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 5 Mon Jul 7 11:25:21 2008 MODEL 5 PARENT N/A ATOM 1 N MET 1 14.309 10.334 26.864 1.00 0.00 ATOM 2 CA MET 1 14.786 8.933 26.854 1.00 0.00 ATOM 3 CB MET 1 13.668 7.924 26.742 1.00 0.00 ATOM 4 CG MET 1 14.263 6.541 26.422 1.00 0.00 ATOM 5 SD MET 1 15.227 5.908 27.784 1.00 0.00 ATOM 6 CE MET 1 14.142 6.203 29.193 1.00 0.00 ATOM 7 O MET 1 15.052 9.396 24.501 1.00 0.00 ATOM 8 C MET 1 15.485 8.806 25.495 1.00 0.00 ATOM 9 N THR 2 16.626 8.107 25.459 1.00 0.00 ATOM 10 CA THR 2 17.347 7.947 24.204 1.00 0.00 ATOM 11 CB THR 2 18.640 7.235 24.361 1.00 0.00 ATOM 12 CG2 THR 2 19.518 7.995 25.378 1.00 0.00 ATOM 13 OG1 THR 2 18.398 5.913 24.839 1.00 0.00 ATOM 14 O THR 2 16.689 7.328 21.981 1.00 0.00 ATOM 15 C THR 2 16.510 7.174 23.190 1.00 0.00 ATOM 16 N GLN 3 15.598 6.342 23.684 1.00 0.00 ATOM 17 CA GLN 3 14.726 5.540 22.799 1.00 0.00 ATOM 18 CB GLN 3 14.351 4.166 23.527 1.00 0.00 ATOM 19 CG GLN 3 13.206 3.376 22.796 1.00 0.00 ATOM 20 CD GLN 3 11.817 3.811 23.266 1.00 0.00 ATOM 21 OE1 GLN 3 11.538 3.824 24.467 1.00 0.00 ATOM 22 NE2 GLN 3 10.949 4.187 22.321 1.00 0.00 ATOM 23 O GLN 3 13.544 6.310 20.903 1.00 0.00 ATOM 24 C GLN 3 13.802 6.453 22.099 1.00 0.00 ATOM 25 N LYS 4 13.276 7.424 22.839 1.00 0.00 ATOM 26 CA LYS 4 12.350 8.394 22.265 1.00 0.00 ATOM 27 CB LYS 4 11.703 9.222 23.373 1.00 0.00 ATOM 28 CG LYS 4 10.812 8.393 24.313 1.00 0.00 ATOM 29 CD LYS 4 9.943 9.278 25.327 1.00 0.00 ATOM 30 CE LYS 4 8.952 8.324 26.115 1.00 0.00 ATOM 31 NZ LYS 4 8.421 8.936 27.422 1.00 0.00 ATOM 32 O LYS 4 12.617 9.673 20.253 1.00 0.00 ATOM 33 C LYS 4 13.099 9.345 21.338 1.00 0.00 ATOM 34 N PHE 5 14.277 9.787 21.766 1.00 0.00 ATOM 35 CA PHE 5 15.073 10.695 20.964 1.00 0.00 ATOM 36 CB PHE 5 15.169 12.074 21.609 1.00 0.00 ATOM 37 CG PHE 5 13.845 12.756 21.719 1.00 0.00 ATOM 38 CD1 PHE 5 13.099 12.678 22.884 1.00 0.00 ATOM 39 CD2 PHE 5 13.309 13.410 20.626 1.00 0.00 ATOM 40 CE1 PHE 5 11.842 13.301 22.967 1.00 0.00 ATOM 41 CE2 PHE 5 12.062 14.019 20.697 1.00 0.00 ATOM 42 CZ PHE 5 11.332 13.964 21.867 1.00 0.00 ATOM 43 O PHE 5 17.186 9.885 21.722 1.00 0.00 ATOM 44 C PHE 5 16.451 10.120 20.762 1.00 0.00 ATOM 45 N THR 6 16.819 9.885 19.500 1.00 0.00 ATOM 46 CA THR 6 18.113 9.339 19.191 1.00 0.00 ATOM 47 CB THR 6 17.985 8.401 17.967 1.00 0.00 ATOM 48 CG2 THR 6 19.319 7.916 17.450 1.00 0.00 ATOM 49 OG1 THR 6 17.143 7.316 18.340 1.00 0.00 ATOM 50 O THR 6 18.888 11.317 18.073 1.00 0.00 ATOM 51 C THR 6 19.089 10.490 18.964 1.00 0.00 ATOM 52 N LYS 7 20.145 10.541 19.770 1.00 0.00 ATOM 53 CA LYS 7 21.153 11.604 19.643 1.00 0.00 ATOM 54 CB LYS 7 22.031 11.627 20.925 1.00 0.00 ATOM 55 CG LYS 7 22.756 10.319 21.195 1.00 0.00 ATOM 56 CD LYS 7 23.684 10.439 22.403 1.00 0.00 ATOM 57 CE LYS 7 24.393 9.124 22.689 1.00 0.00 ATOM 58 NZ LYS 7 25.252 9.192 23.907 1.00 0.00 ATOM 59 O LYS 7 22.742 12.462 18.046 1.00 0.00 ATOM 60 C LYS 7 22.054 11.503 18.396 1.00 0.00 ATOM 61 N ASP 8 22.040 10.348 17.740 1.00 0.00 ATOM 62 CA ASP 