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 1 Mon Jul 7 11:25:21 2008 MODEL 1 PARENT N/A ATOM 1 N MET 1 11.344 13.895 22.581 1.00 0.00 ATOM 2 CA MET 1 10.948 12.881 23.567 1.00 0.00 ATOM 3 CB MET 1 9.579 12.343 23.142 1.00 0.00 ATOM 4 CG MET 1 8.640 13.477 22.714 1.00 0.00 ATOM 5 SD MET 1 6.836 13.210 22.846 1.00 0.00 ATOM 6 CE MET 1 6.682 11.549 22.256 1.00 0.00 ATOM 7 O MET 1 12.246 11.297 22.384 1.00 0.00 ATOM 8 C MET 1 12.009 11.772 23.487 1.00 0.00 ATOM 9 N THR 2 12.542 11.331 24.617 1.00 0.00 ATOM 10 CA THR 2 13.620 10.308 24.646 1.00 0.00 ATOM 11 CB THR 2 14.197 10.081 26.054 1.00 0.00 ATOM 12 CG2 THR 2 15.299 9.020 26.152 1.00 0.00 ATOM 13 OG1 THR 2 14.861 11.283 26.403 1.00 0.00 ATOM 14 O THR 2 13.904 8.358 23.275 1.00 0.00 ATOM 15 C THR 2 13.167 8.984 24.037 1.00 0.00 ATOM 16 N GLN 3 11.953 8.560 24.374 1.00 0.00 ATOM 17 CA GLN 3 11.416 7.305 23.852 1.00 0.00 ATOM 18 CB GLN 3 10.071 7.114 24.534 1.00 0.00 ATOM 19 CG GLN 3 10.258 6.932 26.045 1.00 0.00 ATOM 20 CD GLN 3 8.918 6.950 26.775 1.00 0.00 ATOM 21 OE1 GLN 3 8.070 7.814 26.573 1.00 0.00 ATOM 22 NE2 GLN 3 8.670 5.909 27.528 1.00 0.00 ATOM 23 O GLN 3 11.300 6.155 21.739 1.00 0.00 ATOM 24 C GLN 3 11.266 7.239 22.324 1.00 0.00 ATOM 25 N LYS 4 11.100 8.395 21.689 1.00 0.00 ATOM 26 CA LYS 4 10.950 8.447 20.240 1.00 0.00 ATOM 27 CB LYS 4 9.381 8.402 19.953 1.00 0.00 ATOM 28 CG LYS 4 8.991 7.229 19.094 1.00 0.00 ATOM 29 CD LYS 4 8.348 6.129 19.911 1.00 0.00 ATOM 30 CE LYS 4 6.888 5.937 19.536 1.00 0.00 ATOM 31 NZ LYS 4 6.493 4.508 19.479 1.00 0.00 ATOM 32 O LYS 4 12.078 9.352 18.301 1.00 0.00 ATOM 33 C LYS 4 12.091 9.200 19.509 1.00 0.00 ATOM 34 N PHE 5 13.113 9.609 20.273 1.00 0.00 ATOM 35 CA PHE 5 14.265 10.358 19.752 1.00 0.00 ATOM 36 CB PHE 5 14.281 11.779 20.321 1.00 0.00 ATOM 37 CG PHE 5 15.489 12.610 19.878 1.00 0.00 ATOM 38 CD1 PHE 5 15.416 13.391 18.747 1.00 0.00 ATOM 39 CD2 PHE 5 16.681 12.573 20.575 1.00 0.00 ATOM 40 CE1 PHE 5 16.532 14.104 18.364 1.00 0.00 ATOM 41 CE2 PHE 5 17.777 13.296 20.173 1.00 0.00 ATOM 42 CZ PHE 5 17.724 14.087 19.051 1.00 0.00 ATOM 43 O PHE 5 15.997 9.478 21.230 1.00 0.00 ATOM 44 C PHE 5 15.569 9.627 20.090 1.00 0.00 ATOM 45 N THR 6 16.271 9.349 19.009 1.00 0.00 ATOM 46 CA THR 6 17.648 8.827 19.077 1.00 0.00 ATOM 47 CB THR 6 17.879 7.649 18.118 1.00 0.00 ATOM 48 CG2 THR 6 19.306 7.095 18.176 1.00 0.00 ATOM 49 OG1 THR 6 16.993 6.571 18.421 1.00 0.00 ATOM 50 O THR 6 18.509 10.668 17.803 1.00 0.00 ATOM 51 C THR 6 18.591 10.000 18.835 1.00 0.00 ATOM 52 N LYS 7 19.487 10.249 19.786 1.00 0.00 ATOM 53 CA LYS 7 20.439 11.343 19.657 1.00 0.00 ATOM 54 CB LYS 7 21.367 11.174 20.877 1.00 0.00 ATOM 55 CG LYS 7 20.685 10.592 22.119 1.00 0.00 ATOM 56 CD LYS 7 21.233 9.190 22.431 1.00 0.00 ATOM 57 CE LYS 7 20.159 8.146 22.745 1.00 0.00 ATOM 58 NZ LYS 7 19.468 8.445 23.995 1.00 0.00 ATOM 59 O LYS 7 21.805 12.304 17.886 1.00 0.00 ATOM 60 C LYS 7 21.265 11.286 18.320 1.00 0.00 ATOM 61 N ASP 8 21.342 10.110 17.705 1.00 0.00 ATOM 62 CA ASP 