from __future__ import absolute_import, division, print_function from cctbx.array_family import flex import os import mmtbx.model import libtbx.load_env from six.moves import cStringIO as StringIO from libtbx.utils import format_cpu_times, null_out from libtbx.test_utils import approx_equal, show_diff import iotbx.pdb from mmtbx.refinement import geometry_minimization from six.moves import range pdb_str_00=""" CRYST1 107.161 107.161 93.144 90.00 90.00 120.00 H 3 9 ATOM 1 O5' DG A 101 30.353 -5.691 -5.826 1.00 80.00 O ATOM 2 C5' DG A 101 30.297 -7.106 -5.681 1.00 80.00 C ATOM 3 C4' DG A 101 31.674 -7.699 -5.430 1.00 80.00 C ATOM 4 O4' DG A 101 32.464 -7.647 -6.648 1.00 80.00 O ATOM 5 C3' DG A 101 32.550 -6.981 -4.410 1.00 80.00 C ATOM 6 O3' DG A 101 32.270 -7.276 -3.034 1.00 80.00 O ATOM 7 C2' DG A 101 33.901 -7.575 -4.788 1.00 80.00 C ATOM 8 C1' DG A 101 33.833 -7.502 -6.309 1.00 80.00 C ATOM 9 N9 DG A 101 34.347 -6.243 -6.849 1.00 80.00 N ATOM 10 C8 DG A 101 34.042 -5.661 -8.057 1.00 80.00 C ATOM 11 N7 DG A 101 34.661 -4.530 -8.261 1.00 80.00 N ATOM 12 C5 DG A 101 35.428 -4.345 -7.115 1.00 80.00 C ATOM 13 C6 DG A 101 36.313 -3.295 -6.755 1.00 80.00 C ATOM 14 O6 DG A 101 36.612 -2.277 -7.397 1.00 80.00 O ATOM 15 N1 DG A 101 36.884 -3.505 -5.501 1.00 80.00 N ATOM 16 C2 DG A 101 36.635 -4.591 -4.694 1.00 80.00 C ATOM 17 N2 DG A 101 37.276 -4.631 -3.515 1.00 80.00 N ATOM 18 N3 DG A 101 35.812 -5.576 -5.021 1.00 80.00 N ATOM 19 C4 DG A 101 35.243 -5.392 -6.238 1.00 80.00 C ATOM 20 P DA A 102 30.891 -7.850 -2.448 1.00 80.00 P ATOM 21 OP1 DA A 102 30.412 -8.967 -3.293 1.00 80.00 O ATOM 22 OP2 DA A 102 30.002 -6.702 -2.162 1.00 80.00 O ATOM 23 O5' DA A 102 31.376 -8.460 -1.047 1.00 80.00 O ATOM 24 C5' DA A 102 31.097 -7.804 0.189 1.00 80.00 C ATOM 25 C4' DA A 102 32.133 -6.759 0.563 1.00 80.00 C ATOM 26 O4' DA A 102 32.644 -6.131 -0.644 1.00 80.00 O ATOM 27 C3' DA A 102 31.556 -5.636 1.422 1.00 80.00 C ATOM 28 O3' DA A 102 32.520 -5.085 2.335 1.00 80.00 O ATOM 29 C2' DA A 102 31.162 -4.648 0.332 1.00 80.00 C ATOM 30 C1' DA A 102 32.411 -4.745 -0.532 1.00 80.00 C ATOM 31 N9 DA A 102 32.281 -4.091 -1.831 1.00 80.00 N ATOM 32 C8 DA A 102 31.274 -4.232 -2.743 1.00 80.00 C ATOM 33 N7 DA A 102 31.432 -3.498 -3.820 1.00 80.00 N ATOM 34 C5 DA A 102 32.622 -2.824 -3.594 1.00 80.00 C ATOM 35 C6 DA A 102 33.346 -1.887 -4.362 1.00 80.00 C ATOM 36 N6 DA A 102 32.949 -1.453 -5.565 1.00 80.00 N ATOM 37 N1 DA A 102 34.499 -1.412 -3.839 1.00 80.00 N ATOM 38 C2 DA A 102 34.895 -1.846 -2.634 1.00 80.00 C ATOM 39 N3 DA A 102 34.299 -2.721 -1.825 1.00 80.00 N ATOM 40 C4 DA A 102 33.157 -3.176 -2.369 1.00 80.00 C ATOM 41 P DG A 103 32.892 -3.523 2.296 1.00 80.00 P ATOM 42 OP1 DG A 103 31.640 -2.754 2.139 1.00 80.00 O ATOM 43 OP2 DG A 103 34.006 -3.355 1.337 1.00 80.00 O ATOM 44 O5' DG A 103 33.448 -3.176 3.750 1.00 80.00 O ATOM 45 C5' DG A 103 34.359 -2.085 3.897 1.00 80.00 C ATOM 46 C4' DG A 103 33.856 -0.766 3.315 1.00 80.00 C ATOM 47 O4' DG A 103 33.647 -0.832 1.878 1.00 80.00 O ATOM 48 C3' DG A 103 32.546 -0.221 3.892 1.00 80.00 C ATOM 49 O3' DG A 103 32.798 0.912 4.728 1.00 80.00 O ATOM 50 C2' DG A 103 31.711 0.163 2.669 1.00 80.00 C ATOM 51 C1' DG A 103 32.785 0.248 1.593 1.00 80.00 C ATOM 52 N9 DG A 103 32.290 0.224 0.218 1.00 80.00 N ATOM 53 C8 DG A 103 31.420 -0.663 -0.371 1.00 80.00 C ATOM 54 N7 DG A 103 31.177 -0.390 -1.626 1.00 80.00 N ATOM 55 C5 DG A 103 31.930 0.751 -1.886 1.00 80.00 C ATOM 56 C6 DG A 103 32.073 1.512 -3.074 1.00 80.00 C ATOM 57 O6 DG A 103 31.547 1.330 -4.185 1.00 80.00 O ATOM 58 N1 DG A 103 32.939 2.590 -2.882 1.00 80.00 N ATOM 59 C2 DG A 103 33.581 2.892 -1.700 1.00 80.00 C ATOM 60 N2 DG A 103 34.377 3.970 -1.703 1.00 80.00 N ATOM 61 N3 DG A 103 33.453 2.187 -0.586 1.00 80.00 N ATOM 62 C4 DG A 103 32.616 1.137 -0.755 1.00 80.00 C ATOM 63 P DC A 104 33.914 2.007 4.370 1.00 80.00 P ATOM 64 OP1 DC A 104 33.746 2.431 2.963 1.00 80.00 O ATOM 65 OP2 DC A 104 35.221 1.487 4.828 1.00 80.00 O ATOM 66 O5' DC A 104 33.518 3.233 5.318 1.00 80.00 O ATOM 67 C5' DC A 104 32.464 4.116 4.954 1.00 80.00 C ATOM 68 C4' DC A 104 32.995 5.260 4.108 1.00 80.00 C ATOM 69 O4' DC A 104 33.087 4.852 2.719 1.00 80.00 O ATOM 70 C3' DC A 104 32.140 6.517 4.153 1.00 80.00 C ATOM 71 O3' DC A 104 32.959 7.623 4.504 1.00 80.00 O ATOM 72 C2' DC A 104 31.561 6.667 2.748 1.00 80.00 C ATOM 73 C1' DC A 104 32.386 5.736 1.867 1.00 80.00 C ATOM 74 N1 DC A 104 31.555 4.918 0.935 1.00 80.00 N ATOM 75 C2 DC A 104 31.268 5.380 -0.358 1.00 80.00 C ATOM 76 O2 DC A 104 31.708 6.476 -0.729 1.00 80.00 O ATOM 77 N3 DC A 104 30.510 4.607 -1.178 1.00 80.00 N ATOM 78 C4 DC A 104 30.047 3.428 -0.756 1.00 80.00 C ATOM 79 N4 DC A 104 29.303 2.699 -1.599 1.00 80.00 N ATOM 80 C5 DC A 104 30.329 2.944 0.557 1.00 80.00 C ATOM 81 C6 DC A 104 31.078 3.711 1.357 1.00 80.00 C ATOM 82 P DA A 105 32.348 9.101 4.508 1.00 80.00 P ATOM 83 OP1 DA A 105 33.057 9.891 5.540 1.00 80.00 O ATOM 84 OP2 DA A 105 30.874 8.987 4.560 1.00 80.00 O ATOM 85 O5' DA A 105 32.742 9.657 3.061 1.00 80.00 O ATOM 86 C5' DA A 105 32.655 11.052 2.825 1.00 80.00 C ATOM 87 C4' DA A 105 31.977 11.333 1.502 1.00 80.00 C ATOM 88 O4' DA A 105 31.468 10.103 0.922 1.00 80.00 O ATOM 89 C3' DA A 105 30.771 12.251 1.639 1.00 80.00 C ATOM 90 O3' DA A 105 30.631 13.044 0.476 1.00 80.00 O ATOM 91 C2' DA A 105 29.635 11.242 1.738 1.00 80.00 C ATOM 92 C1' DA A 105 30.103 10.319 0.626 1.00 80.00 C ATOM 93 N9 DA A 105 29.385 9.052 0.528 1.00 80.00 N ATOM 94 C8 DA A 105 29.276 8.056 1.456 1.00 80.00 C ATOM 95 N7 DA A 105 28.553 7.035 1.056 1.00 80.00 N ATOM 96 C5 DA A 105 28.157 7.390 -0.224 1.00 80.00 C ATOM 97 C6 DA A 105 27.371 6.744 -1.202 1.00 80.00 C ATOM 98 N6 DA A 105 26.808 5.541 -1.035 1.00 80.00 N ATOM 99 N1 DA A 105 27.180 7.393 -2.369 1.00 80.00 N ATOM 100 C2 DA A 105 27.737 8.597 -2.550 1.00 80.00 C ATOM 101 N3 DA A 105 28.492 9.298 -1.711 1.00 80.00 N ATOM 102 C4 DA A 105 28.663 8.631 -0.560 1.00 80.00 C ATOM 103 P DG A 106 29.602 14.269 0.500 1.00 80.00 P ATOM 104 OP1 DG A 106 30.398 15.515 0.488 1.00 80.00 O ATOM 105 OP2 DG A 106 28.639 14.023 1.596 1.00 80.00 O ATOM 106 O5' DG A 106 28.803 14.154 -0.882 1.00 80.00 O ATOM 107 C5' DG A 106 27.826 15.145 -1.198 1.00 80.00 C ATOM 108 C4' DG A 106 26.772 14.584 -2.133 1.00 80.00 C ATOM 109 O4' DG A 106 26.868 13.141 -2.116 1.00 80.00 O ATOM 110 C3' DG A 106 25.340 14.942 -1.740 1.00 80.00 C ATOM 111 O3' DG A 106 24.833 16.023 -2.560 1.00 80.00 O ATOM 112 C2' DG A 106 24.552 13.634 -1.861 1.00 80.00 C ATOM 113 C1' DG A 106 25.585 12.567 -2.228 1.00 80.00 C ATOM 114 N9 DG A 106 25.534 11.397 -1.358 1.00 80.00 N ATOM 115 C8 DG A 106 25.934 11.315 -0.046 1.00 80.00 C ATOM 116 N7 DG A 106 25.762 10.132 0.476 1.00 80.00 N ATOM 117 C5 DG A 106 25.214 9.382 -0.557 1.00 80.00 C ATOM 118 C6 DG A 106 24.814 8.026 -0.587 1.00 80.00 C ATOM 119 O6 DG A 106 24.869 7.190 0.326 1.00 80.00 O ATOM 120 N1 DG A 106 24.309 7.667 -1.836 1.00 80.00 N ATOM 121 C2 DG A 106 24.205 8.514 -2.916 1.00 80.00 C ATOM 122 N2 DG A 106 23.693 7.995 -4.040 1.00 80.00 N ATOM 123 N3 DG A 106 24.575 9.786 -2.899 1.00 80.00 N ATOM 124 C4 DG A 106 25.068 10.148 -1.691 1.00 80.00 C ATOM 125 P DC A 107 23.670 15.874 -3.663 1.00 80.00 P ATOM 126 OP1 DC A 107 23.922 16.896 -4.704 1.00 80.00 O ATOM 127 OP2 DC A 107 22.371 15.869 -2.955 1.00 80.00 O ATOM 128 O5' DC A 107 23.890 14.422 -4.301 1.00 80.00 O ATOM 129 C5' DC A 107 23.186 14.007 -5.467 1.00 80.00 C ATOM 130 C4' DC A 107 22.016 13.088 -5.146 1.00 80.00 C ATOM 131 O4' DC A 107 22.408 11.990 -4.275 1.00 80.00 O ATOM 132 C3' DC A 107 20.823 13.746 -4.452 1.00 80.00 C ATOM 133 O3' DC A 107 19.648 13.446 -5.181 1.00 80.00 O ATOM 134 C2' DC A 107 20.782 13.047 -3.098 1.00 80.00 C ATOM 135 C1' DC A 107 21.224 11.674 -3.575 1.00 80.00 C ATOM 136 N1 DC A 107 21.443 10.667 -2.497 1.00 80.00 N ATOM 137 C2 DC A 107 21.175 9.318 -2.763 1.00 80.00 C ATOM 138 O2 DC A 107 20.780 8.993 -3.891 1.00 80.00 O ATOM 139 N3 DC A 107 21.367 8.406 -1.776 1.00 80.00 N ATOM 140 C4 DC A 107 21.795 8.797 -0.574 1.00 80.00 C ATOM 141 N4 DC A 107 21.968 7.861 0.368 1.00 80.00 N ATOM 142 C5 DC A 107 22.064 10.168 -0.286 1.00 80.00 C ATOM 143 C6 DC A 107 21.873 11.060 -1.265 1.00 80.00 C ATOM 144 P DC A 108 18.566 14.590 -5.437 1.00 80.00 P ATOM 145 OP1 DC A 108 19.277 15.771 -5.984 1.00 80.00 O ATOM 146 OP2 DC A 108 17.761 14.715 -4.201 1.00 80.00 O ATOM 147 O5' DC A 108 17.622 13.954 -6.563 1.00 80.00 O ATOM 148 C5' DC A 108 16.332 13.473 -6.207 1.00 80.00 C ATOM 149 C4' DC A 108 16.257 11.958 -6.195 1.00 80.00 C ATOM 150 O4' DC A 108 17.371 11.392 -5.470 1.00 80.00 O ATOM 151 C3' DC A 108 15.028 11.417 -5.486 1.00 80.00 C ATOM 152 O3' DC A 108 13.942 11.422 -6.406 1.00 80.00 O ATOM 153 C2' DC A 108 15.469 10.012 -5.091 1.00 80.00 C ATOM 154 C1' DC A 108 16.977 10.159 -4.897 1.00 80.00 C ATOM 155 N1 DC A 108 17.412 10.157 -3.471 1.00 80.00 N ATOM 156 C2 DC A 108 17.296 8.999 -2.689 1.00 80.00 C ATOM 157 O2 DC A 108 16.820 7.970 -3.182 1.00 80.00 O ATOM 158 N3 DC A 108 