*********************************** ************** ****** CURVES 5.3 R.L. 1998 ***** * 22 Oct 98 * *********************************** ************** FILE : ideal_B.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) C5 1 0.003 1 : 2) A 2 0.007 1 : 3) T 3 0.003 1 : 4) G 4 0.004 1 : 5) G 5 0.004 1 : 6) C 6 0.003 1 : 7) C 7 0.003 1 : 8) A 8 0.007 1 : 9) T 9 0.003 1 : 10) G3 10 0.004 2 : 1) G3 20 0.004 2 : 2) T 19 0.003 2 : 3) A 18 0.007 2 : 4) C 17 0.003 2 : 5) C 16 0.003 2 : 6) G 15 0.004 2 : 7) G 14 0.004 2 : 8) T 13 0.003 2 : 9) A 12 0.007 2 : 10) C5 11 0.003 Strand= 2 Nucleo= 20 Atoms = 632 Units = 20 Input 1) Xdisp= 0.00 Ydisp= 0.00 Inclin= 0.00 Tip= 0.00 Combined strands have 10 levels ... Strand 1 has 10 bases (5'-3'): CATGGCCATG Strand 2 has 10 bases (3'-5'): GTACCGGTAC FIRST SUM= 11.600 CPTS: 0.000 0.005 0.824 10.772 MINIMISATION: ACC = 0.100E-05 MAXN= 500 NVAR= 40 STEP 1 SUM= 11.600 DEL= 0.000E+00 STEP 2 SUM= 6.669 DEL= -0.493E+01 STEP 3 SUM= 5.047 DEL= -0.162E+01 STEP 4 SUM= 3.848 DEL= -0.120E+01 STEP 5 SUM= 3.516 DEL= -0.332E+00 STEP 6 SUM= 2.969 DEL= -0.547E+00 STEP 7 SUM= 4.419 DEL= 0.145E+01 STEP 8 SUM= 2.852 DEL= -0.157E+01 STEP 9 SUM= 2.729 DEL= -0.123E+00 STEP 10 SUM= 2.555 DEL= -0.174E+00 STEP 11 SUM= 2.315 DEL= -0.240E+00 STEP 12 SUM= 2.132 DEL= -0.183E+00 STEP 13 SUM= 1.784 DEL= -0.348E+00 STEP 14 SUM= 0.209 DEL= -0.157E+01 STEP 15 SUM= 100.070 DEL= 0.999E+02 STEP 16 SUM= 0.862 DEL= -0.992E+02 STEP 17 SUM= 0.174 DEL= -0.688E+00 STEP 18 SUM= 0.206 DEL= 0.324E-01 STEP 19 SUM= 0.162 DEL= -0.446E-01 STEP 20 SUM= 0.142 DEL= -0.200E-01 STEP 21 SUM= 0.181 DEL= 0.396E-01 STEP 22 SUM= 0.136 DEL= -0.447E-01 STEP 23 SUM= 0.128 DEL= -0.867E-02 STEP 24 SUM= 0.118 DEL= -0.964E-02 STEP 25 SUM= 0.100 DEL= -0.184E-01 STEP 26 SUM= 0.090 DEL= -0.972E-02 STEP 27 SUM= 0.083 DEL= -0.738E-02 STEP 28 SUM= 0.077 DEL= -0.541E-02 STEP 29 SUM= 0.072 DEL= -0.532E-02 STEP 30 SUM= 0.062 DEL= -0.960E-02 STEP 31 SUM= 0.045 DEL= -0.175E-01 STEP 32 SUM= 0.027 DEL= -0.176E-01 STEP 33 SUM= 0.034 DEL= 0.639E-02 STEP 34 SUM= 0.020 DEL= -0.138E-01 STEP 35 SUM= 0.012 DEL= -0.835E-02 STEP 36 SUM= 0.017 DEL= 0.526E-02 STEP 37 SUM= 0.008 DEL= -0.843E-02 STEP 38 SUM= 