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Conformers: ABBIImiBZICOPNSYNN
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Solution RNA structure of stem-bulge-stem region of the HIV-1 dimerization initiation site

Results of the assignment of 308 detected steps in 11 model(s), can be also downloaded as csv or json file. Average confal 0, percentile 0.

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Click a row in table or a step in viewer for analysis of results. Click column headers to sort data.
Define restraints for steps within Å cartesian RMSD, global sigma scaling factor or use per step sigma scaling.
step numberStep nameCANANtCconfalrmsd
0012d17-m10_A_C1_G2AAAAA00740.21 AA00
0022d17-m11_A_C1_G2AAAAA00670.26 AA00
0032d17-m1_A_C1_G2AAAAA00570.37 AA00
0042d17-m2_A_C1_G2AAAAA00630.31 AA00
0052d17-m3_A_C1_G2AAAAA00680.27 AA00
0062d17-m4_A_C1_G2AAAAA00740.20 AA00
0072d17-m5_A_C1_G2AAAAA00590.34 AA00
0082d17-m6_A_C1_G2AAAAA00700.24 AA00
0092d17-m7_A_C1_G2AAAAA00730.20 AA00
0102d17-m8_A_C1_G2AAAAA00750.20 AA00
0112d17-m9_A_C1_G2AAAAA00730.22 AA00
0122d17-m10_A_G2_G3AAAAA00860.17 AA00
0132d17-m11_A_G2_G3AAAAA00850.15 AA00
0142d17-m1_A_G2_G3AAAAA00830.16 AA00
0152d17-m2_A_G2_G3AAAAA00820.14 AA00
0162d17-m3_A_G2_G3AAAAA00860.16 AA00
0172d17-m4_A_G2_G3AAAAA00860.17 AA00
0182d17-m5_A_G2_G3AAAAA00830.17 AA00
0192d17-m6_A_G2_G3AAAAA00840.16 AA00
0202d17-m7_A_G2_G3AAAAA00830.17 AA00
0212d17-m8_A_G2_G3AAAAA00840.17 AA00
0222d17-m9_A_G2_G3AAAAA00880.14 AA00
0232d17-m10_A_G3_C4AAAAA00870.18 AA00
0242d17-m11_A_G3_C4AAAAA00880.18 AA00
0252d17-m1_A_G3_C4AAAAA00840.21 AA00
0262d17-m2_A_G3_C4AAAAA00850.19 AA00
0272d17-m3_A_G3_C4AAAAA00860.18 AA00
0282d17-m4_A_G3_C4AAAAA00880.18 AA00
0292d17-m5_A_G3_C4AAAAA00850.20 AA00
0302d17-m6_A_G3_C4AAAAA00880.18 AA00
0312d17-m7_A_G3_C4AAAAA00880.20 AA00
0322d17-m8_A_G3_C4AAAAA00890.18 AA00
0332d17-m9_A_G3_C4AAAAA00890.20 AA00
0342d17-m10_A_C4_A5AAAAA00770.19 AA00
0352d17-m11_A_C4_A5AAAAA00770.19 AA00
0362d17-m1_A_C4_A5AAwAA01920.23 AA01
0372d17-m2_A_C4_A5AAAAA00740.19 AA00
0382d17-m3_A_C4_A5AAAAA00740.18 AA00
0392d17-m4_A_C4_A5AAwAA01950.23 AA01
0402d17-m5_A_C4_A5AAwAA01920.25 AA01
0412d17-m6_A_C4_A5AAAAA00660.18 AA00
0422d17-m7_A_C4_A5AAwAA01680.33 AA01
