % Rotamer: Outliers : 8.00 % Allowed : 22.38 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.10), residues: 5847 helix: -0.33 (0.11), residues: 1933 sheet: -1.82 (0.16), residues: 992 loop : -2.57 (0.10), residues: 2922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 212 HIS 0.011 0.002 HIS 3 30 PHE 0.019 0.002 PHE 5 69 TYR 0.030 0.002 TYR S 38 ARG 0.011 0.001 ARG f 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11694 Ramachandran restraints generated. 5847 Oldfield, 0 Emsley, 5847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11694 Ramachandran restraints generated. 5847 Oldfield, 0 Emsley, 5847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1404 residues out of total 4853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 386 poor density : 1018 time to evaluate : 6.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 62 ARG cc_start: 0.5163 (ptp-170) cc_final: 0.4665 (mtm-85) REVERT: b 141 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7351 (tm-30) REVERT: b 166 ASP cc_start: 0.5672 (OUTLIER) cc_final: 0.5389 (m-30) REVERT: c 7 ASN cc_start: 0.8333 (t0) cc_final: 0.8019 (t0) REVERT: c 74 ILE cc_start: 0.7499 (OUTLIER) cc_final: 0.7296 (mm) REVERT: c 168 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7791 (ptp90) REVERT: c 171 ARG cc_start: 0.7687 (ttp-110) cc_final: 0.7421 (ttp80) REVERT: d 13 ARG cc_start: 0.8525 (tpt170) cc_final: 0.8088 (tpp-160) REVERT: d 43 ARG cc_start: 0.5363 (OUTLIER) cc_final: 0.4105 (mtp-110) REVERT: d 112 GLU cc_start: -0.1096 (OUTLIER) cc_final: -0.2462 (pt0) REVERT: d 122 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.8132 (tt) REVERT: d 196 GLU cc_start: 0.7634 (pm20) cc_final: 0.6562 (pm20) REVERT: e 25 LYS cc_start: 0.9114 (ttpt) cc_final: 0.8273 (tptt) REVERT: e 145 ASN cc_start: 0.7939 (p0) cc_final: 0.7544 (p0) REVERT: f 2 ARG cc_start: 0.6938 (OUTLIER) cc_final: 0.6559 (mtt90) REVERT: f 54 LEU cc_start: 0.3533 (OUTLIER) cc_final: 0.3115 (mm) REVERT: f 56 LYS cc_start: 0.7375 (ttmt) cc_final: 0.6744 (tttp) REVERT: f 74 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7014 (mm) REVERT: f 86 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.8333 (ttp-110) REVERT: f 92 THR cc_start: 0.5703 (OUTLIER) cc_final: 0.5501 (t) REVERT: g 39 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6650 (mt-10) REVERT: g 135 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8220 (ttmt) REVERT: g 137 ARG cc_start: 0.7884 (tmm160) cc_final: 0.7165 (ttp80) REVERT: h 20 ASN cc_start: 0.8721 (OUTLIER) cc_final: 0.8414 (m-40) REVERT: h 60 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8936 (mp) REVERT: h 103 VAL cc_start: 0.8924 (OUTLIER) cc_final: 0.8688 (p) REVERT: h 116 ARG cc_start: 0.7438 (mtt180) cc_final: 0.6918 (mtt180) REVERT: i 30 ASN cc_start: 0.8440 (m-40) cc_final: 0.8042 (m-40) REVERT: i 67 LYS cc_start: 0.8466 (ptpp) cc_final: 0.8068 (pttt) REVERT: j 16 ARG cc_start: 0.7105 (OUTLIER) cc_final: 0.6719 (mmt-90) REVERT: j 18 ILE cc_start: 0.7821 (OUTLIER) cc_final: 0.7514 (tt) REVERT: j 56 HIS cc_start: 0.7699 (OUTLIER) cc_final: 0.7162 (t-170) REVERT: j 67 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8257 (mp) REVERT: j 92 LEU cc_start: 0.2933 (OUTLIER) cc_final: 0.2680 (pp) REVERT: k 68 ARG cc_start: 0.8057 (mtp-110) cc_final: 0.7611 (mtp-110) REVERT: k 74 LYS cc_start: 0.7981 (mtmm) cc_final: 0.7167 (mmtm) REVERT: l 74 GLN cc_start: 0.6661 (OUTLIER) cc_final: 0.6197 (pm20) REVERT: l 76 HIS cc_start: 0.6916 (OUTLIER) cc_final: 0.6710 (m90) REVERT: m 12 LYS cc_start: 0.7940 (ptpt) cc_final: 0.7415 (mtpt) REVERT: m 40 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8171 (mt-10) REVERT: m 41 ASP cc_start: 0.7229 (m-30) cc_final: 0.6680 (t70) REVERT: m 80 MET cc_start: 0.7680 (ptp) cc_final: 0.7371 (ptm) REVERT: o 70 LYS cc_start: 0.9284 (ttpt) cc_final: 0.8937 (tttt) REVERT: q 32 ILE cc_start: 0.9262 (mt) cc_final: 0.8880 (mt) REVERT: q 33 TYR cc_start: 0.8809 (m-80) cc_final: 0.8361 (m-80) REVERT: q 79 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7317 (tm-30) REVERT: r 20 ILE cc_start: 0.6954 (OUTLIER) cc_final: 0.6670 (mm) REVERT: r 47 ARG cc_start: 0.6817 (mmt-90) cc_final: 0.6420 (ttt180) REVERT: s 5 LYS cc_start: 0.3946 (OUTLIER) cc_final: 0.2996 (ptmm) REVERT: s 6 LYS cc_start: 0.6111 (mmtp) cc_final: 0.5665 (pttm) REVERT: s 15 LEU cc_start: 0.7568 (pp) cc_final: 0.7087 (pp) REVERT: t 23 ARG cc_start: 0.7900 (mmm160) cc_final: 0.7608 (mmt-90) REVERT: t 69 ASN cc_start: 0.8357 (m-40) cc_final: 0.8103 (m-40) REVERT: C 2 VAL cc_start: 0.8598 (t) cc_final: 0.8318 (p) REVERT: C 173 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8644 (mt) REVERT: D 45 TYR cc_start: 0.8685 (p90) cc_final: 0.8371 (p90) REVERT: D 133 THR cc_start: 0.9099 (p) cc_final: 0.8863 (p) REVERT: D 181 ASP cc_start: 0.7949 (t0) cc_final: 0.7499 (t0) REVERT: E 46 GLN cc_start: 0.8973 (mp10) cc_final: 0.8637 (mt0) REVERT: E 115 GLN cc_start: 0.8274 (mt0) cc_final: 0.7985 (mt0) REVERT: F 56 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8024 (tp) REVERT: F 76 PHE cc_start: 0.8017 (m-10) cc_final: 0.7690 (m-10) REVERT: G 25 ILE cc_start: 0.6798 (OUTLIER) cc_final: 0.6484 (mt) REVERT: H 41 LYS cc_start: 0.5572 (OUTLIER) cc_final: 0.5172 (mtpt) REVERT: I 48 ILE cc_start: 0.1270 (OUTLIER) cc_final: 0.0729 (tp) REVERT: I 116 MET cc_start: 0.0805 (tpt) cc_final: 0.0132 (mmm) REVERT: J 31 GLU cc_start: 0.7457 (tp30) cc_final: 0.7217 (tp30) REVERT: J 128 ASN cc_start: 0.8874 (t0) cc_final: 0.8354 (t0) REVERT: K 88 ASN cc_start: 0.7794 (t0) cc_final: 0.7419 (t0) REVERT: K 113 MET cc_start: 0.6944 (mmp) cc_final: 0.6553 (mmp) REVERT: L 82 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8318 (mp) REVERT: L 129 LYS cc_start: 0.8599 (ttmm) cc_final: 0.8325 (mtmm) REVERT: L 136 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6770 (mm-30) REVERT: M 6 ARG cc_start: 0.7032 (ptm-80) cc_final: 0.6636 (ptp90) REVERT: M 9 PHE cc_start: 0.8838 (m-80) cc_final: 0.8581 (m-10) REVERT: M 53 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.7947 (mtm) REVERT: N 2 ARG cc_start: 0.9026 (OUTLIER) cc_final: 0.8813 (tmt170) REVERT: N 23 ASN cc_start: 0.8591 (m-40) cc_final: 0.8206 (m-40) REVERT: O 12 THR cc_start: 0.9303 (m) cc_final: 0.8689 (p) REVERT: Q 48 ASP cc_start: 0.8324 (m-30) cc_final: 0.8039 (m-30) REVERT: R 11 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7590 (mp10) REVERT: S 1 MET cc_start: 0.6521 (tmm) cc_final: 0.6120 (tmm) REVERT: T 26 LYS cc_start: 0.7890 (tmtt) cc_final: 0.7416 (tttp) REVERT: U 13 LEU cc_start: 0.8482 (mt) cc_final: 0.8242 (mt) REVERT: U 87 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6948 (mp0) REVERT: W 7 ARG cc_start: 0.7324 (ttm110) cc_final: 0.7068 (mtm110) REVERT: W 40 LYS cc_start: 0.8946 (mttt) cc_final: 0.8299 (mtpt) REVERT: Y 17 GLU cc_start: 0.8186 (tt0) cc_final: 0.7976 (tt0) REVERT: Y 39 GLN cc_start: 0.7663 (mt0) cc_final: 0.7228 (mp10) REVERT: 4 20 ASP cc_start: 0.7834 (t0) cc_final: 0.7341 (t0) REVERT: 5 23 LEU cc_start: 0.4021 (mm) cc_final: 0.3664 (mt) REVERT: 5 65 GLU cc_start: 0.4038 (OUTLIER) cc_final: 0.3658 (tt0) REVERT: 6 2 LYS cc_start: 0.6711 (mttt) cc_final: 0.6504 (mttm) outliers start: 386 outliers final: 301 residues processed: 1268 average time/residue: 1.2582 time to fit residues: 2796.1509 Evaluate side-chains 1341 residues out of total 4853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 338 poor density : 1003 time to evaluate : 6.