Starting phenix.real_space_refine on Wed Mar 20 16:06:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wnv_21857/03_2024/6wnv_21857.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wnv_21857/03_2024/6wnv_21857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wnv_21857/03_2024/6wnv_21857.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wnv_21857/03_2024/6wnv_21857.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wnv_21857/03_2024/6wnv_21857.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wnv_21857/03_2024/6wnv_21857.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.783 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 4562 5.49 5 S 153 5.16 5 C 71930 2.51 5 N 26651 2.21 5 O 39740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b GLU 22": "OE1" <-> "OE2" Residue "b GLU 81": "OE1" <-> "OE2" Residue "b ASP 113": "OD1" <-> "OD2" Residue "b TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 167": "OD1" <-> "OD2" Residue "b ASP 186": "OD1" <-> "OD2" Residue "c ARG 13": "NH1" <-> "NH2" Residue "c ARG 33": "NH1" <-> "NH2" Residue "c ASP 43": "OD1" <-> "OD2" Residue "c ARG 59": "NH1" <-> "NH2" Residue "c GLU 74": "OE1" <-> "OE2" Residue "c ARG 77": "NH1" <-> "NH2" Residue "c ARG 83": "NH1" <-> "NH2" Residue "c ARG 169": "NH1" <-> "NH2" Residue "c ARG 184": "NH1" <-> "NH2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ARG 44": "NH1" <-> "NH2" Residue "d ARG 49": "NH1" <-> "NH2" Residue "d ARG 61": "NH1" <-> "NH2" Residue "d ARG 88": "NH1" <-> "NH2" Residue "d ARG 102": "NH1" <-> "NH2" Residue "d ARG 162": "NH1" <-> "NH2" Residue "d ARG 170": "NH1" <-> "NH2" Residue "d ASP 191": "OD1" <-> "OD2" Residue "e GLU 31": "OE1" <-> "OE2" Residue "e ASP 45": "OD1" <-> "OD2" Residue "e ARG 70": "NH1" <-> "NH2" Residue "e ARG 79": "NH1" <-> "NH2" Residue "e ARG 91": "NH1" <-> "NH2" Residue "e GLU 97": "OE1" <-> "OE2" Residue "e ARG 101": "NH1" <-> "NH2" Residue "e ARG 109": "NH1" <-> "NH2" Residue "e ARG 111": "NH1" <-> "NH2" Residue "e ASP 112": "OD1" <-> "OD2" Residue "e ARG 114": "NH1" <-> "NH2" Residue "e ARG 132": "NH1" <-> "NH2" Residue "f ARG 2": "NH1" <-> "NH2" Residue "f TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 152": "NH1" <-> "NH2" Residue "f ARG 162": "NH1" <-> "NH2" Residue "f ASP 165": "OD1" <-> "OD2" Residue "f ARG 169": "NH1" <-> "NH2" Residue "g PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 65": "OE1" <-> "OE2" Residue "i ASP 95": "OD1" <-> "OD2" Residue "i ASP 115": "OD1" <-> "OD2" Residue "i GLU 122": "OE1" <-> "OE2" Residue "i ASP 141": "OD1" <-> "OD2" Residue "j GLU 9": "OE1" <-> "OE2" Residue "j ARG 13": "NH1" <-> "NH2" Residue "j ARG 37": "NH1" <-> "NH2" Residue "j ASP 49": "OD1" <-> "OD2" Residue "j TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 96": "NH1" <-> "NH2" Residue "j ARG 120": "NH1" <-> "NH2" Residue "j GLU 129": "OE1" <-> "OE2" Residue "k ASP 80": "OD1" <-> "OD2" Residue "k GLU 106": "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 ARG 78": "NH1" <-> "NH2" Residue "l PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 115": "OE1" <-> "OE2" Residue "l ARG 126": "NH1" <-> "NH2" Residue "n ARG 8": "NH1" <-> "NH2" Residue "n ARG 12": "NH1" <-> "NH2" Residue "n ARG 17": "NH1" <-> "NH2" Residue "n ARG 22": "NH1" <-> "NH2" Residue "n ARG 46": "NH1" <-> "NH2" Residue "n ARG 63": "NH1" <-> "NH2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n ARG 69": "NH1" <-> "NH2" Residue "n ARG 71": "NH1" <-> "NH2" Residue "n ARG 96": "NH1" <-> "NH2" Residue "n ARG 118": "NH1" <-> "NH2" Residue "o ARG 10": "NH1" <-> "NH2" Residue "o ARG 16": "NH1" <-> "NH2" Residue "o ARG 25": "NH1" <-> "NH2" Residue "o ARG 81": "NH1" <-> "NH2" Residue "o GLU 84": "OE1" <-> "OE2" Residue "o ARG 94": "NH1" <-> "NH2" Residue "o ARG 102": "NH1" <-> "NH2" Residue "o ARG 111": "NH1" <-> "NH2" Residue "o PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 20": "NH1" <-> "NH2" Residue "p ARG 38": "NH1" <-> "NH2" Residue "p GLU 43": "OE1" <-> "OE2" Residue "p ARG 61": "NH1" <-> "NH2" Residue "p GLU 67": "OE1" <-> "OE2" Residue "p ARG 88": "NH1" <-> "NH2" Residue "p ARG 100": "NH1" <-> "NH2" Residue "p ARG 108": "NH1" <-> "NH2" Residue "q ARG 2": "NH1" <-> "NH2" Residue "q ARG 5": "NH1" <-> "NH2" Residue "q ARG 12": "NH1" <-> "NH2" Residue "q ARG 32": "NH1" <-> "NH2" Residue "q ARG 47": "NH1" <-> "NH2" Residue "q ASP 48": "OD1" <-> "OD2" Residue "q ARG 69": "NH1" <-> "NH2" Residue "q ASP 101": "OD1" <-> "OD2" Residue "r ARG 21": "NH1" <-> "NH2" Residue "r GLU 23": "OE1" <-> "OE2" Residue "r GLU 37": "OE1" <-> "OE2" Residue "r ARG 68": "NH1" <-> "NH2" Residue "r GLU 70": "OE1" <-> "OE2" Residue "r ARG 78": "NH1" <-> "NH2" Residue "r ARG 79": "NH1" <-> "NH2" Residue "r ARG 84": "NH1" <-> "NH2" Residue "s GLU 59": "OE1" <-> "OE2" Residue "s ASP 65": "OD1" <-> "OD2" Residue "s ASP 77": "OD1" <-> "OD2" 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 4": "OE1" <-> "OE2" Residue "t GLU 56": "OE1" <-> "OE2" Residue "t ARG 73": "NH1" <-> "NH2" Residue "t ASP 79": "OD1" <-> "OD2" Residue "u ARG 5": "NH1" <-> "NH2" Residue "u ARG 6": "NH1" <-> "NH2" Residue "u ASP 7": "OD1" <-> "OD2" Residue "u GLU 36": "OE1" <-> "OE2" Residue "u ARG 81": "NH1" <-> "NH2" Residue "u ARG 85": "NH1" <-> "NH2" Residue "u ARG 93": "NH1" <-> "NH2" Residue "v GLU 11": "OE1" <-> "OE2" Residue "v GLU 35": "OE1" <-> "OE2" Residue "v GLU 55": "OE1" <-> "OE2" Residue "v ASP 90": "OD1" <-> "OD2" Residue "w GLU 13": "OE1" <-> "OE2" Residue "w PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 29": "NH1" <-> "NH2" Residue "y ARG 47": "NH1" <-> "NH2" Residue "y ASP 49": "OD1" <-> "OD2" 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 "A TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 11": "OE1" <-> "OE2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "D ARG 3": "NH1" <-> "NH2" Residue "D ARG 12": "NH1" <-> "NH2" Residue "D ARG 14": "NH1" <-> "NH2" Residue "D ARG 19": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 41": "NH1" <-> "NH2" Residue "E ARG 12": "NH1" <-> "NH2" Residue "E ARG 29": "NH1" <-> "NH2" Residue "E ARG 39": "NH1" <-> "NH2" Residue "E ARG 41": "NH1" <-> "NH2" Residue "F ARG 12": "NH1" <-> "NH2" Residue "F ASP 20": "OD1" <-> "OD2" Residue "F ARG 24": "NH1" <-> "NH2" Residue "G GLU 43": "OE1" <-> "OE2" Residue "G PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 51": "OE1" <-> "OE2" Residue "G ASP 81": "OD1" <-> "OD2" Residue "G ASP 87": "OD1" <-> "OD2" Residue "G GLU 132": "OE1" <-> "OE2" Residue "G GLU 141": "OE1" <-> "OE2" Residue "G GLU 144": "OE1" <-> "OE2" Residue "G ASP 158": "OD1" <-> "OD2" Residue "G GLU 174": "OE1" <-> "OE2" Residue "G ASP 193": "OD1" <-> "OD2" Residue "G ASP 203": "OD1" <-> "OD2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "H ASP 30": "OD1" <-> "OD2" Residue "H ASP 82": "OD1" <-> "OD2" Residue "H GLU 104": "OE1" <-> "OE2" Residue "H ARG 106": "NH1" <-> "NH2" Residue "H ARG 130": "NH1" <-> "NH2" Residue "I GLU 68": "OE1" <-> "OE2" Residue "I GLU 87": "OE1" <-> "OE2" Residue "I ASP 173": "OD1" <-> "OD2" Residue "I GLU 201": "OE1" <-> "OE2" Residue "J GLU 54": "OE1" <-> "OE2" Residue "J ARG 156": "NH1" <-> "NH2" Residue "K GLU 16": "OE1" <-> "OE2" Residue "K GLU 23": "OE1" <-> "OE2" Residue "K TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 72": "OD1" <-> "OD2" Residue "M GLU 46": "OE1" <-> "OE2" Residue "M ASP 47": "OD1" <-> "OD2" Residue "M ASP 53": "OD1" <-> "OD2" Residue "M GLU 57": "OE1" <-> "OE2" Residue "M GLU 90": "OE1" <-> "OE2" Residue "M GLU 123": "OE1" <-> "OE2" Residue "N ASP 55": "OD1" <-> "OD2" Residue "N GLU 58": "OE1" <-> "OE2" Residue "N GLU 111": "OE1" <-> "OE2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "O ASP 19": "OD1" <-> "OD2" Residue "O ASP 91": "OD1" <-> "OD2" Residue "P ASP 35": "OD1" <-> "OD2" Residue "P GLU 93": "OE1" <-> "OE2" Residue "Q GLU 24": "OE1" <-> "OE2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "S PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 5": "OE1" <-> "OE2" Residue "T GLU 13": "OE1" <-> "OE2" Residue "T ASP 67": "OD1" <-> "OD2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 45": "OE1" <-> "OE2" Residue "U ASP 55": "OD1" <-> "OD2" Residue "V PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 51": "OE1" <-> "OE2" Residue "W ARG 11": "NH1" <-> "NH2" Residue "X GLU 23": "OE1" <-> "OE2" Residue "X ASP 26": "OD1" <-> "OD2" Residue "Y GLU 39": "OE1" <-> "OE2" Residue "Y ASP 42": "OD1" <-> "OD2" Residue "Z ARG 66": "NH1" <-> "NH2" Residue "a ARG 7": "NH1" <-> "NH2" Residue "a ARG 12": "NH1" <-> "NH2" Residue "a GLU 40": "OE1" <-> "OE2" Residue "a ARG 162": "NH1" <-> "NH2" Residue "a ASP 179": "OD1" <-> "OD2" Residue "a ASP 183": "OD1" <-> "OD2" Residue "a TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 225": "OD1" <-> "OD2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 143036 Number of models: 1 Model: "" Number of chains: 52 Chain: "b" 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: "c" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1564 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "d" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1551 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "e" 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: "f" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1322 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "g" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 409 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "h" 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: "i" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1031 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "j" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1128 Classifications: {'peptide': 142} 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: 1044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1044 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 4, 'TRANS': 138} 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: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 891 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "p" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 916 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "q" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 946 Classifications: {'peptide': 117} Link IDs: {'TRANS': 116} Chain: "r" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 815 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "s" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 856 Classifications: {'peptide': 110} 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: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 752 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "w" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "x" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 624 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "y" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 508 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "z" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 448 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "A" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 315 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "B" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 443 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "D" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 376 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "E" Number of atoms: 503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 503 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "F" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 301 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "G" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1756 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "H" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "I" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1642 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "J" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1156 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "K" 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: "L" 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: "M" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 978 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "N" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1021 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "O" 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: "P" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 869 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "Q" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 954 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "R" 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: "S" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 804 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "T" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 713 Classifications: {'peptide': 88} Link IDs: {'TRANS': 87} Chain: "U" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 648 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "V" 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: "W" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "X" 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: "Y" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 664 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "Z" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 545 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "a" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1026 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain breaks: 1 Chain: "3" Number of atoms: 33012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33012 Classifications: {'RNA': 1539} Modifications used: {'5*END': 1, 'rna2p_pur': 91, 'rna2p_pyr': 49, 'rna3p_pur': 783, 'rna3p_pyr': 616} Link IDs: {'rna2p': 140, 'rna3p': 1398} Chain: "4" Number of atoms: 64925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3025, 64925 Classifications: {'RNA': 3025} Modifications used: {'5*END': 1, 'rna2p_pur': 218, 'rna2p_pyr': 105, 'rna3p_pur': 1519, 'rna3p_pyr': 1183} Link IDs: {'rna2p': 323, 'rna3p': 2701} Chain breaks: 1 Time building chain proxies: 53.63, per 1000 atoms: 0.37 Number of scatterers: 143036 At special positions: 0 Unit cell: (280.14, 266.22, 248.82, 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 153 16.00 P 4562 15.00 O 39740 8.00 N 26651 7.00 C 71930 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: 56.72 Conformation dependent library (CDL) restraints added in 7.2 seconds 11360 Ramachandran restraints generated. 5680 Oldfield, 0 Emsley, 5680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10632 Finding SS restraints... Secondary structure from input PDB file: 177 helices and 72 sheets defined 30.2% alpha, 15.0% beta 1332 base pairs and 2618 stacking pairs defined. Time for finding SS restraints: 48.75 Creating SS restraints... Processing helix chain 'b' and resid 29 through 31 No H-bonds generated for 'chain 'b' and resid 29 through 31' Processing helix chain 'b' and resid 132 through 134 No H-bonds generated for 'chain 'b' and resid 132 through 134' Processing helix chain 'b' and resid 196 through 202 removed outlier: 4.320A pdb=" N MET b 200 " --> pdb=" O ALA b 197 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG b 202 " --> pdb=" O HIS b 199 " (cutoff:3.500A) Processing helix chain 'b' and resid 206 through 212 removed outlier: 3.794A pdb=" N ALA b 210 " --> pdb=" O LYS b 206 " (cutoff:3.500A) Processing helix chain 'c' and resid 61 through 72 removed outlier: 3.683A pdb=" N ALA c 71 " --> pdb=" O HIS c 67 " (cutoff:3.500A) Processing helix chain 'c' and resid 98 through 103 removed outlier: 3.923A pdb=" N ASP c 103 " --> pdb=" O LEU c 100 " (cutoff:3.500A) Processing helix chain 'c' and resid 120 through 125 Processing helix chain 'd' and resid 24 through 40 removed outlier: 3.585A pdb=" N VAL d 31 " --> pdb=" O LEU d 27 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG d 40 " --> pdb=" O ALA d 36 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 115 removed outlier: 3.761A pdb=" N ARG d 114 " --> pdb=" O SER d 110 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 141 removed outlier: 3.677A pdb=" N LEU d 134 " --> pdb=" O LYS d 130 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 160 Processing helix chain 'd' and resid 178 through 183 removed outlier: 3.589A pdb=" N PHE d 183 " --> pdb=" O SER d 179 " (cutoff:3.500A) Processing helix chain 'd' and resid 190 through 201 Processing helix chain 'e' and resid 2 through 19 removed outlier: 3.599A pdb=" N GLU e 10 " --> pdb=" O TYR e 6 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL e 11 " --> pdb=" O TYR e 7 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N VAL e 12 " --> pdb=" O LYS e 8 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS e 13 " --> pdb=" O ASP e 9 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR e 17 " --> pdb=" O LYS e 13 " (cutoff:3.500A) Processing helix chain 'e' and resid 45 through 60 removed outlier: 4.290A pdb=" N LEU e 49 " --> pdb=" O ASP e 45 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP e 50 " --> pdb=" O LYS e 46 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA e 52 " --> pdb=" O LEU e 48 " (cutoff:3.500A) Processing helix chain 'e' and resid 92 through 104 removed outlier: 3.785A pdb=" N TRP e 96 " --> pdb=" O GLY e 92 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR e 104 " --> pdb=" O GLU e 100 " (cutoff:3.500A) Processing helix chain 'e' and resid 106 through 110 Processing helix chain 'e' and resid 161 through 171 Processing helix chain 'f' and resid 59 through 78 removed outlier: 3.707A pdb=" N ILE f 76 " --> pdb=" O ASN f 72 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL f 78 " --> pdb=" O MET f 74 " (cutoff:3.500A) Processing helix chain 'f' and resid 136 through 150 removed outlier: 3.527A pdb=" N GLY f 141 " --> pdb=" O LYS f 137 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR f 150 " --> pdb=" O ASP f 146 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 28 Processing helix chain 'g' and resid 40 through 46 removed outlier: 3.674A pdb=" N GLU g 45 " --> pdb=" O LYS g 41 " (cutoff:3.500A) Processing helix chain 'h' and resid 3 through 21 removed outlier: 3.743A pdb=" N ALA h 10 " --> pdb=" O GLN h 6 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA h 13 " --> pdb=" O GLN h 9 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER h 16 " --> pdb=" O VAL h 12 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA h 19 " --> pdb=" O VAL h 15 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS h 20 " --> pdb=" O SER h 16 " (cutoff:3.500A) Processing helix chain 'h' and resid 33 through 44 removed outlier: 3.509A pdb=" N THR h 39 " --> pdb=" O VAL h 35 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU h 40 " --> pdb=" O ASP h 36 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU h 41 " --> pdb=" O LYS h 37 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ARG h 42 " --> pdb=" O MET h 38 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA h 44 " --> pdb=" O GLU h 40 " (cutoff:3.500A) Processing helix chain 'h' and resid 63 through 67 removed outlier: 3.695A pdb=" N THR h 67 " --> pdb=" O VAL h 64 " (cutoff:3.500A) Processing helix chain 'h' and resid 71 through 77 removed outlier: 3.854A pdb=" N ALA h 75 " --> pdb=" O LEU h 72 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE h 76 " --> pdb=" O LYS h 73 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL h 77 " --> pdb=" O ASP h 74 " (cutoff:3.500A) Processing helix chain 'h' and resid 94 through 101 removed outlier: 3.842A pdb=" N GLU h 98 " --> pdb=" O ARG h 94 " (cutoff:3.500A) Processing helix chain 'i' and resid 19 through 29 removed outlier: 3.769A pdb=" N VAL i 23 " --> pdb=" O PRO i 19 " (cutoff:3.500A) Proline residue: i 25 - end of helix Processing helix chain 'i' and resid 33 through 42 removed outlier: 3.771A pdb=" N PHE i 37 " --> pdb=" O ASN i 33 " (cutoff:3.500A) Processing helix chain 'i' and resid 74 through 84 removed outlier: 3.693A pdb=" N LEU i 79 " --> pdb=" O ALA i 75 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS i 80 " --> pdb=" O ALA i 76 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS i 81 " --> pdb=" O VAL i 77 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA i 82 " --> pdb=" O LEU i 78 " (cutoff:3.500A) Processing helix chain 'i' and resid 101 through 114 removed outlier: 3.743A pdb=" N GLU i 107 " --> pdb=" O ALA i 103 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR i 111 " --> pdb=" O GLU i 107 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS i 112 " --> pdb=" O ILE i 108 " (cutoff:3.500A) Processing helix chain 'i' and resid 120 through 134 removed outlier: 3.540A pdb=" N SER i 127 " --> pdb=" O ALA i 123 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE i 128 " --> pdb=" O MET i 124 " (cutoff:3.500A) Processing helix chain 'j' and resid 24 through 38 removed outlier: 4.078A pdb=" N GLU j 31 " --> pdb=" O ARG j 27 " (cutoff:3.500A) Processing helix chain 'j' and resid 58 through 62 Processing helix chain 'j' and resid 67 through 72 removed outlier: 3.645A pdb=" N LYS j 72 " --> pdb=" O LYS j 68 " (cutoff:3.500A) Processing helix chain 'j' and resid 88 through 96 Processing helix chain 'j' and resid 96 through 109 removed outlier: 4.113A pdb=" N VAL j 100 " --> pdb=" O ARG j 96 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE j 101 " --> pdb=" O PRO j 97 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA j 104 " --> pdb=" O VAL j 100 " (cutoff:3.500A) Processing helix chain 'j' and resid 112 through 120 removed outlier: 3.621A pdb=" N ARG j 120 " --> pdb=" O ARG j 116 " (cutoff:3.500A) Processing helix chain 'j' and resid 132 through 136 Processing helix chain 'k' and resid 104 through 108 Processing helix chain 'k' and resid 112 through 117 Processing helix chain 'l' and resid 56 through 61 removed outlier: 3.692A pdb=" N LEU l 61 " --> pdb=" O LEU l 57 " (cutoff:3.500A) Processing helix chain 'l' and resid 68 through 72 Processing helix chain 'l' and resid 80 through 82 No H-bonds generated for 'chain 'l' and resid 80 through 82' Processing helix chain 'l' and resid 128 through 137 removed outlier: 3.678A pdb=" N ALA l 133 " --> pdb=" O LYS l 129 " (cutoff:3.500A) Processing helix chain 'n' and resid 13 through 32 removed outlier: 3.545A pdb=" N HIS n 31 " --> pdb=" O SER n 27 " (cutoff:3.500A) Processing helix chain 'n' and resid 38 through 57 removed outlier: 4.986A pdb=" N ARG n 46 " --> pdb=" O LYS n 42 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL n 47 " --> pdb=" O GLU n 43 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) Proline residue: n 50 - end of helix removed outlier: 4.119A pdb=" N THR n 57 " --> pdb=" O THR n 53 " (cutoff:3.500A) Processing helix chain 'n' and resid 59 through 69 Processing helix chain 'n' and resid 74 through 79 Processing helix chain 'n' and resid 82 through 87 removed outlier: 3.560A pdb=" N PHE n 87 " --> pdb=" O LEU n 83 " (cutoff:3.500A) Processing helix chain 'o' and resid 3 through 22 removed outlier: 5.003A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS o 17 " --> pdb=" O ARG o 13 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 60 Processing helix chain 'o' and resid 67 through 86 Processing helix chain 'o' and resid 101 through 114 Processing helix chain 'p' and resid 2 through 10 removed outlier: 3.620A pdb=" N GLU p 8 " --> pdb=" O ILE p 4 " (cutoff:3.500A) Processing