0.006 DEL= -0.277E-02 STEP 39 SUM= 0.005 DEL= -0.180E-03 STEP 40 SUM= 0.004 DEL= -0.125E-02 STEP 41 SUM= 0.004 DEL= 0.171E-03 STEP 42 SUM= 0.003 DEL= -0.847E-03 STEP 43 SUM= 0.006 DEL= 0.259E-02 STEP 44 SUM= 0.003 DEL= -0.271E-02 STEP 45 SUM= 0.003 DEL= -0.583E-04 STEP 46 SUM= 0.003 DEL= 0.269E-04 STEP 47 SUM= 0.003 DEL= -0.506E-04 STEP 48 SUM= 0.003 DEL= -0.768E-05 STEP 49 SUM= 0.003 DEL= -0.341E-05 STEP 50 SUM= 0.003 DEL= -0.735E-06 STEP 51 SUM= 0.003 DEL= -0.128E-05 STEP 52 SUM= 0.003 DEL= -0.153E-05 STEP 53 SUM= 0.003 DEL= 0.821E-05 STEP 54 SUM= 0.003 DEL= -0.859E-05 STEP 55 SUM= 0.003 DEL= -0.217E-06 STEP 56 SUM= 0.003 DEL= -0.150E-06 STEP 57 SUM= 0.003 DEL= -0.891E-08 STEP 58 SUM= 0.003 DEL= -0.684E-07 STEP 59 SUM= 0.003 DEL= 0.143E-06 STEP 60 SUM= 0.003 DEL= -0.151E-06 STEP 61 SUM= 0.003 DEL= -0.828E-08 STEP 62 SUM= 0.003 DEL= -0.672E-09 STEP 63 SUM= 0.003 DEL= -0.364E-08 STEP 64 SUM= 0.003 DEL= 0.105E-10 STEP 65 SUM= 0.003 DEL= -0.308E-09 STEP 66 SUM= 0.003 DEL= -0.137E-09 STEP 67 SUM= 0.003 DEL= -0.418E-10 STEP 68 SUM= 0.003 DEL= -0.336E-13 STEP 69 SUM= 0.003 DEL= -0.924E-16 STEP 70 SUM= 0.003 DEL= 0.000E+00 FINAL SUM= 0.003 CPTS: 0.000 0.003 0.000 0.000 GRA=-0.10E-10 0.98E-12 0.39E-12 0.17E-12 0.93E-11-0.82E-11-0.25E-11-0.10E-12 GRA= 0.12E-11-0.12E-10 0.37E-11 0.18E-11 0.31E-11 0.69E-11 0.43E-12-0.54E-13 GRA= 0.64E-11 0.38E-11 0.73E-12 0.10E-11-0.51E-11-0.28E-12 0.70E-14-0.10E-11 GRA=-0.42E-11-0.18E-11-0.18E-12 0.33E-12 0.99E-11-0.16E-11-0.15E-11 0.15E-11 GRA= 0.46E-11 0.61E-11 0.37E-11 0.19E-12-0.18E-10-0.11E-10-0.94E-13 0.92E-12 ---------------------------- |A| Global axis parameters | ---------------------------- 1) U: -0.001 0.000 1.000 P: 0.008 -0.002 0.002 D: 0.000 2) U: -0.001 0.000 1.000 P: 0.001 -0.005 3.378 D: 0.001 3) U: -0.001 0.001 1.000 P: -0.005 -0.002 6.761 D: 0.001 4) U: 0.000 0.000 1.000 P: -0.003 0.005 10.138 D: 0.000 5) U: 0.000 0.000 1.000 P: -0.005 0.003 13.517 D: 0.000 6) U: 0.000 0.000 1.000 P: -0.006 0.000 16.903 D: 0.000 7) U: 0.000 0.000 1.000 P: -0.005 -0.002 20.282 D: 0.001 8) U: 0.001 0.000 1.000 P: -0.003 0.004 23.659 D: 0.001 9) U: 0.001 -0.001 1.000 P: 0.004 0.004 27.042 D: 0.000 10) U: 0.001 -0.001 1.000 