PFRMAT TS TARGET T0469 AUTHOR 4008-1775-0004 METHOD The SAM-T08 hand predictions use methods similar to SAM_T06 in CASP7. METHOD METHOD We start with a fully automated method (implemented as the SAM-T08-server): METHOD METHOD Use the SAM-T2K, SAM-T04, and SAM-T06 methods for finding homologs METHOD of the target and aligning them. METHOD METHOD Make local structure predictions using neural nets and the METHOD multiple alignments. These neural nets have been newly trained METHOD for CASP8 with an improved training protocol. The neural nets for METHOD the 3 different multiple sequence alignments are independently METHOD trained, so combining them should offer improved performance. METHOD METHOD We currently use 15 local-structure alphabets: METHOD STR2 an extended version of DSSP that splits the beta strands METHOD into multiple classes (parallel/antiparallel/mixed, METHOD edge/center) METHOD STR4 an attempt at an alphabet like STR2, but not requiring DSSP. METHOD This alphabet may be trying to make some irrelevant METHOD distinctions as well. METHOD ALPHA an discretization of the alpha torsion angle: METHOD CA(i-i), CA(i), CA(i+1), CA(i+2) METHOD BYS a discretization of Ramachandran plots, due to Bystroff METHOD PB de Brevern's protein blocks METHOD METHOD N_NOTOR METHOD N_NOTOR2 METHOD O_NOTOR METHOD O_NOTOR2 alphabets based on the torsion angle of METHOD backbone hydrogen bonds METHOD METHOD N_SEP METHOD O_SEP alphabets based on the separation of donor and METHOD acceptor for backbone hydrogen bonds METHOD METHOD CB_burial_14_7 a 7-state discretization of the number of C_beta METHOD atoms in a 14 Angstrom radius sphere around the C_beta. METHOD near-backbone-11 an 11-state discretization of the number of METHOD residues (represented by near-backbone points) in a METHOD 9.65 Angstrom radius sphere around the sidechain proxy METHOD spot for the residue. METHOD METHOD DSSP_EHL2 CASP's collapse of the DSSP alphabet METHOD DSSP_EHL2 is not predicted directly by a METHOD neural net, but is computed as a weighted METHOD average of the other backbone alphabet predictions. METHOD METHOD We make 2-track HMMs with each alphabet with the amino-acid track METHOD having a weight of 1 and the local structure track having a weight METHOD of 0.1 (for backbone alphabets) or 0.3 (for burial alphabets). METHOD We use these HMMs to score a template library of about METHOD 14000 (t06), 16000 (t04), or 18000 (t2k) templates. METHOD The template libraries are expanded weekly, but old template HMMs METHOD are not rebuilt. The target HMMs are used to score consensus METHOD sequences for the templates, to get a cheap approximation of METHOD profile-profile scoring, which does not yet work in the SAM package. METHOD METHOD We also used single-track HMMs to score not just the template METHOD library, but a non-redundant copy of the entire PDB. This scoring METHOD is done with real sequences, not consensus sequences. METHOD METHOD All the target HMMs use a new calibration method the provides more METHOD accurate E-values than before, and can be used even with METHOD local-structure alphabets that used to give us trouble (such as METHOD protein blocks). METHOD METHOD One-track HMMs built from the template library multiple alignments METHOD were used to score the target sequence. Later this summer, we METHOD hope to be able to use multi-track template HMMs, but we have not METHOD had time to calibrate such models while keeping the code METHOD compatible with the old libraries, so the template libraries METHOD currently use old calibrations, with somewhat optimistic E-values. METHOD METHOD All the logs of e-values were combined in a weighted average (with METHOD rather arbitrary weights, since we still have not taken the time METHOD to optimize them), and the best templates ranked. METHOD METHOD Alignments of the target to the top templates were made using METHOD several different alignment settings on the SAM alignment software. METHOD METHOD Generate fragments (short 9-residue alignments for each position) METHOD