diff --git a/CHANGES/v2.11.md b/CHANGES/v2.11.md index bbb1eee3f9..aaf421e666 100644 --- a/CHANGES/v2.11.md +++ b/CHANGES/v2.11.md @@ -5,6 +5,7 @@ This page contains changes that will end up in 2.11 ### Changes relevant for users: - When using [MOLINFO](MOLINFO.md) with the `WHOLE` flag, PBCs in the following actions will be reconstructed using a minimum spanning tree based on the coordinates stored in the MOLFILE reference pdb. + - When the reference pdb of [MOLINFO](MOLINFO.md) with the `WHOLE` flag has a CRYST1 record with space group P 1, PLUMED now checks along each chain that the reference is whole in that box, and writes a warning to the log naming the atoms that are across the periodic boundary from the atom before them. Before, a split reference made [WHOLEMOLECULES](WHOLEMOLECULES.md) split whole molecules without any warning. - When using the benchmark now it is possible to scale the atom distances in the synthetic atom distribution (the base atomic distance is 1) - [SAXS](SAXS.md) now accepts the `MARTINI_FF` keyword to select the Martini form-factor generation: `MARTINI_FF=2` (default) keeps the existing Martini 2.2 protein and nucleic-acid form factors, while `MARTINI_FF=3` selects Martini 3 protein form factors. - Added environment variable `PLUMED_LOG_FILE` to control the log file pathname when runnning with GROMACS (the log file was hardcoded as `PLUMED.OUT`) diff --git a/regtest/basic/rt-molinfo-whole-check/Makefile b/regtest/basic/rt-molinfo-whole-check/Makefile new file mode 100644 index 0000000000..3703b27cea --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-check/Makefile @@ -0,0 +1 @@ +include ../../scripts/test.make diff --git a/regtest/basic/rt-molinfo-whole-check/config b/regtest/basic/rt-molinfo-whole-check/config new file mode 100644 index 0000000000..df1f95bf3e --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-check/config @@ -0,0 +1 @@ +type=make diff --git a/regtest/basic/rt-molinfo-whole-check/dna_torn.pdb b/regtest/basic/rt-molinfo-whole-check/dna_torn.pdb new file mode 100644 index 0000000000..060cf91ff4 --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-check/dna_torn.pdb @@ -0,0 +1,245 @@ +CRYST1 47.018 47.018 47.018 60.00 60.00 90.00 P 1 1 +ATOM 1 O5' DC A 1 31.610 35.993 16.129 1.00 64.35 O +ATOM 2 C5' DC A 1 31.805 35.719 14.731 1.00 44.69 C +ATOM 3 C4' DC A 1 32.636 34.466 14.612 1.00 31.28 C +ATOM 4 O4' DC A 1 32.035 33.381 15.364 1.00 37.45 O +ATOM 5 C3' DC A 1 32.847 33.920 13.206 1.00 46.72 C +ATOM 6 O3' DC A 1 34.025 33.123 13.193 1.00 48.89 O +ATOM 7 C2' DC A 1 31.623 33.021 13.159 1.00 30.88 C +ATOM 8 C1' DC A 1 31.906 32.280 14.456 1.00 36.58 C +ATOM 9 N1 DC A 1 30.745 31.459 14.892 1.00 40.51 N +ATOM 10 C2 DC A 1 30.899 30.252 15.527 1.00 16.62 C +ATOM 11 O2 DC A 1 32.035 29.812 15.726 1.00 27.75 O +ATOM 12 N3 DC A 1 29.818 29.559 15.889 1.00 20.55 N +ATOM 13 C4 DC A 1 28.592 30.024 15.632 1.00 34.72 C +ATOM 14 N4 DC A 1 27.503 29.275 15.956 1.00 40.31 N +ATOM 15 C5 DC A 1 28.394 31.240 14.983 1.00 30.78 C +ATOM 16 C6 DC A 1 29.518 31.969 14.613 1.00 25.90 C +ATOM 17 P DG A 2 35.084 33.084 11.995 1.00 58.85 P +ATOM 18 OP1 DG A 2 36.211 33.955 12.363 1.00 57.82 O +ATOM 19 OP2 DG A 2 34.497 33.257 10.651 1.00 78.33 O +ATOM 20 O5' DG A 2 35.515 31.549 12.010 1.00 40.36 O +ATOM 21 C5' DG A 2 36.218 30.973 13.106 1.00 47.19 C +ATOM 22 C4' DG A 2 36.169 29.507 12.791 1.00 47.81 C +ATOM 23 O4' DG A 2 34.868 29.050 13.186 1.00 38.76 O +ATOM 24 C3' DG A 2 36.368 29.123 11.319 1.00 28.58 C +ATOM 25 O3' DG A 2 37.398 28.118 11.165 1.00 40.44 O +ATOM 26 C2' DG A 2 34.948 28.683 10.928 1.00 21.14 C +ATOM 27 C1' DG A 2 34.396 28.102 12.228 1.00 33.95 C +ATOM 28 N9 DG A 2 32.912 28.268 12.292 1.00 34.00 N +ATOM 29 C8 DG A 2 32.201 29.382 11.941 1.00 36.47 C +ATOM 30 N7 DG A 2 30.882 29.253 12.148 1.00 32.37 N +ATOM 31 C5 DG A 2 30.758 28.010 12.654 1.00 15.06 C +ATOM 32 C6 DG A 2 29.579 27.323 13.057 1.00 11.88 C +ATOM 33 O6 DG A 2 28.414 27.714 13.030 1.00 21.30 O +ATOM 34 N1 DG A 2 29.872 26.077 13.549 1.00 15.44 N +ATOM 35 C2 DG A 2 31.109 25.515 13.667 1.00 9.63 C +ATOM 36 N2 DG A 2 31.183 24.254 14.180 1.00 16.69 N +ATOM 37 N3 DG A 2 32.212 26.158 13.282 1.00 30.98 N +ATOM 38 C4 DG A 2 31.965 27.392 12.786 1.00 18.56 C +ATOM 39 P DC A 3 37.739 27.419 9.764 1.00 44.67 P +ATOM 40 OP1 DC A 3 39.181 27.114 9.732 1.00 53.89 O +ATOM 41 OP2 DC A 3 37.234 28.210 8.627 1.00 57.79 O +ATOM 42 O5' DC A 3 36.935 26.044 9.839 1.00 35.42 O +ATOM 43 C5' DC A 3 37.259 25.083 10.847 1.00 45.75 C +ATOM 44 C4' DC A 3 36.198 24.031 10.757 1.00 43.02 C +ATOM 45 O4' DC A 3 34.931 24.642 10.965 1.00 36.85 O +ATOM 46 C3' DC A 3 36.099 23.355 9.415 1.00 40.14 C +ATOM 47 O3' DC A 3 36.796 22.107 9.440 1.00 49.62 O +ATOM 48 C2' DC A 3 34.605 23.204 9.173 1.00 53.79 C +ATOM 49 C1' DC A 3 33.953 23.764 10.421 1.00 22.18 C +ATOM 50 N1 DC A 3 32.871 24.687 10.033 1.00 25.44 N +ATOM 51 C2 DC A 3 31.584 24.382 10.328 1.00 19.81 C +ATOM 52 O2 DC A 3 31.360 23.310 10.894 1.00 29.92 O +ATOM 53 N3 DC A 3 30.610 25.245 10.014 1.00 21.59 N +ATOM 54 C4 DC A 3 30.892 26.401 9.409 1.00 14.01 C +ATOM 55 N4 DC A 3 29.896 27.297 9.141 1.00 26.88 N +ATOM 56 C5 DC A 3 32.201 26.743 9.083 1.00 27.59 C +ATOM 57 C6 DC A 3 33.212 25.846 9.411 1.00 27.05 C +ATOM 58 P DG A 4 36.924 21.210 8.129 1.00 44.54 P +ATOM 59 OP1 DG A 4 38.095 20.333 8.277 1.00 61.90 O +ATOM 60 OP2 DG A 4 36.883 22.094 6.952 1.00 37.36 O +ATOM 61 O5' DG A 4 35.606 20.335 8.182 1.00 32.01 O +ATOM 62 C5' DG A 4 35.389 19.423 9.265 1.00 37.89 C +ATOM 63 C4' DG A 4 34.068 18.758 9.017 1.00 53.00 C +ATOM 64 O4' DG A 4 33.028 19.750 9.008 1.00 38.79 O +ATOM 65 C3' DG A 4 33.939 18.027 7.688 1.00 56.72 C +ATOM 66 O3' DG A 4 32.959 17.012 7.750 1.00 64.12 O +ATOM 67 C2' DG A 4 33.468 19.166 6.800 1.00 40.81 C +ATOM 68 C1' DG A 4 32.391 19.699 7.730 1.00 30.52 C +ATOM 69 N9 DG A 4 31.980 21.079 7.381 1.00 28.53 N +ATOM 70 C8 DG A 4 32.692 22.061 6.744 1.00 27.82 C +ATOM 71 N7 DG A 4 31.988 23.192 6.589 1.00 28.01 N +ATOM 72 C5 DG A 4 30.796 22.898 7.147 1.00 23.22 C +ATOM 73 C6 DG A 4 29.627 23.702 7.261 1.00 29.21 C +ATOM 74 O6 DG A 4 29.444 24.855 6.880 1.00 38.58 O +ATOM 75 N1 DG A 4 28.608 23.012 7.864 1.00 27.94 N +ATOM 76 C2 DG A 4 28.647 21.728 8.328 1.00 23.44 C +ATOM 77 N2 DG A 4 27.506 21.214 8.865 1.00 42.64 N +ATOM 78 N3 DG A 4 29.743 20.977 8.229 1.00 21.56 N +ATOM 79 C4 DG A 4 30.759 21.623 7.633 1.00 23.44 C +ATOM 80 P DA A 5 33.031 15.767 6.757 1.00 57.01 P +ATOM 81 OP1 DA A 5 33.791 14.689 7.404 1.00 58.59 O +ATOM 82 OP2 DA A 5 33.512 16.221 5.422 1.00 51.96 O +ATOM 83 O5' DA A 5 31.485 15.379 6.673 1.00 47.12 O +ATOM 84 C5' DA A 5 30.690 15.367 7.874 1.00 47.67 C +ATOM 85 C4' DA A 5 29.347 15.886 7.469 1.00 64.79 C +ATOM 86 O4' DA A 5 29.517 17.245 7.073 1.00 47.60 O +ATOM 87 C3' DA A 5 28.694 15.191 6.276 1.00 51.50 C +ATOM 88 O3' DA A 5 27.437 14.594 6.632 1.00 52.18 O +ATOM 89 C2' DA A 5 28.627 16.296 5.208 1.00 45.00 C +ATOM 90 C1' DA A 5 28.526 17.530 6.081 1.00 26.88 C +ATOM 91 N9 DA A 5 29.066 18.714 5.379 1.00 16.69 N +ATOM 92 C8 DA A 5 30.333 18.901 4.894 1.00 28.14 C +ATOM 93 N7 DA A 5 30.538 20.144 4.425 1.00 34.85 N +ATOM 94 C5 DA A 5 29.348 20.751 4.610 1.00 22.49 C +ATOM 95 C6 DA A 5 28.905 22.077 4.331 1.00 18.12 C +ATOM 96 N6 DA A 5 29.720 23.020 3.780 1.00 29.30 N +ATOM 97 N1 DA A 5 27.641 22.376 4.630 1.00 27.61 N +ATOM 98 C2 DA A 5 26.853 21.450 5.181 1.00 18.53 C +ATOM 99 N3 DA A 5 27.138 20.190 5.496 1.00 29.16 N +ATOM 100 C4 DA A 5 28.425 19.908 5.173 1.00 15.08 C +ATOM 101 P DA A 6 26.541 13.804 5.575 1.00 43.68 P +ATOM 102 OP1 DA A 6 25.703 12.837 6.312 1.00 42.55 O +ATOM 103 OP2 DA A 6 27.390 13.297 4.480 1.00 54.20 O +ATOM 104 O5' DA A 6 25.554 14.909 4.992 1.00 28.20 O +ATOM 105 C5' DA A 6 24.477 15.395 5.802 1.00 42.29 C +ATOM 106 C4' DA A 6 23.786 16.401 4.947 1.00 33.23 C +ATOM 107 O4' DA A 6 24.827 17.258 4.474 1.00 41.48 O +ATOM 108 C3' DA A 6 23.092 15.868 3.699 1.00 18.16 C +ATOM 109 O3' DA A 6 21.682 16.167 3.693 1.00 30.42 O +ATOM 110 C2' DA A 6 23.915 16.490 2.573 1.00 52.97 C +ATOM 111 C1' DA A 6 24.374 17.772 3.231 1.00 38.93 C +ATOM 112 N9 DA A 6 25.593 18.324 2.590 1.00 19.06 N +ATOM 113 C8 DA A 6 26.790 17.697 2.380 1.00 17.83 C +ATOM 114 N7 DA A 6 27.724 18.512 1.868 1.00 29.55 N +ATOM 115 C5 DA A 6 27.091 19.699 1.758 1.00 19.88 C +ATOM 116 C6 DA A 6 27.548 20.985 1.327 1.00 17.26 C +ATOM 117 N6 DA A 6 28.836 21.216 0.939 1.00 19.85 N +ATOM 118 N1 DA A 6 26.674 21.989 1.364 1.00 17.93 N +ATOM 119 C2 DA A 6 25.428 21.760 1.784 1.00 23.00 C +ATOM 120 N3 DA A 6 24.885 20.622 2.210 1.00 21.37 N +ATOM 121 C4 DA A 6 25.791 19.621 2.169 1.00 15.93 C +ATOM 122 P DT A 7 44.265 39.357 35.674 1.00 40.72 P +ATOM 123 OP1 DT A 7 42.852 39.267 36.101 1.00 46.75 O +ATOM 124 OP2 DT A 7 44.784 38.201 34.896 1.00 42.53 O +ATOM 125 O5' DT A 7 44.423 40.694 34.835 1.00 35.21 O +ATOM 126 C5' DT A 7 44.091 41.942 35.445 1.00 34.88 C +ATOM 127 C4' DT A 7 44.346 42.935 34.357 1.00 31.45 C +ATOM 128 O4' DT A 7 45.727 42.887 34.038 1.00 46.82 O +ATOM 129 C3' DT A 7 43.645 42.591 33.055 1.00 23.76 C +ATOM 130 O3' DT A 7 42.435 43.341 32.921 1.00 44.27 O +ATOM 131 C2' DT A 7 44.716 42.834 31.982 1.00 26.30 C +ATOM 132 C1' DT A 7 45.828 43.516 32.778 1.00 28.96 C +ATOM 133 N1 DT A 7 47.205 43.210 32.324 1.00 20.47 N +ATOM 134 C2 DT A 7 48.006 44.230 31.935 1.00 28.01 C +ATOM 135 O2 DT A 7 47.567 45.384 31.902 1.00 40.01 O +ATOM 136 N3 DT A 7 49.303 43.948 31.611 1.00 27.94 N +ATOM 137 C4 DT A 7 49.817 42.679 31.641 1.00 15.14 C +ATOM 138 O4 DT A 7 51.014 42.529 31.378 1.00 32.54 O +ATOM 139 C5 DT A 7 48.965 41.632 31.994 1.00 10.83 C +ATOM 140 C7 DT A 7 49.453 40.209 31.995 1.00 36.33 C +ATOM 141 C6 DT A 7 47.649 41.923 32.353 1.00 12.19 C +ATOM 142 P DT A 8 41.568 43.297 31.583 1.00 49.10 P +ATOM 143 OP1 DT A 8 40.209 43.751 31.939 1.00 41.11 O +ATOM 144 OP2 DT A 8 41.642 41.975 30.919 1.00 39.21 O +ATOM 145 O5' DT A 8 42.270 44.425 30.686 1.00 48.80 O +ATOM 146 C5' DT A 8 42.330 45.785 31.177 1.00 34.73 C +ATOM 147 C4' DT A 8 43.179 46.536 30.197 1.00 28.73 C +ATOM 148 O4' DT A 8 44.372 45.765 30.043 1.00 39.07 O +ATOM 149 C3' DT A 8 42.602 46.639 28.788 1.00 37.88 C +ATOM 150 O3' DT A 8 42.151 47.974 28.455 1.00 52.04 O +ATOM 151 C2' DT A 8 43.697 46.025 27.898 1.00 32.80 C +ATOM 152 C1' DT A 8 44.920 46.162 28.793 1.00 36.58 C +ATOM 153 N1 DT A 8 46.007 45.183 28.518 1.00 24.57 N +ATOM 154 C2 DT A 8 47.270 45.623 28.253 1.00 19.41 C +ATOM 155 O2 DT A 8 47.508 46.823 28.148 1.00 32.74 O +ATOM 156 N3 DT A 8 48.278 44.710 28.171 1.00 25.12 N +ATOM 157 C4 DT A 8 48.060 43.367 28.310 1.00 31.35 C +ATOM 158 O4 DT A 8 49.042 42.624 28.262 1.00 28.53 O +ATOM 159 C5 DT A 8 46.753 42.918 28.524 1.00 22.80 C +ATOM 160 C7 DT A 8 46.445 41.447 28.655 1.00 24.98 C +ATOM 161 C6 DT A 8 45.729 43.855 28.663 1.00 20.28 C +ATOM 162 P DC A 9 41.715 48.378 26.968 1.00 48.97 P +ATOM 163 OP1 DC A 9 40.832 49.551 27.028 1.00 62.33 O +ATOM 164 OP2 DC A 9 41.194 47.212 26.229 1.00 51.53 O +ATOM 165 O5' DC A 9 43.110 48.854 26.370 1.00 43.99 O +ATOM 166 C5' DC A 9 43.820 49.934 27.008 1.00 50.86 C +ATOM 167 C4' DC A 9 45.081 50.160 26.216 1.00 46.66 C +ATOM 168 O4' DC A 9 45.822 48.934 26.207 1.00 42.69 O +ATOM 169 C3' DC A 9 44.901 50.547 24.757 1.00 56.96 C +ATOM 170 O3' DC A 9 45.654 51.721 24.426 1.00 63.54 O +ATOM 171 C2' DC A 9 45.310 49.272 24.012 1.00 50.41 C +ATOM 172 C1' DC A 9 46.425 48.790 24.916 1.00 41.08 C +ATOM 173 N1 DC A 9 46.708 47.329 24.774 1.00 37.23 N +ATOM 174 C2 DC A 9 47.998 46.910 24.599 1.00 40.54 C +ATOM 175 O2 DC A 9 48.875 47.754 24.429 1.00 43.89 O +ATOM 176 N3 DC A 9 48.290 45.604 24.632 1.00 32.57 N +ATOM 177 C4 DC A 9 47.325 44.702 24.805 1.00 24.65 C +ATOM 178 N4 DC A 9 47.645 43.382 24.848 1.00 27.84 N +ATOM 179 C5 DC A 9 45.987 45.082 24.936 1.00 17.61 C +ATOM 180 C6 DC A 9 45.683 46.440 24.926 1.00 30.63 C +ATOM 181 P DG A 10 45.239 52.640 23.178 1.00 65.48 P +ATOM 182 OP1 DG A 10 45.680 54.024 23.501 1.00 59.09 O +ATOM 183 OP2 DG A 10 43.816 52.413 22.812 1.00 45.71 O +ATOM 184 O5' DG A 10 46.138 52.072 21.988 1.00 70.30 O +ATOM 185 C5' DG A 10 47.566 52.247 22.039 1.00 71.73 C +ATOM 186 C4' DG A 10 48.156 51.397 20.957 1.00 58.69 C +ATOM 187 O4' DG A 10 47.986 50.031 21.355 1.00 41.03 O +ATOM 188 C3' DG A 10 47.511 51.485 19.571 1.00 45.61 C +ATOM 189 O3' DG A 10 48.495 51.403 18.545 1.00 52.70 O +ATOM 190 C2' DG A 10 46.598 50.269 19.573 1.00 36.02 C +ATOM 191 C1' DG A 10 47.613 49.335 20.172 1.00 50.90 C +ATOM 192 N9 DG A 10 47.074 48.020 20.559 1.00 45.86 N +ATOM 193 C8 DG A 10 45.800 47.622 20.849 1.00 44.49 C +ATOM 194 N7 DG A 10 45.725 46.316 21.146 1.00 39.96 N +ATOM 195 C5 DG A 10 47.002 45.895 21.041 1.00 38.99 C +ATOM 196 C6 DG A 10 47.560 44.599 21.248 1.00 35.78 C +ATOM 197 O6 DG A 10 46.997 43.559 21.580 1.00 34.90 O +ATOM 198 N1 DG A 10 48.913 44.606 21.039 1.00 23.54 N +ATOM 199 C2 DG A 10 49.682 45.672 20.677 1.00 8.73 C +ATOM 200 N2 DG A 10 51.018 45.476 20.522 1.00 23.15 N +ATOM 201 N3 DG A 10 49.166 46.880 20.492 1.00 24.68 N +ATOM 202 C4 DG A 10 47.840 46.908 20.698 1.00 31.53 C +ATOM 203 P DC A 11 48.947 52.728 17.779 1.00 60.62 P +ATOM 204 OP1 DC A 11 48.980 53.879 18.710 1.00 63.74 O +ATOM 205 OP2 DC A 11 48.070 52.849 16.595 1.00 52.44 O +ATOM 206 O5' DC A 11 50.456 52.393 17.393 1.00 57.57 O +ATOM 207 C5' DC A 11 51.459 52.415 18.441 1.00 54.70 C +ATOM 208 C4' DC A 11 52.406 51.253 18.249 1.00 72.51 C +ATOM 209 O4' DC A 11 51.627 50.061 18.362 1.00 47.18 O +ATOM 210 C3' DC A 11 53.126 51.134 16.911 1.00 29.82 C +ATOM 211 O3' DC A 11 54.524 50.818 17.058 1.00 43.53 O +ATOM 212 C2' DC A 11 52.302 50.074 16.181 1.00 51.34 C +ATOM 213 C1' DC A 11 52.040 49.143 17.345 1.00 30.07 C +ATOM 214 N1 DC A 11 50.856 48.282 17.122 1.00 23.25 N +ATOM 215 C2 DC A 11 50.986 46.935 17.230 1.00 20.38 C +ATOM 216 O2 DC A 11 52.108 46.485 17.445 1.00 38.77 O +ATOM 217 N3 DC A 11 49.907 46.149 17.132 1.00 15.92 N +ATOM 218 C4 DC A 11 48.699 46.680 16.923 1.00 15.82 C +ATOM 219 N4 DC A 11 47.594 45.881 16.887 1.00 28.04 N +ATOM 220 C5 DC A 11 48.532 48.051 16.781 1.00 26.17 C +ATOM 221 C6 DC A 11 49.654 48.865 16.890 1.00 35.50 C +ATOM 222 P DG A 12 55.515 51.081 15.834 1.00 55.98 P +ATOM 223 OP1 DG A 12 56.888 51.283 16.351 1.00 45.83 O +ATOM 224 OP2 DG A 12 54.947 52.158 15.001 1.00 44.26 O +ATOM 225 O5' DG A 12 55.486 49.719 14.996 1.00 62.63 O +ATOM 226 C5' DG A 12 56.293 48.591 15.400 1.00 69.50 C +ATOM 227 C4' DG A 12 55.932 47.474 14.460 1.00 39.92 C +ATOM 228 O4' DG A 12 54.534 47.276 14.620 1.00 32.00 O +ATOM 229 C3' DG A 12 56.105 47.711 12.944 1.00 50.39 C +ATOM 230 O3' DG A 12 57.169 46.942 12.358 1.00 64.13 O +ATOM 231 C2' DG A 12 54.719 47.369 12.378 1.00 36.18 C +ATOM 232 C1' DG A 12 54.149 46.507 13.490 1.00 24.79 C +ATOM 233 N9 DG A 12 52.677 46.527 13.494 1.00 28.44 N +ATOM 234 C8 DG A 12 51.847 47.596 13.281 1.00 31.85 C +ATOM 235 N7 DG A 12 50.552 47.265 13.369 1.00 38.26 N +ATOM 236 C5 DG A 12 50.572 45.947 13.657 1.00 28.99 C +ATOM 237 C6 DG A 12 49.485 45.049 13.903 1.00 42.63 C +ATOM 238 O6 DG A 12 48.275 45.274 13.902 1.00 49.17 O +ATOM 239 N1 DG A 12 49.934 43.773 14.134 1.00 40.15 N +ATOM 240 C2 DG A 12 51.226 43.350 14.154 1.00 33.42 C +ATOM 241 N2 DG A 12 51.443 42.024 14.353 1.00 40.53 N +ATOM 242 N3 DG A 12 52.245 44.192 13.967 1.00 37.34 N +ATOM 243 C4 DG A 12 51.844 45.463 13.732 1.00 31.14 C +END diff --git a/regtest/basic/rt-molinfo-whole-check/dna_whole.pdb b/regtest/basic/rt-molinfo-whole-check/dna_whole.pdb new file mode 100644 index 0000000000..2123faf43b --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-check/dna_whole.pdb @@ -0,0 +1,245 @@ +CRYST1 47.018 47.018 47.018 60.00 60.00 90.00 P 1 1 +ATOM 1 O5' DC A 1 55.119 59.502 49.376 1.00 64.35 O +ATOM 2 C5' DC A 1 55.314 59.228 47.978 1.00 44.69 C +ATOM 3 C4' DC A 1 56.145 57.975 47.859 1.00 31.28 C +ATOM 4 O4' DC A 1 55.544 56.890 48.611 1.00 37.45 O +ATOM 5 C3' DC A 1 56.356 57.429 46.453 1.00 46.72 C +ATOM 6 O3' DC A 1 57.534 56.632 46.440 1.00 48.89 O +ATOM 7 C2' DC A 1 55.132 56.530 46.406 1.00 30.88 C +ATOM 8 C1' DC A 1 55.415 55.789 47.703 1.00 36.58 C +ATOM 9 N1 DC A 1 54.254 54.968 48.139 1.00 40.51 N +ATOM 10 C2 DC A 1 54.408 53.761 48.774 1.00 16.62 C +ATOM 11 O2 DC A 1 55.544 53.321 48.973 1.00 27.75 O +ATOM 12 N3 DC A 1 53.327 53.068 49.136 1.00 20.55 N +ATOM 13 C4 DC A 1 52.101 53.533 48.879 1.00 34.72 C +ATOM 14 N4 DC A 1 51.012 52.784 49.203 1.00 40.31 N +ATOM 15 C5 DC A 1 51.903 54.749 48.230 1.00 30.78 C +ATOM 16 C6 DC A 1 53.027 55.478 47.860 1.00 25.90 C +ATOM 17 P DG A 2 58.593 56.593 45.242 1.00 58.85 P +ATOM 18 OP1 DG A 2 59.720 57.464 45.610 1.00 57.82 O +ATOM 19 OP2 DG A 2 58.006 56.766 43.898 1.00 78.33 O +ATOM 20 O5' DG A 2 59.024 55.058 45.257 1.00 40.36 O +ATOM 21 C5' DG A 2 59.727 54.482 46.353 1.00 47.19 C +ATOM 22 C4' DG A 2 59.678 53.016 46.038 1.00 47.81 C +ATOM 23 O4' DG A 2 58.377 52.559 46.433 1.00 38.76 O +ATOM 24 C3' DG A 2 59.877 52.632 44.566 1.00 28.58 C +ATOM 25 O3' DG A 2 60.907 51.627 44.412 1.00 40.44 O +ATOM 26 C2' DG A 2 58.457 52.192 44.175 1.00 21.14 C +ATOM 27 C1' DG A 2 57.905 51.611 45.475 1.00 33.95 C +ATOM 28 N9 DG A 2 56.421 51.777 45.539 1.00 34.00 N +ATOM 29 C8 DG A 2 55.710 52.891 45.188 1.00 36.47 C +ATOM 30 N7 DG A 2 54.391 52.762 45.395 1.00 32.37 N +ATOM 31 C5 DG A 2 54.267 51.519 45.901 1.00 15.06 C +ATOM 32 C6 DG A 2 53.088 50.832 46.304 1.00 11.88 C +ATOM 33 O6 DG A 2 51.923 51.223 46.277 1.00 21.30 O +ATOM 34 N1 DG A 2 53.381 49.586 46.796 1.00 15.44 N +ATOM 35 C2 DG A 2 54.618 49.024 46.914 1.00 9.63 C +ATOM 36 N2 DG A 2 54.692 47.763 47.427 1.00 16.69 N +ATOM 37 N3 DG A 2 55.721 49.667 46.529 1.00 30.98 N +ATOM 38 C4 DG A 2 55.474 50.901 46.033 1.00 18.56 C +ATOM 39 P DC A 3 61.248 50.928 43.011 1.00 44.67 P +ATOM 40 OP1 DC A 3 62.690 50.623 42.979 1.00 53.89 O +ATOM 41 OP2 DC A 3 60.743 51.719 41.874 1.00 57.79 O +ATOM 42 O5' DC A 3 60.444 49.553 43.086 1.00 35.42 O +ATOM 43 C5' DC A 3 60.768 48.592 44.094 1.00 45.75 C +ATOM 44 C4' DC A 3 59.707 47.540 44.004 1.00 43.02 C +ATOM 45 O4' DC A 3 58.440 48.151 44.212 1.00 36.85 O +ATOM 46 C3' DC A 3 59.608 46.864 42.662 1.00 40.14 C +ATOM 47 O3' DC A 3 60.305 45.616 42.687 1.00 49.62 O +ATOM 48 C2' DC A 3 58.114 46.713 42.420 1.00 53.79 C +ATOM 49 C1' DC A 3 57.462 47.273 43.668 1.00 22.18 C +ATOM 50 N1 DC A 3 56.380 48.196 43.280 1.00 25.44 N +ATOM 51 C2 DC A 3 55.093 47.891 43.575 1.00 19.81 C +ATOM 52 O2 DC A 3 54.869 46.819 44.141 1.00 29.92 O +ATOM 53 N3 DC A 3 54.119 48.754 43.261 1.00 21.59 N +ATOM 54 C4 DC A 3 54.401 49.910 42.656 1.00 14.01 C +ATOM 55 N4 DC A 3 53.405 50.806 42.388 1.00 26.88 N +ATOM 56 C5 DC A 3 55.710 50.252 42.330 1.00 27.59 C +ATOM 57 C6 DC A 3 56.721 49.355 42.658 1.00 27.05 C +ATOM 58 P DG A 4 60.433 44.719 41.376 1.00 44.54 P +ATOM 59 OP1 DG A 4 61.604 43.842 41.524 1.00 61.90 O +ATOM 60 OP2 DG A 4 60.392 45.603 40.199 1.00 37.36 O +ATOM 61 O5' DG A 4 59.115 43.844 41.429 1.00 32.01 O +ATOM 62 C5' DG A 4 58.898 42.932 42.512 1.00 37.89 C +ATOM 63 C4' DG A 4 57.577 42.267 42.264 1.00 53.00 C +ATOM 64 O4' DG A 4 56.537 43.259 42.255 1.00 38.79 O +ATOM 65 C3' DG A 4 57.448 41.536 40.935 1.00 56.72 C +ATOM 66 O3' DG A 4 56.468 40.521 40.997 1.00 64.12 O +ATOM 67 C2' DG A 4 56.977 42.675 40.047 1.00 40.81 C +ATOM 68 C1' DG A 4 55.900 43.208 40.977 1.00 30.52 C +ATOM 69 N9 DG A 4 55.489 44.588 40.628 1.00 28.53 N +ATOM 70 C8 DG A 4 56.201 45.570 39.991 1.00 27.82 C +ATOM 71 N7 DG A 4 55.497 46.701 39.836 1.00 28.01 N +ATOM 72 C5 DG A 4 54.305 46.407 40.394 1.00 23.22 C +ATOM 73 C6 DG A 4 53.136 47.211 40.508 1.00 29.21 C +ATOM 74 O6 DG A 4 52.953 48.364 40.127 1.00 38.58 O +ATOM 75 N1 DG A 4 52.117 46.521 41.111 1.00 27.94 N +ATOM 76 C2 DG A 4 52.156 45.237 41.575 1.00 23.44 C +ATOM 77 N2 DG A 4 51.015 44.723 42.112 1.00 42.64 N +ATOM 78 N3 DG A 4 53.252 44.486 41.476 1.00 21.56 N +ATOM 79 C4 DG A 4 54.268 45.132 40.880 1.00 23.44 C +ATOM 80 P DA A 5 56.540 39.276 40.004 1.00 57.01 P +ATOM 81 OP1 DA A 5 57.300 38.198 40.651 1.00 58.59 O +ATOM 82 OP2 DA A 5 57.021 39.730 38.669 1.00 51.96 O +ATOM 83 O5' DA A 5 54.994 38.888 39.920 1.00 47.12 O +ATOM 84 C5' DA A 5 54.199 38.876 41.121 1.00 47.67 C +ATOM 85 C4' DA A 5 52.856 39.395 40.716 1.00 64.79 C +ATOM 86 O4' DA A 5 53.026 40.754 40.320 1.00 47.60 O +ATOM 87 C3' DA A 5 52.203 38.700 39.523 1.00 51.50 C +ATOM 88 O3' DA A 5 50.946 38.103 39.879 1.00 52.18 O +ATOM 89 C2' DA A 5 52.136 39.805 38.455 1.00 45.00 C +ATOM 90 C1' DA A 5 52.035 41.039 39.328 1.00 26.88 C +ATOM 91 N9 DA A 5 52.575 42.223 38.626 1.00 16.69 N +ATOM 92 C8 DA A 5 53.842 42.410 38.141 1.00 28.14 C +ATOM 93 N7 DA A 5 54.047 43.653 37.672 1.00 34.85 N +ATOM 94 C5 DA A 5 52.857 44.260 37.857 1.00 22.49 C +ATOM 95 C6 DA A 5 52.414 45.586 37.578 1.00 18.12 C +ATOM 96 N6 DA A 5 53.229 46.529 37.027 1.00 29.30 N +ATOM 97 N1 DA A 5 51.150 45.885 37.877 1.00 27.61 N +ATOM 98 C2 DA A 5 50.362 44.959 38.428 1.00 18.53 C +ATOM 99 N3 DA A 5 50.647 43.699 38.743 1.00 29.16 N +ATOM 100 C4 DA A 5 51.934 43.417 38.420 1.00 15.08 C +ATOM 101 P DA A 6 50.050 37.313 38.822 1.00 43.68 P +ATOM 102 OP1 DA A 6 49.212 36.346 39.559 1.00 42.55 O +ATOM 103 OP2 DA A 6 50.899 36.806 37.727 1.00 54.20 O +ATOM 104 O5' DA A 6 49.063 38.418 38.239 1.00 28.20 O +ATOM 105 C5' DA A 6 47.986 38.904 39.049 1.00 42.29 C +ATOM 106 C4' DA A 6 47.295 39.910 38.194 1.00 33.23 C +ATOM 107 O4' DA A 6 48.336 40.767 37.721 1.00 41.48 O +ATOM 108 C3' DA A 6 46.601 39.377 36.946 1.00 18.16 C +ATOM 109 O3' DA A 6 45.191 39.676 36.940 1.00 30.42 O +ATOM 110 C2' DA A 6 47.424 39.999 35.820 1.00 52.97 C +ATOM 111 C1' DA A 6 47.883 41.281 36.478 1.00 38.93 C +ATOM 112 N9 DA A 6 49.102 41.833 35.837 1.00 19.06 N +ATOM 113 C8 DA A 6 50.299 41.206 35.627 1.00 17.83 C +ATOM 114 N7 DA A 6 51.233 42.021 35.115 1.00 29.55 N +ATOM 115 C5 DA A 6 50.600 43.208 35.005 1.00 19.88 C +ATOM 116 C6 DA A 6 51.057 44.494 34.574 1.00 17.26 C +ATOM 117 N6 DA A 6 52.345 44.725 34.186 1.00 19.85 N +ATOM 118 N1 DA A 6 50.183 45.498 34.611 1.00 17.93 N +ATOM 119 C2 DA A 6 48.937 45.269 35.031 1.00 23.00 C +ATOM 120 N3 DA A 6 48.394 44.131 35.457 1.00 21.37 N +ATOM 121 C4 DA A 6 49.300 43.130 35.416 1.00 15.93 C +ATOM 122 P DT A 7 44.265 39.357 35.674 1.00 40.72 P +ATOM 123 OP1 DT A 7 42.852 39.267 36.101 1.00 46.75 O +ATOM 124 OP2 DT A 7 44.784 38.201 34.896 1.00 42.53 O +ATOM 125 O5' DT A 7 44.423 40.694 34.835 1.00 35.21 O +ATOM 126 C5' DT A 7 44.091 41.942 35.445 1.00 34.88 C +ATOM 127 C4' DT A 7 44.346 42.935 34.357 1.00 31.45 C +ATOM 128 O4' DT A 7 45.727 42.887 34.038 1.00 46.82 O +ATOM 129 C3' DT A 7 43.645 42.591 33.055 1.00 23.76 C +ATOM 130 O3' DT A 7 42.435 43.341 32.921 1.00 44.27 O +ATOM 131 C2' DT A 7 44.716 42.834 31.982 1.00 26.30 C +ATOM 132 C1' DT A 7 45.828 43.516 32.778 1.00 28.96 C +ATOM 133 N1 DT A 7 47.205 43.210 32.324 1.00 20.47 N +ATOM 134 C2 DT A 7 48.006 44.230 31.935 1.00 28.01 C +ATOM 135 O2 DT A 7 47.567 45.384 31.902 1.00 40.01 O +ATOM 136 N3 DT A 7 49.303 43.948 31.611 1.00 27.94 N +ATOM 137 C4 DT A 7 49.817 42.679 31.641 1.00 15.14 C +ATOM 138 O4 DT A 7 51.014 42.529 31.378 1.00 32.54 O +ATOM 139 C5 DT A 7 48.965 41.632 31.994 1.00 10.83 C +ATOM 140 C7 DT A 7 49.453 40.209 31.995 1.00 36.33 C +ATOM 141 C6 DT A 7 47.649 41.923 32.353 1.00 12.19 C +ATOM 142 P DT A 8 41.568 43.297 31.583 1.00 49.10 P +ATOM 143 OP1 DT A 8 40.209 43.751 31.939 1.00 41.11 O +ATOM 144 OP2 DT A 8 41.642 41.975 30.919 1.00 39.21 O +ATOM 145 O5' DT A 8 42.270 44.425 30.686 1.00 48.80 O +ATOM 146 C5' DT A 8 42.330 45.785 31.177 1.00 34.73 C +ATOM 147 C4' DT A 8 43.179 46.536 30.197 1.00 28.73 C +ATOM 148 O4' DT A 8 44.372 45.765 30.043 1.00 39.07 O +ATOM 149 C3' DT A 8 42.602 46.639 28.788 1.00 37.88 C +ATOM 150 O3' DT A 8 42.151 47.974 28.455 1.00 52.04 O +ATOM 151 C2' DT A 8 43.697 46.025 27.898 1.00 32.80 C +ATOM 152 C1' DT A 8 44.920 46.162 28.793 1.00 36.58 C +ATOM 153 N1 DT A 8 46.007 45.183 28.518 1.00 24.57 N +ATOM 154 C2 DT A 8 47.270 45.623 28.253 1.00 19.41 C +ATOM 155 O2 DT A 8 47.508 46.823 28.148 1.00 32.74 O +ATOM 156 N3 DT A 8 48.278 44.710 28.171 1.00 25.12 N +ATOM 157 C4 DT A 8 48.060 43.367 28.310 1.00 31.35 C +ATOM 158 O4 DT A 8 49.042 42.624 28.262 1.00 28.53 O +ATOM 159 C5 DT A 8 46.753 42.918 28.524 1.00 22.80 C +ATOM 160 C7 DT A 8 46.445 41.447 28.655 1.00 24.98 C +ATOM 161 C6 DT A 8 45.729 43.855 28.663 1.00 20.28 C +ATOM 162 P DC A 9 41.715 48.378 26.968 1.00 48.97 P +ATOM 163 OP1 DC A 9 40.832 49.551 27.028 1.00 62.33 O +ATOM 164 OP2 DC A 9 41.194 47.212 26.229 1.00 51.53 O +ATOM 165 O5' DC A 9 43.110 48.854 26.370 1.00 43.99 O +ATOM 166 C5' DC A 9 43.820 49.934 27.008 1.00 50.86 C +ATOM 167 C4' DC A 9 45.081 50.160 26.216 1.00 46.66 C +ATOM 168 O4' DC A 9 45.822 48.934 26.207 1.00 42.69 O +ATOM 169 C3' DC A 9 44.901 50.547 24.757 1.00 56.96 C +ATOM 170 O3' DC A 9 45.654 51.721 24.426 1.00 63.54 O +ATOM 171 C2' DC A 9 45.310 49.272 24.012 1.00 50.41 C +ATOM 172 C1' DC A 9 46.425 48.790 24.916 1.00 41.08 C +ATOM 173 N1 DC A 9 46.708 47.329 24.774 1.00 37.23 N +ATOM 174 C2 DC A 9 47.998 46.910 24.599 1.00 40.54 C +ATOM 175 O2 DC A 9 48.875 47.754 24.429 1.00 43.89 O +ATOM 176 N3 DC A 9 48.290 45.604 24.632 1.00 32.57 N +ATOM 177 C4 DC A 9 47.325 44.702 24.805 1.00 24.65 C +ATOM 178 N4 DC A 9 47.645 43.382 24.848 1.00 27.84 N +ATOM 179 C5 DC A 9 45.987 45.082 24.936 1.00 17.61 C +ATOM 180 C6 DC A 9 45.683 46.440 24.926 1.00 30.63 C +ATOM 181 P DG A 10 45.239 52.640 23.178 1.00 65.48 P +ATOM 182 OP1 DG A 10 45.680 54.024 23.501 1.00 59.09 O +ATOM 183 OP2 DG A 10 43.816 52.413 22.812 1.00 45.71 O +ATOM 184 O5' DG A 10 46.138 52.072 21.988 1.00 70.30 O +ATOM 185 C5' DG A 10 47.566 52.247 22.039 1.00 71.73 C +ATOM 186 C4' DG A 10 48.156 51.397 20.957 1.00 58.69 C +ATOM 187 O4' DG A 10 47.986 50.031 21.355 1.00 41.03 O +ATOM 188 C3' DG A 10 47.511 51.485 19.571 1.00 45.61 C +ATOM 189 O3' DG A 10 48.495 51.403 18.545 1.00 52.70 O +ATOM 190 C2' DG A 10 46.598 50.269 19.573 1.00 36.02 C +ATOM 191 C1' DG A 10 47.613 49.335 20.172 1.00 50.90 C +ATOM 192 N9 DG A 10 47.074 48.020 20.559 1.00 45.86 N +ATOM 193 C8 DG A 10 45.800 47.622 20.849 1.00 44.49 C +ATOM 194 N7 DG A 10 45.725 46.316 21.146 1.00 39.96 N +ATOM 195 C5 DG A 10 47.002 45.895 21.041 1.00 38.99 C +ATOM 196 C6 DG A 10 47.560 44.599 21.248 1.00 35.78 C +ATOM 197 O6 DG A 10 46.997 43.559 21.580 1.00 34.90 O +ATOM 198 N1 DG A 10 48.913 44.606 21.039 1.00 23.54 N +ATOM 199 C2 DG A 10 49.682 45.672 20.677 1.00 8.73 C +ATOM 200 N2 DG A 10 51.018 45.476 20.522 1.00 23.15 N +ATOM 201 N3 DG A 10 49.166 46.880 20.492 1.00 24.68 N +ATOM 202 C4 DG A 10 47.840 46.908 20.698 1.00 31.53 C +ATOM 203 P DC A 11 48.947 52.728 17.779 1.00 60.62 P +ATOM 204 OP1 DC A 11 48.980 53.879 18.710 1.00 63.74 O +ATOM 205 OP2 DC A 11 48.070 52.849 16.595 1.00 52.44 O +ATOM 206 O5' DC A 11 50.456 52.393 17.393 1.00 57.57 O +ATOM 207 C5' DC A 11 51.459 52.415 18.441 1.00 54.70 C +ATOM 208 C4' DC A 11 52.406 51.253 18.249 1.00 72.51 C +ATOM 209 O4' DC A 11 51.627 50.061 18.362 1.00 47.18 O +ATOM 210 C3' DC A 11 53.126 51.134 16.911 1.00 29.82 C +ATOM 211 O3' DC A 11 54.524 50.818 17.058 1.00 43.53 O +ATOM 212 C2' DC A 11 52.302 50.074 16.181 1.00 51.34 C +ATOM 213 C1' DC A 11 52.040 49.143 17.345 1.00 30.07 C +ATOM 214 N1 DC A 11 50.856 48.282 17.122 1.00 23.25 N +ATOM 215 C2 DC A 11 50.986 46.935 17.230 1.00 20.38 C +ATOM 216 O2 DC A 11 52.108 46.485 17.445 1.00 38.77 O +ATOM 217 N3 DC A 11 49.907 46.149 17.132 1.00 15.92 N +ATOM 218 C4 DC A 11 48.699 46.680 16.923 1.00 15.82 C +ATOM 219 N4 DC A 11 47.594 45.881 16.887 1.00 28.04 N +ATOM 220 C5 DC A 11 48.532 48.051 16.781 1.00 26.17 C +ATOM 221 C6 DC A 11 49.654 48.865 16.890 1.00 35.50 C +ATOM 222 P DG A 12 55.515 51.081 15.834 1.00 55.98 P +ATOM 223 OP1 DG A 12 56.888 51.283 16.351 1.00 45.83 O +ATOM 224 OP2 DG A 12 54.947 52.158 15.001 1.00 44.26 O +ATOM 225 O5' DG A 12 55.486 49.719 14.996 1.00 62.63 O +ATOM 226 C5' DG A 12 56.293 48.591 15.400 1.00 69.50 C +ATOM 227 C4' DG A 12 55.932 47.474 14.460 1.00 39.92 C +ATOM 228 O4' DG A 12 54.534 47.276 14.620 1.00 32.00 O +ATOM 229 C3' DG A 12 56.105 47.711 12.944 1.00 50.39 C +ATOM 230 O3' DG A 12 57.169 46.942 12.358 1.00 64.13 O +ATOM 231 C2' DG A 12 54.719 47.369 12.378 1.00 36.18 C +ATOM 232 C1' DG A 12 54.149 46.507 13.490 1.00 24.79 C +ATOM 233 N9 DG A 12 52.677 46.527 13.494 1.00 28.44 N +ATOM 234 C8 DG A 12 51.847 47.596 13.281 1.00 31.85 C +ATOM 235 N7 DG A 12 50.552 47.265 13.369 1.00 38.26 N +ATOM 236 C5 DG A 12 50.572 45.947 13.657 1.00 28.99 C +ATOM 237 C6 DG A 12 49.485 45.049 13.903 1.00 42.63 C +ATOM 238 O6 DG A 12 48.275 45.274 13.902 1.00 49.17 O +ATOM 239 N1 DG A 12 49.934 43.773 14.134 1.00 40.15 N +ATOM 240 C2 DG A 12 51.226 43.350 14.154 1.00 33.42 C +ATOM 241 N2 DG A 12 51.443 42.024 14.353 1.00 40.53 N +ATOM 242 N3 DG A 12 52.245 44.192 13.967 1.00 37.34 N +ATOM 243 C4 DG A 12 51.844 45.463 13.732 1.00 31.14 C +END diff --git a/regtest/basic/rt-molinfo-whole-check/main.cpp b/regtest/basic/rt-molinfo-whole-check/main.cpp new file mode 100644 index 0000000000..b7094a8624 --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-check/main.cpp @@ -0,0 +1,62 @@ +#include "plumed/wrapper/Plumed.h" +#include +#include +#include +#include + +// MOLINFO WHOLE takes the reference structure as whole. Here each reference is read with +// MOLINFO ... WHOLE and used by WHOLEMOLECULES, and we report whether PLUMED accepts it or +// writes a warning that a chain looks split by the periodic boundary of its CRYST1 record. +// torn.pdb is whole.pdb with 15 atoms wrapped across a face of its (rhombic dodecahedron) cell. +// Its copies without a usable cell (no CRYST1, the 1 A placeholder, a zero cell, a crystallographic +// space group) cannot be checked and are accepted. +// dna_torn.pdb is dna_whole.pdb (chain A of 1BNA) wrapped nucleotide by nucleotide: each nucleotide is +// whole, and the chain is split between them. +int main(int, char**) { + std::ofstream out("output"); + unsigned natoms=304; + std::vector positions(3*natoms,0.0); + const std::vector> cases{ + {"whole.pdb","1-304"}, + {"torn.pdb","1-304"}, + {"torn_nocryst.pdb","1-304"}, + {"torn_placeholder.pdb","1-304"}, + {"torn_zero.pdb","1-304"}, + {"torn_crystal.pdb","1-304"}, + {"dna_whole.pdb","1-243"}, + {"dna_torn.pdb","1-243"} + }; + for(unsigned i=0; i out_sep 2> err_sep || return 1 +} + +# the WHOLEMOLECULES lines of the log and the warnings, up to the list of atoms +function plumed_regtest_after() { + for f in out_sep out; do + echo "# $f" + grep -E "^PLUMED: (Action WHOLEMOLECULES|WARNING for action MOLINFO)" $f | sed -e "s/^PLUMED: //" -e "s/\\. WHOLEMOLECULES will.