Output of DNA/RNA backbone conformational parameters DSSR v1.9.9-2020feb06 by xiangjun@x3dna.org ****************************************************************************************** Main chain conformational parameters: alpha: O3'(i-1)-P-O5'-C5' beta: P-O5'-C5'-C4' gamma: O5'-C5'-C4'-C3' delta: C5'-C4'-C3'-O3' epsilon: C4'-C3'-O3'-P(i+1) zeta: C3'-O3'-P(i+1)-O5'(i+1) e-z: epsilon-zeta (BI/BII backbone classification) chi for pyrimidines(Y): O4'-C1'-N1-C2; purines(R): O4'-C1'-N9-C4 Range [170, -50(310)] is assigned to anti, and [50, 90] to syn phase-angle: the phase angle of pseudorotation and puckering sugar-type: ~C2'-endo for C2'-endo like conformation, or ~C3'-endo for C3'-endo like conformation Note the ONE column offset (for easy visual distinction) ssZp: single-stranded Zp, defined as the z-coordinate of the 3' phosphorus atom (P) expressed in the standard reference frame of the 5' base; the value is POSITIVE when P lies on the +z-axis side (base in anti conformation); NEGATIVE if P is on the -z-axis side (base in syn conformation) Dp: perpendicular distance of the 3' P atom to the glycosidic bond [Ref: Chen et al. (2010): "MolProbity: all-atom structure validation for macromolecular crystallography." Acta Crystallogr D Biol Crystallogr, 66(1):12-21] splay: angle between the bridging P to the two base-origins of a dinucleotide. nt alpha beta gamma delta epsilon zeta e-z chi phase-angle sugar-type ssZp Dp splay 1 C A.C1 --- -100.4 87.8 79.7 -135.4 -85.2 -50(BI) -172.1(anti) 8.2(C3'-endo) ~C3'-endo 4.69 4.75 20.54 2 G A.G2 -48.5 162.3 46.7 80.6 -142.2 -89.7 -52(BI) -162.7(anti) 9.8(C3'-endo) ~C3'-endo 4.45 4.68 22.26 3 U A.U3 -42.5 153.0 47.7 74.9 -139.2 -82.8 -56(BI) -164.4(anti) 11.4(C3'-endo) ~C3'-endo 4.47 4.70 24.36 4 G A.G4 -44.2 164.2 50.4 79.7 -154.3 -71.4 -83(BI) -162.5(anti) 16.9(C3'-endo) ~C3'-endo 4.43 4.57 21.85 5 G A.G5 -80.9 -174.5 57.7 78.7 -148.1 67.0 145(..) -155.5(anti) 21.3(C3'-endo) ~C3'-endo 4.32 4.68 112.78 6 U A.U6 71.9 128.5 32.7 83.1 -161.1 -69.3 -92(BI) -173.5(anti) 14.5(C3'-endo) ~C3'-endo 4.60 4.55 29.35 7 U A.U7 -76.4 -155.2 49.8 85.1 -159.0 -62.0 -97(BI) -161.8(anti) 11.0(C3'-endo) ~C3'-endo 4.32 4.49 20.15 8 A A.A8 -93.6 -165.8 60.9 81.5 -145.5 -78.6 -67(BI) -159.3(anti) 23.4(C3'-endo) ~C3'-endo 4.30 4.51 21.15 9 G A.G9 -56.3 163.4 45.2 74.2 -134.4 -75.1 -59(BI) -161.9(anti) 17.5(C3'-endo) ~C3'-endo 4.44 4.74 22.19 10 G A.G10 -65.0 150.3 73.3 70.8 -138.0 -73.0 -65(BI) -175.0(anti) 21.0(C3'-endo) ~C3'-endo 4.75 4.74 