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 13 VAL Chi-restraints excluded: chain b residue 14 HIS Chi-restraints excluded: chain b residue 17 HIS Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 20 ARG Chi-restraints excluded: chain b residue 66 ILE Chi-restraints excluded: chain b residue 89 PHE Chi-restraints excluded: chain b residue 93 HIS Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 141 GLU Chi-restraints excluded: chain b residue 166 ASP Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 203 ASP Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 50 SER Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 74 ILE Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 151 GLU Chi-restraints excluded: chain c residue 168 ARG Chi-restraints excluded: chain c residue 183 TYR Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 43 ARG Chi-restraints excluded: chain d residue 63 ILE Chi-restraints excluded: chain d residue 66 VAL Chi-restraints excluded: chain d residue 77 GLU Chi-restraints excluded: chain d residue 112 GLU Chi-restraints excluded: chain d residue 122 ILE Chi-restraints excluded: chain d residue 123 MET Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 144 ILE Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain e residue 14 LEU Chi-restraints excluded: chain e residue 36 THR Chi-restraints excluded: chain e residue 79 THR Chi-restraints excluded: chain e residue 85 LYS Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 96 GLN Chi-restraints excluded: chain e residue 119 VAL Chi-restraints excluded: chain e residue 133 ILE Chi-restraints excluded: chain f residue 2 ARG Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 13 ASP Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 54 LEU Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 74 LEU Chi-restraints excluded: chain f residue 86 ARG Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 37 THR Chi-restraints excluded: chain g residue 39 GLU Chi-restraints excluded: chain g residue 83 THR Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 103 ILE Chi-restraints excluded: chain g residue 105 GLU Chi-restraints excluded: chain g residue 135 LYS Chi-restraints excluded: chain g residue 147 ASN Chi-restraints excluded: chain h residue 10 LEU Chi-restraints excluded: chain h residue 20 ASN Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 41 GLU Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 57 GLU Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 73 SER Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain h residue 100 ILE Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain i residue 46 VAL Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain i residue 57 VAL Chi-restraints excluded: chain i residue 62 LEU Chi-restraints excluded: chain i residue 71 ILE Chi-restraints excluded: chain i residue 93 LEU Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain i residue 106 ASP Chi-restraints excluded: chain i residue 126 PHE Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 16 ARG Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 56 HIS Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain k residue 63 GLN Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain k residue 95 THR Chi-restraints excluded: chain k residue 113 THR Chi-restraints excluded: chain l residue 54 VAL Chi-restraints excluded: chain l residue 69 GLU Chi-restraints excluded: chain l residue 74 GLN Chi-restraints excluded: chain l residue 76 HIS Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain l residue 80 LEU Chi-restraints excluded: chain l residue 89 LEU Chi-restraints excluded: chain l residue 96 THR Chi-restraints excluded: chain l residue 97 VAL Chi-restraints excluded: chain l residue 101 LEU Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain l residue 118 VAL Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 19 THR Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain m residue 76 ILE Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain o residue 1 SER Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 50 THR Chi-restraints excluded: chain p residue 52 LEU Chi-restraints excluded: chain p residue 57 ILE Chi-restraints excluded: chain p residue 63 GLN Chi-restraints excluded: chain q residue 20 ILE Chi-restraints excluded: chain q residue 37 ILE Chi-restraints excluded: chain q residue 64 ARG Chi-restraints excluded: chain q residue 68 LYS Chi-restraints excluded: chain r residue 20 ILE Chi-restraints excluded: chain r residue 25 ILE Chi-restraints excluded: chain r residue 27 THR Chi-restraints excluded: chain r residue 33 THR Chi-restraints excluded: chain r residue 65 SER Chi-restraints excluded: chain s residue 3 SER Chi-restraints excluded: chain s residue 5 LYS Chi-restraints excluded: chain s residue 28 LYS Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 48 ILE Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 72 GLU Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 123 LYS Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 174 PHE Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain N residue 24 MET Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 35 LYS Chi-restraints excluded: chain N residue 45 ARG Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 82 SER Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 11 GLN Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 39 ASN Chi-restraints excluded: chain U residue 87 GLU Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain U residue 100 GLU Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 66 ASP Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 66 GLU Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain W residue 74 LYS Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 22 LEU Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain Z residue 4 ILE Chi-restraints excluded: chain Z residue 18 LYS Chi-restraints excluded: chain Z residue 24 LEU Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain Z residue 55 LYS Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 10 SER Chi-restraints excluded: chain 0 residue 42 ILE Chi-restraints excluded: chain 2 residue 22 MET Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 