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 2 Thu Aug 14 14:48:22 2008 MODEL 2 PARENT N/A ATOM 1 N GLN 3 8.602 11.498 21.787 1.00 0.00 ATOM 2 CA GLN 3 8.367 10.024 21.820 1.00 0.00 ATOM 3 CB GLN 3 7.496 9.621 20.609 1.00 0.00 ATOM 4 CG GLN 3 7.162 8.137 20.555 1.00 0.00 ATOM 5 CD GLN 3 6.465 7.741 19.267 1.00 0.00 ATOM 6 OE1 GLN 3 6.984 7.967 18.173 1.00 0.00 ATOM 7 NE2 GLN 3 5.285 7.143 19.391 1.00 0.00 ATOM 8 O GLN 3 10.377 9.155 22.801 1.00 0.00 ATOM 9 C GLN 3 9.702 9.280 21.782 1.00 0.00 ATOM 10 N LYS 4 10.069 8.715 20.569 1.00 0.00 ATOM 11 CA LYS 4 11.278 7.965 20.526 1.00 0.00 ATOM 12 CB LYS 4 11.046 6.633 19.778 1.00 0.00 ATOM 13 CG LYS 4 9.939 5.777 20.366 1.00 0.00 ATOM 14 CD LYS 4 9.700 4.525 19.538 1.00 0.00 ATOM 15 CE LYS 4 8.538 3.718 20.110 1.00 0.00 ATOM 16 NZ LYS 4 8.178 2.553 19.250 1.00 0.00 ATOM 17 O LYS 4 12.323 9.252 18.810 1.00 0.00 ATOM 18 C LYS 4 12.370 8.792 19.951 1.00 0.00 ATOM 19 N PHE 5 13.390 9.055 20.782 1.00 0.00 ATOM 20 CA PHE 5 14.415 9.913 20.303 1.00 0.00 ATOM 21 CB PHE 5 14.465 11.213 21.118 1.00 0.00 ATOM 22 CG PHE 5 15.594 12.131 20.722 1.00 0.00 ATOM 23 CD1 PHE 5 15.507 12.900 19.564 1.00 0.00 ATOM 24 CD2 PHE 5 16.752 12.203 21.488 1.00 0.00 ATOM 25 CE1 PHE 5 16.564 13.727 19.174 1.00 0.00 ATOM 26 CE2 PHE 5 17.815 13.024 21.108 1.00 0.00 ATOM 27 CZ PHE 5 17.719 13.787 19.949 1.00 0.00 ATOM 28 O PHE 5 16.357 8.938 21.321 1.00 0.00 ATOM 29 C PHE 5 15.805 9.284 20.276 1.00 0.00 ATOM 30 N THR 6 16.369 9.139 19.081 1.00 0.00 ATOM 31 CA THR 6 17.643 8.575 18.959 1.00 0.00 ATOM 32 CB THR 6 17.699 7.700 17.695 1.00 0.00 ATOM 33 CG2 THR 6 19.071 7.054 17.554 1.00 0.00 ATOM 34 OG1 THR 6 16.707 6.669 17.778 1.00 0.00 ATOM 35 O THR 6 18.537 10.549 17.929 1.00 0.00 ATOM 36 C THR 6 18.621 9.741 18.854 1.00 0.00 ATOM 37 N LYS 7 19.548 9.826 19.803 1.00 0.00 ATOM 38 CA LYS 7 20.494 10.865 19.787 1.00 0.00 ATOM 39 CB LYS 7 21.175 10.765 21.258 1.00 0.00 ATOM 40 CG LYS 7 22.062 9.435 21.443 1.00 0.00 ATOM 41 CD LYS 7 21.404 8.094 20.982 1.00 0.00 ATOM 42 CE LYS 7 22.397 7.175 20.263 1.00 0.00 ATOM 43 NZ LYS 7 21.830 5.873 19.793 1.00 0.00 ATOM 44 O LYS 7 21.975 11.983 18.284 1.00 0.00 ATOM 45 C LYS 7 21.341 10.958 18.540 1.00 0.00 ATOM 46 N ASP 8 21.357 9.886 17.755 1.00 0.00 ATOM 47 CA ASP 8 22.137 9.863 16.524 1.00 0.00 ATOM 48 CB ASP 8 22.147 8.450 15.936 1.00 0.00 ATOM 49 CG ASP 8 23.015 7.495 16.732 1.00 0.00 ATOM 50 OD1 ASP 8 23.785 7.969 17.593 1.00 0.00 ATOM 51 OD2 ASP 8 22.929 6.274 16.491 1.00 0.00 ATOM 52 O ASP 8 22.386 11.121 14.501 1.00 0.00 ATOM 53 C ASP 8 21.633 10.758 15.405 1.00 0.00 ATOM 54 N MET 9 20.353 11.118 15.466 1.00 0.00 ATOM 55 CA MET 9 19.761 11.976 14.448 1.00 0.00 ATOM 56 CB MET 9 18.248 11.703 14.371 1.00 0.00 ATOM 57 CG MET 9 17.856 10.236 14.363 1.00 0.00 ATOM 58 SD MET 9 16.037 10.077 14.177 1.00 0.00 ATOM 59 CE MET 9 15.462 11.202 15.457 1.00 0.00 ATOM 60 O MET 9 