Output of DNA/RNA backbone conformational parameters ****************************************************************************************** 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. d22: distance between the midpoints of the C5-C6 bonds in adjacent pyrimidine bases. d64: distance between the C5 atom of the 5' pyrimidine and either the N4 (for cytosine) or O4 (for thymine/uracil) atom of the adjacent 3' pyrimidine. [Ref: Gordan et al. (2025): "High-throughput characterization of transcription factors that modulate UV damage formation and repair at single-nucleotide resolution." (https://doi.org/10.21203/rs.3.rs-8197218/v1)] nt alpha beta gamma delta epsilon zeta e-z chi phase-angle sugar-type ssZp Dp splay d22 d64 1 U ///A/2647 --- --- -76.0 70.7 -129.8 -73.1 -57(--) -179.6(anti) 9.9(C3'-endo) ~C3'-endo 4.88 4.90 33.43 --- --- 2 G ///A/2648 -33.9 161.9 32.0 91.9 -144.8 -73.1 -72(BI) -167.8(anti) 5.3(C3'-endo) ~C3'-endo 4.47 4.56 22.83 --- --- 3 C ///A/2649 -58.2 167.1 47.6 84.1 -146.6 -77.1 -69(BI) -160.5(anti) 12.9(C3'-endo) ~C3'-endo 4.41 4.66 23.50 3.85 3.89 4 U ///A/2650 -64.2 164.2 60.3 79.8 -154.5 -73.1 -81(BI) -167.2(anti) 21.3(C3'-endo) ~C3'-endo 4.40 4.55 21.63 4.50 4.36 5 C ///A/2651 -62.3 173.8 46.2 84.3 -154.6 -71.3 -83(BI) -159.0(anti) 12.9(C3'-endo) ~C3'-endo 4.29 4.58 24.06 4.15 4.43 6 C ///A/2652 -67.5 175.2 58.1 78.0 -154.0 -67.0 -87(BI) -158.8(anti) 15.5(C3'-endo) ~C3'-endo 4.28 4.53 22.84 3.99 3.83 7 U ///A/2653 -61.8 167.4 55.9 82.4 -149.4 55.3 155(--) -151.0(anti) 15.7(C3'-endo) ~C3'-endo 4.00 4.62 22.57 --- --- 8 A ///A/2654 165.2 133.8 56.7 149.4 -98.3 161.4 100(BII) -145.3(anti) 151.0(C2'-endo) ~C2'-endo 0.91 0.92 43.08 --- --- 9 G ///A/2655 -96.2 91.7 179.3 149.3 -167.2 141.4 51(--) -93.5(anti) 151.5(C2'-endo) ~C2'-endo 2.15 2.14 54.21 --- --- 10 U ///A/2656 -72.5 157.8 37.9 91.6 -141.0 -65.6 -75(BI) -173.9(anti) 0.4(C3'-endo) ~C3'-endo 4.35 4.42 27.39 --- --- 11 A ///A/2657 -68.7 174.5 50.2 83.7 -145.1 -61.1 -84(BI) -171.1(anti) 26.5(C3'-endo) ~C3'-endo 4.49 4.52 32.91 --- --- 12 C ///A/2658 -72.0 172.7 51.5 84.0 -151.8 -62.9 -89(BI) -165.5(anti) 17.9(C3'-endo) ~C3'-endo 4.49 4.70 26.73 --- --- 13 G ///A/2659 -71.8 -179.4 49.4 80.9 -135.7 -64.4 -71(BI) -172.9(anti) 29.4(C3'-endo) ~C3'-endo 4.76 4.95 95.33 --- --- 14 U ///A/2660 166.2 136.3 51.8 89.0 -124.3 -88.1 -36(--) -157.3(anti) 32.3(C3'-endo) ~C3'-endo 3.51 3.95 27.58 --- --- 15 A ///A/2661 -63.6 139.7 65.6 89.3 -148.7 -74.8 -74(BI) -130.9(anti) 8.0(C3'-endo) ~C3'-endo 3.09 4.24 24.88 --- --- 16 A ///A/2662 -65.4 164.6 51.4 89.5 -135.4 -65.8 -70(BI) -130.9(anti) 18.7(C3'-endo) ~C3'-endo 2.71 4.68 44.81 --- --- 17 G ///A/2663 145.7 -139.8 -168.8 82.7 -146.0 -59.6 -86(BI) -170.9(anti) 