18 LYS Chi-restraints excluded: chain 4 residue 37 GLN Chi-restraints excluded: chain 5 residue 17 GLU Chi-restraints excluded: chain 5 residue 27 VAL Chi-restraints excluded: chain 5 residue 33 VAL Chi-restraints excluded: chain 5 residue 65 GLU Chi-restraints excluded: chain 5 residue 77 VAL Chi-restraints excluded: chain 5 residue 114 GLU Chi-restraints excluded: chain 6 residue 4 ASP Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 57 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 616 optimal weight: 10.0000 chunk 397 optimal weight: 20.0000 chunk 595 optimal weight: 50.0000 chunk 300 optimal weight: 2.9990 chunk 195 optimal weight: 5.9990 chunk 193 optimal weight: 10.0000 chunk 633 optimal weight: 8.9990 chunk 678 optimal weight: 20.0000 chunk 492 optimal weight: 20.0000 chunk 92 optimal weight: 10.0000 chunk 783 optimal weight: 5.9990 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 40 HIS ** g 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 62 ASN q 8 GLN ** t 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 17 ASN W 72 ASN ** 6 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 158507 Z= 0.384 Angle : 0.750 15.068 236990 Z= 0.394 Chirality : 0.042 0.359 30193 Planarity : 0.007 0.137 12798 Dihedral : 23.645 178.534 78902 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.42 % Favored : 88.27 % Rotamer: Outliers : 7.81 % Allowed : 23.11 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.10), residues: 5847 helix: -0.27 (0.11), residues: 1930 sheet: -1.82 (0.16), residues: 983 loop : -2.52 (0.11), residues: 2934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP c 200 HIS 0.011 0.001 HIS 3 30 PHE 0.025 0.002 PHE s 73 TYR 0.030 0.002 TYR S 38 ARG 0.009 0.001 ARG f 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11694 Ramachandran restraints generated. 5847 Oldfield, 0 Emsley, 5847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11694 Ramachandran restraints generated. 5847 Oldfield, 0 Emsley, 5847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1389 residues out of total 4853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 377 poor density : 1012 time to evaluate : 6.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 26 MET cc_start: 0.7181 (mmm) cc_final: 0.6940 (mmt) REVERT: b 62 ARG cc_start: 0.5168 (ptp-170) cc_final: 0.4659 (mtm-85) REVERT: b 141 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7368 (tm-30) REVERT: b 166 ASP cc_start: 0.5625 (OUTLIER) cc_final: 0.5351 (m-30) REVERT: c 168 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7784 (ptp90) REVERT: d 13 ARG cc_start: 0.8526 (tpt170) cc_final: 0.8103 (tpp-160) REVERT: d 43 ARG cc_start: 0.5348 (OUTLIER) cc_final: 0.4122 (mtp-110) REVERT: d 122 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8139 (tt) REVERT: d 196 GLU cc_start: 0.7752 (pm20) cc_final: 0.6681 (pm20) REVERT: e 25 LYS cc_start: 0.9092 (ttpt) cc_final: 0.8295 (tptt) REVERT: e 145 ASN cc_start: 0.7903 (p0) cc_final: 0.7489 (p0) REVERT: f 2 ARG cc_start: 0.6949 (OUTLIER) cc_final: 0.6646 (mtt90) REVERT: f 54 LEU cc_start: 0.3462 (OUTLIER) cc_final: 0.3062 (mm) REVERT: f 56 LYS cc_start: 0.7377 (ttmt) cc_final: 0.6739 (tttp) REVERT: f 74 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.6889 (mm) REVERT: f 86 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8332 (ttp-110) REVERT: g 135 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8218 (ttmt) REVERT: g 137 ARG cc_start: 0.7865 (tmm160) cc_final: 0.7392 (ttp80) REVERT: h 103 VAL cc_start: 0.8915 (OUTLIER) cc_final: 0.8670 (p) REVERT: h 116 ARG cc_start: 0.7227 (mtt180) cc_final: 0.6654 (mtt180) REVERT: i 30 ASN cc_start: 0.8452 (m-40) cc_final: 0.8073 (m-40) REVERT: i 67 LYS cc_start: 0.8468 (ptpp) cc_final: 0.8071 (pttt) REVERT: j 16 ARG cc_start: 0.7107 (OUTLIER) cc_final: 0.6734 (mmt-90) REVERT: j 18 ILE cc_start: 0.7821 (OUTLIER) cc_final: 0.7541 (tt) REVERT: j 56 HIS cc_start: 0.7692 (OUTLIER) cc_final: 0.7162 (t-170) REVERT: j 62 ARG cc_start: 0.8405 (mtt90) cc_final: 0.8125 (mtt90) REVERT: j 67 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8187 (mp) REVERT: j 92 LEU cc_start: 0.2877 (OUTLIER) cc_final: 0.2622 (pp) REVERT: k 68 ARG cc_start: 0.8057 (mtp-110) cc_final: 0.7610 (mtp-110) REVERT: k 74 LYS cc_start: 0.7986 (mtmm) cc_final: 0.7173 (mmtm) REVERT: l 74 GLN cc_start: 0.6743 (OUTLIER) cc_final: 0.6284 (pm20) REVERT: l 76 HIS cc_start: 0.6832 (OUTLIER) cc_final: 0.6615 (m90) REVERT: m 12 LYS cc_start: 0.7937 (ptpt) cc_final: 0.7415 (mtpt) REVERT: m 40 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8179 (mt-10) REVERT: m 41 ASP cc_start: 0.7226 (m-30) cc_final: 0.6674 (t70) REVERT: m 80 MET cc_start: 0.7687 (ptp) cc_final: 0.7375 (ptm) REVERT: n 22 LYS cc_start: 0.6491 (mmtt) cc_final: 0.6037 (tmtt) REVERT: o 70 LYS cc_start: 0.9274 (ttpt) cc_final: 0.8935 (tttt) REVERT: q 32 ILE cc_start: 0.9264 (OUTLIER) cc_final: 0.8885 (mt) REVERT: q 33 TYR cc_start: 0.8806 (m-80) cc_final: 0.8359 (m-80) REVERT: q 79 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7303 (tm-30) REVERT: r 20 ILE cc_start: 0.6935 (OUTLIER) cc_final: 0.6664 (mm) REVERT: r 47 ARG cc_start: 0.6811 (mmt-90) cc_final: 0.6411 (ttt180) REVERT: s 5 LYS cc_start: 0.4032 (OUTLIER) cc_final: 0.3019 (ptmm) REVERT: s 6 LYS cc_start: 0.6098 (mmtp) cc_final: 0.5655 (pttm) REVERT: s 15 LEU cc_start: 0.7344 (pp) cc_final: 0.6777 (pp) REVERT: t 23 ARG cc_start: 0.7958 (mmm160) cc_final: 0.7691 (mmt-90) REVERT: t 69 ASN cc_start: 0.8347 (m-40) cc_final: 0.8101 (m-40) REVERT: C 43 ASN cc_start: 0.8793 (p0) cc_final: 0.8544 (p0) REVERT: C 173 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8624 (mt) REVERT: D 45 TYR cc_start: 0.8654 (p90) cc_final: 0.8378 (p90) REVERT: D 133 THR cc_start: 0.9078 (p) cc_final: 0.8839 (p) REVERT: D 181 ASP cc_start: 0.7975 (t0) cc_final: 0.7480 (t0) REVERT: E 46 GLN cc_start: 0.8971 (mp10) cc_final: 0.8645 (mt0) REVERT: E 115 GLN cc_start: 0.8272 (mt0) cc_final: 0.7980 (mt0) REVERT: F 25 MET cc_start: 0.8570 (mmt) cc_final: 0.7958 (mmm) REVERT: F 56 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.7902 (tp) REVERT: F 76 PHE cc_start: 0.8018 (m-10) cc_final: 0.7709 (m-10) REVERT: G 25 ILE cc_start: 0.6770 (OUTLIER) cc_final: 0.6453 (mt) REVERT: H 41 LYS cc_start: 0.5571 (OUTLIER) cc_final: 0.5096 (mtpt) REVERT: I 48 ILE cc_start: 0.1014 (OUTLIER) cc_final: 0.0427 (tp) REVERT: I 116 MET cc_start: 0.0811 (tpt) cc_final: 0.0138 (mmm) REVERT: J 31 GLU cc_start: 0.7432 (tp30) cc_final: 0.7209 (tp30) REVERT: J 128 ASN cc_start: 0.8856 (t0) cc_final: 0.8350 (t0) REVERT: K 88 ASN cc_start: 0.7783 (t0) cc_final: 0.7403 (t0) REVERT: K 113 MET cc_start: 0.6903 (mmp) cc_final: 0.6516 (mmp) REVERT: L 82 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8296 (mp) REVERT: L 129 LYS cc_start: 0.8579 (ttmm) cc_final: 0.8304 (mtmm) REVERT: L 136 