From 1fcad041893ac0796c38b9ce0a18fa5af12b4546 Mon Sep 17 00:00:00 2001 From: Justas Dauparas Date: Mon, 19 Feb 2024 19:33:59 +0000 Subject: [PATCH] add a flag for parse_atoms_with_zero_occupancy --- README.md | 11 + data_utils.py | 7 +- .../backbones/1BC8_1.pdb | 782 ++++++++++++++++++ .../seqs/1BC8.fa | 4 + run.py | 9 +- 5 files changed, 809 insertions(+), 4 deletions(-) create mode 100644 outputs/parse_atoms_with_zero_occupancy/backbones/1BC8_1.pdb create mode 100644 outputs/parse_atoms_with_zero_occupancy/seqs/1BC8.fa diff --git a/README.md b/README.md index 332d7a4..5123ec4 100644 --- a/README.md +++ b/README.md @@ -450,6 +450,17 @@ python run.py \ --parse_these_chains_only "B" ``` +### 34 parse atoms with zero occupancy +Parse atoms in the PDB files with zero occupancy too. +``` +python run.py \ + --model_type "ligand_mpnn" \ + --seed 111 \ + --pdb_path "./inputs/1BC8.pdb" \ + --out_folder "./outputs/parse_atoms_with_zero_occupancy" \ + --parse_atoms_with_zero_occupancy 1 +``` + ### Things to add - Support for ProteinMPNN CA-only model. - Examples for scoring sequences only. diff --git a/data_utils.py b/data_utils.py index 5d471a2..8380bd8 100644 --- a/data_utils.py +++ b/data_utils.py @@ -513,17 +513,17 @@ def get_aligned_coordinates(protein_atoms, CA_dict: dict, atom_name: str): def parse_PDB( input_path: str, - atom_context_num=8, device: str = "cpu", chains: list = [], parse_all_atoms: bool = False, + parse_atoms_with_zero_occupancy: bool = False ): """ input_path : path for the input PDB - atom_context_num: number of nearest ligand context atoms per residue device: device for the torch.Tensor chains: a list specifying which chains need to be parsed; e.g. ["A", "B"] parse_all_atoms: if False parse only N,CA,C,O otherwise all 37 atoms + parse_atoms_with_zero_occupancy: if True atoms with zero occupancy will be parsed """ element_list = [ "H", @@ -776,7 +776,8 @@ def parse_PDB( ] atoms = parsePDB(input_path) - atoms = atoms.select("occupancy > 0") + if not parse_atoms_with_zero_occupancy: + atoms = atoms.select("occupancy > 0") if chains: str_out = "" for item in chains: diff --git a/outputs/parse_atoms_with_zero_occupancy/backbones/1BC8_1.pdb b/outputs/parse_atoms_with_zero_occupancy/backbones/1BC8_1.pdb new file mode 100644 index 0000000..9beea0b --- /dev/null +++ b/outputs/parse_atoms_with_zero_occupancy/backbones/1BC8_1.pdb @@ -0,0 +1,782 @@ +REMARK AtomMap (Selection '(backbone) and (protein)') + (Selection 'not protein and not water') +ATOM 1 N MET C 1 -14.358 13.416 9.007 1.00 0.15 N +ATOM 2 CA MET C 1 -14.660 12.744 7.707 1.00 0.15 C +ATOM 3 C MET C 1 -13.362 12.270 7.055 1.00 0.15 C +ATOM 4 O MET C 1 -13.026 12.659 5.930 1.00 0.15 O +ATOM 5 N LYS C 2 -12.633 11.425 7.779 1.00 0.14 N +ATOM 6 CA LYS C 2 -11.368 10.876 7.296 1.00 0.14 C +ATOM 7 C LYS C 2 -11.590 9.499 6.655 1.00 0.14 C +ATOM 8 O LYS C 2 -12.731 9.052 6.492 1.00 0.14 O +ATOM 9 N SER C 3 -10.499 8.834 6.284 1.00 0.76 N +ATOM 10 CA SER C 3 -10.591 7.502 5.691 1.00 0.76 C +ATOM 11 C SER C 3 -10.700 6.479 6.821 1.00 0.76 C +ATOM 12 O SER C 3 -9.978 6.570 7.826 1.00 0.76 O +ATOM 13 N PRO C 4 -11.609 5.518 6.662 1.00 0.19 N +ATOM 14 CA PRO C 4 -11.808 4.473 7.667 1.00 0.19 C +ATOM 15 C PRO C 4 -10.742 3.401 7.494 1.00 0.19 C +ATOM 16 O PRO C 4 -10.769 2.359 8.155 1.00 0.19 O +ATOM 17 N ILE C 5 -9.810 3.666 6.585 1.00 0.72 N +ATOM 18 CA ILE C 5 -8.735 2.739 6.294 1.00 0.72 C +ATOM 19 C ILE C 5 -7.933 2.403 7.549 1.00 0.72 C +ATOM 20 O ILE C 5 -7.698 3.252 8.412 1.00 0.72 O +ATOM 21 N SER C 6 -7.537 1.141 7.630 1.00 0.42 N +ATOM 22 CA SER C 6 -6.743 0.612 8.726 1.00 0.42 C +ATOM 23 C SER C 6 -5.270 0.853 8.347 1.00 0.42 C +ATOM 24 O SER C 6 -4.983 1.093 7.175 1.00 0.42 O +ATOM 25 N LEU C 7 -4.339 0.805 9.302 1.00 0.63 N +ATOM 26 CA LEU C 7 -2.934 1.042 8.934 1.00 0.63 C +ATOM 27 C LEU C 7 -2.346 -0.105 8.111 1.00 0.63 C +ATOM 28 O LEU C 7 -1.597 0.127 7.163 1.00 0.63 O +ATOM 29 N HIS C 8 -2.672 -1.342 8.456 1.00 0.51 N +ATOM 30 CA HIS C 8 -2.122 -2.445 7.691 1.00 0.51 C +ATOM 31 C HIS C 8 -2.766 -2.496 6.303 1.00 0.51 C +ATOM 32 O HIS C 8 -2.176 -3.028 5.373 1.00 0.51 O +ATOM 33 N GLU C 9 -3.956 -1.915 6.159 1.00 0.31 N +ATOM 34 CA GLU C 9 -4.644 -1.901 4.861 1.00 0.31 C +ATOM 35 C GLU C 9 -4.031 -0.811 3.997 1.00 0.31 C +ATOM 36 O GLU C 9 -3.926 -0.942 2.779 1.00 0.31 O +ATOM 37 N PHE C 10 -3.644 0.277 4.654 1.00 0.92 N +ATOM 38 CA PHE C 10 -3.032 1.420 4.001 1.00 0.92 C +ATOM 39 C PHE C 10 -1.670 1.009 3.451 1.00 0.92 C +ATOM 40 O PHE C 10 -1.290 1.417 2.357 1.00 0.92 O +ATOM 41 N LEU C 11 -0.944 0.193 4.211 1.00 0.51 N +ATOM 42 CA LEU C 11 0.369 -0.277 3.776 1.00 0.51 C +ATOM 43 C LEU C 11 0.181 -1.185 2.575 1.00 0.51 C +ATOM 44 O LEU C 11 0.926 -1.104 1.598 1.00 0.51 O +ATOM 45 N LEU C 12 -0.833 -2.043 2.660 1.00 0.46 N +ATOM 46 CA LEU C 12 -1.168 -2.966 1.583 1.00 0.46 C +ATOM 47 C LEU C 12 -1.523 -2.162 0.331 1.00 0.46 C +ATOM 48 O LEU C 12 -1.217 -2.566 -0.785 1.00 0.46 O +ATOM 49 N GLU C 13 -2.155 -1.015 0.517 1.00 0.13 N +ATOM 50 CA GLU C 13 -2.525 -0.179 -0.615 1.00 0.13 C +ATOM 51 C GLU C 13 -1.292 0.389 -1.324 1.00 0.13 C +ATOM 52 O GLU C 13 -1.210 0.358 -2.554 1.00 0.13 O +ATOM 53 N LEU C 14 -0.335 0.897 -0.549 1.00 0.91 N +ATOM 54 CA LEU C 14 0.901 1.459 -1.108 1.00 0.91 C +ATOM 55 C LEU C 14 1.700 0.372 -1.809 1.00 0.91 C +ATOM 56 O LEU C 14 2.312 0.602 -2.858 1.00 0.91 O +ATOM 57 N LEU C 15 1.689 -0.816 -1.217 1.00 0.92 N +ATOM 58 CA LEU C 15 2.410 -1.956 -1.759 1.00 0.92 C +ATOM 59 C LEU C 15 1.807 -2.461 -3.092 1.00 0.92 C +ATOM 60 O LEU C 15 2.419 -3.262 -3.791 1.00 0.92 O +ATOM 61 N SER C 16 0.615 -1.991 -3.438 1.00 0.47 N +ATOM 62 CA SER C 16 -0.045 -2.417 -4.672 1.00 0.47 C +ATOM 