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 4 Mon Jul 7 11:25:21 2008 MODEL 4 PARENT N/A ATOM 1 N MET 1 19.723 9.479 22.599 1.00 0.00 ATOM 2 CA MET 1 18.727 10.077 23.494 1.00 0.00 ATOM 3 CB MET 1 17.801 11.075 22.773 1.00 0.00 ATOM 4 CG MET 1 18.380 12.395 22.326 1.00 0.00 ATOM 5 SD MET 1 19.342 13.299 23.582 1.00 0.00 ATOM 6 CE MET 1 17.869 13.819 24.410 1.00 0.00 ATOM 7 O MET 1 18.535 8.022 24.602 1.00 0.00 ATOM 8 C MET 1 17.918 8.887 24.003 1.00 0.00 ATOM 9 N THR 2 16.658 8.802 23.594 1.00 0.00 ATOM 10 CA THR 2 15.741 7.732 23.990 1.00 0.00 ATOM 11 CB THR 2 14.599 8.335 24.839 1.00 0.00 ATOM 12 CG2 THR 2 13.661 9.272 24.073 1.00 0.00 ATOM 13 OG1 THR 2 13.822 7.274 25.393 1.00 0.00 ATOM 14 O THR 2 15.620 7.193 21.622 1.00 0.00 ATOM 15 C THR 2 15.255 6.947 22.755 1.00 0.00 ATOM 16 N GLN 3 14.311 6.049 22.997 1.00 0.00 ATOM 17 CA GLN 3 13.652 5.337 21.887 1.00 0.00 ATOM 18 CB GLN 3 12.765 4.231 22.397 1.00 0.00 ATOM 19 CG GLN 3 13.620 3.049 22.826 1.00 0.00 ATOM 20 CD GLN 3 12.733 1.833 23.041 1.00 0.00 ATOM 21 OE1 GLN 3 11.821 1.571 22.272 1.00 0.00 ATOM 22 NE2 GLN 3 12.918 1.167 24.154 1.00 0.00 ATOM 23 O GLN 3 13.000 6.284 19.796 1.00 0.00 ATOM 24 C GLN 3 12.814 6.266 21.008 1.00 0.00 ATOM 25 N LYS 4 12.087 7.171 21.667 1.00 0.00 ATOM 26 CA LYS 4 11.247 8.158 20.950 1.00 0.00 ATOM 27 CB LYS 4 10.436 9.034 21.906 1.00 0.00 ATOM 28 CG LYS 4 9.363 8.205 22.601 1.00 0.00 ATOM 29 CD LYS 4 8.494 9.107 23.465 1.00 0.00 ATOM 30 CE LYS 4 7.436 8.299 24.193 1.00 0.00 ATOM 31 NZ LYS 4 6.557 9.172 24.961 1.00 0.00 ATOM 32 O LYS 4 11.770 9.330 18.918 1.00 0.00 ATOM 33 C LYS 4 12.097 9.082 20.063 1.00 0.00 ATOM 34 N PHE 5 13.224 9.514 20.631 1.00 0.00 ATOM 35 CA PHE 5 14.172 10.346 19.886 1.00 0.00 ATOM 36 CB PHE 5 14.290 11.739 20.478 1.00 0.00 ATOM 37 CG PHE 5 12.981 12.519 20.478 1.00 0.00 ATOM 38 CD1 PHE 5 12.091 12.452 21.558 1.00 0.00 ATOM 39 CD2 PHE 5 12.687 13.300 19.377 1.00 0.00 ATOM 40 CE1 PHE 5 10.913 13.186 21.524 1.00 0.00 ATOM 41 CE2 PHE 5 11.510 14.030 19.352 1.00 0.00 ATOM 42 CZ PHE 5 10.629 13.970 20.423 1.00 0.00 ATOM 43 O PHE 5 16.144 9.458 20.922 1.00 0.00 ATOM 44 C PHE 5 15.567 9.728 19.885 1.00 0.00 ATOM 45 N THR 6 16.239 9.994 18.765 1.00 0.00 ATOM 46 CA THR 6 17.626 9.555 18.588 1.00 0.00 ATOM 47 CB THR 6 17.838 8.859 17.242 1.00 0.00 ATOM 48 CG2 THR 6 19.245 8.317 17.085 1.00 0.00 ATOM 49 OG1 THR 6 16.991 7.737 17.227 1.00 0.00 ATOM 50 O THR 6 18.607 11.569 17.805 1.00 0.00 ATOM 51 C THR 6 18.562 10.749 18.713 1.00 0.00 ATOM 52 N LYS 7 19.373 10.705 19.764 1.00 0.00 ATOM 53 CA LYS 7 20.449 11.712 19.947 1.00 0.00 ATOM 54 CB LYS 7 21.326 11.570 21.211 1.00 0.00 ATOM 55 CG LYS 7 22.288 10.383 21.251 1.00 0.00 ATOM 56 CD LYS 7 22.981 10.318 22.609 1.00 0.00 ATOM 57 CE LYS 7 24.181 9.349 22.598 1.00 0.00 ATOM 58 NZ LYS 7 25.120 9.567 21.481 1.00 0.00 ATOM 59 O LYS 7 22.181 12.701 18.631 1.00 0.00 ATOM 60 C LYS 7 21.427 11.738 18.785 1.00 0.00 ATOM 61 N ASP 8 21.592 10.542 18.240 1.00 0.00 ATOM 62 CA