PFRMAT TS TARGET T0214 AUTHOR 4204-4258-2837 METHOD The SAM-T04 human predictions for CASP6 use a very similar method to METHOD the SAM-T02 method in CASP5. METHOD METHOD We start with a fully automated method: METHOD METHOD Use the SAM-T2K and SAM-T04 methods for finding homologs of the METHOD target and aligning them. METHOD METHOD Make local structure predictions using neural nets and the METHOD multiple alignments. Different neural nets are used for the METHOD SAM-T2K alignments and the SAM-T04 alignments. METHOD We currently use 7 local-structure alphabets: METHOD DSSP METHOD STRIDE METHOD STR2 an extended version of DSSP that splits the beta strands METHOD into multiple classes (parallel/antiparallel/mixed, METHOD edge/center) METHOD ALPHA an discretization of the alpha torsion angle: METHOD CA(i-i), CA(i), CA(i+1), CA(i+2) METHOD BYS a discretization of Ramachandran plots, due to Bystroff METHOD CB_burial_14_7 a 7-state discretization of the number of C_beta METHOD atoms in a 14 Angstrom radius sphere around the C_beta. METHOD DSSP_EHL2 CASP's collapse of the DSSP alphabet METHOD DSSP_EHL2 is not predicted directly by a METHOD neural net, but is computed as a weighted METHOD average of the other backbone alphabet predictions. METHOD METHOD We make 2-track HMMs with each alphabet (1.0 amino acid + 0.3 local structure) METHOD and use them to score a template library of 6400 (t04) or 9900 (t2k) templates METHOD We also used a single-track HMM to score not just the template METHOD library, but a non-redundant copy of the entire PDB. METHOD METHOD We also made a few 3-track HMMs (AA, str2, CB_burial_14_7) for METHOD finding and aligning more remote homologs. METHOD METHOD One-track HMMs built from the template library multiple alignments METHOD were used to score the target sequence (for early targets, only METHOD t2k template library was searched this way). METHOD METHOD All the logs of e-values were combined in a weighted average (with METHOD rather arbitrary weights, since we did not have time to METHOD optimize them), and the best templates ranked. Ranking was METHOD separate for predictions from the t2k and t04 multiple alignments. METHOD METHOD Alignments of the target to the top templates were made using METHOD several different alignment methods (mainly using the SAM hmmscore METHOD program, but a few alignments were made with Bob Edgar's MUSCLE METHOD profile-profile aligner). METHOD METHOD Generate fragments (short 9-residue alignments for each position) METHOD using SAM's "fragfinder" program