20.430 14.009 15.484 1.00 0.00 ATOM 61 C MET 9 20.075 13.456 14.448 1.00 0.00 ATOM 62 N THR 10 19.803 14.060 13.263 1.00 0.00 ATOM 63 CA THR 10 20.071 15.491 13.178 1.00 0.00 ATOM 64 CB THR 10 19.768 15.991 11.754 1.00 0.00 ATOM 65 CG2 THR 10 20.753 15.397 10.760 1.00 0.00 ATOM 66 OG1 THR 10 18.440 15.601 11.381 1.00 0.00 ATOM 67 O THR 10 18.010 15.688 14.383 1.00 0.00 ATOM 68 C THR 10 19.105 16.190 14.123 1.00 0.00 ATOM 69 N PHE 11 19.523 17.258 14.666 1.00 0.00 ATOM 70 CA PHE 11 18.638 17.987 15.560 1.00 0.00 ATOM 71 CB PHE 11 19.419 19.204 16.132 1.00 0.00 ATOM 72 CG PHE 11 18.603 20.061 17.062 1.00 0.00 ATOM 73 CD1 PHE 11 17.661 20.956 16.562 1.00 0.00 ATOM 74 CD2 PHE 11 18.776 19.972 18.440 1.00 0.00 ATOM 75 CE1 PHE 11 16.901 21.749 17.422 1.00 0.00 ATOM 76 CE2 PHE 11 18.022 20.762 19.307 1.00 0.00 ATOM 77 CZ PHE 11 17.084 21.651 18.797 1.00 0.00 ATOM 78 O PHE 11 16.293 18.492 15.512 1.00 0.00 ATOM 79 C PHE 11 17.349 18.434 14.880 1.00 0.00 ATOM 80 N ALA 12 17.435 18.753 13.591 1.00 0.00 ATOM 81 CA ALA 12 16.298 19.177 12.879 1.00 0.00 ATOM 82 CB ALA 12 16.651 19.525 11.428 1.00 0.00 ATOM 83 O ALA 12 14.028 18.410 12.975 1.00 0.00 ATOM 84 C ALA 12 15.212 18.108 12.816 1.00 0.00 ATOM 85 N GLN 13 15.615 16.864 12.589 1.00 0.00 ATOM 86 CA GLN 13 14.679 15.795 12.514 1.00 0.00 ATOM 87 CB GLN 13 15.332 14.457 12.127 1.00 0.00 ATOM 88 CG GLN 13 15.893 14.498 10.682 1.00 0.00 ATOM 89 CD GLN 13 16.572 13.200 10.310 1.00 0.00 ATOM 90 OE1 GLN 13 17.708 12.982 10.737 1.00 0.00 ATOM 91 NE2 GLN 13 15.916 12.317 9.567 1.00 0.00 ATOM 92 O GLN 13 12.725 15.484 13.872 1.00 0.00 ATOM 93 C GLN 13 13.946 15.646 13.843 1.00 0.00 ATOM 94 N ALA 14 14.692 15.702 14.943 1.00 0.00 ATOM 95 CA ALA 14 14.102 15.576 16.224 1.00 0.00 ATOM 96 CB ALA 14 15.388 16.133 17.186 1.00 0.00 ATOM 97 O ALA 14 12.014 16.447 16.981 1.00 0.00 ATOM 98 C ALA 14 13.108 16.683 16.468 1.00 0.00 ATOM 99 N LEU 15 13.483 17.903 16.098 1.00 0.00 ATOM 100 CA LEU 15 12.604 19.052 16.282 1.00 0.00 ATOM 101 CB LEU 15 13.342 20.327 15.858 1.00 0.00 ATOM 102 CG LEU 15 12.509 21.620 15.825 1.00 0.00 ATOM 103 CD1 LEU 15 12.008 21.937 17.222 1.00 0.00 ATOM 104 CD2 LEU 15 13.349 22.780 15.288 1.00 0.00 ATOM 105 O LEU 15 10.221 19.222 16.044 1.00 0.00 ATOM 106 C LEU 15 11.292 18.915 15.518 1.00 0.00 ATOM 107 N GLN 16 11.397 18.442 14.304 1.00 0.00 ATOM 108 CA GLN 16 10.209 18.285 13.477 1.00 0.00 ATOM 109 CB GLN 16 10.567 17.982 12.007 1.00 0.00 ATOM 110 CG GLN 16 11.581 18.874 11.337 1.00 0.00 ATOM 111 CD GLN 16 11.458 20.310 11.711 1.00 0.00 ATOM 112 OE1 GLN 16 10.391 20.915 11.509 1.00 0.00 ATOM 113 NE2 GLN 16 12.561 20.907 12.204 1.00 0.00 ATOM 114 O GLN 16 8.077 17.272 13.821 1.00 0.00 ATOM 115 C GLN 16 9.297 17.197 13.970 1.00 0.00 ATOM 116 N THR 17 9.873 16.141 14.570 1.00 0.00 ATOM 117 CA THR 17 9.068 15.040 15.030 1.00 0.00 ATOM 118 CB THR 17 9.918 13.795 15.346 1.00 0.00 ATOM 119 CG2 