ASP 8 22.604 10.244 17.224 1.00 0.00 ATOM 63 CB ASP 8 22.708 8.748 16.936 1.00 0.00 ATOM 64 CG ASP 8 23.168 7.895 18.122 1.00 0.00 ATOM 65 OD1 ASP 8 23.881 8.421 18.990 1.00 0.00 ATOM 66 OD2 ASP 8 22.716 6.742 18.169 1.00 0.00 ATOM 67 O ASP 8 23.308 11.238 15.181 1.00 0.00 ATOM 68 C ASP 8 22.357 10.962 15.895 1.00 0.00 ATOM 69 N MET 9 21.079 11.166 15.561 1.00 0.00 ATOM 70 CA MET 9 20.714 11.756 14.257 1.00 0.00 ATOM 71 CB MET 9 19.332 11.322 13.795 1.00 0.00 ATOM 72 CG MET 9 19.246 9.833 13.493 1.00 0.00 ATOM 73 SD MET 9 17.698 9.400 12.627 1.00 0.00 ATOM 74 CE MET 9 16.472 9.832 13.844 1.00 0.00 ATOM 75 O MET 9 20.563 13.866 15.402 1.00 0.00 ATOM 76 C MET 9 20.712 13.280 14.338 1.00 0.00 ATOM 77 N THR 10 20.684 13.855 13.138 1.00 0.00 ATOM 78 CA THR 10 20.617 15.308 12.944 1.00 0.00 ATOM 79 CB THR 10 20.614 15.696 11.447 1.00 0.00 ATOM 80 CG2 THR 10 21.647 14.861 10.679 1.00 0.00 ATOM 81 OG1 THR 10 19.322 15.523 10.867 1.00 0.00 ATOM 82 O THR 10 18.325 15.164 13.722 1.00 0.00 ATOM 83 C THR 10 19.369 15.826 13.656 1.00 0.00 ATOM 84 N PHE 11 19.513 16.998 14.245 1.00 0.00 ATOM 85 CA PHE 11 18.444 17.644 15.004 1.00 0.00 ATOM 86 CB PHE 11 18.976 18.951 15.578 1.00 0.00 ATOM 87 CG PHE 11 17.847 19.808 16.141 1.00 0.00 ATOM 88 CD1 PHE 11 17.447 19.628 17.444 1.00 0.00 ATOM 89 CD2 PHE 11 17.167 20.727 15.362 1.00 0.00 ATOM 90 CE1 PHE 11 16.424 20.422 17.909 1.00 0.00 ATOM 91 CE2 PHE 11 16.105 21.475 15.841 1.00 0.00 ATOM 92 CZ PHE 11 15.708 21.319 17.146 1.00 0.00 ATOM 93 O PHE 11 16.072 17.699 14.608 1.00 0.00 ATOM 94 C PHE 11 17.194 17.871 14.134 1.00 0.00 ATOM 95 N ALA 12 17.422 18.201 12.873 1.00 0.00 ATOM 96 CA ALA 12 16.323 18.458 11.917 1.00 0.00 ATOM 97 CB ALA 12 16.932 18.879 10.592 1.00 0.00 ATOM 98 O ALA 12 14.208 17.318 11.775 1.00 0.00 ATOM 99 C ALA 12 15.432 17.223 11.726 1.00 0.00 ATOM 100 N GLN 13 16.069 16.051 11.648 1.00 0.00 ATOM 101 CA GLN 13 15.346 14.774 11.537 1.00 0.00 ATOM 102 CB GLN 13 16.345 13.617 11.449 1.00 0.00 ATOM 103 CG GLN 13 15.637 12.276 11.171 1.00 0.00 ATOM 104 CD GLN 13 14.914 12.265 9.821 1.00 0.00 ATOM 105 OE1 GLN 13 15.362 12.741 8.796 1.00 0.00 ATOM 106 NE2 GLN 13 13.699 11.793 9.824 1.00 0.00 ATOM 107 O GLN 13 13.237 14.351 12.605 1.00 0.00 ATOM 108 C GLN 13 14.433 14.567 12.749 1.00 0.00 ATOM 109 N ALA 14 14.993 14.849 13.930 1.00 0.00 ATOM 110 CA ALA 14 14.250 14.762 15.198 1.00 0.00 ATOM 111 CB ALA 14 15.192 14.993 16.386 1.00 0.00 ATOM 112 O ALA 14 11.957 15.409 15.545 1.00 0.00 ATOM 113 C ALA 14 13.101 15.766 15.256 1.00 0.00 ATOM 114 N LEU 15 13.405 16.991 14.818 1.00 0.00 ATOM 115 CA LEU 15 12.435 18.097 14.827 1.00 0.00 ATOM 116 CB LEU 15 13.156 19.364 14.363 1.00 0.00 ATOM 117 CG LEU 15 12.228 20.577 14.299 1.00 0.00 ATOM 118 CD1 LEU 15 11.634 20.882 15.663 1.00 0.00 ATOM 119 CD2 LEU 15 13.060 21.727 13.788 1.00 0.00 ATOM 120 O LEU 15 10.102 18.038 14.302 1.00 0.00 ATOM 121 C LEU 15 11.248 17.821 13.916 1.00 0.00 ATOM 122 N GLN 16 11.544 17.313 12.723 1.00 0.00 ATOM 123 