Output of DNA/RNA backbone conformational parameters DSSR v2.4.5-2024sep24 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 G A.G1 --- -128.1 67.8 82.9 -155.6 -68.6 -87(BI) -167.8(anti) 16.1(C3'-endo) ~C3'-endo 4.59 4.57 24.92 2 C A.C2 -67.4 -178.4 53.8 83.4 -145.1 -76.8 -68(BI) -163.8(anti) 16.1(C3'-endo) ~C3'-endo 4.52 4.63 21.15 3 G A.G3 -74.5 169.7 59.5 80.7 -148.3 -80.0 -68(BI) -161.9(anti) 14.6(C3'-endo) ~C3'-endo 4.75 4.69 22.28 4 G A.G4 -64.4 162.2 60.7 82.2 -157.4 -68.7 -89(BI) -168.7(anti) 20.8(C3'-endo) ~C3'-endo 4.68 4.57 25.22 5 A A.A5 -74.7 -176.5 53.4 84.9 -137.5 -81.7 -56(BI) -162.9(anti) 4.8(C3'-endo) ~C3'-endo 4.49 4.76 22.04 6 U A.U6 -48.8 157.6 55.3 81.3 -151.0 -77.0 -74(BI) -160.0(anti) 18.2(C3'-endo) ~C3'-endo 4.31 4.51 22.89 7 U A.U7 -59.5 -178.7 62.5 137.3 -105.9 -52.0 -54(--) -133.1(anti) 156.1(C2'-endo) ~C2'-endo 1.55 1.41 126.99 8 U A.U8 -83.8 -145.6 55.4 78.6 -142.8 -118.6 -24(--) -161.5(anti) 10.5(C3'-endo) ~C3'-endo 4.60 4.76 62.37 9 A A.A9 -69.7 -141.7 52.3 147.8 -106.2 -77.3 -29(--) -70.5(anti) 149.8(C2'-endo) ~C2'-endo 1.00 1.14 57.38 10 g A.2MG10 177.8 147.2 60.1 89.3 -126.2 -88.7 -37(--) 169.6(anti) 6.6(C3'-endo) ~C3'-endo 4.68 4.63 23.87 11 C A.C11 -56.1 167.9 48.2 87.2 -150.5 -69.9 -81(BI) -160.9(anti) 16.8(C3'-endo) ~C3'-endo 4.28 4.46 21.20 12 U A.U12 -67.8 172.9 51.8 80.7 -158.5 -65.2 -93(BI) -158.3(anti) 25.2(C3'-endo) ~C3'-endo 4.29 4.45 21.01 13 C A.C13 166.6 -169.9 178.6 82.5 -153.1 -97.4 -56(BI) -168.3(anti) 23.7(C3'-endo) ~C3'-endo 4.28 4.36 31.59 14 A A.A14 83.4 -158.3 -114.6 92.0 -125.5 -57.3 -68(--) -170.7(anti) 358.9(C2'-exo) ~C3'-endo 4.67 4.74 38.01 15 G A.G15 -55.1 162.5 51.9 79.8 -136.3 -143.9 8(--) -164.5(anti) 16.0(C3'-endo) ~C3'-endo 4.72 4.74 26.17 16 u A.H2U16 -6.1 91.2 76.8 96.8 -61.8 -131.2 69(--) -85.8(anti) 18.8(C3'-endo) ~C3'-endo -0.71 3.38 145.77 17 u A.H2U17 27.8 107.7 174.1 94.8 178.0 76.2 102(--) -142.5(anti) 341.4(C2'-exo) ~C3'-endo -0.90 4.20 105.55 18 G A.G18 45.4 -159.4 59.0 150.6 -95.2 -179.1 84(BII) -99.5(anti) 154.3(C2'-endo) ~C2'-endo 1.60 1.09 51.64 19 G A.G19 -71.4 -178.9 53.8 153.8 -91.6 -83.7 -8(--) -80.3(anti) 167.6(C2'-endo) ~C2'-endo -1.14 0.48 130.30 20 G A.G20 -81.3 -150.7 47.8 89.9 -122.3 -54.1 -68(--) 177.8(anti) 8.7(C3'-endo) ~C3'-endo 4.90 4.76 57.04 21 A A.A21 -75.6 148.6 -176.6 78.2 -168.9 -75.6 -93(BI) -160.2(anti) 