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 2 Mon Jul 7 11:25:21 2008 MODEL 2 PARENT N/A ATOM 1 N MET 1 11.026 11.813 26.022 1.00 0.00 ATOM 2 CA MET 1 11.508 12.202 24.702 1.00 0.00 ATOM 3 CB MET 1 11.583 13.717 24.672 1.00 0.00 ATOM 4 CG MET 1 11.844 14.253 23.288 1.00 0.00 ATOM 5 SD MET 1 10.488 13.952 22.106 1.00 0.00 ATOM 6 CE MET 1 11.312 12.830 21.008 1.00 0.00 ATOM 7 O MET 1 12.958 11.045 23.260 1.00 0.00 ATOM 8 C MET 1 12.829 11.511 24.380 1.00 0.00 ATOM 9 N THR 2 13.638 11.163 25.390 1.00 0.00 ATOM 10 CA THR 2 14.862 10.392 25.133 1.00 0.00 ATOM 11 CB THR 2 15.647 10.099 26.402 1.00 0.00 ATOM 12 CG2 THR 2 16.933 9.315 26.118 1.00 0.00 ATOM 13 OG1 THR 2 15.952 11.354 26.962 1.00 0.00 ATOM 14 O THR 2 15.128 8.524 23.650 1.00 0.00 ATOM 15 C THR 2 14.478 9.029 24.567 1.00 0.00 ATOM 16 N GLN 3 13.423 8.435 25.113 1.00 0.00 ATOM 17 CA GLN 3 12.969 7.139 24.650 1.00 0.00 ATOM 18 CB GLN 3 11.727 6.694 25.409 1.00 0.00 ATOM 19 CG GLN 3 11.948 6.446 26.877 1.00 0.00 ATOM 20 CD GLN 3 10.658 6.108 27.587 1.00 0.00 ATOM 21 OE1 GLN 3 10.312 6.717 28.606 1.00 0.00 ATOM 22 NE2 GLN 3 9.922 5.153 27.043 1.00 0.00 ATOM 23 O GLN 3 12.624 6.143 22.460 1.00 0.00 ATOM 24 C GLN 3 12.575 7.173 23.134 1.00 0.00 ATOM 25 N LYS 4 12.199 8.345 22.634 1.00 0.00 ATOM 26 CA LYS 4 11.813 8.480 21.234 1.00 0.00 ATOM 27 CB LYS 4 10.091 8.724 21.391 1.00 0.00 ATOM 28 CG LYS 4 9.426 8.614 22.771 1.00 0.00 ATOM 29 CD LYS 4 9.412 7.228 23.311 1.00 0.00 ATOM 30 CE LYS 4 8.223 7.048 24.273 1.00 0.00 ATOM 31 NZ LYS 4 8.227 5.623 24.762 1.00 0.00 ATOM 32 O LYS 4 12.293 9.777 19.250 1.00 0.00 ATOM 33 C LYS 4 12.659 9.444 20.377 1.00 0.00 ATOM 34 N PHE 5 13.811 9.867 20.898 1.00 0.00 ATOM 35 CA PHE 5 14.670 10.884 20.263 1.00 0.00 ATOM 36 CB PHE 5 14.807 12.078 21.225 1.00 0.00 ATOM 37 CG PHE 5 15.377 13.319 20.548 1.00 0.00 ATOM 38 CD1 PHE 5 14.528 14.341 20.156 1.00 0.00 ATOM 39 CD2 PHE 5 16.743 13.440 20.342 1.00 0.00 ATOM 40 CE1 PHE 5 15.033 15.481 19.568 1.00 0.00 ATOM 41 CE2 PHE 5 17.246 14.590 19.738 1.00 0.00 ATOM 42 CZ PHE 5 16.393 15.614 19.358 1.00 0.00 ATOM 43 O PHE 5 16.717 9.870 20.995 1.00 0.00 ATOM 44 C PHE 5 16.067 10.312 20.047 1.00 0.00 ATOM 45 N THR 6 16.526 10.320 18.800 1.00 0.00 ATOM 46 CA THR 6 17.859 9.796 18.474 1.00 0.00 ATOM 47 CB THR 6 17.835 9.084 17.122 1.00 0.00 ATOM 