CA GLN 16 10.501 16.950 11.753 1.00 0.00 ATOM 124 CB GLN 16 11.064 16.436 10.436 1.00 0.00 ATOM 125 CG GLN 16 11.735 17.586 9.682 1.00 0.00 ATOM 126 CD GLN 16 12.313 17.091 8.362 1.00 0.00 ATOM 127 OE1 GLN 16 11.908 17.419 7.262 1.00 0.00 ATOM 128 NE2 GLN 16 13.424 16.401 8.466 1.00 0.00 ATOM 129 O GLN 16 8.356 16.076 12.349 1.00 0.00 ATOM 130 C GLN 16 9.567 15.886 12.329 1.00 0.00 ATOM 131 N THR 17 10.177 14.872 12.948 1.00 0.00 ATOM 132 CA THR 17 9.392 13.795 13.564 1.00 0.00 ATOM 133 CB THR 17 10.275 12.680 14.155 1.00 0.00 ATOM 134 CG2 THR 17 9.426 11.544 14.735 1.00 0.00 ATOM 135 OG1 THR 17 11.080 12.137 13.111 1.00 0.00 ATOM 136 O THR 17 7.269 14.199 14.630 1.00 0.00 ATOM 137 C THR 17 8.481 14.373 14.655 1.00 0.00 ATOM 138 N HIS 18 9.098 15.140 15.536 1.00 0.00 ATOM 139 CA HIS 18 8.368 15.705 16.663 1.00 0.00 ATOM 140 CB HIS 18 8.738 14.933 17.908 1.00 0.00 ATOM 141 CG HIS 18 8.116 13.552 17.978 1.00 0.00 ATOM 142 CD2 HIS 18 6.837 13.205 18.120 1.00 0.00 ATOM 143 ND1 HIS 18 8.812 12.431 17.828 1.00 0.00 ATOM 144 CE1 HIS 18 7.977 11.405 17.842 1.00 0.00 ATOM 145 NE2 HIS 18 6.746 11.883 18.018 1.00 0.00 ATOM 146 O HIS 18 9.543 17.656 17.463 1.00 0.00 ATOM 147 C HIS 18 8.612 17.208 16.788 1.00 0.00 ATOM 148 N PRO 19 7.731 18.014 16.205 1.00 0.00 ATOM 149 CA PRO 19 7.852 19.479 16.269 1.00 0.00 ATOM 150 CB PRO 19 6.719 19.974 15.384 1.00 0.00 ATOM 151 CG PRO 19 5.677 18.865 15.462 1.00 0.00 ATOM 152 CD PRO 19 6.497 17.595 15.521 1.00 0.00 ATOM 153 O PRO 19 8.510 20.945 18.053 1.00 0.00 ATOM 154 C PRO 19 7.765 20.035 17.690 1.00 0.00 ATOM 155 N GLY 20 7.000 19.347 18.536 1.00 0.00 ATOM 156 CA GLY 20 6.821 19.729 19.954 1.00 0.00 ATOM 157 O GLY 20 8.356 20.680 21.535 1.00 0.00 ATOM 158 C GLY 20 8.168 19.809 20.694 1.00 0.00 ATOM 159 N VAL 21 9.103 18.915 20.324 1.00 0.00 ATOM 160 CA VAL 21 10.405 18.774 21.003 1.00 0.00 ATOM 161 CB VAL 21 11.204 17.558 20.470 1.00 0.00 ATOM 162 CG1 VAL 21 11.816 17.740 19.079 1.00 0.00 ATOM 163 CG2 VAL 21 12.310 17.174 21.458 1.00 0.00 ATOM 164 O VAL 21 12.178 20.256 21.715 1.00 0.00 ATOM 165 C VAL 21 11.273 20.041 20.913 1.00 0.00 ATOM 166 N ALA 22 11.066 20.777 19.832 1.00 0.00 ATOM 167 CA ALA 22 11.931 21.934 19.563 1.00 0.00 ATOM 168 CB ALA 22 11.482 22.684 18.351 1.00 0.00 ATOM 169 O ALA 22 12.923 23.573 20.967 1.00 0.00 ATOM 170 C ALA 22 11.890 22.977 20.675 1.00 0.00 ATOM 171 N GLY 23 10.703 23.138 21.268 1.00 0.00 ATOM 172 CA GLY 23 10.517 24.041 22.414 1.00 0.00 ATOM 173 O GLY 23 12.310 24.398 23.966 1.00 0.00 ATOM 174 C GLY 23 11.474 23.619 23.541 1.00 0.00 ATOM 175 N VAL 24 11.578 22.314 23.732 1.00 0.00 ATOM 176 CA VAL 24 12.520 21.784 24.730 1.00 0.00 ATOM 177 CB VAL 24 12.258 20.304 24.992 1.00 0.00 ATOM 178 CG1 VAL 24 13.239 19.711 25.995 1.00 0.00 ATOM 179 CG2 VAL 24 10.921 20.330 25.704 1.00 0.00 ATOM 180 O VAL 24 14.788 22.434 25.173 1.00 0.00 ATOM 181 C VAL 24 13.980 22.007 24.352 1.00 0.00 ATOM 182 N LEU 25 14.267 21.702 23.102 1.00 0.00 ATOM 183 CA LEU 25 15.631 21.742 