PFRMAT TS TARGET TR469 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 This refinement started with two models: the provided Zhang-Server_TS3 METHOD model and SAM-T08-hand_TS1 (here called from-try13-opt3), which was METHOD very similar (closer to the Zhang model than the Zhang model is to the METHOD real structure). METHOD METHOD The main hand addition was to add clustering constraints for the C32, METHOD C35, and H50 residues, trying to create a metal-binding site. METHOD METHOD I don't think that the undertaker cost fcns are really fine tuend METHOD enough to refine a model that is this close to being correct. METHOD METHOD Model METHOD 1 TR469.try12-opt3.pdb # < try11-opt3 < chimera-try10-try7 METHOD chimera-try10-try7 METHOD mostly TR469.try7-opt3.pdb METHOD Q3 and K4 from try10-opt3. METHOD METHOD 2 TR469.try10-opt3.pdb # < try4-opt3 < try3-opt3 < try2-opt3 < TR469 METHOD METHOD 3 TR469.try9-opt3.pdb # < try8-opt3 < try7-opt3.gromacs0 < try6-opt3 < try5-opt3 < from-try13-opt3.pdb< try6-opt3 < try5-opt3 < from-try13-opt3 METHOD METHOD 4 TR469.try8-opt3.gromacs0.repack-nonPC.pdb # < try7-opt3.gromacs0 < try6-opt3 < try5-opt3 < from-try13-opt3 METHOD # best rosetta energy METHOD METHOD 5 TR469.try4-opt3.pdb # < try3-opt3 < try2-opt3 < TR469 REMARK 6 REMARK 6 TR469 model 5 Thu Aug 14 14:48:22 2008 MODEL 5 PARENT N/A ATOM 1 N GLN 3 8.572 11.526 21.746 1.00 0.00 ATOM 2 CA GLN 3 8.348 10.052 21.806 1.00 0.00 ATOM 3 CB GLN 3 7.491 9.620 20.596 1.00 0.00 ATOM 4 CG GLN 3 7.167 8.132 20.565 1.00 0.00 ATOM 5 CD GLN 3 6.485 7.707 19.280 1.00 0.00 ATOM 6 OE1 GLN 3 7.011 7.916 18.186 1.00 0.00 ATOM 7 NE2 GLN 3 5.307 7.101 19.405 1.00 0.00 ATOM 8 O GLN 3 10.327 9.165 22.834 1.00 0.00 ATOM 9 C GLN 3 9.680 9.302 21.798 1.00 0.00 ATOM 10 N LYS 4 10.079 8.746 20.590 1.00 0.00 ATOM 11 CA LYS 4 11.285 7.990 20.575 1.00 0.00 ATOM 12 CB LYS 4 11.069 6.643 19.849 1.00 0.00 ATOM 13 CG LYS 4 9.963 5.790 20.445 1.00 0.00 ATOM 14 CD LYS 4 9.741 4.520 19.638 1.00 0.00 ATOM 15 CE LYS 4 8.579 3.716 20.215 1.00 0.00 ATOM 16 NZ LYS 4 8.236 2.533 19.375 1.00 0.00 ATOM 17 O LYS 4 12.351 9.227 18.834 1.00 0.00 ATOM 18 C LYS 4 12.380 8.808 19.990 1.00 0.00 ATOM 19 N PHE 5 13.383 9.107 20.830 1.00 0.00 ATOM 20 CA PHE 5 14.410 9.958 20.341 1.00 0.00 ATOM 21 CB PHE 5 14.446 11.271 21.135 1.00 0.00 ATOM 22 CG PHE 5 15.571 12.190 20.731 1.00 0.00 ATOM 23 CD1 PHE 5 15.487 12.939 19.561 1.00 0.00 ATOM 24 CD2 PHE 5 16.724 12.282 21.503 1.00 0.00 ATOM 25 CE1 PHE 5 16.542 13.766 19.164 1.00 0.00 ATOM 26 CE2 PHE 5 17.785 13.103 21.117 1.00 0.00 ATOM 27 CZ PHE 5 17.691 13.847 19.945 1.00 0.00 ATOM 28 O PHE 5 16.353 9.016 21.388 1.00 0.00 ATOM 29 C PHE 5 15.804 9.339 20.333 1.00 0.00 ATOM 30 N THR 6 16.376 9.176 19.144 1.00 0.00 ATOM 31 CA THR 6 17.654 8.619 19.040 1.00 0.00 ATOM 32 CB THR 6 17.725 7.723 17.790 1.00 0.00 ATOM 33 CG2 THR 6 19.101 7.084 17.669 1.00 0.00 ATOM 34 OG1 THR 6 16.739 6.687 17.884 1.00 0.00 ATOM 35 O THR 6 18.617 10.483 17.990 1.00 0.00 ATOM 36 C THR 6 18.638 9.723 18.945 1.00 0.00 ATOM 37 N LYS 7 