17.708 9.034 -1.397 1.00 80.00 N ATOM 159 C4 DC A 108 18.217 10.157 -0.889 1.00 80.00 C ATOM 160 N4 DC A 108 18.608 10.144 0.389 1.00 80.00 N ATOM 161 C5 DC A 108 18.343 11.343 -1.670 1.00 80.00 C ATOM 162 C6 DC A 108 17.935 11.298 -2.942 1.00 80.00 C ATOM 163 P DT A 109 12.767 10.335 -6.352 1.00 80.00 P ATOM 164 OP1 DT A 109 13.346 9.044 -6.792 1.00 80.00 O ATOM 165 OP2 DT A 109 11.601 10.895 -7.072 1.00 80.00 O ATOM 166 O5' DT A 109 12.371 10.262 -4.802 1.00 80.00 O ATOM 167 C5' DT A 109 11.341 9.374 -4.378 1.00 80.00 C ATOM 168 C4' DT A 109 11.748 7.948 -4.691 1.00 80.00 C ATOM 169 O4' DT A 109 13.164 7.820 -4.404 1.00 80.00 O ATOM 170 C3' DT A 109 11.038 6.875 -3.875 1.00 80.00 C ATOM 171 O3' DT A 109 10.032 6.201 -4.629 1.00 80.00 O ATOM 172 C2' DT A 109 12.157 5.904 -3.516 1.00 80.00 C ATOM 173 C1' DT A 109 13.364 6.830 -3.418 1.00 80.00 C ATOM 174 N1 DT A 109 13.566 7.503 -2.089 1.00 80.00 N ATOM 175 C2 DT A 109 13.223 6.852 -0.921 1.00 80.00 C ATOM 176 O2 DT A 109 12.741 5.734 -0.882 1.00 80.00 O ATOM 177 N3 DT A 109 13.462 7.566 0.226 1.00 80.00 N ATOM 178 C4 DT A 109 14.001 8.834 0.334 1.00 80.00 C ATOM 179 O4 DT A 109 14.171 9.378 1.425 1.00 80.00 O ATOM 180 C5 DT A 109 14.342 9.457 -0.924 1.00 80.00 C ATOM 181 C7 DT A 109 14.933 10.836 -0.951 1.00 80.00 C ATOM 182 C6 DT A 109 14.113 8.772 -2.054 1.00 80.00 C ATOM 183 P DG A 110 8.773 6.966 -5.255 1.00 80.00 P ATOM 184 OP1 DG A 110 7.794 5.926 -5.644 1.00 80.00 O ATOM 185 OP2 DG A 110 9.264 7.931 -6.263 1.00 80.00 O ATOM 186 O5' DG A 110 8.163 7.793 -4.030 1.00 80.00 O ATOM 187 C5' DG A 110 7.217 7.175 -3.170 1.00 80.00 C ATOM 188 C4' DG A 110 7.900 6.082 -2.381 1.00 80.00 C ATOM 189 O4' DG A 110 9.169 6.610 -1.957 1.00 80.00 O ATOM 190 C3' DG A 110 7.209 5.673 -1.094 1.00 80.00 C ATOM 191 O3' DG A 110 6.337 4.602 -1.358 1.00 80.00 O ATOM 192 C2' DG A 110 8.355 5.237 -0.192 1.00 80.00 C ATOM 193 C1' DG A 110 9.541 6.033 -0.729 1.00 80.00 C ATOM 194 N9 DG A 110 10.003 7.124 0.119 1.00 80.00 N ATOM 195 C8 DG A 110 10.514 8.324 -0.310 1.00 80.00 C ATOM 196 N7 DG A 110 10.859 9.116 0.665 1.00 80.00 N ATOM 197 C5 DG A 110 10.561 8.393 1.814 1.00 80.00 C ATOM 198 C6 DG A 110 10.716 8.740 3.177 1.00 80.00 C ATOM 199 O6 DG A 110 11.170 9.789 3.657 1.00 80.00 O ATOM 200 N1 DG A 110 10.283 7.718 4.019 1.00 80.00 N ATOM 201 C2 DG A 110 9.767 6.516 3.596 1.00 80.00 C ATOM 202 N2 DG A 110 9.401 5.650 4.551 1.00 80.00 N ATOM 203 N3 DG A 110 9.615 6.181 2.323 1.00 80.00 N ATOM 204 C4 DG A 110 10.031 7.164 1.492 1.00 80.00 C ATOM 205 P DT A 111 4.960 4.916 -2.099 1.00 80.00 P ATOM 206 OP1 DT A 111 5.092 4.516 -3.518 1.00 80.00 O ATOM 207 OP2 DT A 111 4.587 6.305 -1.757 1.00 80.00 O ATOM 208 O5' DT A 111 3.929 3.946 -1.358 1.00 80.00 O ATOM 209 C5' DT A 111 3.218 4.420 -0.224 1.00 80.00 C ATOM 210 C4' DT A 111 3.932 4.139 1.088 1.00 80.00 C ATOM 211 O4' DT A 111 5.168 4.904 1.195 1.00 80.00 O ATOM 212 C3' DT A 111 3.082 4.523 2.294 1.00 80.00 C ATOM 213 O3' DT A 111 2.994 3.461 3.244 1.00 80.00 O ATOM 214 C2' DT A 111 3.809 5.741 2.863 1.00 80.00 C ATOM 215 C1' DT A 111 5.255 5.454 2.495 1.00 80.00 C ATOM 216 N1 DT A 111 6.098 6.689 2.477 1.00 80.00 N ATOM 217 C2 DT A 111 6.650 7.188 3.644 1.00 80.00 C ATOM 218 O2 DT A 111 6.513 6.684 4.745 1.00 80.00 O ATOM 219 N3 DT A 111 7.394 8.329 3.480 1.00 80.00 N ATOM 220 C4 DT A 111 7.635 9.008 2.301 1.00 80.00 C ATOM 221 O4 DT A 111 8.317 10.026 2.252 1.00 80.00 O ATOM 222 C5 DT A 111 7.032 8.437 1.128 1.00 80.00 C ATOM 223 C7 DT A 111 7.228 9.091 -0.206 1.00 80.00 C ATOM 224 C6 DT A 111 6.300 7.328 1.274 1.00 80.00 C ATOM 225 P DA A 112 2.965 3.884 4.784 1.00 80.00 P ATOM 226 OP1 DA A 112 1.999 4.996 4.916 1.00 80.00 O ATOM 227 OP2 DA A 112 4.381 4.040 5.191 1.00 80.00 O ATOM 228 O5' DA A 112 2.356 2.660 5.606 1.00 80.00 O ATOM 229 C5' DA A 112 1.577 2.955 6.768 1.00 80.00 C ATOM 230 C4' DA A 112 2.349 3.720 7.837 1.00 80.00 C ATOM 231 O4' DA A 112 3.444 4.490 7.280 1.00 80.00 O ATOM 232 C3' DA A 112 1.513 4.734 8.604 1.00 80.00 C ATOM 233 O3' DA A 112 0.910 4.105 9.734 1.00 80.00 O ATOM 234 C2' DA A 112 2.519 5.808 9.014 1.00 80.00 C ATOM 235 C1' DA A 112 3.697 5.647 8.055 1.00 80.00 C ATOM 236 N9 DA A 112 3.925 6.796 7.169 1.00 80.00 N ATOM 237 C8 DA A 112 3.695 6.853 5.824 1.00 80.00 C ATOM 238 N7 DA A 112 3.988 8.003 5.267 1.00 80.00 N ATOM 239 C5 DA A 112 4.449 8.768 6.323 1.00 80.00 C ATOM 240 C6 DA A 112 4.920 10.095 6.393 1.00 80.00 C ATOM 241 N6 DA A 112 5.006 10.912 5.336 1.00 80.00 N ATOM 242 N1 DA A 112 5.305 10.555 7.601 1.00 80.00 N ATOM 243 C2 DA A 112 5.221 9.740 8.659 1.00 80.00 C ATOM 244 N3 DA A 112 4.795 8.477 8.715 1.00 80.00 N ATOM 245 C4 DA A 112 4.419 8.042 7.502 1.00 80.00 C ATOM 246 P DC A 113 1.755 3.812 11.063 1.00 80.00 P ATOM 247 OP1 DC A 113 3.072 3.272 10.660 1.00 80.00 O ATOM 248 OP2 DC A 113 0.895 3.026 11.975 1.00 80.00 O ATOM 249 O5' DC A 113 1.962 5.264 11.707 1.00 80.00 O ATOM 250 C5' DC A 113 3.125 5.543 12.481 1.00 80.00 C ATOM 251 C4' DC A 113 3.028 6.911 13.131 1.00 80.00 C ATOM 252 O4' DC A 113 3.173 7.957 12.138 1.00 80.00 O ATOM 253 C3' DC A 113 1.705 7.169 13.839 1.00 80.00 C ATOM 254 O3' DC A 113 1.962 7.721 15.127 1.00 80.00 O ATOM 255 C2' DC A 113 0.971 8.124 12.896 1.00 80.00 C ATOM 256 C1' DC A 113 2.122 8.892 12.260 1.00 80.00 C ATOM 257 N1 DC A 113 1.847 9.424 10.891 1.00 80.00 N ATOM 258 C2 DC A 113 1.880 10.800 10.648 1.00 80.00 C ATOM 259 O2 DC A 113 2.128 11.565 11.582 1.00 80.00 O ATOM 260 N3 DC A 113 1.635 11.260 9.396 1.00 80.00 N ATOM 261 C4 DC A 113 1.370 10.404 8.409 1.00 80.00 C ATOM 262 N4 DC A 113 1.135 10.903 7.189 1.00 80.00 N ATOM 263 C5 DC A 113 1.334 8.997 8.633 1.00 80.00 C ATOM 264 C6 DC A 113 1.576 8.560 9.875 1.00 80.00 C ATOM 265 P DG A 114 1.600 6.848 16.418 1.00 80.00 P ATOM 266 OP1 DG A 114 1.787 5.427 16.053 1.00 80.00 O ATOM 267 OP2 DG A 114 0.290 7.315 16.917 1.00 80.00 O ATOM 268 O5' DG A 114 2.700 7.244 17.509 1.00 80.00 O ATOM 269 C5' DG A 114 2.480 8.349 18.378 1.00 80.00 C ATOM 270 C4' DG A 114 3.302 9.539 17.924 1.00 80.00 C ATOM 271 O4' DG A 114 3.208 9.629 16.484 1.00 80.00 O ATOM 272 C3' DG A 114 2.866 10.886 18.484 1.00 80.00 C ATOM 273 O3' DG A 114 3.685 11.197 19.606 1.00 80.00 O ATOM 274 C2' DG A 114 3.112 11.853 17.331 1.00 80.00 C ATOM 275 C1' DG A 114 3.061 10.974 16.084 1.00 80.00 C ATOM 276 N9 DG A 114 1.839 11.066 15.289 1.00 80.00 N ATOM 277 C8 DG A 114 0.794 10.177 15.251 1.00 80.00 C ATOM 278 N7 DG A 114 -0.157 10.523 14.427 1.00 80.00 N ATOM 279 C5 DG A 114 0.285 11.720 13.880 1.00 80.00 C ATOM 280 C6 DG A 114 -0.319 12.573 12.925 1.00 80.00 C ATOM 281 O6 DG A 114 -1.403 12.447 12.339 1.00 80.00 O ATOM 282 N1 DG A 114 0.479 13.680 12.659 1.00 80.00 N ATOM 283 C2 DG A 114 1.700 13.927 13.239 1.00 80.00 C ATOM 284 N2 DG A 114 2.328 15.048 12.859 1.00 80.00 N ATOM 285 N3 DG A 114 2.276 13.140 14.133 1.00 80.00 N ATOM 286 C4 DG A 114 1.513 12.061 14.402 1.00 80.00 C ATOM 287 P DG A 115 3.482 12.544 20.444 1.00 80.00 P ATOM 288 OP1 DG A 115 3.569 12.198 21.880 1.00 80.00 O ATOM 289 OP2 DG A 115 2.290 13.247 19.927 1.00 80.00 O ATOM 290 O5' DG A 115 4.767 13.407 20.053 1.00 80.00 O ATOM 291 C5' DG A 115 4.748 14.805 20.275 1.00 80.00 C ATOM 292 C4' DG A 115 4.431 15.527 18.982 1.00 80.00 C ATOM 293 O4' DG A 115 3.747 14.642 18.061 1.00 80.00 O ATOM 294 C3' DG A 115 3.453 16.678 19.113 1.00 80.00 C ATOM 295 O3' DG A 115 4.061 17.824 19.729 1.00 80.00 O ATOM 296 C2' DG A 115 3.074 16.876 17.649 1.00 80.00 C ATOM 297 C1' DG A 115 3.037 15.440 17.129 1.00 80.00 C ATOM 298 N9 DG A 115 1.685 14.911 16.941 1.00 80.00 N ATOM 299 C8 DG A 115 1.063 13.944 17.688 1.00 80.00 C ATOM 300 N7 DG A 115 -0.145 13.664 17.289 1.00 80.00 N ATOM 301 C5 DG A 115 -0.345 14.505 16.203 1.00 80.00 C ATOM 302 C6 DG A 115 -1.473 14.655 15.360 1.00 80.00 C ATOM 303 O6 DG A 115 -2.554 14.058 15.406 1.00 80.00 O ATOM 304 N1 DG A 115 -1.269 15.616 14.377 1.00 80.00 N ATOM 305 C2 DG A 115 -0.115 16.342 14.230 1.00 80.00 C ATOM 306 N2 DG A 115 -0.108 17.224 13.220 1.00 80.00 N ATOM 307 N3 DG A 115 0.952 16.214 15.012 1.00 80.00 N ATOM 308 C4 DG A 115 0.770 15.279 15.976 1.00 80.00 C ATOM 309 P DA A 116 5.043 18.849 18.982 1.00 80.00 P ATOM 310 OP1 DA A 116 5.270 18.413 17.588 1.00 80.00 O ATOM 311 OP2 DA A 116 6.205 19.060 19.873 1.00 80.00 O ATOM 312 O5' DA A 116 4.200 20.208 18.971 1.00 80.00 O ATOM 313 C5' DA A 116 4.399 21.132 17.916 1.00 80.00 C ATOM 314 C4' DA A 116 3.267 21.056 16.910 1.00 80.00 C ATOM 315 O4' DA A 116 2.561 19.797 17.037 1.00 80.00 O ATOM 316 C3' DA A 116 2.201 22.127 17.103 1.00 80.00 C ATOM 317 O3' DA A 116 2.289 23.067 16.054 1.00 80.00 O ATOM 318 C2' DA A 116 0.866 21.388 17.055 1.00 80.00 C ATOM 319 C1' DA A 116 1.260 20.012 16.535 1.00 80.00 C ATOM 320 N9 DA A 116 0.333 18.952 16.941 1.00 80.00 N ATOM 321 C8 DA A 116 0.447 18.043 17.956 1.00 80.00 C ATOM 322 N7 DA A 116 -0.571 17.217 18.058 1.00 80.00 N ATOM 323 C5 DA A 116 -1.422 17.616 17.042 1.00 80.00 C ATOM 324 C6 DA A 116 -2.682 17.156 16.606 1.00 80.00 C ATOM 325 N6 