PFRMAT TS TARGET T0480 AUTHOR 4008-1775-0004 METHOD The SAM-T08 hand predictions use methods similar to SAM_T06 in CASP7. METHOD METHOD We start with a fully automated method (implemented as the SAM-T08-server): METHOD METHOD Use the SAM-T2K, SAM-T04, and SAM-T06 methods for finding homologs METHOD of the target and aligning them. METHOD METHOD Make local structure predictions using neural nets and the METHOD multiple alignments. These neural nets have been newly trained METHOD for CASP8 with an improved training protocol. The neural nets for METHOD the 3 different multiple sequence alignments are independently METHOD trained, so combining them should offer improved performance. METHOD METHOD We currently use 15 local-structure alphabets: METHOD STR2 an extended version of DSSP that splits the beta strands METHOD into multiple classes (parallel/antiparallel/mixed, METHOD edge/center) METHOD STR4 an attempt at an alphabet like STR2, but not requiring DSSP. METHOD This alphabet may be trying to make some irrelevant METHOD distinctions as well. 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 PB de Brevern's protein blocks METHOD METHOD N_NOTOR METHOD N_NOTOR2 METHOD O_NOTOR METHOD O_NOTOR2 alphabets based on the torsion angle of METHOD backbone hydrogen bonds METHOD METHOD N_SEP METHOD O_SEP alphabets based on the separation of donor and METHOD acceptor for backbone hydrogen bonds METHOD 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 near-backbone-11 an 11-state discretization of the number of METHOD residues (represented by near-backbone points) in a METHOD 9.65 Angstrom radius sphere around the sidechain proxy METHOD spot for the residue. METHOD 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 with the amino-acid track METHOD having a weight of 1 and the local structure track having a weight METHOD of 0.1 (for backbone alphabets) or 0.3 (for burial alphabets). METHOD We use these HMMs to score a template library of about METHOD 14000 (t06), 16000 (t04), or 18000 (t2k) templates. METHOD The template libraries are expanded weekly, but old template HMMs METHOD are not rebuilt. The target HMMs are used to score consensus METHOD sequences for the templates, to get a cheap approximation of METHOD profile-profile scoring, which does not yet work in the SAM package. METHOD METHOD We also used single-track HMMs to score not just the template METHOD library, but a non-redundant copy of the entire PDB. This scoring METHOD is done with real sequences, not consensus sequences. METHOD METHOD All the target HMMs use a new calibration method the provides more METHOD accurate E-values than before, and can be used even with METHOD local-structure alphabets that used to give us trouble (such as METHOD protein blocks). METHOD METHOD One-track HMMs built from the template library multiple alignments METHOD were used to score the target sequence. Later this summer, we METHOD hope to be able to use multi-track template HMMs, but we have not METHOD had time to calibrate such models while keeping the code METHOD compatible with the old libraries, so the template libraries METHOD currently use old calibrations, with somewhat optimistic E-values. METHOD METHOD All the logs of e-values were combined in a weighted average (with METHOD rather arbitrary weights, since we still have not taken the time METHOD to optimize them), and the best templates ranked. METHOD METHOD Alignments of the target to the top templates were made using METHOD several different alignment settings on the SAM alignment software. METHOD METHOD Generate fragments (short 9-residue alignments for each position) METHOD using SAM's "fragfinder" program and the 3-track HMM which