8 22.853 10.148 16.545 1.00 0.00 ATOM 63 CB ASP 8 23.340 8.709 16.634 1.00 0.00 ATOM 64 CG ASP 8 24.126 8.428 17.885 1.00 0.00 ATOM 65 OD1 ASP 8 24.804 9.363 18.390 1.00 0.00 ATOM 66 OD2 ASP 8 24.129 7.297 18.429 1.00 0.00 ATOM 67 O ASP 8 22.967 10.252 14.151 1.00 0.00 ATOM 68 C ASP 8 22.286 10.441 15.160 1.00 0.00 ATOM 69 N MET 9 21.041 10.903 15.113 1.00 0.00 ATOM 70 CA MET 9 20.383 11.227 13.824 1.00 0.00 ATOM 71 CB MET 9 18.863 11.007 13.925 1.00 0.00 ATOM 72 CG MET 9 18.155 12.011 14.868 1.00 0.00 ATOM 73 SD MET 9 16.170 11.878 14.966 1.00 0.00 ATOM 74 CE MET 9 16.054 10.468 16.317 1.00 0.00 ATOM 75 O MET 9 21.000 13.478 14.510 1.00 0.00 ATOM 76 C MET 9 20.483 12.782 13.635 1.00 0.00 ATOM 77 N THR 10 19.989 13.289 12.510 1.00 0.00 ATOM 78 CA THR 10 20.033 14.722 12.242 1.00 0.00 ATOM 79 CB THR 10 19.836 15.054 10.757 1.00 0.00 ATOM 80 CG2 THR 10 20.678 14.204 9.850 1.00 0.00 ATOM 81 OG1 THR 10 18.451 14.992 10.400 1.00 0.00 ATOM 82 O THR 10 17.933 14.865 13.395 1.00 0.00 ATOM 83 C THR 10 19.029 15.386 13.180 1.00 0.00 ATOM 84 N PHE 11 19.404 16.534 13.735 1.00 0.00 ATOM 85 CA PHE 11 18.521 17.260 14.648 1.00 0.00 ATOM 86 CB PHE 11 19.281 18.467 15.218 1.00 0.00 ATOM 87 CG PHE 11 18.797 18.874 16.592 1.00 0.00 ATOM 88 CD1 PHE 11 17.550 19.437 16.750 1.00 0.00 ATOM 89 CD2 PHE 11 19.564 18.665 17.735 1.00 0.00 ATOM 90 CE1 PHE 11 17.110 19.718 18.020 1.00 0.00 ATOM 91 CE2 PHE 11 19.133 18.960 18.972 1.00 0.00 ATOM 92 CZ PHE 11 17.884 19.532 19.121 1.00 0.00 ATOM 93 O PHE 11 16.155 17.647 14.593 1.00 0.00 ATOM 94 C PHE 11 17.230 17.741 13.999 1.00 0.00 ATOM 95 N ALA 12 17.336 18.256 12.778 1.00 0.00 ATOM 96 CA ALA 12 16.166 18.745 12.059 1.00 0.00 ATOM 97 CB ALA 12 16.553 19.340 10.731 1.00 0.00 ATOM 98 O ALA 12 13.998 17.742 11.974 1.00 0.00 ATOM 99 C ALA 12 15.215 17.590 11.841 1.00 0.00 ATOM 100 N GLN 13 15.745 16.409 11.510 1.00 0.00 ATOM 101 CA GLN 13 14.905 15.218 11.361 1.00 0.00 ATOM 102 CB GLN 13 15.703 14.032 10.861 1.00 0.00 ATOM 103 CG GLN 13 14.828 12.852 10.455 1.00 0.00 ATOM 104 CD GLN 13 15.623 11.616 10.065 1.00 0.00 ATOM 105 OE1 GLN 13 15.069 10.656 9.529 1.00 0.00 ATOM 106 NE2 GLN 13 16.921 11.630 10.341 1.00 0.00 ATOM 107 O GLN 13 13.119 14.512 12.719 1.00 0.00 ATOM 108 C GLN 13 14.280 14.842 12.669 1.00 0.00 ATOM 109 N ALA 14 15.035 14.926 13.704 1.00 0.00 ATOM 110 CA ALA 14 14.437 14.683 14.981 1.00 0.00 ATOM 111 CB ALA 14 15.449 14.867 16.100 1.00 0.00 ATOM 112 O ALA 14 12.194 15.218 15.659 1.00 0.00 ATOM 113 C ALA 14 13.252 15.631 15.179 1.00 0.00 ATOM 114 N LEU 15 13.433 16.897 14.817 1.00 0.00 ATOM 115 CA LEU 15 12.372 17.886 14.968 1.00 0.00 ATOM 116 CB LEU 15 12.962 19.287 14.714 1.00 0.00 ATOM 117 CG LEU 15 11.979 20.456 14.868 1.00 0.00 ATOM 118 CD1 LEU 15 11.460 20.500 16.304 1.00 0.00 ATOM 119 CD2 LEU 15 12.662 21.767 14.510 1.00 0.00 ATOM 120 O LEU 15 10.082 17.797 14.449 1.00 0.00 ATOM 121 C LEU 15 11.224 17.593 14.060 1.00 0.00 ATOM 122 N GLN 16 11.538 17.221 12.861 1.00 0.00 ATOM 123 CA