PFRMAT TS TARGET T0215 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 is the result of sidechain replacement on the backbone of METHOD our top-scoring template 1lqlA. Sidechains were optimized by SCWRL. METHOD METHOD The alignment was created with an amino-acid-only HMM: METHOD T0215-1lqlA-t2k-global-adpstyle5 METHOD REMARK 6 REMARK 6 T0215 model 5 Mon Aug 16 17:36:36 2004 MODEL 5 PARENT 1lql_A ATOM 2 N ARG 24 -25.658 -14.379 -27.765 1.00 0.00 ATOM 3 CA ARG 24 -25.242 -15.760 -27.585 1.00 0.00 ATOM 4 CB ARG 24 -24.990 -16.425 -28.939 1.00 0.00 ATOM 5 CG ARG 24 -26.251 -16.683 -29.748 1.00 0.00 ATOM 6 CD ARG 24 -25.924 -17.301 -31.098 1.00 0.00 ATOM 7 NE ARG 24 -27.122 -17.512 -31.908 1.00 0.00 ATOM 8 CZ ARG 24 -27.110 -17.986 -33.149 1.00 0.00 ATOM 9 NH1 ARG 24 -28.250 -18.144 -33.810 1.00 0.00 ATOM 10 NH2 ARG 24 -25.959 -18.301 -33.729 1.00 0.00 ATOM 11 O ARG 24 -23.882 -16.607 -25.810 1.00 0.00 ATOM 12 C ARG 24 -23.961 -15.844 -26.772 1.00 0.00 ATOM 13 N ASN 25 -22.955 -15.061 -27.153 1.00 0.00 ATOM 14 CA ASN 25 -21.690 -15.115 -26.442 1.00 0.00 ATOM 15 CB ASN 25 -20.540 -14.701 -27.363 1.00 0.00 ATOM 16 CG ASN 25 -19.182 -14.865 -26.708 1.00 0.00 ATOM 17 ND2 ASN 25 -18.152 -15.046 -27.525 1.00 0.00 ATOM 18 OD1 ASN 25 -19.064 -14.830 -25.483 1.00 0.00 ATOM 19 O ASN 25 -21.718 -12.987 -25.317 1.00 0.00 ATOM 20 C ASN 25 -21.595 -14.215 -25.228 1.00 0.00 ATOM 21 N LEU 26 -21.374 -14.859 -24.086 1.00 0.00 ATOM 22 CA LEU 26 -21.252 -14.179 -22.806 1.00 0.00 ATOM 23 CB LEU 26 -22.108 -14.874 -21.746 1.00 0.00 ATOM 24 CG LEU 26 -23.604 -14.990 -22.052 1.00 0.00 ATOM 25 CD1 LEU 26 -24.314 -15.783 -20.967 1.00 0.00 ATOM 26 CD2 LEU 26 -24.245 -13.613 -22.131 1.00 0.00 ATOM 27 O LEU 26 -19.017 -15.064 -22.753 1.00 0.00 ATOM 28 C LEU 26 -19.793 -14.196 -22.350 1.00 0.00 ATOM 29 N SER 27 -19.430 -13.233 -21.511 1.00 0.00 ATOM 30 CA SER 27 -18.074 -13.132 -20.996 1.00 0.00 ATOM 31 CB SER 27 -17.300 -12.041 -21.738 1.00 0.00 ATOM 32 OG SER 27 -15.979 -11.923 -21.238 1.00 0.00 ATOM 33 O SER 27 -18.880 -11.896 -19.113 1.00 0.00 ATOM 34 C SER 27 -18.130 -12.787 -19.520 1.00 0.00 ATOM 35 N ASP 28 -17.340 -13.491 -18.717 1.00 0.00 ATOM 36 CA ASP 28 -17.306 -13.215 -17.294 1.00 0.00 ATOM 37 CB ASP 28 -18.019 -14.322 -16.516 1.00 0.00 ATOM 38 CG ASP 28 -18.064 -14.051 -15.024 1.00 0.00 ATOM 39 OD1 ASP 28 -17.430 -13.070 -14.581 1.00 0.00 ATOM 40 OD2 ASP 28 -18.732 -14.818 -14.301 1.00 0.00 ATOM 41 O ASP 28 -15.185 -14.129 -16.641 1.00 0.00 ATOM 42 C ASP 28 -15.884 -13.125 -16.766 1.00 0.00 ATOM 43 N ARG 29 -15.486 -11.910 -16.417 1.00 0.00 ATOM 44 CA ARG 29 -14.154 -11.642 -15.917 1.00 0.00 ATOM 45 CB ARG 29 -13.397 -10.723 -16.877 1.00 0.00 ATOM 46 CG ARG 29 -13.062 -11.361 -18.214 1.00 0.00 ATOM 47 CD ARG 29 -12.294 -10.402 -19.108 1.00 0.00 ATOM 48 NE ARG 29 -12.066 -10.959 -20.440 1.00 0.00 ATOM 49 CZ ARG 29 -11.039 -11.740 -20.758 1.00 0.00 ATOM 50 NH1 ARG 29 -10.912 -12.200 -21.994 1.00 0.00 ATOM 51 NH2 ARG 29 -10.139 -12.059 -19.837 1.00 0.00 ATOM 52 O ARG 29 -15.175 -10.389 -14.117 1.00 0.00 ATOM 53 C ARG 29 -14.160 -10.953 -14.536 1.00 0.00 ATOM 57 N GLU 33 -13.030 -11.013 -13.832 1.00 0.00 ATOM 58 CA GLU 33 -12.909 -10.380 -12.521 1.00 0.00 ATOM 59 CB GLU 33 -13.406 -11.321 -11.422 1.00 0.00 ATOM 60 CG GLU 33 -13.381 -10.717 -10.028 1.00 0.00 ATOM 61 CD GLU 33 -13.964 -11.646 -8.981 1.00 0.00 ATOM 62 OE1 GLU 33 -14.441 -12.737 -9.354 1.00 0.00 ATOM 63 OE2 GLU 33 -13.945 -11.280 -7.786 1.00 0.00 ATOM 64 O GLU 33 -10.547 -10.865 -12.321 1.00 0.00 ATOM 65 C GLU 33 -11.447 -10.022 -12.224 1.00 0.00 ATOM 66 N SER 34 -11.221 -8.769 -11.846 1.00 0.00 ATOM 67 CA SER 34 -9.885 -8.296 -11.537 1.00 0.00 ATOM 68 CB SER 34 -9.502 -7.132 -12.452 1.00 0.00 ATOM 69 OG SER 34 -9.410 -7.555 -13.802 1.00 0.00 ATOM 70 O SER 34 -10.731 -7.184 -9.576 1.00 0.00 ATOM 71 C SER 34 -9.802 -7.815 -10.094 1.00 0.00 ATOM 72 N MET 35 -8.677 -8.108 -9.452 1.00 0.00 ATOM 73 CA MET 35 -8.459 -7.711 -8.076 1.00 0.00 ATOM 74 CB MET 35 -8.185 -8.937 -7.203 1.00 0.00 ATOM 75 CG MET 35 -9.368 -9.884 -7.075 1.00 0.00 ATOM 76 SD MET 35 -9.042 -11.257 -5.952 1.00 0.00 ATOM 77 CE MET 35 -8.905 -10.391 -4.390 1.00 0.00 ATOM 78 O MET 35 -6.271 -6.902 -8.645 1.00 0.00 ATOM 79 C MET 35 -7.273 -6.774 -7.944 1.00 0.00 ATOM 80 N ILE 36 -7.396 -5.827 -7.030 1.00 0.00 ATOM 81 CA ILE 36 -6.322 -4.897 -6.770 1.00 0.00 ATOM 82 CB ILE 36 -6.860 -3.518 -6.345 1.00 0.00 ATOM 83 CG1 ILE 36 -7.739 -2.925 -7.447 1.00 0.00 ATOM 84 CG2 ILE 36 -5.711 -2.559 -6.075 1.00 0.00 ATOM 85 CD1 ILE 36 -8.479 -1.672 -7.031 1.00 0.00 ATOM 86 O ILE 36 -6.064 -5.708 -4.563 1.00 0.00 ATOM 