THR 17 10.604 13.284 14.087 1.00 0.00 ATOM 120 OG1 THR 17 10.917 14.128 16.316 1.00 0.00 ATOM 121 O THR 17 7.063 14.948 16.358 1.00 0.00 ATOM 122 C THR 17 8.209 15.390 16.250 1.00 0.00 ATOM 123 N HIS 18 8.862 16.202 17.012 1.00 0.00 ATOM 124 CA HIS 18 8.200 16.611 18.252 1.00 0.00 ATOM 125 CB HIS 18 8.509 15.659 19.425 1.00 0.00 ATOM 126 CG HIS 18 8.512 14.196 19.115 1.00 0.00 ATOM 127 CD2 HIS 18 7.521 13.268 19.162 1.00 0.00 ATOM 128 ND1 HIS 18 9.646 13.526 18.712 1.00 0.00 ATOM 129 CE1 HIS 18 9.363 12.251 18.508 1.00 0.00 ATOM 130 NE2 HIS 18 8.077 12.070 18.778 1.00 0.00 ATOM 131 O HIS 18 9.550 18.418 19.019 1.00 0.00 ATOM 132 C HIS 18 8.420 17.999 18.785 1.00 0.00 ATOM 133 N PRO 19 7.341 18.779 18.868 1.00 0.00 ATOM 134 CA PRO 19 7.325 20.053 19.562 1.00 0.00 ATOM 135 CB PRO 19 5.874 20.514 19.429 1.00 0.00 ATOM 136 CG PRO 19 5.458 19.924 18.112 1.00 0.00 ATOM 137 CD PRO 19 6.055 18.531 18.180 1.00 0.00 ATOM 138 O PRO 19 8.474 20.822 21.523 1.00 0.00 ATOM 139 C PRO 19 7.766 19.951 21.018 1.00 0.00 ATOM 140 N GLY 20 7.345 18.882 21.692 1.00 0.00 ATOM 141 CA GLY 20 7.704 18.693 23.057 1.00 0.00 ATOM 142 O GLY 20 9.865 19.067 24.041 1.00 0.00 ATOM 143 C GLY 20 9.214 18.553 23.124 1.00 0.00 ATOM 144 N VAL 21 9.723 17.870 22.141 1.00 0.00 ATOM 145 CA VAL 21 11.169 17.699 22.095 1.00 0.00 ATOM 146 CB VAL 21 11.599 16.734 20.984 1.00 0.00 ATOM 147 CG1 VAL 21 13.116 16.714 20.803 1.00 0.00 ATOM 148 CG2 VAL 21 11.121 15.319 21.295 1.00 0.00 ATOM 149 O VAL 21 12.989 19.278 22.533 1.00 0.00 ATOM 150 C VAL 21 11.897 19.065 21.942 1.00 0.00 ATOM 151 N ALA 22 11.338 19.986 21.202 1.00 0.00 ATOM 152 CA ALA 22 11.972 21.314 21.023 1.00 0.00 ATOM 153 CB ALA 22 11.167 22.192 20.115 1.00 0.00 ATOM 154 O ALA 22 13.016 22.657 22.703 1.00 0.00 ATOM 155 C ALA 22 12.017 22.074 22.336 1.00 0.00 ATOM 156 N GLY 23 10.917 21.971 23.040 1.00 0.00 ATOM 157 CA GLY 23 10.884 22.581 24.362 1.00 0.00 ATOM 158 O GLY 23 12.626 22.725 26.004 1.00 0.00 ATOM 159 C GLY 23 11.929 21.991 25.302 1.00 0.00 ATOM 160 N VAL 24 12.038 20.666 25.315 1.00 0.00 ATOM 161 CA VAL 24 12.971 20.039 26.143 1.00 0.00 ATOM 162 CB VAL 24 12.674 18.505 26.257 1.00 0.00 ATOM 163 CG1 VAL 24 13.096 17.751 25.016 1.00 0.00 ATOM 164 CG2 VAL 24 13.364 17.925 27.470 1.00 0.00 ATOM 165 O VAL 24 15.263 20.537 26.658 1.00 0.00 ATOM 166 C VAL 24 14.418 20.358 25.779 1.00 0.00 ATOM 167 N LEU 25 14.724 20.442 24.481 1.00 0.00 ATOM 168 CA LEU 25 16.078 20.762 24.054 1.00 0.00 ATOM 169 CB LEU 25 16.213 20.567 22.524 1.00 0.00 ATOM 170 CG LEU 25 16.148 19.084 22.142 1.00 0.00 ATOM 171 CD1 LEU 25 15.764 18.917 20.671 1.00 0.00 ATOM 172 CD2 LEU 25 17.499 18.386 22.457 1.00 0.00 ATOM 173 O LEU 25 17.572 22.346 24.999 1.00 0.00 ATOM 174 C LEU 25 16.464 22.128 24.512 1.00 0.00 ATOM 175 N ARG 26 15.544 23.093 24.354 1.00 0.00 ATOM 176 CA ARG 26 15.888 24.419 24.747 1.00 0.00 ATOM 177 CB ARG 26 14.843 25.458 24.298 