63 C SER C 16 0.300 -1.509 -5.867 1.00 0.47 C +ATOM 64 O SER C 16 0.163 -1.903 -7.024 1.00 0.47 O +ATOM 65 N ASP C 17 0.766 -0.300 -5.581 1.00 0.36 N +ATOM 66 CA ASP C 17 1.094 0.654 -6.628 1.00 0.36 C +ATOM 67 C ASP C 17 2.595 0.875 -6.823 1.00 0.36 C +ATOM 68 O ASP C 17 3.308 1.257 -5.893 1.00 0.36 O +ATOM 69 N PRO C 18 3.088 0.651 -8.056 1.00 0.55 N +ATOM 70 CA PRO C 18 4.506 0.820 -8.397 1.00 0.55 C +ATOM 71 C PRO C 18 5.018 2.202 -8.032 1.00 0.55 C +ATOM 72 O PRO C 18 6.188 2.374 -7.705 1.00 0.55 O +ATOM 73 N LYS C 19 4.128 3.184 -8.093 1.00 0.21 N +ATOM 74 CA LYS C 19 4.476 4.559 -7.780 1.00 0.21 C +ATOM 75 C LYS C 19 5.068 4.718 -6.385 1.00 0.21 C +ATOM 76 O LYS C 19 5.790 5.683 -6.128 1.00 0.21 O +ATOM 77 N TYR C 20 4.756 3.785 -5.489 1.00 0.51 N +ATOM 78 CA TYR C 20 5.246 3.857 -4.110 1.00 0.51 C +ATOM 79 C TYR C 20 6.346 2.871 -3.777 1.00 0.51 C +ATOM 80 O TYR C 20 6.733 2.745 -2.610 1.00 0.51 O +ATOM 81 N ALA C 21 6.839 2.163 -4.791 1.00 0.16 N +ATOM 82 CA ALA C 21 7.899 1.180 -4.591 1.00 0.16 C +ATOM 83 C ALA C 21 9.150 1.832 -4.004 1.00 0.16 C +ATOM 84 O ALA C 21 9.897 1.197 -3.257 1.00 0.16 O +ATOM 85 N ASP C 22 9.378 3.098 -4.334 1.00 0.21 N +ATOM 86 CA ASP C 22 10.550 3.795 -3.815 1.00 0.21 C +ATOM 87 C ASP C 22 10.450 4.075 -2.319 1.00 0.21 C +ATOM 88 O ASP C 22 11.466 4.326 -1.680 1.00 0.21 O +ATOM 89 N ILE C 23 9.241 4.039 -1.756 1.00 0.39 N +ATOM 90 CA ILE C 23 9.090 4.302 -0.325 1.00 0.39 C +ATOM 91 C ILE C 23 8.722 3.068 0.499 1.00 0.39 C +ATOM 92 O ILE C 23 8.972 3.021 1.713 1.00 0.39 O +ATOM 93 N ILE C 24 8.132 2.075 -0.158 1.00 0.83 N +ATOM 94 CA ILE C 24 7.755 0.821 0.492 1.00 0.83 C +ATOM 95 C ILE C 24 7.678 -0.280 -0.570 1.00 0.83 C +ATOM 96 O ILE C 24 6.964 -0.156 -1.564 1.00 0.83 O +ATOM 97 N GLU C 25 8.434 -1.354 -0.367 1.00 0.40 N +ATOM 98 CA GLU C 25 8.470 -2.438 -1.343 1.00 0.40 C +ATOM 99 C GLU C 25 8.447 -3.820 -0.703 1.00 0.40 C +ATOM 100 O GLU C 25 8.791 -3.980 0.470 1.00 0.40 O +ATOM 101 N TRP C 26 8.031 -4.821 -1.474 1.00 0.85 N +ATOM 102 CA TRP C 26 8.006 -6.191 -0.972 1.00 0.85 C +ATOM 103 C TRP C 26 9.446 -6.677 -1.057 1.00 0.85 C +ATOM 104 O TRP C 26 10.159 -6.364 -2.021 1.00 0.85 O +ATOM 105 N VAL C 27 9.876 -7.430 -0.052 1.00 0.49 N +ATOM 106 CA VAL C 27 11.232 -7.957 -0.026 1.00 0.49 C +ATOM 107 C VAL C 27 11.215 -9.474 -0.020 1.00 0.49 C +ATOM 108 O VAL C 27 12.252 -10.122 0.112 1.00 0.49 O +ATOM 109 N SER C 28 10.022 -10.040 -0.159 1.00 0.80 N +ATOM 110 CA SER C 28 9.868 -11.486 -0.203 1.00 0.80 C +ATOM 111 C SER C 28 8.556 -11.828 -0.896 1.00 0.80 C +ATOM 112 O SER C 28 7.742 -10.939 -1.162 1.00 0.80 O +ATOM 113 N ASP C 29 8.365 -13.114 -1.195 1.00 0.40 N +ATOM 114 CA ASP C 29 7.139 -13.584 -1.834 1.00 0.40 C +ATOM 115 C ASP C 29 6.224 -14.245 -0.796 1.00 0.40 C +ATOM 116 O ASP C 29 5.378 -15.085 -1.139 1.00 0.40 O +ATOM 117 N ASN C 30 6.406 -13.875 0.475 1.00 0.21 N +ATOM 118 CA ASN C 30 5.564 -14.422 1.534 1.00 0.21 C +ATOM 119 C ASN C 30 5.128 -13.409 2.596 1.00 0.21 C +ATOM 120 O ASN C 30 4.908 -13.765 3.757 1.00 0.21 O +ATOM 121 N GLY C 31 5.001 -12.145 2.190 1.00 0.93 N +ATOM 122 CA GLY C 31 4.542 -11.109 3.104 1.00 0.93 C +ATOM 123 C GLY C 31 5.525 -10.097 3.664 1.00 0.93 C +ATOM 124 O GLY C 31 5.108 -9.128 4.297 1.00 0.93 O +ATOM 125 N GLU C 32 6.816 -10.309 3.436 1.00 0.45 N +ATOM 126 CA GLU C 32 7.860 -9.414 3.937 1.00 0.45 C +ATOM 127 C GLU C 32 7.968 -8.122 3.119 1.00 0.45 C +ATOM 128 O GLU C 32 7.941 -8.145 1.888 1.00 0.45 O +ATOM 129 N PHE C 33 8.091 -6.992 3.803 1.00 0.92 N +ATOM 130 CA PHE C 33 8.195 -5.713 3.119 1.00 0.92 C +ATOM 131 C PHE C 33 9.123 -4.791 3.883 1.00 0.92 C +ATOM 132 O PHE C 33 9.396 -5.025 5.056 1.00 0.92 O +ATOM 133 N ARG C 34 9.606 -3.748 3.211 1.00 0.31 N +ATOM 134 CA ARG C 34 10.522 -2.791 3.819 1.00 0.31 C +ATOM 135 C ARG C 34 10.136 -1.342 3.532 1.00 0.31 C +ATOM 136 O ARG C 34 9.821 -0.972 2.391 1.00 0.31 O +ATOM 137 N LEU C 35 10.147 -0.527 4.587 1.00 0.67 N +ATOM 138 CA LEU C 35 9.837 0.890 4.475 1.00 0.67 C +ATOM 139 C LEU C 35 11.118 1.607 4.045 1.00 0.67 C +ATOM 140 O LEU C 35 11.896 2.086 4.884 1.00 0.67 O +ATOM 141 N VAL C 36 11.337 1.666 2.731 1.00 0.38 N +ATOM 142 CA VAL C 36 12.523 2.307 2.177 1.00 0.38 C +ATOM 143 C VAL C 36 12.591 3.754 2.608 1.00 0.38 C +ATOM 144 O VAL C 36 13.658 4.253 2.933 1.00 0.38 O +ATOM 145 N ASP C 37 11.441 4.422 2.595 1.00 0.33 N +ATOM 146 CA ASP C 37 11.324 5.820 2.996 1.00 0.33 C +ATOM 147 C ASP C 37 10.264 5.872 4.111 1.00 0.33 C +ATOM 148 O ASP C 37 9.114 6.265 3.882 1.00 0.33 O +ATOM 149 N PRO C 38 10.682 5.474 5.314 1.00 0.90 N +ATOM 150 CA PRO C 38 9.828 5.395 6.496 1.00 0.90 C +ATOM 151 C PRO C 38 9.088 6.667 6.895 1.00 0.90 C +ATOM 152 O PRO C 38 7.893 6.616 7.199 1.00 0.90 O +ATOM 153 N GLU C 39 9.785 7.801 6.900 1.00 0.57 N +ATOM 154 CA GLU C 39 9.163 9.073 7.247 1.00 0.57 C +ATOM 155 C GLU C 39 8.218 9.536 6.129 1.00 0.57 C +ATOM 156 O GLU C 39 7.218 10.212 6.385 1.00 0.57 O +ATOM 157 N ARG C 40 8.537 9.187 4.883 1.00 0.29 N +ATOM 158 CA ARG C 40 7.668 9.576 3.785 1.00 0.29 C +ATOM 159 C ARG C 40 6.354 8.786 3.881 1.00 0.29 C +ATOM 160 O ARG C 40 5.276 9.342 3.668 1.00 0.29 O +ATOM 161 N VAL C 41 6.441 7.498 4.213 1.00 0.89 N +ATOM 162 CA VAL C 41 5.245 6.659 4.362 1.00 0.89 C +ATOM 163 C VAL C 41 4.414 7.203 5.534 1.00 0.89 C +ATOM 164 O VAL C 41 3.185 7.242 5.464 1.00 0.89 O +ATOM 165 N ALA C 42 5.091 7.633 6.602 1.00 0.88 N +ATOM 166 CA ALA C 42 4.412 8.161 7.792 1.00 0.88 C +ATOM 167 C ALA C 42 3.652 9.457 7.514 1.00 0.88 C +ATOM 168 O ALA C 42 2.543 9.671 8.025 1.00 0.88 O +ATOM 169 N LYS C 43 4.250 10.330 6.715 1.00 0.43 N +ATOM 170 CA LYS C 43 3.610 11.592 6.367 1.00 0.43 C +ATOM 171 C LYS C 43 2.358 11.292 5.542 1.00 