48 CG2 THR 6 19.213 8.514 16.813 1.00 0.00 ATOM 49 OG1 THR 6 16.948 7.971 17.233 1.00 0.00 ATOM 50 O THR 6 18.978 11.672 17.498 1.00 0.00 ATOM 51 C THR 6 18.912 10.884 18.443 1.00 0.00 ATOM 52 N LYS 7 19.742 10.932 19.480 1.00 0.00 ATOM 53 CA LYS 7 20.798 11.936 19.558 1.00 0.00 ATOM 54 CB LYS 7 21.579 11.448 21.066 1.00 0.00 ATOM 55 CG LYS 7 20.789 10.697 22.117 1.00 0.00 ATOM 56 CD LYS 7 21.695 10.213 23.244 1.00 0.00 ATOM 57 CE LYS 7 22.737 9.225 22.743 1.00 0.00 ATOM 58 NZ LYS 7 23.614 8.724 23.842 1.00 0.00 ATOM 59 O LYS 7 22.538 12.869 18.166 1.00 0.00 ATOM 60 C LYS 7 21.782 11.912 18.416 1.00 0.00 ATOM 61 N ASP 8 21.856 10.785 17.702 1.00 0.00 ATOM 62 CA ASP 8 22.778 10.603 16.588 1.00 0.00 ATOM 63 CB ASP 8 22.943 9.080 16.511 1.00 0.00 ATOM 64 CG ASP 8 23.719 8.486 17.689 1.00 0.00 ATOM 65 OD1 ASP 8 24.480 9.214 18.346 1.00 0.00 ATOM 66 OD2 ASP 8 23.420 7.321 18.014 1.00 0.00 ATOM 67 O ASP 8 23.069 11.184 14.279 1.00 0.00 ATOM 68 C ASP 8 22.294 11.107 15.233 1.00 0.00 ATOM 69 N MET 9 21.012 11.449 15.149 1.00 0.00 ATOM 70 CA MET 9 20.440 11.948 13.900 1.00 0.00 ATOM 71 CB MET 9 18.936 11.616 13.788 1.00 0.00 ATOM 72 CG MET 9 18.602 10.216 14.139 1.00 0.00 ATOM 73 SD MET 9 16.890 9.808 13.798 1.00 0.00 ATOM 74 CE MET 9 16.033 10.772 14.993 1.00 0.00 ATOM 75 O MET 9 20.560 14.153 14.803 1.00 0.00 ATOM 76 C MET 9 20.499 13.451 13.794 1.00 0.00 ATOM 77 N THR 10 20.480 13.955 12.564 1.00 0.00 ATOM 78 CA THR 10 20.529 15.394 12.336 1.00 0.00 ATOM 79 CB THR 10 20.552 15.760 10.846 1.00 0.00 ATOM 80 CG2 THR 10 21.768 15.127 10.174 1.00 0.00 ATOM 81 OG1 THR 10 19.360 15.292 10.207 1.00 0.00 ATOM 82 O THR 10 18.226 15.329 13.112 1.00 0.00 ATOM 83 C THR 10 19.283 15.974 13.042 1.00 0.00 ATOM 84 N PHE 11 19.486 17.098 13.706 1.00 0.00 ATOM 85 CA PHE 11 18.456 17.723 14.550 1.00 0.00 ATOM 86 CB PHE 11 19.088 18.953 15.203 1.00 0.00 ATOM 87 CG PHE 11 18.151 19.676 16.169 1.00 0.00 ATOM 88 CD1 PHE 11 18.216 19.444 17.536 1.00 0.00 ATOM 89 CD2 PHE 11 17.203 20.545 15.656 1.00 0.00 ATOM 90 CE1 PHE 11 17.334 20.091 18.370 1.00 0.00 ATOM 91 CE2 PHE 11 16.296 21.172 16.495 1.00 0.00 ATOM 92 CZ PHE 11 16.361 20.939 17.861 1.00 0.00 ATOM 93 O PHE 11 16.082 17.973 14.299 1.00 0.00 ATOM 94 C PHE 11 17.188 18.015 13.755 1.00 0.00 ATOM 95 N ALA 12 17.347 18.309 12.469 1.00 0.00 ATOM 96 CA ALA 