1.00 0.00 ATOM 178 CG ARG 26 14.806 25.676 22.778 1.00 0.00 ATOM 179 CD ARG 26 16.083 26.281 22.191 1.00 0.00 ATOM 180 NE ARG 26 16.325 27.626 22.696 1.00 0.00 ATOM 181 CZ ARG 26 15.891 28.729 22.108 1.00 0.00 ATOM 182 NH1 ARG 26 15.202 28.652 20.979 1.00 0.00 ATOM 183 NH2 ARG 26 16.149 29.915 22.644 1.00 0.00 ATOM 184 O ARG 26 17.078 25.204 26.684 1.00 0.00 ATOM 185 C ARG 26 16.179 24.487 26.246 1.00 0.00 ATOM 186 N SER 27 15.423 23.728 27.022 1.00 0.00 ATOM 187 CA SER 27 15.600 23.726 28.467 1.00 0.00 ATOM 188 CB SER 27 14.452 22.896 29.117 1.00 0.00 ATOM 189 OG SER 27 13.192 23.494 28.862 1.00 0.00 ATOM 190 O SER 27 17.563 23.675 29.888 1.00 0.00 ATOM 191 C SER 27 16.989 23.182 28.915 1.00 0.00 ATOM 192 N TYR 28 17.504 22.184 28.205 1.00 0.00 ATOM 193 CA TYR 28 18.799 21.606 28.542 1.00 0.00 ATOM 194 CB TYR 28 18.563 20.037 28.622 1.00 0.00 ATOM 195 CG TYR 28 17.495 19.596 29.595 1.00 0.00 ATOM 196 CD1 TYR 28 17.466 20.080 30.898 1.00 0.00 ATOM 197 CD2 TYR 28 16.538 18.663 29.219 1.00 0.00 ATOM 198 CE1 TYR 28 16.494 19.658 31.793 1.00 0.00 ATOM 199 CE2 TYR 28 15.561 18.237 30.111 1.00 0.00 ATOM 200 CZ TYR 28 15.542 18.744 31.389 1.00 0.00 ATOM 201 OH TYR 28 14.575 18.321 32.273 1.00 0.00 ATOM 202 O TYR 28 21.106 22.098 28.125 1.00 0.00 ATOM 203 C TYR 28 19.943 22.505 28.105 1.00 0.00 ATOM 204 N ASN 29 19.615 23.730 27.711 1.00 0.00 ATOM 205 CA ASN 29 20.631 24.681 27.274 1.00 0.00 ATOM 206 CB ASN 29 21.700 24.816 28.384 1.00 0.00 ATOM 207 CG ASN 29 21.165 25.366 29.675 1.00 0.00 ATOM 208 ND2 ASN 29 21.491 24.689 30.771 1.00 0.00 ATOM 209 OD1 ASN 29 20.490 26.394 29.732 1.00 0.00 ATOM 210 O ASN 29 22.238 25.049 25.576 1.00 0.00 ATOM 211 C ASN 29 21.299 24.370 25.984 1.00 0.00 ATOM 212 N LEU 30 20.792 23.342 25.286 1.00 0.00 ATOM 213 CA LEU 30 21.247 23.080 23.957 1.00 0.00 ATOM 214 CB LEU 30 20.633 21.769 23.410 1.00 0.00 ATOM 215 CG LEU 30 20.960 21.404 21.937 1.00 0.00 ATOM 216 CD1 LEU 30 22.451 21.199 21.781 1.00 0.00 ATOM 217 CD2 LEU 30 20.228 20.126 21.483 1.00 0.00 ATOM 218 O LEU 30 21.901 24.798 22.416 1.00 0.00 ATOM 219 C LEU 30 21.031 24.372 23.176 1.00 0.00 ATOM 220 N GLY 31 19.871 24.991 23.364 1.00 0.00 ATOM 221 CA GLY 31 19.567 26.219 22.677 1.00 0.00 ATOM 222 O GLY 31 19.813 26.925 20.435 1.00 0.00 ATOM 223 C GLY 31 19.472 26.030 21.206 1.00 0.00 ATOM 224 N CYS 32 19.004 24.860 20.760 1.00 0.00 ATOM 225 CA CYS 32 18.980 24.718 19.341 1.00 0.00 ATOM 226 CB CYS 32 19.804 23.495 18.936 1.00 0.00 ATOM 227 SG CYS 32 21.554 23.592 19.381 1.00 0.00 ATOM 228 O CYS 32 17.295 26.376 19.240 1.00 0.00 ATOM 229 C CYS 32 17.842 25.413 18.701 1.00 0.00 ATOM 230 N ILE 33 17.458 24.933 17.523 1.00 0.00 ATOM 231 CA ILE 33 16.348 25.530 16.789 1.00 0.00 ATOM 232 CB ILE 33 15.156 25.867 17.582 1.00 0.00 ATOM 233 CG1 ILE 33 14.497 24.553 17.960 1.00 0.00 ATOM 234 CG2 ILE 33 14.236 26.761 16.786 1.00 0.00 ATOM 235 CD1 ILE 33 13.537 