GLN 16 10.451 16.953 11.965 1.00 0.00 ATOM 124 CB GLN 16 10.947 16.483 10.614 1.00 0.00 ATOM 125 CG GLN 16 11.353 17.584 9.683 1.00 0.00 ATOM 126 CD GLN 16 11.860 17.016 8.384 1.00 0.00 ATOM 127 OE1 GLN 16 12.933 16.415 8.335 1.00 0.00 ATOM 128 NE2 GLN 16 11.079 17.179 7.325 1.00 0.00 ATOM 129 O GLN 16 8.379 15.823 12.400 1.00 0.00 ATOM 130 C GLN 16 9.604 15.820 12.534 1.00 0.00 ATOM 131 N THR 17 10.257 14.852 13.171 1.00 0.00 ATOM 132 CA THR 17 9.548 13.725 13.757 1.00 0.00 ATOM 133 CB THR 17 10.270 12.494 14.054 1.00 0.00 ATOM 134 CG2 THR 17 10.988 11.985 12.817 1.00 0.00 ATOM 135 OG1 THR 17 11.227 12.755 15.090 1.00 0.00 ATOM 136 O THR 17 7.652 13.688 15.254 1.00 0.00 ATOM 137 C THR 17 8.771 14.148 15.028 1.00 0.00 ATOM 138 N HIS 18 9.371 15.017 15.837 1.00 0.00 ATOM 139 CA HIS 18 8.725 15.483 17.058 1.00 0.00 ATOM 140 CB HIS 18 9.546 14.917 18.224 1.00 0.00 ATOM 141 CG HIS 18 9.655 13.425 18.233 1.00 0.00 ATOM 142 CD2 HIS 18 8.772 12.462 18.596 1.00 0.00 ATOM 143 ND1 HIS 18 10.800 12.766 17.844 1.00 0.00 ATOM 144 CE1 HIS 18 10.620 11.463 17.967 1.00 0.00 ATOM 145 NE2 HIS 18 9.401 11.252 18.429 1.00 0.00 ATOM 146 O HIS 18 9.646 17.578 17.777 1.00 0.00 ATOM 147 C HIS 18 8.744 17.018 17.140 1.00 0.00 ATOM 148 N PRO 19 7.763 17.707 16.509 1.00 0.00 ATOM 149 CA PRO 19 7.770 19.186 16.518 1.00 0.00 ATOM 150 CB PRO 19 6.507 19.571 15.725 1.00 0.00 ATOM 151 CG PRO 19 6.155 18.372 14.901 1.00 0.00 ATOM 152 CD PRO 19 6.738 17.157 15.597 1.00 0.00 ATOM 153 O PRO 19 8.329 20.810 18.188 1.00 0.00 ATOM 154 C PRO 19 7.724 19.773 17.940 1.00 0.00 ATOM 155 N GLY 20 7.048 19.109 18.865 1.00 0.00 ATOM 156 CA GLY 20 6.925 19.563 20.253 1.00 0.00 ATOM 157 O GLY 20 8.324 20.286 22.063 1.00 0.00 ATOM 158 C GLY 20 8.219 19.580 21.059 1.00 0.00 ATOM 159 N VAL 21 9.204 18.804 20.618 1.00 0.00 ATOM 160 CA VAL 21 10.505 18.741 21.313 1.00 0.00 ATOM 161 CB VAL 21 10.825 17.050 20.759 1.00 0.00 ATOM 162 CG1 VAL 21 9.528 16.277 20.438 1.00 0.00 ATOM 163 CG2 VAL 21 11.722 17.195 19.555 1.00 0.00 ATOM 164 O VAL 21 12.463 20.134 21.669 1.00 0.00 ATOM 165 C VAL 21 11.451 19.946 20.992 1.00 0.00 ATOM 166 N ALA 22 11.109 20.730 19.974 1.00 0.00 ATOM 167 CA ALA 22 11.924 21.878 19.598 1.00 0.00 ATOM 168 CB ALA 22 11.359 22.539 18.324 1.00 0.00 ATOM 169 O ALA 22 13.057 23.388 21.091 1.00 0.00 ATOM 170 C ALA 22 11.987 22.866 20.769 1.00 0.00 ATOM 171 N GLY 23 10.844 23.118 21.401 1.00 0.00 ATOM 172 CA GLY 23 10.791 24.039 22.530 1.00 0.00 ATOM 173 O GLY 23 12.384 24.329 24.323 1.00 0.00 ATOM 174 C GLY 23 11.654 23.563 23.689 1.00 0.00 ATOM 175 N VAL 24 11.599 22.270 23.974 1.00 0.00 ATOM 176 CA VAL 24 12.409 21.695 25.028 1.00 0.00 ATOM 177 CB VAL 24 11.824 20.021 24.812 1.00 0.00 ATOM 178 CG1 VAL 24 10.358 19.917 24.340 1.00 0.00 ATOM 179 CG2 VAL 24 12.766 19.485 23.749 1.00 0.00 ATOM 180 O VAL 24 14.726 22.075 25.520 1.00 0.00 ATOM 181 C VAL 24 13.886 21.782 24.667 1.00 0.00 ATOM 182 N LEU 25 14.204 21.528 23.401 1.00 0.00 ATOM 183 CA LEU 25 15.549 21.586 