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6769 (mm-30) REVERT: M 6 ARG cc_start: 0.7026 (ptm-80) cc_final: 0.6629 (ptp90) REVERT: M 9 PHE cc_start: 0.8843 (m-80) cc_final: 0.8586 (m-10) REVERT: M 53 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.7877 (mtm) REVERT: N 2 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8540 (tmt170) REVERT: N 23 ASN cc_start: 0.8688 (m-40) cc_final: 0.8301 (m-40) REVERT: O 12 THR cc_start: 0.9301 (m) cc_final: 0.8706 (p) REVERT: P 71 ARG cc_start: 0.8106 (ttt180) cc_final: 0.7723 (ttt-90) REVERT: Q 48 ASP cc_start: 0.8283 (m-30) cc_final: 0.7993 (m-30) REVERT: R 11 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7579 (mp10) REVERT: S 1 MET cc_start: 0.6525 (tmm) cc_final: 0.6135 (tmm) REVERT: T 26 LYS cc_start: 0.7886 (tmtt) cc_final: 0.7416 (tttp) REVERT: U 13 LEU cc_start: 0.8471 (mt) cc_final: 0.8231 (mt) REVERT: U 87 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6911 (mp0) REVERT: V 1 MET cc_start: 0.6729 (tmm) cc_final: 0.6465 (tmm) REVERT: W 7 ARG cc_start: 0.7328 (ttm110) cc_final: 0.7071 (mtm110) REVERT: W 40 LYS cc_start: 0.8945 (mttt) cc_final: 0.8267 (mtpt) REVERT: Y 39 GLN cc_start: 0.7637 (mt0) cc_final: 0.7221 (mp10) REVERT: 4 20 ASP cc_start: 0.7819 (t0) cc_final: 0.7294 (t0) REVERT: 5 23 LEU cc_start: 0.3889 (mm) cc_final: 0.3559 (mt) REVERT: 5 65 GLU cc_start: 0.4240 (OUTLIER) cc_final: 0.3915 (tt0) REVERT: 6 2 LYS cc_start: 0.6695 (mttt) cc_final: 0.6387 (mttm) outliers start: 377 outliers final: 315 residues processed: 1259 average time/residue: 1.3397 time to fit residues: 2979.4157 Evaluate side-chains 1345 residues out of total 4853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 347 poor density : 998 time to evaluate : 6.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 13 VAL Chi-restraints excluded: chain b residue 14 HIS Chi-restraints excluded: chain b residue 17 HIS Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 20 ARG Chi-restraints excluded: chain b residue 35 ASN Chi-restraints excluded: chain b residue 66 ILE Chi-restraints excluded: chain b residue 89 PHE Chi-restraints excluded: chain b residue 93 HIS Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 141 GLU Chi-restraints excluded: chain b residue 166 ASP Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 203 ASP Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 50 SER Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 151 GLU Chi-restraints excluded: chain c residue 168 ARG Chi-restraints excluded: chain c residue 183 TYR Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 43 ARG Chi-restraints excluded: chain d residue 63 ILE Chi-restraints excluded: chain d residue 66 VAL Chi-restraints excluded: chain d residue 77 GLU Chi-restraints excluded: chain d residue 122 ILE Chi-restraints excluded: chain d residue 123 MET Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 144 ILE Chi-restraints excluded: chain d residue 158 LEU Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain e residue 14 LEU Chi-restraints excluded: chain e residue 36 THR Chi-restraints excluded: chain e residue 79 THR Chi-restraints excluded: chain e residue 85 LYS Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 96 GLN Chi-restraints excluded: chain e residue 119 VAL Chi-restraints excluded: chain e residue 135 VAL Chi-restraints excluded: chain f residue 2 ARG Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 13 ASP Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 54 LEU Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 74 LEU Chi-restraints excluded: chain f residue 86 ARG Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 37 THR Chi-restraints excluded: chain g residue 83 THR Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 103 ILE Chi-restraints excluded: chain g residue 105 GLU Chi-restraints excluded: chain g residue 123 LEU Chi-restraints excluded: chain g residue 135 LYS Chi-restraints excluded: chain g residue 147 ASN Chi-restraints excluded: chain h residue 10 LEU Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 41 GLU Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 57 GLU Chi-restraints excluded: chain h residue 73 SER Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain h residue 100 ILE Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain i residue 46 VAL Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain i residue 62 LEU Chi-restraints excluded: chain i residue 71 ILE Chi-restraints excluded: chain i residue 93 LEU Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain i residue 106 ASP Chi-restraints excluded: chain i residue 126 PHE Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 16 ARG Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 56 HIS Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain k residue 19 VAL Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain k residue 63 GLN Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain k residue 95 THR Chi-restraints excluded: chain k residue 113 THR Chi-restraints excluded: chain l residue 54 VAL Chi-restraints excluded: chain l residue 69 GLU Chi-restraints excluded: chain l residue 74 GLN Chi-restraints excluded: chain l residue 76 HIS Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain l residue 80 LEU Chi-restraints excluded: chain l residue 89 LEU Chi-restraints excluded: chain l residue 96 THR Chi-restraints excluded: chain l residue 97 VAL Chi-restraints excluded: chain l residue 101 LEU Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain l residue 118 VAL Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 19 THR Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain m residue 76 ILE Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain o residue 1 SER Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 50 THR Chi-restraints excluded: chain p residue 52 LEU Chi-restraints excluded: chain p residue 57 ILE Chi-restraints excluded: chain p residue 63 GLN Chi-restraints excluded: chain q residue 20 ILE Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 37 ILE Chi-restraints excluded: chain q residue 64 ARG Chi-restraints excluded: chain q residue 68 LYS Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain r residue 20 ILE Chi-restraints excluded: chain r residue 25 ILE Chi-restraints excluded: chain r residue 27 THR Chi-restraints excluded: chain r residue 33 THR Chi-restraints excluded: chain r residue 65 SER Chi-restraints excluded: chain s residue 3 SER Chi-restraints excluded: chain s residue 5 LYS Chi-restraints excluded: chain s residue 28 LYS Chi-restraints excluded: chain s residue 47 THR Chi-restraints excluded: chain s residue 48 ILE Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 72 GLU Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 31 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 123 