P: 0.008 -0.003 30.418 --------------------------------- |B| Global Base-Axis Parameters | --------------------------------- 1st strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) C5 1 -0.70 0.01 -6.02 1.88 3 0 2) A 2 -0.69 0.02 -6.00 1.89 2 30 3) T 3 -0.70 0.02 -6.02 1.92 4 -30 4) G 4 -0.70 0.01 -5.95 1.94 1 11 5) G 5 -0.70 0.01 -5.96 1.93 1 5 6) C 6 -0.70 0.01 -6.04 1.95 3 -5 7) C 7 -0.70 0.01 -6.04 1.94 3 -11 8) A 8 -0.69 0.02 -6.01 1.94 2 30 9) T 9 -0.70 0.02 -6.02 1.96 4 -30 10) G3 10 -0.69 0.01 -5.94 2.00 1 0 2nd strand Xdisp Ydisp Inclin Tip Bc Tc (dx) (dy) (eta) (theta) 1) G3 20 -0.69 0.01 -5.94 2.00 1 0 2) T 19 -0.70 0.02 -6.02 1.96 4 -30 3) A 18 -0.69 0.02 -6.01 1.93 2 30 4) C 17 -0.70 0.01 -6.04 1.94 3 -11 5) C 16 -0.70 0.01 -6.04 1.95 3 -5 6) G 15 -0.70 0.01 -5.96 1.93 1 5 7) G 14 -0.70 0.01 -5.96 1.94 1 11 8) T 13 -0.70 0.02 -6.02 1.92 4 -30 9) A 12 -0.69 0.02 -6.00 1.89 2 30 10) C5 11 -0.70 0.01 -6.02 1.88 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 20 -0.70 0.00 -5.98 -0.06 3 0 2) A 2-T 19 -0.69 0.00 -6.01 -0.03 2 30 3) T 3-A 18 -0.70 0.00 -6.01 -0.01 4 -30 4) G 4-C 17 -0.70 0.00 -6.00 0.00 1 11 5) G 5-C 16 -0.70 0.00 -6.00 -0.01 1 5 6) C 6-G 15 -0.70 0.00 -6.00 0.01 3 -5 7) C 7-G 14 -0.70 0.00 -6.00 0.00 3 -11 8) A 8-T 13 -0.70 0.00 -6.01 0.01 2 30 9) T 9-A 12 -0.69 0.00 -6.01 0.03 4 -30 10) G 10-C 11 -0.70 0.00 -5.98 0.06 1 0 Average: -0.70 0.00 -6.00 0.00 --------------------------------- |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 20 -0.01 0.02 0.06 -0.08 3.88 -4.06 3 0 2) A 2-T 19 0.02 0.04 0.05 0.02 3.85 -3.65 2 30 3) T 3-A 18 -0.01 0.04 0.05 -0.01 3.85 -3.65 4 -30 4) G 4-C 17 0.01 0.02 0.06 0.08 3.88 -4.06 1 11 5) G 5-C 16 0.01 0.02 0.06 0.08 3.88 -4.06 1 5 6) C 6-G 15 -0.01 0.02 0.06 -0.09 3.88 -4.06 3 -5 7) C 7-G 14 -0.01 0.02 0.06 -0.08 3.88 -4.06 3 -11 8) A 8-T 13 0.02 0.04 0.05 0.01 3.85 -3.65 2 30 9) T 9-A 12 -0.02 0.04 0.05 -0.02 3.85 -3.65 4 -30 10) G 10-C 11 0.01 0.02 0.06 0.08 3.88 -4.06 1 0 Average: 0.00 0.03 0.06 0.00 3.87 -3.90 ---------------------------------- |E| Global Inter-Base Parameters | ---------------------------------- 1st strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C 