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). 2.DAT YOUR REFERENCE ATOM INPUT FILENAME IS- [MARLA.RNASTAT]BASES.INN Checking Numbers and RMS Values CHAIN a BASE 1 G RMS = 0.347479E-01 CHAIN a BASE 2 A RMS = 0.142439E-01 CHAIN a BASE 3 A RMS = 0.144256E-01 CHAIN a BASE 4 G RMS = 0.348641E-01 CHAIN a BASE 5 A RMS = 0.143979E-01 CHAIN a BASE 6 A RMS = 0.143028E-01 CHAIN a BASE 7 G RMS = 0.346757E-01 CHAIN a BASE 8 A RMS = 0.142538E-01 CHAIN a BASE 9 A RMS = 0.142938E-01 CHAIN a BASE 10 G RMS = 0.346914E-01 CHAIN a BASE 11 A RMS = 0.143524E-01 CHAIN a BASE 12 A RMS = 0.142394E-01 CHAIN a BASE 13 T RMS = 0.817933E-02 CHAIN a BASE 14 T RMS = 0.794264E-02 CHAIN a BASE 15 C RMS = 0.203920E-01 CHAIN a BASE 16 T RMS = 0.803282E-02 CHAIN a BASE 17 T RMS = 0.769840E-02 CHAIN a BASE 18 C RMS = 0.203675E-01 CHAIN a BASE 19 T RMS = 0.791428E-02 CHAIN a BASE 20 T RMS = 0.788951E-02 CHAIN a BASE 21 C RMS = 0.203656E-01 CHAIN a BASE 22 T RMS = 0.767137E-02 CHAIN a BASE 23 T RMS = 0.784920E-02 CHAIN a BASE 24 C RMS = 0.204510E-01 2.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 G 24a C 5.650 -2.325 6.068 6.107 -0.188 0.141 0.159 0.284 2a A 23a T 4.565 -11.391 4.493 12.269 0.103 -0.012 0.077 0.129 3a A 22a T 8.310 -7.921 5.876 11.475 0.153 0.000 0.233 0.279 4a G 21a C 6.313 -1.933 4.846 6.601 -0.051 0.099 0.139 0.178 5a A 20a T 5.848 -10.439 6.456 11.959 0.166 -0.005 0.198 0.259 6a A 19a T 8.763 -6.553 7.149 10.935 0.187 0.046 0.465 0.504 7a G 18a C -1.835 -1.928 5.429 2.661 -0.038 0.100 -0.074 0.130 8a A 17a T -0.810 -6.129 10.353 6.173 0.241 0.060 0.135 0.283 9a A 16a T 6.687 -2.811 11.110 7.242 0.148 0.082 0.332 0.373 10a G 15a C -2.660 -3.492 5.657 4.388 -0.059 0.095 -0.098 0.149 11a A 14a T -1.668 -11.599 16.540 11.678 0.217 0.153 0.209 0.338 12a A 13a T -3.712 -6.052 3.701 7.098 0.180 0.062 0.160 0.248 THE NUMBER OF SAMPLES= 12 -------------------------------------------------------------------------------------------- MEAN= 2.954 -6.048 7.306 8.215 0.088 0.068 0.161 0.263 STANDARD DEVIATION= 4.475 3.502 3.495 3.154 0.131 0.052 0.147 0.105 2.