24.649 19.153 1.00 0.00 ATOM 236 O ILE 33 16.812 26.983 14.938 1.00 0.00 ATOM 237 C ILE 33 16.830 26.834 16.160 1.00 0.00 ATOM 238 N GLY 34 17.258 27.772 16.997 1.00 0.00 ATOM 239 CA GLY 34 17.727 29.016 16.508 1.00 0.00 ATOM 240 O GLY 34 19.665 30.011 15.509 1.00 0.00 ATOM 241 C GLY 34 19.101 28.972 15.858 1.00 0.00 ATOM 242 N CYS 35 19.643 27.769 15.693 1.00 0.00 ATOM 243 CA CYS 35 20.956 27.609 15.082 1.00 0.00 ATOM 244 CB CYS 35 22.028 27.880 16.244 1.00 0.00 ATOM 245 SG CYS 35 22.119 26.577 17.501 1.00 0.00 ATOM 246 O CYS 35 20.382 25.469 14.160 1.00 0.00 ATOM 247 C CYS 35 20.914 26.564 13.971 1.00 0.00 ATOM 248 N MET 36 21.475 26.903 12.815 1.00 0.00 ATOM 249 CA MET 36 21.497 25.972 11.670 1.00 0.00 ATOM 250 CB MET 36 22.091 26.594 10.432 1.00 0.00 ATOM 251 CG MET 36 21.173 27.502 9.669 1.00 0.00 ATOM 252 SD MET 36 22.061 28.017 8.185 1.00 0.00 ATOM 253 CE MET 36 22.541 29.577 8.651 1.00 0.00 ATOM 254 O MET 36 22.232 23.732 11.265 1.00 0.00 ATOM 255 C MET 36 22.407 24.780 11.889 1.00 0.00 ATOM 256 N GLY 37 23.382 24.934 12.779 1.00 0.00 ATOM 257 CA GLY 37 24.315 23.854 13.073 1.00 0.00 ATOM 258 O GLY 37 24.201 21.521 13.623 1.00 0.00 ATOM 259 C GLY 37 23.620 22.607 13.612 1.00 0.00 ATOM 260 N ALA 38 22.377 22.765 14.056 1.00 0.00 ATOM 261 CA ALA 38 21.626 21.647 14.586 1.00 0.00 ATOM 262 CB ALA 38 20.285 22.300 15.083 1.00 0.00 ATOM 263 O ALA 38 21.484 19.360 13.876 1.00 0.00 ATOM 264 C ALA 38 21.422 20.546 13.551 1.00 0.00 ATOM 265 N GLN 39 21.180 20.940 12.304 1.00 0.00 ATOM 266 CA GLN 39 20.981 19.994 11.275 1.00 0.00 ATOM 267 CB GLN 39 20.532 20.771 10.007 1.00 0.00 ATOM 268 CG GLN 39 19.084 21.292 10.144 1.00 0.00 ATOM 269 CD GLN 39 18.698 22.432 9.199 1.00 0.00 ATOM 270 OE1 GLN 39 17.562 22.909 9.234 1.00 0.00 ATOM 271 NE2 GLN 39 19.622 22.879 8.376 1.00 0.00 ATOM 272 O GLN 39 22.190 17.932 10.873 1.00 0.00 ATOM 273 C GLN 39 22.273 19.136 11.120 1.00 0.00 ATOM 274 N ASN 40 23.435 19.763 11.268 1.00 0.00 ATOM 275 CA ASN 40 24.700 19.049 11.146 1.00 0.00 ATOM 276 CB ASN 40 25.841 20.097 10.945 1.00 0.00 ATOM 277 CG ASN 40 25.762 20.840 9.607 1.00 0.00 ATOM 278 ND2 ASN 40 26.490 21.948 9.495 1.00 0.00 ATOM 279 OD1 ASN 40 25.047 20.411 8.693 1.00 0.00 ATOM 280 O ASN 40 25.811 17.244 12.232 1.00 0.00 ATOM 281 C ASN 40 25.003 18.164 12.346 1.00 0.00 ATOM 282 N GLU 41 24.406 18.401 13.540 1.00 0.00 ATOM 283 CA GLU 41 24.939 17.744 14.722 1.00 0.00 ATOM 284 CB GLU 41 25.469 18.692 15.801 1.00 0.00 ATOM 285 CG GLU 41 26.701 19.479 15.387 1.00 0.00 ATOM 286 CD GLU 41 27.223 20.369 16.498 1.00 0.00 ATOM 287 OE1 GLU 41 26.616 20.377 17.590 1.00 0.00 ATOM 288 OE2 GLU 41 28.242 21.058 16.277 1.00 0.00 ATOM 289 O GLU 41 22.717 17.074 15.326 1.00 0.00 ATOM 290 C GLU 41 23.924 16.849 15.424 1.00 0.00 ATOM 291 N SER 42 24.413 15.835 16.130 1.00 0.00 ATOM 292 CA SER 42 23.538 14.928 16.835 1.00 0.00 ATOM 293 CB SER 42 24.173 13.536 16.863 1.00 