87 C ILE 36 -5.539 -5.544 -5.659 1.00 0.00 ATOM 88 N ASN 37 -4.307 -5.951 -5.949 1.00 0.00 ATOM 89 CA ASN 37 -3.449 -6.571 -4.942 1.00 0.00 ATOM 90 CB ASN 37 -2.444 -7.518 -5.602 1.00 0.00 ATOM 91 CG ASN 37 -3.094 -8.777 -6.138 1.00 0.00 ATOM 92 ND2 ASN 37 -2.507 -9.348 -7.182 1.00 0.00 ATOM 93 OD1 ASN 37 -4.114 -9.231 -5.617 1.00 0.00 ATOM 94 O ASN 37 -2.985 -4.255 -4.566 1.00 0.00 ATOM 95 C ASN 37 -2.735 -5.418 -4.246 1.00 0.00 ATOM 96 N SER 38 -1.861 -5.724 -3.291 1.00 0.00 ATOM 97 CA SER 38 -1.107 -4.670 -2.623 1.00 0.00 ATOM 98 CB SER 38 -0.428 -5.214 -1.364 1.00 0.00 ATOM 99 OG SER 38 0.595 -6.136 -1.695 1.00 0.00 ATOM 100 O SER 38 -0.155 -4.730 -4.805 1.00 0.00 ATOM 101 C SER 38 -0.100 -4.244 -3.678 1.00 0.00 ATOM 102 N PRO 39 0.808 -3.341 -3.341 1.00 0.00 ATOM 103 CA PRO 39 1.804 -2.897 -4.314 1.00 0.00 ATOM 104 CB PRO 39 2.673 -4.136 -4.545 1.00 0.00 ATOM 105 CG PRO 39 1.762 -5.287 -4.276 1.00 0.00 ATOM 106 CD PRO 39 0.845 -4.843 -3.171 1.00 0.00 ATOM 107 O PRO 39 1.778 -2.381 -6.652 1.00 0.00 ATOM 108 C PRO 39 1.142 -2.433 -5.604 1.00 0.00 ATOM 109 N SER 40 -0.144 -2.116 -5.517 1.00 0.00 ATOM 110 CA SER 40 -0.938 -1.629 -6.643 1.00 0.00 ATOM 111 CB SER 40 -0.500 -0.217 -7.036 1.00 0.00 ATOM 112 OG SER 40 -0.679 0.690 -5.963 1.00 0.00 ATOM 113 O SER 40 -1.257 -1.816 -9.019 1.00 0.00 ATOM 114 C SER 40 -0.926 -2.389 -7.977 1.00 0.00 ATOM 115 N LYS 41 -0.549 -3.662 -7.967 1.00 0.00 ATOM 116 CA LYS 41 -0.583 -4.437 -9.203 1.00 0.00 ATOM 117 CB LYS 41 0.555 -5.459 -9.226 1.00 0.00 ATOM 118 CG LYS 41 1.943 -4.843 -9.288 1.00 0.00 ATOM 119 CD LYS 41 3.024 -5.910 -9.243 1.00 0.00 ATOM 120 CE LYS 41 4.410 -5.297 -9.349 1.00 0.00 ATOM 121 NZ LYS 41 5.480 -6.333 -9.314 1.00 0.00 ATOM 122 O LYS 41 -2.488 -5.382 -8.088 1.00 0.00 ATOM 123 C LYS 41 -1.960 -5.114 -9.169 1.00 0.00 ATOM 124 N SER 42 -2.549 -5.385 -10.329 1.00 0.00 ATOM 125 CA SER 42 -3.873 -6.019 -10.370 1.00 0.00 ATOM 126 CB SER 42 -4.870 -5.130 -11.115 1.00 0.00 ATOM 127 OG SER 42 -5.094 -3.918 -10.413 1.00 0.00 ATOM 128 O SER 42 -3.229 -7.511 -12.115 1.00 0.00 ATOM 129 C SER 42 -3.858 -7.370 -11.076 1.00 0.00 ATOM 130 N VAL 43 -4.530 -8.376 -10.533 1.00 0.00 ATOM 131 CA VAL 43 -4.549 -9.644 -11.250 1.00 0.00 ATOM 132 CB VAL 43 -4.090 -10.808 -10.351 1.00 0.00 ATOM 133 CG1 VAL 43 -2.626 -10.642 -9.971 1.00 0.00 ATOM 134 CG2 VAL 43 -4.915 -10.853 -9.075 1.00 0.00 ATOM 135 O VAL 43 -6.928 -9.792 -10.963 1.00 0.00 ATOM 136 C VAL 43 -5.964 -9.924 -11.723 1.00 0.00 ATOM 137 N PHE 44 -7.506 -19.234 -16.120 1.00 0.00 ATOM 138 CA PHE 44 -6.331 -18.495 -16.565 1.00 0.00 ATOM 139 CB PHE 44 -6.465 -18.113 -18.042 1.00 0.00 ATOM 140 CG PHE 44 -6.325 -19.275 -18.983 1.00 0.00 ATOM 141 CD1 PHE 44 -7.442 -19.872 -19.540 1.00 0.00 ATOM 142 CD2 PHE 44 -5.075 -19.772 -19.311 1.00 0.00 ATOM 143 CE1 PHE 44 -7.313 -20.941 -20.407 1.00 0.00 ATOM 144 CE2 PHE 44 -4.947 -20.840 -20.178 1.00 0.00 ATOM 145 CZ PHE 44 -6.058 -21.425 -20.725 1.00 0.00 ATOM 146 O PHE 44 -7.176 -16.686 -15.263 1.00 0.00 ATOM 147 C PHE 44 -6.176 -17.222 -15.743 1.00 0.00 ATOM 148 N VAL 45 -4.950 -16.719 -15.603 1.00 0.00 ATOM 149 CA VAL 45 -4.721 -15.508 -14.816 1.00 0.00 ATOM 150 CB VAL 45 -4.220 -15.843 -13.399 1.00 0.00 ATOM 151 CG1 VAL 45 -3.980 -14.568 -12.604 1.00 0.00 ATOM 152 CG2 VAL 45 -5.244 -16.687 -12.656 1.00 0.00 ATOM 153 O VAL 45 -2.606 -14.993 -15.800 1.00 0.00 ATOM 154 C VAL 45 -3.692 -14.572 -15.414 1.00 0.00 ATOM 155 N ARG 46 -4.041 -13.294 -15.477 1.00 0.00 ATOM 156 CA ARG 46 -3.156 -12.268 -16.016 1.00 0.00 ATOM 157 CB ARG 46 -3.805 -11.579 -17.217 1.00 0.00 ATOM 158 CG ARG 46 -3.989 -12.481 -18.426 1.00 0.00 ATOM 159 CD ARG 46 -4.622 -11.730 -19.586 1.00 0.00 ATOM 160 NE ARG 46 -4.803 -12.583 -20.757 1.00 0.00 ATOM 161 CZ ARG 46 -5.387 -12.190 -21.885 1.00 0.00 ATOM 162 NH1 ARG 46 -5.509 -13.036 -22.898 1.00 0.00 ATOM 163 NH2 ARG 46 -5.849 -10.953 -21.995 1.00 0.00 ATOM 164 O ARG 46 -3.801 -10.893 -14.160 1.00 0.00 ATOM 165 C ARG 46 -2.893 -11.243 -14.917 1.00 0.00 ATOM 166 N ASN 47 -1.660 -10.765 -14.811 1.00 0.00 ATOM 167 CA ASN 47 -1.371 -9.744 -13.817 1.00 0.00 ATOM 168 CB ASN 47 -0.150 -10.138 -12.984 1.00 0.00 ATOM 169 CG ASN 47 0.163 -9.128 -11.897 1.00 0.00 ATOM 170 ND2 ASN 47 0.923 -9.556 -10.895 1.00 0.00 ATOM 171 OD1 ASN 47 -0.273 -7.979 -11.959 1.00 0.00 ATOM 172 O ASN 47 -0.209 -8.363 -15.411 1.00 0.00 ATOM 173 C ASN 47 -1.092 -8.427 -14.558 1.00 0.00 ATOM 174 N LEU 48 -1.871 -7.392 -14.249 1.00 0.00 ATOM 175 CA LEU 48 -1.724 -6.082 -14.884 1.00 0.00 ATOM 176 CB LEU 48 -3.074 -5.585 -15.404 1.00 0.00 ATOM 177 CG LEU 48 -3.790 -6.491 -16.406 1.00 0.00 ATOM 178 