and the 3-track HMM. METHOD METHOD Then the "undertaker" program (named because it optimizes burial) METHOD is used to try to combine the alignments and the fragments into METHOD a consistent 3D model. No single alignment or parent template METHOD was used, though in many cases one had much more influence than METHOD the others. The alignment scores were not passed to undertaker, METHOD but were used only to pick the set of alignments and fragments METHOD that undertaker would see. METHOD METHOD After the initial automatic run was finished, the results were METHOD examined by hand, and various tweaks were made to the undertaker METHOD cost function to improve the models. Many of the tweaks consisted of METHOD adding specific Hbonds, SSbonds, or distance constraints, to make the METHOD model look better to us. METHOD METHOD Undertaker uses a genetic algorithm with about 28 different operators METHOD to minimize its cost function. The cost function has many components, METHOD including various definitions of burial and compactness, sidechain METHOD rotamer preferences, steric clashes, chain breaks, predicted local METHOD backbone conformation, hydrogen bonding, disulfide bonds, and user METHOD specified constraints. The relative weights of these components were METHOD tweaked for each target, as we have not found a generally applicable METHOD set of weights. METHOD METHOD Because undertaker does not (yet) handle multimers, we sometimes added METHOD "scaffolding" constraints by hand to try to retain structure in METHOD dimerization interfaces. METHOD METHOD For multiple-domain models, we generally broke the sequence into METHOD chunks (often somewhat arbitrary overlapping chunks), and did the full METHOD method for each subchain. The alignments found were all tossed into METHOD the undertaker conformation search. In some cases, we performed METHOD undertaker runs for the subchains, and cut-and-pasted the pieces into METHOD one PDB file (with bad breaks) and let undertaker try to assemble the METHOD pieces. METHOD METHOD This model was created by sidechain replacement on the backbone of our METHOD top-scoring target (1jnyA). Sidechains were optimized by SCWRL. METHOD METHOD The alignment was created by a 3-track HMM: METHOD T0214-1jnyA-t2k-local-str2+CB_burial_14_7-0.4+0.4-adpstyle5 METHOD REMARK 6 REMARK 6 T0214 model 5 Thu Aug 12 17:37:26 2004 MODEL 5 PARENT 1jny_A ATOM 2 N LEU 17 -14.275 -1.137 12.637 1.00 0.00 ATOM 3 CA LEU 17 -15.630 -1.608 12.917 1.00 0.00 ATOM 4 CB LEU 17 -15.925 -1.529 