0432d17-m8_A_C4_A5AAAAA00800.18 AA00
0442d17-m9_A_C4_A5AAwAA01950.23 AA01
0452d17-m10_A_A5_A6AAwAA01840.21 AA01
0462d17-m11_A_A5_A6AAwAA01760.23 AA01
0472d17-m1_A_A5_A6AAAAA00650.25 AA00
0482d17-m2_A_A5_A6AAAAA00710.20 AA00
0492d17-m3_A_A5_A6AAAAA00690.20 AA00
0502d17-m4_A_A5_A6AAAAA00720.23 AA00
0512d17-m5_A_A5_A6AAAAA00700.21 AA00
0522d17-m6_A_A5_A6AAwAA01750.22 AA01
0532d17-m7_A_A5_A6NANNANT01.36 OP24
0542d17-m8_A_A5_A6AAwAA01820.23 AA01
0552d17-m9_A_A5_A6AAAAA00520.23 AA00
0562d17-m10_A_A6_G7NANNANT00.60 AB2S
0572d17-m11_A_A6_G7NANNANT02.07 OP1S
0582d17-m1_A_A6_G7AAwAA01230.36 AA01
0592d17-m2_A_A6_G7AAwAA01840.25 AA01
0602d17-m3_A_A6_G7AAAAA00740.19 AA00
0612d17-m4_A_A6_G7AAAAA00810.13 AA00
0622d17-m5_A_A6_G7NANNANT00.47 AA01
0632d17-m6_A_A6_G7NANNANT01.35 OP24
0642d17-m7_A_A6_G7AAAAA00460.23 AA00
0652d17-m8_A_A6_G7AAAAA00730.25 AA00
0662d17-m9_A_A6_G7NANNANT01.22 OP24
0672d17-m10_A_G7_A8NANNANT00.64 AA04
0682d17-m11_A_G7_A8NANNANT00.69 AA01
0692d17-m1_A_G7_A8NANNANT00.52 AA01
0702d17-m2_A_G7_A8AAAAA00870.17 AA00
0712d17-m3_A_G7_A8AAwAA01700.33 AA01
0722d17-m4_A_G7_A8AAAAA00820.12 AA00
0732d17-m5_A_G7_A8NANNANT00.67 AA11
0742d17-m6_A_G7_A8AAAAA00840.15 AA00
0752d17-m7_A_G7_A8NANNANT00.77 AB02
0762d17-m8_A_G7_A8AAwAA01690.28 AA01
0772d17-m9_A_G7_A8NANNANT00.76 AA00
0782d17-m10_A_A8_G9AAAAA04800.14 AA04
0792d17-m11_A_A8_G9AAwAA01410.44 AA01
0802d17-m1_A_A8_G9AAwAA01540.31 AA01
0812d17-m2_A_A8_G9AAwAA01650.26 AA01
0822d17-m3_A_A8_G9NANNANT01.35 OP24
0832d17-m4_A_A8_G9AAwAA01810.30 AA01
0842d17-m5_A_A8_G9AAwAA01460.38 AA01
0852d17-m6_A_A8_G9AAwAA01730.35 AA01
0862d17-m7_A_A8_G9AAAAA00730.30 AA00
0872d17-m8_A_A8_G9AAwAA01260.44 AA01
0882d17-m9_A_A8_G9NANNANT00.39 AA01
0892d17-m10_A_G9_G10NANNANT00.66 AA01
0902d17-m11_A_G9_G10NANNANT00.88 AA10
0912d17-m1_A_G9_G10NANNANT01.07 AA10
0922d17-m2_A_G9_G10NANNANT01.23 OP08
0932d17-m3_A_G9_G10NANNANT00.55 AA01
0942d17-m4_A_G9_G10NANNANT00.98 AA01
0952d17-m5_A_G9_G10NANNANT00.57 AA01
0962d17-m6_A_G9_G10NANNANT00.89 AA04
0972d17-m7_A_G9_G10NANNANT00.70 AA11
0982d17-m8_A_G9_G10NANNANT00.99 AB2S
0992d17-m9_A_G9_G10NANNANT00.93 OP23
1002d17-m10_A_G10_C11NANNANT01.26 AA07
1012d17-m11_A_G10_C11NANNANT00.68 AA07
1022d17-m1_A_G10_C11NANNANT00.76 AA07
1032d17-m2_A_G10_C11NANNANT01.39 ZZS1