DA A 116 -3.351 16.137 17.160 1.00 80.00 N ATOM 326 N1 DA A 116 -3.241 17.791 15.559 1.00 80.00 N ATOM 327 C2 DA A 116 -2.588 18.811 14.992 1.00 80.00 C ATOM 328 N3 DA A 116 -1.408 19.332 15.309 1.00 80.00 N ATOM 329 C4 DA A 116 -0.876 18.683 16.351 1.00 80.00 C ATOM 330 P DC A 117 2.105 24.611 16.411 1.00 80.00 P ATOM 331 OP1 DC A 117 2.988 25.393 15.519 1.00 80.00 O ATOM 332 OP2 DC A 117 2.223 24.748 17.879 1.00 80.00 O ATOM 333 O5' DC A 117 0.588 24.892 15.994 1.00 80.00 O ATOM 334 C5' DC A 117 0.266 24.938 14.615 1.00 80.00 C ATOM 335 C4' DC A 117 -1.169 24.516 14.361 1.00 80.00 C ATOM 336 O4' DC A 117 -1.470 23.276 15.052 1.00 80.00 O ATOM 337 C3' DC A 117 -2.249 25.510 14.796 1.00 80.00 C ATOM 338 O3' DC A 117 -2.890 26.015 13.623 1.00 80.00 O ATOM 339 C2' DC A 117 -3.190 24.677 15.668 1.00 80.00 C ATOM 340 C1' DC A 117 -2.873 23.265 15.194 1.00 80.00 C ATOM 341 N1 DC A 117 -3.312 22.171 16.114 1.00 80.00 N ATOM 342 C2 DC A 117 -4.452 21.432 15.782 1.00 80.00 C ATOM 343 O2 DC A 117 -5.064 21.706 14.744 1.00 80.00 O ATOM 344 N3 DC A 117 -4.861 20.438 16.607 1.00 80.00 N ATOM 345 C4 DC A 117 -4.175 20.174 17.718 1.00 80.00 C ATOM 346 N4 DC A 117 -4.619 19.181 18.495 1.00 80.00 N ATOM 347 C5 DC A 117 -3.008 20.913 18.075 1.00 80.00 C ATOM 348 C6 DC A 117 -2.616 21.894 17.253 1.00 80.00 C ATOM 349 P DA A 118 -4.112 27.051 13.667 1.00 80.00 P ATOM 350 OP1 DA A 118 -3.583 28.391 13.332 1.00 80.00 O ATOM 351 OP2 DA A 118 -4.873 26.851 14.920 1.00 80.00 O ATOM 352 O5' DA A 118 -5.026 26.539 12.457 1.00 80.00 O ATOM 353 C5' DA A 118 -5.272 25.145 12.319 1.00 80.00 C ATOM 354 C4' DA A 118 -6.637 24.866 11.721 1.00 80.00 C ATOM 355 O4' DA A 118 -7.241 23.799 12.487 1.00 80.00 O ATOM 356 C3' DA A 118 -7.664 25.969 11.880 1.00 80.00 C ATOM 357 O3' DA A 118 -8.848 25.575 11.204 1.00 80.00 O ATOM 358 C2' DA A 118 -7.856 25.891 13.384 1.00 80.00 C ATOM 359 C1' DA A 118 -8.005 24.381 13.528 1.00 80.00 C ATOM 360 N9 DA A 118 -7.512 23.861 14.797 1.00 80.00 N ATOM 361 C8 DA A 118 -6.366 24.199 15.461 1.00 80.00 C ATOM 362 N7 DA A 118 -6.197 23.545 16.588 1.00 80.00 N ATOM 363 C5 DA A 118 -7.306 22.719 16.665 1.00 80.00 C ATOM 364 C6 DA A 118 -7.733 21.769 17.617 1.00 80.00 C ATOM 365 N6 DA A 118 -7.065 21.462 18.736 1.00 80.00 N ATOM 366 N1 DA A 118 -8.895 21.133 17.367 1.00 80.00 N ATOM 367 C2 DA A 118 -9.575 21.424 16.253 1.00 80.00 C ATOM 368 N3 DA A 118 -9.279 22.291 15.292 1.00 80.00 N ATOM 369 C4 DA A 118 -8.123 22.906 15.565 1.00 80.00 C ATOM 370 P DT A 119 -10.214 26.387 11.386 1.00 80.00 P ATOM 371 OP1 DT A 119 -10.052 27.708 10.741 1.00 80.00 O ATOM 372 OP2 DT A 119 -10.622 26.317 12.805 1.00 80.00 O ATOM 373 O5' DT A 119 -11.237 25.517 10.520 1.00 80.00 O ATOM 374 C5' DT A 119 -11.341 24.119 10.739 1.00 80.00 C ATOM 375 C4' DT A 119 -12.159 23.825 11.983 1.00 80.00 C ATOM 376 O4' DT A 119 -11.315 23.827 13.158 1.00 80.00 O ATOM 377 C3' DT A 119 -13.270 24.833 12.284 1.00 80.00 C ATOM 378 O3' DT A 119 -14.542 24.302 11.891 1.00 80.00 O ATOM 379 C2' DT A 119 -13.161 25.091 13.791 1.00 80.00 C ATOM 380 C1' DT A 119 -12.201 23.996 14.239 1.00 80.00 C ATOM 381 N1 DT A 119 -11.443 24.293 15.482 1.00 80.00 N ATOM 382 C2 DT A 119 -11.767 23.570 16.600 1.00 80.00 C ATOM 383 O2 DT A 119 -12.635 22.721 16.593 1.00 80.00 O ATOM 384 N3 DT A 119 -11.038 23.879 17.719 1.00 80.00 N ATOM 385 C4 DT A 119 -10.036 24.823 17.826 1.00 80.00 C ATOM 386 O4 DT A 119 -9.438 25.026 18.881 1.00 80.00 O ATOM 387 C5 DT A 119 -9.746 25.546 16.612 1.00 80.00 C ATOM 388 C7 DT A 119 -8.678 26.597 16.607 1.00 80.00 C ATOM 389 C6 DT A 119 -10.454 25.253 15.511 1.00 80.00 C ATOM 390 P DC A 120 -15.468 23.453 12.885 1.00 80.00 P ATOM 391 OP1 DC A 120 -14.618 22.442 13.552 1.00 80.00 O ATOM 392 OP2 DC A 120 -16.663 23.023 12.125 1.00 80.00 O ATOM 393 O5' DC A 120 -15.936 24.536 13.965 1.00 80.00 O ATOM 394 C5' DC A 120 -17.013 24.233 14.835 1.00 80.00 C ATOM 395 C4' DC A 120 -16.925 22.791 15.292 1.00 80.00 C ATOM 396 O4' DC A 120 -15.683 22.617 16.015 1.00 80.00 O ATOM 397 C3' DC A 120 -18.006 22.358 16.267 1.00 80.00 C ATOM 398 O3' DC A 120 -18.104 20.946 16.280 1.00 80.00 O ATOM 399 C2' DC A 120 -17.431 22.871 17.577 1.00 80.00 C ATOM 400 C1' DC A 120 -15.965 22.499 17.395 1.00 80.00 C ATOM 401 N1 DC A 120 -15.035 23.383 18.138 1.00 80.00 N ATOM 402 C2 DC A 120 -14.632 23.001 19.417 1.00 80.00 C ATOM 403 O2 DC A 120 -15.067 21.941 19.878 1.00 80.00 O ATOM 404 N3 DC A 120 -13.781 23.797 20.110 1.00 80.00 N ATOM 405 C4 DC A 120 -13.342 24.930 19.564 1.00 80.00 C ATOM 406 N4 DC A 120 -12.505 25.682 20.286 1.00 80.00 N ATOM 407 C5 DC A 120 -13.746 25.339 18.257 1.00 80.00 C ATOM 408 C6 DC A 120 -14.587 24.544 17.584 1.00 80.00 C ATOM 409 P DA A 121 -19.416 20.260 16.881 1.00 80.00 P ATOM 410 OP1 DA A 121 -19.577 18.929 16.255 1.00 80.00 O ATOM 411 OP2 DA A 121 -20.516 21.244 16.799 1.00 80.00 O ATOM 412 O5' DA A 121 -19.044 20.078 18.425 1.00 80.00 O ATOM 413 C5' DA A 121 -20.069 19.733 19.343 1.00 80.00 C ATOM 414 C4' DA A 121 -19.576 19.889 20.766 1.00 80.00 C ATOM 415 O4' DA A 121 -18.465 20.820 20.781 1.00 80.00 O ATOM 416 C3' DA A 121 -20.600 20.475 21.731 1.00 80.00 C ATOM 417 O3' DA A 121 -20.330 20.010 23.045 1.00 80.00 O ATOM 418 C2' DA A 121 -20.290 21.960 21.615 1.00 80.00 C ATOM 419 C1' DA A 121 -18.785 21.806 21.738 1.00 80.00 C ATOM 420 N9 DA A 121 -17.974 22.997 21.524 1.00 80.00 N ATOM 421 C8 DA A 121 -18.031 23.959 20.555 1.00 80.00 C ATOM 422 N7 DA A 121 -17.109 24.890 20.695 1.00 80.00 N ATOM 423 C5 DA A 121 -16.403 24.507 21.829 1.00 80.00 C ATOM 424 C6 DA A 121 -15.300 25.047 22.534 1.00 80.00 C ATOM 425 N6 DA A 121 -14.643 26.166 22.206 1.00 80.00 N ATOM 426 N1 DA A 121 -14.881 24.373 23.625 1.00 80.00 N ATOM 427 C2 DA A 121 -15.510 23.251 23.991 1.00 80.00 C ATOM 428 N3 DA A 121 -16.542 22.652 23.417 1.00 80.00 N ATOM 429 C4 DA A 121 -16.935 23.340 22.339 1.00 80.00 C TER 430 DA A 121 ATOM 431 P DC B 119 -4.997 12.691 6.730 1.00 80.00 P ATOM 432 OP1 DC B 119 -5.064 11.667 5.666 1.00 80.00 O ATOM 433 OP2 DC B 119 -4.773 12.292 8.137 1.00 80.00 O ATOM 434 O5' DC B 119 -3.872 13.760 6.342 1.00 80.00 O ATOM 435 C5' DC B 119 -4.236 14.912 5.593 1.00 80.00 C ATOM 436 C4' DC B 119 -4.388 16.143 6.471 1.00 80.00 C ATOM 437 O4' DC B 119 -4.859 15.775 7.793 1.00 80.00 O ATOM 438 C3' DC B 119 -3.106 16.943 6.679 1.00 80.00 C ATOM 439 O3' DC B 119 -3.373 18.319 6.438 1.00 80.00 O ATOM 440 C2' DC B 119 -2.742 16.678 8.138 1.00 80.00 C ATOM 441 C1' DC B 119 -4.118 16.492 8.759 1.00 80.00 C ATOM 442 N1 DC B 119 -4.159 15.715 10.033 1.00 80.00 N ATOM 443 C2 DC B 119 -3.232 15.927 11.066 1.00 80.00 C ATOM 444 O2 DC B 119 -2.336 16.770 10.943 1.00 80.00 O ATOM 445 N3 DC B 119 -3.335 15.188 12.197 1.00 80.00 N ATOM 446 C4 DC B 119 -4.306 14.282 12.317 1.00 80.00 C ATOM 447 N4 DC B 119 -4.368 13.577 13.451 1.00 80.00 N ATOM 448 C5 DC B 119 -5.259 14.054 11.284 1.00 80.00 C ATOM 449 C6 DC B 119 -5.144 14.785 10.175 1.00 80.00 C ATOM 450 P DC B 120 -2.194 19.307 6.004 1.00 80.00 P ATOM 451 OP1 DC B 120 -1.448 19.684 7.226 1.00 80.00 O ATOM 452 OP2 DC B 120 -2.775 20.360 5.139 1.00 80.00 O ATOM 453 O5' DC B 120 -1.261 18.359 5.118 1.00 80.00 O ATOM 454 C5' DC B 120 0.058 18.758 4.765 1.00 80.00 C ATOM 455 C4' DC B 120 1.014 18.542 5.924 1.00 80.00 C ATOM 456 O4' DC B 120 0.382 17.708 6.931 1.00 80.00 O ATOM 457 C3' DC B 120 2.318 17.849 5.540 1.00 80.00 C ATOM 458 O3' DC B 120 3.426 18.520 6.135 1.00 80.00 O ATOM 459 C2' DC B 120 2.118 16.436 6.078 1.00 80.00 C ATOM 460 C1' DC B 120 1.306 16.719 7.331 1.00 80.00 C ATOM 461 N1 DC B 120 0.576 15.535 7.880 1.00 80.00 N ATOM 462 C2 DC B 120 0.854 15.128 9.186 1.00 80.00 C ATOM 463 O2 DC B 120 1.692 15.765 9.832 1.00 80.00 O ATOM 464 N3 DC B 120 0.204 14.057 9.705 1.00 80.00 N ATOM 465 C4 DC B 120 -0.692 13.400 8.970 1.00 80.00 C ATOM 466 N4 DC B 120 -1.304 12.351 9.535 1.00 80.00 N ATOM 467 C5 DC B 120 -0.991 13.797 7.631 1.00 80.00 C ATOM 468 C6 DC B 120 -0.340 14.856 7.130 1.00 80.00 C ATOM 469 P DG B 121 3.831 19.954 5.556 1.00 80.00 P ATOM 470 OP1 DG B 121 3.397 20.965 6.540 1.00 80.00 O ATOM 471 OP2 DG B 121 3.342 20.031 4.163 1.00 80.00 O ATOM 472 O5' DG B 121 5.429 19.953 5.538 1.00 80.00 O ATOM 473 C5' DG B 121 6.145 20.665 6.542 1.00 80.00 C ATOM 474 C4' DG B 121 6.754 19.720 7.558 1.00 80.00 C ATOM 475 O4' DG B 121 5.784 18.690 7.847 1.00 80.00 O ATOM 476 C3' DG B 121 8.010 19.007 7.067 1.00 80.00 C ATOM 477 O3' DG B 121 9.207 19.685 7.518 1.00 80.00 O ATOM 478 C2' DG B 121 7.881 17.572 7.578 1.00 80.00 C ATOM 479 C1' DG B 121 6.438 17.458 8.062 1.00 80.00 C ATOM 480 N9 DG B 121 5.671 16.422 7.381 1.00 80.00 N ATOM 481 C8 DG B 121 5.376 16.317 6.044 1.00 80.00 C ATOM 482 N7 DG B 121 4.665 15.260 5.754 1.00 80.00 N ATOM 483 C5 DG B 121 4.474 14.628 6.977 1.00 80.00 C ATOM 484 C6 DG B 121 3.779 13.437 7.307 1.00 80.00 C ATOM 485 O6 DG B 121 3.162 12.662 6.562 1.00 80.00 O ATOM 486 N1 DG B 121 3.843 13.170 8.672 1.00 80.00 N ATOM 487 C2 DG B 121 4.494 13.952 9.598 1.00 80.00 C ATOM 488 N2 DG B 