1/A 2 0.02 0.01 3.37 0.02 0.01 36.40 9 3) A 2/T 3 -0.02 -0.01 3.38 -0.03 -0.02 35.73 7 4) T 3/G 4 0.00 0.00 3.38 0.04 0.04 35.99 -9 5) G 4/G 5 0.00 0.00 3.38 0.01 0.01 36.00 1 6) G 5/C 6 -0.01 0.00 3.39 -0.08 0.05 35.89 5 7) C 6/C 7 0.00 0.00 3.38 -0.01 0.01 36.00 -1 8) C 7/A 8 0.02 0.02 3.37 0.05 0.01 36.40 9 9) A 8/T 9 -0.01 -0.01 3.38 0.00 -0.03 35.73 7 10) T 9/G 10 0.01 0.00 3.38 0.07 0.04 35.99 -9 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 20/T 19 -0.01 0.00 3.38 -0.07 -0.04 35.99 -9 3) T 19/A 18 0.01 0.01 3.38 0.00 0.02 35.73 7 4) A 18/C 17 -0.02 -0.02 3.37 -0.05 -0.01 36.40 9 5) C 17/C 16 0.00 0.00 3.38 0.01 -0.01 36.00 -1 6) C 16/G 15 0.01 0.00 3.39 0.08 -0.05 35.89 5 7) G 15/G 14 0.00 0.00 3.38 -0.01 -0.01 35.99 1 8) G 14/T 13 0.00 0.00 3.38 -0.04 -0.04 35.99 -9 9) T 13/A 12 0.02 0.01 3.38 0.03 0.03 35.73 7 10) A 12/C 11 -0.02 -0.01 3.37 -0.02 -0.01 36.40 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 1/A 2 0.01 0.01 3.38 -0.03 0.02 36.19 9 3) A 2/T 3 0.00 -0.01 3.38 -0.01 -0.02 35.73 7 4) T 3/G 4 -0.01 0.01 3.38 0.00 0.03 36.19 -9 5) G 4/G 5 0.00 0.00 3.38 0.01 0.01 36.00 1 6) G 5/C 6 0.00 0.00 3.39 0.00 0.05 35.89 5 7) C 6/C 7 0.00 0.00 3.38 -0.01 0.01 35.99 -1 8) C 7/A 8 0.01 0.01 3.38 0.01 0.03 36.19 9 9) A 8/T 9 0.00 -0.01 3.38 0.01 -0.03 35.73 7 10) T 9/G 10 -0.01 0.01 3.38 0.03 0.02 36.20 -9 Average: 0.00 0.00 3.38 0.00 0.01 36.01 --------------------------------- |G| Local Inter-Base Parameters | --------------------------------- 1st strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) C 1/A 2 -0.10 -0.75 3.32 -1.15 -3.74 36.19 9 3) A 2/T 3 -0.13 -0.77 3.32 -1.19 -3.71 35.52 7 4) T 3/G 4 -0.12 -0.77 3.32 -1.15 -3.65 35.79 -9 5) G 4/G 5 -0.11 -0.76 3.32 -1.18 -3.66 35.80 1 6) G 5/C 6 -0.12 -0.77 3.33 -1.27 -3.64 35.69 5 7) C 6/C 7 -0.11 -0.77 3.32 -1.20 -3.72 35.79 -1 8) C 7/A 8 -0.10 -0.75 3.32 -1.15 -3.74 36.20 9 9) A 8/T 9 -0.13 -0.77 3.32 -1.19 -3.71 35.52 7 10) T 9/G 10 -0.11 -0.77 3.32 -1.15 -3.65 35.79 -9 2nd strand Shift Slide Rise Tilt Roll Twist Dc (Dx) (Dy) (Dz) (tau) (rho) (Omega) 2) G 20/T 19 0.12 -0.77 3.32 1.15 -3.65 35.78 -9 3) T 19/A 18 0.13 -0.77 3.32 1.19 -3.71 35.52 7 4) A 18/C 17 