8 22.082 9.957 16.458 1.00 0.00 ATOM 63 CB ASP 8 22.117 8.476 16.099 1.00 0.00 ATOM 64 CG ASP 8 23.019 7.645 16.999 1.00 0.00 ATOM 65 OD1 ASP 8 23.784 8.228 17.808 1.00 0.00 ATOM 66 OD2 ASP 8 22.810 6.420 16.981 1.00 0.00 ATOM 67 O ASP 8 22.275 10.884 14.251 1.00 0.00 ATOM 68 C ASP 8 21.554 10.691 15.230 1.00 0.00 ATOM 69 N MET 9 20.281 11.072 15.305 1.00 0.00 ATOM 70 CA MET 9 19.611 11.764 14.190 1.00 0.00 ATOM 71 CB MET 9 18.093 11.841 14.353 1.00 0.00 ATOM 72 CG MET 9 17.421 10.486 14.235 1.00 0.00 ATOM 73 SD MET 9 15.605 10.720 14.198 1.00 0.00 ATOM 74 CE MET 9 15.260 11.220 15.868 1.00 0.00 ATOM 75 O MET 9 20.522 13.849 14.944 1.00 0.00 ATOM 76 C MET 9 20.149 13.166 13.981 1.00 0.00 ATOM 77 N THR 10 20.031 13.605 12.746 1.00 0.00 ATOM 78 CA THR 10 20.277 15.027 12.435 1.00 0.00 ATOM 79 CB THR 10 20.211 15.337 10.935 1.00 0.00 ATOM 80 CG2 THR 10 21.159 14.434 10.144 1.00 0.00 ATOM 81 OG1 THR 10 18.869 15.269 10.467 1.00 0.00 ATOM 82 O THR 10 18.139 15.333 13.480 1.00 0.00 ATOM 83 C THR 10 19.234 15.827 13.209 1.00 0.00 ATOM 84 N PHE 11 19.575 17.062 13.562 1.00 0.00 ATOM 85 CA PHE 11 18.654 17.918 14.302 1.00 0.00 ATOM 86 CB PHE 11 19.406 19.156 14.731 1.00 0.00 ATOM 87 CG PHE 11 20.229 18.974 15.980 1.00 0.00 ATOM 88 CD1 PHE 11 21.566 19.300 15.932 1.00 0.00 ATOM 89 CD2 PHE 11 19.627 18.501 17.129 1.00 0.00 ATOM 90 CE1 PHE 11 22.339 19.123 17.051 1.00 0.00 ATOM 91 CE2 PHE 11 20.410 18.333 18.248 1.00 0.00 ATOM 92 CZ PHE 11 21.767 18.629 18.219 1.00 0.00 ATOM 93 O PHE 11 16.326 18.468 14.087 1.00 0.00 ATOM 94 C PHE 11 17.414 18.355 13.521 1.00 0.00 ATOM 95 N ALA 12 17.582 18.599 12.225 1.00 0.00 ATOM 96 CA ALA 12 16.467 19.018 11.385 1.00 0.00 ATOM 97 CB ALA 12 16.945 19.356 9.970 1.00 0.00 ATOM 98 O ALA 12 14.253 18.101 11.500 1.00 0.00 ATOM 99 C ALA 12 15.459 17.874 11.395 1.00 0.00 ATOM 100 N GLN 13 15.954 16.645 11.287 1.00 0.00 ATOM 101 CA GLN 13 15.073 15.453 11.288 1.00 0.00 ATOM 102 CB GLN 13 15.880 14.166 11.125 1.00 0.00 ATOM 103 CG GLN 13 16.332 14.058 9.674 1.00 0.00 ATOM 104 CD GLN 13 17.251 12.870 9.412 1.00 0.00 ATOM 105 OE1 GLN 13 18.208 12.534 10.111 1.00 0.00 ATOM 106 NE2 GLN 13 17.026 12.258 8.285 1.00 0.00 ATOM 107 O GLN 13 13.090 15.199 12.620 1.00 0.00 ATOM 108 C GLN 13 14.302 15.423 12.607 1.00 0.00 ATOM 109 N ALA 14 15.005 15.646 13.713 1.00 0.00 ATOM 110 CA ALA 14 14.369 15.643 15.026 1.00 0.00 ATOM 111 CB ALA 14 15.679 16.356 15.891 1.00 0.00 ATOM 112 O ALA 14 12.189 16.447 15.650 1.00 0.00 ATOM 113 C ALA 14 13.281 16.718 15.149 1.00 0.00 ATOM 114 N LEU 15 13.582 17.929 14.691 1.00 0.00 ATOM 115 CA LEU 15 12.621 19.022 14.755 1.00 0.00 ATOM 116 CB LEU 15 13.337 20.294 14.291 1.00 0.00 ATOM 117 CG LEU 15 12.387 21.483 14.100 1.00 0.00 ATOM 118 CD1 LEU 15 11.740 21.891 15.403 1.00 0.00 ATOM 119 CD2 LEU 15 13.133 22.674 13.497 1.00 0.00 ATOM 120 O LEU 15 10.269 18.968 14.313 1.00 0.00 ATOM 121 C LEU 15 11.400 18.718 13.898 1.00 0.00 ATOM 122 N GLN 16 11.615 18.162 12.710 1.00 0.00 ATOM 123 CA