0.00 ATOM 294 OG SER 42 25.344 13.524 17.659 1.00 0.00 ATOM 295 O SER 42 23.853 16.459 18.630 1.00 0.00 ATOM 296 C SER 42 23.283 15.448 18.217 1.00 0.00 ATOM 297 N LEU 43 22.419 14.757 18.955 1.00 0.00 ATOM 298 CA LEU 43 22.090 15.166 20.315 1.00 0.00 ATOM 299 CB LEU 43 20.985 14.366 20.945 1.00 0.00 ATOM 300 CG LEU 43 20.837 14.392 22.462 1.00 0.00 ATOM 301 CD1 LEU 43 19.918 15.518 22.925 1.00 0.00 ATOM 302 CD2 LEU 43 20.316 13.065 22.999 1.00 0.00 ATOM 303 O LEU 43 23.560 16.005 22.008 1.00 0.00 ATOM 304 C LEU 43 23.335 15.117 21.186 1.00 0.00 ATOM 305 N GLU 44 24.122 14.109 20.987 1.00 0.00 ATOM 306 CA GLU 44 25.342 13.968 21.775 1.00 0.00 ATOM 307 CB GLU 44 26.092 12.668 21.516 1.00 0.00 ATOM 308 CG GLU 44 25.298 11.434 21.944 1.00 0.00 ATOM 309 CD GLU 44 26.086 10.132 21.801 1.00 0.00 ATOM 310 OE1 GLU 44 27.057 10.083 21.018 1.00 0.00 ATOM 311 OE2 GLU 44 25.711 9.146 22.462 1.00 0.00 ATOM 312 O GLU 44 26.909 15.680 22.373 1.00 0.00 ATOM 313 C GLU 44 26.326 15.086 21.465 1.00 0.00 ATOM 314 N GLN 45 26.510 15.374 20.180 1.00 0.00 ATOM 315 CA GLN 45 27.429 16.429 19.767 1.00 0.00 ATOM 316 CB GLN 45 27.588 16.415 18.214 1.00 0.00 ATOM 317 CG GLN 45 28.287 15.166 17.655 1.00 0.00 ATOM 318 CD GLN 45 28.066 14.987 16.159 1.00 0.00 ATOM 319 OE1 GLN 45 27.001 14.544 15.716 1.00 0.00 ATOM 320 NE2 GLN 45 29.078 15.331 15.369 1.00 0.00 ATOM 321 O GLN 45 27.784 18.594 20.730 1.00 0.00 ATOM 322 C GLN 45 26.962 17.784 20.274 1.00 0.00 ATOM 323 N GLY 46 25.663 18.058 20.187 1.00 0.00 ATOM 324 CA GLY 46 25.097 19.323 20.686 1.00 0.00 ATOM 325 O GLY 46 25.660 20.509 22.693 1.00 0.00 ATOM 326 C GLY 46 25.298 19.444 22.192 1.00 0.00 ATOM 327 N ALA 47 25.064 18.352 22.913 1.00 0.00 ATOM 328 CA ALA 47 25.229 18.342 24.400 1.00 0.00 ATOM 329 CB ALA 47 24.890 17.015 24.987 1.00 0.00 ATOM 330 O ALA 47 26.986 19.445 25.641 1.00 0.00 ATOM 331 C ALA 47 26.698 18.612 24.766 1.00 0.00 ATOM 332 N ASN 48 27.619 17.923 24.087 1.00 0.00 ATOM 333 CA ASN 48 29.048 18.143 24.316 1.00 0.00 ATOM 334 CB ASN 48 29.933 17.325 23.435 1.00 0.00 ATOM 335 CG ASN 48 29.974 15.885 23.886 1.00 0.00 ATOM 336 ND2 ASN 48 30.073 14.958 22.935 1.00 0.00 ATOM 337 OD1 ASN 48 29.925 15.608 25.085 1.00 0.00 ATOM 338 O ASN 48 30.124 20.212 24.878 1.00 0.00 ATOM 339 C ASN 48 29.422 19.601 24.073 1.00 0.00 ATOM 340 N ALA 49 28.953 20.156 22.960 1.00 0.00 ATOM 341 CA ALA 49 29.246 21.556 22.622 1.00 0.00 ATOM 342 CB ALA 49 28.668 21.837 21.231 1.00 0.00 ATOM 343 O ALA 49 29.324 23.478 24.048 1.00 0.00 ATOM 344 C ALA 49 28.654 22.537 23.619 1.00 0.00 ATOM 345 N HIS 50 27.397 22.320 23.989 1.00 0.00 ATOM 346 CA HIS 50 26.727 23.197 24.944 1.00 0.00 ATOM 347 CB HIS 50 25.263 23.229 24.508 1.00 0.00 ATOM 348 CG HIS 50 25.072 24.056 23.220 1.00 0.00 ATOM 349 CD2 HIS 50 24.585 23.675 22.034 1.00 0.00 ATOM 350 ND1 HIS 50 25.279 25.365 23.144 1.00 0.00 ATOM 351 CE1 HIS 50 24.903 25.784 21.943 