0.43 C +ATOM 172 O LYS C 43 1.308 11.923 5.724 1.00 0.43 O +ATOM 173 N LEU C 44 2.468 10.309 4.653 1.00 0.54 N +ATOM 174 CA LEU C 44 1.354 9.894 3.790 1.00 0.54 C +ATOM 175 C LEU C 44 0.209 9.334 4.630 1.00 0.54 C +ATOM 176 O LEU C 44 -0.964 9.530 4.322 1.00 0.54 O +ATOM 177 N TRP C 45 0.569 8.623 5.692 1.00 0.92 N +ATOM 178 CA TRP C 45 -0.403 8.025 6.606 1.00 0.92 C +ATOM 179 C TRP C 45 -1.100 9.140 7.400 1.00 0.92 C +ATOM 180 O TRP C 45 -2.317 9.114 7.613 1.00 0.92 O +ATOM 181 N GLY C 46 -0.324 10.133 7.818 1.00 0.93 N +ATOM 182 CA GLY C 46 -0.893 11.245 8.559 1.00 0.93 C +ATOM 183 C GLY C 46 -1.851 12.069 7.706 1.00 0.93 C +ATOM 184 O GLY C 46 -2.833 12.613 8.213 1.00 0.93 O +ATOM 185 N GLU C 47 -1.563 12.179 6.411 1.00 0.28 N +ATOM 186 CA GLU C 47 -2.429 12.931 5.512 1.00 0.28 C +ATOM 187 C GLU C 47 -3.747 12.161 5.392 1.00 0.28 C +ATOM 188 O GLU C 47 -4.834 12.741 5.446 1.00 0.28 O +ATOM 189 N VAL C 48 -3.642 10.844 5.257 1.00 0.21 N +ATOM 190 CA VAL C 48 -4.813 9.987 5.133 1.00 0.21 C +ATOM 191 C VAL C 48 -5.712 10.021 6.381 1.00 0.21 C +ATOM 192 O VAL C 48 -6.934 10.081 6.273 1.00 0.21 O +ATOM 193 N LYS C 49 -5.100 9.988 7.562 1.00 0.44 N +ATOM 194 CA LYS C 49 -5.845 9.991 8.817 1.00 0.44 C +ATOM 195 C LYS C 49 -6.034 11.386 9.389 1.00 0.44 C +ATOM 196 O LYS C 49 -6.663 11.553 10.427 1.00 0.44 O +ATOM 197 N GLY C 50 -5.481 12.387 8.716 1.00 0.71 N +ATOM 198 CA GLY C 50 -5.598 13.761 9.178 1.00 0.71 C +ATOM 199 C GLY C 50 -4.805 14.041 10.468 1.00 0.71 C +ATOM 200 O GLY C 50 -5.278 14.755 11.353 1.00 0.71 O +ATOM 201 N LYS C 51 -3.605 13.471 10.567 1.00 0.50 N +ATOM 202 CA LYS C 51 -2.727 13.671 11.730 1.00 0.50 C +ATOM 203 C LYS C 51 -1.411 14.280 11.218 1.00 0.50 C +ATOM 204 O LYS C 51 -0.425 13.570 11.007 1.00 0.50 O +ATOM 205 N PRO C 52 -1.381 15.610 11.033 1.00 0.83 N +ATOM 206 CA PRO C 52 -0.212 16.345 10.537 1.00 0.83 C +ATOM 207 C PRO C 52 1.104 16.112 11.244 1.00 0.83 C +ATOM 208 O PRO C 52 2.155 16.373 10.672 1.00 0.83 O +ATOM 209 N LYS C 53 1.060 15.627 12.479 1.00 0.31 N +ATOM 210 CA LYS C 53 2.297 15.396 13.219 1.00 0.31 C +ATOM 211 C LYS C 53 2.729 13.937 13.211 1.00 0.31 C +ATOM 212 O LYS C 53 3.606 13.539 13.977 1.00 0.31 O +ATOM 213 N MET C 54 2.114 13.144 12.334 1.00 0.83 N +ATOM 214 CA MET C 54 2.438 11.727 12.221 1.00 0.83 C +ATOM 215 C MET C 54 3.869 11.546 11.720 1.00 0.83 C +ATOM 216 O MET C 54 4.325 12.263 10.824 1.00 0.83 O +ATOM 217 N ASN C 55 4.588 10.605 12.317 1.00 0.66 N +ATOM 218 CA ASN C 55 5.947 10.331 11.880 1.00 0.66 C +ATOM 219 C ASN C 55 6.185 8.840 12.036 1.00 0.66 C +ATOM 220 O ASN C 55 5.294 8.108 12.496 1.00 0.66 O +ATOM 221 N TRP C 56 7.368 8.378 11.644 1.00 0.28 N +ATOM 222 CA TRP C 56 7.657 6.957 11.734 1.00 0.28 C +ATOM 223 C TRP C 56 7.709 6.457 13.178 1.00 0.28 C +ATOM 224 O TRP C 56 7.413 5.294 13.448 1.00 0.28 O +ATOM 225 N LYS C 57 8.089 7.333 14.100 1.00 0.24 N +ATOM 226 CA LYS C 57 8.156 6.952 15.508 1.00 0.24 C +ATOM 227 C LYS C 57 6.808 6.390 15.949 1.00 0.24 C +ATOM 228 O LYS C 57 6.719 5.256 16.418 1.00 0.24 O +ATOM 229 N ASN C 58 5.761 7.191 15.778 1.00 0.76 N +ATOM 230 CA ASN C 58 4.413 6.796 16.162 1.00 0.76 C +ATOM 231 C ASN C 58 3.806 5.728 15.251 1.00 0.76 C +ATOM 232 O ASN C 58 3.042 4.896 15.714 1.00 0.76 O +ATOM 233 N LEU C 59 4.131 5.745 13.959 1.00 0.58 N +ATOM 234 CA LEU C 59 3.596 4.726 13.054 1.00 0.58 C +ATOM 235 C LEU C 59 4.143 3.365 13.478 1.00 0.58 C +ATOM 236 O LEU C 59 3.419 2.372 13.518 1.00 0.58 O +ATOM 237 N HIS C 60 5.430 3.329 13.806 1.00 0.40 N +ATOM 238 CA HIS C 60 6.062 2.097 14.238 1.00 0.40 C +ATOM 239 C HIS C 60 5.406 1.599 15.537 1.00 0.40 C +ATOM 240 O HIS C 60 5.298 0.392 15.756 1.00 0.40 O +ATOM 241 N ARG C 61 4.961 2.509 16.402 1.00 0.27 N +ATOM 242 CA ARG C 61 4.311 2.062 17.636 1.00 0.27 C +ATOM 243 C ARG C 61 3.026 1.323 17.282 1.00 0.27 C +ATOM 244 O ARG C 61 2.678 0.328 17.920 1.00 0.27 O +ATOM 245 N ALA C 62 2.321 1.818 16.262 1.00 0.73 N +ATOM 246 CA ALA C 62 1.086 1.187 15.794 1.00 0.73 C +ATOM 247 C ALA C 62 1.404 -0.187 15.209 1.00 0.73 C +ATOM 248 O ALA C 62 0.632 -1.138 15.361 1.00 0.73 O +ATOM 249 N LEU C 63 2.544 -0.301 14.529 1.00 0.67 N +ATOM 250 CA LEU C 63 2.934 -1.583 13.961 1.00 0.67 C +ATOM 251 C LEU C 63 3.232 -2.545 15.106 1.00 0.67 C +ATOM 252 O LEU C 63 2.899 -3.727 15.039 1.00 0.67 O +ATOM 253 N ARG C 64 3.853 -2.034 16.162 1.00 0.76 N +ATOM 254 CA ARG C 64 4.197 -2.873 17.304 1.00 0.76 C +ATOM 255 C ARG C 64 2.961 -3.443 17.983 1.00 0.76 C +ATOM 256 O ARG C 64 3.001 -4.522 18.564 1.00 0.76 O +ATOM 257 N GLY C 65 1.852 -2.726 17.888 1.00 0.28 N +ATOM 258 CA GLY C 65 0.602 -3.202 18.471 1.00 0.28 C +ATOM 259 C GLY C 65 0.064 -4.378 17.654 1.00 0.28 C +ATOM 260 O GLY C 65 -0.732 -5.179 18.144 1.00 0.28 O +ATOM 261 N TYR C 66 0.508 -4.485 16.405 1.00 0.74 N +ATOM 262 CA TYR C 66 0.065 -5.565 15.534 1.00 0.74 C +ATOM 263 C TYR C 66 0.768 -6.874 15.891 1.00 0.74 C +ATOM 264 O TYR C 66 0.320 -7.946 15.492 1.00 0.74 O +ATOM 265 N LYS C 67 1.871 -6.792 16.632 1.00 0.74 N +ATOM 266 CA LYS C 67 2.606 -7.999 17.015 1.00 0.74 C +ATOM 267 C LYS C 67 1.705 -8.898 17.852 1.00 0.74 C +ATOM 268 O LYS C 67 1.666 -10.115 17.673 1.00 0.74 O +ATOM 269 N LYS C 68 1.000 -8.272 18.785 1.00 0.49 N +ATOM 270 CA LYS C 68 0.084 -8.964 19.684 1.00 0.49 C +ATOM 271 C LYS C 68 -1.109 -9.530 18.910 1.00 0.49 C +ATOM 272 O LYS C 68 -1.571 -10.649 19.168 1.00 0.49 O +ATOM 273 N LYS C 69 -1.598 -8.736 17.962 1.00 0.57 N +ATOM 274 CA LYS C 69 -2.733 -9.109 17.137 1.00 0.57 C +ATOM 275 C LYS C 69 -2.364 -10.141 16.087 1.00 0.57 C +ATOM 276 O LYS C 69 -3.232 -10.741 15.458 1.00 0.57 O +ATOM 277 N LYS C 70 -1.071 -10.350 15.899 1.00 0.29 N +ATOM 278 CA LYS C 70 -0.596 -11.309 14.916 