22.967 1.00 0.00 ATOM 184 CB LEU 25 15.665 21.038 21.540 1.00 0.00 ATOM 185 CG LEU 25 15.239 19.570 21.403 1.00 0.00 ATOM 186 CD1 LEU 25 15.311 19.149 19.942 1.00 0.00 ATOM 187 CD2 LEU 25 16.149 18.683 22.267 1.00 0.00 ATOM 188 O LEU 25 17.246 23.184 23.520 1.00 0.00 ATOM 189 C LEU 25 16.104 22.994 23.098 1.00 0.00 ATOM 190 N ARG 26 15.295 23.985 22.736 1.00 0.00 ATOM 191 CA ARG 26 15.721 25.377 22.821 1.00 0.00 ATOM 192 CB ARG 26 14.724 26.277 22.117 1.00 0.00 ATOM 193 CG ARG 26 15.050 27.745 22.115 1.00 0.00 ATOM 194 CD ARG 26 14.251 28.553 21.107 1.00 0.00 ATOM 195 NE ARG 26 14.693 28.147 19.794 1.00 0.00 ATOM 196 CZ ARG 26 15.620 28.744 19.040 1.00 0.00 ATOM 197 NH1 ARG 26 16.197 29.890 19.373 1.00 0.00 ATOM 198 NH2 ARG 26 15.956 28.166 17.909 1.00 0.00 ATOM 199 O ARG 26 16.936 26.422 24.611 1.00 0.00 ATOM 200 C ARG 26 15.921 25.817 24.273 1.00 0.00 ATOM 201 N SER 27 14.978 25.523 25.131 1.00 0.00 ATOM 202 CA SER 27 15.041 25.937 26.533 1.00 0.00 ATOM 203 CB SER 27 13.630 25.664 27.197 1.00 0.00 ATOM 204 OG SER 27 13.400 24.276 27.339 1.00 0.00 ATOM 205 O SER 27 16.568 25.835 28.380 1.00 0.00 ATOM 206 C SER 27 16.154 25.294 27.354 1.00 0.00 ATOM 207 N TYR 28 16.635 24.141 26.903 1.00 0.00 ATOM 208 CA TYR 28 17.705 23.435 27.609 1.00 0.00 ATOM 209 CB TYR 28 17.219 22.127 28.137 1.00 0.00 ATOM 210 CG TYR 28 16.077 22.336 29.071 1.00 0.00 ATOM 211 CD1 TYR 28 16.262 23.033 30.245 1.00 0.00 ATOM 212 CD2 TYR 28 14.808 21.856 28.783 1.00 0.00 ATOM 213 CE1 TYR 28 15.237 23.246 31.122 1.00 0.00 ATOM 214 CE2 TYR 28 13.765 22.042 29.662 1.00 0.00 ATOM 215 CZ TYR 28 13.991 22.753 30.848 1.00 0.00 ATOM 216 OH TYR 28 12.982 22.998 31.754 1.00 0.00 ATOM 217 O TYR 28 19.938 22.631 27.135 1.00 0.00 ATOM 218 C TYR 28 19.139 23.561 27.025 1.00 0.00 ATOM 219 N ASN 29 19.442 24.704 26.416 1.00 0.00 ATOM 220 CA ASN 29 20.762 24.924 25.837 1.00 0.00 ATOM 221 CB ASN 29 21.877 24.643 26.864 1.00 0.00 ATOM 222 CG ASN 29 23.138 25.420 26.506 1.00 0.00 ATOM 223 ND2 ASN 29 24.291 24.744 26.610 1.00 0.00 ATOM 224 OD1 ASN 29 23.095 26.600 26.138 1.00 0.00 ATOM 225 O ASN 29 22.018 24.505 23.829 1.00 0.00 ATOM 226 C ASN 29 20.905 24.558 24.355 1.00 0.00 ATOM 227 N LEU 30 19.782 24.301 23.693 1.00 0.00 ATOM 228 CA LEU 30 19.803 23.936 22.281 1.00 0.00 ATOM 229 CB LEU 30 19.784 22.433 22.085 1.00 0.00 ATOM 230 CG LEU 30 21.252 21.949 22.261 1.00 0.00 ATOM 231 CD1 LEU 30 21.419 20.600 22.688 1.00 0.00 ATOM 232 CD2 LEU 30 22.061 22.223 20.959 1.00 0.00 ATOM 233 O LEU 30 18.660 24.732 20.329 1.00 0.00 ATOM 234 C LEU 30 19.174 25.015 21.415 1.00 0.00 ATOM 235 N GLY 31 19.254 26.261 21.871 1.00 0.00 ATOM 236 CA GLY 31 18.490 27.330 21.232 1.00 0.00 ATOM 237 O GLY 31 18.289 28.409 19.093 1.00 0.00 ATOM 238 C GLY 31 19.013 27.748 19.849 1.00 0.00 ATOM 239 N CYS 32 20.271 27.456 19.526 1.00 0.00 ATOM 240 CA CYS 32 20.778 27.732 18.186 1.00 0.00 ATOM 241 CB CYS 32 22.201 27.151 18.081 1.00 0.00 ATOM 242 SG CYS 32 23.082 27.653 16.578 1.00 0.00 ATOM 243 O CYS 