tested METHOD best for alignment. METHOD METHOD Residue-residue contact predictions are made using mutual METHOD information, pairwise contact potentials, joint entropy, and other METHOD signals combined by a neural net. Two different neural net METHOD methods were used, and the results submitted separately. METHOD METHOD CB-CB constraints were extracted from the alignments and a METHOD combinatorial optimization done to choose a most-believable METHOD subset. METHOD METHOD Then the "undertaker" program (named because it originally METHOD optimized burial) is used to try to combine the alignments and the METHOD fragments into a consistent 3D model. No single alignment or METHOD parent template was used as a frozen core, though in many cases METHOD one had much more influence than the others. The alignment scores METHOD were not used by undertaker, but were used only to pick the set METHOD of alignments and fragments that undertaker would see. METHOD METHOD The cost functions used by undertaker rely heavily on the METHOD alignment constraints, on helix and strand constraints generated METHOD from the secondary-structure predictions, and on the neural-net METHOD predictions of local properties that undertaker can measure. METHOD The residue-residue contact predictions are also given to METHOD undertaker, but have less weight. There are also a number of METHOD built-in cost functions (breaks, clashes, burial, ...) that are METHOD included in the cost function. METHOD METHOD The automatic script runs the undertaker-optimized model through METHOD gromacs (to fix small clashes and breaks) and repacks the METHOD sidechains using Rosetta, but these post-undertaker optimizations METHOD are not included in the server predictions. They can be used in METHOD subsequent re-optimization. METHOD METHOD After the automatic prediction is done, we examine it by hand and try METHOD to fix any flaws that we see. This generally involves rerunning METHOD undertaker with new cost functions, increasing the weights for METHOD features we want to see and decreasing the weights where we think the METHOD optimization has gone overboard. Sometimes we will add new templates METHOD or remove ones that we think are misleading the optimization process. METHOD We often do "polishing" runs, where all the current models are read in METHOD and optimization with undertaker's genetic algorithm is done with high METHOD crossover. METHOD METHOD Some improvements in undertaker include better communication with METHOD SCWRL for initial model building form alignments (now using the METHOD standard protocol that identical residues have fixed rotamers, rather METHOD than being reoptimized by SCWRL), more cost functions based on the METHOD neural net predictions, multiple constraint sets (for easier METHOD weighting of the importance of different constraints), and some new METHOD conformation-change operators (Backrub and BigBackrub). METHOD METHOD We also created model-quality-assessment methods for CASP8, which we METHOD are applying to the server predictions. We do two optimizations from the METHOD top 10 models with two of the MQA methods, and consider these models METHOD as possible alternatives to our natively-generated models. METHOD METHOD The most distinctive feature of T0480 were the conserved CYS residues: METHOD C21, C24, C39, and C42. I decided to make these into a tetrahedral METHOD zinc-binding site. METHOD METHOD Most of my models came from SAM+undertaker alone, but the first model METHOD was optimized from a meta-server model. I'm a bit dubious about the METHOD flat sheet in that model, but it consistently scored best in several METHOD variants of the cost