1.00 0.29 C +ATOM 279 C LYS C 70 -0.943 -10.912 13.490 1.00 0.29 C +ATOM 280 O LYS C 70 -1.236 -11.763 12.661 1.00 0.29 O +ATOM 281 N ILE C 71 -0.916 -9.615 13.215 1.00 0.49 N +ATOM 282 CA ILE C 71 -1.207 -9.113 11.879 1.00 0.49 C +ATOM 283 C ILE C 71 0.127 -8.886 11.176 1.00 0.49 C +ATOM 284 O ILE C 71 0.306 -9.250 10.014 1.00 0.49 O +ATOM 285 N ILE C 72 1.058 -8.290 11.912 1.00 0.86 N +ATOM 286 CA ILE C 72 2.390 -7.989 11.409 1.00 0.86 C +ATOM 287 C ILE C 72 3.421 -8.258 12.508 1.00 0.86 C +ATOM 288 O ILE C 72 3.170 -8.020 13.692 1.00 0.86 O +ATOM 289 N GLU C 73 4.574 -8.777 12.103 1.00 0.19 N +ATOM 290 CA GLU C 73 5.657 -9.043 13.026 1.00 0.19 C +ATOM 291 C GLU C 73 6.886 -8.323 12.487 1.00 0.19 C +ATOM 292 O GLU C 73 6.925 -7.929 11.320 1.00 0.19 O +ATOM 293 N THR C 74 7.876 -8.120 13.343 1.00 0.62 N +ATOM 294 CA THR C 74 9.099 -7.454 12.934 1.00 0.62 C +ATOM 295 C THR C 74 10.081 -8.490 12.388 1.00 0.62 C +ATOM 296 O THR C 74 10.115 -9.625 12.870 1.00 0.62 O +ATOM 297 N VAL C 75 10.838 -8.128 11.350 1.00 0.90 N +ATOM 298 CA VAL C 75 11.859 -9.038 10.829 1.00 0.90 C +ATOM 299 C VAL C 75 13.081 -8.613 11.652 1.00 0.90 C +ATOM 300 O VAL C 75 13.637 -7.535 11.449 1.00 0.90 O +ATOM 301 N LYS C 76 13.467 -9.452 12.608 1.00 0.38 N +ATOM 302 CA LYS C 76 14.576 -9.143 13.503 1.00 0.38 C +ATOM 303 C LYS C 76 15.916 -8.827 12.830 1.00 0.38 C +ATOM 304 O LYS C 76 16.351 -9.525 11.908 1.00 0.38 O +ATOM 305 N GLY C 77 16.560 -7.762 13.306 1.00 0.35 N +ATOM 306 CA GLY C 77 17.860 -7.362 12.789 1.00 0.35 C +ATOM 307 C GLY C 77 17.910 -6.851 11.361 1.00 0.35 C +ATOM 308 O GLY C 77 18.944 -6.946 10.703 1.00 0.35 O +ATOM 309 N LYS C 78 16.796 -6.310 10.882 1.00 0.34 N +ATOM 310 CA LYS C 78 16.718 -5.771 9.526 1.00 0.34 C +ATOM 311 C LYS C 78 15.926 -4.480 9.563 1.00 0.34 C +ATOM 312 O LYS C 78 14.704 -4.496 9.476 1.00 0.34 O +ATOM 313 N PRO C 79 16.639 -3.367 9.695 1.00 0.36 N +ATOM 314 CA PRO C 79 16.029 -2.045 9.769 1.00 0.36 C +ATOM 315 C PRO C 79 14.916 -1.814 8.754 1.00 0.36 C +ATOM 316 O PRO C 79 15.066 -2.109 7.569 1.00 0.36 O +ATOM 317 N TYR C 80 13.795 -1.295 9.254 1.00 0.84 N +ATOM 318 CA TYR C 80 12.615 -0.972 8.454 1.00 0.84 C +ATOM 319 C TYR C 80 11.898 -2.143 7.774 1.00 0.84 C +ATOM 320 O TYR C 80 10.962 -1.936 6.998 1.00 0.84 O +ATOM 321 N GLN C 81 12.325 -3.367 8.079 1.00 0.41 N +ATOM 322 CA GLN C 81 11.723 -4.553 7.489 1.00 0.41 C +ATOM 323 C GLN C 81 10.730 -5.217 8.435 1.00 0.41 C +ATOM 324 O GLN C 81 11.028 -5.455 9.611 1.00 0.41 O +ATOM 325 N TYR C 82 9.552 -5.515 7.899 1.00 0.63 N +ATOM 326 CA TYR C 82 8.475 -6.140 8.649 1.00 0.63 C +ATOM 327 C TYR C 82 7.896 -7.264 7.810 1.00 0.63 C +ATOM 328 O TYR C 82 8.253 -7.438 6.647 1.00 0.63 O +ATOM 329 N ARG C 83 6.977 -8.016 8.397 1.00 0.42 N +ATOM 330 CA ARG C 83 6.372 -9.119 7.685 1.00 0.42 C +ATOM 331 C ARG C 83 4.920 -9.292 8.044 1.00 0.42 C +ATOM 332 O ARG C 83 4.553 -9.245 9.214 1.00 0.42 O +ATOM 333 N PHE C 84 4.089 -9.482 7.030 1.00 0.87 N +ATOM 334 CA PHE C 84 2.678 -9.712 7.264 1.00 0.87 C +ATOM 335 C PHE C 84 2.607 -11.164 7.727 1.00 0.87 C +ATOM 336 O PHE C 84 3.049 -12.067 7.017 1.00 0.87 O +ATOM 337 N VAL C 85 2.071 -11.388 8.925 1.00 0.68 N +ATOM 338 CA VAL C 85 1.985 -12.740 9.467 1.00 0.68 C +ATOM 339 C VAL C 85 1.360 -13.705 8.479 1.00 0.68 C +ATOM 340 O VAL C 85 1.939 -14.754 8.183 1.00 0.68 O +ATOM 341 N ASN C 86 0.183 -13.359 7.967 1.00 0.28 N +ATOM 342 CA ASN C 86 -0.487 -14.222 7.002 1.00 0.28 C +ATOM 343 C ASN C 86 -1.010 -13.449 5.796 1.00 0.28 C +ATOM 344 O ASN C 86 -2.179 -13.051 5.728 1.00 0.28 O +ATOM 345 N TYR C 87 -0.102 -13.221 4.855 1.00 0.80 N +ATOM 346 CA TYR C 87 -0.418 -12.532 3.617 1.00 0.80 C +ATOM 347 C TYR C 87 -0.442 -13.663 2.600 1.00 0.80 C +ATOM 348 O TYR C 87 0.460 -14.490 2.588 1.00 0.80 O +ATOM 349 N PRO C 88 -1.474 -13.726 1.743 1.00 0.91 N +ATOM 350 CA PRO C 88 -2.643 -12.851 1.604 1.00 0.91 C +ATOM 351 C PRO C 88 -3.914 -13.295 2.337 1.00 0.91 C +ATOM 352 O PRO C 88 -5.005 -12.823 2.027 1.00 0.91 O +ATOM 353 N GLU C 89 -3.787 -14.208 3.290 1.00 0.80 N +ATOM 354 CA GLU C 89 -4.942 -14.690 4.047 1.00 0.80 C +ATOM 355 C GLU C 89 -5.803 -13.534 4.586 1.00 0.80 C +ATOM 356 O GLU C 89 -7.038 -13.619 4.636 1.00 0.80 O +ATOM 357 N LEU C 90 -5.140 -12.452 4.982 1.00 0.15 N +ATOM 358 CA LEU C 90 -5.826 -11.287 5.531 1.00 0.15 C +ATOM 359 C LEU C 90 -6.670 -10.532 4.491 1.00 0.15 C +ATOM 360 O LEU C 90 -7.395 -9.588 4.829 1.00 0.15 O +ATOM 361 N LEU C 91 -6.577 -10.948 3.228 1.00 0.73 N +ATOM 362 CA LEU C 91 -7.338 -10.295 2.160 1.00 0.73 C +ATOM 363 C LEU C 91 -8.600 -11.055 1.730 1.00 0.73 C +ATOM 364 O LEU C 91 -9.434 -10.527 1.002 1.00 0.73 O +ATOM 365 N HIS C 92 -8.733 -12.301 2.167 1.00 0.63 N +ATOM 366 CA HIS C 92 -9.945 -13.070 1.889 1.00 0.63 C +ATOM 367 C HIS C 92 -10.546 -13.404 3.247 1.00 0.63 C +ATOM 368 O HIS C 92 -10.434 -14.541 3.724 1.00 0.63 O +ATOM 369 N PRO C 93 -11.152 -12.402 3.878 1.00 0.32 N +ATOM 370 CA PRO C 93 -11.779 -12.611 5.167 1.00 0.32 C +ATOM 371 C PRO C 93 -13.050 -13.403 4.882 1.00 0.32 C +ATOM 372 O PRO C 93 -13.476 -14.188 5.762 1.00 0.32 O +ATOM 373 O5' DT A 1 18.304 10.313 14.820 1.00 0.00 O +ATOM 374 C5' DT A 1 19.094 9.803 13.737 1.00 0.00 C +ATOM 375 C4' DT A 1 18.917 8.315 13.559 1.00 0.00 C +ATOM 376 O4' DT A 1 19.697 7.616 14.562 1.00 0.00 O +ATOM 377 C3' DT A 1 17.470 7.855 13.741 1.00 0.00 C +ATOM 378 O3' DT A 1 17.095 6.863 12.788 1.00 0.00 O +ATOM 379 C2' DT A 1 17.458 7.238 15.125 1.00 0.00 C +ATOM 380 C1' DT A 1 18.865 6.691 15.255 1.00 0.00 C +ATOM 381 N1 DT A 1 19.304 6.626 16.668 1.00 0.00 N +ATOM 382 C2 DT A 1 19.705 5.412 17.182 1.00 0.00 C +ATOM 383 O2 DT A 1 19.791 4.385 16.537 1.00 0.00 O +ATOM 384 N3 DT A 1 20.012 5.437 