22.575 1.00 0.00 ATOM 184 CB LEU 25 15.589 21.125 21.184 1.00 0.00 ATOM 185 CG LEU 25 15.167 19.635 21.279 1.00 0.00 ATOM 186 CD1 LEU 25 14.871 18.918 19.973 1.00 0.00 ATOM 187 CD2 LEU 25 16.225 18.793 21.954 1.00 0.00 ATOM 188 O LEU 25 17.358 23.324 23.061 1.00 0.00 ATOM 189 C LEU 25 16.223 23.144 22.615 1.00 0.00 ATOM 190 N ARG 26 15.367 24.138 22.391 1.00 0.00 ATOM 191 CA ARG 26 15.755 25.552 22.479 1.00 0.00 ATOM 192 CB ARG 26 14.580 26.467 22.176 1.00 0.00 ATOM 193 CG ARG 26 14.198 26.350 20.704 1.00 0.00 ATOM 194 CD ARG 26 12.966 27.200 20.535 1.00 0.00 ATOM 195 NE ARG 26 12.550 27.118 19.145 1.00 0.00 ATOM 196 CZ ARG 26 11.512 27.777 18.676 1.00 0.00 ATOM 197 NH1 ARG 26 11.226 27.633 17.417 1.00 0.00 ATOM 198 NH2 ARG 26 10.695 28.486 19.445 1.00 0.00 ATOM 199 O ARG 26 17.237 26.646 23.999 1.00 0.00 ATOM 200 C ARG 26 16.262 25.915 23.877 1.00 0.00 ATOM 201 N SER 27 15.684 25.255 24.874 1.00 0.00 ATOM 202 CA SER 27 16.078 25.407 26.296 1.00 0.00 ATOM 203 CB SER 27 15.160 24.664 27.249 1.00 0.00 ATOM 204 OG SER 27 13.859 25.253 27.208 1.00 0.00 ATOM 205 O SER 27 18.104 25.374 27.557 1.00 0.00 ATOM 206 C SER 27 17.482 24.935 26.597 1.00 0.00 ATOM 207 N TYR 28 17.954 24.024 25.775 1.00 0.00 ATOM 208 CA TYR 28 19.229 23.395 26.063 1.00 0.00 ATOM 209 CB TYR 28 18.895 21.941 26.363 1.00 0.00 ATOM 210 CG TYR 28 17.959 21.776 27.556 1.00 0.00 ATOM 211 CD1 TYR 28 18.226 22.252 28.821 1.00 0.00 ATOM 212 CD2 TYR 28 16.747 21.185 27.258 1.00 0.00 ATOM 213 CE1 TYR 28 17.254 22.122 29.819 1.00 0.00 ATOM 214 CE2 TYR 28 15.785 21.055 28.243 1.00 0.00 ATOM 215 CZ TYR 28 16.041 21.531 29.522 1.00 0.00 ATOM 216 OH TYR 28 15.094 21.425 30.495 1.00 0.00 ATOM 217 O TYR 28 20.565 22.741 24.158 1.00 0.00 ATOM 218 C TYR 28 20.211 23.647 24.913 1.00 0.00 ATOM 219 N ASN 29 20.468 24.934 24.704 1.00 0.00 ATOM 220 CA ASN 29 21.497 25.419 23.773 1.00 0.00 ATOM 221 CB ASN 29 22.833 24.784 24.164 1.00 0.00 ATOM 222 CG ASN 29 23.194 24.463 25.623 1.00 0.00 ATOM 223 ND2 ASN 29 24.398 24.004 25.856 1.00 0.00 ATOM 224 OD1 ASN 29 22.447 24.589 26.583 1.00 0.00 ATOM 225 O ASN 29 21.854 25.604 21.376 1.00 0.00 ATOM 226 C ASN 29 21.156 25.134 22.279 1.00 0.00 ATOM 227 N LEU 30 19.941 24.653 22.021 1.00 0.00 ATOM 228 CA LEU 30 19.437 24.444 20.653 1.00 0.00 ATOM 229 CB LEU 30 18.866 23.015 20.549 1.00 0.00 ATOM 230 CG LEU 30 19.903 21.901 20.491 1.00 0.00 ATOM 231 CD1 LEU 30 19.144 20.595 20.485 1.00 0.00 ATOM 232 CD2 LEU 30 20.760 21.921 19.215 1.00 0.00 ATOM 233 O LEU 30 17.613 25.391 19.304 1.00 0.00 ATOM 234 C LEU 30 18.427 25.517 20.219 1.00 0.00 ATOM 235 N GLY 31 18.512 26.670 20.887 1.00 0.00 ATOM 236 CA GLY 31 17.693 27.859 20.584 1.00 0.00 ATOM 237 O GLY 31 17.072 28.878 18.472 1.00 0.00 ATOM 238 C GLY 31 17.967 28.425 19.184 1.00 0.00 ATOM 239 N CYS 32 19.218 28.308 18.770 1.00 0.00 ATOM 240 CA CYS 32 19.650 28.796 17.441 1.00 0.00 ATOM 241 CB CYS 32 21.102 28.427 17.166 1.00 0.00 ATOM 242 SG CYS 32 21.420 26.630 17.023 1.00 0.00 ATOM 243 O CYS 