GLN 16 10.481 17.857 11.854 1.00 0.00 ATOM 124 CB GLN 16 11.000 17.455 10.490 1.00 0.00 ATOM 125 CG GLN 16 11.628 18.700 9.855 1.00 0.00 ATOM 126 CD GLN 16 12.199 18.385 8.491 1.00 0.00 ATOM 127 OE1 GLN 16 11.609 18.609 7.454 1.00 0.00 ATOM 128 NE2 GLN 16 13.421 17.915 8.504 1.00 0.00 ATOM 129 O GLN 16 8.414 16.686 12.192 1.00 0.00 ATOM 130 C GLN 16 9.621 16.739 12.435 1.00 0.00 ATOM 131 N THR 17 10.242 15.849 13.201 1.00 0.00 ATOM 132 CA THR 17 9.508 14.711 13.830 1.00 0.00 ATOM 133 CB THR 17 10.448 13.652 14.320 1.00 0.00 ATOM 134 CG2 THR 17 9.675 12.518 14.959 1.00 0.00 ATOM 135 OG1 THR 17 11.177 13.128 13.191 1.00 0.00 ATOM 136 O THR 17 7.493 14.853 15.109 1.00 0.00 ATOM 137 C THR 17 8.650 15.247 14.956 1.00 0.00 ATOM 138 N HIS 18 9.214 16.152 15.749 1.00 0.00 ATOM 139 CA HIS 18 8.482 16.741 16.865 1.00 0.00 ATOM 140 CB HIS 18 9.057 16.187 18.152 1.00 0.00 ATOM 141 CG HIS 18 8.794 14.717 18.430 1.00 0.00 ATOM 142 CD2 HIS 18 7.669 14.243 18.929 1.00 0.00 ATOM 143 ND1 HIS 18 9.666 13.720 18.351 1.00 0.00 ATOM 144 CE1 HIS 18 9.036 12.626 18.765 1.00 0.00 ATOM 145 NE2 HIS 18 7.814 12.956 19.162 1.00 0.00 ATOM 146 O HIS 18 9.703 18.782 17.246 1.00 0.00 ATOM 147 C HIS 18 8.623 18.265 16.965 1.00 0.00 ATOM 148 N PRO 19 7.456 18.904 17.102 1.00 0.00 ATOM 149 CA PRO 19 7.397 20.278 17.610 1.00 0.00 ATOM 150 CB PRO 19 5.969 20.704 17.317 1.00 0.00 ATOM 151 CG PRO 19 5.645 19.952 16.080 1.00 0.00 ATOM 152 CD PRO 19 6.198 18.582 16.381 1.00 0.00 ATOM 153 O PRO 19 8.419 21.411 19.461 1.00 0.00 ATOM 154 C PRO 19 7.775 20.433 19.079 1.00 0.00 ATOM 155 N GLY 20 7.375 19.468 19.901 1.00 0.00 ATOM 156 CA GLY 20 7.685 19.508 21.348 1.00 0.00 ATOM 157 O GLY 20 9.746 19.997 22.473 1.00 0.00 ATOM 158 C GLY 20 9.195 19.412 21.541 1.00 0.00 ATOM 159 N VAL 21 9.860 18.676 20.657 1.00 0.00 ATOM 160 CA VAL 21 11.318 18.514 20.742 1.00 0.00 ATOM 161 CB VAL 21 11.765 17.400 19.773 1.00 0.00 ATOM 162 CG1 VAL 21 13.267 17.328 19.552 1.00 0.00 ATOM 163 CG2 VAL 21 11.487 16.042 20.401 1.00 0.00 ATOM 164 O VAL 21 13.002 20.186 21.130 1.00 0.00 ATOM 165 C VAL 21 12.008 19.863 20.472 1.00 0.00 ATOM 166 N ALA 22 11.423 20.660 19.578 1.00 0.00 ATOM 167 CA ALA 22 11.915 22.008 19.215 1.00 0.00 ATOM 168 CB ALA 22 10.981 22.679 18.226 1.00 0.00 ATOM 169 O ALA 22 12.997 23.505 20.744 1.00 0.00 ATOM 170 C ALA 22 11.973 22.882 20.462 1.00 0.00 ATOM 171 N GLY 23 10.874 22.928 21.208 1.00 0.00 ATOM 172 CA GLY 23 10.827 23.715 22.397 1.00 0.00 ATOM 173 O GLY 23 12.446 24.202 24.052 1.00 0.00 ATOM 174 C GLY 23 11.824 23.344 23.424 1.00 0.00 ATOM 175 N VAL 24 11.999 22.041 23.620 1.00 0.00 ATOM 176 CA VAL 24 12.955 21.544 24.603 1.00 0.00 ATOM 177 CB VAL 24 12.922 19.998 24.666 1.00 0.00 ATOM 178 CG1 VAL 24 14.032 19.483 25.581 1.00 0.00 ATOM 179 CG2 VAL 24 11.567 19.534 25.179 1.00 0.00 ATOM 180 O VAL 24 15.161 22.415 25.042 1.00 0.00 ATOM 181 C VAL 24 14.390 21.948 24.204 1.00 0.00 ATOM 182 N LEU 25 14.733 21.765 22.933 1.00 0.00 ATOM 183 CA LEU 25 16.064 22.115 