1.00 0.00 ATOM 352 NE2 HIS 50 24.484 24.741 21.248 1.00 0.00 ATOM 353 O HIS 50 26.411 23.565 27.309 1.00 0.00 ATOM 354 C HIS 50 27.016 22.949 26.438 1.00 0.00 ATOM 355 N GLY 51 27.921 22.000 26.709 1.00 0.00 ATOM 356 CA GLY 51 28.348 21.645 28.056 1.00 0.00 ATOM 357 O GLY 51 27.456 20.855 30.138 1.00 0.00 ATOM 358 C GLY 51 27.354 20.867 28.910 1.00 0.00 ATOM 359 N LEU 52 26.394 20.216 28.260 1.00 0.00 ATOM 360 CA LEU 52 25.360 19.413 28.987 1.00 0.00 ATOM 361 CB LEU 52 24.042 19.711 28.274 1.00 0.00 ATOM 362 CG LEU 52 22.854 18.946 28.907 1.00 0.00 ATOM 363 CD1 LEU 52 22.678 19.234 30.319 1.00 0.00 ATOM 364 CD2 LEU 52 21.577 19.374 28.124 1.00 0.00 ATOM 365 O LEU 52 25.973 17.453 27.747 1.00 0.00 ATOM 366 C LEU 52 25.742 17.942 28.853 1.00 0.00 ATOM 367 N ASN 53 25.807 17.241 29.980 1.00 0.00 ATOM 368 CA ASN 53 26.159 15.829 29.969 1.00 0.00 ATOM 369 CB ASN 53 26.146 15.271 31.396 1.00 0.00 ATOM 370 CG ASN 53 27.164 15.941 32.294 1.00 0.00 ATOM 371 ND2 ASN 53 26.761 16.255 33.514 1.00 0.00 ATOM 372 OD1 ASN 53 28.303 16.179 31.891 1.00 0.00 ATOM 373 O ASN 53 23.912 15.344 29.214 1.00 0.00 ATOM 374 C ASN 53 25.108 15.065 29.120 1.00 0.00 ATOM 375 N VAL 54 25.565 14.115 28.309 1.00 0.00 ATOM 376 CA VAL 54 24.661 13.337 27.472 1.00 0.00 ATOM 377 CB VAL 54 25.543 12.493 26.449 1.00 0.00 ATOM 378 CG1 VAL 54 24.669 11.523 25.671 1.00 0.00 ATOM 379 CG2 VAL 54 26.281 13.417 25.488 1.00 0.00 ATOM 380 O VAL 54 22.544 12.338 27.975 1.00 0.00 ATOM 381 C VAL 54 23.715 12.489 28.325 1.00 0.00 ATOM 382 N GLU 55 24.247 11.931 29.409 1.00 0.00 ATOM 383 CA GLU 55 23.443 11.133 30.349 1.00 0.00 ATOM 384 CB GLU 55 24.258 10.595 31.493 1.00 0.00 ATOM 385 CG GLU 55 23.508 9.565 32.410 1.00 0.00 ATOM 386 CD GLU 55 24.427 8.849 33.433 1.00 0.00 ATOM 387 OE1 GLU 55 25.341 8.057 33.019 1.00 0.00 ATOM 388 OE2 GLU 55 24.250 9.080 34.666 1.00 0.00 ATOM 389 O GLU 55 21.123 11.442 30.943 1.00 0.00 ATOM 390 C GLU 55 22.236 11.961 30.845 1.00 0.00 ATOM 391 N ASP 56 22.467 13.234 31.149 1.00 0.00 ATOM 392 CA ASP 56 21.397 14.104 31.624 1.00 0.00 ATOM 393 CB ASP 56 21.907 15.507 31.996 1.00 0.00 ATOM 394 CG ASP 56 22.741 15.565 33.271 1.00 0.00 ATOM 395 OD1 ASP 56 22.725 14.581 34.019 1.00 0.00 ATOM 396 OD2 ASP 56 23.428 16.591 33.459 1.00 0.00 ATOM 397 O ASP 56 19.122 14.063 30.875 1.00 0.00 ATOM 398 C ASP 56 20.303 14.225 30.570 1.00 0.00 ATOM 399 N ILE 57 20.705 14.482 29.320 1.00 0.00 ATOM 400 CA ILE 57 19.758 14.642 28.215 1.00 0.00 ATOM 401 CB ILE 57 20.478 15.073 26.917 1.00 0.00 ATOM 402 CG1 ILE 57 21.078 16.470 27.110 1.00 0.00 ATOM 403 CG2 ILE 57 19.503 15.059 25.739 1.00 0.00 ATOM 404 CD1 ILE 57 21.902 16.959 25.934 1.00 0.00 ATOM 405 O ILE 57 17.784 13.361 27.685 1.00 0.00 ATOM 406 C ILE 57 18.989 13.356 27.930 1.00 0.00 ATOM 407 N LEU 58 19.668 12.206 27.973 1.00 0.00 ATOM 408 CA LEU 58 19.037 10.909 27.713 1.00 0.00 ATOM 409 CB LEU 58 20.077 9.788 27.632 