function. METHOD METHOD Model METHOD 1 T0480.try10-opt3.pdb # < MQAU5-opt3 < RBO-Proteus_TS4 METHOD METHOD 2 T0480.try11-opt3.pdb # < try9-opt3 < try8-opt3.gromacs0 < align(2bmoA) METHOD METHOD 3 T0480.try5-opt3.pdb # < align(2hf1A) METHOD METHOD 4 T0480.try4-opt3.pdb # < align(1v6kA) METHOD METHOD 5 T0480.MQAC5-opt3.gromacs0.pdb # < SAM-T08-server_TS1 METHOD REMARK 6 REMARK 6 T0480 model 3 Fri Jul 25 05:17:40 2008 MODEL 3 PARENT 2ct7_A 2bmo_A REMARK 7 REMARK 7 ALLPARENTS 2ct7_A 2bmo_A ATOM 1 N MET 1 19.733 2.414 6.650 1.00 0.00 ATOM 2 CA MET 1 19.013 3.555 7.265 1.00 0.00 ATOM 3 CB MET 1 19.432 4.852 6.567 1.00 0.00 ATOM 4 CG MET 1 18.990 6.123 7.266 1.00 0.00 ATOM 5 SD MET 1 19.656 7.618 6.422 1.00 0.00 ATOM 6 CE MET 1 21.380 7.553 6.899 1.00 0.00 ATOM 7 O MET 1 17.017 3.158 5.998 1.00 0.00 ATOM 8 C MET 1 17.507 3.338 7.111 1.00 0.00 ATOM 9 N GLN 2 16.815 3.337 8.180 1.00 0.00 ATOM 10 CA GLN 2 15.355 3.150 8.189 1.00 0.00 ATOM 11 CB GLN 2 14.790 3.262 9.606 1.00 0.00 ATOM 12 CG GLN 2 15.166 2.089 10.470 1.00 0.00 ATOM 13 CD GLN 2 14.733 2.299 11.920 1.00 0.00 ATOM 14 OE1 GLN 2 14.549 3.423 12.437 1.00 0.00 ATOM 15 NE2 GLN 2 14.621 1.237 12.580 1.00 0.00 ATOM 16 O GLN 2 13.492 4.014 6.944 1.00 0.00 ATOM 17 C GLN 2 14.652 4.196 7.335 1.00 0.00 ATOM 18 N LYS 3 15.294 5.344 7.073 1.00 0.00 ATOM 19 CA LYS 3 14.630 6.459 6.473 1.00 0.00 ATOM 20 CB LYS 3 15.323 7.780 6.746 1.00 0.00 ATOM 21 CG LYS 3 15.209 8.130 8.234 1.00 0.00 ATOM 22 CD LYS 3 15.820 9.378 8.737 1.00 0.00 ATOM 23 CE LYS 3 15.257 9.701 10.141 1.00 0.00 ATOM 24 NZ LYS 3 15.105 8.464 10.946 1.00 0.00 ATOM 25 O LYS 3 15.703 5.777 4.438 1.00 0.00 ATOM 26 C LYS 3 14.701 6.265 4.962 1.00 0.00 ATOM 27 N ARG 4 13.638 6.651 4.263 1.00 0.00 ATOM 28 CA ARG 4 13.604 6.514 2.835 1.00 0.00 ATOM 29 CB ARG 4 12.302 7.062 2.255 1.00 0.00 ATOM 30 CG ARG 4 12.246 6.914 0.742 1.00 0.00 ATOM 31 CD ARG 4 10.899 7.456 0.251 1.00 0.00 ATOM 32 NE ARG 4 10.790 7.225 -1.209 1.00 0.00 ATOM 33 CZ ARG 4 9.716 7.570 -1.915 1.00 0.00 ATOM 34 NH1 ARG 4 8.651 8.137 -1.318 1.00 0.00 ATOM 35 NH2 ARG 4 9.657 7.325 -3.221 1.00 0.00 ATOM 36 O ARG 4 15.294 6.876 1.138 1.00 0.00 ATOM 37 C ARG 4 14.769 7.301 2.168 1.00 0.00 ATOM 38 N GLU 5 15.153 8.427 2.761 1.00 0.00 ATOM 39 CA GLU 5 16.236 9.236 2.217 1.00 0.00 ATOM 40 CB GLU 5 16.083 10.715 2.289 1.00 0.00 ATOM 41 CG GLU 5 17.252 11.497 1.698 1.00 0.00 ATOM 42 CD GLU 5 17.153 12.984 1.965 1.00 0.00 ATOM 43 OE1 GLU 5 16.237 13.398 2.710 1.00 0.00 ATOM 44 OE2 GLU 5 18.003 13.732 1.434 1.00 0.00 ATOM 45 O GLU 5 17.670 8.871 4.105 1.00 0.00 ATOM 46 C GLU 5 17.507 8.732 2.892 1.00 0.00 ATOM 47 N LEU 6 18.406 8.147 2.107 1.00 0.00 ATOM 48 CA LEU 6 19.670 7.626 2.648 1.00 0.00 ATOM 49 CB LEU 6 19.953 6.271 2.019 1.00 0.00 ATOM 50 CG LEU 6 21.187 5.542 2.555 1.00 0.00 ATOM 51 CD1 LEU 6 21.039 5.289 4.050 1.00 0.00 ATOM 52 CD2 LEU 6 21.349 4.229 1.810 1.00 0.00 ATOM 53 O LEU 6 20.928 8.877 1.057 1.00 0.00 ATOM 54 C LEU 6 20.788 8.587 2.248 1.00 0.00 ATOM 55 N TYR 7 21.565 9.076 3.226 1.00 0.00 ATOM 56 CA TYR 7 22.792 9.855 2.949 1.00 0.00 ATOM 57 CB TYR 7 22.750 11.199 3.694 1.00 0.00 ATOM 58 CG TYR 7 22.963 11.090 5.168 1.00 0.00 ATOM 59 CD1 TYR 7 24.248 11.067 5.694 1.00 0.00 ATOM 60 CD2 TYR 7 21.879 11.029 6.044 1.00 0.00 ATOM 61 CE1 TYR 7 24.462 10.994 7.049 1.00 0.00 ATOM 62 CE2 TYR 7 22.075 10.960 7.402 1.00 0.00 ATOM 63 CZ TYR 7 23.374 10.943 7.899 1.00 0.00 ATOM 64 OH TYR 7 23.601 10.893 9.256 1.00 0.00 ATOM 65 O TYR 7 24.180 8.267 4.099 1.00 0.00 ATOM 66 C TYR 7 24.058 8.982 3.119 1.00 0.00 ATOM 67 N GLU 8 24.967 9.101 2.219 1.00 0.00 ATOM 68 CA GLU 8 26.271 8.437 2.351 1.00 0.00 ATOM 69 CB GLU 8 26.089 6.967 1.903 1.00 0.00 ATOM 70 CG GLU 8 27.143 6.014 2.448 1.00 