14.416 1.00 0.00 ATOM 5 CG LEU 17 -17.283 -2.070 14.870 1.00 0.00 ATOM 6 CD1 LEU 17 -17.368 -3.571 14.637 1.00 0.00 ATOM 7 CD2 LEU 17 -17.498 -1.807 16.353 1.00 0.00 ATOM 8 O LEU 17 -16.584 0.502 12.229 1.00 0.00 ATOM 9 C LEU 17 -16.644 -0.736 12.165 1.00 0.00 ATOM 10 N ARG 18 -17.527 -1.383 11.410 1.00 0.00 ATOM 11 CA ARG 18 -18.519 -0.651 10.643 1.00 0.00 ATOM 12 CB ARG 18 -18.915 0.635 11.370 1.00 0.00 ATOM 13 CG ARG 18 -19.677 0.406 12.666 1.00 0.00 ATOM 14 CD ARG 18 -20.017 1.722 13.347 1.00 0.00 ATOM 15 NE ARG 18 -20.738 1.518 14.602 1.00 0.00 ATOM 16 CZ ARG 18 -21.071 2.496 15.439 1.00 0.00 ATOM 17 NH1 ARG 18 -21.726 2.216 16.557 1.00 0.00 ATOM 18 NH2 ARG 18 -20.744 3.750 15.157 1.00 0.00 ATOM 19 O ARG 18 -18.857 -0.055 8.354 1.00 0.00 ATOM 20 C ARG 18 -18.039 -0.243 9.258 1.00 0.00 ATOM 21 N LYS 19 -16.724 -0.093 9.088 1.00 0.00 ATOM 22 CA LYS 19 -16.139 0.291 7.800 1.00 0.00 ATOM 23 CB LYS 19 -14.912 1.178 8.013 1.00 0.00 ATOM 24 CG LYS 19 -15.214 2.505 8.690 1.00 0.00 ATOM 25 CD LYS 19 -13.970 3.372 8.788 1.00 0.00 ATOM 26 CE LYS 19 -14.253 4.662 9.539 1.00 0.00 ATOM 27 NZ LYS 19 -13.022 5.481 9.723 1.00 0.00 ATOM 28 O LYS 19 -16.125 -1.138 5.869 1.00 0.00 ATOM 29 C LYS 19 -15.707 -0.943 7.011 1.00 0.00 ATOM 30 N LYS 20 -14.865 -1.767 7.625 1.00 0.00 ATOM 31 CA LYS 20 -14.380 -2.967 6.966 1.00 0.00 ATOM 32 CB LYS 20 -14.947 -3.067 5.548 1.00 0.00 ATOM 33 CG LYS 20 -16.448 -3.297 5.495 1.00 0.00 ATOM 34 CD LYS 20 -16.940 -3.401 4.061 1.00 0.00 ATOM 35 CE LYS 20 -18.444 -3.615 4.008 1.00 0.00 ATOM 36 NZ LYS 20 -18.942 -3.708 2.608 1.00 0.00 ATOM 37 O LYS 20 -12.146 -2.458 7.710 1.00 0.00 ATOM 38 C LYS 20 -12.863 -2.996 6.851 1.00 0.00 ATOM 39 N LYS 21 -12.378 -3.654 5.798 1.00 0.00 ATOM 40 CA LYS 21 -10.949 -3.790 5.515 1.00 0.00 ATOM 41 CB LYS 21 -10.708 -4.909 4.499 1.00 0.00 ATOM 42 CG LYS 21 -9.241 -5.184 4.216 1.00 0.00 ATOM 43 CD LYS 21 -9.073 -6.338 3.243 1.00 0.00 ATOM 44 CE LYS 21 -7.605 -6.609 2.954 1.00 0.00 ATOM 45 NZ LYS 21 -7.427 -7.724 1.984 1.00 0.00 ATOM 46 O LYS 21 -10.779 -2.016 3.887 1.00 0.00 ATOM 47 C LYS 21 -10.351 -2.500 4.937 1.00 0.00 ATOM 48 N ILE 22 -9.366 -1.940 5.625 1.00 0.00 ATOM 49 CA ILE 22 -8.748 -0.720 5.145 1.00 0.00 ATOM 50 CB ILE 22 -9.200 0.502 5.966 1.00 0.00 ATOM 51 CG1 ILE 22 -10.726 0.613 5.963 1.00 0.00 ATOM 52 CG2 ILE 22 -8.622 1.781 5.379 1.00 0.00 ATOM 53 CD1 ILE 22 -11.260 1.730 6.832 1.00 0.00 ATOM 54 O ILE 22 -6.619 -0.467 6.245 1.00 0.00 ATOM 55 C ILE 22 -7.222 -0.701 5.196 1.00 0.00 ATOM 56 N GLU 23 -6.580 -1.076 4.079 1.00 0.00 ATOM 57 