121 4.455 13.542 10.873 1.00 80.00 N ATOM 489 N3 DG B 121 5.145 15.066 9.304 1.00 80.00 N ATOM 490 C4 DG B 121 5.089 15.337 7.982 1.00 80.00 C ATOM 491 P DT B 122 9.955 19.429 8.918 1.00 80.00 P ATOM 492 OP1 DT B 122 10.186 20.750 9.545 1.00 80.00 O ATOM 493 OP2 DT B 122 11.112 18.548 8.651 1.00 80.00 O ATOM 494 O5' DT B 122 8.898 18.634 9.816 1.00 80.00 O ATOM 495 C5' DT B 122 9.274 18.108 11.084 1.00 80.00 C ATOM 496 C4' DT B 122 9.561 16.614 11.029 1.00 80.00 C ATOM 497 O4' DT B 122 8.714 15.959 10.053 1.00 80.00 O ATOM 498 C3' DT B 122 10.989 16.214 10.658 1.00 80.00 C ATOM 499 O3' DT B 122 11.650 15.728 11.827 1.00 80.00 O ATOM 500 C2' DT B 122 10.825 15.122 9.595 1.00 80.00 C ATOM 501 C1' DT B 122 9.355 14.745 9.726 1.00 80.00 C ATOM 502 N1 DT B 122 8.742 14.194 8.486 1.00 80.00 N ATOM 503 C2 DT B 122 7.718 13.280 8.599 1.00 80.00 C ATOM 504 O2 DT B 122 7.278 12.890 9.665 1.00 80.00 O ATOM 505 N3 DT B 122 7.215 12.829 7.406 1.00 80.00 N ATOM 506 C4 DT B 122 7.626 13.193 6.139 1.00 80.00 C ATOM 507 O4 DT B 122 7.104 12.726 5.129 1.00 80.00 O ATOM 508 C5 DT B 122 8.703 14.152 6.093 1.00 80.00 C ATOM 509 C7 DT B 122 9.236 14.622 4.772 1.00 80.00 C ATOM 510 C6 DT B 122 9.204 14.601 7.252 1.00 80.00 C ATOM 511 P DA B 123 13.116 15.081 11.762 1.00 80.00 P ATOM 512 OP1 DA B 123 13.781 15.326 13.063 1.00 80.00 O ATOM 513 OP2 DA B 123 13.764 15.544 10.513 1.00 80.00 O ATOM 514 O5' DA B 123 12.815 13.511 11.650 1.00 80.00 O ATOM 515 C5' DA B 123 11.968 12.864 12.598 1.00 80.00 C ATOM 516 C4' DA B 123 11.689 11.434 12.178 1.00 80.00 C ATOM 517 O4' DA B 123 10.834 11.423 11.002 1.00 80.00 O ATOM 518 C3' DA B 123 12.930 10.654 11.764 1.00 80.00 C ATOM 519 O3' DA B 123 12.687 9.266 11.879 1.00 80.00 O ATOM 520 C2' DA B 123 12.986 11.019 10.296 1.00 80.00 C ATOM 521 C1' DA B 123 11.529 10.700 10.011 1.00 80.00 C ATOM 522 N9 DA B 123 11.114 11.085 8.674 1.00 80.00 N ATOM 523 C8 DA B 123 11.492 12.199 7.981 1.00 80.00 C ATOM 524 N7 DA B 123 10.962 12.273 6.785 1.00 80.00 N ATOM 525 C5 DA B 123 10.187 11.128 6.693 1.00 80.00 C ATOM 526 C6 DA B 123 9.365 10.616 5.671 1.00 80.00 C ATOM 527 N6 DA B 123 9.188 11.231 4.499 1.00 80.00 N ATOM 528 N1 DA B 123 8.730 9.446 5.896 1.00 80.00 N ATOM 529 C2 DA B 123 8.909 8.831 7.070 1.00 80.00 C ATOM 530 N3 DA B 123 9.657 9.217 8.106 1.00 80.00 N ATOM 531 C4 DA B 123 10.273 10.382 7.849 1.00 80.00 C ATOM 532 P DC B 124 12.749 8.568 13.313 1.00 80.00 P ATOM 533 OP1 DC B 124 11.376 8.134 13.650 1.00 80.00 O ATOM 534 OP2 DC B 124 13.491 9.470 14.222 1.00 80.00 O ATOM 535 O5' DC B 124 13.622 7.252 13.059 1.00 80.00 O ATOM 536 C5' DC B 124 12.998 5.981 13.162 1.00 80.00 C ATOM 537 C4' DC B 124 12.292 5.574 11.881 1.00 80.00 C ATOM 538 O4' DC B 124 12.213 6.680 10.948 1.00 80.00 O ATOM 539 C3' DC B 124 12.965 4.437 11.115 1.00 80.00 C ATOM 540 O3' DC B 124 12.069 3.341 11.055 1.00 80.00 O ATOM 541 C2' DC B 124 13.231 5.011 9.726 1.00 80.00 C ATOM 542 C1' DC B 124 12.170 6.096 9.666 1.00 80.00 C ATOM 543 N1 DC B 124 12.402 7.130 8.628 1.00 80.00 N ATOM 544 C2 DC B 124 11.731 7.022 7.411 1.00 80.00 C ATOM 545 O2 DC B 124 10.971 6.065 7.240 1.00 80.00 O ATOM 546 N3 DC B 124 11.935 7.962 6.457 1.00 80.00 N ATOM 547 C4 DC B 124 12.768 8.976 6.689 1.00 80.00 C ATOM 548 N4 DC B 124 12.940 9.884 5.723 1.00 80.00 N ATOM 549 C5 DC B 124 13.462 9.100 7.926 1.00 80.00 C ATOM 550 C6 DC B 124 13.252 8.166 8.860 1.00 80.00 C ATOM 551 P DA B 125 12.623 1.875 10.755 1.00 80.00 P ATOM 552 OP1 DA B 125 12.258 1.006 11.893 1.00 80.00 O ATOM 553 OP2 DA B 125 14.035 2.002 10.337 1.00 80.00 O ATOM 554 O5' DA B 125 11.759 1.416 9.495 1.00 80.00 O ATOM 555 C5' DA B 125 11.939 2.071 8.254 1.00 80.00 C ATOM 556 C4' DA B 125 12.557 1.098 7.274 1.00 80.00 C ATOM 557 O4' DA B 125 12.842 1.780 6.034 1.00 80.00 O ATOM 558 C3' DA B 125 13.908 0.563 7.706 1.00 80.00 C ATOM 559 O3' DA B 125 14.225 -0.600 6.948 1.00 80.00 O ATOM 560 C2' DA B 125 14.805 1.746 7.359 1.00 80.00 C ATOM 561 C1' DA B 125 14.186 2.215 6.046 1.00 80.00 C ATOM 562 N9 DA B 125 14.169 3.658 5.849 1.00 80.00 N ATOM 563 C8 DA B 125 14.221 4.660 6.775 1.00 80.00 C ATOM 564 N7 DA B 125 14.180 5.862 6.245 1.00 80.00 N ATOM 565 C5 DA B 125 14.089 5.631 4.881 1.00 80.00 C ATOM 566 C6 DA B 125 14.008 6.476 3.753 1.00 80.00 C ATOM 567 N6 DA B 125 14.004 7.813 3.796 1.00 80.00 N ATOM 568 N1 DA B 125 13.930 5.884 2.546 1.00 80.00 N ATOM 569 C2 DA B 125 13.931 4.549 2.471 1.00 80.00 C ATOM 570 N3 DA B 125 14.002 3.658 3.449 1.00 80.00 N ATOM 571 C4 DA B 125 14.080 4.274 4.632 1.00 80.00 C TER 572 DA B 125 ATOM 573 P DG C 209 19.189 -1.072 6.886 1.00 80.00 P ATOM 574 OP1 DG C 209 19.987 0.135 7.191 1.00 80.00 O ATOM 575 OP2 DG C 209 19.863 -2.336 6.525 1.00 80.00 O ATOM 576 O5' DG C 209 18.144 -0.722 5.726 1.00 80.00 O ATOM 577 C5' DG C 209 18.596 -0.403 4.410 1.00 80.00 C ATOM 578 C4' DG C 209 17.449 0.114 3.554 1.00 80.00 C ATOM 579 O4' DG C 209 17.113 1.466 3.947 1.00 80.00 O ATOM 580 C3' DG C 209 17.734 0.202 2.061 1.00 80.00 C ATOM 581 O3' DG C 209 17.401 -1.046 1.458 1.00 80.00 O ATOM 582 C2' DG C 209 16.802 1.322 1.594 1.00 80.00 C ATOM 583 C1' DG C 209 16.555 2.163 2.847 1.00 80.00 C ATOM 584 N9 DG C 209 17.102 3.525 2.838 1.00 80.00 N ATOM 585 C8 DG C 209 17.843 4.106 3.842 1.00 80.00 C ATOM 586 N7 DG C 209 18.203 5.333 3.592 1.00 80.00 N ATOM 587 C5 DG C 209 17.666 5.595 2.339 1.00 80.00 C ATOM 588 C6 DG C 209 17.734 6.773 1.555 1.00 80.00 C ATOM 589 O6 DG C 209 18.296 7.847 1.814 1.00 80.00 O ATOM 590 N1 DG C 209 17.058 6.625 0.348 1.00 80.00 N ATOM 591 C2 DG C 209 16.401 5.484 -0.047 1.00 80.00 C ATOM 592 N2 DG C 209 15.810 5.539 -1.251 1.00 80.00 N ATOM 593 N3 DG C 209 16.330 4.371 0.678 1.00 80.00 N ATOM 594 C4 DG C 209 16.984 4.495 1.860 1.00 80.00 C ATOM 595 P DG C 210 18.164 -1.598 0.162 1.00 80.00 P ATOM 596 OP1 DG C 210 18.646 -2.963 0.466 1.00 80.00 O ATOM 597 OP2 DG C 210 19.126 -0.572 -0.288 1.00 80.00 O ATOM 598 O5' DG C 210 16.985 -1.722 -0.912 1.00 80.00 O ATOM 599 C5' DG C 210 17.270 -2.156 -2.235 1.00 80.00 C ATOM 600 C4' DG C 210 17.298 -0.977 -3.190 1.00 80.00 C ATOM 601 O4' DG C 210 17.216 0.268 -2.442 1.00 80.00 O ATOM 602 C3' DG C 210 18.568 -0.909 -4.038 1.00 80.00 C ATOM 603 O3' DG C 210 18.286 -0.626 -5.424 1.00 80.00 O ATOM 604 C2' DG C 210 19.343 0.201 -3.336 1.00 80.00 C ATOM 605 C1' DG C 210 18.204 1.136 -2.952 1.00 80.00 C ATOM 606 N9 DG C 210 18.599 2.133 -1.966 1.00 80.00 N ATOM 607 C8 DG C 210 18.627 1.983 -0.606 1.00 80.00 C ATOM 608 N7 DG C 210 19.034 3.043 0.032 1.00 80.00 N ATOM 609 C5 DG C 210 19.301 3.959 -0.976 1.00 80.00 C ATOM 610 C6 DG C 210 19.774 5.289 -0.888 1.00 80.00 C ATOM 611 O6 DG C 210 20.058 5.935 0.133 1.00 80.00 O ATOM 612 N1 DG C 210 19.907 5.868 -2.149 1.00 80.00 N ATOM 613 C2 DG C 210 19.621 5.241 -3.340 1.00 80.00 C ATOM 614 N2 DG C 210 19.810 5.965 -4.455 1.00 80.00 N ATOM 615 N3 DG C 210 19.177 3.993 -3.433 1.00 80.00 N ATOM 616 C4 DG C 210 19.041 3.414 -2.214 1.00 80.00 C ATOM 617 P DC C 211 18.468 0.841 -6.054 1.00 80.00 P ATOM 618 OP1 DC C 211 19.776 1.371 -5.621 1.00 80.00 O ATOM 619 OP2 DC C 211 17.225 1.596 -5.782 1.00 80.00 O ATOM 620 O5' DC C 211 18.604 0.607 -7.630 1.00 80.00 O ATOM 621 C5' DC C 211 18.366 1.695 -8.529 1.00 80.00 C ATOM 622 C4' DC C 211 19.477 2.743 -8.586 1.00 80.00 C ATOM 623 O4' DC C 211 19.807 3.279 -7.275 1.00 80.00 O ATOM 624 C3' DC C 211 20.804 2.292 -9.206 1.00 80.00 C ATOM 625 O3' DC C 211 21.049 3.043 -10.410 1.00 80.00 O ATOM 626 C2' DC C 211 21.830 2.554 -8.101 1.00 80.00 C ATOM 627 C1' DC C 211 21.152 3.695 -7.359 1.00 80.00 C ATOM 628 N1 DC C 211 21.713 3.986 -6.010 1.00 80.00 N ATOM 629 C2 DC C 211 22.175 5.276 -5.744 1.00 80.00 C ATOM 630 O2 DC C 211 22.097 6.135 -6.632 1.00 80.00 O ATOM 631 N3 DC C 211 22.685 5.550 -4.520 1.00 80.00 N ATOM 632 C4 DC C 211 22.748 4.595 -3.592 1.00 80.00 C ATOM 633 N4 DC C 211 23.262 4.917 -2.401 1.00 80.00 N ATOM 634 C5 DC C 211 22.286 3.271 -3.845 1.00 80.00 C ATOM 635 C6 DC C 211 21.785 3.014 -5.056 1.00 80.00 C ATOM 636 P DT C 212 22.296 4.036 -10.603 1.00 80.00 P ATOM 637 OP1 DT C 212 22.133 5.165 -9.658 1.00 80.00 O ATOM 638 OP2 DT C 212 22.421 4.329 -12.048 1.00 80.00 O ATOM 639 O5' DT C 212 23.540 3.129 -10.155 1.00 80.00 O ATOM 640 C5' DT C 212 24.877 3.495 -10.472 1.00 80.00 C ATOM 641 C4' DT C 212 25.155 4.920 -10.040 1.00 80.00 C ATOM 642 O4' DT C 212 24.485 5.180 -8.782 1.00 80.00 O ATOM 643 C3' DT C 212 26.609 5.236 -9.729 1.00 80.00 C ATOM 644 O3' DT C 212 27.391 5.443 -10.909 1.00 80.00 O ATOM 645 C2' DT C 212 26.448 6.495 -8.886 1.00 80.00 C ATOM 646 C1' DT C 212 25.242 6.114 -8.033 1.00 80.00 C ATOM 647 N1 DT C 212 25.636 5.497 -6.739 1.00 80.00 N ATOM 648 C2 DT C 212 26.039 6.322 -5.713 1.00 80.00 C ATOM 649 O2 DT C 212 26.083 7.537 -5.814 1.00 80.00 O ATOM 650 N3 DT C 212 26.386 5.665 -4.559 1.00 80.00 N ATOM 651 C4 DT C 212 26.374 4.300 -4.334 1.00 80.00 C ATOM 652 O4 DT C 212 26.706 3.812 -3.255 1.00 80.00 O ATOM 653 C5 DT C 212 25.943 3.496 -5.454 1.00 80.00 C ATOM 654 C7 DT C 212 25.887 2.002 -5.335 