using SAM's "fragfinder" program and the 3-track HMM which tested METHOD best for alignment. METHOD METHOD Residue-residue contact predictions are made using mutual METHOD information, pairwise contact potentials, joint entropy, and other METHOD signals combined by a neural net. Two different neural net METHOD methods were used, and the results submitted separately. METHOD METHOD CB-CB constraints were extracted from the alignments and a METHOD combinatorial optimization done to choose a most-believable METHOD subset. METHOD METHOD Then the "undertaker" program (named because it originally METHOD optimized burial) is used to try to combine the alignments and the METHOD fragments into a consistent 3D model. No single alignment or METHOD parent template was used as a frozen core, though in many cases METHOD one had much more influence than the others. The alignment scores METHOD were not used by undertaker, but were used only to pick the set METHOD of alignments and fragments that undertaker would see. METHOD METHOD The cost functions used by undertaker rely heavily on the METHOD alignment constraints, on helix and strand constraints generated METHOD from the secondary-structure predictions, and on the neural-net METHOD predictions of local properties that undertaker can measure. METHOD The residue-residue contact predictions are also given to METHOD undertaker, but have less weight. There are also a number of METHOD built-in cost functions (breaks, clashes, burial, ...) that are METHOD included in the cost function. METHOD METHOD The automatic script runs the undertaker-optimized model through METHOD gromacs (to fix small clashes and breaks) and repacks the METHOD sidechains using Rosetta, but these post-undertaker optimizations METHOD are not included in the server predictions. They can be used in METHOD subsequent re-optimization. METHOD METHOD After the automatic prediction is done, we examine it by hand and try METHOD to fix any flaws that we see. This generally involves rerunning METHOD undertaker with new cost functions, increasing the weights for METHOD features we want to see and decreasing the weights where we think the METHOD optimization has gone overboard. Sometimes we will add new templates METHOD or remove ones that we think are misleading the optimization process. METHOD We often do "polishing" runs, where all the current models are read in METHOD and optimization with undertaker's genetic algorithm is done with high METHOD crossover. METHOD METHOD Some improvements in undertaker include better communication with METHOD SCWRL for initial model building form alignments (now using the METHOD standard protocol that identical residues have fixed rotamers, rather METHOD than being reoptimized by SCWRL), more cost functions based on the METHOD neural net predictions, multiple constraint sets (for easier METHOD weighting of the importance of different constraints), and some new METHOD conformation-change operators (Backrub and BigBackrub). METHOD METHOD We also created model-quality-assessment methods for CASP8, which we METHOD are applying to the server predictions. We do two optimizations from the METHOD top 10 models with two of the MQA methods, and consider these models METHOD as possible alternatives to our natively-generated models. METHOD METHOD The HMMs found a weak but reasonably convincing relationship to 2fi0A, METHOD which seems to be the same as what half the servers found. The METHOD interesting thing as that there were two conserved CYS residues and a METHOD conserved HIS in the loop that did not align to 2fi0A. METHOD METHOD I tried clustering these 3 residues (which may indicate a METHOD metal-binding site) for three of my models. I tried basing my models METHOD both on SAM+undertaker models and on metaserver models from the METHOD servers---there did not seem to be much difference. METHOD METHOD Model METHOD 1 T0469.try13-opt3.pdb # < try12-opt3.gromacs0 < try11-opt3 < try10-opt3 < MQAX5-opt3 < Zhang-Server_TS4 METHOD attempts to cluster C32, C35, H50. The