helix chain 'p' and resid 52 through 55 removed outlier: 3.654A pdb=" N HIS p 55 " --> pdb=" O ARG p 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 52 through 55' Processing helix chain 'p' and resid 96 through 101 removed outlier: 3.918A pdb=" N GLU p 101 " --> pdb=" O TYR p 98 " (cutoff:3.500A) Processing helix chain 'p' and resid 103 through 107 Processing helix chain 'q' and resid 5 through 18 removed outlier: 3.783A pdb=" N ALA q 9 " --> pdb=" O ARG q 5 " (cutoff:3.500A) Processing helix chain 'q' and resid 24 through 29 removed outlier: 3.734A pdb=" N SER q 28 " --> pdb=" O GLY q 25 " (cutoff:3.500A) Processing helix chain 'q' and resid 30 through 71 removed outlier: 4.435A pdb=" N GLN q 36 " --> pdb=" O ARG q 32 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG q 50 " --> pdb=" O TYR q 46 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LYS q 53 " --> pdb=" O ARG q 49 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG q 54 " --> pdb=" O ARG q 50 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG q 57 " --> pdb=" O LYS q 53 " (cutoff:3.500A) Processing helix chain 'q' and resid 74 through 85 Processing helix chain 'q' and resid 90 through 101 Processing helix chain 'q' and resid 101 through 116 Processing helix chain 's' and resid 13 through 22 removed outlier: 3.726A pdb=" N VAL s 20 " --> pdb=" O LYS s 16 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 38 removed outlier: 3.742A pdb=" N ASP s 34 " --> pdb=" O SER s 30 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR s 38 " --> pdb=" O ASP s 34 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 62 Processing helix chain 's' and resid 89 through 91 No H-bonds generated for 'chain 's' and resid 89 through 91' Processing helix chain 't' and resid 2 through 10 removed outlier: 4.019A pdb=" N LEU t 8 " --> pdb=" O GLU t 4 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS t 9 " --> pdb=" O GLU t 5 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL t 10 " --> pdb=" O ARG t 6 " (cutoff:3.500A) Processing helix chain 't' and resid 17 through 26 removed outlier: 3.536A pdb=" N GLU t 25 " --> pdb=" O SER t 21 " (cutoff:3.500A) Processing helix chain 't' and resid 39 through 51 Processing helix chain 'v' and resid 13 through 21 Processing helix chain 'v' and resid 44 through 51 removed outlier: 3.551A pdb=" N ASN v 49 " --> pdb=" O ASP v 45 " (cutoff:3.500A) Processing helix chain 'v' and resid 54 through 59 Processing helix chain 'x' and resid 52 through 61 Processing helix chain 'x' and resid 62 through 74 removed outlier: 3.523A pdb=" N LEU x 67 " --> pdb=" O ILE x 63 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA x 68 " --> pdb=" O ASP x 64 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU x 69 " --> pdb=" O THR x 65 " (cutoff:3.500A) Processing helix chain 'y' and resid 2 through 6 removed outlier: 3.788A pdb=" N GLU y 5 " --> pdb=" O LYS y 2 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU y 6 " --> pdb=" O ALA y 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 2 through 6' Processing helix chain 'y' and resid 9 through 22 removed outlier: 3.608A pdb=" N LEU y 21 " --> pdb=" O GLU y 17 " (cutoff:3.500A) Processing helix chain 'y' and resid 23 through 32 removed outlier: 3.516A pdb=" N ASN y 27 " --> pdb=" O ARG y 23 " (cutoff:3.500A) Processing helix chain 'y' and resid 40 through 60 Processing helix chain 'z' and resid 16 through 27 Processing helix chain 'z' and resid 40 through 50 removed outlier: 3.521A pdb=" N MET z 46 " --> pdb=" O ALA z 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 16 removed outlier: 3.546A pdb=" N ARG B 16 " --> pdb=" O ARG B 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 14 Processing helix chain 'D' and resid 17 through 22 Processing helix chain 'D' and resid 24 through 38 Processing helix chain 'E' and resid 8 through 12 removed outlier: 3.593A pdb=" N LYS E 11 " --> pdb=" O GLY E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 35 Processing helix chain 'E' and resid 36 through 42 Processing helix chain 'E' and resid 50 through 52 No H-bonds generated for 'chain 'E' and resid 50 through 52' Processing helix chain 'E' and resid 53 through 61 removed outlier: 3.765A pdb=" N VAL E 57 " --> pdb=" O ASP E 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 22 removed outlier: 3.610A pdb=" N GLY F 21 " --> pdb=" O LYS F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 33 Processing helix chain 'G' and resid 20 through 22 No H-bonds generated for 'chain 'G' and resid 20 through 22' Processing helix chain 'G' and resid 23 through 30 removed outlier: 3.705A pdb=" N LYS G 27 " --> pdb=" O PRO G 24 " (cutoff:3.500A) Proline residue: G 28 - end of helix Processing helix chain 'G' and resid 45 through 60 removed outlier: 3.553A pdb=" N ASN G 50 " --> pdb=" O VAL G 46 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU G 51 " --> pdb=" O PRO G 47 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU G 55 " --> pdb=" O GLU G 51 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 75 Processing helix chain 'G' and resid 76 through 85 removed outlier: 3.685A pdb=" N ASP G 81 " --> pdb=" O GLU G 77 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA G 82 " --> pdb=" O ALA G 78 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER G 85 " --> pdb=" O ASP G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 107 Processing helix chain 'G' and resid 110 through 115 removed outlier: 3.603A pdb=" N ASP G 115 " --> pdb=" O LYS G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 121 removed outlier: 3.779A pdb=" N SER G 120 " --> pdb=" O GLU G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 147 removed outlier: 3.718A pdb=" N LEU G 134 " --> pdb=" O LYS G 130 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR G 137 " --> pdb=" O ALA G 133 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU G 140 " --> pdb=" O ARG G 136 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER G 146 " --> pdb=" O LYS G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 174 removed outlier: 3.874A pdb=" N LYS G 173 " --> pdb=" O HIS G 169 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU G 174 " --> pdb=" O ILE G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 224 removed outlier: 4.282A pdb=" N THR G 210 " --> pdb=" O ILE G 206 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N LEU G 211 " --> pdb=" O ARG G 207 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR G 212 " --> pdb=" O ALA G 208 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY G 214 " --> pdb=" O THR G 210 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL G 220 " --> pdb=" O VAL G 216 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG G 221 " --> pdb=" O ALA G 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 32 removed outlier: 3.541A pdb=" N LEU H 32 " --> pdb=" O PHE H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 41 removed outlier: 4.227A pdb=" N ARG H 39 " --> pdb=" O ASP H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 45 Processing helix chain 'H' and resid 71 through 76 removed outlier: 3.991A pdb=" N VAL H 75 " --> pdb=" O ARG H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 91 removed outlier: 3.816A pdb=" N VAL H 89 " --> pdb=" O LYS H 85 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL H 90 " --> pdb=" O LEU H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 138 removed outlier: 3.761A pdb=" N ARG H 135 " --> pdb=" O ARG H 131 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA H 136 " --> pdb=" O ALA H 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 13 Processing helix chain 'I' and resid 50 through 65 removed outlier: 4.316A pdb=" N GLU I 56 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE I 63 " --> pdb=" O LYS I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 81 removed outlier: 4.308A pdb=" N ASN I 73 " --> pdb=" O ARG I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 95 removed outlier: 3.829A pdb=" N LEU I 90 " --> pdb=" O GLY I 86 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA I 91 " --> pdb=" O GLU I 87 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU I 92 " --> pdb=" O ASN I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 103 removed outlier: 3.681A pdb=" N TYR I 102 " --> pdb=" O ASP I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 119 removed outlier: 3.876A pdb=" N SER I 118 " --> pdb=" O ARG I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 161 removed outlier: 3.511A pdb=" N LEU I 160 " --> pdb=" O ALA I 157 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 67 removed outlier: 3.742A pdb=" N ILE J 59 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU J 64 " --> pdb=" O GLN J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 118 removed outlier: 4.225A pdb=" N VAL J 116 " --> pdb=" O ALA J 112 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY J 118 " --> pdb=" O LEU J 114 " (cutoff:3.500A) Processing helix chain 'J' and resid 134 through 144 removed outlier: 3.707A pdb=" N ASP J 141 " --> pdb=" O ARG J 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 156 Processing helix chain 'K' and resid 17 through 31 removed outlier: 3.697A pdb=" N ARG K 24 " --> pdb=" O GLY K 20 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA K 27 " --> pdb=" O GLU K 23 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA K 28 " --> pdb=" O ARG K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 80 removed outlier: 3.545A pdb=" N ILE K 71 " --> pdb=" O PRO K 67 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP K 72 " --> pdb=" O GLN K 68 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU K 73 " --> pdb=" O GLU K 69 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU K 75 " --> pdb=" O ILE K 71 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 21 through 30 removed outlier: 3.630A pdb=" N VAL L 26 " --> pdb=" O LEU L 22 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASN L 27 " --> pdb=" O ALA L 23 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE L 28 " --> pdb=" O LYS L 24 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU L 29 " --> pdb=" O PHE L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 43 removed outlier: 4.430A pdb=" N SER L 40 " --> pdb=" O SER L 36 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE L 41 " --> pdb=" O THR L 37 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL L 42 " --> pdb=" O ALA L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 101 removed outlier: 3.934A pdb=" N ARG L 101 " --> pdb=" O ALA L 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 110 removed outlier: 3.987A pdb=" N LYS L 109 " --> pdb=" O ALA L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 125 removed outlier: 4.751A pdb=" N ALA L 120 " --> pdb=" O ALA L 116 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN L 121 " --> pdb=" O LEU L 117 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU L 122 " --> pdb=" O ARG L 118 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER L 124 " --> pdb=" O ALA L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 133 through 139 removed outlier: 3.741A pdb=" N ARG L 137 " --> pdb=" O ALA L 133 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 20 removed outlier: 3.611A pdb=" N ASP M 8 " --> pdb=" O ASP M 4 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN M 15 " --> pdb=" O THR M 11 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA M 18 " --> pdb=" O ARG M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 31 through 42 removed outlier: 3.863A pdb=" N VAL M 38 " --> pdb=" O ALA M 34 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU M 39 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS M 40 " --> pdb=" O ALA M 36 " (cutoff:3.500A) Processing helix chain 'M' and resid 93 through 98 removed outlier: 4.168A pdb=" N ALA M 96 " --> pdb=" O LYS M 93 " (cutoff:3.500A) Processing helix chain 'M' and resid 112 through 119 removed outlier: 4.217A pdb=" N GLN M 117 " --> pdb=" O ARG M 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 53 Processing helix chain 'N' and resid 70 through 80 removed outlier: 3.854A pdb=" N ILE N 78 " --> pdb=" O GLN N 74 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG N 79 " --> pdb=" O ALA N 75 " (cutoff:3.500A) Processing helix chain 'O' and resid 21 through 31 removed outlier: 3.632A pdb=" N ILE O 25 " --> pdb=" O ALA O 21 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA O 29 " --> pdb=" O ILE O 25 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 85 removed outlier: 3.819A pdb=" N VAL O 84 " --> pdb=" O THR O 80 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP O 85 " --> pdb=" O GLU O 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 80 through 85' Processing helix chain 'P' and resid 58 through 69 removed outlier: 3.593A pdb=" N GLU P 67 " --> pdb=" O GLN P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 94 through 100 removed outlier: 3.660A pdb=" N ALA P 98 " --> pdb=" O SER P 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 15 through 19 removed outlier: 3.739A pdb=" N THR R 19 " --> pdb=" O ILE R 16 " (cutoff:3.500A) Processing helix chain 'R' and resid 29 through 34 removed outlier: 3.639A pdb=" N ALA R 34 " --> pdb=" O LYS R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 53 removed outlier: 3.748A pdb=" N ASP R 53 " --> pdb=" O GLU R 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 54 through 57 Processing helix chain 'R' and resid 64 through 75 removed outlier: 3.559A pdb=" N ILE R 72 " --> pdb=" O LEU R 68 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER R 73 " --> pdb=" O ARG R 69 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER R 75 " --> pdb=" O GLU R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 81 removed outlier: 3.729A pdb=" N MET R 80 " --> pdb=" O LYS R 77 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASP R 81 " --> pdb=" O ARG R 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 77 through 81' Processing helix chain 'R' and resid 87 through 92 removed outlier: 3.518A pdb=" N ARG R 92 " --> pdb=" O LEU R 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 3 through 10 Processing helix chain 'S' and resid 18 through 22 removed outlier: 3.739A pdb=" N ALA S 21 " --> pdb=" O LYS S 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 49 removed outlier: 3.565A pdb=" N THR S 49 " --> pdb=" O LYS S 46 " (cutoff:3.500A) Processing helix chain 'S' and resid 81 through 86 Processing helix chain 'T' and resid 3 through 14 removed outlier: 3.503A pdb=" N ALA T 8 " --> pdb=" O THR T 4 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU T 13 " --> pdb=" O LYS T 9 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE T 14 " --> pdb=" O ILE T 10 " (cutoff:3.500A) Processing helix chain 'T' and resid 23 through 40 removed outlier: 3.634A pdb=" N VAL T 28 " --> pdb=" O THR T 24 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA T 29 " --> pdb=" O GLU T 25 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN T 34 " --> pdb=" O LEU T 30 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN T 36 " --> pdb=" O THR T 32 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N HIS T 37 " --> pdb=" O ALA T 33 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY T 40 " --> pdb=" O ASN T 36 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 73 removed outlier: 4.672A pdb=" N GLY T 54 " --> pdb=" O HIS T 50 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG T 63 " --> pdb=" O VAL T 59 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP T 67 " --> pdb=" O ARG T 63 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N TYR T 68 " --> pdb=" O LYS T 64 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 85 removed outlier: 3.606A pdb=" N TYR T 77 " --> pdb=" O ASP T 73 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU T 82 " --> pdb=" O THR T 78 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG T 83 " --> pdb=" O GLN T 79 " (cutoff:3.500A) Processing helix chain 'U' and resid 53 through 61 removed outlier: 3.575A pdb=" N ILE U 57 " --> pdb=" O ASP U 53 " (cutoff:3.500A) Processing helix chain 'U' and resid 62 through 64 No H-bonds generated for 'chain 'U' and resid 62 through 64' Processing helix chain 'U' and resid 69 through 72 Processing helix chain 'U' and resid 73 through 78 removed outlier: 3.525A pdb=" N VAL U 78 " --> pdb=" O LEU U 74 " (cutoff:3.500A) Processing helix chain 'W' and resid 24 through 29 removed outlier: 3.960A pdb=" N LEU W 28 " --> pdb=" O ASP W 24 " (cutoff:3.500A) Processing helix chain 'W' and resid 30 through 32 No H-bonds generated for 'chain 'W' and resid 30 through 32' Processing helix chain 'W' and resid 40 through 45 removed outlier: 3.652A pdb=" N THR W 44 " --> pdb=" O PRO W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 47 through 62 removed outlier: 3.726A pdb=" N ARG W 52 " --> pdb=" O ALA W 48 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU W 54 " --> pdb=" O TYR W 50 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA W 57 " --> pdb=" O GLN W 53 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 16 Processing helix chain 'X' and resid 18 through 23 Processing helix chain 'Y' and resid 6 through 39 removed outlier: 3.680A pdb=" N HIS Y 19 " --> pdb=" O LYS Y 15 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER Y 22 " --> pdb=" O LYS Y 18 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE Y 30 " --> pdb=" O MET Y 26 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE Y 31 " --> pdb=" O MET Y 27 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS Y 32 " --> pdb=" O ARG Y 28 " (cutoff:3.500A) Processing helix chain 'Y' and resid 43 through 52 Processing helix chain 'Y' and resid 53 through 64 removed outlier: 3.654A pdb=" N GLN Y 60 " --> pdb=" O ILE Y 56 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA Y 61 " --> pdb=" O VAL Y 57 " (cutoff:3.500A) Processing helix chain 'Y' and resid 68 through 86 removed outlier: 3.711A pdb=" N LEU Y 78 " --> pdb=" O HIS Y 74 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR Y 79 " --> pdb=" O LYS Y 75 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN Y 81 " --> pdb=" O ASN Y 77 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASN Y 83 " --> pdb=" O THR Y 79 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N LYS Y 84 " --> pdb=" O ALA Y 80 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 21 Processing helix chain 'Z' and resid 26 through 30 Processing helix chain 'Z' and resid 38 through 41 Processing helix chain 'Z' and resid 42 through 50 removed outlier: 3.854A pdb=" N ARG Z 46 " --> pdb=" O THR Z 42 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA Z 47 " --> pdb=" O GLU Z 43 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS Z 48 " --> pdb=" O ARG Z 44 " (cutoff:3.500A) Processing helix chain 'Z' and resid 51 through 56 removed outlier: 3.526A pdb=" N HIS Z 55 " --> pdb=" O ALA Z 51 " (cutoff:3.500A) Processing helix chain 'a' and resid 5 through 12 removed outlier: 3.812A pdb=" N VAL a 10 " --> pdb=" O LYS a 6 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE a 11 " --> pdb=" O ARG a 7 " (cutoff:3.500A) Processing helix chain 'a' and resid 22 through 30 removed outlier: 3.512A pdb=" N ALA a 26 " --> pdb=" O ASP a 22 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE a 27 " --> pdb=" O ILE a 23 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ALA a 28 " --> pdb=" O ASN a 24 " (cutoff:3.500A) Processing helix chain 'a' and resid 54 through 58 removed outlier: 3.730A pdb=" N GLN a 57 " --> pdb=" O LYS a 54 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN a 58 " --> pdb=" O SER a 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 54 through 58' Processing helix chain 'a' and resid 181 through 198 removed outlier: 3.574A pdb=" N GLU a 187 " --> pdb=" O ASP a 183 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN a 188 " --> pdb=" O LYS a 184 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA a 191 " --> pdb=" O GLU a 187 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU a 192 " --> pdb=" O ASN a 188 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU a 193 " --> pdb=" O LEU a 189 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA a 195 " --> pdb=" O ALA a 191 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS a 198 " --> pdb=" O VAL a 194 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'b' and resid 2 through 4 Processing sheet with id=AA2, first strand: chain 'b' and resid 33 through 34 Processing sheet with id=AA3, first strand: chain 'b' and resid 100 through 104 removed outlier: 6.808A pdb=" N ILE b 90 " --> pdb=" O LEU b 80 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LEU b 80 " --> pdb=" O ILE b 90 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU b 92 " --> pdb=" O GLU b 78 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'b' and resid 128 through 130 removed outlier: 5.811A pdb=" N ILE b 163 " --> pdb=" O ARG b 174 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ARG b 174 " --> pdb=" O ILE b 163 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N MET b 180 " --> pdb=" O VAL b 267 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'c' and resid 170 through 171 removed outlier: 5.491A pdb=" N VAL c 26 " --> pdb=" O VAL c 9 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N MET c 11 " --> pdb=" O VAL c 24 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL c 24 " --> pdb=" O MET c 11 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ARG c 13 " --> pdb=" O ILE c 22 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE c 22 " --> pdb=" O ARG c 13 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL c 189 " --> pdb=" O THR c 25 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU c 188 " --> pdb=" O VAL c 178 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASP c 176 " --> pdb=" O LYS c 190 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'c' and resid 79 through 83 removed outlier: 6.336A pdb=" N ALA c 47 " --> pdb=" O VAL c 37 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N VAL c 37 " --> pdb=" O ALA c 47 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLN c 49 " --> pdb=" O THR c 35 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'c' and resid 117 through 119 removed outlier: 3.504A pdb=" N GLY c 117 " --> pdb=" O MET c 165 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'd' and resid 2 through 3 Processing sheet with id=AA9, first strand: chain 'd' and resid 118 through 121 Processing sheet with id=AB1, first strand: chain 'd' and resid 146 through 150 removed outlier: 3.588A pdb=" N THR d 150 " --> pdb=" O ARG d 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'e' and resid 65 through 68 removed outlier: 3.828A pdb=" N LYS e 32 " --> pdb=" O THR e 156 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'f' and resid 8 through 9 removed outlier: 3.546A pdb=" N LYS f 43 " --> pdb=" O THR f 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'f' and resid 15 through 19 Processing sheet with id=AB5, first strand: chain 'f' and resid 121 through 126 removed outlier: 7.158A pdb=" N GLU f 129 " --> pdb=" O PRO f 125 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'f' and resid 93 through 98 Processing sheet with id=AB7, first strand: chain 'g' and resid 18 through 20 removed outlier: 3.665A pdb=" N VAL g 3 " --> pdb=" O VAL g 19 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'h' and resid 23 through 27 removed outlier: 3.524A pdb=" N ALA h 25 " --> pdb=" O SER h 85 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER h 85 " --> pdb=" O ALA h 25 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL h 27 " --> pdb=" O ALA h 83 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'i' and resid 8 through 10 removed outlier: 3.987A pdb=" N VAL i 8 " --> pdb=" O ILE i 58 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL i 56 " --> pdb=" O LEU i 10 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR i 59 " --> pdb=" O THR i 67 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'i' and resid 99 through 100 Processing sheet with id=AC2, first strand: chain 'j' and resid 122 through 124 removed outlier: 6.474A pdb=" N ILE j 54 " --> pdb=" O LYS j 123 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TYR j 16 " --> pdb=" O ILE j 55 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N LEU j 57 " --> pdb=" O TYR j 16 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL j 18 " --> pdb=" O LEU j 57 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP j 15 " --> pdb=" O GLN j 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'j' and resid 74 through 77 Processing sheet with id=AC4, first strand: chain 'k' and resid 7 through 10 removed outlier: 3.559A pdb=" N VAL k 10 " --> pdb=" O ARG k 17 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG k 17 " --> pdb=" O VAL k 10 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ALA k 16 " --> pdb=" O ALA k 46 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ALA k 46 " --> pdb=" O ALA k 16 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ARG k 18 " --> pdb=" O LYS k 44 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LYS k 40 " --> pdb=" O ILE k 22 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL k 24 " --> pdb=" O ILE k 38 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N ILE k 38 " --> pdb=" O VAL k 24 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N VAL k 62 " --> pdb=" O VAL k 85 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL k 85 " --> pdb=" O VAL k 62 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N CYS k 84 " --> pdb=" O MET k 7 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ASN k 9 " --> pdb=" O CYS k 84 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N LEU k 86 " --> pdb=" O ASN k 9 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'l' and resid 74 through 78 removed outlier: 6.628A pdb=" N ALA l 75 " --> pdb=" O LYS l 109 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ILE l 111 " --> pdb=" O ALA l 75 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE l 77 " --> pdb=" O ILE l 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'l' and resid 89 through 90 Processing sheet with id=AC7, first strand: chain 'n' and resid 33 through 37 Processing sheet with id=AC8, first strand: chain 'o' and resid 47 through 52 removed outlier: 6.533A pdb=" N VAL o 39 " --> pdb=" O LEU o 48 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ALA o 50 " --> pdb=" O ALA o 37 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA o 37 " --> pdb=" O ALA o 50 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N SER o 52 " --> pdb=" O ILE o 35 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ILE o 35 " --> pdb=" O SER o 52 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'p' and resid 68 through 74 removed outlier: 3.984A pdb=" N ALA p 48 " --> pdb=" O THR p 59 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG p 61 " --> pdb=" O VAL p 46 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N VAL p 46 " --> pdb=" O ARG p 61 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N ILE p 63 " --> pdb=" O GLY p 44 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N GLY p 44 " --> pdb=" O ILE p 63 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LYS p 28 " --> pdb=" O ASP p 81 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'p' and resid 68 through 74 removed outlier: 3.984A pdb=" N ALA p 48 " --> pdb=" O THR p 59 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG p 61 " --> pdb=" O VAL p 46 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N VAL p 46 " --> pdb=" O ARG p 61 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N ILE p 63 " --> pdb=" O GLY p 44 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N GLY p 44 " --> pdb=" O ILE p 63 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N THR p 24 " --> pdb=" O LYS p 86 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'r' and resid 11 through 15 removed outlier: 3.564A pdb=" N MET r 40 " --> pdb=" O VAL r 4 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLN r 6 " --> pdb=" O VAL r 38 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL r 38 " --> pdb=" O GLN r 6 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'r' and resid 19 through 23 removed outlier: 6.645A pdb=" N PHE r 93 " --> pdb=" O HIS r 66 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N HIS r 66 " --> pdb=" O PHE r 93 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASP r 95 " --> pdb=" O VAL r 64 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LYS r 60 " --> pdb=" O THR r 99 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ILE r 101 " --> pdb=" O VAL r 58 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL r 58 " --> pdb=" O ILE r 101 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE r 35 " --> pdb=" O ILE r 59 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'r' and resid 72 through 78 removed outlier: 4.358A pdb=" N TYR r 83 " --> pdb=" O ARG r 78 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 's' and resid 4 through 10 removed outlier: 5.515A pdb=" N SER s 101 " --> pdb=" O HIS s 9 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP s 77 " --> pdb=" O HIS s 102 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS s 73 " --> pdb=" O VAL s 106 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N SER s 108 " --> pdb=" O VAL s 71 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL s 71 " --> pdb=" O SER s 108 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 's' and resid 82 through 87 Processing sheet with id=AD7, first strand: chain 't' and resid 11 through 14 removed outlier: 3.888A pdb=" N LYS t 81 " --> pdb=" O VAL t 34 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 't' and resid 69 through 70 Processing sheet with id=AD9, first strand: chain 'u' and resid 64 through 65 removed outlier: 6.602A pdb=" N GLU u 9 " --> pdb=" O PHE u 72 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE u 71 " --> pdb=" O ASP u 80 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP u 80 " --> pdb=" O ILE u 71 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'u' and resid 40 through 44 Processing sheet with id=AE2, first strand: chain 'u' and resid 82 through 86 Processing sheet with id=AE3, first strand: chain 'v' and resid 7 through 8 removed outlier: 3.605A pdb=" N GLU v 7 " --> pdb=" O GLU v 41 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N GLN v 87 " --> pdb=" O LYS v 25 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N HIS v 88 " --> pdb=" O GLN v 78 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL v 92 " --> pdb=" O ALA v 74 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ALA v 74 " --> pdb=" O VAL v 92 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'w' and resid 18 through 19 removed outlier: 6.678A pdb=" N LEU w 55 " --> pdb=" O ILE w 33 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'w' and resid 26 through 27 Processing sheet with id=AE6, first strand: chain 'x' and resid 12 through 15 Processing sheet with id=AE7, first strand: chain 'x' and resid 32 through 39 Processing sheet with id=AE8, first strand: chain 'z' and resid 34 through 36 removed outlier: 3.726A pdb=" N LYS z 5 " --> pdb=" O GLU z 57 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 22 through 26 removed outlier: 8.399A pdb=" N LEU A 34 " --> pdb=" O THR A 13 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N SER A 15 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 14 through 15 Processing sheet with id=AF2, first strand: chain 'F' and resid 2 through 3 removed outlier: 3.821A pdb=" N ARG F 36 " --> pdb=" O LYS F 2 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'F' and resid 15 through 17 Processing sheet with id=AF4, first strand: chain 'G' and resid 17 through 18 removed outlier: 4.000A pdb=" N HIS G 17 " --> pdb=" O HIS G 38 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 89 through 91 removed outlier: 6.374A pdb=" N ILE G 66 " --> pdb=" O PHE G 89 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL G 91 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N PHE G 68 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N LEU G 67 " --> pdb=" O PHE G 161 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LEU G 160 " --> pdb=" O PHE G 183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'H' and resid 51 through 57 removed outlier: 3.661A pdb=" N ARG H 53 " --> pdb=" O HIS H 68 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA H 103 " --> pdb=" O ILE H 67 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR H 69 " --> pdb=" O ALA H 103 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 165 through 168 removed outlier: 3.880A pdb=" N VAL H 150 " --> pdb=" O TYR H 167 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY H 147 " --> pdb=" O PHE H 202 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER H 186 " --> pdb=" O VAL H 197 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 140 through 142 Processing sheet with id=AF9, first strand: chain 'J' and resid 12 through 14 removed outlier: 3.613A pdb=" N THR J 36 " --> pdb=" O GLY J 48 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY J 48 " --> pdb=" O THR J 36 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 18 through 21 Processing sheet with id=AG2, first strand: chain 'J' and resid 94 through 96 Processing sheet with id=AG3, first strand: chain 'K' and resid 2 through 3 removed outlier: 3.664A pdb=" N ARG K 2 " --> pdb=" O ALA K 66 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 60 through 61 removed outlier: 3.652A pdb=" N VAL K 60 " --> pdb=" O PHE K 8 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE K 8 " --> pdb=" O VAL K 60 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL K 7 " --> pdb=" O SER K 87 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N SER K 87 " --> pdb=" O VAL K 7 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'M' and resid 23 through 27 removed outlier: 6.434A pdb=" N GLU M 57 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL M 50 " --> pdb=" O GLU M 57 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLU M 59 " --> pdb=" O PHE M 48 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE M 48 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR M 61 " --> pdb=" O GLU M 46 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'M' and resid 73 through 76 removed outlier: 3.696A pdb=" N SER M 73 " --> pdb=" O ALA M 129 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR M 127 " --> pdb=" O GLN M 75 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL M 102 " --> pdb=" O ILE M 125 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N TYR M 127 " --> pdb=" O ILE M 100 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ILE M 100 " --> pdb=" O TYR M 127 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'N' and resid 5 through 7 removed outlier: 3.553A pdb=" N TYR N 5 " --> pdb=" O ILE N 20 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE N 20 " --> pdb=" O TYR N 5 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY N 7 " --> pdb=" O VAL N 18 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL N 18 " --> pdb=" O GLY N 7 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR N 65 " --> pdb=" O ARG N 17 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL N 28 " --> pdb=" O ILE N 64 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N VAL N 66 " --> pdb=" O VAL N 28 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'O' and resid 9 through 10 removed outlier: 3.520A pdb=" N ARG O 72 " --> pdb=" O LEU O 10 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'O' and resid 45 through 46 Processing sheet with id=AH1, first strand: chain 'O' and resid 49 through 52 Processing sheet with id=AH2, first strand: chain 'P' and resid 40 through 45 removed outlier: 6.707A pdb=" N ALA P 40 " --> pdb=" O ASP P 35 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ASP P 35 " --> pdb=" O ALA P 40 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLY P 42 " --> pdb=" O ILE P 33 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE P 33 " --> pdb=" O GLY P 42 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL P 31 " --> pdb=" O ALA P 44 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS P 21 " --> pdb=" O THR P 32 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N LEU P 81 " --> pdb=" O ASN P 108 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N THR P 110 " --> pdb=" O LEU P 81 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL P 83 " --> pdb=" O THR P 110 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Q' and resid 34 through 39 removed outlier: 4.880A pdb=" N ARG Q 35 " --> pdb=" O ARG Q 53 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LYS Q 50 " --> pdb=" O ILE Q 66 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'U' and resid 34 through 35 Processing sheet with id=AH5, first strand: chain 'U' and resid 8 through 11 Processing sheet with id=AH6, first strand: chain 'V' and resid 6 through 13 removed outlier: 17.291A pdb=" N THR V 6 " --> pdb=" O PHE V 27 " (cutoff:3.500A) removed outlier: 12.934A pdb=" N PHE V 27 " --> pdb=" O THR V 6 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N GLN V 8 " --> pdb=" O GLU V 25 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N GLU V 25 " --> pdb=" O GLN V 8 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL V 21 " --> pdb=" O VAL V 12 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N LYS V 70 " --> pdb=" O LYS V 42 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N HIS V 44 " --> pdb=" O LYS V 70 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TRP V 72 " --> pdb=" O HIS V 44 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'X' and resid 31 through 32 removed outlier: 7.259A pdb=" N THR X 32 " --> pdb=" O HIS X 51 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'a' and resid 172 through 174 Processing sheet with id=AH9, first strand: chain 'a' and resid 61 through 63 removed outlier: 3.690A pdb=" N GLY a 61 " --> pdb=" O TYR a 163 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR a 163 " --> pdb=" O GLY a 61 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL a 161 " --> pdb=" O THR a 63 " (cutoff:3.500A) 1304 hydrogen bonds defined for protein. 3561 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3312 hydrogen bonds 5344 hydrogen bond angles 0 basepair planarities 1332 basepair parallelities 2618 stacking parallelities Total time for adding SS restraints: 260.51 Time building geometry restraints manager: 61.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 30484 1.34 - 1.47: 64367 1.47 - 1.59: 51141 1.59 - 1.71: 9122 1.71 - 1.84: 272 Bond restraints: 155386 Sorted by residual: bond pdb=" CA VAL X 57 " pdb=" CB VAL X 57 " ideal model delta sigma weight residual 1.535 1.574 -0.039 1.02e-02 9.61e+03 1.46e+01 bond pdb=" CA THR h 67 " pdb=" CB THR h 67 " ideal model delta sigma weight residual 1.525 1.569 -0.043 1.24e-02 6.50e+03 1.23e+01 bond pdb=" CA ILE S 92 " pdb=" CB ILE S 92 " ideal model delta sigma weight residual 1.539 1.565 -0.026 7.50e-03 1.78e+04 1.22e+01 bond pdb=" CA VAL a 64 " pdb=" CB VAL a 64 " ideal model delta sigma weight residual 1.538 1.572 -0.034 1.03e-02 9.43e+03 1.12e+01 bond pdb=" CA VAL e 107 " pdb=" CB VAL e 107 " ideal model delta sigma weight residual 1.537 1.580 -0.043 1.29e-02 6.01e+03 1.11e+01 ... (remaining 155381 not shown) Histogram of bond angle deviations from ideal: 99.76 - 106.60: 28003 106.60 - 113.44: 91029 113.44 - 120.28: 57713 120.28 - 127.12: 44506 127.12 - 133.96: 11138 Bond angle restraints: 232389 Sorted by residual: angle pdb=" N VAL R 96 " pdb=" CA VAL R 96 " pdb=" C VAL R 96 " ideal model delta sigma weight residual 110.42 120.09 -9.67 9.60e-01 1.09e+00 1.01e+02 angle pdb=" N GLU N 52 " pdb=" CA GLU N 52 " pdb=" C GLU N 52 " ideal model delta sigma weight residual 113.12 101.89 11.23 1.25e+00 6.40e-01 8.07e+01 angle pdb=" N ILE H 76 " pdb=" CA ILE H 76 " pdb=" C ILE H 76 " ideal model delta sigma weight residual 111.45 103.22 8.23 9.30e-01 1.16e+00 7.83e+01 angle pdb=" N HIS R 11 " pdb=" CA HIS R 11 " pdb=" C HIS R 11 " ideal model delta sigma weight residual 111.74 123.28 -11.54 1.35e+00 5.49e-01 7.31e+01 angle pdb=" N PRO h 89 " pdb=" CA PRO h 89 " pdb=" C PRO h 89 " ideal model delta sigma weight residual 114.68 103.98 10.70 1.28e+00 6.10e-01 6.99e+01 ... (remaining 232384 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 88476 35.90 - 71.80: 9850 71.80 - 107.70: 1222 107.70 - 143.60: 8 143.60 - 179.50: 15 Dihedral angle restraints: 99571 sinusoidal: 83096 harmonic: 16475 Sorted by residual: dihedral pdb=" C4' C 4 490 " pdb=" C3' C 4 490 " pdb=" C2' C 4 490 " pdb=" C1' C 4 490 " ideal model delta sinusoidal sigma weight residual -35.00 34.53 -69.53 1 8.00e+00 1.56e-02 9.75e+01 dihedral pdb=" C5' C 4 490 " pdb=" C4' C 4 490 " pdb=" C3' C 4 490 " pdb=" O3' C 4 490 " ideal model delta sinusoidal sigma weight residual 147.00 79.89 67.11 1 8.00e+00 1.56e-02 9.17e+01 dihedral pdb=" O4' U 42680 " pdb=" C1' U 42680 " pdb=" N1 U 42680 " pdb=" C2 U 42680 " ideal model delta sinusoidal sigma weight residual 200.00 36.25 163.75 1 1.50e+01 4.44e-03 8.36e+01 ... (remaining 99568 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 23061 0.096 - 0.192: 6066 0.192 - 0.287: 541 0.287 - 0.383: 44 0.383 - 0.479: 4 Chirality restraints: 29716 Sorted by residual: chirality pdb=" CA GLU Z 9 " pdb=" N GLU Z 9 " pdb=" C GLU Z 9 " pdb=" CB GLU Z 9 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.73e+00 chirality pdb=" C1' A 31256 " pdb=" O4' A 31256 " pdb=" C2' A 31256 " pdb=" N9 A 31256 " both_signs ideal model delta sigma weight residual False 2.46 2.00 0.46 2.00e-01 2.50e+01 5.31e+00 chirality pdb=" CA ASN Z 8 " pdb=" N ASN Z 8 " pdb=" C ASN Z 8 " pdb=" CB ASN Z 8 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.04e+00 ... (remaining 29713 not shown) Planarity restraints: 12463 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U 42237 " 0.099 2.00e-02 2.50e+03 5.22e-02 6.13e+01 pdb=" N1 U 42237 " -0.006 2.00e-02 2.50e+03 pdb=" C2 U 42237 " -0.019 2.00e-02 2.50e+03 pdb=" O2 U 42237 " -0.041 2.00e-02 2.50e+03 pdb=" N3 U 42237 " -0.010 2.00e-02 2.50e+03 pdb=" C4 U 42237 " -0.009 2.00e-02 2.50e+03 pdb=" O4 U 42237 " 0.086 2.00e-02 2.50e+03 pdb=" C5 U 42237 " -0.049 2.00e-02 2.50e+03 pdb=" C6 U 42237 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 41191 " -0.101 2.00e-02 2.50e+03 4.26e-02 5.45e+01 pdb=" N9 G 41191 " 0.008 2.00e-02 2.50e+03 pdb=" C8 G 41191 " 0.051 2.00e-02 2.50e+03 pdb=" N7 G 41191 " 0.043 2.00e-02 2.50e+03 pdb=" C5 G 41191 " 0.016 2.00e-02 2.50e+03 pdb=" C6 G 41191 " -0.021 2.00e-02 2.50e+03 pdb=" O6 G 41191 " -0.063 2.00e-02 2.50e+03 pdb=" N1 G 41191 " -0.018 2.00e-02 2.50e+03 pdb=" C2 G 41191 " 0.009 2.00e-02 2.50e+03 pdb=" N2 G 41191 " 0.030 2.00e-02 2.50e+03 pdb=" N3 G 41191 " 0.021 2.00e-02 2.50e+03 pdb=" C4 G 41191 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 41024 " -0.094 2.00e-02 2.50e+03 3.98e-02 4.75e+01 pdb=" N9 G 41024 " 0.006 2.00e-02 2.50e+03 pdb=" C8 G 41024 " 0.048 2.00e-02 2.50e+03 pdb=" N7 G 41024 " 0.044 2.00e-02 2.50e+03 pdb=" C5 G 41024 " 0.012 2.00e-02 2.50e+03 pdb=" C6 G 41024 " -0.023 2.00e-02 2.50e+03 pdb=" O6 G 41024 " -0.057 2.00e-02 2.50e+03 pdb=" N1 G 41024 " -0.016 2.00e-02 2.50e+03 pdb=" C2 G 41024 " 0.009 2.00e-02 2.50e+03 pdb=" N2 G 41024 " 0.028 2.00e-02 2.50e+03 pdb=" N3 G 41024 " 0.021 2.00e-02 2.50e+03 pdb=" C4 G 41024 " 0.022 2.00e-02 2.50e+03 ... (remaining 12460 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 22616 2.77 - 3.31: 128346 3.31 - 3.84: 294714 3.84 - 4.37: 363937 4.37 - 4.90: 482428 Nonbonded interactions: 1292041 Sorted by model distance: nonbonded pdb=" O LYS l 29 " pdb=" OG1 THR l 30 " model vdw 2.243 2.440 nonbonded pdb=" O ASN l 93 " pdb=" OG1 THR l 94 " model vdw 2.283 2.440 nonbonded pdb=" O GLU k 92 " pdb=" O GLN k 93 " model vdw 2.296 3.040 nonbonded pdb=" O ARG n 69 " pdb=" OG1 THR n 70 " model vdw 2.314 2.440 nonbonded pdb=" OG1 THR K 92 " pdb=" N LYS K 93 " model vdw 2.315 2.520 ... (remaining 1292036 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.880 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: 0.100 Extract box with map and model: 48.320 Check model and map are aligned: 1.500 Set scattering table: 0.990 Process input model: 516.200 Find NCS groups from input model: 2.770 Set up NCS constraints: 0.370 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:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 583.410 ------------------------------------------------------------------------------- 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 : 0.007 0.073 155386 Z= 0.430 Angle : 0.961 13.844 232389 Z= 0.643 Chirality : 0.081 0.479 29716 Planarity : 0.007 0.076 12463 Dihedral : 22.446 179.498 88939 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 1.60 % Allowed : 12.98 % Favored : 85.42 % Rotamer: Outliers : 0.89 % Allowed : 6.82 % Favored : 92.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.34 (0.08), residues: 5680 helix: -4.36 (0.07), residues: 1612 sheet: -2.96 (0.15), residues: 862 loop : -3.35 (0.09), residues: 3206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.007 TRP I 169 HIS 0.002 0.000 HIS E 30 PHE 0.048 0.005 PHE Z 11 TYR 0.066 0.007 TYR I 102 ARG 0.006 0.001 ARG r 84 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11360 Ramachandran restraints generated. 5680 Oldfield, 0 Emsley, 5680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11360 Ramachandran restraints generated. 5680 Oldfield, 0 Emsley, 5680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1447 residues out of total 4720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 1405 time to evaluate : 7.