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 1.273 -1.068 37.471 1.633 0.024 -0.769 3.004 3.101 2a: 23a 3a: 22a -1.667 -3.279 37.942 3.612 0.118 -0.596 2.926 2.988 3a: 22a 4a: 21a -1.925 -3.000 36.624 3.504 -0.229 -0.766 3.033 3.136 4a: 21a 5a: 20a 1.825 -7.260 41.153 7.326 0.093 -0.403 3.067 3.094 5a: 20a 6a: 19a -3.045 -14.016 40.275 14.048 0.163 -0.511 3.097 3.143 6a: 19a 7a: 18a 1.770 -12.948 37.633 12.834 -0.058 -1.109 3.416 3.591 7a: 18a 8a: 17a 1.818 -13.934 39.939 13.767 0.379 -0.580 3.267 3.339 8a: 17a 9a: 16a -2.026 -14.182 38.783 14.053 -0.036 -0.634 3.129 3.193 9a: 16a 10a: 15a 1.499 -13.498 37.600 13.338 -0.441 -1.030 3.466 3.642 10a: 15a 11a: 14a 2.305 -12.697 41.331 12.625 0.628 -0.376 3.244 3.325 11a: 14a 12a: 13a -3.712 -6.334 40.415 7.190 -1.106 -0.236 2.995 3.201 THE NUMBER OF SAMPLES= 11 ------------------------------------------------------------------------------------------------- MEAN= -0.171 -9.292 39.015 9.448 -0.042 -0.637 3.149 3.250 STANDARD DEVIATION= 2.180 4.924 1.583 4.649 0.431 0.255 0.169 0.197 2.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 G 2a A 2.854 -3.883 36.678 4.737 -0.872 -0.657 3.099 3.286 2a A 3a A 3.304 0.507 38.643 3.280 -0.812 -0.343 3.055 3.180 3a A 4a G -1.338 2.295 36.203 2.613 -1.377 -0.456 3.025 3.354 4a G 5a A 3.453 -9.246 42.289 9.647 -0.944 -0.194 3.232 3.373 5a A 6a A 0.680 -9.481 41.433 9.299 -0.904 -0.166 3.246 3.374 6a A 7a G -2.558 -9.558 37.109 9.722 -1.280 -0.899 3.297 3.649 7a G 8a A 2.705 -16.613 42.165 16.451 -0.673 -0.551 3.460 3.567 8a A 9a A 1.882 -11.581 39.471 11.501 -1.266 -0.360 3.241 3.498 9a A 10a G -2.968 -13.102 35.148 13.224 -1.694 -0.819 3.381 3.870 10a G 11a A 4.211 -17.788 46.307 17.782 -0.368 -0.334 3.504 3.539 11a A 12a A -2.275 -4.240 34.094 4.741 -2.197 -0.078 3.043 3.754 13a T 14a T 5.480 -8.404 46.660 9.757 0.025 -0.177 3.139 3.144 14a T 15a C -0.263 -7.887 36.142 7.761 -1.652 -0.212 3.128 3.544 15a C 16a T -5.904 -13.626 40.188 14.545 -0.812 -1.065 3.635 3.874 16a T 17a T 5.644 -17.123 37.895 17.699 -1.219 -0.663 3.097 3.394 17a T 18a C -0.828 -11.344 37.653 11.170 -1.439 -0.461 3.149 3.493 18a C 19a T -6.247 -16.122 38.250 16.968 -1.157 -1.196 3.642 4.004 19a T 20a T 6.394 -18.676 38.577 19.365 -1.260 -0.706 3.096 3.416 20a T 21a C -0.164 -5.286 40.043 5.182 -1.146 -0.490 3.016 3.264 21a C 22a T 2.276 -8.333 36.700 8.491 -0.927 -0.974 3.129 3.405 22a T 23a T 6.379 -7.230 36.631 9.478 -1.065 -0.749 2.954 3.228 23a T 24a C 0.484 1.629 38.297 1.668 -0.920 -0.790 3.028 3.261 THE NUMBER OF SAMPLES= 22 -------------------------------------------------------------------------------------------- MEAN= 1.055 -9.322 38.935 10.231 -1.089 -0.561 3.209 3.476 STANDARD DEVIATION= 3.577 6.004 3.167 5.166 0.451 0.309 0.195 0.229 2.