CA GLU 23 -5.122 -1.079 4.016 1.00 0.00 ATOM 58 CB GLU 23 -4.639 -1.880 2.807 1.00 0.00 ATOM 59 CG GLU 23 -4.899 -3.375 2.907 1.00 0.00 ATOM 60 CD GLU 23 -4.407 -4.135 1.693 1.00 0.00 ATOM 61 OE1 GLU 23 -3.896 -3.488 0.753 1.00 0.00 ATOM 62 OE2 GLU 23 -4.529 -5.378 1.679 1.00 0.00 ATOM 63 O GLU 23 -5.361 1.247 3.447 1.00 0.00 ATOM 64 C GLU 23 -4.629 0.359 3.896 1.00 0.00 ATOM 65 N GLY 24 -3.399 0.589 4.337 1.00 0.00 ATOM 66 CA GLY 24 -2.776 1.911 4.282 1.00 0.00 ATOM 67 O GLY 24 -0.696 0.805 3.803 1.00 0.00 ATOM 68 C GLY 24 -1.422 1.774 3.584 1.00 0.00 ATOM 69 N ARG 25 -1.114 2.718 2.709 1.00 0.00 ATOM 70 CA ARG 25 0.144 2.684 1.990 1.00 0.00 ATOM 71 CB ARG 25 0.199 1.468 1.065 1.00 0.00 ATOM 72 CG ARG 25 -0.854 1.473 -0.032 1.00 0.00 ATOM 73 CD ARG 25 -0.722 0.253 -0.929 1.00 0.00 ATOM 74 NE ARG 25 -1.806 0.174 -1.907 1.00 0.00 ATOM 75 CZ ARG 25 -1.793 0.788 -3.086 1.00 0.00 ATOM 76 NH1 ARG 25 -2.822 0.660 -3.912 1.00 0.00 ATOM 77 NH2 ARG 25 -0.750 1.528 -3.437 1.00 0.00 ATOM 78 O ARG 25 -0.611 4.734 1.012 1.00 0.00 ATOM 79 C ARG 25 0.313 3.931 1.149 1.00 0.00 ATOM 80 N LEU 26 1.488 4.099 0.572 1.00 0.00 ATOM 81 CA LEU 26 1.742 5.263 -0.241 1.00 0.00 ATOM 82 CB LEU 26 3.108 5.865 0.096 1.00 0.00 ATOM 83 CG LEU 26 3.300 6.350 1.534 1.00 0.00 ATOM 84 CD1 LEU 26 4.720 6.850 1.747 1.00 0.00 ATOM 85 CD2 LEU 26 2.341 7.488 1.849 1.00 0.00 ATOM 86 O LEU 26 2.345 3.882 -2.093 1.00 0.00 ATOM 87 C LEU 26 1.723 4.872 -1.701 1.00 0.00 ATOM 88 N TYR 27 0.969 5.620 -2.498 1.00 0.00 ATOM 89 CA TYR 27 0.900 5.368 -3.932 1.00 0.00 ATOM 90 CB TYR 27 -0.175 6.244 -4.579 1.00 0.00 ATOM 91 CG TYR 27 -1.587 5.874 -4.183 1.00 0.00 ATOM 92 CD1 TYR 27 -2.262 6.592 -3.206 1.00 0.00 ATOM 93 CD2 TYR 27 -2.239 4.808 -4.790 1.00 0.00 ATOM 94 CE1 TYR 27 -3.553 6.262 -2.837 1.00 0.00 ATOM 95 CE2 TYR 27 -3.529 4.463 -4.435 1.00 0.00 ATOM 96 CZ TYR 27 -4.184 5.201 -3.450 1.00 0.00 ATOM 97 OH TYR 27 -5.470 4.869 -3.086 1.00 0.00 ATOM 98 O TYR 27 2.782 6.821 -4.242 1.00 0.00 ATOM 99 C TYR 27 2.275 5.712 -4.463 1.00 0.00 ATOM 100 N ASP 28 2.896 4.740 -5.118 1.00 0.00 ATOM 101 CA ASP 28 4.224 4.935 -5.668 1.00 0.00 ATOM 102 CB ASP 28 5.069 3.670 -5.490 1.00 0.00 ATOM 103 CG ASP 28 5.307 3.329 -4.033 1.00 0.00 ATOM 104 OD1 ASP 28 5.811 4.200 -3.294 1.00 0.00 ATOM 105 OD2 ASP 28 4.989 2.191 -3.629 1.00 0.00 ATOM 106 O ASP 28 5.046 6.010 -7.677 1.00 0.00 ATOM 107 C ASP 28 4.195 5.261 -7.171 1.00 0.00 ATOM 111 N ARG 31 3.196 4.733 -7.871 1.00 0.00 ATOM 112 CA ARG 31 3.030 4.982 -9.302 1.00 0.00 ATOM 113 CB ARG 31 3.855 3.983 -10.117 1.00 