32 19.526 25.917 17.240 1.00 0.00 ATOM 244 C CYS 32 19.881 27.091 17.132 1.00 0.00 ATOM 245 N ILE 33 19.516 27.864 16.114 1.00 0.00 ATOM 246 CA ILE 33 18.657 27.355 15.041 1.00 0.00 ATOM 247 CB ILE 33 18.241 28.498 14.079 1.00 0.00 ATOM 248 CG1 ILE 33 17.212 29.398 14.774 1.00 0.00 ATOM 249 CG2 ILE 33 17.676 27.924 12.777 1.00 0.00 ATOM 250 CD1 ILE 33 16.915 30.704 14.046 1.00 0.00 ATOM 251 O ILE 33 18.870 25.264 13.883 1.00 0.00 ATOM 252 C ILE 33 19.434 26.284 14.284 1.00 0.00 ATOM 253 N GLY 34 20.729 26.514 14.090 1.00 0.00 ATOM 254 CA GLY 34 21.559 25.562 13.387 1.00 0.00 ATOM 255 O GLY 34 21.490 23.174 13.546 1.00 0.00 ATOM 256 C GLY 34 21.571 24.246 14.146 1.00 0.00 ATOM 257 N CYS 35 21.670 24.326 15.469 1.00 0.00 ATOM 258 CA CYS 35 21.688 23.128 16.299 1.00 0.00 ATOM 259 CB CYS 35 21.130 23.409 17.783 1.00 0.00 ATOM 260 SG CYS 35 21.519 25.051 18.515 1.00 0.00 ATOM 261 O CYS 35 20.337 21.145 16.277 1.00 0.00 ATOM 262 C CYS 35 20.362 22.376 16.248 1.00 0.00 ATOM 263 N MET 36 19.262 23.117 16.169 1.00 0.00 ATOM 264 CA MET 36 17.945 22.504 16.111 1.00 0.00 ATOM 265 CB MET 36 16.837 23.494 16.210 1.00 0.00 ATOM 266 CG MET 36 16.797 24.141 17.591 1.00 0.00 ATOM 267 SD MET 36 15.457 25.296 17.890 1.00 0.00 ATOM 268 CE MET 36 14.060 24.333 17.697 1.00 0.00 ATOM 269 O MET 36 17.370 20.516 14.876 1.00 0.00 ATOM 270 C MET 36 17.775 21.677 14.822 1.00 0.00 ATOM 271 N GLY 37 18.087 22.280 13.679 1.00 0.00 ATOM 272 CA GLY 37 17.965 21.586 12.402 1.00 0.00 ATOM 273 O GLY 37 20.260 21.796 11.795 1.00 0.00 ATOM 274 C GLY 37 19.271 21.066 11.868 1.00 0.00 ATOM 275 N ALA 38 19.285 19.793 11.485 1.00 0.00 ATOM 276 CA ALA 38 20.493 19.179 10.948 1.00 0.00 ATOM 277 CB ALA 38 20.280 17.704 10.737 1.00 0.00 ATOM 278 O ALA 38 20.067 19.655 8.655 1.00 0.00 ATOM 279 C ALA 38 20.840 19.772 9.607 1.00 0.00 ATOM 280 N GLN 39 22.050 20.311 9.490 1.00 0.00 ATOM 281 CA GLN 39 22.539 20.799 8.206 1.00 0.00 ATOM 282 CB GLN 39 22.602 22.433 8.581 1.00 0.00 ATOM 283 CG GLN 39 22.681 23.361 7.368 1.00 0.00 ATOM 284 CD GLN 39 24.024 23.336 6.650 1.00 0.00 ATOM 285 OE1 GLN 39 25.022 23.868 7.152 1.00 0.00 ATOM 286 NE2 GLN 39 24.059 22.711 5.471 1.00 0.00 ATOM 287 O GLN 39 23.861 20.208 6.327 1.00 0.00 ATOM 288 C GLN 39 23.300 19.806 7.333 1.00 0.00 ATOM 289 N ASN 40 23.710 19.002 9.212 1.00 0.00 ATOM 290 CA ASN 40 25.030 18.403 9.384 1.00 0.00 ATOM 291 CB ASN 40 26.071 19.497 8.681 1.00 0.00 ATOM 292 CG ASN 40 26.082 19.538 7.165 1.00 0.00 ATOM 293 ND2 ASN 40 26.510 20.672 6.613 1.00 0.00 ATOM 294 OD1 ASN 40 25.735 18.562 6.495 1.00 0.00 ATOM 295 O ASN 40 26.257 17.155 11.035 1.00 0.00 ATOM 296 C ASN 40 25.307 17.920 10.809 1.00 0.00 ATOM 297 N GLU 41 24.540 18.402 11.781 1.00 0.00 ATOM 298 CA GLU 41 24.876 18.162 13.178 1.00 0.00 ATOM 299 CB GLU 41 25.253 19.408 13.935 1.00 0.00 ATOM 300 CG GLU 41 26.369 20.230 13.317 1.00 0.00 ATOM 301 CD GLU 41 26.448 21.630 13.904 1.00 0.00 ATOM 302 OE1 GLU 41 27.368 22.382 13.520 1.00 0.00 ATOM 303 OE2 GLU 41 25.587 