==> seq1_ss1_simrna_rpr.pdb <== REMARK 250 Model edited with rna-tools REMARK 250 ver 3.8.13.1+39.gca2dada6.dirty REMARK 250 https://github.com/mmagnus/rna-tools REMARK 250 Tue Jan 27 20:38:32 2026 ATOM 1 P U A 1 -4.765 18.652 99.203 1.00 0.00 P ATOM 2 OP1 U A 1 -4.792 17.173 99.360 1.00 0.00 O ATOM 3 OP2 U A 1 -3.468 19.340 98.958 1.00 0.00 O ATOM 4 O5' U A 1 -5.798 19.077 98.068 1.00 0.00 O ATOM 5 C5' U A 1 -7.137 18.573 98.099 1.00 0.00 C ATOM 6 C4' U A 1 -7.898 19.023 96.882 1.00 0.00 C ==> seq1_ss2_farfar_rpr.pdb <== REMARK 250 Model edited with rna-tools REMARK 250 ver 3.8.13.1+39.gca2dada6.dirty REMARK 250 https://github.com/mmagnus/rna-tools REMARK 250 Tue Jan 27 20:38:32 2026 REMARK 250 Fixed atoms/residues: REMARK 250 - add OP3 at the beginning of the chain in chain: A residue # 1 ATOM 1 P U A 1 12.859 -13.444 -23.952 1.00 11.89 P ATOM 2 OP1 U A 1 11.963 -13.439 -25.134 1.00 14.35 O ATOM 3 OP2 U A 1 12.335 -13.783 -22.619 1.00 12.68 O ATOM 4 O5' U A 1 14.104 -14.400 -24.191 1.00 10.34 O ==> seq1_ss2_simrna_rpr.pdb <== REMARK 250 Model edited with rna-tools REMARK 250 ver 3.8.13.1+39.gca2dada6.dirty REMARK 250 https://github.com/mmagnus/rna-tools REMARK 250 Tue Jan 27 20:38:33 2026 ATOM 1 P U A 1 -13.969 11.086 50.612 1.00 0.00 P ATOM 2 OP1 U A 1 -12.621 11.289 51.189 1.00 0.00 O ATOM 3 OP2 U A 1 -14.466 12.031 49.586 1.00 0.00 O ATOM 4 O5' U A 1 -14.102 9.646 49.914 1.00 0.00 O ATOM 5 C5' U A 1 -13.113 8.687 50.262 1.00 0.00 C ATOM 6 C4' U A 1 -13.499 7.234 50.102 1.00 0.00 C ==> seq1_ss2_trrosetta_simrna_rpr.pdb <== REMARK 250 Model edited with rna-tools REMARK 250 ver 3.8.13.1+39.gca2dada6.dirty REMARK 250 https://github.com/mmagnus/rna-tools REMARK 250 Tue Jan 27 20:38:33 2026 ATOM 1 P U A 1 36.635 -47.789 -16.284 1.00 17.92 P ATOM 2 OP1 U A 1 37.246 -46.527 -16.759 1.00 17.92 O ATOM 3 OP2 U A 1 35.581 -48.469 -17.073 1.00 17.92 O ATOM 4 O5' U A 1 37.774 -48.895 -16.115 1.00 17.92 O ATOM 5 C5' U A 1 38.297 -49.525 -17.269 1.00 17.92 C ATOM 6 C4' U A 1 38.607 -50.975 -17.016 1.00 17.92 C ==> seq1_ss3_farfar_rpr.pdb <== REMARK 250 Model edited with rna-tools REMARK 250 ver 3.8.13.1+39.gca2dada6.dirty REMARK 250 https://github.com/mmagnus/rna-tools REMARK 250 Tue Jan 27 20:38:34 2026 REMARK 250 Fixed atoms/residues: REMARK 250 - add OP3 at the beginning of the chain in chain: A residue # 1 ATOM 1 P U A 1 -21.736 -5.457 -2.277 1.00 11.89 P ATOM 2 OP1 U A 1 -21.443 -4.101 -1.755 1.00 14.35 O ATOM 3 OP2 U A 1 -21.171 -6.649 -1.624 1.00 12.68 O ATOM 4 O5' U A 1 -23.303 -5.704 -2.361 1.00 10.34 O ==> seq2_ss1_af_rpr.pdb <== REMARK 250 Model edited with rna-tools REMARK 250 ver 3.8.13.1+39.gca2dada6.dirty REMARK 250 