23.57 11 G A.G11 -61.5 167.6 63.2 73.4 -146.1 -71.9 -74(BI) -164.4(anti) 17.1(C3'-endo) ~C3'-endo 4.48 4.67 23.87 12 C A.C12 -58.2 165.3 57.5 77.7 -162.5 -69.3 -93(BI) -156.5(anti) 13.9(C3'-endo) ~C3'-endo 4.21 4.49 22.30 13 C A.C13 151.0 -158.4 176.1 85.0 -122.6 -109.4 -13(..) -175.6(anti) 13.1(C3'-endo) ~C3'-endo 4.64 4.68 20.23 14 A A.A14 -20.1 131.7 45.3 76.0 -138.9 -80.5 -58(BI) -158.7(anti) 31.2(C3'-endo) ~C3'-endo 3.96 4.32 19.21 15 C A.C15 -73.7 144.7 86.6 81.9 -140.1 -75.1 -65(BI) -162.6(anti) 35.6(C3'-endo) ~C3'-endo 4.00 4.27 20.55 16 G A.G16 -60.9 179.1 54.7 139.3 -90.6 106.9 163(..) -121.2(anti) 154.0(C2'-endo) ~C2'-endo 1.12 1.07 14.15 17 U A.U17 136.6 -157.1 152.0 149.7 -56.9 93.5 210(..) 22.9(syn) 166.2(C2'-endo) ~C2'-endo 0.37 0.30 23.16 18 U A.U18 -124.1 -167.4 31.1 142.2 -149.6 -135.3 -14(..) -39.0(...) 161.5(C2'-endo) ~C2'-endo 0.14 2.05 24.69 19 A A.A19 -72.5 147.9 45.3 143.7 -67.4 92.8 200(..) -44.8(...) 150.2(C2'-endo) ~C2'-endo 1.81 1.32 21.57 20 A A.A20 85.0 -148.8 -173.4 82.6 -126.4 -91.2 -35(..) -162.9(anti) 22.6(C3'-endo) ~C3'-endo 4.07 4.42 20.06 21 A A.A21 -62.2 147.1 67.8 89.5 -149.9 -108.6 -41(BI) -140.0(anti) 25.0(C3'-endo) ~C3'-endo 3.43 4.24 110.37 22 U A.U22 -168.0 162.7 49.0 151.5 -99.1 -71.9 -27(..) -114.0(anti) 165.5(C2'-endo) ~C2'-endo 0.70 0.71 106.30 23 A A.A23 -60.0 -169.2 36.4 88.7 -137.6 -77.4 -60(BI) -151.3(anti) 7.7(C3'-endo) ~C3'-endo 3.96 4.53 23.12 24 G A.G24 -45.6 156.6 35.8 83.9 -150.0 78.3 132(..) -145.0(anti) 5.3(C3'-endo) ~C3'-endo 3.93 4.68 111.33 25 U A.U25 43.9 129.9 52.3 78.4 -147.7 -105.9 -42(BI) 154.7(anti) 11.2(C3'-endo) ~C3'-endo 4.18 4.73 13.69 26 U A.U26 30.4 125.3 6.9 76.1 -149.1 -112.6 -37(BI) -135.1(anti) 18.1(C3'-endo) ~C3'-endo 3.46 4.66 20.80 27 G A.G27 2.0 131.3 8.6 75.5 -153.6 -77.1 -76(BI) -153.2(anti) 23.4(C3'-endo) ~C3'-endo 4.19 4.55 21.05 28 C A.C28 -53.7 160.0 52.7 80.4 -145.7 -74.8 -71(BI) -163.9(anti) 15.8(C3'-endo) ~C3'-endo 4.52 4.65 29.16 29 U A.U29 -46.3 156.8 55.6 81.4 -156.1 -106.1 -50(BI) -173.2(anti) 16.2(C3'-endo) ~C3'-endo 4.59 4.57 24.81 30 U A.U30 164.1 -137.3 161.9 75.5 -112.2 -50.6 -62(..) -177.8(anti) 20.7(C3'-endo) ~C3'-endo 4.62 4.70 67.61 31 A A.A31 -158.4 122.3 36.9 79.5 -142.4 -62.3 -80(BI) -167.6(anti) 6.4(C3'-endo) ~C3'-endo 4.62 4.76 20.46 32 A A.A32 -80.0 178.3 62.7 82.8 -126.9 155.3 78(BII) -150.3(anti) 19.7(C3'-endo) ~C3'-endo 3.92 4.73 77.63 33 G A.G33 -67.8 124.6 48.0 74.7 -175.8 76.9 107(..) -143.6(anti) 15.6(C3'-endo) ~C3'-endo 3.92 4.46 98.77 