13.0(C3'-endo) ~C3'-endo 4.00 4.26 40.66 22 G A.G22 158.8 153.5 179.3 82.0 -145.0 -80.4 -65(BI) -175.5(anti) 353.8(C2'-exo) ~C3'-endo 4.60 4.73 25.62 23 A A.A23 -53.3 174.8 52.5 82.3 -155.3 -66.4 -89(BI) -158.0(anti) 12.6(C3'-endo) ~C3'-endo 4.18 4.61 22.96 24 G A.G24 -68.8 178.2 46.8 83.6 -144.3 -72.8 -71(BI) -160.7(anti) 13.4(C3'-endo) ~C3'-endo 4.63 4.74 20.51 25 C A.C25 -65.1 168.9 53.9 83.3 -145.1 -68.4 -77(BI) -160.3(anti) 17.4(C3'-endo) ~C3'-endo 4.56 4.70 30.70 26 g A.M2G26 -53.8 170.8 47.7 86.0 -136.3 -76.9 -59(BI) -163.4(anti) 9.3(C3'-endo) ~C3'-endo 4.57 4.67 27.36 27 C A.C27 -53.0 166.9 43.6 83.4 -148.5 -73.4 -75(BI) -168.2(anti) 18.3(C3'-endo) ~C3'-endo 4.53 4.62 23.07 28 C A.C28 -72.4 178.3 49.3 80.1 -152.1 -67.0 -85(BI) -160.6(anti) 9.2(C3'-endo) ~C3'-endo 4.55 4.73 21.61 29 A A.A29 -66.6 174.0 55.6 81.4 -155.5 -78.3 -77(BI) -165.9(anti) 13.7(C3'-endo) ~C3'-endo 4.73 4.65 26.96 30 G A.G30 -54.0 165.9 56.9 83.6 -144.7 -62.3 -82(BI) -171.7(anti) 14.5(C3'-endo) ~C3'-endo 4.67 4.65 25.72 31 A A.A31 -69.9 177.8 52.3 83.7 -137.0 -75.5 -61(BI) -156.7(anti) 14.6(C3'-endo) ~C3'-endo 4.24 4.72 21.52 32 c A.OMC32 -52.7 161.4 49.3 80.1 -145.9 -71.2 -75(BI) -149.9(anti) 20.4(C3'-endo) ~C3'-endo 4.16 4.63 25.94 33 U A.U33 -67.7 -177.0 47.0 82.1 -148.0 -53.7 -94(BI) -148.2(anti) 13.3(C3'-endo) ~C3'-endo 4.19 4.64 75.47 34 g A.OMG34 171.1 148.1 52.5 83.4 -132.5 -71.8 -61(BI) -171.2(anti) 12.2(C3'-endo) ~C3'-endo 4.15 4.58 22.09 35 A A.A35 -47.7 163.7 40.2 80.9 -143.7 -59.5 -84(BI) -154.4(anti) 21.9(C3'-endo) ~C3'-endo 4.20 4.54 20.57 36 A A.A36 -52.4 165.7 51.3 72.2 -160.4 -85.2 -75(BI) -158.4(anti) 45.8(C4'-exo) ~C3'-endo 4.49 4.31 24.48 37 g A.YYG37 -57.5 163.0 47.8 81.1 -148.1 -67.0 -81(BI) -168.8(anti) 15.4(C3'-endo) ~C3'-endo 4.63 4.65 32.08 38 A A.A38 -61.8 -180.0 46.9 82.5 -136.8 -76.4 -60(BI) -169.4(anti) 2.4(C3'-endo) ~C3'-endo 4.63 4.78 23.75 39 P A.PSU39 -47.7 160.4 53.3 79.3 -140.1 -68.6 -72(BI) -165.6(anti) 15.8(C3'-endo) ~C3'-endo 4.55 4.68 26.68 40 c A.5MC40 -67.4 172.0 56.2 83.2 -154.2 -74.9 -79(BI) -162.6(anti) 17.3(C3'-endo) ~C3'-endo 4.52 4.60 27.71 41 U A.U41 -68.2 -179.4 52.4 78.9 -137.3 -84.7 -53(BI) -169.0(anti) 13.4(C3'-endo) ~C3'-endo 4.54 4.75 24.14 42 G A.G42 -47.9 158.7 55.6 79.8 -160.3 -70.3 -90(BI) -169.0(anti) 20.9(C3'-endo) ~C3'-endo 4.43 4.51 23.54 43 G A.G43 -67.0 -178.3 