PFRMAT TS TARGET T0499 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 METHOD All the models, whether native SAM+undertaker models or metaserver METHOD models, were very similar. I added some constraints to keep the OH METHOD atoms of Y3 and Y45 close together (as seen in the template 2igdA) and METHOD to keep W43 buried. METHOD METHOD The first model is the best scoring with my constrained cost function. METHOD The second is the same model followed by energy minimization by METHOD gromacs and repacking the sidechains by rosetta. Although many of the METHOD solvent-exposed residues have been changed to more canonical rotamers, METHOD I don't really like the way rosetta moved Y29, so I ranked this model METHOD lower. METHOD METHOD The third model is a meta-server model, optimized by undertaker using METHOD the same constrained cost function used to generate the first model, METHOD but starting from non-SAM server models. METHOD METHOD The fourth model is from an earlier metaserver run, without the METHOD constraints on Y45, so it ended up kicked out of position. METHOD METHOD The fifth model is the fully automatic one, with no human intervention METHOD other than choosing the gromacs-minimized version of the model to METHOD minimize clashes. METHOD METHOD Model METHOD 1 T0499.try4-opt3.pdb # < try3-gromacs0.repack-nonPC < try2-opt3 < align(2igdA) METHOD METHOD 2 T0499.try4-opt3.gromacs0.repack-nonPC.pdb # < try3-gromacs0.repack-nonPC < try2-opt3 < align(2igdA) METHOD # best rosetta energy METHOD METHOD 3 T0499.MQAX4-opt3.pdb # < pipe_int_TS1 METHOD METHOD 4 T0499.MQAC1-opt3.gromacs0.repack-nonPC.pdb # < SAM-T08-server_TS1 METHOD METHOD 5 T0499.try1-opt3.gromacs0.pdb # < align(2gi9A) REMARK 6 REMARK 6 T0499 model 3 Tue Jul 15 16:01:45 2008 MODEL 3 PARENT 2i38_A 2i2y_A 1ibx_B 1pn5_A 2cwb_A REMARK 7 REMARK 7 ALLPARENTS 2i38_A 2i2y_A 1ibx_B 1pn5_A 2cwb_A 1pgx_A 2igg_A REMARK 7 ALLPARENTS 1pgb_A 2igd_A 2igh_A 2qmt_A ATOM 1 N THR 1 15.174 9.481 17.392 1.00 0.00 ATOM 2 CA THR 1 13.848 9.287 18.119 1.00 0.00 ATOM 3 CB THR 1 14.060 8.342 19.299 1.00 0.00 ATOM 4 CG2 THR 1 14.541 6.952 18.890 1.00 0.00 ATOM 5 OG1 THR 1 14.997 8.816 20.263 1.00 0.00 ATOM 6 O THR 1 13.136 11.511 17.567 1.00 0.00 ATOM 7 C THR 1 13.375 10.695 18.459 1.00 0.00 ATOM 8 N THR 2 13.236 10.992 19.747 1.00 0.00 ATOM 9 CA THR 2 12.799 12.289 20.197 1.00 0.00 ATOM 10 CB THR 2 11.876 12.224 21.469 1.00 0.00 ATOM 11 CG2 THR 2 11.419 13.587 21.869 1.00 0.00 ATOM 12 OG1 THR 2 10.743 11.415 21.107 1.00 0.00 ATOM 13 O THR 2 14.826 12.766 21.402 1.00 0.00 ATOM 14 C THR 2 14.026 13.129 20.526 1.00 0.00 ATOM 15 N TYR 3 14.164 14.233 19.849 1.00 0.00 ATOM 16 CA TYR 3 15.212 15.198 20.062 1.00 0.00 ATOM 17 CB TYR 3 15.876 15.615 18.727 1.00 0.00 ATOM 18 CG TYR 3 16.605 14.511 18.074 1.00 0.00 ATOM 19 CD1 TYR 3 15.923 13.621 17.230 1.00 0.00 ATOM 20 CD2 TYR 3 17.952 14.284 18.281 1.00 0.00 ATOM 21 CE1 TYR 3 16.612 12.560 16.621 1.00 0.00 ATOM 22 CE2 TYR 3 18.632 13.206 17.679 1.00 0.00 ATOM 23 