34 C A.C34 47.1 145.4 67.6 77.2 -159.6 -66.1 -94(BI) -149.6(anti) 13.9(C3'-endo) ~C3'-endo 4.07 4.57 28.23 35 C A.C35 -83.9 -173.0 70.3 78.4 -149.6 -71.7 -78(BI) -168.5(anti) 24.7(C3'-endo) ~C3'-endo 4.47 4.54 25.46 36 C A.C36 -87.9 -179.3 70.0 80.9 -124.6 -103.8 -21(..) -174.1(anti) 15.4(C3'-endo) ~C3'-endo 4.58 4.70 21.65 37 U A.U37 -39.1 154.4 33.8 80.6 -150.2 -68.9 -81(BI) -161.3(anti) 16.1(C3'-endo) ~C3'-endo 4.50 4.66 21.12 38 A A.A38 -62.7 175.0 47.8 80.5 -162.1 -68.0 -94(BI) -158.0(anti) 18.3(C3'-endo) ~C3'-endo 4.42 4.57 25.31 39 A A.A39 145.0 -157.2 -162.3 84.7 -141.2 -46.9 -94(BI) -172.4(anti) 20.0(C3'-endo) ~C3'-endo 4.43 4.49 36.44 40 G A.G40 -75.0 -176.5 64.2 155.7 -83.9 100.1 176(..) -113.1(anti) 169.8(C2'-endo) ~C2'-endo 0.34 0.46 43.18 41 C A.C41 -176.5 -127.1 57.3 86.9 -150.3 -68.7 -82(BI) -164.3(anti) 9.0(C3'-endo) ~C3'-endo 4.57 4.62 22.79 42 G A.G42 -54.6 168.5 46.4 84.9 -142.3 -73.1 -69(BI) -160.6(anti) 20.3(C3'-endo) ~C3'-endo 4.36 4.55 23.50 43 U A.U43 -66.0 158.1 59.3 77.6 -132.2 -72.2 -60(BI) -164.6(anti) 14.9(C3'-endo) ~C3'-endo 4.57 4.80 35.76 44 U A.U44 -79.6 177.7 79.6 80.0 -134.2 -107.6 -27(..) -158.4(anti) 22.4(C3'-endo) ~C3'-endo 4.24 4.64 27.57 45 G A.G45 -42.0 152.8 40.0 80.6 -147.8 -70.0 -78(BI) -163.3(anti) 12.2(C3'-endo) ~C3'-endo 4.50 4.65 21.52 46 A A.A46 -64.6 174.3 54.3 77.7 -142.3 -71.6 -71(BI) -161.0(anti) 18.1(C3'-endo) ~C3'-endo 4.35 4.62 25.27 47 U A.U47 -52.3 174.0 42.2 81.9 --- --- --- -153.3(anti) 11.1(C3'-endo) ~C3'-endo --- --- --- 48 A A.A52 --- 124.5 163.4 138.4 -157.5 4.1 198(..) 23.1(syn) 153.3(C2'-endo) ~C2'-endo -1.68 2.15 120.73 49 U A.U53 -105.2 -135.5 65.1 81.6 -146.7 -82.3 -64(BI) -162.5(anti) 16.3(C3'-endo) ~C3'-endo 4.38 4.58 19.79 50 C A.C54 -58.3 164.1 48.6 76.7 -139.4 -86.4 -53(BI) -157.6(anti) 14.5(C3'-endo) ~C3'-endo 4.33 4.72 24.28 51 A A.A55 -34.6 151.9 50.1 76.2 -146.5 -71.9 -75(BI) -158.9(anti) 23.9(C3'-endo) ~C3'-endo 4.34 4.61 27.50 52 G A.G56 -46.0 173.1 36.5 75.4 157.9 -75.1 -127(BI) -143.8(anti) 10.1(C3'-endo) ~C3'-endo 3.93 4.31 19.39 53 G A.G57 168.0 -103.5 151.3 108.4 180.0 119.4 61(..) -162.6(anti) 104.5(O4'-endo) .... 