55.6 81.6 -154.9 -76.4 -78(BI) -160.2(anti) 12.6(C3'-endo) ~C3'-endo 4.24 4.61 20.95 44 A A.A44 -59.7 162.1 60.0 85.3 -142.8 -57.2 -86(BI) -159.4(anti) 16.9(C3'-endo) ~C3'-endo 4.25 4.61 31.07 45 G A.G45 -71.9 -176.9 51.0 87.6 -135.1 -78.7 -56(BI) -149.3(anti) 15.4(C3'-endo) ~C3'-endo 4.01 4.58 40.27 46 g A.7MG46 -56.8 -146.5 48.4 141.6 -102.7 -137.9 35(--) -65.8(anti) 154.5(C2'-endo) ~C2'-endo 0.21 0.96 139.04 47 U A.U47 62.4 -164.0 44.4 146.1 -93.7 -78.0 -16(--) -112.0(anti) 164.9(C2'-endo) ~C2'-endo 0.26 0.39 157.37 48 C A.C48 -73.5 -174.3 161.5 145.6 -143.5 75.6 141(--) -140.1(anti) 158.2(C2'-endo) ~C2'-endo 1.92 1.80 147.54 49 c A.5MC49 50.7 168.5 42.2 84.3 -145.0 -82.1 -63(BI) -173.6(anti) 10.1(C3'-endo) ~C3'-endo 4.77 4.75 25.83 50 U A.U50 -51.7 177.2 42.1 80.4 -150.6 -67.8 -83(BI) -165.3(anti) 5.6(C3'-endo) ~C3'-endo 4.38 4.75 23.15 51 G A.G51 -63.9 176.8 52.8 79.4 -150.4 -71.3 -79(BI) -156.6(anti) 11.5(C3'-endo) ~C3'-endo 4.44 4.67 21.28 52 U A.U52 -64.7 173.6 48.5 80.3 -156.5 -69.4 -87(BI) -164.0(anti) 14.1(C3'-endo) ~C3'-endo 4.64 4.74 25.47 53 G A.G53 -56.9 171.5 56.2 83.9 -159.4 -64.9 -95(BI) -169.2(anti) 19.8(C3'-endo) ~C3'-endo 4.59 4.57 24.53 54 t A.5MU54 -79.7 -172.8 57.7 77.6 -128.6 -70.7 -58(BI) -161.5(anti) 20.6(C3'-endo) ~C3'-endo 4.56 4.80 30.73 55 P A.PSU55 -49.7 168.8 44.1 76.6 -140.8 -69.9 -71(BI) -147.0(anti) 10.1(C3'-endo) ~C3'-endo 4.15 4.74 71.28 56 C A.C56 166.4 171.8 53.3 83.4 -132.7 -70.6 -62(BI) -161.5(anti) 12.6(C3'-endo) ~C3'-endo 4.37 4.76 28.07 57 G A.G57 -65.7 167.1 57.5 81.7 -145.2 -67.6 -78(BI) -159.3(anti) 12.8(C3'-endo) ~C3'-endo 4.36 4.65 42.47 58 a A.1MA58 -60.8 -146.1 71.8 156.7 -78.3 -169.3 91(BII) -86.3(anti) 161.1(C2'-endo) ~C2'-endo 0.48 0.68 73.92 59 U A.U59 72.6 -158.8 63.7 84.6 -148.8 -53.7 -95(BI) -165.6(anti) 25.8(C3'-endo) ~C3'-endo 4.67 4.42 27.88 60 C A.C60 -72.2 179.5 66.0 148.3 -97.1 -66.4 -31(--) -117.8(anti) 154.8(C2'-endo) ~C2'-endo 0.99 0.86 90.64 61 C A.C61 -84.3 179.8 38.2 83.0 -152.3 -74.5 -78(BI) -166.7(anti) 14.8(C3'-endo) ~C3'-endo 4.45 4.52 25.80 62 A A.A62 -60.1 179.6 46.9 80.5 -145.6 -74.1 -71(BI) -158.7(anti) 9.9(C3'-endo) ~C3'-endo 4.18 4.66 19.23 63 C A.C63 -62.0 167.3 50.9 80.7 -152.3 -70.7 -82(BI) -152.6(anti) 10.7(C3'-endo) ~C3'-endo 4.32 4.62 23.62 64 A A.A64 -66.9 180.0 44.1 75.8 -147.5 -76.5 -71(BI) -161.8(anti) 12.9(C3'-endo) ~C3'-endo 