CZ TYR 3 17.908 12.353 16.850 1.00 0.00 ATOM 24 OH TYR 3 18.526 11.275 16.241 1.00 0.00 ATOM 25 O TYR 3 13.396 16.690 20.589 1.00 0.00 ATOM 26 C TYR 3 14.578 16.428 20.731 1.00 0.00 ATOM 27 N LYS 4 15.379 17.142 21.512 1.00 0.00 ATOM 28 CA LYS 4 14.931 18.274 22.305 1.00 0.00 ATOM 29 CB LYS 4 15.575 18.173 23.687 1.00 0.00 ATOM 30 CG LYS 4 14.783 18.806 24.790 1.00 0.00 ATOM 31 CD LYS 4 13.649 17.885 25.234 1.00 0.00 ATOM 32 CE LYS 4 14.114 16.889 26.294 1.00 0.00 ATOM 33 NZ LYS 4 13.255 15.653 26.303 1.00 0.00 ATOM 34 O LYS 4 16.673 19.537 21.270 1.00 0.00 ATOM 35 C LYS 4 15.539 19.542 21.772 1.00 0.00 ATOM 36 N LEU 5 14.816 20.651 21.904 1.00 0.00 ATOM 37 CA LEU 5 15.306 21.999 21.642 1.00 0.00 ATOM 38 CB LEU 5 14.550 22.678 20.496 1.00 0.00 ATOM 39 CG LEU 5 14.934 24.087 20.190 1.00 0.00 ATOM 40 CD1 LEU 5 16.363 24.201 19.697 1.00 0.00 ATOM 41 CD2 LEU 5 13.997 24.710 19.172 1.00 0.00 ATOM 42 O LEU 5 13.997 22.993 23.381 1.00 0.00 ATOM 43 C LEU 5 15.124 22.832 22.892 1.00 0.00 ATOM 44 N ILE 6 16.219 23.377 23.396 1.00 0.00 ATOM 45 CA ILE 6 16.266 24.338 24.487 1.00 0.00 ATOM 46 CB ILE 6 17.449 24.065 25.436 1.00 0.00 ATOM 47 CG1 ILE 6 17.392 22.616 25.959 1.00 0.00 ATOM 48 CG2 ILE 6 17.502 25.109 26.561 1.00 0.00 ATOM 49 CD1 ILE 6 16.076 22.220 26.637 1.00 0.00 ATOM 50 O ILE 6 17.274 25.995 23.075 1.00 0.00 ATOM 51 C ILE 6 16.347 25.742 23.832 1.00 0.00 ATOM 52 N LEU 7 15.364 26.587 24.112 1.00 0.00 ATOM 53 CA LEU 7 15.266 27.903 23.488 1.00 0.00 ATOM 54 CB LEU 7 13.808 28.122 22.936 1.00 0.00 ATOM 55 CG LEU 7 13.299 27.257 21.758 1.00 0.00 ATOM 56 CD1 LEU 7 12.581 26.019 22.273 1.00 0.00 ATOM 57 CD2 LEU 7 12.346 28.069 20.861 1.00 0.00 ATOM 58 O LEU 7 14.692 29.128 25.470 1.00 0.00 ATOM 59 C LEU 7 15.468 28.996 24.513 1.00 0.00 ATOM 60 N ASN 8 16.522 29.786 24.327 1.00 0.00 ATOM 61 CA ASN 8 16.827 30.947 25.133 1.00 0.00 ATOM 62 CB ASN 8 18.021 30.545 26.189 1.00 0.00 ATOM 63 CG ASN 8 18.038 29.103 26.657 1.00 0.00 ATOM 64 ND2 ASN 8 19.205 28.472 26.575 1.00 0.00 ATOM 65 OD1 ASN 8 17.025 28.568 27.107 1.00 0.00 ATOM 66 O ASN 8 17.700 32.657 23.712 1.00 0.00 ATOM 67 C ASN 8 16.708 32.148 24.200 1.00 0.00 ATOM 68 N LEU 9 15.485 32.581 23.921 1.00 0.00 ATOM 69 CA LEU 9 15.191 33.675 23.031 1.00 0.00 ATOM 70 CB LEU 9 14.105 33.280 22.001 1.00 0.00 ATOM 71 CG LEU 9 14.289 31.960 21.259 1.00 0.00 ATOM 72 CD1 LEU 9 13.051 31.574 20.440 1.00 0.00 ATOM 73 CD2 LEU 9 15.490 31.998 20.307 1.00 0.00 ATOM 74 O LEU 9 14.331 34.859 24.946 1.00 0.00 ATOM 75 C LEU 9 14.749 34.931 23.787 1.00 0.00 ATOM 76 N LYS 10 14.804 36.003 23.061 1.00 0.00 ATOM 77 CA LYS 10 14.449 37.296 23.644 1.00 0.00 ATOM 78 CB LYS 10 14.769 38.390 22.552 1.00 0.00 ATOM 79 CG LYS 10 14.327 39.784 22.965 1.00 0.00 ATOM 80 CD LYS 10 14.663 40.815 21.904 1.00 0.00 ATOM 81 CE LYS 10 14.288 42.217 22.357 1.00 0.00 ATOM 82 NZ LYS 10 14.672 43.247 21.344 1.00 0.00 ATOM 83 O LYS 10 12.721 37.852 25.213 1.00 0.00 ATOM 84 C LYS 10 13.007 37.319 24.141 1.00 0.00 ATOM 85 N GLN 11 12.101 36.738 23.361 