2.76 2.90 155.62 54 U A.U58 78.4 -82.3 -76.6 90.3 -148.0 -60.4 -88(BI) -167.8(anti) 359.9(C2'-exo) ~C3'-endo 4.61 4.70 17.60 55 G A.G59 -99.7 166.4 83.2 80.1 -143.6 -83.0 -61(BI) -169.8(anti) 20.8(C3'-endo) ~C3'-endo 4.51 4.60 21.32 56 C A.C60 -64.6 172.8 53.3 83.9 -151.3 -57.0 -94(BI) -156.3(anti) 12.2(C3'-endo) ~C3'-endo 4.27 4.57 21.73 57 A A.A61 -105.9 163.0 95.9 77.3 -126.8 -71.8 -55(BI) -168.8(anti) 17.1(C3'-endo) ~C3'-endo 4.59 4.75 20.71 58 A A.A62 -98.2 121.4 123.8 77.8 --- --- --- 177.3(anti) 19.6(C3'-endo) ~C3'-endo --- --- --- ****************************************************************************************** Virtual eta/theta torsion angles: eta: C4'(i-1)-P(i)-C4'(i)-P(i+1) theta: P(i)-C4'(i)-P(i+1)-C4'(i+1) [Ref: Olson (1980): "Configurational statistics of polynucleotide chains. An updated virtual bond model to treat effects of base stacking." Macromolecules, 13(3):721-728] eta': C1'(i-1)-P(i)-C1'(i)-P(i+1) theta': P(i)-C1'(i)-P(i+1)-C1'(i+1) [Ref: Keating et al. (2011): "A new way to see RNA." Quarterly Reviews of Biophysics, 44(4):433-466] eta": base(i-1)-P(i)-base(i)-P(i+1) theta": P(i)-base(i)-P(i+1)-base(i+1) nt eta theta eta' theta' eta" theta" 1 C A.C1 --- -126.8 --- -128.3 --- -116.0 2 G A.G2 167.9 -150.4 -178.9 -149.0 -141.8 -127.1 3 U A.U3 168.1 -145.2 180.0 -143.4 -143.1 -121.6 4 G A.G4 174.8 -148.5 -172.6 -149.6 -136.8 -137.2 5 G A.G5 166.9 22.8 173.7 -16.6 -163.3 -122.3 6 U A.U6 -85.3 -141.5 -29.4 -141.3 77.5 -128.6 7 U A.U7 176.1 -137.2 -177.0 -135.3 -153.1 -112.7 8 A A.A8 161.4 -144.8 173.3 -143.7 -151.3 -114.9 9 G A.G9 161.4 -143.1 172.7 -142.9 -145.1 -118.7 10 G A.G10 163.3 -145.2 178.7 -145.2 -139.2 -117.1 11 G A.G11 170.4 -148.0 -174.7 -145.4 -130.8 -96.6 12 C A.C12 168.3 -122.2 -172.6 -132.3 -107.5 -108.2 13 C A.C13 165.4 -167.5 -177.2 -158.7 -130.4 -133.3 14 A A.A14 173.0 -142.9 -169.7 -146.1 -136.9 -113.1 15 C A.C15 169.9 -141.4 -172.8 -141.1 -125.1 -120.8 16 G A.G16 -165.0 134.2 -143.0 131.8 -118.0 175.0 17 U A.U17 -114.0 78.8 -145.1 88.6 -123.2 89.1 18 U A.U18 157.8 -163.8 156.8 -172.0 163.5 167.0 19 A A.A19 177.5 157.0 -171.2 123.0 164.9 172.4 20 A A.A20 -177.9 -174.4 166.0 -165.0 -145.6 -114.0 21 A A.A21 168.3 -165.0 -170.6 156.4 -113.4 109.2 22 U A.U22 73.6 -49.3 92.9 -74.3 76.8 -41.4 23 A A.A23 159.0 -137.0 -159.9 -129.6 -137.0 -74.0 24 G A.G24 155.8 43.0 -179.9 13.6 -109.8 -101.9 25 U A.U25 -88.0 -131.7 -44.0 -133.4 82.0 -103.9 26 U A.U26 176.6 -157.5 -171.0 -156.8 -122.3 -155.6 27 G A.G27 161.3 -152.2 165.6 -150.1 175.9 -111.5 28 C A.C28 168.5 -139.2 -178.4 -137.0 -126.5 -104.9 29 U A.U29 171.0 -139.1 -166.4 -147.1 -112.5 -148.5 30 U A.U30 164.2 -111.7 172.9 -161.8 -175.5 131.6 31 A A.A31 12.4 -120.1 48.3 -125.0 23.7 -103.1 32 A A.A32 169.4 99.9 -175.0 101.6 -131.8 116.0 33 G A.G33 162.6 17.1 174.3 -45.4 176.6 -124.8 34 C A.C34 -66.3 -143.3 4.1 -150.4 70.8 -139.4 