32 18.379 28.964 15.414 1.00 0.00 ATOM 244 C CYS 32 18.824 28.222 16.295 1.00 0.00 ATOM 245 N ILE 33 18.492 26.944 16.450 1.00 0.00 ATOM 246 CA ILE 33 17.700 26.211 15.441 1.00 0.00 ATOM 247 CB ILE 33 18.192 24.776 15.199 1.00 0.00 ATOM 248 CG1 ILE 33 19.698 24.670 14.963 1.00 0.00 ATOM 249 CG2 ILE 33 17.438 24.034 14.086 1.00 0.00 ATOM 250 CD1 ILE 33 20.132 25.415 13.711 1.00 0.00 ATOM 251 O ILE 33 15.424 25.327 15.609 1.00 0.00 ATOM 252 C ILE 33 16.212 26.247 15.820 1.00 0.00 ATOM 253 N GLY 34 15.790 27.396 16.364 1.00 0.00 ATOM 254 CA GLY 34 14.362 27.709 16.406 1.00 0.00 ATOM 255 O GLY 34 12.777 27.170 14.684 1.00 0.00 ATOM 256 C GLY 34 13.840 27.702 14.958 1.00 0.00 ATOM 257 N CYS 35 14.701 28.248 14.097 1.00 0.00 ATOM 258 CA CYS 35 14.567 28.240 12.639 1.00 0.00 ATOM 259 CB CYS 35 15.440 29.364 12.072 1.00 0.00 ATOM 260 SG CYS 35 17.217 29.202 12.483 1.00 0.00 ATOM 261 O CYS 35 15.607 26.069 12.929 1.00 0.00 ATOM 262 C CYS 35 15.086 26.877 12.156 1.00 0.00 ATOM 263 N MET 36 14.997 26.675 10.858 1.00 0.00 ATOM 264 CA MET 36 15.566 25.470 10.226 1.00 0.00 ATOM 265 CB MET 36 15.006 25.242 8.820 1.00 0.00 ATOM 266 CG MET 36 13.488 25.250 8.735 1.00 0.00 ATOM 267 SD MET 36 12.715 24.025 9.834 1.00 0.00 ATOM 268 CE MET 36 11.074 24.623 9.500 1.00 0.00 ATOM 269 O MET 36 17.670 26.652 10.276 1.00 0.00 ATOM 270 C MET 36 17.083 25.586 10.091 1.00 0.00 ATOM 271 N GLY 37 17.666 24.491 9.624 1.00 0.00 ATOM 272 CA GLY 37 19.093 24.445 9.248 1.00 0.00 ATOM 273 O GLY 37 21.161 23.667 10.158 1.00 0.00 ATOM 274 C GLY 37 19.938 23.558 10.160 1.00 0.00 ATOM 275 N ALA 38 19.312 22.606 10.836 1.00 0.00 ATOM 276 CA ALA 38 20.074 21.657 11.667 1.00 0.00 ATOM 277 CB ALA 38 19.560 21.629 13.097 1.00 0.00 ATOM 278 O ALA 38 19.996 19.223 11.752 1.00 0.00 ATOM 279 C ALA 38 20.127 20.252 11.067 1.00 0.00 ATOM 280 N GLN 39 20.246 20.228 9.747 1.00 0.00 ATOM 281 CA GLN 39 20.478 18.967 9.028 1.00 0.00 ATOM 282 CB GLN 39 20.429 19.098 7.508 1.00 0.00 ATOM 283 CG GLN 39 19.071 19.576 7.006 1.00 0.00 ATOM 284 CD GLN 39 18.897 21.061 7.276 1.00 0.00 ATOM 285 OE1 GLN 39 19.719 21.919 6.994 1.00 0.00 ATOM 286 NE2 GLN 39 17.830 21.403 7.954 1.00 0.00 ATOM 287 O GLN 39 22.096 17.262 9.325 1.00 0.00 ATOM 288 C GLN 39 21.874 18.453 9.353 1.00 0.00 ATOM 289 N ASN 40 22.794 19.389 9.530 1.00 0.00 ATOM 290 CA ASN 40 24.194 19.037 9.773 1.00 0.00 ATOM 291 CB ASN 40 25.046 20.283 9.708 1.00 0.00 ATOM 292 CG ASN 40 25.199 20.802 8.298 1.00 0.00 ATOM 293 ND2 ASN 40 25.505 22.051 8.258 1.00 0.00 ATOM 294 OD1 ASN 40 25.024 20.172 7.292 1.00 0.00 ATOM 295 O ASN 40 25.141 17.367 11.176 1.00 0.00 ATOM 296 C ASN 40 24.463 18.382 11.112 1.00 0.00 ATOM 297 N GLU 41 23.877 18.926 12.171 1.00 0.00 ATOM 298 CA GLU 41 24.269 18.483 13.508 1.00 0.00 ATOM 299 CB GLU 41 24.493 19.669 14.431 1.00 0.00 ATOM 300 CG GLU 41 25.730 20.480 14.049 1.00 0.00 ATOM 301 CD GLU 41 25.941 21.676 14.990 1.00 0.00 ATOM 302 OE1 GLU 41 25.181 21.810 15.969 1.00 0.00 ATOM 303 OE2 GLU 41 26.899 