1.00 80.00 C ATOM 655 C6 DT C 212 25.600 4.124 -6.588 1.00 80.00 C ATOM 656 P DG C 213 26.985 6.465 -12.076 1.00 80.00 P ATOM 657 OP1 DG C 213 26.124 7.530 -11.515 1.00 80.00 O ATOM 658 OP2 DG C 213 26.503 5.669 -13.226 1.00 80.00 O ATOM 659 O5' DG C 213 28.397 7.124 -12.451 1.00 80.00 O ATOM 660 C5' DG C 213 28.753 8.401 -11.929 1.00 80.00 C ATOM 661 C4' DG C 213 29.542 8.334 -10.629 1.00 80.00 C ATOM 662 O4' DG C 213 29.077 7.274 -9.756 1.00 80.00 O ATOM 663 C3' DG C 213 31.048 8.097 -10.766 1.00 80.00 C ATOM 664 O3' DG C 213 31.726 9.284 -10.363 1.00 80.00 O ATOM 665 C2' DG C 213 31.334 6.932 -9.814 1.00 80.00 C ATOM 666 C1' DG C 213 30.150 7.063 -8.867 1.00 80.00 C ATOM 667 N9 DG C 213 29.904 5.917 -7.990 1.00 80.00 N ATOM 668 C8 DG C 213 29.368 4.691 -8.307 1.00 80.00 C ATOM 669 N7 DG C 213 29.278 3.882 -7.285 1.00 80.00 N ATOM 670 C5 DG C 213 29.788 4.617 -6.219 1.00 80.00 C ATOM 671 C6 DG C 213 29.951 4.271 -4.852 1.00 80.00 C ATOM 672 O6 DG C 213 29.667 3.207 -4.280 1.00 80.00 O ATOM 673 N1 DG C 213 30.509 5.320 -4.120 1.00 80.00 N ATOM 674 C2 DG C 213 30.864 6.545 -4.638 1.00 80.00 C ATOM 675 N2 DG C 213 31.389 7.433 -3.777 1.00 80.00 N ATOM 676 N3 DG C 213 30.716 6.877 -5.914 1.00 80.00 N ATOM 677 C4 DG C 213 30.174 5.870 -6.642 1.00 80.00 C ATOM 678 P DC C 214 33.306 9.458 -10.562 1.00 80.00 P ATOM 679 OP1 DC C 214 33.524 10.612 -11.464 1.00 80.00 O ATOM 680 OP2 DC C 214 33.869 8.133 -10.905 1.00 80.00 O ATOM 681 O5' DC C 214 33.814 9.885 -9.104 1.00 80.00 O ATOM 682 C5' DC C 214 33.600 9.022 -7.994 1.00 80.00 C ATOM 683 C4' DC C 214 34.777 9.064 -7.038 1.00 80.00 C ATOM 684 O4' DC C 214 34.622 8.000 -6.068 1.00 80.00 O ATOM 685 C3' DC C 214 36.130 8.780 -7.668 1.00 80.00 C ATOM 686 O3' DC C 214 37.170 9.216 -6.802 1.00 80.00 O ATOM 687 C2' DC C 214 36.099 7.258 -7.763 1.00 80.00 C ATOM 688 C1' DC C 214 35.405 6.886 -6.455 1.00 80.00 C ATOM 689 N1 DC C 214 34.511 5.694 -6.550 1.00 80.00 N ATOM 690 C2 DC C 214 34.537 4.749 -5.521 1.00 80.00 C ATOM 691 O2 DC C 214 35.302 4.930 -4.566 1.00 80.00 O ATOM 692 N3 DC C 214 33.727 3.664 -5.596 1.00 80.00 N ATOM 693 C4 DC C 214 32.916 3.506 -6.643 1.00 80.00 C ATOM 694 N4 DC C 214 32.136 2.416 -6.667 1.00 80.00 N ATOM 695 C5 DC C 214 32.874 4.460 -7.705 1.00 80.00 C ATOM 696 C6 DC C 214 33.678 5.529 -7.619 1.00 80.00 C TER 697 DC C 214 ATOM 698 O5' DT D 101 -11.214 36.668 23.965 1.00 80.00 O ATOM 699 C5' DT D 101 -12.609 36.525 24.185 1.00 80.00 C ATOM 700 C4' DT D 101 -12.892 36.191 25.637 1.00 80.00 C ATOM 701 O4' DT D 101 -14.285 36.476 25.930 1.00 80.00 O ATOM 702 C3' DT D 101 -12.734 34.723 26.016 1.00 80.00 C ATOM 703 O3' DT D 101 -11.375 34.358 26.273 1.00 80.00 O ATOM 704 C2' DT D 101 -13.619 34.671 27.251 1.00 80.00 C ATOM 705 C1' DT D 101 -14.823 35.400 26.678 1.00 80.00 C ATOM 706 N1 DT D 101 -15.622 34.523 25.774 1.00 80.00 N ATOM 707 C2 DT D 101 -15.951 33.245 26.186 1.00 80.00 C ATOM 708 O2 DT D 101 -15.631 32.771 27.263 1.00 80.00 O ATOM 709 N3 DT D 101 -16.685 32.522 25.279 1.00 80.00 N ATOM 710 C4 DT D 101 -17.112 32.935 24.031 1.00 80.00 C ATOM 711 O4 DT D 101 -17.768 32.208 23.291 1.00 80.00 O ATOM 712 C5 DT D 101 -16.733 34.277 23.663 1.00 80.00 C ATOM 713 C7 DT D 101 -17.143 34.829 22.330 1.00 80.00 C ATOM 714 C6 DT D 101 -16.015 34.998 24.537 1.00 80.00 C ATOM 715 P DC D 102 -10.685 34.423 27.721 1.00 80.00 P ATOM 716 OP1 DC D 102 -11.394 35.418 28.557 1.00 80.00 O ATOM 717 OP2 DC D 102 -9.235 34.591 27.489 1.00 80.00 O ATOM 718 O5' DC D 102 -10.893 32.947 28.317 1.00 80.00 O ATOM 719 C5' DC D 102 -10.248 32.568 29.542 1.00 80.00 C ATOM 720 C4' DC D 102 -10.650 31.174 29.997 1.00 80.00 C ATOM 721 O4' DC D 102 -11.953 30.875 29.427 1.00 80.00 O ATOM 722 C3' DC D 102 -9.734 30.044 29.533 1.00 80.00 C ATOM 723 O3' DC D 102 -9.801 28.887 30.393 1.00 80.00 O ATOM 724 C2' DC D 102 -10.339 29.760 28.167 1.00 80.00 C ATOM 725 C1' DC D 102 -11.822 29.805 28.513 1.00 80.00 C ATOM 726 N1 DC D 102 -12.689 30.033 27.325 1.00 80.00 N ATOM 727 C2 DC D 102 -13.545 29.015 26.894 1.00 80.00 C ATOM 728 O2 DC D 102 -13.573 27.948 27.515 1.00 80.00 O ATOM 729 N3 DC D 102 -14.325 29.230 25.808 1.00 80.00 N ATOM 730 C4 DC D 102 -14.266 30.397 25.167 1.00 80.00 C ATOM 731 N4 DC D 102 -15.054 30.562 24.100 1.00 80.00 N ATOM 732 C5 DC D 102 -13.397 31.445 25.589 1.00 80.00 C ATOM 733 C6 DC D 102 -12.632 31.222 26.661 1.00 80.00 C ATOM 734 P DT D 103 -9.742 27.408 29.757 1.00 80.00 P ATOM 735 OP1 DT D 103 -8.653 27.402 28.756 1.00 80.00 O ATOM 736 OP2 DT D 103 -11.127 27.069 29.356 1.00 80.00 O ATOM 737 O5' DT D 103 -9.322 26.402 30.937 1.00 80.00 O ATOM 738 C5' DT D 103 -8.623 25.175 30.645 1.00 80.00 C ATOM 739 C4' DT D 103 -9.475 24.128 29.936 1.00 80.00 C ATOM 740 O4' DT D 103 -10.440 24.766 29.058 1.00 80.00 O ATOM 741 C3' DT D 103 -8.679 23.162 29.052 1.00 80.00 C ATOM 742 O3' DT D 103 -8.976 21.764 29.316 1.00 80.00 O ATOM 743 C2' DT D 103 -9.015 23.609 27.628 1.00 80.00 C ATOM 744 C1' DT D 103 -10.447 24.090 27.818 1.00 80.00 C ATOM 745 N1 DT D 103 -11.003 24.949 26.718 1.00 80.00 N ATOM 746 C2 DT D 103 -12.034 24.430 25.972 1.00 80.00 C ATOM 747 O2 DT D 103 -12.494 23.323 26.173 1.00 80.00 O ATOM 748 N3 DT D 103 -12.507 25.251 24.981 1.00 80.00 N ATOM 749 C4 DT D 103 -12.065 26.519 24.662 1.00 80.00 C ATOM 750 O4 DT D 103 -12.555 27.182 23.750 1.00 80.00 O ATOM 751 C5 DT D 103 -10.984 27.005 25.480 1.00 80.00 C ATOM 752 C7 DT D 103 -10.426 28.371 25.217 1.00 80.00 C ATOM 753 C6 DT D 103 -10.508 26.211 26.455 1.00 80.00 C ATOM 754 P DG D 104 -10.432 21.076 29.251 1.00 80.00 P ATOM 755 OP1 DG D 104 -11.129 21.475 28.009 1.00 80.00 O ATOM 756 OP2 DG D 104 -11.073 21.312 30.562 1.00 80.00 O ATOM 757 O5' DG D 104 -10.103 19.510 29.135 1.00 80.00 O ATOM 758 C5' DG D 104 -11.141 18.530 29.257 1.00 80.00 C ATOM 759 C4' DG D 104 -11.682 18.044 27.919 1.00 80.00 C ATOM 760 O4' DG D 104 -11.943 19.164 27.033 1.00 80.00 O ATOM 761 C3' DG D 104 -10.746 17.143 27.123 1.00 80.00 C ATOM 762 O3' DG D 104 -11.473 16.393 26.164 1.00 80.00 O ATOM 763 C2' DG D 104 -9.943 18.195 26.379 1.00 80.00 C ATOM 764 C1' DG D 104 -11.135 19.001 25.884 1.00 80.00 C ATOM 765 N9 DG D 104 -10.819 20.306 25.321 1.00 80.00 N ATOM 766 C8 DG D 104 -9.750 21.118 25.604 1.00 80.00 C ATOM 767 N7 DG D 104 -9.751 22.234 24.927 1.00 80.00 N ATOM 768 C5 DG D 104 -10.895 22.155 24.148 1.00 80.00 C ATOM 769 C6 DG D 104 -11.423 23.072 23.212 1.00 80.00 C ATOM 770 O6 DG D 104 -10.969 24.173 22.871 1.00 80.00 O ATOM 771 N1 DG D 104 -12.602 22.591 22.649 1.00 80.00 N ATOM 772 C2 DG D 104 -13.188 21.385 22.956 1.00 80.00 C ATOM 773 N2 DG D 104 -14.323 21.091 22.310 1.00 80.00 N ATOM 774 N3 DG D 104 -12.703 20.518 23.830 1.00 80.00 N ATOM 775 C4 DG D 104 -11.560 20.974 24.383 1.00 80.00 C ATOM 776 P DA D 105 -12.709 15.446 26.533 1.00 80.00 P ATOM 777 OP1 DA D 105 -12.866 15.434 28.004 1.00 80.00 O ATOM 778 OP2 DA D 105 -12.545 14.167 25.806 1.00 80.00 O ATOM 779 O5' DA D 105 -13.943 16.220 25.870 1.00 80.00 O ATOM 780 C5' DA D 105 -13.723 17.284 24.953 1.00 80.00 C ATOM 781 C4' DA D 105 -13.471 16.809 23.536 1.00 80.00 C ATOM 782 O4' DA D 105 -12.949 17.930 22.780 1.00 80.00 O ATOM 783 C3' DA D 105 -12.428 15.711 23.364 1.00 80.00 C ATOM 784 O3' DA D 105 -12.672 14.997 22.160 1.00 80.00 O ATOM 785 C2' DA D 105 -11.149 16.530 23.285 1.00 80.00 C ATOM 786 C1' DA D 105 -11.657 17.587 22.321 1.00 80.00 C ATOM 787 N9 DA D 105 -10.845 18.789 22.180 1.00 80.00 N ATOM 788 C8 DA D 105 -9.655 19.109 22.770 1.00 80.00 C ATOM 789 N7 DA D 105 -9.190 20.286 22.405 1.00 80.00 N ATOM 790 C5 DA D 105 -10.134 20.764 21.508 1.00 80.00 C ATOM 791 C6 DA D 105 -10.247 21.953 20.752 1.00 80.00 C ATOM 792 N6 DA D 105 -9.362 22.957 20.761 1.00 80.00 N ATOM 793 N1 DA D 105 -11.334 22.079 19.968 1.00 80.00 N ATOM 794 C2 DA D 105 -12.235 21.092 19.939 1.00 80.00 C ATOM 795 N3 DA D 105 -12.240 19.939 20.594 1.00 80.00 N ATOM 796 C4 DA D 105 -11.153 19.842 21.364 1.00 80.00 C ATOM 797 P DT D 106 -13.616 13.707 22.181 1.00 80.00 P ATOM 798 OP1 DT D 106 -14.095 13.505 23.565 1.00 80.00 O ATOM 799 OP2 DT D 106 -12.912 12.622 21.469 1.00 80.00 O ATOM 800 O5' DT D 106 -14.845 14.133 21.259 1.00 80.00 O ATOM 801 C5' DT D 106 -15.043 15.493 20.926 1.00 80.00 C ATOM 802 C4' DT D 106 -14.211 15.836 19.708 1.00 80.00 C ATOM 803 O4' DT D 106 -13.046 16.617 20.057 1.00 80.00 O ATOM 804 C3' DT D 106 -13.664 14.624 18.960 1.00 80.00 C ATOM 805 O3' DT D 106 -14.110 14.704 17.632 1.00 80.00 O ATOM 806 C2' DT D 106 -12.149 14.788 19.039 1.00 80.00 C ATOM 807 C1' DT D 106 -12.120 16.304 19.045 1.00 80.00 C ATOM 808 N1 DT D 106 -10.805 16.957 19.301 1.00 80.00 N ATOM 809 C2 DT D 106 -10.613 18.180 18.712 1.00 80.00 C ATOM 810 O2 DT D 106 -11.469 18.700 18.027 1.00 80.00 O ATOM 811 N3 DT D 106 -9.399 18.767 18.952 1.00 80.00 N ATOM 812 C4 DT D 106 -8.366 18.258 19.712 1.00 80.00 C ATOM 813 O4 DT D 106 -7.312 18.870 19.865 1.00 80.00 O ATOM 814 C5 DT D 106 -8.636 16.968 20.297 1.00 80.00 C ATOM 815 C7 DT D 106 -7.584 16.275 21.169 1.00 30.00 C ATOM 816 