22.451 1.00 0.00 ATOM 184 CB LEU 25 16.258 21.653 21.009 1.00 0.00 ATOM 185 CG LEU 25 16.257 20.133 20.853 1.00 0.00 ATOM 186 CD1 LEU 25 16.499 19.829 19.374 1.00 0.00 ATOM 187 CD2 LEU 25 17.335 19.448 21.704 1.00 0.00 ATOM 188 O LEU 25 17.389 24.014 23.080 1.00 0.00 ATOM 189 C LEU 25 16.325 23.609 22.610 1.00 0.00 ATOM 190 N ARG 26 15.353 24.427 22.218 1.00 0.00 ATOM 191 CA ARG 26 15.491 25.886 22.326 1.00 0.00 ATOM 192 CB ARG 26 14.268 26.587 21.759 1.00 0.00 ATOM 193 CG ARG 26 14.246 26.510 20.239 1.00 0.00 ATOM 194 CD ARG 26 12.909 27.034 19.751 1.00 0.00 ATOM 195 NE ARG 26 12.798 26.970 18.282 1.00 0.00 ATOM 196 CZ ARG 26 11.622 26.920 17.647 1.00 0.00 ATOM 197 NH1 ARG 26 11.553 26.912 16.317 1.00 0.00 ATOM 198 NH2 ARG 26 10.464 26.888 18.314 1.00 0.00 ATOM 199 O ARG 26 16.479 27.173 24.094 1.00 0.00 ATOM 200 C ARG 26 15.694 26.276 23.787 1.00 0.00 ATOM 201 N SER 27 14.984 25.600 24.685 1.00 0.00 ATOM 202 CA SER 27 15.096 25.888 26.154 1.00 0.00 ATOM 203 CB SER 27 14.097 25.058 26.933 1.00 0.00 ATOM 204 OG SER 27 12.817 25.598 26.639 1.00 0.00 ATOM 205 O SER 27 16.714 26.207 27.862 1.00 0.00 ATOM 206 C SER 27 16.401 25.620 26.825 1.00 0.00 ATOM 207 N TYR 28 17.187 24.722 26.239 1.00 0.00 ATOM 208 CA TYR 28 18.488 24.377 26.800 1.00 0.00 ATOM 209 CB TYR 28 18.518 22.846 26.909 1.00 0.00 ATOM 210 CG TYR 28 17.575 22.400 28.038 1.00 0.00 ATOM 211 CD1 TYR 28 17.908 22.615 29.370 1.00 0.00 ATOM 212 CD2 TYR 28 16.380 21.747 27.747 1.00 0.00 ATOM 213 CE1 TYR 28 17.076 22.179 30.389 1.00 0.00 ATOM 214 CE2 TYR 28 15.547 21.311 28.766 1.00 0.00 ATOM 215 CZ TYR 28 15.890 21.527 30.088 1.00 0.00 ATOM 216 OH TYR 28 15.137 21.059 31.116 1.00 0.00 ATOM 217 O TYR 28 20.790 24.605 26.088 1.00 0.00 ATOM 218 C TYR 28 19.692 25.153 26.201 1.00 0.00 ATOM 219 N ASN 29 19.472 26.410 25.828 1.00 0.00 ATOM 220 CA ASN 29 20.538 27.226 25.256 1.00 0.00 ATOM 221 CB ASN 29 21.666 27.387 26.285 1.00 0.00 ATOM 222 CG ASN 29 21.187 28.034 27.571 1.00 0.00 ATOM 223 ND2 ASN 29 21.477 27.398 28.700 1.00 0.00 ATOM 224 OD1 ASN 29 20.565 29.097 27.548 1.00 0.00 ATOM 225 O ASN 29 22.150 27.272 23.449 1.00 0.00 ATOM 226 C ASN 29 21.160 26.719 23.944 1.00 0.00 ATOM 227 N LEU 30 20.500 25.762 23.291 1.00 0.00 ATOM 228 CA LEU 30 20.839 25.442 21.883 1.00 0.00 ATOM 229 CB LEU 30 20.049 24.275 21.282 1.00 0.00 ATOM 230 CG LEU 30 20.588 22.902 21.698 1.00 0.00 ATOM 231 CD1 LEU 30 20.101 22.490 23.086 1.00 0.00 ATOM 232 CD2 LEU 30 20.207 21.863 20.650 1.00 0.00 ATOM 233 O LEU 30 21.547 27.151 20.363 1.00 0.00 ATOM 234 C LEU 30 20.645 26.730 21.079 1.00 0.00 ATOM 235 N GLY 31 19.542 27.426 21.362 1.00 0.00 ATOM 236 CA GLY 31 19.212 28.746 20.792 1.00 0.00 ATOM 237 O GLY 31 19.220 29.552 18.506 1.00 0.00 ATOM 238 C GLY 31 18.988 28.633 19.291 1.00 0.00 ATOM 239 N CYS 32 18.367 27.509 18.956 1.00 0.00 ATOM 240 CA CYS 32 18.165 27.107 17.565 1.00 0.00 ATOM 241 CB CYS 32 19.467 26.266 17.074 1.00 0.00 ATOM 242 SG CYS 32 19.763 24.864 18.242 1.00 0.00 ATOM 243 O CYS 32 