12 16.172 18.614 11.572 1.00 0.00 ATOM 97 CB ALA 12 16.659 18.974 10.193 1.00 0.00 ATOM 98 O ALA 12 14.049 17.498 11.608 1.00 0.00 ATOM 99 C ALA 12 15.271 17.386 11.507 1.00 0.00 ATOM 100 N GLN 13 15.876 16.214 11.338 1.00 0.00 ATOM 101 CA GLN 13 15.102 14.936 11.260 1.00 0.00 ATOM 102 CB GLN 13 15.990 13.768 11.117 1.00 0.00 ATOM 103 CG GLN 13 16.709 13.696 9.772 1.00 0.00 ATOM 104 CD GLN 13 17.747 12.582 9.770 1.00 0.00 ATOM 105 OE1 GLN 13 18.916 12.819 10.083 1.00 0.00 ATOM 106 NE2 GLN 13 17.330 11.366 9.432 1.00 0.00 ATOM 107 O GLN 13 13.178 14.363 12.575 1.00 0.00 ATOM 108 C GLN 13 14.360 14.711 12.573 1.00 0.00 ATOM 109 N ALA 14 15.054 14.909 13.689 1.00 0.00 ATOM 110 CA ALA 14 14.442 14.725 15.011 1.00 0.00 ATOM 111 CB ALA 14 15.518 15.003 16.057 1.00 0.00 ATOM 112 O ALA 14 12.177 15.291 15.659 1.00 0.00 ATOM 113 C ALA 14 13.239 15.697 15.185 1.00 0.00 ATOM 114 N LEU 15 13.422 16.957 14.800 1.00 0.00 ATOM 115 CA LEU 15 12.357 17.945 14.917 1.00 0.00 ATOM 116 CB LEU 15 12.824 19.320 14.512 1.00 0.00 ATOM 117 CG LEU 15 11.773 20.430 14.582 1.00 0.00 ATOM 118 CD1 LEU 15 11.104 20.439 15.955 1.00 0.00 ATOM 119 CD2 LEU 15 12.438 21.773 14.291 1.00 0.00 ATOM 120 O LEU 15 10.031 17.613 14.466 1.00 0.00 ATOM 121 C LEU 15 11.177 17.595 14.022 1.00 0.00 ATOM 122 N GLN 16 11.452 17.270 12.765 1.00 0.00 ATOM 123 CA GLN 16 10.387 16.893 11.845 1.00 0.00 ATOM 124 CB GLN 16 10.893 16.496 10.500 1.00 0.00 ATOM 125 CG GLN 16 11.433 17.677 9.722 1.00 0.00 ATOM 126 CD GLN 16 11.761 17.249 8.306 1.00 0.00 ATOM 127 OE1 GLN 16 11.324 17.971 7.432 1.00 0.00 ATOM 128 NE2 GLN 16 12.464 16.168 8.142 1.00 0.00 ATOM 129 O GLN 16 8.395 15.695 12.422 1.00 0.00 ATOM 130 C GLN 16 9.626 15.725 12.450 1.00 0.00 ATOM 131 N THR 17 10.358 14.762 12.999 1.00 0.00 ATOM 132 CA THR 17 9.735 13.595 13.613 1.00 0.00 ATOM 133 CB THR 17 10.865 12.581 13.878 1.00 0.00 ATOM 134 CG2 THR 17 10.360 11.301 14.555 1.00 0.00 ATOM 135 OG1 THR 17 11.502 12.295 12.628 1.00 0.00 ATOM 136 O THR 17 7.867 13.420 15.154 1.00 0.00 ATOM 137 C THR 17 8.918 14.002 14.882 1.00 0.00 ATOM 138 N HIS 18 9.410 14.986 15.628 1.00 0.00 ATOM 139 CA HIS 18 8.722 15.440 16.830 1.00 0.00 ATOM 140 CB HIS 18 9.561 14.938 17.988 1.00 0.00 ATOM 141 CG HIS 18 9.395 13.456 18.146 1.00 0.00 ATOM 142 CD2 HIS 18 10.241 12.432 17.888 1.00 0.00 ATOM 