0.00 ATOM 71 CD GLU 8 26.755 4.552 2.288 1.00 0.00 ATOM 72 OE1 GLU 8 25.587 4.206 2.578 1.00 0.00 ATOM 73 OE2 GLU 8 27.621 3.746 1.891 1.00 0.00 ATOM 74 O GLU 8 27.196 9.685 0.495 1.00 0.00 ATOM 75 C GLU 8 27.399 9.126 1.592 1.00 0.00 ATOM 76 N ILE 9 28.582 9.101 2.193 1.00 0.00 ATOM 77 CA ILE 9 29.761 9.584 1.521 1.00 0.00 ATOM 78 CB ILE 9 30.657 10.295 2.533 1.00 0.00 ATOM 79 CG1 ILE 9 29.849 11.430 3.184 1.00 0.00 ATOM 80 CG2 ILE 9 31.859 10.884 1.816 1.00 0.00 ATOM 81 CD1 ILE 9 30.602 12.158 4.373 1.00 0.00 ATOM 82 O ILE 9 30.907 7.508 1.484 1.00 0.00 ATOM 83 C ILE 9 30.442 8.451 0.841 1.00 0.00 ATOM 84 N ALA 10 30.512 8.524 -0.484 1.00 0.00 ATOM 85 CA ALA 10 31.158 7.476 -1.266 1.00 0.00 ATOM 86 CB ALA 10 30.150 6.374 -1.704 1.00 0.00 ATOM 87 O ALA 10 31.340 9.014 -3.086 1.00 0.00 ATOM 88 C ALA 10 31.880 8.130 -2.418 1.00 0.00 ATOM 89 N ASP 11 33.137 7.668 -2.636 1.00 0.00 ATOM 90 CA ASP 11 33.983 8.178 -3.714 1.00 0.00 ATOM 91 CB ASP 11 33.627 7.607 -5.100 1.00 0.00 ATOM 92 CG ASP 11 34.052 6.166 -5.257 1.00 0.00 ATOM 93 OD1 ASP 11 35.042 5.768 -4.604 1.00 0.00 ATOM 94 OD2 ASP 11 33.410 5.439 -6.038 1.00 0.00 ATOM 95 O ASP 11 34.002 10.307 -4.858 1.00 0.00 ATOM 96 C ASP 11 34.031 9.725 -3.768 1.00 0.00 ATOM 97 N GLY 12 34.118 10.377 -2.605 1.00 0.00 ATOM 98 CA GLY 12 34.310 11.828 -2.544 1.00 0.00 ATOM 99 O GLY 12 33.155 13.891 -2.941 1.00 0.00 ATOM 100 C GLY 12 33.066 12.672 -2.800 1.00 0.00 ATOM 101 N LYS 13 31.909 12.021 -2.861 1.00 0.00 ATOM 102 CA LYS 13 30.624 12.736 -3.104 1.00 0.00 ATOM 103 CB LYS 13 29.886 11.955 -4.277 1.00 0.00 ATOM 104 CG LYS 13 30.481 12.299 -5.639 1.00 0.00 ATOM 105 CD LYS 13 30.019 11.364 -6.747 1.00 0.00 ATOM 106 CE LYS 13 30.855 10.095 -6.794 1.00 0.00 ATOM 107 NZ LYS 13 30.592 9.298 -8.025 1.00 0.00 ATOM 108 O LYS 13 29.474 11.343 -1.516 1.00 0.00 ATOM 109 C LYS 13 29.584 12.464 -2.012 1.00 0.00 ATOM 110 N LEU 14 28.825 13.492 -1.643 1.00 0.00 ATOM 111 CA LEU 14 27.801 13.345 -0.615 1.00 0.00 ATOM 112 CB LEU 14 27.727 14.495 0.361 1.00 0.00 ATOM 113 CG LEU 14 29.084 15.076 0.789 1.00 0.00 ATOM 114 CD1 LEU 14 28.873 16.266 1.703 1.00 0.00 ATOM 115 CD2 LEU 14 29.960 14.023 1.460 1.00 0.00 ATOM 116 O LEU 14 25.914 13.791 -2.023 1.00 0.00 ATOM 117 C LEU 14 26.548 12.959 -1.388 1.00 0.00 ATOM 118 N VAL 15 26.239 11.655 -1.347 1.00 0.00 ATOM 119 CA VAL 15 25.125 11.070 -2.069 1.00 0.00 ATOM 120 CB VAL 15 25.363 9.599 -2.428 1.00 0.00 ATOM 121 CG1 VAL 15 24.074 9.008 -2.957 1.00 0.00 ATOM 122 CG2 VAL 15 26.475 9.528 -3.500 1.00 0.00 ATOM 123 O VAL 15 23.991 10.668 0.019 1.00 0.00 ATOM 124 C VAL 15 23.904 11.072 -1.139 1.00 0.00 ATOM 125 N ARG 16 22.779 11.544 -1.662 1.00 0.00 ATOM 126 CA ARG 16 21.478 11.350 -1.038 1.00 0.00 ATOM 127 CB ARG 16 21.081 12.551 -0.132 1.00 0.00 ATOM 128 CG ARG 16 22.035 12.804 1.003 1.00 0.00 ATOM 129 CD ARG 16 21.861 14.138 1.660 1.00 0.00 ATOM 130 NE ARG 16 22.758 14.249 2.785 1.00 0.00 ATOM 131 CZ ARG 16 24.080 14.390 2.696 1.00 0.00 ATOM 132 NH1 ARG 16 24.691 14.468 1.514 1.00 0.00 ATOM 133 NH2 ARG 16 24.803 14.465 3.809 1.00 0.00 ATOM 134 O ARG 16 20.319 11.492 -3.134 1.00 0.00 ATOM 135 C ARG 16 20.515 10.843 -2.106 1.00 0.00 ATOM 136 N LYS 17 19.915 9.681 -1.863 1.00 0.00 ATOM 137 CA LYS 17 18.971 9.101 -2.816 1.00 0.00 ATOM 138 CB LYS 17 19.650 8.029 -3.661 1.00 0.00 ATOM 139 CG LYS 17 18.758 7.456 -4.791 1.00 0.00 ATOM 140 CD LYS 17 19.208 7.939 -6.183 1.00 0.00 ATOM 141 CE LYS 17 18.256 7.489 -7.302 1.00 0.00 ATOM 142 NZ LYS 17 18.159 5.999 -7.405 1.00 0.00 ATOM 143 O LYS 17 17.927 8.083 -0.914 1.00 0.00 ATOM 144 C LYS 17 17.775 8.593 -2.025 1.00 0.00 ATOM 145 N HIS 18 16.584 8.732 -2.596 1.00 0.00 ATOM 146 CA HIS 18 15.368 8.279 -1.929 1.00 0.00 ATOM 147 CB