16.171 25.932 18.199 1.00 0.00 ATOM 244 C CYS 32 16.762 26.563 17.321 1.00 0.00 ATOM 245 N ILE 33 16.230 26.808 16.127 1.00 0.00 ATOM 246 CA ILE 33 14.875 26.328 15.773 1.00 0.00 ATOM 247 CB ILE 33 14.397 27.009 14.479 1.00 0.00 ATOM 248 CG1 ILE 33 15.239 26.633 13.255 1.00 0.00 ATOM 249 CG2 ILE 33 14.351 28.527 14.749 1.00 0.00 ATOM 250 CD1 ILE 33 14.760 27.339 11.986 1.00 0.00 ATOM 251 O ILE 33 14.358 24.306 17.035 1.00 0.00 ATOM 252 C ILE 33 14.923 24.824 16.075 1.00 0.00 ATOM 253 N GLY 34 15.775 24.332 15.252 1.00 0.00 ATOM 254 CA GLY 34 16.355 23.008 15.419 1.00 0.00 ATOM 255 O GLY 34 18.281 22.013 14.508 1.00 0.00 ATOM 256 C GLY 34 17.781 23.059 14.876 1.00 0.00 ATOM 257 N CYS 35 18.337 24.227 14.902 1.00 0.00 ATOM 258 CA CYS 35 19.595 24.600 14.222 1.00 0.00 ATOM 259 CB CYS 35 20.638 23.572 14.698 1.00 0.00 ATOM 260 SG CYS 35 20.587 23.000 16.448 1.00 0.00 ATOM 261 O CYS 35 18.263 24.134 12.287 1.00 0.00 ATOM 262 C CYS 35 19.300 24.632 12.692 1.00 0.00 ATOM 263 N MET 36 20.022 25.417 11.861 1.00 0.00 ATOM 264 CA MET 36 19.934 25.265 10.379 1.00 0.00 ATOM 265 CB MET 36 20.467 26.687 9.738 1.00 0.00 ATOM 266 CG MET 36 19.737 28.015 10.013 1.00 0.00 ATOM 267 SD MET 36 19.346 28.385 11.723 1.00 0.00 ATOM 268 CE MET 36 21.001 28.460 12.414 1.00 0.00 ATOM 269 O MET 36 21.007 23.408 9.320 1.00 0.00 ATOM 270 C MET 36 21.104 24.339 10.121 1.00 0.00 ATOM 271 N GLY 37 22.219 24.591 10.800 1.00 0.00 ATOM 272 CA GLY 37 23.408 23.764 10.635 1.00 0.00 ATOM 273 O GLY 37 23.339 21.371 10.416 1.00 0.00 ATOM 274 C GLY 37 22.944 22.356 11.055 1.00 0.00 ATOM 275 N ALA 38 21.958 22.313 11.942 1.00 0.00 ATOM 276 CA ALA 38 21.150 21.139 12.325 1.00 0.00 ATOM 277 CB ALA 38 19.495 21.450 12.020 1.00 0.00 ATOM 278 O ALA 38 21.314 18.829 11.838 1.00 0.00 ATOM 279 C ALA 38 21.232 19.971 11.366 1.00 0.00 ATOM 280 N GLN 39 20.921 20.264 10.108 1.00 0.00 ATOM 281 CA GLN 39 20.783 19.287 9.000 1.00 0.00 ATOM 282 CB GLN 39 20.753 19.827 7.637 1.00 0.00 ATOM 283 CG GLN 39 21.913 20.615 7.194 1.00 0.00 ATOM 284 CD GLN 39 21.658 21.330 5.876 1.00 0.00 ATOM 285 OE1 GLN 39 21.183 22.457 5.856 1.00 0.00 ATOM 286 NE2 GLN 39 21.997 20.669 4.773 1.00 0.00 ATOM 287 O GLN 39 21.757 17.090 9.092 1.00 0.00 ATOM 288 C GLN 39 21.938 18.294 9.154 1.00 0.00 ATOM 289 N ASN 40 23.103 18.881 9.375 1.00 0.00 ATOM 290 CA ASN 40 24.374 18.148 9.423 1.00 0.00 ATOM 291 CB ASN 40 25.499 19.095 9.091 1.00 0.00 ATOM 292 CG ASN 40 25.363 19.624 7.670 1.00 0.00 ATOM 293 ND2 ASN 40 26.208 20.587 7.458 1.00 0.00 ATOM 294 OD1 ASN 40 24.535 19.300 6.813 1.00 0.00 ATOM 295 O ASN 40 25.697 16.652 10.690 1.00 0.00 ATOM 296 C ASN 40 24.796 17.484 10.733 1.00 0.00 ATOM 297 N GLU 41 24.162 17.833 11.840 1.00 0.00 ATOM 298 CA GLU 41 24.686 17.422 13.151 1.00 0.00 ATOM 299 CB GLU 41 25.164 18.574 14.031 1.00 0.00 ATOM 300 CG GLU 41 26.441 19.232 13.514 1.00 0.00 ATOM 301 CD GLU 41 27.008 20.240 14.523 1.00 0.00 ATOM 302 OE1 GLU 41 26.373 20.477 15.587 1.00 0.00 ATOM 303 OE2 GLU 41 28.043 