19.622 9.758 19.850 1.00 0.00 ATOM 38 CA LYS 7 20.528 10.870 19.892 1.00 0.00 ATOM 39 CB LYS 7 21.722 10.243 20.989 1.00 0.00 ATOM 40 CG LYS 7 21.251 9.273 22.106 1.00 0.00 ATOM 41 CD LYS 7 22.485 8.463 22.535 1.00 0.00 ATOM 42 CE LYS 7 22.291 7.639 23.791 1.00 0.00 ATOM 43 NZ LYS 7 21.067 6.863 23.715 1.00 0.00 ATOM 44 O LYS 7 21.845 12.084 18.340 1.00 0.00 ATOM 45 C LYS 7 21.301 11.019 18.619 1.00 0.00 ATOM 46 N ASP 8 21.361 9.960 17.805 1.00 0.00 ATOM 47 CA ASP 8 22.156 9.895 16.612 1.00 0.00 ATOM 48 CB ASP 8 22.179 8.473 16.048 1.00 0.00 ATOM 49 CG ASP 8 23.048 7.537 16.865 1.00 0.00 ATOM 50 OD1 ASP 8 23.809 8.030 17.723 1.00 0.00 ATOM 51 OD2 ASP 8 22.971 6.311 16.644 1.00 0.00 ATOM 52 O ASP 8 22.410 11.122 14.571 1.00 0.00 ATOM 53 C ASP 8 21.654 10.770 15.476 1.00 0.00 ATOM 54 N MET 9 20.372 11.122 15.523 1.00 0.00 ATOM 55 CA MET 9 19.780 11.959 14.487 1.00 0.00 ATOM 56 CB MET 9 18.269 11.675 14.405 1.00 0.00 ATOM 57 CG MET 9 17.887 10.206 14.419 1.00 0.00 ATOM 58 SD MET 9 16.070 10.033 14.224 1.00 0.00 ATOM 59 CE MET 9 15.480 11.174 15.482 1.00 0.00 ATOM 60 O MET 9 20.430 14.013 15.494 1.00 0.00 ATOM 61 C MET 9 20.084 13.441 14.465 1.00 0.00 ATOM 62 N THR 10 19.817 14.024 13.269 1.00 0.00 ATOM 63 CA THR 10 20.077 15.454 13.162 1.00 0.00 ATOM 64 CB THR 10 19.779 15.929 11.728 1.00 0.00 ATOM 65 CG2 THR 10 20.775 15.326 10.750 1.00 0.00 ATOM 66 OG1 THR 10 18.457 15.525 11.353 1.00 0.00 ATOM 67 O THR 10 18.006 15.657 14.351 1.00 0.00 ATOM 68 C THR 10 19.100 16.162 14.089 1.00 0.00 ATOM 69 N PHE 11 19.508 17.242 14.617 1.00 0.00 ATOM 70 CA PHE 11 18.612 17.980 15.494 1.00 0.00 ATOM 71 CB PHE 11 19.381 19.211 16.051 1.00 0.00 ATOM 72 CG PHE 11 18.554 20.078 16.961 1.00 0.00 ATOM 73 CD1 PHE 11 17.609 20.959 16.441 1.00 0.00 ATOM 74 CD2 PHE 11 18.718 20.013 18.342 1.00 0.00 ATOM 75 CE1 PHE 11 16.839 21.761 17.282 1.00 0.00 ATOM 76 CE2 PHE 11 17.954 20.812 19.191 1.00 0.00 ATOM 77 CZ PHE 11 17.013 21.687 18.660 1.00 0.00 ATOM 78 O PHE 11 16.265 18.469 15.422 1.00 0.00 ATOM 79 C PHE 11 17.324 18.408 14.798 1.00 0.00 ATOM 80 N ALA 12 17.417 18.706 13.504 1.00 0.00 ATOM 81 CA ALA 12 16.282 19.110 12.779 1.00 0.00 ATOM 82 CB ALA 12 16.643 19.437 11.324 1.00 0.00 ATOM 83 O ALA 12 14.016 18.331 12.872 1.00 0.00 ATOM 84 C ALA 12 15.203 18.035 12.726 1.00 0.00 ATOM 85 N GLN 13 15.615 16.789 12.521 1.00 0.00 ATOM 86 CA GLN 13 14.687 15.713 12.459 1.00 0.00 ATOM 87 CB GLN 13 15.351 14.373 12.097 1.00 0.00 ATOM 88 CG GLN 13 15.921 14.394 10.656 1.00 0.00 ATOM 89 CD GLN 13 16.611 13.096 10.310 1.00 0.00 ATOM 90 OE1 GLN 13 17.745 12.892 10.747 1.00 0.00 ATOM 91 NE2 GLN 13 15.964 12.195 9.577 1.00 0.00 ATOM 92 O GLN 13 12.718 15.431 13.799 1.00 0.00 ATOM 93 C GLN 13 13.939 15.585 13.781 1.00 0.00 ATOM 94 N ALA 14 14.673 15.650 14.888 1.00 0.00 ATOM 95 CA ALA 14 14.069 15.544 16.164 1.00 0.00 ATOM 96 CB ALA 14 15.343 16.114 17.133 1.00 0.00 ATOM 97 O ALA 14 11.977 16.425 16.899 1.00 0.00 ATOM 98 C ALA 14 13.073 16.652 16.386 1.00 0.00 ATOM 99 N LEU 15 13.448 17.867 15.998 1.00 0.00 ATOM 100 CA LEU 15 