21.980 14.741 1.00 0.00 ATOM 304 O GLU 41 22.587 17.804 13.799 1.00 0.00 ATOM 305 C GLU 41 23.758 17.443 13.924 1.00 0.00 ATOM 306 N SER 42 24.119 16.426 14.700 1.00 0.00 ATOM 307 CA SER 42 23.128 15.663 15.467 1.00 0.00 ATOM 308 CB SER 42 23.617 14.230 15.753 1.00 0.00 ATOM 309 OG SER 42 24.836 14.258 16.501 1.00 0.00 ATOM 310 O SER 42 23.771 17.293 17.109 1.00 0.00 ATOM 311 C SER 42 23.037 16.336 16.828 1.00 0.00 ATOM 312 N LEU 43 22.126 15.862 17.674 1.00 0.00 ATOM 313 CA LEU 43 22.034 16.386 19.048 1.00 0.00 ATOM 314 CB LEU 43 20.956 15.222 19.712 1.00 0.00 ATOM 315 CG LEU 43 20.186 15.436 21.013 1.00 0.00 ATOM 316 CD1 LEU 43 18.874 16.141 20.738 1.00 0.00 ATOM 317 CD2 LEU 43 19.929 14.118 21.761 1.00 0.00 ATOM 318 O LEU 43 23.807 16.898 20.575 1.00 0.00 ATOM 319 C LEU 43 23.341 16.095 19.764 1.00 0.00 ATOM 320 N GLU 44 23.938 14.945 19.465 1.00 0.00 ATOM 321 CA GLU 44 25.198 14.563 20.089 1.00 0.00 ATOM 322 CB GLU 44 25.590 13.153 19.722 1.00 0.00 ATOM 323 CG GLU 44 26.793 12.620 20.467 1.00 0.00 ATOM 324 CD GLU 44 27.044 11.156 20.174 1.00 0.00 ATOM 325 OE1 GLU 44 26.087 10.353 20.251 1.00 0.00 ATOM 326 OE2 GLU 44 28.197 10.812 19.863 1.00 0.00 ATOM 327 O GLU 44 27.017 16.041 20.577 1.00 0.00 ATOM 328 C GLU 44 26.304 15.562 19.713 1.00 0.00 ATOM 329 N GLN 45 26.422 15.877 18.422 1.00 0.00 ATOM 330 CA GLN 45 27.391 16.875 17.935 1.00 0.00 ATOM 331 CB GLN 45 27.409 16.891 16.403 1.00 0.00 ATOM 332 CG GLN 45 28.002 15.628 15.766 1.00 0.00 ATOM 333 CD GLN 45 27.557 15.399 14.318 1.00 0.00 ATOM 334 OE1 GLN 45 26.490 15.835 13.893 1.00 0.00 ATOM 335 NE2 GLN 45 28.377 14.685 13.567 1.00 0.00 ATOM 336 O GLN 45 27.953 19.038 18.806 1.00 0.00 ATOM 337 C GLN 45 27.061 18.282 18.419 1.00 0.00 ATOM 338 N GLY 46 25.779 18.633 18.398 1.00 0.00 ATOM 339 CA GLY 46 25.352 19.951 18.840 1.00 0.00 ATOM 340 O GLY 46 25.870 21.326 20.742 1.00 0.00 ATOM 341 C GLY 46 25.555 20.207 20.336 1.00 0.00 ATOM 342 N ALA 47 25.375 19.170 21.147 1.00 0.00 ATOM 343 CA ALA 47 25.545 19.301 22.590 1.00 0.00 ATOM 344 CB ALA 47 25.083 18.022 23.310 1.00 0.00 ATOM 345 O ALA 47 27.267 20.495 23.770 1.00 0.00 ATOM 346 C ALA 47 26.993 19.646 22.910 1.00 0.00 ATOM 347 N ASN 48 27.952 18.992 22.208 1.00 0.00 ATOM 348 CA ASN 48 29.373 19.294 22.376 1.00 0.00 ATOM 349 CB ASN 48 30.250 18.343 21.604 1.00 0.00 ATOM 350 CG ASN 48 30.118 16.935 22.083 1.00 0.00 ATOM 351 ND2 ASN 48 30.492 15.984 21.243 1.00 0.00 ATOM 352 OD1 ASN 48 29.704 16.697 23.210 1.00 0.00 ATOM 353 O ASN 48 30.410 21.439 22.660 1.00 0.00 ATOM 354 C ASN 48 29.689 20.726 21.959 1.00 0.00 ATOM 355 N ALA 49 29.150 21.146 20.820 1.00 0.00 ATOM 356 CA ALA 49 29.382 22.495 20.328 1.00 0.00 ATOM 357 CB ALA 49 28.841 22.659 18.897 1.00 0.00 ATOM 358 O ALA 49 29.260 24.657 21.355 1.00 0.00 ATOM 359 C ALA 49 28.745 23.545 21.224 1.00 0.00 ATOM 360 N HIS 50 27.621 23.194 21.841 1.00 0.00 ATOM 361 CA HIS 50 26.923 24.121 22.724 1.00 0.00 ATOM 362 CB HIS 50 25.440 24.201 22.352 1.00 0.00 ATOM 363 CG HIS 50 