ID code: 2L8U *********************************** ************** ****** CURVES 5.3 R.L. 1998 ***** * 17 May 24 * *********************************** ************** FILE : duplex.pdb lis : dna : axin : axout: daf : pdb : acc : 0.000 wid : 0.750 maxn : 500 ior : 0 ibond: 0 splin: 3 break: -1 NLEVE: 0 NBAC : 7 ends : F supp : T COMB : T dinu : F mini : T rest : F LINE : F zaxe : F FIT : T test : F GRV : F old : T axonl: F Least squares fitting of standard bases ... Str Pos Base Rms (ang) 1 : 1) CA 1 0.036 1 : 2) CA 2 0.022 1 : 3) GA 3 0.029 1 : 4) CA 4 0.031 1 : 5) UA 5 0.036 1 : 6) GA 6 0.032 1 : 7) CA 7 0.040 1 : 8) GA 8 0.025 1 : 9) GA 9 0.038 2 : 1) GB 18 0.032 2 : 2) GB 17 0.026 2 : 3) CB 16 0.037 2 : 4) GB 15 0.058 2 : 5) UB 14 0.055 2 : 6) CB 13 0.033 2 : 7) GB 12 0.038 2 : 8) CB 11 0.042 2 : 9) CB 10 0.030 Strand= 2 Nucleo= 18 Atoms = 418 Units = 18 Input 1) Xdisp= 0.00 Ydisp= 0.00 Inclin= 0.00 Tip= 0.00 Combined strands have 9 levels ... Strand 1 has 9 bases (5'-3'): CCGCUGCGG Strand 2 has 9 bases (3'-5'): GGCGUCGCC FIRST SUM= 142.869 CPTS: 8.792 22.243 10.745 101.089 MINIMISATION: ACC = 0.100E-05 MAXN= 500 NVAR= 36 STEP 1 SUM= 142.869 DEL= 0.000E+00 STEP 2 SUM= 118.415 DEL= -0.245E+02 STEP 3 SUM= 98.849 DEL= -0.196E+02 STEP 4 SUM= 73.448 DEL= -0.254E+02 STEP 5 SUM= 82.109 DEL= 0.866E+01 STEP 6 SUM= 62.599 DEL= -0.195E+02 STEP 7 SUM= 55.253 DEL= -0.735E+01 STEP 8 SUM= 60.747 DEL= 0.549E+01 STEP 9 SUM= 52.579 DEL= -0.817E+01 STEP 10 SUM= 50.839 DEL= -0.174E+01 STEP 11 SUM= 47.840 DEL= -0.300E+01 STEP 12 SUM= 44.636 DEL= -0.320E+01 STEP 13 SUM= 48.458 DEL= 0.382E+01 STEP 14 SUM= 42.263 DEL= -0.619E+01 STEP 15 SUM= 52.304 DEL= 0.100E+02 STEP 16 SUM= 41.882 DEL= -0.104E+02 STEP 17 SUM= 41.179 DEL= -0.703E+00 STEP 18 SUM= 39.418 DEL= -0.176E+01 STEP 19 SUM= 45.611 DEL= 0.619E+01 STEP 20 SUM= 38.870 DEL= -0.674E+01 STEP 21 SUM= 39.211 DEL= 0.340E+00 STEP 22 SUM= 38.661 DEL= -0.549E+00 STEP 23 SUM= 38.377 DEL= -0.285E+00 STEP 24 SUM= 38.194 DEL= -0.183E+00 STEP 25 SUM= 37.931 DEL= -0.262E+00 STEP 26 SUM= 37.651 DEL= -0.281E+00 STEP 27 SUM= 37.147 DEL= -0.503E+00 STEP 28 SUM= 36.315 DEL= -0.832E+00 STEP 29 SUM= 41.214 DEL= 0.490E+01 STEP 30 SUM= 36.078 DEL= -0.514E+01 STEP 31 SUM= 35.720 DEL= -0.358E+00 STEP 32 SUM= 35.248 DEL= -0.472E+00 STEP 33 SUM= 35.078 DEL= -0.170E+00 STEP 34 SUM= 34.882 DEL= -0.196E+00 STEP 35 SUM= 34.868 DEL= -0.143E-01 STEP 36 SUM= 34.801 DEL= -0.672E-01 STEP 37 SUM= 34.826 DEL= 0.258E-01 STEP 38 SUM= 34.765 DEL= -0.609E-01 STEP 39 SUM= 34.735 DEL= -0.300E-01 STEP 40 SUM= 34.725 DEL= -0.109E-01 STEP 41 SUM= 34.719 