The base morphology parameters were calculated using the program by M. Babcock (Babcock, M.S. and Olson, W.K., 1994, J. Mol. Biol., 237, 98-156). 4.DAT YOUR REFERENCE ATOM INPUT FILENAME IS- [MARLA.RNASTAT]BASES.INN Checking Numbers and RMS Values CHAIN a BASE 1 C RMS = 0.203663E-01 CHAIN a BASE 2 G RMS = 0.346725E-01 CHAIN a BASE 3 A RMS = 0.143256E-01 CHAIN a BASE 4 C RMS = 0.203704E-01 CHAIN a BASE 5 G RMS = 0.347060E-01 CHAIN a BASE 6 T RMS = 0.775331E-02 CHAIN a BASE 7 C RMS = 0.205687E-01 CHAIN a BASE 8 A RMS = 0.141006E-01 CHAIN a BASE 9 T RMS = 0.779356E-02 CHAIN a BASE 10 A RMS = 0.142335E-01 CHAIN a BASE 11 G RMS = 0.347478E-01 CHAIN a BASE 12 T RMS = 0.779159E-02 CHAIN a BASE 13 A RMS = 0.143290E-01 CHAIN a BASE 14 C RMS = 0.202881E-01 CHAIN a BASE 15 T RMS = 0.789313E-02 CHAIN a BASE 16 A RMS = 0.144025E-01 CHAIN a BASE 17 T RMS = 0.780394E-02 CHAIN a BASE 18 G RMS = 0.347541E-01 CHAIN a BASE 19 A RMS = 0.141677E-01 CHAIN a BASE 20 C RMS = 0.202596E-01 CHAIN a BASE 21 G RMS = 0.349264E-01 CHAIN a BASE 22 T RMS = 0.782458E-02 CHAIN a BASE 23 C RMS = 0.205715E-01 CHAIN a BASE 24 G RMS = 0.349683E-01 4.DAT YOUR REFERENCE ATOM INPUT FILENAME IS- [MARLA.RNASTAT]BASES.INN YOUR PIVOT POINT WAS: 0.000 1.808 0.000 Calculations Across a Basepair #Ch Base #Ch Base Buckle Prop Open Angle Shear Stretch Stagger Dist -------------------------------------------------------------------------------------------- 1a C 24a G -0.714 -1.926 3.917 2.054 -0.055 0.107 0.056 0.133 2a G 23a C -3.138 -4.898 5.051 5.815 -0.043 0.079 0.001 0.089 3a A 22a T -0.834 -5.904 4.996 5.960 0.118 -0.001 0.072 0.138 4a C 21a G 2.163 -2.795 5.111 3.533 0.096 0.083 0.098 0.161 5a G 20a C -1.560 -7.085 5.341 7.252 -0.091 0.086 0.105 0.164 6a T 19a A -6.414 -11.456 7.442 13.120 -0.057 0.010 0.238 0.245 7a C 18a G -5.857 -3.459 3.915 6.801 0.029 0.101 0.089 0.138 8a A 17a T -2.647 -3.334 7.789 4.253 0.018 0.012 0.150 0.151 9a T 16a A 6.191 -4.476 8.373 7.633 -0.054 0.020 0.194 0.202 10a A 15a T 5.878 -10.178 2.073 11.753 0.108 0.009 0.096 0.144 11a G 14a C -4.010 -8.537 4.954 9.429 -0.037 0.084 0.110 0.143 12a T 13a A -12.380 -9.464 4.006 15.580 -0.074 0.000 0.162 0.178 THE NUMBER OF SAMPLES= 12 -------------------------------------------------------------------------------------------- MEAN= -1.944 -6.126 5.247 7.765 -0.004 0.049 0.114 0.157 STANDARD DEVIATION= 4.979 3.036 1.742 3.868 0.072 0.042 0.061 0.037 4.DAT YOUR REFERENCE ATOM INPUT FILENAME IS- [MARLA.RNASTAT]BASES.INN Calculations of Basepairs #Ch: #Ch #Ch: #Ch Tilt Roll Twist Angle Shift Slide Rise Dist ------------------------------------------------------------------------------------------------- 1a: 24a 2a: 23a -0.135 0.472 36.937 0.482 0.130 -0.870 3.013 3.139 2a: 23a 3a: 22a 0.599 -1.413 39.012 1.505 0.093 -0.404 2.960 2.989 3a: 22a 4a: 21a -1.949 -1.446 37.561 2.384 -0.140 -0.449 3.013 3.050 4a: 21a 5a: 20a 0.194 1.981 37.364 1.956 0.016 -0.602 2.929 2.990 5a: 20a 6a: 19a 1.518 -4.877 39.294 5.008 0.308 -0.530 3.073 3.134 6a: 19a 7a: 18a -0.469 -4.126 40.132 4.068 -0.294 -0.427 2.992 3.036 7a: 18a 8a: 17a 0.386 1.698 38.282 1.710 0.478 -0.323 2.912 2.969 8a: 17a 9a: 16a -0.494 -4.326 36.181 4.282 0.075 -0.639 3.055 3.122 9a: 16a 10a: 15a -1.170 2.085 39.328 2.344 -0.826 -0.284 2.896 3.025 10a: 15a 11a: 14a -1.800 -0.117 36.061 1.774 0.138 -0.992 3.076 3.235 11a: 14a 12a: 13a 2.257 -3.535 37.817 4.118 0.068 -0.729 3.113 3.198 THE NUMBER OF SAMPLES= 11 ------------------------------------------------------------------------------------------------- MEAN= -0.097 -1.237 37.997 2.694 0.004 -0.568 3.003 3.081 STANDARD DEVIATION= 1.233 2.535 1.276 1.371 0.326 0.215 0.069 0.086 4.DAT YOUR REFERENCE ATOM INPUT FILENAME IS- [MARLA.RNASTAT]BASES.INN Calculations of Adjacent Single Bases #Ch Base #Ch Base Tilt Roll Twist Angle Shift Slide Rise Dist -------------------------------------------------------------------------------------------- 1a C 2a G -0.217 -1.581 37.500 1.567 -0.980 -0.904 3.000 3.283 2a G 3a A 3.453 -2.660 38.857 4.276 -0.933 -0.436 3.053 3.222 3a A 4a C 0.897 0.294 37.641 0.927 -1.237 -0.307 3.014 3.272 4a C 5a G 0.057 0.006 37.468 0.056 -1.146 -0.528 2.996 3.251 5a G 6a T 2.030 -8.460 39.977 8.525 -0.677 -0.652 3.232 3.366 6a T 7a C 2.182 -2.416 38.125 3.196 -1.351 -0.490 2.968 3.298 7a C 8a A 3.144 0.214 40.206 3.087 -0.669 -0.431 2.959 3.064 8a A 9a T 4.705 -4.467 36.479 6.378 -1.048 -0.514 3.101 3.313 9a T 10a A 1.169 1.318 36.082 1.733 -1.791 -0.031 2.940 3.443 10a A 11a G -3.550 1.059 37.729 3.638 -0.820 -0.893 3.116 3.344 11a G 12a T 0.956 -6.713 36.845 6.664 -0.900 -0.979 3.232 3.495 13a A 14a C -3.356 -0.244 38.659 3.301 -1.034 -0.405 3.153 3.343 14a C 15a T -0.127 -1.224 34.542 1.212 -1.091 -1.025 3.225 3.556 15a T 16a A 3.751 2.556 42.450 4.436 -0.141 -0.448 2.976 3.013 16a A 17a T 5.678 -4.548 35.726 7.158 -1.202 -0.600 3.073 3.354 17a T 18a G 2.385 2.966 36.230 3.742 -1.617 -0.097 2.923 3.341 18a G 19a A 3.168 -5.849 42.065 6.503 -0.746 -0.239 3.157 3.252 19a A 20a C -0.877 -1.353 38.446 1.582 -1.295 -0.292 3.094 3.367 20a C 21a G -0.244 3.962 37.272 3.900 -1.180 -0.564 2.972 3.247 21a G 22a T 4.712 -3.308 37.372 5.656 -0.961 -0.492 3.094 3.277 22a T 23a C 2.311 -0.291 39.014 2.284 -1.119 -0.279 2.964 3.180 23a C 24a G 0.114 2.517 36.344 2.477 -1.234 -0.746 3.096 3.415 THE NUMBER OF SAMPLES= 22 -------------------------------------------------------------------------------------------- MEAN= 1.470 -1.283 37.956 3.741 -1.053 -0.516 3.061 3.304 STANDARD DEVIATION= 2.362 3.201 1.901 2.217 0.334 0.263 0.095 0.121 4.DAT YOUR REFERENCE