1.00 0.00 ATOM 86 CA GLN 11 10.660 36.694 23.739 1.00 0.00 ATOM 87 CB GLN 11 9.805 36.957 22.318 1.00 0.00 ATOM 88 CG GLN 11 10.480 37.692 21.186 1.00 0.00 ATOM 89 CD GLN 11 10.504 39.196 21.396 1.00 0.00 ATOM 90 OE1 GLN 11 9.513 39.799 21.833 1.00 0.00 ATOM 91 NE2 GLN 11 11.627 39.810 21.057 1.00 0.00 ATOM 92 O GLN 11 9.166 35.042 24.695 1.00 0.00 ATOM 93 C GLN 11 10.122 35.247 23.946 1.00 0.00 ATOM 94 N ALA 12 10.742 34.273 23.287 1.00 0.00 ATOM 95 CA ALA 12 10.316 32.884 23.415 1.00 0.00 ATOM 96 CB ALA 12 9.972 32.286 22.072 1.00 0.00 ATOM 97 O ALA 12 12.546 32.145 23.904 1.00 0.00 ATOM 98 C ALA 12 11.358 32.118 24.225 1.00 0.00 ATOM 99 N LYS 13 10.909 31.436 25.273 1.00 0.00 ATOM 100 CA LYS 13 11.809 30.676 26.104 1.00 0.00 ATOM 101 CB LYS 13 12.094 31.414 27.408 1.00 0.00 ATOM 102 CG LYS 13 11.355 32.743 27.578 1.00 0.00 ATOM 103 CD LYS 13 9.842 32.559 27.638 1.00 0.00 ATOM 104 CE LYS 13 9.121 33.899 27.716 1.00 0.00 ATOM 105 NZ LYS 13 9.482 34.664 28.941 1.00 0.00 ATOM 106 O LYS 13 9.948 29.286 26.725 1.00 0.00 ATOM 107 C LYS 13 11.152 29.359 26.492 1.00 0.00 ATOM 108 N GLU 14 11.966 28.319 26.632 1.00 0.00 ATOM 109 CA GLU 14 11.537 27.046 27.148 1.00 0.00 ATOM 110 CB GLU 14 10.155 26.761 27.338 1.00 0.00 ATOM 111 CG GLU 14 9.621 27.332 28.639 1.00 0.00 ATOM 112 CD GLU 14 8.304 26.698 29.050 1.00 0.00 ATOM 113 OE1 GLU 14 8.286 25.468 29.281 1.00 0.00 ATOM 114 OE2 GLU 14 7.289 27.421 29.139 1.00 0.00 ATOM 115 O GLU 14 13.303 25.937 25.990 1.00 0.00 ATOM 116 C GLU 14 12.109 25.894 26.363 1.00 0.00 ATOM 117 N GLU 15 11.332 24.847 26.182 1.00 0.00 ATOM 118 CA GLU 15 11.766 23.634 25.506 1.00 0.00 ATOM 119 CB GLU 15 11.969 22.498 26.511 1.00 0.00 ATOM 120 CG GLU 15 10.913 22.380 27.614 1.00 0.00 ATOM 121 CD GLU 15 11.139 21.176 28.524 1.00 0.00 ATOM 122 OE1 GLU 15 10.488 21.088 29.587 1.00 0.00 ATOM 123 OE2 GLU 15 11.966 20.310 28.172 1.00 0.00 ATOM 124 O GLU 15 9.464 23.175 24.971 1.00 0.00 ATOM 125 C GLU 15 10.645 23.085 24.646 1.00 0.00 ATOM 126 N ALA 16 11.014 22.447 23.538 1.00 0.00 ATOM 127 CA ALA 16 10.090 21.741 22.672 1.00 0.00 ATOM 128 CB ALA 16 9.502 22.609 21.554 1.00 0.00 ATOM 129 O ALA 16 12.046 20.482 22.097 1.00 0.00 ATOM 130 C ALA 16 10.784 20.527 22.071 1.00 0.00 ATOM 131 N ILE 17 10.028 19.560 21.551 1.00 0.00 ATOM 132 CA ILE 17 10.612 18.284 21.137 1.00 0.00 ATOM 133 CB ILE 17 10.225 17.135 22.058 1.00 0.00 ATOM 134 CG1 ILE 17 8.694 16.944 22.216 1.00 0.00 ATOM 135 CG2 ILE 17 10.966 17.167 23.415 1.00 0.00 ATOM 136 CD1 ILE 17 8.302 15.618 22.875 1.00 0.00 ATOM 137 O ILE 17 9.087 18.487 19.281 1.00 0.00 ATOM 138 C ILE 17 10.141 17.990 19.721 1.00 0.00 ATOM 139 N LYS 18 10.862 17.104 19.052 1.00 0.00 ATOM 140 CA LYS 18 10.440 16.549 17.772 1.00 0.00 ATOM 141 CB LYS 18 10.923 17.447 16.593 1.00 0.00 ATOM 142 CG LYS 18 10.515 17.005 15.175 1.00 0.00 ATOM 143 CD LYS 18 9.019 17.103 14.970 1.00 0.00 ATOM 144 CE LYS 18 8.539 16.436 13.686 1.00 0.00 ATOM 145 NZ LYS 18 8.452 14.964 13.959 1.00 0.00 ATOM 146 O LYS 18 12.087 14.854 18.094 