35 C A.C35 172.5 -148.6 -178.5 -147.0 -151.7 -120.0 36 C A.C36 168.3 -148.7 178.5 -145.0 -143.0 -122.2 37 U A.U37 163.2 -138.0 171.3 -137.7 -154.6 -110.6 38 A A.A38 164.4 -120.5 179.2 -127.0 -136.4 -108.0 39 A A.A39 -174.6 -148.8 -159.3 -129.7 -120.9 -64.4 40 G A.G40 -174.2 142.0 -123.2 127.7 -56.8 144.8 41 C A.C41 153.9 -131.2 135.6 -127.5 149.0 -88.6 42 G A.G42 169.6 -136.9 -172.8 -135.5 -117.6 -99.1 43 U A.U43 160.3 -132.5 179.3 -129.1 -125.6 -100.4 44 U A.U44 178.3 -164.4 -166.1 -162.9 -124.2 -140.6 45 G A.G45 168.1 -141.2 173.4 -142.1 -156.6 -129.8 46 A A.A46 168.7 -142.5 -179.2 -137.8 -151.6 -89.3 47 U A.U47 --- --- --- --- --- --- 48 A A.A52 --- -99.5 --- -86.4 --- -60.2 49 U A.U53 -174.7 -149.5 -131.5 -146.7 -130.1 -127.2 50 C A.C54 163.1 -146.2 173.5 -142.8 -155.6 -121.8 51 A A.A55 175.4 -140.6 -169.1 -139.4 -135.2 -84.6 52 G A.G56 169.2 -145.4 -170.5 -139.7 -98.6 -124.3 53 G A.G57 161.9 115.6 -148.8 68.8 -120.8 81.3 54 U A.U58 -62.6 163.0 -82.6 -178.4 -103.4 -134.6 55 G A.G59 156.3 -150.9 178.2 -151.9 -132.6 -121.9 56 C A.C60 167.9 -130.9 178.8 -135.1 -138.1 -115.9 57 A A.A61 162.9 -149.8 -179.4 -158.1 -140.6 -158.0 58 A A.A62 --- --- --- --- --- --- ****************************************************************************************** Sugar conformational parameters: v0: C4'-O4'-C1'-C2' v1: O4'-C1'-C2'-C3' v2: C1'-C2'-C3'-C4' v3: C2'-C3'-C4'-O4' v4: C3'-C4'-O4'-C1' tm: the amplitude of pucker P: the phase angle of pseudorotation [Ref: Altona & Sundaralingam (1972): "Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation." J Am Chem Soc, 94(23):8205-8212] nt v0 v1 v2 v3 v4 tm P Puckering 1 C A.C1 7.1 -28.3 37.8 -34.7 17.4 38.2 8.2 C3'-endo 2 G A.G2 6.0 -27.6 37.8 -35.3 18.5 38.4 9.8 C3'-endo 3 U A.U3 5.4 -29.3 41.3 -39.2 21.3 42.2 11.4 C3'-endo 4 G A.G4 1.2 -24.2 36.7 -37.2 22.7 38.4 16.9 C3'-endo 5 G A.G5 -1.9 -23.2 38.1 -40.4 26.8 40.9 21.3 C3'-endo 6 U A.U6 2.5 -23.5 34.2 -33.6 19.6 35.3 14.5 C3'-endo 7 U A.U7 4.7 -24.2 33.4 -31.9 17.1 34.1 11.0 C3'-endo 8 A A.A8 -3.0 -18.7 32.3 -34.8 23.9 35.2 23.4 C3'-endo 9 G A.G9 0.9 -25.8 39.9 -40.3 24.9 41.8 17.5 C3'-endo 10 G A.G10 -1.8 -23.9 39.4 -41.5 27.2 42.2 21.0 C3'-endo 11 G A.G11 1.1 -26.3 40.4 -40.5 25.1 42.2 17.1 C3'-endo 12 C A.C12 3.4 -26.7 38.9 -37.8 21.9 40.0 13.9 C3'-endo 13 C A.C13 3.4 -23.6 33.9 -32.9 18.4 34.8 13.1 C3'-endo 14 A A.A14 -9.0 -16.4 34.2 -40.2 30.9 40.0 31.2 C3'-endo 15 C A.C15 -11.1 -12.8 30.2 -37.5 30.6 37.1 35.6 C3'-endo 16 G A.G16 -24.6 34.5 -30.7 17.4 4.3 