chain got broken in METHOD forcing the cluster, and took several attempts to rejoin METHOD without losing the clustering. METHOD METHOD 2 T0469.try9-opt3.pdb # < try8-opt3 < try7-opt3.gromacs0 < try6-opt3 < MQAU1-opt3 < SAM-T08-server_TS1 METHOD attempts to cluster C32, C35, H50. METHOD METHOD 3 T0469.try4-opt3.pdb # < try3-opt3.gromacs0 < align(2fi0A) METHOD no attempt to cluster. METHOD METHOD 4 T0469.MQAC1-opt3.gromacs0.pdb # < MULTICOM-CMFR_TS3 METHOD no attempt to cluster. METHOD METHOD 5 T0469.try5-opt3.pdb # < align(2fi0A+2cs8A) METHOD attempts to cluster C32, C35, H50. REMARK 6 REMARK 6 T0469 model 3 Mon Jul 7 11:25:21 2008 MODEL 3 PARENT N/A ATOM 1 N MET 1 6.197 10.874 21.341 1.00 0.00 ATOM 2 CA MET 1 5.121 9.942 21.676 1.00 0.00 ATOM 3 CB MET 1 5.275 8.625 20.641 1.00 0.00 ATOM 4 CG MET 1 6.164 8.899 19.435 1.00 0.00 ATOM 5 SD MET 1 6.193 7.261 18.627 1.00 0.00 ATOM 6 CE MET 1 4.510 7.333 17.960 1.00 0.00 ATOM 7 O MET 1 4.800 9.366 23.981 1.00 0.00 ATOM 8 C MET 1 5.533 9.294 22.994 1.00 0.00 ATOM 9 N THR 2 6.739 8.723 23.001 1.00 0.00 ATOM 10 CA THR 2 7.220 8.122 24.251 1.00 0.00 ATOM 11 CB THR 2 7.299 6.587 24.151 1.00 0.00 ATOM 12 CG2 THR 2 5.961 5.910 23.914 1.00 0.00 ATOM 13 OG1 THR 2 8.170 6.146 23.113 1.00 0.00 ATOM 14 O THR 2 9.399 8.019 25.310 1.00 0.00 ATOM 15 C THR 2 8.604 8.710 24.672 1.00 0.00 ATOM 16 N GLN 3 8.890 9.942 24.260 1.00 0.00 ATOM 17 CA GLN 3 10.172 10.563 24.569 1.00 0.00 ATOM 18 CB GLN 3 10.407 10.818 26.073 1.00 0.00 ATOM 19 CG GLN 3 9.475 11.848 26.705 1.00 0.00 ATOM 20 CD GLN 3 8.043 11.318 26.769 1.00 0.00 ATOM 21 OE1 GLN 3 7.746 10.355 27.441 1.00 0.00 ATOM 22 NE2 GLN 3 7.134 11.996 26.098 1.00 0.00 ATOM 23 O GLN 3 12.442 9.682 24.546 1.00 0.00 ATOM 24 C GLN 3 11.350 9.754 23.995 1.00 0.00 ATOM 25 N LYS 4 11.097 9.184 22.818 1.00 0.00 ATOM 26 CA LYS 4 12.119 8.435 22.095 1.00 0.00 ATOM 27 CB LYS 4 11.585 7.171 21.425 1.00 0.00 ATOM 28 CG LYS 4 11.228 6.040 22.398 1.00 0.00 ATOM 29 CD LYS 4 11.494 4.700 21.747 1.00 0.00 ATOM 30 CE LYS 4 11.481 3.541 22.747 1.00 0.00 ATOM 31 NZ LYS 4 10.123 3.171 23.150 1.00 0.00 ATOM 32 O LYS 4 12.235 9.686 20.050 1.00 0.00 ATOM 33 C LYS 4 12.813 9.340 21.082 1.00 0.00 ATOM 34 N PHE 5 14.051 9.722 21.376 1.00 0.00 ATOM 35 CA PHE 5 14.831 10.600 20.466 1.00 0.00 ATOM 36 CB PHE 5 14.820 12.045 21.018 1.00 0.00 ATOM 37 CG PHE 5 13.449 12.623 21.243 1.00 0.00 ATOM 38 CD1 PHE 5 12.689 12.244 22.343 1.00 0.00 ATOM 39 CD2 PHE 5 12.922 13.555 20.353 1.00 0.00 ATOM 40 CE1 PHE 5 11.420 12.785 22.556 1.00 0.00 ATOM 41 CE2 PHE 5 11.658 14.101 20.555 1.00 0.00 ATOM 42 CZ PHE 5 10.907 13.717 21.658 1.00 0.00 ATOM 43 O PHE 5 16.832 9.445 21.147 1.00 0.00 ATOM 44 C PHE 5 16.212 9.973 20.222 1.00 0.00 ATOM 45 N THR 6 16.686 10.034 18.981 1.00 0.00 ATOM 46 CA THR 6 17.987 9.472 18.639 1.00 0.00 ATOM 47 CB THR 6 17.937 8.699 17.312 1.00 0.00 ATOM 48 CG2 THR 6 19.276 8.091 16.919 1.00 0.00 ATOM 49 OG1 THR 6 16.947 7.674 17.483 1.00 0.00 ATOM 50 O THR 6 19.013 11.472 17.721 1.00 0.00 ATOM 51 C THR 6 19.018 10.617 18.606 1.00 0.00 ATOM 52 N LYS 7 19.860 10.620 19.626 1.00 0.00 ATOM 53 CA LYS 7 20.947 11.605 19.843 1.00 0.00 ATOM 54 CB LYS 7 21.498 11.514 21.292 1.00 0.00 ATOM 55 CG LYS 7 20.627 10.823 22.374 1.00 0.00 ATOM 56 CD LYS 7 21.533 10.183 23.444 1.00 0.00 ATOM 57 CE LYS 7 20.793 9.456 24.558 1.00 0.00 ATOM 58 NZ LYS 7 19.734 8.564 24.072 1.00 0.00 ATOM 59 O LYS 7 22.636 12.571 18.421 1.00 0.00 ATOM 60 C LYS 7 22.034 11.536 18.731 1.00 0.00 ATOM 61 N ASP 8 22.012 10.468 17.913 1.00 0.00 ATOM 62 CA ASP 8 23.021 10.237 16.848 1.00 0.00 ATOM 63 CB ASP 8 23.485 8.770 16.863 1.00 0.00 ATOM 64 CG ASP 8 24.014 8.287 18.211 1.00 0.00 ATOM 65 OD1 ASP 8 24.336 9.162 19.036 1.00 0.00 ATOM 66 OD2 ASP 8 23.945 7.054 18.380 1.00 0.00 ATOM 67 O ASP 8 23.305 10.542 14.486 1.00 0.00 ATOM 68 C ASP 8 22.548 10.631 15.454 1.00 0.00 ATOM 69 N MET 9 21.297 11.069 15.353 1.00 0.00 ATOM 70 CA MET 9 20.716 11.487 14.040 1.00 0.00 ATOM 71 CB MET 9 19.217 11.208 13.927 1.00 0.00 ATOM 72 CG MET 9 18.786 9.788 14.249 1.00 0.00 ATOM 73 SD MET 9 17.067 