HIS 18 14.252 9.362 -2.044 1.00 0.00 ATOM 148 CG HIS 18 14.697 10.768 -1.779 1.00 0.00 ATOM 149 CD2 HIS 18 14.479 11.587 -0.724 1.00 0.00 ATOM 150 ND1 HIS 18 15.452 11.492 -2.675 1.00 0.00 ATOM 151 CE1 HIS 18 15.675 12.701 -2.187 1.00 0.00 ATOM 152 NE2 HIS 18 15.096 12.783 -1.002 1.00 0.00 ATOM 153 O HIS 18 14.529 6.707 -3.537 1.00 0.00 ATOM 154 C HIS 18 14.999 6.879 -2.412 1.00 0.00 ATOM 155 N ARG 19 15.212 5.882 -1.559 1.00 0.00 ATOM 156 CA ARG 19 14.892 4.492 -1.913 1.00 0.00 ATOM 157 CB ARG 19 16.075 4.046 -2.703 1.00 0.00 ATOM 158 CG ARG 19 16.129 4.751 -4.061 1.00 0.00 ATOM 159 CD ARG 19 14.923 4.442 -4.954 1.00 0.00 ATOM 160 NE ARG 19 14.843 5.381 -6.035 1.00 0.00 ATOM 161 CZ ARG 19 13.894 5.336 -6.969 1.00 0.00 ATOM 162 NH1 ARG 19 13.054 4.303 -7.041 1.00 0.00 ATOM 163 NH2 ARG 19 13.793 6.311 -7.817 1.00 0.00 ATOM 164 O ARG 19 13.951 4.320 0.271 1.00 0.00 ATOM 165 C ARG 19 14.154 3.776 -0.815 1.00 0.00 ATOM 166 N PHE 20 13.748 2.540 -1.089 1.00 0.00 ATOM 167 CA PHE 20 13.026 1.746 -0.101 1.00 0.00 ATOM 168 CB PHE 20 11.489 1.906 -0.225 1.00 0.00 ATOM 169 CG PHE 20 10.919 1.359 -1.519 1.00 0.00 ATOM 170 CD1 PHE 20 10.739 -0.013 -1.698 1.00 0.00 ATOM 171 CD2 PHE 20 10.611 2.215 -2.571 1.00 0.00 ATOM 172 CE1 PHE 20 10.266 -0.528 -2.906 1.00 0.00 ATOM 173 CE2 PHE 20 10.131 1.702 -3.796 1.00 0.00 ATOM 174 CZ PHE 20 9.965 0.334 -3.956 1.00 0.00 ATOM 175 O PHE 20 13.818 -0.096 -1.389 1.00 0.00 ATOM 176 C PHE 20 13.391 0.302 -0.305 1.00 0.00 ATOM 177 N CYS 21 13.223 -0.499 0.743 1.00 0.00 ATOM 178 CA CYS 21 13.540 -1.920 0.666 1.00 0.00 ATOM 179 CB CYS 21 14.593 -2.311 1.704 1.00 0.00 ATOM 180 SG CYS 21 14.697 -4.066 2.144 1.00 0.00 ATOM 181 O CYS 21 11.496 -2.435 1.806 1.00 0.00 ATOM 182 C CYS 21 12.213 -2.662 0.811 1.00 0.00 ATOM 183 N PRO 22 11.965 -3.625 -0.058 1.00 0.00 ATOM 184 CA PRO 22 10.723 -4.378 0.104 1.00 0.00 ATOM 185 CB PRO 22 10.746 -5.345 -1.087 1.00 0.00 ATOM 186 CG PRO 22 12.186 -5.442 -1.478 1.00 0.00 ATOM 187 CD PRO 22 12.763 -4.067 -1.219 1.00 0.00 ATOM 188 O PRO 22 9.603 -5.861 1.620 1.00 0.00 ATOM 189 C PRO 22 10.652 -5.289 1.330 1.00 0.00 ATOM 190 N ARG 23 11.772 -5.372 2.086 1.00 0.00 ATOM 191 CA ARG 23 11.787 -6.209 3.281 1.00 0.00 ATOM 192 CB ARG 23 13.010 -6.969 3.493 1.00 0.00 ATOM 193 CG ARG 23 13.121 -8.172 2.581 1.00 0.00 ATOM 194 CD ARG 23 14.519 -8.816 2.741 1.00 0.00 ATOM 195 NE ARG 23 14.709 -9.995 1.893 1.00 0.00 ATOM 196 CZ ARG 23 15.081 -9.949 0.616 1.00 0.00 ATOM 197 NH1 ARG 23 15.290 -8.795 0.010 1.00 0.00 ATOM 198 NH2 ARG 23 15.229 -11.053 -0.074 1.00 0.00 ATOM 199 O ARG 23 10.628 -5.421 5.227 1.00 0.00 ATOM 200 C ARG 23 11.662 -5.387 4.559 1.00 0.00 ATOM 201 N CYS 24 12.714 -4.649 4.896 1.00 0.00 ATOM 202 CA CYS 24 12.705 -3.814 6.104 1.00 0.00 ATOM 203 CB CYS 24 14.145 -3.636 6.589 1.00 0.00 ATOM 204 SG CYS 24 15.164 -2.591 5.499 1.00 0.00 ATOM 205 O CYS 24 11.901 -1.711 6.920 1.00 0.00 ATOM 206 C CYS 24 12.071 -2.437 5.939 1.00 0.00 ATOM 207 N GLY 25 11.729 -2.079 4.705 1.00 0.00 ATOM 208 CA GLY 25 11.138 -0.774 4.412 1.00 0.00 ATOM 209 O GLY 25 11.672 1.524 4.865 1.00 0.00 ATOM 210 C GLY 25 12.097 0.381 4.689 1.00 0.00 ATOM 211 N PRO 26 13.393 0.084 4.719 1.00 0.00 ATOM 212 CA PRO 26 14.383 1.122 4.958 1.00 0.00 ATOM 213 CB PRO 26 15.585 0.326 5.449 1.00 0.00 ATOM 214 CG PRO 26 15.510 -0.952 4.634 1.00 0.00 ATOM 215 CD PRO 26 14.026 -1.232 4.475 1.00 0.00 ATOM 216 O PRO 26 14.421 1.326 2.541 1.00 0.00 ATOM 217 C PRO 26 14.801 1.798 3.613 1.00 0.00 ATOM 218 N GLY 27 15.569 2.880 3.693 1.00 0.00 ATOM 219 CA GLY 27 16.015 3.581 2.494 1.00 0.00 ATOM 220 O GLY 27 17.756 1.939 2.333 1.00 0.00 ATOM 221 C GLY 27 17.083 2.789 1.749 1.00 0.00 ATOM 222 N VAL 28 17.239 3.070 0.459 1.00 0.00 ATOM 223 