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 224 MET cc_start: 0.8669 (mtt) cc_final: 0.8468 (mtm) REVERT: c 150 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7788 (pt0) REVERT: c 186 LEU cc_start: 0.9382 (mt) cc_final: 0.9167 (mt) REVERT: d 77 ILE cc_start: 0.9411 (pt) cc_final: 0.9174 (mt) REVERT: d 100 MET cc_start: 0.8170 (mtp) cc_final: 0.7814 (mtm) REVERT: d 111 GLU cc_start: 0.8583 (tp30) cc_final: 0.8317 (tp30) REVERT: e 99 PHE cc_start: 0.8261 (t80) cc_final: 0.8029 (t80) REVERT: e 172 PHE cc_start: 0.7860 (m-80) cc_final: 0.7632 (m-80) REVERT: e 174 PHE cc_start: 0.7626 (m-80) cc_final: 0.7137 (m-80) REVERT: f 46 ASP cc_start: 0.8481 (m-30) cc_final: 0.8244 (m-30) REVERT: f 130 ILE cc_start: 0.9234 (tt) cc_final: 0.9005 (mp) REVERT: g 22 LYS cc_start: 0.8993 (mttp) cc_final: 0.8468 (mtpp) REVERT: g 35 LYS cc_start: 0.8816 (mttt) cc_final: 0.8540 (mmmm) REVERT: g 42 LYS cc_start: 0.9054 (mtmm) cc_final: 0.8609 (ptmm) REVERT: g 46 PHE cc_start: 0.8392 (m-10) cc_final: 0.8166 (m-80) REVERT: h 1 MET cc_start: 0.5686 (ptt) cc_final: 0.5305 (ptm) REVERT: j 16 TYR cc_start: 0.8989 (m-80) cc_final: 0.8672 (m-80) REVERT: j 36 LEU cc_start: 0.9182 (mt) cc_final: 0.8596 (mt) REVERT: k 1 MET cc_start: 0.8032 (mmp) cc_final: 0.7460 (mmp) REVERT: k 3 GLN cc_start: 0.8865 (pt0) cc_final: 0.8607 (pt0) REVERT: k 12 ASP cc_start: 0.8415 (p0) cc_final: 0.7957 (p0) REVERT: k 53 LYS cc_start: 0.9002 (pttp) cc_final: 0.8646 (pttp) REVERT: l 55 MET cc_start: 0.9072 (tpp) cc_final: 0.8867 (mmt) REVERT: l 57 LEU cc_start: 0.8720 (tt) cc_final: 0.8511 (tt) REVERT: l 58 TYR cc_start: 0.8336 (p90) cc_final: 0.7981 (p90) REVERT: l 100 ILE cc_start: 0.9066 (pt) cc_final: 0.8822 (mp) REVERT: n 53 THR cc_start: 0.8406 (m) cc_final: 0.8074 (p) REVERT: n 72 ASP cc_start: 0.8663 (t0) cc_final: 0.8431 (t0) REVERT: n 100 CYS cc_start: 0.8111 (t) cc_final: 0.7392 (t) REVERT: n 110 MET cc_start: 0.8764 (mmm) cc_final: 0.8508 (mpp) REVERT: o 17 LYS cc_start: 0.9099 (tppp) cc_final: 0.8891 (tptp) REVERT: p 9 GLN cc_start: 0.9424 (pt0) cc_final: 0.8774 (pt0) REVERT: p 54 LEU cc_start: 0.9359 (tp) cc_final: 0.8681 (tp) REVERT: p 70 GLU cc_start: 0.8015 (tt0) cc_final: 0.7762 (tt0) REVERT: p 81 ASP cc_start: 0.8707 (t70) cc_final: 0.8426 (t70) REVERT: p 82 SER cc_start: 0.8859 (m) cc_final: 0.8540 (m) REVERT: p 108 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7403 (pmt-80) REVERT: q 51 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8441 (mm-40) REVERT: r 81 LYS cc_start: 0.9034 (mmtt) cc_final: 0.8729 (mmmm) REVERT: s 1 MET cc_start: 0.8534 (mtm) cc_final: 0.8159 (mtp) REVERT: s 15 GLN cc_start: 0.8333 (tt0) cc_final: 0.8044 (tt0) REVERT: s 38 TYR cc_start: 0.8937 (m-80) cc_final: 0.8681 (m-10) REVERT: s 86 MET cc_start: 0.8709 (tpt) cc_final: 0.8448 (tpp) REVERT: t 79 ASP cc_start: 0.8764 (m-30) cc_final: 0.8544 (m-30) REVERT: v 25 LYS cc_start: 0.9119 (mttt) cc_final: 0.8825 (mtpp) REVERT: v 49 ASN cc_start: 0.8456 (m-40) cc_final: 0.8024 (m110) REVERT: w 78 ILE cc_start: 0.8785 (mt) cc_final: 0.8580 (tt) REVERT: x 55 MET cc_start: 0.8564 (mtp) cc_final: 0.8281 (ttm) REVERT: x 61 LYS cc_start: 0.8540 (mttt) cc_final: 0.8033 (mmmt) REVERT: z 18 LYS cc_start: 0.8275 (mmmt) cc_final: 0.8039 (mmmt) REVERT: A 12 ILE cc_start: 0.8537 (mm) cc_final: 0.8265 (tt) REVERT: B 53 VAL cc_start: 0.8989 (p) cc_final: 0.8684 (p) REVERT: E 56 LEU cc_start: 0.8965 (mt) cc_final: 0.8727 (mp) REVERT: F 36 ARG cc_start: 0.8576 (mtp180) cc_final: 0.8241 (mtp180) REVERT: G 6 ARG cc_start: 0.8601 (mpt-90) cc_final: 0.8131 (mtm-85) REVERT: G 48 MET cc_start: 0.6880 (mtt) cc_final: 0.6636 (mtp) REVERT: G 89 PHE cc_start: 0.8003 (m-80) cc_final: 0.7071 (m-80) REVERT: G 95 TRP cc_start: 0.8222 (t-100) cc_final: 0.7843 (t-100) REVERT: G 99 MET cc_start: 0.8844 (ttm) cc_final: 0.8572 (mtp) REVERT: G 135 MET cc_start: 0.6168 (mmp) cc_final: 0.5658 (mmm) REVERT: G 158 ASP cc_start: 0.7921 (m-30) cc_final: 0.7605 (t0) REVERT: H 5 HIS cc_start: 0.8456 (t-90) cc_final: 0.7813 (t-90) REVERT: H 17 TRP cc_start: 0.8093 (m-90) cc_final: 0.7792 (m-90) REVERT: H 24 ASN cc_start: 0.8649 (m-40) cc_final: 0.8405 (m-40) REVERT: H 40 GLN cc_start: 0.8296 (tt0) cc_final: 0.8087 (tt0) REVERT: H 133 MET cc_start: 0.8504 (mtp) cc_final: 0.8201 (mtm) REVERT: H 139 ASN cc_start: 0.8590 (m110) cc_final: 0.7799 (m110) REVERT: H 142 ARG cc_start: 0.9218 (tpt170) cc_final: 0.8994 (tpp80) REVERT: H 151 GLU cc_start: 0.8306 (tt0) cc_final: 0.7441 (tm-30) REVERT: H 167 TYR cc_start: 0.7574 (t80) cc_final: 0.7207 (t80) REVERT: H 180 ASP cc_start: 0.9019 (t70) cc_final: 0.7669 (p0) REVERT: I 70 GLN cc_start: 0.8775 (tt0) cc_final: 0.8218 (tt0) REVERT: I 122 ILE cc_start: 0.9063 (mm) cc_final: 0.8651 (tp) REVERT: I 140 ASP cc_start: 0.7364 (m-30) cc_final: 0.7109 (m-30) REVERT: I 144 ILE cc_start: 0.8839 (mp) cc_final: 0.8612 (mp) REVERT: I 203 TYR cc_start: 0.7570 (m-80) cc_final: 0.7344 (m-80) REVERT: J 18 ASN cc_start: 0.8999 (t0) cc_final: 0.8695 (t0) REVERT: J 32 PHE cc_start: 0.7227 (m-80) cc_final: 0.6887 (m-80) REVERT: J 54 GLU cc_start: 0.8549 (mp0) cc_final: 0.8090 (mm-30) REVERT: J 92 ARG cc_start: 0.8686 (mtt90) cc_final: 0.8249 (mtt-85) REVERT: K 62 MET cc_start: 0.8674 (mmm) cc_final: 0.8397 (mmm) REVERT: K 90 MET cc_start: 0.7874 (mmt) cc_final: 0.7272 (mmm) REVERT: L 4 ARG cc_start: 0.8300 (mtt90) cc_final: 0.7853 (mmm160) REVERT: L 28 ILE cc_start: 0.5996 (mt) cc_final: 0.5532 (mt) REVERT: L 101 ARG cc_start: 0.4563 (mmt180) cc_final: 0.2838 (mtt180) REVERT: L 115 MET cc_start: 0.8144 (mmt) cc_final: 0.7770 (mmt) REVERT: L 143 MET cc_start: 0.7091 (mmt) cc_final: 0.6806 (mpp) REVERT: M 26 MET cc_start: 0.8575 (ptp) cc_final: 0.8294 (ptm) REVERT: M 65 PHE cc_start: 0.8725 (t80) cc_final: 0.8400 (t80) REVERT: M 91 LEU cc_start: 0.9280 (mt) cc_final: 0.8973 (mt) REVERT: N 21 LYS cc_start: 0.8155 (tppp) cc_final: 0.7738 (mttp) REVERT: P 35 ASP cc_start: 0.8409 (t70) cc_final: 0.7953 (t70) REVERT: P 74 LYS cc_start: 0.8832 (mtpp) cc_final: 0.8193 (mmmt) REVERT: P 93 GLU cc_start: 0.8379 (pm20) cc_final: 0.8175 (pm20) REVERT: P 109 ILE cc_start: 0.8962 (mt) cc_final: 0.8683 (pt) REVERT: Q 34 THR cc_start: 0.8059 (t) cc_final: 0.7002 (p) REVERT: R 68 LEU cc_start: 0.4186 (OUTLIER) cc_final: 0.3848 (tt) REVERT: R 74 MET cc_start: 0.6842 (mtm) cc_final: 0.6387 (mtm) REVERT: S 27 LYS cc_start: 0.7336 (pptt) cc_final: 0.6865 (pttp) REVERT: S 76 PHE cc_start: 0.8384 (m-80) cc_final: 0.8162 (m-10) REVERT: S 88 MET cc_start: 0.8326 (mtp) cc_final: 0.7052 (mtp) REVERT: T 57 ARG cc_start: 0.8896 (ttt-90) cc_final: 0.8630 (ttt-90) REVERT: T 77 TYR cc_start: 0.9223 (t80) cc_final: 0.8952 (t80) REVERT: V 43 LEU cc_start: 0.9002 (mt) cc_final: 0.8700 (mp) REVERT: W 69 TYR cc_start: 0.8459 (m-80) cc_final: 0.8084 (m-10) REVERT: X 43 MET cc_start: 0.6540 (mtp) cc_final: 0.6154 (ttp) REVERT: Y 38 ILE cc_start: 0.9558 (mt) cc_final: 0.9022 (tp) REVERT: Y 47 GLN cc_start: 0.9234 (tp-100) cc_final: 0.8982 (tp-100) REVERT: Y 52 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8161 (mt-10) REVERT: Y 78 LEU cc_start: 0.9046 (mt) cc_final: 0.8822 (mt) REVERT: Y 81 GLN cc_start: 0.8844 (tt0) cc_final: 0.8490 (tm-30) REVERT: a 168 ASN cc_start: 0.1779 (m110) cc_final: 0.1031 (t0) REVERT: a 200 LYS cc_start: 0.0708 (tttt) cc_final: 0.0504 (tppt) outliers start: 42 outliers final: 16 residues processed: 1432 average time/residue: 1.3783 time to fit residues: 3417.4453 Evaluate side-chains 1011 residues out of total 4720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 991 time to evaluate : 5.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 150 GLN Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain h residue 34 THR Chi-restraints excluded: chain h residue 77 VAL Chi-restraints excluded: chain h residue 99 PHE Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain p residue 108 ARG Chi-restraints excluded: chain q residue 51 GLN Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain Z residue 31 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1012 random chunks: chunk 854 optimal weight: 10.0000 chunk 767 optimal weight: 10.0000 chunk 425 optimal weight: 5.9990 chunk 262 optimal weight: 6.9990 chunk 517 optimal weight: 20.0000 chunk 409 optimal weight: 8.9990 chunk 793 optimal weight: 10.0000 chunk 306 optimal weight: 0.9980 chunk 482 optimal weight: 10.0000 chunk 590 optimal weight: 10.0000 chunk 919 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 85 ASN ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 196 ASN b 225 ASN b 259 ASN d 46 GLN d 115 GLN d 165 HIS f 37 ASN ** f 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 4 ASN h 88 HIS i 5 GLN ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 5 GLN k 82 ASN ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 3 HIS n 9 GLN n 18 GLN o 100 HIS q 55 GLN t 15 HIS t 59 ASN u 39 ASN u 73 ASN ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 78 GLN w 53 HIS x 15 ASN y 20 ASN ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 ASN ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 HIS I 130 ASN ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 134 ASN ** J 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 63 ASN L 51 GLN ** L 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 141 HIS L 147 ASN ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 66 GLN N 3 ASN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 HIS P 27 ASN P 63 GLN Q 111 GLN R 11 HIS R 51 GLN ** S 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 27 GLN U 18 GLN U 29 ASN V 30 HIS W 30 ASN Y 51 ASN Y 67 HIS Y 69 ASN Z 8 ASN ** a 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 155386 Z= 0.313 Angle : 0.697 12.205 232389 Z= 0.362 Chirality : 0.039 0.366 29716 Planarity : 0.006 0.085 12463 Dihedral : 23.238 176.589 77635 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.61 % Favored : 90.11 % Rotamer: Outliers : 3.90 % Allowed : 16.04 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -4.08 (0.09), residues: 5680 helix: -2.69 (0.10), residues: 1643 sheet: -2.53 (0.15), residues: 913 loop : -2.81 (0.10), residues: 3124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP b 212 HIS 0.009 0.001 HIS I 197 PHE 0.030 0.002 PHE G 125 TYR 0.029 0.002 TYR M 127 ARG 0.009 0.001 ARG Q 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11360 Ramachandran restraints generated. 5680 Oldfield, 0 Emsley, 5680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11360 Ramachandran restraints generated. 5680 Oldfield, 0 Emsley, 5680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1260 residues out of total 4720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 1076 time to evaluate : 6.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 224 MET cc_start: 0.8760 (mtt) cc_final: 0.8311 (mtt) REVERT: c 150 GLN cc_start: 0.8330 (pt0) cc_final: 0.8082 (pt0) REVERT: d 100 MET cc_start: 0.8173 (mtp) cc_final: 0.7749 (mtm) REVERT: d 198 GLU cc_start: 0.9255 (tm-30) cc_final: 0.9041 (tm-30) REVERT: f 46 ASP cc_start: 0.8397 (m-30) cc_final: 0.8133 (m-30) REVERT: f 57 TYR cc_start: 0.8084 (m-80) cc_final: 0.7685 (m-10) REVERT: g 22 LYS cc_start: 0.8957 (mttp) cc_final: 0.8415 (mtpp) REVERT: g 35 LYS cc_start: 0.8812 (mttt) cc_final: 0.8556 (mmmt) REVERT: h 1 MET cc_start: 0.5514 (ptt) cc_final: 0.5045 (ptm) REVERT: j 36 LEU cc_start: 0.9135 (mt) cc_final: 0.8913 (mt) REVERT: k 1 MET cc_start: 0.8012 (mmp) cc_final: 0.7180 (mmm) REVERT: k 12 ASP cc_start: 0.8494 (p0) cc_final: 0.8091 (p0) REVERT: k 17 ARG cc_start: 0.8654 (tpp80) cc_final: 0.8299 (tpp80) REVERT: l 57 LEU cc_start: 0.8732 (tt) cc_final: 0.8515 (tt) REVERT: l 58 TYR cc_start: 0.8525 (p90) cc_final: 0.8016 (p90) REVERT: l 67 THR cc_start: 0.8929 (m) cc_final: 0.8613 (p) REVERT: l 100 ILE cc_start: 0.9157 (pt) cc_final: 0.8933 (mp) REVERT: n 4 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7775 (tpt170) REVERT: n 53 THR cc_start: 0.8346 (m) cc_final: 0.7982 (p) REVERT: n 72 ASP cc_start: 0.8794 (t0) cc_final: 0.8467 (t0) REVERT: n 110 MET cc_start: 0.8626 (mmm) cc_final: 0.8262 (mmm) REVERT: o 16 ARG cc_start: 0.8298 (mmp80) cc_final: 0.8008 (mmp80) REVERT: o 17 LYS cc_start: 0.9265 (tppp) cc_final: 0.9033 (tptp) REVERT: p 9 GLN cc_start: 0.9207 (pt0) cc_final: 0.8677 (pp30) REVERT: p 70 GLU cc_start: 0.7942 (tt0) cc_final: 0.7656 (tt0) REVERT: r 74 ILE cc_start: 0.9179 (mt) cc_final: 0.8636 (mp) REVERT: r 76 LYS cc_start: 0.9190 (mtpt) cc_final: 0.8928 (mttm) REVERT: s 1 MET cc_start: 0.8469 (mtm) cc_final: 0.8043 (mtp) REVERT: s 11 ARG cc_start: 0.8171 (tpp-160) cc_final: 0.7967 (tpp-160) REVERT: u 36 GLU cc_start: 0.8158 (pp20) cc_final: 0.7417 (pp20) REVERT: v 40 ILE cc_start: 0.8697 (mm) cc_final: 0.8421 (mm) REVERT: v 49 ASN cc_start: 0.8351 (m-40) cc_final: 0.7891 (p0) REVERT: x 61 LYS cc_start: 0.8647 (mttt) cc_final: 0.8184 (mmmt) REVERT: B 27 LEU cc_start: 0.8599 (tp) cc_final: 0.7844 (tt) REVERT: B 53 VAL cc_start: 0.9015 (p) cc_final: 0.8792 (p) REVERT: F 1 MET cc_start: 0.8790 (ptp) cc_final: 0.8047 (ptp) REVERT: G 6 ARG cc_start: 0.8665 (mpt-90) cc_final: 0.8162 (mtm-85) REVERT: G 48 MET cc_start: 0.6561 (mtt) cc_final: 0.6356 (mtp) REVERT: G 88 GLN cc_start: 0.8510 (mm-40) cc_final: 0.8260 (mm-40) REVERT: G 135 MET cc_start: 0.6104 (mmp) cc_final: 0.5588 (mmm) REVERT: G 158 ASP cc_start: 0.7937 (m-30) cc_final: 0.7601 (t0) REVERT: H 5 HIS cc_start: 0.8473 (t-90) cc_final: 0.7906 (t-90) REVERT: H 17 TRP cc_start: 0.8016 (m-90) cc_final: 0.7751 (m-90) REVERT: H 40 GLN cc_start: 0.8108 (tt0) cc_final: 0.7847 (tt0) REVERT: H 142 ARG cc_start: 0.9272 (tpt170) cc_final: 0.9046 (tpp80) REVERT: H 151 GLU cc_start: 0.8162 (tt0) cc_final: 0.7244 (tm-30) REVERT: I 53 GLN cc_start: 0.8526 (pt0) cc_final: 0.7835 (pt0) REVERT: I 70 GLN cc_start: 0.9116 (tt0) cc_final: 0.8804 (tt0) REVERT: I 122 ILE cc_start: 0.9150 (mm) cc_final: 0.8741 (tp) REVERT: I 140 ASP cc_start: 0.8002 (m-30) cc_final: 0.7539 (m-30) REVERT: J 12 GLU cc_start: 0.7835 (mp0) cc_final: 0.7466 (mp0) REVERT: J 13 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.8011 (tttp) REVERT: K 13 ASP cc_start: 0.8429 (p0) cc_final: 0.8111 (p0) REVERT: K 90 MET cc_start: 0.7771 (mmt) cc_final: 0.7050 (mmm) REVERT: L 4 ARG cc_start: 0.8224 (mtt90) cc_final: 0.7830 (mmm160) REVERT: L 115 MET cc_start: 0.7978 (mmt) cc_final: 0.7614 (mmt) REVERT: L 143 MET cc_start: 0.7029 (mmt) cc_final: 0.6810 (mpp) REVERT: M 2 MET cc_start: 0.8219 (tpp) cc_final: 0.7939 (tpp) REVERT: M 26 MET cc_start: 0.8483 (ptp) cc_final: 0.7569 (ptm) REVERT: M 41 GLU cc_start: 0.9213 (mm-30) cc_final: 0.8995 (mm-30) REVERT: M 91 LEU cc_start: 0.9295 (mt) cc_final: 0.9094 (mt) REVERT: N 45 MET cc_start: 0.8653 (tmm) cc_final: 0.8411 (tmm) REVERT: P 35 ASP cc_start: 0.8278 (t70) cc_final: 0.8048 (t70) REVERT: P 74 LYS cc_start: 0.8808 (mtpp) cc_final: 0.8160 (mmmt) REVERT: P 109 ILE cc_start: 0.8957 (mt) cc_final: 0.8641 (pt) REVERT: Q 111 GLN cc_start: 0.8219 (mt0) cc_final: 0.7952 (mt0) REVERT: R 85 TYR cc_start: 0.6396 (m-80) cc_final: 0.6021 (m-80) REVERT: S 5 MET cc_start: 0.4038 (mmp) cc_final: 0.3812 (mmp) REVERT: U 26 ASN cc_start: 0.8536 (m-40) cc_final: 0.8290 (m110) REVERT: V 20 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8730 (mm) REVERT: X 43 MET cc_start: 0.6783 (mtp) cc_final: 0.6354 (ttp) REVERT: Y 47 GLN cc_start: 0.9433 (tp-100) cc_final: 0.8930 (tp-100) REVERT: Y 58 ASP cc_start: 0.9321 (t70) cc_final: 0.8867 (p0) REVERT: Y 78 LEU cc_start: 0.9125 (mt) cc_final: 0.8831 (mt) REVERT: Z 9 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6913 (tt0) REVERT: a 168 ASN cc_start: 0.1597 (m110) cc_final: 0.0772 (t0) REVERT: a 200 LYS cc_start: 0.0973 (tttt) cc_final: 0.0689 (tppt) outliers start: 184 outliers final: 111 residues processed: 1178 average time/residue: 1.2202 time to fit residues: 2508.1681 Evaluate side-chains 1069 residues out of total 4720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 954 time to evaluate : 5.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain b residue 87 SER Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 112 LEU Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain d residue 181 ILE Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain f residue 37 ASN Chi-restraints excluded: chain f residue 75 VAL Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain f residue 152 ARG Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain i residue 120 ASP Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 100 PHE Chi-restraints excluded: chain k residue 110 GLU Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain n residue 4 ARG Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 67 ASN Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 62 LYS Chi-restraints excluded: chain p residue 67 GLU Chi-restraints excluded: chain p residue 108 ARG Chi-restraints excluded: chain q residue 17 LEU Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 52 ASN Chi-restraints excluded: chain v residue 34 LYS Chi-restraints excluded: chain v residue 38 LEU Chi-restraints excluded: chain v residue 41 GLU Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain y residue 11 VAL Chi-restraints excluded: chain y residue 23 ARG Chi-restraints excluded: chain z residue 9 THR Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 120 SER Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain H residue 182 ASP Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain J residue 13 LYS Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 161 GLU Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 15 HIS Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 46 SER Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain Q residue 103 CYS Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain T residue 1 SER Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 75 ILE Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain V residue 20 ILE Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain Z residue 9 GLU Chi-restraints excluded: chain Z residue 31 VAL Chi-restraints excluded: chain a residue 178 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1012 random chunks: chunk 510 optimal weight: 10.0000 chunk 285 optimal weight: 6.9990 chunk 764 optimal weight: 10.0000 chunk 625 optimal weight: 20.0000 chunk 253 optimal weight: 0.0970 chunk 920 optimal weight: 10.0000 chunk 994 optimal weight: 10.0000 chunk 819 optimal weight: 20.0000 chunk 912 optimal weight: 10.0000 chunk 313 optimal weight: 8.9990 chunk 738 optimal weight: 20.0000 overall best weight: 7.2190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 115 GLN f 37 ASN ** f 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 110 HIS g 20 ASN g 43 ASN i 5 GLN ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 82 ASN ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 62 ASN t 28 ASN ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 42 HIS ** y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 11 HIS ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 13 HIS ** S 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 50 ASN W 53 GLN X 52 ASN Y 67 HIS ** a 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.126 155386 Z= 0.337 Angle : 0.674 13.493 232389 Z= 0.349 Chirality : 0.039 0.318 29716 Planarity : 0.005 0.081 12463 Dihedral : 23.511 176.694 77618 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.41 % Favored : 88.36 % Rotamer: Outliers : 4.85 % Allowed : 18.77 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.10), residues: 5680 helix: -1.91 (0.11), residues: 1667 sheet: -2.34 (0.16), residues: 902 loop : -2.52 (0.10), residues: 3111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 169 HIS 0.025 0.002 HIS v 80 PHE 0.026 0.002 PHE I 106 TYR 0.034 0.002 TYR M 127 ARG 0.014 0.001 ARG q 10 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11360 Ramachandran restraints generated. 5680 Oldfield, 0 Emsley, 5680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11360 Ramachandran restraints generated. 5680 Oldfield, 0 Emsley, 5680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1238 residues out of total 4720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 1009 time to evaluate : 6.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 150 GLN cc_start: 0.8311 (pt0) cc_final: 0.8109 (pt0) REVERT: d 100 MET cc_start: 0.8077 (mtp) cc_final: 0.7687 (mtm) REVERT: e 137 PHE cc_start: 0.8492 (m-80) cc_final: 0.8222 (m-80) REVERT: e 141 ASP cc_start: 0.6561 (OUTLIER) cc_final: 0.5072 (p0) REVERT: f 46 ASP cc_start: 0.8533 (m-30) cc_final: 0.8254 (m-30) REVERT: g 22 LYS cc_start: 0.8918 (mttp) cc_final: 0.8439 (mtpt) REVERT: g 33 GLN cc_start: 0.8561 (mm110) cc_final: 0.8357 (mt0) REVERT: h 1 MET cc_start: 0.5337 (ptt) cc_final: 0.4972 (ptm) REVERT: h 6 GLN cc_start: 0.8299 (tp40) cc_final: 0.8011 (mp10) REVERT: j 13 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8404 (mtm-85) REVERT: k 12 ASP cc_start: 0.8375 (p0) cc_final: 0.7991 (p0) REVERT: l 58 TYR cc_start: 0.8582 (p90) cc_final: 0.8331 (p90) REVERT: l 67 THR cc_start: 0.8929 (m) cc_final: 0.8572 (p) REVERT: l 100 ILE cc_start: 0.9261 (pt) cc_final: 0.9013 (tp) REVERT: n 4 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7931 (tpt170) REVERT: n 53 THR cc_start: 0.8333 (m) cc_final: 0.8009 (p) REVERT: n 72 ASP cc_start: 0.8795 (t0) cc_final: 0.8497 (t0) REVERT: n 110 MET cc_start: 0.8686 (mmm) cc_final: 0.8321 (mmm) REVERT: o 17 LYS cc_start: 0.9262 (tppp) cc_final: 0.9051 (tptp) REVERT: p 70 GLU cc_start: 0.7942 (tt0) cc_final: 0.7651 (tt0) REVERT: r 76 LYS cc_start: 0.9205 (mtpt) cc_final: 0.8965 (mttm) REVERT: s 1 MET cc_start: 0.8498 (mtm) cc_final: 0.8089 (mtp) REVERT: s 86 MET cc_start: 0.8570 (tpt) cc_final: 0.8345 (tpp) REVERT: v 1 MET cc_start: 0.7339 (tpt) cc_final: 0.6261 (ptt) REVERT: v 40 ILE cc_start: 0.8595 (mm) cc_final: 0.8341 (mm) REVERT: v 85 LYS cc_start: 0.8586 (ptpp) cc_final: 0.8343 (ptpp) REVERT: w 78 ILE cc_start: 0.8956 (mt) cc_final: 0.8611 (tt) REVERT: w 79 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8475 (mp0) REVERT: x 61 LYS cc_start: 0.8689 (mttt) cc_final: 0.8282 (mmmt) REVERT: B 27 LEU cc_start: 0.8725 (tp) cc_final: 0.8481 (tt) REVERT: F 1 MET cc_start: 0.8829 (ptp) cc_final: 0.8397 (ptp) REVERT: G 48 MET cc_start: 0.6455 (mtt) cc_final: 0.6183 (mtp) REVERT: G 88 GLN cc_start: 0.8640 (mm-40) cc_final: 0.8310 (mm-40) REVERT: G 135 MET cc_start: 0.6111 (mmp) cc_final: 0.5609 (mmm) REVERT: G 158 ASP cc_start: 0.7752 (m-30) cc_final: 0.7316 (t0) REVERT: G 161 PHE cc_start: 0.8945 (t80) cc_final: 0.8745 (t80) REVERT: H 5 HIS cc_start: 0.8409 (t-90) cc_final: 0.7888 (t-90) REVERT: H 17 TRP cc_start: 0.7978 (m-90) cc_final: 0.7699 (m-90) REVERT: H 40 GLN cc_start: 0.8010 (tt0) cc_final: 0.7742 (tt0) REVERT: H 142 ARG cc_start: 0.9342 (tpt170) cc_final: 0.9126 (tpp80) REVERT: H 151 GLU cc_start: 0.8081 (tt0) cc_final: 0.7108 (tm-30) REVERT: I 53 GLN cc_start: 0.8622 (pt0) cc_final: 0.8026 (pt0) REVERT: I 70 GLN cc_start: 0.9001 (tt0) cc_final: 0.8701 (tt0) REVERT: I 140 ASP cc_start: 0.8069 (m-30) cc_final: 0.7622 (m-30) REVERT: J 13 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.8002 (tttp) REVERT: J 40 ASP cc_start: 0.8359 (p0) cc_final: 0.8047 (p0) REVERT: J 150 GLU cc_start: 0.9276 (mp0) cc_final: 0.8972 (mp0) REVERT: K 1 MET cc_start: 0.7794 (tpt) cc_final: 0.7495 (tpt) REVERT: K 90 MET cc_start: 0.7729 (mmt) cc_final: 0.7351 (mmm) REVERT: L 4 ARG cc_start: 0.8249 (mtt90) cc_final: 0.7875 (mmm160) REVERT: L 30 MET cc_start: 0.6101 (ttt) cc_final: 0.5792 (ttt) REVERT: L 115 MET cc_start: 0.7885 (mmt) cc_final: 0.7538 (mmt) REVERT: L 143 MET cc_start: 0.7024 (mmt) cc_final: 0.6796 (mpp) REVERT: M 75 GLN cc_start: 0.7676 (mm110) cc_final: 0.7458 (mm110) REVERT: M 91 LEU cc_start: 0.9354 (mt) cc_final: 0.9104 (mt) REVERT: M 110 MET cc_start: 0.8329 (ptp) cc_final: 0.8106 (ptp) REVERT: N 21 LYS cc_start: 0.8199 (tppp) cc_final: 0.7585 (ptpp) REVERT: P 35 ASP cc_start: 0.8437 (t70) cc_final: 0.8114 (t0) REVERT: P 37 GLN cc_start: 0.8445 (mm-40) cc_final: 0.8243 (mm-40) REVERT: P 109 ILE cc_start: 0.8953 (mt) cc_final: 0.8654 (pt) REVERT: Q 75 GLU cc_start: 0.8489 (tp30) cc_final: 0.8174 (tp30) REVERT: R 85 TYR cc_start: 0.6385 (m-80) cc_final: 0.6143 (m-80) REVERT: S 59 GLN cc_start: 0.6830 (mt0) cc_final: 0.6158 (mp10) REVERT: S 85 GLU cc_start: 0.9198 (tt0) cc_final: 0.8781 (tp30) REVERT: T 25 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.7970 (pm20) REVERT: T 77 TYR cc_start: 0.9224 (t80) cc_final: 0.8996 (t80) REVERT: U 1 MET cc_start: 0.7692 (ttm) cc_final: 0.7243 (mtt) REVERT: U 26 ASN cc_start: 0.8565 (m-40) cc_final: 0.8272 (m110) REVERT: V 39 ARG cc_start: 0.8231 (mmm-85) cc_final: 0.7796 (mmm-85) REVERT: W 69 TYR cc_start: 0.8501 (m-80) cc_final: 0.8293 (m-10) REVERT: Y 47 GLN cc_start: 0.9363 (tp-100) cc_final: 0.8919 (tp-100) REVERT: Y 52 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8251 (mt-10) REVERT: Z 35 GLU cc_start: 0.5042 (OUTLIER) cc_final: 0.4752 (pp20) REVERT: a 30 LEU cc_start: 0.0893 (OUTLIER) cc_final: 0.0666 (pp) outliers start: 229 outliers final: 165 residues processed: 1144 average time/residue: 1.2153 time to fit residues: 2441.0730 Evaluate side-chains 1094 residues out of total 4720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 922 time to evaluate : 5.