*//" + done > warnings +} diff --git a/regtest/basic/rt-molinfo-whole-ligand/plumed.dat b/regtest/basic/rt-molinfo-whole-ligand/plumed.dat new file mode 100644 index 0000000000..a05e51816a --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-ligand/plumed.dat @@ -0,0 +1,5 @@ +# trp-cage and a ligand away from it, closer to a periodic image of the protein than to the protein itself +MOLINFO STRUCTURE=ref.pdb WHOLE +# protein and ligand in one group: no warning (the ligand is a chain of its own), and the frames are made whole as the reference +WHOLEMOLECULES ENTITY0=1-313 +DUMPATOMS ATOMS=1-313 FILE=whole.xyz PRECISION=3 diff --git a/regtest/basic/rt-molinfo-whole-ligand/plumed_sep.dat b/regtest/basic/rt-molinfo-whole-ligand/plumed_sep.dat new file mode 100644 index 0000000000..0353ca9ec9 --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-ligand/plumed_sep.dat @@ -0,0 +1,3 @@ +MOLINFO STRUCTURE=ref.pdb WHOLE +# protein and ligand in separate groups: no warning +WHOLEMOLECULES ENTITY0=1-304 ENTITY1=305-313 diff --git a/regtest/basic/rt-molinfo-whole-ligand/ref.pdb b/regtest/basic/rt-molinfo-whole-ligand/ref.pdb new file mode 100644 index 0000000000..f7e56173c9 --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-ligand/ref.pdb @@ -0,0 +1,316 @@ +CRYST1 40.000 40.000 40.000 60.00 60.00 60.00 P 1 1 +ATOM 1 N ASN A 1 30.997 27.202 15.779 1.00 0.00 N +ATOM 2 CA ASN A 1 31.290 26.210 14.716 1.00 0.00 C +ATOM 3 C ASN A 1 32.781 26.039 14.437 1.00 0.00 C +ATOM 4 O ASN A 1 33.264 24.924 14.576 1.00 0.00 O +ATOM 5 CB ASN A 1 30.461 26.471 13.445 1.00 0.00 C +ATOM 6 CG ASN A 1 28.983 26.205 13.723 1.00 0.00 C +ATOM 7 OD1 ASN A 1 28.629 25.775 14.810 1.00 0.00 O +ATOM 8 ND2 ASN A 1 28.092 26.481 12.791 1.00 0.00 N +ATOM 9 H1 ASN A 1 31.568 27.032 16.595 1.00 0.00 H +ATOM 10 H2 ASN A 1 31.158 28.143 15.445 1.00 0.00 H +ATOM 11 H3 ASN A 1 30.021 27.116 16.041 1.00 0.00 H +ATOM 12 HA ASN A 1 30.968 25.237 15.095 1.00 0.00 H +ATOM 13 HB2 ASN A 1 30.588 27.492 13.141 1.00 0.00 H +ATOM 14 HB3 ASN A 1 30.790 25.794 12.655 1.00 0.00 H +ATOM 15 HD21 ASN A 1 28.326 26.866 11.890 1.00 0.00 H +ATOM 16 HD22 ASN A 1 27.141 26.258 13.040 1.00 0.00 H +ATOM 17 N LEU A 2 33.519 27.106 14.106 1.00 0.00 N +ATOM 18 CA LEU A 2 34.975 27.077 13.882 1.00 0.00 C +ATOM 19 C LEU A 2 35.762 26.262 14.930 1.00 0.00 C +ATOM 20 O LEU A 2 36.507 25.349 14.574 1.00 0.00 O +ATOM 21 CB LEU A 2 35.487 28.525 13.715 1.00 0.00 C +ATOM 22 CG LEU A 2 35.103 29.525 14.839 1.00 0.00 C +ATOM 23 CD1 LEU A 2 36.286 29.878 15.735 1.00 0.00 C +ATOM 24 CD2 LEU A 2 34.547 30.823 14.250 1.00 0.00 C +ATOM 25 H LEU A 2 33.077 27.998 13.940 1.00 0.00 H +ATOM 26 HA LEU A 2 35.148 26.569 12.931 1.00 0.00 H +ATOM 27 HB2 LEU A 2 36.558 28.489 13.662 1.00 0.00 H +ATOM 28 HB3 LEU A 2 35.085 28.892 12.770 1.00 0.00 H +ATOM 29 HG LEU A 2 34.330 29.097 15.476 1.00 0.00 H +ATOM 30 HD11 LEU A 2 36.691 28.980 16.188 1.00 0.00 H +ATOM 31 HD12 LEU A 2 37.057 30.379 15.151 1.00 0.00 H +ATOM 32 HD13 LEU A 2 35.969 30.552 16.531 1.00 0.00 H +ATOM 33 HD21 LEU A 2 35.291 31.284 13.598 1.00 0.00 H +ATOM 34 HD22 LEU A 2 33.643 30.619 13.677 1.00 0.00 H +ATOM 35 HD23 LEU A 2 34.306 31.520 15.053 1.00 0.00 H +ATOM 36 N TYR A 3 35.544 26.530 16.223 1.00 0.00 N +ATOM 37 CA TYR A 3 36.208 25.813 17.315 1.00 0.00 C +ATOM 38 C TYR A 3 35.796 24.331 17.408 1.00 0.00 C +ATOM 39 O TYR A 3 36.607 23.484 17.776 1.00 0.00 O +ATOM 40 CB TYR A 3 35.934 26.547 18.636 1.00 0.00 C +ATOM 41 CG TYR A 3 37.074 26.414 19.624 1.00 0.00 C +ATOM 42 CD1 TYR A 3 37.152 25.292 20.472 1.00 0.00 C +ATOM 43 CD2 TYR A 3 38.078 27.401 19.666 1.00 0.00 C +ATOM 44 CE1 TYR A 3 38.241 25.151 21.352 1.00 0.00 C +ATOM 45 CE2 TYR A 3 39.173 27.260 20.539 1.00 0.00 C +ATOM 46 CZ TYR A 3 39.259 26.128 21.377 1.00 0.00 C +ATOM 47 OH TYR A 3 40.331 25.956 22.195 1.00 0.00 O +ATOM 48 H TYR A 3 34.964 27.320 16.454 1.00 0.00 H +ATOM 49 HA TYR A 3 37.283 25.843 17.130 1.00 0.00 H +ATOM 50 HB2 TYR A 3 35.781 27.588 18.425 1.00 0.00 H +ATOM 51 HB3 TYR A 3 35.012 26.171 19.084 1.00 0.00 H +ATOM 52 HD1 TYR A 3 36.385 24.531 20.435 1.00 0.00 H +ATOM 53 HD2 TYR A 3 38.021 28.275 19.029 1.00 0.00 H +ATOM 54 HE1 TYR A 3 38.322 24.296 22.003 1.00 0.00 H +ATOM 55 HE2 TYR A 3 39.931 28.027 20.567 1.00 0.00 H +ATOM 56 HH TYR A 3 41.085 26.470 21.901 1.00 0.00 H +ATOM 57 N ILE A 4 34.556 24.000 17.023 1.00 0.00 N +ATOM 58 CA ILE A 4 34.041 22.626 16.947 1.00 0.00 C +ATOM 59 C ILE A 4 34.809 21.854 15.864 1.00 0.00 C +ATOM 60 O ILE A 4 35.277 20.741 16.108 1.00 0.00 O +ATOM 61 CB ILE A 4 32.512 22.609 16.677 1.00 0.00 C +ATOM 62 CG1 ILE A 4 31.701 23.615 17.531 1.00 0.00 C +ATOM 63 CG2 ILE A 4 31.939 21.191 16.835 1.00 0.00 C +ATOM 64 CD1 ILE A 4 31.879 23.487 19.049 1.00 0.00 C +ATOM 65 H ILE A 4 33.992 24.731 16.617 1.00 0.00 H +ATOM 66 HA ILE A 4 34.228 22.134 17.902 1.00 0.00 H +ATOM 67 HB ILE A 4 32.344 22.883 15.637 1.00 0.00 H +ATOM 68 HG12 ILE A 4 31.998 24.606 17.246 1.00 0.00 H +ATOM 69 HG13 ILE A 4 30.641 23.499 17.298 1.00 0.00 H +ATOM 70 HG21 ILE A 4 32.389 20.520 16.102 1.00 0.00 H +ATOM 71 HG22 ILE A 4 32.139 20.804 17.835 1.00 0.00 H +ATOM 72 HG23 ILE A 4 30.862 21.204 16.666 1.00 0.00 H +ATOM 73 HD11 ILE A 4 31.592 22.490 19.383 1.00 0.00 H +ATOM 74 HD12 ILE A 4 32.915 23.681 19.329 1.00 0.00 H +ATOM 75 HD13 ILE A 4 31.242 24.219 19.547 1.00 0.00 H +ATOM 76 N GLN A 5 34.991 22.474 14.689 1.00 0.00 N +ATOM 77 CA GLN A 5 35.776 21.908 13.591 1.00 0.00 C +ATOM 78 C GLN A 5 37.269 21.754 13.944 1.00 0.00 C +ATOM 79 O GLN A 5 37.912 20.835 13.450 1.00 0.00 O +ATOM 80 CB GLN A 5 35.606 22.762 12.321 1.00 0.00 C +ATOM 81 CG GLN A 5 35.654 21.904 11.044 1.00 0.00 C +ATOM 82 CD GLN A 5 34.322 21.215 10.749 1.00 0.00 C +ATOM 83 OE1 GLN A 5 34.129 20.031 10.999 1.00 0.00 O +ATOM 84 NE2 GLN A 5 33.366 21.929 10.182 1.00 0.00 N +ATOM 85 H GLN A 5 34.571 23.393 14.571 1.00 0.00 H +ATOM 86 HA GLN A 5 35.381 20.913 13.394 1.00 0.00 H +ATOM 87 HB2 GLN A 5 34.660 23.266 12.365 1.00 0.00 H +ATOM 88 HB3 GLN A 5 36.406 23.504 12.281 1.00 0.00 H +ATOM 89 HG2 GLN A 5 35.905 22.536 10.214 1.00 0.00 H +ATOM 90 HG3 GLN A 5 36.440 21.152 11.129 1.00 0.00 H +ATOM 91 HE21 GLN A 5 33.509 22.891 9.926 1.00 0.00 H +ATOM 92 HE22 GLN A 5 32.506 21.440 9.999 1.00 0.00 H +ATOM 93 N TRP A 6 37.824 22.616 14.806 1.00 0.00 N +ATOM 94 CA TRP A 6 39.182 22.444 15.341 1.00 0.00 C +ATOM 95 C TRP A 6 39.267 21.309 16.378 1.00 0.00 C +ATOM 96 O TRP A 6 40.193 20.496 16.330 1.00 0.00 O +ATOM 97 CB TRP A 6 39.677 23.778 15.917 1.00 0.00 C +ATOM 98 CG TRP A 6 41.046 23.727 16.528 1.00 0.00 C +ATOM 99 CD1 TRP A 6 42.217 23.739 15.852 1.00 0.00 C +ATOM 100 CD2 TRP A 6 41.406 23.639 17.940 1.00 0.00 C +ATOM 101 NE1 TRP A 6 43.269 23.635 16.745 1.00 0.00 N +ATOM 102 CE2 TRP A 6 42.826 23.590 18.044 1.00 0.00 C +ATOM 103 CE3 TRP A 6 40.677 23.599 19.146 1.00 0.00 C +ATOM 104 CZ2 TRP A 6 43.497 23.520 19.272 1.00 0.00 C +ATOM 105 CZ3 TRP A 6 41.337 23.508 20.387 1.00 0.00 C +ATOM 106 CH2 TRP A 6 42.740 23.482 20.454 1.00 0.00 C +ATOM 107 H TRP A 6 37.274 23.418 15.092 1.00 0.00 H +ATOM 108 HA TRP A 6 39.846 22.167 14.521 1.00 0.00 H +ATOM 109 HB2 TRP A 6 39.692 24.500 15.123 1.00 0.00 H +ATOM 110 HB3 TRP A 6 38.977 24.119 16.678 1.00 0.00 H +ATOM 111 HD1 TRP A 6 42.310 23.808 14.776 1.00 0.00 H +ATOM 112 HE1 TRP A 6 44.258 23.611 16.490 1.00 0.00 H +ATOM 113 HE3 TRP A 6 39.599 23.646 19.107 1.00 0.00 H +ATOM 114 HZ2 TRP A 6 44.577 23.493 19.295 1.00 0.00 H +ATOM 115 HZ3 TRP A 6 40.760 23.475 21.300 1.00 0.00 H +ATOM 116 HH2 TRP A 6 43.232 23.435 21.415 1.00 0.00 H +ATOM 117 N LEU A 7 38.298 21.215 17.301 1.00 0.00 N +ATOM 118 CA LEU A 7 38.257 20.143 18.297 1.00 0.00 C +ATOM 119 C LEU A 7 38.051 18.756 17.676 1.00 0.00 C +ATOM 120 O LEU A 7 38.754 17.827 18.076 1.00 0.00 O +ATOM 121 CB LEU A 7 37.188 20.430 19.367 1.00 0.00 C +ATOM 122 CG LEU A 7 37.597 21.496 20.403 1.00 0.00 C +ATOM 123 CD1 LEU A 7 36.423 21.752 21.352 1.00 0.00 C +ATOM 124 CD2 LEU A 7 38.805 21.068 21.248 1.00 0.00 C +ATOM 125 H LEU A 7 37.582 21.938 17.328 1.00 0.00 H +ATOM 126 HA LEU A 7 39.232 20.097 18.779 1.00 0.00 H +ATOM 127 HB2 LEU A 7 36.298 20.767 18.871 1.00 0.00 H +ATOM 128 HB3 LEU A 7 36.977 19.504 19.906 1.00 0.00 H +ATOM 129 HG LEU A 7 37.837 22.426 19.894 1.00 0.00 H +ATOM 130 HD11 LEU A 7 35.555 22.083 20.783 1.00 0.00 H +ATOM 131 HD12 LEU A 7 36.173 20.838 21.894 1.00 0.00 H +ATOM 132 HD13 LEU A 7 36.687 22.526 22.073 1.00 0.00 H +ATOM 133 HD21 LEU A 7 38.628 20.086 21.688 1.00 0.00 H +ATOM 134 HD22 LEU A 7 39.703 21.030 20.634 1.00 0.00 H +ATOM 135 HD23 LEU A 7 38.976 21.789 22.046 1.00 0.00 H +ATOM 136 N LYS A 8 37.145 18.594 16.694 1.00 0.00 N +ATOM 137 CA LYS A 8 36.874 17.284 16.065 1.00 0.00 C +ATOM 138 C LYS A 8 38.102 16.648 15.397 1.00 0.00 C +ATOM 139 O LYS A 8 38.179 15.427 15.304 1.00 0.00 O +ATOM 140 CB LYS A 8 35.674 17.378 15.102 1.00 0.00 C +ATOM 141 CG LYS A 8 35.968 18.066 13.757 1.00 0.00 C +ATOM 142 CD LYS A 8 36.216 17.089 12.598 1.00 0.00 C +ATOM 143 CE LYS A 8 36.404 17.876 11.295 1.00 0.00 C +ATOM 144 NZ LYS A 8 35.335 17.592 10.311 1.00 0.00 N +ATOM 145 H LYS A 8 36.577 19.400 16.431 1.00 0.00 H +ATOM 146 HA LYS A 8 36.589 16.597 16.863 1.00 0.00 H +ATOM 147 HB2 LYS A 8 35.333 16.381 14.898 1.00 0.00 H +ATOM 148 HB3 LYS A 8 34.879 17.932 15.603 1.00 0.00 H +ATOM 149 HG2 LYS A 8 35.129 18.685 13.504 1.00 0.00 H +ATOM 150 HG3 LYS A 8 36.836 18.707 13.865 1.00 0.00 H +ATOM 151 HD2 LYS A 8 37.099 16.513 12.798 1.00 0.00 H +ATOM 152 HD3 LYS A 8 35.374 16.401 12.516 1.00 0.00 H +ATOM 153 HE2 LYS A 8 36.396 18.925 11.521 1.00 0.00 H +ATOM 154 HE3 LYS A 8 37.387 17.636 10.877 1.00 0.00 H +ATOM 155 HZ1 LYS A 8 35.277 16.601 10.123 1.00 0.00 H +ATOM 156 HZ2 LYS A 8 34.456 17.951 10.677 1.00 0.00 H +ATOM 157 HZ3 LYS A 8 35.516 18.092 9.453 1.00 0.00 H +ATOM 158 N ASP A 9 39.070 17.468 14.979 1.00 0.00 N +ATOM 159 CA ASP A 9 40.364 17.059 14.429 1.00 0.00 C +ATOM 160 C ASP A 9 41.379 16.611 15.502 1.00 0.00 C +ATOM 161 O ASP A 9 42.443 16.104 15.140 1.00 0.00 O +ATOM 162 CB ASP A 9 40.931 18.236 13.610 1.00 0.00 C +ATOM 163 CG ASP A 9 40.570 18.169 12.124 1.00 0.00 C +ATOM 164 OD1 ASP A 9 39.366 18.024 11.812 1.00 0.00 O +ATOM 165 OD2 ASP A 9 41.525 18.260 11.317 1.00 0.00 O +ATOM 166 H ASP A 9 38.888 18.459 15.043 1.00 0.00 H +ATOM 167 HA ASP A 9 40.217 16.208 13.760 1.00 0.00 H +ATOM 168 HB2 ASP A 9 40.542 19.151 14.014 1.00 0.00 H +ATOM 169 HB3 ASP A 9 42.014 18.238 13.684 1.00 0.00 H +ATOM 170 N GLY A 10 41.083 16.797 16.798 1.00 0.00 N +ATOM 171 CA GLY A 10 41.958 16.457 17.927 1.00 0.00 C +ATOM 172 C GLY A 10 42.526 17.663 18.687 1.00 0.00 C +ATOM 173 O GLY A 10 43.394 17.481 19.542 1.00 0.00 O +ATOM 174 H GLY A 10 40.163 17.167 17.027 1.00 0.00 H +ATOM 175 HA2 GLY A 10 41.384 15.861 18.638 1.00 0.00 H +ATOM 176 HA3 GLY A 10 42.795 15.847 17.586 1.00 0.00 H +ATOM 177 N GLY A 11 42.070 18.888 18.389 1.00 0.00 N +ATOM 178 CA GLY A 11 42.524 20.108 19.057 1.00 0.00 C +ATOM 179 C GLY A 11 44.055 20.273 18.988 1.00 0.00 C +ATOM 180 O GLY A 11 44.608 20.246 17.885 1.00 0.00 O +ATOM 181 H GLY A 11 41.379 18.986 17.653 1.00 0.00 H +ATOM 182 HA2 GLY A 11 42.062 20.966 18.571 1.00 0.00 H +ATOM 183 HA3 GLY A 11 42.178 20.078 20.087 1.00 0.00 H +ATOM 184 N PRO A 12 44.769 20.424 20.128 1.00 0.00 N +ATOM 185 CA PRO A 12 46.231 20.542 20.140 1.00 0.00 C +ATOM 186 C PRO A 12 46.956 19.346 19.499 1.00 0.00 C +ATOM 187 O PRO A 12 48.037 19.513 18.935 1.00 0.00 O +ATOM 188 CB PRO A 12 46.638 20.688 21.613 1.00 0.00 C +ATOM 189 CG PRO A 12 45.358 21.123 22.321 1.00 0.00 C +ATOM 190 CD PRO A 12 44.260 20.460 21.494 1.00 0.00 C +ATOM 191 HA PRO A 12 46.509 21.449 19.601 1.00 0.00 H +ATOM 192 HB2 PRO A 12 46.989 19.752 22.004 1.00 0.00 H +ATOM 193 HB3 PRO A 12 47.429 21.428 21.737 1.00 0.00 H +ATOM 194 HG2 PRO A 12 45.341 20.773 23.335 1.00 0.00 H +ATOM 195 HG3 PRO A 12 45.256 22.208 22.263 1.00 0.00 H +ATOM 196 HD2 PRO A 12 44.071 19.466 21.850 1.00 0.00 H +ATOM 197 HD3 PRO A 12 43.338 21.033 21.580 1.00 0.00 H +ATOM 198 N SER A 13 46.361 18.146 19.539 1.00 0.00 N +ATOM 199 CA SER A 13 46.947 16.896 19.038 1.00 0.00 C +ATOM 200 C SER A 13 46.795 16.706 17.519 1.00 0.00 C +ATOM 201 O SER A 13 46.923 15.587 17.031 1.00 0.00 O +ATOM 202 CB SER A 13 46.356 15.704 19.806 1.00 0.00 C +ATOM 203 OG SER A 13 46.661 15.811 21.184 1.00 0.00 O +ATOM 204 H SER A 13 45.433 18.076 19.947 1.00 0.00 H +ATOM 205 HA SER A 13 48.019 16.916 19.237 1.00 0.00 H +ATOM 206 HB2 SER A 13 45.291 15.693 19.678 1.00 0.00 H +ATOM 207 HB3 SER A 13 46.778 14.773 19.427 1.00 0.00 H +ATOM 208 HG SER A 13 47.605 15.681 21.304 1.00 0.00 H +ATOM 209 N SER A 14 46.535 17.785 16.768 1.00 0.00 N +ATOM 210 CA SER A 14 46.287 17.760 15.319 1.00 0.00 C +ATOM 211 C SER A 14 47.230 18.670 14.511 1.00 0.00 C +ATOM 212 O SER A 14 46.980 18.952 13.341 1.00 0.00 O +ATOM 213 CB SER A 14 44.812 18.082 15.069 1.00 0.00 C +ATOM 214 OG SER A 14 44.329 17.332 13.976 1.00 0.00 O +ATOM 215 H SER A 14 46.407 18.660 17.264 1.00 0.00 H +ATOM 216 HA SER A 14 46.460 16.746 14.956 1.00 0.00 H +ATOM 217 HB2 SER A 14 44.242 17.839 15.945 1.00 0.00 H +ATOM 218 HB3 SER A 14 44.676 19.141 14.877 1.00 0.00 H +ATOM 219 HG SER A 14 43.612 16.751 14.347 1.00 0.00 H +ATOM 220 N GLY A 15 48.317 19.155 15.132 1.00 0.00 N +ATOM 221 CA GLY A 15 49.349 19.959 14.464 1.00 0.00 C +ATOM 222 C GLY A 15 48.882 21.350 14.018 1.00 0.00 C +ATOM 223 O GLY A 15 49.437 21.898 13.067 1.00 0.00 O +ATOM 224 H GLY A 15 48.471 18.865 16.088 1.00 0.00 H +ATOM 225 HA2 GLY A 15 50.195 20.088 15.140 1.00 0.00 H +ATOM 226 HA3 GLY A 15 49.703 19.423 13.582 1.00 0.00 H +ATOM 227 N ARG A 16 47.854 21.911 14.674 1.00 0.00 N +ATOM 228 CA ARG A 16 47.187 23.159 14.280 1.00 0.00 C +ATOM 229 C ARG A 16 46.753 23.991 15.505 1.00 0.00 C +ATOM 230 O ARG A 16 46.120 23.441 16.410 1.00 0.00 O +ATOM 231 CB ARG A 16 46.008 22.832 13.340 1.00 0.00 C +ATOM 232 CG ARG A 16 44.944 21.904 13.956 1.00 0.00 C +ATOM 233 CD ARG A 16 43.821 21.483 12.996 1.00 0.00 C +ATOM 234 NE ARG A 16 44.149 20.264 12.234 1.00 0.00 N +ATOM 235 CZ ARG A 16 44.757 20.161 11.060 1.00 0.00 C +ATOM 236 NH1 ARG A 16 45.187 21.211 10.397 1.00 0.00 N +ATOM 237 NH2 ARG A 16 44.933 18.980 10.525 1.00 0.00 N +ATOM 238 H ARG A 16 47.477 21.399 15.460 1.00 0.00 H +ATOM 239 HA ARG A 16 47.907 23.738 13.704 1.00 0.00 H +ATOM 240 HB2 ARG A 16 45.532 23.753 13.065 1.00 0.00 H +ATOM 241 HB3 ARG A 16 46.422 22.355 12.454 1.00 0.00 H +ATOM 242 HG2 ARG A 16 45.436 21.016 14.303 1.00 0.00 H +ATOM 243 HG3 ARG A 16 44.477 22.423 14.785 1.00 0.00 H +ATOM 244 HD2 ARG A 16 42.931 21.301 13.568 1.00 0.00 H +ATOM 245 HD3 ARG A 16 43.567 22.310 12.331 1.00 0.00 H +ATOM 246 HE ARG A 16 43.861 19.381 12.636 1.00 0.00 H +ATOM 247 HH11 ARG A 16 45.048 22.113 10.813 1.00 0.00 H +ATOM 248 HH12 ARG A 16 45.659 21.113 9.519 1.00 0.00 H +ATOM 249 HH21 ARG A 16 44.547 18.181 11.007 1.00 0.00 H +ATOM 250 HH22 ARG A 16 45.406 18.870 9.650 1.00 0.00 H +ATOM 251 N PRO A 17 47.054 25.305 15.554 1.00 0.00 N +ATOM 252 CA PRO A 17 46.680 26.163 16.679 1.00 0.00 C +ATOM 253 C PRO A 17 45.159 26.406 16.729 1.00 0.00 C +ATOM 254 O PRO A 17 44.484 26.240 15.710 1.00 0.00 O +ATOM 255 CB PRO A 17 47.452 27.469 16.453 1.00 0.00 C +ATOM 256 CG PRO A 17 47.575 27.549 14.933 1.00 0.00 C +ATOM 257 CD PRO A 17 47.718 26.085 14.518 1.00 0.00 C +ATOM 258 HA PRO A 17 47.005 25.703 17.613 1.00 0.00 H +ATOM 259 HB2 PRO A 17 46.907 28.309 16.839 1.00 0.00 H +ATOM 260 HB3 PRO A 17 48.446 27.383 16.895 1.00 0.00 H +ATOM 261 HG2 PRO A 17 46.698 27.989 14.498 1.00 0.00 H +ATOM 262 HG3 PRO A 17 48.438 28.141 14.627 1.00 0.00 H +ATOM 263 HD2 PRO A 17 47.247 25.919 13.568 1.00 0.00 H +ATOM 264 HD3 PRO A 17 48.774 25.814 14.479 1.00 0.00 H +ATOM 265 N PRO A 18 44.608 26.814 17.889 1.00 0.00 N +ATOM 266 CA PRO A 18 43.185 27.106 18.020 1.00 0.00 C +ATOM 267 C PRO A 18 42.799 28.380 17.247 1.00 0.00 C +ATOM 268 O PRO A 18 43.582 29.331 17.205 1.00 0.00 O +ATOM 269 CB PRO A 18 42.933 27.265 19.521 1.00 0.00 C +ATOM 270 CG PRO A 18 44.283 27.730 20.063 1.00 0.00 C +ATOM 271 CD PRO A 18 45.291 27.024 19.157 1.00 0.00 C +ATOM 272 HA PRO A 18 42.617 26.256 17.650 1.00 0.00 H +ATOM 273 HB2 PRO A 18 42.172 27.999 19.706 1.00 0.00 H +ATOM 274 HB3 PRO A 18 42.679 26.298 19.952 1.00 0.00 H +ATOM 275 HG2 PRO A 18 44.380 28.796 19.988 1.00 0.00 H +ATOM 276 HG3 PRO A 18 44.416 27.452 21.109 1.00 0.00 H +ATOM 277 HD2 PRO A 18 46.160 27.637 19.016 1.00 0.00 H +ATOM 278 HD3 PRO A 18 45.560 26.058 19.587 1.00 0.00 H +ATOM 279 N PRO A 19 41.586 28.435 16.670 1.00 0.00 N +ATOM 280 CA PRO A 19 41.083 29.618 15.981 1.00 0.00 C +ATOM 281 C PRO A 19 40.613 30.682 16.989 1.00 0.00 C +ATOM 282 O PRO A 19 39.774 30.399 17.847 1.00 0.00 O +ATOM 283 CB PRO A 19 39.946 29.089 15.105 1.00 0.00 C +ATOM 284 CG PRO A 19 39.379 27.927 15.922 1.00 0.00 C +ATOM 285 CD PRO A 19 40.614 27.350 16.606 1.00 0.00 C +ATOM 286 HA PRO A 19 41.859 30.041 15.343 1.00 0.00 H +ATOM 287 HB2 PRO A 19 39.201 29.845 14.945 1.00 0.00 H +ATOM 288 HB3 PRO A 19 40.361 28.705 14.172 1.00 0.00 H +ATOM 289 HG2 PRO A 19 38.666 28.276 16.644 1.00 0.00 H +ATOM 290 HG3 PRO A 19 38.879 27.189 15.293 1.00 0.00 H +ATOM 291 HD2 PRO A 19 40.368 27.012 17.594 1.00 0.00 H +ATOM 292 HD3 PRO A 19 41.019 26.536 16.005 1.00 0.00 H +ATOM 293 N SER A 20 41.169 31.897 16.883 1.00 0.00 N +ATOM 294 CA SER A 20 40.750 33.102 17.619 1.00 0.00 C +ATOM 295 C SER A 20 39.492 33.732 17.017 1.00 0.00 C +ATOM 296 O SER A 20 39.511 33.991 15.794 1.00 0.00 O +ATOM 297 CB SER A 20 41.870 34.146 17.618 1.00 0.00 C +ATOM 298 OG SER A 20 43.018 33.616 18.245 1.00 0.00 O +ATOM 299 OXT SER A 20 38.557 33.978 17.807 1.00 0.00 O +ATOM 300 H SER A 20 41.867 32.036 16.169 1.00 0.00 H +ATOM 301 HA SER A 20 40.499 32.835 18.644 1.00 0.00 H +ATOM 302 HB2 SER A 20 42.108 34.413 16.606 1.00 0.00 H +ATOM 303 HB3 SER A 20 41.534 35.034 18.158 1.00 0.00 H +ATOM 304 HG SER A 20 42.729 33.115 19.010 1.00 0.00 H +TER +HETATM 305 C1 BEN B 21 39.867 33.011 36.900 1.00 0.00 C +HETATM 306 C2 BEN B 21 40.534 32.219 37.826 1.00 0.00 C +HETATM 307 C3 BEN B 21 41.748 32.641 38.356 1.00 0.00 C +HETATM 308 C4 BEN B 21 42.294 33.857 37.959 1.00 0.00 C +HETATM 309 C5 BEN B 21 41.626 34.649 37.033 1.00 0.00 C +HETATM 310 C6 BEN B 21 40.412 34.227 36.503 1.00 0.00 C +HETATM 311 C7 BEN B 21 38.557 32.555 36.328 1.00 0.00 C +HETATM 312 N1 BEN B 21 38.039 31.396 36.708 1.00 0.00 N +HETATM 313 N2 BEN B 21 37.922 33.314 35.445 1.00 0.00 N +END diff --git a/regtest/basic/rt-molinfo-whole-ligand/traj.gro b/regtest/basic/rt-molinfo-whole-ligand/traj.gro new file mode 100644 index 0000000000..241a7f60de --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-ligand/traj.gro @@ -0,0 +1,948 @@ +trp-cage and a ligand nearer a periodic image of the protein + 313 + 1ASN N 1 5.100 1.565 3.211 + 1ASN CA 2 5.129 1.466 3.105 + 1ASN C 3 5.278 1.449 3.077 + 1ASN O 4 5.326 1.338 3.091 + 1ASN CB 5 5.046 1.492 2.977 + 1ASN CG 6 4.898 1.466 3.005 + 1ASN OD1 7 4.863 1.423 3.114 + 1ASN ND2 8 4.809 1.493 2.912 + 1ASN H1 9 3.157 0.394 0.027 + 1ASN H2 10 5.116 1.660 3.177 + 1ASN H3 11 5.002 1.557 3.237 + 1ASN HA 12 5.097 1.369 3.142 + 1ASN HB2 13 5.059 1.594 2.947 + 1ASN HB3 14 5.079 1.425 2.898 + 1ASN HD21 15 4.833 1.532 2.822 + 1ASN HD22 16 4.714 1.471 2.937 + 2LEU N 17 5.352 1.556 3.044 + 2LEU CA 18 5.497 1.553 3.021 + 2LEU C 19 5.576 1.471 3.126 + 2LEU O 20 5.651 1.380 3.090 + 2LEU CB 21 5.549 1.698 3.004 + 2LEU CG 22 5.510 1.798 3.117 + 2LEU CD1 23 5.629 1.833 3.206 + 2LEU CD2 24 5.455 1.928 3.058 + 2LEU H 25 5.308 1.645 3.027 + 2LEU HA 26 5.515 1.502 2.926 + 2LEU HB2 27 5.656 1.694 2.999 + 2LEU HB3 28 5.509 1.734 2.910 + 2LEU HG 29 5.433 1.755 3.181 + 2LEU HD11 30 5.669 1.743 3.252 + 2LEU HD12 31 5.706 1.883 3.148 + 2LEU HD13 32 3.597 0.746 0.020 + 2LEU HD21 33 5.529 1.974 2.993 + 2LEU HD22 34 5.364 1.907 3.001 + 2LEU HD23 35 5.431 1.997 3.138 + 3TYR N 36 5.554 1.498 3.255 + 3TYR CA 37 3.621 0.272 0.099 + 3TYR C 38 3.580 0.124 0.108 + 3TYR O 39 5.661 3.503 0.145 + 3TYR CB 40 3.593 0.345 0.231 + 3TYR CG 41 3.707 0.332 0.329 + 3TYR CD1 42 3.715 0.220 0.414 + 3TYR CD2 43 3.808 0.431 0.334 + 3TYR CE1 44 3.824 0.206 0.502 + 3TYR CE2 45 3.917 0.417 0.421 + 3TYR CZ 46 3.926 0.303 0.505 + 3TYR OH 47 4.033 0.286 0.587 + 3TYR H 48 3.496 0.423 0.012 + 3TYR HA 49 3.728 0.275 0.080 + 3TYR HB2 50 3.578 0.449 0.210 + 3TYR HB3 51 3.501 0.308 0.275 + 3TYR HD1 52 5.638 3.608 0.411 + 3TYR HD2 53 3.802 0.518 0.270 + 3TYR HE1 54 5.832 3.584 0.567 + 3TYR HE2 55 3.993 0.493 0.424 + 3TYR HH 56 4.109 0.338 0.557 + 4ILE N 57 3.456 0.091 0.069 + 4ILE CA 58 5.404 3.417 0.062 + 4ILE C 59 7.481 4.495 3.219 + 4ILE O 60 7.528 4.384 3.244 + 4ILE CB 61 5.251 3.416 0.035 + 4ILE CG1 62 3.170 0.052 0.120 + 4ILE CG2 63 5.194 3.274 0.051 + 4ILE CD1 64 5.188 3.503 0.272 + 4ILE H 65 3.399 0.164 0.029 + 4ILE HA 66 5.423 3.368 0.157 + 4ILE HB 67 5.234 1.134 3.197 + 4ILE HG12 68 3.200 0.151 0.092 + 4ILE HG13 69 3.064 0.040 0.097 + 4ILE HG21 70 7.239 4.361 3.243 + 4ILE HG22 71 5.214 3.235 0.151 + 4ILE HG23 72 5.086 3.275 0.034 + 4ILE HD11 73 5.159 3.404 0.305 + 4ILE HD12 74 5.292 3.523 0.300 + 4ILE HD13 75 5.124 3.577 0.322 + 5GLN N 76 7.499 4.557 3.102 + 5GLN CA 77 7.578 4.500 2.992 + 5GLN C 78 7.727 4.485 3.027 + 5GLN O 79 3.791 4.393 2.978 + 5GLN CB 80 5.561 1.121 2.865 + 5GLN CG 81 5.565 1.036 2.737 + 5GLN CD 82 5.432 0.967 2.708 + 5GLN OE1 83 7.413 4.313 2.733 + 5GLN NE2 84 5.337 1.038 2.651 + 5GLN H 85 5.457 1.185 3.090 + 5GLN HA 86 7.538 4.401 2.972 + 5GLN HB2 87 5.466 1.172 2.869 + 5GLN HB3 88 5.641 1.196 2.861 + 5GLN HG2 89 5.590 1.099 2.654 + 5GLN HG3 90 7.644 4.425 2.746 + 5GLN HE21 91 5.351 1.134 2.626 + 5GLN HE22 92 5.251 0.989 2.633 + 6TRP N 93 5.782 1.107 3.114 + 6TRP CA 94 7.918 4.554 3.167 + 6TRP C 95 1.927 3.286 0.005 + 6TRP O 96 2.019 3.204 0.000 + 6TRP CB 97 5.968 1.223 3.225 + 6TRP CG 98 0.105 0.063 0.020 + 6TRP CD1 99 2.222 1.219 3.218 + 6TRP CD2 100 2.141 3.519 0.161 + 6TRP NE1 101 0.327 0.054 0.042 + 6TRP CE2 102 2.283 3.514 0.171 + 6TRP CE3 103 6.068 3.515 0.282 + 6TRP CZ2 104 2.350 3.507 0.294 + 6TRP CZ3 105 6.134 3.506 0.406 + 6TRP CH2 106 2.274 3.503 0.412 + 6TRP H 107 5.727 1.187 3.142 + 6TRP HA 108 3.985 4.526 3.085 + 6TRP HB2 109 5.969 1.295 3.145 + 6TRP HB3 110 3.898 0.102 0.035 + 6TRP HD1 111 2.231 1.226 3.111 + 6TRP HE1 112 0.426 0.052 0.016 + 6TRP HE3 113 5.960 3.519 0.278 + 6TRP HZ2 114 2.458 3.504 0.297 + 6TRP HZ3 115 6.076 3.502 0.497 + 6TRP HH2 116 2.323 3.498 0.509 + 7LEU N 117 5.830 3.276 0.097 + 7LEU CA 118 5.826 3.169 0.197 + 7LEU C 119 1.805 3.030 0.135 + 7LEU O 120 1.875 2.937 0.175 + 7LEU CB 121 5.719 3.198 0.304 + 7LEU CG 122 5.760 3.304 0.407 + 7LEU CD1 123 5.642 3.330 0.502 + 7LEU CD2 124 5.881 3.262 0.492 + 7LEU H 125 5.758 3.349 0.100 + 7LEU HA 126 5.923 3.164 0.245 + 7LEU HB2 127 5.630 3.231 0.254 + 7LEU HB3 128 5.698 3.105 0.358 + 7LEU HG 129 5.784 3.397 0.356 + 7LEU HD11 130 5.556 3.363 0.445 + 7LEU HD12 131 5.617 3.239 0.556 + 7LEU HD13 132 5.669 3.407 0.574 + 7LEU HD21 133 5.863 3.163 0.536 + 7LEU HD22 134 5.970 3.258 0.430 + 7LEU HD23 135 5.898 3.334 0.572 + 8LYS N 136 5.715 3.014 0.036 + 8LYS CA 137 3.687 4.038 3.239 + 8LYS C 138 3.810 3.974 3.173 + 8LYS O 139 3.818 3.852 3.163 + 8LYS CB 140 7.567 4.047 3.143 + 8LYS CG 141 7.597 4.116 3.009 + 8LYS CD 142 3.622 4.018 2.893 + 8LYS CE 143 3.640 4.097 2.762 + 8LYS NZ 144 3.534 4.069 2.664 + 8LYS H 145 5.658 3.095 0.010 + 8LYS HA 146 1.659 2.814 0.053 + 8LYS HB2 147 7.533 3.948 3.123 + 8LYS HB3 148 7.488 4.103 3.193 + 8LYS HG2 149 7.513 4.178 2.983 + 8LYS HG3 150 3.684 4.180 3.019 + 8LYS HD2 151 3.710 3.961 2.913 + 8LYS HD3 152 3.537 3.950 2.885 + 8LYS HE2 153 3.640 4.202 2.785 + 8LYS HE3 154 3.739 4.073 2.721 + 8LYS HZ1 155 3.528 3.970 2.645 + 8LYS HZ2 156 7.446 4.105 2.701 + 8LYS HZ3 157 3.552 4.119 2.578 + 9ASP N 158 3.907 4.056 3.131 + 9ASP CA 159 4.036 4.015 3.076 + 9ASP C 160 4.138 3.971 3.183 + 9ASP O 161 4.244 3.920 3.147 + 9ASP CB 162 4.093 4.133 2.994 + 9ASP CG 163 4.057 4.126 2.845 + 9ASP OD1 164 3.937 4.112 2.814 + 9ASP OD2 165 4.153 4.135 2.765 + 9ASP H 166 3.889 4.155 3.137 + 9ASP HA 167 4.022 3.930 3.009 + 9ASP HB2 168 4.054 4.225 3.034 + 9ASP HB3 169 4.201 4.133 3.001 + 10GLY N 170 2.108 2.834 0.047 + 10GLY CA 171 2.196 2.800 0.160 + 10GLY C 172 2.253 2.921 0.236 + 10GLY O 173 2.339 2.903 0.321 + 10GLY H 174 2.016 2.871 0.070 + 10GLY HA2 175 2.138 2.741 0.231 + 10GLY HA3 176 2.280 2.739 0.126 + 11GLY N 177 2.207 3.044 0.206 + 11GLY CA 178 2.252 3.166 0.273 + 11GLY C 179 2.406 3.182 0.266 + 11GLY O 180 2.461 3.179 0.156 + 11GLY H 181 2.138 3.053 0.132 + 11GLY HA2 182 2.206 3.251 0.224 + 11GLY HA3 183 2.218 3.163 0.376 + 12PRO N 184 2.477 3.197 0.380 + 12PRO CA 185 2.623 3.209 0.381 + 12PRO C 186 2.696 3.089 0.317 + 12PRO O 187 2.804 3.106 0.261 + 12PRO CB 188 2.664 3.224 0.528 + 12PRO CG 189 2.536 3.267 0.599 + 12PRO CD 190 2.426 3.201 0.516 + 12PRO HA 191 2.651 3.300 0.327 + 12PRO HB2 192 2.699 3.130 0.567 + 12PRO HB3 193 2.743 3.298 0.541 + 12PRO HG2 194 2.534 3.232 0.701 + 12PRO HG3 195 2.526 3.376 0.593 + 12PRO HD2 196 2.407 3.101 0.552 + 12PRO HD3 197 2.334 3.258 0.525 + 13SER N 198 2.636 2.969 0.321 + 13SER CA 199 2.695 2.844 0.271 + 13SER C 200 2.680 2.825 0.119 + 13SER O 201 2.692 2.713 0.070 + 13SER CB 202 2.636 2.725 0.348 + 13SER OG 203 2.666 2.736 0.485 + 13SER H 204 2.543 2.962 0.362 + 13SER HA 205 2.802 2.846 0.291 + 13SER HB2 206 2.529 2.724 0.335 + 13SER HB3 207 2.678 2.632 0.310 + 13SER HG 208 2.760 2.723 0.497 + 14SER N 209 2.653 2.933 0.044 + 14SER CA 210 4.629 4.085 3.165 + 14SER C 211 4.723 4.176 3.084 + 14SER O 212 4.698 4.205 2.967 + 14SER CB 213 4.481 4.118 3.140 + 14SER OG 214 4.433 4.043 3.031 + 14SER H 215 2.641 3.021 0.093 + 14SER HA 216 4.646 3.984 3.129 + 14SER HB2 217 4.424 4.093 3.227 + 14SER HB3 218 4.468 4.224 3.121 + 14SER HG 219 4.361 3.985 3.068 + 15GLY N 220 4.832 4.225 3.146 + 15GLY CA 221 4.935 4.305 3.079 + 15GLY C 222 4.888 4.444 3.035 + 15GLY O 223 4.944 4.499 2.940 + 15GLY H 224 4.847 4.196 3.242 + 15GLY HA2 225 5.019 4.318 3.147 + 15GLY HA3 226 4.970 4.252 2.991 + 16ARG N 227 4.785 4.501 3.100 + 16ARG CA 228 2.719 1.161 3.061 + 16ARG C 229 2.675 1.244 3.183 + 16ARG O 230 0.612 0.035 0.008 + 16ARG CB 231 2.601 1.128 2.967 + 16ARG CG 232 4.494 4.500 3.029 + 16ARG CD 233 4.382 4.458 2.933 + 16ARG NE 234 4.415 4.336 2.856 + 16ARG CZ 235 4.476 4.326 2.739 + 16ARG NH1 236 2.519 0.966 2.673 + 16ARG NH2 237 4.493 4.207 2.685 + 16ARG H 238 4.748 4.449 3.179 + 16ARG HA 239 2.791 1.219 3.003 + 16ARG HB2 240 2.553 1.221 2.939 + 16ARG HB3 241 2.642 1.081 2.878 + 16ARG HG2 242 4.544 4.411 3.063 + 16ARG HG3 243 4.448 4.552 3.111 + 16ARG HD2 244 4.293 4.440 2.990 + 16ARG HD3 245 2.357 1.076 2.866 + 16ARG HE 246 4.386 4.248 2.897 + 16ARG HH11 247 2.505 1.057 2.714 + 16ARG HH12 248 2.566 0.957 2.585 + 16ARG HH21 249 4.455 4.128 2.734 + 16ARG HH22 250 4.541 4.196 2.598 + 17PRO N 251 2.705 1.376 3.188 + 17PRO CA 252 0.668 0.307 0.035 + 17PRO C 253 0.516 0.331 0.040 + 17PRO O 254 2.448 1.469 3.204 + 17PRO CB 255 0.745 0.437 0.012 + 17PRO CG 256 2.757 1.600 3.126 + 17PRO CD 257 2.772 1.454 3.085 + 17PRO HA 258 0.700 0.261 0.128 + 17PRO HB2 259 0.691 0.521 0.051 + 17PRO HB3 260 0.845 0.429 0.057 + 17PRO HG2 261 2.670 1.644 3.083 + 17PRO HG3 262 2.844 1.659 3.096 + 17PRO HD2 263 2.725 1.437 2.990 + 17PRO HD3 264 2.877 1.427 3.081 + 18PRO N 265 0.461 0.372 0.156 + 18PRO CA 266 0.318 0.401 0.169 + 18PRO C 267 4.280 0.529 0.092 + 18PRO O 268 4.358 0.624 0.088 + 18PRO CB 269 4.293 0.417 0.319 + 18PRO CG 270 0.428 0.464 0.373 + 18PRO CD 271 0.529 0.393 0.283 + 18PRO HA 272 0.262 0.316 0.132 + 18PRO HB2 273 4.217 0.490 0.338 + 18PRO HB3 274 4.268 0.320 0.362 + 18PRO HG2 275 4.438 0.570 0.366 + 18PRO HG3 276 4.442 0.436 0.478 + 18PRO HD2 277 0.616 0.454 0.269 + 18PRO HD3 278 0.556 0.296 0.326 + 19PRO N 279 4.159 0.534 0.034 + 19PRO CA 280 6.108 1.807 3.231 + 19PRO C 281 4.061 0.759 0.066 + 19PRO O 282 3.977 0.730 0.152 + 19PRO CB 283 5.995 1.754 3.143 + 19PRO CG 284 5.938 1.638 3.225 + 19PRO CD 285 4.061 0.426 0.028 + 19PRO HA 286 6.186 1.849 3.167 + 19PRO HB2 287 5.920 1.830 3.127 + 19PRO HB3 288 6.036 1.716 3.050 + 19PRO HG2 289 3.867 0.518 0.031 + 19PRO HG3 290 5.888 1.564 3.162 + 19PRO HD2 291 4.037 0.392 0.126 + 19PRO HD3 292 6.102 1.499 3.233 + 20SER N 293 4.117 0.880 0.055 + 20SER CA 294 4.075 1.001 0.129 + 20SER C 295 3.949 1.064 0.069 + 20SER O 296 5.951 2.244 3.212 + 20SER CB 297 4.187 1.105 0.129 + 20SER OG 298 4.302 1.052 0.192 + 20SER OXT 299 3.856 1.088 0.148 + 20SER H 300 6.187 2.049 3.250 + 20SER HA 301 4.050 0.974 0.231 + 20SER HB2 302 4.211 1.132 0.028 + 20SER HB3 303 4.153 1.194 0.183 + 20SER HG 304 4.273 1.002 0.268 + 21BEN C1 305 3.987 0.992 2.057 + 21BEN C2 306 4.053 0.912 2.150 + 21BEN C3 307 4.175 0.955 2.203 + 21BEN C4 308 4.229 1.076 2.163 + 21BEN C5 309 4.163 1.155 2.070 + 21BEN C6 310 4.041 1.113 2.017 + 21BEN C7 311 3.856 0.946 2.000 + 21BEN N1 312 3.804 0.830 2.038 + 21BEN N2 313 3.792 1.022 1.912 + 4.00000 3.46410 3.26599 0.00000 0.00000 2.00000 0.00000 2.00000 1.15470 +trp-cage and a ligand nearer a periodic image of the protein + 313 + 1ASN N 1 4.311 1.790 2.862 + 1ASN CA 2 4.388 1.679 2.773 + 1ASN C 3 4.481 1.666 2.737 + 1ASN O 4 4.541 1.578 2.784 + 1ASN CB 5 4.258 1.727 2.664 + 1ASN CG 6 4.121 1.683 2.684 + 1ASN OD1 7 4.028 1.674 2.800 + 1ASN ND2 8 3.993 1.726 2.617 + 1ASN H1 9 4.362 1.794 2.978 + 1ASN H2 10 4.350 1.857 2.823 + 1ASN H3 11 4.184 1.773 2.888 + 1ASN HA 12 4.301 1.604 2.805 + 1ASN HB2 13 4.226 1.808 2.638 + 1ASN HB3 14 4.292 1.634 2.560 + 1ASN HD21 15 4.039 1.769 2.550 + 1ASN HD22 16 3.902 1.679 2.603 + 2LEU N 17 4.536 1.806 2.764 + 2LEU CA 18 4.723 1.806 2.691 + 2LEU C 19 4.734 1.689 2.813 + 2LEU O 20 4.880 1.599 2.794 + 2LEU CB 21 4.719 1.961 2.682 + 2LEU CG 22 4.732 2.046 2.812 + 2LEU CD1 23 4.831 2.068 2.892 + 2LEU CD2 24 4.615 2.164 2.755 + 2LEU H 25 4.520 1.880 2.728 + 2LEU HA 26 4.699 1.729 2.576 + 2LEU HB2 27 4.864 1.924 2.657 + 2LEU HB3 28 4.666 1.961 2.613 + 2LEU HG 29 4.659 1.987 2.832 + 2LEU HD11 30 4.889 1.991 2.946 + 2LEU HD12 31 4.875 2.155 2.847 + 2LEU HD13 32 4.785 2.136 2.951 + 2LEU HD21 33 4.730 2.190 2.665 + 2LEU HD22 34 4.572 2.148 2.646 + 2LEU HD23 35 4.620 2.228 2.807 + 3TYR N 36 4.760 1.715 2.899 + 3TYR CA 37 4.800 1.653 3.077 + 3TYR C 38 4.801 1.524 3.040 + 3TYR O 39 4.864 1.425 3.099 + 3TYR CB 40 4.789 1.721 3.198 + 3TYR CG 41 4.928 1.669 3.255 + 3TYR CD1 42 2.886 0.461 0.097 + 3TYR CD2 43 3.001 0.662 0.047 + 3TYR CE1 44 3.003 0.408 0.196 + 3TYR CE2 45 3.116 0.671 0.081 + 3TYR CZ 46 3.113 0.523 0.196 + 3TYR OH 47 3.236 0.499 0.232 + 3TYR H 48 4.704 1.836 2.940 + 3TYR HA 49 4.944 1.655 3.041 + 3TYR HB2 50 4.773 1.843 3.168 + 3TYR HB3 51 4.681 1.699 3.206 + 3TYR HD1 52 2.803 0.369 0.088 + 3TYR HD2 53 5.045 1.903 3.210 + 3TYR HE1 54 3.037 0.354 0.235 + 3TYR HE2 55 3.172 0.728 0.065 + 3TYR HH 56 3.275 0.577 0.243 + 4ILE N 57 4.659 1.511 3.049 + 4ILE CA 58 4.595 1.324 3.029 + 4ILE C 59 4.671 1.265 2.866 + 4ILE O 60 4.716 1.126 2.923 + 4ILE CB 61 4.445 1.335 2.957 + 4ILE CG1 62 4.337 1.465 3.068 + 4ILE CG2 63 4.379 1.189 2.979 + 4ILE CD1 64 4.391 1.428 3.201 + 4ILE H 65 4.588 1.567 2.968 + 4ILE HA 66 4.631 1.275 3.118 + 4ILE HB 67 4.431 1.361 2.849 + 4ILE HG12 68 4.399 1.540 3.039 + 4ILE HG13 69 4.284 1.439 3.055 + 4ILE HG21 70 4.467 1.102 2.921 + 4ILE HG22 71 4.421 1.130 3.072 + 4ILE HG23 72 4.308 1.196 3.008 + 4ILE HD11 73 4.390 1.320 3.257 + 4ILE HD12 74 2.516 0.308 0.004 + 4ILE HD13 75 2.282 0.319 0.005 + 5GLN N 76 4.683 1.323 2.779 + 5GLN CA 77 4.770 1.262 2.648 + 5GLN C 78 4.931 1.256 2.716 + 5GLN O 79 4.996 1.201 2.592 + 5GLN CB 80 4.773 1.373 2.550 + 5GLN CG 81 4.772 1.255 2.407 + 5GLN CD 82 4.636 1.219 2.395 + 5GLN OE1 83 4.593 1.108 2.408 + 5GLN NE2 84 4.547 1.275 2.304 + 5GLN H 85 4.655 1.403 2.718 + 5GLN HA 86 4.706 1.185 2.645 + 5GLN HB2 87 4.669 1.408 2.510 + 5GLN HB3 88 4.860 1.454 2.502 + 5GLN HG2 89 4.797 1.357 2.346 + 5GLN HG3 90 4.832 1.194 2.439 + 5GLN HE21 91 4.555 1.360 2.278 + 5GLN HE22 92 4.464 1.219 2.290 + 6TRP N 93 4.973 1.398 2.778 + 6TRP CA 94 5.108 1.347 2.870 + 6TRP C 95 5.114 1.205 2.923 + 6TRP O 96 5.224 1.083 2.945 + 6TRP CB 97 5.131 1.455 2.875 + 6TRP CG 98 5.324 1.462 2.960 + 6TRP CD1 99 5.433 1.439 2.893 + 6TRP CD2 100 5.314 1.447 3.112 + 6TRP NE1 101 5.543 1.460 3.003 + 6TRP CE2 102 5.510 1.439 3.101 + 6TRP CE3 103 5.262 1.464 3.203 + 6TRP CZ2 104 5.563 1.433 3.228 + 6TRP CZ3 105 3.345 0.272 0.078 + 6TRP CH2 106 3.437 0.298 0.097 + 6TRP H 107 4.965 1.400 2.807 + 6TRP HA 108 5.183 1.280 2.727 + 6TRP HB2 109 5.172 1.510 2.852 + 6TRP HB3 110 5.108 1.470 2.966 + 6TRP HD1 111 5.466 1.477 2.744 + 6TRP HE1 112 5.660 1.445 2.975 + 6TRP HE3 113 5.159 1.417 3.205 + 6TRP HZ2 114 5.656 1.409 3.236 + 6TRP HZ3 115 3.284 0.311 0.133 + 6TRP HH2 116 3.499 0.281 0.204 + 7LEU N 117 5.033 1.186 3.016 + 7LEU CA 118 7.027 4.552 3.137 + 7LEU C 119 7.035 4.401 3.074 + 7LEU O 120 7.028 4.352 3.098 + 7LEU CB 121 6.915 4.593 3.204 + 7LEU CG 122 2.935 0.050 0.076 + 7LEU CD1 123 2.851 0.078 0.167 + 7LEU CD2 124 5.080 3.494 0.169 + 7LEU H 125 4.973 1.262 3.063 + 7LEU HA 126 7.135 4.538 3.204 + 7LEU HB2 127 4.856 1.144 3.193 + 7LEU HB3 128 4.913 3.355 0.030 + 7LEU HG 129 3.001 0.190 0.046 + 7LEU HD11 130 2.766 0.113 0.125 + 7LEU HD12 131 4.855 3.430 0.227 + 7LEU HD13 132 2.876 0.199 0.244 + 7LEU HD21 133 5.072 3.412 0.221 + 7LEU HD22 134 5.168 3.488 0.107 + 7LEU HD23 135 3.073 0.107 0.223 + 8LYS N 136 6.895 4.393 3.029 + 8LYS CA 137 6.891 4.265 2.905 + 8LYS C 138 7.051 4.162 2.853 + 8LYS O 139 7.005 4.087 2.862 + 8LYS CB 140 6.771 4.253 2.821 + 8LYS CG 141 6.795 4.335 2.673 + 8LYS CD 142 6.813 4.267 2.542 + 8LYS CE 143 4.855 0.873 2.400 + 8LYS NZ 144 4.798 0.857 2.343 + 8LYS H 145 6.877 4.470 2.918 + 8LYS HA 146 6.880 4.192 3.011 + 8LYS HB2 147 6.710 4.184 2.813 + 8LYS HB3 148 6.676 4.308 2.844 + 8LYS HG2 149 4.679 0.968 2.667 + 8LYS HG3 150 6.893 4.395 2.692 + 8LYS HD2 151 6.939 4.197 2.547 + 8LYS HD3 152 6.771 4.214 2.575 + 8LYS HE2 153 4.865 1.015 2.436 + 8LYS HE3 154 4.979 0.875 2.401 + 8LYS HZ1 155 6.764 4.181 2.317 + 8LYS HZ2 156 4.661 0.873 2.365 + 8LYS HZ3 157 4.738 0.860 2.250 + 9ASP N 158 7.118 4.283 2.773 + 9ASP CA 159 7.222 4.240 2.789 + 9ASP C 160 7.313 4.216 2.860 + 9ASP O 161 7.476 4.192 2.838 + 9ASP CB 162 7.313 4.335 2.676 + 9ASP CG 163 5.276 0.913 2.504 + 9ASP OD1 164 7.136 4.340 2.479 + 9ASP OD2 165 7.347 4.326 2.455 + 9ASP H 166 7.118 4.391 2.788 + 9ASP HA 167 7.250 4.167 2.634 + 9ASP HB2 168 5.273 0.988 2.737 + 9ASP HB3 169 7.379 4.351 2.684 + 10GLY N 170 7.329 4.194 2.963 + 10GLY CA 171 7.400 4.172 3.140 + 10GLY C 172 7.455 4.285 3.213 + 10GLY O 173 5.552 3.113 0.012 + 10GLY H 174 7.243 4.232 3.017 + 10GLY HA2 175 7.327 4.151 3.163 + 10GLY HA3 176 7.492 4.104 3.096 + 11GLY N 177 7.428 4.459 3.158 + 11GLY CA 178 7.404 4.530 3.205 + 11GLY C 179 7.587 4.581 3.189 + 11GLY O 180 5.688 1.151 3.099 + 11GLY H 181 7.336 4.425 3.050 + 11GLY HA2 182 5.416 1.196 3.148 + 11GLY HA3 183 5.412 3.392 0.056 + 12PRO N 184 5.686 3.434 0.063 + 12PRO CA 185 5.838 3.433 0.036 + 12PRO C 186 7.884 4.462 3.257 + 12PRO O 187 4.010 4.483 3.183 + 12PRO CB 188 5.839 3.445 0.205 + 12PRO CG 189 5.743 3.508 0.273 + 12PRO CD 190 5.625 3.444 0.197 + 12PRO HA 191 3.868 0.064 0.032 + 12PRO HB2 192 5.885 3.354 0.263 + 12PRO HB3 193 5.939 3.521 0.245 + 12PRO HG2 194 5.701 3.490 0.389 + 12PRO HG3 195 3.725 0.099 0.247 + 12PRO HD2 196 5.605 3.339 0.256 + 12PRO HD3 197 5.537 3.509 0.218 + 13SER N 198 5.825 3.238 0.014 + 13SER CA 199 3.879 4.233 3.206 + 13SER C 200 3.867 4.169 3.073 + 13SER O 201 3.884 4.130 3.009 + 13SER CB 202 1.833 2.972 0.014 + 13SER OG 203 1.887 2.936 0.151 + 13SER H 204 5.753 3.177 0.041 + 13SER HA 205 3.991 4.223 3.243 + 13SER HB2 206 5.739 2.994 0.038 + 13SER HB3 207 3.911 3.998 3.222 + 13SER HG 208 1.970 2.949 0.166 + 14SER N 209 3.886 4.318 3.000 + 14SER CA 210 3.857 4.319 2.830 + 14SER C 211 3.880 4.393 2.760 + 14SER O 212 1.907 0.975 2.676 + 14SER CB 213 7.667 4.388 2.797 + 14SER OG 214 3.599 4.268 2.698 + 14SER H 215 3.837 4.385 3.041 + 14SER HA 216 3.831 4.176 2.819 + 14SER HB2 217 7.661 4.360 2.884 + 14SER HB3 218 5.656 1.019 2.810 + 14SER HG 219 3.584 4.209 2.757 + 15GLY N 220 4.017 4.435 2.831 + 15GLY CA 221 2.165 1.067 2.736 + 15GLY C 222 2.064 1.188 2.685 + 15GLY O 223 2.112 1.268 2.619 + 15GLY H 224 4.052 4.421 2.938 + 15GLY HA2 225 2.203 1.070 2.797 + 15GLY HA3 226 2.159 1.010 2.672 + 16ARG N 227 1.984 1.282 2.766 + 16ARG CA 228 1.930 1.394 2.711 + 16ARG C 229 5.879 1.493 2.869 + 16ARG O 230 5.827 1.449 2.960 + 16ARG CB 231 5.806 1.340 2.611 + 16ARG CG 232 5.696 1.310 2.695 + 16ARG CD 233 5.591 1.209 2.619 + 16ARG NE 234 5.607 1.082 2.554 + 16ARG CZ 235 1.690 1.073 2.403 + 16ARG NH1 236 1.707 1.185 2.382 + 16ARG NH2 237 1.672 0.973 2.392 + 16ARG H 238 1.946 1.191 2.841 + 16ARG HA 239 2.020 1.452 2.657 + 16ARG HB2 240 5.764 1.459 2.619 + 16ARG HB3 241 1.851 1.276 2.547 + 16ARG HG2 242 5.716 1.190 2.736 + 16ARG HG3 243 5.669 1.306 2.781 + 16ARG HD2 244 5.521 1.257 2.684 + 16ARG HD3 245 5.555 1.326 2.560 + 16ARG HE 246 5.578 0.996 2.551 + 16ARG HH11 247 5.653 1.285 2.423 + 16ARG HH12 248 1.783 1.183 2.330 + 16ARG HH21 249 1.660 0.904 2.394 + 16ARG HH22 250 1.726 0.969 2.277 + 17PRO N 251 5.866 1.586 2.842 + 17PRO CA 252 5.876 1.689 2.918 + 17PRO C 253 5.731 1.689 2.995 + 17PRO O 254 5.664 1.714 2.905 + 17PRO CB 255 5.966 1.810 2.911 + 17PRO CG 256 5.950 1.839 2.789 + 17PRO CD 257 5.984 1.690 2.734 + 17PRO HA 258 5.888 1.669 3.086 + 17PRO HB2 259 5.898 1.953 2.996 + 17PRO HB3 260 6.033 1.802 2.992 + 17PRO HG2 261 5.863 1.870 2.785 + 17PRO HG3 262 6.047 1.898 2.771 + 17PRO HD2 263 5.906 1.706 2.693 + 17PRO HD3 264 6.066 1.671 2.751 + 18PRO N 265 5.677 1.747 3.086 + 18PRO CA 266 5.482 1.791 3.065 + 18PRO C 267 5.474 1.926 3.003 + 18PRO O 268 5.589 1.983 3.023 + 18PRO CB 269 5.525 1.777 3.266 + 18PRO CG 270 3.606 0.666 0.046 + 18PRO CD 271 5.716 1.792 3.223 + 18PRO HA 272 5.454 1.717 3.068 + 18PRO HB2 273 5.404 1.879 3.249 + 18PRO HB3 274 3.441 0.540 0.018 + 18PRO HG2 275 3.646 0.789 0.025 + 18PRO HG3 276 3.649 0.653 0.154 + 18PRO HD2 277 5.808 1.838 3.199 + 18PRO HD3 278 3.775 0.514 0.042 + 19PRO N 279 5.401 1.932 2.978 + 19PRO CA 280 5.315 2.045 2.888 + 19PRO C 281 5.240 2.121 3.075 + 19PRO O 282 5.171 2.153 3.114 + 19PRO CB 283 5.197 1.974 2.800 + 19PRO CG 284 5.162 1.840 2.882 + 19PRO CD 285 5.282 1.773 2.980 + 19PRO HA 286 5.389 2.089 2.818 + 19PRO HB2 287 5.128 2.105 2.796 + 19PRO HB3 288 5.263 1.983 2.723 + 19PRO HG2 289 5.042 1.905 2.950 + 19PRO HG3 290 5.130 1.776 2.850 + 19PRO HD2 291 5.213 1.782 3.063 + 19PRO HD3 292 5.303 1.706 2.914 + 20SER N 293 5.289 2.256 2.960 + 20SER CA 294 5.272 2.382 3.032 + 20SER C 295 5.183 2.423 3.004 + 20SER O 296 5.190 2.449 2.885 + 20SER CB 297 5.406 2.497 3.051 + 20SER OG 298 5.481 2.457 3.134 + 20SER OXT 299 5.059 2.493 3.067 + 20SER H 300 5.397 2.281 2.950 + 20SER HA 301 5.229 2.360 3.171 + 20SER HB2 302 5.416 2.544 2.977 + 20SER HB3 303 5.362 2.616 3.100 + 20SER HG 304 5.475 2.383 3.229 + 21BEN C1 305 3.375 1.097 1.750 + 21BEN C2 306 3.393 1.062 1.857 + 21BEN C3 307 3.539 1.073 1.918 + 21BEN C4 308 3.596 1.211 1.866 + 21BEN C5 309 3.507 1.313 1.803 + 21BEN C6 310 3.399 1.231 1.722 + 21BEN C7 311 3.183 1.032 1.738 + 21BEN N1 312 3.157 0.951 1.763 + 21BEN N2 313 3.157 1.154 1.639 + 4.00000 3.46410 3.26599 0.00000 0.00000 2.00000 0.00000 2.00000 1.15470 +trp-cage and a ligand nearer a periodic image of the protein + 313 + 1ASN N 1 3.872 2.056 1.020 + 1ASN CA 2 3.882 1.937 0.958 + 1ASN C 3 4.026 1.883 0.908 + 1ASN O 4 4.097 1.808 0.937 + 1ASN CB 5 3.828 1.948 0.813 + 1ASN CG 6 3.655 1.922 0.839 + 1ASN OD1 7 3.659 1.895 0.935 + 1ASN ND2 8 3.583 1.948 0.770 + 1ASN H1 9 3.906 1.978 1.121 + 1ASN H2 10 3.889 2.114 1.015 + 1ASN H3 11 3.803 2.004 1.059 + 1ASN HA 12 3.860 1.844 0.961 + 1ASN HB2 13 3.821 2.035 0.777 + 1ASN HB3 14 3.866 1.850 0.736 + 1ASN HD21 15 3.594 1.979 0.660 + 1ASN HD22 16 3.494 1.916 0.794 + 2LEU N 17 4.152 2.021 0.869 + 2LEU CA 18 4.307 2.010 0.846 + 2LEU C 19 4.381 1.917 0.994 + 2LEU O 20 4.472 1.833 0.971 + 2LEU CB 21 4.342 2.156 0.807 + 2LEU CG 22 4.251 2.280 0.963 + 2LEU CD1 23 4.418 2.286 1.030 + 2LEU CD2 24 4.228 2.359 0.893 + 2LEU H 25 4.060 2.074 0.854 + 2LEU HA 26 4.282 1.922 0.768 + 2LEU HB2 27 4.445 2.138 0.843 + 2LEU HB3 28 4.255 2.194 0.738 + 2LEU HG 29 4.208 2.210 1.006 + 2LEU HD11 30 4.435 2.183 1.103 + 2LEU HD12 31 4.488 2.378 1.016 + 2LEU HD13 32 4.385 2.361 1.122 + 2LEU HD21 33 4.295 2.413 0.808 + 2LEU HD22 34 4.162 2.357 0.813 + 2LEU HD23 35 4.223 2.449 0.984 + 3TYR N 36 4.335 1.947 1.093 + 3TYR CA 37 4.371 1.863 1.203 + 3TYR C 38 4.331 1.723 1.206 + 3TYR O 39 4.463 1.629 1.258 + 3TYR CB 40 4.361 1.984 1.316 + 3TYR CG 41 4.438 1.936 1.392 + 3TYR CD1 42 4.486 1.863 1.533 + 3TYR CD2 43 4.574 2.041 1.422 + 3TYR CE1 44 4.594 1.791 1.583 + 3TYR CE2 45 4.694 2.044 1.532 + 3TYR CZ 46 4.703 1.884 1.566 + 3TYR OH 47 4.830 1.880 1.668 + 3TYR H 48 4.295 2.016 1.103 + 3TYR HA 49 4.563 1.904 1.193 + 3TYR HB2 50 4.376 2.058 1.290 + 3TYR HB3 51 4.301 1.903 1.342 + 3TYR HD1 52 4.391 1.749 1.521 + 3TYR HD2 53 4.554 2.139 1.362 + 3TYR HE1 54 4.640 1.710 1.692 + 3TYR HE2 55 4.778 2.096 1.527 + 3TYR HH 56 4.892 1.942 1.631 + 4ILE N 57 4.222 1.740 1.175 + 4ILE CA 58 4.168 1.551 1.194 + 4ILE C 59 4.296 1.483 1.031 + 4ILE O 60 4.284 1.394 1.046 + 4ILE CB 61 4.002 1.544 1.101 + 4ILE CG1 62 3.904 1.655 1.236 + 4ILE CG2 63 4.019 1.370 1.135 + 4ILE CD1 64 3.953 1.684 1.388 + 4ILE H 65 4.149 1.761 1.090 + 4ILE HA 66 4.177 1.534 1.273 + 4ILE HB 67 4.017 1.575 1.008 + 4ILE HG12 68 3.985 1.739 1.183 + 4ILE HG13 69 3.854 1.632 1.205 + 4ILE HG21 70 3.981 1.325 1.052 + 4ILE HG22 71 3.978 1.396 1.265 + 4ILE HG23 72 3.878 1.404 1.148 + 4ILE HD11 73 3.930 1.559 1.392 + 4ILE HD12 74 4.081 1.662 1.356 + 4ILE HD13 75 3.865 1.712 1.430 + 5GLN N 76 4.309 1.538 0.924 + 5GLN CA 77 4.342 1.488 0.791 + 5GLN C 78 4.511 1.503 0.837 + 5GLN O 79 4.552 1.368 0.770 + 5GLN CB 80 4.368 1.593 0.701 + 5GLN CG 81 4.300 1.504 0.516 + 5GLN CD 82 4.187 1.440 0.499 + 5GLN OE1 83 4.168 1.296 0.577 + 5GLN NE2 84 4.135 1.480 0.489 + 5GLN H 85 4.250 1.641 0.915 + 5GLN HA 86 4.330 1.381 0.797 + 5GLN HB2 87 4.253 1.634 0.703 + 5GLN HB3 88 4.419 1.668 0.686 + 5GLN HG2 89 4.332 1.572 0.468 + 5GLN HG3 90 4.399 1.399 0.591 + 5GLN HE21 91 4.155 1.592 0.462 + 5GLN HE22 92 4.020 1.436 0.473 + 6TRP N 93 4.552 1.607 0.937 + 6TRP CA 94 4.702 1.555 0.966 + 6TRP C 95 4.711 1.448 1.090 + 6TRP O 96 4.809 1.350 1.076 + 6TRP CB 97 4.758 1.685 1.051 + 6TRP CG 98 4.876 1.655 1.127 + 6TRP CD1 99 4.998 1.687 1.037 + 6TRP CD2 100 4.896 1.681 1.238 + 6TRP NE1 101 5.077 1.635 1.151 + 6TRP CE2 102 5.086 1.671 1.308 + 6TRP CE3 103 4.869 1.653 1.391 + 6TRP CZ2 104 5.114 1.646 1.379 + 6TRP CZ3 105 4.898 1.617 1.498 + 6TRP CH2 106 5.031 1.616 1.513 + 6TRP H 107 4.504 1.640 0.980 + 6TRP HA 108 4.773 1.545 0.943 + 6TRP HB2 109 4.702 1.775 0.980 + 6TRP HB3 110 4.659 1.703 1.114 + 6TRP HD1 111 4.973 1.689 0.930 + 6TRP HE1 112 5.181 1.660 1.112 + 6TRP HE3 113 4.755 1.669 1.356 + 6TRP HZ2 114 5.211 1.647 1.402 + 6TRP HZ3 115 4.820 1.598 1.551 + 6TRP HH2 116 5.076 1.658 1.578 + 7LEU N 117 4.602 1.411 1.218 + 7LEU CA 118 4.591 1.307 1.275 + 7LEU C 119 4.573 1.163 1.239 + 7LEU O 120 4.658 1.044 1.255 + 7LEU CB 121 4.503 1.340 1.394 + 7LEU CG 122 4.540 1.434 1.509 + 7LEU CD1 123 4.423 1.493 1.628 + 7LEU CD2 124 4.668 1.432 1.546 + 7LEU H 125 4.535 1.446 1.193 + 7LEU HA 126 4.712 1.291 1.369 + 7LEU HB2 127 4.376 1.376 1.372 + 7LEU HB3 128 4.484 1.249 1.426 + 7LEU HG 129 4.503 1.544 1.435 + 7LEU HD11 130 4.290 1.475 1.483 + 7LEU HD12 131 4.410 1.359 1.637 + 7LEU HD13 132 4.456 1.543 1.661 + 7LEU HD21 133 4.657 1.302 1.651 + 7LEU HD22 134 4.733 1.397 1.528 + 7LEU HD23 135 4.682 1.525 1.688 + 8LYS N 136 4.505 1.134 1.124 + 8LYS CA 137 4.456 1.049 1.046 + 8LYS C 138 4.570 0.972 0.975 + 8LYS O 139 4.604 0.857 0.960 + 8LYS CB 140 4.343 1.018 0.978 + 8LYS CG 141 4.360 1.105 0.847 + 8LYS CD 142 4.412 0.997 0.725 + 8LYS CE 143 4.422 1.072 0.628 + 8LYS NZ 144 4.285 1.095 0.504 + 8LYS H 145 4.454 1.193 1.084 + 8LYS HA 146 4.413 0.949 1.138 + 8LYS HB2 147 4.309 0.930 0.924 + 8LYS HB3 148 4.314 1.068 1.010 + 8LYS HG2 149 4.263 1.182 0.772 + 8LYS HG3 150 4.427 1.181 0.875 + 8LYS HD2 151 4.490 0.946 0.754 + 8LYS HD3 152 4.346 0.927 0.711 + 8LYS HE2 153 4.407 1.179 0.638 + 8LYS HE3 154 4.502 1.059 0.532 + 8LYS HZ1 155 4.315 0.963 0.456 + 8LYS HZ2 156 4.225 1.112 0.529 + 8LYS HZ3 157 4.316 1.052 0.399 + 9ASP N 158 4.689 1.034 0.917 + 9ASP CA 159 4.778 1.023 0.885 + 9ASP C 160 4.878 0.980 1.015 + 9ASP O 161 5.015 0.913 0.971 + 9ASP CB 162 4.866 1.158 0.838 + 9ASP CG 163 4.813 1.118 0.688 + 9ASP OD1 164 4.719 1.085 0.664 + 9ASP OD2 165 4.908 1.117 0.588 + 9ASP H 166 4.668 1.144 0.949 + 9ASP HA 167 4.818 0.909 0.831 + 9ASP HB2 168 4.835 1.205 0.864 + 9ASP HB3 169 4.962 1.135 0.854 + 10GLY N 170 4.920 0.987 1.153 + 10GLY CA 171 4.986 0.965 1.244 + 10GLY C 172 5.038 1.077 1.332 + 10GLY O 173 5.130 1.048 1.410 + 10GLY H 174 4.777 0.995 1.169 + 10GLY HA2 175 4.914 0.908 1.321 + 10GLY HA3 176 5.037 0.880 1.211 + 11GLY N 177 4.958 1.189 1.304 + 11GLY CA 178 5.040 1.318 1.366 + 11GLY C 179 5.175 1.358 1.360 + 11GLY O 180 5.238 1.337 1.263 + 11GLY H 181 4.912 1.220 1.227 + 11GLY HA2 182 4.969 1.399 1.300 + 11GLY HA3 183 4.991 1.311 1.449 + 12PRO N 184 5.258 1.363 1.466 + 12PRO CA 185 5.381 1.358 1.456 + 12PRO C 186 5.472 1.264 1.379 + 12PRO O 187 5.576 1.254 1.340 + 12PRO CB 188 5.438 1.362 1.644 + 12PRO CG 189 5.333 1.420 1.709 + 12PRO CD 190 5.219 1.313 1.601 + 12PRO HA 191 5.424 1.454 1.448 + 12PRO HB2 192 5.458 1.277 1.638 + 12PRO HB3 193 5.501 1.417 1.612 + 12PRO HG2 194 5.343 1.387 1.826 + 12PRO HG3 195 5.313 1.532 1.639 + 12PRO HD2 196 5.193 1.226 1.653 + 12PRO HD3 197 5.102 1.384 1.622 + 13SER N 198 5.409 1.143 1.436 + 13SER CA 199 5.460 0.986 1.377 + 13SER C 200 5.441 1.001 1.192 + 13SER O 201 5.442 0.882 1.188 + 13SER CB 202 5.458 0.849 1.456 + 13SER OG 203 5.447 0.852 1.595 + 13SER H 204 5.310 1.096 1.494 + 13SER HA 205 5.564 0.980 1.409 + 13SER HB2 206 5.279 0.826 1.468 + 13SER HB3 207 3.472 4.208 1.386 + 13SER HG 208 3.528 4.340 1.603 + 14SER N 209 5.456 1.067 1.102 + 14SER CA 210 5.413 1.033 0.981 + 14SER C 211 5.547 1.127 0.907 + 14SER O 212 5.502 1.231 0.782 + 14SER CB 213 5.288 1.080 0.955 + 14SER OG 214 5.227 1.054 0.867 + 14SER H 215 5.427 1.152 1.186 + 14SER HA 216 5.398 1.007 0.937 + 14SER HB2 217 5.180 1.062 1.050 + 14SER HB3 218 5.226 1.228 0.969 + 14SER HG 219 5.129 0.975 0.913 + 15GLY N 220 5.621 1.209 0.996 + 15GLY CA 221 5.673 1.282 0.901 + 15GLY C 222 5.699 1.369 0.863 + 15GLY O 223 5.731 1.466 0.790 + 15GLY H 224 5.627 1.161 1.059 + 15GLY HA2 225 5.786 1.319 0.972 + 15GLY HA3 226 5.729 1.198 0.863 + 16ARG N 227 5.559 1.487 0.945 + 16ARG CA 228 5.484 1.622 0.872 + 16ARG C 229 5.447 1.683 1.011 + 16ARG O 230 5.404 1.617 1.127 + 16ARG CB 231 5.341 1.571 0.802 + 16ARG CG 232 5.246 1.491 0.882 + 16ARG CD 233 5.157 1.443 0.780 + 16ARG NE 234 5.179 1.338 0.682 + 16ARG CZ 235 5.300 1.326 0.584 + 16ARG NH1 236 5.310 1.452 0.487 + 16ARG NH2 237 5.256 1.196 0.533 + 16ARG H 238 5.514 1.412 1.033 + 16ARG HA 239 5.513 1.664 0.823 + 16ARG HB2 240 5.348 1.692 0.768 + 16ARG HB3 241 5.387 1.539 0.712 + 16ARG HG2 242 5.344 1.403 0.871 + 16ARG HG3 243 5.198 1.509 0.956 + 16ARG HD2 244 5.079 1.427 0.819 + 16ARG HD3 245 5.188 1.517 0.669 + 16ARG HE 246 5.147 1.241 0.687 + 16ARG HH11 247 5.291 1.494 0.548 + 16ARG HH12 248 5.350 1.408 0.409 + 16ARG HH21 249 5.252 1.116 0.578 + 16ARG HH22 250 3.298 2.304 3.639 + 17PRO N 251 5.440 1.818 1.013 + 17PRO CA 252 5.486 1.910 1.156 + 17PRO C 253 5.294 1.963 1.173 + 17PRO O 254 5.194 1.883 1.035 + 17PRO CB 255 5.515 2.042 1.131 + 17PRO CG 256 5.503 2.064 0.975 + 17PRO CD 257 5.562 1.866 0.910 + 17PRO HA 258 5.467 1.847 1.198 + 17PRO HB2 259 5.448 2.106 1.118 + 17PRO HB3 260 5.620 2.038 1.156 + 17PRO HG2 261 5.433 2.088 0.906 + 17PRO HG3 262 5.654 2.106 0.934 + 17PRO HD2 263 5.502 1.832 0.811 + 17PRO HD3 264 5.650 1.894 0.896 + 18PRO N 265 5.201 1.965 1.253 + 18PRO CA 266 5.080 1.991 1.277 + 18PRO C 267 5.017 2.149 1.187 + 18PRO O 268 5.134 2.252 1.188 + 18PRO CB 269 5.039 2.044 1.392 + 18PRO CG 270 5.205 2.060 1.449 + 18PRO CD 271 5.298 1.963 1.389 + 18PRO HA 272 5.051 1.935 1.216 + 18PRO HB2 273 4.945 2.068 1.428 + 18PRO HB3 274 5.044 1.947 1.471 + 18PRO HG2 275 5.229 2.167 1.442 + 18PRO HG3 276 5.203 2.014 1.628 + 18PRO HD2 277 5.390 2.075 1.365 + 18PRO HD3 278 5.342 1.882 1.460 + 19PRO N 279 4.947 2.092 1.082 + 19PRO CA 280 4.893 2.264 1.053 + 19PRO C 281 4.825 2.373 1.161 + 19PRO O 282 4.753 2.324 1.252 + 19PRO CB 283 4.752 2.211 0.937 + 19PRO CG 284 4.729 2.090 1.047 + 19PRO CD 285 4.835 2.061 1.105 + 19PRO HA 286 4.949 2.296 0.989 + 19PRO HB2 287 4.692 2.273 0.990 + 19PRO HB3 288 4.789 2.162 0.877 + 19PRO HG2 289 4.656 2.136 1.144 + 19PRO HG3 290 4.631 2.019 0.955 + 19PRO HD2 291 4.795 1.973 1.233 + 19PRO HD3 292 4.897 1.923 1.023 + 20SER N 293 4.918 2.496 1.142 + 20SER CA 294 4.893 2.589 1.218 + 20SER C 295 4.752 2.670 1.161 + 20SER O 296 4.747 2.693 1.043 + 20SER CB 297 4.962 2.728 1.241 + 20SER OG 298 5.054 2.632 1.295 + 20SER OXT 299 4.623 2.683 1.243 + 20SER H 300 4.980 2.453 1.088 + 20SER HA 301 4.825 2.590 1.339 + 20SER HB2 302 4.974 2.728 1.116 + 20SER HB3 303 4.932 2.765 1.309 + 20SER HG 304 5.036 2.585 1.377 + 21BEN C1 305 4.766 2.605 3.151 + 21BEN C2 306 4.837 2.518 3.266 + 21BEN C3 307 4.990 2.568 3.323 + 21BEN C4 308 4.969 2.672 3.243 + 21BEN C5 309 4.976 2.738 3.146 + 21BEN C6 310 4.815 2.713 3.103 + 21BEN C7 311 4.642 2.583 3.078 + 21BEN N1 312 4.608 2.433 3.162 + 21BEN N2 313 4.588 2.601 3.004 + 4.00000 3.46410 3.26599 0.00000 0.00000 2.00000 0.00000 2.00000 1.15470 diff --git a/regtest/basic/rt-molinfo-whole-ligand/warnings.reference b/regtest/basic/rt-molinfo-whole-ligand/warnings.reference new file mode 100644 index 0000000000..99de63f898 --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-ligand/warnings.reference @@ -0,0 +1,4 @@ +# out_sep +Action WHOLEMOLECULES +# out +Action WHOLEMOLECULES diff --git a/regtest/basic/rt-molinfo-whole-ligand/whole.xyz.reference b/regtest/basic/rt-molinfo-whole-ligand/whole.xyz.reference new file mode 100644 index 0000000000..485041d7c1 --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-ligand/whole.xyz.reference @@ -0,0 +1,945 @@ +313 + 4.000 0.000 0.000 2.000 3.464 0.000 2.000 1.155 3.266 +N 5.100 1.565 3.211 +CA 5.129 1.466 3.105 +C 5.278 1.449 3.077 +O 5.326 1.338 3.091 +CB 5.046 1.492 2.977 +CG 4.898 1.466 3.005 +OD1 4.863 1.423 3.114 +ND2 4.809 1.493 2.912 +H1 5.157 1.549 3.293 +H2 5.116 1.660 3.177 +H3 5.002 1.557 3.237 +HA 5.097 1.369 3.142 +HB2 5.059 1.594 2.947 +HB3 5.079 1.425 2.898 +HD21 4.833 1.532 2.822 +HD22 4.714 1.471 2.937 +N 5.352 1.556 3.044 +CA 5.497 1.553 3.021 +C 5.576 1.471 3.126 +O 5.651 1.380 3.090 +CB 5.549 1.698 3.004 +CG 5.510 1.798 3.117 +CD1 5.629 1.833 3.206 +CD2 5.455 1.928 3.058 +H 5.308 1.645 3.027 +HA 5.515 1.502 2.926 +HB2 5.656 1.694 2.999 +HB3 5.509 1.734 2.910 +HG 5.433 1.755 3.181 +HD11 5.669 1.743 3.252 +HD12 5.706 1.883 3.148 +HD13 5.597 1.901 3.286 +HD21 5.529 1.974 2.993 +HD22 5.364 1.907 3.001 +HD23 5.431 1.997 3.138 +N 5.554 1.498 3.255 +CA 5.621 1.427 3.365 +C 5.580 1.279 3.374 +O 5.661 1.194 3.411 +CB 5.593 1.500 3.497 +CG 5.707 1.487 3.595 +CD1 5.715 1.375 3.680 +CD2 5.808 1.586 3.600 +CE1 5.824 1.361 3.768 +CE2 5.917 1.572 3.687 +CZ 5.926 1.458 3.771 +OH 6.033 1.441 3.853 +H 5.496 1.578 3.278 +HA 5.728 1.430 3.346 +HB2 5.578 1.604 3.476 +HB3 5.501 1.463 3.541 +HD1 5.638 1.299 3.677 +HD2 5.802 1.673 3.536 +HE1 5.832 1.275 3.833 +HE2 5.993 1.648 3.690 +HH 6.109 1.493 3.823 +N 5.456 1.246 3.335 +CA 5.404 1.108 3.328 +C 5.481 1.031 3.219 +O 5.528 0.920 3.244 +CB 5.251 1.107 3.301 +CG1 5.170 1.207 3.386 +CG2 5.194 0.965 3.317 +CD1 5.188 1.194 3.538 +H 5.399 1.319 3.295 +HA 5.423 1.059 3.423 +HB 5.234 1.134 3.197 +HG12 5.200 1.306 3.358 +HG13 5.064 1.195 3.363 +HG21 5.239 0.897 3.243 +HG22 5.214 0.926 3.417 +HG23 5.086 0.966 3.300 +HD11 5.159 1.095 3.571 +HD12 5.292 1.214 3.566 +HD13 5.124 1.268 3.588 +N 5.499 1.093 3.102 +CA 5.578 1.036 2.992 +C 5.727 1.021 3.027 +O 5.791 0.929 2.978 +CB 5.561 1.121 2.865 +CG 5.565 1.036 2.737 +CD 5.432 0.967 2.708 +OE1 5.413 0.849 2.733 +NE2 5.337 1.038 2.651 +H 5.457 1.185 3.090 +HA 5.538 0.937 2.972 +HB2 5.466 1.172 2.869 +HB3 5.641 1.196 2.861 +HG2 5.590 1.099 2.654 +HG3 5.644 0.961 2.746 +HE21 5.351 1.134 2.626 +HE22 5.251 0.989 2.633 +N 5.782 1.107 3.114 +CA 5.918 1.090 3.167 +C 5.927 0.977 3.271 +O 6.019 0.895 3.266 +CB 5.968 1.223 3.225 +CG 6.105 1.218 3.286 +CD1 6.222 1.219 3.218 +CD2 6.141 1.210 3.427 +NE1 6.327 1.209 3.308 +CE2 6.283 1.205 3.437 +CE3 6.068 1.206 3.548 +CZ2 6.350 1.198 3.560 +CZ3 6.134 1.197 3.672 +CH2 6.274 1.194 3.678 +H 5.727 1.187 3.142 +HA 5.985 1.062 3.085 +HB2 5.969 1.295 3.145 +HB3 5.898 1.257 3.301 +HD1 6.231 1.226 3.111 +HE1 6.426 1.207 3.282 +HE3 5.960 1.210 3.544 +HZ2 6.458 1.195 3.563 +HZ3 6.076 1.193 3.763 +HH2 6.323 1.189 3.775 +N 5.830 0.967 3.363 +CA 5.826 0.860 3.463 +C 5.805 0.721 3.401 +O 5.875 0.628 3.441 +CB 5.719 0.889 3.570 +CG 5.760 0.995 3.673 +CD1 5.642 1.021 3.768 +CD2 5.881 0.953 3.758 +H 5.758 1.040 3.366 +HA 5.923 0.855 3.511 +HB2 5.630 0.922 3.520 +HB3 5.698 0.796 3.624 +HG 5.784 1.088 3.622 +HD11 5.556 1.054 3.711 +HD12 5.617 0.930 3.822 +HD13 5.669 1.098 3.840 +HD21 5.863 0.854 3.802 +HD22 5.970 0.949 3.696 +HD23 5.898 1.025 3.838 +N 5.715 0.705 3.302 +CA 5.687 0.574 3.239 +C 5.810 0.510 3.173 +O 5.818 0.388 3.163 +CB 5.567 0.583 3.143 +CG 5.597 0.652 3.009 +CD 5.622 0.554 2.893 +CE 5.640 0.633 2.762 +NZ 5.534 0.605 2.664 +H 5.658 0.786 3.276 +HA 5.659 0.505 3.319 +HB2 5.533 0.484 3.123 +HB3 5.488 0.639 3.193 +HG2 5.513 0.714 2.983 +HG3 5.684 0.716 3.019 +HD2 5.710 0.497 2.913 +HD3 5.537 0.486 2.885 +HE2 5.640 0.738 2.785 +HE3 5.739 0.609 2.721 +HZ1 5.528 0.506 2.645 +HZ2 5.446 0.641 2.701 +HZ3 5.552 0.655 2.578 +N 5.907 0.592 3.131 +CA 6.036 0.551 3.076 +C 6.138 0.507 3.183 +O 6.244 0.456 3.147 +CB 6.093 0.669 2.994 +CG 6.057 0.662 2.845 +OD1 5.937 0.648 2.814 +OD2 6.153 0.671 2.765 +H 5.889 0.691 3.137 +HA 6.022 0.466 3.009 +HB2 6.054 0.761 3.034 +HB3 6.201 0.669 3.001 +N 6.108 0.525 3.313 +CA 6.196 0.491 3.426 +C 6.253 0.612 3.502 +O 6.339 0.594 3.587 +H 6.016 0.562 3.336 +HA2 6.138 0.432 3.497 +HA3 6.280 0.430 3.392 +N 6.207 0.735 3.472 +CA 6.252 0.857 3.539 +C 6.406 0.873 3.532 +O 6.461 0.870 3.422 +H 6.138 0.744 3.398 +HA2 6.206 0.942 3.490 +HA3 6.218 0.854 3.642 +N 6.477 0.888 3.646 +CA 6.623 0.900 3.647 +C 6.696 0.780 3.583 +O 6.804 0.797 3.527 +CB 6.664 0.915 3.794 +CG 6.536 0.958 3.865 +CD 6.426 0.892 3.782 +HA 6.651 0.991 3.593 +HB2 6.699 0.821 3.833 +HB3 6.743 0.989 3.807 +HG2 6.534 0.923 3.967 +HG3 6.526 1.067 3.859 +HD2 6.407 0.792 3.818 +HD3 6.334 0.949 3.791 +N 6.636 0.660 3.587 +CA 6.695 0.535 3.537 +C 6.680 0.516 3.385 +O 6.692 0.404 3.336 +CB 6.636 0.416 3.614 +OG 6.666 0.427 3.751 +H 6.543 0.653 3.628 +HA 6.802 0.537 3.557 +HB2 6.529 0.415 3.601 +HB3 6.678 0.323 3.576 +HG 6.760 0.414 3.763 +N 6.653 0.624 3.310 +CA 6.629 0.621 3.165 +C 6.723 0.712 3.084 +O 6.698 0.741 2.967 +CB 6.481 0.654 3.140 +OG 6.433 0.579 3.031 +H 6.641 0.712 3.359 +HA 6.646 0.520 3.129 +HB2 6.424 0.629 3.227 +HB3 6.468 0.760 3.121 +HG 6.361 0.521 3.068 +N 6.832 0.761 3.146 +CA 6.935 0.841 3.079 +C 6.888 0.980 3.035 +O 6.944 1.035 2.940 +H 6.847 0.732 3.242 +HA2 7.019 0.854 3.147 +HA3 6.970 0.788 2.991 +N 6.785 1.037 3.100 +CA 6.719 1.161 3.061 +C 6.675 1.244 3.183 +O 6.612 1.190 3.274 +CB 6.601 1.128 2.967 +CG 6.494 1.036 3.029 +CD 6.382 0.994 2.933 +NE 6.415 0.872 2.856 +CZ 6.476 0.862 2.739 +NH1 6.519 0.966 2.673 +NH2 6.493 0.743 2.685 +H 6.748 0.985 3.179 +HA 6.791 1.219 3.003 +HB2 6.553 1.221 2.939 +HB3 6.642 1.081 2.878 +HG2 6.544 0.947 3.063 +HG3 6.448 1.088 3.111 +HD2 6.293 0.976 2.990 +HD3 6.357 1.076 2.866 +HE 6.386 0.784 2.897 +HH11 6.505 1.057 2.714 +HH12 6.566 0.957 2.585 +HH21 6.455 0.664 2.734 +HH22 6.541 0.732 2.598 +N 6.705 1.376 3.188 +CA 6.668 1.462 3.301 +C 6.516 1.486 3.306 +O 6.448 1.469 3.204 +CB 6.745 1.592 3.278 +CG 6.757 1.600 3.126 +CD 6.772 1.454 3.085 +HA 6.700 1.416 3.394 +HB2 6.691 1.676 3.317 +HB3 6.845 1.584 3.323 +HG2 6.670 1.644 3.083 +HG3 6.844 1.659 3.096 +HD2 6.725 1.437 2.990 +HD3 6.877 1.427 3.081 +N 6.461 1.527 3.422 +CA 6.318 1.556 3.435 +C 6.280 1.684 3.358 +O 6.358 1.779 3.354 +CB 6.293 1.572 3.585 +CG 6.428 1.619 3.639 +CD 6.529 1.548 3.549 +HA 6.262 1.471 3.398 +HB2 6.217 1.645 3.604 +HB3 6.268 1.475 3.628 +HG2 6.438 1.725 3.632 +HG3 6.442 1.591 3.744 +HD2 6.616 1.609 3.535 +HD3 6.556 1.451 3.592 +N 6.159 1.689 3.300 +CA 6.108 1.807 3.231 +C 6.061 1.914 3.332 +O 5.977 1.885 3.418 +CB 5.995 1.754 3.143 +CG 5.938 1.638 3.225 +CD 6.061 1.581 3.294 +HA 6.186 1.849 3.167 +HB2 5.920 1.830 3.127 +HB3 6.036 1.716 3.050 +HG2 5.867 1.673 3.297 +HG3 5.888 1.564 3.162 +HD2 6.037 1.547 3.392 +HD3 6.102 1.499 3.233 +N 6.117 2.035 3.321 +CA 6.075 2.156 3.395 +C 5.949 2.219 3.335 +O 5.951 2.244 3.212 +CB 6.187 2.260 3.395 +OG 6.302 2.207 3.458 +OXT 5.856 2.243 3.414 +H 6.187 2.049 3.250 +HA 6.050 2.129 3.497 +HB2 6.211 2.287 3.294 +HB3 6.153 2.349 3.449 +HG 6.273 2.157 3.534 +C1 5.987 2.147 5.323 +C2 6.053 2.067 5.416 +C3 6.175 2.110 5.469 +C4 6.229 2.231 5.429 +C5 6.163 2.310 5.336 +C6 6.041 2.268 5.283 +C7 5.856 2.101 5.266 +N1 5.804 1.985 5.304 +N2 5.792 2.177 5.178 +313 + 4.000 0.000 0.000 2.000 3.464 0.000 2.000 1.155 3.266 +N 4.311 1.790 2.862 +CA 4.388 1.679 2.773 +C 4.481 1.666 2.737 +O 4.541 1.578 2.784 +CB 4.258 1.727 2.664 +CG 4.121 1.683 2.684 +OD1 4.028 1.674 2.800 +ND2 3.993 1.726 2.617 +H1 4.362 1.794 2.978 +H2 4.350 1.857 2.823 +H3 4.184 1.773 2.888 +HA 4.301 1.604 2.805 +HB2 4.226 1.808 2.638 +HB3 4.292 1.634 2.560 +HD21 4.039 1.769 2.550 +HD22 3.902 1.679 2.603 +N 4.536 1.806 2.764 +CA 4.723 1.806 2.691 +C 4.734 1.689 2.813 +O 4.880 1.599 2.794 +CB 4.719 1.961 2.682 +CG 4.732 2.046 2.812 +CD1 4.831 2.068 2.892 +CD2 4.615 2.164 2.755 +H 4.520 1.880 2.728 +HA 4.699 1.729 2.576 +HB2 4.864 1.924 2.657 +HB3 4.666 1.961 2.613 +HG 4.659 1.987 2.832 +HD11 4.889 1.991 2.946 +HD12 4.875 2.155 2.847 +HD13 4.785 2.136 2.951 +HD21 4.730 2.190 2.665 +HD22 4.572 2.148 2.646 +HD23 4.620 2.228 2.807 +N 4.760 1.715 2.899 +CA 4.800 1.653 3.077 +C 4.801 1.524 3.040 +O 4.864 1.425 3.099 +CB 4.789 1.721 3.198 +CG 4.928 1.669 3.255 +CD1 4.886 1.616 3.363 +CD2 5.001 1.817 3.313 +CE1 5.003 1.563 3.462 +CE2 5.116 1.826 3.347 +CZ 5.113 1.678 3.462 +OH 5.236 1.654 3.498 +H 4.704 1.836 2.940 +HA 4.944 1.655 3.041 +HB2 4.773 1.843 3.168 +HB3 4.681 1.699 3.206 +HD1 4.803 1.524 3.354 +HD2 5.045 1.903 3.210 +HE1 5.037 1.509 3.501 +HE2 5.172 1.883 3.331 +HH 5.275 1.732 3.509 +N 4.659 1.511 3.049 +CA 4.595 1.324 3.029 +C 4.671 1.265 2.866 +O 4.716 1.126 2.923 +CB 4.445 1.335 2.957 +CG1 4.337 1.465 3.068 +CG2 4.379 1.189 2.979 +CD1 4.391 1.428 3.201 +H 4.588 1.567 2.968 +HA 4.631 1.275 3.118 +HB 4.431 1.361 2.849 +HG12 4.399 1.540 3.039 +HG13 4.284 1.439 3.055 +HG21 4.467 1.102 2.921 +HG22 4.421 1.130 3.072 +HG23 4.308 