143 ND1 HIS 18 8.199 12.883 18.525 1.00 0.00 ATOM 144 CE1 HIS 18 8.324 11.566 18.517 1.00 0.00 ATOM 145 NE2 HIS 18 9.554 11.266 18.133 1.00 0.00 ATOM 146 O HIS 18 9.480 17.594 17.595 1.00 0.00 ATOM 147 C HIS 18 8.677 16.980 16.887 1.00 0.00 ATOM 148 N PRO 19 7.705 17.635 16.235 1.00 0.00 ATOM 149 CA PRO 19 7.625 19.113 16.252 1.00 0.00 ATOM 150 CB PRO 19 6.393 19.458 15.425 1.00 0.00 ATOM 151 CG PRO 19 6.361 18.298 14.448 1.00 0.00 ATOM 152 CD PRO 19 6.729 17.080 15.293 1.00 0.00 ATOM 153 O PRO 19 8.033 20.771 17.938 1.00 0.00 ATOM 154 C PRO 19 7.541 19.674 17.668 1.00 0.00 ATOM 155 N GLY 20 6.917 18.922 18.569 1.00 0.00 ATOM 156 CA GLY 20 6.770 19.363 19.998 1.00 0.00 ATOM 157 O GLY 20 8.252 20.270 21.653 1.00 0.00 ATOM 158 C GLY 20 8.097 19.452 20.743 1.00 0.00 ATOM 159 N VAL 21 9.053 18.612 20.358 1.00 0.00 ATOM 160 CA VAL 21 10.379 18.609 21.004 1.00 0.00 ATOM 161 CB VAL 21 11.137 17.324 20.647 1.00 0.00 ATOM 162 CG1 VAL 21 11.883 17.349 19.309 1.00 0.00 ATOM 163 CG2 VAL 21 12.153 17.034 21.752 1.00 0.00 ATOM 164 O VAL 21 12.300 20.053 21.291 1.00 0.00 ATOM 165 C VAL 21 11.219 19.866 20.718 1.00 0.00 ATOM 166 N ALA 22 10.808 20.654 19.730 1.00 0.00 ATOM 167 CA ALA 22 11.555 21.850 19.313 1.00 0.00 ATOM 168 CB ALA 22 10.920 22.555 18.156 1.00 0.00 ATOM 169 O ALA 22 12.757 23.382 20.714 1.00 0.00 ATOM 170 C ALA 22 11.680 22.838 20.467 1.00 0.00 ATOM 171 N GLY 23 10.578 23.069 21.173 1.00 0.00 ATOM 172 CA GLY 23 10.572 24.015 22.329 1.00 0.00 ATOM 173 O GLY 23 12.234 24.468 24.001 1.00 0.00 ATOM 174 C GLY 23 11.569 23.614 23.412 1.00 0.00 ATOM 175 N VAL 24 11.671 22.314 23.673 1.00 0.00 ATOM 176 CA VAL 24 12.608 21.802 24.703 1.00 0.00 ATOM 177 CB VAL 24 12.373 20.377 25.226 1.00 0.00 ATOM 178 CG1 VAL 24 11.074 20.336 26.001 1.00 0.00 ATOM 179 CG2 VAL 24 12.444 19.274 24.161 1.00 0.00 ATOM 180 O VAL 24 14.954 22.219 24.987 1.00 0.00 ATOM 181 C VAL 24 14.056 21.854 24.228 1.00 0.00 ATOM 182 N LEU 25 14.281 21.488 22.970 1.00 0.00 ATOM 183 CA LEU 25 15.608 21.502 22.422 1.00 0.00 ATOM 184 CB LEU 25 15.542 20.780 21.080 1.00 0.00 ATOM 185 CG LEU 25 15.213 19.297 21.224 1.00 0.00 ATOM 186 CD1 LEU 25 14.769 18.762 19.872 1.00 0.00 ATOM 187 CD2 LEU 25 16.412 18.478 21.722 1.00 0.00 ATOM 188 O LEU 25 17.435 23.088 22.496 1.00 0.00 ATOM 189 C LEU 25 16.222 22.928 22.353 1.00 0.00 