CA VAL 28 18.232 2.377 -0.351 1.00 0.00 ATOM 224 CB VAL 28 17.465 1.628 -1.473 1.00 0.00 ATOM 225 CG1 VAL 28 18.389 1.094 -2.563 1.00 0.00 ATOM 226 CG2 VAL 28 16.648 0.454 -0.890 1.00 0.00 ATOM 227 O VAL 28 19.009 4.537 -1.022 1.00 0.00 ATOM 228 C VAL 28 19.285 3.351 -0.838 1.00 0.00 ATOM 229 N PHE 29 20.499 2.852 -1.050 1.00 0.00 ATOM 230 CA PHE 29 21.591 3.696 -1.518 1.00 0.00 ATOM 231 CB PHE 29 22.857 3.397 -0.705 1.00 0.00 ATOM 232 CG PHE 29 24.055 4.218 -1.113 1.00 0.00 ATOM 233 CD1 PHE 29 24.987 3.714 -2.015 1.00 0.00 ATOM 234 CD2 PHE 29 24.238 5.502 -0.605 1.00 0.00 ATOM 235 CE1 PHE 29 26.086 4.477 -2.406 1.00 0.00 ATOM 236 CE2 PHE 29 25.339 6.276 -0.992 1.00 0.00 ATOM 237 CZ PHE 29 26.261 5.760 -1.893 1.00 0.00 ATOM 238 O PHE 29 21.814 2.218 -3.396 1.00 0.00 ATOM 239 C PHE 29 21.789 3.384 -2.998 1.00 0.00 ATOM 240 N LEU 30 21.930 4.426 -3.812 1.00 0.00 ATOM 241 CA LEU 30 22.124 4.240 -5.220 1.00 0.00 ATOM 242 CB LEU 30 21.586 5.474 -5.994 1.00 0.00 ATOM 243 CG LEU 30 21.778 5.449 -7.519 1.00 0.00 ATOM 244 CD1 LEU 30 20.844 4.417 -8.127 1.00 0.00 ATOM 245 CD2 LEU 30 21.490 6.820 -8.113 1.00 0.00 ATOM 246 O LEU 30 24.421 4.885 -5.154 1.00 0.00 ATOM 247 C LEU 30 23.588 4.061 -5.535 1.00 0.00 ATOM 248 N ALA 31 23.912 2.979 -6.236 1.00 0.00 ATOM 249 CA ALA 31 25.297 2.703 -6.602 1.00 0.00 ATOM 250 CB ALA 31 25.671 1.324 -6.012 1.00 0.00 ATOM 251 O ALA 31 24.932 2.225 -8.925 1.00 0.00 ATOM 252 C ALA 31 25.394 3.008 -8.093 1.00 0.00 ATOM 253 N GLU 32 25.993 4.146 -8.429 1.00 0.00 ATOM 254 CA GLU 32 26.143 4.537 -9.826 1.00 0.00 ATOM 255 CB GLU 32 26.893 5.863 -9.914 1.00 0.00 ATOM 256 CG GLU 32 27.035 6.409 -11.321 1.00 0.00 ATOM 257 CD GLU 32 27.921 7.636 -11.374 1.00 0.00 ATOM 258 OE1 GLU 32 28.092 8.287 -10.325 1.00 0.00 ATOM 259 OE2 GLU 32 28.436 7.952 -12.466 1.00 0.00 ATOM 260 O GLU 32 26.643 3.288 -11.821 1.00 0.00 ATOM 261 C GLU 32 26.988 3.581 -10.673 1.00 0.00 ATOM 262 N HIS 33 28.084 3.094 -10.105 1.00 0.00 ATOM 263 CA HIS 33 28.992 2.199 -10.820 1.00 0.00 ATOM 264 CB HIS 33 30.330 1.950 -10.253 1.00 0.00 ATOM 265 CG HIS 33 30.226 1.279 -8.916 1.00 0.00 ATOM 266 CD2 HIS 33 30.475 -0.002 -8.554 1.00 0.00 ATOM 267 ND1 HIS 33 29.818 1.935 -7.771 1.00 0.00 ATOM 268 CE1 HIS 33 29.829 1.079 -6.760 1.00 0.00 ATOM 269 NE2 HIS 33 30.221 -0.101 -7.207 1.00 0.00 ATOM 270 O HIS 33 28.761 0.239 -12.177 1.00 0.00 ATOM 271 C HIS 33 28.419 0.820 -11.151 1.00 0.00 ATOM 272 N ALA 34 27.564 0.284 -10.288 1.00 0.00 ATOM 273 CA ALA 34 26.976 -1.031 -10.541 1.00 0.00 ATOM 274 CB ALA 34 27.801 -2.016 -9.602 1.00 0.00 ATOM 275 O ALA 34 24.798 -1.900 -11.045 1.00 0.00 ATOM 276 C ALA 34 25.494 -0.899 -10.874 1.00 0.00 ATOM 277 N ASP 35 25.013 0.337 -10.967 1.00 0.00 ATOM 278 CA ASP 35 23.606 0.584 -11.285 1.00 0.00 ATOM 279 CB ASP 35 23.299 0.458 -12.775 1.00 0.00 ATOM 280 CG ASP 35 21.932 1.023 -13.115 1.00 0.00 ATOM 281 OD1 ASP 35 21.547 2.057 -12.509 1.00 0.00 ATOM 282 OD2 ASP 35 21.226 0.434 -13.965 1.00 0.00 ATOM 283 O ASP 35 21.910 -1.085 -11.010 1.00 0.00 ATOM 284 C ASP 35 22.709 -0.325 -10.462 1.00 0.00 ATOM 285 N ARG 36 22.840 -0.247 -9.141 1.00 0.00 ATOM 286 CA ARG 36 22.029 -1.071 -8.252 1.00 0.00 ATOM 287 CB ARG 36 22.859 -2.201 -7.687 1.00 0.00 ATOM 288 CG ARG 36 24.037 -1.753 -6.818 1.00 0.00 ATOM 289 CD ARG 36 24.868 -2.952 -6.394 1.00 0.00 ATOM 290 NE ARG 36 25.645 -3.480 -7.517 1.00 0.00 ATOM 291 CZ ARG 36 26.381 -4.585 -7.466 1.00 0.00 ATOM 292 NH1 ARG 36 27.055 -4.980 -8.536 1.00 0.00 ATOM 293 NH2 ARG 36 26.425 -5.310 -6.351 1.00 0.00 ATOM 294 O ARG 36 22.056 0.882 -6.867 1.00 0.00 ATOM 295 C ARG 36 21.529 -0.203 -7.107 1.00 0.00 ATOM 296 N TYR 37 20.507 -0.689 -6.417 1.00 0.00 ATOM 297 CA TYR 37 19.963 0.005 -5.252 1.00 0.00 