12.567 19.018 16.159 1.00 0.00 ATOM 101 CB LEU 15 13.300 20.291 15.719 1.00 0.00 ATOM 102 CG LEU 15 12.459 21.578 15.659 1.00 0.00 ATOM 103 CD1 LEU 15 11.947 21.914 17.048 1.00 0.00 ATOM 104 CD2 LEU 15 13.294 22.734 15.110 1.00 0.00 ATOM 105 O LEU 15 10.185 19.168 15.903 1.00 0.00 ATOM 106 C LEU 15 11.261 18.859 15.389 1.00 0.00 ATOM 107 N GLN 16 11.376 18.368 14.184 1.00 0.00 ATOM 108 CA GLN 16 10.195 18.190 13.351 1.00 0.00 ATOM 109 CB GLN 16 10.565 17.866 11.890 1.00 0.00 ATOM 110 CG GLN 16 11.577 18.752 11.211 1.00 0.00 ATOM 111 CD GLN 16 11.442 20.194 11.560 1.00 0.00 ATOM 112 OE1 GLN 16 10.373 20.788 11.342 1.00 0.00 ATOM 113 NE2 GLN 16 12.539 20.805 12.051 1.00 0.00 ATOM 114 O GLN 16 8.066 17.176 13.711 1.00 0.00 ATOM 115 C GLN 16 9.287 17.107 13.860 1.00 0.00 ATOM 116 N THR 17 9.865 16.060 14.475 1.00 0.00 ATOM 117 CA THR 17 9.065 14.963 14.951 1.00 0.00 ATOM 118 CB THR 17 9.920 13.730 15.292 1.00 0.00 ATOM 119 CG2 THR 17 10.619 13.202 14.049 1.00 0.00 ATOM 120 OG1 THR 17 10.910 14.085 16.265 1.00 0.00 ATOM 121 O THR 17 7.051 14.880 16.266 1.00 0.00 ATOM 122 C THR 17 8.195 15.328 16.158 1.00 0.00 ATOM 123 N HIS 18 8.836 16.157 16.911 1.00 0.00 ATOM 124 CA HIS 18 8.164 16.583 18.140 1.00 0.00 ATOM 125 CB HIS 18 8.472 15.653 19.331 1.00 0.00 ATOM 126 CG HIS 18 8.487 14.186 19.046 1.00 0.00 ATOM 127 CD2 HIS 18 7.503 13.251 19.102 1.00 0.00 ATOM 128 ND1 HIS 18 9.628 13.517 18.663 1.00 0.00 ATOM 129 CE1 HIS 18 9.356 12.236 18.479 1.00 0.00 ATOM 130 NE2 HIS 18 8.071 12.050 18.743 1.00 0.00 ATOM 131 O HIS 18 9.495 18.412 18.884 1.00 0.00 ATOM 132 C HIS 18 8.369 17.981 18.650 1.00 0.00 ATOM 133 N PRO 19 7.285 18.754 18.712 1.00 0.00 ATOM 134 CA PRO 19 7.255 20.040 19.384 1.00 0.00 ATOM 135 CB PRO 19 5.800 20.487 19.234 1.00 0.00 ATOM 136 CG PRO 19 5.398 19.872 17.924 1.00 0.00 ATOM 137 CD PRO 19 6.004 18.484 18.020 1.00 0.00 ATOM 138 O PRO 19 8.382 20.852 21.339 1.00 0.00 ATOM 139 C PRO 19 7.685 19.966 20.844 1.00 0.00 ATOM 140 N GLY 20 7.270 18.906 21.533 1.00 0.00 ATOM 141 CA GLY 20 7.620 18.744 22.904 1.00 0.00 ATOM 142 O GLY 20 9.769 19.154 23.899 1.00 0.00 ATOM 143 C GLY 20 9.130 18.617 22.986 1.00 0.00 ATOM 144 N VAL 21 9.653 17.922 22.018 1.00 0.00 ATOM 145 CA VAL 21 11.100 17.764 21.987 1.00 0.00 ATOM 146 CB VAL 21 11.548 16.784 20.896 1.00 0.00 ATOM 147 CG1 VAL 21 13.066 16.775 20.726 1.00 0.00 ATOM 148 CG2 VAL 21 11.080 15.370 21.226 1.00 0.00 ATOM 149 O VAL 21 12.906 19.363 22.406 1.00 0.00 ATOM 150 C VAL 21 11.818 19.131 21.814 1.00 0.00 ATOM 151 N ALA 22 11.255 20.037 21.056 1.00 0.00 ATOM 152 CA ALA 22 11.879 21.367 20.857 1.00 0.00 ATOM 153 CB ALA 22 11.074 22.222 19.928 1.00 0.00 ATOM 154 O ALA 22 12.899 22.749 22.522 1.00 0.00 ATOM 155 C ALA 22 11.907 22.149 22.157 1.00 0.00 ATOM 156 N GLY 23 10.803 22.049 22.854 1.00 0.00 ATOM 157 CA GLY 23 10.755 22.681 24.165 1.00 0.00 ATOM 158 O GLY 23 12.445 22.842 25.860 1.00 0.00 ATOM 159 C GLY 23 11.781 22.102 25.132 1.00 0.00 ATOM 160 N VAL 24 11.911 20.779 25.138 1.00 0.00 ATOM 161 CA VAL 24 12.827 20.161 25.993 1.00 0.00 ATOM 