CD1 LEU 48 -5.157 -5.925 -16.763 1.00 0.00 ATOM 179 CD2 LEU 48 -2.982 -6.622 -17.687 1.00 0.00 ATOM 180 O LEU 48 -1.316 -5.142 -12.698 1.00 0.00 ATOM 181 C LEU 48 -1.186 -5.018 -13.919 1.00 0.00 ATOM 182 N ASN 49 -0.614 -3.952 -14.477 1.00 0.00 ATOM 183 CA ASN 49 -0.024 -2.894 -13.671 1.00 0.00 ATOM 184 CB ASN 49 1.407 -3.260 -13.270 1.00 0.00 ATOM 185 CG ASN 49 2.031 -2.237 -12.340 1.00 0.00 ATOM 186 ND2 ASN 49 3.357 -2.180 -12.329 1.00 0.00 ATOM 187 OD1 ASN 49 1.326 -1.510 -11.640 1.00 0.00 ATOM 188 O ASN 49 0.537 -1.466 -15.527 1.00 0.00 ATOM 189 C ASN 49 0.042 -1.543 -14.406 1.00 0.00 ATOM 190 N GLU 50 3.189 -6.529 -15.241 1.00 0.00 ATOM 191 CA GLU 50 2.466 -7.041 -16.389 1.00 0.00 ATOM 192 CB GLU 50 1.245 -7.844 -15.937 1.00 0.00 ATOM 193 CG GLU 50 1.585 -9.143 -15.225 1.00 0.00 ATOM 194 CD GLU 50 2.377 -10.097 -16.095 1.00 0.00 ATOM 195 OE1 GLU 50 1.924 -10.385 -17.224 1.00 0.00 ATOM 196 OE2 GLU 50 3.449 -10.556 -15.651 1.00 0.00 ATOM 197 O GLU 50 2.473 -4.734 -17.004 1.00 0.00 ATOM 198 C GLU 50 2.022 -5.862 -17.225 1.00 0.00 ATOM 199 N LEU 51 1.123 -6.144 -18.165 1.00 0.00 ATOM 200 CA LEU 51 0.563 -5.172 -19.093 1.00 0.00 ATOM 201 CB LEU 51 -0.454 -5.839 -20.021 1.00 0.00 ATOM 202 CG LEU 51 0.099 -6.881 -20.996 1.00 0.00 ATOM 203 CD1 LEU 51 -1.029 -7.554 -21.761 1.00 0.00 ATOM 204 CD2 LEU 51 1.036 -6.230 -22.003 1.00 0.00 ATOM 205 O LEU 51 -0.792 -4.178 -17.395 1.00 0.00 ATOM 206 C LEU 51 -0.161 -4.014 -18.429 1.00 0.00 ATOM 207 N GLU 52 -0.068 -2.837 -19.026 1.00 0.00 ATOM 208 CA GLU 52 -0.795 -1.721 -18.475 1.00 0.00 ATOM 209 CB GLU 52 -0.381 -0.420 -19.164 1.00 0.00 ATOM 210 CG GLU 52 1.049 0.011 -18.873 1.00 0.00 ATOM 211 CD GLU 52 1.406 1.331 -19.529 1.00 0.00 ATOM 212 OE1 GLU 52 0.546 1.891 -20.239 1.00 0.00 ATOM 213 OE2 GLU 52 2.544 1.802 -19.331 1.00 0.00 ATOM 214 O GLU 52 -2.501 -2.966 -19.564 1.00 0.00 ATOM 215 C GLU 52 -2.238 -2.080 -18.754 1.00 0.00 ATOM 216 N ALA 53 -3.204 -1.431 -18.103 1.00 0.00 ATOM 217 CA ALA 53 -4.592 -1.792 -18.387 1.00 0.00 ATOM 218 CB ALA 53 -5.543 -0.895 -17.609 1.00 0.00 ATOM 219 O ALA 53 -5.257 -2.596 -20.549 1.00 0.00 ATOM 220 C ALA 53 -4.872 -1.634 -19.876 1.00 0.00 ATOM 221 N LEU 54 -4.669 -0.410 -20.371 1.00 0.00 ATOM 222 CA LEU 54 -4.893 -0.076 -21.778 1.00 0.00 ATOM 223 CB LEU 54 -4.517 1.382 -22.050 1.00 