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 -1.633 -1.945 37.507 -1.062 0.122 3.024 2a: 23a 3a: 22a -4.937 2.509 38.120 -0.524 -0.378 2.959 3a: 22a 4a: 21a -4.678 3.002 36.797 -0.816 0.108 3.093 4a: 21a 5a: 20a -9.998 -2.513 41.829 0.190 0.060 3.091 5a: 20a 6a: 19a -19.155 4.162 42.753 0.728 -0.533 3.073 6a: 19a 7a: 18a -18.974 -2.594 39.838 0.090 0.320 3.584 7a: 18a 8a: 17a -19.220 -2.507 42.339 0.734 -0.324 3.289 8a: 17a 9a: 16a -20.071 2.868 41.344 0.677 -0.174 3.155 9a: 16a 10a: 15a -19.739 -2.192 39.977 0.290 0.845 3.591 10a: 15a 11a: 14a -17.061 -3.097 43.299 0.808 -0.612 3.240 11a: 14a 12a: 13a -8.882 5.206 41.076 0.337 1.182 3.083 THE NUMBER OF SAMPLES= 11 ------------------------------------------------------------------------------- MEAN= -13.123 0.264 40.444 0.132 0.056 3.198 STANDARD DEVIATION= 6.832 3.085 2.091 0.625 0.535 0.203 2.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 G 2a A -6.032 -4.432 36.994 -0.522 -0.057 3.074 2a A 3a A 0.751 -4.887 38.787 -0.577 -0.199 2.970 3a A 4a G 3.626 2.113 36.301 -1.039 0.223 3.039 4a G 5a A -12.307 -4.596 43.425 0.663 -0.187 3.114 5a A 6a A -12.888 -0.925 42.509 0.773 -0.489 3.186 6a A 7a G -14.421 3.860 38.405 -0.059 -0.212 3.495 7a G 8a A -21.479 -3.497 45.401 0.966 -0.663 3.375 8a A 9a A -16.340 -2.656 41.178 0.793 0.205 3.150 9a A 10a G -20.401 4.622 37.628 0.672 0.379 3.577 10a G 11a A -20.963 -4.962 49.784 1.110 -1.014 3.347 11a A 12a A -7.079 3.797 34.432 0.517 1.556 3.168 13a T 14a T -10.165 -6.628 47.727 0.468 -1.391 3.103 14a T 15a C -12.310 0.411 36.994 0.726 0.761 3.113 15a C 16a T -18.608 8.062 42.844 0.226 -1.426 3.860 16a T 17a T -24.165 -7.965 41.965 0.871 0.487 2.903 17a T 18a C -16.763 1.224 39.333 0.699 0.229 3.178 18a C 19a T -22.682 8.789 41.976 0.460 -1.018 3.950 19a T 20a T -25.639 -8.777 43.334 0.887 0.530 2.875 20a T 21a C -7.520 0.233 40.391 -0.132 -0.166 3.059 21a C 22a T -12.776 -3.490 37.703 -0.409 -0.074 3.205 22a T 23a T -11.058 -9.756 37.879 -0.291 0.594 2.820 23a T 24a C 2.435 -0.724 38.335 -1.397 -0.349 2.980 THE NUMBER OF SAMPLES= 22 -------------------------------------------------------------------------- MEAN= -13.036 -1.372 40.606 0.246 -0.104 3.206 STANDARD DEVIATION= 8.139 5.043 3.744 0.680 0.704 0.287 2.