34.1 154.0 C2'-endo 17 U A.U17 -21.7 37.8 -38.5 26.9 -3.5 39.6 166.2 C2'-endo 18 U A.U18 -22.4 35.4 -34.4 22.3 -0.1 36.3 161.5 C2'-endo 19 A A.A19 -32.4 43.5 -36.5 19.3 7.8 42.1 150.2 C2'-endo 20 A A.A20 -2.5 -19.3 32.6 -35.0 23.7 35.3 22.6 C3'-endo 21 A A.A21 -3.5 -16.0 28.2 -31.1 21.9 31.1 25.0 C3'-endo 22 U A.U22 -22.0 37.5 -38.1 26.3 -2.9 39.3 165.5 C2'-endo 23 A A.A23 6.3 -24.3 31.9 -29.3 14.6 32.2 7.7 C3'-endo 24 G A.G24 8.8 -29.5 37.7 -33.4 15.5 37.8 5.3 C3'-endo 25 U A.U25 5.3 -29.3 40.6 -38.4 20.8 41.4 11.2 C3'-endo 26 U A.U26 0.3 -24.7 38.4 -39.1 24.5 40.4 18.1 C3'-endo 27 G A.G27 -3.5 -21.7 37.3 -40.3 27.6 40.7 23.4 C3'-endo 28 C A.C28 1.8 -23.0 34.4 -34.3 20.5 35.8 15.8 C3'-endo 29 U A.U29 1.4 -22.2 33.5 -33.4 20.2 34.8 16.2 C3'-endo 30 U A.U30 -1.5 -22.7 37.0 -39.0 25.4 39.6 20.7 C3'-endo 31 A A.A31 8.5 -30.1 39.1 -35.2 17.0 39.3 6.4 C3'-endo 32 A A.A32 -0.7 -22.3 35.4 -36.8 23.7 37.6 19.7 C3'-endo 33 G A.G33 2.2 -26.7 39.6 -39.4 23.7 41.1 15.6 C3'-endo 34 C A.C34 3.5 -27.7 40.6 -39.4 22.7 41.8 13.9 C3'-endo 35 C A.C35 -4.1 -19.5 34.7 -37.9 26.6 38.2 24.7 C3'-endo 36 C A.C36 2.4 -26.9 39.9 -39.7 23.4 41.4 15.4 C3'-endo 37 U A.U37 1.7 -24.2 36.6 -36.5 21.9 38.1 16.1 C3'-endo 38 A A.A38 0.2 -23.8 36.8 -37.8 23.7 38.8 18.3 C3'-endo 39 A A.A39 -0.8 -20.2 32.2 -33.7 21.8 34.3 20.0 C3'-endo 40 G A.G40 -19.3 36.4 -38.6 28.4 -5.9 39.3 169.8 C2'-endo 41 C A.C41 5.7 -24.3 32.7 -30.4 15.6 33.1 9.0 C3'-endo 42 G A.G42 -1.0 -18.0 29.3 -30.5 20.0 31.3 20.3 C3'-endo 43 U A.U43 2.6 -25.6 37.8 -37.3 21.9 39.1 14.9 C3'-endo 44 U A.U44 -2.5 -21.2 35.6 -38.1 25.6 38.4 22.4 C3'-endo 45 G A.G45 4.4 -26.7 37.7 -36.1 19.9 38.5 12.2 C3'-endo 46 A A.A46 0.4 -24.6 38.2 -39.1 24.4 40.2 18.1 C3'-endo 47 U A.U47 5.2 -26.9 37.5 -35.5 19.1 38.2 11.1 C3'-endo 48 A A.A52 -26.1 36.3 -32.0 17.7 4.9 35.8 153.3 C2'-endo 49 U A.U53 1.5 -23.6 35.5 -35.6 21.5 37.0 16.3 C3'-endo 50 C A.C54 3.0 -27.1 39.7 -39.0 22.6 41.0 14.5 C3'-endo 51 A A.A55 -3.7 -20.5 35.7 -38.8 26.7 39.1 23.9 C3'-endo 52 G A.G56 6.3 -29.6 40.5 -38.0 20.0 41.1 10.1 C3'-endo 53 G A.G57 -42.1 31.0 -10.1 -13.2 34.4 40.5 104.5 O4'-endo 54 U A.U58 11.6 -29.4 35.1 -29.3 11.5 35.1 359.9 C2'-exo 55 G A.G59 -1.5 -21.9 35.7 -37.6 24.6 38.2 20.8 C3'-endo 56 C A.C60 4.1 -24.6 34.7 -33.3 18.4 35.5 12.2 C3'-endo 57 A A.A61 1.1 -23.8 36.3 -36.7 22.5 38.0 17.1 C3'-endo 58 A A.A62 -0.7 -23.0 36.5 -38.0 24.3 38.8 19.6 C3'-endo ****************************************************************************************** Assignment of sugar-phosphate backbone suites bin: name of the 12 bins based on [delta(i-1), delta, gamma], where delta(i-1) and delta can be either 3 (for C3'-endo sugar) or 2 (for C2'-endo) and gamma can be p/t/m (for gauche+/trans/gauche- conformations, respectively) (2x2x3=12 combinations: 33p, 33t, ... 