4.68 4.86 25.64 65 G A.G65 -44.0 164.2 49.9 79.8 -152.0 -73.3 -79(BI) -172.8(anti) 16.5(C3'-endo) ~C3'-endo 4.92 4.76 25.20 66 A A.A66 -57.9 178.5 52.0 81.7 -151.0 -73.5 -77(BI) -164.9(anti) 22.5(C3'-endo) ~C3'-endo 4.56 4.60 22.73 67 A A.A67 -62.0 164.1 54.2 83.2 -152.2 -78.3 -74(BI) -162.8(anti) 15.0(C3'-endo) ~C3'-endo 4.71 4.67 23.30 68 U A.U68 -59.8 175.3 47.3 82.2 -152.9 -65.4 -88(BI) -160.1(anti) 11.2(C3'-endo) ~C3'-endo 4.30 4.60 24.35 69 U A.U69 -63.8 168.1 55.1 79.1 -155.4 -85.6 -70(BI) -161.4(anti) 14.7(C3'-endo) ~C3'-endo 4.55 4.61 19.23 70 C A.C70 -61.7 164.6 53.1 79.0 -158.5 -64.5 -94(BI) -152.0(anti) 15.0(C3'-endo) ~C3'-endo 4.20 4.56 20.96 71 G A.G71 -78.4 173.6 60.3 80.3 -149.6 -68.4 -81(BI) -162.8(anti) 13.5(C3'-endo) ~C3'-endo 4.50 4.71 22.80 72 C A.C72 -73.2 176.2 62.1 83.0 -152.3 -67.9 -84(BI) -161.6(anti) 19.5(C3'-endo) ~C3'-endo 4.56 4.63 26.14 73 A A.A73 -63.3 177.7 50.4 81.6 -148.2 -66.1 -82(BI) -167.4(anti) 15.0(C3'-endo) ~C3'-endo 4.65 4.71 26.33 74 C A.C74 -66.9 -174.9 50.7 85.9 -145.0 -58.8 -86(BI) -153.1(anti) 11.8(C3'-endo) ~C3'-endo 4.22 4.61 33.45 75 C A.C75 -52.3 175.7 42.3 85.6 -131.9 163.9 64(BII) -151.7(anti) 15.1(C3'-endo) ~C3'-endo 3.96 4.60 159.78 76 A A.A76 -71.0 130.2 164.6 160.9 --- --- --- 138.5(anti) 176.1(C2'-endo) ~C2'-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 G A.G1 --- -139.3 --- -136.5 --- -110.8 2 C A.C2 171.9 -144.6 -175.5 -144.1 -136.1 -118.1 3 G A.G3 160.2 -151.4 173.9 -153.9 -145.0 -143.7 4 G A.G4 164.3 -144.6 177.7 -144.1 -154.8 -98.7 5 A A.A5 166.9 -138.1 -178.3 -135.8 -116.3 -111.6 6 U A.U6 172.1 -149.7 -170.8 -143.9 -130.1 -126.5 7 U A.U7 -158.0 -42.7 -138.7 -60.7 -120.5 -31.5 8 U A.U8 162.7 160.7 -159.9 -163.8 -142.6 176.2 9 A A.A9 -140.6 -38.9 -159.3 -112.7 157.1 -105.5 10 g A.2MG10 27.8 -130.3 97.2 -130.1 134.8 -110.3 11 C A.C11 170.3 -135.8 -175.7 -136.7 -137.8 -119.9 12 U A.U12 159.9 -121.6 176.5 -130.6 -148.5 -101.4 13 C A.C13 178.1 -179.1 -166.8 176.7 -118.5 178.4 14 A A.A14 171.9 -146.5 172.1 -133.4 -179.7 -74.6 15 G A.G15 164.3 -177.9 -166.6 -161.0 -92.6 -101.8 16 u A.H2U16 -124.1 -77.5 -114.2 -108.3 -72.5 -127.0 17 u A.H2U17 -10.5 -64.3 7.7 -94.7 17.3 -125.4 18 G A.G18 -21.0 -167.4 45.3 -160.9 61.3 -124.2 19 G A.G19 -127.4 -43.3 -122.0 -72.9 -105.8 -7.8 20 G A.G20 165.3 -100.4 -160.4 -101.1 -177.9 -115.4 21 A A.A21 -78.3 