0.10 -0.75 3.32 1.15 -3.74 36.19 9 5) C 17/C 16 0.11 -0.77 3.32 1.21 -3.72 35.79 -1 6) C 16/G 15 0.12 -0.77 3.33 1.27 -3.64 35.69 5 7) G 15/G 14 0.11 -0.76 3.32 1.18 -3.66 35.79 1 8) G 14/T 13 0.11 -0.77 3.32 1.15 -3.65 35.79 -9 9) T 13/A 12 0.13 -0.77 3.32 1.19 -3.71 35.52 7 10) A 12/C 11 0.10 -0.75 3.32 1.15 -3.74 36.20 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 1/A 2 0.01 -0.76 3.32 0.00 -3.66 36.01 9 3) A 2/T 3 0.00 -0.76 3.33 0.00 -3.67 35.55 7 4) T 3/G 4 -0.01 -0.76 3.32 0.01 -3.66 36.01 -9 5) G 4/G 5 0.00 -0.76 3.32 0.01 -3.65 35.82 1 6) G 5/C 6 0.00 -0.77 3.33 0.00 -3.59 35.71 5 7) C 6/C 7 0.00 -0.76 3.32 -0.01 -3.65 35.82 -1 8) C 7/A 8 0.01 -0.76 3.32 0.00 -3.66 36.02 9 9) A 8/T 9 0.00 -0.76 3.33 0.00 -3.67 35.54 7 10) T 9/G 10 -0.01 -0.76 3.32 0.00 -3.66 36.02 -9 Average: 0.00 -0.76 3.32 0.00 -3.65 35.83 --------------------------- |I| Global Axis Curvature | --------------------------- Duplex Ax Ay Ainc Atip Adis Angle Path Dc 2) C 1/A 2 0.00 0.00 0.00 0.00 0.00 0.00 3.38 9 3) A 2/T 3 0.00 0.00 -0.01 -0.05 0.00 0.05 3.38 7 4) T 3/G 4 0.00 0.00 -0.02 0.02 0.01 0.03 3.38 -9 5) G 4/G 5 0.00 0.00 0.01 0.02 0.00 0.02 3.38 1 6) G 5/C 6 0.00 0.00 0.00 0.03 0.00 0.03 3.39 5 7) C 6/C 7 0.00 0.00 -0.01 0.02 0.00 0.02 3.38 -1 8) C 7/A 8 0.00 0.00 0.02 0.02 0.01 0.03 3.38 9 9) A 8/T 9 0.00 0.00 0.01 -0.05 0.00 0.05 3.38 7 10) T 9/G 10 0.00 0.00 0.00 0.00 0.00 0.00 3.38 -9 Overall axis bend ... UU= 0.15 PP= 0.20 Duplex Offset L.Dir ... wrt end-to-end vector 1) C 1 0.00 0.00 2) A 2 0.01 169.41 3) T 3 0.01 106.47 4) G 4 0.01 42.53 5) G 5 0.01 14.04 6) C 6 0.01 -10.64 7) C 7 0.01 -39.30 8) A 8 0.01 -103.28 9) T 9 0.01 -166.44 10) G 10 0.00 0.00 Path length= 30.42 End-to-end= 30.42 Shortening= 0.00 % ------------------------- |J| Backbone Parameters | ------------------------- 1st strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)C5 1 24.92 -34.92 191.64 36.33 C3'-exo 108.0 102.1 102.9 2)A 2 24.90 -34.86 191.60 36.26 C3'-exo 107.9 102.1 102.9 3)T 3 24.91 -34.88 191.59 36.28 C3'-exo 108.0 102.1 102.9 4)G 4 24.96 -34.94 191.59 36.35 C3'-exo 108.0 102.0 102.9 5)G 5 24.93 -34.92 191.60 36.31 C3'-exo 107.9 102.0 102.9 6)C 6 24.92 -34.92 