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 5 CYS Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain b residue 87 SER Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 144 GLU Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain c residue 193 VAL Chi-restraints excluded: chain c residue 202 ILE Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 112 LEU Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 167 VAL Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain d residue 181 ILE Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain e residue 141 ASP Chi-restraints excluded: chain f residue 75 VAL Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain f residue 152 ARG Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain g residue 15 LEU Chi-restraints excluded: chain g residue 21 VAL Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain i residue 120 ASP Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 13 ARG Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 21 CYS Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 100 PHE Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain l residue 90 VAL Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain n residue 4 ARG Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 100 CYS Chi-restraints excluded: chain n residue 106 ASP Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 67 ASN Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 62 LYS Chi-restraints excluded: chain p residue 67 GLU Chi-restraints excluded: chain p residue 75 THR Chi-restraints excluded: chain p residue 81 ASP Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 17 LEU Chi-restraints excluded: chain q residue 116 LEU Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain s residue 53 SER Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain t residue 86 THR Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 52 ASN Chi-restraints excluded: chain v residue 3 THR Chi-restraints excluded: chain v residue 34 LYS Chi-restraints excluded: chain v residue 41 GLU Chi-restraints excluded: chain v residue 61 LEU Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 32 LEU Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain y residue 11 VAL Chi-restraints excluded: chain y residue 23 ARG Chi-restraints excluded: chain z residue 9 THR Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 120 SER Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 182 ASP Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 73 ASN Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain J residue 13 LYS Chi-restraints excluded: chain J residue 64 GLU Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 161 GLU Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 102 PHE Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 46 SER Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain Q residue 80 LEU Chi-restraints excluded: chain Q residue 103 CYS Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 13 HIS Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain T residue 1 SER Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 77 GLU Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain V residue 26 ARG Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 53 MET Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Z residue 35 GLU Chi-restraints excluded: chain a residue 30 LEU Chi-restraints excluded: chain a residue 59 VAL Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain a residue 178 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1012 random chunks: chunk 909 optimal weight: 10.0000 chunk 692 optimal weight: 40.0000 chunk 477 optimal weight: 7.9990 chunk 101 optimal weight: 20.0000 chunk 439 optimal weight: 20.0000 chunk 618 optimal weight: 20.0000 chunk 923 optimal weight: 10.0000 chunk 978 optimal weight: 10.0000 chunk 482 optimal weight: 30.0000 chunk 875 optimal weight: 10.0000 chunk 263 optimal weight: 4.9990 overall best weight: 8.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 134 HIS d 115 GLN ** e 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 103 ASN ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 82 ASN ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 38 GLN n 9 GLN n 107 ASN ** o 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 74 GLN q 19 GLN ** q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 40 ASN ** v 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 19 HIS ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 GLN ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 70 GLN I 135 GLN ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 121 ASN ** J 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN ** L 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 HIS ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 37 GLN ** P 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 67 HIS ** a 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.130 155386 Z= 0.395 Angle : 0.713 13.386 232389 Z= 0.367 Chirality : 0.040 0.347 29716 Planarity : 0.005 0.076 12463 Dihedral : 23.711 175.910 77613 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 24.11 Ramachandran Plot: Outliers : 0.21 % Allowed : 11.41 % Favored : 88.38 % Rotamer: Outliers : 5.64 % Allowed : 21.59 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.22 (0.10), residues: 5680 helix: -1.63 (0.12), residues: 1657 sheet: -2.25 (0.16), residues: 894 loop : -2.43 (0.10), residues: 3129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP e 96 HIS 0.037 0.002 HIS R 13 PHE 0.043 0.003 PHE g 46 TYR 0.032 0.002 TYR e 142 ARG 0.013 0.001 ARG n 118 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11360 Ramachandran restraints generated. 5680 Oldfield, 0 Emsley, 5680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11360 Ramachandran restraints generated. 5680 Oldfield, 0 Emsley, 5680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1226 residues out of total 4720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 960 time to evaluate : 5.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 100 MET cc_start: 0.8143 (mtp) cc_final: 0.7764 (mtm) REVERT: f 46 ASP cc_start: 0.8630 (m-30) cc_final: 0.8310 (m-30) REVERT: f 165 ASP cc_start: 0.8989 (p0) cc_final: 0.8728 (p0) REVERT: g 22 LYS cc_start: 0.8855 (mttp) cc_final: 0.8371 (mtpt) REVERT: g 51 ARG cc_start: 0.6939 (tpt90) cc_final: 0.6486 (mmp-170) REVERT: h 1 MET cc_start: 0.4855 (ptt) cc_final: 0.4624 (ptt) REVERT: h 6 GLN cc_start: 0.8338 (tp40) cc_final: 0.8112 (mp10) REVERT: j 142 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7954 (tp) REVERT: k 12 ASP cc_start: 0.8345 (p0) cc_final: 0.7972 (p0) REVERT: l 58 TYR cc_start: 0.8558 (p90) cc_final: 0.8283 (p90) REVERT: l 100 ILE cc_start: 0.9272 (OUTLIER) cc_final: 0.9029 (tp) REVERT: n 4 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7970 (tpt170) REVERT: n 53 THR cc_start: 0.8217 (m) cc_final: 0.7899 (p) REVERT: n 110 MET cc_start: 0.8697 (mmm) cc_final: 0.8311 (mmm) REVERT: p 54 LEU cc_start: 0.9201 (tp) cc_final: 0.8753 (tp) REVERT: p 70 GLU cc_start: 0.7976 (tt0) cc_final: 0.7568 (tt0) REVERT: q 90 ASP cc_start: 0.7789 (p0) cc_final: 0.6190 (p0) REVERT: r 11 GLN cc_start: 0.8844 (mp10) cc_final: 0.8375 (mp10) REVERT: r 76 LYS cc_start: 0.9231 (mtpt) cc_final: 0.8944 (mttm) REVERT: s 1 MET cc_start: 0.8380 (mtm) cc_final: 0.7855 (mtp) REVERT: s 77 ASP cc_start: 0.7912 (p0) cc_final: 0.7647 (p0) REVERT: s 86 MET cc_start: 0.8633 (tpt) cc_final: 0.8359 (tpp) REVERT: s 95 ARG cc_start: 0.8689 (tmm-80) cc_final: 0.8372 (tmm-80) REVERT: v 1 MET cc_start: 0.7883 (tpt) cc_final: 0.6581 (ptt) REVERT: v 59 GLU cc_start: 0.8048 (tt0) cc_final: 0.7444 (tt0) REVERT: v 80 HIS cc_start: 0.7315 (OUTLIER) cc_final: 0.7017 (m-70) REVERT: v 85 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7822 (ptpp) REVERT: v 86 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7945 (tp) REVERT: w 64 LYS cc_start: 0.8968 (tppt) cc_final: 0.8761 (tppt) REVERT: w 79 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8473 (mp0) REVERT: x 61 LYS cc_start: 0.8680 (mttt) cc_final: 0.8316 (mmmt) REVERT: B 27 LEU cc_start: 0.8749 (tp) cc_final: 0.8429 (tt) REVERT: F 1 MET cc_start: 0.8671 (ptp) cc_final: 0.8326 (ptp) REVERT: F 37 GLN cc_start: 0.8533 (mt0) cc_final: 0.8328 (tt0) REVERT: G 48 MET cc_start: 0.6397 (mtt) cc_final: 0.6139 (mtp) REVERT: G 88 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8303 (mm-40) REVERT: G 135 MET cc_start: 0.6213 (mmp) cc_final: 0.5719 (mmm) REVERT: G 158 ASP cc_start: 0.7678 (m-30) cc_final: 0.7310 (t0) REVERT: G 197 PHE cc_start: 0.8198 (m-80) cc_final: 0.7951 (m-80) REVERT: H 5 HIS cc_start: 0.8417 (t-90) cc_final: 0.7941 (t-90) REVERT: H 17 TRP cc_start: 0.8059 (m-90) cc_final: 0.7615 (m-90) REVERT: H 41 TYR cc_start: 0.8711 (t80) cc_final: 0.8480 (t80) REVERT: H 142 ARG cc_start: 0.9361 (tpt170) cc_final: 0.9132 (tpp80) REVERT: H 151 GLU cc_start: 0.7941 (tt0) cc_final: 0.7098 (tm-30) REVERT: I 53 GLN cc_start: 0.8652 (pt0) cc_final: 0.8044 (pt0) REVERT: I 70 GLN cc_start: 0.8953 (tt0) cc_final: 0.8681 (tt0) REVERT: I 140 ASP cc_start: 0.7987 (m-30) cc_final: 0.7572 (m-30) REVERT: I 144 ILE cc_start: 0.8797 (mp) cc_final: 0.8369 (pt) REVERT: I 169 TRP cc_start: 0.8294 (p90) cc_final: 0.7377 (p90) REVERT: J 13 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7926 (tttp) REVERT: J 19 ARG cc_start: 0.8786 (ptm-80) cc_final: 0.8543 (ptm160) REVERT: J 63 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8324 (ttt) REVERT: J 67 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7776 (mpt-90) REVERT: J 80 LEU cc_start: 0.8796 (mp) cc_final: 0.8566 (mt) REVERT: J 85 LYS cc_start: 0.9080 (mmmm) cc_final: 0.8853 (mmmm) REVERT: J 115 GLU cc_start: 0.8637 (pt0) cc_final: 0.8346 (pt0) REVERT: K 54 LEU cc_start: 0.8811 (pp) cc_final: 0.8551 (pp) REVERT: K 90 MET cc_start: 0.7775 (mmt) cc_final: 0.7321 (mmm) REVERT: L 4 ARG cc_start: 0.8186 (mtt90) cc_final: 0.7868 (mmm160) REVERT: L 115 MET cc_start: 0.7876 (mmt) cc_final: 0.7578 (mmt) REVERT: L 143 MET cc_start: 0.7146 (mmt) cc_final: 0.6887 (mpp) REVERT: M 26 MET cc_start: 0.7433 (ptm) cc_final: 0.7217 (ptm) REVERT: M 91 LEU cc_start: 0.9395 (mt) cc_final: 0.9148 (mt) REVERT: N 21 LYS cc_start: 0.8037 (tppp) cc_final: 0.7779 (mtmm) REVERT: N 45 MET cc_start: 0.8665 (tmm) cc_final: 0.8207 (tmm) REVERT: N 114 LYS cc_start: 0.6958 (mtmm) cc_final: 0.6743 (pttm) REVERT: P 109 ILE cc_start: 0.8897 (mt) cc_final: 0.8657 (pt) REVERT: Q 61 GLU cc_start: 0.7429 (tp30) cc_final: 0.6025 (mm-30) REVERT: S 5 MET cc_start: 0.3624 (mmp) cc_final: 0.3312 (mmp) REVERT: S 59 GLN cc_start: 0.7024 (mt0) cc_final: 0.6496 (mp10) REVERT: S 85 GLU cc_start: 0.9117 (tt0) cc_final: 0.8767 (tp30) REVERT: T 25 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.7940 (pm20) REVERT: U 26 ASN cc_start: 0.8562 (m-40) cc_final: 0.8251 (m110) REVERT: V 36 PHE cc_start: 0.8538 (m-10) cc_final: 0.8306 (m-10) REVERT: W 69 TYR cc_start: 0.8705 (m-80) cc_final: 0.8439 (m-10) REVERT: X 43 MET cc_start: 0.6540 (ttp) cc_final: 0.6272 (tpp) REVERT: X 65 MET cc_start: 0.3320 (tpt) cc_final: 0.3088 (tpp) REVERT: Y 47 GLN cc_start: 0.9339 (tp-100) cc_final: 0.8859 (tp-100) REVERT: Y 52 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8308 (mt-10) REVERT: Y 58 ASP cc_start: 0.9377 (t70) cc_final: 0.8854 (p0) REVERT: Y 78 LEU cc_start: 0.9291 (mt) cc_final: 0.9029 (mt) REVERT: Z 35 GLU cc_start: 0.5217 (OUTLIER) cc_final: 0.4873 (pp20) outliers start: 266 outliers final: 189 residues processed: 1116 average time/residue: 1.2593 time to fit residues: 2485.2330 Evaluate side-chains 1088 residues out of total 4720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 888 time to evaluate : 5.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 73 ILE Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain b residue 87 SER Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 132 ARG Chi-restraints excluded: chain b residue 144 GLU Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 193 VAL Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain c residue 202 ILE Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 112 LEU Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 167 VAL Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain d residue 181 ILE Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain d residue 195 GLN Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 141 ASP Chi-restraints excluded: chain e residue 172 PHE Chi-restraints excluded: chain f residue 75 VAL Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain f residue 126 THR Chi-restraints excluded: chain f residue 152 ARG Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain g residue 21 VAL Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain i residue 120 ASP Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 88 THR Chi-restraints excluded: chain j residue 101 ILE Chi-restraints excluded: chain j residue 103 ILE Chi-restraints excluded: chain j residue 142 ILE Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 37 ASP Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 91 SER Chi-restraints excluded: chain k residue 100 PHE Chi-restraints excluded: chain k residue 105 ARG Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain l residue 100 ILE Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain n residue 4 ARG Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 100 CYS Chi-restraints excluded: chain n residue 106 ASP Chi-restraints excluded: chain o residue 26 LEU Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 67 ASN Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain p residue 62 LYS Chi-restraints excluded: chain p residue 67 GLU Chi-restraints excluded: chain p residue 81 ASP Chi-restraints excluded: chain p residue 101 GLU Chi-restraints excluded: chain q residue 17 LEU Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain t residue 86 THR Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 52 ASN Chi-restraints excluded: chain v residue 34 LYS Chi-restraints excluded: chain v residue 41 GLU Chi-restraints excluded: chain v residue 49 ASN Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 80 HIS Chi-restraints excluded: chain v residue 85 LYS Chi-restraints excluded: chain v residue 86 LEU Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain x residue 6 VAL Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 32 LEU Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain y residue 11 VAL Chi-restraints excluded: chain y residue 23 ARG Chi-restraints excluded: chain z residue 3 THR Chi-restraints excluded: chain z residue 9 THR Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 120 SER Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 182 ASP Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 73 ASN Chi-restraints excluded: chain I residue 139 ASN Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain J residue 13 LYS Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 67 ARG Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 161 GLU Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 102 PHE Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 15 HIS Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 113 THR Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 46 SER Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain Q residue 103 CYS Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain S residue 20 PHE Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain T residue 1 SER Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 77 GLU Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain V residue 26 ARG Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 35 GLU Chi-restraints excluded: chain a residue 59 VAL Chi-restraints excluded: chain a residue 168 ASN Chi-restraints excluded: chain a residue 173 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1012 random chunks: chunk 814 optimal weight: 10.0000 chunk 555 optimal weight: 20.0000 chunk 14 optimal weight: 8.9990 chunk 728 optimal weight: 10.0000 chunk 403 optimal weight: 7.9990 chunk 834 optimal weight: 20.0000 chunk 676 optimal weight: 30.0000 chunk 1 optimal weight: 4.9990 chunk 499 optimal weight: 10.0000 chunk 878 optimal weight: 10.0000 chunk 246 optimal weight: 20.0000 overall best weight: 8.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 36 GLN c 94 GLN ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 115 GLN ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 136 GLN k 82 ASN ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 65 ASN ** q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 45 GLN ** z 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 145 ASN ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 74 GLN ** S 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 67 HIS ** a 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.113 155386 Z= 0.383 Angle : 0.704 13.198 232389 Z= 0.362 Chirality : 0.040 0.472 29716 Planarity : 0.005 0.075 12463 Dihedral : 23.799 176.539 77612 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 24.37 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.92 % Favored : 87.89 % Rotamer: Outliers : 6.31 % Allowed : 22.10 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.08 (0.10), residues: 5680 helix: -1.41 (0.12), residues: 1658 sheet: -2.28 (0.16), residues: 921 loop : -2.36 (0.10), residues: 3101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 169 HIS 0.010 0.002 HIS R 13 PHE 0.054 0.002 PHE g 46 TYR 0.029 0.002 TYR T 77 ARG 0.022 0.001 ARG G 6 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11360 Ramachandran restraints generated. 5680 Oldfield, 0 Emsley, 5680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11360 Ramachandran restraints generated. 5680 Oldfield, 0 Emsley, 5680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1236 residues out of total 4720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 298 poor density : 938 time to evaluate : 6.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 100 MET cc_start: 0.8160 (mtp) cc_final: 0.7772 (mtm) REVERT: e 95 MET cc_start: 0.9065 (tmm) cc_final: 0.8693 (tmm) REVERT: e 137 PHE cc_start: 0.8645 (m-80) cc_final: 0.8408 (m-80) REVERT: e 174 PHE cc_start: 0.8141 (OUTLIER) cc_final: 0.7452 (m-80) REVERT: f 46 ASP cc_start: 0.8704 (m-30) cc_final: 0.8390 (m-30) REVERT: f 57 TYR cc_start: 0.8238 (m-80) cc_final: 0.8022 (m-80) REVERT: f 152 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8072 (ptm160) REVERT: f 165 ASP cc_start: 0.8997 (p0) cc_final: 0.8744 (p0) REVERT: g 22 LYS cc_start: 0.8836 (mttp) cc_final: 0.8368 (mtpt) REVERT: h 1 MET cc_start: 0.4924 (ptt) cc_final: 0.4703 (ptt) REVERT: h 6 GLN cc_start: 0.8340 (tp40) cc_final: 0.8082 (mp10) REVERT: j 142 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.8030 (tp) REVERT: k 12 ASP cc_start: 0.8319 (p0) cc_final: 0.7962 (p0) REVERT: l 58 TYR cc_start: 0.8575 (p90) cc_final: 0.8253 (p90) REVERT: l 100 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.8976 (tp) REVERT: n 4 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7951 (tpt170) REVERT: n 53 THR cc_start: 0.8166 (m) cc_final: 0.7863 (p) REVERT: n 110 MET cc_start: 0.8710 (mmm) cc_final: 0.8312 (mmm) REVERT: p 70 GLU cc_start: 0.7840 (tt0) cc_final: 0.7573 (tt0) REVERT: q 90 ASP cc_start: 0.7781 (p0) cc_final: 0.6457 (p0) REVERT: r 11 GLN cc_start: 0.8833 (mp10) cc_final: 0.8368 (mp10) REVERT: r 76 LYS cc_start: 0.9201 (mtpt) cc_final: 0.8918 (mttm) REVERT: s 1 MET cc_start: 0.8371 (mtm) cc_final: 0.8108 (mtp) REVERT: s 53 SER cc_start: 0.9295 (OUTLIER) cc_final: 0.9002 (p) REVERT: s 77 ASP cc_start: 0.7889 (p0) cc_final: 0.7579 (p0) REVERT: s 86 MET cc_start: 0.8686 (tpt) cc_final: 0.8404 (tpp) REVERT: s 95 ARG cc_start: 0.8697 (tmm-80) cc_final: 0.8380 (tmm-80) REVERT: v 80 HIS cc_start: 0.7520 (OUTLIER) cc_final: 0.7167 (m-70) REVERT: v 86 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7662 (tp) REVERT: w 64 LYS cc_start: 0.9004 (tppt) cc_final: 0.8747 (tppt) REVERT: w 79 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8511 (mp0) REVERT: x 61 LYS cc_start: 0.8690 (mttt) cc_final: 0.8329 (mmmt) REVERT: y 17 GLU cc_start: 0.8606 (tp30) cc_final: 0.8371 (tp30) REVERT: B 27 LEU cc_start: 0.8805 (tp) cc_final: 0.8440 (tt) REVERT: F 1 MET cc_start: 0.8335 (ptp) cc_final: 0.8120 (ptp) REVERT: G 7 ASP cc_start: 0.8488 (t0) cc_final: 0.8154 (p0) REVERT: G 48 MET cc_start: 0.6486 (mtt) cc_final: 0.6186 (mtp) REVERT: G 88 GLN cc_start: 0.8672 (mm-40) cc_final: 0.8285 (mm-40) REVERT: G 135 MET cc_start: 0.6225 (mmp) cc_final: 0.5725 (mmm) REVERT: G 158 ASP cc_start: 0.7593 (m-30) cc_final: 0.7215 (t0) REVERT: H 17 TRP cc_start: 0.7918 (m-90) cc_final: 0.7511 (m-90) REVERT: H 41 TYR cc_start: 0.8762 (t80) cc_final: 0.8529 (t80) REVERT: H 142 ARG cc_start: 0.9377 (tpt170) cc_final: 0.9016 (tpp80) REVERT: H 192 TYR cc_start: 0.8525 (m-10) cc_final: 0.8245 (m-10) REVERT: I 46 ARG cc_start: 0.7648 (pmt170) cc_final: 0.7277 (pmt170) REVERT: I 70 GLN cc_start: 0.8949 (tt0) cc_final: 0.8629 (tt0) REVERT: I 130 ASN cc_start: 0.8581 (m-40) cc_final: 0.8208 (t0) REVERT: I 131 ILE cc_start: 0.6229 (mm) cc_final: 0.6000 (mm) REVERT: I 140 ASP cc_start: 0.8002 (m-30) cc_final: 0.7597 (m-30) REVERT: I 169 TRP cc_start: 0.8363 (p90) cc_final: 0.7383 (p90) REVERT: J 63 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8450 (ttt) REVERT: J 115 GLU cc_start: 0.8644 (pt0) cc_final: 0.8368 (pt0) REVERT: K 1 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7921 (tpt) REVERT: K 90 MET cc_start: 0.7724 (mmt) cc_final: 0.7344 (mmm) REVERT: L 4 ARG cc_start: 0.8146 (mtt90) cc_final: 0.7853 (mmm160) REVERT: L 101 ARG cc_start: 0.5076 (mmt180) cc_final: 0.3121 (mtt180) REVERT: L 115 MET cc_start: 0.7789 (mmt) cc_final: 0.7537 (mmt) REVERT: L 143 MET cc_start: 0.7208 (mmt) cc_final: 0.6933 (mpp) REVERT: M 26 MET cc_start: 0.7512 (ptm) cc_final: 0.7219 (ptm) REVERT: M 91 LEU cc_start: 0.9400 (mt) cc_final: 0.9155 (mt) REVERT: N 21 LYS cc_start: 0.7962 (tppp) cc_final: 0.7671 (mtmm) REVERT: O 13 PHE cc_start: 0.5484 (OUTLIER) cc_final: 0.4410 (m-80) REVERT: O 88 MET cc_start: 0.6757 (mmt) cc_final: 0.6551 (mtt) REVERT: P 109 ILE cc_start: 0.8895 (mt) cc_final: 0.8646 (pt) REVERT: Q 55 ARG cc_start: 0.8140 (tpp80) cc_final: 0.7515 (tpp80) REVERT: Q 61 GLU cc_start: 0.7418 (tp30) cc_final: 0.7185 (tp30) REVERT: R 85 TYR cc_start: 0.7016 (m-80) cc_final: 0.6558 (m-80) REVERT: S 59 GLN cc_start: 0.6985 (mt0) cc_final: 0.6454 (mp10) REVERT: S 85 GLU cc_start: 0.9117 (tt0) cc_final: 0.8802 (tp30) REVERT: T 25 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.7834 (pm20) REVERT: U 26 ASN cc_start: 0.8545 (m-40) cc_final: 0.8202 (m110) REVERT: V 36 PHE cc_start: 0.8683 (m-10) cc_final: 0.8145 (m-10) REVERT: W 69 TYR cc_start: 0.8659 (m-80) cc_final: 0.8453 (m-10) REVERT: X 65 MET cc_start: 0.3306 (tpt) cc_final: 0.2984 (tpp) REVERT: Y 52 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8292 (mt-10) REVERT: Y 78 LEU cc_start: 0.9290 (mt) cc_final: 0.9011 (mt) REVERT: Z 35 GLU cc_start: 0.5177 (OUTLIER) cc_final: 0.4797 (pp20) REVERT: a 200 LYS cc_start: 0.1793 (tttt) cc_final: 0.1159 (tppt) outliers start: 298 outliers final: 215 residues processed: 1130 average time/residue: 1.1962 time to fit residues: 2382.8311 Evaluate side-chains 1116 residues out of total 4720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 888 time to evaluate : 5.