152.7 -68.0 155.1 -61.1 154.8 22 G A.G22 159.5 167.6 156.6 178.8 157.1 -162.6 23 A A.A23 178.4 -141.8 -173.5 -141.2 -156.1 -112.0 24 G A.G24 163.7 -139.5 177.7 -137.6 -137.6 -103.8 25 C A.C25 161.4 -132.6 179.2 -131.0 -128.2 -89.0 26 g A.M2G26 173.0 -133.0 -167.7 -130.4 -106.9 -93.6 27 C A.C27 163.5 -142.3 -178.0 -141.5 -123.6 -105.6 28 C A.C28 157.5 -143.8 171.1 -144.3 -136.3 -125.5 29 A A.A29 163.5 -152.9 179.0 -150.8 -142.9 -124.7 30 G A.G30 178.3 -127.8 -167.7 -126.5 -128.2 -72.5 31 A A.A31 165.4 -133.9 -174.3 -131.0 -101.0 -93.9 32 c A.OMC32 164.5 -139.2 -175.9 -138.0 -122.3 -108.9 33 U A.U33 165.1 -114.0 177.8 -158.5 -141.1 138.3 34 g A.OMG34 27.3 -121.7 50.5 -123.7 22.7 -84.4 35 A A.A35 162.5 -127.7 -177.7 -128.5 -116.8 -113.4 36 A A.A36 164.9 -172.7 -174.4 -169.2 -142.3 -115.1 37 g A.YYG37 163.1 -135.2 174.1 -131.3 -119.8 -79.8 38 A A.A38 170.2 -133.9 -173.3 -129.0 -104.3 -105.5 39 P A.PSU39 174.0 -132.6 -168.6 -131.2 -127.5 -89.6 40 c A.5MC40 163.1 -148.5 -177.6 -149.3 -115.9 -131.7 41 U A.U41 169.4 -148.8 177.2 -144.0 -152.9 -120.5 42 G A.G42 171.2 -150.4 -171.5 -151.6 -133.9 -124.5 43 G A.G43 174.2 -151.6 -174.4 -150.0 -134.0 -124.5 44 A A.A44 173.2 -120.4 -171.8 -120.0 -133.3 -72.6 45 G A.G45 168.6 -141.6 -168.3 -128.4 -103.4 -133.4 46 g A.7MG46 -143.2 -107.3 -133.6 -149.6 -148.2 -162.7 47 U A.U47 -31.5 -56.8 4.8 -91.0 24.9 -110.7 48 C A.C48 -82.5 53.9 -29.3 17.5 1.5 -107.6 49 c A.5MC49 -56.7 -145.3 -36.6 -142.8 103.2 -130.2 50 U A.U50 174.8 -146.6 -176.9 -142.8 -153.6 -113.8 51 G A.G51 170.3 -147.3 -175.5 -148.2 -134.2 -122.1 52 U A.U52 160.3 -145.8 173.9 -144.3 -141.8 -119.6 53 G A.G53 174.9 -141.5 -167.2 -142.4 -124.7 -111.6 54 t A.5MU54 171.1 -129.2 -177.4 -122.6 -133.3 -76.4 55 P A.PSU55 165.3 -115.2 -173.6 -155.4 -112.1 145.1 56 C A.C56 31.4 -126.9 51.6 -124.1 25.3 -87.4 57 G A.G57 164.3 -142.5 -174.1 -131.9 -119.2 -113.8 58 a A.1MA58 -131.5 -108.7 -105.3 -171.2 -104.2 159.8 59 U A.U59 1.8 -119.4 26.8 -109.9 49.0 -56.9 60 C A.C60 -171.8 -40.7 -130.1 -68.5 -70.2 -35.8 61 C A.C61 122.4 -148.3 168.6 -144.1 -158.2 -117.4 62 A A.A62 173.0 -146.6 -176.9 -144.9 -142.0 -119.6 63 C A.C63 164.5 -148.3 177.9 -149.6 -143.9 -128.6 64 A A.A64 158.4 -151.0 168.5 -148.2 -154.8 -122.8 65 G A.G65 173.6 -147.3 -172.0 -145.4 -130.5 -121.2 66 A A.A66 177.6 -145.4 -170.1 -142.7 -133.5 -111.9 67 A A.A67 165.6 -149.3 -176.9 -149.8 -129.8 -126.7 68 U A.U68 168.9 -138.2 179.4 -136.1 -143.2 -96.5 69 U A.U69 165.6 -160.5 -176.0 -161.2 -118.8 -156.9 70 C A.C70 166.7 -146.2 173.6 -149.0 -171.6 -127.0 71 G A.G71 161.0 -143.0 174.0 -142.3 -146.3 -113.4 72 C A.C72 166.1 -141.5 -177.5 -141.9 -131.5 -110.2 73 A A.A73 167.6 -137.8 -177.2 -133.3 -127.1 -89.8 74 C A.C74 171.2 -122.1 -172.8 -116.5 -116.2 -72.1 75 C A.C75 174.9 106.5 -161.9 109.8 -102.9 -139.3 76 A A.A76 --- --- --- --- --- --- ****************************************************************************************** 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 G A.G1 1.7 -23.4 35.1 -35.2 21.1 36.5 16.1 C3'-endo 2 C A.C2 1.6 -23.2 34.8 -34.8 20.9 36.2 16.1 C3'-endo 3 G A.G3 2.7 -25.1 36.8 -36.1 21.2 38.1 14.6 C3'-endo 4 G A.G4 -1.6 -22.3 36.3 -38.2 25.0 38.8 20.8 C3'-endo 5 A A.A5 10.1 -32.6 41.5 -36.6 16.7 41.7 4.8 C3'-endo 6 U A.U6 0.3 -24.0 37.3 -38.1 23.9 39.2 18.2 C3'-endo 7 U A.U7 -24.4 35.4 -32.4 18.9 3.3 35.4 156.1 C2'-endo 8 U A.U8 5.8 -28.7 39.7 -37.2 19.7 40.4 10.5 C3'-endo 9 A A.A9 -31.7 41.8 -35.6 18.1 8.4 41.2 149.8 C2'-endo 10 g A.2MG10 7.8 -28.0 36.7 -33.0 15.9 37.0 6.6 C3'-endo 11 C A.C11 1.2 -21.2 32.1 -32.5 19.8 33.5 16.8 C3'-endo 12 U A.U12 -4.6 -19.3 34.5 -37.9 26.7 38.1 25.2 C3'-endo 13 C A.C13 -3.4 -19.4 33.8 -36.4 25.1 36.9 23.7 C3'-endo 14 A A.A14 12.6 -30.8 36.8 -30.2 11.0 36.8 358.9 C2'-exo 15 G A.G15 1.9 -24.6 36.8 -36.8 22.2 38.3 16.0 C3'-endo 16 u A.H2U16 0.0 -18.7 29.2 -30.2 19.2 30.9 18.8 C3'-endo 17 u A.H2U17 23.0 -36.7 35.1 -23.2 0.2 37.0 341.4 C2'-exo 18 G A.G18 -27.9 39.5 -35.0 20.2 4.8 38.9 154.3 C2'-endo 19 G A.G19 -17.6 31.0 -31.9 23.1 -3.8 32.7 167.6 C2'-endo 20 G A.G20 6.6 -27.8 36.6 -34.2 17.5 37.0 8.7 C3'-endo 21 A A.A21 3.8 -25.0 35.1 -34.4 19.4 36.0 13.0 C3'-endo 22 G A.G22 16.4 -34.1 38.1 -29.5 8.3 38.3 353.8 C2'-exo 23 A A.A23 4.2 -26.6 37.4 -36.5 20.1 38.3 12.6 C3'-endo 24 G A.G24 3.9 -28.4 40.3 -39.3 22.4 41.5 13.4 C3'-endo 25 C A.C25 0.6 -24.5 37.8 -38.0 23.6 39.6 17.4 C3'-endo 26 g A.M2G26 6.3 -27.5 37.1 -34.7 17.9 37.6 9.3 C3'-endo 27 C A.C27 0.2 -23.5 36.5 -37.2 23.6 38.4 18.3 C3'-endo 28 C A.C28 6.6 -29.0 39.1 -36.3 18.8 39.6 9.2 C3'-endo 29 A A.A29 3.4 -26.6 38.4 -37.4 21.4 39.5 13.7 C3'-endo 30 G A.G30 2.6 -24.2 35.7 -34.9 20.4 36.9 14.5 C3'-endo 31 A A.A31 2.6 -24.0 35.0 -34.6 20.2 36.2 14.6 C3'-endo 