191.64 36.33 C3'-exo 108.0 102.1 102.9 7)C 7 24.90 -34.86 191.60 36.26 C3'-exo 107.9 102.1 102.9 8)A 8 24.91 -34.88 191.59 36.28 C3'-exo 108.0 102.1 102.9 9)T 9 24.96 -34.94 191.59 36.35 C3'-exo 108.0 102.0 102.9 10)G3 10 24.93 -34.92 191.60 36.31 C3'-exo 107.9 102.0 102.9 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)C5 1 -97.94 45.40 148.70 154.98 -95.17 -46.85 -146.05 2)A 2 -97.82 36.41 156.38 154.97 -95.18 -46.82 -146.05 3)T 3 -98.02 36.32 156.35 155.01 -95.11 -46.84 -146.03 4)G 4 -97.79 36.38 156.36 154.97 -95.11 -46.85 -145.97 5)G 5 -97.77 36.29 156.39 155.01 -95.13 -46.83 -146.02 6)C 6 -97.94 36.36 156.40 154.98 -95.17 -46.85 -146.05 7)C 7 -97.96 36.41 156.38 154.97 -95.18 -46.82 -146.05 8)A 8 -97.83 36.32 156.35 155.01 -95.11 -46.84 -146.03 9)T 9 -98.02 36.38 156.36 154.97 -95.11 -46.85 -145.97 10)G3 10 -97.77 36.29 154.95 ...... ...... ...... ...... 2nd strand C1'-C2' C2'-C3' Phase Ampli Pucker C1' C2' C3' 1)G3 20 24.92 -34.92 191.64 36.33 C3'-exo 108.0 102.1 102.9 2)T 19 24.93 -34.92 191.60 36.31 C3'-exo 107.9 102.0 102.9 3)A 18 24.96 -34.94 191.59 36.35 C3'-exo 108.0 102.0 102.9 4)C 17 24.91 -34.88 191.59 36.28 C3'-exo 108.0 102.1 102.9 5)C 16 24.90 -34.86 191.60 36.26 C3'-exo 107.9 102.1 102.9 6)G 15 24.92 -34.92 191.64 36.33 C3'-exo 108.0 102.1 102.9 7)G 14 24.93 -34.92 191.60 36.31 C3'-exo 107.9 102.0 102.9 8)T 13 24.96 -34.94 191.59 36.35 C3'-exo 108.0 102.0 102.9 9)A 12 24.91 -34.88 191.59 36.28 C3'-exo 108.0 102.1 102.9 10)C5 11 24.90 -34.86 191.60 36.26 C3'-exo 107.9 102.1 102.9 Torsions Chi Gamma Delta Epsil Zeta Alpha Beta C1'-N C5'-C4' C4'-C3' C3'-O3' O3'-P P-O5' O5'-C5' 1)G3 20 -97.76 36.36 154.88 ...... ...... ...... ...... 2)T 19 -98.01 36.29 156.39 155.01 -95.13 -46.83 -146.02 3)A 18 -97.82 36.38 156.36 154.97 -95.11 -46.85 -145.97 4)C 17 -97.96 36.32 156.35 155.01 -95.11 -46.84 -146.03 5)C 16 -97.96 36.41 156.38 154.97 -95.18 -46.82 -146.05 6)G 15 -97.76 36.36 156.40 154.98 -95.17 -46.85 -146.05 7)G 14 -97.77 36.29 156.39 155.01 -95.13 -46.83 -146.02 8)T 13 -98.02 44.53 153.49 154.97 -95.11 -46.85 -145.97 9)A 12 -97.83 36.32 156.35 155.01 -95.11 -51.90 -150.47 10)C5 11 -97.96 26.51 156.38 154.97 -95.18 -46.82 -146.05