0.00 ATOM 224 CG LEU 54 -5.415 2.443 -21.413 1.00 0.00 ATOM 225 CD1 LEU 54 -4.835 3.834 -21.622 1.00 0.00 ATOM 226 CD2 LEU 54 -6.806 2.411 -22.028 1.00 0.00 ATOM 227 O LEU 54 -4.521 -1.189 -23.871 1.00 0.00 ATOM 228 C LEU 54 -4.079 -0.928 -22.747 1.00 0.00 ATOM 229 N ALA 55 -2.895 -1.354 -22.319 1.00 0.00 ATOM 230 CA ALA 55 -2.068 -2.210 -23.158 1.00 0.00 ATOM 231 CB ALA 55 -0.772 -2.561 -22.442 1.00 0.00 ATOM 232 O ALA 55 -3.084 -3.876 -24.580 1.00 0.00 ATOM 233 C ALA 55 -2.881 -3.478 -23.436 1.00 0.00 ATOM 234 N VAL 56 -3.357 -4.085 -22.359 1.00 0.00 ATOM 235 CA VAL 56 -4.144 -5.307 -22.424 1.00 0.00 ATOM 236 CB VAL 56 -4.590 -5.765 -21.022 1.00 0.00 ATOM 237 CG1 VAL 56 -5.569 -6.923 -21.128 1.00 0.00 ATOM 238 CG2 VAL 56 -3.392 -6.222 -20.205 1.00 0.00 ATOM 239 O VAL 56 -5.809 -6.095 -23.959 1.00 0.00 ATOM 240 C VAL 56 -5.417 -5.170 -23.255 1.00 0.00 ATOM 241 N ARG 57 -6.068 -4.021 -23.171 1.00 0.00 ATOM 242 CA ARG 57 -7.293 -3.829 -23.930 1.00 0.00 ATOM 243 CB ARG 57 -7.961 -2.507 -23.545 1.00 0.00 ATOM 244 CG ARG 57 -8.577 -2.504 -22.156 1.00 0.00 ATOM 245 CD ARG 57 -9.152 -1.141 -21.809 1.00 0.00 ATOM 246 NE ARG 57 -9.745 -1.121 -20.475 1.00 0.00 ATOM 247 CZ ARG 57 -10.246 -0.033 -19.897 1.00 0.00 ATOM 248 NH1 ARG 57 -10.765 -0.109 -18.678 1.00 0.00 ATOM 249 NH2 ARG 57 -10.227 1.128 -20.537 1.00 0.00 ATOM 250 O ARG 57 -7.575 -4.440 -26.249 1.00 0.00 ATOM 251 C ARG 57 -6.919 -3.811 -25.411 1.00 0.00 ATOM 252 N LEU 58 -5.839 -3.102 -25.720 1.00 0.00 ATOM 253 CA LEU 58 -5.362 -2.999 -27.087 1.00 0.00 ATOM 254 CB LEU 58 -4.188 -2.021 -27.172 1.00 0.00 ATOM 255 CG LEU 58 -4.512 -0.548 -26.914 1.00 0.00 ATOM 256 CD1 LEU 58 -3.240 0.285 -26.877 1.00 0.00 ATOM 257 CD2 LEU 58 -5.410 0.005 -28.010 1.00 0.00 ATOM 258 O LEU 58 -4.983 -4.610 -28.812 1.00 0.00 ATOM 259 C LEU 58 -4.891 -4.345 -27.610 1.00 0.00 ATOM 260 N GLY 59 -4.389 -5.196 -26.712 1.00 0.00 ATOM 261 CA GLY 59 -3.921 -6.527 -27.087 1.00 0.00 ATOM 262 O GLY 59 -5.163 -8.362 -28.012 1.00 0.00 ATOM 263 C GLY 59 -5.148 -7.404 -27.231 1.00 0.00 ATOM 264 N LYS 60 -6.178 -7.067 -26.464 1.00 0.00 ATOM 265 CA LYS 60 -7.411 -7.822 -26.529 1.00 0.00 ATOM 266 CB LYS 60 -8.359 -7.398 -25.406 1.00 0.00 ATOM 267 CG LYS 60 -9.652 -8.196 -25.351 1.00 0.00 ATOM 268 CD LYS 60 -10.498 -7.792 -24.156 1.00 0.00 ATOM 269 