1042d17-m3_A_G10_C11NANNANT01.31 AA07
1052d17-m4_A_G10_C11NANNANT01.25 AA11
1062d17-m5_A_G10_C11NANNANT00.96 OP25
1072d17-m6_A_G10_C11NANNANT01.53 BA16
1082d17-m7_A_G10_C11NANNANT01.23 BA16
1092d17-m8_A_G10_C11NANNANT00.83 ZZ02
1102d17-m9_A_G10_C11NANNANT01.36 AA07
1112d17-m10_A_C11_G12AAAAA00260.39 AA00
1122d17-m11_A_C11_G12AAAAA08160.49 AA08
1132d17-m1_A_C11_G12AAAAA00660.26 AA00
1142d17-m2_A_C11_G12AAAAA00830.16 AA00
1152d17-m3_A_C11_G12NANNANT00.36 AA12
1162d17-m4_A_C11_G12AAAAA08610.29 AA08
1172d17-m5_A_C11_G12AAuAA12370.48 AA12
1182d17-m6_A_C11_G12AAAAA00890.19 AA00
1192d17-m7_A_C11_G12AAAAA00870.17 AA00
1202d17-m8_A_C11_G12AAAAA00440.37 AA00
1212d17-m9_A_C11_G12AAAAA00630.31 AA00
1222d17-m10_A_G12_A13AAAAA00750.18 AA00
1232d17-m11_A_G12_A13AAAAA00890.17 AA00
1242d17-m1_A_G12_A13AAAAA00880.13 AA00
1252d17-m2_A_G12_A13AAAAA00840.17 AA00
1262d17-m3_A_G12_A13AAAAA00890.17 AA00
1272d17-m4_A_G12_A13AAAAA00920.14 AA00
1282d17-m5_A_G12_A13AAAAA00450.28 AA00
1292d17-m6_A_G12_A13AAAAA00910.15 AA00
1302d17-m7_A_G12_A13AAAAA00900.13 AA00
1312d17-m8_A_G12_A13AAAAA00760.19 AA00
1322d17-m9_A_G12_A13AAAAA00830.17 AA00
1332d17-m10_A_A13_C14AAAAA00890.18 AA00
1342d17-m11_A_A13_C14AAAAA00890.18 AA00
1352d17-m1_A_A13_C14AAAAA00880.20 AA00
1362d17-m2_A_A13_C14AAAAA00880.18 AA00
1372d17-m3_A_A13_C14AAAAA00900.16 AA00
1382d17-m4_A_A13_C14AAAAA00900.20 AA00
1392d17-m5_A_A13_C14AAAAA00870.20 AA00
1402d17-m6_A_A13_C14AAAAA00890.17 AA00
1412d17-m7_A_A13_C14AAAAA00900.16 AA00
1422d17-m8_A_A13_C14AAAAA00910.17 AA00
1432d17-m9_A_A13_C14AAAAA00880.19 AA00
1442d17-m10_A_C14_C15AAAAA00890.20 AA00
1452d17-m11_A_C14_C15AAAAA00900.18 AA00
1462d17-m1_A_C14_C15AAAAA00900.17 AA00
1472d17-m2_A_C14_C15AAAAA00830.20 AA00
1482d17-m3_A_C14_C15AAAAA00900.18 AA00
1492d17-m4_A_C14_C15AAAAA00890.18 AA00
1502d17-m5_A_C14_C15AAAAA00890.18 AA00
1512d17-m6_A_C14_C15AAAAA00850.20 AA00
1522d17-m7_A_C14_C15AAAAA00900.18 AA00
1532d17-m8_A_C14_C15AAAAA00920.17 AA00
1542d17-m9_A_C14_C15AAAAA00890.19 AA00
1552d17-m10_A_C15_C16AAAAA00880.18 AA00
1562d17-m11_A_C15_C16AAAAA00860.21 AA00
1572d17-m1_A_C15_C16AAAAA00880.22 AA00
1582d17-m2_A_C15_C16AAAAA00860.20 AA00
1592d17-m3_A_C15_C16AAAAA00900.19 AA00
1602d17-m4_A_C15_C16AAAAA00870.19 AA00