9.366 13.806 1.00 0.00 ATOM 74 CE MET 9 16.181 10.395 14.943 1.00 0.00 ATOM 75 O MET 9 20.829 13.705 14.947 1.00 0.00 ATOM 76 C MET 9 20.723 13.009 13.937 1.00 0.00 ATOM 77 N THR 10 20.607 13.523 12.716 1.00 0.00 ATOM 78 CA THR 10 20.597 14.975 12.497 1.00 0.00 ATOM 79 CB THR 10 20.585 15.366 11.011 1.00 0.00 ATOM 80 CG2 THR 10 21.683 14.594 10.251 1.00 0.00 ATOM 81 OG1 THR 10 19.325 15.105 10.397 1.00 0.00 ATOM 82 O THR 10 18.302 15.024 13.256 1.00 0.00 ATOM 83 C THR 10 19.414 15.550 13.318 1.00 0.00 ATOM 84 N PHE 11 19.667 16.616 14.072 1.00 0.00 ATOM 85 CA PHE 11 18.622 17.234 14.880 1.00 0.00 ATOM 86 CB PHE 11 19.210 18.421 15.643 1.00 0.00 ATOM 87 CG PHE 11 18.301 18.751 16.835 1.00 0.00 ATOM 88 CD1 PHE 11 18.439 18.079 18.034 1.00 0.00 ATOM 89 CD2 PHE 11 17.309 19.706 16.696 1.00 0.00 ATOM 90 CE1 PHE 11 17.571 18.377 19.069 1.00 0.00 ATOM 91 CE2 PHE 11 16.512 20.084 17.732 1.00 0.00 ATOM 92 CZ PHE 11 16.642 19.389 18.895 1.00 0.00 ATOM 93 O PHE 11 16.229 17.559 14.685 1.00 0.00 ATOM 94 C PHE 11 17.318 17.596 14.110 1.00 0.00 ATOM 95 N ALA 12 17.446 17.938 12.832 1.00 0.00 ATOM 96 CA ALA 12 16.285 18.292 12.024 1.00 0.00 ATOM 97 CB ALA 12 16.746 18.728 10.644 1.00 0.00 ATOM 98 O ALA 12 14.138 17.223 11.956 1.00 0.00 ATOM 99 C ALA 12 15.354 17.086 11.867 1.00 0.00 ATOM 100 N GLN 13 15.951 15.893 11.837 1.00 0.00 ATOM 101 CA GLN 13 15.222 14.627 11.768 1.00 0.00 ATOM 102 CB GLN 13 16.267 13.551 11.505 1.00 0.00 ATOM 103 CG GLN 13 16.642 13.411 10.041 1.00 0.00 ATOM 104 CD GLN 13 17.653 12.278 9.889 1.00 0.00 ATOM 105 OE1 GLN 13 17.467 11.084 10.074 1.00 0.00 ATOM 106 NE2 GLN 13 18.824 12.639 9.459 1.00 0.00 ATOM 107 O GLN 13 13.288 14.008 13.063 1.00 0.00 ATOM 108 C GLN 13 14.451 14.411 13.085 1.00 0.00 ATOM 109 N ALA 14 15.080 14.686 14.235 1.00 0.00 ATOM 110 CA ALA 14 14.388 14.578 15.516 1.00 0.00 ATOM 111 CB ALA 14 15.307 14.944 16.684 1.00 0.00 ATOM 112 O ALA 14 12.110 15.170 15.982 1.00 0.00 ATOM 113 C ALA 14 13.206 15.541 15.560 1.00 0.00 ATOM 114 N LEU 15 13.431 16.777 15.126 1.00 0.00 ATOM 115 CA LEU 15 12.355 17.808 15.118 1.00 0.00 ATOM 116 CB LEU 15 12.958 19.159 14.713 1.00 0.00 ATOM 117 CG LEU 15 13.904 19.725 15.770 1.00 0.00 ATOM 118 CD1 LEU 15 14.562 21.034 15.229 1.00 0.00 ATOM 119 CD2 LEU 15 13.161 19.969 17.065 1.00 0.00 ATOM 120 O LEU 15 10.026 17.653 14.446 1.00 0.00 ATOM 121 C LEU 15 11.196 17.421 14.139 1.00 0.00 ATOM 122 N GLN 16 11.539 16.845 12.991 1.00 0.00 ATOM 123 CA GLN 16 10.532 16.445 12.015 1.00 0.00 ATOM 124 CB GLN 16 11.208 15.819 10.795 1.00 0.00 ATOM 125 CG GLN 16 11.987 16.871 10.013 1.00 0.00 ATOM 126 CD GLN 16 12.920 16.217 8.994 1.00 0.00 ATOM 127 OE1 GLN 16 13.481 15.145 9.136 1.00 0.00 ATOM 128 NE2 GLN 16 13.066 16.898 7.890 1.00 0.00 ATOM 129 O GLN 16 8.386 15.486 12.484 1.00 0.00 ATOM 130 C GLN 16 9.593 15.417 12.650 1.00 0.00 ATOM 131 N THR 17 10.186 14.476 13.351 1.00 0.00 ATOM 132 CA THR 17 9.411 13.394 13.976 1.00 0.00 ATOM 133 CB THR 17 10.327 12.197 14.290 1.00 0.00 ATOM 134 CG2 THR 17 9.570 11.026 14.947 1.00 0.00 ATOM 135 OG1 THR 17 10.857 11.727 13.048 1.00 0.00 ATOM 136 O THR 17 7.421 13.593 15.306 1.00 0.00 ATOM 137 C THR 17 8.594 13.933 15.150 1.00 0.00 ATOM 138 N HIS 18 9.216 14.773 15.972 1.00 0.00 ATOM 139 CA HIS 18 8.532 15.351 17.123 1.00 0.00 ATOM 140 CB HIS 18 9.226 14.793 18.334 1.00 0.00 ATOM 141 CG HIS 18 8.713 13.422 18.626 1.00 0.00 ATOM 142 CD2 HIS 18 7.666 13.006 19.379 1.00 0.00 ATOM 143 ND1 HIS 18 9.254 12.288 18.055 1.00 0.00 ATOM 144 CE1 HIS 18 8.583 11.231 18.478 1.00 0.00 ATOM 145 NE2 HIS 18 7.610 11.639 19.274 1.00 0.00 ATOM 146 O HIS 18 9.547 17.457 17.720 1.00 0.00 ATOM 147 C HIS 18 8.634 16.840 17.119 1.00 0.00 ATOM 148 N PRO 19 7.663 17.622 16.513 1.00 0.00 ATOM 149 CA PRO 19 7.674 19.058 16.458 1.00 0.00 ATOM 150 CB PRO 19 6.454 19.451 15.586 1.00 0.00 ATOM 151 CG PRO 19 5.637 18.213 15.596 1.00 0.00 ATOM 152 CD PRO 19 6.538 17.013 15.707 1.00 0.00 ATOM 153 O PRO 19 8.109 20.788 18.062 1.00 0.00 ATOM 154 C PRO 19 7.565 19.707 17.834 1.00 0.00 ATOM 155 N GLY 20 6.862 19.047 18.749 1.00 0.00 ATOM 