162 CB VAL 24 12.528 18.629 26.126 1.00 0.00 ATOM 163 CG1 VAL 24 12.956 17.857 24.897 1.00 0.00 ATOM 164 CG2 VAL 24 13.210 18.065 27.351 1.00 0.00 ATOM 165 O VAL 24 15.131 20.548 26.540 1.00 0.00 ATOM 166 C VAL 24 14.285 20.440 25.649 1.00 0.00 ATOM 167 N LEU 25 14.581 20.557 24.359 1.00 0.00 ATOM 168 CA LEU 25 15.952 20.828 23.912 1.00 0.00 ATOM 169 CB LEU 25 16.102 20.623 22.385 1.00 0.00 ATOM 170 CG LEU 25 16.040 19.139 22.011 1.00 0.00 ATOM 171 CD1 LEU 25 15.669 18.964 20.537 1.00 0.00 ATOM 172 CD2 LEU 25 17.388 18.443 22.341 1.00 0.00 ATOM 173 O LEU 25 17.437 22.418 24.861 1.00 0.00 ATOM 174 C LEU 25 16.334 22.197 24.365 1.00 0.00 ATOM 175 N ARG 26 15.414 23.159 24.195 1.00 0.00 ATOM 176 CA ARG 26 15.754 24.488 24.584 1.00 0.00 ATOM 177 CB ARG 26 14.711 25.524 24.123 1.00 0.00 ATOM 178 CG ARG 26 14.684 25.734 22.601 1.00 0.00 ATOM 179 CD ARG 26 15.964 26.337 22.020 1.00 0.00 ATOM 180 NE ARG 26 16.201 27.685 22.520 1.00 0.00 ATOM 181 CZ ARG 26 15.770 28.785 21.923 1.00 0.00 ATOM 182 NH1 ARG 26 15.089 28.701 20.789 1.00 0.00 ATOM 183 NH2 ARG 26 16.023 29.973 22.455 1.00 0.00 ATOM 184 O ARG 26 16.901 25.272 26.532 1.00 0.00 ATOM 185 C ARG 26 16.032 24.529 26.074 1.00 0.00 ATOM 186 N SER 27 15.293 23.730 26.836 1.00 0.00 ATOM 187 CA SER 27 15.474 23.685 28.282 1.00 0.00 ATOM 188 CB SER 27 14.336 22.820 28.906 1.00 0.00 ATOM 189 OG SER 27 13.068 23.403 28.659 1.00 0.00 ATOM 190 O SER 27 17.452 23.666 29.683 1.00 0.00 ATOM 191 C SER 27 16.876 23.163 28.716 1.00 0.00 ATOM 192 N TYR 28 17.400 22.173 28.002 1.00 0.00 ATOM 193 CA TYR 28 18.708 21.616 28.324 1.00 0.00 ATOM 194 CB TYR 28 18.497 20.042 28.366 1.00 0.00 ATOM 195 CG TYR 28 17.432 19.561 29.322 1.00 0.00 ATOM 196 CD1 TYR 28 17.388 20.013 30.637 1.00 0.00 ATOM 197 CD2 TYR 28 16.491 18.621 28.919 1.00 0.00 ATOM 198 CE1 TYR 28 16.419 19.554 31.516 1.00 0.00 ATOM 199 CE2 TYR 28 15.518 18.158 29.796 1.00 0.00 ATOM 200 CZ TYR 28 15.484 18.634 31.085 1.00 0.00 ATOM 201 OH TYR 28 14.520 18.174 31.954 1.00 0.00 ATOM 202 O TYR 28 21.015 22.182 27.990 1.00 0.00 ATOM 203 C TYR 28 19.843 22.556 27.931 1.00 0.00 ATOM 204 N ASN 29 19.495 23.775 27.534 1.00 0.00 ATOM 205 CA ASN 29 20.495 24.750 27.140 1.00 0.00 ATOM 206 CB ASN 29 21.555 24.892 28.257 1.00 0.00 ATOM 207 CG ASN 29 21.011 25.448 29.541 1.00 0.00 ATOM 208 ND2 ASN 29 21.330 24.777 30.642 1.00 0.00 ATOM 209 OD1 ASN 29 20.335 26.476 29.589 1.00 0.00 ATOM 210 O ASN 29 22.145 25.076 25.476 1.00 0.00 ATOM 211 C ASN 29 21.181 24.422 25.864 1.00 0.00 ATOM 212 N LEU 30 20.659 23.408 25.155 1.00 0.00 ATOM 213 CA LEU 30 21.135 23.133 23.836 1.00 0.00 ATOM 214 CB LEU 30 20.534 21.888 23.237 1.00 0.00 ATOM 215 CG LEU 30 21.108 21.470 21.955 1.00 0.00 ATOM 216 CD1 LEU 30 22.603 21.293 22.000 1.00 0.00 ATOM 217 CD2 LEU 30 20.466 20.139 21.574 1.00 0.00 ATOM 218 O LEU 30 21.798 24.844 22.291 1.00 0.00 ATOM 219 C LEU 30 20.923 24.421 23.047 1.00 0.00 ATOM 220 N GLY 31 19.761 25.040 23.224 1.00 0.00 ATOM 221 CA GLY 31 19.461 26.263 22.529 1.00 0.00 ATOM 222 O GLY 31 19.749 26.948 20.284 1.00 0.00 