LYS Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 60 GLU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 17 ASN Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 45 ARG Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 62 LYS Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 82 SER Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 11 GLN Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 39 ASN Chi-restraints excluded: chain U residue 87 GLU Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain U residue 100 GLU Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 66 ASP Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 66 GLU Chi-restraints excluded: chain W residue 74 LYS Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 22 LEU Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain Z residue 4 ILE Chi-restraints excluded: chain Z residue 18 LYS Chi-restraints excluded: chain Z residue 24 LEU Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain Z residue 55 LYS Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 10 SER Chi-restraints excluded: chain 0 residue 42 ILE Chi-restraints excluded: chain 2 residue 22 MET Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 18 LYS Chi-restraints excluded: chain 4 residue 37 GLN Chi-restraints excluded: chain 5 residue 17 GLU Chi-restraints excluded: chain 5 residue 27 VAL Chi-restraints excluded: chain 5 residue 33 VAL Chi-restraints excluded: chain 5 residue 65 GLU Chi-restraints excluded: chain 5 residue 77 VAL Chi-restraints excluded: chain 5 residue 114 GLU Chi-restraints excluded: chain 6 residue 4 ASP Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 57 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 906 optimal weight: 0.9990 chunk 954 optimal weight: 8.9990 chunk 871 optimal weight: 3.9990 chunk 928 optimal weight: 0.9980 chunk 558 optimal weight: 10.0000 chunk 404 optimal weight: 10.0000 chunk 729 optimal weight: 4.9990 chunk 285 optimal weight: 5.9990 chunk 839 optimal weight: 7.9990 chunk 878 optimal weight: 0.7980 chunk 925 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 67 ASN g 129 ASN j 70 HIS ** n 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 62 ASN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 GLN I 104 GLN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 17 ASN R 86 GLN S 61 ASN ** 6 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 158507 Z= 0.144 Angle : 0.619 14.035 236990 Z= 0.336 Chirality : 0.034 0.389 30193 Planarity : 0.006 0.123 12798 Dihedral : 23.555 179.454 78902 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.41 % Favored : 90.32 % Rotamer: Outliers : 5.41 % Allowed : 25.62 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.11), residues: 5847 helix: 0.16 (0.12), residues: 1921 sheet: -1.64 (0.16), residues: 990 loop : -2.26 (0.11), residues: 2936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP c 200 HIS 0.007 0.001 HIS 3 30 PHE 0.033 0.001 PHE H 46 TYR 0.025 0.001 TYR i 6 ARG 0.010 0.000 ARG f 44 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11694 Ramachandran restraints generated. 5847 Oldfield, 0 Emsley, 5847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11694 Ramachandran restraints generated. 5847 Oldfield, 0 Emsley, 5847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1341 residues out of total 4853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 1080 time to evaluate : 6.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 141 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7346 (tm-30) REVERT: b 166 ASP cc_start: 0.6050 (OUTLIER) cc_final: 0.5793 (m-30) REVERT: c 168 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7738 (ttp80) REVERT: d 13 ARG cc_start: 0.8365 (tpt170) cc_final: 0.8068 (tpp-160) REVERT: d 33 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8113 (mt) REVERT: d 43 ARG cc_start: 0.5242 (OUTLIER) cc_final: 0.3945 (mtp-110) REVERT: d 46 ARG cc_start: 0.7331 (mtm180) cc_final: 0.6957 (mmt180) REVERT: d 104 MET cc_start: 0.7244 (ttm) cc_final: 0.6807 (ttm) REVERT: d 122 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.8106 (tt) REVERT: d 130 ASN cc_start: 0.8718 (t0) cc_final: 0.8345 (t0) REVERT: d 196 GLU cc_start: 0.7669 (pm20) cc_final: 0.6807 (pm20) REVERT: e 12 GLU cc_start: 0.7592 (tt0) cc_final: 0.7378 (tt0) REVERT: e 25 LYS cc_start: 0.9033 (ttpt) cc_final: 0.8412 (tptt) REVERT: e 69 ASN cc_start: 0.8302 (t0) cc_final: 0.8098 (t0) REVERT: e 145 ASN cc_start: 0.7465 (p0) cc_final: 0.6803 (p0) REVERT: f 2 ARG cc_start: 0.6732 (OUTLIER) cc_final: 0.6445 (mtt90) REVERT: f 54 LEU cc_start: 0.3265 (OUTLIER) cc_final: 0.2941 (mm) REVERT: f 70 VAL cc_start: 0.6711 (OUTLIER) cc_final: 0.6259 (p) REVERT: f 74 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.6702 (mm) REVERT: f 86 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.8247 (ttm170) REVERT: g 91 ARG cc_start: 0.7792 (mmm-85) cc_final: 0.6843 (mtm110) REVERT: g 135 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8331 (ttmt) REVERT: g 137 ARG cc_start: 0.7719 (tmm160) cc_final: 0.7277 (ttp80) REVERT: h 103 VAL cc_start: 0.8708 (OUTLIER) cc_final: 0.8459 (p) REVERT: h 116 ARG cc_start: 0.7537 (mtt180) cc_final: 0.7103 (mtt180) REVERT: i 30 ASN cc_start: 0.8165 (m-40) cc_final: 0.7844 (m-40) REVERT: i 67 LYS cc_start: 0.8408 (ptpp) cc_final: 0.8009 (pttt) REVERT: j 16 ARG cc_start: 0.6873 (OUTLIER) cc_final: 0.6487 (mmt90) REVERT: j 56 HIS cc_start: 0.7653 (OUTLIER) cc_final: 0.7150 (t-170) REVERT: j 67 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8143 (mp) REVERT: j 88 MET cc_start: 0.7150 (tpt) cc_final: 0.6818 (tpt) REVERT: k 68 ARG cc_start: 0.7931 (mtp-110) cc_final: 0.7508 (mtp-110) REVERT: k 74 LYS cc_start: 0.8047 (mtmm) cc_final: 0.7277 (mmtm) REVERT: l 106 VAL cc_start: 0.7434 (OUTLIER) cc_final: 0.7210 (p) REVERT: m 12 LYS cc_start: 0.7795 (ptpt) cc_final: 0.7295 (mtpt) REVERT: m 40 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8110 (mt-10) REVERT: m 41 ASP cc_start: 0.7223 (m-30) cc_final: 0.6689 (t0) REVERT: m 67 ASP cc_start: 0.7499 (OUTLIER) cc_final: 0.6305 (t70) REVERT: m 80 MET cc_start: 0.7654 (ptp) cc_final: 0.7336 (ptm) REVERT: m 99 GLN cc_start: 0.7631 (mm-40) cc_final: 0.7401 (mm-40) REVERT: n 22 LYS cc_start: 0.6204 (mmtt) cc_final: 0.5919 (tmtt) REVERT: n 74 LEU cc_start: 0.9063 (mt) cc_final: 0.8853 (mt) REVERT: o 70 LYS cc_start: 0.9176 (ttpt) cc_final: 0.8869 (tttt) REVERT: p 23 ASP cc_start: 0.8094 (t70) cc_final: 0.7726 (t70) REVERT: q 10 ARG cc_start: 0.7027 (ptm-80) cc_final: 0.6645 (mtp85) REVERT: q 32 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.8874 (mt) REVERT: q 79 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7369 (tm-30) REVERT: r 47 ARG cc_start: 0.6604 (mmt-90) cc_final: 0.6253 (ttt180) REVERT: s 6 LYS cc_start: 0.6339 (mmtp) cc_final: 0.5561 (pttm) REVERT: s 28 LYS cc_start: 