20.830 14.184 1.00 0.00 ATOM 304 O GLU 41 22.474 16.802 13.911 1.00 0.00 ATOM 305 C GLU 41 23.697 16.584 13.948 1.00 0.00 ATOM 306 N SER 42 24.245 15.721 14.783 1.00 0.00 ATOM 307 CA SER 42 23.449 14.899 15.683 1.00 0.00 ATOM 308 CB SER 42 24.172 13.578 15.907 1.00 0.00 ATOM 309 OG SER 42 25.429 13.789 16.555 1.00 0.00 ATOM 310 O SER 42 23.971 16.591 17.311 1.00 0.00 ATOM 311 C SER 42 23.307 15.588 17.046 1.00 0.00 ATOM 312 N LEU 43 22.445 15.049 17.901 1.00 0.00 ATOM 313 CA LEU 43 22.234 15.622 19.225 1.00 0.00 ATOM 314 CB LEU 43 21.165 14.818 19.954 1.00 0.00 ATOM 315 CG LEU 43 20.912 15.385 21.355 1.00 0.00 ATOM 316 CD1 LEU 43 20.137 16.710 21.310 1.00 0.00 ATOM 317 CD2 LEU 43 20.237 14.334 22.203 1.00 0.00 ATOM 318 O LEU 43 23.777 16.681 20.750 1.00 0.00 ATOM 319 C LEU 43 23.533 15.702 20.032 1.00 0.00 ATOM 320 N GLU 44 24.384 14.659 19.962 1.00 0.00 ATOM 321 CA GLU 44 25.632 14.664 20.719 1.00 0.00 ATOM 322 CB GLU 44 26.317 13.313 20.680 1.00 0.00 ATOM 323 CG GLU 44 25.535 12.253 21.453 1.00 0.00 ATOM 324 CD GLU 44 26.259 10.912 21.455 1.00 0.00 ATOM 325 OE1 GLU 44 27.109 10.746 20.561 1.00 0.00 ATOM 326 OE2 GLU 44 25.869 10.049 22.260 1.00 0.00 ATOM 327 O GLU 44 27.218 16.454 20.927 1.00 0.00 ATOM 328 C GLU 44 26.558 15.743 20.166 1.00 0.00 ATOM 329 N GLN 45 26.605 15.865 18.843 1.00 0.00 ATOM 330 CA GLN 45 27.464 16.878 18.192 1.00 0.00 ATOM 331 CB GLN 45 27.384 16.794 16.672 1.00 0.00 ATOM 332 CG GLN 45 28.109 15.556 16.210 1.00 0.00 ATOM 333 CD GLN 45 27.957 15.353 14.721 1.00 0.00 ATOM 334 OE1 GLN 45 26.946 15.686 14.132 1.00 0.00 ATOM 335 NE2 GLN 45 28.853 14.574 14.175 1.00 0.00 ATOM 336 O GLN 45 27.833 19.097 19.003 1.00 0.00 ATOM 337 C GLN 45 27.021 18.291 18.561 1.00 0.00 ATOM 338 N GLY 46 25.700 18.452 18.619 1.00 0.00 ATOM 339 CA GLY 46 25.078 19.724 19.007 1.00 0.00 ATOM 340 O GLY 46 25.688 21.153 20.837 1.00 0.00 ATOM 341 C GLY 46 25.378 20.016 20.474 1.00 0.00 ATOM 342 N ALA 47 25.286 18.991 21.314 1.00 0.00 ATOM 343 CA ALA 47 25.555 19.153 22.750 1.00 0.00 ATOM 344 CB ALA 47 25.319 17.825 23.450 1.00 0.00 ATOM 345 O ALA 47 27.287 20.484 23.744 1.00 0.00 ATOM 346 C ALA 47 27.003 19.588 22.947 1.00 0.00 ATOM 347 N ASN 48 27.918 18.955 22.219 1.00 0.00 ATOM 348 CA ASN 48 29.347 19.292 22.323 1.00 0.00 ATOM 349 CB ASN 48 30.157 18.307 21.488 1.00 0.00 ATOM 350 CG ASN 48 30.310 16.968 22.209 1.00 0.00 ATOM 351 ND2 ASN 48 30.867 16.054 21.499 1.00 0.00 ATOM 352 OD1 ASN 48 29.739 16.657 23.235 1.00 0.00 ATOM 353 O ASN 48 30.308 21.501 22.543 1.00 0.00 ATOM 354 C ASN 48 29.585 20.759 21.877 1.00 0.00 ATOM 355 N ALA 49 28.976 21.155 20.764 1.00 0.00 ATOM 356 CA ALA 49 29.133 22.515 20.259 1.00 0.00 ATOM 357 CB ALA 49 28.569 22.602 18.842 1.00 0.00 ATOM 358 O ALA 49 28.977 24.682 21.317 1.00 0.00 ATOM 359 C ALA 49 28.458 23.576 21.163 1.00 0.00 ATOM 360 N HIS 50 27.314 23.228 21.745 1.00 0.00 ATOM 361 CA HIS 50 26.600 24.154 22.618 1.00 0.00 ATOM 362 CB HIS 50 25.121 23.812 22.502 1.00 0.00 ATOM 363 CG HIS 50 