156 CA GLY 20 6.682 19.579 20.145 1.00 0.00 ATOM 157 O GLY 20 8.075 20.265 21.982 1.00 0.00 ATOM 158 C GLY 20 7.964 19.550 20.985 1.00 0.00 ATOM 159 N VAL 21 8.926 18.727 20.578 1.00 0.00 ATOM 160 CA VAL 21 10.188 18.622 21.302 1.00 0.00 ATOM 161 CB VAL 21 10.869 17.294 20.951 1.00 0.00 ATOM 162 CG1 VAL 21 11.738 17.278 19.686 1.00 0.00 ATOM 163 CG2 VAL 21 11.606 16.805 22.194 1.00 0.00 ATOM 164 O VAL 21 11.942 20.154 21.954 1.00 0.00 ATOM 165 C VAL 21 11.086 19.868 21.126 1.00 0.00 ATOM 166 N ALA 22 10.860 20.614 20.043 1.00 0.00 ATOM 167 CA ALA 22 11.677 21.806 19.730 1.00 0.00 ATOM 168 CB ALA 22 11.240 22.443 18.412 1.00 0.00 ATOM 169 O ALA 22 12.721 23.448 21.152 1.00 0.00 ATOM 170 C ALA 22 11.697 22.839 20.869 1.00 0.00 ATOM 171 N GLY 23 10.536 23.062 21.505 1.00 0.00 ATOM 172 CA GLY 23 10.396 23.982 22.652 1.00 0.00 ATOM 173 O GLY 23 11.895 24.468 24.482 1.00 0.00 ATOM 174 C GLY 23 11.319 23.603 23.820 1.00 0.00 ATOM 175 N VAL 24 11.470 22.303 24.015 1.00 0.00 ATOM 176 CA VAL 24 12.385 21.744 25.038 1.00 0.00 ATOM 177 CB VAL 24 12.171 20.225 25.211 1.00 0.00 ATOM 178 CG1 VAL 24 13.205 19.561 26.139 1.00 0.00 ATOM 179 CG2 VAL 24 10.764 19.954 25.740 1.00 0.00 ATOM 180 O VAL 24 14.643 22.513 25.410 1.00 0.00 ATOM 181 C VAL 24 13.844 21.997 24.647 1.00 0.00 ATOM 182 N LEU 25 14.167 21.615 23.434 1.00 0.00 ATOM 183 CA LEU 25 15.571 21.628 23.017 1.00 0.00 ATOM 184 CB LEU 25 15.655 20.776 21.773 1.00 0.00 ATOM 185 CG LEU 25 15.291 19.353 22.204 1.00 0.00 ATOM 186 CD1 LEU 25 14.444 18.661 21.152 1.00 0.00 ATOM 187 CD2 LEU 25 16.518 18.515 22.525 1.00 0.00 ATOM 188 O LEU 25 17.260 23.306 23.306 1.00 0.00 ATOM 189 C LEU 25 16.099 23.058 22.980 1.00 0.00 ATOM 190 N ARG 26 15.245 23.996 22.583 1.00 0.00 ATOM 191 CA ARG 26 15.642 25.418 22.508 1.00 0.00 ATOM 192 CB ARG 26 14.510 26.256 21.936 1.00 0.00 ATOM 193 CG ARG 26 14.281 25.928 20.467 1.00 0.00 ATOM 194 CD ARG 26 13.101 26.717 19.923 1.00 0.00 ATOM 195 NE ARG 26 12.995 26.373 18.506 1.00 0.00 ATOM 196 CZ ARG 26 11.874 26.136 17.832 1.00 0.00 ATOM 197 NH1 ARG 26 10.694 26.234 18.386 1.00 0.00 ATOM 198 NH2 ARG 26 11.909 25.801 16.556 1.00 0.00 ATOM 199 O ARG 26 16.821 26.896 23.963 1.00 0.00 ATOM 200 C ARG 26 16.071 25.924 23.861 1.00 0.00 ATOM 201 N SER 27 15.597 25.266 24.914 1.00 0.00 ATOM 202 CA SER 27 15.946 25.663 26.273 1.00 0.00 ATOM 203 CB SER 27 14.594 25.540 26.978 1.00 0.00 ATOM 204 OG SER 27 14.276 24.245 27.500 1.00 0.00 ATOM 205 O SER 27 17.671 25.153 27.867 1.00 0.00 ATOM 206 C SER 27 17.124 24.818 26.818 1.00 0.00 ATOM 207 N TYR 28 17.729 24.005 25.945 1.00 0.00 ATOM 208 CA TYR 28 18.911 23.190 26.311 1.00 0.00 ATOM 209 CB TYR 28 18.440 21.772 26.684 1.00 0.00 ATOM 210 CG TYR 28 17.613 21.761 27.980 1.00 0.00 ATOM 211 CD1 TYR 28 18.088 22.291 29.178 1.00 0.00 ATOM 212 CD2 TYR 28 16.308 21.286 27.946 1.00 0.00 ATOM 213 CE1 TYR 28 17.281 22.325 30.314 1.00 0.00 ATOM 214 CE2 TYR 28 15.499 21.328 29.076 1.00 0.00 ATOM 215 CZ TYR 28 15.978 21.859 30.260 1.00 0.00 ATOM 216 OH TYR 28 15.112 22.092 31.292 1.00 0.00 ATOM 217 O TYR 28 20.703 22.370 24.829 1.00 0.00 ATOM 218 C TYR 28 20.070 23.312 25.301 1.00 0.00 ATOM 219 N ASN 29 20.292 24.557 24.901 1.00 0.00 ATOM 220 CA ASN 29 21.468 25.009 24.112 1.00 0.00 ATOM 221 CB ASN 29 22.857 24.692 24.807 1.00 0.00 ATOM 222 CG ASN 29 22.932 25.184 26.247 1.00 0.00 ATOM 223 ND2 ASN 29 24.095 24.927 26.849 1.00 0.00 ATOM 224 OD1 ASN 29 22.035 25.719 26.871 1.00 0.00 ATOM 225 O ASN 29 22.532 24.146 22.121 1.00 0.00 ATOM 226 C ASN 29 21.502 24.494 22.671 1.00 0.00 ATOM 227 N LEU 30 20.306 24.374 22.116 1.00 0.00 ATOM 228 CA LEU 30 20.136 23.924 20.721 1.00 0.00 ATOM 229 CB LEU 30 19.374 22.592 20.597 1.00 0.00 ATOM 230 CG LEU 30 19.821 21.498 21.566 1.00 0.00 ATOM 231 CD1 LEU 30 18.928 20.259 21.350 1.00 0.00 ATOM 232 CD2 LEU 30 21.293 21.159 21.407 1.00 0.00 ATOM 233 O LEU 30 18.639 24.673 18.919 1.00 0.00 ATOM 234 C LEU 30 19.262 24.949 19.954 1.00 0.00 ATOM 235 N GLY 31 19.298 26.208 20.386 1.00 0.00 ATOM 236 CA GLY 31 18.424 27.301 19.900 1.00 0.00 ATOM 237 O GLY 31 17.473 27.821 