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 A 3.817 -4.584 1.914 5.964 0.050 -0.092 0.066 0.123 G: C A: T 23a T 0.769 -6.876 2.381 6.918 0.060 0.080 0.064 0.118 TOTAL 4.586 -11.459 4.295 12.882 0.110 -0.012 0.130 0.242 ACTUAL 4.565 -11.391 4.493 12.269 0.103 -0.012 0.077 0.129 0.128 2a: 23a 4a: 21a 3a A 4.309 -4.083 3.597 5.935 0.299 0.083 -0.012 0.311 A: T G: C 22a T 4.039 -3.797 2.280 5.543 -0.168 -0.099 0.229 0.301 TOTAL 8.348 -7.880 5.878 11.478 0.131 -0.016 0.217 0.612 ACTUAL 8.310 -7.921 5.876 11.475 0.153 0.000 0.233 0.279 0.279 3a: 22a 5a: 20a 4a G 1.232 1.216 0.124 1.731 -0.133 -0.130 -0.024 0.188 A: T A: T 21a C 5.136 -3.191 4.634 6.045 0.149 0.235 0.113 0.300 TOTAL 6.368 -1.975 4.758 7.775 0.015 0.105 0.089 0.487 ACTUAL 6.313 -1.933 4.846 6.601 -0.051 0.099 0.139 0.178 0.275 4a: 21a 6a: 19a 5a A 5.590 -1.747 3.500 5.856 0.111 0.072 0.072 0.151 G: C A: T 20a T 0.497 -8.808 2.540 8.821 0.048 -0.083 0.197 0.219 TOTAL 6.087 -10.555 6.040 14.677 0.159 -0.012 0.269 0.370 ACTUAL 5.848 -10.439 6.456 11.959 0.166 -0.005 0.198 0.259 0.110 5a: 20a 7a: 18a 6a A 1.888 -3.683 4.983 4.137 0.243 0.335 -0.049 0.417 A: T G: C 19a T 6.916 -2.611 2.350 7.392 -0.090 -0.301 0.403 0.511 TOTAL 8.804 -6.294 7.332 11.529 0.152 0.034 0.354 0.928 ACTUAL 8.763 -6.553 7.149 10.935 0.187 0.046 0.465 0.504 0.443 6a: 19a 8a: 17a 7a G -0.938 -0.458 1.567 1.044 -0.196 -0.224 0.047 0.301 A: T A: T 18a C -0.893 -1.451 3.870 1.703 0.183 0.332 -0.123 0.399 TOTAL -1.831 -1.908 5.437 2.747 -0.013 0.109 -0.076 0.700 ACTUAL -1.835 -1.928 5.429 2.661 -0.038 0.100 -0.074 0.130 0.505 7a: 18a 9a: 16a 8a A 1.627 -3.019 5.706 3.428 0.433 0.043 0.165 0.465 G: C A: T 17a T -2.393 -3.295 4.539 4.071 -0.203 -0.010 0.019 0.205 TOTAL -0.766 -6.314 10.245 7.499 0.229 0.033 0.185 0.670 ACTUAL -0.810 -6.129 10.353 6.173 0.241 0.060 0.135 0.283 0.307 8a: 17a 10a: 15a 9a A 1.495 -1.645 6.175 2.222 0.368 0.232 -0.093 0.445 A: T G: C 16a T 5.172 -0.953 4.999 5.257 -0.225 -0.180 0.348 0.452 TOTAL 6.667 -2.598 11.174 7.480 0.143 0.051 0.255 0.897 ACTUAL 6.687 -2.811 11.110 7.242 0.148 0.082 0.332 0.373 0.248 9a: 16a 11a: 14a 10a G -1.787 -2.157 0.951 2.801 -0.535 -0.290 0.076 0.614 A: T A: T 15a C -0.952 -1.271 4.709 1.587 0.524 0.410 -0.179 0.689 TOTAL -2.739 -3.427 5.660 4.388 -0.012 0.120 -0.103 1.303 ACTUAL -2.660 -3.492 5.657 4.388 -0.059 0.095 -0.098 0.149 0.629 10a: 15a 12a: 13a 11a A 2.092 -9.343 8.514 9.566 1.182 -0.099 0.240 1.211 G: C A: T 14a T -4.193 -2.714 7.650 4.991 -0.987 0.098 -0.028 0.992 TOTAL -2.100 -12.057 16.164 14.557 0.195 -0.001 0.212 2.203 ACTUAL -1.668 -11.599 16.540 11.678 0.217 0.153 0.209 0.338 1.121