22.430 14.711 1.00 0.00 ATOM 304 O GLU 41 22.016 17.831 14.003 1.00 0.00 ATOM 305 C GLU 41 23.211 17.609 14.164 1.00 0.00 ATOM 306 N SER 42 23.740 16.612 14.852 1.00 0.00 ATOM 307 CA SER 42 22.940 15.672 15.652 1.00 0.00 ATOM 308 CB SER 42 23.586 14.282 15.774 1.00 0.00 ATOM 309 OG SER 42 24.848 14.270 16.439 1.00 0.00 ATOM 310 O SER 42 23.636 17.153 17.393 1.00 0.00 ATOM 311 C SER 42 22.846 16.290 17.029 1.00 0.00 ATOM 312 N LEU 43 21.948 15.765 17.837 1.00 0.00 ATOM 313 CA LEU 43 21.871 16.190 19.240 1.00 0.00 ATOM 314 CB LEU 43 20.768 15.456 19.982 1.00 0.00 ATOM 315 CG LEU 43 19.384 15.814 19.462 1.00 0.00 ATOM 316 CD1 LEU 43 18.402 14.896 20.151 1.00 0.00 ATOM 317 CD2 LEU 43 19.016 17.242 19.821 1.00 0.00 ATOM 318 O LEU 43 23.699 16.816 20.674 1.00 0.00 ATOM 319 C LEU 43 23.185 15.935 19.991 1.00 0.00 ATOM 320 N GLU 44 23.771 14.774 19.730 1.00 0.00 ATOM 321 CA GLU 44 25.054 14.393 20.333 1.00 0.00 ATOM 322 CB GLU 44 25.391 12.970 19.912 1.00 0.00 ATOM 323 CG GLU 44 26.599 12.445 20.688 1.00 0.00 ATOM 324 CD GLU 44 27.135 11.133 20.151 1.00 0.00 ATOM 325 OE1 GLU 44 26.532 10.630 19.186 1.00 0.00 ATOM 326 OE2 GLU 44 28.042 10.607 20.830 1.00 0.00 ATOM 327 O GLU 44 26.749 16.056 20.730 1.00 0.00 ATOM 328 C GLU 44 26.171 15.359 19.895 1.00 0.00 ATOM 329 N GLN 45 26.245 15.616 18.592 1.00 0.00 ATOM 330 CA GLN 45 27.223 16.565 18.048 1.00 0.00 ATOM 331 CB GLN 45 27.208 16.584 16.529 1.00 0.00 ATOM 332 CG GLN 45 27.713 15.278 15.930 1.00 0.00 ATOM 333 CD GLN 45 27.570 15.304 14.411 1.00 0.00 ATOM 334 OE1 GLN 45 27.088 16.247 13.777 1.00 0.00 ATOM 335 NE2 GLN 45 28.083 14.278 13.796 1.00 0.00 ATOM 336 O GLN 45 27.898 18.707 18.927 1.00 0.00 ATOM 337 C GLN 45 26.975 18.004 18.511 1.00 0.00 ATOM 338 N GLY 46 25.696 18.381 18.509 1.00 0.00 ATOM 339 CA GLY 46 25.218 19.727 18.861 1.00 0.00 ATOM 340 O GLY 46 25.926 21.200 20.641 1.00 0.00 ATOM 341 C GLY 46 25.504 20.087 20.324 1.00 0.00 ATOM 342 N ALA 47 25.367 19.094 21.205 1.00 0.00 ATOM 343 CA ALA 47 25.613 19.283 22.647 1.00 0.00 ATOM 344 CB ALA 47 25.283 17.980 23.356 1.00 0.00 ATOM 345 O ALA 47 27.352 20.538 23.686 1.00 0.00 ATOM 346 C ALA 47 27.078 19.636 22.910 1.00 0.00 ATOM 347 N ASN 48 27.972 19.016 22.134 1.00 0.00 ATOM 348 CA ASN 48 29.414 19.322 22.224 1.00 0.00 ATOM 349 CB ASN 48 30.246 18.481 21.261 1.00 0.00 ATOM 350 CG ASN 48 30.307 17.052 21.748 1.00 0.00 ATOM 351 ND2 ASN 48 30.678 16.170 20.865 1.00 0.00 ATOM 352 OD1 ASN 48 30.118 16.740 22.921 1.00 0.00 ATOM 353 O ASN 48 30.300 21.494 22.693 1.00 0.00 ATOM 354 C ASN 48 29.696 20.776 21.897 1.00 0.00 ATOM 355 N ALA 49 29.118 21.225 20.788 1.00 0.00 ATOM 356 CA ALA 49 29.269 22.609 20.348 1.00 0.00 ATOM 357 CB ALA 49 28.729 22.758 18.934 1.00 0.00 ATOM 358 O ALA 49 29.249 24.577 21.752 1.00 0.00 ATOM 359 C ALA 49 28.613 23.628 21.293 1.00 0.00 ATOM 360 N HIS 50 27.458 23.249 21.828 1.00 0.00 ATOM 361 CA HIS 50 26.759 24.175 22.704 1.00 0.00 ATOM 362 CB HIS 50 25.297 24.031 22.303 1.00 0.00 ATOM 363 CG HIS 50 24.872 