17.760 1.00 0.00 ATOM 238 C GLY 31 18.487 27.524 18.393 1.00 0.00 ATOM 239 N CYS 32 19.678 27.382 17.821 1.00 0.00 ATOM 240 CA CYS 32 19.861 27.571 16.366 1.00 0.00 ATOM 241 CB CYS 32 21.374 27.816 16.271 1.00 0.00 ATOM 242 SG CYS 32 22.264 26.222 16.230 1.00 0.00 ATOM 243 O CYS 32 19.218 26.567 14.285 1.00 0.00 ATOM 244 C CYS 32 19.277 26.453 15.510 1.00 0.00 ATOM 245 N ILE 33 18.844 25.375 16.156 1.00 0.00 ATOM 246 CA ILE 33 18.260 24.236 15.435 1.00 0.00 ATOM 247 CB ILE 33 18.432 22.941 16.239 1.00 0.00 ATOM 248 CG1 ILE 33 19.786 22.841 16.961 1.00 0.00 ATOM 249 CG2 ILE 33 18.396 21.872 15.151 1.00 0.00 ATOM 250 CD1 ILE 33 20.179 21.546 17.694 1.00 0.00 ATOM 251 O ILE 33 16.468 23.654 13.923 1.00 0.00 ATOM 252 C ILE 33 16.890 24.460 14.754 1.00 0.00 ATOM 253 N GLY 34 16.212 25.546 15.113 1.00 0.00 ATOM 254 CA GLY 34 14.911 25.851 14.530 1.00 0.00 ATOM 255 O GLY 34 14.172 25.310 12.312 1.00 0.00 ATOM 256 C GLY 34 15.058 25.802 13.013 1.00 0.00 ATOM 257 N CYS 35 16.177 26.310 12.507 1.00 0.00 ATOM 258 CA CYS 35 16.425 26.312 11.070 1.00 0.00 ATOM 259 CB CYS 35 17.603 27.236 10.787 1.00 0.00 ATOM 260 SG CYS 35 17.825 27.444 9.023 1.00 0.00 ATOM 261 O CYS 35 17.611 24.190 11.265 1.00 0.00 ATOM 262 C CYS 35 16.808 24.852 10.607 1.00 0.00 ATOM 263 N MET 36 16.232 24.393 9.500 1.00 0.00 ATOM 264 CA MET 36 16.526 23.058 8.993 1.00 0.00 ATOM 265 CB MET 36 15.633 22.708 7.799 1.00 0.00 ATOM 266 CG MET 36 14.173 22.513 8.192 1.00 0.00 ATOM 267 SD MET 36 13.835 21.325 9.543 1.00 0.00 ATOM 268 CE MET 36 13.831 22.366 10.995 1.00 0.00 ATOM 269 O MET 36 18.395 21.683 8.296 1.00 0.00 ATOM 270 C MET 36 17.981 22.814 8.583 1.00 0.00 ATOM 271 N GLY 37 18.728 23.970 8.539 1.00 0.00 ATOM 272 CA GLY 37 20.166 23.926 8.260 1.00 0.00 ATOM 273 O GLY 37 21.852 22.454 9.085 1.00 0.00 ATOM 274 C GLY 37 20.760 22.978 9.278 1.00 0.00 ATOM 275 N ALA 38 19.933 22.757 10.310 1.00 0.00 ATOM 276 CA ALA 38 20.300 21.711 11.261 1.00 0.00 ATOM 277 CB ALA 38 18.907 21.310 12.091 1.00 0.00 ATOM 278 O ALA 38 21.174 19.492 11.520 1.00 0.00 ATOM 279 C ALA 38 20.639 20.309 10.768 1.00 0.00 ATOM 280 N GLN 39 20.328 20.030 9.506 1.00 0.00 ATOM 281 CA GLN 39 20.609 18.722 8.931 1.00 0.00 ATOM 282 CB GLN 39 20.319 18.870 7.445 1.00 0.00 ATOM 283 CG GLN 39 18.832 19.114 7.122 1.00 0.00 ATOM 284 CD GLN 39 18.620 19.928 5.831 1.00 0.00 ATOM 285 OE1 GLN 39 17.629 20.590 5.582 1.00 0.00 ATOM 286 NE2 GLN 39 19.621 19.931 4.990 1.00 0.00 ATOM 287 O GLN 39 22.403 17.088 9.087 1.00 0.00 ATOM 288 C GLN 39 22.102 18.281 9.129 1.00 0.00 ATOM 289 N ASN 40 22.995 19.243 9.340 1.00 0.00 ATOM 290 CA ASN 40 24.406 18.934 9.539 1.00 0.00 ATOM 291 CB ASN 40 25.207 20.273 9.202 1.00 0.00 ATOM 292 CG ASN 40 25.068 20.741 7.766 1.00 0.00 ATOM 293 ND2 ASN 40 25.120 22.054 7.563 1.00 0.00 ATOM 294 OD1 ASN 40 24.933 19.932 6.845 1.00 0.00 ATOM 295 O ASN 40 25.864 17.752 11.010 1.00 0.00 ATOM 296 C ASN 40 24.830 18.413 10.908 1.00 0.00 ATOM 297 N GLU 41 24.009 18.697 11.922 1.00 0.00 ATOM 298 CA GLU 41 24.420 18.463 13.317 1.00 0.00 ATOM 299 CB GLU 41 24.667 19.778 14.055 1.00 0.00 ATOM 300 CG GLU 41 25.579 20.742 13.272 1.00 0.00 ATOM 301 CD GLU 41 26.044 21.975 14.048 1.00 0.00 ATOM 302 OE1 GLU 41 25.257 22.454 14.899 1.00 0.00 ATOM 303 OE2 GLU 41 27.172 22.422 13.754 1.00 0.00 ATOM 304 O GLU 41 22.179 17.795 13.940 1.00 0.00 ATOM 305 C GLU 41 23.391 17.600 14.066 1.00 0.00 ATOM 306 N SER 42 23.878 16.519 14.664 1.00 0.00 ATOM 307 CA SER 42 23.065 15.671 15.558 1.00 0.00 ATOM 308 CB SER 42 23.647 14.267 15.755 1.00 0.00 ATOM 309 OG SER 42 24.754 14.238 16.667 1.00 0.00 ATOM 310 O SER 42 23.587 17.335 17.231 1.00 0.00 ATOM 311 C SER 42 22.913 16.351 16.921 1.00 0.00 ATOM 312 N LEU 43 22.103 15.736 17.778 1.00 0.00 ATOM 313 CA LEU 43 22.026 16.142 19.191 1.00 0.00 ATOM 314 CB LEU 43 20.978 15.277 19.916 1.00 0.00 ATOM 315 CG LEU 43 20.789 15.571 21.408 1.00 0.00 ATOM 316 CD1 LEU 43 20.342 17.006 21.599 1.00 0.00 ATOM 317 CD2 LEU 43 19.764 14.620 21.994 1.00 0.00 ATOM 318 O LEU 43 23.867 16.872 20.545 1.00 0.00 ATOM 319 C LEU 43 23.397 15.981 19.837 1.00 