ATOM 298 CB TYR 37 18.649 0.736 -5.663 1.00 0.00 ATOM 299 CG TYR 37 17.508 -0.142 -6.110 1.00 0.00 ATOM 300 CD1 TYR 37 17.529 -0.783 -7.340 1.00 0.00 ATOM 301 CD2 TYR 37 16.379 -0.328 -5.313 1.00 0.00 ATOM 302 CE1 TYR 37 16.484 -1.586 -7.757 1.00 0.00 ATOM 303 CE2 TYR 37 15.324 -1.126 -5.722 1.00 0.00 ATOM 304 CZ TYR 37 15.382 -1.752 -6.942 1.00 0.00 ATOM 305 OH TYR 37 14.343 -2.553 -7.382 1.00 0.00 ATOM 306 O TYR 37 19.730 -2.113 -4.148 1.00 0.00 ATOM 307 C TYR 37 20.245 -0.993 -4.134 1.00 0.00 ATOM 308 N SER 38 21.061 -0.587 -3.167 1.00 0.00 ATOM 309 CA SER 38 21.397 -1.457 -2.050 1.00 0.00 ATOM 310 CB SER 38 22.923 -1.482 -1.776 1.00 0.00 ATOM 311 OG SER 38 23.204 -2.381 -0.711 1.00 0.00 ATOM 312 O SER 38 20.535 0.035 -0.418 1.00 0.00 ATOM 313 C SER 38 20.728 -1.133 -0.759 1.00 0.00 ATOM 314 N CYS 39 20.362 -2.171 -0.014 1.00 0.00 ATOM 315 CA CYS 39 19.702 -1.983 1.272 1.00 0.00 ATOM 316 CB CYS 39 18.431 -2.805 1.438 1.00 0.00 ATOM 317 SG CYS 39 17.907 -2.813 3.187 1.00 0.00 ATOM 318 O CYS 39 21.089 -3.644 2.309 1.00 0.00 ATOM 319 C CYS 39 20.733 -2.465 2.287 1.00 0.00 ATOM 320 N GLY 40 21.211 -1.553 3.127 1.00 0.00 ATOM 321 CA GLY 40 22.191 -1.902 4.130 1.00 0.00 ATOM 322 O GLY 40 22.296 -3.886 5.475 1.00 0.00 ATOM 323 C GLY 40 21.656 -2.877 5.174 1.00 0.00 ATOM 324 N ARG 41 20.482 -2.577 5.722 1.00 0.00 ATOM 325 CA ARG 41 19.870 -3.442 6.733 1.00 0.00 ATOM 326 CB ARG 41 18.451 -2.748 7.027 1.00 0.00 ATOM 327 CG ARG 41 18.573 -1.384 7.700 1.00 0.00 ATOM 328 CD ARG 41 18.427 -1.527 9.209 1.00 0.00 ATOM 329 NE ARG 41 17.057 -1.883 9.563 1.00 0.00 ATOM 330 CZ ARG 41 16.675 -2.297 10.764 1.00 0.00 ATOM 331 NH1 ARG 41 17.565 -2.416 11.744 1.00 0.00 ATOM 332 NH2 ARG 41 15.404 -2.584 10.990 1.00 0.00 ATOM 333 O ARG 41 19.737 -5.778 7.273 1.00 0.00 ATOM 334 C ARG 41 19.686 -4.918 6.391 1.00 0.00 ATOM 335 N CYS 42 19.474 -5.211 5.112 1.00 0.00 ATOM 336 CA CYS 42 19.288 -6.589 4.672 1.00 0.00 ATOM 337 CB CYS 42 18.000 -6.555 3.827 1.00 0.00 ATOM 338 SG CYS 42 16.577 -5.801 4.681 1.00 0.00 ATOM 339 O CYS 42 20.485 -8.383 3.622 1.00 0.00 ATOM 340 C CYS 42 20.448 -7.179 3.878 1.00 0.00 ATOM 341 N GLY 43 21.395 -6.331 3.490 1.00 0.00 ATOM 342 CA GLY 43 22.548 -6.785 2.726 1.00 0.00 ATOM 343 O GLY 43 22.415 -8.475 1.028 1.00 0.00 ATOM 344 C GLY 43 22.044 -7.364 1.409 1.00 0.00 ATOM 345 N TYR 44 21.200 -6.609 0.712 1.00 0.00 ATOM 346 CA TYR 44 20.662 -7.060 -0.553 1.00 0.00 ATOM 347 CB TYR 44 19.179 -7.354 -0.476 1.00 0.00 ATOM 348 CG TYR 44 18.873 -8.664 0.202 1.00 0.00 ATOM 349 CD1 TYR 44 18.476 -8.712 1.527 1.00 0.00 ATOM 350 CD2 TYR 44 18.997 -9.853 -0.480 1.00 0.00 ATOM 351 CE1 TYR 44 18.204 -9.910 2.133 1.00 0.00 ATOM 352 CE2 TYR 44 18.729 -11.055 0.120 1.00 0.00 ATOM 353 CZ TYR 44 18.323 -11.081 1.433 1.00 0.00 ATOM 354 OH TYR 44 18.042 -12.274 2.048 1.00 0.00 ATOM 355 O TYR 44 20.829 -4.795 -1.326 1.00 0.00 ATOM 356 C TYR 44 20.877 -5.990 -1.619 1.00 0.00 ATOM 357 N THR 45 21.113 -6.421 -2.855 1.00 0.00 ATOM 358 CA THR 45 21.328 -5.489 -3.945 1.00 0.00 ATOM 359 CB THR 45 22.701 -5.668 -4.633 1.00 0.00 ATOM 360 CG2 THR 45 23.809 -5.479 -3.578 1.00 0.00 ATOM 361 OG1 THR 45 22.877 -7.009 -5.109 1.00 0.00 ATOM 362 O THR 45 20.217 -6.868 -5.555 1.00 0.00 ATOM 363 C THR 45 20.285 -5.765 -5.011 1.00 0.00 ATOM 364 N GLU 46 19.470 -4.760 -5.314 1.00 0.00 ATOM 365 CA GLU 46 18.430 -4.909 -6.326 1.00 0.00 ATOM 366 CB GLU 46 17.171 -4.176 -5.971 1.00 0.00 ATOM 367 CG GLU 46 16.105 -5.247 -5.929 1.00 0.00 ATOM 368 CD GLU 46 15.799 -5.599 -4.517 1.00 0.00 ATOM 369 OE1 GLU 46 15.862 -4.685 -3.689 1.00 0.00 ATOM 370 OE2 GLU 46 15.532 -6.755 -4.211 1.00 0.00 ATOM 371 O GLU 46 19.585 -3.162 -7.497 1.00 0.00 ATOM 372 C GLU 46 18.949 -4.213 -7.580 1.00 0.00 