1.00 0.00 ATOM 147 C LYS 18 11.003 15.147 17.624 1.00 0.00 ATOM 148 N GLU 19 10.302 14.307 16.886 1.00 0.00 ATOM 149 CA GLU 19 10.757 12.936 16.602 1.00 0.00 ATOM 150 CB GLU 19 9.627 11.933 16.603 1.00 0.00 ATOM 151 CG GLU 19 10.115 10.532 16.254 1.00 0.00 ATOM 152 CD GLU 19 8.988 9.521 16.277 1.00 0.00 ATOM 153 OE1 GLU 19 7.867 9.915 15.883 1.00 0.00 ATOM 154 OE2 GLU 19 9.206 8.363 16.691 1.00 0.00 ATOM 155 O GLU 19 10.704 13.439 14.239 1.00 0.00 ATOM 156 C GLU 19 11.302 12.879 15.164 1.00 0.00 ATOM 157 N ALA 20 12.438 12.203 14.988 1.00 0.00 ATOM 158 CA ALA 20 13.002 12.071 13.672 1.00 0.00 ATOM 159 CB ALA 20 13.823 13.313 13.308 1.00 0.00 ATOM 160 O ALA 20 14.517 10.422 14.564 1.00 0.00 ATOM 161 C ALA 20 13.928 10.856 13.579 1.00 0.00 ATOM 162 N VAL 21 14.111 10.393 12.351 1.00 0.00 ATOM 163 CA VAL 21 15.016 9.285 12.070 1.00 0.00 ATOM 164 CB VAL 21 14.474 8.623 10.675 1.00 0.00 ATOM 165 CG1 VAL 21 15.406 7.506 10.221 1.00 0.00 ATOM 166 CG2 VAL 21 13.060 8.085 10.831 1.00 0.00 ATOM 167 O VAL 21 17.290 8.748 12.569 1.00 0.00 ATOM 168 C VAL 21 16.474 9.629 12.289 1.00 0.00 ATOM 169 N ASP 22 16.873 10.887 12.139 1.00 0.00 ATOM 170 CA ASP 22 18.257 11.279 12.285 1.00 0.00 ATOM 171 CB ASP 22 19.056 11.022 11.011 1.00 0.00 ATOM 172 CG ASP 22 18.544 11.797 9.798 1.00 0.00 ATOM 173 OD1 ASP 22 18.076 12.898 9.931 1.00 0.00 ATOM 174 OD2 ASP 22 18.633 11.256 8.697 1.00 0.00 ATOM 175 O ASP 22 17.316 13.477 12.783 1.00 0.00 ATOM 176 C ASP 22 18.312 12.735 12.757 1.00 0.00 ATOM 177 N ALA 23 19.508 13.155 13.137 1.00 0.00 ATOM 178 CA ALA 23 19.692 14.524 13.719 1.00 0.00 ATOM 179 CB ALA 23 21.116 14.590 14.337 1.00 0.00 ATOM 180 O ALA 23 18.971 16.681 12.954 1.00 0.00 ATOM 181 C ALA 23 19.525 15.617 12.670 1.00 0.00 ATOM 182 N GLY 24 20.003 15.356 11.457 1.00 0.00 ATOM 183 CA GLY 24 19.894 16.319 10.394 1.00 0.00 ATOM 184 O GLY 24 18.141 17.861 9.866 1.00 0.00 ATOM 185 C GLY 24 18.453 16.694 10.105 1.00 0.00 ATOM 186 N THR 25 17.568 15.702 10.128 1.00 0.00 ATOM 187 CA THR 25 16.154 15.945 9.870 1.00 0.00 ATOM 188 CB THR 25 15.426 14.597 9.659 1.00 0.00 ATOM 189 CG2 THR 25 13.938 14.770 9.456 1.00 0.00 ATOM 190 OG1 THR 25 16.002 13.878 8.579 1.00 0.00 ATOM 191 O THR 25 14.721 17.669 10.772 1.00 0.00 ATOM 192 C THR 25 15.526 16.766 10.993 1.00 0.00 ATOM 193 N ALA 26 15.911 16.432 12.236 1.00 0.00 ATOM 194 CA ALA 26 15.450 17.220 13.379 1.00 0.00 ATOM 195 CB ALA 26 15.881 16.559 14.677 1.00 0.00 ATOM 196 O ALA 26 15.232 19.598 13.615 1.00 0.00 ATOM 197 C ALA 26 15.966 18.654 13.323 1.00 0.00 ATOM 198 N GLU 27 17.231 18.815 12.945 1.00 0.00 ATOM 199 CA GLU 27 17.825 20.138 12.852 1.00 0.00 ATOM 200 CB GLU 27 19.271 20.009 12.363 1.00 0.00 ATOM 201 CG GLU 27 20.063 21.284 12.466 1.00 0.00 ATOM 202 CD GLU 27 21.412 21.177 11.786 1.00 0.00 ATOM 203 OE1 GLU 27 21.468 20.639 10.660 1.00 0.00 ATOM 204 OE2 GLU 27 22.415 21.628 12.378 1.00 0.00 ATOM 205 O GLU 27 16.735 22.163 12.134 1.00 0.00 ATOM 206 C GLU 27 17.041 21.010 11.861 1.00 0.00 ATOM 207 N LYS 28 16.701 20.474 