DEL= -0.556E-02 STEP 42 SUM= 34.717 DEL= -0.161E-02 STEP 43 SUM= 34.717 DEL= -0.503E-03 STEP 44 SUM= 34.717 DEL= -0.130E-03 STEP 45 SUM= 34.717 DEL= -0.218E-04 STEP 46 SUM= 34.717 DEL= -0.652E-05 STEP 47 SUM= 34.717 DEL= -0.448E-05 STEP 48 SUM= 34.717 DEL= -0.267E-05 STEP 49 SUM= 34.717 DEL= -0.321E-05 STEP 50 SUM= 34.717 DEL= -0.158E-05 STEP 51 SUM= 34.717 DEL= -0.108E-05 STEP 52 SUM= 34.717 DEL= -0.971E-06 STEP 53 SUM= 34.717 DEL= -0.618E-06 STEP 54 SUM= 34.717 DEL= -0.132E-06 STEP 55 SUM= 34.717 DEL= -0.126E-07 STEP 56 SUM= 34.717 DEL= -0.394E-09 STEP 57 SUM= 34.717 DEL= -0.109E-10 STEP 58 SUM= 34.717 DEL= -0.490E-12 STEP 59 SUM= 34.717 DEL= 0.000E+00 STEP 60 SUM= 34.717 DEL= -0.711E-14 STEP 61 SUM= 34.717 DEL= 0.000E+00 FINAL SUM= 34.717 CPTS: 4.569 18.365 6.586 5.197 GRA=-0.61E-09 0.15E-09 0.76E-11 0.62E-10 0.89E-09 0.61E-09 0.53E-10 0.23E-09 GRA=-0.64E-09-0.92E-09 0.84E-10-0.84E-10 0.10E-08 0.27E-09-0.12E-09-0.14E-09 GRA= 0.48E-09-0.64E-09-0.20E-09-0.31E-10 0.18E-09 0.53E-09-0.78E-10-0.89E-10 GRA=-0.24E-09 0.46E-09 0.16E-09 0.55E-10-0.43E-09-0.47E-09 0.10E-09-0.10E-09 GRA= 0.22E-09-0.55E-09-0.39E-10 0.54E-10 ---------------------------- |A| Global axis parameters | ---------------------------- 1) U: -0.318 0.850 0.419 P: 6.308 -17.699 5.604 D: 1.712 2) U: -0.284 0.919 0.273 P: 5.430 -15.053 6.778 D: 2.471 3) U: -0.391 0.909 0.143 P: 4.723 -12.025 7.809 D: 5.816 4) U: -0.359 0.932 -0.044 P: 3.716 -8.791 7.276 D: 7.010 5) U: -0.489 0.848 -0.205 P: 2.557 -5.443 7.100 D: 12.443 6) U: -0.648 0.662 -0.376 P: 1.464 -3.720 5.469 D: 2.382 7) U: -0.781 0.584 -0.222 P: -0.370 -1.573 4.732 D: 1.391 8) U: -0.866 0.479 -0.144 P: -2.908 -0.406 4.425 D: 1.490 9) U: -0.916 0.401 -0.011 P: -5.771 0.591 4.318 --------------------------------- |B| Global Base-Axis Parameters | --------------------------------- 1st strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) CA 1 -3.49 3.08 17.74 -29.45 3 0 2) CA 2 -3.98 2.55 7.68 -16.72 3 -9 3) GA 3 -4.14 2.01 4.90 -10.83 1 13 4) CA 4 -2.81 1.96 -3.03 -21.56 3 -7 5) UA 5 -2.07 0.99 -12.72 -12.25 4 -25 6) GA 6 -2.98 1.05 -5.62 -14.07 1 15 7) CA 7 -3.56 0.72 -5.11 -6.88 3 -13 8) GA 8 -3.18 0.51 -2.31 -10.94 1 9 9) GA 9 -3.10 0.20 -3.96 -12.27 1 0 2nd strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) GB 18 -4.49 -2.20 0.11 6.44 1 0 2) GB 17 -4.25 -2.28 -3.27 9.46 1 9 3) CB 16 -4.00 -1.64 -9.72 17.53 3 -13 4) GB 15 -3.35 -1.76 1.07 4.21 1 15 5) UB 14 -4.26 -3.19 6.89 6.07 4 -25 6) CB 13 -2.90 -0.82 8.07 -4.92 3 -7 7) GB 12 -3.34 -0.82 6.11 3.21 1 13 8) CB 11 -3.16 -0.40 7.02 1.26 3 -9 9) CB 10 -2.80 0.04 9.65 -6.75 3 0 -------------------------------------- |C| Global Base pair-Axis Parameters | -------------------------------------- Strand 1 with strand 2 ... Duplex Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) C 1-G 18 -3.99 2.64 8.93 -17.95 3 0 2) C 2-G 17 -4.12 2.41 2.20 -13.09 3 -9 3) G 3-C 16 -4.07 1.83 -2.41 -14.18 1 13 4) C 4-G 15 -3.08 1.86 -0.98 -12.88 3 -7 5) U 5-U 14 -3.16 2.09 -2.91 -9.16 4 -25 6) G 6-C 13 -2.94 0.93 1.22 -4.57 1 15 7) C 7-G 12 -3.45 0.77 0.50 -5.05 3 -13 8) G 8-C 11 -3.17 0.46 2.35 -6.10 1 9 9) G 9-C 10 -2.95 0.08 2.85 -2.76 1 0 Average: -3.44 1.45 1.31 -9.53 --------------------------------- |D| Global Base-Base Parameters | --------------------------------- Strand 1 with strand 2 ... Duplex Shear Stretch Stagger Buckle Propel Opening Bc Tc (Sx) (Sy) (Sz) (kappa) (omega) (sigma) 1) C 1-G 18 1.00 0.87 -0.60 17.63 -23.01 9.92 3 0 2) C 2-G 17 0.27 0.27 -0.19 10.95 -7.26 2.05 3 -9 3) G 3-C 16 -0.13 0.37 0.43 14.62 6.70 3.36 1 13 4) C 4-G 15 0.54 0.20 -0.76 -4.09 -17.35 4.48 3 -7 5) U 5-U 14 2.19 -2.20 0.19 -19.60 -6.19 -25.48 4 -25 6) G 6-C 13 -0.07 0.23 -0.52 -13.69 -18.99 2.93 1 15 7) C 7-G 12 -0.22 -0.10 0.37 -11.22 -3.66 -4.08 3 -13 8) G 8-C 11 -0.02 0.11 -0.19 -9.34 -9.68 -0.20 1 9 9) G 9-C 10 -0.31 0.24 -0.49 -13.61 -19.01 2.57 1 0 Average: 0.36 -0.00 -0.20 -3.15 -10.94 -0.50 ---------------------------------- |E| Global Inter-Base Parameters | ---------------------------------- 1st strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C 1/C 2 -0.54 -0.66 3.24 -16.55 19.65 25.71 -1 3) C 2/G 3 -0.23 -1.06 3.55 -12.02 8.65 25.35 8 4) G 3/C 4 2.05 -0.29 2.77 -6.45 0.13 39.34 5 5) C 4/U 5 0.29 -1.14 4.01 -11.39 22.04 25.09 -3 6) U 5/G 6 -0.59 -0.86 2.10 9.53 15.19 19.18 -9 7) G 6/C 7 -1.01 -0.23 3.35 -9.62 14.59 30.09 5 8) C 7/G 8 0.83 -0.23 2.50 2.61 4.89 34.89 8 9) G 8/G 9 0.36 -0.59 2.86 -0.48 7.85 32.57 1 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 18/G 17 0.19 0.05 2.83 -9.87 -3.90 33.58 1 3) G 17/C 16 0.18 1.16 2.94 -15.69 5.30 24.04 8 4) C 16/G 15 1.37 0.13 3.95 12.27 -24.17 38.21 5 5) G 15/U 14 -1.36 -1.27 3.07 4.12 -10.87 55.05 -9 6) U 14/C 13 1.67 3.29 2.80 3.61 -27.99 -9.24 -3 7) C 13/G 12 -0.86 -0.10 2.46 -12.09 0.73 37.11 5 8) G 12/C 11 0.62 0.44 3.06 0.72 -10.90 31.01 8 9) C 11/C 10 0.65 0.72 3.17 3.79 -17.18 29.79 -1 --------------------------------------- |F| Global Inter-Base pair Parameters | --------------------------------------- Strand 1 with strand 2 ... Duplex Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C 1/C 2 -0.17 -0.36 3.03 -13.21 11.77 29.65 -1 3) C 2/G 3 -0.03 -1.11 3.24 -13.86 1.68 24.69 8 4) G 3/C 4 1.71 -0.21 3.36 2.91 12.15 38.77 5 5) C 4/U 5 -0.53 0.07 3.54 -3.64 16.45 40.07 -3 6) U 5/G 6 0.54 -2.08 2.45 6.57 21.59 4.97 -9 7) G 6/C 7 -0.94 -0.07 2.90 -10.86 6.93 33.60 5 8) C 7/G 8 0.73 -0.33 2.78 1.66 7.89 32.95 8 9) G 8/G 9 0.51 -0.65 3.02 1.65 12.52 31.18 1 Average: 0.23 -0.59 3.04 -3.60 11.37 29.48 --------------------------------- |G| Local Inter-Base Parameters | --------------------------------- 1st strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C 1/C 2 -0.11 -1.66 4.28 -5.74 24.99 28.54 -1 3) C 2/G 3 -0.31 -2.48 3.85 -5.72 11.42 27.11 8 4) G 3/C 4 1.58 -2.49 3.24 5.29 1.33 39.05 5 5) C 4/U 5 0.88 -2.87 3.99 -4.17 17.99 29.33 -3 6) U 5/G 6 -0.27 -2.08 2.69 12.44 12.05 19.37 -9 7) G 6/C 7 -0.82 -2.30 3.59 -4.03 11.48 31.97 5 8) C 7/G 8 0.85 -2.38 2.79 7.67 2.82 34.59 8 9) G 8/G 9 0.76 -2.49 3.14 6.24 6.11 32.40 1 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 18/G 17 -0.65 -2.61 3.12 -5.35 2.79 34.81 1 3) G 17/C 16 -0.05 -3.12 2.60 -9.60 -7.94 27.30 8 4) C 16/G 15 0.85 -3.01 4.37 18.87 20.25 36.94 5 5) G 15/U 14 -3.26 -2.09 4.25 9.38 14.78 53.51 -9 6) U 14/C 13 1.94 -2.16 4.42 5.36 26.24 -11.60 -3 7) C 13/G 12 -1.37 -1.47 2.95 -12.45 4.19 35.67 5 8) G 12/C 11 0.42 -1.78 3.76 2.03 14.28 29.83 8 9) C 11/C 10 0.37 -1.77 3.96 2.34 21.12 28.64 -1 -------------------------------------- |H| Local Inter-Base pair Parameters | -------------------------------------- Strand 1 with strand 2 ... Duplex Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C 1/C 2 -0.41 -2.18 3.71 -5.75 13.88 33.05 -1 3) C 2/G 3 -0.17 -2.85 3.23 -7.58 1.73 28.07 8 4) G 3/C 4 1.26 -2.69 3.81 12.22 10.79 37.24 5 5) C 4/U 5 -1.22 -2.63 4.32 2.67 16.97 41.24 -3 6) U 5/G 6 0.88 -2.13 3.34 8.36 18.89 5.82 -9 7) G 6/C 7 -1.14 -1.83 3.30 -8.29 8.00 33.33 5 8) C 7/G 8 0.64 -2.11 3.29 4.80 8.52 32.62 8 9) G 8/G 9 0.59 -2.16 3.56 4.48 13.64 31.32 1 Average: 0.05 -2.32 3.57 1.36 11.55 30.34 --------------------------- |I| Global Axis Curvature | --------------------------- Duplex Ax Ay Ainc Atip Adis Angle Path Dc 2) C 1/C 2 -0.04 -0.13 -6.48 6.92 0.14 9.48 3.02 -1 3) C 2/G 3 -0.08 -0.53 -9.24 2.77 0.53 9.65 3.28 8 4) G 3/C 4 0.72 -0.24 1.48 10.85 0.76 10.95 3.43 5 5) C 4/U 5 -0.45 -0.16 -1.70 12.73 0.48 12.84 3.55 -3 6) U 5/G 6 0.32 -0.92 2.43 17.00 0.98 17.17 2.61 -9 7) G 6/C 7 -0.43 0.09 -10.13 7.40 0.44 12.54 2.92 5 8) C 7/G 8 0.45 -0.02 -0.19 8.95 0.45 8.95 2.81 8 9) G 8/G 9 0.29 -0.27 1.16 9.18 0.39 9.25 3.03 1 Overall axis bend ... UU= 51.13 PP= 56.78 Duplex Offset L.Dir ... wrt end-to-end vector 1) C 1 0.00 0.00 