0.00 ATOM 114 CG ARG 31 3.419 2.537 -9.950 1.00 0.00 ATOM 115 CD ARG 31 4.303 1.597 -10.754 1.00 0.00 ATOM 116 NE ARG 31 3.852 0.210 -10.664 1.00 0.00 ATOM 117 CZ ARG 31 4.470 -0.815 -11.240 1.00 0.00 ATOM 118 NH1 ARG 31 3.987 -2.042 -11.105 1.00 0.00 ATOM 119 NH2 ARG 31 5.571 -0.610 -11.953 1.00 0.00 ATOM 120 O ARG 31 0.805 4.230 -8.867 1.00 0.00 ATOM 121 C ARG 31 1.554 4.826 -9.636 1.00 0.00 ATOM 122 N ARG 32 1.136 5.367 -10.773 1.00 0.00 ATOM 123 CA ARG 32 -0.253 5.262 -11.167 1.00 0.00 ATOM 124 CB ARG 32 -0.762 3.834 -10.959 1.00 0.00 ATOM 125 CG ARG 32 -0.113 2.805 -11.869 1.00 0.00 ATOM 126 CD ARG 32 -0.655 1.410 -11.599 1.00 0.00 ATOM 127 NE ARG 32 -0.020 0.403 -12.448 1.00 0.00 ATOM 128 CZ ARG 32 -0.259 -0.901 -12.364 1.00 0.00 ATOM 129 NH1 ARG 32 0.365 -1.742 -13.178 1.00 0.00 ATOM 130 NH2 ARG 32 -1.121 -1.362 -11.467 1.00 0.00 ATOM 131 O ARG 32 -0.742 7.112 -9.705 1.00 0.00 ATOM 132 C ARG 32 -1.179 6.174 -10.386 1.00 0.00 ATOM 133 N GLN 33 -2.473 5.902 -10.509 1.00 0.00 ATOM 134 CA GLN 33 -3.516 6.671 -9.849 1.00 0.00 ATOM 135 CB GLN 33 -4.140 7.673 -10.821 1.00 0.00 ATOM 136 CG GLN 33 -5.189 8.577 -10.195 1.00 0.00 ATOM 137 CD GLN 33 -5.739 9.597 -11.171 1.00 0.00 ATOM 138 OE1 GLN 33 -5.291 9.678 -12.315 1.00 0.00 ATOM 139 NE2 GLN 33 -6.714 10.379 -10.723 1.00 0.00 ATOM 140 O GLN 33 -4.958 4.742 -10.065 1.00 0.00 ATOM 141 C GLN 33 -4.581 5.692 -9.360 1.00 0.00 ATOM 142 N ILE 34 -5.015 5.887 -8.126 1.00 0.00 ATOM 143 CA ILE 34 -6.040 5.053 -7.549 1.00 0.00 ATOM 144 CB ILE 34 -5.650 4.570 -6.141 1.00 0.00 ATOM 145 CG1 ILE 34 -4.310 3.831 -6.182 1.00 0.00 ATOM 146 CG2 ILE 34 -6.705 3.625 -5.590 1.00 0.00 ATOM 147 CD1 ILE 34 -4.319 2.602 -7.064 1.00 0.00 ATOM 148 O ILE 34 -7.178 7.103 -7.099 1.00 0.00 ATOM 149 C ILE 34 -7.273 5.940 -7.498 1.00 0.00 ATOM 150 N LYS 35 -8.423 5.391 -7.874 1.00 0.00 ATOM 151 CA LYS 35 -9.668 6.149 -7.871 1.00 0.00 ATOM 152 CB LYS 35 -10.086 6.498 -9.301 1.00 0.00 ATOM 153 CG LYS 35 -9.136 7.447 -10.012 1.00 0.00 ATOM 154 CD LYS 35 -9.633 7.785 -11.408 1.00 0.00 ATOM 155 CE LYS 35 -8.648 8.677 -12.145 1.00 0.00 ATOM 156 NZ LYS 35 -9.122 9.014 -13.515 1.00 0.00 ATOM 157 O LYS 35 -10.842 4.114 -7.355 1.00 0.00 ATOM 158 C LYS 35 -10.790 5.340 -7.226 1.00 0.00 ATOM 159 N PRO 36 -11.675 6.023 -6.505 1.00 0.00 ATOM 160 CA PRO 36 -12.797 5.355 -5.856 1.00 0.00 ATOM 161 CB PRO 36 -13.583 6.497 -5.210 1.00 0.00 ATOM 162 CG PRO 36 -12.573 7.574 -4.999 1.00 0.00 ATOM 163 CD PRO 36 -11.649 7.516 -6.184 1.00 0.00 ATOM 164 O PRO 36 -13.867 5.187 -8.002 1.00 0.00 ATOM 165 C