10.698 1.00 0.00 ATOM 208 CA LYS 28 15.952 21.216 9.722 1.00 0.00 ATOM 209 CB LYS 28 15.833 20.403 8.431 1.00 0.00 ATOM 210 CG LYS 28 17.088 20.274 7.641 1.00 0.00 ATOM 211 CD LYS 28 16.923 19.424 6.383 1.00 0.00 ATOM 212 CE LYS 28 18.289 19.221 5.699 1.00 0.00 ATOM 213 NZ LYS 28 18.130 18.072 4.713 1.00 0.00 ATOM 214 O LYS 28 14.111 22.721 10.041 1.00 0.00 ATOM 215 C LYS 28 14.581 21.605 10.265 1.00 0.00 ATOM 216 N TYR 29 13.941 20.683 10.978 1.00 0.00 ATOM 217 CA TYR 29 12.599 20.945 11.562 1.00 0.00 ATOM 218 CB TYR 29 12.017 19.691 12.222 1.00 0.00 ATOM 219 CG TYR 29 11.533 18.684 11.230 1.00 0.00 ATOM 220 CD1 TYR 29 10.989 19.113 9.968 1.00 0.00 ATOM 221 CD2 TYR 29 11.541 17.329 11.551 1.00 0.00 ATOM 222 CE1 TYR 29 10.539 18.136 9.021 1.00 0.00 ATOM 223 CE2 TYR 29 11.044 16.361 10.637 1.00 0.00 ATOM 224 CZ TYR 29 10.536 16.827 9.427 1.00 0.00 ATOM 225 OH TYR 29 10.046 15.863 8.536 1.00 0.00 ATOM 226 O TYR 29 11.811 22.992 12.556 1.00 0.00 ATOM 227 C TYR 29 12.659 22.097 12.577 1.00 0.00 ATOM 228 N PHE 30 13.655 22.070 13.454 1.00 0.00 ATOM 229 CA PHE 30 13.807 23.116 14.459 1.00 0.00 ATOM 230 CB PHE 30 14.689 22.628 15.597 1.00 0.00 ATOM 231 CG PHE 30 14.103 21.594 16.497 1.00 0.00 ATOM 232 CD1 PHE 30 12.756 21.569 16.843 1.00 0.00 ATOM 233 CD2 PHE 30 14.911 20.629 17.081 1.00 0.00 ATOM 234 CE1 PHE 30 12.281 20.649 17.756 1.00 0.00 ATOM 235 CE2 PHE 30 14.422 19.719 17.987 1.00 0.00 ATOM 236 CZ PHE 30 13.094 19.742 18.340 1.00 0.00 ATOM 237 O PHE 30 13.729 25.504 14.246 1.00 0.00 ATOM 238 C PHE 30 14.246 24.455 13.838 1.00 0.00 ATOM 239 N LYS 31 15.162 24.383 12.902 1.00 0.00 ATOM 240 CA LYS 31 15.585 25.652 12.262 1.00 0.00 ATOM 241 CB LYS 31 16.734 25.342 11.266 1.00 0.00 ATOM 242 CG LYS 31 17.160 26.518 10.387 1.00 0.00 ATOM 243 CD LYS 31 17.608 27.723 11.197 1.00 0.00 ATOM 244 CE LYS 31 18.227 28.775 10.282 1.00 0.00 ATOM 245 NZ LYS 31 18.410 30.085 10.958 1.00 0.00 ATOM 246 O LYS 31 14.268 27.519 11.582 1.00 0.00 ATOM 247 C LYS 31 14.409 26.305 11.544 1.00 0.00 ATOM 248 N LEU 32 13.567 25.498 10.900 1.00 0.00 ATOM 249 CA LEU 32 12.379 26.045 10.254 1.00 0.00 ATOM 250 CB LEU 32 11.660 24.924 9.464 1.00 0.00 ATOM 251 CG LEU 32 10.311 25.312 8.844 1.00 0.00 ATOM 252 CD1 LEU 32 10.510 26.442 7.846 1.00 0.00 ATOM 253 CD2 LEU 32 9.687 24.094 8.164 1.00 0.00 ATOM 254 O LEU 32 10.850 27.714 11.043 1.00 0.00 ATOM 255 C LEU 32 11.423 26.646 11.270 1.00 0.00 ATOM 256 N ILE 33 11.212 25.970 12.394 1.00 0.00 ATOM 257 CA ILE 33 10.393 26.499 13.483 1.00 0.00 ATOM 258 CB ILE 33 10.359 25.446 14.599 1.00 0.00 ATOM 259 CG1 ILE 33 9.503 24.247 14.157 1.00 0.00 ATOM 260 CG2 ILE 33 9.805 26.039 15.890 1.00 0.00 ATOM 261 CD1 ILE 33 9.413 23.113 15.146 1.00 0.00 ATOM 262 O ILE 33 10.171 28.778 14.211 1.00 0.00 ATOM 263 C ILE 33 10.935 27.822 13.972 1.00 0.00 ATOM 264 N ALA 34 12.252 27.923 14.186 1.00 0.00 ATOM 265 CA ALA 34 12.833 29.159 14.695 1.00 0.00 ATOM 266 CB ALA 34 14.320 28.997 14.925 1.00 0.00 ATOM 267 O ALA 34 12.292 31.405 14.079 1.00 0.00 ATOM 268 