27.7(C3'-endo) ~C3'-endo 4.71 4.82 35.71 --- --- 18 G ///A/2664 -61.4 173.1 52.3 77.6 -159.1 -80.8 -78(BI) -162.8(anti) 9.7(C3'-endo) ~C3'-endo 4.48 4.63 74.59 --- --- 19 A ///A/2665 -100.9 72.3 170.4 85.5 -153.2 -77.2 -76(BI) -179.1(anti) 4.5(C3'-endo) ~C3'-endo 4.74 4.75 25.77 --- --- 20 C ///A/2666 -58.9 171.7 58.5 80.6 -139.4 -61.2 -78(BI) -165.3(anti) 16.0(C3'-endo) ~C3'-endo 4.57 4.74 32.11 3.54 3.80 21 C ///A/2667 -61.9 166.8 51.2 82.1 -138.5 -56.7 -82(BI) -165.7(anti) 16.5(C3'-endo) ~C3'-endo 4.53 4.79 37.34 --- --- 22 G ///A/2668 -65.3 169.3 57.9 74.7 -148.6 -79.7 -69(BI) -167.2(anti) 7.3(C3'-endo) ~C3'-endo 4.59 4.73 24.02 --- --- 23 G ///A/2669 -47.6 158.2 54.6 77.5 -153.5 -66.0 -87(BI) -168.5(anti) 13.0(C3'-endo) ~C3'-endo 4.59 4.65 24.40 --- --- 24 A ///A/2670 -66.2 171.4 58.1 80.7 -148.9 -83.1 -66(BI) -165.5(anti) 12.6(C3'-endo) ~C3'-endo 4.44 4.57 22.81 --- --- 25 G ///A/2671 -63.3 167.5 56.5 82.0 -151.2 -63.9 -87(BI) -163.7(anti) 9.2(C3'-endo) ~C3'-endo 4.47 4.62 22.80 --- --- 26 U ///A/2672 -60.3 168.4 54.7 85.1 -154.5 -92.4 -62(BI) -152.8(anti) 19.2(C3'-endo) ~C3'-endo 4.00 4.37 27.53 --- --- 27 G ///A/2673 -47.5 -171.1 14.6 88.1 --- --- --- -141.9(anti) 357.2(C2'-exo) ~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 U ///A/2647 --- --- --- --- --- --- 2 G ///A/2648 172.1 -133.3 -163.5 -131.2 -97.6 -93.1 3 C ///A/2649 162.7 -140.1 -178.0 -138.9 -120.5 -104.8 4 U ///A/2650 167.0 -148.3 -174.5 -150.1 -122.6 -127.9 5 C ///A/2651 165.4 -147.2 177.6 -145.6 -144.3 -123.9 6 C ///A/2652 171.3 -142.0 -176.3 -139.3 -142.0 -91.5 7 U ///A/2653 172.2 -18.3 -170.0 -63.3 -107.9 -99.1 8 A ///A/2654 46.3 172.0 120.5 135.6 126.4 150.3 9 G ///A/2655 -44.2 24.9 -82.3 59.0 -98.6 91.3 10 U ///A/2656 170.9 -121.7 163.1 -122.7 161.9 -94.8 11 A ///A/2657 162.1 -127.4 -177.7 -123.2 -126.9 -67.0 12 C ///A/2658 159.4 -135.3 -176.0 -135.4 -98.2 -106.5 13 G ///A/2659 167.6 -117.7 -179.4 -160.6 -134.1 156.9 14 U ///A/2660 15.1 -126.1 43.5 -124.9 21.0 -65.2 15 A ///A/2661 160.4 -132.0 -169.4 -138.7 -95.8 -93.3 16 A ///A/2662 167.0 -83.0 -174.8 -81.7 -117.0 -64.2 17 G ///A/2663 172.6 -154.0 -148.2 -148.6 -101.2 -97.0 18 G ///A/2664 166.2 166.9 -168.9 147.4 -95.5 137.9 19 A ///A/2665 -155.6 141.6 175.0 164.3 154.7 -178.6 20 C ///A/2666 -178.4 -125.3 -169.0 -123.0 -153.9 -74.8 21 C ///A/2667 164.6 -120.7 -172.9 -116.0 -101.6 -71.6 22 G ///A/2668 164.9 -150.0 -168.4 -145.8 -97.4 -120.2 23 G ///A/2669 171.3 -139.8 -172.8 -139.5 -131.7 -111.7 24 A ///A/2670 170.6 -153.2 -173.8 -152.7 -127.2 -132.0 25 G ///A/2671 170.4 -134.4 -180.0 -133.1 -147.1 -94.7 26 U ///A/2672 172.2 -167.9 -166.6 -170.6 -110.6 -171.6 27 G ///A/2673 --- --- --- --- --- --- ****************************************************************************************** 