0.6676 (OUTLIER) cc_final: 0.5929 (mtmt) REVERT: s 33 TRP cc_start: 0.8551 (m-90) cc_final: 0.7457 (m-90) REVERT: C 43 ASN cc_start: 0.8459 (p0) cc_final: 0.8171 (p0) REVERT: C 78 GLU cc_start: 0.7832 (tp30) cc_final: 0.7569 (mm-30) REVERT: C 97 ASP cc_start: 0.8784 (p0) cc_final: 0.8557 (p0) REVERT: C 170 TYR cc_start: 0.8460 (m-80) cc_final: 0.6804 (m-80) REVERT: C 250 GLN cc_start: 0.8588 (tm-30) cc_final: 0.8309 (tm-30) REVERT: D 161 MET cc_start: 0.8997 (ptp) cc_final: 0.8755 (mtm) REVERT: E 46 GLN cc_start: 0.8774 (mp10) cc_final: 0.8571 (mt0) REVERT: E 115 GLN cc_start: 0.8238 (mt0) cc_final: 0.7926 (mt0) REVERT: E 158 PHE cc_start: 0.8639 (t80) cc_final: 0.8385 (t80) REVERT: E 171 ASP cc_start: 0.7488 (OUTLIER) cc_final: 0.7154 (p0) REVERT: F 25 MET cc_start: 0.8412 (mmt) cc_final: 0.7907 (mmm) REVERT: F 100 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7966 (tm-30) REVERT: G 123 GLU cc_start: 0.6894 (mp0) cc_final: 0.6662 (mp0) REVERT: I 116 MET cc_start: 0.0065 (tpt) cc_final: -0.0465 (mmm) REVERT: J 128 ASN cc_start: 0.8618 (t0) cc_final: 0.8112 (t0) REVERT: K 59 LYS cc_start: 0.8521 (mttp) cc_final: 0.8263 (ttmt) REVERT: K 88 ASN cc_start: 0.7772 (t0) cc_final: 0.7482 (t0) REVERT: K 114 LYS cc_start: 0.8199 (tppp) cc_final: 0.7963 (mmtt) REVERT: L 129 LYS cc_start: 0.8413 (ttmm) cc_final: 0.8150 (mtmm) REVERT: M 6 ARG cc_start: 0.7289 (ptm-80) cc_final: 0.6907 (ptp90) REVERT: M 9 PHE cc_start: 0.8761 (m-80) cc_final: 0.8424 (m-10) REVERT: M 53 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7698 (mtm) REVERT: M 136 MET cc_start: 0.7177 (tmm) cc_final: 0.6426 (tmm) REVERT: O 12 THR cc_start: 0.9174 (m) cc_final: 0.8911 (p) REVERT: O 112 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7408 (mt-10) REVERT: P 71 ARG cc_start: 0.7986 (ttt180) cc_final: 0.7695 (ttt-90) REVERT: Q 48 ASP cc_start: 0.8139 (m-30) cc_final: 0.7931 (m-30) REVERT: Q 58 GLN cc_start: 0.8075 (pt0) cc_final: 0.7725 (pt0) REVERT: S 1 MET cc_start: 0.6521 (tmm) cc_final: 0.6016 (tmm) REVERT: T 26 LYS cc_start: 0.7598 (tmtt) cc_final: 0.7074 (tttp) REVERT: U 5 ARG cc_start: 0.8106 (ptp-170) cc_final: 0.7892 (mtt180) REVERT: U 13 LEU cc_start: 0.8475 (mt) cc_final: 0.8270 (mt) REVERT: U 87 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6871 (mp0) REVERT: V 76 ASP cc_start: 0.6551 (m-30) cc_final: 0.6106 (m-30) REVERT: W 7 ARG cc_start: 0.7329 (ttm110) cc_final: 0.6892 (mtm110) REVERT: W 40 LYS cc_start: 0.8824 (mttt) cc_final: 0.8182 (mtpt) REVERT: Y 39 GLN cc_start: 0.7355 (mt0) cc_final: 0.6870 (mp10) REVERT: 3 14 LYS cc_start: 0.8174 (mptt) cc_final: 0.7959 (mttp) REVERT: 4 20 ASP cc_start: 0.7671 (t0) cc_final: 0.7048 (t0) REVERT: 5 23 LEU cc_start: 0.3377 (mm) cc_final: 0.3136 (mt) REVERT: 5 65 GLU cc_start: 0.3201 (OUTLIER) cc_final: 0.2888 (tt0) REVERT: 6 2 LYS cc_start: 0.6609 (mttt) cc_final: 0.6203 (mttm) outliers start: 261 outliers final: 178 residues processed: 1224 average time/residue: 1.2670 time to fit residues: 2693.8028 Evaluate side-chains 1219 residues out of total 4853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 1017 time to evaluate : 5.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 14 HIS Chi-restraints excluded: chain b residue 66 ILE Chi-restraints excluded: chain b residue 89 PHE Chi-restraints excluded: chain b residue 93 HIS Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 141 GLU Chi-restraints excluded: chain b residue 166 ASP Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 50 SER Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 168 ARG Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 33 ILE Chi-restraints excluded: chain d residue 43 ARG Chi-restraints excluded: chain d residue 122 ILE Chi-restraints excluded: chain d residue 123 MET Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain e residue 14 LEU Chi-restraints excluded: chain e residue 36 THR Chi-restraints excluded: chain e residue 85 LYS Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 96 GLN Chi-restraints excluded: chain e residue 119 VAL Chi-restraints excluded: chain e residue 120 HIS Chi-restraints excluded: chain e residue 133 ILE Chi-restraints excluded: chain f residue 2 ARG Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 13 ASP Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 54 LEU Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 74 LEU Chi-restraints excluded: chain f residue 86 ARG Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 47 GLU Chi-restraints excluded: chain g residue 83 THR Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 135 LYS Chi-restraints excluded: chain h residue 10 LEU Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 57 GLU Chi-restraints excluded: chain h residue 73 SER Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain i residue 62 LEU Chi-restraints excluded: chain i residue 71 ILE Chi-restraints excluded: chain i residue 93 LEU Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain i residue 106 ASP Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 16 ARG Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 56 HIS Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain k residue 63 GLN Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain k residue 95 THR Chi-restraints excluded: chain k residue 113 THR Chi-restraints excluded: chain l residue 54 VAL Chi-restraints excluded: chain l residue 69 GLU Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain l residue 96 THR Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 19 THR Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain o residue 1 SER Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 52 LEU Chi-restraints excluded: chain p residue 57 ILE Chi-restraints excluded: chain p residue 63 GLN Chi-restraints excluded: chain q residue 20 ILE Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 64 ARG Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain r residue 27 THR Chi-restraints excluded: chain s residue 28 LYS Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 31 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain P residue 3 ILE Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 62 LYS Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 82 SER Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 87 GLU Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 66 ASP Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 66 GLU Chi-restraints excluded: chain W residue 74 LYS Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 10 SER Chi-restraints excluded: chain 0 residue 42 ILE Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 4 residue 18 LYS Chi-restraints excluded: chain 4 residue 37 GLN Chi-restraints excluded: chain 5 residue 33 VAL Chi-restraints excluded: chain 5 residue 65 GLU Chi-restraints excluded: chain 5 residue 114 GLU Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 57 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 609 optimal weight: 10.0000 chunk 982 optimal weight: 10.0000 chunk 599 optimal weight: 50.0000 chunk 465 optimal weight: 10.0000 chunk 682 optimal weight: 10.0000 chunk 1030 optimal weight: 10.0000 chunk 948 optimal weight: 9.9990 chunk 820 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 633 optimal weight: 10.0000 chunk 502 optimal weight: 10.0000 overall best weight: 8.