22m); 'inc' refers to incomplete cases (i.e., with missing torsions), and 'trig' to triages (i.e., with torsion angle outliers) cluster: 2-char suite name, for one of 53 reported clusters (46 certain and 7 wannabes), '__' for incomplete cases, and '!!' for outliers suiteness: measure of conformer-match quality (low to high in range 0 to 1) [Ref: Richardson et al. (2008): "RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)." RNA, 14(3):465-481] nt bin cluster suiteness 1 C A.C1 inc __ 0 2 G A.G2 33p 1a 0.626 3 U A.U3 33p 1a 0.412 4 G A.G4 33p 1a 0.552 5 G A.G5 33p 1a 0.736 6 U A.U6 33p 5d 0.493 7 U A.U7 33p 1a 0.527 8 A A.A8 33p 1a 0.324 9 G A.G9 33p 1a 0.740 10 G A.G10 33p 1a 0.251 11 G A.G11 33p 1a 0.549 12 C A.C12 33p 1a 0.774 13 C A.C13 33t 1c 0.954 14 A A.A14 trig !! 0 15 C A.C15 33p 1a 0.010 16 G A.G16 32p 1b 0.889 17 U A.U17 22t !! 0 18 U A.U18 22p !! 0 19 A A.A19 22p !! 0 20 A A.A20 23t 6n 0.362 21 A A.A21 33p 1a 0.307 22 U A.U22 32p 1z 0.490 23 A A.A23 23p 2a 0.478 24 G A.G24 33p 1a 0.328 25 U A.U25 33p 5d 0.446 26 U A.U26 trig !! 0 27 G A.G27 trig !! 0 28 C A.C28 33p 1a 0.772 29 U A.U29 33p 1a 0.643 30 U A.U30 33t 1c 0.085 31 A A.A31 33p 1g 0.029 32 A A.A32 33p 1a 0.699 33 G A.G33 33p 3a 0.259 34 C A.C34 33p 5d 0.281 35 C A.C35 33p 1a 0.396 36 C A.C36 33p 1a 0.367 37 U A.U37 33p 1a 0.057 38 A A.A38 33p 1a 0.932 39 A A.A39 33t 1c 0.437 40 G A.G40 32p 1b 0.396 41 C A.C41 23p 6g 0.150 42 G A.G42 33p 1a 0.788 43 U A.U43 33p 1a 0.826 44 U A.U44 33p 1a 0.124 45 G A.G45 33p 1a 0.108 46 A A.A46 33p 1a 0.964 47 U A.U47 33p 1a 0.688 48 A A.A52 inc __ 0 49 U A.U53 trig !! 0 50 C A.C54 33p 1a 0.829 51 A A.A55 33p 1a 0.254 52 G A.G56 33p 1a 0.390 53 G A.G57 33t !! 0 54 U A.U58 33m !! 0 55 G A.G59 33p 1a 0.010 56 C A.C60 33p 1a 0.880 57 A A.A61 trig !! 0 58 A A.A62 trig !! 0 Concatenated suite string per chain. To avoid confusion of lower case modified nucleotide name (e.g., 'a') with suite cluster (e.g., '1a'), use --suite-delimiter to add delimiters (matched '()' by default). 1 A RNA[57]/1* nts=58 C1aG1aU1aG1aG5dU1aU1aA1aG1aG1aG1aC1cC!!A1aC1bG!!U!!U!!A6nA1aA1zU2aA1aG5dU!!U!!G1aC1aU1cU1gA1aA3aG5dC1aC1aC1aU1aA1cA1bG6gC1aG1aU1aU1aG1aA1aU..A!!U1aC1aA1aG!!G!!U1aG1aC!!A!!A