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 5 CYS Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 73 ILE Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain b residue 87 SER Chi-restraints excluded: chain b residue 132 ARG Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 86 GLU Chi-restraints excluded: chain c residue 151 THR Chi-restraints excluded: chain c residue 193 VAL Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain c residue 202 ILE Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 112 LEU Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 167 VAL Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain d residue 181 ILE Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain d residue 195 GLN Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 99 PHE Chi-restraints excluded: chain e residue 141 ASP Chi-restraints excluded: chain e residue 155 ILE Chi-restraints excluded: chain e residue 174 PHE Chi-restraints excluded: chain f residue 55 ASP Chi-restraints excluded: chain f residue 75 VAL Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain f residue 126 THR Chi-restraints excluded: chain f residue 152 ARG Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain g residue 19 VAL Chi-restraints excluded: chain g residue 21 VAL Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain i residue 120 ASP Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 88 THR Chi-restraints excluded: chain j residue 142 ILE Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 52 VAL Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 91 SER Chi-restraints excluded: chain k residue 100 PHE Chi-restraints excluded: chain k residue 105 ARG Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain l residue 100 ILE Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain n residue 4 ARG Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 100 CYS Chi-restraints excluded: chain n residue 106 ASP Chi-restraints excluded: chain o residue 26 LEU Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 67 ASN Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 45 VAL Chi-restraints excluded: chain p residue 62 LYS Chi-restraints excluded: chain p residue 67 GLU Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 81 ASP Chi-restraints excluded: chain p residue 101 GLU Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 17 LEU Chi-restraints excluded: chain q residue 116 LEU Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 84 ARG Chi-restraints excluded: chain s residue 53 SER Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain t residue 74 ILE Chi-restraints excluded: chain t residue 86 THR Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 52 ASN Chi-restraints excluded: chain u residue 90 LYS Chi-restraints excluded: chain v residue 34 LYS Chi-restraints excluded: chain v residue 38 LEU Chi-restraints excluded: chain v residue 41 GLU Chi-restraints excluded: chain v residue 49 ASN Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 80 HIS Chi-restraints excluded: chain v residue 86 LEU Chi-restraints excluded: chain w residue 27 VAL Chi-restraints excluded: chain w residue 34 VAL Chi-restraints excluded: chain x residue 6 VAL Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 32 LEU Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain y residue 11 VAL Chi-restraints excluded: chain y residue 23 ARG Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 6 ILE Chi-restraints excluded: chain z residue 9 THR Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 30 HIS Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 120 SER Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 167 HIS Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 182 ASP Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 73 ASN Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 64 GLU Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 161 GLU Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 13 PHE Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 118 ASN Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 46 SER Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain Q residue 103 CYS Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain S residue 20 PHE Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 41 TRP Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain T residue 1 SER Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 24 SER Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 77 GLU Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain V residue 26 ARG Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 35 GLU Chi-restraints excluded: chain a residue 168 ASN Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain a residue 178 VAL Chi-restraints excluded: chain a residue 192 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1012 random chunks: chunk 329 optimal weight: 30.0000 chunk 880 optimal weight: 10.0000 chunk 193 optimal weight: 1.9990 chunk 574 optimal weight: 20.0000 chunk 241 optimal weight: 6.9990 chunk 979 optimal weight: 10.0000 chunk 812 optimal weight: 10.0000 chunk 453 optimal weight: 10.0000 chunk 81 optimal weight: 0.0010 chunk 323 optimal weight: 20.0000 chunk 514 optimal weight: 20.0000 overall best weight: 5.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 115 GLN e 26 GLN ** f 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 43 ASN ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 82 ASN ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 65 ASN ** q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 20 ASN D 13 ASN ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN ** G 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 HIS ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 37 GLN ** P 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 13 HIS ** S 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 19 ASN Y 69 ASN ** a 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 155386 Z= 0.278 Angle : 0.629 11.556 232389 Z= 0.325 Chirality : 0.037 0.440 29716 Planarity : 0.005 0.070 12463 Dihedral : 23.752 177.288 77612 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 21.53 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.14 % Favored : 89.67 % Rotamer: Outliers : 5.44 % Allowed : 23.58 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.11), residues: 5680 helix: -1.19 (0.12), residues: 1657 sheet: -2.14 (0.15), residues: 977 loop : -2.18 (0.11), residues: 3046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 169 HIS 0.013 0.001 HIS H 5 PHE 0.016 0.002 PHE I 106 TYR 0.035 0.002 TYR g 25 ARG 0.009 0.001 ARG K 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11360 Ramachandran restraints generated. 5680 Oldfield, 0 Emsley, 5680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11360 Ramachandran restraints generated. 5680 Oldfield, 0 Emsley, 5680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1232 residues out of total 4720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 975 time to evaluate : 6.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 165 MET cc_start: 0.8951 (ttp) cc_final: 0.8728 (ttm) REVERT: d 100 MET cc_start: 0.8128 (mtp) cc_final: 0.7756 (mtm) REVERT: e 95 MET cc_start: 0.9001 (tmm) cc_final: 0.8623 (tmm) REVERT: e 137 PHE cc_start: 0.8697 (m-80) cc_final: 0.8453 (m-80) REVERT: e 141 ASP cc_start: 0.6837 (OUTLIER) cc_final: 0.5275 (p0) REVERT: f 46 ASP cc_start: 0.8625 (m-30) cc_final: 0.8311 (m-30) REVERT: f 57 TYR cc_start: 0.8204 (m-80) cc_final: 0.7996 (m-80) REVERT: f 152 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7854 (ptm160) REVERT: f 165 ASP cc_start: 0.8969 (p0) cc_final: 0.8687 (p0) REVERT: g 22 LYS cc_start: 0.8811 (mttp) cc_final: 0.8326 (mtpt) REVERT: g 42 LYS cc_start: 0.9366 (mppt) cc_final: 0.8986 (tttm) REVERT: g 46 PHE cc_start: 0.8278 (m-80) cc_final: 0.7686 (m-80) REVERT: h 1 MET cc_start: 0.4905 (ptt) cc_final: 0.4687 (ptt) REVERT: h 6 GLN cc_start: 0.8342 (tp40) cc_final: 0.8111 (mp10) REVERT: k 12 ASP cc_start: 0.8323 (p0) cc_final: 0.7975 (p0) REVERT: l 58 TYR cc_start: 0.8504 (p90) cc_final: 0.8208 (p90) REVERT: l 100 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8963 (tp) REVERT: n 4 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7910 (tpt170) REVERT: n 53 THR cc_start: 0.8112 (m) cc_final: 0.7813 (p) REVERT: n 110 MET cc_start: 0.8666 (mmm) cc_final: 0.8325 (mmm) REVERT: p 70 GLU cc_start: 0.7743 (tt0) cc_final: 0.7472 (tt0) REVERT: q 90 ASP cc_start: 0.7791 (p0) cc_final: 0.6547 (p0) REVERT: r 11 GLN cc_start: 0.8822 (mp10) cc_final: 0.8363 (mp10) REVERT: r 76 LYS cc_start: 0.9142 (mtpt) cc_final: 0.8843 (mttm) REVERT: s 1 MET cc_start: 0.8408 (mtm) cc_final: 0.8112 (mtp) REVERT: s 11 ARG cc_start: 0.8456 (tpp-160) cc_final: 0.8225 (tpp-160) REVERT: s 53 SER cc_start: 0.9285 (m) cc_final: 0.9009 (p) REVERT: s 77 ASP cc_start: 0.8061 (p0) cc_final: 0.7729 (p0) REVERT: s 95 ARG cc_start: 0.8663 (tmm-80) cc_final: 0.8310 (tmm-80) REVERT: u 7 ASP cc_start: 0.8468 (m-30) cc_final: 0.8177 (m-30) REVERT: v 1 MET cc_start: 0.8021 (tpp) cc_final: 0.6528 (ptt) REVERT: v 59 GLU cc_start: 0.8166 (tt0) cc_final: 0.6987 (tt0) REVERT: v 80 HIS cc_start: 0.7425 (OUTLIER) cc_final: 0.7117 (m-70) REVERT: w 79 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8559 (mp0) REVERT: x 31 ASN cc_start: 0.8831 (t0) cc_final: 0.8534 (m-40) REVERT: x 61 LYS cc_start: 0.8656 (mttt) cc_final: 0.8315 (mmmt) REVERT: y 17 GLU cc_start: 0.8604 (tp30) cc_final: 0.8378 (tp30) REVERT: G 26 MET cc_start: 0.8513 (mmm) cc_final: 0.8148 (ttt) REVERT: G 48 MET cc_start: 0.6548 (mtt) cc_final: 0.6202 (mtp) REVERT: G 88 GLN cc_start: 0.8669 (mm-40) cc_final: 0.8310 (mm-40) REVERT: G 135 MET cc_start: 0.6269 (mmp) cc_final: 0.5754 (mmm) REVERT: G 156 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8886 (pp) REVERT: G 158 ASP cc_start: 0.7596 (m-30) cc_final: 0.7220 (t0) REVERT: H 2 GLN cc_start: 0.4326 (OUTLIER) cc_final: 0.4012 (pt0) REVERT: H 17 TRP cc_start: 0.7882 (m-90) cc_final: 0.7483 (m-90) REVERT: H 41 TYR cc_start: 0.8758 (t80) cc_final: 0.8531 (t80) REVERT: H 142 ARG cc_start: 0.9371 (tpt170) cc_final: 0.9012 (tpp80) REVERT: I 46 ARG cc_start: 0.7599 (pmt170) cc_final: 0.7222 (pmt170) REVERT: I 70 GLN cc_start: 0.8902 (tt0) cc_final: 0.8547 (tt0) REVERT: I 130 ASN cc_start: 0.8554 (m-40) cc_final: 0.8181 (t0) REVERT: I 131 ILE cc_start: 0.6392 (mm) cc_final: 0.6159 (mm) REVERT: I 140 ASP cc_start: 0.7920 (m-30) cc_final: 0.7502 (m-30) REVERT: I 169 TRP cc_start: 0.8339 (p90) cc_final: 0.7445 (p90) REVERT: J 80 LEU cc_start: 0.8744 (mt) cc_final: 0.7945 (mm) REVERT: J 85 LYS cc_start: 0.9206 (mmmt) cc_final: 0.8757 (tppt) REVERT: J 94 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.7028 (t80) REVERT: J 115 GLU cc_start: 0.8679 (pt0) cc_final: 0.8381 (pt0) REVERT: J 146 MET cc_start: 0.8283 (tmm) cc_final: 0.7804 (ttt) REVERT: K 90 MET cc_start: 0.7619 (mmt) cc_final: 0.7219 (mmm) REVERT: L 4 ARG cc_start: 0.8125 (mtt90) cc_final: 0.7836 (mmm160) REVERT: L 115 MET cc_start: 0.7792 (mmt) cc_final: 0.7509 (mmt) REVERT: L 143 MET cc_start: 0.7253 (mmt) cc_final: 0.6948 (mpp) REVERT: M 26 MET cc_start: 0.7283 (ptm) cc_final: 0.7061 (ptm) REVERT: M 91 LEU cc_start: 0.9365 (mt) cc_final: 0.9138 (mt) REVERT: N 21 LYS cc_start: 0.7924 (tppp) cc_final: 0.7667 (mtmm) REVERT: N 45 MET cc_start: 0.8682 (tmm) cc_final: 0.8076 (tpp) REVERT: N 49 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8640 (mm-40) REVERT: O 53 ILE cc_start: 0.7183 (tt) cc_final: 0.6935 (tt) REVERT: P 93 GLU cc_start: 0.8090 (pm20) cc_final: 0.7787 (pm20) REVERT: P 109 ILE cc_start: 0.8892 (mt) cc_final: 0.8650 (pt) REVERT: Q 55 ARG cc_start: 0.7925 (tpp80) cc_final: 0.7712 (tpp80) REVERT: Q 60 PHE cc_start: 0.7527 (m-10) cc_final: 0.7275 (m-10) REVERT: Q 65 TYR cc_start: 0.8632 (t80) cc_final: 0.8389 (t80) REVERT: S 59 GLN cc_start: 0.6971 (mt0) cc_final: 0.6423 (mp10) REVERT: S 85 GLU cc_start: 0.9076 (tt0) cc_final: 0.8851 (tm-30) REVERT: T 25 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.7828 (pm20) REVERT: U 26 ASN cc_start: 0.8522 (m-40) cc_final: 0.8175 (m110) REVERT: V 36 PHE cc_start: 0.8647 (m-10) cc_final: 0.8094 (m-10) REVERT: W 50 TYR cc_start: 0.8134 (m-80) cc_final: 0.7432 (m-80) REVERT: Y 47 GLN cc_start: 0.9299 (tp40) cc_final: 0.8822 (tp40) REVERT: Y 58 ASP cc_start: 0.9344 (t70) cc_final: 0.8679 (p0) REVERT: Z 35 GLU cc_start: 0.5060 (OUTLIER) cc_final: 0.4746 (pp20) REVERT: a 200 LYS cc_start: 0.1914 (tttt) cc_final: 0.1335 (tppt) outliers start: 257 outliers final: 188 residues processed: 1134 average time/residue: 1.1936 time to fit residues: 2386.5292 Evaluate side-chains 1109 residues out of total 4720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 910 time to evaluate : 6.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain b residue 87 SER Chi-restraints excluded: chain b residue 132 ARG Chi-restraints excluded: chain b residue 219 VAL Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 43 ASP Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 86 GLU Chi-restraints excluded: chain c residue 151 THR Chi-restraints excluded: chain c residue 193 VAL Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain c residue 202 ILE Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 167 VAL Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain d residue 181 ILE Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain d residue 195 GLN Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 99 PHE Chi-restraints excluded: chain e residue 141 ASP Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain e residue 155 ILE Chi-restraints excluded: chain e residue 172 PHE Chi-restraints excluded: chain f residue 55 ASP Chi-restraints excluded: chain f residue 126 THR Chi-restraints excluded: chain f residue 152 ARG Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain g residue 15 LEU Chi-restraints excluded: chain g residue 19 VAL Chi-restraints excluded: chain g residue 21 VAL Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain i residue 120 ASP Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 88 THR Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 52 VAL Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 100 PHE Chi-restraints excluded: chain k residue 109 SER Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain l residue 100 ILE Chi-restraints excluded: chain n residue 4 ARG Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 100 CYS Chi-restraints excluded: chain n residue 106 ASP Chi-restraints excluded: chain o residue 26 LEU Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 67 ASN Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 62 LYS Chi-restraints excluded: chain p residue 67 GLU Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 81 ASP Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain p residue 86 LYS Chi-restraints excluded: chain p residue 101 GLU Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 116 LEU Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 84 ARG Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain t residue 86 THR Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 52 ASN Chi-restraints excluded: chain v residue 34 LYS Chi-restraints excluded: chain v residue 41 GLU Chi-restraints excluded: chain v residue 49 ASN Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 80 HIS Chi-restraints excluded: chain x residue 6 VAL Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 32 LEU Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain y residue 11 VAL Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 6 ILE Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 30 HIS Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 120 SER Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 167 HIS Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain H residue 2 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 182 ASP Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 73 ASN Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 94 PHE Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 161 GLU Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 130 LYS Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 113 THR Chi-restraints excluded: chain P residue 118 ASN Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 46 SER Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 103 CYS Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain S residue 20 PHE Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain T residue 1 SER Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 54 LEU Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain V residue 26 ARG Chi-restraints excluded: chain V residue 40 THR Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 53 MET Chi-restraints excluded: chain Z residue 11 PHE Chi-restraints excluded: chain Z residue 35 GLU Chi-restraints excluded: chain a residue 178 VAL Chi-restraints excluded: chain a residue 192 LEU Chi-restraints excluded: chain a residue 222 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1012 random chunks: chunk 944 optimal weight: 10.0000 chunk 110 optimal weight: 20.0000 chunk 557 optimal weight: 20.0000 chunk 715 optimal weight: 10.0000 chunk 554 optimal weight: 8.9990 chunk 824 optimal weight: 10.0000 chunk 546 optimal weight: 9.9990 chunk 975 optimal weight: 10.0000 chunk 610 optimal weight: 20.0000 chunk 594 optimal weight: 20.0000 chunk 450 optimal weight: 30.0000 overall best weight: 9.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 20 ASN ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 82 ASN ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 65 ASN ** q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 92 ASN ** y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 45 GLN ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 51 GLN Y 67 HIS ** a 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 155386 Z= 0.442 Angle : 0.754 13.045 232389 Z= 0.385 Chirality : 0.042 0.378 29716 Planarity : 0.005 0.073 12463 Dihedral : 23.902 177.616 77612 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 27.43 Ramachandran Plot: Outliers : 0.21 % Allowed : 12.64 % Favored : 87.15 % Rotamer: Outliers : 6.25 % Allowed : 23.94 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.10), residues: 5680 helix: -1.32 (0.12), residues: 1656 sheet: -2.13 (0.16), residues: 930 loop : -2.29 (0.11), residues: 3094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 169 HIS 0.013 0.002 HIS H 5 PHE 0.025 0.003 PHE X 9 TYR 0.049 0.003 TYR g 25 ARG 0.011 0.001 ARG V 10 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11360 Ramachandran restraints generated. 5680 Oldfield, 0 Emsley, 5680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11360 Ramachandran restraints generated. 5680 Oldfield, 0 Emsley, 5680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1191 residues out of total 4720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 295 poor density : 896 time to evaluate : 6.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 100 MET cc_start: 0.8140 (mtp) cc_final: 0.7759 (mtm) REVERT: e 95 MET cc_start: 0.9020 (tmm) cc_final: 0.8622 (tmm) REVERT: e 137 PHE cc_start: 0.8714 (m-80) cc_final: 0.8472 (m-80) REVERT: e 174 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7588 (m-80) REVERT: f 46 ASP cc_start: 0.8782 (m-30) cc_final: 0.8464 (m-30) REVERT: f 165 ASP cc_start: 0.9097 (p0) cc_final: 0.8851 (p0) REVERT: g 22 LYS cc_start: 0.8829 (mttp) cc_final: 0.8338 (mtpt) REVERT: j 142 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.8047 (tp) REVERT: k 12 ASP cc_start: 0.8332 (p0) cc_final: 0.7889 (p0) REVERT: l 58 TYR cc_start: 0.8586 (p90) cc_final: 0.8224 (p90) REVERT: n 4 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7974 (tpt170) REVERT: n 53 THR cc_start: 0.8181 (m) cc_final: 0.7878 (p) REVERT: p 70 GLU cc_start: 0.7865 (tt0) cc_final: 0.7571 (tt0) REVERT: r 76 LYS cc_start: 0.9188 (mtpt) cc_final: 0.8874 (mttm) REVERT: s 1 MET cc_start: 0.8411 (mtm) cc_final: 0.8155 (mtp) REVERT: s 77 ASP cc_start: 0.8013 (p0) cc_final: 0.7705 (p0) REVERT: v 1 MET cc_start: 0.8053 (tpp) cc_final: 0.6551 (ptt) REVERT: v 59 GLU cc_start: 0.8185 (tt0) cc_final: 0.7217 (tt0) REVERT: v 80 HIS cc_start: 0.7533 (OUTLIER) cc_final: 0.7134 (m-70) REVERT: v 85 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7842 (ptpp) REVERT: v 86 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7849 (tp) REVERT: w 40 LYS cc_start: 0.9002 (mmtm) cc_final: 0.8782 (mmtm) REVERT: w 79 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8531 (mp0) REVERT: x 61 LYS cc_start: 0.8838 (mttt) cc_final: 0.8438 (mmmt) REVERT: y 17 GLU cc_start: 0.8704 (tp30) cc_final: 0.8463 (tp30) REVERT: G 48 MET cc_start: 0.6545 (mtt) cc_final: 0.6208 (mtp) REVERT: G 88 GLN cc_start: 0.8699 (mm-40) cc_final: 0.8335 (mm-40) REVERT: G 135 MET cc_start: 0.6329 (mmp) cc_final: 0.5807 (mmm) REVERT: G 156 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8945 (pp) REVERT: G 158 ASP cc_start: 0.7635 (m-30) cc_final: 0.7290 (t0) REVERT: H 2 GLN cc_start: 0.4416 (OUTLIER) cc_final: 0.4001 (pt0) REVERT: H 41 TYR cc_start: 0.8705 (t80) cc_final: 0.8496 (t80) REVERT: H 142 ARG cc_start: 0.9374 (tpt170) cc_final: 0.9042 (tpp80) REVERT: I 70 GLN cc_start: 0.8958 (tt0) cc_final: 0.8627 (tt0) REVERT: I 130 ASN cc_start: 0.8469 (m-40) cc_final: 0.8082 (t0) REVERT: I 140 ASP cc_start: 0.7964 (m-30) cc_final: 0.7567 (m-30) REVERT: I 169 TRP cc_start: 0.8446 (p90) cc_final: 0.7620 (p90) REVERT: J 115 GLU cc_start: 0.8652 (pt0) cc_final: 0.8382 (pt0) REVERT: J 146 MET cc_start: 0.8122 (tmm) cc_final: 0.7907 (tpp) REVERT: K 90 MET cc_start: 0.7778 (mmt) cc_final: 0.7434 (mmm) REVERT: L 4 ARG cc_start: 0.8162 (mtt90) cc_final: 0.7839 (mmm160) REVERT: L 101 ARG cc_start: 0.4998 (mmt180) cc_final: 0.3047 (mtt180) REVERT: L 115 MET cc_start: 0.7832 (mmt) cc_final: 0.7585 (mmt) REVERT: L 143 MET cc_start: 0.7207 (mmt) cc_final: 0.6901 (mpp) REVERT: M 89 ASP cc_start: 0.8894 (p0) cc_final: 0.8676 (p0) REVERT: M 91 LEU cc_start: 0.9386 (mt) cc_final: 0.9181 (mt) REVERT: N 21 LYS cc_start: 0.8052 (tppp) cc_final: 0.7431 (pttm) REVERT: O 13 PHE cc_start: 0.5734 (OUTLIER) cc_final: 0.4912 (m-80) REVERT: P 75 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8581 (tm-30) REVERT: P 109 ILE cc_start: 0.8872 (mt) cc_final: 0.8640 (pt) REVERT: Q 65 TYR cc_start: 0.8614 (t80) cc_final: 0.8414 (t80) REVERT: S 85 GLU cc_start: 0.9050 (tt0) cc_final: 0.8831 (tm-30) REVERT: T 25 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7857 (pm20) REVERT: U 26 ASN cc_start: 0.8575 (m-40) cc_final: 0.8217 (m110) REVERT: U 51 ARG cc_start: 0.8283 (tmm160) cc_final: 0.7655 (tmm160) REVERT: Y 47 GLN cc_start: 0.9322 (tp40) cc_final: 0.8843 (tp-100) REVERT: Y 52 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8295 (mt-10) REVERT: Y 78 LEU cc_start: 0.9306 (mt) cc_final: 0.9017 (mt) REVERT: Z 35 GLU cc_start: 0.5356 (OUTLIER) cc_final: 0.4889 (pp20) outliers start: 295 outliers final: 244 residues processed: 1081 average time/residue: 1.2015 time to fit residues: 2298.7892 Evaluate side-chains 1114 residues out of total 4720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 256 poor density : 858 time to evaluate : 5.