32 c A.OMC32 -1.2 -21.7 35.1 -36.7 23.9 37.4 20.4 C3'-endo 33 U A.U33 3.5 -25.4 36.5 -35.3 20.1 37.5 13.3 C3'-endo 34 g A.OMG34 3.9 -22.7 32.2 -30.8 17.1 32.9 12.2 C3'-endo 35 A A.A35 -2.0 -19.9 32.7 -34.9 23.4 35.2 21.9 C3'-endo 36 A A.A36 -20.6 -7.3 30.6 -43.2 40.5 43.9 45.8 C4'-exo 37 g A.YYG37 2.1 -24.1 36.0 -35.6 21.0 37.4 15.4 C3'-endo 38 A A.A38 10.9 -30.3 37.6 -32.5 13.6 37.7 2.4 C3'-endo 39 P A.PSU39 2.1 -25.6 38.5 -38.4 22.8 40.0 15.8 C3'-endo 40 c A.5MC40 0.8 -22.5 34.6 -35.0 21.5 36.3 17.3 C3'-endo 41 U A.U41 3.8 -27.7 39.9 -38.6 22.0 41.0 13.4 C3'-endo 42 G A.G42 -1.7 -22.4 36.8 -38.6 25.4 39.4 20.9 C3'-endo 43 G A.G43 4.3 -27.6 39.1 -37.6 21.1 40.1 12.6 C3'-endo 44 A A.A44 1.0 -23.0 35.2 -35.4 21.6 36.8 16.9 C3'-endo 45 G A.G45 2.1 -24.3 35.7 -35.4 21.2 37.0 15.4 C3'-endo 46 g A.7MG46 -27.4 38.6 -34.7 19.7 4.7 38.5 154.5 C2'-endo 47 U A.U47 -20.9 34.8 -35.1 24.3 -2.2 36.4 164.9 C2'-endo 48 C A.C48 -25.6 38.4 -35.6 22.1 2.1 38.4 158.2 C2'-endo 49 c A.5MC49 5.8 -28.1 38.7 -36.0 19.1 39.3 10.1 C3'-endo 50 U A.U50 9.4 -32.2 41.0 -36.4 17.6 41.2 5.6 C3'-endo 51 G A.G51 4.9 -27.9 38.9 -36.8 20.3 39.7 11.5 C3'-endo 52 U A.U52 3.2 -28.5 41.4 -40.1 23.6 42.7 14.1 C3'-endo 53 G A.G53 -1.0 -23.1 37.0 -38.3 24.9 39.4 19.8 C3'-endo 54 t A.5MU54 -1.4 -22.2 35.9 -37.7 24.8 38.3 20.6 C3'-endo 55 P A.PSU55 6.2 -29.9 40.9 -38.3 20.4 41.5 10.1 C3'-endo 56 C A.C56 3.8 -25.3 35.7 -34.5 19.2 36.6 12.6 C3'-endo 57 G A.G57 4.0 -26.7 37.9 -36.5 20.6 38.9 12.8 C3'-endo 58 a A.1MA58 -24.3 38.4 -36.9 23.9 0.2 39.0 161.1 C2'-endo 59 U A.U59 -4.4 -18.3 31.8 -35.7 25.4 35.3 25.8 C3'-endo 60 C A.C60 -28.8 40.5 -36.4 21.2 4.7 40.3 154.8 C2'-endo 61 C A.C61 2.6 -25.5 36.8 -36.6 21.5 38.1 14.8 C3'-endo 62 A A.A62 5.9 -27.8 38.1 -35.4 18.8 38.7 9.9 C3'-endo 63 C A.C63 5.4 -27.3 37.5 -35.5 19.1 38.1 10.7 C3'-endo 64 A A.A64 4.1 -28.6 40.2 -38.8 22.2 41.2 12.9 C3'-endo 65 G A.G65 1.5 -26.6 39.5 -39.9 24.3 41.2 16.5 C3'-endo 66 A A.A66 -2.9 -21.6 36.5 -38.8 26.5 39.5 22.5 C3'-endo 67 A A.A67 2.4 -24.9 36.5 -36.1 21.4 37.8 15.0 C3'-endo 68 U A.U68 5.3 -28.4 39.5 -37.5 20.3 40.3 11.2 C3'-endo 69 U A.U69 2.9 -26.3 38.3 -37.9 22.3 39.6 14.7 C3'-endo 70 C A.C70 2.4 -25.9 38.7 -37.9 22.4 40.1 15.0 C3'-endo 71 G A.G71 3.7 -27.4 39.2 -38.3 21.8 40.3 13.5 C3'-endo 72 C A.C72 -0.6 -21.9 34.9 -36.2 23.1 37.0 19.5 C3'-endo 73 A A.A73 2.4 -25.4 