ATOM 373 N PHE 47 18.677 -4.801 -8.741 1.00 0.00 ATOM 374 CA PHE 47 19.122 -4.223 -10.002 1.00 0.00 ATOM 375 CB PHE 47 20.424 -4.886 -10.474 1.00 0.00 ATOM 376 CG PHE 47 20.307 -6.365 -10.729 1.00 0.00 ATOM 377 CD1 PHE 47 19.728 -6.842 -11.902 1.00 0.00 ATOM 378 CD2 PHE 47 20.778 -7.281 -9.793 1.00 0.00 ATOM 379 CE1 PHE 47 19.621 -8.210 -12.141 1.00 0.00 ATOM 380 CE2 PHE 47 20.677 -8.652 -10.022 1.00 0.00 ATOM 381 CZ PHE 47 20.096 -9.116 -11.199 1.00 0.00 ATOM 382 O PHE 47 17.195 -5.307 -10.925 1.00 0.00 ATOM 383 C PHE 47 18.002 -4.382 -11.018 1.00 0.00 ATOM 384 N LYS 48 17.954 -3.478 -11.991 1.00 0.00 ATOM 385 CA LYS 48 16.924 -3.533 -13.023 1.00 0.00 ATOM 386 CB LYS 48 16.605 -2.103 -13.464 1.00 0.00 ATOM 387 CG LYS 48 16.132 -1.200 -12.336 1.00 0.00 ATOM 388 CD LYS 48 15.841 0.206 -12.840 1.00 0.00 ATOM 389 CE LYS 48 15.370 1.115 -11.718 1.00 0.00 ATOM 390 NZ LYS 48 15.141 2.508 -12.193 1.00 0.00 ATOM 391 O LYS 48 16.606 -4.999 -14.891 1.00 0.00 ATOM 392 C LYS 48 17.399 -4.328 -14.229 1.00 0.00 ATOM 393 N LYS 49 18.695 -4.254 -14.515 1.00 0.00 ATOM 394 CA LYS 49 19.261 -4.976 -15.649 1.00 0.00 ATOM 395 CB LYS 49 19.596 -4.020 -16.796 1.00 0.00 ATOM 396 CG LYS 49 19.995 -4.706 -18.094 1.00 0.00 ATOM 397 CD LYS 49 20.185 -3.693 -19.223 1.00 0.00 ATOM 398 CE LYS 49 18.884 -2.974 -19.560 1.00 0.00 ATOM 399 NZ LYS 49 17.825 -3.921 -20.020 1.00 0.00 ATOM 400 O LYS 49 21.294 -5.246 -14.402 1.00 0.00 ATOM 401 C LYS 49 20.515 -5.734 -15.221 1.00 0.00 ATOM 402 N ALA 50 20.708 -6.926 -15.776 1.00 0.00 ATOM 403 CA ALA 50 21.874 -7.736 -15.443 1.00 0.00 ATOM 404 CB ALA 50 21.758 -9.113 -16.094 1.00 0.00 ATOM 405 O ALA 50 24.127 -6.986 -15.098 1.00 0.00 ATOM 406 C ALA 50 23.161 -7.032 -15.861 1.00 0.00 ATOM 407 N LYS 51 23.171 -6.484 -17.072 1.00 0.00 ATOM 408 CA LYS 51 24.350 -5.781 -17.575 1.00 0.00 ATOM 409 CB LYS 51 24.130 -5.394 -19.040 1.00 0.00 ATOM 410 CG LYS 51 24.070 -6.599 -19.981 1.00 0.00 ATOM 411 CD LYS 51 23.812 -6.183 -21.418 1.00 0.00 ATOM 412 CE LYS 51 23.821 -7.400 -22.335 1.00 0.00 ATOM 413 NZ LYS 51 23.613 -7.036 -23.772 1.00 0.00 ATOM 414 O LYS 51 25.784 -4.274 -16.403 1.00 0.00 ATOM 415 C LYS 51 24.634 -4.556 -16.740 1.00 0.00 ATOM 416 N LYS 52 23.581 -3.819 -16.400 1.00 0.00 ATOM 417 CA LYS 52 23.733 -2.612 -15.595 1.00 0.00 ATOM 418 CB LYS 52 22.417 -1.856 -15.474 1.00 0.00 ATOM 419 CG LYS 52 21.941 -1.244 -16.784 1.00 0.00 ATOM 420 CD LYS 52 23.017 -0.367 -17.431 1.00 0.00 ATOM 421 CE LYS 52 23.383 0.831 -16.563 1.00 0.00 ATOM 422 NZ LYS 52 22.222 1.742 -16.346 1.00 0.00 ATOM 423 O LYS 52 24.940 -2.181 -13.567 1.00 0.00 ATOM 424 C LYS 52 24.215 -2.957 -14.190 1.00 0.00 ATOM 425 N SER 53 23.812 -4.123 -13.693 1.00 0.00 ATOM 426 CA SER 53 24.210 -4.538 -12.389 1.00 0.00 ATOM 427 CB SER 53 23.280 -5.681 -11.930 1.00 0.00 ATOM 428 OG SER 53 23.601 -6.118 -10.629 1.00 0.00 ATOM 429 O SER 53 26.440 -4.574 -11.498 1.00 0.00 ATOM 430 C SER 53 25.683 -4.942 -12.400 1.00 0.00 ATOM 431 N LYS 54 26.095 -5.688 -13.404 1.00 0.00 ATOM 432 CA LYS 54 27.479 -6.139 -13.507 1.00 0.00 ATOM 433 CB LYS 54 27.576 -7.216 -14.592 1.00 0.00 ATOM 434 CG LYS 54 28.955 -7.816 -14.801 1.00 0.00 ATOM 435 CD LYS 54 28.932 -8.839 -15.930 1.00 0.00 ATOM 436 CE LYS 54 30.287 -9.494 -16.131 1.00 0.00 ATOM 437 NZ LYS 54 30.212 -10.644 -17.078 1.00 0.00 ATOM 438 O LYS 54 29.540 -5.023 -13.351 1.00 0.00 ATOM 439 C LYS 54 28.421 -5.010 -13.851 1.00 0.00 ATOM 440 N SER 55 28.014 -4.075 -14.701 1.00 0.00 ATOM 441 CA SER 55 28.860 -2.975 -15.120 1.00 0.00 ATOM 442 CB SER 55 29.479 -3.234 -16.495 1.00 0.00 ATOM 443 OG SER 55 28.502 -3.152 -17.519 1.00 0.00 ATOM 444 O SER 55 26.801 -1.753 -15.237 1.00 0.00 ATOM 445 C SER 55 28.029 -1.689 -15.194 1.00 0.00 TER END