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 5 CYS Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain b residue 87 SER Chi-restraints excluded: chain b residue 120 ASP Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 219 VAL Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 43 ASP Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 86 GLU Chi-restraints excluded: chain c residue 151 THR Chi-restraints excluded: chain c residue 193 VAL Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain c residue 202 ILE Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 112 LEU Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 167 VAL Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain d residue 181 ILE Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain d residue 195 GLN Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 99 PHE Chi-restraints excluded: chain e residue 141 ASP Chi-restraints excluded: chain e residue 154 THR Chi-restraints excluded: chain e residue 155 ILE Chi-restraints excluded: chain e residue 172 PHE Chi-restraints excluded: chain e residue 174 PHE Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 55 ASP Chi-restraints excluded: chain f residue 75 VAL Chi-restraints excluded: chain f residue 91 VAL Chi-restraints excluded: chain f residue 126 THR Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain g residue 15 LEU Chi-restraints excluded: chain g residue 19 VAL Chi-restraints excluded: chain g residue 21 VAL Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain i residue 120 ASP Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 88 THR Chi-restraints excluded: chain j residue 142 ILE Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 52 VAL Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 91 SER Chi-restraints excluded: chain k residue 100 PHE Chi-restraints excluded: chain k residue 110 GLU Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain l residue 100 ILE Chi-restraints excluded: chain n residue 4 ARG Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 100 CYS Chi-restraints excluded: chain n residue 106 ASP Chi-restraints excluded: chain n residue 113 ILE Chi-restraints excluded: chain o residue 26 LEU Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 62 LYS Chi-restraints excluded: chain p residue 67 GLU Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 81 ASP Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain p residue 86 LYS Chi-restraints excluded: chain p residue 101 GLU Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain q residue 116 LEU Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 84 ARG Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain s residue 7 HIS Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 52 GLU Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain t residue 74 ILE Chi-restraints excluded: chain t residue 86 THR Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 52 ASN Chi-restraints excluded: chain u residue 90 LYS Chi-restraints excluded: chain v residue 24 ASN Chi-restraints excluded: chain v residue 34 LYS Chi-restraints excluded: chain v residue 41 GLU Chi-restraints excluded: chain v residue 49 ASN Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 80 HIS Chi-restraints excluded: chain v residue 85 LYS Chi-restraints excluded: chain v residue 86 LEU Chi-restraints excluded: chain x residue 6 VAL Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 32 LEU Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain x residue 67 LEU Chi-restraints excluded: chain y residue 11 VAL Chi-restraints excluded: chain y residue 22 LEU Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 3 THR Chi-restraints excluded: chain z residue 6 ILE Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 30 HIS Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 120 SER Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 167 HIS Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain H residue 2 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 182 ASP Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 73 ASN Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 67 ARG Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 161 GLU Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 130 LYS Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 13 PHE Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 75 GLU Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 113 THR Chi-restraints excluded: chain P residue 118 ASN Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 46 SER Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 103 CYS Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain S residue 19 TYR Chi-restraints excluded: chain S residue 20 PHE Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 41 TRP Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 99 SER Chi-restraints excluded: chain T residue 1 SER Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 58 MET Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 54 LEU Chi-restraints excluded: chain U residue 77 GLU Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain V residue 26 ARG Chi-restraints excluded: chain V residue 40 THR Chi-restraints excluded: chain V residue 52 CYS Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain W residue 46 THR Chi-restraints excluded: chain W residue 51 GLN Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Y residue 53 MET Chi-restraints excluded: chain Y residue 67 HIS Chi-restraints excluded: chain Z residue 11 PHE Chi-restraints excluded: chain Z residue 35 GLU Chi-restraints excluded: chain a residue 11 ILE Chi-restraints excluded: chain a residue 168 ASN Chi-restraints excluded: chain a residue 178 VAL Chi-restraints excluded: chain a residue 192 LEU Chi-restraints excluded: chain a residue 222 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1012 random chunks: chunk 603 optimal weight: 30.0000 chunk 389 optimal weight: 6.9990 chunk 582 optimal weight: 10.0000 chunk 293 optimal weight: 5.9990 chunk 191 optimal weight: 5.9990 chunk 188 optimal weight: 8.9990 chunk 620 optimal weight: 10.0000 chunk 664 optimal weight: 10.0000 chunk 482 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 766 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 43 ASN ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 82 ASN ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 4 ASN ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 65 ASN ** q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 45 GLN ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 8 GLN Y 67 HIS ** a 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 155386 Z= 0.317 Angle : 0.666 11.555 232389 Z= 0.343 Chirality : 0.038 0.341 29716 Planarity : 0.005 0.072 12463 Dihedral : 23.863 178.874 77612 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 23.55 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.58 % Favored : 89.19 % Rotamer: Outliers : 5.76 % Allowed : 25.19 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.11), residues: 5680 helix: -1.16 (0.12), residues: 1656 sheet: -2.10 (0.16), residues: 939 loop : -2.18 (0.11), residues: 3085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 169 HIS 0.020 0.001 HIS Y 67 PHE 0.054 0.002 PHE g 46 TYR 0.051 0.002 TYR I 102 ARG 0.023 0.001 ARG b 132 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11360 Ramachandran restraints generated. 5680 Oldfield, 0 Emsley, 5680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11360 Ramachandran restraints generated. 5680 Oldfield, 0 Emsley, 5680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1182 residues out of total 4720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 910 time to evaluate : 6.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 100 MET cc_start: 0.8122 (mtp) cc_final: 0.7744 (mtm) REVERT: e 95 MET cc_start: 0.9000 (tmm) cc_final: 0.8589 (tmm) REVERT: e 137 PHE cc_start: 0.8707 (m-80) cc_final: 0.8461 (m-80) REVERT: e 174 PHE cc_start: 0.8179 (OUTLIER) cc_final: 0.7546 (m-80) REVERT: f 46 ASP cc_start: 0.8780 (m-30) cc_final: 0.8446 (m-30) REVERT: f 165 ASP cc_start: 0.9040 (p0) cc_final: 0.8785 (p0) REVERT: g 22 LYS cc_start: 0.8824 (mttp) cc_final: 0.8333 (mtpt) REVERT: h 6 GLN cc_start: 0.8043 (mm110) cc_final: 0.7471 (mp10) REVERT: j 142 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.8037 (tp) REVERT: k 12 ASP cc_start: 0.8331 (p0) cc_final: 0.7973 (p0) REVERT: l 58 TYR cc_start: 0.8522 (p90) cc_final: 0.8215 (p90) REVERT: n 4 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7964 (tpt170) REVERT: n 53 THR cc_start: 0.8101 (m) cc_final: 0.7796 (p) REVERT: n 110 MET cc_start: 0.8667 (mmm) cc_final: 0.8274 (mmm) REVERT: p 70 GLU cc_start: 0.7765 (tt0) cc_final: 0.7499 (tt0) REVERT: r 76 LYS cc_start: 0.9131 (mtpt) cc_final: 0.8832 (mttm) REVERT: s 1 MET cc_start: 0.8410 (mtm) cc_final: 0.8133 (mtp) REVERT: s 77 ASP cc_start: 0.8097 (p0) cc_final: 0.7726 (p0) REVERT: t 1 MET cc_start: 0.5225 (mtp) cc_final: 0.4379 (mtt) REVERT: v 1 MET cc_start: 0.8079 (tpp) cc_final: 0.6463 (ptt) REVERT: v 7 GLU cc_start: 0.7538 (pm20) cc_final: 0.7156 (pm20) REVERT: v 59 GLU cc_start: 0.8253 (tt0) cc_final: 0.7291 (tt0) REVERT: v 80 HIS cc_start: 0.7485 (OUTLIER) cc_final: 0.7161 (m-70) REVERT: v 85 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7995 (ptpp) REVERT: v 86 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7897 (tp) REVERT: w 79 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8530 (mp0) REVERT: x 17 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8226 (tpp-160) REVERT: x 61 LYS cc_start: 0.8799 (mttt) cc_final: 0.8473 (mmmt) REVERT: E 51 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8451 (tttp) REVERT: G 48 MET cc_start: 0.6539 (mtt) cc_final: 0.6180 (mtp) REVERT: G 88 GLN cc_start: 0.8709 (mm-40) cc_final: 0.8384 (mm-40) REVERT: G 95 TRP cc_start: 0.7799 (t-100) cc_final: 0.7569 (t-100) REVERT: G 119 GLN cc_start: 0.8178 (mm-40) cc_final: 0.7880 (mp10) REVERT: G 135 MET cc_start: 0.6377 (mmp) cc_final: 0.5854 (mmm) REVERT: G 156 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8950 (pp) REVERT: G 158 ASP cc_start: 0.7624 (m-30) cc_final: 0.7224 (t0) REVERT: H 2 GLN cc_start: 0.4304 (OUTLIER) cc_final: 0.3914 (pt0) REVERT: H 142 ARG cc_start: 0.9377 (tpt170) cc_final: 0.9167 (tpp80) REVERT: I 46 ARG cc_start: 0.7686 (pmt170) cc_final: 0.7201 (pmt170) REVERT: I 70 GLN cc_start: 0.8878 (tt0) cc_final: 0.8558 (tt0) REVERT: I 115 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7375 (pp30) REVERT: I 130 ASN cc_start: 0.8399 (m-40) cc_final: 0.8052 (t0) REVERT: I 140 ASP cc_start: 0.7973 (m-30) cc_final: 0.7583 (m-30) REVERT: I 169 TRP cc_start: 0.8413 (p90) cc_final: 0.7552 (p90) REVERT: J 94 PHE cc_start: 0.8449 (OUTLIER) cc_final: 0.7396 (t80) REVERT: J 115 GLU cc_start: 0.8690 (pt0) cc_final: 0.8346 (pt0) REVERT: K 54 LEU cc_start: 0.8816 (pp) cc_final: 0.8610 (pp) REVERT: K 90 MET cc_start: 0.7524 (mmt) cc_final: 0.7226 (mmm) REVERT: L 4 ARG cc_start: 0.8125 (mtt90) cc_final: 0.7833 (mmm160) REVERT: L 115 MET cc_start: 0.7784 (mmt) cc_final: 0.7516 (mmt) REVERT: L 143 MET cc_start: 0.7262 (mmt) cc_final: 0.6933 (mpp) REVERT: L 145 GLU cc_start: 0.5530 (OUTLIER) cc_final: 0.4878 (pt0) REVERT: M 75 GLN cc_start: 0.7836 (mm-40) cc_final: 0.7537 (mm-40) REVERT: M 91 LEU cc_start: 0.9335 (mt) cc_final: 0.9110 (mt) REVERT: M 95 MET cc_start: 0.9066 (tpp) cc_final: 0.8646 (tpp) REVERT: N 21 LYS cc_start: 0.7919 (tppp) cc_final: 0.7321 (pttm) REVERT: N 45 MET cc_start: 0.8645 (tmm) cc_final: 0.8043 (tpp) REVERT: N 49 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8635 (mm-40) REVERT: O 11 LYS cc_start: 0.7263 (tppt) cc_final: 0.7030 (ttmt) REVERT: O 13 PHE cc_start: 0.5729 (OUTLIER) cc_final: 0.4842 (m-80) REVERT: P 75 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8623 (tm-30) REVERT: P 109 ILE cc_start: 0.8887 (mt) cc_final: 0.8655 (pt) REVERT: S 5 MET cc_start: 0.3946 (mmp) cc_final: 0.3667 (mmm) REVERT: S 59 GLN cc_start: 0.6952 (mt0) cc_final: 0.6416 (mp10) REVERT: S 85 GLU cc_start: 0.9046 (tt0) cc_final: 0.8846 (tm-30) REVERT: T 25 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7809 (pm20) REVERT: U 26 ASN cc_start: 0.8542 (m-40) cc_final: 0.8177 (m110) REVERT: Y 47 GLN cc_start: 0.9322 (tp40) cc_final: 0.8817 (tp40) REVERT: Y 58 ASP cc_start: 0.9371 (t70) cc_final: 0.8691 (p0) REVERT: Y 78 LEU cc_start: 0.9322 (mt) cc_final: 0.9020 (mt) REVERT: Z 35 GLU cc_start: 0.5245 (OUTLIER) cc_final: 0.4872 (pp20) REVERT: a 200 LYS cc_start: 0.1969 (tttt) cc_final: 0.1241 (tppt) outliers start: 272 outliers final: 221 residues processed: 1087 average time/residue: 1.2192 time to fit residues: 2342.6956 Evaluate side-chains 1121 residues out of total 4720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 882 time to evaluate : 5.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain b residue 87 SER Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 215 VAL Chi-restraints excluded: chain b residue 219 VAL Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 43 ASP Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 86 GLU Chi-restraints excluded: chain c residue 151 THR Chi-restraints excluded: chain c residue 188 LEU Chi-restraints excluded: chain c residue 193 VAL Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain c residue 202 ILE Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 167 VAL Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain d residue 181 ILE Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain d residue 195 GLN Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 99 PHE Chi-restraints excluded: chain e residue 141 ASP Chi-restraints excluded: chain e residue 155 ILE Chi-restraints excluded: chain e residue 172 PHE Chi-restraints excluded: chain e residue 174 PHE Chi-restraints excluded: chain f residue 55 ASP Chi-restraints excluded: chain f residue 75 VAL Chi-restraints excluded: chain f residue 126 THR Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain g residue 15 LEU Chi-restraints excluded: chain g residue 19 VAL Chi-restraints excluded: chain g residue 21 VAL Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain i residue 120 ASP Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 88 THR Chi-restraints excluded: chain j residue 142 ILE Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 52 VAL Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 91 SER Chi-restraints excluded: chain k residue 100 PHE Chi-restraints excluded: chain k residue 105 ARG Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain l residue 100 ILE Chi-restraints excluded: chain n residue 4 ARG Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 106 ASP Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 67 ASN Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 45 VAL Chi-restraints excluded: chain p residue 62 LYS Chi-restraints excluded: chain p residue 67 GLU Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 81 ASP Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain p residue 86 LYS Chi-restraints excluded: chain p residue 92 ARG Chi-restraints excluded: chain p residue 101 GLU Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain q residue 116 LEU Chi-restraints excluded: chain r residue 32 THR Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 84 ARG Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain s residue 52 GLU Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain t residue 74 ILE Chi-restraints excluded: chain t residue 86 THR Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 52 ASN Chi-restraints excluded: chain u residue 90 LYS Chi-restraints excluded: chain v residue 34 LYS Chi-restraints excluded: chain v residue 41 GLU Chi-restraints excluded: chain v residue 49 ASN Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 80 HIS Chi-restraints excluded: chain v residue 85 LYS Chi-restraints excluded: chain v residue 86 LEU Chi-restraints excluded: chain x residue 6 VAL Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 17 ARG Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 32 LEU Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain y residue 11 VAL Chi-restraints excluded: chain y residue 22 LEU Chi-restraints excluded: chain y residue 23 ARG Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 30 HIS Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain F residue 8 LYS Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 120 SER Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 167 HIS Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain H residue 2 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 182 ASP Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 73 ASN Chi-restraints excluded: chain I residue 115 GLN Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 67 ARG Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 94 PHE Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 161 GLU Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 130 LYS Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 13 PHE Chi-restraints excluded: chain O residue 15 HIS Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 75 GLU Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 113 THR Chi-restraints excluded: chain P residue 118 ASN Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 46 SER Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 103 CYS Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain S residue 20 PHE Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 99 SER Chi-restraints excluded: chain T residue 1 SER Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 24 SER Chi-restraints excluded: chain U residue 77 GLU Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain V residue 26 ARG Chi-restraints excluded: chain V residue 40 THR Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain Y residue 53 MET Chi-restraints excluded: chain Y residue 67 HIS Chi-restraints excluded: chain Z residue 11 PHE Chi-restraints excluded: chain Z residue 35 GLU Chi-restraints excluded: chain a residue 168 ASN Chi-restraints excluded: chain a residue 178 VAL Chi-restraints excluded: chain a residue 192 LEU Chi-restraints excluded: chain a residue 222 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1012 random chunks: chunk 887 optimal weight: 10.0000 chunk 934 optimal weight: 50.0000 chunk 852 optimal weight: 10.0000 chunk 908 optimal weight: 10.0000 chunk 547 optimal weight: 10.0000 chunk 395 optimal weight: 20.0000 chunk 713 optimal weight: 10.0000 chunk 278 optimal weight: 3.9990 chunk 821 optimal weight: 20.0000 chunk 859 optimal weight: 10.0000 chunk 905 optimal weight: 10.0000 overall best weight: 8.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 43 ASN ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 136 GLN k 82 ASN ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 69 ASN ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 51 GLN Y 67 HIS ** a 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 155386 Z= 0.403 Angle : 0.725 14.528 232389 Z= 0.371 Chirality : 0.041 0.368 29716 Planarity : 0.005 0.072 12463 Dihedral : 23.886 179.741 77612 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 26.20 Ramachandran Plot: Outliers : 0.23 % Allowed : 12.39 % Favored : 87.38 % Rotamer: Outliers : 5.83 % Allowed : 25.57 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.10), residues: 5680 helix: -1.24 (0.12), residues: 1656 sheet: -2.15 (0.16), residues: 888 loop : -2.22 (0.11), residues: 3136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 169 HIS 0.053 0.002 HIS Y 67 PHE 0.053 0.002 PHE g 46 TYR 0.052 0.002 TYR I 102 ARG 0.015 0.001 ARG A 25 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11360 Ramachandran restraints generated. 5680 Oldfield, 0 Emsley, 5680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11360 Ramachandran restraints generated. 5680 Oldfield, 0 Emsley, 5680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1170 residues out of total 4720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 275 poor density : 895 time to evaluate : 6.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 100 MET cc_start: 0.8134 (mtp) cc_final: 0.7753 (mtm) REVERT: e 95 MET cc_start: 0.9037 (tmm) cc_final: 0.8606 (tmm) REVERT: e 137 PHE cc_start: 0.8704 (m-80) cc_final: 0.8447 (m-80) REVERT: e 174 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.7546 (m-80) REVERT: f 46 ASP cc_start: 0.8782 (m-30) cc_final: 0.8464 (m-30) REVERT: f 165 ASP cc_start: 0.9056 (p0) cc_final: 0.8824 (p0) REVERT: g 22 LYS cc_start: 0.8827 (mttp) cc_final: 0.8320 (mtpt) REVERT: g 41 LYS cc_start: 0.8709 (tptt) cc_final: 0.8324 (ptpt) REVERT: h 6 GLN cc_start: 0.8057 (mm110) cc_final: 0.7734 (mp10) REVERT: j 142 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.8020 (tp) REVERT: k 12 ASP cc_start: 0.8298 (p0) cc_final: 0.7957 (p0) REVERT: l 10 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7745 (mm-30) REVERT: l 58 TYR cc_start: 0.8570 (p90) cc_final: 0.8210 (p90) REVERT: n 4 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7900 (tpt170) REVERT: n 53 THR cc_start: 0.8162 (m) cc_final: 0.7857 (p) REVERT: p 12 MET cc_start: 0.7847 (mmm) cc_final: 0.7499 (mmm) REVERT: p 70 GLU cc_start: 0.7827 (tt0) cc_final: 0.7554 (tt0) REVERT: r 76 LYS cc_start: 0.9141 (mtpt) cc_final: 0.8817 (mttm) REVERT: s 1 MET cc_start: 0.8386 (mtm) cc_final: 0.8109 (mtp) REVERT: s 77 ASP cc_start: 0.8129 (p0) cc_final: 0.7779 (p0) REVERT: t 1 MET cc_start: 0.5298 (mtp) cc_final: 0.4434 (mtt) REVERT: v 1 MET cc_start: 0.8103 (tpp) cc_final: 0.6493 (ptt) REVERT: v 7 GLU cc_start: 0.7594 (pm20) cc_final: 0.7210 (pm20) REVERT: v 59 GLU cc_start: 0.8300 (tt0) cc_final: 0.7436 (tt0) REVERT: v 80 HIS cc_start: 0.7539 (OUTLIER) cc_final: 0.7212 (m-70) REVERT: v 85 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7928 (ptpp) REVERT: v 86 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7947 (tp) REVERT: x 17 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8353 (tpp-160) REVERT: x 61 LYS cc_start: 0.8849 (mttt) cc_final: 0.8492 (mmmt) REVERT: y 2 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7410 (pttm) REVERT: G 48 MET cc_start: 0.6562 (mtt) cc_final: 0.6197 (mtp) REVERT: G 88 GLN cc_start: 0.8704 (mm-40) cc_final: 0.8377 (mm-40) REVERT: G 95 TRP cc_start: 0.7810 (t-100) cc_final: 0.7592 (t-100) REVERT: G 119 GLN cc_start: 0.8208 (mm-40) cc_final: 0.7913 (mp10) REVERT: G 135 MET cc_start: 0.6373 (mmp) cc_final: 0.5886 (mmm) REVERT: G 156 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8961 (pp) REVERT: G 158 ASP cc_start: 0.7567 (m-30) cc_final: 0.7142 (t0) REVERT: H 2 GLN cc_start: 0.4346 (OUTLIER) cc_final: 0.3943 (pt0) REVERT: H 142 ARG cc_start: 0.9376 (tpt170) cc_final: 0.9032 (tpp80) REVERT: I 70 GLN cc_start: 0.8980 (tt0) cc_final: 0.8682 (tt0) REVERT: I 115 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7211 (pp30) REVERT: I 130 ASN cc_start: 0.8202 (m-40) cc_final: 0.7949 (t0) REVERT: I 140 ASP cc_start: 0.8027 (m-30) cc_final: 0.7632 (m-30) REVERT: I 169 TRP cc_start: 0.8458 (p90) cc_final: 0.7633 (p90) REVERT: J 32 PHE cc_start: 0.7789 (m-80) cc_final: 0.7562 (m-80) REVERT: J 44 ARG cc_start: 0.7836 (ttm110) cc_final: 0.7306 (ttm110) REVERT: J 64 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8653 (mm-30) REVERT: J 85 LYS cc_start: 0.9259 (mmmt) cc_final: 0.8905 (tppt) REVERT: J 94 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.7103 (t80) REVERT: J 115 GLU cc_start: 0.8634 (pt0) cc_final: 0.8341 (pt0) REVERT: J 144 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8490 (mm-30) REVERT: K 44 ARG cc_start: 0.7964 (mmm160) cc_final: 0.7656 (mmm160) REVERT: K 90 MET cc_start: 0.7527 (mmt) cc_final: 0.7272 (mmm) REVERT: L 4 ARG cc_start: 0.8181 (mtt90) cc_final: 0.7871 (mmm160) REVERT: L 101 ARG cc_start: 0.5059 (mmt180) cc_final: 0.3131 (mtt180) REVERT: L 115 MET cc_start: 0.7789 (mmt) cc_final: 0.7533 (mmt) REVERT: L 143 MET cc_start: 0.7213 (mmt) cc_final: 0.6907 (mpp) REVERT: M 91 LEU cc_start: 0.9336 (mt) cc_final: 0.9093 (mt) REVERT: N 21 LYS cc_start: 0.8011 (tppp) cc_final: 0.7400 (pttm) REVERT: N 45 MET cc_start: 0.8647 (tmm) cc_final: 0.8053 (tpp) REVERT: N 49 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8630 (mm-40) REVERT: O 13 PHE cc_start: 0.5808 (OUTLIER) cc_final: 0.4991 (m-80) REVERT: P 75 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8611 (tm-30) REVERT: P 109 ILE cc_start: 0.8889 (mt) cc_final: 0.8648 (pt) REVERT: R 40 GLU cc_start: 0.3393 (OUTLIER) cc_final: 0.2975 (pt0) REVERT: S 5 MET cc_start: 0.4013 (mmp) cc_final: 0.3707 (mmm) REVERT: S 59 GLN cc_start: 0.6911 (mt0) cc_final: 0.6435 (mp10) REVERT: S 85 GLU cc_start: 0.9027 (tt0) cc_final: 0.8825 (tm-30) REVERT: T 25 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7865 (pm20) REVERT: U 26 ASN cc_start: 0.8563 (m-40) cc_final: 0.8188 (m110) REVERT: W 51 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8292 (tm-30) REVERT: Y 14 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8126 (tp30) REVERT: Y 47 GLN cc_start: 0.9332 (tp40) cc_final: 0.8859 (tp-100) REVERT: Y 52 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8306 (mt-10) REVERT: Y 58 ASP cc_start: 0.9378 (t70) cc_final: 0.8699 (p0) REVERT: Z 35 GLU cc_start: 0.5209 (OUTLIER) cc_final: 0.4680 (pp20) REVERT: a 200 LYS cc_start: 0.2101 (tttt) cc_final: 0.1331 (tppt) outliers start: 275 outliers final: 234 residues processed: 1074 average time/residue: 1.2273 time to fit residues: 2325.1513 Evaluate side-chains 1129 residues out of total 4720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 875 time to evaluate : 5.