18.502 1.00 0.00 N +ATOM 385 C4 DT A 1 19.951 6.509 19.368 1.00 0.00 C +ATOM 386 O4 DT A 1 20.205 6.342 20.562 1.00 0.00 O +ATOM 387 C5 DT A 1 19.567 7.762 18.762 1.00 0.00 C +ATOM 388 C7 DT A 1 19.513 8.999 19.602 1.00 0.00 C +ATOM 389 C6 DT A 1 19.273 7.759 17.458 1.00 0.00 C +ATOM 390 P DA A 2 15.599 6.249 12.825 1.00 0.00 P +ATOM 391 OP1 DA A 2 15.051 6.238 11.437 1.00 0.00 O +ATOM 392 OP2 DA A 2 14.829 6.923 13.914 1.00 0.00 O +ATOM 393 O5' DA A 2 15.831 4.747 13.296 1.00 0.00 O +ATOM 394 C5' DA A 2 16.645 3.854 12.539 1.00 0.00 C +ATOM 395 C4' DA A 2 16.501 2.449 13.077 1.00 0.00 C +ATOM 396 O4' DA A 2 17.058 2.395 14.415 1.00 0.00 O +ATOM 397 C3' DA A 2 15.052 1.969 13.198 1.00 0.00 C +ATOM 398 O3' DA A 2 14.977 0.578 12.848 1.00 0.00 O +ATOM 399 C2' DA A 2 14.719 2.214 14.663 1.00 0.00 C +ATOM 400 C1' DA A 2 16.062 2.014 15.360 1.00 0.00 C +ATOM 401 N9 DA A 2 16.254 2.824 16.570 1.00 0.00 N +ATOM 402 C8 DA A 2 16.103 4.182 16.715 1.00 0.00 C +ATOM 403 N7 DA A 2 16.322 4.612 17.935 1.00 0.00 N +ATOM 404 C5 DA A 2 16.643 3.462 18.643 1.00 0.00 C +ATOM 405 C6 DA A 2 16.964 3.235 20.000 1.00 0.00 C +ATOM 406 N6 DA A 2 17.022 4.194 20.924 1.00 0.00 N +ATOM 407 N1 DA A 2 17.226 1.969 20.377 1.00 0.00 N +ATOM 408 C2 DA A 2 17.176 1.003 19.457 1.00 0.00 C +ATOM 409 N3 DA A 2 16.887 1.084 18.163 1.00 0.00 N +ATOM 410 C4 DA A 2 16.619 2.355 17.813 1.00 0.00 C +ATOM 411 P DC A 3 13.558 -0.169 12.821 1.00 0.00 P +ATOM 412 OP1 DC A 3 13.640 -1.321 11.905 1.00 0.00 O +ATOM 413 OP2 DC A 3 12.525 0.871 12.617 1.00 0.00 O +ATOM 414 O5' DC A 3 13.380 -0.737 14.299 1.00 0.00 O +ATOM 415 C5' DC A 3 14.400 -1.524 14.907 1.00 0.00 C +ATOM 416 C4' DC A 3 13.967 -2.001 16.275 1.00 0.00 C +ATOM 417 O4' DC A 3 14.336 -1.015 17.272 1.00 0.00 O +ATOM 418 C3' DC A 3 12.472 -2.279 16.468 1.00 0.00 C +ATOM 419 O3' DC A 3 12.313 -3.566 17.075 1.00 0.00 O +ATOM 420 C2' DC A 3 12.009 -1.161 17.390 1.00 0.00 C +ATOM 421 C1' DC A 3 13.266 -0.839 18.181 1.00 0.00 C +ATOM 422 N1 DC A 3 13.361 0.526 18.749 1.00 0.00 N +ATOM 423 C2 DC A 3 13.811 0.679 20.081 1.00 0.00 C +ATOM 424 O2 DC A 3 14.117 -0.328 20.740 1.00 0.00 O +ATOM 425 N3 DC A 3 13.895 1.920 20.611 1.00 0.00 N +ATOM 426 C4 DC A 3 13.551 2.986 19.881 1.00 0.00 C +ATOM 427 N4 DC A 3 13.648 4.189 20.454 1.00 0.00 N +ATOM 428 C5 DC A 3 13.090 2.863 18.530 1.00 0.00 C +ATOM 429 C6 DC A 3 13.015 1.628 18.010 1.00 0.00 C +ATOM 430 P DC A 4 10.841 -4.169 17.337 1.00 0.00 P +ATOM 431 OP1 DC A 4 10.889 -5.642 17.128 1.00 0.00 O +ATOM 432 OP2 DC A 4 9.841 -3.354 16.599 1.00 0.00 O +ATOM 433 O5' DC A 4 10.610 -3.896 18.887 1.00 0.00 O +ATOM 434 C5' DC A 4 11.624 -4.211 19.840 1.00 0.00 C +ATOM 435 C4' DC A 4 11.077 -4.102 21.242 1.00 0.00 C +ATOM 436 O4' DC A 4 11.519 -2.836 21.796 1.00 0.00 O +ATOM 437 C3' DC A 4 9.548 -4.087 21.270 1.00 0.00 C +ATOM 438 O3' DC A 4 8.983 -5.058 22.133 1.00 0.00 O +ATOM 439 C2' DC A 4 9.174 -2.695 21.730 1.00 0.00 C +ATOM 440 C1' DC A 4 10.429 -2.136 22.378 1.00 0.00 C +ATOM 441 N1 DC A 4 10.556 -0.702 22.049 1.00 0.00 N +ATOM 442 C2 DC A 4 10.557 0.249 23.091 1.00 0.00 C +ATOM 443 O2 DC A 4 10.547 -0.140 24.273 1.00 0.00 O +ATOM 444 N3 DC A 4 10.560 1.564 22.778 1.00 0.00 N +ATOM 445 C4 DC A 4 10.559 1.949 21.496 1.00 0.00 C +ATOM 446 N4 DC A 4 10.505 3.253 21.236 1.00 0.00 N +ATOM 447 C5 DC A 4 10.602 1.011 20.425 1.00 0.00 C +ATOM 448 C6 DC A 4 10.612 -0.291 20.743 1.00 0.00 C +ATOM 449 P DG A 5 7.455 -5.511 21.910 1.00 0.00 P +ATOM 450 OP1 DG A 5 7.431 -6.984 21.812 1.00 0.00 O +ATOM 451 OP2 DG A 5 6.832 -4.697 20.834 1.00 0.00 O +ATOM 452 O5' DG A 5 6.759 -5.086 23.279 1.00 0.00 O +ATOM 453 C5' DG A 5 7.337 -5.436 24.539 1.00 0.00 C +ATOM 454 C4' DG A 5 6.876 -4.472 25.610 1.00 0.00 C +ATOM 455 O4' DG A 5 7.321 -3.132 25.288 1.00 0.00 O +ATOM 456 C3' DG A 5 5.362 -4.373 25.791 1.00 0.00 C +ATOM 457 O3' DG A 5 5.084 -4.149 27.177 1.00 0.00 O +ATOM 458 C2' DG A 5 4.998 -3.139 24.982 1.00 0.00 C +ATOM 459 C1' DG A 5 6.203 -2.256 25.230 1.00 0.00 C +ATOM 460 N9 DG A 5 6.465 -1.239 24.213 1.00 0.00 N +ATOM 461 C8 DG A 5 6.402 -1.381 22.845 1.00 0.00 C +ATOM 462 N7 DG A 5 6.676 -0.276 22.204 1.00 0.00 N +ATOM 463 C5 DG A 5 6.938 0.650 23.208 1.00 0.00 C +ATOM 464 C6 DG A 5 7.280 2.026 23.126 1.00 0.00 C +ATOM 465 O6 DG A 5 7.421 2.721 22.118 1.00 0.00 O +ATOM 466 N1 DG A 5 7.454 2.589 24.393 1.00 0.00 N +ATOM 467 C2 DG A 5 7.313 1.908 25.583 1.00 0.00 C +ATOM 468 N2 DG A 5 7.525 2.605 26.721 1.00 0.00 N +ATOM 469 N3 DG A 5 6.988 0.633 25.665 1.00 0.00 N +ATOM 470 C4 DG A 5 6.816 0.069 24.451 1.00 0.00 C +ATOM 471 P DG A 6 3.574 -4.238 27.728 1.00 0.00 P +ATOM 472 OP1 DG A 6 3.439 -5.516 28.484 1.00 0.00 O +ATOM 473 OP2 DG A 6 2.597 -3.914 26.651 1.00 0.00 O +ATOM 474 O5' DG A 6 3.529 -3.055 28.788 1.00 0.00 O +ATOM 475 C5' DG A 6 4.595 -2.864 29.713 1.00 0.00 C +ATOM 476 C4' DG A 6 4.483 -1.505 30.357 1.00 0.00 C +ATOM 477 O4' DG A 6 4.861 -0.450 29.443 1.00 0.00 O +ATOM 478 C3' DG A 6 3.078 -1.162 30.839 1.00 0.00 C +ATOM 479 O3' DG A 6 3.181 -0.493 32.087 1.00 0.00 O +ATOM 480 C2' DG A 6 2.543 -0.236 29.760 1.00 0.00 C +ATOM 481 C1' DG A 6 3.794 0.483 29.279 1.00 0.00 C +ATOM 482 N9 DG A 6 3.768 0.876 27.870 1.00 0.00 N +ATOM 483 C8 DG A 6 3.526 0.057 26.790 1.00 0.00 C +ATOM 484 N7 DG A 6 3.640 0.671 25.646 1.00 0.00 N +ATOM 485 C5 DG A 6 3.957 1.979 25.985 1.00 0.00 C +ATOM 486 C6 DG A 6 4.211 3.105 25.157 1.00 0.00 C +ATOM 487 O6 DG A 6 4.217 3.166 23.918 1.00 0.00 O +ATOM 488 N1 DG A 6 4.481 4.244 25.909 1.00 0.00 N +ATOM 489 C2 DG A 6 4.495 4.294 27.286 1.00 0.00 C +ATOM 490 N2 DG A 6 4.734 5.494 27.835 1.00 0.00 N +ATOM 491 N3 DG A 6 4.280 3.244 28.067 1.00 0.00 N +ATOM 492 C4 DG A 6 4.019 2.130 27.355 1.00 0.00 