24.779 21.028 1.00 0.00 ATOM 364 CD2 HIS 50 24.268 24.260 19.951 1.00 0.00 ATOM 365 ND1 HIS 50 24.984 26.095 20.834 1.00 0.00 ATOM 366 CE1 HIS 50 24.478 26.352 19.639 1.00 0.00 ATOM 367 NE2 HIS 50 24.032 25.240 19.071 1.00 0.00 ATOM 368 O HIS 50 26.831 24.882 25.012 1.00 0.00 ATOM 369 C HIS 50 27.139 24.028 24.188 1.00 0.00 ATOM 370 N GLY 51 28.014 23.067 24.486 1.00 0.00 ATOM 371 CA GLY 51 28.505 22.775 25.849 1.00 0.00 ATOM 372 O GLY 51 27.298 22.625 27.938 1.00 0.00 ATOM 373 C GLY 51 27.391 22.263 26.777 1.00 0.00 ATOM 374 N LEU 52 26.486 21.482 26.221 1.00 0.00 ATOM 375 CA LEU 52 25.419 20.895 27.020 1.00 0.00 ATOM 376 CB LEU 52 24.118 21.107 26.287 1.00 0.00 ATOM 377 CG LEU 52 22.913 20.473 26.951 1.00 0.00 ATOM 378 CD1 LEU 52 22.611 20.943 28.379 1.00 0.00 ATOM 379 CD2 LEU 52 21.859 20.954 26.012 1.00 0.00 ATOM 380 O LEU 52 25.669 18.673 26.167 1.00 0.00 ATOM 381 C LEU 52 25.657 19.401 27.153 1.00 0.00 ATOM 382 N ASN 53 25.871 18.967 28.383 1.00 0.00 ATOM 383 CA ASN 53 26.054 17.536 28.642 1.00 0.00 ATOM 384 CB ASN 53 25.981 17.363 30.144 1.00 0.00 ATOM 385 CG ASN 53 26.388 15.971 30.578 1.00 0.00 ATOM 386 ND2 ASN 53 26.616 15.862 31.840 1.00 0.00 ATOM 387 OD1 ASN 53 26.287 14.975 29.885 1.00 0.00 ATOM 388 O ASN 53 23.711 17.096 28.214 1.00 0.00 ATOM 389 C ASN 53 24.882 16.745 28.039 1.00 0.00 ATOM 390 N VAL 54 25.216 15.657 27.369 1.00 0.00 ATOM 391 CA VAL 54 24.203 14.756 26.772 1.00 0.00 ATOM 392 CB VAL 54 24.846 13.630 25.953 1.00 0.00 ATOM 393 CG1 VAL 54 23.822 12.623 25.402 1.00 0.00 ATOM 394 CG2 VAL 54 25.619 14.222 24.772 1.00 0.00 ATOM 395 O VAL 54 22.092 13.957 27.579 1.00 0.00 ATOM 396 C VAL 54 23.263 14.175 27.845 1.00 0.00 ATOM 397 N GLU 55 23.802 13.911 29.030 1.00 0.00 ATOM 398 CA GLU 55 23.020 13.326 30.135 1.00 0.00 ATOM 399 CB GLU 55 23.911 13.075 31.346 1.00 0.00 ATOM 400 CG GLU 55 23.154 12.595 32.589 1.00 0.00 ATOM 401 CD GLU 55 22.429 11.261 32.468 1.00 0.00 ATOM 402 OE1 GLU 55 22.866 10.393 31.676 1.00 0.00 ATOM 403 OE2 GLU 55 21.411 11.165 33.191 1.00 0.00 ATOM 404 O GLU 55 20.731 13.842 30.617 1.00 0.00 ATOM 405 C GLU 55 21.887 14.279 30.521 1.00 0.00 ATOM 406 N ASP 56 22.204 15.556 30.518 1.00 0.00 ATOM 407 CA ASP 56 21.198 16.585 30.790 1.00 0.00 ATOM 408 CB ASP 56 21.872 17.944 31.001 1.00 0.00 ATOM 409 CG ASP 56 22.581 18.029 32.361 1.00 0.00 ATOM 410 OD1 ASP 56 22.282 17.250 33.285 1.00 0.00 ATOM 411 OD2 ASP 56 23.378 18.962 32.498 1.00 0.00 ATOM 412 O ASP 56 18.943 16.535 30.015 1.00 0.00 ATOM 413 C ASP 56 20.117 16.660 29.704 1.00 0.00 ATOM 414 N ILE 57 20.562 16.522 28.445 1.00 0.00 ATOM 415 CA ILE 57 19.648 16.505 27.281 1.00 0.00 ATOM 416 CB ILE 57 20.443 16.494 25.962 1.00 0.00 ATOM 417 CG1 ILE 57 21.221 17.783 25.829 1.00 0.00 ATOM 418 CG2 ILE 57 19.523 16.469 24.749 1.00 0.00 ATOM 419 CD1 ILE 57 22.103 17.894 24.577 1.00 0.00 ATOM 420 O ILE 57 17.490 15.429 27.230 1.00 0.00 ATOM 421 C ILE 57 18.698 15.302 27.362 1.00 0.00 ATOM 422 N LEU 58 19.309 14.124 27.517 1.00 0.00 ATOM 