0.00 ATOM 320 N GLU 44 24.039 14.842 19.592 1.00 0.00 ATOM 321 CA GLU 44 25.387 14.569 20.164 1.00 0.00 ATOM 322 CB GLU 44 25.952 13.275 19.638 1.00 0.00 ATOM 323 CG GLU 44 25.208 12.055 20.148 1.00 0.00 ATOM 324 CD GLU 44 25.484 11.772 21.615 1.00 0.00 ATOM 325 OE1 GLU 44 24.682 11.053 22.244 1.00 0.00 ATOM 326 OE2 GLU 44 26.509 12.255 22.141 1.00 0.00 ATOM 327 O GLU 44 27.058 16.243 20.584 1.00 0.00 ATOM 328 C GLU 44 26.376 15.657 19.742 1.00 0.00 ATOM 329 N GLN 45 26.450 15.922 18.442 1.00 0.00 ATOM 330 CA GLN 45 27.357 16.942 17.929 1.00 0.00 ATOM 331 CB GLN 45 27.282 17.054 16.423 1.00 0.00 ATOM 332 CG GLN 45 27.869 15.844 15.725 1.00 0.00 ATOM 333 CD GLN 45 27.585 16.023 14.246 1.00 0.00 ATOM 334 OE1 GLN 45 26.532 16.478 13.805 1.00 0.00 ATOM 335 NE2 GLN 45 28.489 15.533 13.448 1.00 0.00 ATOM 336 O GLN 45 27.850 19.079 18.910 1.00 0.00 ATOM 337 C GLN 45 26.969 18.320 18.481 1.00 0.00 ATOM 338 N GLY 46 25.674 18.691 18.413 1.00 0.00 ATOM 339 CA GLY 46 25.232 19.972 18.849 1.00 0.00 ATOM 340 O GLY 46 26.009 21.298 20.690 1.00 0.00 ATOM 341 C GLY 46 25.548 20.217 20.319 1.00 0.00 ATOM 342 N ALA 47 25.302 19.214 21.155 1.00 0.00 ATOM 343 CA ALA 47 25.573 19.331 22.615 1.00 0.00 ATOM 344 CB ALA 47 25.092 18.129 23.384 1.00 0.00 ATOM 345 O ALA 47 27.436 20.418 23.694 1.00 0.00 ATOM 346 C ALA 47 27.073 19.590 22.857 1.00 0.00 ATOM 347 N ASN 48 27.929 18.884 22.125 1.00 0.00 ATOM 348 CA ASN 48 29.370 19.053 22.273 1.00 0.00 ATOM 349 CB ASN 48 30.118 18.134 21.334 1.00 0.00 ATOM 350 CG ASN 48 30.018 16.691 21.791 1.00 0.00 ATOM 351 ND2 ASN 48 30.347 15.794 20.907 1.00 0.00 ATOM 352 OD1 ASN 48 29.870 16.411 22.958 1.00 0.00 ATOM 353 O ASN 48 30.420 21.166 22.711 1.00 0.00 ATOM 354 C ASN 48 29.701 20.508 21.958 1.00 0.00 ATOM 355 N ALA 49 29.175 21.008 20.844 1.00 0.00 ATOM 356 CA ALA 49 29.424 22.391 20.444 1.00 0.00 ATOM 357 CB ALA 49 28.882 22.605 19.026 1.00 0.00 ATOM 358 O ALA 49 29.351 24.535 21.566 1.00 0.00 ATOM 359 C ALA 49 28.786 23.457 21.379 1.00 0.00 ATOM 360 N HIS 50 27.627 23.142 21.948 1.00 0.00 ATOM 361 CA HIS 50 26.948 24.072 22.844 1.00 0.00 ATOM 362 CB HIS 50 25.458 24.076 22.623 1.00 0.00 ATOM 363 CG HIS 50 25.108 24.475 21.238 1.00 0.00 ATOM 364 CD2 HIS 50 24.662 23.751 20.194 1.00 0.00 ATOM 365 ND1 HIS 50 25.223 25.774 20.790 1.00 0.00 ATOM 366 CE1 HIS 50 24.856 25.828 19.520 1.00 0.00 ATOM 367 NE2 HIS 50 24.521 24.610 19.130 1.00 0.00 ATOM 368 O HIS 50 26.781 24.550 25.205 1.00 0.00 ATOM 369 C HIS 50 27.319 23.881 24.329 1.00 0.00 ATOM 370 N GLY 51 28.247 22.922 24.573 1.00 0.00 ATOM 371 CA GLY 51 28.742 22.615 25.909 1.00 0.00 ATOM 372 O GLY 51 27.789 22.288 28.086 1.00 0.00 ATOM 373 C GLY 51 27.672 22.114 26.873 1.00 0.00 ATOM 374 N LEU 52 26.630 21.490 26.332 1.00 0.00 ATOM 375 CA LEU 52 25.517 20.953 27.172 1.00 0.00 ATOM 376 CB LEU 52 24.109 21.274 26.655 1.00 0.00 ATOM 377 CG LEU 52 23.047 20.699 27.597 1.00 0.00 ATOM 378 CD1 LEU 52 22.960 21.434 28.935 1.00 0.00 ATOM 379 CD2 LEU 52 21.686 20.800 26.971 1.00 0.00 ATOM 380 O LEU 52 25.673 18.839 26.048 1.00 0.00 ATOM 381 C LEU 52 25.707 19.441 27.123 1.00 0.00 ATOM 382 N ASN 53 25.909 18.830 28.286 1.00 0.00 ATOM 383 CA ASN 53 26.108 17.360 28.366 1.00 0.00 ATOM 384 CB ASN 53 26.151 16.836 29.795 1.00 0.00 ATOM 385 CG ASN 53 27.358 17.294 30.581 1.00 0.00 ATOM 386 ND2 ASN 53 27.032 17.841 31.710 1.00 0.00 ATOM 387 OD1 ASN 53 28.511 17.316 30.204 1.00 0.00 ATOM 388 O ASN 53 23.759 17.061 27.977 1.00 0.00 ATOM 389 C ASN 53 24.899 16.648 27.766 1.00 0.00 ATOM 390 N VAL 54 25.152 15.576 27.020 1.00 0.00 ATOM 391 CA VAL 54 24.077 14.822 26.405 1.00 0.00 ATOM 392 CB VAL 54 24.620 13.712 25.499 1.00 0.00 ATOM 393 CG1 VAL 54 23.518 12.754 25.027 1.00 0.00 ATOM 394 CG2 VAL 54 25.203 14.365 24.266 1.00 0.00 ATOM 395 O VAL 54 21.929 14.114 27.283 1.00 0.00 ATOM 396 C VAL 54 23.143 14.186 27.482 1.00 0.00 ATOM 397 N GLU 55 23.719 13.741 28.594 1.00 0.00 ATOM 398 CA GLU 55 22.933 13.134 29.661 1.00 0.00 ATOM 399 CB GLU 55 23.780 12.693 30.862 1.00 0.00 ATOM 400 CG GLU 55 24.794 11.587 30.555 1.00 0.00 ATOM 401 CD GLU 55 