ATOM 223 C GLY 31 19.384 26.064 21.058 1.00 0.00 ATOM 224 N CYS 32 18.904 24.898 20.613 1.00 0.00 ATOM 225 CA CYS 32 18.897 24.744 19.196 1.00 0.00 ATOM 226 CB CYS 32 19.726 23.520 18.803 1.00 0.00 ATOM 227 SG CYS 32 21.473 23.622 19.260 1.00 0.00 ATOM 228 O CYS 32 17.212 26.400 19.075 1.00 0.00 ATOM 229 C CYS 32 17.764 25.435 18.545 1.00 0.00 ATOM 230 N ILE 33 17.389 24.949 17.366 1.00 0.00 ATOM 231 CA ILE 33 16.283 25.540 16.622 1.00 0.00 ATOM 232 CB ILE 33 15.015 25.770 17.287 1.00 0.00 ATOM 233 CG1 ILE 33 14.530 24.410 17.810 1.00 0.00 ATOM 234 CG2 ILE 33 14.009 26.394 16.321 1.00 0.00 ATOM 235 CD1 ILE 33 13.309 24.447 18.713 1.00 0.00 ATOM 236 O ILE 33 16.695 27.010 14.772 1.00 0.00 ATOM 237 C ILE 33 16.748 26.849 15.991 1.00 0.00 ATOM 238 N GLY 34 17.202 27.780 16.824 1.00 0.00 ATOM 239 CA GLY 34 17.659 29.027 16.334 1.00 0.00 ATOM 240 O GLY 34 19.641 30.024 15.427 1.00 0.00 ATOM 241 C GLY 34 19.050 28.983 15.718 1.00 0.00 ATOM 242 N CYS 35 19.573 27.777 15.519 1.00 0.00 ATOM 243 CA CYS 35 20.898 27.616 14.932 1.00 0.00 ATOM 244 CB CYS 35 21.960 27.292 15.999 1.00 0.00 ATOM 245 SG CYS 35 21.689 25.755 16.882 1.00 0.00 ATOM 246 O CYS 35 20.355 25.482 13.980 1.00 0.00 ATOM 247 C CYS 35 20.884 26.582 13.811 1.00 0.00 ATOM 248 N MET 36 21.465 26.936 12.670 1.00 0.00 ATOM 249 CA MET 36 21.515 26.017 11.517 1.00 0.00 ATOM 250 CB MET 36 22.150 26.647 10.303 1.00 0.00 ATOM 251 CG MET 36 21.264 27.576 9.527 1.00 0.00 ATOM 252 SD MET 36 22.199 28.098 8.075 1.00 0.00 ATOM 253 CE MET 36 22.684 29.647 8.576 1.00 0.00 ATOM 254 O MET 36 22.191 23.752 11.151 1.00 0.00 ATOM 255 C MET 36 22.391 24.804 11.759 1.00 0.00 ATOM 256 N GLY 37 23.365 24.947 12.652 1.00 0.00 ATOM 257 CA GLY 37 24.267 23.846 12.968 1.00 0.00 ATOM 258 O GLY 37 24.156 21.524 13.533 1.00 0.00 ATOM 259 C GLY 37 23.575 22.610 13.507 1.00 0.00 ATOM 260 N ALA 38 22.328 22.771 13.937 1.00 0.00 ATOM 261 CA ALA 38 21.563 21.651 14.473 1.00 0.00 ATOM 262 CB ALA 38 20.210 22.298 14.943 1.00 0.00 ATOM 263 O ALA 38 21.411 19.366 13.755 1.00 0.00 ATOM 264 C ALA 38 21.369 20.554 13.432 1.00 0.00 ATOM 265 N GLN 39 21.159 20.953 12.181 1.00 0.00 ATOM 266 CA GLN 39 20.971 20.010 11.145 1.00 0.00 ATOM 267 CB GLN 39 20.565 20.794 9.868 1.00 0.00 ATOM 268 CG GLN 39 19.117 21.326 9.965 1.00 0.00 ATOM 269 CD GLN 39 18.768 22.472 9.012 1.00 0.00 ATOM 270 OE1 GLN 39 17.634 22.958 9.015 1.00 0.00 ATOM 271 NE2 GLN 39 19.718 22.914 8.217 1.00 0.00 ATOM 272 O GLN 39 22.094 17.951 10.775 1.00 0.00 ATOM 273 C GLN 39 22.215 19.144 11.022 1.00 0.00 ATOM 274 N ASN 40 23.394 19.734 11.183 1.00 0.00 ATOM 275 CA ASN 40 24.685 19.035 11.122 1.00 0.00 ATOM 276 CB ASN 40 25.811 20.097 10.916 1.00 0.00 ATOM 277 CG ASN 40 25.736 20.816 9.565 1.00 0.00 ATOM 278 ND2 ASN 40 26.448 21.933 9.441 1.00 0.00 ATOM 279 OD1 ASN 40 25.037 20.361 8.650 1.00 0.00 ATOM 280 O ASN 40 25.788 17.250 12.249 1.00 0.00 ATOM 281 C ASN 40 24.980 18.172 12.340 1.00 0.00 ATOM 282 N GLU 41 24.376 18.432 13.527 1.00 0.00 ATOM 283 CA GLU 41 24.903 17.798 14.724 1.00 0.00 ATOM 284 CB GLU 41 25.401 