ATOM INPUT FILENAME IS- [MARLA.RNASTAT]BASES.INN Local Helical Calculations of Basepairs #Ch: #Ch #Ch: #Ch Incl Tip H-Twist DX DY DZ ------------------------------------------------------------------------------- 1a: 24a 2a: 23a 0.732 0.209 36.940 -1.434 -0.223 3.001 2a: 23a 3a: 22a -2.074 -0.879 39.042 -0.444 -0.071 2.973 3a: 22a 4a: 21a -2.202 2.970 37.640 -0.516 -0.026 3.032 4a: 21a 5a: 20a 3.035 -0.297 37.417 -1.179 -0.001 2.893 5a: 20a 6a: 19a -7.072 -2.201 39.625 -0.217 -0.278 3.125 6a: 19a 7a: 18a -5.869 0.667 40.347 -0.172 0.376 3.023 7a: 18a 8a: 17a 2.540 -0.577 38.322 -0.688 -0.684 2.900 8a: 17a 9a: 16a -6.818 0.779 36.442 -0.435 -0.188 3.108 9a: 16a 10a: 15a 3.034 1.702 39.400 -0.649 1.098 2.901 10a: 15a 11a: 14a -0.186 2.858 36.106 -1.584 -0.470 3.068 11a: 14a 12a: 13a -5.334 -3.406 38.049 -0.669 0.183 3.166 THE NUMBER OF SAMPLES= 11 ------------------------------------------------------------------------------- MEAN= -1.838 0.166 38.121 -0.726 -0.026 3.017 STANDARD DEVIATION= 3.776 1.866 1.306 0.450 0.450 0.090 4.DAT YOUR REFERENCE ATOM INPUT FILENAME IS- [MARLA.RNASTAT]BASES.INN Local Helical Calculations of Adjacent Single Bases #Ch Base #Ch Base Incl Tip H-Twist DX DY DZ -------------------------------------------------------------------------- 1a C 2a G -2.414 0.331 37.534 -1.207 -0.312 3.041 2a G 3a A -3.906 -5.070 39.101 -0.344 -0.014 2.981 3a A 4a C 0.447 -1.366 37.653 -0.511 0.219 2.981 4a C 5a G 0.008 -0.087 37.468 -0.823 -0.016 2.995 5a G 6a T -11.939 -2.864 40.913 0.039 -0.607 3.259 6a T 7a C -3.622 -3.271 38.264 -0.464 0.509 2.912 7a C 8a A 0.304 -4.472 40.329 -0.648 -0.506 2.895 8a A 9a T -6.943 -7.313 37.051 -0.227 0.453 2.982 9a T 10a A 2.091 -1.856 36.125 -0.221 1.232 2.877 10a A 11a G 1.602 5.374 37.911 -1.509 -0.998 3.153 11a G 12a T -10.323 -1.470 37.463 -0.601 -0.275 3.331 13a A 14a C -0.361 4.961 38.805 -0.579 -0.669 3.233 14a C 15a T -2.029 0.210 34.564 -1.532 0.009 3.264 15a T 16a A 3.436 -5.044 42.692 -0.859 -1.257 2.920 16a A 17a T -7.196 -8.984 36.459 -0.358 0.864 2.899 17a T 18a G 4.673 -3.757 36.429 -0.528 1.078 2.793 18a G 19a A -7.902 -4.279 42.588 0.266 -0.459 3.095 19a A 20a C -2.015 1.306 38.480 -0.277 0.049 3.131 20a C 21a G 6.067 0.374 37.483 -1.363 -0.002 2.904 21a G 22a T -5.033 -7.168 37.812 -0.346 0.263 2.982 22a T 23a C -0.426 -3.389 39.084 -0.384 0.124 2.894 23a C 24a G 3.962 -0.179 36.431 -1.533 0.181 3.033 THE NUMBER OF SAMPLES= 22 -------------------------------------------------------------------------- MEAN= -1.887 -2.182 38.211 -0.637 -0.006 3.025 STANDARD DEVIATION= 4.741 3.553 1.955 0.496 0.606 0.144 4.DAT YOUR REFERENCE ATOM INPUT FILENAME IS- [MARLA.RNASTAT]BASES.INN Relative Positions of Bases with respect to Neighboring Basepairs Basepair-1 Basepair+1 #Ch #Ch #Ch #Ch Base