ATOM 190 N ARG 26 15.382 23.934 22.137 1.00 0.00 ATOM 191 CA ARG 26 15.857 25.311 22.058 1.00 0.00 ATOM 192 CB ARG 26 14.713 26.251 21.526 1.00 0.00 ATOM 193 CG ARG 26 14.026 25.777 20.270 1.00 0.00 ATOM 194 CD ARG 26 14.988 25.660 19.067 1.00 0.00 ATOM 195 NE ARG 26 14.247 25.365 17.844 1.00 0.00 ATOM 196 CZ ARG 26 13.717 26.296 17.037 1.00 0.00 ATOM 197 NH1 ARG 26 13.891 27.609 17.295 1.00 0.00 ATOM 198 NH2 ARG 26 13.013 25.907 15.972 1.00 0.00 ATOM 199 O ARG 26 17.406 26.551 23.396 1.00 0.00 ATOM 200 C ARG 26 16.411 25.828 23.404 1.00 0.00 ATOM 201 N SER 27 15.969 25.216 24.501 1.00 0.00 ATOM 202 CA SER 27 16.364 25.594 25.868 1.00 0.00 ATOM 203 CB SER 27 14.718 25.312 26.572 1.00 0.00 ATOM 204 OG SER 27 14.928 24.049 27.122 1.00 0.00 ATOM 205 O SER 27 18.116 25.137 27.441 1.00 0.00 ATOM 206 C SER 27 17.625 24.881 26.342 1.00 0.00 ATOM 207 N TYR 28 18.148 23.984 25.509 1.00 0.00 ATOM 208 CA TYR 28 19.387 23.219 25.859 1.00 0.00 ATOM 209 CB TYR 28 19.013 21.786 26.253 1.00 0.00 ATOM 210 CG TYR 28 18.668 21.746 27.749 1.00 0.00 ATOM 211 CD1 TYR 28 17.354 21.826 28.185 1.00 0.00 ATOM 212 CD2 TYR 28 19.669 21.692 28.691 1.00 0.00 ATOM 213 CE1 TYR 28 17.049 21.831 29.541 1.00 0.00 ATOM 214 CE2 TYR 28 19.376 21.699 30.035 1.00 0.00 ATOM 215 CZ TYR 28 18.062 21.757 30.484 1.00 0.00 ATOM 216 OH TYR 28 17.796 21.905 31.809 1.00 0.00 ATOM 217 O TYR 28 21.228 22.643 24.431 1.00 0.00 ATOM 218 C TYR 28 20.516 23.539 24.885 1.00 0.00 ATOM 219 N ASN 29 20.678 24.820 24.566 1.00 0.00 ATOM 220 CA ASN 29 21.729 25.242 23.646 1.00 0.00 ATOM 221 CB ASN 29 23.059 25.366 24.645 1.00 0.00 ATOM 222 CG ASN 29 22.923 26.413 25.778 1.00 0.00 ATOM 223 ND2 ASN 29 23.609 26.181 26.899 1.00 0.00 ATOM 224 OD1 ASN 29 22.217 27.412 25.630 1.00 0.00 ATOM 225 O ASN 29 22.481 24.846 21.400 1.00 0.00 ATOM 226 C ASN 29 21.558 24.790 22.211 1.00 0.00 ATOM 227 N LEU 30 20.287 24.693 21.849 1.00 0.00 ATOM 228 CA LEU 30 19.894 24.368 20.479 1.00 0.00 ATOM 229 CB LEU 30 19.487 22.879 20.383 1.00 0.00 ATOM 230 CG LEU 30 20.318 21.903 21.274 1.00 0.00 ATOM 231 CD1 LEU 30 19.631 20.547 21.390 1.00 0.00 ATOM 232 CD2 LEU 30 21.770 21.697 20.833 1.00 0.00 ATOM 233 O LEU 30 18.397 25.458 18.883 1.00 0.00 ATOM 234 C LEU 30 18.939 25.498 19.977 1.00 0.00 ATOM 235 N GLY 31 19.004 26.656 20.645 1.00 0.00 ATOM 236 CA GLY 31 