C +ATOM 493 P DA A 7 1.858 -0.155 32.916 1.00 0.00 P +ATOM 494 OP1 DA A 7 2.280 -0.017 34.333 1.00 0.00 O +ATOM 495 OP2 DA A 7 0.793 -1.130 32.549 1.00 0.00 O +ATOM 496 O5' DA A 7 1.457 1.274 32.352 1.00 0.00 O +ATOM 497 C5' DA A 7 2.256 2.408 32.638 1.00 0.00 C +ATOM 498 C4' DA A 7 1.571 3.659 32.146 1.00 0.00 C +ATOM 499 O4' DA A 7 1.761 3.835 30.718 1.00 0.00 O +ATOM 500 C3' DA A 7 0.062 3.741 32.403 1.00 0.00 C +ATOM 501 O3' DA A 7 -0.223 5.027 32.953 1.00 0.00 O +ATOM 502 C2' DA A 7 -0.543 3.574 31.013 1.00 0.00 C +ATOM 503 C1' DA A 7 0.526 4.180 30.110 1.00 0.00 C +ATOM 504 N9 DA A 7 0.561 3.700 28.723 1.00 0.00 N +ATOM 505 C8 DA A 7 0.339 2.431 28.248 1.00 0.00 C +ATOM 506 N7 DA A 7 0.472 2.322 26.946 1.00 0.00 N +ATOM 507 C5 DA A 7 0.796 3.608 26.534 1.00 0.00 C +ATOM 508 C6 DA A 7 1.071 4.161 25.263 1.00 0.00 C +ATOM 509 N6 DA A 7 1.055 3.462 24.126 1.00 0.00 N +ATOM 510 N1 DA A 7 1.367 5.481 25.204 1.00 0.00 N +ATOM 511 C2 DA A 7 1.386 6.182 26.342 1.00 0.00 C +ATOM 512 N3 DA A 7 1.145 5.776 27.587 1.00 0.00 N +ATOM 513 C4 DA A 7 0.852 4.467 27.616 1.00 0.00 C +ATOM 514 P DA A 8 -1.702 5.389 33.460 1.00 0.00 P +ATOM 515 OP1 DA A 8 -1.561 6.127 34.742 1.00 0.00 O +ATOM 516 OP2 DA A 8 -2.599 4.209 33.379 1.00 0.00 O +ATOM 517 O5' DA A 8 -2.185 6.443 32.385 1.00 0.00 O +ATOM 518 C5' DA A 8 -1.409 7.602 32.152 1.00 0.00 C +ATOM 519 C4' DA A 8 -1.868 8.288 30.891 1.00 0.00 C +ATOM 520 O4' DA A 8 -1.571 7.465 29.737 1.00 0.00 O +ATOM 521 C3' DA A 8 -3.366 8.586 30.831 1.00 0.00 C +ATOM 522 O3' DA A 8 -3.512 9.915 30.341 1.00 0.00 O +ATOM 523 C2' DA A 8 -3.890 7.566 29.830 1.00 0.00 C +ATOM 524 C1' DA A 8 -2.708 7.462 28.894 1.00 0.00 C +ATOM 525 N9 DA A 8 -2.646 6.287 28.027 1.00 0.00 N +ATOM 526 C8 DA A 8 -2.861 4.961 28.316 1.00 0.00 C +ATOM 527 N7 DA A 8 -2.739 4.168 27.273 1.00 0.00 N +ATOM 528 C5 DA A 8 -2.417 5.031 26.231 1.00 0.00 C +ATOM 529 C6 DA A 8 -2.153 4.819 24.852 1.00 0.00 C +ATOM 530 N6 DA A 8 -2.167 3.618 24.263 1.00 0.00 N +ATOM 531 N1 DA A 8 -1.865 5.902 24.097 1.00 0.00 N +ATOM 532 C2 DA A 8 -1.838 7.105 24.684 1.00 0.00 C +ATOM 533 N3 DA A 8 -2.065 7.431 25.958 1.00 0.00 N +ATOM 534 C4 DA A 8 -2.352 6.337 26.685 1.00 0.00 C +ATOM 535 P DG A 9 -4.956 10.607 30.276 1.00 0.00 P +ATOM 536 OP1 DG A 9 -4.885 11.863 31.061 1.00 0.00 O +ATOM 537 OP2 DG A 9 -6.006 9.603 30.576 1.00 0.00 O +ATOM 538 O5' DG A 9 -5.074 10.984 28.734 1.00 0.00 O +ATOM 539 C5' DG A 9 -4.136 11.869 28.135 1.00 0.00 C +ATOM 540 C4' DG A 9 -4.463 12.060 26.674 1.00 0.00 C +ATOM 541 O4' DG A 9 -4.156 10.846 25.948 1.00 0.00 O +ATOM 542 C3' DG A 9 -5.927 12.387 26.371 1.00 0.00 C +ATOM 543 O3' DG A 9 -5.991 13.394 25.360 1.00 0.00 O +ATOM 544 C2' DG A 9 -6.494 11.069 25.879 1.00 0.00 C +ATOM 545 C1' DG A 9 -5.294 10.411 25.218 1.00 0.00 C +ATOM 546 N9 DG A 9 -5.318 8.951 25.254 1.00 0.00 N +ATOM 547 C8 DG A 9 -5.424 8.148 26.366 1.00 0.00 C +ATOM 548 N7 DG A 9 -5.433 6.876 26.080 1.00 0.00 N +ATOM 549 C5 DG A 9 -5.321 6.831 24.700 1.00 0.00 C +ATOM 550 C6 DG A 9 -5.280 5.728 23.832 1.00 0.00 C +ATOM 551 O6 DG A 9 -5.335 4.529 24.121 1.00 0.00 O +ATOM 552 N1 DG A 9 -5.165 6.122 22.498 1.00 0.00 N +ATOM 553 C2 DG A 9 -5.094 7.428 22.065 1.00 0.00 C +ATOM 554 N2 DG A 9 -4.988 7.619 20.737 1.00 0.00 N +ATOM 555 N3 DG A 9 -5.127 8.474 22.875 1.00 0.00 N +ATOM 556 C4 DG A 9 -5.244 8.103 24.171 1.00 0.00 C +ATOM 557 P DT A 10 -7.414 13.887 24.796 1.00 0.00 P +ATOM 558 OP1 DT A 10 -7.222 15.289 24.332 1.00 0.00 O +ATOM 559 OP2 DT A 10 -8.502 13.575 25.763 1.00 0.00 O +ATOM 560 O5' DT A 10 -7.631 12.962 23.511 1.00 0.00 O +ATOM 561 C5' DT A 10 -6.781 13.101 22.371 1.00 0.00 C +ATOM 562 C4' DT A 10 -7.422 12.481 21.152 1.00 0.00 C +ATOM 563 O4' DT A 10 -7.287 11.044 21.195 1.00 0.00 O +ATOM 564 C3' DT A 10 -8.913 12.766 20.979 1.00 0.00 C +ATOM 565 O3' DT A 10 -9.196 12.942 19.592 1.00 0.00 O +ATOM 566 C2' DT A 10 -9.566 11.479 21.453 1.00 0.00 C +ATOM 567 C1' DT A 10 -8.549 10.431 21.020 1.00 0.00 C +ATOM 568 N1 DT A 10 -8.545 9.162 21.790 1.00 0.00 N +ATOM 569 C2 DT A 10 -8.395 7.963 21.106 1.00 0.00 C +ATOM 570 O2 DT A 10 -8.268 7.885 19.896 1.00 0.00 O +ATOM 571 N3 DT A 10 -8.402 6.847 21.907 1.00 0.00 N +ATOM 572 C4 DT A 10 -8.544 6.798 23.283 1.00 0.00 C +ATOM 573 O4 DT A 10 -8.535 5.711 23.865 1.00 0.00 O +ATOM 574 C5 DT A 10 -8.698 8.081 23.932 1.00 0.00 C +ATOM 575 C7 DT A 10 -8.860 8.129 25.419 1.00 0.00 C +ATOM 576 C6 DT A 10 -8.689 9.183 23.166 1.00 0.00 C +TER 577 DT A 10 +ATOM 578 O5' DA B 11 -11.321 -3.165 21.625 1.00 0.00 O +ATOM 579 C5' DA B 11 -12.292 -3.560 20.649 1.00 0.00 C +ATOM 580 C4' DA B 11 -12.040 -2.969 19.280 1.00 0.00 C +ATOM 581 O4' DA B 11 -12.252 -1.543 19.299 1.00 0.00 O +ATOM 582 C3' DA B 11 -10.634 -3.172 18.721 1.00 0.00 C +ATOM 583 O3' DA B 11 -10.731 -3.375 17.306 1.00 0.00 O +ATOM 584 C2' DA B 11 -9.907 -1.883 19.079 1.00 0.00 C +ATOM 585 C1' DA B 11 -11.009 -0.837 19.267 1.00 0.00 C +ATOM 586 N9 DA B 11 -10.895 -0.158 20.561 1.00 0.00 N +ATOM 587 C8 DA B 11 -10.718 -0.787 21.775 1.00 0.00 C +ATOM 588 N7 DA B 11 -10.705 0.020 22.795 1.00 0.00 N +ATOM 589 C5 DA B 11 -10.869 1.266 22.226 1.00 0.00 C +ATOM 590 C6 DA B 11 -10.952 2.518 22.793 1.00 0.00 C +ATOM 591 N6 DA B 11 -10.919 2.716 24.101 1.00 0.00 N +ATOM 592 N1 DA B 11 -11.095 3.571 21.975 1.00 0.00 N +ATOM 593 C2 DA B 11 -11.181 3.342 20.659 1.00 0.00 C +ATOM 594 N3 DA B 11 -11.138 2.195 19.991 1.00 0.00 N +ATOM 595 C4 DA B 11 -10.974 1.177 20.848 1.00 0.00 C +ATOM 596 P DA B 12 -9.435 -3.789 16.458 1.00 0.00 P +ATOM 597 OP1 DA B 12 -9.943 -4.405 15.206 1.00 0.00 O +ATOM 598 OP2 DA B 12 -8.497 -4.550 17.314 1.00 0.00 O +ATOM 599 O5' DA B 12 -8.783 -2.383 16.114 1.00 0.00 O +ATOM 600 C5' DA B 