1.196 3.008 +HD11 4.390 1.320 3.257 +HD12 4.516 1.463 3.270 +HD13 4.282 1.474 3.271 +N 4.683 1.323 2.779 +CA 4.770 1.262 2.648 +C 4.931 1.256 2.716 +O 4.996 1.201 2.592 +CB 4.773 1.373 2.550 +CG 4.772 1.255 2.407 +CD 4.636 1.219 2.395 +OE1 4.593 1.108 2.408 +NE2 4.547 1.275 2.304 +H 4.655 1.403 2.718 +HA 4.706 1.185 2.645 +HB2 4.669 1.408 2.510 +HB3 4.860 1.454 2.502 +HG2 4.797 1.357 2.346 +HG3 4.832 1.194 2.439 +HE21 4.555 1.360 2.278 +HE22 4.464 1.219 2.290 +N 4.973 1.398 2.778 +CA 5.108 1.347 2.870 +C 5.114 1.205 2.923 +O 5.224 1.083 2.945 +CB 5.131 1.455 2.875 +CG 5.324 1.462 2.960 +CD1 5.433 1.439 2.893 +CD2 5.314 1.447 3.112 +NE1 5.543 1.460 3.003 +CE2 5.510 1.439 3.101 +CE3 5.262 1.464 3.203 +CZ2 5.563 1.433 3.228 +CZ3 5.345 1.427 3.344 +CH2 5.437 1.453 3.363 +H 4.965 1.400 2.807 +HA 5.183 1.280 2.727 +HB2 5.172 1.510 2.852 +HB3 5.108 1.470 2.966 +HD1 5.466 1.477 2.744 +HE1 5.660 1.445 2.975 +HE3 5.159 1.417 3.205 +HZ2 5.656 1.409 3.236 +HZ3 5.284 1.466 3.399 +HH2 5.499 1.436 3.470 +N 5.033 1.186 3.016 +CA 5.027 1.088 3.137 +C 5.035 0.937 3.074 +O 5.028 0.888 3.098 +CB 4.915 1.129 3.204 +CG 4.935 1.205 3.342 +CD1 4.851 1.233 3.433 +CD2 5.080 1.185 3.435 +H 4.973 1.262 3.063 +HA 5.135 1.074 3.204 +HB2 4.856 1.144 3.193 +HB3 4.913 1.046 3.296 +HG 5.001 1.345 3.312 +HD11 4.766 1.268 3.391 +HD12 4.855 1.121 3.493 +HD13 4.876 1.354 3.510 +HD21 5.072 1.103 3.487 +HD22 5.168 1.179 3.373 +HD23 5.073 1.262 3.489 +N 4.895 0.929 3.029 +CA 4.891 0.801 2.905 +C 5.051 0.698 2.853 +O 5.005 0.623 2.862 +CB 4.771 0.789 2.821 +CG 4.795 0.871 2.673 +CD 4.813 0.803 2.542 +CE 4.855 0.873 2.400 +NZ 4.798 0.857 2.343 +H 4.877 1.006 2.918 +HA 4.880 0.728 3.011 +HB2 4.710 0.720 2.813 +HB3 4.676 0.844 2.844 +HG2 4.679 0.968 2.667 +HG3 4.893 0.931 2.692 +HD2 4.939 0.733 2.547 +HD3 4.771 0.750 2.575 +HE2 4.865 1.015 2.436 +HE3 4.979 0.875 2.401 +HZ1 4.764 0.717 2.317 +HZ2 4.661 0.873 2.365 +HZ3 4.738 0.860 2.250 +N 5.118 0.819 2.773 +CA 5.222 0.776 2.789 +C 5.313 0.752 2.860 +O 5.476 0.728 2.838 +CB 5.313 0.871 2.676 +CG 5.276 0.913 2.504 +OD1 5.136 0.876 2.479 +OD2 5.347 0.862 2.455 +H 5.118 0.927 2.788 +HA 5.250 0.703 2.634 +HB2 5.273 0.988 2.737 +HB3 5.379 0.887 2.684 +N 5.329 0.730 2.963 +CA 5.400 0.708 3.140 +C 5.455 0.821 3.213 +O 5.552 0.804 3.278 +H 5.243 0.768 3.017 +HA2 5.327 0.687 3.163 +HA3 5.492 0.640 3.096 +N 5.428 0.995 3.158 +CA 5.404 1.066 3.205 +C 5.587 1.117 3.189 +O 5.688 1.151 3.099 +H 5.336 0.961 3.050 +HA2 5.416 1.196 3.148 +HA3 5.412 1.083 3.322 +N 5.686 1.125 3.329 +CA 5.838 1.124 3.302 +C 5.884 0.998 3.257 +O 6.010 1.019 3.183 +CB 5.839 1.136 3.471 +CG 5.743 1.199 3.539 +CD 5.625 1.135 3.463 +HA 5.868 1.219 3.298 +HB2 5.885 1.045 3.529 +HB3 5.939 1.212 3.511 +HG2 5.701 1.181 3.655 +HG3 5.725 1.254 3.513 +HD2 5.605 1.030 3.522 +HD3 5.537 1.200 3.484 +N 5.825 0.929 3.280 +CA 5.879 0.769 3.206 +C 5.867 0.705 3.073 +O 5.884 0.666 3.009 +CB 5.833 0.663 3.280 +OG 5.887 0.627 3.417 +H 5.753 0.868 3.307 +HA 5.991 0.759 3.243 +HB2 5.739 0.685 3.304 +HB3 5.911 0.534 3.222 +HG 5.970 0.640 3.432 +N 5.886 0.854 3.000 +CA 5.857 0.855 2.830 +C 5.880 0.929 2.760 +O 5.907 0.975 2.676 +CB 5.667 0.924 2.797 +OG 5.599 0.804 2.698 +H 5.837 0.921 3.041 +HA 5.831 0.712 2.819 +HB2 5.661 0.896 2.884 +HB3 5.656 1.019 2.810 +HG 5.584 0.745 2.757 +N 6.017 0.971 2.831 +CA 6.165 1.067 2.736 +C 6.064 1.188 2.685 +O 6.112 1.268 2.619 +H 6.052 0.957 2.938 +HA2 6.203 1.070 2.797 +HA3 6.159 1.010 2.672 +N 5.984 1.282 2.766 +CA 5.930 1.394 2.711 +C 5.879 1.493 2.869 +O 5.827 1.449 2.960 +CB 5.806 1.340 2.611 +CG 5.696 1.310 2.695 +CD 5.591 1.209 2.619 +NE 5.607 1.082 2.554 +CZ 5.690 1.073 2.403 +NH1 5.707 1.185 2.382 +NH2 5.672 0.973 2.392 +H 5.946 1.191 2.841 +HA 6.020 1.452 2.657 +HB2 5.764 1.459 2.619 +HB3 5.851 1.276 2.547 +HG2 5.716 1.190 2.736 +HG3 5.669 1.306 2.781 +HD2 5.521 1.257 2.684 +HD3 5.555 1.326 2.560 +HE 5.578 0.996 2.551 +HH11 5.653 1.285 2.423 +HH12 5.783 1.183 2.330 +HH21 5.660 0.904 2.394 +HH22 5.726 0.969 2.277 +N 5.866 1.586 2.842 +CA 5.876 1.689 2.918 +C 5.731 1.689 2.995 +O 5.664 1.714 2.905 +CB 5.966 1.810 2.911 +CG 5.950 1.839 2.789 +CD 5.984 1.690 2.734 +HA 5.888 1.669 3.086 +HB2 5.898 1.953 2.996 +HB3 6.033 1.802 2.992 +HG2 5.863 1.870 2.785 +HG3 6.047 1.898 2.771 +HD2 5.906 1.706 2.693 +HD3 6.066 1.671 2.751 +N 5.677 1.747 3.086 +CA 5.482 1.791 3.065 +C 5.474 1.926 3.003 +O 5.589 1.983 3.023 +CB 5.525 1.777 3.266 +CG 5.606 1.821 3.312 +CD 5.716 1.792 3.223 +HA 5.454 1.717 3.068 +HB2 5.404 1.879 3.249 +HB3 5.441 1.695 3.284 +HG2 5.646 1.944 3.291 +HG3 5.649 1.808 3.420 +HD2 5.808 1.838 3.199 +HD3 5.775 1.669 3.308 +N 5.401 1.932 2.978 +CA 5.315 2.045 2.888 +C 5.240 2.121 3.075 +O 5.171 2.153 3.114 +CB 5.197 1.974 2.800 +CG 5.162 1.840 2.882 +CD 5.282 1.773 2.980 +HA 5.389 2.089 2.818 +HB2 5.128 2.105 2.796 +HB3 5.263 1.983 2.723 +HG2 5.042 1.905 2.950 +HG3 5.130 1.776 2.850 +HD2 5.213 1.782 3.063 +HD3 5.303 1.706 2.914 +N 5.289 2.256 2.960 +CA 5.272 2.382 3.032 +C 5.183 2.423 3.004 +O 5.190 2.449 2.885 +CB 5.406 2.497 3.051 +OG 5.481 2.457 3.134 +OXT 5.059 2.493 3.067 +H 5.397 2.281 2.950 +HA 5.229 2.360 3.171 +HB2 5.416 2.544 2.977 +HB3 5.362 2.616 3.100 +HG 5.475 2.383 3.229 +C1 5.375 2.252 5.016 +C2 5.393 2.217 5.123 +C3 5.539 2.228 5.184 +C4 5.596 2.366 5.132 +C5 5.507 2.468 5.069 +C6 5.399 2.386 4.988 +C7 5.183 2.187 5.004 +N1 5.157 2.106 5.029 +N2 5.157 2.309 4.905 +313 + 4.000 0.000 0.000 2.000 3.464 0.000 2.000 1.155 3.266 +N 3.872 2.056 1.020 +CA 3.882 1.937 0.958 +C 4.026 1.883 0.908 +O 4.097 1.808 0.937 +CB 3.828 1.948 0.813 +CG 3.655 1.922 0.839 +OD1 3.659 1.895 0.935 +ND2 3.583 1.948 0.770 +H1 3.906 1.978 1.121 +H2 3.889 2.114 1.015 +H3 3.803 2.004 1.059 +HA 3.860 1.844 0.961 +HB2 3.821 2.035 0.777 +HB3 3.866 1.850 0.736 +HD21 3.594 1.979 0.660 +HD22 3.494 1.916 0.794 +N 4.152 2.021 0.869 +CA 4.307 2.010 0.846 +C 4.381 1.917 0.994 +O 4.472 1.833 0.971 +CB 4.342 2.156 0.807 +CG 4.251 2.280 0.963 +CD1 4.418 2.286 1.030 +CD2 4.228 2.359 0.893 +H 4.060 2.074 0.854 +HA 4.282 1.922 0.768 +HB2 4.445 2.138 0.843 +HB3 4.255 2.194 0.738 +HG 4.208 2.210 1.006 +HD11 4.435 2.183 1.103 +HD12 4.488 2.378 1.016 +HD13 4.385 2.361 1.122 +HD21 4.295 2.413 0.808 +HD22 4.162 2.357 0.813 +HD23 4.223 2.449 0.984 +N 4.335 1.947 1.093 +CA 4.371 1.863 1.203 +C 4.331 1.723 1.206 +O 4.463 1.629 1.258 +CB 4.361 1.984 1.316 +CG 4.438 1.936 1.392 +CD1 4.486 1.863 1.533 +CD2 4.574 2.041 1.422 +CE1 4.594 1.791 1.583 +CE2 4.694 2.044 1.532 +CZ 4.703 1.884 1.566 +OH 4.830 1.880 1.668 +H 4.295 2.016 1.103 +HA 4.563 1.904 1.193 +HB2 4.376 2.058 1.290 +HB3 4.301 1.903 1.342 +HD1 4.391 1.749 1.521 +HD2 4.554 2.139 1.362 +HE1 4.640 1.710 1.692 +HE2 4.778 2.096 1.527 +HH 4.892 1.942 1.631 +N 4.222 1.740 1.175 +CA 4.168 1.551 1.194 +C 4.296 1.483 1.031 +O 4.284 1.394 1.046 +CB 4.002 1.544 1.101 +CG1 3.904 1.655 1.236 +CG2 4.019 1.370 1.135 +CD1 3.953 1.684 1.388 +H 4.149 1.761 1.090 +HA 4.177 1.534 1.273 +HB 4.017 1.575 1.008 +HG12 3.985 1.739 1.183 +HG13 3.854 1.632 1.205 +HG21 3.981 1.325 1.052 +HG22 3.978 1.396 1.265 +HG23 3.878 1.404 1.148 +HD11 3.930 1.559 1.392 +HD12 4.081 1.662 1.356 +HD13 3.865 1.712 1.430 +N 4.309 1.538 0.924 +CA 4.342 1.488 0.791 +C 4.511 1.503 0.837 +O 4.552 1.368 0.770 +CB 4.368 1.593 0.701 +CG 4.300 1.504 0.516 +CD 4.187 1.440 0.499 +OE1 4.168 1.296 0.577 +NE2 4.135 1.480 0.489 +H 4.250 1.641 0.915 +HA 4.330 1.381 0.797 +HB2 4.253 1.634 0.703 +HB3 4.419 1.668 0.686 +HG2 4.332 1.572 0.468 +HG3 4.399 1.399 0.591 +HE21 4.155 1.592 0.462 +HE22 4.020 1.436 0.473 +N 4.552 1.607 0.937 +CA 4.702 1.555 0.966 +C 4.711 1.448 1.090 +O 4.809 1.350 1.076 +CB 4.758 1.685 1.051 +CG 4.876 1.655 1.127 +CD1 4.998 1.687 1.037 +CD2 4.896 1.681 1.238 +NE1 5.077 1.635 1.151 +CE2 5.086 1.671 1.308 +CE3 4.869 1.653 1.391 +CZ2 5.114 1.646 1.379 +CZ3 4.898 1.617 1.498 +CH2 5.031 1.616 1.513 +H 4.504 1.640 0.980 +HA 4.773 1.545 0.943 +HB2 4.702 1.775 0.980 +HB3 4.659 1.703 1.114 +HD1 4.973 1.689 0.930 +HE1 5.181 1.660 1.112 +HE3 4.755 1.669 1.356 +HZ2 5.211 1.647 1.402 +HZ3 4.820 1.598 1.551 +HH2 5.076 1.658 1.578 +N 4.602 1.411 1.218 +CA 4.591 1.307 1.275 +C 4.573 1.163 1.239 +O 4.658 1.044 1.255 +CB 4.503 1.340 1.394 +CG 4.540 1.434 1.509 +CD1 4.423 1.493 1.628 +CD2 4.668 1.432 1.546 +H 4.535 1.446 1.193 +HA 4.712 1.291 1.369 +HB2 4.376 1.376 1.372 +HB3 4.484 1.249 1.426 +HG 4.503 1.544 1.435 +HD11 4.290 1.475 1.483 +HD12 4.410 1.359 1.637 +HD13 4.456 1.543 1.661 +HD21 4.657 1.302 1.651 +HD22 4.733 1.397 1.528 +HD23 4.682 1.525 1.688 +N 4.505 1.134 1.124 +CA 4.456 1.049 1.046 +C 4.570 0.972 0.975 +O 4.604 0.857 0.960 +CB 4.343 1.018 0.978 +CG 4.360 1.105 0.847 +CD 4.412 0.997 0.725 +CE 4.422 1.072 0.628 +NZ 4.285 1.095 0.504 +H 4.454 1.193 1.084 +HA 4.413 0.949 1.138 +HB2 4.309 0.930 0.924 +HB3 4.314 1.068 1.010 +HG2 4.263 1.182 0.772 +HG3 4.427 1.181 0.875 +HD2 4.490 0.946 0.754 +HD3 4.346 0.927 0.711 +HE2 4.407 1.179 0.638 +HE3 4.502 1.059 0.532 +HZ1 4.315 0.963 0.456 +HZ2 4.225 1.112 0.529 +HZ3 4.316 1.052 0.399 +N 4.689 1.034 0.917 +CA 4.778 1.023 0.885 +C 4.878 0.980 1.015 +O 5.015 0.913 0.971 +CB 4.866 1.158 0.838 +CG 4.813 1.118 0.688 +OD1 4.719 1.085 0.664 +OD2 4.908 1.117 0.588 +H 4.668 1.144 0.949 +HA 4.818 0.909 0.831 +HB2 4.835 1.205 0.864 +HB3 4.962 1.135 0.854 +N 4.920 0.987 1.153 +CA 4.986 0.965 1.244 +C 5.038 1.077 1.332 +O 5.130 1.048 1.410 +H 4.777 0.995 1.169 +HA2 4.914 0.908 1.321 +HA3 5.037 0.880 1.211 +N 4.958 1.189 1.304 +CA 5.040 1.318 1.366 +C 5.175 1.358 1.360 +O 5.238 1.337 1.263 +H 4.912 1.220 1.227 +HA2 4.969 1.399 1.300 +HA3 4.991 1.311 1.449 +N 5.258 1.363 1.466 +CA 5.381 1.358 1.456 +C 5.472 1.264 1.379 +O 5.576 1.254 1.340 +CB 5.438 1.362 1.644 +CG 5.333 1.420 1.709 +CD 5.219 1.313 1.601 +HA 5.424 1.454 1.448 +HB2 5.458 1.277 1.638 +HB3 5.501 1.417 1.612 +HG2 5.343 1.387 1.826 +HG3 5.313 1.532 1.639 +HD2 5.193 1.226 1.653 +HD3 5.102 1.384 1.622 +N 5.409 1.143 1.436 +CA 5.460 0.986 1.377 +C 5.441 1.001 1.192 +O 5.442 0.882 1.188 +CB 5.458 0.849 1.456 +OG 5.447 0.852 1.595 +H 5.310 1.096 1.494 +HA 5.564 0.980 1.409 +HB2 5.279 0.826 1.468 +HB3 5.472 0.744 1.386 +HG 5.528 0.876 1.603 +N 5.456 1.067 1.102 +CA 5.413 1.033 0.981 +C 5.547 1.127 0.907 +O 5.502 1.231 0.782 +CB 5.288 1.080 0.955 +OG 5.227 1.054 0.867 +H 5.427 1.152 1.186 +HA 5.398 1.007 0.937 +HB2 5.180 1.062 1.050 +HB3 5.226 1.228 0.969 +HG 5.129 0.975 0.913 +N 5.621 1.209 0.996 +CA 5.673 1.282 0.901 +C 5.699 1.369 0.863 +O 5.731 1.466 0.790 +H 5.627 1.161 1.059 +HA2 5.786 1.319 0.972 +HA3 5.729 1.198 0.863 +N 5.559 1.487 0.945 +CA 5.484 1.622 0.872 +C 5.447 1.683 1.011 +O 5.404 1.617 1.127 +CB 5.341 1.571 0.802 +CG 5.246 1.491 0.882 +CD 5.157 1.443 0.780 +NE 5.179 1.338 0.682 +CZ 5.300 1.326 0.584 +NH1 5.310 1.452 0.487 +NH2 5.256 1.196 0.533 +H 5.514 1.412 1.033 +HA 5.513 1.664 0.823 +HB2 5.348 1.692 0.768 +HB3 5.387 1.539 0.712 +HG2 5.344 1.403 0.871 +HG3 5.198 1.509 0.956 +HD2 5.079 1.427 0.819 +HD3 5.188 1.517 0.669 +HE 5.147 1.241 0.687 +HH11 5.291 1.494 0.548 +HH12 5.350 1.408 0.409 +HH21 5.252 1.116 0.578 +HH22 5.298 1.149 0.373 +N 5.440 1.818 1.013 +CA 5.486 1.910 1.156 +C 5.294 1.963 1.173 +O 5.194 1.883 1.035 +CB 5.515 2.042 1.131 +CG 5.503 2.064 0.975 +CD 5.562 1.866 0.910 +HA 5.467 1.847 1.198 +HB2 5.448 2.106 1.118 +HB3 5.620 2.038 1.156 +HG2 5.433 2.088 0.906 +HG3 5.654 2.106 0.934 +HD2 5.502 1.832 0.811 +HD3 5.650 1.894 0.896 +N 5.201 1.965 1.253 +CA 5.080 1.991 1.277 +C 5.017 2.149 1.187 +O 5.134 2.252 1.188 +CB 5.039 2.044 1.392 +CG 5.205 2.060 1.449 +CD 5.298 1.963 1.389 +HA 5.051 1.935 1.216 +HB2 4.945 2.068 1.428 +HB3 5.044 1.947 1.471 +HG2 5.229 2.167 1.442 +HG3 5.203 2.014 1.628 +HD2 5.390 2.075 1.365 +HD3 5.342 1.882 1.460 +N 4.947 2.092 1.082 +CA 4.893 2.264 1.053 +C 4.825 2.373 1.161 +O 4.753 2.324 1.252 +CB 4.752 2.211 0.937 +CG 4.729 2.090 1.047 +CD 4.835 2.061 1.105 +HA 4.949 2.296 0.989 +HB2 4.692 2.273 0.990 +HB3 4.789 2.162 0.877 +HG2 4.656 2.136 1.144 +HG3 4.631 2.019 0.955 +HD2 4.795 1.973 1.233 +HD3 4.897 1.923 1.023 +N 4.918 2.496 1.142 +CA 4.893 2.589 1.218 +C 4.752 2.670 1.161 +O 4.747 2.693 1.043 +CB 4.962 2.728 1.241 +OG 5.054 2.632 1.295 +OXT 4.623 2.683 1.243 +H 4.980 2.453 1.088 +HA 4.825 2.590 1.339 +HB2 4.974 2.728 1.116 +HB3 4.932 2.765 1.309 +HG 5.036 2.585 1.377 +C1 4.766 2.605 3.151 +C2 4.837 2.518 3.266 +C3 4.990 2.568 3.323 +C4 4.969 2.672 3.243 +C5 4.976 2.738 3.146 +C6 4.815 2.713 3.103 +C7 4.642 2.583 3.078 +N1 4.608 2.433 3.162 +N2 4.588 2.601 3.004 diff --git a/regtest/basic/rt-molinfo-whole-membrane/Makefile b/regtest/basic/rt-molinfo-whole-membrane/Makefile new file mode 100644 index 0000000000..3703b27cea --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-membrane/Makefile @@ -0,0 +1 @@ +include ../../scripts/test.make diff --git a/regtest/basic/rt-molinfo-whole-membrane/config b/regtest/basic/rt-molinfo-whole-membrane/config new file mode 100644 index 0000000000..3bac19a409 --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-membrane/config @@ -0,0 +1,16 @@ +type=driver +# a small bilayer, continuous across the box, in one group and in separate groups. +# There is no warning, and the frames are made whole right. +arg="--plumed plumed.dat --igro traj.gro" + +function plumed_regtest_before() { + $valgrind $plumed driver --plumed plumed_sep.dat --igro traj.gro > out_sep 2> err_sep || return 1 +} + +# the WHOLEMOLECULES lines of the log and the warnings, up to the list of atoms +function plumed_regtest_after() { + for f in out_sep out; do + echo "# $f" + grep -E "^PLUMED: (Action WHOLEMOLECULES|WARNING for action MOLINFO)" $f | sed -e "s/^PLUMED: //" -e "s/\\. WHOLEMOLECULES will.*//" + done > warnings +} diff --git a/regtest/basic/rt-molinfo-whole-membrane/plumed.dat b/regtest/basic/rt-molinfo-whole-membrane/plumed.dat new file mode 100644 index 0000000000..81db707076 --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-membrane/plumed.dat @@ -0,0 +1,5 @@ +# a small bilayer: 18 lipids of 6 beads, continuous across the box in x and y +MOLINFO STRUCTURE=ref.pdb WHOLE +# all lipids in one group: no warning (the check does not go from one lipid to the next), and every lipid is made whole +WHOLEMOLECULES ENTITY0=1-108 +DUMPATOMS ATOMS=1-108 FILE=whole.xyz PRECISION=3 diff --git a/regtest/basic/rt-molinfo-whole-membrane/plumed_sep.dat b/regtest/basic/rt-molinfo-whole-membrane/plumed_sep.dat new file mode 100644 index 0000000000..20d4e8018a --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-membrane/plumed_sep.dat @@ -0,0 +1,3 @@ +MOLINFO STRUCTURE=ref.pdb WHOLE +# one group per lipid: no warning +WHOLEMOLECULES ENTITY0=1-6 ENTITY1=7-12 ENTITY2=13-18 ENTITY3=19-24 ENTITY4=25-30 ENTITY5=31-36 ENTITY6=37-42 ENTITY7=43-48 ENTITY8=49-54 ENTITY9=55-60 ENTITY10=61-66 ENTITY11=67-72 ENTITY12=73-78 ENTITY13=79-84 ENTITY14=85-90 ENTITY15=91-96 ENTITY16=97-102 ENTITY17=103-108 diff --git a/regtest/basic/rt-molinfo-whole-membrane/ref.pdb b/regtest/basic/rt-molinfo-whole-membrane/ref.pdb new file mode 100644 index 0000000000..22b370b11c --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-membrane/ref.pdb @@ -0,0 +1,110 @@ +CRYST1 24.000 24.000 70.000 90.00 90.00 90.00 P 1 1 +ATOM 1 NC3 LIP A 1 -3.055 0.735 61.000 1.00 0.00 +ATOM 2 PO4 LIP A 1 -2.520 0.673 56.300 1.00 0.00 +ATOM 3 GL1 LIP A 1 -1.984 0.610 51.600 1.00 0.00 +ATOM 4 C1A LIP A 1 -1.449 0.548 46.900 1.00 0.00 +ATOM 5 C2A LIP A 1 -0.914 0.486 42.200 1.00 0.00 +ATOM 6 C3A LIP A 1 -0.378 0.423 37.500 1.00 0.00 +ATOM 7 NC3 LIP A 2 -2.399 9.042 61.000 1.00 0.00 +ATOM 8 PO4 LIP A 2 -1.982 8.886 56.300 1.00 0.00 +ATOM 9 GL1 LIP A 2 -1.565 8.731 51.600 1.00 0.00 +ATOM 10 C1A LIP A 2 -1.149 8.575 46.900 1.00 0.00 +ATOM 11 C2A LIP A 2 -0.732 8.419 42.200 1.00 0.00 +ATOM 12 C3A LIP A 2 -0.315 8.263 37.500 1.00 0.00 +ATOM 13 NC3 LIP A 3 -2.157 18.212 61.000 1.00 0.00 +ATOM 14 PO4 LIP A 3 -1.684 17.729 56.300 1.00 0.00 +ATOM 15 GL1 LIP A 3 -1.210 17.246 51.600 1.00 0.00 +ATOM 16 C1A LIP A 3 -0.737 16.763 46.900 1.00 0.00 +ATOM 17 C2A LIP A 3 -0.263 16.280 42.200 1.00 0.00 +ATOM 18 C3A LIP A 3 0.210 15.797 37.500 1.00 0.00 +ATOM 19 NC3 LIP A 4 9.787 -0.105 61.000 1.00 0.00 +ATOM 20 PO4 LIP A 4 9.387 -0.034 56.300 1.00 0.00 +ATOM 21 GL1 LIP A 4 8.987 0.036 51.600 1.00 0.00 +ATOM 22 C1A LIP A 4 8.586 0.107 46.900 1.00 0.00 +ATOM 23 C2A LIP A 4 8.186 0.178 42.200 1.00 0.00 +ATOM 24 C3A LIP A 4 7.786 0.249 37.500 1.00 0.00 +ATOM 25 NC3 LIP A 5 10.167 9.011 61.000 1.00 0.00 +ATOM 26 PO4 LIP A 5 9.860 8.741 56.300 1.00 0.00 +ATOM 27 GL1 LIP A 5 9.553 8.472 51.600 1.00 0.00 +ATOM 28 C1A LIP A 5 9.246 8.202 46.900 1.00 0.00 +ATOM 29 C2A LIP A 5 8.939 7.932 42.200 1.00 0.00 +ATOM 30 C3A LIP A 5 8.632 7.663 37.500 1.00 0.00 +ATOM 31 NC3 LIP A 6 9.236 15.883 61.000 1.00 0.00 +ATOM 32 PO4 LIP A 6 9.070 15.901 56.300 1.00 0.00 +ATOM 33 GL1 LIP A 6 8.904 15.919 51.600 1.00 0.00 +ATOM 34 C1A LIP A 6 8.738 15.937 46.900 1.00 0.00 +ATOM 35 C2A LIP A 6 8.572 15.954 42.200 1.00 0.00 +ATOM 36 C3A LIP A 6 8.406 15.972 37.500 1.00 0.00 +ATOM 37 NC3 LIP A 7 17.634 -1.408 61.000 1.00 0.00 +ATOM 38 PO4 LIP A 7 17.406 -1.145 56.300 1.00 0.00 +ATOM 39 GL1 LIP A 7 17.178 -0.882 51.600 1.00 0.00 +ATOM 40 C1A LIP A 7 16.950 -0.619 46.900 1.00 0.00 +ATOM 41 C2A LIP A 7 16.722 -0.356 42.200 1.00 0.00 +ATOM 42 C3A LIP A 7 16.494 -0.093 37.500 1.00 0.00 +ATOM 43 NC3 LIP A 8 16.118 8.167 61.000 1.00 0.00 +ATOM 44 PO4 LIP A 8 16.052 8.147 56.300 1.00 0.00 +ATOM 45 GL1 LIP A 8 15.986 8.128 51.600 1.00 0.00 +ATOM 46 C1A LIP A 8 15.920 8.108 46.900 1.00 0.00 +ATOM 47 C2A LIP A 8 15.855 8.088 42.200 1.00 0.00 +ATOM 48 C3A LIP A 8 15.789 8.069 37.500 1.00 0.00 +ATOM 49 NC3 LIP A 9 16.186 16.441 61.000 1.00 0.00 +ATOM 50 PO4 LIP A 9 16.108 16.310 56.300 1.00 0.00 +ATOM 51 GL1 LIP A 9 16.029 16.179 51.600 1.00 0.00 +ATOM 52 C1A LIP A 9 15.951 16.047 46.900 1.00 0.00 +ATOM 53 C2A LIP A 9 15.872 15.916 42.200 1.00 0.00 +ATOM 54 C3A LIP A 9 15.794 15.785 37.500 1.00 0.00 +ATOM 55 NC3 LIP A 10 1.873 8.314 9.000 1.00 0.00 +ATOM 56 PO4 LIP A 10 2.259 7.452 13.700 1.00 0.00 +ATOM 57 GL1 LIP A 10 2.645 6.589 18.400 1.00 0.00 +ATOM 58 C1A LIP A 10 3.031 5.727 23.100 1.00 0.00 +ATOM 59 C2A LIP A 10 3.417 4.865 27.800 1.00 0.00 +ATOM 60 C3A LIP A 10 3.802 4.002 32.500 1.00 0.00 +ATOM 61 NC3 LIP A 11 3.198 11.272 9.000 1.00 0.00 +ATOM 62 PO4 LIP A 11 3.360 11.485 13.700 1.00 0.00 +ATOM 63 GL1 LIP A 11 3.523 11.699 18.400 1.00 0.00 +ATOM 64 C1A LIP A 11 3.686 11.912 23.100 1.00 0.00 +ATOM 65 C2A LIP A 11 3.849 12.125 27.800 1.00 0.00 +ATOM 66 C3A LIP A 11 4.012 12.338 32.500 1.00 0.00 +ATOM 67 NC3 LIP A 12 9.154 18.993 9.000 1.00 0.00 +ATOM 68 PO4 LIP A 12 8.190 19.248 13.700 1.00 0.00 +ATOM 69 GL1 LIP A 12 7.226 19.502 18.400 1.00 0.00 +ATOM 70 C1A LIP A 12 6.262 19.757 23.100 1.00 0.00 +ATOM 71 C2A LIP A 12 5.299 20.011 27.800 1.00 0.00 +ATOM 72 C3A LIP A 12 4.335 20.265 32.500 1.00 0.00 +ATOM 73 NC3 LIP A 13 13.266 6.937 9.000 1.00 0.00 +ATOM 74 PO4 LIP A 13 12.956 6.343 13.700 1.00 0.00 +ATOM 75 GL1 LIP A 13 12.645 5.750 18.400 1.00 0.00 +ATOM 76 C1A LIP A 13 12.334 5.156 23.100 1.00 0.00 +ATOM 77 C2A LIP A 13 12.024 4.563 27.800 1.00 0.00 +ATOM 78 C3A LIP A 13 11.713 3.969 32.500 1.00 0.00 +ATOM 79 NC3 LIP A 14 6.929 13.039 9.000 1.00 0.00 +ATOM 80 PO4 LIP A 14 7.831 12.898 13.700 1.00 0.00 +ATOM 81 GL1 LIP A 14 8.733 12.758 18.400 1.00 0.00 +ATOM 82 C1A LIP A 14 9.636 12.618 23.100 1.00 0.00 +ATOM 83 C2A LIP A 14 10.538 12.477 27.800 1.00 0.00 +ATOM 84 C3A LIP A 14 11.440 12.337 32.500 1.00 0.00 +ATOM 85 NC3 LIP A 15 9.256 18.728 9.000 1.00 0.00 +ATOM 86 PO4 LIP A 15 9.819 18.918 13.700 1.00 0.00 +ATOM 87 GL1 LIP A 15 10.382 19.108 18.400 1.00 0.00 +ATOM 88 C1A LIP A 15 10.946 19.298 23.100 1.00 0.00 +ATOM 89 C2A LIP A 15 11.509 19.488 27.800 1.00 0.00 +ATOM 90 C3A LIP A 15 12.072 19.678 32.500 1.00 0.00 +ATOM 91 NC3 LIP A 16 18.586 3.034 9.000 1.00 0.00 +ATOM 92 PO4 LIP A 16 18.844 3.222 13.700 1.00 0.00 +ATOM 93 GL1 LIP A 16 19.101 3.410 18.400 1.00 0.00 +ATOM 94 C1A LIP A 16 19.358 3.598 23.100 1.00 0.00 +ATOM 95 C2A LIP A 16 19.616 3.786 27.800 1.00 0.00 +ATOM 96 C3A LIP A 16 19.873 3.974 32.500 1.00 0.00 +ATOM 97 NC3 LIP A 17 18.304 13.126 9.000 1.00 0.00 +ATOM 98 PO4 LIP A 17 18.640 12.968 13.700 1.00 0.00 +ATOM 99 GL1 LIP A 17 18.977 12.810 18.400 1.00 0.00 +ATOM 100 C1A LIP A 17 19.313 12.651 23.100 1.00 0.00 +ATOM 101 C2A LIP A 17 19.649 12.493 27.800 1.00 0.00 +ATOM 102 C3A LIP A 17 19.986 12.335 32.500 1.00 0.00 +ATOM 103 NC3 LIP A 18 21.363 18.683 9.000 1.00 0.00 +ATOM 104 PO4 LIP A 18 21.117 18.913 13.700 1.00 0.00 +ATOM 105 GL1 LIP A 18 20.872 19.144 18.400 1.00 0.00 +ATOM 106 C1A LIP A 18 20.626 19.374 23.100 1.00 0.00 +ATOM 107 C2A LIP A 18 20.380 19.605 27.800 1.00 0.00 +ATOM 108 C3A LIP A 18 20.135 19.836 32.500 1.00 0.00 +END diff --git a/regtest/basic/rt-molinfo-whole-membrane/traj.gro b/regtest/basic/rt-molinfo-whole-membrane/traj.gro new file mode 100644 index 0000000000..79523e7351 --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-membrane/traj.gro @@ -0,0 +1,333 @@ +a small bilayer, each lipid moved and wrapped atom by atom + 108 + 1LIP NC3 1 2.374 0.135 1.087 + 1LIP PO4 2 2.377 0.135 0.572 + 1LIP GL1 3 0.080 0.160 0.143 + 1LIP C1A 4 0.095 0.121 6.655 + 1LIP C2A 5 0.175 0.115 6.180 + 1LIP C3A 6 0.225 0.114 5.688 + 2LIP NC3 7 2.047 0.894 1.137 + 2LIP PO4 8 2.103 0.831 0.671 + 2LIP GL1 9 2.128 0.838 0.184 + 2LIP C1A 10 2.202 0.874 6.707 + 2LIP C2A 11 2.214 0.815 6.265 + 2LIP C3A 12 2.295 0.804 5.799 + 3LIP NC3 13 2.354 2.071 1.062 + 3LIP PO4 14 2.354 1.995 0.576 + 3LIP GL1 15 0.025 1.919 0.114 + 3LIP C1A 16 0.030 1.881 6.661 + 3LIP C2A 17 0.116 1.852 6.170 + 3LIP C3A 18 0.092 1.830 5.708 + 4LIP NC3 19 1.371 2.323 1.185 + 4LIP PO4 20 1.297 2.284 0.678 + 4LIP GL1 21 1.275 2.296 0.229 + 4LIP C1A 22 1.267 2.334 6.736 + 4LIP C2A 23 1.232 2.303 6.249 + 4LIP C3A 24 1.185 2.303 5.750 + 5LIP NC3 25 1.486 0.681 1.119 + 5LIP PO4 26 1.432 0.678 0.643 + 5LIP GL1 27 1.450 0.682 0.139 + 5LIP C1A 28 1.381 0.613 6.690 + 5LIP C2A 29 1.289 0.611 6.217 + 5LIP C3A 30 1.286 0.594 5.765 + 6LIP NC3 31 1.630 1.314 1.137 + 6LIP PO4 32 1.594 1.327 0.659 + 6LIP GL1 33 1.600 1.312 0.172 + 6LIP C1A 34 1.581 1.303 6.728 + 6LIP C2A 35 1.563 1.364 6.274 + 6LIP C3A 36 1.511 1.322 5.765 + 7LIP NC3 37 0.058 0.051 1.098 + 7LIP PO4 38 2.369 0.076 0.613 + 7LIP GL1 39 2.370 0.052 0.158 + 7LIP C1A 40 2.287 0.136 6.717 + 7LIP C2A 41 2.277 0.144 6.233 + 7LIP C3A 42 2.317 0.211 5.720 + 8LIP NC3 43 1.724 0.920 1.104 + 8LIP PO4 44 1.698 0.890 0.638 + 8LIP GL1 45 1.683 0.941 0.141 + 8LIP C1A 46 1.700 0.934 6.647 + 8LIP C2A 47 1.674 0.915 6.209 + 8LIP C3A 48 1.678 0.928 5.768 + 9LIP NC3 49 1.704 1.872 1.091 + 9LIP PO4 50 1.735 1.908 0.632 + 9LIP GL1 51 1.692 1.835 0.167 + 9LIP C1A 52 1.727 1.855 6.704 + 9LIP C2A 53 1.647 1.851 6.244 + 9LIP C3A 54 1.686 1.838 5.753 + 10LIP NC3 55 0.770 1.306 2.842 + 10LIP PO4 56 0.796 1.239 3.308 + 10LIP GL1 57 0.864 1.077 3.809 + 10LIP C1A 58 0.845 1.054 4.244 + 10LIP C2A 59 0.900 0.949 4.723 + 10LIP C3A 60 0.989 0.881 5.190 + 11LIP NC3 61 0.592 0.833 2.919 + 11LIP PO4 62 0.562 0.843 3.335 + 11LIP GL1 63 0.625 0.856 3.824 + 11LIP C1A 64 0.603 0.896 4.311 + 11LIP C2A 65 0.640 0.916 4.785 + 11LIP C3A 66 0.639 0.973 5.247 + 12LIP NC3 67 1.319 2.090 2.877 + 12LIP PO4 68 1.255 2.086 3.319 + 12LIP GL1 69 1.133 2.155 3.841 + 12LIP C1A 70 1.096 2.213 4.254 + 12LIP C2A 71 0.969 2.183 4.764 + 12LIP C3A 72 0.855 2.221 5.215 + 13LIP NC3 73 1.519 0.339 2.929 + 13LIP PO4 74 1.470 0.256 3.380 + 13LIP GL1 75 1.395 0.212 3.859 + 13LIP C1A 76 1.392 0.104 4.326 + 13LIP C2A 77 1.318 0.085 4.820 + 13LIP C3A 78 1.370 0.004 5.261 + 14LIP NC3 79 1.104 1.326 2.901 + 14LIP PO4 80 1.192 1.309 3.384 + 14LIP GL1 81 1.210 1.299 3.879 + 14LIP C1A 82 1.339 1.274 4.305 + 14LIP C2A 83 1.410 1.302 4.803 + 14LIP C3A 84 1.510 1.265 5.236 + 15LIP NC3 85 1.099 1.738 2.988 + 15LIP PO4 86 1.136 1.751 3.439 + 15LIP GL1 87 1.157 1.795 3.922 + 15LIP C1A 88 1.227 1.783 4.419 + 15LIP C2A 89 1.303 1.850 4.914 + 15LIP C3A 90 1.371 1.881 5.355 + 16LIP NC3 91 1.952 0.348 2.878 + 16LIP PO4 92 2.015 0.387 3.406 + 16LIP GL1 93 2.031 0.433 3.816 + 16LIP C1A 94 2.076 0.421 4.307 + 16LIP C2A 95 2.092 0.443 4.766 + 16LIP C3A 96 2.046 0.475 5.269 + 17LIP NC3 97 2.112 1.210 2.994 + 17LIP PO4 98 2.139 1.202 3.426 + 17LIP GL1 99 2.166 1.196 3.915 + 17LIP C1A 100 2.218 1.170 4.336 + 17LIP C2A 101 2.256 1.098 4.854 + 17LIP C3A 102 2.260 1.145 5.278 + 18LIP NC3 103 2.309 2.019 2.930 + 18LIP PO4 104 2.328 1.999 3.398 + 18LIP GL1 105 2.340 2.046 3.861 + 18LIP C1A 106 2.303 2.059 4.361 + 18LIP C2A 107 2.268 2.089 4.809 + 18LIP C3A 108 2.217 2.095 5.332 + 2.40000 2.40000 7.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 +a small bilayer, each lipid moved and wrapped atom by atom + 108 + 1LIP NC3 1 0.026 0.918 4.147 + 1LIP PO4 2 0.081 0.897 3.661 + 1LIP GL1 3 0.127 0.936 3.210 + 1LIP C1A 4 0.180 0.878 2.726 + 1LIP C2A 5 0.254 0.922 2.250 + 1LIP C3A 6 0.268 0.887 1.749 + 2LIP NC3 7 2.255 1.289 4.083 + 2LIP PO4 8 2.311 1.289 3.626 + 2LIP GL1 9 2.359 1.265 3.136 + 2LIP C1A 10 0.002 1.262 2.623 + 2LIP C2A 11 0.048 1.258 2.207 + 2LIP C3A 12 0.095 1.214 1.688 + 3LIP NC3 13 2.040 0.118 4.105 + 3LIP PO4 14 2.074 0.109 3.607 + 3LIP GL1 15 2.143 0.039 3.148 + 3LIP C1A 16 2.202 0.004 2.682 + 3LIP C2A 17 2.217 2.343 2.179 + 3LIP C3A 18 2.251 2.274 1.728 + 4LIP NC3 19 0.860 0.239 4.066 + 4LIP PO4 20 0.790 0.230 3.552 + 4LIP GL1 21 0.780 0.230 3.081 + 4LIP C1A 22 0.724 0.242 2.607 + 4LIP C2A 23 0.696 0.232 2.161 + 4LIP C3A 24 0.639 0.261 1.713 + 5LIP NC3 25 1.028 1.275 4.117 + 5LIP PO4 26 0.994 1.234 3.693 + 5LIP GL1 27 1.003 1.237 3.208 + 5LIP C1A 28 0.946 1.226 2.736 + 5LIP C2A 29 0.876 1.153 2.258 + 5LIP C3A 30 0.841 1.142 1.759 + 6LIP NC3 31 0.812 1.933 4.168 + 6LIP PO4 32 0.822 1.992 3.630 + 6LIP GL1 33 0.810 2.001 3.194 + 6LIP C1A 34 0.827 1.993 2.724 + 6LIP C2A 35 0.767 2.019 2.284 + 6LIP C3A 36 0.738 1.975 1.792 + 7LIP NC3 37 1.637 0.106 4.081 + 7LIP PO4 38 1.644 0.129 3.647 + 7LIP GL1 39 1.642 0.166 3.151 + 7LIP C1A 40 1.601 0.193 2.681 + 7LIP C2A 41 1.569 0.225 2.208 + 7LIP C3A 42 1.558 0.279 1.776 + 8LIP NC3 43 1.650 1.382 4.244 + 8LIP PO4 44 1.656 1.377 3.804 + 8LIP GL1 45 1.624 1.368 3.292 + 8LIP C1A 46 1.596 1.379 2.825 + 8LIP C2A 47 1.598 1.359 2.397 + 8LIP C3A 48 1.565 1.378 1.891 + 9LIP NC3 49 1.464 1.710 4.086 + 9LIP PO4 50 1.456 1.722 3.626 + 9LIP GL1 51 1.482 1.697 3.172 + 9LIP C1A 52 1.432 1.695 2.695 + 9LIP C2A 53 1.451 1.680 2.179 + 9LIP C3A 54 1.446 1.660 1.726 + 10LIP NC3 55 2.286 1.693 5.868 + 10LIP PO4 56 2.328 1.601 6.339 + 10LIP GL1 57 2.343 1.523 6.839 + 10LIP C1A 58 0.001 1.407 0.258 + 10LIP C2A 59 0.026 1.358 0.702 + 10LIP C3A 60 0.063 1.252 1.208 + 11LIP NC3 61 0.053 1.723 5.830 + 11LIP PO4 62 0.059 1.765 6.367 + 11LIP GL1 63 0.063 1.747 6.808 + 11LIP C1A 64 0.077 1.751 0.298 + 11LIP C2A 65 0.069 1.800 0.739 + 11LIP C3A 66 0.104 1.823 1.236 + 12LIP NC3 67 1.171 2.194 5.861 + 12LIP PO4 68 1.048 2.233 6.367 + 12LIP GL1 69 0.979 2.260 6.809 + 12LIP C1A 70 0.854 2.292 0.282 + 12LIP C2A 71 0.743 2.318 0.779 + 12LIP C3A 72 0.673 2.374 1.215 + 13LIP NC3 73 1.267 1.369 5.866 + 13LIP PO4 74 1.247 1.305 6.366 + 13LIP GL1 75 1.219 1.260 6.830 + 13LIP C1A 76 1.165 1.169 0.286 + 13LIP C2A 77 1.153 1.158 0.769 + 13LIP C3A 78 1.126 1.075 1.244 + 14LIP NC3 79 0.841 1.785 5.939 + 14LIP PO4 80 0.917 1.761 6.395 + 14LIP GL1 81 1.029 1.697 6.853 + 14LIP C1A 82 1.138 1.700 0.337 + 14LIP C2A 83 1.221 1.684 0.816 + 14LIP C3A 84 1.269 1.699 1.308 + 15LIP NC3 85 1.169 2.105 5.882 + 15LIP PO4 86 1.175 2.108 6.393 + 15LIP GL1 87 1.230 2.136 6.856 + 15LIP C1A 88 1.333 2.124 0.356 + 15LIP C2A 89 1.381 2.184 0.805 + 15LIP C3A 90 1.446 2.222 1.295 + 16LIP NC3 91 1.745 0.775 5.926 + 16LIP PO4 92 1.789 0.777 6.389 + 16LIP GL1 93 1.826 0.824 6.859 + 16LIP C1A 94 1.863 0.829 0.349 + 16LIP C2A 95 1.866 0.817 0.841 + 16LIP C3A 96 1.890 0.851 1.277 + 17LIP NC3 97 1.853 1.493 5.937 + 17LIP PO4 98 1.847 1.522 6.406 + 17LIP GL1 99 1.842 1.490 6.843 + 17LIP C1A 100 1.907 1.514 0.304 + 17LIP C2A 101 1.964 1.473 0.753 + 17LIP C3A 102 1.979 1.461 1.222 + 18LIP NC3 103 2.078 0.152 5.914 + 18LIP PO4 104 2.010 0.202 6.348 + 18LIP GL1 105 1.980 0.216 6.821 + 18LIP C1A 106 1.967 0.262 0.314 + 18LIP C2A 107 1.978 0.269 0.765 + 18LIP C3A 108 1.940 0.251 1.240 + 2.40000 2.40000 7.