37.3 -36.9 21.8 38.6 15.0 C3'-endo 74 C A.C74 4.4 -25.4 35.6 -34.0 18.6 36.4 11.8 C3'-endo 75 C A.C75 2.3 -22.5 33.1 -33.0 19.2 34.3 15.1 C3'-endo 76 A A.A76 -13.6 30.5 -34.8 27.7 -9.1 34.8 176.1 C2'-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 G A.G1 inc __ 0 2 C A.C2 33p 1a 0.935 3 G A.G3 33p 1a 0.868 4 G A.G4 33p 1a 0.842 5 A A.A5 33p 1a 0.847 6 U A.U6 33p 1a 0.664 7 U A.U7 32p 1b 0.803 8 U A.U8 23p 2a 0.509 9 A A.A9 32p 1[ 0.046 10 g A.2MG10 23p 2g 0.640 11 C A.C11 33p 1a 0.507 12 U A.U12 33p 1a 0.898 13 C A.C13 33t 1c 0.824 14 A A.A14 trig !! 0 15 G A.G15 33p 1a 0.484 16 u A.H2U16 trig !! 0 17 u A.H2U17 33t !! 0 18 G A.G18 32p 5p 0.026 19 G A.G19 22p 4b 0.512 20 G A.G20 23p 2a 0.623 21 A A.A21 33t !! 0 22 G A.G22 33t 1f 0.714 23 A A.A23 33p 1a 0.840 24 G A.G24 33p 1a 0.881 25 C A.C25 33p 1a 0.967 26 g A.M2G26 33p 1a 0.819 27 C A.C27 33p 1a 0.698 28 C A.C28 33p 1a 0.923 29 A A.A29 33p 1a 0.973 30 G A.G30 33p 1a 0.838 31 A A.A31 33p 1a 0.914 32 c A.OMC32 33p 1a 0.782 33 U A.U33 33p 1a 0.897 34 g A.OMG34 33p 1g 0.784 35 A A.A35 33p 1a 0.517 36 A A.A36 33p 1a 0.670 37 g A.YYG37 33p 1a 0.625 38 A A.A38 33p 1a 0.903 39 P A.PSU39 33p 1a 0.680 40 c A.5MC40 33p 1a 0.942 41 U A.U41 33p 1a 0.945 42 G A.G42 33p 1a 0.630 43 G A.G43 33p 1a 0.882 44 A A.A44 33p 1a 0.837 45 G A.G45 33p 1a 0.749 46 g A.7MG46 32p 1[ 0.849 47 U A.U47 22p 4p 0.589 48 C A.C48 22t 2u 0.283 49 c A.5MC49 23p 6d 0.520 50 U A.U50 33p 1a 0.656 51 G A.G51 33p 1a 0.981 52 U A.U52 33p 1a 0.945 53 G A.G53 33p 1a 0.896 54 t A.5MU54 33p 1a 0.720 55 P A.PSU55 33p 1a 0.586 56 C A.C56 33p 1g 0.894 57 G A.G57 33p 1a 0.837 58 a A.1MA58 32p 1[ 0.332 59 U A.U59 23p 4d 0.411 60 C A.C60 32p 1b 0.662 61 C A.C61 23p 2a 0.553 62 A A.A62 33p 1a 0.895 63 C A.C63 33p 1a 0.964 64 A A.A64 33p 1a 0.791 65 G A.G65 33p 1a 0.586 66 A A.A66 33p 1a 0.940 67 A A.A67 33p 1a 0.941 68 U A.U68 33p 1a 0.891 69 U A.U69 33p 1a 0.951 70 C A.C70 33p 1a 0.809 71 G A.G71 33p 1a 0.761 72 C A.C72 33p 1a 0.832 73 A A.A73 33p 1a 0.965 74 C A.C74 33p 1a 0.886 75 C A.C75 33p 1a 0.639 76 A A.A76 32t !! 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 nts=76 G1aC1aG1aG1aA1aU1bU2aU1[A2gg1aC1aU1cC!!A1aG!!u!!u5pG4bG2aG!!A1fG1aA1aG1aC1ag1aC1aC1aA1aG1aA1ac1aU1gg1aA1aA1ag1aA1aP1ac1aU1aG1aG1aA1aG1[g4pU2uC6dc1aU1aG1aU1aG1at1aP1gC1aG1[a4dU1bC2aC1aA1aC1aA1aG1aA1aA1aU1aU1aC1aG1aC1aA1aC1aC!!A