18.772 15.793 1.00 0.00 ATOM 285 CG GLU 41 26.623 19.576 15.382 1.00 0.00 ATOM 286 CD GLU 41 27.116 20.493 16.484 1.00 0.00 ATOM 287 OE1 GLU 41 26.494 20.507 17.568 1.00 0.00 ATOM 288 OE2 GLU 41 28.124 21.197 16.265 1.00 0.00 ATOM 289 O GLU 41 22.683 17.155 15.324 1.00 0.00 ATOM 290 C GLU 41 23.888 16.925 15.425 1.00 0.00 ATOM 291 N SER 42 24.372 15.917 16.143 1.00 0.00 ATOM 292 CA SER 42 23.487 15.011 16.867 1.00 0.00 ATOM 293 CB SER 42 24.115 13.617 16.913 1.00 0.00 ATOM 294 OG SER 42 25.286 13.611 17.709 1.00 0.00 ATOM 295 O SER 42 23.898 16.491 18.684 1.00 0.00 ATOM 296 C SER 42 23.261 15.528 18.254 1.00 0.00 ATOM 297 N LEU 43 22.344 14.891 18.977 1.00 0.00 ATOM 298 CA LEU 43 22.038 15.301 20.342 1.00 0.00 ATOM 299 CB LEU 43 20.929 14.514 20.981 1.00 0.00 ATOM 300 CG LEU 43 20.782 14.560 22.498 1.00 0.00 ATOM 301 CD1 LEU 43 19.868 15.696 22.947 1.00 0.00 ATOM 302 CD2 LEU 43 20.254 13.242 23.052 1.00 0.00 ATOM 303 O LEU 43 23.527 16.082 22.054 1.00 0.00 ATOM 304 C LEU 43 23.280 15.208 21.221 1.00 0.00 ATOM 305 N GLU 44 24.062 14.149 21.036 1.00 0.00 ATOM 306 CA GLU 44 25.240 13.976 21.802 1.00 0.00 ATOM 307 CB GLU 44 25.952 12.657 21.527 1.00 0.00 ATOM 308 CG GLU 44 25.126 11.443 21.947 1.00 0.00 ATOM 309 CD GLU 44 25.874 10.119 21.787 1.00 0.00 ATOM 310 OE1 GLU 44 26.841 10.051 21.000 1.00 0.00 ATOM 311 OE2 GLU 44 25.475 9.138 22.440 1.00 0.00 ATOM 312 O GLU 44 26.888 15.598 22.429 1.00 0.00 ATOM 313 C GLU 44 26.270 15.056 21.511 1.00 0.00 ATOM 314 N GLN 45 26.466 15.360 20.233 1.00 0.00 ATOM 315 CA GLN 45 27.422 16.388 19.837 1.00 0.00 ATOM 316 CB GLN 45 27.570 16.394 18.283 1.00 0.00 ATOM 317 CG GLN 45 28.213 15.128 17.697 1.00 0.00 ATOM 318 CD GLN 45 27.974 14.984 16.201 1.00 0.00 ATOM 319 OE1 GLN 45 26.888 14.595 15.758 1.00 0.00 ATOM 320 NE2 GLN 45 28.993 15.301 15.408 1.00 0.00 ATOM 321 O GLN 45 27.817 18.466 21.004 1.00 0.00 ATOM 322 C GLN 45 26.991 17.746 20.442 1.00 0.00 ATOM 323 N GLY 46 25.709 18.077 20.322 1.00 0.00 ATOM 324 CA GLY 46 25.199 19.333 20.859 1.00 0.00 ATOM 325 O GLY 46 25.843 20.463 22.908 1.00 0.00 ATOM 326 C GLY 46 25.436 19.416 22.401 1.00 0.00 ATOM 327 N ALA 47 25.180 18.323 23.111 1.00 0.00 ATOM 328 CA ALA 47 25.372 18.298 24.557 1.00 0.00 ATOM 329 CB ALA 47 24.983 16.997 25.119 1.00 0.00 ATOM 330 O ALA 47 27.183 19.328 25.776 1.00 0.00 ATOM 331 C ALA 47 26.862 18.528 24.897 1.00 0.00 ATOM 332 N ASN 48 27.751 17.828 24.198 1.00 0.00 ATOM 333 CA ASN 48 29.182 17.971 24.439 1.00 0.00 ATOM 334 CB ASN 48 30.033 17.146 23.531 1.00 0.00 ATOM 335 CG ASN 48 30.048 15.699 23.962 1.00 0.00 ATOM 336 ND2 ASN 48 30.109 14.782 22.997 1.00 0.00 ATOM 337 OD1 ASN 48 30.013 15.406 25.159 1.00 0.00 ATOM 338 O ASN 48 30.386 19.977 24.971 1.00 0.00 ATOM 339 C ASN 48 29.609 19.415 24.198 1.00 0.00 ATOM 340 N ALA 49 29.101 20.013 23.125 1.00 0.00 ATOM 341 CA ALA 49 29.439 21.404 22.795 1.00 0.00 ATOM 342 CB ALA 49 28.850 21.721 21.416 1.00 0.00 ATOM 343 O ALA 49 29.615 23.242 24.350 1.00 0.00 ATOM 344 C ALA 49 28.894 22.386 23.835 1.00 0.00 ATOM 345 N HIS 50 27.646 22.154 