ID code: 1MWL, DR0008 *********************************** ************** ****** 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 8 0.015 1 : 2) AA 9 0.012 1 : 3) CA 10 0.029 1 : 4) CA 11 0.017 1 : 5) GA 12 0.019 1 : 6) GA 13 0.020 1 : 7) UA 14 0.027 1 : 8) GA 15 0.024 2 : 1) GB 37 0.019 2 : 2) UB 36 0.013 2 : 3) GB 35 0.023 2 : 4) GB 34 0.026 2 : 5) CB 33 0.013 2 : 6) CB 32 0.016 2 : 7) AB 31 0.021 2 : 8) CB 30 0.012 Strand= 2 Nucleo= 16 Atoms = 342 Units = 16 Input 1) Xdisp= 0.00 Ydisp= 0.00 Inclin= 0.00 Tip= 0.00 Combined strands have 8 levels ... Strand 1 has 8 bases (5'-3'): CACCGGUG Strand 2 has 8 bases (3'-5'): GUGGCCAC FIRST SUM= 75.179 CPTS: 1.318 0.783 4.314 68.763 MINIMISATION: ACC = 0.100E-05 MAXN= 500 NVAR= 32 STEP 1 SUM= 75.179 DEL= 0.000E+00 STEP 2 SUM= 60.983 DEL= -0.142E+02 STEP 3 SUM= 40.508 DEL= -0.205E+02 STEP 4 SUM= 47.384 DEL= 0.688E+01 STEP 5 SUM= 31.748 DEL= -0.156E+02 STEP 6 SUM= 25.822 DEL= -0.593E+01 STEP 7 SUM= 21.184 DEL= -0.464E+01 STEP 8 SUM= 21.880 DEL= 0.696E+00 STEP 9 SUM= 19.026 DEL= -0.285E+01 STEP 10 SUM= 16.844 DEL= -0.218E+01 STEP 11 SUM= 13.294 DEL= -0.355E+01 STEP 12 SUM= 71.250 DEL= 0.580E+02 STEP 13 SUM= 13.234 DEL= -0.580E+02 STEP 14 SUM= 13.100 DEL= -0.134E+00 STEP 15 SUM= 12.722 DEL= -0.378E+00 STEP 16 SUM= 10.184 DEL= -0.254E+01 STEP 17 SUM= 14.702 DEL= 0.452E+01 STEP 18 SUM= 9.360 DEL= -0.534E+01 STEP 19 SUM= 9.914 DEL= 0.554E+00 STEP 20 SUM= 9.052 DEL= -0.862E+00 STEP 21 SUM= 8.540 DEL= -0.511E+00 STEP 22 SUM= 10.872 DEL= 0.233E+01 STEP 23 SUM= 8.462 DEL= -0.241E+01 STEP 24 SUM= 8.324 DEL= -0.138E+00 STEP 25 SUM= 8.123 DEL= -0.201E+00 STEP 26 SUM= 7.649 DEL= -0.474E+00 STEP 27 SUM= 7.514 DEL= -0.136E+00 STEP 28 SUM= 7.295 DEL= -0.219E+00 STEP 29 SUM= 7.055 DEL= -0.240E+00 STEP 30 SUM= 6.802 DEL= -0.253E+00 STEP 31 SUM= 6.848 DEL= 0.462E-01 STEP 32 SUM= 6.704 DEL= -0.144E+00 STEP 33 SUM= 6.555 DEL= -0.150E+00 STEP 34 SUM= 6.362 DEL= -0.193E+00 STEP 35 SUM= 6.397 DEL= 0.354E-01 STEP 36 SUM= 6.272 DEL= -0.126E+00 STEP 37 SUM= 6.256 DEL= -0.154E-01 STEP 38 SUM= 6.222 DEL= -0.341E-01 STEP 39 SUM= 6.227 DEL= 0.502E-02 STEP 40 SUM= 6.209 DEL= -0.180E-01 STEP 41 SUM= 6.201 DEL= -0.771E-02 STEP 42 SUM= 6.205 DEL= 0.336E-02 STEP 43 SUM= 6.199 DEL= -0.550E-02 STEP 44 SUM= 6.198 DEL= -0.123E-02 STEP 45 SUM= 6.198 DEL= -0.312E-03 STEP 46 SUM= 6.197 DEL= -0.214E-03 STEP 47 SUM= 6.197 DEL= -0.296E-03 STEP 48 SUM= 6.197 DEL= -0.207E-03 STEP 49 SUM= 6.197 DEL= -0.562E-04 STEP 50 SUM= 6.197 DEL= -0.194E-04 STEP 51 SUM= 6.197 DEL= -0.197E-05 STEP 52 SUM= 6.197 DEL= -0.357E-05 STEP 53 SUM= 6.197 DEL= -0.200E-05 STEP 54 SUM= 6.197 DEL= -0.122E-06 STEP 55 SUM= 6.197 DEL= -0.154E-08 STEP 56 SUM= 6.197 DEL= -0.818E-11 STEP 57 SUM= 6.197 DEL= -0.108E-11 STEP 58 SUM= 6.197 DEL= 0.178E-14 STEP 59 