C ALA 34 12.630 30.279 13.676 1.00 0.00 ATOM 269 N ASN 35 12.823 29.978 12.379 1.00 0.00 ATOM 270 CA ASN 35 12.666 30.991 11.339 1.00 0.00 ATOM 271 CB ASN 35 13.203 30.456 9.972 1.00 0.00 ATOM 272 CG ASN 35 14.782 30.355 9.917 1.00 0.00 ATOM 273 ND2 ASN 35 15.288 29.541 9.004 1.00 0.00 ATOM 274 OD1 ASN 35 15.489 30.977 10.713 1.00 0.00 ATOM 275 O ASN 35 10.966 32.654 11.020 1.00 0.00 ATOM 276 C ASN 35 11.222 31.466 11.221 1.00 0.00 ATOM 277 N ALA 36 10.279 30.537 11.345 1.00 0.00 ATOM 278 CA ALA 36 8.826 30.876 11.251 1.00 0.00 ATOM 279 CB ALA 36 7.991 29.585 11.236 1.00 0.00 ATOM 280 O ALA 36 7.383 32.507 12.260 1.00 0.00 ATOM 281 C ALA 36 8.382 31.796 12.384 1.00 0.00 ATOM 282 N LYS 37 9.124 31.784 13.485 1.00 0.00 ATOM 283 CA LYS 37 8.794 32.638 14.656 1.00 0.00 ATOM 284 CB LYS 37 8.755 31.739 15.938 1.00 0.00 ATOM 285 CG LYS 37 7.633 30.761 15.965 1.00 0.00 ATOM 286 CD LYS 37 6.303 31.390 16.243 1.00 0.00 ATOM 287 CE LYS 37 5.171 30.333 16.283 1.00 0.00 ATOM 288 NZ LYS 37 4.722 29.877 14.961 1.00 0.00 ATOM 289 O LYS 37 9.575 34.598 15.716 1.00 0.00 ATOM 290 C LYS 37 9.692 33.797 14.788 1.00 0.00 ATOM 291 N THR 38 10.613 34.042 13.907 1.00 0.00 ATOM 292 CA THR 38 11.451 35.234 13.887 1.00 0.00 ATOM 293 CB THR 38 10.725 36.552 14.198 1.00 0.00 ATOM 294 CG2 THR 38 11.514 37.861 13.957 1.00 0.00 ATOM 295 OG1 THR 38 9.507 36.502 13.353 1.00 0.00 ATOM 296 O THR 38 13.064 36.182 15.390 1.00 0.00 ATOM 297 C THR 38 12.606 35.158 14.881 1.00 0.00 ATOM 298 N VAL 39 13.074 33.945 15.155 1.00 0.00 ATOM 299 CA VAL 39 14.180 33.753 16.090 1.00 0.00 ATOM 300 CB VAL 39 13.643 32.930 17.360 1.00 0.00 ATOM 301 CG1 VAL 39 12.493 33.611 18.077 1.00 0.00 ATOM 302 CG2 VAL 39 13.200 31.560 16.884 1.00 0.00 ATOM 303 O VAL 39 15.614 32.732 14.462 1.00 0.00 ATOM 304 C VAL 39 15.478 33.621 15.304 1.00 0.00 ATOM 305 N GLU 40 16.431 34.506 15.578 1.00 0.00 ATOM 306 CA GLU 40 17.715 34.472 14.888 1.00 0.00 ATOM 307 CB GLU 40 17.864 35.754 14.093 1.00 0.00 ATOM 308 CG GLU 40 16.761 36.075 13.069 1.00 0.00 ATOM 309 CD GLU 40 16.853 35.231 11.810 1.00 0.00 ATOM 310 OE1 GLU 40 17.922 34.693 11.500 1.00 0.00 ATOM 311 OE2 GLU 40 15.838 35.089 11.125 1.00 0.00 ATOM 312 O GLU 40 19.205 35.443 16.446 1.00 0.00 ATOM 313 C GLU 40 18.777 34.418 15.914 1.00 0.00 ATOM 314 N GLY 41 19.231 33.206 16.217 1.00 0.00 ATOM 315 CA GLY 41 20.280 33.018 17.212 1.00 0.00 ATOM 316 O GLY 41 21.570 31.763 15.626 1.00 0.00 ATOM 317 C GLY 41 21.363 32.074 16.801 1.00 0.00 ATOM 318 N VAL 42 22.146 31.653 17.812 1.00 0.00 ATOM 319 CA VAL 42 23.249 30.720 17.614 1.00 0.00 ATOM 320 CB VAL 42 24.598 31.166 18.248 1.00 0.00 ATOM 321 CG1 VAL 42 25.100 32.336 17.507 1.00 0.00 ATOM 322 CG2 VAL 42 24.465 31.543 19.736 1.00 0.00 ATOM 323 O VAL 42 22.108 29.349 19.227 1.00 0.00 ATOM 324 C VAL 42 22.876 29.402 18.269 1.00 0.00 ATOM 325 N TRP 43 23.445 28.325 17.721 1.00 0.00 ATOM 326 CA TRP 43 22.988 26.969 17.974 1.00 0.00 ATOM 327 CB TRP 43 22.402 26.358 16.673 1.00 0.00 ATOM 328 CG TRP 43 21.131 27.010 16.231 1.00 