CE LYS 60 -11.789 -8.592 -24.097 1.00 0.00 ATOM 270 NZ LYS 60 -12.623 -8.220 -22.922 1.00 0.00 ATOM 271 O LYS 60 -8.671 -8.386 -28.454 1.00 0.00 ATOM 272 C LYS 60 -8.021 -7.530 -27.870 1.00 0.00 ATOM 273 N SER 61 -7.806 -6.313 -28.362 1.00 0.00 ATOM 274 CA SER 61 -8.326 -5.891 -29.665 1.00 0.00 ATOM 275 CB SER 61 -8.160 -4.380 -29.843 1.00 0.00 ATOM 276 OG SER 61 -8.975 -3.666 -28.929 1.00 0.00 ATOM 277 O SER 61 -8.117 -7.246 -31.655 1.00 0.00 ATOM 278 C SER 61 -7.540 -6.626 -30.759 1.00 0.00 ATOM 279 N TYR 62 -6.218 -6.554 -30.671 1.00 0.00 ATOM 280 CA TYR 62 -5.365 -7.212 -31.646 1.00 0.00 ATOM 281 CB TYR 62 -3.900 -7.143 -31.212 1.00 0.00 ATOM 282 CG TYR 62 -2.949 -7.859 -32.144 1.00 0.00 ATOM 283 CD1 TYR 62 -2.512 -7.253 -33.316 1.00 0.00 ATOM 284 CD2 TYR 62 -2.491 -9.136 -31.849 1.00 0.00 ATOM 285 CE1 TYR 62 -1.644 -7.900 -34.174 1.00 0.00 ATOM 286 CE2 TYR 62 -1.622 -9.798 -32.696 1.00 0.00 ATOM 287 CZ TYR 62 -1.200 -9.168 -33.866 1.00 0.00 ATOM 288 OH TYR 62 -0.334 -9.814 -34.719 1.00 0.00 ATOM 289 O TYR 62 -6.034 -9.143 -32.885 1.00 0.00 ATOM 290 C TYR 62 -5.765 -8.664 -31.780 1.00 0.00 ATOM 291 N ARG 63 -5.806 -9.368 -30.654 1.00 0.00 ATOM 292 CA ARG 63 -6.171 -10.773 -30.687 1.00 0.00 ATOM 293 CB ARG 63 -6.268 -11.335 -29.268 1.00 0.00 ATOM 294 CG ARG 63 -4.928 -11.484 -28.566 1.00 0.00 ATOM 295 CD ARG 63 -5.104 -11.977 -27.139 1.00 0.00 ATOM 296 NE ARG 63 -3.826 -12.098 -26.441 1.00 0.00 ATOM 297 CZ ARG 63 -3.704 -12.438 -25.162 1.00 0.00 ATOM 298 NH1 ARG 63 -2.501 -12.525 -24.611 1.00 0.00 ATOM 299 NH2 ARG 63 -4.785 -12.691 -24.437 1.00 0.00 ATOM 300 O ARG 63 -7.684 -12.070 -32.016 1.00 0.00 ATOM 301 C ARG 63 -7.522 -11.043 -31.365 1.00 0.00 ATOM 302 N ILE 64 -8.488 -10.140 -31.204 1.00 0.00 ATOM 303 CA ILE 64 -9.803 -10.318 -31.835 1.00 0.00 ATOM 304 CB ILE 64 -10.806 -9.251 -31.360 1.00 0.00 ATOM 305 CG1 ILE 64 -11.135 -9.449 -29.880 1.00 0.00 ATOM 306 CG2 ILE 64 -12.098 -9.343 -32.159 1.00 0.00 ATOM 307 CD1 ILE 64 -11.902 -8.299 -29.265 1.00 0.00 ATOM 308 O ILE 64 -10.257 -10.884 -34.113 1.00 0.00 ATOM 309 C ILE 64 -9.607 -10.200 -33.329 1.00 0.00 ATOM 310 N GLN 65 -8.706 -9.307 -33.711 1.00 0.00 ATOM 311 CA GLN 65 -8.408 -9.069 -35.112 1.00 0.00 ATOM 312 CB GLN 65 -7.408 -7.920 -35.260 1.00 0.00 ATOM 313 CG GLN 65 -7.980 -6.552 -34.925 1.00 