24.236 1.00 0.00 ATOM 346 CA HIS 50 26.990 23.067 25.175 1.00 0.00 ATOM 347 CB HIS 50 25.525 23.155 24.745 1.00 0.00 ATOM 348 CG HIS 50 25.358 24.007 23.470 1.00 0.00 ATOM 349 CD2 HIS 50 24.854 23.660 22.281 1.00 0.00 ATOM 350 ND1 HIS 50 25.608 25.309 23.413 1.00 0.00 ATOM 351 CE1 HIS 50 25.243 25.758 22.220 1.00 0.00 ATOM 352 NE2 HIS 50 24.786 24.740 21.511 1.00 0.00 ATOM 353 O HIS 50 26.712 23.427 27.546 1.00 0.00 ATOM 354 C HIS 50 27.281 22.793 26.664 1.00 0.00 ATOM 355 N GLY 51 28.145 21.802 26.917 1.00 0.00 ATOM 356 CA GLY 51 28.568 21.416 28.257 1.00 0.00 ATOM 357 O GLY 51 27.574 20.633 30.329 1.00 0.00 ATOM 358 C GLY 51 27.502 20.641 29.099 1.00 0.00 ATOM 359 N LEU 52 26.544 20.010 28.428 1.00 0.00 ATOM 360 CA LEU 52 25.505 19.259 29.123 1.00 0.00 ATOM 361 CB LEU 52 24.206 19.609 28.398 1.00 0.00 ATOM 362 CG LEU 52 22.988 18.874 29.007 1.00 0.00 ATOM 363 CD1 LEU 52 22.804 19.147 30.420 1.00 0.00 ATOM 364 CD2 LEU 52 21.735 19.352 28.215 1.00 0.00 ATOM 365 O LEU 52 26.038 17.287 27.869 1.00 0.00 ATOM 366 C LEU 52 25.825 17.778 28.977 1.00 0.00 ATOM 367 N ASN 53 25.858 17.066 30.100 1.00 0.00 ATOM 368 CA ASN 53 26.151 15.638 30.080 1.00 0.00 ATOM 369 CB ASN 53 26.108 15.053 31.496 1.00 0.00 ATOM 370 CG ASN 53 27.149 15.660 32.411 1.00 0.00 ATOM 371 ND2 ASN 53 26.754 15.966 33.635 1.00 0.00 ATOM 372 OD1 ASN 53 28.300 15.856 32.017 1.00 0.00 ATOM 373 O ASN 53 23.900 15.213 29.301 1.00 0.00 ATOM 374 C ASN 53 25.088 14.895 29.226 1.00 0.00 ATOM 375 N VAL 54 25.526 13.924 28.432 1.00 0.00 ATOM 376 CA VAL 54 24.608 13.164 27.592 1.00 0.00 ATOM 377 CB VAL 54 25.467 12.281 26.582 1.00 0.00 ATOM 378 CG1 VAL 54 24.565 11.330 25.813 1.00 0.00 ATOM 379 CG2 VAL 54 26.233 13.172 25.611 1.00 0.00 ATOM 380 O VAL 54 22.478 12.185 28.073 1.00 0.00 ATOM 381 C VAL 54 23.641 12.338 28.444 1.00 0.00 ATOM 382 N GLU 55 24.147 11.804 29.552 1.00 0.00 ATOM 383 CA GLU 55 23.320 11.030 30.492 1.00 0.00 ATOM 384 CB GLU 55 24.117 10.480 31.643 1.00 0.00 ATOM 385 CG GLU 55 23.335 9.484 32.571 1.00 0.00 ATOM 386 CD GLU 55 24.229 8.751 33.602 1.00 0.00 ATOM 387 OE1 GLU 55 25.118 7.925 33.199 1.00 0.00 ATOM 388 OE2 GLU 55 24.060 9.002 34.832 1.00 0.00 ATOM 389 O GLU 55 21.007 11.412 30.999 1.00 0.00 ATOM 390 C GLU 55 22.142 11.888 30.939 1.00 0.00 ATOM 391 N ASP 56 22.411 13.151 31.252 1.00 0.00 ATOM 392 CA ASP 56 21.350 14.081 31.697 1.00 0.00 ATOM 393 CB ASP 56 21.930 15.447 32.103 1.00 0.00 ATOM 394 CG ASP 56 22.778 15.429 33.370 1.00 0.00 ATOM 395 OD1 ASP 56 22.721 14.427 34.091 1.00 0.00 ATOM 396 OD2 ASP 56 23.516 16.416 33.579 1.00 0.00 ATOM 397 O ASP 56 19.086 14.155 30.870 1.00 0.00 ATOM 398 C ASP 56 20.283 14.258 30.599 1.00 0.00 ATOM 399 N ILE 57 20.725 14.520 29.374 1.00 0.00 ATOM 400 CA ILE 57 19.800 14.704 28.261 1.00 0.00 ATOM 401 CB ILE 57 20.555 15.088 26.968 1.00 0.00 ATOM 402 CG1 ILE 57 21.210 16.461 27.150 1.00 0.00 ATOM 403 CG2 ILE 57 19.594 15.099 25.778 1.00 0.00 ATOM 404 CD1 ILE 57 22.069 16.899 25.980 1.00 0.00 ATOM 405 O ILE 57 17.771 13.494 27.772 1.00 0.00 ATOM 406 C ILE 57 18.979 13.447 