24.510 23.958 21.102 1.00 0.00 ATOM 364 CD2 HIS 50 23.738 23.082 20.470 1.00 0.00 ATOM 365 ND1 HIS 50 24.710 24.981 20.294 1.00 0.00 ATOM 366 CE1 HIS 50 24.055 24.749 19.167 1.00 0.00 ATOM 367 NE2 HIS 50 23.484 23.559 19.252 1.00 0.00 ATOM 368 O HIS 50 26.511 24.844 24.942 1.00 0.00 ATOM 369 C HIS 50 26.997 24.061 24.125 1.00 0.00 ATOM 370 N GLY 51 27.868 23.114 24.463 1.00 0.00 ATOM 371 CA GLY 51 28.305 22.949 25.844 1.00 0.00 ATOM 372 O GLY 51 27.232 22.631 27.937 1.00 0.00 ATOM 373 C GLY 51 27.241 22.356 26.721 1.00 0.00 ATOM 374 N LEU 52 26.316 21.632 26.140 1.00 0.00 ATOM 375 CA LEU 52 25.250 21.004 26.906 1.00 0.00 ATOM 376 CB LEU 52 23.943 21.110 26.139 1.00 0.00 ATOM 377 CG LEU 52 22.746 20.471 26.844 1.00 0.00 ATOM 378 CD1 LEU 52 22.634 20.792 28.343 1.00 0.00 ATOM 379 CD2 LEU 52 21.494 20.997 26.146 1.00 0.00 ATOM 380 O LEU 52 25.728 18.810 26.057 1.00 0.00 ATOM 381 C LEU 52 25.586 19.524 27.052 1.00 0.00 ATOM 382 N ASN 53 25.711 19.062 28.292 1.00 0.00 ATOM 383 CA ASN 53 26.020 17.693 28.535 1.00 0.00 ATOM 384 CB ASN 53 26.194 17.416 30.020 1.00 0.00 ATOM 385 CG ASN 53 27.459 17.991 30.624 1.00 0.00 ATOM 386 ND2 ASN 53 27.427 18.122 31.923 1.00 0.00 ATOM 387 OD1 ASN 53 28.372 18.443 29.948 1.00 0.00 ATOM 388 O ASN 53 23.780 17.088 27.941 1.00 0.00 ATOM 389 C ASN 53 24.972 16.778 27.923 1.00 0.00 ATOM 390 N VAL 54 25.415 15.649 27.380 1.00 0.00 ATOM 391 CA VAL 54 24.498 14.695 26.765 1.00 0.00 ATOM 392 CB VAL 54 25.294 13.648 25.882 1.00 0.00 ATOM 393 CG1 VAL 54 24.398 12.495 25.408 1.00 0.00 ATOM 394 CG2 VAL 54 25.933 14.353 24.736 1.00 0.00 ATOM 395 O VAL 54 22.352 13.870 27.498 1.00 0.00 ATOM 396 C VAL 54 23.533 14.083 27.811 1.00 0.00 ATOM 397 N GLU 55 24.019 13.853 29.018 1.00 0.00 ATOM 398 CA GLU 55 23.172 13.314 30.094 1.00 0.00 ATOM 399 CB GLU 55 23.959 12.943 31.350 1.00 0.00 ATOM 400 CG GLU 55 25.052 11.897 31.184 1.00 0.00 ATOM 401 CD GLU 55 26.419 12.428 30.739 1.00 0.00 ATOM 402 OE1 GLU 55 26.535 13.563 30.232 1.00 0.00 ATOM 403 OE2 GLU 55 27.352 11.610 30.913 1.00 0.00 ATOM 404 O GLU 55 20.901 13.842 30.587 1.00 0.00 ATOM 405 C GLU 55 22.035 14.285 30.405 1.00 0.00 ATOM 406 N ASP 56 22.300 15.596 30.420 1.00 0.00 ATOM 407 CA ASP 56 21.251 16.603 30.672 1.00 0.00 ATOM 408 CB ASP 56 21.888 17.982 30.818 1.00 0.00 ATOM 409 CG ASP 56 22.810 18.127 32.029 1.00 0.00 ATOM 410 OD1 ASP 56 22.613 17.462 33.068 1.00 0.00 ATOM 411 OD2 ASP 56 23.784 18.889 31.854 1.00 0.00 ATOM 412 O ASP 56 18.967 16.635 29.901 1.00 0.00 ATOM 413 C ASP 56 20.158 16.584 29.588 1.00 0.00 ATOM 414 N ILE 57 20.568 16.510 28.326 1.00 0.00 ATOM 415 CA ILE 57 19.615 16.483 27.222 1.00 0.00 ATOM 416 CB ILE 57 20.356 16.557 25.879 1.00 0.00 ATOM 417 CG1 ILE 57 20.913 17.957 25.666 1.00 0.00 ATOM 418 CG2 ILE 57 19.390 16.265 24.737 1.00 0.00 ATOM 419 CD1 ILE 57 21.915 18.080 24.509 1.00 0.00 ATOM 420 O ILE 57 17.493 15.332 26.972 1.00 0.00 ATOM 421 C ILE 57 18.686 15.254 27.292 1.00 0.00 ATOM 422 N LEU 58 19.308 14.101 27.476 1.00 0.00 ATOM 