1.00 0.00 ATOM 410 CG LEU 58 21.009 9.906 26.416 1.00 0.00 ATOM 411 CD1 LEU 58 22.116 8.862 26.525 1.00 0.00 ATOM 412 CD2 LEU 58 20.258 9.768 25.062 1.00 0.00 ATOM 413 O LEU 58 16.894 10.120 28.451 1.00 0.00 ATOM 414 C LEU 58 18.000 10.555 28.775 1.00 0.00 ATOM 415 N ARG 59 18.358 10.742 30.040 1.00 0.00 ATOM 416 CA ARG 59 17.446 10.440 31.135 1.00 0.00 ATOM 417 CB ARG 59 18.113 10.835 32.448 1.00 0.00 ATOM 418 CG ARG 59 18.890 9.789 33.080 1.00 0.00 ATOM 419 CD ARG 59 19.363 10.221 34.466 1.00 0.00 ATOM 420 NE ARG 59 20.782 10.442 34.403 1.00 0.00 ATOM 421 CZ ARG 59 21.406 11.559 34.702 1.00 0.00 ATOM 422 NH1 ARG 59 20.761 12.639 35.157 1.00 0.00 ATOM 423 NH2 ARG 59 22.712 11.576 34.556 1.00 0.00 ATOM 424 O ARG 59 15.113 10.818 31.271 1.00 0.00 ATOM 425 C ARG 59 16.233 11.290 31.075 1.00 0.00 ATOM 426 N ASP 60 16.436 12.574 30.798 1.00 0.00 ATOM 427 CA ASP 60 15.325 13.513 30.708 1.00 0.00 ATOM 428 CB ASP 60 15.830 14.940 30.519 1.00 0.00 ATOM 429 CG ASP 60 16.303 15.561 31.822 1.00 0.00 ATOM 430 OD1 ASP 60 15.532 15.559 32.801 1.00 0.00 ATOM 431 OD2 ASP 60 17.439 16.060 31.875 1.00 0.00 ATOM 432 O ASP 60 13.179 13.273 29.678 1.00 0.00 ATOM 433 C ASP 60 14.400 13.232 29.532 1.00 0.00 ATOM 434 N LEU 61 14.971 12.956 28.343 1.00 0.00 ATOM 435 CA LEU 61 14.170 12.656 27.159 1.00 0.00 ATOM 436 CB LEU 61 15.033 12.570 25.921 1.00 0.00 ATOM 437 CG LEU 61 15.570 13.944 25.447 1.00 0.00 ATOM 438 CD1 LEU 61 16.724 13.708 24.511 1.00 0.00 ATOM 439 CD2 LEU 61 14.449 14.703 24.760 1.00 0.00 ATOM 440 O LEU 61 12.225 11.259 27.001 1.00 0.00 ATOM 441 C LEU 61 13.394 11.343 27.358 1.00 0.00 ATOM 442 N ASN 62 14.034 10.327 27.927 1.00 0.00 ATOM 443 CA ASN 62 13.284 9.095 28.231 1.00 0.00 ATOM 444 CB ASN 62 14.196 8.051 28.855 1.00 0.00 ATOM 445 CG ASN 62 15.126 7.385 27.825 1.00 0.00 ATOM 446 ND2 ASN 62 16.283 6.994 28.253 1.00 0.00 ATOM 447 OD1 ASN 62 14.756 7.217 26.680 1.00 0.00 ATOM 448 O ASN 62 11.006 8.878 28.949 1.00 0.00 ATOM 449 C ASN 62 12.105 9.392 29.145 1.00 0.00 ATOM 450 N ALA 63 12.345 10.237 30.145 1.00 0.00 ATOM 451 CA ALA 63 11.293 10.601 31.086 1.00 0.00 ATOM 452 CB ALA 63 11.887 11.507 32.181 1.00 0.00 ATOM 453 O ALA 63 8.995 11.104 30.631 1.00 0.00 ATOM 454 C ALA 63 10.174 11.375 30.404 1.00 0.00 ATOM 455 N LEU 64 10.545 12.338 29.567 1.00 0.00 ATOM 456 CA LEU 64 9.558 13.142 28.855 1.00 0.00 ATOM 457 CB LEU 64 10.461 13.851 27.623 1.00 0.00 ATOM 458 CG LEU 64 10.177 15.237 27.062 1.00 0.00 ATOM 459 CD1 LEU 64 10.808 16.303 27.936 1.00 0.00 ATOM 460 CD2 LEU 64 10.713 15.321 25.648 1.00 0.00 ATOM 461 O LEU 64 7.519 12.570 27.727 1.00 0.00 ATOM 462 C LEU 64 8.709 12.308 27.901 1.00 0.00 ATOM 463 N ALA 65 9.325 11.309 27.278 1.00 0.00 ATOM 464 CA ALA 65 8.613 10.450 26.338 1.00 0.00 ATOM 465 CB ALA 65 8.924 10.975 24.946 1.00 0.00 ATOM 466 O ALA 65 10.308 8.761 26.363 1.00 0.00 ATOM 467 C ALA 65 9.109 9.019 26.453 1.00 0.00 TER END