423 CA LEU 58 18.567 12.860 27.590 1.00 0.00 ATOM 424 CB LEU 58 19.580 11.712 27.633 1.00 0.00 ATOM 425 CG LEU 58 19.009 10.340 27.990 1.00 0.00 ATOM 426 CD1 LEU 58 17.970 9.902 26.965 1.00 0.00 ATOM 427 CD2 LEU 58 20.150 9.321 28.030 1.00 0.00 ATOM 428 O LEU 58 16.384 12.552 28.514 1.00 0.00 ATOM 429 C LEU 58 17.555 12.843 28.740 1.00 0.00 ATOM 430 N ARG 59 17.975 13.374 29.898 1.00 0.00 ATOM 431 CA ARG 59 17.092 13.448 31.068 1.00 0.00 ATOM 432 CB ARG 59 17.895 13.993 32.248 1.00 0.00 ATOM 433 CG ARG 59 17.037 14.143 33.505 1.00 0.00 ATOM 434 CD ARG 59 17.725 15.080 34.484 1.00 0.00 ATOM 435 NE ARG 59 17.745 16.453 33.952 1.00 0.00 ATOM 436 CZ ARG 59 18.589 17.414 34.364 1.00 0.00 ATOM 437 NH1 ARG 59 19.514 17.180 35.290 1.00 0.00 ATOM 438 NH2 ARG 59 18.479 18.627 33.865 1.00 0.00 ATOM 439 O ARG 59 14.745 13.965 31.025 1.00 0.00 ATOM 440 C ARG 59 15.887 14.357 30.778 1.00 0.00 ATOM 441 N ASP 60 16.153 15.519 30.184 1.00 0.00 ATOM 442 CA ASP 60 15.078 16.484 29.872 1.00 0.00 ATOM 443 CB ASP 60 15.626 17.808 29.362 1.00 0.00 ATOM 444 CG ASP 60 16.375 18.536 30.456 1.00 0.00 ATOM 445 OD1 ASP 60 15.802 18.695 31.572 1.00 0.00 ATOM 446 OD2 ASP 60 17.536 18.870 30.174 1.00 0.00 ATOM 447 O ASP 60 12.942 15.919 29.006 1.00 0.00 ATOM 448 C ASP 60 14.148 15.933 28.812 1.00 0.00 ATOM 449 N LEU 61 14.739 15.336 27.781 1.00 0.00 ATOM 450 CA LEU 61 13.942 14.763 26.689 1.00 0.00 ATOM 451 CB LEU 61 14.809 14.197 25.576 1.00 0.00 ATOM 452 CG LEU 61 13.989 13.635 24.414 1.00 0.00 ATOM 453 CD1 LEU 61 13.075 14.658 23.739 1.00 0.00 ATOM 454 CD2 LEU 61 14.914 13.113 23.340 1.00 0.00 ATOM 455 O LEU 61 11.881 13.560 26.795 1.00 0.00 ATOM 456 C LEU 61 13.037 13.648 27.185 1.00 0.00 ATOM 457 N ASN 62 13.614 12.787 28.013 1.00 0.00 ATOM 458 CA ASN 62 12.856 11.667 28.554 1.00 0.00 ATOM 459 CB ASN 62 13.719 10.763 29.385 1.00 0.00 ATOM 460 CG ASN 62 12.932 9.539 29.824 1.00 0.00 ATOM 461 ND2 ASN 62 12.942 9.356 31.111 1.00 0.00 ATOM 462 OD1 ASN 62 12.366 8.765 29.059 1.00 0.00 ATOM 463 O ASN 62 10.657 11.700 29.292 1.00 0.00 ATOM 464 C ASN 62 11.740 12.181 29.441 1.00 0.00 ATOM 465 N ALA 63 12.010 13.156 30.317 1.00 0.00 ATOM 466 CA ALA 63 10.949 13.772 31.128 1.00 0.00 ATOM 467 CB ALA 63 11.581 14.865 31.983 1.00 0.00 ATOM 468 O ALA 63 8.692 14.352 30.538 1.00 0.00 ATOM 469 C ALA 63 9.876 14.413 30.236 1.00 0.00 ATOM 470 N LEU 64 10.334 14.997 29.120 1.00 0.00 ATOM 471 CA LEU 64 9.456 15.625 28.134 1.00 0.00 ATOM 472 CB LEU 64 10.285 16.200 26.993 1.00 0.00 ATOM 473 CG LEU 64 9.417 16.906 25.945 1.00 0.00 ATOM 474 CD1 LEU 64 8.618 18.081 26.525 1.00 0.00 ATOM 475 CD2 LEU 64 10.325 17.194 24.757 1.00 0.00 ATOM 476 O LEU 64 7.294 14.969 27.382 1.00 0.00 ATOM 477 C LEU 64 8.453 14.621 27.570 1.00 0.00 ATOM 478 N ALA 65 8.978 13.463 27.214 1.00 0.00 ATOM 479 CA ALA 65 8.173 12.359 26.680 1.00 0.00 ATOM 480 CB ALA 65 8.829 11.948 25.362 1.00 0.00 ATOM 481 O ALA 65 8.306 11.416 28.885 1.00 0.00 ATOM 482 C ALA 65 8.073 11.199 27.693 1.00 0.00 TER END