PRO 36 -13.587 4.627 -6.933 1.00 0.00 ATOM 166 N GLY 37 -13.881 3.364 -6.663 1.00 0.00 ATOM 167 CA GLY 37 -14.622 2.545 -7.602 1.00 0.00 ATOM 168 O GLY 37 -14.206 0.583 -8.914 1.00 0.00 ATOM 169 C GLY 37 -13.727 1.581 -8.363 1.00 0.00 ATOM 170 N ASP 38 -12.426 1.861 -8.377 1.00 0.00 ATOM 171 CA ASP 38 -11.468 1.017 -9.077 1.00 0.00 ATOM 172 CB ASP 38 -10.049 1.567 -8.913 1.00 0.00 ATOM 173 CG ASP 38 -9.814 2.824 -9.727 1.00 0.00 ATOM 174 OD1 ASP 38 -10.683 3.165 -10.559 1.00 0.00 ATOM 175 OD2 ASP 38 -8.762 3.468 -9.535 1.00 0.00 ATOM 176 O ASP 38 -11.757 -0.659 -7.394 1.00 0.00 ATOM 177 C ASP 38 -11.462 -0.394 -8.565 1.00 0.00 ATOM 178 N VAL 39 -11.109 -1.305 -9.454 1.00 0.00 ATOM 179 CA VAL 39 -10.953 -2.683 -9.064 1.00 0.00 ATOM 180 CB VAL 39 -11.429 -3.640 -10.171 1.00 0.00 ATOM 181 CG1 VAL 39 -11.183 -5.086 -9.767 1.00 0.00 ATOM 182 CG2 VAL 39 -12.917 -3.460 -10.428 1.00 0.00 ATOM 183 O VAL 39 -8.699 -2.025 -9.561 1.00 0.00 ATOM 184 C VAL 39 -9.447 -2.711 -8.843 1.00 0.00 ATOM 185 N ILE 40 -9.013 -3.422 -7.810 1.00 0.00 ATOM 186 CA ILE 40 -7.583 -3.538 -7.494 1.00 0.00 ATOM 187 CB ILE 40 -7.189 -2.625 -6.318 1.00 0.00 ATOM 188 CG1 ILE 40 -7.986 -2.997 -5.064 1.00 0.00 ATOM 189 CG2 ILE 40 -7.473 -1.170 -6.654 1.00 0.00 ATOM 190 CD1 ILE 40 -7.519 -2.289 -3.813 1.00 0.00 ATOM 191 O ILE 40 -8.092 -5.727 -6.673 1.00 0.00 ATOM 192 C ILE 40 -7.229 -4.960 -7.112 1.00 0.00 ATOM 193 N SER 41 -5.965 -5.321 -7.301 1.00 0.00 ATOM 194 CA SER 41 -5.509 -6.656 -6.934 1.00 0.00 ATOM 195 CB SER 41 -4.993 -7.403 -8.167 1.00 0.00 ATOM 196 OG SER 41 -6.040 -7.642 -9.092 1.00 0.00 ATOM 197 O SER 41 -3.497 -5.686 -5.988 1.00 0.00 ATOM 198 C SER 41 -4.373 -6.565 -5.907 1.00 0.00 ATOM 199 N PHE 42 -4.458 -7.418 -4.893 1.00 0.00 ATOM 200 CA PHE 42 -3.461 -7.491 -3.829 1.00 0.00 ATOM 201 CB PHE 42 -4.138 -7.690 -2.471 1.00 0.00 ATOM 202 CG PHE 42 -3.179 -7.721 -1.315 1.00 0.00 ATOM 203 CD1 PHE 42 -2.612 -6.553 -0.836 1.00 0.00 ATOM 204 CD2 PHE 42 -2.845 -8.917 -0.706 1.00 0.00 ATOM 205 CE1 PHE 42 -1.731 -6.580 0.228 1.00 0.00 ATOM 206 CE2 PHE 42 -1.964 -8.945 0.358 1.00 0.00 ATOM 207 CZ PHE 42 -1.408 -7.785 0.826 1.00 0.00 ATOM 208 O PHE 42 -3.014 -9.789 -4.272 1.00 0.00 ATOM 209 C PHE 42 -2.544 -8.658 -4.110 1.00 0.00 ATOM 210 N GLU 43 -1.253 -8.376 -4.233 1.00 0.00 ATOM 211 CA GLU 43 -0.257 -9.411 -4.464 1.00 0.00 ATOM 212 CB GLU 43 0.602 -9.066 -5.682 1.00 0.00 ATOM 213 CG GLU 43 -0.162 -9.052 -6.997 1.00 0.00 ATOM 214 CD GLU 43 0.734 -8.787 -8.189 1.00 0.00 ATOM 215 OE1 GLU 43 1.946 -8.564 -7.983 1.00 0.00 ATOM 216 