SUM= 6.197 DEL= -0.178E-14 FINAL SUM= 6.197 CPTS: 0.842 2.697 0.539 2.119 GRA= 0.66E-08-0.36E-07-0.62E-09-0.17E-08 0.10E-07 0.60E-07 0.88E-09 0.47E-08 GRA=-0.13E-07-0.19E-07 0.10E-08-0.30E-08 0.12E-08 0.11E-07-0.83E-09 0.29E-08 GRA= 0.14E-09-0.24E-07-0.35E-08-0.50E-08-0.66E-08-0.62E-08-0.15E-08-0.15E-08 GRA= 0.12E-07-0.14E-07 0.35E-08-0.11E-08 0.11E-07 0.25E-07 0.13E-08 0.12E-08 ---------------------------- |A| Global axis parameters | ---------------------------- 1) U: 0.776 -0.530 -0.340 P: -6.132 4.478 16.255 D: 0.603 2) U: 0.742 -0.524 -0.417 P: -4.009 3.320 15.342 D: 1.574 3) U: 0.709 -0.574 -0.409 P: -2.006 1.758 13.483 D: 2.140 4) U: 0.732 -0.576 -0.364 P: -0.186 -0.480 12.355 D: 0.601 5) U: 0.788 -0.509 -0.346 P: 2.057 -2.226 11.438 D: 0.595 6) U: 0.815 -0.478 -0.326 P: 4.235 -3.214 10.754 D: 0.298 7) U: 0.798 -0.476 -0.369 P: 6.687 -4.743 9.485 D: 0.385 8) U: 0.819 -0.459 -0.344 P: 8.651 -5.914 8.676 --------------------------------- |B| Global Base-Axis Parameters | --------------------------------- 1st strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) CA 8 -4.49 0.13 12.56 -10.03 3 0 2) AA 9 -4.45 0.33 9.96 -10.09 2 29 3) CA 10 -4.10 0.24 9.83 -9.96 3 -6 4) CA 11 -4.83 -0.25 11.97 -3.59 3 -9 5) GA 12 -4.76 -0.15 8.16 -4.98 1 9 6) GA 13 -4.36 -0.27 9.13 -4.04 1 6 7) UA 14 -4.46 -0.29 7.16 -6.52 4 -29 8) GA 15 -4.35 -0.22 12.31 -2.71 1 0 2nd strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) GB 37 -4.45 0.14 8.63 -4.99 1 0 2) UB 36 -4.77 -0.08 6.45 -7.54 4 -29 3) GB 35 -4.23 0.36 3.58 -9.43 1 6 4) GB 34 -4.50 0.34 5.43 -5.83 1 9 5) CB 33 -4.68 0.40 14.18 -8.74 3 -9 6) CB 32 -4.41 0.45 12.54 -8.46 3 -6 7) AB 31 -4.62 0.42 16.73 -9.26 2 29 8) CB 30 -4.58 0.49 15.82 -5.72 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 8-G 37 -4.47 -0.00 10.59 -2.52 3 0 2) A 9-U 36 -4.61 0.21 8.20 -1.28 2 29 3) C 10-G 35 -4.16 -0.06 6.70 -0.26 3 -6 4) C 11-G 34 -4.66 -0.30 8.70 1.12 3 -9 5) G 12-C 33 -4.72 -0.27 11.17 1.88 1 9 6) G 13-C 32 -4.38 -0.36 10.83 2.21 1 6 7) U 14-A 31 -4.54 -0.36 11.95 1.37 4 -29 8) G 15-C 30 -4.47 -0.35 14.06 1.50 1 0 Average: -4.50 -0.19 10.28 0.50 --------------------------------- |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 8-G 37 -0.04 0.27 -0.22 3.93 -15.02 3.26 3 0 2) A 9-U 36 0.32 0.25 -0.18 3.51 -17.63 4.66 2 29 3) C 10-G 35 0.13 0.60 -0.19 6.25 -19.39 6.49 3 -6 4) C 11-G 34 -0.32 0.09 -0.30 6.55 -9.42 1.60 3 -9 5) G 12-C 33 -0.09 0.25 -0.43 -6.02 -13.72 0.29 1 9 6) G 13-C 32 0.05 0.18 -0.01 -3.41 -12.50 2.48 1 6 7) U 14-A 31 0.16 0.13 -0.02 -9.58 -15.78 1.97 4 -29 8) G 15-C 30 0.23 0.27 -0.00 -3.51 -8.44 2.78 1 0 Average: 0.06 0.26 -0.17 -0.28 -13.99 2.94 ---------------------------------- |E| Global Inter-Base Parameters | ---------------------------------- 1st strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C 8/A 9 -0.03 0.46 2.60 -1.77 4.71 36.32 9 3) A 9/C 10 0.89 -0.45 3.08 2.57 -2.05 27.93 -6 4) C 10/C 11 -1.28 -0.77 2.98 -0.63 5.50 26.85 -1 5) C 11/G 12 -0.05 0.26 2.92 -4.81 3.62 33.64 8 6) G 12/G 13 0.74 -0.17 2.68 1.32 3.54 33.25 1 7) G 13/U 14 -0.30 -0.03 3.15 -1.40 -5.05 32.45 6 8) U 14/G 15 0.17 0.10 2.43 6.89 5.03 34.66 -9 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 37/U 36 -0.39 -0.48 2.55 -1.34 -7.32 34.91 -9 3) U 36/G 35 1.08 0.80 3.09 -0.17 0.28 26.10 6 4) G 35/G 34 -0.82 0.26 3.09 -0.92 4.46 31.74 1 5) G 34/C 33 -0.29 -0.10 3.05 7.76 -7.92 34.95 8 6) C 33/C 32 0.60 0.10 2.25 -1.29 -2.33 31.06 -1 7) C 32/A 31 -0.41 -0.02 3.15 4.77 1.77 32.95 -6 8) A 31/C 30 0.10 0.05 2.42 0.82 2.31 33.86 9 --------------------------------------- |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 8/A 9 -0.21 0.47 2.57 -1.56 6.02 35.61 9 3) A 9/C 10 0.98 -0.63 3.08 1.20 -1.16 27.01 -6 4) C 10/C 11 -1.05 -0.52 3.04 -0.77 0.52 29.30 -1 5) C 11/G 12 -0.17 0.18 2.98 1.48 5.77 34.29 8 6) G 12/G 13 0.67 -0.13 2.47 0.02 2.93 32.16 1 7) G 13/U 14 -0.36 -0.01 3.15 1.69 -3.41 32.70 6 8) U 14/G 15 0.14 0.02 2.43 3.85 1.36 34.26 -9 Average: 0.00 -0.09 2.82 0.84 1.72 32.19 --------------------------------- |G| Local Inter-Base Parameters | --------------------------------- 1st strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C 8/A 9 0.40 -1.74 3.33 4.55 11.57 34.52 9 3) A 9/C 10 1.28 -2.01 3.14 7.25 2.60 27.08 -6 4) C 10/C 11 -0.88 -2.27 3.50 2.41 10.47 26.51 -1 5) C 11/G 12 0.35 -1.92 3.70 -2.23 9.41 32.54 8 6) G 12/G 13 1.07 -2.34 3.18 3.85 8.40 32.34 1 7) G 13/U 14 0.16 -2.05 3.28 1.59 -0.40 32.48 6 8) U 14/G 15 0.50 -2.13 2.86 9.43 10.54 33.52 -9 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 37/U 36 -0.67 -1.93 3.14 -5.10 11.70 33.76 -9 3) U 36/G 35 0.69 -2.55 3.28 -3.83 2.07 25.90 6 4) G 35/G 34 -1.03 -2.40 3.15 -5.11 -1.96 31.33 1 5) G 34/C 33 -0.59 -2.09 3.79 3.10 13.57 34.45 8 6) C 33/C 32 0.40 -1.91 3.05 -5.66 9.36 29.17 -1 7) C 32/A 31 -0.70 -1.76 3.42 -0.36 6.51 32.92 -6 8) A 31/C 30 -0.03 -1.93 3.19 -3.32 7.17 32.00 9 -------------------------------------- |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 8/A 9 -0.14 -1.82 3.29 -0.27 11.80 34.42 9 3) A 9/C 10 0.98 -2.26 3.24 1.71 2.61 26.78 -6 4) C 10/C 11 -0.96 -2.34 3.31 -1.60 4.38 29.40 -1 5) C 11/G 12 -0.12 -2.00 3.77 0.46 11.47 33.65 8 6) G 12/G 13 0.72 -2.12 3.14 -0.90 8.95 30.92 1 7) G 13/U 14 -0.27 -1.90 3.38 0.68 3.07 33.08 6 8) U 14/G 15 0.24 -2.03 3.04 3.03 8.99 32.71 -9 Average: 0.07 -2.07 3.31 0.44 7.33 31.57 --------------------------- |I| Global Axis Curvature | --------------------------- Duplex Ax Ay Ainc Atip Adis Angle Path Dc 2) C 8/A 9 -0.07 0.26 0.83 4.77 0.27 4.85 2.58 9 