12 -9.447 -1.484 15.234 1.00 0.00 C +ATOM 601 C4' DA B 12 -8.656 -0.207 15.093 1.00 0.00 C +ATOM 602 O4' DA B 12 -8.760 0.577 16.303 1.00 0.00 O +ATOM 603 C3' DA B 12 -7.159 -0.372 14.821 1.00 0.00 C +ATOM 604 O3' DA B 12 -6.742 0.602 13.862 1.00 0.00 O +ATOM 605 C2' DA B 12 -6.528 -0.057 16.164 1.00 0.00 C +ATOM 606 C1' DA B 12 -7.470 1.013 16.682 1.00 0.00 C +ATOM 607 N9 DA B 12 -7.470 1.240 18.129 1.00 0.00 N +ATOM 608 C8 DA B 12 -7.200 0.351 19.140 1.00 0.00 C +ATOM 609 N7 DA B 12 -7.262 0.878 20.336 1.00 0.00 N +ATOM 610 C5 DA B 12 -7.602 2.203 20.099 1.00 0.00 C +ATOM 611 C6 DA B 12 -7.821 3.294 20.961 1.00 0.00 C +ATOM 612 N6 DA B 12 -7.723 3.223 22.298 1.00 0.00 N +ATOM 613 N1 DA B 12 -8.148 4.479 20.399 1.00 0.00 N +ATOM 614 C2 DA B 12 -8.248 4.549 19.063 1.00 0.00 C +ATOM 615 N3 DA B 12 -8.068 3.597 18.155 1.00 0.00 N +ATOM 616 C4 DA B 12 -7.741 2.436 18.744 1.00 0.00 C +ATOM 617 P DC B 13 -5.372 0.389 13.051 1.00 0.00 P +ATOM 618 OP1 DC B 13 -5.270 1.456 12.022 1.00 0.00 O +ATOM 619 OP2 DC B 13 -5.353 -1.032 12.637 1.00 0.00 O +ATOM 620 O5' DC B 13 -4.245 0.619 14.163 1.00 0.00 O +ATOM 621 C5' DC B 13 -3.370 1.748 14.127 1.00 0.00 C +ATOM 622 C4' DC B 13 -4.079 2.979 14.641 1.00 0.00 C +ATOM 623 O4' DC B 13 -4.685 2.724 15.936 1.00 0.00 O +ATOM 624 C3' DC B 13 -3.171 4.195 14.829 1.00 0.00 C +ATOM 625 O3' DC B 13 -3.707 5.358 14.202 1.00 0.00 O +ATOM 626 C2' DC B 13 -3.130 4.401 16.333 1.00 0.00 C +ATOM 627 C1' DC B 13 -4.457 3.836 16.783 1.00 0.00 C +ATOM 628 N1 DC B 13 -4.442 3.375 18.189 1.00 0.00 N +ATOM 629 C2 DC B 13 -4.721 4.309 19.207 1.00 0.00 C +ATOM 630 O2 DC B 13 -5.002 5.485 18.896 1.00 0.00 O +ATOM 631 N3 DC B 13 -4.668 3.910 20.503 1.00 0.00 N +ATOM 632 C4 DC B 13 -4.347 2.649 20.802 1.00 0.00 C +ATOM 633 N4 DC B 13 -4.276 2.311 22.095 1.00 0.00 N +ATOM 634 C5 DC B 13 -4.079 1.679 19.790 1.00 0.00 C +ATOM 635 C6 DC B 13 -4.142 2.080 18.511 1.00 0.00 C +ATOM 636 P DT B 14 -2.714 6.556 13.795 1.00 0.00 P +ATOM 637 OP1 DT B 14 -3.371 7.413 12.777 1.00 0.00 O +ATOM 638 OP2 DT B 14 -1.372 5.981 13.524 1.00 0.00 O +ATOM 639 O5' DT B 14 -2.575 7.406 15.129 1.00 0.00 O +ATOM 640 C5' DT B 14 -3.595 8.305 15.516 1.00 0.00 C +ATOM 641 C4' DT B 14 -3.146 9.115 16.706 1.00 0.00 C +ATOM 642 O4' DT B 14 -3.105 8.274 17.880 1.00 0.00 O +ATOM 643 C3' DT B 14 -1.766 9.768 16.586 1.00 0.00 C +ATOM 644 O3' DT B 14 -1.906 11.127 17.016 1.00 0.00 O +ATOM 645 C2' DT B 14 -0.890 8.928 17.513 1.00 0.00 C +ATOM 646 C1' DT B 14 -1.880 8.450 18.567 1.00 0.00 C +ATOM 647 N1 DT B 14 -1.594 7.183 19.306 1.00 0.00 N +ATOM 648 C2 DT B 14 -1.690 7.217 20.684 1.00 0.00 C +ATOM 649 O2 DT B 14 -1.860 8.243 21.323 1.00 0.00 O +ATOM 650 N3 DT B 14 -1.558 5.999 21.294 1.00 0.00 N +ATOM 651 C4 DT B 14 -1.306 4.785 20.705 1.00 0.00 C +ATOM 652 O4 DT B 14 -1.257 3.777 21.393 1.00 0.00 O +ATOM 653 C5 DT B 14 -1.134 4.822 19.274 1.00 0.00 C +ATOM 654 C7 DT B 14 -0.793 3.554 18.555 1.00 0.00 C +ATOM 655 C6 DT B 14 -1.289 6.004 18.650 1.00 0.00 C +ATOM 656 P DT B 15 -0.725 12.189 16.780 1.00 0.00 P +ATOM 657 OP1 DT B 15 -1.366 13.512 16.581 1.00 0.00 O +ATOM 658 OP2 DT B 15 0.236 11.679 15.770 1.00 0.00 O +ATOM 659 O5' DT B 15 -0.011 12.208 18.204 1.00 0.00 O +ATOM 660 C5' DT B 15 -0.766 12.517 19.362 1.00 0.00 C +ATOM 661 C4' DT B 15 0.029 12.250 20.618 1.00 0.00 C +ATOM 662 O4' DT B 15 0.024 10.847 20.979 1.00 0.00 O +ATOM 663 C3' DT B 15 1.490 12.705 20.639 1.00 0.00 C +ATOM 664 O3' DT B 15 1.678 13.512 21.802 1.00 0.00 O +ATOM 665 C2' DT B 15 2.270 11.401 20.765 1.00 0.00 C +ATOM 666 C1' DT B 15 1.286 10.537 21.536 1.00 0.00 C +ATOM 667 N1 DT B 15 1.458 9.060 21.517 1.00 0.00 N +ATOM 668 C2 DT B 15 1.364 8.409 22.734 1.00 0.00 C +ATOM 669 O2 DT B 15 1.195 8.992 23.790 1.00 0.00 O +ATOM 670 N3 DT B 15 1.481 7.044 22.671 1.00 0.00 N +ATOM 671 C4 DT B 15 1.691 6.275 21.544 1.00 0.00 C +ATOM 672 O4 DT B 15 1.760 5.055 21.649 1.00 0.00 O +ATOM 673 C5 DT B 15 1.811 7.017 20.300 1.00 0.00 C +ATOM 674 C7 DT B 15 2.069 6.265 19.031 1.00 0.00 C +ATOM 675 C6 DT B 15 1.686 8.354 20.347 1.00 0.00 C +ATOM 676 P DC B 16 2.846 14.608 21.847 1.00 0.00 P +ATOM 677 OP1 DC B 16 2.259 15.928 22.192 1.00 0.00 O +ATOM 678 OP2 DC B 16 3.742 14.475 20.662 1.00 0.00 O +ATOM 679 O5' DC B 16 3.694 14.128 23.085 1.00 0.00 O +ATOM 680 C5' DC B 16 4.153 12.811 23.124 1.00 0.00 C +ATOM 681 C4' DC B 16 4.366 12.395 24.552 1.00 0.00 C +ATOM 682 O4' DC B 16 3.941 11.024 24.639 1.00 0.00 O +ATOM 683 C3' DC B 16 5.835 12.424 24.942 1.00 0.00 C +ATOM 684 O3' DC B 16 5.990 12.882 26.286 1.00 0.00 O +ATOM 685 C2' DC B 16 6.288 10.992 24.741 1.00 0.00 C +ATOM 686 C1' DC B 16 5.023 10.184 24.968 1.00 0.00 C +ATOM 687 N1 DC B 16 4.916 8.977 24.134 1.00 0.00 N +ATOM 688 C2 DC B 16 4.779 7.746 24.769 1.00 0.00 C +ATOM 689 O2 DC B 16 4.671 7.719 26.008 1.00 0.00 O +ATOM 690 N3 DC B 16 4.759 6.617 24.027 1.00 0.00 N +ATOM 691 C4 DC B 16 4.848 6.688 22.696 1.00 0.00 C +ATOM 692 N4 DC B 16 4.842 5.546 22.012 1.00 0.00 N +ATOM 693 C5 DC B 16 4.949 7.933 22.013 1.00 0.00 C +ATOM 694 C6 DC B 16 4.975 9.047 22.764 1.00 0.00 C +ATOM 695 P DC B 17 7.458 13.230 26.845 1.00 0.00 P +ATOM 696 OP1 DC B 17 7.322 14.261 27.894 1.00 0.00 O +ATOM 697 OP2 DC B 17 8.393 13.457 25.712 1.00 0.00 O +ATOM 698 O5' DC B 17 7.925 11.870 27.513 1.00 0.00 O +ATOM 699 C5' DC B 17 6.986 10.967 28.080 1.00 0.00 C +ATOM 700 C4' DC B 17 7.703 9.812 28.733 1.00 0.00 C +ATOM 701 O4' DC B 17 7.405 8.604 27.996 1.00 0.00 O +ATOM 702 C3' DC B 17 9.228 9.932 28.780 1.00 0.00 C +ATOM 703 O3' DC B 17 9.708 9.565 30.071 1.00 0.00 O +ATOM 704 C2' DC B 17 9.717 8.960 27.719 1.00 0.00 C +ATOM 705 C1' DC B 17 8.596 7.933 27.619 1.00 0.00 C +ATOM 706 N1 DC B 17 8.397 7.391 26.256 