0.00 ATOM 329 CD1 TRP 43 20.957 28.250 15.666 1.00 0.00 ATOM 330 CD2 TRP 43 19.807 26.446 16.346 1.00 0.00 ATOM 331 CE2 TRP 43 18.916 27.416 15.819 1.00 0.00 ATOM 332 CE3 TRP 43 19.306 25.273 16.811 1.00 0.00 ATOM 333 NE1 TRP 43 19.659 28.479 15.410 1.00 0.00 ATOM 334 CZ2 TRP 43 17.547 27.168 15.778 1.00 0.00 ATOM 335 CZ3 TRP 43 17.928 25.038 16.775 1.00 0.00 ATOM 336 CH2 TRP 43 17.076 26.018 16.257 1.00 0.00 ATOM 337 O TRP 43 25.238 26.114 17.956 1.00 0.00 ATOM 338 C TRP 43 24.097 26.067 18.451 1.00 0.00 ATOM 339 N THR 44 23.752 25.115 19.333 1.00 0.00 ATOM 340 CA THR 44 24.556 23.959 19.619 1.00 0.00 ATOM 341 CB THR 44 25.323 24.111 20.974 1.00 0.00 ATOM 342 CG2 THR 44 26.150 25.391 20.974 1.00 0.00 ATOM 343 OG1 THR 44 24.371 24.160 22.042 1.00 0.00 ATOM 344 O THR 44 22.509 22.683 19.726 1.00 0.00 ATOM 345 C THR 44 23.716 22.686 19.494 1.00 0.00 ATOM 346 N TYR 45 24.413 21.584 19.191 1.00 0.00 ATOM 347 CA TYR 45 23.858 20.253 19.233 1.00 0.00 ATOM 348 CB TYR 45 23.911 19.667 17.837 1.00 0.00 ATOM 349 CG TYR 45 23.443 18.235 17.774 1.00 0.00 ATOM 350 CD1 TYR 45 22.150 17.884 18.168 1.00 0.00 ATOM 351 CD2 TYR 45 24.288 17.228 17.312 1.00 0.00 ATOM 352 CE1 TYR 45 21.715 16.564 18.110 1.00 0.00 ATOM 353 CE2 TYR 45 23.863 15.906 17.250 1.00 0.00 ATOM 354 CZ TYR 45 22.575 15.583 17.650 1.00 0.00 ATOM 355 OH TYR 45 22.145 14.279 17.591 1.00 0.00 ATOM 356 O TYR 45 25.984 19.316 19.798 1.00 0.00 ATOM 357 C TYR 45 24.785 19.334 20.040 1.00 0.00 ATOM 358 N LYS 46 24.204 18.583 20.969 1.00 0.00 ATOM 359 CA LYS 46 24.913 17.587 21.753 1.00 0.00 ATOM 360 CB LYS 46 24.848 17.802 23.241 1.00 0.00 ATOM 361 CG LYS 46 25.885 17.032 24.026 1.00 0.00 ATOM 362 CD LYS 46 27.281 17.419 23.550 1.00 0.00 ATOM 363 CE LYS 46 28.351 16.937 24.505 1.00 0.00 ATOM 364 NZ LYS 46 28.321 15.459 24.654 1.00 0.00 ATOM 365 O LYS 46 23.240 15.868 21.742 1.00 0.00 ATOM 366 C LYS 46 24.377 16.203 21.407 1.00 0.00 ATOM 367 N ASP 47 25.197 15.398 20.738 1.00 0.00 ATOM 368 CA ASP 47 24.790 14.070 20.365 1.00 0.00 ATOM 369 CB ASP 47 26.402 13.527 19.995 1.00 0.00 ATOM 370 CG ASP 47 26.729 12.681 18.772 1.00 0.00 ATOM 371 OD1 ASP 47 26.439 11.458 18.771 1.00 0.00 ATOM 372 OD2 ASP 47 27.326 13.234 17.821 1.00 0.00 ATOM 373 O ASP 47 23.506 12.432 21.526 1.00 0.00 ATOM 374 C ASP 47 24.480 13.193 21.560 1.00 0.00 ATOM 375 N GLU 48 25.266 13.312 22.624 1.00 0.00 ATOM 376 CA GLU 48 25.077 12.498 23.814 1.00 0.00 ATOM 377 CB GLU 48 26.143 12.812 24.891 1.00 0.00 ATOM 378 CG GLU 48 26.016 12.072 26.197 1.00 0.00 ATOM 379 CD GLU 48 26.204 10.572 26.108 1.00 0.00 ATOM 380 OE1 GLU 48 26.873 10.079 25.183 1.00 0.00 ATOM 381 OE2 GLU 48 25.678 9.847 26.987 1.00 0.00 ATOM 382 O GLU 48 23.180 11.649 24.919 1.00 0.00 ATOM 383 C GLU 48 23.697 12.627 24.376 1.00 0.00 ATOM 384 N ILE 49 23.203 13.872 24.593 1.00 0.00 ATOM 385 CA ILE 49 21.896 14.137 25.220 1.00 0.00 ATOM 386 CB ILE 49 21.948 15.344 26.188 1.00 0.00 ATOM 387 CG1 ILE 49 22.442 16.574 25.487 1.00 0.00 ATOM 388 CG2 ILE 49 22.851 14.929 27.330 1.00 