1612d17-m5_A_C15_C16AAAAA00860.19 AA00
1622d17-m6_A_C15_C16AAAAA00860.20 AA00
1632d17-m7_A_C15_C16AAAAA00880.21 AA00
1642d17-m8_A_C15_C16AAAAA00870.19 AA00
1652d17-m9_A_C15_C16AAAAA00870.19 AA00
1662d17-m10_B_G1_G2AAAAA00870.12 AA00
1672d17-m11_B_G1_G2AAAAA00840.11 AA00
1682d17-m1_B_G1_G2AAAAA00910.13 AA00
1692d17-m2_B_G1_G2AAAAA00860.15 AA00
1702d17-m3_B_G1_G2AAAAA00840.13 AA00
1712d17-m4_B_G1_G2AAAAA00890.10 AA00
1722d17-m5_B_G1_G2AAAAA00840.12 AA00
1732d17-m6_B_G1_G2AAAAA00830.15 AA00
1742d17-m7_B_G1_G2AAAAA00900.10 AA00
1752d17-m8_B_G1_G2AAAAA00880.11 AA00
1762d17-m9_B_G1_G2AAAAA00880.11 AA00
1772d17-m10_B_G2_G3AAAAA00890.13 AA00
1782d17-m11_B_G2_G3AAAAA00880.16 AA00
1792d17-m1_B_G2_G3AAAAA00910.12 AA00
1802d17-m2_B_G2_G3AAAAA00830.19 AA00
1812d17-m3_B_G2_G3AAAAA00870.14 AA00
1822d17-m4_B_G2_G3AAAAA00910.11 AA00
1832d17-m5_B_G2_G3AAAAA00890.12 AA00
1842d17-m6_B_G2_G3AAAAA00930.12 AA00
1852d17-m7_B_G2_G3AAAAA00910.12 AA00
1862d17-m8_B_G2_G3AAAAA00910.11 AA00
1872d17-m9_B_G2_G3AAAAA00890.12 AA00
1882d17-m10_B_G3_U4AAAAA00880.19 AA00
1892d17-m11_B_G3_U4AAAAA00890.20 AA00
1902d17-m1_B_G3_U4AAAAA00880.17 AA00
1912d17-m2_B_G3_U4AAAAA00830.21 AA00
1922d17-m3_B_G3_U4AAAAA00870.19 AA00
1932d17-m4_B_G3_U4AAAAA00890.17 AA00
1942d17-m5_B_G3_U4AAAAA00890.18 AA00
1952d17-m6_B_G3_U4AAAAA00860.21 AA00
1962d17-m7_B_G3_U4AAAAA00890.17 AA00
1972d17-m8_B_G3_U4AAAAA00890.18 AA00
1982d17-m9_B_G3_U4AAAAA00890.19 AA00
1992d17-m10_B_U4_C5AAAAA00890.20 AA00
2002d17-m11_B_U4_C5AAAAA00930.15 AA00
2012d17-m1_B_U4_C5AAAAA00910.21 AA00
2022d17-m2_B_U4_C5AAAAA00860.20 AA00
2032d17-m3_B_U4_C5AAAAA00910.14 AA00
2042d17-m4_B_U4_C5AAAAA00890.19 AA00
2052d17-m5_B_U4_C5AAAAA00930.17 AA00
2062d17-m6_B_U4_C5AAAAA00910.17 AA00
2072d17-m7_B_U4_C5AAAAA00920.17 AA00
2082d17-m8_B_U4_C5AAAAA00930.17 AA00
2092d17-m9_B_U4_C5AAAAA00900.20 AA00
2102d17-m10_B_C5_G6AAwAA01750.27 AA01
2112d17-m11_B_C5_G6AAAAA00290.21 AA00
2122d17-m1_B_C5_G6AAwAA01950.17 AA01
2132d17-m2_B_C5_G6AAAAA00790.17 AA00
2142d17-m3_B_C5_G6AAwAA01680.23 AA01
2152d17-m4_B_C5_G6AAwAA01890.24 AA01
2162d17-m5_B_C5_G6AAAAA00320.39 AA00
2172d17-m6_B_C5_G6AAAAA00650.18 AA00
2182d17-m7_B_C5_G6AAwAA01840.29 AA01
2192d17-m8_B_C5_G6AAwAA01920.15 AA01
2202d17-m9_B_C5_G6AAwAA01950.21 AA01