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 U ///A/2647 7.5 -34.5 46.2 -43.8 23.1 46.9 9.9 C3'-endo 2 G ///A/2648 9.5 -31.5 39.4 -35.5 16.8 39.6 5.3 C3'-endo 3 C ///A/2649 4.0 -28.3 39.9 -38.4 21.9 40.9 12.9 C3'-endo 4 U ///A/2650 -2.4 -25.5 41.9 -44.0 29.4 44.9 21.3 C3'-endo 5 C ///A/2651 4.8 -32.5 45.7 -44.6 25.0 46.9 12.9 C3'-endo 6 C ///A/2652 2.9 -29.7 43.8 -44.0 25.9 45.4 15.5 C3'-endo 7 U ///A/2653 1.6 -28.2 42.3 -41.3 25.2 44.0 15.7 C3'-endo 8 A ///A/2654 -33.2 44.3 -38.7 20.1 8.5 44.3 151.0 C2'-endo 9 G ///A/2655 -37.3 50.1 -43.9 22.9 8.9 50.0 151.5 C2'-endo 10 U ///A/2656 12.7 -32.9 39.6 -33.2 13.3 39.6 0.4 C3'-endo 11 A ///A/2657 -6.4 -21.7 39.9 -44.5 32.0 44.6 26.5 C3'-endo 12 C ///A/2658 -0.0 -28.5 44.6 -44.4 28.4 46.9 17.9 C3'-endo 13 G ///A/2659 -9.4 -20.6 40.1 -45.3 35.5 46.1 29.4 C3'-endo 14 U ///A/2660 -8.9 -14.6 31.3 -37.4 29.0 37.0 32.3 C3'-endo 15 A ///A/2661 7.2 -28.7 38.3 -35.0 17.5 38.6 8.0 C3'-endo 16 A ///A/2662 0.0 -21.1 32.9 -33.9 21.4 34.8 18.7 C3'-endo 17 G ///A/2663 -7.9 -22.7 42.3 -47.3 35.7 47.8 27.7 C3'-endo 18 G ///A/2664 7.4 -33.6 45.9 -43.1 22.1 46.5 9.7 C3'-endo 19 A ///A/2665 11.2 -35.6 45.2 -39.6 18.1 45.4 4.5 C3'-endo 20 C ///A/2666 2.0 -27.6 41.2 -41.2 24.6 42.8 16.0 C3'-endo 21 C ///A/2667 1.9 -30.7 45.7 -46.0 28.2 47.6 16.5 C3'-endo 22 G ///A/2668 9.1 -34.4 44.4 -40.9 20.0 44.7 7.3 C3'-endo 23 G ///A/2669 4.5 -31.3 45.1 -43.5 24.4 46.3 13.0 C3'-endo 24 A ///A/2670 5.3 -32.9 46.7 -45.3 25.1 47.9 12.6 C3'-endo 25 G ///A/2671 7.6 -33.2 44.6 -41.4 21.7 45.2 9.2 C3'-endo 26 U ///A/2672 -0.3 -23.0 35.9 -37.6 23.6 38.0 19.2 C3'-endo 27 G ///A/2673 17.1 -39.6 45.4 -37.1 12.9 45.4 357.2 C2'-exo ****************************************************************************************** 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 U ///A/2647 inc __ 0 2 G ///A/2648 33p 1a 0.052 3 C ///A/2649 33p 1a 0.665 4 U ///A/2650 33p 1a 0.875 5 C ///A/2651 33p 1a 0.871 6 C ///A/2652 33p 1a 0.919 7 U ///A/2653 33p 1a 0.929 8 A ///A/2654 32p 5z 0.849 9 G ///A/2655 22t 4s 0.730 10 U ///A/2656 23p #a 0.842 11 A ///A/2657 33p 1a 0.693 12 C ///A/2658 33p 1a 0.884 13 G ///A/2659 33p 1a 0.894 14 U ///A/2660 33p 1g 0.736 15 A ///A/2661 33p 1L 0.688 16 A ///A/2662 33p 1a 0.692 17 G ///A/2663 33t 1c 0.321 18 G ///A/2664 33p 1a 0.878 19 A ///A/2665 33t 1e 0.875 20 C ///A/2666 33p 1a 0.891 21 C ///A/2667 33p 1a 0.887 22 G ///A/2668 33p 1a 0.756 23 G ///A/2669 33p 1a 0.625 24 A ///A/2670 33p 1a 0.914 25 G ///A/2671 33p 1a 0.878 26 U ///A/2672 33p 1a 0.912 27 G ///A/2673 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 m1-A RNA nts=27 U1aG1aC1aU1aC1aC1aU5zA4sG#aU1aA1aC1aG1gU1LA1aA1cG1aG1eA1aC1aC1aG1aG1aA1aG1aU!!G