25.183 24.758 20.988 1.00 0.00 ATOM 364 CD2 HIS 50 25.124 26.037 20.545 1.00 0.00 ATOM 365 ND1 HIS 50 25.012 23.958 19.879 1.00 0.00 ATOM 366 CE1 HIS 50 24.836 24.721 18.810 1.00 0.00 ATOM 367 NE2 HIS 50 24.906 25.988 19.187 1.00 0.00 ATOM 368 O HIS 50 26.400 24.592 25.030 1.00 0.00 ATOM 369 C HIS 50 27.077 23.952 24.212 1.00 0.00 ATOM 370 N GLY 51 27.979 23.069 24.564 1.00 0.00 ATOM 371 CA GLY 51 28.235 22.853 25.955 1.00 0.00 ATOM 372 O GLY 51 27.186 22.564 28.094 1.00 0.00 ATOM 373 C GLY 51 27.167 22.298 26.891 1.00 0.00 ATOM 374 N LEU 52 26.236 21.525 26.339 1.00 0.00 ATOM 375 CA LEU 52 25.175 20.942 27.139 1.00 0.00 ATOM 376 CB LEU 52 23.786 21.199 26.596 1.00 0.00 ATOM 377 CG LEU 52 22.617 20.696 27.440 1.00 0.00 ATOM 378 CD1 LEU 52 22.705 21.206 28.909 1.00 0.00 ATOM 379 CD2 LEU 52 21.287 21.062 26.863 1.00 0.00 ATOM 380 O LEU 52 25.216 18.849 25.924 1.00 0.00 ATOM 381 C LEU 52 25.324 19.401 27.020 1.00 0.00 ATOM 382 N ASN 53 25.567 18.731 28.143 1.00 0.00 ATOM 383 CA ASN 53 25.720 17.281 28.140 1.00 0.00 ATOM 384 CB ASN 53 25.605 16.822 29.692 1.00 0.00 ATOM 385 CG ASN 53 26.729 17.369 30.551 1.00 0.00 ATOM 386 ND2 ASN 53 27.966 17.283 30.055 1.00 0.00 ATOM 387 OD1 ASN 53 26.492 17.838 31.667 1.00 0.00 ATOM 388 O ASN 53 23.358 17.068 27.757 1.00 0.00 ATOM 389 C ASN 53 24.482 16.614 27.538 1.00 0.00 ATOM 390 N VAL 54 24.691 15.540 26.783 1.00 0.00 ATOM 391 CA VAL 54 23.581 14.825 26.163 1.00 0.00 ATOM 392 CB VAL 54 24.170 13.693 25.240 1.00 0.00 ATOM 393 CG1 VAL 54 23.057 12.735 24.813 1.00 0.00 ATOM 394 CG2 VAL 54 24.799 14.339 24.005 1.00 0.00 ATOM 395 O VAL 54 21.469 14.289 27.064 1.00 0.00 ATOM 396 C VAL 54 22.676 14.239 27.242 1.00 0.00 ATOM 397 N GLU 55 23.238 13.704 28.313 1.00 0.00 ATOM 398 CA GLU 55 22.416 13.133 29.375 1.00 0.00 ATOM 399 CB GLU 55 23.277 12.640 30.543 1.00 0.00 ATOM 400 CG GLU 55 24.216 11.482 30.210 1.00 0.00 ATOM 401 CD GLU 55 25.605 11.932 29.780 1.00 0.00 ATOM 402 OE1 GLU 55 25.779 13.103 29.366 1.00 0.00 ATOM 403 OE2 GLU 55 26.535 11.105 29.874 1.00 0.00 ATOM 404 O GLU 55 20.233 13.810 30.090 1.00 0.00 ATOM 405 C GLU 55 21.383 14.153 29.878 1.00 0.00 ATOM 406 N ASP 56 21.792 15.406 30.034 1.00 0.00 ATOM 407 CA ASP 56 20.893 16.485 30.434 1.00 0.00 ATOM 408 CB ASP 56 21.647 17.828 30.535 1.00 0.00 ATOM 409 CG ASP 56 22.632 17.907 31.694 1.00 0.00 ATOM 410 OD1 ASP 56 22.405 17.278 32.759 1.00 0.00 ATOM 411 OD2 ASP 56 23.621 18.661 31.523 1.00 0.00 ATOM 412 O ASP 56 18.624 16.845 29.697 1.00 0.00 ATOM 413 C ASP 56 19.802 16.668 29.372 1.00 0.00 ATOM 414 N ILE 57 20.203 16.621 28.102 1.00 0.00 ATOM 415 CA ILE 57 19.256 16.772 26.997 1.00 0.00 ATOM 416 CB ILE 57 19.998 16.892 25.639 1.00 0.00 ATOM 417 CG1 ILE 57 20.691 18.258 25.563 1.00 0.00 ATOM 418 CG2 ILE 57 19.019 16.699 24.459 1.00 0.00 ATOM 419 CD1 ILE 57 21.848 18.312 24.641 1.00 0.00 ATOM 420 O ILE 57 17.075 15.782 26.758 1.00 0.00 ATOM 421 C ILE 57 18.269 15.603 26.950 1.00 0.00 ATOM 422 N LEU 58 18.775 14.385 27.107 1.00 0.00 ATOM 