0.00 ATOM 389 CD1 ILE 49 22.445 17.823 26.416 1.00 0.00 ATOM 390 O ILE 49 19.646 14.711 24.536 1.00 0.00 ATOM 391 C ILE 49 20.779 14.396 24.170 1.00 0.00 ATOM 392 N LYS 50 21.112 14.258 22.890 1.00 0.00 ATOM 393 CA LYS 50 20.135 14.475 21.829 1.00 0.00 ATOM 394 CB LYS 50 19.454 12.957 21.543 1.00 0.00 ATOM 395 CG LYS 50 20.261 11.744 22.003 1.00 0.00 ATOM 396 CD LYS 50 19.548 10.445 21.753 1.00 0.00 ATOM 397 CE LYS 50 20.434 9.292 22.203 1.00 0.00 ATOM 398 NZ LYS 50 21.686 9.112 21.389 1.00 0.00 ATOM 399 O LYS 50 18.209 15.886 21.848 1.00 0.00 ATOM 400 C LYS 50 19.431 15.792 22.020 1.00 0.00 ATOM 401 N THR 51 20.182 16.838 22.327 1.00 0.00 ATOM 402 CA THR 51 19.631 18.151 22.645 1.00 0.00 ATOM 403 CB THR 51 19.802 18.469 24.131 1.00 0.00 ATOM 404 CG2 THR 51 19.199 19.844 24.490 1.00 0.00 ATOM 405 OG1 THR 51 19.116 17.495 24.907 1.00 0.00 ATOM 406 O THR 51 21.505 19.270 21.628 1.00 0.00 ATOM 407 C THR 51 20.272 19.202 21.752 1.00 0.00 ATOM 408 N PHE 52 19.411 20.051 21.188 1.00 0.00 ATOM 409 CA PHE 52 19.780 21.256 20.488 1.00 0.00 ATOM 410 CB PHE 52 18.911 21.459 19.234 1.00 0.00 ATOM 411 CG PHE 52 19.113 20.434 18.159 1.00 0.00 ATOM 412 CD1 PHE 52 18.455 19.218 18.181 1.00 0.00 ATOM 413 CD2 PHE 52 19.979 20.695 17.098 1.00 0.00 ATOM 414 CE1 PHE 52 18.635 18.277 17.184 1.00 0.00 ATOM 415 CE2 PHE 52 20.156 19.757 16.096 1.00 0.00 ATOM 416 CZ PHE 52 19.451 18.572 16.139 1.00 0.00 ATOM 417 O PHE 52 18.554 22.393 22.192 1.00 0.00 ATOM 418 C PHE 52 19.524 22.437 21.420 1.00 0.00 ATOM 419 N THR 53 20.330 23.472 21.303 1.00 0.00 ATOM 420 CA THR 53 20.114 24.722 22.073 1.00 0.00 ATOM 421 CB THR 53 21.127 24.819 23.224 1.00 0.00 ATOM 422 CG2 THR 53 20.931 26.126 23.976 1.00 0.00 ATOM 423 OG1 THR 53 20.946 23.723 24.130 1.00 0.00 ATOM 424 O THR 53 21.139 25.926 20.311 1.00 0.00 ATOM 425 C THR 53 20.215 25.893 21.123 1.00 0.00 ATOM 426 N VAL 54 19.313 26.841 21.232 1.00 0.00 ATOM 427 CA VAL 54 19.409 28.101 20.507 1.00 0.00 ATOM 428 CB VAL 54 18.312 28.191 19.395 1.00 0.00 ATOM 429 CG1 VAL 54 16.893 28.139 19.902 1.00 0.00 ATOM 430 CG2 VAL 54 18.540 29.473 18.572 1.00 0.00 ATOM 431 O VAL 54 18.571 29.235 22.435 1.00 0.00 ATOM 432 C VAL 54 19.380 29.233 21.509 1.00 0.00 ATOM 433 N THR 55 20.256 30.217 21.293 1.00 0.00 ATOM 434 CA THR 55 20.285 31.451 22.093 1.00 0.00 ATOM 435 CB THR 55 21.601 31.532 22.854 1.00 0.00 ATOM 436 CG2 THR 55 21.690 30.502 23.977 1.00 0.00 ATOM 437 OG1 THR 55 22.698 31.268 21.985 1.00 0.00 ATOM 438 O THR 55 21.075 32.713 20.248 1.00 0.00 ATOM 439 C THR 55 20.287 32.641 21.207 1.00 0.00 ATOM 440 N GLU 56 19.502 33.645 21.575 1.00 0.00 ATOM 441 CA GLU 56 19.591 34.999 21.030 1.00 0.00 ATOM 442 CB GLU 56 18.459 35.861 21.561 1.00 0.00 ATOM 443 CG GLU 56 17.095 35.433 21.016 1.00 0.00 ATOM 444 CD GLU 56 16.828 35.905 19.610 1.00 0.00 ATOM 445 OE1 GLU 56 17.466 36.859 19.128 1.00 0.00 ATOM 446 OE2 GLU 56 15.944 35.311 18.940 1.00 0.00 ATOM 447 O GLU 56 21.645 36.044 20.442 1.00 0.00 ATOM 448 C GLU 56 20.964 35.553 21.330 1.00 0.00 TER END