3) A 9/C 10 0.54 -0.36 2.70 -2.18 0.64 3.47 3.15 -6 4) C 10/C 11 -0.55 -0.28 -2.77 -0.87 0.61 2.90 3.10 -1 5) C 11/G 12 -0.12 0.15 -1.00 5.01 0.19 5.11 2.99 8 6) G 12/G 13 0.33 -0.05 0.36 2.60 0.34 2.63 2.49 1 7) G 13/U 14 -0.20 -0.01 0.57 -2.57 0.20 2.64 3.16 6 8) U 14/G 15 0.06 0.02 1.74 1.23 0.07 2.13 2.43 -9 Overall axis bend ... UU= 4.75 PP= 2.39 Duplex Offset L.Dir ... wrt end-to-end vector 1) C 8 0.00 0.00 2) A 9 0.29 -92.38 3) C 10 0.66 144.92 4) C 11 0.88 59.17 5) G 12 0.85 6.64 6) G 13 0.34 -37.54 7) U 14 0.22 -45.65 8) G 15 0.00 0.00 Path length= 19.89 End-to-end= 19.60 Shortening= 1.46 % ------------------------- |J| Backbone Parameters | ------------------------- 1st strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)CA 8 -28.00 40.46 13.96 42.62 C3'-endo 106.8 100.9 100.9 2)AA 9 -27.51 41.09 15.40 43.33 C3'-endo 106.8 100.9 101.4 3)CA 10 -19.63 40.83 31.40 48.72 C3'-endo 106.3 101.3 99.0 4)CA 11 -27.93 43.74 17.60 46.43 C3'-endo 106.1 100.2 100.8 5)GA 12 -27.13 42.99 18.61 45.98 C3'-endo 106.6 100.5 100.7 6)GA 13 -23.04 39.94 23.68 44.36 C3'-endo 107.2 101.1 100.9 7)UA 14 -27.43 41.52 16.12 43.93 C3'-endo 106.5 100.8 101.0 8)GA 15 -26.89 40.47 16.45 43.21 C3'-endo 107.1 100.4 100.9 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)CA 8 -161.87 45.34 86.79 -151.30 -75.43 -59.65 174.79 2)AA 9 -154.43 42.11 86.65 -152.60 -63.04 -71.91 163.66 3)CA 10 -165.26 68.42 80.37 -166.30 -80.15 -71.32 -178.62 4)CA 11 -157.30 52.77 82.57 -158.08 -69.70 -67.22 179.92 5)GA 12 -162.14 47.51 83.98 -153.29 -69.04 -58.59 172.18 6)GA 13 -161.60 50.26 83.78 -167.07 -71.61 -63.18 -179.40 7)UA 14 -161.48 44.91 83.92 -163.67 -60.27 -68.48 -167.96 8)GA 15 -151.24 41.84 81.85 ...... ...... ...... ...... 2nd strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)GB 37 -23.80 38.41 19.99 41.63 C3'-endo 107.2 101.4 101.6 2)UB 36 -29.14 45.05 17.27 47.81 C3'-endo 105.8 100.4 99.8 3)GB 35 -25.12 42.87 22.65 47.15 C3'-endo 106.5 100.6 100.1 4)GB 34 -28.33 45.03 18.76 48.17 C3'-endo 105.6 100.2 99.8 5)CB 33 -24.98 40.24 19.73 43.46 C3'-endo 107.3 100.7 101.3 6)CB 32 -24.78 39.08 18.75 42.06 C3'-endo 107.1 101.1 101.4 7)AB 31 -26.75 41.14 17.58 44.01 C3'-endo 106.5 101.1 100.4 8)CB 30 -27.84 40.42 13.81 42.45 C3'-endo 106.6 100.9 101.2 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)GB 37 -157.46 52.32 86.18 ...... ...... ...... ...... 2)UB 36 -159.51 51.70 83.47 -154.85 -69.61 -68.97 178.57 3)GB 35 -170.22 68.85 82.61 -162.72 -73.42 -69.53 -174.29 4)GB 34 -164.18 44.13 82.92 -159.57 -66.89 -70.85 168.32 5)CB 33 -159.82 53.94 84.54 -150.89 -70.93 -66.01 176.98 6)CB 32 -164.17 49.39 85.11 -156.47 -73.34 -75.54 178.04 7)AB 31 -158.88 44.54 84.32 -157.28 -69.71 -59.63 169.23 8)CB 30 -163.64 37.97 84.43 -157.75 -67.95 -65.25 -178.08