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 40 HIS e 77 ASN g 67 ASN g 129 ASN ** i 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 34 ASN ** n 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 62 ASN q 8 GLN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 17 ASN N 23 ASN O 61 GLN O 104 GLN R 11 GLN R 86 GLN W 72 ASN ** 6 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.099 158507 Z= 0.449 Angle : 0.784 15.115 236990 Z= 0.407 Chirality : 0.043 0.376 30193 Planarity : 0.007 0.142 12798 Dihedral : 23.549 179.270 78902 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.22 % Favored : 88.49 % Rotamer: Outliers : 5.49 % Allowed : 25.95 % Favored : 68.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.11), residues: 5847 helix: -0.14 (0.12), residues: 1928 sheet: -1.67 (0.16), residues: 988 loop : -2.41 (0.11), residues: 2931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 212 HIS 0.009 0.002 HIS 3 30 PHE 0.035 0.002 PHE H 46 TYR 0.036 0.003 TYR S 38 ARG 0.012 0.001 ARG f 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11694 Ramachandran restraints generated. 5847 Oldfield, 0 Emsley, 5847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11694 Ramachandran restraints generated. 5847 Oldfield, 0 Emsley, 5847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1268 residues out of total 4853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 1003 time to evaluate : 6.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 141 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7376 (tm-30) REVERT: b 166 ASP cc_start: 0.5643 (OUTLIER) cc_final: 0.5369 (m-30) REVERT: c 7 ASN cc_start: 0.8350 (t0) cc_final: 0.8034 (t0) REVERT: d 13 ARG cc_start: 0.8546 (tpt170) cc_final: 0.8101 (tpp-160) REVERT: d 43 ARG cc_start: 0.5362 (OUTLIER) cc_final: 0.4089 (mtp-110) REVERT: d 122 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8121 (tt) REVERT: d 196 GLU cc_start: 0.7738 (pm20) cc_final: 0.6647 (pm20) REVERT: e 25 LYS cc_start: 0.9093 (ttpt) cc_final: 0.8399 (tptt) REVERT: e 63 MET cc_start: 0.6717 (OUTLIER) cc_final: 0.6266 (tmm) REVERT: e 69 ASN cc_start: 0.8376 (t0) cc_final: 0.8101 (t0) REVERT: e 145 ASN cc_start: 0.7720 (p0) cc_final: 0.7240 (p0) REVERT: f 2 ARG cc_start: 0.6930 (OUTLIER) cc_final: 0.6639 (mtt90) REVERT: f 54 LEU cc_start: 0.3146 (OUTLIER) cc_final: 0.2809 (mm) REVERT: f 74 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.6858 (mm) REVERT: f 86 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8290 (ttp-110) REVERT: g 39 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6694 (mt-10) REVERT: g 135 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8412 (ttmt) REVERT: g 137 ARG cc_start: 0.7892 (tmm160) cc_final: 0.7420 (ttp80) REVERT: h 20 ASN cc_start: 0.8716 (OUTLIER) cc_final: 0.8415 (m-40) REVERT: h 60 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8910 (mp) REVERT: h 116 ARG cc_start: 0.7236 (mtt180) cc_final: 0.6657 (mtt180) REVERT: i 67 LYS cc_start: 0.8478 (ptpp) cc_final: 0.8069 (pttt) REVERT: j 56 HIS cc_start: 0.7694 (OUTLIER) cc_final: 0.7149 (t-170) REVERT: j 67 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8275 (mp) REVERT: j 88 MET cc_start: 0.7298 (tpt) cc_final: 0.6944 (tpt) REVERT: k 68 ARG cc_start: 0.8091 (mtp-110) cc_final: 0.7659 (mtp-110) REVERT: k 74 LYS cc_start: 0.7999 (mtmm) cc_final: 0.7169 (mmtm) REVERT: m 40 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8211 (mt-10) REVERT: m 41 ASP cc_start: 0.7232 (m-30) cc_final: 0.6669 (t70) REVERT: m 80 MET cc_start: 0.7666 (ptp) cc_final: 0.7346 (ptm) REVERT: n 15 LEU cc_start: 0.8447 (mt) cc_final: 0.8202 (mt) REVERT: n 22 LYS cc_start: 0.6644 (mmtt) cc_final: 0.6175 (tmtt) REVERT: o 70 LYS cc_start: 0.9269 (ttpt) cc_final: 0.8937 (tttt) REVERT: q 32 ILE cc_start: 0.9277 (OUTLIER) cc_final: 0.8892 (mt) REVERT: q 33 TYR cc_start: 0.8838 (m-80) cc_final: 0.8380 (m-80) REVERT: q 79 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7353 (tm-30) REVERT: r 20 ILE cc_start: 0.6952 (OUTLIER) cc_final: 0.6735 (mm) REVERT: r 47 ARG cc_start: 0.6818 (mmt-90) cc_final: 0.6412 (ttt180) REVERT: s 6 LYS cc_start: 0.6135 (mmtp) cc_final: 0.5837 (pttm) REVERT: t 29 THR cc_start: 0.9031 (p) cc_final: 0.8790 (p) REVERT: C 78 GLU cc_start: 0.7788 (tp30) cc_final: 0.7553 (tp30) REVERT: D 45 TYR cc_start: 0.8728 (p90) cc_final: 0.8522 (p90) REVERT: D 133 THR cc_start: 0.9115 (p) cc_final: 0.8877 (p) REVERT: D 181 ASP cc_start: 0.7912 (t0) cc_final: 0.7557 (t0) REVERT: E 46 GLN cc_start: 0.8972 (mp10) cc_final: 0.8635 (mt0) REVERT: E 115 GLN cc_start: 0.8278 (mt0) cc_final: 0.7998 (mt0) REVERT: F 25 MET cc_start: 0.8523 (mmt) cc_final: 0.7938 (mmm) REVERT: I 116 MET cc_start: 0.0751 (tpt) cc_final: 0.0073 (mmm) REVERT: J 128 ASN cc_start: 0.8850 (t0) cc_final: 0.8341 (t0) REVERT: K 88 ASN cc_start: 0.7761 (t0) cc_final: 0.7382 (t0) REVERT: L 118 THR cc_start: 0.8050 (OUTLIER) cc_final: 0.7827 (p) REVERT: L 136 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6789 (mm-30) REVERT: M 6 ARG cc_start: 0.7396 (ptm-80) cc_final: 0.6958 (ptp90) REVERT: M 9 PHE cc_start: 0.8855 (m-80) cc_final: 0.8592 (m-10) REVERT: M 53 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.7958 (mtm) REVERT: M 136 MET cc_start: 0.7227 (tmm) cc_final: 0.6514 (tmm) REVERT: O 12 THR cc_start: 0.9302 (m) cc_final: 0.8695 (p) REVERT: Q 48 ASP cc_start: 0.8244 (m-30) cc_final: 0.7975 (m-30) REVERT: S 1 MET cc_start: 0.6564 (tmm) cc_final: 0.6177 (tmm) REVERT: T 26 LYS cc_start: 0.7892 (tmtt) cc_final: 0.7422 (tttp) REVERT: U 13 LEU cc_start: 0.8536 (mt) cc_final: 0.8241 (mt) REVERT: U 87 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6899 (mp0) REVERT: V 76 ASP cc_start: 0.6602 (m-30) cc_final: 0.6176 (m-30) REVERT: W 7 ARG cc_start: 0.7331 (ttm110) cc_final: 0.7071 (mtm110) REVERT: W 40 LYS cc_start: 0.8951 (mttt) cc_final: 0.8266 (mtpt) REVERT: Y 39 GLN cc_start: 0.7622 (mt0) cc_final: 0.7022 (mp10) REVERT: 4 20 ASP cc_start: 0.7833 (t0) cc_final: 0.7328 (t0) REVERT: 5 23 LEU cc_start: 0.3870 (mm) cc_final: 0.3546 (mt) REVERT: 5 65 GLU cc_start: 0.4110 (OUTLIER) cc_final: 0.3832 (tt0) REVERT: 6 2 LYS cc_start: 0.6700 (mttt) cc_final: 0.6153 (mttm) REVERT: 6 28 VAL cc_start: 0.6888 (m) cc_final: 0.6507 (m) outliers start: 265 outliers final: 222 residues processed: 1162 average time/residue: 1.2393 time to fit residues: 2521.0920 Evaluate side-chains 1233 residues out of total 4853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 990 time to evaluate : 6.