18.238 27.879 20.301 1.00 0.00 ATOM 237 O GLY 31 17.719 28.907 18.195 1.00 0.00 ATOM 238 C GLY 31 18.596 28.464 18.939 1.00 0.00 ATOM 239 N CYS 32 19.884 28.466 18.613 1.00 0.00 ATOM 240 CA CYS 32 20.344 29.001 17.329 1.00 0.00 ATOM 241 CB CYS 32 21.592 29.880 17.533 1.00 0.00 ATOM 242 SG CYS 32 22.866 29.085 18.525 1.00 0.00 ATOM 243 O CYS 32 20.960 26.826 16.525 1.00 0.00 ATOM 244 C CYS 32 20.326 27.861 16.316 1.00 0.00 ATOM 245 N ILE 33 19.599 28.052 15.220 1.00 0.00 ATOM 246 CA ILE 33 19.513 27.028 14.181 1.00 0.00 ATOM 247 CB ILE 33 18.538 27.447 13.061 1.00 0.00 ATOM 248 CG1 ILE 33 17.182 27.881 13.632 1.00 0.00 ATOM 249 CG2 ILE 33 18.376 26.312 12.023 1.00 0.00 ATOM 250 CD1 ILE 33 16.555 26.889 14.624 1.00 0.00 ATOM 251 O ILE 33 21.290 25.561 13.461 1.00 0.00 ATOM 252 C ILE 33 20.954 26.718 13.716 1.00 0.00 ATOM 253 N GLY 34 21.786 27.750 13.612 1.00 0.00 ATOM 254 CA GLY 34 23.168 27.566 13.184 1.00 0.00 ATOM 255 O GLY 34 24.728 25.869 13.752 1.00 0.00 ATOM 256 C GLY 34 23.927 26.717 14.146 1.00 0.00 ATOM 257 N CYS 35 23.685 26.935 15.435 1.00 0.00 ATOM 258 CA CYS 35 24.364 26.166 16.472 1.00 0.00 ATOM 259 CB CYS 35 23.597 26.513 17.733 1.00 0.00 ATOM 260 SG CYS 35 22.360 25.520 18.626 1.00 0.00 ATOM 261 O CYS 35 25.020 23.881 16.558 1.00 0.00 ATOM 262 C CYS 35 24.151 24.677 16.278 1.00 0.00 ATOM 263 N MET 36 22.852 24.427 16.153 1.00 0.00 ATOM 264 CA MET 36 22.270 23.103 16.273 1.00 0.00 ATOM 265 CB MET 36 20.685 23.717 16.780 1.00 0.00 ATOM 266 CG MET 36 19.778 23.568 15.567 1.00 0.00 ATOM 267 SD MET 36 18.078 24.054 15.950 1.00 0.00 ATOM 268 CE MET 36 17.429 23.872 14.327 1.00 0.00 ATOM 269 O MET 36 22.284 21.115 14.933 1.00 0.00 ATOM 270 C MET 36 22.489 22.329 14.978 1.00 0.00 ATOM 271 N GLY 37 22.905 23.029 13.928 1.00 0.00 ATOM 272 CA GLY 37 23.154 22.385 12.622 1.00 0.00 ATOM 273 O GLY 37 22.024 20.272 12.552 1.00 0.00 ATOM 274 C GLY 37 21.968 21.479 12.316 1.00 0.00 ATOM 275 N ALA 38 20.896 22.063 11.789 1.00 0.00 ATOM 276 CA ALA 38 19.704 21.291 11.453 1.00 0.00 ATOM 277 CB ALA 38 18.734 22.025 10.607 1.00 0.00 ATOM 278 O ALA 38 19.687 18.866 11.205 1.00 0.00 ATOM 279 C ALA 38 20.020 19.954 10.755 1.00 0.00 ATOM 280 N GLN 39 20.702 20.092 9.639 1.00 0.00 ATOM 281 CA GLN 39 20.912 18.926 8.771 1.00 0.00 ATOM 282 CB GLN 39 20.573 19.272 7.325 1.00 0.00 ATOM 283 