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain b residue 87 SER Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 215 VAL Chi-restraints excluded: chain b residue 219 VAL Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 43 ASP Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 86 GLU Chi-restraints excluded: chain c residue 122 VAL Chi-restraints excluded: chain c residue 151 THR Chi-restraints excluded: chain c residue 188 LEU Chi-restraints excluded: chain c residue 193 VAL Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain c residue 202 ILE Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 112 LEU Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 167 VAL Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain d residue 181 ILE Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain d residue 195 GLN Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 99 PHE Chi-restraints excluded: chain e residue 141 ASP Chi-restraints excluded: chain e residue 155 ILE Chi-restraints excluded: chain e residue 172 PHE Chi-restraints excluded: chain e residue 174 PHE Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 55 ASP Chi-restraints excluded: chain f residue 75 VAL Chi-restraints excluded: chain f residue 126 THR Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain g residue 15 LEU Chi-restraints excluded: chain g residue 19 VAL Chi-restraints excluded: chain g residue 21 VAL Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain i residue 120 ASP Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 88 THR Chi-restraints excluded: chain j residue 136 GLN Chi-restraints excluded: chain j residue 142 ILE Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 52 VAL Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 91 SER Chi-restraints excluded: chain k residue 105 ARG Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain l residue 100 ILE Chi-restraints excluded: chain n residue 4 ARG Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 100 CYS Chi-restraints excluded: chain n residue 106 ASP Chi-restraints excluded: chain n residue 113 ILE Chi-restraints excluded: chain o residue 26 LEU Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 45 VAL Chi-restraints excluded: chain p residue 67 GLU Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 81 ASP Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain p residue 86 LYS Chi-restraints excluded: chain p residue 92 ARG Chi-restraints excluded: chain p residue 101 GLU Chi-restraints excluded: chain q residue 116 LEU Chi-restraints excluded: chain r residue 32 THR Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 84 ARG Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 52 GLU Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain t residue 74 ILE Chi-restraints excluded: chain t residue 86 THR Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 52 ASN Chi-restraints excluded: chain u residue 90 LYS Chi-restraints excluded: chain v residue 34 LYS Chi-restraints excluded: chain v residue 41 GLU Chi-restraints excluded: chain v residue 49 ASN Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 80 HIS Chi-restraints excluded: chain v residue 85 LYS Chi-restraints excluded: chain v residue 86 LEU Chi-restraints excluded: chain x residue 6 VAL Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 17 ARG Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 32 LEU Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain y residue 2 LYS Chi-restraints excluded: chain y residue 11 VAL Chi-restraints excluded: chain y residue 22 LEU Chi-restraints excluded: chain y residue 23 ARG Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 30 HIS Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain F residue 8 LYS Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 120 SER Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 167 HIS Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain H residue 2 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 182 ASP Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 73 ASN Chi-restraints excluded: chain I residue 115 GLN Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 94 PHE Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 161 GLU Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 130 LYS Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 13 PHE Chi-restraints excluded: chain O residue 15 HIS Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 75 GLU Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 113 THR Chi-restraints excluded: chain P residue 118 ASN Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 46 SER Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 103 CYS Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 40 GLU Chi-restraints excluded: chain S residue 20 PHE Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 41 TRP Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 99 SER Chi-restraints excluded: chain T residue 1 SER Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 24 SER Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 54 LEU Chi-restraints excluded: chain U residue 77 GLU Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain V residue 26 ARG Chi-restraints excluded: chain V residue 40 THR Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain W residue 51 GLN Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain Y residue 14 GLU Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Y residue 53 MET Chi-restraints excluded: chain Z residue 11 PHE Chi-restraints excluded: chain Z residue 35 GLU Chi-restraints excluded: chain a residue 168 ASN Chi-restraints excluded: chain a residue 178 VAL Chi-restraints excluded: chain a residue 192 LEU Chi-restraints excluded: chain a residue 222 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1012 random chunks: chunk 596 optimal weight: 20.0000 chunk 961 optimal weight: 10.0000 chunk 586 optimal weight: 10.0000 chunk 455 optimal weight: 0.9990 chunk 668 optimal weight: 40.0000 chunk 1008 optimal weight: 10.0000 chunk 927 optimal weight: 8.9990 chunk 802 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 620 optimal weight: 10.0000 chunk 492 optimal weight: 30.0000 overall best weight: 7.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 43 ASN ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 136 GLN k 82 ASN ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 92 ASN ** v 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 155386 Z= 0.368 Angle : 0.710 17.345 232389 Z= 0.364 Chirality : 0.040 0.346 29716 Planarity : 0.005 0.073 12463 Dihedral : 23.921 178.085 77612 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 25.62 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.88 % Favored : 87.87 % Rotamer: Outliers : 5.74 % Allowed : 25.97 % Favored : 68.28 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.10), residues: 5680 helix: -1.24 (0.12), residues: 1656 sheet: -2.11 (0.16), residues: 901 loop : -2.18 (0.11), residues: 3123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 169 HIS 0.013 0.001 HIS H 5 PHE 0.052 0.002 PHE g 46 TYR 0.051 0.002 TYR I 102 ARG 0.011 0.001 ARG b 132 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11360 Ramachandran restraints generated. 5680 Oldfield, 0 Emsley, 5680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11360 Ramachandran restraints generated. 5680 Oldfield, 0 Emsley, 5680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1172 residues out of total 4720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 901 time to evaluate : 6.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 61 ARG cc_start: 0.5880 (mtp180) cc_final: 0.4300 (mmp-170) REVERT: d 100 MET cc_start: 0.8130 (mtp) cc_final: 0.7751 (mtm) REVERT: e 95 MET cc_start: 0.9007 (tmm) cc_final: 0.8581 (tmm) REVERT: e 137 PHE cc_start: 0.8699 (m-80) cc_final: 0.8450 (m-80) REVERT: e 174 PHE cc_start: 0.8242 (OUTLIER) cc_final: 0.7580 (m-80) REVERT: f 46 ASP cc_start: 0.8727 (m-30) cc_final: 0.8402 (m-30) REVERT: f 74 MET cc_start: 0.8900 (mtp) cc_final: 0.8581 (mtp) REVERT: f 165 ASP cc_start: 0.9035 (p0) cc_final: 0.8811 (p0) REVERT: g 22 LYS cc_start: 0.8826 (mttp) cc_final: 0.8334 (mtpt) REVERT: g 41 LYS cc_start: 0.8744 (tptt) cc_final: 0.8330 (ptpt) REVERT: j 142 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.8072 (tp) REVERT: k 12 ASP cc_start: 0.8295 (p0) cc_final: 0.7953 (p0) REVERT: l 10 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7812 (mm-30) REVERT: l 58 TYR cc_start: 0.8546 (p90) cc_final: 0.8218 (p90) REVERT: n 4 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7977 (tpt170) REVERT: n 53 THR cc_start: 0.8136 (m) cc_final: 0.7838 (p) REVERT: o 92 PHE cc_start: 0.8372 (t80) cc_final: 0.8132 (t80) REVERT: p 12 MET cc_start: 0.7775 (mmm) cc_final: 0.7484 (mmm) REVERT: p 70 GLU cc_start: 0.7828 (tt0) cc_final: 0.7566 (tt0) REVERT: r 76 LYS cc_start: 0.9148 (mtpt) cc_final: 0.8845 (mttm) REVERT: s 1 MET cc_start: 0.8388 (mtm) cc_final: 0.8143 (mtp) REVERT: s 77 ASP cc_start: 0.8176 (p0) cc_final: 0.7778 (p0) REVERT: v 1 MET cc_start: 0.8074 (tpp) cc_final: 0.6440 (ptt) REVERT: v 7 GLU cc_start: 0.7529 (pm20) cc_final: 0.7182 (pm20) REVERT: v 59 GLU cc_start: 0.8373 (tt0) cc_final: 0.7473 (tt0) REVERT: v 80 HIS cc_start: 0.7575 (OUTLIER) cc_final: 0.7249 (m-70) REVERT: v 85 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7983 (ptpp) REVERT: x 17 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8283 (tpp-160) REVERT: x 61 LYS cc_start: 0.8828 (mttt) cc_final: 0.8498 (mmmt) REVERT: y 2 LYS cc_start: 0.7575 (OUTLIER) cc_final: 0.7346 (pttm) REVERT: G 48 MET cc_start: 0.6609 (mtt) cc_final: 0.6282 (mtp) REVERT: G 88 GLN cc_start: 0.8690 (mm-40) cc_final: 0.8349 (mm-40) REVERT: G 95 TRP cc_start: 0.7790 (t-100) cc_final: 0.7569 (t-100) REVERT: G 119 GLN cc_start: 0.8148 (mm-40) cc_final: 0.7866 (mp10) REVERT: G 135 MET cc_start: 0.6376 (mmp) cc_final: 0.5873 (mmm) REVERT: G 156 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8976 (pp) REVERT: G 158 ASP cc_start: 0.7542 (m-30) cc_final: 0.7139 (t0) REVERT: H 2 GLN cc_start: 0.4388 (OUTLIER) cc_final: 0.4000 (pt0) REVERT: H 142 ARG cc_start: 0.9373 (tpt170) cc_final: 0.9032 (tpp80) REVERT: I 70 GLN cc_start: 0.8981 (tt0) cc_final: 0.8669 (tt0) REVERT: I 130 ASN cc_start: 0.8249 (m-40) cc_final: 0.7948 (t0) REVERT: I 140 ASP cc_start: 0.8059 (m-30) cc_final: 0.7659 (m-30) REVERT: I 169 TRP cc_start: 0.8477 (p90) cc_final: 0.7597 (p90) REVERT: J 32 PHE cc_start: 0.7815 (m-80) cc_final: 0.7608 (m-80) REVERT: J 64 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8610 (mm-30) REVERT: J 85 LYS cc_start: 0.9283 (mmmt) cc_final: 0.8932 (tppt) REVERT: J 94 PHE cc_start: 0.8457 (OUTLIER) cc_final: 0.7104 (t80) REVERT: J 115 GLU cc_start: 0.8607 (pt0) cc_final: 0.8305 (pt0) REVERT: K 44 ARG cc_start: 0.8076 (mmm160) cc_final: 0.7804 (mmm160) REVERT: K 90 MET cc_start: 0.7489 (mmt) cc_final: 0.7229 (mmm) REVERT: L 4 ARG cc_start: 0.8131 (mtt90) cc_final: 0.7840 (mmm160) REVERT: L 101 ARG cc_start: 0.5015 (mmt180) cc_final: 0.3078 (mtt180) REVERT: L 115 MET cc_start: 0.7775 (mmt) cc_final: 0.7511 (mmt) REVERT: L 143 MET cc_start: 0.7233 (mmt) cc_final: 0.6923 (mpp) REVERT: M 91 LEU cc_start: 0.9331 (mt) cc_final: 0.9086 (mt) REVERT: N 21 LYS cc_start: 0.8023 (tppp) cc_final: 0.7432 (pttm) REVERT: N 45 MET cc_start: 0.8648 (tmm) cc_final: 0.8048 (tpp) REVERT: N 49 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8628 (mm-40) REVERT: O 13 PHE cc_start: 0.5813 (OUTLIER) cc_final: 0.4975 (m-80) REVERT: O 88 MET cc_start: 0.6974 (mmt) cc_final: 0.6767 (mtt) REVERT: P 75 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8600 (tm-30) REVERT: P 109 ILE cc_start: 0.8864 (mt) cc_final: 0.8646 (pt) REVERT: R 40 GLU cc_start: 0.3356 (OUTLIER) cc_final: 0.2998 (pt0) REVERT: S 5 MET cc_start: 0.4116 (mmp) cc_final: 0.3780 (mmm) REVERT: S 59 GLN cc_start: 0.6929 (mt0) cc_final: 0.6453 (mp10) REVERT: T 25 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7867 (pm20) REVERT: U 26 ASN cc_start: 0.8533 (m-40) cc_final: 0.8158 (m110) REVERT: Y 47 GLN cc_start: 0.9324 (tp40) cc_final: 0.8851 (tp-100) REVERT: Y 52 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8284 (mt-10) REVERT: Y 67 HIS cc_start: 0.7338 (OUTLIER) cc_final: 0.7047 (t70) REVERT: Z 35 GLU cc_start: 0.5135 (OUTLIER) cc_final: 0.4600 (pp20) REVERT: a 200 LYS cc_start: 0.2130 (tttt) cc_final: 0.1349 (tppt) outliers start: 271 outliers final: 235 residues processed: 1078 average time/residue: 1.1955 time to fit residues: 2269.6147 Evaluate side-chains 1137 residues out of total 4720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 885 time to evaluate : 5.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain b residue 87 SER Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 215 VAL Chi-restraints excluded: chain b residue 219 VAL Chi-restraints excluded: chain c residue 39 ASP Chi-restraints excluded: chain c residue 43 ASP Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 86 GLU Chi-restraints excluded: chain c residue 122 VAL Chi-restraints excluded: chain c residue 151 THR Chi-restraints excluded: chain c residue 188 LEU Chi-restraints excluded: chain c residue 193 VAL Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain c residue 202 ILE Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 73 ILE Chi-restraints excluded: chain d residue 112 LEU Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 150 THR Chi-restraints excluded: chain d residue 167 VAL Chi-restraints excluded: chain d residue 180 LEU Chi-restraints excluded: chain d residue 181 ILE Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain d residue 187 VAL Chi-restraints excluded: chain d residue 195 GLN Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 99 PHE Chi-restraints excluded: chain e residue 141 ASP Chi-restraints excluded: chain e residue 155 ILE Chi-restraints excluded: chain e residue 172 PHE Chi-restraints excluded: chain e residue 174 PHE Chi-restraints excluded: chain f residue 55 ASP Chi-restraints excluded: chain f residue 75 VAL Chi-restraints excluded: chain f residue 126 THR Chi-restraints excluded: chain f residue 161 VAL Chi-restraints excluded: chain g residue 15 LEU Chi-restraints excluded: chain g residue 19 VAL Chi-restraints excluded: chain g residue 21 VAL Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain i residue 120 ASP Chi-restraints excluded: chain j residue 10 THR Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 88 THR Chi-restraints excluded: chain j residue 136 GLN Chi-restraints excluded: chain j residue 142 ILE Chi-restraints excluded: chain k residue 10 VAL Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 52 VAL Chi-restraints excluded: chain k residue 69 VAL Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 91 SER Chi-restraints excluded: chain k residue 100 PHE Chi-restraints excluded: chain k residue 105 ARG Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain l residue 100 ILE Chi-restraints excluded: chain n residue 4 ARG Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 37 THR Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 106 ASP Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 35 ILE Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 45 VAL Chi-restraints excluded: chain p residue 67 GLU Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 81 ASP Chi-restraints excluded: chain p residue 85 VAL Chi-restraints excluded: chain p residue 86 LYS Chi-restraints excluded: chain p residue 92 ARG Chi-restraints excluded: chain p residue 101 GLU Chi-restraints excluded: chain q residue 116 LEU Chi-restraints excluded: chain r residue 11 GLN Chi-restraints excluded: chain r residue 29 THR Chi-restraints excluded: chain r residue 32 THR Chi-restraints excluded: chain r residue 41 ILE Chi-restraints excluded: chain r residue 58 VAL Chi-restraints excluded: chain r residue 84 ARG Chi-restraints excluded: chain r residue 99 THR Chi-restraints excluded: chain s residue 33 LEU Chi-restraints excluded: chain s residue 52 GLU Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 76 VAL Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 16 VAL Chi-restraints excluded: chain t residue 30 ILE Chi-restraints excluded: chain t residue 74 ILE Chi-restraints excluded: chain t residue 86 THR Chi-restraints excluded: chain t residue 92 ASN Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 52 ASN Chi-restraints excluded: chain u residue 90 LYS Chi-restraints excluded: chain v residue 34 LYS Chi-restraints excluded: chain v residue 41 GLU Chi-restraints excluded: chain v residue 49 ASN Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 64 VAL Chi-restraints excluded: chain v residue 80 HIS Chi-restraints excluded: chain v residue 85 LYS Chi-restraints excluded: chain x residue 6 VAL Chi-restraints excluded: chain x residue 7 THR Chi-restraints excluded: chain x residue 17 ARG Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 32 LEU Chi-restraints excluded: chain x residue 47 THR Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain y residue 2 LYS Chi-restraints excluded: chain y residue 11 VAL Chi-restraints excluded: chain y residue 22 LEU Chi-restraints excluded: chain y residue 23 ARG Chi-restraints excluded: chain y residue 55 THR Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 30 HIS Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain F residue 8 LYS Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 120 SER Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 167 HIS Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain H residue 2 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 182 ASP Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 73 ASN Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain J residue 94 PHE Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 161 GLU Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 130 LYS Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 102 PHE Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 13 PHE Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 75 GLU Chi-restraints excluded: chain P residue 78 ILE Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 113 THR Chi-restraints excluded: chain P residue 118 ASN Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 46 SER Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain Q residue 103 CYS Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 40 GLU Chi-restraints excluded: chain S residue 20 PHE Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 41 TRP Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 99 SER Chi-restraints excluded: chain T residue 1 SER Chi-restraints excluded: chain T residue 24 THR Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 24 SER Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 54 LEU Chi-restraints excluded: chain U residue 77 GLU Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain V residue 26 ARG Chi-restraints excluded: chain V residue 40 THR Chi-restraints excluded: chain V residue 45 VAL Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain Y residue 53 MET Chi-restraints excluded: chain Y residue 67 HIS Chi-restraints excluded: chain Z residue 11 PHE Chi-restraints excluded: chain Z residue 35 GLU Chi-restraints excluded: chain a residue 168 ASN Chi-restraints excluded: chain a residue 178 VAL Chi-restraints excluded: chain a residue 192 LEU Chi-restraints excluded: chain a residue 222 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1012 random chunks: chunk 637 optimal weight: 10.0000 chunk 855 optimal weight: 10.0000 chunk 245 optimal weight: 5.9990 chunk 740 optimal weight: 10.0000 chunk 118 optimal weight: 0.4980 chunk 223 optimal weight: 10.0000 chunk 804 optimal weight: 10.0000 chunk 336 optimal weight: 20.0000 chunk 825 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 148 optimal weight: 0.9990 overall best weight: 5.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 43 ASN ** j 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 82 ASN ** k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 39 GLN ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 69 ASN ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 51 GLN ** a 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.051689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.037131 restraints weight = 995117.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.037997 restraints weight = 338673.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.038550 restraints weight = 189275.068| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.211 155386 Z= 0.342 Angle : 0.739 59.200 232389 Z= 0.387 Chirality : 0.039 0.355 29716 Planarity : 0.005 0.107 12463 Dihedral : 23.923 178.075 77612 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 26.34 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.95 % Favored : 87.80 % Rotamer: Outliers : 5.70 % Allowed : 26.21 % Favored : 68.09 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.11), residues: 5680 helix: -1.23 (0.12), residues: 1656 sheet: -2.11 (0.16), residues: 901 loop : -2.18 (0.11), residues: 3123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 169 HIS 0.020 0.001 HIS H 5 PHE 0.049 0.002 PHE g 46 TYR 0.045 0.002 TYR I 102 ARG 0.029 0.001 ARG z 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 35119.57 seconds wall clock time: 616 minutes 22.35 seconds (36982.35 seconds total)