Base Base Base #Ch Base Buckle Prop Open Angle Shear Stretch Stagger Dist Dev ---------------------------------------------------------------------------------------------------------------------- 1a: 24a 3a: 22a 2a G -1.950 -1.449 1.510 2.429 0.049 -0.204 0.043 0.214 C: G A: T 23a C -1.189 -3.404 3.584 3.605 -0.068 0.280 -0.063 0.294 TOTAL -3.139 -4.853 5.093 6.034 -0.018 0.076 -0.019 0.508 ACTUAL -3.138 -4.898 5.051 5.815 -0.043 0.079 0.001 0.089 0.298 2a: 23a 4a: 21a 3a A 0.926 -2.965 3.190 3.106 0.217 0.019 0.032 0.220 G: C C: G 22a T -1.722 -3.001 1.737 3.460 -0.123 -0.027 0.075 0.146 TOTAL -0.796 -5.966 4.927 6.566 0.095 -0.007 0.107 0.367 ACTUAL -0.834 -5.904 4.996 5.960 0.118 -0.001 0.072 0.138 0.184 3a: 22a 5a: 20a 4a C -0.068 -3.149 2.684 3.149 0.002 0.116 0.055 0.128 A: T G: C 21a G 2.154 0.405 2.487 2.192 0.093 -0.028 0.009 0.098 TOTAL 2.086 -2.743 5.171 5.341 0.095 0.087 0.064 0.226 ACTUAL 2.163 -2.795 5.111 3.533 0.096 0.083 0.098 0.161 0.155 4a: 21a 6a: 19a 5a G -1.413 0.041 1.755 1.413 -0.144 0.026 -0.009 0.146 C: G T: A 20a C -0.040 -7.081 3.676 7.080 0.081 0.068 0.103 0.148 TOTAL -1.452 -7.040 5.431 8.493 -0.062 0.094 0.093 0.294 ACTUAL -1.560 -7.085 5.341 7.252 -0.091 0.086 0.105 0.164 0.170 5a: 20a 7a: 18a 6a T -2.206 -6.142 3.237 6.526 0.369 -0.069 0.208 0.429 G: C C: G 19a A -4.276 -5.357 4.079 6.853 -0.411 0.050 0.024 0.414 TOTAL -6.482 -11.499 7.316 13.378 -0.042 -0.019 0.231 0.843 ACTUAL -6.414 -11.456 7.442 13.120 -0.057 0.010 0.238 0.245 0.328 6a: 19a 8a: 17a 7a C -3.411 -4.775 2.808 5.867 -0.382 -0.015 0.128 0.403 T: A A: T 18a G -2.520 1.284 0.965 2.828 0.379 0.126 -0.044 0.401 TOTAL -5.931 -3.491 3.773 8.696 -0.003 0.111 0.083 0.804 ACTUAL -5.857 -3.459 3.915 6.801 0.029 0.101 0.089 0.138 0.556 7a: 18a 9a: 16a 8a A -0.745 1.429 4.977 1.611 0.277 0.178 0.031 0.331 C: G T: A 17a T -1.658 -4.817 2.869 5.094 -0.278 -0.182 0.130 0.357 TOTAL -2.403 -3.388 7.846 6.705 -0.001 -0.004 0.161 0.688 ACTUAL -2.647 -3.334 7.789 4.253 0.018 0.012 0.150 0.151 0.359 8a: 17a 10a: 15a 9a T 3.291 -5.619 2.692 6.511 0.535 -0.207 0.127 0.588 A: T A: T 16a A 2.592 1.033 5.843 2.789 -0.558 0.192 0.067 0.594 TOTAL 5.884 -4.586 8.536 9.301 -0.023 -0.015 0.194 1.182 ACTUAL 6.191 -4.476 8.373 7.633 -0.054 0.020 0.194 0.202 0.708 9a: 16a 11a: 14a 10a A 3.350 -3.909 2.624 5.148 -0.462 0.386 -0.074 0.607 T: A G: C 15a T 2.693 -6.190 -0.639 6.750 0.516 -0.374 0.203 0.669 TOTAL 6.043 -10.099 1.985 11.898 0.054 0.012 0.130 1.276 ACTUAL 5.878 -10.178 2.073 11.753 0.108 0.009 0.096 0.144 0.794 10a: 15a 12a: 13a 11a G -4.099 -2.439 1.711 4.769 0.062 -0.089 0.033 0.114 A: T T: A 14a C 0.101 -5.976 3.460 5.976 -0.075 0.173 0.001 0.188 TOTAL -3.998 -8.414 5.172 10.745 -0.013 0.084 0.034 0.302 ACTUAL -4.010 -8.537 4.954 9.429 -0.037 0.084 0.110 0.143 0.175