423 CA LEU 58 18.558 12.826 27.489 1.00 0.00 ATOM 424 CB LEU 58 19.511 11.624 27.561 1.00 0.00 ATOM 425 CG LEU 58 20.318 11.601 26.255 1.00 0.00 ATOM 426 CD1 LEU 58 21.418 10.566 26.276 1.00 0.00 ATOM 427 CD2 LEU 58 19.386 11.392 25.067 1.00 0.00 ATOM 428 O LEU 58 16.400 12.390 28.442 1.00 0.00 ATOM 429 C LEU 58 17.539 12.823 28.615 1.00 0.00 ATOM 430 N ARG 59 17.955 13.300 29.766 1.00 0.00 ATOM 431 CA ARG 59 17.054 13.347 30.899 1.00 0.00 ATOM 432 CB ARG 59 17.756 13.879 32.156 1.00 0.00 ATOM 433 CG ARG 59 16.761 14.077 33.303 1.00 0.00 ATOM 434 CD ARG 59 17.422 14.546 34.576 1.00 0.00 ATOM 435 NE ARG 59 18.052 15.849 34.433 1.00 0.00 ATOM 436 CZ ARG 59 19.309 16.090 34.780 1.00 0.00 ATOM 437 NH1 ARG 59 20.053 15.115 35.281 1.00 0.00 ATOM 438 NH2 ARG 59 19.818 17.310 34.647 1.00 0.00 ATOM 439 O ARG 59 14.743 13.934 30.704 1.00 0.00 ATOM 440 C ARG 59 15.900 14.315 30.543 1.00 0.00 ATOM 441 N ASP 60 16.240 15.429 29.903 1.00 0.00 ATOM 442 CA ASP 60 15.248 16.434 29.492 1.00 0.00 ATOM 443 CB ASP 60 15.920 17.678 28.893 1.00 0.00 ATOM 444 CG ASP 60 16.702 18.441 29.962 1.00 0.00 ATOM 445 OD1 ASP 60 16.319 18.282 31.135 1.00 0.00 ATOM 446 OD2 ASP 60 17.690 19.102 29.603 1.00 0.00 ATOM 447 O ASP 60 13.043 16.112 28.604 1.00 0.00 ATOM 448 C ASP 60 14.247 15.881 28.483 1.00 0.00 ATOM 449 N LEU 61 14.745 15.151 27.491 1.00 0.00 ATOM 450 CA LEU 61 13.885 14.577 26.485 1.00 0.00 ATOM 451 CB LEU 61 14.708 13.961 25.366 1.00 0.00 ATOM 452 CG LEU 61 15.160 14.977 24.343 1.00 0.00 ATOM 453 CD1 LEU 61 16.128 14.291 23.376 1.00 0.00 ATOM 454 CD2 LEU 61 13.953 15.625 23.656 1.00 0.00 ATOM 455 O LEU 61 11.754 13.520 26.792 1.00 0.00 ATOM 456 C LEU 61 12.943 13.557 27.112 1.00 0.00 ATOM 457 N ASN 62 13.474 12.732 28.009 1.00 0.00 ATOM 458 CA ASN 62 12.664 11.718 28.675 1.00 0.00 ATOM 459 CB ASN 62 13.558 10.844 29.555 1.00 0.00 ATOM 460 CG ASN 62 12.743 9.662 30.104 1.00 0.00 ATOM 461 ND2 ASN 62 12.820 9.455 31.398 1.00 0.00 ATOM 462 OD1 ASN 62 12.135 8.911 29.372 1.00 0.00 ATOM 463 O ASN 62 10.435 11.955 29.540 1.00 0.00 ATOM 464 C ASN 62 11.582 12.402 29.513 1.00 0.00 ATOM 465 N ALA 63 11.950 13.482 30.194 1.00 0.00 ATOM 466 CA ALA 63 10.998 14.214 31.022 1.00 0.00 ATOM 467 CB ALA 63 11.742 15.344 31.731 1.00 0.00 ATOM 468 O ALA 63 8.703 14.781 30.585 1.00 0.00 ATOM 469 C ALA 63 9.864 14.770 30.165 1.00 0.00 ATOM 470 N LEU 64 10.201 15.225 28.969 1.00 0.00 ATOM 471 CA LEU 64 9.188 15.752 28.066 1.00 0.00 ATOM 472 CB LEU 64 9.730 16.281 26.786 1.00 0.00 ATOM 473 CG LEU 64 8.705 16.854 25.793 1.00 0.00 ATOM 474 CD1 LEU 64 7.775 17.867 26.472 1.00 0.00 ATOM 475 CD2 LEU 64 9.459 17.503 24.640 1.00 0.00 ATOM 476 O LEU 64 7.005 14.887 27.749 1.00 0.00 ATOM 477 C LEU 64 8.202 14.637 27.638 1.00 0.00 ATOM 478 N ALA 65 8.768 13.551 27.118 1.00 0.00 ATOM 479 CA ALA 65 8.009 12.333 26.756 1.00 0.00 ATOM 480 CB ALA 65 9.003 11.322 26.190 1.00 0.00 ATOM 481 O ALA 65 7.694 12.115 29.100 1.00 0.00 ATOM 482 C ALA 65 7.328 11.704 27.979 1.00 0.00 TER END