C6 DT D 106 -9.820 16.374 20.073 1.00 80.00 C ATOM 817 P DG D 107 -14.206 13.357 16.795 1.00 80.00 P ATOM 818 OP1 DG D 107 -15.637 13.030 16.608 1.00 80.00 O ATOM 819 OP2 DG D 107 -13.314 12.373 17.442 1.00 80.00 O ATOM 820 O5' DG D 107 -13.575 13.784 15.391 1.00 80.00 O ATOM 821 C5' DG D 107 -14.392 14.473 14.460 1.00 80.00 C ATOM 822 C4' DG D 107 -13.692 15.725 13.979 1.00 80.00 C ATOM 823 O4' DG D 107 -12.779 16.166 15.009 1.00 80.00 O ATOM 824 C3' DG D 107 -12.860 15.564 12.711 1.00 80.00 C ATOM 825 O3' DG D 107 -13.367 16.436 11.713 1.00 80.00 O ATOM 826 C2' DG D 107 -11.445 15.962 13.125 1.00 80.00 C ATOM 827 C1' DG D 107 -11.691 16.791 14.374 1.00 80.00 C ATOM 828 N9 DG D 107 -10.575 16.778 15.306 1.00 80.00 N ATOM 829 C8 DG D 107 -10.456 15.991 16.421 1.00 80.00 C ATOM 830 N7 DG D 107 -9.346 16.190 17.076 1.00 80.00 N ATOM 831 C5 DG D 107 -8.687 17.172 16.349 1.00 80.00 C ATOM 832 C6 DG D 107 -7.433 17.790 16.576 1.00 80.00 C ATOM 833 O6 DG D 107 -6.627 17.591 17.495 1.00 80.00 O ATOM 834 N1 DG D 107 -7.143 18.732 15.594 1.00 80.00 N ATOM 835 C2 DG D 107 -7.962 19.034 14.532 1.00 80.00 C ATOM 836 N2 DG D 107 -7.510 19.971 13.689 1.00 80.00 N ATOM 837 N3 DG D 107 -9.137 18.461 14.306 1.00 80.00 N ATOM 838 C4 DG D 107 -9.434 17.544 15.254 1.00 80.00 C ATOM 839 P DT D 108 -13.261 16.062 10.162 1.00 80.00 P ATOM 840 OP1 DT D 108 -14.311 16.797 9.424 1.00 80.00 O ATOM 841 OP2 DT D 108 -13.216 14.591 10.061 1.00 80.00 O ATOM 842 O5' DT D 108 -11.841 16.670 9.752 1.00 80.00 O ATOM 843 C5' DT D 108 -10.665 15.894 9.901 1.00 80.00 C ATOM 844 C4' DT D 108 -9.467 16.798 10.079 1.00 80.00 C ATOM 845 O4' DT D 108 -9.212 16.988 11.487 1.00 80.00 O ATOM 846 C3' DT D 108 -8.155 16.231 9.575 1.00 80.00 C ATOM 847 O3' DT D 108 -8.061 16.397 8.176 1.00 80.00 O ATOM 848 C2' DT D 108 -7.166 17.136 10.292 1.00 80.00 C ATOM 849 C1' DT D 108 -7.865 17.394 11.624 1.00 80.00 C ATOM 850 N1 DT D 108 -7.233 16.701 12.786 1.00 80.00 N ATOM 851 C2 DT D 108 -5.968 17.085 13.161 1.00 80.00 C ATOM 852 O2 DT D 108 -5.349 17.952 12.584 1.00 80.00 O ATOM 853 N3 DT D 108 -5.446 16.419 14.237 1.00 80.00 N ATOM 854 C4 DT D 108 -6.051 15.422 14.970 1.00 80.00 C ATOM 855 O4 DT D 108 -5.499 14.881 15.926 1.00 80.00 O ATOM 856 C5 DT D 108 -7.374 15.067 14.525 1.00 80.00 C ATOM 857 C7 DT D 108 -8.126 13.993 15.248 1.00 80.00 C ATOM 858 C6 DT D 108 -7.900 15.710 13.471 1.00 80.00 C END """ def exercise_00(): def get_ab(params): pdb_inp = iotbx.pdb.input(lines=pdb_str_00.split('\n'), source_info=None) m = mmtbx.model.manager(model_input=pdb_inp) m.process(make_restraints=True) xray_structure = m.get_xray_structure() assert xray_structure is not None s = flex.bool(xray_structure.scatterers().size(),flex.size_t(range(40,504))) geometry = m.get_restraints_manager().geometry geometry = geometry.select(s) es = geometry.energies_sites( sites_cart = xray_structure.sites_cart().select(s)) a = es.angle_deviations()[2] b = es.bond_deviations()[2] return a, b # default a1,b1 = get_ab(params=None) # using custom bonds params = mmtbx.model.manager.get_default_pdb_interpretation_params() params.pdb_interpretation.automatic_linking.link_all=True params.pdb_interpretation.secondary_structure.enabled=True params.pdb_interpretation.secondary_structure.nucleic_acid.base_pair[0].restrain_hbonds=True params.pdb_interpretation.secondary_structure.nucleic_acid.base_pair[0].restrain_hb_angles=True a2,b2 = get_ab(params=params) # assert approx_equal(a1,a2) assert approx_equal(b1,b2) def exercise(): pdb_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/enk.pdb", test=os.path.isfile) mol = mmtbx.model.manager( model_input = iotbx.pdb.input(file_name=pdb_file)) mol.process(make_restraints=True) mol.setup_scattering_dictionaries(scattering_table = "wk1995") ################ # Not clear why one needed 2 identical files... mol_copy = mol.deep_copy() assert mol.number_of_ordered_solvent_molecules() == 9 f1 = open("test_model_out.pdb","w") f2 = open("test_model_out_nohydrogens.pdb","w") pdb_str = mol.model_as_pdb() f1.write(pdb_str) pdb_str = mol.model_as_pdb() f2.write(pdb_str) f1.close() f2.close() mol = mol.remove_solvent() assert mol.number_of_ordered_solvent_molecules() == 0 f1 = open("test_model_out_nosolvent.pdb","w") f2 = open("test_model_out_noO.pdb","w") pdb_str = mol.model_as_pdb() f1.write(pdb_str) pdb_str = mol.model_as_pdb() f2.write(pdb_str) f1.close() f2.close() mol.geometry_statistics().show() mol.geometry_statistics().show() ################ selection = flex.bool(mol.get_number_of_atoms(), True) mol_other = mol.select(selection) mol_other.setup_scattering_dictionaries(scattering_table = "wk1995") ################ mol_other.geometry_statistics() print() mol.geometry_statistics() ##### class iso: pass iso.sphere_radius = 5.0 iso.distance_power = 1.57 iso.average_power = 0.58 iso.wilson_b_weight_auto = False iso.wilson_b_weight = None iso.plain_pairs_radius = 5.0 iso.refine_ap_and_dp = False iso.use_u_local_only = False ##### import sys mol.show_adp_statistics(out=sys.stdout) print() mol.show_adp_statistics(out=sys.stdout) rm = mol.restraints_manager # Not clear why one needed 2 identical files... f1 = open("XXX.pdb","w") f2 = open("XXXr.pdb","w") pdb_str = mol_copy.model_as_pdb() f1.write(pdb_str) pdb_str = mol_copy.model_as_pdb() f2.write(pdb_str) f1.close() f2.close() def exercise_2(): pdb_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/adp_out_stat.pdb", test=os.path.isfile) params = mmtbx.model.manager.get_default_pdb_interpretation_params() params.pdb_interpretation.nonbonded_weight = 16 params.pdb_interpretation.clash_guard.nonbonded_distance_threshold = None # disable clash_guard mol = mmtbx.model.manager( model_input = iotbx.pdb.input(file_name=pdb_file)) mol.process(pdb_interpretation_params=params, make_restraints=True) mol.setup_scattering_dictionaries(scattering_table = "wk1995") out = StringIO() adp_stat = mol.show_adp_statistics(out = out) def exercise_3(): pdb_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/arg_h_hohh1_sh.pdb", test=os.path.isfile) params = mmtbx.model.manager.get_default_pdb_interpretation_params() params.pdb_interpretation.nonbonded_weight = 16 mol = mmtbx.model.manager( model_input = iotbx.pdb.input(file_name=pdb_file)) mol.process(pdb_interpretation_params=params, make_restraints=True) mol.setup_scattering_dictionaries(scattering_table = "wk1995") out = StringIO() mol.set_log(out) mol.idealize_h_minimization() assert out.getvalue().splitlines()[0] == \ "X-H deviation from ideal before regularization (bond): mean= 0.198 max= 0.626", \ out.getvalue().splitlines()[0] assert out.getvalue().splitlines()[1] == \ "X-H deviation from ideal after regularization (bond): mean= 0.000 max= 0.000" #diffs = flex.double() #for it in mol.xh_connectivity_table(): # diffs.append(abs(it[3]-it[4])) #mmm = diffs.min_max_mean() #print mmm.as_tuple() #assert mmm.max <0.01 , mmm.max #assert mmm.mean<0.001, mmm.mean def exercise_4(): pdb_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/lysozyme_noH.pdb", test=os.path.isfile) mol = mmtbx.model.manager( model_input = iotbx.pdb.input(file_name=pdb_file)) mol.process(make_restraints=True) result = mol.isolated_atoms_selection() solvent_sel = mol.solvent_selection() assert solvent_sel.count(True)+1 == result.count(True) def exercise_convert_atom(): from iotbx.pdb import hierarchy from cctbx import crystal from cctbx.xray import anomalous_scatterer_group coords = [ (2.12, 0., 0.), (0., 2.12, 0.), (0, 0, 2.12), (0,0,0), (-2.12, 0, 0), (0, -2.12, 0), (0, 0, -2.12) ] root = hierarchy.root() model = hierarchy.model() chain = hierarchy.chain(id="S") root.append_model(model) model.append_chain(chain) for k, xyz in enumerate(coords): rg = hierarchy.residue_group(resseq=str(k+1)) ag = hierarchy.atom_group(resname="HOH") atom = hierarchy.atom() atom.serial = str(k+1) atom.name = " O " atom.occ = 1.0 atom.b = 20.0 atom.xyz= xyz atom.element = " O" ag.append_atom(atom) rg.append_atom_group(ag) chain.append_residue_group(rg) symm = crystal.symmetry( space_group_symbol="P1", unit_cell=(10,10,10,90,90,90)) open("tmp_tst_model_5.pdb", "w").write(root.as_pdb_string(symm)) mol = mmtbx.model.manager( model_input = iotbx.pdb.input(file_name="tmp_tst_model_5.pdb")) mol.process(make_restraints=True) mol.convert_atom( i_seq=4, scattering_type="Mg2+", atom_name="MG", element="MG", charge=2, residue_name="MG", initial_occupancy=0.99, chain_id='X') mol.set_anomalous_scatterer_groups( [anomalous_scatterer_group( iselection=flex.size_t([4]), f_prime=0, f_double_prime=0, refine=["f_prime","f_double_prime"], selection_string="element MG", update_from_selection=True),] ) geometry_minimization.run2( restraints_manager = mol.get_restraints_manager(), pdb_hierarchy = mol.get_hierarchy(), correct_special_position_tolerance = 1., nonbonded = True, ) mol.set_sites_cart_from_hierarchy() # if the nonbonded type is set correctly, the nonbonded restraints should # not push the for atom in mol.get_hierarchy().atoms(): xyz_max = max([ abs(n) for n in atom.xyz]) assert (xyz_max < 2.6), 'max %s is larger than 2.6' % xyz_max mol = mol.select(flex.size_t([1,2,3,4,5,6])) assert mol.have_anomalous_scatterer_groups() # assert mol.update_anomalous_groups(out=null_out()) # not needed because select() processed groups correctly isel = mol.get_anomalous_scatterer_groups()[0].iselection assert list(isel) == [3] pdb_file_exercise_h_counts=""" CRYST1 8.228 11.366 10.991 90.00 90.00 90.00 P 1 ATOM 1 N AGLY B 1 3.102 3.878 3.794 0.70 7.85 N ATOM 2 CA AGLY B 1 3.985 4.960 4.314 0.70 6.79 C ATOM 3 C AGLY B 1 5.454 4.600 4.162 0.70 5.59 C ATOM 4 O AGLY B 1 5.756 3.431 3.920 0.70 6.04 O ATOM 5 H1 AGLY B 1 2.660 4.173 3.080 0.70 7.85 H ATOM 6 H2 AGLY B 1 3.597 3.175 3.566 0.70 7.85 H ATOM 7 H3 AGLY B 1 2.522 3.640 4.425 0.70 7.85 H ATOM 8 HA2AGLY B 1 3.815 5.782 3.828 0.70 6.79 H ATOM 9 HA3AGLY B 1 3.798 5.111 5.254 0.70 6.79 H ATOM 10 N BGLY B 1 4.731 2.369 3.426 0.30 7.85 N ATOM 11 CA BGLY B 1 5.847 3.227 3.917 0.30 6.79 C ATOM 12 C BGLY B 1 5.408 4.661 4.138 0.30 5.59 C ATOM 13 O BGLY B 1 4.212 4.956 4.163 0.30 6.04 O ATOM 14 H1 BGLY B 1 4.655 1.653 3.949 0.30 7.85 H ATOM 15 H2 BGLY B 1 3.971 2.832 3.444 0.30 7.85 H ATOM 16 H3 BGLY B 1 4.901 2.110 2.592 0.30 7.85 H ATOM 17 HA2BGLY B 1 6.182 2.874 4.756 0.30 6.79 H ATOM 18 HA3BGLY B 1 6.569 3.222 3.269 0.30 6.79 H ATOM 19 N CYS B 2 6.380 5.555 4.293 1.00 5.95 N ATOM 20 CA CYS B 2 6.109 6.982 4.531 1.00 5.17 C ATOM 21 C CYS B 2 5.169 7.274 5.709 1.00 4.74 C ATOM 22 O CYS B 2 5.516 7.016 6.861 1.00 4.51 O ATOM 23 CB CYS B 2 5.631 7.673 3.244 1.00 5.99 C ATOM 24 SG CYS B 2 5.163 9.405 3.466 1.00 5.51 S ATOM 25 H CYS B 2 7.222 5.382 4.256 1.00 5.95 H ATOM 26 HA CYS B 2 6.956 7.396 4.758 1.00 5.17 H ATOM 27 HB2 CYS B 2 6.346 7.642 2.590 1.00 5.99 H ATOM 28 HB3 CYS B 2 4.856 7.199 2.905 1.00 5.99 H ATOM 29 HG CYS B 2 4.807 9.852 2.411 1.00 5.51 H ATOM 30 N CYS B 3 3.986 7.810 5.419 1.00 4.88 N ATOM 31 CA CYS B 3 3.018 8.129 6.461 1.00 5.24 C ATOM 32 C CYS B 3 2.431 6.857 7.062 1.00 6.13 C ATOM 33 O CYS B 3 1.976 6.851 8.205 1.00 7.85 O ATOM 34 CB CYS B 3 1.896 9.003 5.897 1.00 4.92 C ATOM 35 SG CYS B 3 2.450 10.600 5.255 1.00 6.13 S ATOM 36 H CYS B 3 3.720 7.999 4.623 1.00 4.88 H ATOM 37 HA CYS B 3 3.461 8.623 7.169 1.00 5.24 H ATOM 38 HB2 CYS B 3 1.466 8.526 5.170 0.30 4.92 H ATOM 39 HB3 CYS B 3 1.252 9.176 6.602 0.10 4.92 H ATOM 40 HG CYS B 3 3.237 10.413 4.368 1.00 6.13 H TER ATOM 41 O HOH C 1 1.194 0.871 7.026 1.00 7.85 O ATOM 42 H1 HOH C 1 2.011 1.046 7.112 1.00 7.85 H ATOM 43 H2 HOH C 1 0.786 1.605 7.030 1.00 7.85 H ATOM 44 O HOH C 2 2.387 2.996 6.915 1.00 6.79 O ATOM 45 H1 HOH C 2 3.061 3.497 6.915 1.00 6.79 H ATOM 46 H2 HOH C 2 1.712 3.496 6.915 1.00 6.79 H ATOM 47 O HOH C 3 6.169 4.601 8.563 1.00 5.59 O ATOM 48 D1 HOH C 3 6.992 4.768 8.578 1.00 5.59 D ATOM 49 D2 HOH C 3 5.784 5.301 8.302 1.00 5.59 D TER END """ def exercise_h_counts(): of = open("exercise_h_counts.pdb", "w") print(pdb_file_exercise_h_counts, file=of) of.close() pdb_inp = iotbx.pdb.input(file_name = "exercise_h_counts.pdb") model = mmtbx.model.manager( model_input = pdb_inp) model.process(make_restraints=True) model.setup_scattering_dictionaries(scattering_table="n_gaussian") hc = model.h_counts() assert approx_equal(hc.h_count , 26 , 0.01) assert approx_equal(hc.h_occ_sum , 19.4 , 0.01) assert approx_equal(hc.h_fraction_of_total , 50.52, 0.01) assert approx_equal(hc.hrot_count , 8 , 0.01) assert approx_equal(hc.hrot_occ_sum , 5 , 0.01) assert approx_equal(hc.hrot_fraction_of_total , 13.02, 0.01) model.show_h_counts() def exercise_5(): pdb_str = """ CRYST1 98.237 98.237 87.605 90.00 90.00 120.00 P 31 2 1 18 HETATM 2731 O AHOH A 380 19.567 26.060 41.021 0.50 32.01 O ANISOU 2731 O AHOH A 380 4916 4203 3042 782 151 -1380 O HETATM 2732 O BHOH A 380 19.179 25.528 38.229 0.50 20.88 O ANISOU 2732 O BHOH A 380 3169 2234 2532 1183 675 -168 O """ of = open("exercise_5.pdb", "w") print(pdb_str, file=of) of.close() pdb_inp = iotbx.pdb.input(file_name = "exercise_5.pdb") model = mmtbx.model.manager( model_input = pdb_inp) model.process(make_restraints=True) model.setup_scattering_dictionaries(scattering_table="n_gaussian") result = model.extract_water_residue_groups() assert len(result)==1 def exercise_6(): pdb_inp = iotbx.pdb.input(lines=pdb_str_00.split('\n'), source_info=None) m = mmtbx.model.manager(model_input=pdb_inp) m.process(make_restraints=True) ms = m.geometry_statistics() ms.show() # # IF you are about to change this - STOP! Likely you're doing something wrong! # Essentially, this test is to prevent inserting parameters into # mmtbx.model.statistics without much thinking. Most of parameters should # go elsewhere. # from libtbx.introspection import getfullargspec r = getfullargspec(mmtbx.model.statistics.geometry.__init__) assert r.args == ['self', 'model', 'fast_clash', 'condensed_probe', 'use_hydrogens'], r.args def exercise_from_hierarchy(): def check_consistency(m1, m2): assert approx_equal(m1.get_sites_cart(), m2.get_sites_cart()) assert approx_equal(m1.get_xray_structure().sites_cart(), m2.get_xray_structure().sites_cart()) assert m1.crystal_symmetry().is_similar_symmetry(m2.crystal_symmetry()) assert not show_diff(m1.model_as_pdb(), m2.model_as_pdb()) assert not show_diff(m1.model_as_mmcif(), m2.model_as_mmcif()) grm1 = m1.get_restraints_manager() grm2 = m2.get_restraints_manager() geo1 = m1.restraints_as_geo() geo2 = m2.restraints_as_geo() # mixed order in nonbonded. It is fine since everything else below # matches perfectly # assert not show_diff(geo1, geo2) es1 = grm1.energies_sites(m1.get_sites_cart(), compute_gradients=True) es2 = grm2.energies_sites(m2.get_sites_cart(), compute_gradients=True) print(es1.residual_sum) print(es1.target) assert approx_equal(es1.residual_sum, es2.residual_sum) assert approx_equal(es1.target, es2.target) assert approx_equal(es1.gradients, es2.gradients) pdb_inp1 = iotbx.pdb.input(lines=pdb_str_00.split('\n'), source_info=None) pdb_inp2 = iotbx.pdb.input(lines=pdb_str_00.split('\n'), source_info=None) m1 = mmtbx.model.manager(model_input = pdb_inp1) m1.process(make_restraints=True) m2 = mmtbx.model.manager( model_input = None, crystal_symmetry = pdb_inp2.crystal_symmetry(), pdb_hierarchy=pdb_inp2.construct_hierarchy()) m2.process(make_restraints=True) check_consistency(m1, m2) sel = m1.selection("chain A") m11 = m1.select(sel) m22 = m2.select(sel) check_consistency(m11, m22) def exercise_7(): lines = """ CRYST1 43.974 32.795 33.672 90.00 90.00 90.00 P 1 ATOM 56 N ARG A 10 27.185 16.460 17.483 1.00 2.08 N ATOM 57 CA ARG A 10 26.022 16.782 18.294 1.00 2.02 C ATOM 58 C ARG A 10 25.096 17.774 17.594 1.00 2.02 C ATOM 59 O ARG A 10 23.865 17.608 17.611 1.00 2.22 O ATOM 60 CB ARG A 10 26.464 17.332 19.652 1.00 2.22 C ATOM 61 CG ARG A 10 25.307 17.788 20.546 1.00 2.51 C ATOM 62 CD ARG A 10 24.394 16.657 21.045 1.00 2.89 C ATOM 63 NE ARG A 10 25.123 15.776 21.930 1.00 3.18 N ATOM 64 CZ ARG A 10 24.571 14.673 22.470 1.00 4.37 C ATOM 65 NH1 ARG A 10 23.310 14.331 22.245 1.00 6.14 N ATOM 66 NH2 ARG A 10 25.349 13.908 23.244 1.00 5.58 N ATOM 67 H ARG A 10 28.082 16.725 17.890 1.00 2.08 H ATOM 68 HA ARG A 10 25.458 15.861 18.445 1.00 2.02 H ATOM 69 HB2 ARG A 10 27.033 16.564 20.176 1.00 2.22 H ATOM 70 HB3 ARG A 10 27.138 18.173 19.490 1.00 2.22 H ATOM 71 HG2 ARG A 10 25.718 18.312 21.409 1.00 2.51 H ATOM 72 HG3 ARG A 10 24.702 18.508 19.995 1.00 2.51 H ATOM 73 HD2 ARG A 10 23.535 17.078 21.567 1.00 2.89 H ATOM 74 HD3 ARG A 10 24.007 16.092 20.197 1.00 2.89 H ATOM 75 HE ARG A 10 26.093 15.999 22.154 1.00 3.18 H ATOM 76 HH11 ARG A 10 22.723 14.911 21.645 1.00 6.14 H ATOM 77 HH12 ARG A 10 22.926 13.488 22.672 1.00 6.14 H ATOM 78 HH21 ARG A 10 26.322 14.169 23.406 1.00 5.58 H ATOM 79 HH22 ARG A 10 24.970 13.064 23.672 1.00 5.58 H TER END """ for use_neutron_distances in [True, False]: params = mmtbx.model.manager.get_default_pdb_interpretation_params() params.pdb_interpretation.use_neutron_distances=use_neutron_distances model = mmtbx.model.manager( model_input = iotbx.pdb.input(source_info=None, lines=lines), log = null_out()) model.process(pdb_interpretation_params=params, make_restraints=True) gs = model.geometry_statistics(use_hydrogens = True).result() if(use_neutron_distances): assert approx_equal(gs.bond.mean, 0.0068, 0.0001) else: assert approx_equal(gs.bond.mean, 0.1054, 0.0001) bps, asu = model.get_restraints_manager().geometry.get_all_bond_proxies( sites_cart = model.get_sites_cart()) elems = model.get_hierarchy().atoms().extract_element() cntr=0 for p in bps: i, j = p.i_seqs if([elems[i], elems[j]].count("H")): if(use_neutron_distances): assert p.distance_ideal > 1.0 else: assert p.distance_ideal < 1.0 cntr+=1 assert cntr==13 def exercise_8(): """ Indirectly make sure new model from model.selection() does not inherit pdb_interpretation object as it becomes obsolete as result of selection. """ pdb_str = """ CRYST1 17.862 33.032 12.451 90.00 90.00 90.00 P 21 21 21 0 HETATM 1 O MPR A 5 -3.288 3.784 