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 +a small bilayer, each lipid moved and wrapped atom by atom + 108 + 1LIP NC3 1 0.146 0.735 1.117 + 1LIP PO4 2 0.195 0.704 0.653 + 1LIP GL1 3 0.196 0.673 0.163 + 1LIP C1A 4 0.272 0.694 6.698 + 1LIP C2A 5 0.338 0.674 6.229 + 1LIP C3A 6 0.350 0.694 5.781 + 2LIP NC3 7 2.331 1.390 1.002 + 2LIP PO4 8 0.009 1.401 0.580 + 2LIP GL1 9 0.029 1.381 0.100 + 2LIP C1A 10 0.053 1.337 6.602 + 2LIP C2A 11 0.080 1.364 6.159 + 2LIP C3A 12 0.103 1.315 5.713 + 3LIP NC3 13 0.198 0.100 1.130 + 3LIP PO4 14 0.248 0.062 0.658 + 3LIP GL1 15 0.335 0.033 0.179 + 3LIP C1A 16 0.354 2.345 6.741 + 3LIP C2A 17 0.425 2.289 6.269 + 3LIP C3A 18 0.449 2.248 5.786 + 4LIP NC3 19 1.160 0.553 1.127 + 4LIP PO4 20 1.122 0.554 0.675 + 4LIP GL1 21 1.083 0.577 0.162 + 4LIP C1A 22 1.061 0.584 6.747 + 4LIP C2A 23 1.002 0.580 6.323 + 4LIP C3A 24 0.980 0.628 5.787 + 5LIP NC3 25 1.520 1.548 1.097 + 5LIP PO4 26 1.481 1.561 0.605 + 5LIP GL1 27 1.450 1.527 0.198 + 5LIP C1A 28 1.448 1.475 6.667 + 5LIP C2A 29 1.443 1.458 6.220 + 5LIP C3A 30 1.343 1.432 5.750 + 6LIP NC3 31 1.027 1.686 1.137 + 6LIP PO4 32 1.041 1.721 0.667 + 6LIP GL1 33 1.023 1.700 0.183 + 6LIP C1A 34 0.961 1.664 6.698 + 6LIP C2A 35 0.970 1.702 6.229 + 6LIP C3A 36 0.984 1.743 5.765 + 7LIP NC3 37 2.052 2.303 1.061 + 7LIP PO4 38 2.014 2.334 0.622 + 7LIP GL1 39 2.005 2.375 0.173 + 7LIP C1A 40 1.968 0.014 6.640 + 7LIP C2A 41 1.932 0.056 6.221 + 7LIP C3A 42 1.975 0.045 5.729 + 8LIP NC3 43 2.188 0.880 1.096 + 8LIP PO4 44 2.181 0.863 0.632 + 8LIP GL1 45 2.219 0.861 0.169 + 8LIP C1A 46 2.191 0.920 6.693 + 8LIP C2A 47 2.160 0.894 6.232 + 8LIP C3A 48 2.121 0.877 5.766 + 9LIP NC3 49 1.990 2.075 1.061 + 9LIP PO4 50 1.937 2.086 0.602 + 9LIP GL1 51 1.929 2.038 0.130 + 9LIP C1A 52 1.941 2.061 6.708 + 9LIP C2A 53 1.938 2.073 6.207 + 9LIP C3A 54 1.898 2.039 5.708 + 10LIP NC3 55 0.626 1.564 2.824 + 10LIP PO4 56 0.699 1.441 3.302 + 10LIP GL1 57 0.733 1.364 3.753 + 10LIP C1A 58 0.747 1.245 4.262 + 10LIP C2A 59 0.803 1.176 4.691 + 10LIP C3A 60 0.852 1.090 5.171 + 11LIP NC3 61 1.263 1.473 2.845 + 11LIP PO4 62 1.279 1.531 3.334 + 11LIP GL1 63 1.288 1.542 3.762 + 11LIP C1A 64 1.306 1.572 4.272 + 11LIP C2A 65 1.338 1.547 4.746 + 11LIP C3A 66 1.350 1.617 5.157 + 12LIP NC3 67 1.217 0.076 2.961 + 12LIP PO4 68 1.088 0.170 3.470 + 12LIP GL1 69 0.999 0.214 3.940 + 12LIP C1A 70 0.927 0.210 4.342 + 12LIP C2A 71 0.824 0.218 4.859 + 12LIP C3A 72 0.709 0.241 5.282 + 13LIP NC3 73 1.565 1.371 2.895 + 13LIP PO4 74 1.495 1.338 3.359 + 13LIP GL1 75 1.456 1.251 3.857 + 13LIP C1A 76 1.453 1.205 4.310 + 13LIP C2A 77 1.453 1.126 4.764 + 13LIP C3A 78 1.403 1.070 5.232 + 14LIP NC3 79 1.346 1.542 2.890 + 14LIP PO4 80 1.412 1.546 3.315 + 14LIP GL1 81 1.538 1.547 3.796 + 14LIP C1A 82 1.606 1.518 4.268 + 14LIP C2A 83 1.645 1.491 4.744 + 14LIP C3A 84 1.773 1.478 5.225 + 15LIP NC3 85 1.572 0.121 2.829 + 15LIP PO4 86 1.656 0.095 3.288 + 15LIP GL1 87 1.727 0.161 3.803 + 15LIP C1A 88 1.743 0.127 4.250 + 15LIP C2A 89 1.784 0.166 4.756 + 15LIP C3A 90 1.864 0.196 5.201 + 16LIP NC3 91 1.989 0.911 2.892 + 16LIP PO4 92 2.064 1.015 3.344 + 16LIP GL1 93 2.040 0.965 3.816 + 16LIP C1A 94 2.119 0.965 4.264 + 16LIP C2A 95 2.128 1.012 4.785 + 16LIP C3A 96 2.122 1.097 5.235 + 17LIP NC3 97 2.159 1.345 2.890 + 17LIP PO4 98 2.194 1.283 3.362 + 17LIP GL1 99 2.248 1.276 3.827 + 17LIP C1A 100 2.263 1.273 4.281 + 17LIP C2A 101 2.282 1.236 4.755 + 17LIP C3A 102 2.319 1.257 5.256 + 18LIP NC3 103 0.409 2.225 2.970 + 18LIP PO4 104 0.367 2.283 3.391 + 18LIP GL1 105 0.387 2.268 3.889 + 18LIP C1A 106 0.336 2.302 4.365 + 18LIP C2A 107 0.325 2.345 4.798 + 18LIP C3A 108 0.321 2.359 5.268 + 2.40000 2.40000 7.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 diff --git a/regtest/basic/rt-molinfo-whole-membrane/warnings.reference b/regtest/basic/rt-molinfo-whole-membrane/warnings.reference new file mode 100644 index 0000000000..99de63f898 --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-membrane/warnings.reference @@ -0,0 +1,4 @@ +# out_sep +Action WHOLEMOLECULES +# out +Action WHOLEMOLECULES diff --git a/regtest/basic/rt-molinfo-whole-membrane/whole.xyz.reference b/regtest/basic/rt-molinfo-whole-membrane/whole.xyz.reference new file mode 100644 index 0000000000..8e4d6af5b0 --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-membrane/whole.xyz.reference @@ -0,0 +1,330 @@ +108 + 2.400 2.400 7.000 +NC3 2.374 0.135 1.087 +PO4 2.377 0.135 0.572 +GL1 2.480 0.160 0.143 +C1A 2.495 0.121 -0.345 +C2A 2.575 0.115 -0.820 +C3A 2.625 0.114 -1.312 +NC3 2.047 0.894 1.137 +PO4 2.103 0.831 0.671 +GL1 2.128 0.838 0.184 +C1A 2.202 0.874 -0.293 +C2A 2.214 0.815 -0.735 +C3A 2.295 0.804 -1.201 +NC3 2.354 2.071 1.062 +PO4 2.354 1.995 0.576 +GL1 2.425 1.919 0.114 +C1A 2.430 1.881 -0.339 +C2A 2.516 1.852 -0.830 +C3A 2.492 1.830 -1.292 +NC3 3.771 -0.077 1.185 +PO4 3.697 -0.116 0.678 +GL1 3.675 -0.104 0.229 +C1A 3.667 -0.066 -0.264 +C2A 3.632 -0.097 -0.751 +C3A 3.585 -0.097 -1.250 +NC3 3.886 0.681 1.119 +PO4 3.832 0.678 0.643 +GL1 3.850 0.682 0.139 +C1A 3.781 0.613 -0.310 +C2A 3.689 0.611 -0.783 +C3A 3.686 0.594 -1.235 +NC3 4.030 1.314 1.137 +PO4 3.994 1.327 0.659 +GL1 4.000 1.312 0.172 +C1A 3.981 1.303 -0.272 +C2A 3.963 1.364 -0.726 +C3A 3.911 1.322 -1.235 +NC3 4.858 0.051 1.098 +PO4 4.769 0.076 0.613 +GL1 4.770 0.052 0.158 +C1A 4.687 0.136 -0.283 +C2A 4.677 0.144 -0.767 +C3A 4.717 0.211 -1.280 +NC3 4.124 0.920 1.104 +PO4 4.098 0.890 0.638 +GL1 4.083 0.941 0.141 +C1A 4.100 0.934 -0.353 +C2A 4.074 0.915 -0.791 +C3A 4.078 0.928 -1.232 +NC3 4.104 1.872 1.091 +PO4 4.135 1.908 0.632 +GL1 4.092 1.835 0.167 +C1A 4.127 1.855 -0.296 +C2A 4.047 1.851 -0.756 +C3A 4.086 1.838 -1.247 +NC3 3.170 1.306 -4.158 +PO4 3.196 1.239 -3.692 +GL1 3.264 1.077 -3.191 +C1A 3.245 1.054 -2.756 +C2A 3.300 0.949 -2.277 +C3A 3.389 0.881 -1.810 +NC3 2.992 0.833 -4.081 +PO4 2.962 0.843 -3.665 +GL1 3.025 0.856 -3.176 +C1A 3.003 0.896 -2.689 +C2A 3.040 0.916 -2.215 +C3A 3.039 0.973 -1.753 +NC3 3.719 2.090 -4.123 +PO4 3.655 2.086 -3.681 +GL1 3.533 2.155 -3.159 +C1A 3.496 2.213 -2.746 +C2A 3.369 2.183 -2.236 +C3A 3.255 2.221 -1.785 +NC3 3.919 0.339 -4.071 +PO4 3.870 0.256 -3.620 +GL1 3.795 0.212 -3.141 +C1A 3.792 0.104 -2.674 +C2A 3.718 0.085 -2.180 +C3A 3.770 0.004 -1.739 +NC3 3.504 1.326 -4.099 +PO4 3.592 1.309 -3.616 +GL1 3.610 1.299 -3.121 +C1A 3.739 1.274 -2.695 +C2A 3.810 1.302 -2.197 +C3A 3.910 1.265 -1.764 +NC3 3.499 1.738 -4.012 +PO4 3.536 1.751 -3.561 +GL1 3.557 1.795 -3.078 +C1A 3.627 1.783 -2.581 +C2A 3.703 1.850 -2.086 +C3A 3.771 1.881 -1.645 +NC3 4.352 0.348 -4.122 +PO4 4.415 0.387 -3.594 +GL1 4.431 0.433 -3.184 +C1A 4.476 0.421 -2.693 +C2A 4.492 0.443 -2.234 +C3A 4.446 0.475 -1.731 +NC3 4.512 1.210 -4.006 +PO4 4.539 1.202 -3.574 +GL1 4.566 1.196 -3.085 +C1A 4.618 1.170 -2.664 +C2A 4.656 1.098 -2.146 +C3A 4.660 1.145 -1.722 +NC3 4.709 2.019 -4.070 +PO4 4.728 1.999 -3.602 +GL1 4.740 2.046 -3.139 +C1A 4.703 2.059 -2.639 +C2A 4.668 2.089 -2.191 +C3A 4.617 2.095 -1.668 +108 + 2.400 2.400 7.000 +NC3 0.026 0.918 4.147 +PO4 0.081 0.897 3.661 +GL1 0.127 0.936 3.210 +C1A 0.180 0.878 2.726 +C2A 0.254 0.922 2.250 +C3A 0.268 0.887 1.749 +NC3 -0.145 1.289 4.083 +PO4 -0.089 1.289 3.626 +GL1 -0.041 1.265 3.136 +C1A 0.002 1.262 2.623 +C2A 0.048 1.258 2.207 +C3A 0.095 1.214 1.688 +NC3 -0.360 2.518 4.105 +PO4 -0.326 2.509 3.607 +GL1 -0.257 2.439 3.148 +C1A -0.198 2.404 2.682 +C2A -0.183 2.343 2.179 +C3A -0.149 2.274 1.728 +NC3 0.860 0.239 4.066 +PO4 0.790 0.230 3.552 +GL1 0.780 0.230 3.081 +C1A 0.724 0.242 2.607 +C2A 0.696 0.232 2.161 +C3A 0.639 0.261 1.713 +NC3 1.028 1.275 4.117 +PO4 0.994 1.234 3.693 +GL1 1.003 1.237 3.208 +C1A 0.946 1.226 2.736 +C2A 0.876 1.153 2.258 +C3A 0.841 1.142 1.759 +NC3 0.812 1.933 4.168 +PO4 0.822 1.992 3.630 +GL1 0.810 2.001 3.194 +C1A 0.827 1.993 2.724 +C2A 0.767 2.019 2.284 +C3A 0.738 1.975 1.792 +NC3 1.637 0.106 4.081 +PO4 1.644 0.129 3.647 +GL1 1.642 0.166 3.151 +C1A 1.601 0.193 2.681 +C2A 1.569 0.225 2.208 +C3A 1.558 0.279 1.776 +NC3 1.650 1.382 4.244 +PO4 1.656 1.377 3.804 +GL1 1.624 1.368 3.292 +C1A 1.596 1.379 2.825 +C2A 1.598 1.359 2.397 +C3A 1.565 1.378 1.891 +NC3 1.464 1.710 4.086 +PO4 1.456 1.722 3.626 +GL1 1.482 1.697 3.172 +C1A 1.432 1.695 2.695 +C2A 1.451 1.680 2.179 +C3A 1.446 1.660 1.726 +NC3 -0.114 1.693 -1.132 +PO4 -0.072 1.601 -0.661 +GL1 -0.057 1.523 -0.161 +C1A 0.001 1.407 0.258 +C2A 0.026 1.358 0.702 +C3A 0.063 1.252 1.208 +NC3 0.053 1.723 -1.170 +PO4 0.059 1.765 -0.633 +GL1 0.063 1.747 -0.192 +C1A 0.077 1.751 0.298 +C2A 0.069 1.800 0.739 +C3A 0.104 1.823 1.236 +NC3 1.171 2.194 -1.139 +PO4 1.048 2.233 -0.633 +GL1 0.979 2.260 -0.191 +C1A 0.854 2.292 0.282 +C2A 0.743 2.318 0.779 +C3A 0.673 2.374 1.215 +NC3 1.267 1.369 -1.134 +PO4 1.247 1.305 -0.634 +GL1 1.219 1.260 -0.170 +C1A 1.165 1.169 0.286 +C2A 1.153 1.158 0.769 +C3A 1.126 1.075 1.244 +NC3 0.841 1.785 -1.061 +PO4 0.917 1.761 -0.605 +GL1 1.029 1.697 -0.147 +C1A 1.138 1.700 0.337 +C2A 1.221 1.684 0.816 +C3A 1.269 1.699 1.308 +NC3 1.169 2.105 -1.118 +PO4 1.175 2.108 -0.607 +GL1 1.230 2.136 -0.144 +C1A 1.333 2.124 0.356 +C2A 1.381 2.184 0.805 +C3A 1.446 2.222 1.295 +NC3 1.745 0.775 -1.074 +PO4 1.789 0.777 -0.611 +GL1 1.826 0.824 -0.141 +C1A 1.863 0.829 0.349 +C2A 1.866 0.817 0.841 +C3A 1.890 0.851 1.277 +NC3 1.853 1.493 -1.063 +PO4 1.847 1.522 -0.594 +GL1 1.842 1.490 -0.157 +C1A 1.907 1.514 0.304 +C2A 1.964 1.473 0.753 +C3A 1.979 1.461 1.222 +NC3 2.078 2.552 -1.086 +PO4 2.010 2.602 -0.652 +GL1 1.980 2.616 -0.179 +C1A 1.967 2.662 0.314 +C2A 1.978 2.669 0.765 +C3A 1.940 2.651 1.240 +108 + 2.400 2.400 7.000 +NC3 0.146 0.735 1.117 +PO4 0.195 0.704 0.653 +GL1 0.196 0.673 0.163 +C1A 0.272 0.694 -0.302 +C2A 0.338 0.674 -0.771 +C3A 0.350 0.694 -1.219 +NC3 -0.069 1.390 1.002 +PO4 0.009 1.401 0.580 +GL1 0.029 1.381 0.100 +C1A 0.053 1.337 -0.398 +C2A 0.080 1.364 -0.841 +C3A 0.103 1.315 -1.287 +NC3 0.198 2.500 1.130 +PO4 0.248 2.462 0.658 +GL1 0.335 2.433 0.179 +C1A 0.354 2.345 -0.259 +C2A 0.425 2.289 -0.731 +C3A 0.449 2.248 -1.214 +NC3 1.160 0.553 1.127 +PO4 1.122 0.554 0.675 +GL1 1.083 0.577 0.162 +C1A 1.061 0.584 -0.253 +C2A 1.002 0.580 -0.677 +C3A 0.980 0.628 -1.213 +NC3 1.520 1.548 1.097 +PO4 1.481 1.561 0.605 +GL1 1.450 1.527 0.198 +C1A 1.448 1.475 -0.333 +C2A 1.443 1.458 -0.780 +C3A 1.343 1.432 -1.250 +NC3 1.027 1.686 1.137 +PO4 1.041 1.721 0.667 +GL1 1.023 1.700 0.183 +C1A 0.961 1.664 -0.302 +C2A 0.970 1.702 -0.771 +C3A 0.984 1.743 -1.235 +NC3 2.052 -0.097 1.061 +PO4 2.014 -0.066 0.622 +GL1 2.005 -0.025 0.173 +C1A 1.968 0.014 -0.360 +C2A 1.932 0.056 -0.779 +C3A 1.975 0.045 -1.271 +NC3 2.188 0.880 1.096 +PO4 2.181 0.863 0.632 +GL1 2.219 0.861 0.169 +C1A 2.191 0.920 -0.307 +C2A 2.160 0.894 -0.768 +C3A 2.121 0.877 -1.234 +NC3 1.990 2.075 1.061 +PO4 1.937 2.086 0.602 +GL1 1.929 2.038 0.130 +C1A 1.941 2.061 -0.292 +C2A 1.938 2.073 -0.793 +C3A 1.898 2.039 -1.292 +NC3 0.626 1.564 -4.176 +PO4 0.699 1.441 -3.698 +GL1 0.733 1.364 -3.247 +C1A 0.747 1.245 -2.738 +C2A 0.803 1.176 -2.309 +C3A 0.852 1.090 -1.829 +NC3 1.263 1.473 -4.155 +PO4 1.279 1.531 -3.666 +GL1 1.288 1.542 -3.238 +C1A 1.306 1.572 -2.728 +C2A 1.338 1.547 -2.254 +C3A 1.350 1.617 -1.843 +NC3 1.217 2.476 -4.039 +PO4 1.088 2.570 -3.530 +GL1 0.999 2.614 -3.060 +C1A 0.927 2.610 -2.658 +C2A 0.824 2.618 -2.141 +C3A 0.709 2.641 -1.718 +NC3 1.565 1.371 -4.105 +PO4 1.495 1.338 -3.641 +GL1 1.456 1.251 -3.143 +C1A 1.453 1.205 -2.690 +C2A 1.453 1.126 -2.236 +C3A 1.403 1.070 -1.768 +NC3 1.346 1.542 -4.110 +PO4 1.412 1.546 -3.685 +GL1 1.538 1.547 -3.204 +C1A 1.606 1.518 -2.732 +C2A 1.645 1.491 -2.256 +C3A 1.773 1.478 -1.775 +NC3 1.572 2.521 -4.171 +PO4 1.656 2.495 -3.712 +GL1 1.727 2.561 -3.197 +C1A 1.743 2.527 -2.750 +C2A 1.784 2.566 -2.244 +C3A 1.864 2.596 -1.799 +NC3 1.989 0.911 -4.108 +PO4 2.064 1.015 -3.656 +GL1 2.040 0.965 -3.184 +C1A 2.119 0.965 -2.736 +C2A 2.128 1.012 -2.215 +C3A 2.122 1.097 -1.765 +NC3 2.159 1.345 -4.110 +PO4 2.194 1.283 -3.638 +GL1 2.248 1.276 -3.173 +C1A 2.263 1.273 -2.719 +C2A 2.282 1.236 -2.245 +C3A 2.319 1.257 -1.744 +NC3 2.809 2.225 -4.030 +PO4 2.767 2.283 -3.609 +GL1 2.787 2.268 -3.111 +C1A 2.736 2.302 -2.635 +C2A 2.725 2.345 -2.202 +C3A 2.721 2.359 -1.732 diff --git a/regtest/basic/rt-molinfo-whole-repair/Makefile b/regtest/basic/rt-molinfo-whole-repair/Makefile new file mode 100644 index 0000000000..3703b27cea --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-repair/Makefile @@ -0,0 +1 @@ +include ../../scripts/test.make diff --git a/regtest/basic/rt-molinfo-whole-repair/config b/regtest/basic/rt-molinfo-whole-repair/config new file mode 100644 index 0000000000..7b72bfb742 --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-repair/config @@ -0,0 +1,3 @@ +type=driver +# torn frames in several cell shapes; the reference is whole +arg="--igro traj.gro" diff --git a/regtest/basic/rt-molinfo-whole-repair/plumed.dat b/regtest/basic/rt-molinfo-whole-repair/plumed.dat new file mode 100644 index 0000000000..0c4ffd2071 --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-repair/plumed.dat @@ -0,0 +1,4 @@ +# whole reference with a CRYST1 record: it is checked, and it passes +MOLINFO STRUCTURE=whole.pdb WHOLE +WHOLEMOLECULES ENTITY0=1-304 +DUMPATOMS ATOMS=1-304 FILE=whole.xyz PRECISION=3 diff --git a/regtest/basic/rt-molinfo-whole-repair/traj.gro b/regtest/basic/rt-molinfo-whole-repair/traj.gro new file mode 100644 index 0000000000..87dbb0e15f --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-repair/traj.gro @@ -0,0 +1,1535 @@ +dodecahedron cell, brick wrapping + 304 + 1ASN N 1 1.749 3.804 1.455 + 1ASN CA 2 1.754 3.875 1.325 + 1ASN C 3 1.617 3.915 1.272 + 1ASN O 4 1.596 4.034 1.251 + 1ASN CB 5 1.840 3.800 1.222 + 1ASN CG 6 1.987 3.802 1.266 + 1ASN OD1 7 2.021 3.864 1.365 + 1ASN ND2 8 2.075 3.733 1.196 + 1ASN H1 9 1.690 3.854 1.521 + 1ASN H2 10 1.714 3.710 1.443 + 1ASN H3 11 1.843 3.799 1.494 + 1ASN HA 12 1.805 3.970 1.344 + 1ASN HB2 13 1.807 3.698 1.215 + 1ASN HB3 14 1.832 3.850 1.126 + 1ASN HD21 15 2.052 3.677 1.115 + 1ASN HD22 16 2.170 3.741 1.230 + 2LEU N 17 1.523 3.821 1.254 + 2LEU CA 18 1.386 3.848 1.209 + 2LEU C 19 1.319 3.969 1.279 + 2LEU O 20 1.272 4.061 1.211 + 2LEU CB 21 1.303 3.718 1.220 + 2LEU CG 22 1.306 3.645 1.357 + 2LEU CD1 23 1.174 3.660 1.433 + 2LEU CD2 24 1.334 3.496 1.340 + 2LEU H 25 1.546 3.723 1.266 + 2LEU HA 26 1.390 3.874 1.103 + 2LEU HB2 27 1.201 3.742 1.197 + 2LEU HB3 28 1.342 3.650 1.144 + 2LEU HG 29 1.384 3.687 1.420 + 2LEU HD11 30 1.152 3.765 1.449 + 2LEU HD12 31 1.093 3.614 1.377 + 2LEU HD13 32 1.181 3.612 1.530 + 2LEU HD21 33 1.257 3.451 1.277 + 2LEU HD22 34 1.432 3.481 1.294 + 2LEU HD23 35 1.333 3.447 1.437 + 3TYR N 36 1.321 3.973 1.412 + 3TYR CA 37 1.264 4.084 1.490 + 3TYR C 38 1.338 4.217 1.470 + 3TYR O 39 1.277 4.323 1.473 + 3TYR CB 40 1.260 4.044 1.638 + 3TYR CG 41 4.744 4.106 1.712 + 3TYR CD1 42 4.755 4.236 1.766 + 3TYR CD2 43 4.623 4.035 1.724 + 3TYR CE1 44 4.645 4.295 1.830 + 3TYR CE2 45 4.512 4.094 1.788 + 3TYR CZ 46 4.523 4.225 1.840 + 3TYR OH 47 4.415 4.285 1.898 + 3TYR H 48 1.356 3.893 1.462 + 3TYR HA 49 1.161 4.098 1.456 + 3TYR HB2 50 1.252 3.937 1.645 + 3TYR HB3 51 1.354 4.072 1.686 + 3TYR HD1 52 1.248 4.291 1.756 + 3TYR HD2 53 4.613 3.935 1.685 + 3TYR HE1 54 4.651 4.394 1.871 + 3TYR HE2 55 4.420 4.038 1.797 + 3TYR HH 56 4.333 4.244 1.870 + 4ILE N 57 1.470 4.212 1.444 + 4ILE CA 58 1.553 4.329 1.413 + 4ILE C 59 1.508 4.389 1.279 + 4ILE O 60 1.487 0.910 1.268 + 4ILE CB 61 1.704 4.292 1.410 + 4ILE CG1 62 1.750 4.203 1.528 + 4ILE CG2 63 1.792 4.418 1.400 + 4ILE CD1 64 1.721 4.259 1.668 + 4ILE H 65 1.511 4.121 1.431 + 4ILE HA 66 1.538 4.405 1.490 + 4ILE HB 67 1.723 4.235 1.319 + 4ILE HG12 68 1.700 4.108 1.519 + 4ILE HG13 69 1.857 4.186 1.519 + 4ILE HG21 70 1.771 4.471 1.307 + 4ILE HG22 71 1.772 4.485 1.484 + 4ILE HG23 72 1.897 4.390 1.401 + 4ILE HD11 73 1.770 4.356 1.681 + 4ILE HD12 74 1.614 4.270 1.683 + 4ILE HD13 75 1.760 4.190 1.743 + 5GLN N 76 1.487 4.303 1.178 + 5GLN CA 77 1.435 0.744 1.047 + 5GLN C 78 1.291 0.798 1.054 + 5GLN O 79 1.255 0.885 0.975 + 5GLN CB 80 1.443 4.226 0.948 + 5GLN CG 81 1.471 0.674 0.804 + 5GLN CD 82 1.619 0.703 0.780 + 5GLN OE1 83 1.664 0.818 0.779 + 5GLN NE2 84 1.700 0.601 0.757 + 5GLN H 85 1.506 4.205 1.195 + 5GLN HA 86 1.499 0.824 1.011 + 5GLN HB2 87 1.522 4.160 0.979 + 5GLN HB3 88 1.348 4.172 0.949 + 5GLN HG2 89 1.440 0.598 0.736 + 5GLN HG3 90 1.412 0.763 0.783 + 5GLN HE21 91 1.665 4.107 0.753 + 5GLN HE22 92 1.796 0.625 0.741 + 6TRP N 93 1.208 4.352 1.149 + 6TRP CA 94 1.076 4.410 1.175 + 6TRP C 95 1.085 0.946 1.246 + 6TRP O 96 1.016 1.041 1.208 + 6TRP CB 97 0.991 4.310 1.254 + 6TRP CG 98 4.454 4.359 1.291 + 6TRP CD1 99 4.347 4.364 1.208 + 6TRP CD2 100 4.408 4.412 1.419 + 6TRP NE1 101 4.239 4.420 1.275 + 6TRP CE2 102 4.271 4.449 1.406 + 6TRP CE3 103 4.468 4.433 1.545 + 6TRP CZ2 104 4.196 4.502 1.511 + 6TRP CZ3 105 4.394 4.488 1.651 + 6TRP CH2 106 4.258 4.521 1.636 + 6TRP H 107 1.239 4.272 1.204 + 6TRP HA 108 1.026 0.828 1.080 + 6TRP HB2 109 0.980 4.221 1.195 + 6TRP HB3 110 1.043 4.283 1.346 + 6TRP HD1 111 4.347 4.331 1.105 + 6TRP HE1 112 4.147 4.436 1.235 + 6TRP HE3 113 4.571 4.405 1.558 + 6TRP HZ2 114 4.092 4.528 1.496 + 6TRP HZ3 115 4.442 4.504 1.747 + 6TRP HH2 116 4.203 4.562 1.719 + 7LEU N 117 1.172 0.959 1.348 + 7LEU CA 118 1.192 1.086 1.419 + 7LEU C 119 1.251 1.196 1.329 + 7LEU O 120 1.202 1.308 1.335 + 7LEU CB 121 1.278 4.665 1.544 + 7LEU CG 122 1.203 4.601 1.663 + 7LEU CD1 123 1.302 4.578 1.778 + 7LEU CD2 124 4.689 4.688 1.715 + 7LEU H 125 1.224 4.477 1.378 + 7LEU HA 126 1.094 1.123 1.449 + 7LEU HB2 127 1.361 4.602 1.518 + 7LEU HB3 128 1.316 1.162 1.577 + 7LEU HG 129 1.163 4.505 1.632 + 7LEU HD11 130 1.383 4.513 1.744 + 7LEU HD12 131 1.342 4.673 1.812 + 7LEU HD13 132 4.851 4.529 1.861 + 7LEU HD21 133 4.725 4.789 1.737 + 7LEU HD22 134 4.609 4.694 1.641 + 7LEU HD23 135 4.647 4.645 1.806 + 8LYS N 136 1.352 1.166 1.245 + 8LYS CA 137 1.416 1.267 1.158 + 8LYS C 138 1.319 1.335 1.060 + 8LYS O 139 1.341 1.449 1.021 + 8LYS CB 140 1.539 1.208 1.086 + 8LYS CG 141 1.507 1.114 0.969 + 8LYS CD 142 1.517 1.180 0.831 + 8LYS CE 143 1.493 1.075 0.722 + 8LYS NZ 144 1.612 1.054 0.637 + 8LYS H 145 1.390 1.072 1.248 + 8LYS HA 146 1.452 1.347 1.223 + 8LYS HB2 147 1.597 1.290 1.048 + 8LYS HB3 148 1.597 1.153 1.160 + 8LYS HG2 149 1.575 1.031 0.972 + 8LYS HG3 150 1.406 1.074 0.981 + 8LYS HD2 151 1.444 1.258 0.823 + 8LYS HD3 152 1.616 1.225 0.820 + 8LYS HE2 153 1.466 0.982 0.768 + 8LYS HE3 154 1.407 1.107 0.661 + 8LYS HZ1 155 1.643 1.141 0.596 + 8LYS HZ2 156 1.685 1.012 0.694 + 8LYS HZ3 157 1.591 0.988 0.564 + 9ASP N 158 1.209 1.267 1.024 + 9ASP CA 159 1.099 1.317 0.942 + 9ASP C 160 1.002 1.409 1.019 + 9ASP O 161 0.915 1.469 0.956 + 9ASP CB 162 1.024 1.197 0.883 + 9ASP CG 163 1.075 1.156 0.744 + 9ASP OD1 164 1.198 1.136 0.729 + 9ASP OD2 165 0.988 1.146 0.654 + 9ASP H 166 1.203 1.171 1.057 + 9ASP HA 167 1.140 1.377 0.860 + 9ASP HB2 168 1.036 1.113 0.949 + 9ASP HB3 169 0.919 1.221 0.873 + 10GLY N 170 1.014 1.420 1.152 + 10GLY CA 171 0.926 1.500 1.239 + 10GLY C 172 4.435 1.418 1.332 + 10GLY O 173 4.348 1.476 1.396 + 10GLY H 174 1.091 1.372 1.197 + 10GLY HA2 175 0.989 1.563 1.302 + 10GLY HA3 176 0.863 1.566 1.179 + 11GLY N 177 4.453 1.285 1.339 + 11GLY CA 178 4.373 1.198 1.425 + 11GLY C 179 4.222 1.212 1.399 + 11GLY O 180 4.180 1.197 1.284 + 11GLY H 181 0.924 1.242 1.281 + 11GLY HA2 182 4.402 1.094 1.406 + 11GLY HA3 183 4.398 1.221 1.528 + 12PRO N 184 4.139 1.243 1.501 + 12PRO CA 185 3.995 1.262 1.482 + 12PRO C 186 3.959 1.373 1.381 + 12PRO O 187 3.856 1.365 1.315 + 12PRO CB 188 3.938 1.296 1.621 + 12PRO CG 189 4.044 1.247 1.719 + 12PRO CD 190 4.174 1.265 1.640 + 12PRO HA 191 3.951 1.168 1.448 + 12PRO HB2 192 3.922 1.402 1.631 + 12PRO HB3 193 3.842 1.246 1.638 + 12PRO HG2 194 4.044 1.307 1.808 + 12PRO HG3 195 4.029 4.742 1.740 + 12PRO HD2 196 4.213 1.364 1.654 + 12PRO HD3 197 4.248 1.194 1.676 + 13SER N 198 4.045 1.475 1.366 + 13SER CA 199 4.023 1.591 1.279 + 13SER C 200 4.057 1.566 1.131 + 13SER O 201 4.076 1.661 1.056 + 13SER CB 202 4.101 1.712 1.334 + 13SER OG 203 4.056 1.744 1.464 + 13SER H 204 4.132 1.473 1.418 + 13SER HA 205 3.917 1.617 1.282 + 13SER HB2 206 4.206 1.687 1.338 + 13SER HB3 207 4.087 1.798 1.269 + 13SER HG 208 3.967 1.779 1.458 + 14SER N 209 4.063 1.439 1.089 + 14SER CA 210 4.102 1.398 0.953 + 14SER C 211 3.997 1.310 0.883 + 14SER O 212 4.025 1.247 0.781 + 14SER CB 213 4.239 1.330 0.959 + 14SER OG 214 0.714 1.362 0.844 + 14SER H 215 4.050 1.367 1.159 + 14SER HA 216 4.113 1.487 0.892 + 14SER HB2 217 4.292 1.364 1.046 + 14SER HB3 218 4.229 1.222 0.968 + 14SER HG 219 0.794 1.411 0.877 + 15GLY N 220 3.874 1.303 0.937 + 15GLY CA 221 3.762 1.231 0.876 + 15GLY C 222 3.778 1.079 0.873 + 15GLY O 223 3.720 1.013 0.786 + 15GLY H 224 3.857 1.359 1.019 + 15GLY HA2 225 3.670 1.254 0.931 + 15GLY HA3 226 3.749 1.266 0.773 + 16ARG N 227 3.857 1.022 0.965 + 16ARG CA 228 3.896 0.880 0.967 + 16ARG C 229 3.906 0.825 1.111 + 16ARG O 230 3.972 0.888 1.195 + 16ARG CB 231 4.026 0.862 0.887 + 16ARG CG 232 4.146 0.943 0.941 + 16ARG CD 233 0.673 0.934 0.856 + 16ARG NE 234 0.678 1.036 0.749 + 16ARG CZ 235 0.633 1.027 0.625 + 16ARG NH1 236 0.573 0.919 0.579 + 16ARG NH2 237 0.649 1.128 0.543 + 16ARG H 238 3.898 1.083 1.034 + 16ARG HA 239 3.818 0.825 0.915 + 16ARG HB2 240 4.053 0.758 0.890 + 16ARG HB3 241 4.006 0.892 0.785 + 16ARG HG2 242 4.116 1.046 0.946 + 16ARG HG3 243 4.170 0.907 1.040 + 16ARG HD2 244 0.758 0.948 0.920 + 16ARG HD3 245 0.684 0.834 0.816 + 16ARG HE 246 0.723 1.124 0.771 + 16ARG HH11 247 0.561 0.842 0.643 + 16ARG HH12 248 0.538 0.915 0.486 + 16ARG HH21 249 0.701 1.208 0.576 + 16ARG HH22 250 0.615 1.124 0.449 + 17PRO N 251 3.845 4.309 1.142 + 17PRO CA 252 3.850 4.250 1.276 + 17PRO C 253 3.990 4.197 1.310 + 17PRO O 254 4.069 4.172 1.219 + 17PRO CB 255 3.746 4.137 1.273 + 17PRO CG 256 3.747 4.092 1.128 + 17PRO CD 257 3.772 4.222 1.051 + 17PRO HA 258 3.820 4.325 1.350 + 17PRO HB2 259 3.775 4.057 1.339 + 17PRO HB3 260 3.648 4.178 1.299 + 17PRO HG2 261 3.825 4.021 1.110 + 17PRO HG3 262 3.652 4.046 1.099 + 17PRO HD2 263 3.831 4.203 0.963 + 17PRO HD3 264 3.677 4.268 1.025 + 18PRO N 265 4.023 4.178 1.439 + 18PRO CA 266 4.152 4.125 1.481 + 18PRO C 267 4.166 3.976 1.443 + 18PRO O 268 4.068 3.902 1.449 + 18PRO CB 269 4.158 4.144 1.632 + 18PRO CG 270 4.011 4.143 1.675 + 18PRO CD 271 3.940 4.206 1.556 + 18PRO HA 272 4.231 4.183 1.434 + 18PRO HB2 273 4.212 4.065 1.679 + 18PRO HB3 274 4.202 4.242 1.655 + 18PRO HG2 275 3.977 4.043 1.691 + 18PRO HG3 276 3.995 4.200 1.766 + 18PRO HD2 277 3.842 4.163 1.543 + 18PRO HD3 278 3.933 4.314 1.570 + 19PRO N 279 4.288 3.931 1.407 + 19PRO CA 280 4.315 3.791 1.377 + 19PRO C 281 4.325 3.708 1.506 + 19PRO O 282 4.404 3.740 1.595 + 19PRO CB 283 4.445 3.794 1.298 + 19PRO CG 284 4.520 3.913 1.357 + 19PRO CD 285 4.408 4.011 1.390 + 19PRO HA 286 4.236 3.750 1.314 + 19PRO HB2 287 4.501 3.703 1.312 + 19PRO HB3 288 4.424 3.814 1.193 + 19PRO HG2 289 4.574 3.885 1.446 + 19PRO HG3 290 0.992 3.956 1.287 + 19PRO HD2 291 4.431 4.064 1.481 + 19PRO HD3 292 4.394 4.080 1.307 + 20SER N 293 4.243 3.602 1.516 + 20SER CA 294 4.248 3.499 1.622 + 20SER C 295 4.360 3.398 1.598 + 20SER O 296 4.364 3.341 1.487 + 20SER CB 297 4.114 3.424 1.629 + 20SER OG 298 4.010 3.514 1.659 + 20SER OXT 299 4.437 3.376 1.694 + 20SER H 300 4.179 3.584 1.440 + 20SER HA 301 4.268 3.546 1.717 + 20SER HB2 302 4.095 3.377 1.534 + 20SER HB3 303 4.121 3.348 1.707 + 20SER HG 304 4.043 3.576 1.725 + 3.60000 3.60000 2.54558 0.00000 0.00000 0.00000 0.00000 1.80000 1.80000 +octahedron cell, compact wrapping + 304 + 1ASN N 1 0.011 1.436 1.051 + 1ASN CA 2 0.069 1.373 1.172 + 1ASN C 3 3.563 1.316 1.266 + 1ASN O 4 1.169 4.591 1.292 + 1ASN CB 5 0.169 1.466 1.242 + 1ASN CG 6 0.293 1.484 1.155 + 1ASN OD1 7 0.304 1.424 1.049 + 1ASN ND2 8 0.387 1.570 1.192 + 1ASN H1 9 3.543 1.375 1.007 + 1ASN H2 10 3.567 1.525 1.073 + 1ASN H3 11 0.086 1.454 0.985 + 1ASN HA 12 0.126 1.286 1.138 + 1ASN HB2 13 0.124 1.561 1.260 + 1ASN HB3 14 0.200 1.421 1.337 + 1ASN HD21 15 0.382 1.625 1.277 + 1ASN HD22 16 0.466 1.575 1.131 + 2LEU N 17 3.466 1.395 1.313 + 2LEU CA 18 3.356 1.350 1.399 + 2LEU C 19 3.291 1.217 1.355 + 2LEU O 20 3.283 1.122 1.433 + 2LEU CB 21 3.254 1.465 1.416 + 2LEU CG 22 3.202 1.530 1.285 + 2LEU CD1 23 3.057 1.492 1.255 + 2LEU CD2 24 3.210 1.683 1.293 + 2LEU H 25 3.468 1.495 1.295 + 2LEU HA 26 3.397 1.330 1.498 + 2LEU HB2 27 3.170 1.427 1.470 + 2LEU HB3 28 3.304 1.542 1.475 + 2LEU HG 29 3.262 1.499 1.200 + 2LEU HD11 30 3.049 1.384 1.246 + 2LEU HD12 31 2.992 1.528 1.334 + 2LEU HD13 32 3.025 1.536 1.160 + 2LEU HD21 33 3.151 1.719 1.377 + 2LEU HD22 34 3.313 1.715 1.305 + 2LEU HD23 35 3.170 1.727 1.201 + 3TYR N 36 3.252 1.206 1.227 + 3TYR CA 37 3.191 1.085 1.172 + 3TYR C 38 0.889 4.360 1.167 + 3TYR O 39 0.847 4.245 1.183 + 3TYR CB 40 3.135 1.116 1.032 + 3TYR CG 41 3.013 1.033 0.999 + 3TYR CD1 42 3.027 0.904 0.944 + 3TYR CD2 43 2.884 1.084 1.026 + 3TYR CE1 44 2.913 0.826 0.918 + 3TYR CE2 45 2.770 1.006 1.001 + 3TYR CZ 46 2.785 0.876 0.948 + 3TYR OH 47 2.676 0.798 0.927 + 3TYR H 48 3.256 1.288 1.169 + 3TYR HA 49 3.108 1.057 1.236 + 3TYR HB2 50 3.108 1.220 1.029 + 3TYR HB3 51 3.212 1.100 0.957 + 3TYR HD1 52 0.726 4.259 0.924 + 3TYR HD2 53 2.872 1.184 1.067 + 3TYR HE1 54 0.522 4.121 0.877 + 3TYR HE2 55 2.672 1.047 1.022 + 3TYR HH 56 2.601 0.826 0.979 + 4ILE N 57 1.019 4.386 1.149 + 4ILE CA 58 1.126 4.285 1.153 + 4ILE C 59 1.135 4.225 1.294 + 4ILE O 60 1.138 4.103 1.310 + 4ILE CB 61 1.262 4.345 1.107 + 4ILE CG1 62 1.253 4.433 0.981 + 4ILE CG2 63 1.367 4.234 1.088 + 4ILE CD1 64 1.192 4.367 0.857 + 4ILE H 65 1.047 4.483 1.149 + 4ILE HA 66 1.099 4.204 1.084 + 4ILE HB 67 1.299 4.408 1.187 + 4ILE HG12 68 1.194 4.520 1.005 + 4ILE HG13 69 1.354 4.467 0.955 + 4ILE HG21 70 1.386 4.183 1.183 + 4ILE HG22 71 1.333 4.161 1.015 + 4ILE HG23 72 1.461 4.278 1.054 + 4ILE HD11 73 1.248 4.278 0.829 + 4ILE HD12 74 1.088 4.339 0.877 + 4ILE HD13 75 1.194 4.437 0.774 + 5GLN N 76 1.133 4.312 1.396 + 5GLN CA 77 1.132 4.270 1.537 + 5GLN C 78 1.004 4.194 1.576 + 5GLN O 79 1.010 4.107 1.662 + 5GLN CB 80 1.152 4.393 1.628 + 5GLN CG 81 1.231 4.357 1.755 + 5GLN CD 82 1.382 4.351 1.731 + 5GLN OE1 83 1.442 4.246 1.718 + 5GLN NE2 84 1.448 4.466 1.727 + 5GLN H 85 1.130 4.411 1.374 + 5GLN HA 86 1.216 4.203 1.551 + 5GLN HB2 87 1.206 4.468 1.574 + 5GLN HB3 88 1.054 4.432 1.657 + 5GLN HG2 89 1.211 4.431 1.831 + 5GLN HG3 90 1.197 4.261 1.795 + 5GLN HE21 91 1.402 4.554 1.742 + 5GLN HE22 92 1.547 4.458 1.712 + 6TRP N 93 0.890 4.223 1.512 + 6TRP CA 94 0.767 4.144 1.529 + 6TRP C 95 0.775 4.007 1.458 + 6TRP O 96 0.737 3.905 1.517 + 6TRP CB 97 0.646 4.226 1.481 + 6TRP CG 98 0.515 4.154 1.490 + 6TRP CD1 99 2.841 0.743 1.603 + 6TRP CD2 100 0.440 4.088 1.384 + 6TRP NE1 101 2.728 0.668 1.573 + 6TRP CE2 102 0.321 4.032 1.440 + 6TRP CE3 103 0.459 4.071 1.245 + 6TRP CZ2 104 0.227 3.963 1.363 + 6TRP CZ3 105 0.366 4.000 1.167 + 6TRP CH2 106 0.249 3.947 1.225 + 6TRP H 107 0.889 4.303 1.451 + 6TRP HA 108 0.753 4.123 1.635 + 6TRP HB2 109 3.040 0.920 1.541 + 6TRP HB3 110 0.662 4.255 1.378 + 6TRP HD1 111 2.868 0.780 1.701 + 6TRP HE1 112 2.657 0.640 1.641 + 6TRP HE3 113 0.547 4.113 1.199 + 6TRP HZ2 114 2.538 0.528 1.410 + 6TRP HZ3 115 0.383 3.987 1.061 + 6TRP HH2 116 0.178 3.895 1.164 + 7LEU N 117 0.827 4.002 1.335 + 7LEU CA 118 0.843 3.877 1.261 + 7LEU C 119 0.944 3.782 1.327 + 7LEU O 120 0.914 3.663 1.337 + 7LEU CB 121 0.881 3.904 1.114 + 7LEU CG 122 0.763 3.951 1.026 + 7LEU CD1 123 0.815 3.983 0.886 + 7LEU CD2 124 0.654 3.844 1.013 + 7LEU H 125 0.852 4.090 1.289 + 7LEU HA 126 0.748 3.824 1.263 + 7LEU HB2 127 0.956 3.981 1.113 + 7LEU HB3 128 0.921 3.813 1.071 + 7LEU HG 129 0.720 4.041 1.068 + 7LEU HD11 130 0.892 4.060 0.892 + 7LEU HD12 131 0.858 3.894 0.840 + 7LEU HD13 132 0.734 4.019 0.823 + 7LEU HD21 133 0.697 3.749 0.980 + 7LEU HD22 134 0.603 3.830 1.108 + 7LEU HD23 135 0.580 3.876 0.940 + 8LYS N 136 1.060 3.831 1.374 + 8LYS CA 137 1.163 3.745 1.437 + 8LYS C 138 1.114 3.668 1.560 + 8LYS O 139 1.166 3.561 1.590 + 8LYS CB 140 1.291 3.826 1.466 + 8LYS CG 141 1.283 3.920 1.587 + 8LYS CD 142 1.347 3.863 1.715 + 8LYS CE 143 1.342 3.968 1.826 + 8LYS NZ 144 1.477 4.011 1.869 + 8LYS H 145 1.080 3.930 1.360 + 8LYS HA 146 1.190 3.668 1.364 + 8LYS HB2 147 1.371 3.756 1.483 + 8LYS HB3 148 1.314 3.886 1.377 + 8LYS HG2 149 1.333 4.011 1.562 + 8LYS HG3 150 1.179 3.943 1.608 + 8LYS HD2 151 1.293 3.775 1.745 + 8LYS HD3 152 1.450 3.834 1.694 + 8LYS HE2 153 1.287 4.053 1.791 + 8LYS HE3 154 1.286 3.926 1.911 + 8LYS HZ1 155 1.533 3.932 1.897 + 8LYS HZ2 156 1.520 4.061 1.791 + 8LYS HZ3 157 1.469 4.077 1.945 + 9ASP N 158 1.012 3.721 1.629 + 9ASP CA 159 0.943 3.658 1.742 + 9ASP C 160 0.843 3.549 1.700 + 9ASP O 161 0.791 3.479 1.787 + 9ASP CB 162 0.872 3.769 1.822 + 9ASP CG 163 0.957 3.823 1.938 + 9ASP OD1 164 1.073 3.862 1.913 + 9ASP OD2 165 0.902 3.825 2.051 + 9ASP H 166 0.981 3.812 1.600 + 9ASP HA 167 1.017 3.610 1.806 + 9ASP HB2 168 0.849 3.850 1.756 + 9ASP HB3 169 0.781 3.729 1.865 + 10GLY N 170 0.813 3.533 1.570 + 10GLY CA 171 0.717 3.437 1.515 + 10GLY C 172 0.590 3.499 1.456 + 10GLY O 173 0.497 3.425 1.423 + 10GLY H 174 0.865 3.590 1.503 + 10GLY HA2 175 0.767 3.381 1.435 + 10GLY HA3 176 0.688 3.365 1.592 + 11GLY N 177 0.583 3.632 1.444 + 11GLY CA 178 0.467 3.702 1.388 + 11GLY C 179 0.337 3.667 1.461 + 11GLY O 180 0.331 3.681 1.583 + 11GLY H 181 0.661 3.688 1.476 + 11GLY HA2 182 0.484 3.810 1.397 + 11GLY HA3 183 0.461 3.678 1.282 + 12PRO N 184 0.231 3.618 1.391 + 12PRO CA 185 0.105 3.578 1.454 + 12PRO C 186 0.122 3.468 1.561 + 12PRO O 187 0.045 3.464 1.657 + 12PRO CB 188 0.014 3.529 1.341 + 12PRO CG 189 0.075 3.589 1.214 + 12PRO CD 190 0.224 3.595 1.247 + 12PRO HA 191 0.060 3.666 1.501 + 12PRO HB2 192 0.013 3.422 1.336 + 12PRO HB3 193 3.511 3.563 1.355 + 12PRO HG2 194 0.057 3.526 1.129 + 12PRO HG3 195 0.037 3.690 1.199 + 12PRO HD2 196 0.272 3.502 1.222 + 12PRO HD3 197 0.271 3.674 1.189 + 13SER N 198 0.223 3.382 1.548 + 13SER CA 199 0.249 3.268 1.637 + 13SER C 200 0.323 3.305 1.766 + 13SER O 201 0.379 3.218 1.831 + 13SER CB 202 0.324 3.158 1.560 + 13SER OG 203 0.246 3.113 1.451 + 13SER H 204 0.288 3.394 1.471 + 13SER HA 205 0.153 3.226 1.668 + 13SER HB2 206 0.417 3.198 1.523 + 13SER HB3 207 0.344 3.074 1.626 + 13SER HG 208 0.170 3.065 1.485 + 14SER N 209 0.322 3.434 1.805 + 14SER CA 210 0.394 3.487 1.921 + 14SER C 211 0.303 3.561 2.022 + 14SER O 212 0.352 3.632 2.109 + 14SER CB 213 0.509 3.574 1.872 + 14SER OG 214 0.621 3.560 1.957 + 14SER H 215 0.276 3.499 1.743 + 14SER HA 216 0.438 3.404 1.976 + 14SER HB2 217 0.537 3.544 1.773 + 14SER HB3 218 0.480 3.679 1.867 + 14SER HG 219 0.693 3.522 1.901 + 15GLY N 220 0.171 3.546 2.009 + 15GLY CA 221 0.073 3.603 2.103 + 15GLY C 222 0.064 3.756 2.101 + 15GLY O 223 0.027 3.816 2.201 + 15GLY H 224 0.138 3.484 1.936 + 15GLY HA2 225 3.574 3.564 2.080 + 15GLY HA3 226 0.099 3.572 2.204 + 16ARG N 227 0.101 3.820 1.988 + 16ARG CA 228 2.513 0.571 1.974 + 16ARG C 229 2.469 0.620 1.835 + 16ARG O 230 2.514 0.564 1.735 + 16ARG CB 231 2.658 0.614 2.009 + 16ARG CG 232 0.365 3.943 1.920 + 16ARG CD 233 0.510 3.975 1.960 + 16ARG NE 234 0.565 3.881 2.059 + 16ARG CZ 235 0.560 3.889 2.192 + 16ARG NH1 236 0.501 3.988 2.254 + 16ARG NH2 237 0.617 3.796 2.264 + 16ARG H 238 0.127 3.762 1.910 + 16ARG HA 239 2.448 0.616 2.049 + 16ARG HB2 240 2.665 0.720 1.998 + 16ARG HB3 241 0.276 3.980 2.112 + 16ARG HG2 242 0.353 3.836 1.925 + 16ARG HG3 243 0.352 3.978 1.818 + 16ARG HD2 244 0.572 3.971 1.872 + 16ARG HD3 245 0.517 4.078 1.994 + 16ARG HE 246 0.614 3.800 2.024 + 16ARG HH11 247 0.457 4.059 2.198 + 16ARG HH12 248 1.697 2.295 -0.586 + 16ARG HH21 249 0.668 3.724 2.216 + 16ARG HH22 250 