https://github.com/mmagnus/rna-tools REMARK 250 Tue Jan 27 20:38:35 2026 ATOM 1 P G A 1 -40.020 -5.076 -3.262 1.00 21.31 P ATOM 2 OP1 G A 1 -40.382 -6.316 -3.947 1.00 20.16 O ATOM 3 OP2 G A 1 -38.604 -4.778 -3.057 1.00 20.27 O ATOM 4 O5' G A 1 -40.653 -3.865 -4.093 1.00 21.07 O ATOM 5 C5' G A 1 -41.982 -3.889 -4.554 1.00 21.44 C ATOM 6 C4' G A 1 -42.379 -2.575 -5.168 1.00 21.91 C ==> seq2_ss1_af_simrna_rpr.pdb <== REMARK 250 Model edited with rna-tools REMARK 250 ver 3.8.13.1+39.gca2dada6.dirty REMARK 250 https://github.com/mmagnus/rna-tools REMARK 250 Tue Jan 27 20:38:35 2026 ATOM 1 P G A 1 -40.012 -5.083 -3.260 1.00 21.91 P ATOM 2 OP1 G A 1 -40.451 -6.322 -3.940 1.00 21.91 O ATOM 3 OP2 G A 1 -38.561 -4.800 -3.116 1.00 21.91 O ATOM 4 O5' G A 1 -40.663 -3.840 -4.019 1.00 21.91 O ATOM 5 C5' G A 1 -42.030 -3.870 -4.472 1.00 21.91 C ATOM 6 C4' G A 1 -42.379 -2.575 -5.168 1.00 21.91 C ==> seq2_ss1_farfar_cluster_rpr.pdb <== REMARK 250 Model edited with rna-tools REMARK 250 ver 3.8.13.1+39.gca2dada6.dirty REMARK 250 https://github.com/mmagnus/rna-tools REMARK 250 Tue Jan 27 20:38:36 2026 REMARK 250 Fixed atoms/residues: REMARK 250 - add OP3 at the beginning of the chain in chain: A residue # 1 ATOM 1 P G A 1 -35.793 -13.472 14.414 1.00 11.89 P ATOM 2 OP1 G A 1 -37.254 -13.267 14.564 1.00 14.35 O ATOM 3 OP2 G A 1 -35.165 -14.725 14.861 1.00 12.68 O ATOM 4 O5' G A 1 -35.346 -13.271 12.904 1.00 10.34 O ==> seq2_ss1_simrna_rpr.pdb <== REMARK 250 Model edited with rna-tools REMARK 250 ver 3.8.13.1+39.gca2dada6.dirty REMARK 250 https://github.com/mmagnus/rna-tools REMARK 250 Tue Jan 27 20:38:36 2026 ATOM 1 P G A 1 -15.744 -1.285 -37.227 1.00 0.00 P ATOM 2 OP1 G A 1 -16.679 -0.205 -36.827 1.00 0.00 O ATOM 3 OP2 G A 1 -14.388 -1.344 -36.608 1.00 0.00 O ATOM 4 O5' G A 1 -16.482 -2.674 -36.990 1.00 0.00 O ATOM 5 C5' G A 1 -17.860 -2.850 -37.366 1.00 0.00 C ATOM 6 C4' G A 1 -18.369 -4.179 -36.864 1.00 0.00 C ==> seq2_ss1_trrosetta_simrna_rpr.pdb <== REMARK 250 Model edited with rna-tools REMARK 250 ver 3.8.13.1+39.gca2dada6.dirty REMARK 250 https://github.com/mmagnus/rna-tools REMARK 250 Tue Jan 27 20:38:37 2026 ATOM 1 P G A 1 -72.208 -7.981 25.398 1.00 16.16 P ATOM 2 OP1 G A 1 -73.474 -7.223 25.572 1.00 16.16 O ATOM 3 OP2 G A 1 -70.989 -7.270 24.937 1.00 16.16 O ATOM 4 O5' G A 1 -71.864 -8.695 26.776 1.00 16.16 O ATOM 5 C5' G A 1 -70.748 -8.277 27.552 1.00 16.16 C ATOM 6 C4' G A 1 -69.609 -9.243 27.362 1.00 16.16 C ==> seq3_briq_rpr.pdb <== REMARK 250 Model edited with rna-tools REMARK 250 ver 3.8.13.1+39.gca2dada6.dirty REMARK 250 https://github.com/mmagnus/rna-tools REMARK 250 Tue Jan 27 20:38:38 2026 REMARK 250 Fixed atoms/residues: REMARK 250 - add OP3 at the beginning of the chain in chain: A residue # 1 ATOM 1 P G A 1 250.481 255.074 347.348 1.00 11.89 P ATOM 2 OP1 G A 1 251.925 255.342 347.146 1.00 14.35 O ATOM 3 OP2 G A 1 249.527 255.244 346.241 1.00 12.68 O ATOM 4 O5' G A 1 250.252 253.604 347.904 1.00 10.34 O ==> seq4_farfar_best_1_rpr.pdb <== REMARK 250 Model edited with rna-tools REMARK 250 ver 3.8.13.1+39.gca2dada6.dirty REMARK 250 https://github.com/mmagnus/rna-tools REMARK 250 Tue Jan 27 20:38:39 2026 REMARK 250 Fixed atoms/residues: REMARK 250 - add OP3 at the beginning of the chain in chain: A residue # 1 ATOM 1 P C A 1 -83.347 4.961 -21.830 1.00 11.89 P ATOM 2 OP1 C A 1 -83.267 3.480 -21.845 1.00 14.35 O ATOM 3 OP2 C A 1 -83.639 5.706 -23.066 1.00 12.68 O ATOM 4 O5' C A 1 -84.406 5.459 -20.757 1.00 10.34 O ==> seq4_farfar_best_2_rpr.pdb <== REMARK 250 Model edited with rna-tools REMARK 250 ver 3.8.13.1+39.gca2dada6.dirty REMARK 250 https://github.com/mmagnus/rna-tools REMARK 250 Tue Jan 27 20:38:40 2026 REMARK 250 Fixed atoms/residues: REMARK 250 - add OP3 at the beginning of the chain in chain: A residue # 1 ATOM 1 P C A 1 -28.622 -11.586 -17.736 1.00 11.89 P ATOM 2 OP1 C A 1 -27.426 -11.310 -18.569 1.00 14.35 O ATOM 3 OP2 C A 1 -29.749 -10.639 -17.709 1.00 12.68 O ATOM 4 O5' C A 1 -29.246 -13.001 -18.095 1.00 10.34 O ==> seq4_farfar_cluster_1_rpr.pdb <== REMARK 250 Model edited with rna-tools REMARK 250 ver 3.8.13.1+39.gca2dada6.dirty REMARK 250 https://github.com/mmagnus/rna-tools REMARK 250 Tue Jan 27 20:38:41 2026 REMARK 250 Fixed atoms/residues: REMARK 250 - add OP3 at the beginning of the chain in chain: A residue # 1 ATOM 1 P C A 1 0.104 -0.229 -0.139 1.00 11.89 P ATOM 2 OP1 C A 1 -0.396 0.613 -1.253 1.00 14.35 O ATOM 3 OP2 C A 1 -0.214 -1.665 -0.086 1.00 12.68 O ATOM 4 O5' C A 1 1.684 -0.125 -0.018 1.00 10.34 O ==> seq4_farfar_cluster_2_rpr.pdb <== REMARK 250 Model edited with rna-tools REMARK 250 ver 3.8.13.1+39.gca2dada6.dirty REMARK 250 https://github.com/mmagnus/rna-tools REMARK 250 Tue Jan 27 20:38:42 2026 REMARK 250 Fixed atoms/residues: REMARK 250 - add OP3 at the beginning of the chain in chain: A residue # 1 ATOM 1 P C A 1 -28.622 -11.586 -17.736 1.00 11.89 P ATOM 2 OP1 C A 1 -27.426 -11.310 -18.569 1.00 14.35 O ATOM 3 OP2 C A 1 -29.749 -10.639 -17.709 1.00 12.68 O ATOM 4 O5' C A 1 -29.246 -13.001 -18.095 1.00 10.34 O ==> seq4_trrosetta_rpr.pdb <== REMARK 250 Model edited with rna-tools REMARK 250 ver 3.8.13.1+39.gca2dada6.dirty REMARK 250 https://github.com/mmagnus/rna-tools REMARK 250 Tue Jan 27 20:38:43 2026 ATOM 1 P C A 1 23.261 -45.259 -7.191 1.00 24.61 P ATOM 2 OP1 C A 1 22.543 -46.479 -7.642 1.00 24.61 O ATOM 3 OP2 C A 1 23.169 -44.016 -8.001 1.00 24.61 O ATOM 4 O5' C A 1 22.808 -44.918 -5.695 1.00 24.61 O ATOM 5 C5' C A 1 22.147 -45.880 -4.880 1.00 24.61 C ATOM 6 C4' C A 1 21.941 -45.413 -3.449 1.00 24.61 C ==> seq5_1_refined_rpr.pdb <== REMARK 250 Model edited with rna-tools REMARK 250 ver 3.8.13.1+39.gca2dada6.dirty REMARK 250 https://github.com/mmagnus/rna-tools REMARK 250 Tue Jan 27 20:38:45 2026 ATOM 1 P A A 1 -20.238 -17.509 -9.731 1.00 1.00 P ATOM 2 OP1 A A 1 -19.671 -17.964 -8.355 1.00 1.00 O ATOM 3 OP2 A A 1 -18.970 -16.856 -10.496 1.00 1.00 O ATOM 4 O5' A A 1 -20.867 -18.636 -10.492 1.00 1.00 O ATOM 5 C5' A A 1 -21.950 -19.277 -9.997 1.00 1.00 C ATOM 6 C4' A A 1 -22.498 -20.126 -11.133 1.00 1.00 C ==> seq5_2_refined_rpr.pdb <== REMARK 250 Model edited with rna-tools REMARK 250 ver 3.8.13.1+39.gca2dada6.dirty REMARK 250 https://github.com/mmagnus/rna-tools REMARK 250 Tue Jan 27 20:38:46 2026 ATOM 1 P A A 1 -7.546 -1.448 3.140 1.00 1.00 P ATOM 2 OP1 A A 1 -7.024 -0.976 4.302 1.00 1.00 O ATOM 3 OP2 A A 1 -6.604 -2.266 2.345 1.00 1.00 O ATOM 4 O5' A A 1 -8.721 -2.620 3.432 1.00 1.00 O ATOM 5 C5' A A 1 -9.935 -1.946 3.965 1.00 1.00 C ATOM 6 C4' A A 1 -10.836 -3.199 4.170 1.00 1.00 C ==> seq5_3_refined_rpr.pdb <== REMARK 250 Model edited with rna-tools REMARK 250 ver 3.8.13.1+39.gca2dada6.dirty REMARK 250 https://github.com/mmagnus/rna-tools REMARK 250 Tue Jan 27 20:38:47 2026 ATOM 1 P A A 1 -5.910 -48.021 -12.641 1.00 1.00 P ATOM 2 OP1 A A 1 -7.149 -47.531 -11.997 1.00 1.00 O ATOM 3 OP2 A A 1 -5.602 -47.253 -13.690 1.00 1.00 O ATOM 4 O5' A A 1 -5.146 -49.004 -11.709 1.00 1.00 O ATOM 5 C5' A A 1 -5.741 -49.912 -10.938 1.00 1.00 C ATOM 6 C4' A A 1 -4.664 -50.833 -10.344 1.00 1.00 C ==> seq5_4_refined_rpr.pdb <== REMARK 250 Model edited with rna-tools REMARK 250 ver 3.8.13.1+39.gca2dada6.dirty REMARK 250 https://github.com/mmagnus/rna-tools REMARK 250 Tue Jan 27 20:38:49 2026 ATOM 1 P A A 1 5.287 -25.378 4.951 1.00 1.00 P ATOM 2 OP1 A A 1 5.296 -26.660 4.211 1.00 1.00 O ATOM 3 OP2 A A 1 6.523 -24.419 4.758 1.00 1.00 O ATOM 4 O5' A A 1 3.994 -24.296 4.729 1.00 1.00 O ATOM 5 C5' A A 1 2.770 -24.394 5.183 1.00 1.00 C ATOM 6 C4' A A 1 1.761 -23.479 5.008 1.00 1.00 C ==> seq5_trrosetta_1_rpr.pdb <== REMARK 250 Model edited with rna-tools REMARK 250 ver 3.8.13.1+39.gca2dada6.dirty REMARK 250 https://github.com/mmagnus/rna-tools REMARK 250 Tue Jan 27 20:38:50 2026 ATOM 1 P A A 1 0.063 0.389 -0.682 1.00 13.85 P ATOM 2 OP1 A A 1 -0.489 -0.985 -0.543 1.00 13.85 O ATOM 3 OP2 A A 1 -0.756 1.538 -0.206 1.00 13.85 O ATOM 4 O5' A A 1 1.477 0.447 0.070 1.00 13.85 O ATOM 5 C5' A A 1 2.235 1.652 0.114 1.00 13.85 C ATOM 6 C4' A A 1 3.670 1.442 0.576 1.00 13.85 C DONE!