OE2 GLU 43 0.227 -8.804 -9.330 1.00 0.00 ATOM 217 O GLU 43 0.783 -8.469 -2.509 1.00 0.00 ATOM 218 C GLU 43 0.609 -9.479 -3.207 1.00 0.00 ATOM 219 N GLY 44 1.209 -10.650 -2.920 1.00 0.00 ATOM 220 CA GLY 44 1.177 -11.916 -3.671 1.00 0.00 ATOM 221 O GLY 44 -0.214 -13.719 -4.456 1.00 0.00 ATOM 222 C GLY 44 -0.124 -12.762 -3.679 1.00 0.00 ATOM 223 N GLY 45 -1.106 -12.419 -2.833 1.00 0.00 ATOM 224 CA GLY 45 -2.374 -13.167 -2.721 1.00 0.00 ATOM 225 O GLY 45 -3.807 -14.357 -4.224 1.00 0.00 ATOM 226 C GLY 45 -3.167 -13.328 -4.012 1.00 0.00 ATOM 227 N LYS 46 -3.139 -12.308 -4.859 1.00 0.00 ATOM 228 CA LYS 46 -3.865 -12.365 -6.114 1.00 0.00 ATOM 229 CB LYS 46 -3.615 -13.701 -6.817 1.00 0.00 ATOM 230 CG LYS 46 -2.156 -13.962 -7.152 1.00 0.00 ATOM 231 CD LYS 46 -1.995 -15.247 -7.950 1.00 0.00 ATOM 232 CE LYS 46 -0.528 -15.566 -8.189 1.00 0.00 ATOM 233 NZ LYS 46 -0.355 -16.806 -8.995 1.00 0.00 ATOM 234 O LYS 46 -6.160 -12.781 -6.657 1.00 0.00 ATOM 235 C LYS 46 -5.362 -12.224 -5.907 1.00 0.00 ATOM 236 N LEU 47 -5.748 -11.494 -4.868 1.00 0.00 ATOM 237 CA LEU 47 -7.158 -11.297 -4.583 1.00 0.00 ATOM 238 CB LEU 47 -7.412 -11.346 -3.076 1.00 0.00 ATOM 239 CG LEU 47 -7.056 -12.656 -2.370 1.00 0.00 ATOM 240 CD1 LEU 47 -7.286 -12.540 -0.872 1.00 0.00 ATOM 241 CD2 LEU 47 -7.912 -13.799 -2.895 1.00 0.00 ATOM 242 O LEU 47 -6.898 -8.949 -4.948 1.00 0.00 ATOM 243 C LEU 47 -7.600 -9.947 -5.111 1.00 0.00 ATOM 244 N LYS 48 -8.725 -9.939 -5.818 1.00 0.00 ATOM 245 CA LYS 48 -9.269 -8.716 -6.380 1.00 0.00 ATOM 246 CB LYS 48 -9.868 -8.982 -7.763 1.00 0.00 ATOM 247 CG LYS 48 -8.847 -9.383 -8.815 1.00 0.00 ATOM 248 CD LYS 48 -9.513 -9.671 -10.151 1.00 0.00 ATOM 249 CE LYS 48 -8.499 -10.119 -11.189 1.00 0.00 ATOM 250 NZ LYS 48 -9.141 -10.441 -12.493 1.00 0.00 ATOM 251 O LYS 48 -11.199 -8.873 -4.946 1.00 0.00 ATOM 252 C LYS 48 -10.371 -8.138 -5.491 1.00 0.00 ATOM 253 N VAL 49 -10.357 -6.819 -5.355 1.00 0.00 ATOM 254 CA VAL 49 -11.341 -6.127 -4.551 1.00 0.00 ATOM 255 CB VAL 49 -10.812 -5.844 -3.134 1.00 0.00 ATOM 256 CG1 VAL 49 -10.518 -7.147 -2.404 1.00 0.00 ATOM 257 CG2 VAL 49 -9.531 -5.027 -3.195 1.00 0.00 ATOM 258 O VAL 49 -11.157 -4.495 -6.300 1.00 0.00 ATOM 259 C VAL 49 -11.680 -4.807 -5.217 1.00 0.00 ATOM 260 N ARG 50 -12.566 -4.038 -4.591 1.00 0.00 ATOM 261 CA ARG 50 -12.970 -2.748 -5.132 1.00 0.00 ATOM 262 CB ARG 50 -14.440 -2.781 -5.555 1.00 0.00 ATOM 263 CG ARG 50 -14.729 -3.710 -6.723 1.00 0.00 ATOM 264 CD ARG 50 -16.203 -3.689 -7.093 1.00 0.00 ATOM 265 NE ARG 50 -16.507 -4.614 -8.182 1.00 0.00 ATOM 266 CZ ARG 50 -17.731 -4.850 -8.641 1.00 0.00 ATOM 267 NH1 ARG 50 -17.911 -5.709 -9.636 1.00 0.00 ATOM 268 NH2 ARG 50 -18.772 -4.228 -8.105 1.00 0.00 ATOM 269 O ARG 50 -13.166 -1.824 -2.927 1.00 0.00 ATOM 270 C ARG 50 -12.796 -1.654 -4.096 1.00 0.00 ATOM 271 N VAL 51 -12.270 -0.522 -4.548 1.00 0.00 ATOM 272 CA VAL 51 -12.031 0.628 -3.689 1.00 0.00 ATOM 273 CB VAL 51 -11.020 1.604 -4.321 1.00 0.00 ATOM 274 CG1 VAL 51 -10.840 2.829 -3.439 1.00 0.00 ATOM 275 CG2 VAL 51 -9.666 0.931 -4.492 1.00 0.00 ATOM 276 O VAL 51 -13.878 1.994 -4.349 1.00 0.00 ATOM 277 C VAL 51 -13.314 1.405 -3.431 1.00 0.00 ATOM 278 N LYS 52 -13.743 1.442 -2.175 1.00 0.00 ATOM 279 CA LYS 52 -14.956 2.163 -1.819 1.00 0.00 ATOM 280 CB LYS 52 -15.701 1.437 -0.698 1.00 0.00 ATOM 281 CG LYS 52 -16.254 0.079 -1.098 1.00 0.00 ATOM 282 CD LYS 52 -16.995 -0.576 0.056 1.00 0.00 ATOM 283 CE LYS 52 -17.475 -1.969 -0.317 1.00 0.00 ATOM 284 NZ LYS 52 -18.090 -2.675 0.841 1.00 0.00 ATOM 285 O LYS 52 -15.537 4.457 -1.495 1.00 0.00 ATOM 286 C LYS 52 -14.694 3.584 -1.330 1.00 0.00 ATOM 287 N ALA 53 -13.534 3.822 -0.732 1.00 0.00 ATOM 288 CA ALA 53 -13.195 5.148 -0.240 1.00 0.00 ATOM 289 CB ALA 53 -13.802 5.376 1.136 1.00 0.00 ATOM 290 O ALA 53 -10.970 4.285 -0.035 1.00 0.00 ATOM 291 C ALA 53 -11.685 5.280 -0.143 1.00 0.00 ATOM 292 N ILE 54 -11.217 6.519 -0.150 1.00 0.00 ATOM 293 CA ILE 54 -9.801 6.827 -0.074 1.00 0.00 ATOM 294 CB ILE 54 -9.219 7.160 -1.461 1.00 0.00 ATOM 295 CG1 ILE 54 -9.372 5.964 -2.403 1.00 0.00 ATOM 296 CG2 ILE 54 -7.741 7.502 -1.350 1.00 0.00 ATOM 297 CD1 ILE 54 -8.991 6.265 -3.837 1.00 0.00 ATOM 298 O ILE 54 -10.554 8.907 0.846 1.00 0.00 ATOM 299 C ILE 54 -9.679 8.033 0.852 1.00 0.00 ATOM 300 N ARG 55 -8.650 8.061 1.696 1.00 0.00 ATOM 301 CA ARG 55 -8.449 9.214 2.564 1.00 0.00 ATOM 302 CB ARG 55 -9.146 9.001 3.908 1.00 0.00 ATOM 303 CG ARG 55 -9.153 10.228 4.805 1.00 0.00 ATOM 304 CD ARG 55 -9.909 9.964 6.097 1.00 0.00 ATOM 305 NE ARG 55 -9.784 11.071 7.041 1.00 0.00 ATOM 306 CZ ARG 55 -10.550 11.229 8.115 1.00 0.00 ATOM 307 NH1 ARG 55 -10.365 12.267 8.917 1.00 0.00 ATOM 308 NH2 ARG 55 -11.502 10.345 8.385 1.00 0.00 ATOM 309 O ARG 55 -6.212 8.578 3.153 1.00 0.00 ATOM 310 C ARG 55 -6.979 9.490 2.863 1.00 0.00 ATOM 311 N VAL 56 -6.602 10.748 2.676 1.00 0.00 ATOM 312 CA VAL 56 -5.282 11.219 2.962 1.00 0.00 ATOM 313 CB VAL 56 -4.610 11.811 1.709 1.00 0.00 ATOM 314 CG1 VAL 56 -3.124 12.025 1.953 1.00 0.00 ATOM 315 CG2 VAL 56 -4.773 10.872 0.524 1.00 0.00 ATOM 316 O VAL 56 -6.354 13.152 3.837 1.00 0.00 ATOM 317 C VAL 56 -5.524 12.266 4.015 1.00 0.00 TER END