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 14 HIS Chi-restraints excluded: chain b residue 17 HIS Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 35 ASN Chi-restraints excluded: chain b residue 66 ILE Chi-restraints excluded: chain b residue 89 PHE Chi-restraints excluded: chain b residue 93 HIS Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 141 GLU Chi-restraints excluded: chain b residue 166 ASP Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 203 ASP Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 50 SER Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 151 GLU Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 43 ARG Chi-restraints excluded: chain d residue 122 ILE Chi-restraints excluded: chain d residue 123 MET Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain e residue 14 LEU Chi-restraints excluded: chain e residue 36 THR Chi-restraints excluded: chain e residue 63 MET Chi-restraints excluded: chain e residue 77 ASN Chi-restraints excluded: chain e residue 79 THR Chi-restraints excluded: chain e residue 85 LYS Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 96 GLN Chi-restraints excluded: chain e residue 119 VAL Chi-restraints excluded: chain e residue 120 HIS Chi-restraints excluded: chain f residue 2 ARG Chi-restraints excluded: chain f residue 13 ASP Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 54 LEU Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 74 LEU Chi-restraints excluded: chain f residue 86 ARG Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 37 THR Chi-restraints excluded: chain g residue 39 GLU Chi-restraints excluded: chain g residue 47 GLU Chi-restraints excluded: chain g residue 67 ASN Chi-restraints excluded: chain g residue 83 THR Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 105 GLU Chi-restraints excluded: chain g residue 135 LYS Chi-restraints excluded: chain h residue 10 LEU Chi-restraints excluded: chain h residue 20 ASN Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 57 GLU Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 73 SER Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 62 LEU Chi-restraints excluded: chain i residue 71 ILE Chi-restraints excluded: chain i residue 93 LEU Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain i residue 106 ASP Chi-restraints excluded: chain i residue 126 PHE Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 56 HIS Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain k residue 63 GLN Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain k residue 95 THR Chi-restraints excluded: chain k residue 113 THR Chi-restraints excluded: chain l residue 54 VAL Chi-restraints excluded: chain l residue 69 GLU Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain l residue 96 THR Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 19 THR Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain o residue 1 SER Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 52 LEU Chi-restraints excluded: chain p residue 57 ILE Chi-restraints excluded: chain p residue 63 GLN Chi-restraints excluded: chain q residue 20 ILE Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 37 ILE Chi-restraints excluded: chain q residue 64 ARG Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain r residue 20 ILE Chi-restraints excluded: chain r residue 27 THR Chi-restraints excluded: chain s residue 28 LYS Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 31 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 123 LYS Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 115 GLN Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 106 GLU Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain M residue 17 ASN Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 45 ARG Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 104 GLN Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 62 LYS Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 82 SER Chi-restraints excluded: chain R residue 11 GLN Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 87 GLU Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 66 ASP Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 66 GLU Chi-restraints excluded: chain W residue 74 LYS Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 22 LEU Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain Z residue 18 LYS Chi-restraints excluded: chain Z residue 24 LEU Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain 0 residue 10 SER Chi-restraints excluded: chain 0 residue 42 ILE Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 4 residue 18 LYS Chi-restraints excluded: chain 4 residue 30 GLU Chi-restraints excluded: chain 4 residue 37 GLN Chi-restraints excluded: chain 5 residue 27 VAL Chi-restraints excluded: chain 5 residue 33 VAL Chi-restraints excluded: chain 5 residue 65 GLU Chi-restraints excluded: chain 5 residue 114 GLU Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 57 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1034 random chunks: chunk 651 optimal weight: 8.9990 chunk 873 optimal weight: 4.9990 chunk 251 optimal weight: 10.0000 chunk 756 optimal weight: 6.9990 chunk 121 optimal weight: 20.0000 chunk 227 optimal weight: 9.9990 chunk 821 optimal weight: 4.9990 chunk 343 optimal weight: 0.9990 chunk 843 optimal weight: 6.9990 chunk 104 optimal weight: 20.0000 chunk 151 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 40 HIS ** e 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 67 ASN ** i 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 62 ASN q 8 GLN ** s 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 23 ASN O 61 GLN O 104 GLN P 40 GLN R 11 GLN R 86 GLN W 72 ASN ** 6 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.130576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.101852 restraints weight = 236202.823| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 0.91 r_work: 0.2992 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.290 158507 Z= 0.397 Angle : 0.837 59.196 236990 Z= 0.453 Chirality : 0.042 1.448 30193 Planarity : 0.008 0.192 12798 Dihedral : 23.552 179.221 78902 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.34 % Favored : 88.35 % Rotamer: Outliers : 5.49 % Allowed : 26.07 % Favored : 68.44 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.11), residues: 5847 helix: -0.14 (0.12), residues: 1927 sheet: -1.68 (0.16), residues: 987 loop : -2.42 (0.11), residues: 2933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 212 HIS 0.013 0.002 HIS l 76 PHE 0.031 0.002 PHE H 46 TYR 0.033 0.002 TYR S 38 ARG 0.012 0.001 ARG f 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 38295.58 seconds wall clock time: 670 minutes 30.12 seconds (40230.12 seconds total)