0.614 3.799 2.364 + 17PRO N 251 2.383 0.724 1.825 + 17PRO CA 252 2.336 0.776 1.696 + 17PRO C 253 2.449 0.848 1.620 + 17PRO O 254 2.547 0.890 1.681 + 17PRO CB 255 2.222 0.872 1.732 + 17PRO CG 256 2.261 0.924 1.870 + 17PRO CD 257 2.330 0.803 1.935 + 17PRO HA 258 2.298 0.694 1.636 + 17PRO HB2 259 2.216 0.952 1.661 + 17PRO HB3 260 2.129 0.816 1.740 + 17PRO HG2 261 2.329 1.007 1.862 + 17PRO HG3 262 2.175 0.956 1.928 + 17PRO HD2 263 2.409 0.836 1.999 + 17PRO HD3 264 2.257 0.744 1.990 + 18PRO N 265 2.435 0.865 1.487 + 18PRO CA 266 2.535 0.936 1.407 + 18PRO C 267 2.536 1.086 1.438 + 18PRO O 268 2.431 1.145 1.464 + 18PRO CB 269 2.496 0.910 1.261 + 18PRO CG 270 2.345 0.887 1.267 + 18PRO CD 271 2.326 0.819 1.403 + 18PRO HA 272 2.633 0.893 1.426 + 18PRO HB2 273 2.519 0.995 1.199 + 18PRO HB3 274 2.545 0.820 1.226 + 18PRO HG2 275 2.292 0.980 1.263 + 18PRO HG3 276 2.310 0.824 1.185 + 18PRO HD2 277 2.232 0.848 1.446 + 18PRO HD3 278 2.332 0.711 1.392 + 19PRO N 279 2.654 1.152 1.433 + 19PRO CA 280 2.666 1.296 1.454 + 19PRO C 281 2.622 1.373 1.328 + 19PRO O 282 2.674 1.349 1.219 + 19PRO CB 283 2.814 1.317 1.487 + 19PRO CG 284 2.884 1.207 1.407 + 19PRO CD 285 2.785 1.092 1.411 + 19PRO HA 286 2.605 1.327 1.539 + 19PRO HB2 287 2.847 1.414 1.457 + 19PRO HB3 288 2.829 1.299 1.594 + 19PRO HG2 289 2.902 1.239 1.306 + 19PRO HG3 290 2.980 1.180 1.450 + 19PRO HD2 291 2.786 1.038 1.318 + 19PRO HD3 292 2.809 1.025 1.494 + 20SER N 293 2.525 1.464 1.345 + 20SER CA 294 2.480 1.561 1.244 + 20SER C 295 2.576 1.679 1.231 + 20SER O 296 2.605 1.741 1.335 + 20SER CB 297 2.341 1.615 1.279 + 20SER OG 298 2.248 1.508 1.284 + 20SER OXT 299 2.614 1.708 1.115 + 20SER H 300 2.486 1.476 1.437 + 20SER HA 301 2.477 1.513 1.146 + 20SER HB2 302 2.344 1.663 1.375 + 20SER HB3 303 2.310 1.687 1.204 + 20SER HG 304 2.268 1.449 1.211 + 3.60000 3.39414 2.93950 0.00000 0.00000 1.19993 0.00000 -1.19993 1.69692 +triclinic cell, res wrapping + 304 + 1ASN N 1 0.490 0.686 0.862 + 1ASN CA 2 0.618 0.615 0.886 + 1ASN C 3 0.653 0.602 1.034 + 1ASN O 4 0.668 0.489 1.079 + 1ASN CB 5 0.733 0.674 0.801 + 1ASN CG 6 0.708 0.645 0.653 + 1ASN OD1 7 0.613 0.577 0.619 + 1ASN ND2 8 0.790 0.697 0.564 + 1ASN H1 9 0.416 0.648 0.920 + 1ASN H2 10 0.499 0.785 0.880 + 1ASN H3 11 0.464 0.673 0.764 + 1ASN HA 12 0.604 0.512 0.851 + 1ASN HB2 13 0.737 0.780 0.817 + 1ASN HB3 14 0.827 0.627 0.831 + 1ASN HD21 15 0.868 0.756 0.586 + 1ASN HD22 16 0.769 0.672 0.468 + 2LEU N 17 0.661 0.711 1.110 + 2LEU CA 18 0.687 0.710 1.255 + 2LEU C 19 0.607 0.603 1.333 + 2LEU O 20 0.666 0.522 1.404 + 2LEU CB 21 0.669 0.853 1.311 + 2LEU CG 22 0.534 0.923 1.277 + 2LEU CD1 23 0.442 0.932 1.398 + 2LEU CD2 24 0.558 1.065 1.225 + 2LEU H 25 0.654 0.803 1.069 + 2LEU HA 26 0.792 0.684 1.269 + 2LEU HB2 27 0.677 0.848 1.417 + 2LEU HB3 28 0.750 0.913 1.270 + 2LEU HG 29 0.481 0.868 1.200 + 2LEU HD11 30 0.421 0.833 1.437 + 2LEU HD12 31 0.488 0.993 1.476 + 2LEU HD13 32 0.347 0.979 1.370 + 2LEU HD21 33 0.611 1.124 1.300 + 2LEU HD22 34 0.616 1.062 1.133 + 2LEU HD23 35 0.462 1.113 1.204 + 3TYR N 36 4.075 0.598 1.315 + 3TYR CA 37 3.989 0.500 1.381 + 3TYR C 38 4.015 0.355 1.335 + 3TYR O 39 4.002 0.262 1.414 + 3TYR CB 40 3.842 0.539 1.358 + 3TYR CG 41 3.752 0.499 1.473 + 3TYR CD1 42 3.698 0.369 1.479 + 3TYR CD2 43 3.726 0.590 1.577 + 3TYR CE1 44 3.619 0.330 1.589 + 3TYR CE2 45 3.648 0.552 1.688 + 3TYR CZ 46 3.595 0.422 1.694 + 3TYR OH 47 3.523 0.382 1.802 + 3TYR H 48 4.032 0.670 1.260 + 3TYR HA 49 4.009 0.504 1.488 + 3TYR HB2 50 3.836 0.645 1.346 + 3TYR HB3 51 3.805 0.494 1.266 + 3TYR HD1 52 3.718 0.298 1.400 + 3TYR HD2 53 3.766 0.691 1.573 + 3TYR HE1 54 3.577 0.231 1.596 + 3TYR HE2 55 3.628 0.624 1.766 + 3TYR HH 56 3.541 0.437 1.879 + 4ILE N 57 0.126 4.121 1.209 + 4ILE CA 58 0.166 3.991 1.154 + 4ILE C 59 0.292 3.941 1.226 + 4ILE O 60 0.297 3.826 1.270 + 4ILE CB 61 0.189 4.000 1.000 + 4ILE CG1 62 0.079 4.079 0.924 + 4ILE CG2 63 0.207 3.860 0.939 + 4ILE CD1 64 -0.064 4.028 0.944 + 4ILE H 65 0.146 4.203 1.155 + 4ILE HA 66 0.086 3.919 1.172 + 4ILE HB 67 0.282 4.053 0.982 + 4ILE HG12 68 0.083 4.181 0.956 + 4ILE HG13 69 0.102 4.076 0.817 + 4ILE HG21 70 0.296 3.812 0.980 + 4ILE HG22 71 0.120 3.798 0.959 + 4ILE HG23 72 0.220 3.869 0.831 + 4ILE HD11 73 -0.073 3.924 0.913 + 4ILE HD12 74 -0.094 4.037 1.049 + 4ILE HD13 75 -0.132 4.088 0.884 + 5GLN N 76 0.722 0.244 1.244 + 5GLN CA 77 0.845 0.215 1.319 + 5GLN C 78 0.818 0.187 1.468 + 5GLN O 79 0.890 0.109 1.528 + 5GLN CB 80 0.946 0.329 1.302 + 5GLN CG 81 1.091 0.278 1.302 + 5GLN CD 82 1.133 0.222 1.166 + 5GLN OE1 83 1.138 0.101 1.143 + 5GLN NE2 84 1.168 0.307 1.072 + 5GLN H 85 0.710 0.337 1.205 + 5GLN HA 86 0.887 0.124 1.276 + 5GLN HB2 87 0.927 0.379 1.209 + 5GLN HB3 88 0.934 0.400 1.384 + 5GLN HG2 89 1.157 0.359 1.327 + 5GLN HG3 90 1.103 0.201 1.378 + 5GLN HE21 91 1.170 0.406 1.088 + 5GLN HE22 92 1.196 0.267 0.984 + 6TRP N 93 3.983 4.033 1.528 + 6TRP CA 94 3.939 4.000 1.664 + 6TRP C 95 3.867 3.864 1.671 + 6TRP O 96 3.894 3.784 1.761 + 6TRP CB 97 3.852 4.114 1.719 + 6TRP CG 98 3.797 4.090 1.856 + 6TRP CD1 99 3.866 4.105 1.972 + 6TRP CD2 100 3.664 4.046 1.895 + 6TRP NE1 101 3.784 4.070 2.079 + 6TRP CE2 102 3.658 4.035 2.037 + 6TRP CE3 103 3.546 4.014 1.824 + 6TRP CZ2 104 3.543 3.996 2.106 + 6TRP CZ3 105 3.430 3.973 1.892 + 6TRP CH2 106 3.427 3.965 2.032 + 6TRP H 107 3.935 4.105 1.476 + 6TRP HA 108 4.027 3.992 1.728 + 6TRP HB2 109 3.911 4.203 1.721 + 6TRP HB3 110 3.768 4.130 1.651 + 6TRP HD1 111 3.968 4.138 1.980 + 6TRP HE1 112 3.812 4.071 2.177 + 6TRP HE3 113 3.546 4.022 1.716 + 6TRP HZ2 114 3.544 3.990 2.214 + 6TRP HZ3 115 3.341 3.948 1.836 + 6TRP HH2 116 3.337 3.935 2.083 + 7LEU N 117 3.777 3.835 1.575 + 7LEU CA 118 3.707 3.706 1.570 + 7LEU C 119 3.801 3.588 1.544 + 7LEU O 120 3.787 3.486 1.612 + 7LEU CB 121 3.594 3.711 1.466 + 7LEU CG 122 3.468 3.787 1.512 + 7LEU CD1 123 3.367 3.791 1.397 + 7LEU CD2 124 3.400 3.722 1.633 + 7LEU H 125 3.755 3.906 1.506 + 7LEU HA 126 3.664 3.688 1.668 + 7LEU HB2 127 3.631 3.758 1.377 + 7LEU HB3 128 3.564 3.608 1.443 + 7LEU HG 129 3.495 3.889 1.538 + 7LEU HD11 130 3.412 3.840 1.310 + 7LEU HD12 131 3.336 3.690 1.370 + 7LEU HD13 132 3.279 3.848 1.427 + 7LEU HD21 133 3.381 3.616 1.613 + 7LEU HD22 134 3.463 3.731 1.721 + 7LEU HD23 135 3.305 3.771 1.653 + 8LYS N 136 0.298 3.599 1.451 + 8LYS CA 137 0.391 3.488 1.418 + 8LYS C 138 0.474 3.440 1.538 + 8LYS O 139 0.513 3.324 1.542 + 8LYS CB 140 0.478 3.524 1.297 + 8LYS CG 141 0.593 3.623 1.326 + 8LYS CD 142 0.730 3.557 1.346 + 8LYS CE 143 0.837 3.665 1.364 + 8LYS NZ 144 0.936 3.664 1.255 + 8LYS H 145 0.302 3.685 1.396 + 8LYS HA 146 0.329 3.403 1.389 + 8LYS HB2 147 0.522 3.434 1.259 + 8LYS HB3 148 0.414 3.568 1.220 + 8LYS HG2 149 0.600 3.692 1.244 + 8LYS HG3 150 0.568 3.681 1.415 + 8LYS HD2 151 0.727 3.494 1.432 + 8LYS HD3 152 0.752 3.494 1.259 + 8LYS HE2 153 0.789 3.761 1.367 + 8LYS HE3 154 0.886 3.649 1.461 + 8LYS HZ1 155 0.979 3.573 1.246 + 8LYS HZ2 156 0.890 3.692 1.169 + 8LYS HZ3 157 1.008 3.734 1.273 + 9ASP N 158 0.497 3.527 1.636 + 9ASP CA 159 0.564 3.498 1.763 + 9ASP C 160 0.473 3.425 1.865 + 9ASP O 161 0.523 3.382 1.969 + 9ASP CB 162 0.615 3.631 1.822 + 9ASP CG 163 0.760 3.662 1.783 + 9ASP OD1 164 0.791 3.659 1.662 + 9ASP OD2 165 0.838 3.688 1.877 + 9ASP H 166 0.466 3.622 1.621 + 9ASP HA 167 0.649 3.432 1.745 + 9ASP HB2 168 0.553 3.710 1.787 + 9ASP HB3 169 0.611 3.626 1.931 + 10GLY N 170 3.942 3.412 1.839 + 10GLY CA 171 3.844 3.349 1.927 + 10GLY C 172 3.742 3.446 1.989 + 10GLY O 173 3.665 3.405 2.077 + 10GLY H 174 3.909 3.445 1.748 + 10GLY HA2 175 3.788 3.275 1.869 + 10GLY HA3 176 3.894 3.296 2.008 + 11GLY N 177 3.739 3.573 1.947 + 11GLY CA 178 3.645 3.673 1.997 + 11GLY C 179 3.652 3.687 2.151 + 11GLY O 180 3.761 3.710 2.204 + 11GLY H 181 3.806 3.602 1.877 + 11GLY HA2 182 3.670 3.770 1.953 + 11GLY HA3 183 3.546 3.646 1.965 + 12PRO N 184 3.540 3.672 2.225 + 12PRO CA 185 3.539 3.679 2.371 + 12PRO C 186 3.633 3.577 2.439 + 12PRO O 187 3.686 3.604 2.546 + 12PRO CB 188 3.394 3.656 2.415 + 12PRO CG 189 3.311 3.683 2.290 + 12PRO CD 190 3.405 3.643 2.176 + 12PRO HA 191 3.570 3.779 2.401 + 12PRO HB2 192 3.380 3.554 2.448 + 12PRO HB3 193 3.366 3.722 2.497 + 12PRO HG2 194 3.222 3.625 2.289 + 12PRO HG3 195 3.290 3.790 2.283 + 12PRO HD2 196 3.395 3.538 2.155 + 12PRO HD3 197 3.380 3.698 2.086 + 13SER N 198 3.657 3.461 2.375 + 13SER CA 199 3.738 3.351 2.429 + 13SER C 200 3.889 3.371 2.411 + 13SER O 201 3.964 3.274 2.419 + 13SER CB 202 3.691 3.218 2.368 + 13SER OG 203 3.556 3.194 2.401 + 13SER H 204 3.617 3.447 2.283 + 13SER HA 205 3.721 3.345 2.537 + 13SER HB2 206 3.701 3.223 2.261 + 13SER HB3 207 3.752 3.136 2.406 + 13SER HG 208 3.550 3.176 2.495 + 14SER N 209 0.335 3.494 2.387 + 14SER CA 210 0.475 3.528 2.359 + 14SER C 211 0.533 3.634 2.455 + 14SER O 212 0.639 3.691 2.429 + 14SER CB 213 0.488 3.570 2.212 + 14SER OG 214 0.611 3.525 2.160 + 14SER H 215 0.265 3.567 2.378 + 14SER HA 216 0.536 3.439 2.373 + 14SER HB2 217 0.407 3.526 2.156 + 14SER HB3 218 0.480 3.677 2.202 + 14SER HG 219 0.587 3.462 2.087 + 15GLY N 220 0.464 3.663 2.566 + 15GLY CA 221 0.511 3.755 2.670 + 15GLY C 222 0.519 3.902 2.627 + 15GLY O 223 0.599 3.977 2.683 + 15GLY H 224 0.379 3.611 2.582 + 15GLY HA2 225 0.445 3.748 2.757 + 15GLY HA3 226 0.611 3.724 2.703 + 16ARG N 227 0.439 3.942 2.528 + 16ARG CA 228 0.445 4.075 2.464 + 16ARG C 229 0.305 4.126 2.426 + 16ARG O 230 0.229 4.052 2.362 + 16ARG CB 231 0.541 4.069 2.344 + 16ARG CG 232 0.502 3.967 2.235 + 16ARG CD 233 0.602 3.953 2.120 + 16ARG NE 234 0.707 3.853 2.148 + 16ARG CZ 235 0.825 3.870 2.206 + 16ARG NH1 236 0.864 3.987 2.251 + 16ARG NH2 237 0.906 3.769 2.219 + 16ARG H 238 0.375 3.874 2.490 + 16ARG HA 239 0.488 4.143 2.537 + 16ARG HB2 240 0.544 4.167 2.298 + 16ARG HB3 241 0.640 4.044 2.382 + 16ARG HG2 242 0.491 3.871 2.282 + 16ARG HG3 243 0.407 3.998 2.192 + 16ARG HD2 244 0.549 3.923 2.032 + 16ARG HD3 245 0.645 4.050 2.096 + 16ARG HE 246 0.689 3.758 2.117 + 16ARG HH11 247 0.801 4.065 2.241 + 16ARG HH12 248 0.953 3.998 2.296 + 16ARG HH21 249 0.878 3.680 2.179 + 16ARG HH22 250 0.995 3.778 2.264 + 17PRO N 251 4.199 0.466 2.460 + 17PRO CA 252 4.068 0.522 2.427 + 17PRO C 253 4.054 0.548 2.276 + 17PRO O 254 4.155 0.559 2.206 + 17PRO CB 255 4.060 0.652 2.508 + 17PRO CG 256 4.206 0.697 2.518 + 17PRO CD 257 4.282 0.565 2.527 + 17PRO HA 258 3.990 0.454 2.460 + 17PRO HB2 259 4.000 0.726 2.457 + 17PRO HB3 260 4.022 0.630 2.608 + 17PRO HG2 261 4.235 0.753 2.431 + 17PRO HG3 262 4.223 0.760 2.605 + 17PRO HD2 263 4.377 0.574 2.477 + 17PRO HD3 264 4.295 0.537 2.631 + 18PRO N 265 3.930 0.561 2.224 + 18PRO CA 266 3.906 0.589 2.083 + 18PRO C 267 3.949 0.733 2.047 + 18PRO O 268 3.931 0.824 2.129 + 18PRO CB 269 3.756 0.568 2.061 + 18PRO CG 270 3.696 0.596 2.199 + 18PRO CD 271 3.803 0.548 2.296 + 18PRO HA 272 3.962 0.518 2.023 + 18PRO HB2 273 3.718 0.637 1.988 + 18PRO HB3 274 3.738 0.465 2.034 + 18PRO HG2 275 3.677 0.701 2.212 + 18PRO HG3 276 3.602 0.543 2.213 + 18PRO HD2 277 3.804 0.609 2.384 + 18PRO HD3 278 3.786 0.443 2.320 + 19PRO N 279 4.000 0.756 1.925 + 19PRO CA 280 4.036 0.889 1.877 + 19PRO C 281 3.911 0.968 1.836 + 19PRO O 282 3.833 0.921 1.753 + 19PRO CB 283 4.131 0.862 1.761 + 19PRO CG 284 4.079 0.731 1.702 + 19PRO CD 285 4.031 0.655 1.825 + 19PRO HA 286 4.090 0.943 1.955 + 19PRO HB2 287 4.126 0.941 1.688 + 19PRO HB3 288 4.232 0.847 1.799 + 19PRO HG2 289 3.999 0.748 1.633 + 19PRO HG3 290 4.157 0.676 1.648 + 19PRO HD2 291 3.943 0.598 1.801 + 19PRO HD3 292 4.110 0.590 1.861 + 20SER N 293 3.893 1.087 1.895 + 20SER CA 294 3.791 1.186 1.858 + 20SER C 295 3.830 1.266 1.733 + 20SER O 296 3.943 1.321 1.734 + 20SER CB 297 3.768 1.285 1.973 + 20SER OG 298 3.723 1.215 2.088 + 20SER OXT 299 3.746 1.272 1.642 + 20SER H 300 3.961 1.116 1.964 + 20SER HA 301 3.698 1.136 1.834 + 20SER HB2 302 3.860 1.335 1.996 + 20SER HB3 303 3.693 1.358 1.943 + 20SER HG 304 3.661 1.148 2.058 + 3.60000 3.78554 3.49884 0.00000 0.00000 -0.33119 0.00000 0.95763 0.72873 +cubic cell, brick wrapping + 304 + 1ASN N 1 0.241 0.860 1.865 + 1ASN CA 2 0.115 0.831 1.792 + 1ASN C 3 0.117 0.699 1.716 + 1ASN O 4 0.032 0.615 1.745 + 1ASN CB 5 0.072 0.950 1.704 + 1ASN CG 6 0.030 1.068 1.792 + 1ASN OD1 7 0.028 1.056 1.914 + 1ASN ND2 8 0.001 1.183 1.736 + 1ASN H1 9 0.269 0.780 1.920 + 1ASN H2 10 0.315 0.885 1.801 + 1ASN H3 11 0.224 0.938 1.928 + 1ASN HA 12 0.037 0.819 1.867 + 1ASN HB2 13 0.153 0.980 1.641 + 1ASN HB3 14 3.386 0.921 1.643 + 1ASN HD21 15 0.004 1.200 1.637 + 1ASN HD22 16 3.372 1.255 1.800 + 2LEU N 17 0.214 0.675 1.627 + 2LEU CA 18 0.230 0.549 1.553 + 2LEU C 19 0.214 0.422 1.640 + 2LEU O 20 0.133 0.335 1.609 + 2LEU CB 21 0.363 0.553 1.475 + 2LEU CG 22 0.491 0.588 1.557 + 2LEU CD1 23 0.581 0.467 1.579 + 2LEU CD2 24 0.573 0.697 1.486 + 2LEU H 25 0.279 0.748 1.602 + 2LEU HA 26 0.150 0.543 1.479 + 2LEU HB2 27 0.379 0.456 1.431 + 2LEU HB3 28 0.351 0.627 1.396 + 2LEU HG 29 0.463 0.627 1.655 + 2LEU HD11 30 0.526 0.390 1.631 + 2LEU HD12 31 0.617 0.430 1.484 + 2LEU HD13 32 0.667 0.495 1.640 + 2LEU HD21 33 0.602 0.662 1.387 + 2LEU HD22 34 0.514 0.788 1.477 + 2LEU HD23 35 0.663 0.718 1.544 + 3TYR N 36 0.286 0.414 1.753 + 3TYR CA 37 0.278 0.301 1.845 + 3TYR C 38 0.141 0.288 1.915 + 3TYR O 39 0.095 0.177 1.942 + 3TYR CB 40 0.391 0.312 1.949 + 3TYR CG 41 0.441 0.177 1.996 + 3TYR CD1 42 0.375 0.111 2.102 + 3TYR CD2 43 0.550 0.116 1.931 + 3TYR CE1 44 0.419 3.383 2.142 + 3TYR CE2 45 0.593 3.388 1.971 + 3TYR CZ 46 0.527 3.321 2.075 + 3TYR OH 47 0.565 3.196 2.112 + 3TYR H 48 0.355 0.486 1.771 + 3TYR HA 49 0.294 0.210 1.788 + 3TYR HB2 50 0.473 0.365 1.904 + 3TYR HB3 51 0.358 0.371 2.034 + 3TYR HD1 52 0.291 0.157 2.151 + 3TYR HD2 53 0.602 0.167 1.851 + 3TYR HE1 54 0.370 3.330 2.222 + 3TYR HE2 55 0.678 3.344 1.921 + 3TYR HH 56 0.614 3.152 2.042 + 4ILE N 57 0.072 0.401 1.938 + 4ILE CA 58 3.336 0.406 1.993 + 4ILE C 59 3.238 0.342 1.893 + 4ILE O 60 3.157 0.257 1.931 + 4ILE CB 61 3.294 0.551 2.028 + 4ILE CG1 62 0.003 0.633 2.102 + 4ILE CG2 63 3.162 0.553 2.107 + 4ILE CD1 64 0.055 0.570 2.232 + 4ILE H 65 0.110 0.486 1.901 + 4ILE HA 66 3.333 0.346 2.085 + 4ILE HB 67 3.274 0.604 1.935 + 4ILE HG12 68 0.086 0.646 2.035 + 4ILE HG13 69 3.362 0.732 2.125 + 4ILE HG21 70 3.081 0.512 2.046 + 4ILE HG22 71 3.171 0.495 2.199 + 4ILE HG23 72 3.136 0.656 2.132 + 4ILE HD11 73 3.373 0.555 2.302 + 4ILE HD12 74 0.104 0.475 2.211 + 4ILE HD13 75 0.128 0.637 2.277 + 5GLN N 76 3.250 0.378 1.765 + 5GLN CA 77 3.171 0.319 1.657 + 5GLN C 78 3.200 0.169 1.636 + 5GLN O 79 3.110 0.095 1.597 + 5GLN CB 80 3.194 0.397 1.526 + 5GLN CG 81 3.067 0.401 1.439 + 5GLN CD 82 2.967 0.508 1.485 + 5GLN OE1 83 2.867 0.481 1.550 + 5GLN NE2 84 2.990 0.633 1.449 + 5GLN H 85 3.320 0.448 1.742 + 5GLN HA 86 3.066 0.329 1.685 + 5GLN HB2 87 3.222 0.498 1.550 + 5GLN HB3 88 3.274 0.350 1.469 + 5GLN HG2 89 3.095 0.422 1.337 + 5GLN HG3 90 3.018 0.304 1.440 + 5GLN HE21 91 3.069 0.658 1.392 + 5GLN HE22 92 2.923 0.701 1.481 + 6TRP N 93 3.322 0.122 1.664 + 6TRP CA 94 3.355 3.379 1.664 + 6TRP C 95 3.296 3.306 1.787 + 6TRP O 96 3.239 3.198 1.773 + 6TRP CB 97 0.107 3.361 1.655 + 6TRP CG 98 0.153 3.218 1.658 + 6TRP CD1 99 0.150 3.131 1.555 + 6TRP CD2 100 0.208 3.143 1.771 + 6TRP NE1 101 0.196 3.008 1.596 + 6TRP CE2 102 0.235 3.010 1.728 + 6TRP CE3 103 0.239 3.174 1.905 + 6TRP CZ2 104 0.291 2.913 1.812 + 6TRP CZ3 105 0.293 3.077 1.991 + 6TRP CH2 106 0.320 2.947 1.945 + 6TRP H 107 3.395 0.190 1.685 + 6TRP HA 108 3.310 3.333 1.576 + 6TRP HB2 109 0.140 0.004 1.563 + 6TRP HB3 110 0.154 0.014 1.737 + 6TRP HD1 111 0.115 3.155 1.455 + 6TRP HE1 112 0.203 2.924 1.537 + 6TRP HE3 113 0.221 3.274 1.941 + 6TRP HZ2 114 0.310 2.813 1.774 + 6TRP HZ3 115 0.315 3.103 2.094 + 6TRP HH2 116 0.364 2.874 2.012 + 7LEU N 117 3.306 3.365 1.907 + 7LEU CA 118 3.248 3.307 2.028 + 7LEU C 119 3.095 3.299 2.025 + 7LEU O 120 3.042 3.194 2.062 + 7LEU CB 121 3.296 3.383 2.153 + 7LEU CG 122 0.041 3.351 2.196 + 7LEU CD1 123 0.079 0.039 2.315 + 7LEU CD2 124 0.060 3.204 2.237 + 7LEU H 125 3.358 0.052 1.914 + 7LEU HA 126 3.282 3.204 2.035 + 7LEU HB2 127 3.289 0.088 2.133 + 7LEU HB3 128 3.231 3.358 2.237 + 7LEU HG 129 0.109 3.373 2.113 + 7LEU HD11 130 0.069 0.144 2.288 + 7LEU HD12 131 0.014 0.017 2.400 + 7LEU HD13 132 0.182 0.020 2.344 + 7LEU HD21 133 3.386 3.177 2.312 + 7LEU HD22 134 0.049 3.139 2.151 + 7LEU HD23 135 0.159 3.190 2.278 + 8LYS N 136 3.024 0.003 1.978 + 8LYS CA 137 2.876 0.003 1.974 + 8LYS C 138 2.816 3.290 1.888 + 8LYS O 139 2.705 3.247 1.915 + 8LYS CB 140 2.823 0.142 1.932 + 8LYS CG 141 2.837 0.175 1.782 + 8LYS CD 142 2.708 0.153 1.701 + 8LYS CE 143 2.730 0.198 1.556 + 8LYS NZ 144 2.645 0.313 1.519 + 8LYS H 145 3.075 0.087 1.952 + 8LYS HA 146 2.841 3.385 2.075 + 8LYS HB2 147 2.719 0.146 1.957 + 8LYS HB3 148 2.877 0.217 1.988 + 8LYS HG2 149 2.866 0.277 1.773 + 8LYS HG3 150 2.915 0.113 1.739 + 8LYS HD2 151 2.681 0.049 1.703 + 8LYS HD3 152 2.627 0.210 1.747 + 8LYS HE2 153 2.833 0.226 1.544 + 8LYS HE3 154 2.711 0.113 1.490 + 8LYS HZ1 155 2.547 0.292 1.536 + 8LYS HZ2 156 2.674 0.394 1.574 + 8LYS HZ3 157 2.659 0.336 1.422 + 9ASP N 158 2.892 3.240 1.790 + 9ASP CA 159 2.858 3.125 1.706 + 9ASP C 160 2.880 2.989 1.775 + 9ASP O 161 2.841 2.887 1.719 + 9ASP CB 162 2.942 3.135 1.577 + 9ASP CG 163 2.870 3.207 1.463 + 9ASP OD1 164 2.821 3.320 1.485 + 9ASP OD2 165 2.864 3.145 1.353 + 9ASP H 166 2.980 3.287 1.772 + 9ASP HA 167 2.752 3.130 1.679 + 9ASP HB2 168 3.033 3.188 1.599 + 9ASP HB3 169 2.966 3.034 1.542 + 10GLY N 170 2.943 2.986 1.894 + 10GLY CA 171 2.975 2.864 1.970 + 10GLY C 172 3.124 2.830 1.978 + 10GLY O 173 3.159 2.722 2.025 + 10GLY H 174 2.968 3.075 1.937 + 10GLY HA2 175 2.938 2.877 2.072 + 10GLY HA3 176 2.922 2.779 1.927 + 11GLY N 177 3.213 2.919 1.931 + 11GLY CA 178 3.358 2.898 1.935 + 11GLY C 179 3.399 2.767 1.866 + 11GLY O 180 3.364 2.746 1.750 + 11GLY H 181 3.179 3.005 1.890 + 11GLY HA2 182 0.006 2.981 1.883 + 11GLY HA3 183 3.390 2.900 2.039 + 12PRO N 184 0.072 2.675 1.934 + 12PRO CA 185 0.112 2.546 1.876 + 12PRO C 186 3.393 2.460 1.830 + 12PRO O 187 0.006 2.383 1.734 + 12PRO CB 188 0.191 2.473 1.985 + 12PRO CG 189 0.234 2.583 2.082 + 12PRO CD 190 0.120 2.684 2.071 + 12PRO HA 191 0.177 2.565 1.791 + 12PRO HB2 192 0.130 2.400 2.035 + 12PRO HB3 193 0.278 2.421 1.943 + 12PRO HG2 194 0.243 2.545 2.182 + 12PRO HG3 195 0.327 2.628 2.047 + 12PRO HD2 196 0.042 2.660 2.140 + 12PRO HD3 197 0.157 2.783 2.096 + 13SER N 198 3.275 2.474 1.892 + 13SER CA 199 3.155 2.395 1.865 + 13SER C 200 3.074 2.446 1.744 + 13SER O 201 2.957 2.412 1.731 + 13SER CB 202 3.067 2.390 1.991 + 13SER OG 203 3.137 2.327 2.097 + 13SER H 204 3.267 2.545 1.965 + 13SER HA 205 3.185 2.293 1.841 + 13SER HB2 206 3.040 2.489 2.020 + 13SER HB3 207 2.976 2.332 1.971 + 13SER HG 208 3.149 2.234 2.076 + 14SER N 209 3.136 2.524 1.655 + 14SER CA 210 3.071 2.587 1.539 + 14SER C 211 3.138 2.553 1.404 + 14SER O 212 3.112 2.617 1.303 + 14SER CB 213 3.061 2.737 1.562 + 14SER OG 214 2.941 2.788 1.508 + 14SER H 215 3.231 2.550 1.676 + 14SER HA 216 2.969 2.549 1.531 + 14SER HB2 217 3.063 2.757 1.668 + 14SER HB3 218 3.146 2.789 1.518 + 14SER HG 219 2.890 2.824 1.586 + 15GLY N 220 3.228 2.452 1.403 + 15GLY CA 221 3.293 2.403 1.281 + 15GLY C 222 3.391 2.502 1.217 + 15GLY O 223 0.013 2.496 1.096 + 15GLY H 224 3.243 2.403 1.489 + 15GLY HA2 225 3.348 2.312 1.304 + 15GLY HA3 226 3.217 2.379 1.207 + 16ARG N 227 0.047 2.595 1.295 + 16ARG CA 228 0.131 2.706 1.248 + 16ARG C 229 0.246 2.738 1.346 + 16ARG O 230 0.220 2.753 1.465 + 16ARG CB 231 0.041 2.829 1.220 + 16ARG CG 232 3.362 2.878 1.343 + 16ARG CD 233 3.264 2.993 1.314 + 16ARG NE 234 3.131 2.946 1.273 + 16ARG CZ 235 3.087 2.921 1.150 + 16ARG NH1 236 3.163 2.934 1.044 + 16ARG NH2 237 2.963 2.882 1.133 + 16ARG H 238 0.026 2.591 1.394 + 16ARG HA 239 0.174 2.676 1.152 + 16ARG HB2 240 0.104 2.909 1.186 + 16ARG HB3 241 3.371 2.801 1.142 + 16ARG HG2 242 3.306 2.796 1.382 + 16ARG HG3 243 0.033 2.914 1.417 + 16ARG HD2 244 3.254 3.052 1.403 + 16ARG HD3 245 3.307 3.061 1.240 + 16ARG HE 246 3.062 2.933 1.346 + 16ARG HH11 247 3.257 2.963 1.058 + 16ARG HH12 248 3.128 2.912 0.952 + 16ARG HH21 249 2.903 2.878 1.215 + 16ARG HH22 250 2.927 2.860 1.042 + 17PRO N 251 0.371 2.751 1.298 + 17PRO CA 252 0.486 2.781 1.384 + 17PRO C 253 0.480 2.925 1.438 + 17PRO O 254 0.412 3.010 1.380 + 17PRO CB 255 0.609 2.759 1.295 + 17PRO CG 256 0.558 2.793 1.155 + 17PRO CD 257 0.413 2.745 1.158 + 17PRO HA 258 0.488 2.711 1.467 + 17PRO HB2 259 0.689 2.825 1.323 + 17PRO HB3 260 0.638 2.654 1.299 + 17PRO HG2 261 0.563 2.899 1.137 + 17PRO HG3 262 0.615 2.742 1.078 + 17PRO HD2 263 0.351 2.809 1.098 + 17PRO HD3 264 0.407 2.642 1.124 + 18PRO N 265 0.553 2.956 1.548 + 18PRO CA 266 0.557 3.090 1.604 + 18PRO C 267 0.632 3.188 1.512 + 18PRO O 268 0.731 3.148 1.449 + 18PRO CB 269 0.626 3.076 1.740 + 18PRO CG 270 0.715 2.954 1.722 + 18PRO CD 271 0.635 2.865 1.626 + 18PRO HA 272 0.455 3.125 1.619 + 18PRO HB2 273 0.684 3.164 1.762 + 18PRO HB3 274 0.551 3.057 1.817 + 18PRO HG2 275 0.810 2.981 1.679 + 18PRO HG3 276 0.735 2.904 1.817 + 18PRO HD2 277 0.701 2.810 1.562 + 18PRO HD3 278 0.571 2.798 1.684 + 19PRO N 279 0.591 3.315 1.506 + 19PRO CA 280 0.660 0.018 1.428 + 19PRO C 281 0.786 0.066 1.501 + 19PRO O 282 0.779 0.109 1.616 + 19PRO CB 283 0.556 0.128 1.411 + 19PRO CG 284 0.473 0.120 1.539 + 19PRO CD 285 0.472 3.371 1.570 + 19PRO HA 286 0.687 3.379 1.330 + 19PRO HB2 287 0.603 0.224 1.401 + 19PRO HB3 288 0.492 0.105 1.325 + 19PRO HG2 289 0.519 0.175 1.618 + 19PRO HG3 290 0.372 0.159 1.526 + 19PRO HD2 291 0.477 3.354 1.676 + 19PRO HD3 292 0.383 3.325 1.527 + 20SER N 293 0.902 0.058 1.433 + 20SER CA 294 1.031 0.113 1.476 + 20SER C 295 1.039 0.264 1.452 + 20SER O 296 1.014 0.305 1.336 + 20SER CB 297 1.146 0.045 1.402 + 20SER OG 298 1.146 3.307 1.430 + 20SER OXT 299 1.075 0.335 1.549 + 20SER H 300 0.899 0.019 1.340 + 20SER HA 301 1.043 0.099 1.584 + 20SER HB2 302 1.134 0.061 1.296 + 20SER HB3 303 1.241 0.089 1.434 + 20SER HG 304 1.126 3.296 1.523 + 3.40000 3.40000 3.40000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 +dodecahedron cell, compact wrapping + 304 + 1ASN N 1 3.650 0.231 1.032 + 1ASN CA 2 3.643 0.251 1.179 + 1ASN C 3 3.774 0.222 1.251 + 1ASN O 4 3.824 0.312 1.317 + 1ASN CB 5 3.522 0.178 1.240 + 1ASN CG 6 3.392 0.243 1.192 + 1ASN OD1 7 3.395 0.343 1.122 + 1ASN ND2 8 3.276 0.188 1.225 + 1ASN H1 9 3.732 0.277 0.994 + 1ASN H2 10 3.654 0.133 1.009 + 1ASN H3 11 3.567 0.271 0.989 + 1ASN HA 12 3.625 0.358 1.195 + 1ASN HB2 13 3.523 0.075 1.209 + 1ASN HB3 14 3.526 0.186 1.349 + 1ASN HD21 15 5.068 3.222 1.280 + 1ASN HD22 16 3.195 0.238 1.192 + 2LEU N 17 2.031 3.220 1.237 + 2LEU CA 18 2.161 3.182 1.297 + 2LEU C 19 2.271 3.290 1.283 + 2LEU O 20 2.329 3.332 1.383 + 2LEU CB 21 2.203 3.044 1.242 + 2LEU CG 22 2.204 3.028 1.088 + 2LEU CD1 23 2.346 3.024 1.031 + 2LEU CD2 24 2.132 2.900 1.045 + 2LEU H 25 1.984 3.146 1.188 + 2LEU HA 26 2.145 3.170 1.404 + 2LEU HB2 27 2.302 3.023 1.278 + 2LEU HB3 28 2.133 2.971 1.284 + 2LEU HG 29 2.153 3.112 1.041 + 2LEU HD11 30 2.400 3.114 1.057 + 2LEU HD12 31 2.399 2.936 1.069 + 2LEU HD13 32 2.343 3.016 0.922 + 2LEU HD21 33 2.180 2.813 1.090 + 2LEU HD22 34 2.027 2.904 1.076 + 2LEU HD23 35 2.136 2.890 0.936 + 3TYR N 36 2.294 3.340 1.161 + 3TYR CA 37 2.393 3.444 1.135 + 3TYR C 38 4.158 0.462 1.200 + 3TYR O 39 4.247 0.536 1.241 + 3TYR CB 40 2.412 3.459 0.983 + 3TYR CG 41 2.552 3.500 0.945 + 3TYR CD1 42 4.389 0.519 0.945 + 3TYR CD2 43 2.648 3.402 0.914 + 3TYR CE1 44 4.521 0.556 0.914 + 3TYR CE2 45 2.781 3.439 0.884 + 3TYR CZ 46 2.817 3.575 0.885 + 3TYR OH 47 2.946 3.612 0.861 + 3TYR H 48 2.247 3.298 1.082 + 3TYR HA 49 2.488 3.411 1.177 + 3TYR HB2 50 2.390 3.365 0.937 + 3TYR HB3 51 4.140 0.414 0.944 + 3TYR HD1 52 4.316 0.595 0.969 + 3TYR HD2 53 2.621 3.297 0.913 + 3TYR HE1 54 4.551 0.660 0.914 + 3TYR HE2 55 2.853 3.362 0.860 + 3TYR HH 56 3.007 3.539 0.876 + 4ILE N 57 4.029 0.493 1.214 + 4ILE CA 58 3.978 0.612 1.283 + 4ILE C 59 4.014 0.604 1.432 + 4ILE O 60 4.067 0.700 1.489 + 4ILE CB 61 3.825 0.629 1.263 + 4ILE CG1 62 3.777 0.607 1.117 + 4ILE CG2 63 3.777 0.765 1.315 + 4ILE CD1 64 3.845 0.694 1.011 + 4ILE H 65 3.962 0.422 1.189 + 4ILE HA 66 4.028 0.700 1.242 + 4ILE HB 67 3.774 0.554 1.324 + 4ILE HG12 68 3.795 0.504 1.092 + 4ILE HG13 69 3.669 0.624 1.113 + 4ILE HG21 70 3.795 0.773 1.422 + 4ILE HG22 71 3.830 0.846 1.264 + 4ILE HG23 72 3.670 0.776 1.297 + 4ILE HD11 73 3.830 0.800 1.033 + 4ILE HD12 74 3.952 0.673 1.007 + 4ILE HD13 75 3.802 0.672 0.914 + 5GLN N 76 3.991 0.487 1.494 + 5GLN CA 77 4.028 0.460 1.633 + 5GLN C 78 4.181 0.463 1.655 + 5GLN O 79 4.225 0.500 1.763 + 5GLN CB 80 3.969 0.326 1.679 + 5GLN CG 81 3.931 0.328 1.828 + 5GLN CD 82 3.796 0.395 1.853 + 5GLN OE1 83 3.787 0.510 1.895 + 5GLN NE2 84 3.687 0.324 1.830 + 5GLN H 85 3.947 0.413 1.439 + 5GLN HA 86 3.985 0.540 1.693 + 5GLN HB2 87 3.882 0.305 1.621 + 5GLN HB3 88 2.243 3.365 1.662 + 5GLN HG2 89 3.926 0.227 1.864 + 5GLN HG3 90 4.008 0.380 1.885 + 5GLN HE21 91 3.691 0.229 1.800 + 5GLN HE22 92 3.600 0.372 1.848 + 6TRP N 93 4.262 0.427 1.555 + 6TRP CA 94 2.608 3.561 1.561 + 6TRP C 95 4.451 0.590 1.546 + 6TRP O 96 4.537 0.637 1.621 + 6TRP CB 97 2.673 3.472 1.454 + 6TRP CG 98 2.823 3.482 1.448 + 6TRP CD1 99 2.910 3.422 1.532 + 6TRP CD2 100 2.904 3.557 1.353 + 6TRP NE1 101 3.040 3.458 1.497 + 6TRP CE2 102 3.042 3.539 1.387 + 6TRP CE3 103 2.877 3.638 1.241 + 6TRP CZ2 104 3.146 3.597 1.313 + 6TRP CZ3 105 2.981 3.699 1.168 + 6TRP CH2 106 3.115 3.677 1.203 + 6TRP H 107 4.220 0.386 1.472 + 6TRP HA 108 2.643 3.527 1.658 + 6TRP HB2 109 2.648 3.370 1.476 + 6TRP HB3 110 2.633 3.497 1.357 + 6TRP HD1 111 2.883 3.358 1.614 + 6TRP HE1 112 3.124 3.427 1.546 + 6TRP HE3 113 2.774 3.653 1.211 + 6TRP HZ2 114 3.249 3.580 1.343 + 6TRP HZ3 115 2.957 3.761 1.082 + 6TRP HH2 116 3.194 3.723 1.144 + 7LEU N 117 4.391 0.666 1.453 + 7LEU CA 118 4.421 0.808 1.435 + 7LEU C 119 4.381 0.893 1.556 + 7LEU O 120 4.461 0.978 1.596 + 7LEU CB 121 4.357 0.861 1.306 + 7LEU CG 122 4.430 0.820 1.176 + 7LEU CD1 123 4.351 0.872 1.056 + 7LEU CD2 124 4.572 0.877 1.168 + 7LEU H 125 4.324 0.621 1.390 + 7LEU HA 126 4.529 0.818 1.427 + 7LEU HB2 127 4.256 0.824 1.301 + 7LEU HB3 128 4.355 0.970 1.310 + 7LEU HG 129 4.435 0.712 1.170 + 7LEU HD11 130 4.250 0.831 1.057 + 7LEU HD12 131 4.346 0.981 1.058 + 7LEU HD13 132 4.400 0.841 0.963 + 7LEU HD21 133 4.571 0.985 1.184 + 7LEU HD22 134 4.636 0.830 1.243 + 7LEU HD23 135 4.615 0.856 1.070 + 8LYS N 136 4.263 0.872 1.616 + 8LYS CA 137 4.217 0.952 1.731 + 8LYS C 138 4.310 0.946 1.853 + 8LYS O 139 4.315 1.040 1.931 + 8LYS CB 140 4.071 0.917 1.768 + 8LYS CG 141 4.053 0.783 1.842 + 8LYS CD 142 4.038 0.797 1.994 + 8LYS CE 143 4.011 0.660 2.056 + 8LYS NZ 144 3.878 0.652 2.119 + 8LYS H 145 4.200 0.803 1.575 + 8LYS HA 146 4.217 1.057 1.700 + 8LYS HB2 147 4.033 0.995 1.830 + 8LYS HB3 148 4.013 0.913 1.676 + 8LYS HG2 149 3.966 0.734 1.803 + 8LYS HG3 150 4.139 0.719 1.821 + 8LYS HD2 151 4.128 0.838 2.035 + 8LYS HD3 152 3.956 0.866 2.016 + 8LYS HE2 153 4.018 0.585 1.979 + 8LYS HE3 154 4.090 0.638 2.129 + 8LYS HZ1 155 3.866 0.725 2.188 + 8LYS HZ2 156 3.807 0.658 2.046 + 8LYS HZ3 157 3.866 0.561 2.163 + 9ASP N 158 4.387 0.837 1.866 + 9ASP CA 159 4.490 0.817 1.968 + 9ASP C 160 4.622 0.891 1.938 + 9ASP O 161 4.710 0.893 2.024 + 9ASP CB 162 4.516 0.665 1.981 + 9ASP CG 163 4.432 0.599 2.090 + 9ASP OD1 164 4.308 0.618 2.090 + 9ASP OD2 165 4.494 0.530 2.175 + 9ASP H 166 4.372 0.762 1.800 + 9ASP HA 167 4.454 0.854 2.064 + 9ASP HB2 168 4.492 0.619 1.887 + 9ASP HB3 169 4.620 0.648 2.005 + 10GLY N 170 4.638 0.950 1.818 + 10GLY CA 171 4.758 1.021 1.774 + 10GLY C 172 4.837 0.951 1.662 + 10GLY O 173 4.948 0.994 1.630 + 10GLY H 174 4.559 0.949 1.754 + 10GLY HA2 175 4.729 1.119 1.736 + 10GLY HA3 176 4.826 1.037 1.858 + 11GLY N 177 4.784 0.843 1.604 + 11GLY CA 178 4.849 0.768 1.496 + 11GLY C 179 3.190 3.839 1.534 + 11GLY O 180 3.205 3.773 1.637 + 11GLY H 181 4.694 0.809 1.636 + 11GLY HA2 182 2.988 3.798 1.472 + 11GLY HA3 183 4.851 0.832 1.408 + 12PRO N 184 3.296 3.874 1.457 + 12PRO CA 185 3.434 3.836 1.489 + 12PRO C 186 3.481 3.887 1.627 + 12PRO O 187 3.564 3.823 1.691 + 12PRO CB 188 3.522 3.894 1.378 + 12PRO CG 189 3.425 3.921 1.263 + 12PRO CD 190 3.294 3.953 1.334 + 12PRO HA 191 3.442 3.727 1.488 + 12PRO HB2 192 3.568 3.986 1.410 + 12PRO HB3 193 3.600 3.825 1.348 + 12PRO HG2 194 3.458 4.004 1.203 + 12PRO HG3 195 3.413 3.830 1.203 + 12PRO HD2 196 5.089 0.940 1.357 + 12PRO HD3 197 3.210 3.928 1.270 + 13SER N 198 3.427 4.000 1.675 + 13SER CA 199 3.465 4.065 1.801 + 13SER C 200 3.400 4.003 1.925 + 13SER O 201 5.196 0.950 2.030 + 13SER CB 202 5.236 1.098 1.792 + 13SER OG 203 5.311 1.156 1.687 + 13SER H 204 5.153 0.927 1.621 + 13SER HA 205 3.573 4.053 1.814 + 13SER HB2 206 5.132 1.113 1.773 + 13SER HB3 207 5.263 1.147 1.885 + 13SER HG 208 1.804 1.155 1.711 + 14SER N 209 3.350 3.879 1.916 + 14SER CA 210 3.278 3.810 2.023 + 14SER C 211 3.339 3.673 2.061 + 14SER O 212 3.276 3.593 2.129 + 14SER CB 213 3.130 3.798 1.984 + 14SER OG 214 3.048 3.811 2.097 + 14SER H 215 3.354 3.836 1.824 + 14SER HA 216 3.282 3.871 2.113 + 14SER HB2 217 4.906 0.758 1.913 + 14SER HB3 218 3.111 3.703 1.935 + 14SER HG 219 4.793 0.775 2.082 + 15GLY N 220 3.462 3.645 2.015 + 15GLY CA 221 3.536 3.524 2.050 + 15GLY C 222 3.477 3.394 1.994 + 15GLY O 223 3.497 3.288 2.052 + 15GLY H 224 3.509 3.717 1.961 + 15GLY HA2 225 3.639 3.532 2.014 + 15GLY HA3 226 3.540 3.514 2.159 + 16ARG N 227 3.402 3.402 1.883 + 16ARG CA 228 3.325 3.291 1.824 + 16ARG C 229 3.326 3.296 1.670 + 16ARG O 230 3.297 3.401 1.613 + 16ARG CB 231 3.183 3.291 1.883 + 16ARG CG 232 3.104 3.421 1.858 + 16ARG CD 233 2.966 3.427 1.926 + 16ARG NE 234 2.971 3.481 2.063 + 16ARG CZ 235 2.989 3.415 2.177 + 16ARG NH1 236 3.007 3.285 2.181 + 16ARG NH2 237 2.988 3.481 2.290 + 16ARG H 238 3.393 3.493 1.840 + 16ARG HA 239 3.374 3.199 1.857 + 16ARG HB2 240 3.128 3.210 1.840 + 16ARG HB3 241 3.192 3.276 1.991 + 16ARG HG2 242 3.162 3.503 1.895 + 16ARG HG3 243 3.088 3.431 1.752 + 16ARG HD2 244 2.901 3.489 1.867 + 16ARG HD3 245 2.919 3.328 1.924 + 16ARG HE 246 2.958 3.580 2.073 + 16ARG HH11 247 3.008 3.235 2.094 + 