2212d17-m10_B_G6_G7NANNANT00.94 AA01
2222d17-m11_B_G6_G7NANNANT00.49 AA01
2232d17-m1_B_G6_G7AAAAA00370.44 AA00
2242d17-m2_B_G6_G7AAAAA00140.47 AA00
2252d17-m3_B_G6_G7NANNANT00.77 AA05
2262d17-m4_B_G6_G7NANNANT00.90 AA01
2272d17-m5_B_G6_G7AAAAA00550.17 AA00
2282d17-m6_B_G6_G7NANNANT00.72 AA01
2292d17-m7_B_G6_G7NANNANT01.19 AA04
2302d17-m8_B_G6_G7AAAAA04350.58 AA04
2312d17-m9_B_G6_G7AAAAA00620.33 AA00
2322d17-m10_B_G7_C8AAwAA01830.23 AA01
2332d17-m11_B_G7_C8AAAAA00820.24 AA00
2342d17-m1_B_G7_C8AAwAA01780.21 AA01
2352d17-m2_B_G7_C8AAAAA00540.33 AA00
2362d17-m3_B_G7_C8AAAAA00620.34 AA00
2372d17-m4_B_G7_C8AAwAA01650.31 AA01
2382d17-m5_B_G7_C8NANNANT00.72 AB02
2392d17-m6_B_G7_C8AAwAA01820.21 AA01
2402d17-m7_B_G7_C8AAAAA00270.28 AA00
2412d17-m8_B_G7_C8NANNANT00.89 AB02
2422d17-m9_B_G7_C8AAAAA00700.28 AA00
2432d17-m10_B_C8_U9AAAAA00310.39 AA00
2442d17-m11_B_C8_U9AAAAA00460.39 AA00
2452d17-m1_B_C8_U9AAAAA00690.33 AA00
2462d17-m2_B_C8_U9AAAAA00400.28 AA00
2472d17-m3_B_C8_U9AAAAA00700.29 AA00
2482d17-m4_B_C8_U9NANNANT00.97 AA10
2492d17-m5_B_C8_U9AAwAA01720.40 AA01
2502d17-m6_B_C8_U9AAAAA00440.37 AA00
2512d17-m7_B_C8_U9AAuAA12580.43 AA12
2522d17-m8_B_C8_U9AAAAA00360.19 AA00
2532d17-m9_B_C8_U9AAAAA00330.33 AA00
2542d17-m10_B_U9_U10NANNANT00.48 AA01
2552d17-m11_B_U9_U10AAAAA00770.18 AA00
2562d17-m1_B_U9_U10AAAAA00770.18 AA00
2572d17-m2_B_U9_U10NANNANT00.62 AB02
2582d17-m3_B_U9_U10AAAAA00720.20 AA00
2592d17-m4_B_U9_U10AAAAA00840.20 AA00
2602d17-m5_B_U9_U10AAAAA00790.21 AA00
2612d17-m6_B_U9_U10NANNANT00.59 AB02
2622d17-m7_B_U9_U10AAwAA01740.33 AA01
2632d17-m8_B_U9_U10NANNANT00.73 AB02
2642d17-m9_B_U9_U10NANNANT00.46 AA01
2652d17-m10_B_U10_G11AAAAA00870.13 AA00
2662d17-m11_B_U10_G11AAAAA00890.14 AA00
2672d17-m1_B_U10_G11AAAAA00890.13 AA00
2682d17-m2_B_U10_G11AAAAA00810.18 AA00
2692d17-m3_B_U10_G11AAAAA00880.14 AA00
2702d17-m4_B_U10_G11AAAAA00880.13 AA00
2712d17-m5_B_U10_G11AAAAA00850.15 AA00
2722d17-m6_B_U10_G11AAAAA00820.17 AA00
2732d17-m7_B_U10_G11AAAAA00860.16 AA00
2742d17-m8_B_U10_G11AAAAA00930.14 AA00
2752d17-m9_B_U10_G11AAAAA00850.17 AA00
2762d17-m10_B_G11_C12AAAAA00920.14 AA00
2772d17-m11_B_G11_C12AAAAA00910.16 AA00
2782d17-m1_B_G11_C12AAAAA00890.17 AA00
2792d17-m2_B_G11_C12AAAAA00880.17 AA00