1.00 0.00 N +ATOM 707 C2 DC B 17 8.285 6.003 26.089 1.00 0.00 C +ATOM 708 O2 DC B 17 8.296 5.273 27.090 1.00 0.00 O +ATOM 709 N3 DC B 17 8.164 5.492 24.838 1.00 0.00 N +ATOM 710 C4 DC B 17 8.142 6.310 23.782 1.00 0.00 C +ATOM 711 N4 DC B 17 8.051 5.758 22.567 1.00 0.00 N +ATOM 712 C5 DC B 17 8.219 7.727 23.925 1.00 0.00 C +ATOM 713 C6 DC B 17 8.343 8.220 25.168 1.00 0.00 C +ATOM 714 P DG B 18 11.166 10.040 30.548 1.00 0.00 P +ATOM 715 OP1 DG B 18 11.034 10.651 31.899 1.00 0.00 O +ATOM 716 OP2 DG B 18 11.806 10.821 29.449 1.00 0.00 O +ATOM 717 O5' DG B 18 11.922 8.656 30.729 1.00 0.00 O +ATOM 718 C5' DG B 18 11.366 7.651 31.566 1.00 0.00 C +ATOM 719 C4' DG B 18 11.906 6.297 31.181 1.00 0.00 C +ATOM 720 O4' DG B 18 11.524 5.980 29.820 1.00 0.00 O +ATOM 721 C3' DG B 18 13.431 6.181 31.221 1.00 0.00 C +ATOM 722 O3' DG B 18 13.757 4.851 31.639 1.00 0.00 O +ATOM 723 C2' DG B 18 13.815 6.355 29.759 1.00 0.00 C +ATOM 724 C1' DG B 18 12.682 5.594 29.109 1.00 0.00 C +ATOM 725 N9 DG B 18 12.444 5.808 27.686 1.00 0.00 N +ATOM 726 C8 DG B 18 12.673 6.938 26.939 1.00 0.00 C +ATOM 727 N7 DG B 18 12.337 6.794 25.684 1.00 0.00 N +ATOM 728 C5 DG B 18 11.860 5.493 25.602 1.00 0.00 C +ATOM 729 C6 DG B 18 11.338 4.759 24.493 1.00 0.00 C +ATOM 730 O6 DG B 18 11.174 5.136 23.325 1.00 0.00 O +ATOM 731 N1 DG B 18 10.979 3.465 24.858 1.00 0.00 N +ATOM 732 C2 DG B 18 11.095 2.943 26.125 1.00 0.00 C +ATOM 733 N2 DG B 18 10.697 1.673 26.295 1.00 0.00 N +ATOM 734 N3 DG B 18 11.566 3.616 27.157 1.00 0.00 N +ATOM 735 C4 DG B 18 11.926 4.872 26.827 1.00 0.00 C +ATOM 736 P DG B 19 14.934 4.598 32.701 1.00 0.00 P +ATOM 737 OP1 DG B 19 14.272 4.275 33.993 1.00 0.00 O +ATOM 738 OP2 DG B 19 15.897 5.721 32.631 1.00 0.00 O +ATOM 739 O5' DG B 19 15.618 3.277 32.137 1.00 0.00 O +ATOM 740 C5' DG B 19 14.880 2.066 32.087 1.00 0.00 C +ATOM 741 C4' DG B 19 15.215 1.267 30.847 1.00 0.00 C +ATOM 742 O4' DG B 19 14.518 1.761 29.665 1.00 0.00 O +ATOM 743 C3' DG B 19 16.697 1.151 30.479 1.00 0.00 C +ATOM 744 O3' DG B 19 17.074 -0.224 30.370 1.00 0.00 O +ATOM 745 C2' DG B 19 16.768 1.791 29.109 1.00 0.00 C +ATOM 746 C1' DG B 19 15.369 1.542 28.553 1.00 0.00 C +ATOM 747 N9 DG B 19 15.053 2.496 27.493 1.00 0.00 N +ATOM 748 C8 DG B 19 15.207 3.853 27.554 1.00 0.00 C +ATOM 749 N7 DG B 19 15.039 4.442 26.406 1.00 0.00 N +ATOM 750 C5 DG B 19 14.704 3.416 25.535 1.00 0.00 C +ATOM 751 C6 DG B 19 14.429 3.451 24.138 1.00 0.00 C +ATOM 752 O6 DG B 19 14.446 4.427 23.375 1.00 0.00 O +ATOM 753 N1 DG B 19 14.123 2.186 23.645 1.00 0.00 N +ATOM 754 C2 DG B 19 14.091 1.037 24.394 1.00 0.00 C +ATOM 755 N2 DG B 19 13.773 -0.085 23.737 1.00 0.00 N +ATOM 756 N3 DG B 19 14.352 0.990 25.697 1.00 0.00 N +ATOM 757 C4 DG B 19 14.656 2.211 26.198 1.00 0.00 C +ATOM 758 P DT B 20 18.558 -0.628 29.880 1.00 0.00 P +ATOM 759 OP1 DT B 20 19.093 -1.612 30.860 1.00 0.00 O +ATOM 760 OP2 DT B 20 19.359 0.577 29.549 1.00 0.00 O +ATOM 761 O5' DT B 20 18.278 -1.397 28.509 1.00 0.00 O +ATOM 762 C5' DT B 20 17.371 -2.500 28.462 1.00 0.00 C +ATOM 763 C4' DT B 20 17.458 -3.202 27.125 1.00 0.00 C +ATOM 764 O4' DT B 20 16.921 -2.338 26.091 1.00 0.00 O +ATOM 765 C3' DT B 20 18.870 -3.588 26.675 1.00 0.00 C +ATOM 766 O3' DT B 20 18.878 -4.760 25.881 1.00 0.00 O +ATOM 767 C2' DT B 20 19.255 -2.469 25.727 1.00 0.00 C +ATOM 768 C1' DT B 20 17.917 -2.075 25.104 1.00 0.00 C +ATOM 769 N1 DT B 20 17.828 -0.639 24.740 1.00 0.00 N +ATOM 770 C2 DT B 20 17.473 -0.302 23.449 1.00 0.00 C +ATOM 771 O2 DT B 20 17.233 -1.129 22.581 1.00 0.00 O +ATOM 772 N3 DT B 20 17.413 1.050 23.213 1.00 0.00 N +ATOM 773 C4 DT B 20 17.677 2.071 24.108 1.00 0.00 C +ATOM 774 O4 DT B 20 17.588 3.243 23.750 1.00 0.00 O +ATOM 775 C5 DT B 20 18.053 1.644 25.435 1.00 0.00 C +ATOM 776 C7 DT B 20 18.376 2.676 26.470 1.00 0.00 C +ATOM 777 C6 DT B 20 18.102 0.333 25.680 1.00 0.00 C +TER 778 DT B 20 +HETATM 779 ZN ZN B 2 12.870 8.232 24.146 1.00 0.00 ZN +HETATM 780 ZN ZN C 94 -8.319 -18.103 2.886 1.00 0.00 ZN +END diff --git a/outputs/parse_atoms_with_zero_occupancy/seqs/1BC8.fa b/outputs/parse_atoms_with_zero_occupancy/seqs/1BC8.fa new file mode 100644 index 0000000..3c16415 --- /dev/null +++ b/outputs/parse_atoms_with_zero_occupancy/seqs/1BC8.fa @@ -0,0 +1,4 @@ +>1BC8, T=0.1, seed=111, num_res=93, num_ligand_res=41, use_ligand_context=True, ligand_cutoff_distance=8.0, batch_size=1, number_of_batches=1, model_path=./model_params/ligandmpnn_v_32_010_25.pt +MDSAITLWQFLLQLLQKPQNKHMICWTSNDGQFKLLQAEEVARLWGIRKNKPNMNYDKLSRALRYYYVKNIIKKVNGQKFVYKFVSYPEILNM +>1BC8, id=1, T=0.1, seed=111, overall_confidence=0.4784, ligand_confidence=0.5487, seq_rec=0.4839 +MKSPISLHEFLLELLSDPKYADIIEWVSDNGEFRLVDPERVAKLWGEVKGKPKMNWKNLHRALRGYKKKKIIETVKGKPYQYRFVNYPELLHP \ No newline at end of file diff --git a/run.py b/run.py index a26ccdc..c89c052 100644 --- a/run.py +++ b/run.py @@ -159,9 +159,9 @@ def main(args) -> None: protein_dict, backbone, other_atoms, icodes, _ = parse_PDB( pdb, device=device, - atom_context_num=atom_context_num, chains=args.parse_these_chains_only, parse_all_atoms=args.ligand_mpnn_use_side_chain_context, + parse_atoms_with_zero_occupancy=args.parse_atoms_with_zero_occupancy ) # make chain_letter + residue_idx + insertion_code mapping to integers R_idx_list = list(protein_dict["R_idx"].cpu().numpy()) # residue indices @@ -790,5 +790,12 @@ def main(args) -> None: help="Provide global label for global_label_membrane_mpnn model. 1 - transmembrane, 0 - soluble", ) + argparser.add_argument( + "--parse_atoms_with_zero_occupancy", + type=int, + default=0, + help="To parse atoms with zero occupancy in the PDB input files. 0 - do not parse, 1 - parse atoms with zero occupancy", + ) + args = argparser.parse_args() main(args)