16ARG HH12 248 3.022 3.237 2.268 + 16ARG HH21 249 2.968 3.580 2.287 + 16ARG HH22 250 3.003 3.435 2.377 + 17PRO N 251 3.355 3.184 1.601 + 17PRO CA 252 3.358 3.180 1.454 + 17PRO C 253 3.216 3.192 1.395 + 17PRO O 254 3.118 3.165 1.465 + 17PRO CB 255 3.422 3.045 1.420 + 17PRO CG 256 3.382 2.956 1.537 + 17PRO CD 257 3.382 3.052 1.656 + 17PRO HA 258 3.420 3.261 1.417 + 17PRO HB2 259 3.384 3.007 1.327 + 17PRO HB3 260 3.531 3.057 1.418 + 17PRO HG2 261 3.285 2.913 1.522 + 17PRO HG3 262 3.453 2.874 1.551 + 17PRO HD2 263 3.306 3.024 1.726 + 17PRO HD3 264 3.481 3.052 1.703 + 18PRO N 265 3.203 3.230 1.266 + 18PRO CA 266 3.073 3.240 1.200 + 18PRO C 267 3.011 3.102 1.178 + 18PRO O 268 3.083 3.006 1.149 + 18PRO CB 269 3.100 3.312 1.067 + 18PRO CG 270 3.245 3.276 1.036 + 18PRO CD 271 3.310 3.267 1.175 + 18PRO HA 272 3.008 3.302 1.261 + 18PRO HB2 273 3.035 3.276 0.991 + 18PRO HB3 274 3.091 3.419 1.081 + 18PRO HG2 275 3.252 3.182 0.985 + 18PRO HG3 276 3.293 3.352 0.974 + 18PRO HD2 277 3.387 3.192 1.175 + 18PRO HD3 278 3.350 3.364 1.203 + 19PRO N 279 2.877 3.090 1.186 + 19PRO CA 280 2.806 2.966 1.159 + 19PRO C 281 2.795 2.940 1.008 + 19PRO O 282 2.745 3.025 0.934 + 19PRO CB 283 2.670 2.985 1.226 + 19PRO CG 284 2.644 3.135 1.212 + 19PRO CD 285 2.784 3.195 1.225 + 19PRO HA 286 2.857 2.882 1.206 + 19PRO HB2 287 2.594 2.928 1.175 + 19PRO HB3 288 2.677 2.959 1.331 + 19PRO HG2 289 2.601 3.158 1.116 + 19PRO HG3 290 2.576 3.172 1.289 + 19PRO HD2 291 2.794 3.280 1.161 + 19PRO HD3 292 2.802 3.223 1.329 + 20SER N 293 2.844 2.823 0.963 + 20SER CA 294 2.829 2.771 0.826 + 20SER C 295 2.690 2.711 0.802 + 20SER O 296 2.650 2.625 0.884 + 20SER CB 297 2.934 2.663 0.798 + 20SER OG 298 3.063 2.718 0.811 + 20SER OXT 299 2.628 2.751 0.701 + 20SER H 300 2.885 2.761 1.030 + 20SER HA 301 2.840 2.852 0.754 + 20SER HB2 302 2.922 2.583 0.868 + 20SER HB3 303 2.920 2.625 0.697 + 20SER HG 304 3.062 2.805 0.772 + 3.60000 3.11769 2.93939 0.00000 0.00000 1.80000 0.00000 1.80000 1.03923 diff --git a/regtest/basic/rt-molinfo-whole-repair/whole.pdb b/regtest/basic/rt-molinfo-whole-repair/whole.pdb new file mode 100644 index 0000000000..e729bfec29 --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-repair/whole.pdb @@ -0,0 +1,306 @@ +CRYST1 40.000 40.000 40.000 60.00 60.00 60.00 P 1 1 +ATOM 1 N ASN A 1 30.997 27.202 15.779 1.00 0.00 N +ATOM 2 CA ASN A 1 31.290 26.210 14.716 1.00 0.00 C +ATOM 3 C ASN A 1 32.781 26.039 14.437 1.00 0.00 C +ATOM 4 O ASN A 1 33.264 24.924 14.576 1.00 0.00 O +ATOM 5 CB ASN A 1 30.461 26.471 13.445 1.00 0.00 C +ATOM 6 CG ASN A 1 28.983 26.205 13.723 1.00 0.00 C +ATOM 7 OD1 ASN A 1 28.629 25.775 14.810 1.00 0.00 O +ATOM 8 ND2 ASN A 1 28.092 26.481 12.791 1.00 0.00 N +ATOM 9 H1 ASN A 1 31.568 27.032 16.595 1.00 0.00 H +ATOM 10 H2 ASN A 1 31.158 28.143 15.445 1.00 0.00 H +ATOM 11 H3 ASN A 1 30.021 27.116 16.041 1.00 0.00 H +ATOM 12 HA ASN A 1 30.968 25.237 15.095 1.00 0.00 H +ATOM 13 HB2 ASN A 1 30.588 27.492 13.141 1.00 0.00 H +ATOM 14 HB3 ASN A 1 30.790 25.794 12.655 1.00 0.00 H +ATOM 15 HD21 ASN A 1 28.326 26.866 11.890 1.00 0.00 H +ATOM 16 HD22 ASN A 1 27.141 26.258 13.040 1.00 0.00 H +ATOM 17 N LEU A 2 33.519 27.106 14.106 1.00 0.00 N +ATOM 18 CA LEU A 2 34.975 27.077 13.882 1.00 0.00 C +ATOM 19 C LEU A 2 35.762 26.262 14.930 1.00 0.00 C +ATOM 20 O LEU A 2 36.507 25.349 14.574 1.00 0.00 O +ATOM 21 CB LEU A 2 35.487 28.525 13.715 1.00 0.00 C +ATOM 22 CG LEU A 2 35.103 29.525 14.839 1.00 0.00 C +ATOM 23 CD1 LEU A 2 36.286 29.878 15.735 1.00 0.00 C +ATOM 24 CD2 LEU A 2 34.547 30.823 14.250 1.00 0.00 C +ATOM 25 H LEU A 2 33.077 27.998 13.940 1.00 0.00 H +ATOM 26 HA LEU A 2 35.148 26.569 12.931 1.00 0.00 H +ATOM 27 HB2 LEU A 2 36.558 28.489 13.662 1.00 0.00 H +ATOM 28 HB3 LEU A 2 35.085 28.892 12.770 1.00 0.00 H +ATOM 29 HG LEU A 2 34.330 29.097 15.476 1.00 0.00 H +ATOM 30 HD11 LEU A 2 36.691 28.980 16.188 1.00 0.00 H +ATOM 31 HD12 LEU A 2 37.057 30.379 15.151 1.00 0.00 H +ATOM 32 HD13 LEU A 2 35.969 30.552 16.531 1.00 0.00 H +ATOM 33 HD21 LEU A 2 35.291 31.284 13.598 1.00 0.00 H +ATOM 34 HD22 LEU A 2 33.643 30.619 13.677 1.00 0.00 H +ATOM 35 HD23 LEU A 2 34.306 31.520 15.053 1.00 0.00 H +ATOM 36 N TYR A 3 35.544 26.530 16.223 1.00 0.00 N +ATOM 37 CA TYR A 3 36.208 25.813 17.315 1.00 0.00 C +ATOM 38 C TYR A 3 35.796 24.331 17.408 1.00 0.00 C +ATOM 39 O TYR A 3 36.607 23.484 17.776 1.00 0.00 O +ATOM 40 CB TYR A 3 35.934 26.547 18.636 1.00 0.00 C +ATOM 41 CG TYR A 3 37.074 26.414 19.624 1.00 0.00 C +ATOM 42 CD1 TYR A 3 37.152 25.292 20.472 1.00 0.00 C +ATOM 43 CD2 TYR A 3 38.078 27.401 19.666 1.00 0.00 C +ATOM 44 CE1 TYR A 3 38.241 25.151 21.352 1.00 0.00 C +ATOM 45 CE2 TYR A 3 39.173 27.260 20.539 1.00 0.00 C +ATOM 46 CZ TYR A 3 39.259 26.128 21.377 1.00 0.00 C +ATOM 47 OH TYR A 3 40.331 25.956 22.195 1.00 0.00 O +ATOM 48 H TYR A 3 34.964 27.320 16.454 1.00 0.00 H +ATOM 49 HA TYR A 3 37.283 25.843 17.130 1.00 0.00 H +ATOM 50 HB2 TYR A 3 35.781 27.588 18.425 1.00 0.00 H +ATOM 51 HB3 TYR A 3 35.012 26.171 19.084 1.00 0.00 H +ATOM 52 HD1 TYR A 3 36.385 24.531 20.435 1.00 0.00 H +ATOM 53 HD2 TYR A 3 38.021 28.275 19.029 1.00 0.00 H +ATOM 54 HE1 TYR A 3 38.322 24.296 22.003 1.00 0.00 H +ATOM 55 HE2 TYR A 3 39.931 28.027 20.567 1.00 0.00 H +ATOM 56 HH TYR A 3 41.085 26.470 21.901 1.00 0.00 H +ATOM 57 N ILE A 4 34.556 24.000 17.023 1.00 0.00 N +ATOM 58 CA ILE A 4 34.041 22.626 16.947 1.00 0.00 C +ATOM 59 C ILE A 4 34.809 21.854 15.864 1.00 0.00 C +ATOM 60 O ILE A 4 35.277 20.741 16.108 1.00 0.00 O +ATOM 61 CB ILE A 4 32.512 22.609 16.677 1.00 0.00 C +ATOM 62 CG1 ILE A 4 31.701 23.615 17.531 1.00 0.00 C +ATOM 63 CG2 ILE A 4 31.939 21.191 16.835 1.00 0.00 C +ATOM 64 CD1 ILE A 4 31.879 23.487 19.049 1.00 0.00 C +ATOM 65 H ILE A 4 33.992 24.731 16.617 1.00 0.00 H +ATOM 66 HA ILE A 4 34.228 22.134 17.902 1.00 0.00 H +ATOM 67 HB ILE A 4 32.344 22.883 15.637 1.00 0.00 H +ATOM 68 HG12 ILE A 4 31.998 24.606 17.246 1.00 0.00 H +ATOM 69 HG13 ILE A 4 30.641 23.499 17.298 1.00 0.00 H +ATOM 70 HG21 ILE A 4 32.389 20.520 16.102 1.00 0.00 H +ATOM 71 HG22 ILE A 4 32.139 20.804 17.835 1.00 0.00 H +ATOM 72 HG23 ILE A 4 30.862 21.204 16.666 1.00 0.00 H +ATOM 73 HD11 ILE A 4 31.592 22.490 19.383 1.00 0.00 H +ATOM 74 HD12 ILE A 4 32.915 23.681 19.329 1.00 0.00 H +ATOM 75 HD13 ILE A 4 31.242 24.219 19.547 1.00 0.00 H +ATOM 76 N GLN A 5 34.991 22.474 14.689 1.00 0.00 N +ATOM 77 CA GLN A 5 35.776 21.908 13.591 1.00 0.00 C +ATOM 78 C GLN A 5 37.269 21.754 13.944 1.00 0.00 C +ATOM 79 O GLN A 5 37.912 20.835 13.450 1.00 0.00 O +ATOM 80 CB GLN A 5 35.606 22.762 12.321 1.00 0.00 C +ATOM 81 CG GLN A 5 35.654 21.904 11.044 1.00 0.00 C +ATOM 82 CD GLN A 5 34.322 21.215 10.749 1.00 0.00 C +ATOM 83 OE1 GLN A 5 34.129 20.031 10.999 1.00 0.00 O +ATOM 84 NE2 GLN A 5 33.366 21.929 10.182 1.00 0.00 N +ATOM 85 H GLN A 5 34.571 23.393 14.571 1.00 0.00 H +ATOM 86 HA GLN A 5 35.381 20.913 13.394 1.00 0.00 H +ATOM 87 HB2 GLN A 5 34.660 23.266 12.365 1.00 0.00 H +ATOM 88 HB3 GLN A 5 36.406 23.504 12.281 1.00 0.00 H +ATOM 89 HG2 GLN A 5 35.905 22.536 10.214 1.00 0.00 H +ATOM 90 HG3 GLN A 5 36.440 21.152 11.129 1.00 0.00 H +ATOM 91 HE21 GLN A 5 33.509 22.891 9.926 1.00 0.00 H +ATOM 92 HE22 GLN A 5 32.506 21.440 9.999 1.00 0.00 H +ATOM 93 N TRP A 6 37.824 22.616 14.806 1.00 0.00 N +ATOM 94 CA TRP A 6 39.182 22.444 15.341 1.00 0.00 C +ATOM 95 C TRP A 6 39.267 21.309 16.378 1.00 0.00 C +ATOM 96 O TRP A 6 40.193 20.496 16.330 1.00 0.00 O +ATOM 97 CB TRP A 6 39.677 23.778 15.917 1.00 0.00 C +ATOM 98 CG TRP A 6 41.046 23.727 16.528 1.00 0.00 C +ATOM 99 CD1 TRP A 6 42.217 23.739 15.852 1.00 0.00 C +ATOM 100 CD2 TRP A 6 41.406 23.639 17.940 1.00 0.00 C +ATOM 101 NE1 TRP A 6 43.269 23.635 16.745 1.00 0.00 N +ATOM 102 CE2 TRP A 6 42.826 23.590 18.044 1.00 0.00 C +ATOM 103 CE3 TRP A 6 40.677 23.599 19.146 1.00 0.00 C +ATOM 104 CZ2 TRP A 6 43.497 23.520 19.272 1.00 0.00 C +ATOM 105 CZ3 TRP A 6 41.337 23.508 20.387 1.00 0.00 C +ATOM 106 CH2 TRP A 6 42.740 23.482 20.454 1.00 0.00 C +ATOM 107 H TRP A 6 37.274 23.418 15.092 1.00 0.00 H +ATOM 108 HA TRP A 6 39.846 22.167 14.521 1.00 0.00 H +ATOM 109 HB2 TRP A 6 39.692 24.500 15.123 1.00 0.00 H +ATOM 110 HB3 TRP A 6 38.977 24.119 16.678 1.00 0.00 H +ATOM 111 HD1 TRP A 6 42.310 23.808 14.776 1.00 0.00 H +ATOM 112 HE1 TRP A 6 44.258 23.611 16.490 1.00 0.00 H +ATOM 113 HE3 TRP A 6 39.599 23.646 19.107 1.00 0.00 H +ATOM 114 HZ2 TRP A 6 44.577 23.493 19.295 1.00 0.00 H +ATOM 115 HZ3 TRP A 6 40.760 23.475 21.300 1.00 0.00 H +ATOM 116 HH2 TRP A 6 43.232 23.435 21.415 1.00 0.00 H +ATOM 117 N LEU A 7 38.298 21.215 17.301 1.00 0.00 N +ATOM 118 CA LEU A 7 38.257 20.143 18.297 1.00 0.00 C +ATOM 119 C LEU A 7 38.051 18.756 17.676 1.00 0.00 C +ATOM 120 O LEU A 7 38.754 17.827 18.076 1.00 0.00 O +ATOM 121 CB LEU A 7 37.188 20.430 19.367 1.00 0.00 C +ATOM 122 CG LEU A 7 37.597 21.496 20.403 1.00 0.00 C +ATOM 123 CD1 LEU A 7 36.423 21.752 21.352 1.00 0.00 C +ATOM 124 CD2 LEU A 7 38.805 21.068 21.248 1.00 0.00 C +ATOM 125 H LEU A 7 37.582 21.938 17.328 1.00 0.00 H +ATOM 126 HA LEU A 7 39.232 20.097 18.779 1.00 0.00 H +ATOM 127 HB2 LEU A 7 36.298 20.767 18.871 1.00 0.00 H +ATOM 128 HB3 LEU A 7 36.977 19.504 19.906 1.00 0.00 H +ATOM 129 HG LEU A 7 37.837 22.426 19.894 1.00 0.00 H +ATOM 130 HD11 LEU A 7 35.555 22.083 20.783 1.00 0.00 H +ATOM 131 HD12 LEU A 7 36.173 20.838 21.894 1.00 0.00 H +ATOM 132 HD13 LEU A 7 36.687 22.526 22.073 1.00 0.00 H +ATOM 133 HD21 LEU A 7 38.628 20.086 21.688 1.00 0.00 H +ATOM 134 HD22 LEU A 7 39.703 21.030 20.634 1.00 0.00 H +ATOM 135 HD23 LEU A 7 38.976 21.789 22.046 1.00 0.00 H +ATOM 136 N LYS A 8 37.145 18.594 16.694 1.00 0.00 N +ATOM 137 CA LYS A 8 36.874 17.284 16.065 1.00 0.00 C +ATOM 138 C LYS A 8 38.102 16.648 15.397 1.00 0.00 C +ATOM 139 O LYS A 8 38.179 15.427 15.304 1.00 0.00 O +ATOM 140 CB LYS A 8 35.674 17.378 15.102 1.00 0.00 C +ATOM 141 CG LYS A 8 35.968 18.066 13.757 1.00 0.00 C +ATOM 142 CD LYS A 8 36.216 17.089 12.598 1.00 0.00 C +ATOM 143 CE LYS A 8 36.404 17.876 11.295 1.00 0.00 C +ATOM 144 NZ LYS A 8 35.335 17.592 10.311 1.00 0.00 N +ATOM 145 H LYS A 8 36.577 19.400 16.431 1.00 0.00 H +ATOM 146 HA LYS A 8 36.589 16.597 16.863 1.00 0.00 H +ATOM 147 HB2 LYS A 8 35.333 16.381 14.898 1.00 0.00 H +ATOM 148 HB3 LYS A 8 34.879 17.932 15.603 1.00 0.00 H +ATOM 149 HG2 LYS A 8 35.129 18.685 13.504 1.00 0.00 H +ATOM 150 HG3 LYS A 8 36.836 18.707 13.865 1.00 0.00 H +ATOM 151 HD2 LYS A 8 37.099 16.513 12.798 1.00 0.00 H +ATOM 152 HD3 LYS A 8 35.374 16.401 12.516 1.00 0.00 H +ATOM 153 HE2 LYS A 8 36.396 18.925 11.521 1.00 0.00 H +ATOM 154 HE3 LYS A 8 37.387 17.636 10.877 1.00 0.00 H +ATOM 155 HZ1 LYS A 8 35.277 16.601 10.123 1.00 0.00 H +ATOM 156 HZ2 LYS A 8 34.456 17.951 10.677 1.00 0.00 H +ATOM 157 HZ3 LYS A 8 35.516 18.092 9.453 1.00 0.00 H +ATOM 158 N ASP A 9 39.070 17.468 14.979 1.00 0.00 N +ATOM 159 CA ASP A 9 40.364 17.059 14.429 1.00 0.00 C +ATOM 160 C ASP A 9 41.379 16.611 15.502 1.00 0.00 C +ATOM 161 O ASP A 9 42.443 16.104 15.140 1.00 0.00 O +ATOM 162 CB ASP A 9 40.931 18.236 13.610 1.00 0.00 C +ATOM 163 CG ASP A 9 40.570 18.169 12.124 1.00 0.00 C +ATOM 164 OD1 ASP A 9 39.366 18.024 11.812 1.00 0.00 O +ATOM 165 OD2 ASP A 9 41.525 18.260 11.317 1.00 0.00 O +ATOM 166 H ASP A 9 38.888 18.459 15.043 1.00 0.00 H +ATOM 167 HA ASP A 9 40.217 16.208 13.760 1.00 0.00 H +ATOM 168 HB2 ASP A 9 40.542 19.151 14.014 1.00 0.00 H +ATOM 169 HB3 ASP A 9 42.014 18.238 13.684 1.00 0.00 H +ATOM 170 N GLY A 10 41.083 16.797 16.798 1.00 0.00 N +ATOM 171 CA GLY A 10 41.958 16.457 17.927 1.00 0.00 C +ATOM 172 C GLY A 10 42.526 17.663 18.687 1.00 0.00 C +ATOM 173 O GLY A 10 43.394 17.481 19.542 1.00 0.00 O +ATOM 174 H GLY A 10 40.163 17.167 17.027 1.00 0.00 H +ATOM 175 HA2 GLY A 10 41.384 15.861 18.638 1.00 0.00 H +ATOM 176 HA3 GLY A 10 42.795 15.847 17.586 1.00 0.00 H +ATOM 177 N GLY A 11 42.070 18.888 18.389 1.00 0.00 N +ATOM 178 CA GLY A 11 42.524 20.108 19.057 1.00 0.00 C +ATOM 179 C GLY A 11 44.055 20.273 18.988 1.00 0.00 C +ATOM 180 O GLY A 11 44.608 20.246 17.885 1.00 0.00 O +ATOM 181 H GLY A 11 41.379 18.986 17.653 1.00 0.00 H +ATOM 182 HA2 GLY A 11 42.062 20.966 18.571 1.00 0.00 H +ATOM 183 HA3 GLY A 11 42.178 20.078 20.087 1.00 0.00 H +ATOM 184 N PRO A 12 44.769 20.424 20.128 1.00 0.00 N +ATOM 185 CA PRO A 12 46.231 20.542 20.140 1.00 0.00 C +ATOM 186 C PRO A 12 46.956 19.346 19.499 1.00 0.00 C +ATOM 187 O PRO A 12 48.037 19.513 18.935 1.00 0.00 O +ATOM 188 CB PRO A 12 46.638 20.688 21.613 1.00 0.00 C +ATOM 189 CG PRO A 12 45.358 21.123 22.321 1.00 0.00 C +ATOM 190 CD PRO A 12 44.260 20.460 21.494 1.00 0.00 C +ATOM 191 HA PRO A 12 46.509 21.449 19.601 1.00 0.00 H +ATOM 192 HB2 PRO A 12 46.989 19.752 22.004 1.00 0.00 H +ATOM 193 HB3 PRO A 12 47.429 21.428 21.737 1.00 0.00 H +ATOM 194 HG2 PRO A 12 45.341 20.773 23.335 1.00 0.00 H +ATOM 195 HG3 PRO A 12 45.256 22.208 22.263 1.00 0.00 H +ATOM 196 HD2 PRO A 12 44.071 19.466 21.850 1.00 0.00 H +ATOM 197 HD3 PRO A 12 43.338 21.033 21.580 1.00 0.00 H +ATOM 198 N SER A 13 46.361 18.146 19.539 1.00 0.00 N +ATOM 199 CA SER A 13 46.947 16.896 19.038 1.00 0.00 C +ATOM 200 C SER A 13 46.795 16.706 17.519 1.00 0.00 C +ATOM 201 O SER A 13 46.923 15.587 17.031 1.00 0.00 O +ATOM 202 CB SER A 13 46.356 15.704 19.806 1.00 0.00 C +ATOM 203 OG SER A 13 46.661 15.811 21.184 1.00 0.00 O +ATOM 204 H SER A 13 45.433 18.076 19.947 1.00 0.00 H +ATOM 205 HA SER A 13 48.019 16.916 19.237 1.00 0.00 H +ATOM 206 HB2 SER A 13 45.291 15.693 19.678 1.00 0.00 H +ATOM 207 HB3 SER A 13 46.778 14.773 19.427 1.00 0.00 H +ATOM 208 HG SER A 13 47.605 15.681 21.304 1.00 0.00 H +ATOM 209 N SER A 14 46.535 17.785 16.768 1.00 0.00 N +ATOM 210 CA SER A 14 46.287 17.760 15.319 1.00 0.00 C +ATOM 211 C SER A 14 47.230 18.670 14.511 1.00 0.00 C +ATOM 212 O SER A 14 46.980 18.952 13.341 1.00 0.00 O +ATOM 213 CB SER A 14 44.812 18.082 15.069 1.00 0.00 C +ATOM 214 OG SER A 14 44.329 17.332 13.976 1.00 0.00 O +ATOM 215 H SER A 14 46.407 18.660 17.264 1.00 0.00 H +ATOM 216 HA SER A 14 46.460 16.746 14.956 1.00 0.00 H +ATOM 217 HB2 SER A 14 44.242 17.839 15.945 1.00 0.00 H +ATOM 218 HB3 SER A 14 44.676 19.141 14.877 1.00 0.00 H +ATOM 219 HG SER A 14 43.612 16.751 14.347 1.00 0.00 H +ATOM 220 N GLY A 15 48.317 19.155 15.132 1.00 0.00 N +ATOM 221 CA GLY A 15 49.349 19.959 14.464 1.00 0.00 C +ATOM 222 C GLY A 15 48.882 21.350 14.018 1.00 0.00 C +ATOM 223 O GLY A 15 49.437 21.898 13.067 1.00 0.00 O +ATOM 224 H GLY A 15 48.471 18.865 16.088 1.00 0.00 H +ATOM 225 HA2 GLY A 15 50.195 20.088 15.140 1.00 0.00 H +ATOM 226 HA3 GLY A 15 49.703 19.423 13.582 1.00 0.00 H +ATOM 227 N ARG A 16 47.854 21.911 14.674 1.00 0.00 N +ATOM 228 CA ARG A 16 47.187 23.159 14.280 1.00 0.00 C +ATOM 229 C ARG A 16 46.753 23.991 15.505 1.00 0.00 C +ATOM 230 O ARG A 16 46.120 23.441 16.410 1.00 0.00 O +ATOM 231 CB ARG A 16 46.008 22.832 13.340 1.00 0.00 C +ATOM 232 CG ARG A 16 44.944 21.904 13.956 1.00 0.00 C +ATOM 233 CD ARG A 16 43.821 21.483 12.996 1.00 0.00 C +ATOM 234 NE ARG A 16 44.149 20.264 12.234 1.00 0.00 N +ATOM 235 CZ ARG A 16 44.757 20.161 11.060 1.00 0.00 C +ATOM 236 NH1 ARG A 16 45.187 21.211 10.397 1.00 0.00 N +ATOM 237 NH2 ARG A 16 44.933 18.980 10.525 1.00 0.00 N +ATOM 238 H ARG A 16 47.477 21.399 15.460 1.00 0.00 H +ATOM 239 HA ARG A 16 47.907 23.738 13.704 1.00 0.00 H +ATOM 240 HB2 ARG A 16 45.532 23.753 13.065 1.00 0.00 H +ATOM 241 HB3 ARG A 16 46.422 22.355 12.454 1.00 0.00 H +ATOM 242 HG2 ARG A 16 45.436 21.016 14.303 1.00 0.00 H +ATOM 243 HG3 ARG A 16 44.477 22.423 14.785 1.00 0.00 H +ATOM 244 HD2 ARG A 16 42.931 21.301 13.568 1.00 0.00 H +ATOM 245 HD3 ARG A 16 43.567 22.310 12.331 1.00 0.00 H +ATOM 246 HE ARG A 16 43.861 19.381 12.636 1.00 0.00 H +ATOM 247 HH11 ARG A 16 45.048 22.113 10.813 1.00 0.00 H +ATOM 248 HH12 ARG A 16 45.659 21.113 9.519 1.00 0.00 H +ATOM 249 HH21 ARG A 16 44.547 18.181 11.007 1.00 0.00 H +ATOM 250 HH22 ARG A 16 45.406 18.870 9.650 1.00 0.00 H +ATOM 251 N PRO A 17 47.054 25.305 15.554 1.00 0.00 N +ATOM 252 CA PRO A 17 46.680 26.163 16.679 1.00 0.00 C +ATOM 253 C PRO A 17 45.159 26.406 16.729 1.00 0.00 C +ATOM 254 O PRO A 17 44.484 26.240 15.710 1.00 0.00 O +ATOM 255 CB PRO A 17 47.452 27.469 16.453 1.00 0.00 C +ATOM 256 CG PRO A 17 47.575 27.549 14.933 1.00 0.00 C +ATOM 257 CD PRO A 17 47.718 26.085 14.518 1.00 0.00 C +ATOM 258 HA PRO A 17 47.005 25.703 17.613 1.00 0.00 H +ATOM 259 HB2 PRO A 17 46.907 28.309 16.839 1.00 0.00 H +ATOM 260 HB3 PRO A 17 48.446 27.383 16.895 1.00 0.00 H +ATOM 261 HG2 PRO A 17 46.698 27.989 14.498 1.00 0.00 H +ATOM 262 HG3 PRO A 17 48.438 28.141 14.627 1.00 0.00 H +ATOM 263 HD2 PRO A 17 47.247 25.919 13.568 1.00 0.00 H +ATOM 264 HD3 PRO A 17 48.774 25.814 14.479 1.00 0.00 H +ATOM 265 N PRO A 18 44.608 26.814 17.889 1.00 0.00 N +ATOM 266 CA PRO A 18 43.185 27.106 18.020 1.00 0.00 C +ATOM 267 C PRO A 18 42.799 28.380 17.247 1.00 0.00 C +ATOM 268 O PRO A 18 43.582 29.331 17.205 1.00 0.00 O +ATOM 269 CB PRO A 18 42.933 27.265 19.521 1.00 0.00 C +ATOM 270 CG PRO A 18 44.283 27.730 20.063 1.00 0.00 C +ATOM 271 CD PRO A 18 45.291 27.024 19.157 1.00 0.00 C +ATOM 272 HA PRO A 18 42.617 26.256 17.650 1.00 0.00 H +ATOM 273 HB2 PRO A 18 42.172 27.999 19.706 1.00 0.00 H +ATOM 274 HB3 PRO A 18 42.679 26.298 19.952 1.00 0.00 H +ATOM 275 HG2 PRO A 18 44.380 28.796 19.988 1.00 0.00 H +ATOM 276 HG3 PRO A 18 44.416 27.452 21.109 1.00 0.00 H +ATOM 277 HD2 PRO A 18 46.160 27.637 19.016 1.00 0.00 H +ATOM 278 HD3 PRO A 18 45.560 26.058 19.587 1.00 0.00 H +ATOM 279 N PRO A 19 41.586 28.435 16.670 1.00 0.00 N +ATOM 280 CA PRO A 19 41.083 29.618 15.981 1.00 0.00 C +ATOM 281 C PRO A 19 40.613 30.682 16.989 1.00 0.00 C +ATOM 282 O PRO A 19 39.774 30.399 17.847 1.00 0.00 O +ATOM 283 CB PRO A 19 39.946 29.089 15.105 1.00 0.00 C +ATOM 284 CG PRO A 19 39.379 27.927 15.922 1.00 0.00 C +ATOM 285 CD PRO A 19 40.614 27.350 16.606 1.00 0.00 C +ATOM 286 HA PRO A 19 41.859 30.041 15.343 1.00 0.00 H +ATOM 287 HB2 PRO A 19 39.201 29.845 14.945 1.00 0.00 H +ATOM 288 HB3 PRO A 19 40.361 28.705 14.172 1.00 0.00 H +ATOM 289 HG2 PRO A 19 38.666 28.276 16.644 1.00 0.00 H +ATOM 290 HG3 PRO A 19 38.879 27.189 15.293 1.00 0.00 H +ATOM 291 HD2 PRO A 19 40.368 27.012 17.594 1.00 0.00 H +ATOM 292 HD3 PRO A 19 41.019 26.536 16.005 1.00 0.00 H +ATOM 293 N SER A 20 41.169 31.897 16.883 1.00 0.00 N +ATOM 294 CA SER A 20 40.750 33.102 17.619 1.00 0.00 C +ATOM 295 C SER A 20 39.492 33.732 17.017 1.00 0.00 C +ATOM 296 O SER A 20 39.511 33.991 15.794 1.00 0.00 O +ATOM 297 CB SER A 20 41.870 34.146 17.618 1.00 0.00 C +ATOM 298 OG SER A 20 43.018 33.616 18.245 1.00 0.00 O +ATOM 299 OXT SER A 20 38.557 33.978 17.807 1.00 0.00 O +ATOM 300 H SER A 20 41.867 32.036 16.169 1.00 0.00 H +ATOM 301 HA SER A 20 40.499 32.835 18.644 1.00 0.00 H +ATOM 302 HB2 SER A 20 42.108 34.413 16.606 1.00 0.00 H +ATOM 303 HB3 SER A 20 41.534 35.034 18.158 1.00 0.00 H +ATOM 304 HG SER A 20 42.729 33.115 19.010 1.00 0.00 H +END diff --git a/regtest/basic/rt-molinfo-whole-repair/whole.xyz.reference b/regtest/basic/rt-molinfo-whole-repair/whole.xyz.reference new file mode 100644 index 0000000000..7d2e750e43 --- /dev/null +++ b/regtest/basic/rt-molinfo-whole-repair/whole.xyz.reference @@ -0,0 +1,1530 @@ +304 + 3.600 0.000 0.000 0.000 3.600 0.000 1.800 1.800 2.546 +N 1.749 3.804 1.455 +CA 1.754 3.875 1.325 +C 1.617 3.915 1.272 +O 1.596 4.034 1.251 +CB 1.840 3.800 1.222 +CG 1.987 3.802 1.266 +OD1 2.021 3.864 1.365 +ND2 2.075 3.733 1.196 +H1 1.690 3.854 1.521 +H2 1.714 3.710 1.443 +H3 1.843 3.799 1.494 +HA 1.805 3.970 1.344 +HB2 1.807 3.698 1.215 +HB3 1.832 3.850 1.126 +HD21 2.052 3.677 1.115 +HD22 2.170 3.741 1.230 +N 1.523 3.821 1.254 +CA 1.386 3.848 1.209 +C 1.319 3.969 1.279 +O 1.272 4.061 1.211 +CB 1.303 3.718 1.220 +CG 1.306 3.645 1.357 +CD1 1.174 3.660 1.433 +CD2 1.334 3.496 1.340 +H 1.546 3.723 1.266 +HA 1.390 3.874 1.103 +HB2 1.201 3.742 1.197 +HB3 1.342 3.650 1.144 +HG 1.384 3.687 1.420 +HD11 1.152 3.765 1.449 +HD12 1.093 3.614 1.377 +HD13 1.181 3.612 1.530 +HD21 1.257 3.451 1.277 +HD22 1.432 3.481 1.294 +HD23 1.333 3.447 1.437 +N 1.321 3.973 1.412 +CA 1.264 4.084 1.490 +C 1.338 4.217 1.470 +O 1.277 4.323 1.473 +CB 1.260 4.044 1.638 +CG 1.144 4.106 1.712 +CD1 1.155 4.236 1.766 +CD2 1.023 4.035 1.724 +CE1 1.045 4.295 1.830 +CE2 0.912 4.094 1.788 +CZ 0.923 4.225 1.840 +OH 0.815 4.285 1.898 +H 1.356 3.893 1.462 +HA 1.161 4.098 1.456 +HB2 1.252 3.937 1.645 +HB3 1.354 4.072 1.686 +HD1 1.248 4.291 1.756 +HD2 1.013 3.935 1.685 +HE1 1.051 4.394 1.871 +HE2 0.820 4.038 1.797 +HH 0.733 4.244 1.870 +N 1.470 4.212 1.444 +CA 1.553 4.329 1.413 +C 1.508 4.389 1.279 +O 1.487 4.510 1.268 +CB 1.704 4.292 1.410 +CG1 1.750 4.203 1.528 +CG2 1.792 4.418 1.400 +CD1 1.721 4.259 1.668 +H 1.511 4.121 1.431 +HA 1.538 4.405 1.490 +HB 1.723 4.235 1.319 +HG12 1.700 4.108 1.519 +HG13 1.857 4.186 1.519 +HG21 1.771 4.471 1.307 +HG22 1.772 4.485 1.484 +HG23 1.897 4.390 1.401 +HD11 1.770 4.356 1.681 +HD12 1.614 4.270 1.683 +HD13 1.760 4.190 1.743 +N 1.487 4.303 1.178 +CA 1.435 4.344 1.047 +C 1.291 4.398 1.054 +O 1.255 4.485 0.975 +CB 1.443 4.226 0.948 +CG 1.471 4.274 0.804 +CD 1.619 4.303 0.780 +OE1 1.664 4.418 0.779 +NE2 1.700 4.201 0.757 +H 1.506 4.205 1.195 +HA 1.499 4.424 1.011 +HB2 1.522 4.160 0.979 +HB3 1.348 4.172 0.949 +HG2 1.440 4.198 0.736 +HG3 1.412 4.363 0.783 +HE21 1.665 4.107 0.753 +HE22 1.796 4.225 0.741 +N 1.208 4.352 1.149 +CA 1.076 4.410 1.175 +C 1.085 4.546 1.246 +O 1.016 4.641 1.208 +CB 0.991 4.310 1.254 +CG 0.854 4.359 1.291 +CD1 0.747 4.364 1.208 +CD2 0.808 4.412 1.419 +NE1 0.639 4.420 1.275 +CE2 0.671 4.449 1.406 +CE3 0.868 4.433 1.545 +CZ2 0.596 4.502 1.511 +CZ3 0.794 4.488 1.651 +CH2 0.658 4.521 1.636 +H 1.239 4.272 1.204 +HA 1.026 4.428 1.080 +HB2 0.980 4.221 1.195 +HB3 1.043 4.283 1.346 +HD1 0.747 4.331 1.105 +HE1 0.547 4.436 1.235 +HE3 0.971 4.405 1.558 +HZ2 0.492 4.528 1.496 +HZ3 0.842 4.504 1.747 +HH2 0.603 4.562 1.719 +N 1.172 4.559 1.348 +CA 1.192 4.686 1.419 +C 1.251 4.796 1.329 +O 1.202 4.908 1.335 +CB 1.278 4.665 1.544 +CG 1.203 4.601 1.663 +CD1 1.302 4.578 1.778 +CD2 1.089 4.688 1.715 +H 1.224 4.477 1.378 +HA 1.094 4.723 1.449 +HB2 1.361 4.602 1.518 +HB3 1.316 4.762 1.577 +HG 1.163 4.505 1.632 +HD11 1.383 4.513 1.744 +HD12 1.342 4.673 1.812 +HD13 1.251 4.529 1.861 +HD21 1.125 4.789 1.737 +HD22 1.009 4.694 1.641 +HD23 1.047 4.645 1.806 +N 1.352 4.766 1.245 +CA 1.416 4.867 1.158 +C 1.319 4.935 1.060 +O 1.341 5.049 1.021 +CB 1.539 4.808 1.086 +CG 1.507 4.714 0.969 +CD 1.517 4.780 0.831 +CE 1.493 4.675 0.722 +NZ 1.612 4.654 0.637 +H 1.390 4.672 1.248 +HA 1.452 4.947 1.223 +HB2 1.597 4.890 1.048 +HB3 1.597 4.753 1.160 +HG2 1.575 4.631 0.972 +HG3 1.406 4.674 0.981 +HD2 1.444 4.858 0.823 +HD3 1.616 4.825 0.820 +HE2 1.466 4.582 0.768 +HE3 1.407 4.707 0.661 +HZ1 1.643 4.741 0.596 +HZ2 1.685 4.612 0.694 +HZ3 1.591 4.588 0.564 +N 1.209 4.867 1.024 +CA 1.099 4.917 0.942 +C 1.002 5.009 1.019 +O 0.915 5.069 0.956 +CB 1.024 4.797 0.883 +CG 1.075 4.756 0.744 +OD1 1.198 4.736 0.729 +OD2 0.988 4.746 0.654 +H 1.203 4.771 1.057 +HA 1.140 4.977 0.860 +HB2 1.036 4.713 0.949 +HB3 0.919 4.821 0.873 +N 1.014 5.020 1.152 +CA 0.926 5.100 1.239 +C 0.835 5.018 1.332 +O 0.748 5.076 1.396 +H 1.091 4.972 1.197 +HA2 0.989 5.163 1.302 +HA3 0.863 5.166 1.179 +N 0.853 4.885 1.339 +CA 0.773 4.798 1.425 +C 0.622 4.812 1.399 +O 0.580 4.797 1.284 +H 0.924 4.842 1.281 +HA2 0.802 4.694 1.406 +HA3 0.798 4.821 1.528 +N 0.539 4.843 1.501 +CA 0.395 4.862 1.482 +C 0.359 4.973 1.381 +O 0.256 4.965 1.315 +CB 0.338 4.896 1.621 +CG 0.444 4.847 1.719 +CD 0.574 4.865 1.640 +HA 0.351 4.768 1.448 +HB2 0.322 5.002 1.631 +HB3 0.242 4.846 1.638 +HG2 0.444 4.907 1.808 +HG3 0.429 4.742 1.740 +HD2 0.613 4.964 1.654 +HD3 0.648 4.794 1.676 +N 0.445 5.075 1.366 +CA 0.423 5.191 1.279 +C 0.457 5.166 1.131 +O 0.476 5.261 1.056 +CB 0.501 5.312 1.334 +OG 0.456 5.344 1.464 +H 0.532 5.073 1.418 +HA 0.317 5.217 1.282 +HB2 0.606 5.287 1.338 +HB3 0.487 5.398 1.269 +HG 0.367 5.379 1.458 +N 0.463 5.039 1.089 +CA 0.502 4.998 0.953 +C 0.397 4.910 0.883 +O 0.425 4.847 0.781 +CB 0.639 4.930 0.959 +OG 0.714 4.962 0.844 +H 0.450 4.967 1.159 +HA 0.513 5.087 0.892 +HB2 0.692 4.964 1.046 +HB3 0.629 4.822 0.968 +HG 0.794 5.011 0.877 +N 0.274 4.903 0.937 +CA 0.162 4.831 0.876 +C 0.178 4.679 0.873 +O 0.120 4.613 0.786 +H 0.257 4.959 1.019 +HA2 0.070 4.854 0.931 +HA3 0.149 4.866 0.773 +N 0.257 4.622 0.965 +CA 0.296 4.480 0.967 +C 0.306 4.425 1.111 +O 0.372 4.488 1.195 +CB 0.426 4.462 0.887 +CG 0.546 4.543 0.941 +CD 0.673 4.534 0.856 +NE 0.678 4.636 0.749 +CZ 0.633 4.627 0.625 +NH1 0.573 4.519 0.579 +NH2 0.649 4.728 0.543 +H 0.298 4.683 1.034 +HA 0.218 4.425 0.915 +HB2 0.453 4.358 0.890 +HB3 0.406 4.492 0.785 +HG2 0.516 4.646 0.946 +HG3 0.570 4.507 1.040 +HD2 0.758 4.548 0.920 +HD3 0.684 4.434 0.816 +HE 0.723 4.724 0.771 +HH11 0.561 4.442 0.643 +HH12 0.538 4.515 0.486 +HH21 0.701 4.808 0.576 +HH22 0.615 4.724 0.449 +N 0.245 4.309 1.142 +CA 0.250 4.250 1.276 +C 0.390 4.197 1.310 +O 0.469 4.172 1.219 +CB 0.146 4.137 1.273 +CG 0.147 4.092 1.128 +CD 0.172 4.222 1.051 +HA 0.220 4.325 1.350 +HB2 0.175 4.057 1.339 +HB3 0.048 4.178 1.299 +HG2 0.225 4.021 1.110 +HG3 0.052 4.046 1.099 +HD2 0.231 4.203 0.963 +HD3 0.077 4.268 1.025 +N 0.423 4.178 1.439 +CA 0.552 4.125 1.481 +C 0.566 3.976 1.443 +O 0.468 3.902 1.449 +CB 0.558 4.144 1.632 +CG 0.411 4.143 1.675 +CD 0.340 4.206 1.556 +HA 0.631 4.183 1.434 +HB2 0.612 4.065 1.679 +HB3 0.602 4.242 1.655 +HG2 0.377 4.043 1.691 +HG3 0.395 4.200 1.766 +HD2 0.242 4.163 1.543 +HD3 0.333 4.314 1.570 +N 0.688 3.931 1.407 +CA 0.715 3.791 1.377 +C 0.725 3.708 1.506 +O 0.804 3.740 1.595 +CB 0.845 3.794 1.298 +CG 0.920 3.913 1.357 +CD 0.808 4.011 1.390 +HA 0.636 3.750 1.314 +HB2 0.901 3.703 1.312 +HB3 0.824 3.814 1.193 +HG2 0.974 3.885 1.446 +HG3 0.992 3.956 1.287 +HD2 0.831 4.064 1.481 +HD3 0.794 4.080 1.307 +N 0.643 3.602 1.516 +CA 0.648 3.499 1.622 +C 0.760 3.398 1.598 +O 0.764 3.341 1.487 +CB 0.514 3.424 1.629 +OG 0.410 3.514 1.659 +OXT 0.837 3.376 1.694 +H 0.579 3.584 1.440 +HA 0.668 3.546 1.717 +HB2 0.495 3.377 1.534 +HB3 0.521 3.348 1.707 +HG 0.443 3.576 1.725 +304 + 3.600 0.000 0.000 1.200 3.394 0.000 -1.200 1.697 2.939 +N 0.011 1.436 1.051 +CA 0.069 1.373 1.172 +C -0.037 1.316 1.266 +O -0.031 1.197 1.292 +CB 0.169 1.466 1.242 +CG 0.293 1.484 1.155 +OD1 0.304 1.424 1.049 +ND2 0.387 1.570 1.192 +H1 -0.057 1.375 1.007 +H2 -0.033 1.525 1.073 +H3 0.086 1.454 0.985 +HA 0.126 1.286 1.138 +HB2 0.124 1.561 1.260 +HB3 0.200 1.421 1.337 +HD21 0.382 1.625 1.277 +HD22 0.466 1.575 1.131 +N -0.134 1.395 1.313 +CA -0.244 1.350 1.399 +C -0.309 1.217 1.355 +O -0.317 1.122 1.433 +CB -0.346 1.465 1.416 +CG -0.398 1.530 1.285 +CD1 -0.543 1.492 1.255 +CD2 -0.390 1.683 1.293 +H -0.132 1.495 1.295 +HA -0.203 1.330 1.498 +HB2 -0.430 1.427 1.470 +HB3 -0.296 1.542 1.475 +HG -0.338 1.499 1.200 +HD11 -0.551 1.384 1.246 +HD12 -0.608 1.528 1.334 +HD13 -0.575 1.536 1.160 +HD21 -0.449 1.719 1.377 +HD22 -0.287 1.715 1.305 +HD23 -0.430 1.727 1.201 +N -0.348 1.206 1.227 +CA -0.409 1.085 1.172 +C -0.311 0.966 1.167 +O -0.353 0.851 1.183 +CB -0.465 1.116 1.032 +CG -0.587 1.033 0.999 +CD1 -0.573 0.904 0.944 +CD2 -0.716 1.084 1.026 +CE1 -0.687 0.826 0.918 +CE2 -0.830 1.006 1.001 +CZ -0.815 0.876 0.948 +OH -0.924 0.798 0.927 +H -0.344 1.288 1.169 +HA -0.492 1.057 1.236 +HB2 -0.492 1.220 1.029 +HB3 -0.388 1.100 0.957 +HD1 -0.474 0.865 0.924 +HD2 -0.728 1.184 1.067 +HE1 -0.678 0.727 0.877 +HE2 -0.928 1.047 1.022 +HH -0.999 0.826 0.979 +N -0.181 0.992 1.149 +CA -0.074 0.891 1.153 +C -0.065 0.831 1.294 +O -0.062 0.709 1.310 +CB 0.062 0.951 1.107 +CG1 0.053 1.039 0.981 +CG2 0.167 0.840 1.088 +CD1 -0.008 0.973 0.857 +H -0.153 1.089 1.149 +HA -0.101 0.810 1.084 +HB 0.099 1.014 1.187 +HG12 -0.006 1.126 1.005 +HG13 0.154 1.073 0.955 +HG21 0.186 0.789 1.183 +HG22 0.133 0.767 1.015 +HG23 0.261 0.884 1.054 +HD11 0.048 0.884 0.829 +HD12 -0.112 0.945 0.877 +HD13 -0.006 1.043 0.774 +N -0.067 0.918 1.396 +CA -0.068 0.876 1.537 +C -0.196 0.800 1.576 +O -0.190 0.713 1.662 +CB -0.048 0.999 1.628 +CG 0.031 0.963 1.755 +CD 0.182 0.957 1.731 +OE1 0.242 0.852 1.718 +NE2 0.248 1.072 1.727 +H -0.070 1.017 1.374 +HA 0.016 0.809 1.551 +HB2 0.006 1.074 1.574 +HB3 -0.146 1.038 1.657 +HG2 0.011 1.037 1.831 +HG3 -0.003 0.867 1.795 +HE21 0.202 1.160 1.742 +HE22 0.347 1.064 1.712 +N -0.310 0.829 1.512 +CA -0.433 0.750 1.529 +C -0.425 0.613 1.458 +O -0.463 0.511 1.517 +CB -0.554 0.832 1.481 +CG -0.685 0.760 1.490 +CD1 -0.759 0.743 1.603 +CD2 -0.760 0.694 1.384 +NE1 -0.872 0.668 1.573 +CE2 -0.879 0.638 1.440 +CE3 -0.741 0.677 1.245 +CZ2 -0.973 0.569 1.363 +CZ3 -0.834 0.606 1.167 +CH2 -0.951 0.553 1.225 +H -0.311 0.909 1.451 +HA -0.447 0.729 1.635 +HB2 -0.560 0.920 1.541 +HB3 -0.538 0.861 1.378 +HD1 -0.732 0.780 1.701 +HE1 -0.943 0.640 1.641 +HE3 -0.653 0.719 1.199 +HZ2 -1.062 0.528 1.410 +HZ3 -0.817 0.593 1.061 +HH2 -1.022 0.501 1.164 +N -0.373 0.608 1.335 +CA -0.357 0.483 1.261 +C -0.256 0.388 1.327 +O -0.286 0.269 1.337 +CB -0.319 0.510 1.114 +CG -0.437 0.557 1.026 +CD1 -0.385 0.589 0.886 +CD2 -0.546 0.450 1.013 +H -0.348 0.696 1.289 +HA -0.452 0.430 1.263 +HB2 -0.244 0.587 1.113 +HB3 -0.279 0.419 1.071 +HG -0.480 0.647 1.068 +HD11 -0.308 0.666 0.892 +HD12 -0.342 0.500 0.840 +HD13 -0.466 0.625 0.823 +HD21 -0.503 0.355 0.980 +HD22 -0.597 0.436 1.108 +HD23 -0.620 0.482 0.940 +N -0.140 0.437 1.374 +CA -0.037 0.351 1.437 +C -0.086 0.274 1.560 +O -0.034 0.167 1.590 +CB 0.091 0.432 1.466 +CG 0.083 0.526 1.587 +CD 0.147 0.469 1.715 +CE 0.142 0.574 1.826 +NZ 0.277 0.617 1.869 +H -0.120 0.536 1.360 +HA -0.010 0.274 1.364 +HB2 0.171 0.362 1.483 +HB3 0.114 0.492 1.377 +HG2 0.133 0.617 1.562 +HG3 -0.021 0.549 1.608 +HD2 0.093 0.381 1.745 +HD3 0.250 0.440 1.694 +HE2 0.087 0.659 1.791 +HE3 0.086 0.532 1.911 +HZ1 0.333 0.538 1.897 +HZ2 0.320 0.667 1.791 +HZ3 0.269 0.683 1.945 +N -0.188 0.327 1.629 +CA -0.257 0.264 1.742 +C -0.357 0.155 1.700 +O -0.409 0.085 1.787 +CB -0.328 0.375 1.822 +CG -0.243 0.429 1.938 +OD1 -0.127 0.468 1.913 +OD2 -0.298 