0.00 ATOM 314 CD GLN 65 -6.929 -5.460 -34.952 1.00 0.00 ATOM 315 OE1 GLN 65 -5.744 -5.729 -35.148 1.00 0.00 ATOM 316 NE2 GLN 65 -7.362 -4.219 -34.759 1.00 0.00 ATOM 317 O GLN 65 -8.239 -10.735 -36.829 1.00 0.00 ATOM 318 C GLN 65 -7.808 -10.309 -35.762 1.00 0.00 ATOM 319 N LEU 66 -6.817 -10.888 -35.102 1.00 0.00 ATOM 320 CA LEU 66 -6.159 -12.065 -35.626 1.00 0.00 ATOM 321 CB LEU 66 -4.941 -12.422 -34.772 1.00 0.00 ATOM 322 CG LEU 66 -4.150 -13.659 -35.203 1.00 0.00 ATOM 323 CD1 LEU 66 -3.591 -13.479 -36.606 1.00 0.00 ATOM 324 CD2 LEU 66 -2.987 -13.911 -34.256 1.00 0.00 ATOM 325 O LEU 66 -7.232 -13.947 -36.612 1.00 0.00 ATOM 326 C LEU 66 -7.113 -13.228 -35.621 1.00 0.00 ATOM 327 N ASP 67 -7.816 -13.421 -34.514 1.00 0.00 ATOM 328 CA ASP 67 -8.736 -14.537 -34.441 1.00 0.00 ATOM 329 CB ASP 67 -9.444 -14.560 -33.085 1.00 0.00 ATOM 330 CG ASP 67 -8.527 -14.991 -31.957 1.00 0.00 ATOM 331 OD1 ASP 67 -7.425 -15.499 -32.248 1.00 0.00 ATOM 332 OD2 ASP 67 -8.913 -14.822 -30.781 1.00 0.00 ATOM 333 O ASP 67 -9.992 -15.453 -36.260 1.00 0.00 ATOM 334 C ASP 67 -9.825 -14.489 -35.514 1.00 0.00 ATOM 335 N GLN 68 -10.554 -13.385 -35.639 1.00 0.00 ATOM 336 CA GLN 68 -11.606 -13.387 -36.649 1.00 0.00 ATOM 337 CB GLN 68 -12.403 -12.082 -36.594 1.00 0.00 ATOM 338 CG GLN 68 -13.284 -11.944 -35.364 1.00 0.00 ATOM 339 CD GLN 68 -14.029 -10.625 -35.325 1.00 0.00 ATOM 340 OE1 GLN 68 -13.926 -9.816 -36.248 1.00 0.00 ATOM 341 NE2 GLN 68 -14.782 -10.402 -34.254 1.00 0.00 ATOM 342 O GLN 68 -11.799 -13.977 -38.962 1.00 0.00 ATOM 343 C GLN 68 -11.075 -13.525 -38.080 1.00 0.00 ATOM 344 N ALA 69 -9.818 -13.147 -38.308 1.00 0.00 ATOM 345 CA ALA 69 -9.207 -13.260 -39.640 1.00 0.00 ATOM 346 CB ALA 69 -7.918 -12.454 -39.703 1.00 0.00 ATOM 347 O ALA 69 -9.087 -15.240 -41.007 1.00 0.00 ATOM 348 C ALA 69 -8.903 -14.726 -39.914 1.00 0.00 ATOM 349 N LYS 70 -8.418 -15.394 -38.888 1.00 0.00 ATOM 350 CA LYS 70 -8.088 -16.792 -38.989 1.00 0.00 ATOM 351 CB LYS 70 -7.382 -17.268 -37.719 1.00 0.00 ATOM 352 CG LYS 70 -6.008 -16.655 -37.504 1.00 0.00 ATOM 353 CD LYS 70 -5.334 -17.226 -36.269 1.00 0.00 ATOM 354 CE LYS 70 -3.969 -16.596 -36.041 1.00 0.00 ATOM 355 NZ LYS 70 -3.310 -17.127 -34.816 1.00 0.00 ATOM 356 O LYS 70 -9.331 -18.689 -39.732 1.00 0.00 ATOM 357 C LYS 70 -9.364 -17.600 -39.180 1.00 0.00 TER END