26.179 12.094 30.115 1.00 0.00 ATOM 402 OE1 GLU 55 26.266 13.253 29.649 1.00 0.00 ATOM 403 OE2 GLU 55 27.114 11.282 30.199 1.00 0.00 ATOM 404 O GLU 55 20.713 13.716 30.356 1.00 0.00 ATOM 405 C GLU 55 21.852 14.111 30.110 1.00 0.00 ATOM 406 N ASP 56 22.211 15.387 30.213 1.00 0.00 ATOM 407 CA ASP 56 21.240 16.445 30.641 1.00 0.00 ATOM 408 CB ASP 56 21.933 17.793 30.816 1.00 0.00 ATOM 409 CG ASP 56 22.813 17.888 32.068 1.00 0.00 ATOM 410 OD1 ASP 56 22.422 17.313 33.102 1.00 0.00 ATOM 411 OD2 ASP 56 23.894 18.528 31.977 1.00 0.00 ATOM 412 O ASP 56 18.919 16.619 29.932 1.00 0.00 ATOM 413 C ASP 56 20.117 16.557 29.593 1.00 0.00 ATOM 414 N ILE 57 20.508 16.549 28.315 1.00 0.00 ATOM 415 CA ILE 57 19.527 16.615 27.217 1.00 0.00 ATOM 416 CB ILE 57 20.246 16.703 25.857 1.00 0.00 ATOM 417 CG1 ILE 57 20.854 18.086 25.706 1.00 0.00 ATOM 418 CG2 ILE 57 19.245 16.542 24.718 1.00 0.00 ATOM 419 CD1 ILE 57 21.999 18.168 24.693 1.00 0.00 ATOM 420 O ILE 57 17.395 15.532 27.024 1.00 0.00 ATOM 421 C ILE 57 18.605 15.401 27.214 1.00 0.00 ATOM 422 N LEU 58 19.177 14.220 27.424 1.00 0.00 ATOM 423 CA LEU 58 18.390 12.992 27.445 1.00 0.00 ATOM 424 CB LEU 58 19.255 11.734 27.512 1.00 0.00 ATOM 425 CG LEU 58 18.491 10.391 27.590 1.00 0.00 ATOM 426 CD1 LEU 58 17.548 10.207 26.379 1.00 0.00 ATOM 427 CD2 LEU 58 19.464 9.224 27.703 1.00 0.00 ATOM 428 O LEU 58 16.164 12.733 28.391 1.00 0.00 ATOM 429 C LEU 58 17.336 13.047 28.606 1.00 0.00 ATOM 430 N ARG 59 17.768 13.442 29.800 1.00 0.00 ATOM 431 CA ARG 59 16.865 13.530 30.940 1.00 0.00 ATOM 432 CB ARG 59 17.698 14.041 32.115 1.00 0.00 ATOM 433 CG ARG 59 16.810 14.389 33.318 1.00 0.00 ATOM 434 CD ARG 59 17.517 15.095 34.461 1.00 0.00 ATOM 435 NE ARG 59 17.964 16.383 33.920 1.00 0.00 ATOM 436 CZ ARG 59 19.230 16.779 33.913 1.00 0.00 ATOM 437 NH1 ARG 59 20.188 16.099 34.543 1.00 0.00 ATOM 438 NH2 ARG 59 19.549 17.844 33.202 1.00 0.00 ATOM 439 O ARG 59 14.534 14.181 30.876 1.00 0.00 ATOM 440 C ARG 59 15.704 14.490 30.639 1.00 0.00 ATOM 441 N ASP 60 16.050 15.658 30.085 1.00 0.00 ATOM 442 CA ASP 60 15.108 16.744 29.767 1.00 0.00 ATOM 443 CB ASP 60 15.867 17.959 29.233 1.00 0.00 ATOM 444 CG ASP 60 16.828 18.590 30.246 1.00 0.00 ATOM 445 OD1 ASP 60 16.603 18.479 31.472 1.00 0.00 ATOM 446 OD2 ASP 60 17.816 19.180 29.756 1.00 0.00 ATOM 447 O ASP 60 12.904 16.405 28.883 1.00 0.00 ATOM 448 C ASP 60 14.115 16.247 28.723 1.00 0.00 ATOM 449 N LEU 61 14.628 15.646 27.654 1.00 0.00 ATOM 450 CA LEU 61 13.765 15.119 26.576 1.00 0.00 ATOM 451 CB LEU 61 14.547 14.509 25.494 1.00 0.00 ATOM 452 CG LEU 61 15.208 15.490 24.523 1.00 0.00 ATOM 453 CD1 LEU 61 16.307 14.779 23.730 1.00 0.00 ATOM 454 CD2 LEU 61 14.130 16.052 23.595 1.00 0.00 ATOM 455 O LEU 61 11.605 14.095 26.850 1.00 0.00 ATOM 456 C LEU 61 12.802 14.066 27.139 1.00 0.00 ATOM 457 N ASN 62 13.328 13.145 27.940 1.00 0.00 ATOM 458 CA ASN 62 12.504 12.098 28.532 1.00 0.00 ATOM 459 CB ASN 62 13.319 11.099 29.343 1.00 0.00 ATOM 460 CG ASN 62 14.135 10.151 28.457 1.00 0.00 ATOM 461 ND2 ASN 62 15.136 9.575 29.032 1.00 0.00 ATOM 462 OD1 ASN 62 13.910 9.869 27.297 1.00 0.00 ATOM 463 O ASN 62 10.243 12.288 29.308 1.00 0.00 ATOM 464 C ASN 62 11.405 12.678 29.422 1.00 0.00 ATOM 465 N ALA 63 11.738 13.682 30.220 1.00 0.00 ATOM 466 CA ALA 63 10.758 14.350 31.102 1.00 0.00 ATOM 467 CB ALA 63 11.489 15.314 32.019 1.00 0.00 ATOM 468 O ALA 63 8.560 15.305 30.944 1.00 0.00 ATOM 469 C ALA 63 9.637 15.111 30.376 1.00 0.00 ATOM 470 N LEU 64 9.929 15.522 29.150 1.00 0.00 ATOM 471 CA LEU 64 9.088 16.478 28.404 1.00 0.00 ATOM 472 CB LEU 64 9.921 17.733 28.072 1.00 0.00 ATOM 473 CG LEU 64 10.393 18.530 29.300 1.00 0.00 ATOM 474 CD1 LEU 64 11.150 19.815 28.918 1.00 0.00 ATOM 475 CD2 LEU 64 9.219 18.912 30.203 1.00 0.00 ATOM 476 O LEU 64 8.887 14.659 26.845 1.00 0.00 ATOM 477 C LEU 64 8.531 15.801 27.145 1.00 0.00 ATOM 478 N ALA 65 7.532 16.415 26.524 1.00 0.00 ATOM 479 CA ALA 65 6.794 15.797 25.427 1.00 0.00 ATOM 480 CB ALA 65 5.629 16.701 25.012 1.00 0.00 ATOM 481 O ALA 65 7.486 14.459 23.555 1.00 0.00 ATOM 482 C ALA 65 7.666 15.489 24.210 1.00 0.00 TER END