2802d17-m3_B_G11_C12AAAAA00930.14 AA00
2812d17-m4_B_G11_C12AAAAA00920.14 AA00
2822d17-m5_B_G11_C12AAAAA00910.16 AA00
2832d17-m6_B_G11_C12AAAAA00920.14 AA00
2842d17-m7_B_G11_C12AAAAA00910.14 AA00
2852d17-m8_B_G11_C12AAAAA00920.15 AA00
2862d17-m9_B_G11_C12AAAAA00920.16 AA00
2872d17-m10_B_C12_U13AAAAA00860.23 AA00
2882d17-m11_B_C12_U13AAAAA00860.22 AA00
2892d17-m1_B_C12_U13AAAAA00840.23 AA00
2902d17-m2_B_C12_U13AAAAA00860.22 AA00
2912d17-m3_B_C12_U13AAAAA00850.22 AA00
2922d17-m4_B_C12_U13AAAAA00850.24 AA00
2932d17-m5_B_C12_U13AAAAA00860.22 AA00
2942d17-m6_B_C12_U13AAAAA00850.23 AA00
2952d17-m7_B_C12_U13AAAAA00860.24 AA00
2962d17-m8_B_C12_U13AAAAA00820.25 AA00
2972d17-m9_B_C12_U13AAAAA00850.21 AA00
2982d17-m10_B_U13_G14AAAAA00870.16 AA00
2992d17-m11_B_U13_G14AAAAA00870.16 AA00
3002d17-m1_B_U13_G14AAAAA00860.17 AA00
3012d17-m2_B_U13_G14AAAAA00870.16 AA00
3022d17-m3_B_U13_G14AAAAA00880.16 AA00
3032d17-m4_B_U13_G14AAAAA00880.15 AA00
3042d17-m5_B_U13_G14AAAAA00870.16 AA00
3052d17-m6_B_U13_G14AAAAA00880.16 AA00
3062d17-m7_B_U13_G14AAAAA00880.15 AA00
3072d17-m8_B_U13_G14AAAAA00860.17 AA00
3082d17-m9_B_U13_G14AAAAA00870.16 AA00

Steps with non-standard or missing atoms have not been assigned, description of conformers is defined in the table.
Definition of torsion angles
step:
Table of conformers

δ1ε1ζ1α2β2γ2δ2χ1χ2μNNCC
step_torsions
ntC_average
Δ torsions
torsion scores

commentsstep confal = NaN
cartesian RMSD = NaN Å
pseudorotation: NA
details: NA
Similarity of step to class averages

Download

Results as csv or json file.
Best NtC fitted to input structure.

Restraints

Restraints file for REFMAC (steps with RMSD <= 0.5Å)
Commands file for MMB (steps with RMSD <= 0.5Å)
Restraints file for Phenix (steps with RMSD <= 0.5Å) [?]

Definitions

Average parameters (csv), esd values (csv), and Cartesian coordinates of conformers.

Download the papers

Description of DNATCO server:
Černý et al., Nucleic Acids Research, 44, W284 (2016).
Definition of conformers:
Schneider et al., Acta Cryst D, 74, 52-64 (2018).
Example of application:
Schneider et al., Genes, 8(10), 278, (2017).

Browse conformers

Return up to random steps in PDB structures ( include large structures )

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