0.431 2.051 +H -0.219 0.418 1.600 +HA -0.183 0.216 1.806 +HB2 -0.351 0.456 1.756 +HB3 -0.419 0.335 1.865 +N -0.387 0.139 1.570 +CA -0.483 0.043 1.515 +C -0.610 0.105 1.456 +O -0.703 0.031 1.423 +H -0.335 0.196 1.503 +HA2 -0.433 -0.013 1.435 +HA3 -0.512 -0.029 1.592 +N -0.617 0.238 1.444 +CA -0.733 0.308 1.388 +C -0.863 0.273 1.461 +O -0.869 0.287 1.583 +H -0.539 0.294 1.476 +HA2 -0.716 0.416 1.397 +HA3 -0.739 0.284 1.282 +N -0.969 0.224 1.391 +CA -1.095 0.184 1.454 +C -1.078 0.074 1.561 +O -1.155 0.070 1.657 +CB -1.186 0.135 1.341 +CG -1.125 0.195 1.214 +CD -0.976 0.201 1.247 +HA -1.140 0.272 1.501 +HB2 -1.187 0.028 1.336 +HB3 -1.289 0.169 1.355 +HG2 -1.143 0.132 1.129 +HG3 -1.163 0.296 1.199 +HD2 -0.928 0.108 1.222 +HD3 -0.929 0.280 1.189 +N -0.977 -0.012 1.548 +CA -0.951 -0.126 1.637 +C -0.877 -0.089 1.766 +O -0.821 -0.176 1.831 +CB -0.876 -0.236 1.560 +OG -0.954 -0.281 1.451 +H -0.912 -0.000 1.471 +HA -1.047 -0.168 1.668 +HB2 -0.783 -0.196 1.523 +HB3 -0.856 -0.320 1.626 +HG -1.030 -0.329 1.485 +N -0.878 0.040 1.805 +CA -0.806 0.093 1.921 +C -0.897 0.167 2.022 +O -0.848 0.238 2.109 +CB -0.691 0.180 1.872 +OG -0.579 0.166 1.957 +H -0.924 0.105 1.743 +HA -0.762 0.010 1.976 +HB2 -0.663 0.150 1.773 +HB3 -0.720 0.285 1.867 +HG -0.507 0.128 1.901 +N -1.029 0.152 2.009 +CA -1.127 0.209 2.103 +C -1.136 0.362 2.101 +O -1.173 0.422 2.201 +H -1.062 0.090 1.936 +HA2 -1.226 0.170 2.080 +HA3 -1.101 0.178 2.204 +N -1.099 0.426 1.988 +CA -1.087 0.571 1.974 +C -1.131 0.620 1.835 +O -1.086 0.564 1.735 +CB -0.942 0.614 2.009 +CG -0.835 0.549 1.920 +CD -0.690 0.581 1.960 +NE -0.635 0.487 2.059 +CZ -0.640 0.495 2.192 +NH1 -0.699 0.594 2.254 +NH2 -0.583 0.402 2.264 +H -1.073 0.368 1.910 +HA -1.152 0.616 2.049 +HB2 -0.935 0.720 1.998 +HB3 -0.924 0.586 2.112 +HG2 -0.847 0.442 1.925 +HG3 -0.848 0.584 1.818 +HD2 -0.628 0.577 1.872 +HD3 -0.683 0.684 1.994 +HE -0.586 0.406 2.024 +HH11 -0.743 0.665 2.198 +HH12 -0.703 0.598 2.354 +HH21 -0.532 0.330 2.216 +HH22 -0.586 0.405 2.364 +N -1.217 0.724 1.825 +CA -1.264 0.776 1.696 +C -1.151 0.848 1.620 +O -1.053 0.890 1.681 +CB -1.378 0.872 1.732 +CG -1.339 0.924 1.870 +CD -1.270 0.803 1.935 +HA -1.302 0.694 1.636 +HB2 -1.384 0.952 1.661 +HB3 -1.471 0.816 1.740 +HG2 -1.271 1.007 1.862 +HG3 -1.425 0.956 1.928 +HD2 -1.191 0.836 1.999 +HD3 -1.343 0.744 1.990 +N -1.165 0.865 1.487 +CA -1.065 0.936 1.407 +C -1.064 1.086 1.438 +O -1.169 1.145 1.464 +CB -1.104 0.910 1.261 +CG -1.255 0.887 1.267 +CD -1.274 0.819 1.403 +HA -0.967 0.893 1.426 +HB2 -1.081 0.995 1.199 +HB3 -1.055 0.820 1.226 +HG2 -1.308 0.980 1.263 +HG3 -1.290 0.824 1.185 +HD2 -1.368 0.848 1.446 +HD3 -1.268 0.711 1.392 +N -0.946 1.152 1.433 +CA -0.934 1.296 1.454 +C -0.978 1.373 1.328 +O -0.926 1.349 1.219 +CB -0.786 1.317 1.487 +CG -0.716 1.207 1.407 +CD -0.815 1.092 1.411 +HA -0.995 1.327 1.539 +HB2 -0.753 1.414 1.457 +HB3 -0.771 1.299 1.594 +HG2 -0.698 1.239 1.306 +HG3 -0.620 1.180 1.450 +HD2 -0.814 1.038 1.318 +HD3 -0.791 1.025 1.494 +N -1.075 1.464 1.345 +CA -1.120 1.561 1.244 +C -1.024 1.679 1.231 +O -0.995 1.741 1.335 +CB -1.259 1.615 1.279 +OG -1.352 1.508 1.284 +OXT -0.986 1.708 1.115 +H -1.114 1.476 1.437 +HA -1.123 1.513 1.146 +HB2 -1.256 1.663 1.375 +HB3 -1.290 1.687 1.204 +HG -1.332 1.449 1.211 +304 + 3.600 0.000 0.000 -0.331 3.786 0.000 0.958 0.729 3.499 +N 0.490 0.686 0.862 +CA 0.618 0.615 0.886 +C 0.653 0.602 1.034 +O 0.668 0.489 1.079 +CB 0.733 0.674 0.801 +CG 0.708 0.645 0.653 +OD1 0.613 0.577 0.619 +ND2 0.790 0.697 0.564 +H1 0.416 0.648 0.920 +H2 0.499 0.785 0.880 +H3 0.464 0.673 0.764 +HA 0.604 0.512 0.851 +HB2 0.737 0.780 0.817 +HB3 0.827 0.627 0.831 +HD21 0.868 0.756 0.586 +HD22 0.769 0.672 0.468 +N 0.661 0.711 1.110 +CA 0.687 0.710 1.255 +C 0.607 0.603 1.333 +O 0.666 0.522 1.404 +CB 0.669 0.853 1.311 +CG 0.534 0.923 1.277 +CD1 0.442 0.932 1.398 +CD2 0.558 1.065 1.225 +H 0.654 0.803 1.069 +HA 0.792 0.684 1.269 +HB2 0.677 0.848 1.417 +HB3 0.750 0.913 1.270 +HG 0.481 0.868 1.200 +HD11 0.421 0.833 1.437 +HD12 0.488 0.993 1.476 +HD13 0.347 0.979 1.370 +HD21 0.611 1.124 1.300 +HD22 0.616 1.062 1.133 +HD23 0.462 1.113 1.204 +N 0.475 0.598 1.315 +CA 0.389 0.500 1.381 +C 0.415 0.355 1.335 +O 0.402 0.262 1.414 +CB 0.242 0.539 1.358 +CG 0.152 0.499 1.473 +CD1 0.098 0.369 1.479 +CD2 0.126 0.590 1.577 +CE1 0.019 0.330 1.589 +CE2 0.048 0.552 1.688 +CZ -0.005 0.422 1.694 +OH -0.077 0.382 1.802 +H 0.432 0.670 1.260 +HA 0.409 0.504 1.488 +HB2 0.236 0.645 1.346 +HB3 0.205 0.494 1.266 +HD1 0.118 0.298 1.400 +HD2 0.166 0.691 1.573 +HE1 -0.023 0.231 1.596 +HE2 0.028 0.624 1.766 +HH -0.059 0.437 1.879 +N 0.457 0.335 1.209 +CA 0.497 0.205 1.154 +C 0.623 0.155 1.226 +O 0.628 0.040 1.270 +CB 0.520 0.214 1.000 +CG1 0.410 0.293 0.924 +CG2 0.538 0.074 0.939 +CD1 0.267 0.242 0.944 +H 0.477 0.417 1.155 +HA 0.417 0.133 1.172 +HB 0.613 0.267 0.982 +HG12 0.414 0.395 0.956 +HG13 0.433 0.290 0.817 +HG21 0.627 0.026 0.980 +HG22 0.451 0.012 0.959 +HG23 0.551 0.083 0.831 +HD11 0.258 0.138 0.913 +HD12 0.237 0.251 1.049 +HD13 0.199 0.302 0.884 +N 0.722 0.244 1.244 +CA 0.845 0.215 1.319 +C 0.818 0.187 1.468 +O 0.890 0.109 1.528 +CB 0.946 0.329 1.302 +CG 1.091 0.278 1.302 +CD 1.133 0.222 1.166 +OE1 1.138 0.101 1.143 +NE2 1.168 0.307 1.072 +H 0.710 0.337 1.205 +HA 0.887 0.124 1.276 +HB2 0.927 0.379 1.209 +HB3 0.934 0.400 1.384 +HG2 1.157 0.359 1.327 +HG3 1.103 0.201 1.378 +HE21 1.170 0.406 1.088 +HE22 1.196 0.267 0.984 +N 0.714 0.247 1.528 +CA 0.670 0.214 1.664 +C 0.598 0.078 1.671 +O 0.625 -0.002 1.761 +CB 0.583 0.328 1.719 +CG 0.528 0.304 1.856 +CD1 0.597 0.319 1.972 +CD2 0.395 0.260 1.895 +NE1 0.515 0.284 2.079 +CE2 0.389 0.249 2.037 +CE3 0.277 0.228 1.824 +CZ2 0.274 0.210 2.106 +CZ3 0.161 0.187 1.892 +CH2 0.158 0.179 2.032 +H 0.666 0.319 1.476 +HA 0.758 0.206 1.728 +HB2 0.642 0.417 1.721 +HB3 0.499 0.344 1.651 +HD1 0.699 0.352 1.980 +HE1 0.543 0.285 2.177 +HE3 0.277 0.236 1.716 +HZ2 0.275 0.204 2.214 +HZ3 0.072 0.162 1.836 +HH2 0.068 0.149 2.083 +N 0.508 0.049 1.575 +CA 0.438 -0.080 1.570 +C 0.532 -0.198 1.544 +O 0.518 -0.300 1.612 +CB 0.325 -0.075 1.466 +CG 0.199 0.001 1.512 +CD1 0.098 0.005 1.397 +CD2 0.131 -0.064 1.633 +H 0.486 0.120 1.506 +HA 0.395 -0.098 1.668 +HB2 0.362 -0.028 1.377 +HB3 0.295 -0.178 1.443 +HG 0.226 0.103 1.538 +HD11 0.143 0.054 1.310 +HD12 0.067 -0.096 1.370 +HD13 0.010 0.062 1.427 +HD21 0.112 -0.170 1.613 +HD22 0.194 -0.055 1.721 +HD23 0.036 -0.015 1.653 +N 0.629 -0.187 1.451 +CA 0.722 -0.298 1.418 +C 0.805 -0.346 1.538 +O 0.844 -0.462 1.542 +CB 0.809 -0.262 1.297 +CG 0.924 -0.163 1.326 +CD 1.061 -0.229 1.346 +CE 1.168 -0.121 1.364 +NZ 1.267 -0.122 1.255 +H 0.633 -0.101 1.396 +HA 0.660 -0.383 1.389 +HB2 0.853 -0.352 1.259 +HB3 0.745 -0.218 1.220 +HG2 0.931 -0.094 1.244 +HG3 0.899 -0.105 1.415 +HD2 1.058 -0.292 1.432 +HD3 1.083 -0.292 1.259 +HE2 1.120 -0.025 1.367 +HE3 1.217 -0.137 1.461 +HZ1 1.310 -0.213 1.246 +HZ2 1.221 -0.094 1.169 +HZ3 1.339 -0.052 1.273 +N 0.828 -0.259 1.636 +CA 0.895 -0.288 1.763 +C 0.804 -0.361 1.865 +O 0.854 -0.404 1.969 +CB 0.946 -0.155 1.822 +CG 1.091 -0.124 1.783 +OD1 1.122 -0.127 1.662 +OD2 1.169 -0.098 1.877 +H 0.797 -0.164 1.621 +HA 0.980 -0.354 1.745 +HB2 0.884 -0.076 1.787 +HB3 0.942 -0.160 1.931 +N 0.673 -0.374 1.839 +CA 0.575 -0.437 1.927 +C 0.473 -0.340 1.989 +O 0.396 -0.381 2.077 +H 0.640 -0.341 1.748 +HA2 0.519 -0.511 1.869 +HA3 0.625 -0.490 2.008 +N 0.470 -0.213 1.947 +CA 0.376 -0.113 1.997 +C 0.383 -0.099 2.151 +O 0.492 -0.076 2.204 +H 0.537 -0.184 1.877 +HA2 0.401 -0.016 1.953 +HA3 0.277 -0.140 1.965 +N 0.271 -0.114 2.225 +CA 0.270 -0.107 2.371 +C 0.364 -0.209 2.439 +O 0.417 -0.182 2.546 +CB 0.125 -0.130 2.415 +CG 0.042 -0.103 2.290 +CD 0.136 -0.143 2.176 +HA 0.301 -0.007 2.401 +HB2 0.111 -0.232 2.448 +HB3 0.097 -0.064 2.497 +HG2 -0.047 -0.161 2.289 +HG3 0.021 0.004 2.283 +HD2 0.126 -0.248 2.155 +HD3 0.111 -0.088 2.086 +N 0.388 -0.325 2.375 +CA 0.469 -0.435 2.429 +C 0.620 -0.415 2.411 +O 0.695 -0.512 2.419 +CB 0.422 -0.568 2.368 +OG 0.287 -0.592 2.401 +H 0.348 -0.339 2.283 +HA 0.452 -0.441 2.537 +HB2 0.432 -0.563 2.261 +HB3 0.483 -0.650 2.406 +HG 0.281 -0.610 2.495 +N 0.666 -0.292 2.387 +CA 0.806 -0.258 2.359 +C 0.864 -0.152 2.455 +O 0.970 -0.095 2.429 +CB 0.819 -0.216 2.212 +OG 0.942 -0.261 2.160 +H 0.596 -0.219 2.378 +HA 0.867 -0.347 2.373 +HB2 0.738 -0.260 2.156 +HB3 0.811 -0.109 2.202 +HG 0.918 -0.324 2.087 +N 0.795 -0.123 2.566 +CA 0.842 -0.031 2.670 +C 0.850 0.116 2.627 +O 0.930 0.191 2.683 +H 0.710 -0.175 2.582 +HA2 0.776 -0.038 2.757 +HA3 0.942 -0.062 2.703 +N 0.770 0.156 2.528 +CA 0.776 0.289 2.464 +C 0.636 0.340 2.426 +O 0.560 0.266 2.362 +CB 0.872 0.283 2.344 +CG 0.833 0.181 2.235 +CD 0.933 0.167 2.120 +NE 1.038 0.067 2.148 +CZ 1.156 0.084 2.206 +NH1 1.195 0.201 2.251 +NH2 1.237 -0.017 2.219 +H 0.706 0.088 2.490 +HA 0.819 0.357 2.537 +HB2 0.875 0.381 2.298 +HB3 0.971 0.258 2.382 +HG2 0.822 0.085 2.282 +HG3 0.738 0.212 2.192 +HD2 0.880 0.137 2.032 +HD3 0.976 0.264 2.096 +HE 1.020 -0.028 2.117 +HH11 1.132 0.279 2.241 +HH12 1.284 0.212 2.296 +HH21 1.209 -0.106 2.179 +HH22 1.326 -0.008 2.264 +N 0.599 0.466 2.460 +CA 0.468 0.522 2.427 +C 0.454 0.548 2.276 +O 0.555 0.559 2.206 +CB 0.460 0.652 2.508 +CG 0.606 0.697 2.518 +CD 0.682 0.565 2.527 +HA 0.390 0.454 2.460 +HB2 0.400 0.726 2.457 +HB3 0.422 0.630 2.608 +HG2 0.635 0.753 2.431 +HG3 0.623 0.760 2.605 +HD2 0.777 0.574 2.477 +HD3 0.695 0.537 2.631 +N 0.330 0.561 2.224 +CA 0.306 0.589 2.083 +C 0.349 0.733 2.047 +O 0.331 0.824 2.129 +CB 0.156 0.568 2.061 +CG 0.096 0.596 2.199 +CD 0.203 0.548 2.296 +HA 0.362 0.518 2.023 +HB2 0.118 0.637 1.988 +HB3 0.138 0.465 2.034 +HG2 0.077 0.701 2.212 +HG3 0.002 0.543 2.213 +HD2 0.204 0.609 2.384 +HD3 0.186 0.443 2.320 +N 0.400 0.756 1.925 +CA 0.436 0.889 1.877 +C 0.311 0.968 1.836 +O 0.233 0.921 1.753 +CB 0.531 0.862 1.761 +CG 0.479 0.731 1.702 +CD 0.431 0.655 1.825 +HA 0.490 0.943 1.955 +HB2 0.526 0.941 1.688 +HB3 0.632 0.847 1.799 +HG2 0.399 0.748 1.633 +HG3 0.557 0.676 1.648 +HD2 0.343 0.598 1.801 +HD3 0.510 0.590 1.861 +N 0.293 1.087 1.895 +CA 0.191 1.186 1.858 +C 0.230 1.266 1.733 +O 0.343 1.321 1.734 +CB 0.168 1.285 1.973 +OG 0.123 1.215 2.088 +OXT 0.146 1.272 1.642 +H 0.361 1.116 1.964 +HA 0.098 1.136 1.834 +HB2 0.260 1.335 1.996 +HB3 0.093 1.358 1.943 +HG 0.061 1.148 2.058 +304 + 3.400 3.400 3.400 +N 0.241 0.860 1.865 +CA 0.115 0.831 1.792 +C 0.117 0.699 1.716 +O 0.032 0.615 1.745 +CB 0.072 0.950 1.704 +CG 0.030 1.068 1.792 +OD1 0.028 1.056 1.914 +ND2 0.001 1.183 1.736 +H1 0.269 0.780 1.920 +H2 0.315 0.885 1.801 +H3 0.224 0.938 1.928 +HA 0.037 0.819 1.867 +HB2 0.153 0.980 1.641 +HB3 -0.014 0.921 1.643 +HD21 0.004 1.200 1.637 +HD22 -0.028 1.255 1.800 +N 0.214 0.675 1.627 +CA 0.230 0.549 1.553 +C 0.214 0.422 1.640 +O 0.133 0.335 1.609 +CB 0.363 0.553 1.475 +CG 0.491 0.588 1.557 +CD1 0.581 0.467 1.579 +CD2 0.573 0.697 1.486 +H 0.279 0.748 1.602 +HA 0.150 0.543 1.479 +HB2 0.379 0.456 1.431 +HB3 0.351 0.627 1.396 +HG 0.463 0.627 1.655 +HD11 0.526 0.390 1.631 +HD12 0.617 0.430 1.484 +HD13 0.667 0.495 1.640 +HD21 0.602 0.662 1.387 +HD22 0.514 0.788 1.477 +HD23 0.663 0.718 1.544 +N 0.286 0.414 1.753 +CA 0.278 0.301 1.845 +C 0.141 0.288 1.915 +O 0.095 0.177 1.942 +CB 0.391 0.312 1.949 +CG 0.441 0.177 1.996 +CD1 0.375 0.111 2.102 +CD2 0.550 0.116 1.931 +CE1 0.419 -0.017 2.142 +CE2 0.593 -0.012 1.971 +CZ 0.527 -0.079 2.075 +OH 0.565 -0.204 2.112 +H 0.355 0.486 1.771 +HA 0.294 0.210 1.788 +HB2 0.473 0.365 1.904 +HB3 0.358 0.371 2.034 +HD1 0.291 0.157 2.151 +HD2 0.602 0.167 1.851 +HE1 0.370 -0.070 2.222 +HE2 0.678 -0.056 1.921 +HH 0.614 -0.248 2.042 +N 0.072 0.401 1.938 +CA -0.064 0.406 1.993 +C -0.162 0.342 1.893 +O -0.243 0.257 1.931 +CB -0.106 0.551 2.028 +CG1 0.003 0.633 2.102 +CG2 -0.238 0.553 2.107 +CD1 0.055 0.570 2.232 +H 0.110 0.486 1.901 +HA -0.067 0.346 2.085 +HB -0.126 0.604 1.935 +HG12 0.086 0.646 2.035 +HG13 -0.038 0.732 2.125 +HG21 -0.319 0.512 2.046 +HG22 -0.229 0.495 2.199 +HG23 -0.264 0.656 2.132 +HD11 -0.027 0.555 2.302 +HD12 0.104 0.475 2.211 +HD13 0.128 0.637 2.277 +N -0.150 0.378 1.765 +CA -0.229 0.319 1.657 +C -0.200 0.169 1.636 +O -0.290 0.095 1.597 +CB -0.206 0.397 1.526 +CG -0.333 0.401 1.439 +CD -0.433 0.508 1.485 +OE1 -0.533 0.481 1.550 +NE2 -0.410 0.633 1.449 +H -0.080 0.448 1.742 +HA -0.334 0.329 1.685 +HB2 -0.178 0.498 1.550 +HB3 -0.126 0.350 1.469 +HG2 -0.305 0.422 1.337 +HG3 -0.382 0.304 1.440 +HE21 -0.331 0.658 1.392 +HE22 -0.477 0.701 1.481 +N -0.078 0.122 1.664 +CA -0.045 -0.021 1.664 +C -0.104 -0.094 1.787 +O -0.161 -0.202 1.773 +CB 0.107 -0.039 1.655 +CG 0.153 -0.182 1.658 +CD1 0.150 -0.269 1.555 +CD2 0.208 -0.257 1.771 +NE1 0.196 -0.392 1.596 +CE2 0.235 -0.390 1.728 +CE3 0.239 -0.226 1.905 +CZ2 0.291 -0.487 1.812 +CZ3 0.293 -0.323 1.991 +CH2 0.320 -0.453 1.945 +H -0.005 0.190 1.685 +HA -0.090 -0.067 1.576 +HB2 0.140 0.004 1.563 +HB3 0.154 0.014 1.737 +HD1 0.115 -0.245 1.455 +HE1 0.203 -0.476 1.537 +HE3 0.221 -0.126 1.941 +HZ2 0.310 -0.587 1.774 +HZ3 0.315 -0.297 2.094 +HH2 0.364 -0.526 2.012 +N -0.094 -0.035 1.907 +CA -0.152 -0.093 2.028 +C -0.305 -0.101 2.025 +O -0.358 -0.206 2.062 +CB -0.104 -0.017 2.153 +CG 0.041 -0.049 2.196 +CD1 0.079 0.039 2.315 +CD2 0.060 -0.196 2.237 +H -0.042 0.052 1.914 +HA -0.118 -0.196 2.035 +HB2 -0.111 0.088 2.133 +HB3 -0.169 -0.042 2.237 +HG 0.109 -0.027 2.113 +HD11 0.069 0.144 2.288 +HD12 0.014 0.017 2.400 +HD13 0.182 0.020 2.344 +HD21 -0.014 -0.223 2.312 +HD22 0.049 -0.261 2.151 +HD23 0.159 -0.210 2.278 +N -0.376 0.003 1.978 +CA -0.524 0.003 1.974 +C -0.584 -0.110 1.888 +O -0.695 -0.153 1.915 +CB -0.577 0.142 1.932 +CG -0.563 0.175 1.782 +CD -0.692 0.153 1.701 +CE -0.670 0.198 1.556 +NZ -0.755 0.313 1.519 +H -0.325 0.087 1.952 +HA -0.559 -0.015 2.075 +HB2 -0.681 0.146 1.957 +HB3 -0.523 0.217 1.988 +HG2 -0.534 0.277 1.773 +HG3 -0.485 0.113 1.739 +HD2 -0.719 0.049 1.703 +HD3 -0.773 0.210 1.747 +HE2 -0.567 0.226 1.544 +HE3 -0.689 0.113 1.490 +HZ1 -0.853 0.292 1.536 +HZ2 -0.726 0.394 1.574 +HZ3 -0.741 0.336 1.422 +N -0.508 -0.160 1.790 +CA -0.542 -0.275 1.706 +C -0.520 -0.411 1.775 +O -0.559 -0.513 1.719 +CB -0.458 -0.265 1.577 +CG -0.530 -0.193 1.463 +OD1 -0.579 -0.080 1.485 +OD2 -0.536 -0.255 1.353 +H -0.420 -0.113 1.772 +HA -0.648 -0.270 1.679 +HB2 -0.367 -0.212 1.599 +HB3 -0.434 -0.366 1.542 +N -0.457 -0.414 1.894 +CA -0.425 -0.536 1.970 +C -0.276 -0.570 1.978 +O -0.241 -0.678 2.025 +H -0.432 -0.325 1.937 +HA2 -0.462 -0.523 2.072 +HA3 -0.478 -0.621 1.927 +N -0.187 -0.481 1.931 +CA -0.042 -0.502 1.935 +C -0.001 -0.633 1.866 +O -0.036 -0.654 1.750 +H -0.221 -0.395 1.890 +HA2 0.006 -0.419 1.883 +HA3 -0.010 -0.500 2.039 +N 0.072 -0.725 1.934 +CA 0.112 -0.854 1.876 +C -0.007 -0.940 1.830 +O 0.006 -1.017 1.734 +CB 0.191 -0.927 1.985 +CG 0.234 -0.817 2.082 +CD 0.120 -0.716 2.071 +HA 0.177 -0.835 1.791 +HB2 0.130 -1.000 2.035 +HB3 0.278 -0.979 1.943 +HG2 0.243 -0.855 2.182 +HG3 0.327 -0.772 2.047 +HD2 0.042 -0.740 2.140 +HD3 0.157 -0.617 2.096 +N -0.125 -0.926 1.892 +CA -0.245 -1.005 1.865 +C -0.326 -0.954 1.744 +O -0.443 -0.988 1.731 +CB -0.333 -1.010 1.991 +OG -0.263 -1.073 2.097 +H -0.133 -0.855 1.965 +HA -0.215 -1.107 1.841 +HB2 -0.360 -0.911 2.020 +HB3 -0.424 -1.068 1.971 +HG -0.251 -1.166 2.076 +N -0.264 -0.876 1.655 +CA -0.329 -0.813 1.539 +C -0.262 -0.847 1.404 +O -0.288 -0.783 1.303 +CB -0.339 -0.663 1.562 +OG -0.459 -0.612 1.508 +H -0.169 -0.850 1.676 +HA -0.431 -0.851 1.531 +HB2 -0.337 -0.643 1.668 +HB3 -0.254 -0.611 1.518 +HG -0.510 -0.576 1.586 +N -0.172 -0.948 1.403 +CA -0.107 -0.997 1.281 +C -0.009 -0.898 1.217 +O 0.013 -0.904 1.096 +H -0.157 -0.997 1.489 +HA2 -0.052 -1.088 1.304 +HA3 -0.183 -1.021 1.207 +N 0.047 -0.805 1.295 +CA 0.131 -0.694 1.248 +C 0.246 -0.662 1.346 +O 0.220 -0.647 1.465 +CB 0.041 -0.571 1.220 +CG -0.038 -0.522 1.343 +CD -0.136 -0.407 1.314 +NE -0.269 -0.454 1.273 +CZ -0.313 -0.479 1.150 +NH1 -0.237 -0.466 1.044 +NH2 -0.437 -0.518 1.133 +H 0.026 -0.809 1.394 +HA 0.174 -0.724 1.152 +HB2 0.104 -0.491 1.186 +HB3 -0.029 -0.599 1.142 +HG2 -0.094 -0.604 1.382 +HG3 0.033 -0.486 1.417 +HD2 -0.146 -0.348 1.403 +HD3 -0.093 -0.339 1.240 +HE -0.338 -0.467 1.346 +HH11 -0.143 -0.437 1.058 +HH12 -0.272 -0.488 0.952 +HH21 -0.497 -0.522 1.215 +HH22 -0.473 -0.540 1.042 +N 0.371 -0.649 1.298 +CA 0.486 -0.619 1.384 +C 0.480 -0.475 1.438 +O 0.412 -0.390 1.380 +CB 0.609 -0.641 1.295 +CG 0.558 -0.607 1.155 +CD 0.413 -0.655 1.158 +HA 0.488 -0.689 1.467 +HB2 0.689 -0.575 1.323 +HB3 0.638 -0.746 1.299 +HG2 0.563 -0.501 1.137 +HG3 0.615 -0.658 1.078 +HD2 0.351 -0.591 1.098 +HD3 0.407 -0.758 1.124 +N 0.553 -0.444 1.548 +CA 0.557 -0.310 1.604 +C 0.632 -0.212 1.512 +O 0.731 -0.252 1.449 +CB 0.626 -0.324 1.740 +CG 0.715 -0.446 1.722 +CD 0.635 -0.535 1.626 +HA 0.455 -0.275 1.619 +HB2 0.684 -0.236 1.762 +HB3 0.551 -0.343 1.817 +HG2 0.810 -0.419 1.679 +HG3 0.735 -0.496 1.817 +HD2 0.701 -0.590 1.562 +HD3 0.571 -0.602 1.684 +N 0.591 -0.085 1.506 +CA 0.660 0.018 1.428 +C 0.786 0.066 1.501 +O 0.779 0.109 1.616 +CB 0.556 0.128 1.411 +CG 0.473 0.120 1.539 +CD 0.472 -0.029 1.570 +HA 0.687 -0.021 1.330 +HB2 0.603 0.224 1.401 +HB3 0.492 0.105 1.325 +HG2 0.519 0.175 1.618 +HG3 0.372 0.159 1.526 +HD2 0.477 -0.046 1.676 +HD3 0.383 -0.075 1.527 +N 0.902 0.058 1.433 +CA 1.031 0.113 1.476 +C 1.039 0.264 1.452 +O 1.014 0.305 1.336 +CB 1.146 0.045 1.402 +OG 1.146 -0.093 1.430 +OXT 1.075 0.335 1.549 +H 0.899 0.019 1.340 +HA 1.043 0.099 1.584 +HB2 1.134 0.061 1.296 +HB3 1.241 0.089 1.434 +HG 1.126 -0.104 1.523 +304 + 3.600 0.000 0.000 1.800 3.118 0.000 1.800 1.039 2.939 +N 3.650 0.231 1.032 +CA 3.643 0.251 1.179 +C 3.774 0.222 1.251 +O 3.824 0.312 1.317 +CB 3.522 0.178 1.240 +CG 3.392 0.243 1.192 +OD1 3.395 0.343 1.122 +ND2 3.276 0.188 1.225 +H1 3.732 0.277 0.994 +H2 3.654 0.133 1.009 +H3 3.567 0.271 0.989 +HA 3.625 0.358 1.195 +HB2 3.523 0.075 1.209 +HB3 3.526 0.186 1.349 +HD21 3.268 0.104 1.280 +HD22 3.195 0.238 1.192 +N 3.831 0.102 1.237 +CA 3.961 0.064 1.297 +C 4.071 0.172 1.283 +O 4.129 0.214 1.383 +CB 4.003 -0.074 1.242 +CG 4.004 -0.090 1.088 +CD1 4.146 -0.094 1.031 +CD2 3.932 -0.218 1.045 +H 3.784 0.028 1.188 +HA 3.945 0.052 1.404 +HB2 4.102 -0.095 1.278 +HB3 3.933 -0.147 1.284 +HG 3.953 -0.006 1.041 +HD11 4.200 -0.004 1.057 +HD12 4.199 -0.182 1.069 +HD13 4.143 -0.102 0.922 +HD21 3.980 -0.305 1.090 +HD22 3.827 -0.214 1.076 +HD23 3.936 -0.228 0.936 +N 4.094 0.222 1.161 +CA 4.193 0.326 1.135 +C 4.158 0.462 1.200 +O 4.247 0.536 1.241 +CB 4.212 0.341 0.983 +CG 4.352 0.382 0.945 +CD1 4.389 0.519 0.945 +CD2 4.448 0.284 0.914 +CE1 4.521 0.556 0.914 +CE2 4.581 0.321 0.884 +CZ 4.617 0.457 0.885 +OH 4.746 0.494 0.861 +H 4.047 0.180 1.082 +HA 4.288 0.293 1.177 +HB2 4.190 0.247 0.937 +HB3 4.140 0.414 0.944 +HD1 4.316 0.595 0.969 +HD2 4.421 0.179 0.913 +HE1 4.551 0.660 0.914 +HE2 4.653 0.244 0.860 +HH 4.807 0.421 0.876 +N 4.029 0.493 1.214 +CA 3.978 0.612 1.283 +C 4.014 0.604 1.432 +O 4.067 0.700 1.489 +CB 3.825 0.629 1.263 +CG1 3.777 0.607 1.117 +CG2 3.777 0.765 1.315 +CD1 3.845 0.694 1.011 +H 3.962 0.422 1.189 +HA 4.028 0.700 1.242 +HB 3.774 0.554 1.324 +HG12 3.795 0.504 1.092 +HG13 3.669 0.624 1.113 +HG21 3.795 0.773 1.422 +HG22 3.830 0.846 1.264 +HG23 3.670 0.776 1.297 +HD11 3.830 0.800 1.033 +HD12 3.952 0.673 1.007 +HD13 3.802 0.672 0.914 +N 3.991 0.487 1.494 +CA 4.028 0.460 1.633 +C 4.181 0.463 1.655 +O 4.225 0.500 1.763 +CB 3.969 0.326 1.679 +CG 3.931 0.328 1.828 +CD 3.796 0.395 1.853 +OE1 3.787 0.510 1.895 +NE2 3.687 0.324 1.830 +H 3.947 0.413 1.439 +HA 3.985 0.540 1.693 +HB2 3.882 0.305 1.621 +HB3 4.043 0.247 1.662 +HG2 3.926 0.227 1.864 +HG3 4.008 0.380 1.885 +HE21 3.691 0.229 1.800 +HE22 3.600 0.372 1.848 +N 4.262 0.427 1.555 +CA 4.408 0.443 1.561 +C 4.451 0.590 1.546 +O 4.537 0.637 1.621 +CB 4.473 0.354 1.454 +CG 4.623 0.364 1.448 +CD1 4.710 0.304 1.532 +CD2 4.704 0.439 1.353 +NE1 4.840 0.340 1.497 +CE2 4.842 0.421 1.387 +CE3 4.677 0.520 1.241 +CZ2 4.946 0.479 1.313 +CZ3 4.781 0.581 1.168 +CH2 4.915 0.559 1.203 +H 4.220 0.386 1.472 +HA 4.443 0.409 1.658 +HB2 4.448 0.252 1.476 +HB3 4.433 0.379 1.357 +HD1 4.683 0.240 1.614 +HE1 4.924 0.309 1.546 +HE3 4.574 0.535 1.211 +HZ2 5.049 0.462 1.343 +HZ3 4.757 0.643 1.082 +HH2 4.994 0.605 1.144 +N 4.391 0.666 1.453 +CA 4.421 0.808 1.435 +C 4.381 0.893 1.556 +O 4.461 0.978 1.596 +CB 4.357 0.861 1.306 +CG 4.430 0.820 1.176 +CD1 4.351 0.872 1.056 +CD2 4.572 0.877 1.168 +H 4.324 0.621 1.390 +HA 4.529 0.818 1.427 +HB2 4.256 0.824 1.301 +HB3 4.355 0.970 1.310 +HG 4.435 0.712 1.170 +HD11 4.250 0.831 1.057 +HD12 4.346 0.981 1.058 +HD13 4.400 0.841 0.963 +HD21 4.571 0.985 1.184 +HD22 4.636 0.830 1.243 +HD23 4.615 0.856 1.070 +N 4.263 0.872 1.616 +CA 4.217 0.952 1.731 +C 4.310 0.946 1.853 +O 4.315 1.040 1.931 +CB 4.071 0.917 1.768 +CG 4.053 0.783 1.842 +CD 4.038 0.797 1.994 +CE 4.011 0.660 2.056 +NZ 3.878 0.652 2.119 +H 4.200 0.803 1.575 +HA 4.217 1.057 1.700 +HB2 4.033 0.995 1.830 +HB3 4.013 0.913 1.676 +HG2 3.966 0.734 1.803 +HG3 4.139 0.719 1.821 +HD2 4.128 0.838 2.035 +HD3 3.956 0.866 2.016 +HE2 4.018 0.585 1.979 +HE3 4.090 0.638 2.129 +HZ1 3.866 0.725 2.188 +HZ2 3.807 0.658 2.046 +HZ3 3.866 0.561 2.163 +N 4.387 0.837 1.866 +CA 4.490 0.817 1.968 +C 4.622 0.891 1.938 +O 4.710 0.893 2.024 +CB 4.516 0.665 1.981 +CG 4.432 0.599 2.090 +OD1 4.308 0.618 2.090 +OD2 4.494 0.530 2.175 +H 4.372 0.762 1.800 +HA 4.454 0.854 2.064 +HB2 4.492 0.619 1.887 +HB3 4.620 0.648 2.005 +N 4.638 0.950 1.818 +CA 4.758 1.021 1.774 +C 4.837 0.951 1.662 +O 4.948 0.994 1.630 +H 4.559 0.949 1.754 +HA2 4.729 1.119 1.736 +HA3 4.826 1.037 1.858 +N 4.784 0.843 1.604 +CA 4.849 0.768 1.496 +C 4.990 0.721 1.534 +O 5.005 0.655 1.637 +H 4.694 0.809 1.636 +HA2 4.788 0.680 1.472 +HA3 4.851 0.832 1.408 +N 5.096 0.756 1.457 +CA 5.234 0.718 1.489 +C 5.281 0.769 1.627 +O 5.364 0.705 1.691 +CB 5.322 0.776 1.378 +CG 5.225 0.803 1.263 +CD 5.094 0.835 1.334 +HA 5.242 0.609 1.488 +HB2 5.368 0.868 1.410 +HB3 5.400 0.707 1.348 +HG2 5.258 0.886 1.203 +HG3 5.213 0.712 1.203 +HD2 5.089 0.940 1.357 +HD3 5.010 0.810 1.270 +N 5.227 0.882 1.675 +CA 5.265 0.947 1.801 +C 5.200 0.885 1.925 +O 5.196 0.950 2.030 +CB 5.236 1.098 1.792 +OG 5.311 1.156 1.687 +H 5.153 0.927 1.621 +HA 5.373 0.935 1.814 +HB2 5.132 1.113 1.773 +HB3 5.263 1.147 1.885 +HG 5.404 1.155 1.711 +N 5.150 0.761 1.916 +CA 5.078 0.692 2.023 +C 5.139 0.555 2.061 +O 5.076 0.475 2.129 +CB 4.930 0.680 1.984 +OG 4.848 0.693 2.097 +H 5.154 0.718 1.824 +HA 5.082 0.753 2.113 +HB2 4.906 0.758 1.913 +HB3 4.911 0.585 1.935 +HG 4.793 0.775 2.082 +N 5.262 0.527 2.015 +CA 5.336 0.406 2.050 +C 5.277 0.276 1.994 +O 5.297 0.170 2.052 +H 5.309 0.599 1.961 +HA2 5.439 0.414 2.014 +HA3 5.340 0.396 2.159 +N 5.202 0.284 1.883 +CA 5.125 0.173 1.824 +C 5.126 0.178 1.670 +O 5.097 0.283 1.613 +CB 4.983 0.173 1.883 +CG 4.904 0.303 1.858 +CD 4.766 0.309 1.926 +NE 4.771 0.363 2.063 +CZ 4.789 0.297 2.177 +NH1 4.807 0.167 2.181 +NH2 4.788 0.363 2.290 +H 5.193 0.375 1.840 +HA 5.174 0.081 1.857 +HB2 4.928 0.092 1.840 +HB3 4.992 0.158 1.991 +HG2 4.962 0.385 1.895 +HG3 4.888 0.313 1.752 +HD2 4.701 0.371 1.867 +HD3 4.719 0.210 1.924 +HE 4.758 0.462 2.073 +HH11 4.808 0.117 2.094 +HH12 4.822 0.119 2.268 +HH21 4.768 0.462 2.287 +HH22 4.803 0.317 2.377 +N 5.155 0.066 1.601 +CA 5.158 0.062 1.454 +C 5.016 0.074 1.395 +O 4.918 0.047 1.465 +CB 5.222 -0.073 1.420 +CG 5.182 -0.162 1.537 +CD 5.182 -0.066 1.656 +HA 5.220 0.143 1.417 +HB2 5.184 -0.111 1.327 +HB3 5.331 -0.061 1.418 +HG2 5.085 -0.205 1.522 +HG3 5.253 -0.244 1.551 +HD2 5.106 -0.094 1.726 +HD3 5.281 -0.066 1.703 +N 5.003 0.112 1.266 +CA 4.873 0.122 1.200 +C 4.811 -0.016 1.178 +O 4.883 -0.112 1.149 +CB 4.900 0.194 1.067 +CG 5.045 0.158 1.036 +CD 5.110 0.149 1.175 +HA 4.808 0.184 1.261 +HB2 4.835 0.158 0.991 +HB3 4.891 0.301 1.081 +HG2 5.052 0.064 0.985 +HG3 5.093 0.234 0.974 +HD2 5.187 0.074 1.175 +HD3 5.150 0.246 1.203 +N 4.677 -0.028 1.186 +CA 4.606 -0.152 1.159 +C 4.595 -0.178 1.008 +O 4.545 -0.093 0.934 +CB 4.470 -0.133 1.226 +CG 4.444 0.017 1.212 +CD 4.584 0.077 1.225 +HA 4.657 -0.236 1.206 +HB2 4.394 -0.190 1.175 +HB3 4.477 -0.159 1.331 +HG2 4.401 0.040 1.116 +HG3 4.376 0.054 1.289 +HD2 4.594 0.162 1.161 +HD3 4.602 0.105 1.329 +N 4.644 -0.295 0.963 +CA 4.629 -0.347 0.826 +C 4.490 -0.407 0.802 +O 4.450 -0.493 0.884 +CB 4.734 -0.455 0.798 +OG 4.863 -0.400 0.811 +OXT 4.428 -0.367 0.701 +H 4.685 -0.357 1.030 +HA 4.640 -0.266 0.754 +HB2 4.722 -0.535 0.868 +HB3 4.720 -0.493 0.697 +HG 4.862 -0.313 0.772 diff --git a/src/core/GenericMolInfo.cpp b/src/core/GenericMolInfo.cpp index 9534f5b780..7e9b9249bc 100644 --- a/src/core/GenericMolInfo.cpp +++ b/src/core/GenericMolInfo.cpp @@ -26,7 +26,11 @@ #include "tools/MolDataClass.h" #include "tools/PDB.h" #include "tools/Communicator.h" +#include "tools/Pbc.h" +#include "tools/Tools.h" #include "config/Config.h" +#include +#include namespace PLMD { @@ -47,13 +51,72 @@ void GenericMolInfo::registerKeywords( Keywords& keys ) { keys.add("compulsory","PYTHON_BIN","default","python interpreter"); keys.add("atoms","CHAIN","(for masochists ( mostly Davide Branduardi ) ) The atoms involved in each of the chains of interest in the structure."); keys.add("hidden","STRIDE","frequency for resetting the python interpreter. Should be 1."); - keys.addFlag("WHOLE", false, "The reference structure is whole, i.e. not broken by PBC"); + keys.addFlag("WHOLE", false, "The reference structure is whole, i.e. not broken by PBC. If the pdb file has a CRYST1 record with space group P 1, this is checked along each chain, and a warning is written to the log if consecutive atoms of a residue, or of two consecutive protein or nucleic-acid residues, are on opposite sides of the periodic boundary"); } GenericMolInfo::~GenericMolInfo() { // empty destructor to delete unique_ptr } +namespace { +// MOLINFO WHOLE takes the reference structure as whole. Check it along each chain in the box of the +// CRYST1 record: consecutive atoms of a residue, or of two consecutive protein or nucleic-acid residues, +// are close, so a step between them that is not its own minimum image crosses the periodic boundary. +// Returns a warning, or an empty string. +std::string checkWhole(const PDB & pdb,double scale) { + // skip a cell that cannot be the periodic box: none or degenerate, the 1 A cube written when there + // is no unit cell, or a crystallographic cell (simulation programs write the space group P 1) + const Tensor & box(pdb.getBoxVec()); + const double det=box.determinant(); + bool unitcube=true; + for(unsigned k=0; k<3; k++) { + unitcube=unitcube && std::fabs(pdb.getBoxAxs()[k]-scale)<1e-3*scale && std::fabs(pdb.getBoxAng()[k]-90.0)<1e-3; + } + std::string group=pdb.getSpaceGroup(); + group.erase(std::remove(group.begin(),group.end(),' '),group.end()); + if(unitcube || (group.length()>0 && group!="P1") || !std::isfinite(det) || det<=0.0) { + return ""; + } + Pbc pbc; + pbc.setBox(box); + auto polymer=[](std::string r) { + Tools::ltrim(r); + Tools::trim(r); + return MolDataClass::allowedResidue("protein",r) || MolDataClass::allowedResidue("dna",r) || MolDataClass::allowedResidue("rna",r); + }; + const auto & at(pdb.getAtomNumbers()); + const auto & pos(pdb.getPositions()); + unsigned n=0; + std::string list; + for(unsigned i=1; i1e-3*std::cbrt(det)) { + if(++n<=10) { + std::string r=pdb.getResidueName(at[i]); + Tools::ltrim(r); + Tools::trim(r); + list+=" "+std::to_string(at[i].serial())+" ("+r+std::to_string(pdb.getResidueNumber(at[i]))+")"; + } + } + } + if(n==0) { + return ""; + } + return "the reference structure in the MOLINFO pdb file may not be whole: in the box of its CRYST1 record, " + +std::to_string(n)+" atoms are across the periodic boundary from the atom before them in their chain:"+list + +(n>10 ? " and "+std::to_string(n-10)+" more" : "") + +". WHOLEMOLECULES will then split these molecules in every frame: make the pdb whole" + +" (for example with gmx trjconv -pbc whole), or check that its CRYST1 record is the box the structure was written in"; +} +} + GenericMolInfo::GenericMolInfo( const ActionOptions&ao ): Action(ao), ActionAnyorder(ao), @@ -92,6 +155,12 @@ GenericMolInfo::GenericMolInfo( const ActionOptions&ao ): if( ! pdb.read(reference,usingNaturalUnits(),0.1/getUnits().getLength())) { plumed_merror("missing input file " + reference ); } + if( iswhole_ ) { + const std::string msg=checkWhole(pdb,usingNaturalUnits() ? 1.0 : 0.1/getUnits().getLength()); + if( msg.length()>0 ) { + warning(msg); + } + } std::vector chains; pdb.getChainNames( chains ); diff --git a/src/tools/PDB.cpp b/src/tools/PDB.cpp index 765a3932ec..03946b6a89 100644 --- a/src/tools/PDB.cpp +++ b/src/tools/PDB.cpp @@ -274,6 +274,10 @@ const Tensor & PDB::getBoxVec()const { return Box; } +const std::string & PDB::getSpaceGroup()const { + return spaceGroup; +} + std::string PDB::getAtomName(AtomNumber a)const { const auto p=number2index.find(a); if(p==number2index.end()) { @@ -368,6 +372,8 @@ bool PDB::readFromFilepointer(FILE *fp,bool naturalUnits,double scale) { Tools::convert(BoxA,BoxABG[0]); Tools::convert(BoxB,BoxABG[1]); Tools::convert(BoxG,BoxABG[2]); + spaceGroup=line.substr(55,11); + Tools::trim(spaceGroup); BoxXYZ*=scale; double cosA=std::cos(BoxABG[0]*pi/180.); double cosB=std::cos(BoxABG[1]*pi/180.); diff --git a/src/tools/PDB.h b/src/tools/PDB.h index 8e8f56da9e..903be60ab7 100644 --- a/src/tools/PDB.h +++ b/src/tools/PDB.h @@ -55,6 +55,7 @@ class PDB { std::map > arg_data; Vector BoxXYZ,BoxABG; Tensor Box; + std::string spaceGroup; public: /// Read the pdb from a file, scaling positions by a factor scale bool read(const std::string&file,bool naturalUnits,double scale); @@ -146,6 +147,8 @@ class PDB { const Vector & getBoxAng()const; /// Returns box axis vectors const Tensor & getBoxVec()const; +/// Returns the space group of the CRYST1 record (empty if there is none) + const std::string & getSpaceGroup()const; /// Return true if the residue name is one of the allowed reisude names e.g. one of the 20 amino acids for proteins bool allowedResidue( const std::string& type, const std::string& residuename ) const; };