12.142 1.00 0.05 O HETATM 2 C1 MPR A 5 -2.721 3.156 13.026 1.00 0.04 C HETATM 3 C2 MPR A 5 -3.033 3.296 14.510 1.00 0.05 C HETATM 4 C3 MPR A 5 -3.588 4.658 14.899 1.00 0.05 C HETATM 5 S3 MPR A 5 -2.358 5.908 15.321 1.00 0.06 S HETATM 0 H32 MPR A 5 -4.126 4.992 14.165 1.00 0.05 H HETATM 0 H31 MPR A 5 -4.182 4.543 15.657 1.00 0.05 H HETATM 0 H22 MPR A 5 -3.673 2.612 14.763 1.00 0.05 H HETATM 0 H21 MPR A 5 -2.224 3.129 15.018 1.00 0.05 H ATOM 10 N CYS A 6 -1.838 2.168 12.744 1.00 0.05 N ATOM 11 CA CYS A 6 -1.501 1.856 11.357 1.00 0.04 C ATOM 12 C CYS A 6 -2.711 1.429 10.499 1.00 0.04 C ATOM 13 O CYS A 6 -2.700 1.672 9.296 1.00 0.04 O ATOM 14 CB CYS A 6 -0.431 0.750 11.269 1.00 0.05 C ATOM 15 SG CYS A 6 1.221 1.279 11.825 1.00 0.06 S ATOM 0 HA CYS A 6 -1.159 2.690 10.998 1.00 0.04 H ATOM 0 HB2 CYS A 6 -0.716 -0.007 11.804 1.00 0.05 H ATOM 0 HB3 CYS A 6 -0.371 0.442 10.351 1.00 0.05 H """ pdb_inp = iotbx.pdb.input(source_info=None, lines = pdb_str) model = mmtbx.model.manager( model_input = pdb_inp, log = null_out()) model.process(make_restraints=True) sel = model.selection(string = "element H and not protein") model = model.select(~sel) sel = model.selection(string="protein") assert model.size() == sel.size(), [model.size(), sel.size()] def exercise_9(): """ Exercise rotamer_outlier_selection. """ pdb_str = """ CRYST1 82.497 82.497 134.586 90.00 90.00 120.00 P 32 2 1 ATOM 0 N LYS A 228 16.753 49.364 44.427 1.00 29.71 N ATOM 1 CA LYS A 228 17.316 50.225 45.462 1.00 30.97 C ATOM 2 C LYS A 228 16.971 51.681 45.225 1.00 32.43 C ATOM 3 O LYS A 228 16.594 52.055 44.120 1.00 32.69 O ATOM 4 CB LYS A 228 18.841 50.152 45.390 1.00 32.79 C ATOM 5 CG LYS A 228 19.434 48.982 46.075 1.00 36.99 C ATOM 6 CD LYS A 228 20.099 49.447 47.331 1.00 40.31 C ATOM 7 CE LYS A 228 20.368 48.266 48.182 1.00 41.44 C ATOM 8 NZ LYS A 228 20.323 48.625 49.612 1.00 41.02 N ATOM 9 N GLN A 229 17.130 52.508 46.260 1.00 32.84 N ATOM 10 C GLN A 229 18.360 54.464 45.732 1.00 33.80 C ATOM 11 O GLN A 229 19.348 54.126 46.386 1.00 34.43 O ATOM 12 CA AGLN A 229 16.971 53.942 46.112 0.43 33.76 C ATOM 13 CB AGLN A 229 16.506 54.583 47.431 0.43 35.95 C ATOM 14 CG AGLN A 229 15.176 55.322 47.295 0.43 39.53 C ATOM 15 CD AGLN A 229 14.847 56.184 48.492 0.43 43.68 C ATOM 16 OE1AGLN A 229 15.695 56.481 49.340 0.43 45.16 O ATOM 17 NE2AGLN A 229 13.608 56.636 48.568 0.43 44.89 N ATOM 18 CA BGLN A 229 16.981 53.943 46.113 0.57 33.65 C ATOM 19 CB BGLN A 229 16.529 54.590 47.436 0.57 35.47 C ATOM 20 CG BGLN A 229 15.105 54.230 47.849 0.57 37.90 C ATOM 21 CD BGLN A 229 14.089 54.492 46.764 0.57 40.71 C ATOM 22 OE1BGLN A 229 13.564 53.568 46.135 0.57 41.54 O ATOM 23 NE2BGLN A 229 13.802 55.759 46.510 0.57 41.34 N ATOM 24 N ALA A 230 18.441 55.247 44.673 1.00 33.30 N ATOM 25 CA ALA A 230 19.683 55.848 44.191 1.00 32.95 C ATOM 26 C ALA A 230 19.661 57.363 44.526 1.00 32.70 C ATOM 27 O ALA A 230 18.597 57.905 44.844 1.00 33.61 O ATOM 28 CB ALA A 230 19.790 55.649 42.683 1.00 32.78 C TER END """ pdb_inp = iotbx.pdb.input(source_info=None, lines = pdb_str) model = mmtbx.model.manager( model_input = pdb_inp, log = null_out()) model.process(make_restraints=True) sel = model.rotamer_outlier_selection().iselection() assert list(sel) == [9, 10, 11, 12, 13, 14, 15, 16, 17] def exercise_10(): """ Exercise macromolecule_plus_hetatms_by_chain_selections() method. """ psb_str1 = """ CRYST1 21.937 4.866 23.477 90.00 107.08 90.00 P 1 21 1 2 ATOM 0 CG ASN A 2 -7.584 1.342 0.692 1.00 14.08 C ATOM 1 OD1 ASN A 2 -8.025 0.227 1.016 1.00 17.46 O ATOM 2 ND2 ASN A 2 -8.204 2.155 -0.169 1.00 11.72 N TER ATOM 3 C TYR B 7 10.603 2.331 6.885 1.00 15.91 C ATOM 4 O TYR B 7 11.041 1.811 5.855 1.00 15.76 O ATOM 5 OXT TYR B 7 11.358 2.999 7.612 1.00 17.49 O TER HETATM 6 O HOH C 9 10.431 1.858 3.216 1.00 19.71 O HETATM 7 O HOH C 10 -11.286 1.756 -1.468 1.00 17.08 O HETATM 8 O HOH C 11 11.808 4.179 9.970 1.00 23.99 O HETATM 9 O HOH C 12 13.605 1.327 9.198 1.00 26.17 O END """ psb_str2 = """ CRYST1 21.937 4.866 23.477 90.00 107.08 90.00 P 1 21 1 2 ATOM 0 CG ASN A 2 -7.584 1.342 0.692 1.00 14.08 C ATOM 1 OD1 ASN A 2 -8.025 0.227 1.016 1.00 17.46 O ATOM 2 ND2 ASN A 2 -8.204 2.155 -0.169 1.00 11.72 N ATOM 3 C TYR B 7 10.603 2.331 6.885 1.00 15.91 C ATOM 4 O TYR B 7 11.041 1.811 5.855 1.00 15.76 O ATOM 5 OXT TYR B 7 11.358 2.999 7.612 1.00 17.49 O HETATM 6 O HOH C 9 10.431 1.858 3.216 1.00 19.71 O HETATM 7 O HOH C 10 -11.286 1.756 -1.468 1.00 17.08 O HETATM 8 O HOH C 11 11.808 4.179 9.970 1.00 23.99 O HETATM 9 O HOH C 12 13.605 1.327 9.198 1.00 26.17 O END """ psb_str3 = """ CRYST1 21.937 4.866 23.477 90.00 107.08 90.00 P 1 21 1 2 ATOM 0 CG ASN A 2 -7.584 1.342 0.692 1.00 14.08 C ATOM 1 OD1 ASN A 2 -8.025 0.227 1.016 1.00 17.46 O ATOM 2 ND2 ASN A 2 -8.204 2.155 -0.169 1.00 11.72 N ATOM 3 C TYR B 7 10.603 2.331 6.885 1.00 15.91 C ATOM 4 O TYR B 7 11.041 1.811 5.855 1.00 15.76 O ATOM 5 OXT TYR B 7 11.358 2.999 7.612 1.00 17.49 O HETATM 6 O HOH A 9 10.431 1.858 3.216 1.00 19.71 O HETATM 7 O HOH A 10 -11.286 1.756 -1.468 1.00 17.08 O HETATM 8 O HOH A 11 11.808 4.179 9.970 1.00 23.99 O HETATM 9 O HOH A 12 13.605 1.327 9.198 1.00 26.17 O END """ psb_str4 = """ CRYST1 21.937 4.866 23.477 90.00 107.08 90.00 P 1 21 1 2 ATOM 0 CG ASN A 2 -7.584 1.342 0.692 1.00 14.08 C ATOM 1 OD1 ASN A 2 -8.025 0.227 1.016 1.00 17.46 O ATOM 2 ND2 ASN A 2 -8.204 2.155 -0.169 1.00 11.72 N ATOM 3 C TYR B 7 10.603 2.331 6.885 1.00 15.91 C ATOM 4 O TYR B 7 11.041 1.811 5.855 1.00 15.76 O ATOM 5 OXT TYR B 7 11.358 2.999 7.612 1.00 17.49 O HETATM 6 O HOH B 9 10.431 1.858 3.216 1.00 19.71 O HETATM 7 O HOH B 10 -11.286 1.756 -1.468 1.00 17.08 O HETATM 8 O HOH B 11 11.808 4.179 9.970 1.00 23.99 O HETATM 9 O HOH B 12 13.605 1.327 9.198 1.00 26.17 O END """ psb_str5 = """ CRYST1 21.937 4.866 23.477 90.00 107.08 90.00 P 1 21 1 2 ATOM 0 CG ASN A 2 -7.584 1.342 0.692 1.00 14.08 C ATOM 1 OD1 ASN A 2 -8.025 0.227 1.016 1.00 17.46 O ATOM 2 ND2 ASN A 2 -8.204 2.155 -0.169 1.00 11.72 N TER ATOM 3 C TYR A 7 10.603 2.331 6.885 1.00 15.91 C ATOM 4 O TYR A 7 11.041 1.811 5.855 1.00 15.76 O ATOM 5 OXT TYR A 7 11.358 2.999 7.612 1.00 17.49 O HETATM 6 O HOH A 9 10.431 1.858 3.216 1.00 19.71 O HETATM 7 O HOH A 10 -11.286 1.756 -1.468 1.00 17.08 O HETATM 8 O HOH A 11 11.808 4.179 9.970 1.00 23.99 O HETATM 9 O HOH A 12 13.605 1.327 9.198 1.00 26.17 O END """ for i, pdb_str in enumerate([psb_str1, psb_str2, psb_str3, psb_str4, psb_str5]): pi = iotbx.pdb.input(source_info=None, lines=pdb_str) m = mmtbx.model.manager(model_input = pi) sels = m.macromolecule_plus_hetatms_by_chain_selections() sels = [list(s.iselection()) for s in sels] assert sels == [[0, 1, 2, 7], [3, 4, 5, 6, 8, 9]] # Check first_resseq_as_int in hierarchy and model (same function) ph = pi.construct_hierarchy() assert m.first_resseq_as_int() == ph.first_resseq_as_int() assert m.last_resseq_as_int() == ph.last_resseq_as_int() def exercise_11_ss_annotations(): good_h_str = 'HELIX 1 1 THR A 18 ILE A 20 5 3' bad_h_str = 'HELIX 1 1 THR A 18 ILE A 20 11 3' pdb_str = """ CRYST1 32.501 39.502 44.640 90.00 90.00 90.00 P 21 21 21 4 ATOM 265 N THR A 18 13.114 7.968 6.956 1.00 4.57 N ATOM 266 CA THR A 18 13.581 6.907 6.105 1.00 4.76 C ATOM 267 C THR A 18 14.273 5.867 7.003 1.00 4.60 C ATOM 268 O THR A 18 14.631 6.110 8.149 1.00 4.40 O ATOM 269 CB THR A 18 14.556 7.447 5.032 1.00 5.62 C ATOM 270 OG1 THR A 18 15.710 7.880 5.759 1.00 6.08 O ATOM 271 CG2 THR A 18 13.937 8.551 4.219 1.00 7.48 C ATOM 279 N LEU A 19 14.528 4.681 6.410 1.00 5.15 N ATOM 280 CA LEU A 19 15.074 3.599 7.202 1.00 4.83 C ATOM 281 C LEU A 19 16.437 3.919 7.781 1.00 4.82 C ATOM 282 O LEU A 19 16.736 3.482 8.909 1.00 5.18 O ATOM 283 CB LEU A 19 15.111 2.303 6.373 1.00 5.60 C ATOM 284 CG LEU A 19 13.748 1.663 6.109 1.00 6.04 C ATOM 285 CD1 LEU A 19 13.891 0.508 5.116 1.00 7.36 C ATOM 286 CD2 LEU A 19 13.107 1.170 7.418 1.00 7.22 C ATOM 298 N ILE A 20 17.306 4.658 7.066 1.00 5.11 N ATOM 299 CA ILE A 20 18.645 4.933 7.588 1.00 5.24 C ATOM 300 C ILE A 20 18.601 5.767 8.844 1.00 4.94 C ATOM 301 O ILE A 20 19.565 5.822 9.609 1.00 5.92 O ATOM 302 CB ILE A 20 19.529 5.617 6.519 1.00 6.40 C ATOM 303 CG1 ILE A 20 21.031 5.545 6.877 1.00 9.33 C ATOM 304 CG2 ILE A 20 19.057 7.034 6.234 1.00 7.06 C ATOM 305 CD1 ILE A 20 21.947 6.045 5.765 1.00 12.70 C """ good_inp = iotbx.pdb.input(source_info=None, lines=good_h_str+pdb_str) bad_inp = iotbx.pdb.input(source_info=None, lines=bad_h_str+pdb_str) m1 = mmtbx.model.manager(model_input = good_inp) m2 = mmtbx.model.manager(model_input = bad_inp, skip_ss_annotations=True) try: m2 = mmtbx.model.manager(model_input = bad_inp) except IndexError as e: assert str(e) == 'list index out of range', e else: assert 0 def run(): exercise_00() exercise() exercise_2() exercise_3() exercise_4() exercise_convert_atom() exercise_h_counts() exercise_5() exercise_6() exercise_7() exercise_8() exercise_from_hierarchy() exercise_9() exercise_10() exercise_11_ss_annotations() print(format_cpu_times()) if (__name__ == "__main__"): run()