2) C 2 1.51 77.15 3) G 3 3.11 57.79 4) C 4 3.51 33.67 5) U 5 4.25 14.01 6) G 6 3.73 12.11 7) C 7 3.32 -11.19 8) G 8 1.84 -43.96 9) G 9 0.00 0.00 Path length= 24.65 End-to-end= 21.96 Shortening= 10.94 % ------------------------- |J| Backbone Parameters | ------------------------- 1st strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)CA 1 3.67 19.71 60.65 41.22 C4'-exo 106.5 104.2 102.0 2)CA 2 -30.83 38.27 3.71 39.39 C3'-endo 106.3 101.3 101.1 3)GA 3 -29.37 39.49 11.43 41.95 C3'-endo 107.5 101.3 99.1 4)CA 4 -25.88 36.87 14.82 39.38 C3'-endo 106.4 103.3 99.2 5)UA 5 -2.73 18.41 50.67 30.65 C4'-exo 107.2 105.7 100.6 6)GA 6 -12.97 31.21 36.81 40.24 C4'-exo 107.4 103.5 100.1 7)CA 7 -33.44 28.38 329.70 33.60 C2'-exo 104.5 103.7 102.6 8)GA 8 -25.74 39.99 20.24 44.41 C3'-endo 107.9 100.3 98.8 9)GA 9 -22.98 35.23 19.03 38.60 C3'-endo 107.3 102.2 100.3 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)CA 1 -139.69 -168.22 78.68 -169.30 -78.47 131.51 -179.54 2)CA 2 -158.76 179.70 81.06 -156.56 -66.39 -77.44 175.60 3)GA 3 -169.58 65.88 76.61 -152.63 -60.03 -76.15 178.95 4)CA 4 -161.13 62.68 79.13 -155.38 -61.77 -71.51 178.48 5)UA 5 -158.94 70.34 84.47 -158.06 -72.39 120.32 -165.09 6)GA 6 -157.63 -171.74 78.71 -179.34 -81.70 161.12 177.06 7)CA 7 -174.81 174.89 99.93 -131.85 -60.10 -76.05 169.76 8)GA 8 -164.54 56.81 71.30 -160.31 -64.94 -71.46 176.83 9)GA 9 -160.57 61.25 76.57 ...... ...... ...... ...... 2nd strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)GB 18 -24.46 35.19 15.14 37.76 C3'-endo 107.8 102.0 100.7 2)GB 17 -34.34 38.90 356.89 40.21 C2'-exo 105.9 101.0 100.5 3)CB 16 -28.63 29.17 348.13 30.78 C2'-exo 106.0 104.3 100.9 4)GB 15 -23.24 34.16 16.72 36.88 C3'-endo 107.3 103.0 100.6 5)UB 14 5.97 15.00 65.20 36.64 C4'-exo 105.4 104.9 103.3 6)CB 13 -21.37 30.78 15.70 33.08 C3'-endo 107.5 104.1 100.5 7)GB 12 -27.90 36.17 8.86 38.09 C3'-endo 107.1 102.4 99.6 8)CB 11 -29.31 38.58 9.55 40.51 C3'-endo 106.7 102.1 99.1 9)CB 10 -23.53 34.69 17.13 37.68 C3'-endo 108.0 102.6 100.2 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)GB 18 -161.15 58.64 79.83 ...... ...... ...... ...... 2)GB 17 -173.26 -165.61 84.53 -149.03 -61.89 -74.67 179.76 3)CB 16 -172.51 58.81 90.71 -164.41 -64.13 130.89 -176.03 4)GB 15 -170.91 -167.45 83.28 -159.99 -78.99 -76.38 -166.81 5)UB 14 -177.12 179.39 87.07 -143.14 -58.10 108.85 -172.83 6)CB 13 -149.24 59.79 88.71 -104.29 -54.08 -91.32 60.77 7)GB 12 -155.93 62.77 81.38 -155.45 -59.93 -75.55 174.66 8)CB 11 -151.80 60.37 78.31 -163.21 -67.51 -80.75 -179.58 9)CB 10 -147.71 54.06 78.36 -161.91 -68.36 -81.50 -179.42