27.992 1.00 0.00 ATOM 407 N LEU 58 19.617 12.272 28.027 1.00 0.00 ATOM 408 CA LEU 58 18.933 11.000 27.780 1.00 0.00 ATOM 409 CB LEU 58 19.940 9.847 27.709 1.00 0.00 ATOM 410 CG LEU 58 20.880 9.930 26.495 1.00 0.00 ATOM 411 CD1 LEU 58 21.953 8.854 26.613 1.00 0.00 ATOM 412 CD2 LEU 58 20.128 9.807 25.139 1.00 0.00 ATOM 413 O LEU 58 16.755 10.296 28.526 1.00 0.00 ATOM 414 C LEU 58 17.879 10.686 28.842 1.00 0.00 ATOM 415 N ARG 59 18.235 10.873 30.107 1.00 0.00 ATOM 416 CA ARG 59 17.315 10.599 31.198 1.00 0.00 ATOM 417 CB ARG 59 17.995 10.978 32.509 1.00 0.00 ATOM 418 CG ARG 59 18.760 9.919 33.133 1.00 0.00 ATOM 419 CD ARG 59 19.245 10.338 34.519 1.00 0.00 ATOM 420 NE ARG 59 20.667 10.538 34.449 1.00 0.00 ATOM 421 CZ ARG 59 21.308 11.645 34.751 1.00 0.00 ATOM 422 NH1 ARG 59 20.681 12.732 35.214 1.00 0.00 ATOM 423 NH2 ARG 59 22.613 11.644 34.599 1.00 0.00 ATOM 424 O ARG 59 14.962 11.046 31.331 1.00 0.00 ATOM 425 C ARG 59 16.089 11.503 31.139 1.00 0.00 ATOM 426 N ASP 60 16.309 12.787 30.871 1.00 0.00 ATOM 427 CA ASP 60 15.236 13.703 30.792 1.00 0.00 ATOM 428 CB ASP 60 15.789 15.134 30.754 1.00 0.00 ATOM 429 CG ASP 60 16.249 15.624 32.103 1.00 0.00 ATOM 430 OD1 ASP 60 17.105 16.572 32.163 1.00 0.00 ATOM 431 OD2 ASP 60 15.902 15.030 33.163 1.00 0.00 ATOM 432 O ASP 60 13.078 13.486 29.781 1.00 0.00 ATOM 433 C ASP 60 14.297 13.423 29.626 1.00 0.00 ATOM 434 N LEU 61 14.856 13.124 28.438 1.00 0.00 ATOM 435 CA LEU 61 14.041 12.823 27.263 1.00 0.00 ATOM 436 CB LEU 61 14.892 12.710 26.020 1.00 0.00 ATOM 437 CG LEU 61 15.448 14.070 25.527 1.00 0.00 ATOM 438 CD1 LEU 61 16.591 13.806 24.585 1.00 0.00 ATOM 439 CD2 LEU 61 14.334 14.840 24.841 1.00 0.00 ATOM 440 O LEU 61 12.069 11.459 27.145 1.00 0.00 ATOM 441 C LEU 61 13.244 11.526 27.486 1.00 0.00 ATOM 442 N ASN 62 13.872 10.504 28.055 1.00 0.00 ATOM 443 CA ASN 62 13.104 9.288 28.379 1.00 0.00 ATOM 444 CB ASN 62 14.005 8.236 29.008 1.00 0.00 ATOM 445 CG ASN 62 14.919 7.547 27.977 1.00 0.00 ATOM 446 ND2 ASN 62 16.072 7.142 28.402 1.00 0.00 ATOM 447 OD1 ASN 62 14.540 7.375 26.837 1.00 0.00 ATOM 448 O ASN 62 10.860 9.032 29.161 1.00 0.00 ATOM 449 C ASN 62 11.946 9.596 29.303 1.00 0.00 ATOM 450 N ALA 63 12.173 10.493 30.256 1.00 0.00 ATOM 451 CA ALA 63 11.131 10.871 31.203 1.00 0.00 ATOM 452 CB ALA 63 11.740 11.774 32.293 1.00 0.00 ATOM 453 O ALA 63 8.831 11.321 30.698 1.00 0.00 ATOM 454 C ALA 63 10.008 11.630 30.510 1.00 0.00 ATOM 455 N LEU 64 10.373 12.625 29.706 1.00 0.00 ATOM 456 CA LEU 64 9.382 13.419 28.990 1.00 0.00 ATOM 457 CB LEU 64 10.115 14.639 28.367 1.00 0.00 ATOM 458 CG LEU 64 9.270 15.575 27.494 1.00 0.00 ATOM 459 CD1 LEU 64 8.094 16.155 28.241 1.00 0.00 ATOM 460 CD2 LEU 64 10.168 16.671 26.882 1.00 0.00 ATOM 461 O LEU 64 7.375 12.822 27.817 1.00 0.00 ATOM 462 C LEU 64 8.567 12.580 28.012 1.00 0.00 ATOM 463 N ALA 65 9.218 11.610 27.377 1.00 0.00 ATOM 464 CA ALA 65 8.544 10.762 26.399 1.00 0.00 ATOM 465 CB ALA 65 8.831 11.310 25.010 1.00 0.00 ATOM 466 O ALA 65 10.283 9.118 26.392 1.00 0.00 ATOM 467 C ALA 65 9.077 9.343 26.495 1.00 0.00 TER END