423 CA LEU 58 17.931 13.205 27.030 1.00 0.00 ATOM 424 CB LEU 58 18.720 11.915 27.370 1.00 0.00 ATOM 425 CG LEU 58 19.540 11.442 26.138 1.00 0.00 ATOM 426 CD1 LEU 58 20.586 10.397 26.507 1.00 0.00 ATOM 427 CD2 LEU 58 18.629 10.907 25.065 1.00 0.00 ATOM 428 O LEU 58 15.701 12.943 27.875 1.00 0.00 ATOM 429 C LEU 58 16.878 13.193 28.133 1.00 0.00 ATOM 430 N ARG 59 17.304 13.467 29.363 1.00 0.00 ATOM 431 CA ARG 59 16.369 13.489 30.527 1.00 0.00 ATOM 432 CB ARG 59 17.168 13.647 31.798 1.00 0.00 ATOM 433 CG ARG 59 16.446 13.133 33.024 1.00 0.00 ATOM 434 CD ARG 59 17.252 13.432 34.279 1.00 0.00 ATOM 435 NE ARG 59 18.604 12.872 34.240 1.00 0.00 ATOM 436 CZ ARG 59 19.461 12.954 35.255 1.00 0.00 ATOM 437 NH1 ARG 59 19.105 13.571 36.386 1.00 0.00 ATOM 438 NH2 ARG 59 20.676 12.431 35.139 1.00 0.00 ATOM 439 O ARG 59 14.113 14.290 30.611 1.00 0.00 ATOM 440 C ARG 59 15.289 14.542 30.346 1.00 0.00 ATOM 441 N ASP 60 15.687 15.727 29.891 1.00 0.00 ATOM 442 CA ASP 60 14.736 16.811 29.677 1.00 0.00 ATOM 443 CB ASP 60 15.384 18.123 29.345 1.00 0.00 ATOM 444 CG ASP 60 16.305 18.639 30.453 1.00 0.00 ATOM 445 OD1 ASP 60 16.099 18.262 31.628 1.00 0.00 ATOM 446 OD2 ASP 60 17.228 19.434 30.159 1.00 0.00 ATOM 447 O ASP 60 12.515 16.605 28.792 1.00 0.00 ATOM 448 C ASP 60 13.718 16.405 28.616 1.00 0.00 ATOM 449 N LEU 61 14.201 15.836 27.517 1.00 0.00 ATOM 450 CA LEU 61 13.324 15.409 26.449 1.00 0.00 ATOM 451 CB LEU 61 14.078 14.807 25.301 1.00 0.00 ATOM 452 CG LEU 61 14.801 15.802 24.427 1.00 0.00 ATOM 453 CD1 LEU 61 15.893 15.128 23.616 1.00 0.00 ATOM 454 CD2 LEU 61 13.731 16.506 23.550 1.00 0.00 ATOM 455 O LEU 61 11.168 14.363 26.563 1.00 0.00 ATOM 456 C LEU 61 12.339 14.355 26.944 1.00 0.00 ATOM 457 N ASN 62 12.815 13.451 27.794 1.00 0.00 ATOM 458 CA ASN 62 11.969 12.416 28.321 1.00 0.00 ATOM 459 CB ASN 62 12.743 11.472 29.248 1.00 0.00 ATOM 460 CG ASN 62 11.905 10.281 29.683 1.00 0.00 ATOM 461 ND2 ASN 62 11.653 10.175 30.993 1.00 0.00 ATOM 462 OD1 ASN 62 11.475 9.471 28.849 1.00 0.00 ATOM 463 O ASN 62 9.618 12.794 28.667 1.00 0.00 ATOM 464 C ASN 62 10.768 13.107 28.979 1.00 0.00 ATOM 465 N ALA 63 11.039 14.042 29.884 1.00 0.00 ATOM 466 CA ALA 63 9.973 14.763 30.569 1.00 0.00 ATOM 467 CB ALA 63 10.566 15.635 31.656 1.00 0.00 ATOM 468 O ALA 63 7.935 15.791 29.785 1.00 0.00 ATOM 469 C ALA 63 9.139 15.625 29.594 1.00 0.00 ATOM 470 N LEU 64 9.787 16.160 28.564 1.00 0.00 ATOM 471 CA LEU 64 9.093 16.987 27.583 1.00 0.00 ATOM 472 CB LEU 64 10.172 18.056 27.114 1.00 0.00 ATOM 473 CG LEU 64 10.436 19.200 28.110 1.00 0.00 ATOM 474 CD1 LEU 64 11.850 19.812 27.829 1.00 0.00 ATOM 475 CD2 LEU 64 9.374 20.269 27.988 1.00 0.00 ATOM 476 O LEU 64 7.669 16.854 25.662 1.00 0.00 ATOM 477 C LEU 64 8.371 16.246 26.471 1.00 0.00 ATOM 478 N ALA 65 8.542 14.928 26.429 1.00 0.00 ATOM 479 CA ALA 65 7.895 14.114 25.408 1.00 0.00 ATOM 480 CB ALA 65 6.424 14.494 25.343 1.00 0.00 ATOM 481 O ALA 65 7.804 13.494 23.094 1.00 0.00 ATOM 482 C ALA 65 8.377 14.162 23.964 1.00 0.00 TER END