CG GLN 39 21.553 20.265 6.712 1.00 0.00 ATOM 284 CD GLN 39 21.137 21.719 6.894 1.00 0.00 ATOM 285 OE1 GLN 39 20.517 22.200 7.841 1.00 0.00 ATOM 286 NE2 GLN 39 21.634 22.478 5.982 1.00 0.00 ATOM 287 O GLN 39 22.554 17.223 8.380 1.00 0.00 ATOM 288 C GLN 39 22.315 18.336 8.848 1.00 0.00 ATOM 289 N ASN 40 23.243 19.082 9.439 1.00 0.00 ATOM 290 CA ASN 40 24.623 18.616 9.573 1.00 0.00 ATOM 291 CB ASN 40 25.541 19.661 8.925 1.00 0.00 ATOM 292 CG ASN 40 25.269 19.834 7.448 1.00 0.00 ATOM 293 ND2 ASN 40 25.211 21.079 6.994 1.00 0.00 ATOM 294 OD1 ASN 40 25.101 18.856 6.725 1.00 0.00 ATOM 295 O ASN 40 26.291 18.038 11.208 1.00 0.00 ATOM 296 C ASN 40 25.118 18.353 11.001 1.00 0.00 ATOM 297 N GLU 41 24.223 18.484 11.976 1.00 0.00 ATOM 298 CA GLU 41 24.587 18.255 13.369 1.00 0.00 ATOM 299 CB GLU 41 25.017 19.581 14.095 1.00 0.00 ATOM 300 CG GLU 41 26.108 20.338 13.368 1.00 0.00 ATOM 301 CD GLU 41 26.579 21.621 14.024 1.00 0.00 ATOM 302 OE1 GLU 41 26.727 21.666 15.260 1.00 0.00 ATOM 303 OE2 GLU 41 26.802 22.565 13.251 1.00 0.00 ATOM 304 O GLU 41 22.277 17.725 13.904 1.00 0.00 ATOM 305 C GLU 41 23.471 17.508 14.102 1.00 0.00 ATOM 306 N SER 42 23.912 16.440 14.740 1.00 0.00 ATOM 307 CA SER 42 23.008 15.598 15.546 1.00 0.00 ATOM 308 CB SER 42 23.573 14.147 15.580 1.00 0.00 ATOM 309 OG SER 42 24.716 14.111 16.403 1.00 0.00 ATOM 310 O SER 42 23.724 17.093 17.275 1.00 0.00 ATOM 311 C SER 42 22.969 16.177 16.956 1.00 0.00 ATOM 312 N LEU 43 22.098 15.632 17.827 1.00 0.00 ATOM 313 CA LEU 43 21.978 16.111 19.198 1.00 0.00 ATOM 314 CB LEU 43 20.878 15.334 19.923 1.00 0.00 ATOM 315 CG LEU 43 20.777 15.698 21.411 1.00 0.00 ATOM 316 CD1 LEU 43 20.427 17.185 21.550 1.00 0.00 ATOM 317 CD2 LEU 43 19.721 14.815 22.069 1.00 0.00 ATOM 318 O LEU 43 23.689 16.838 20.714 1.00 0.00 ATOM 319 C LEU 43 23.298 15.959 19.946 1.00 0.00 ATOM 320 N GLU 44 23.983 14.842 19.722 1.00 0.00 ATOM 321 CA GLU 44 25.279 14.583 20.387 1.00 0.00 ATOM 322 CB GLU 44 25.889 13.305 19.949 1.00 0.00 ATOM 323 CG GLU 44 25.945 12.301 21.060 1.00 0.00 ATOM 324 CD GLU 44 26.918 11.167 20.768 1.00 0.00 ATOM 325 OE1 GLU 44 27.278 10.977 19.594 1.00 0.00 ATOM 326 OE2 GLU 44 27.281 10.524 21.768 1.00 0.00 ATOM 327 O GLU 44 26.906 16.325 20.737 1.00 0.00 ATOM 328 C GLU 44 26.273 15.659 19.917 1.00 0.00 ATOM 329 N GLN 45 26.403 15.820 18.604 1.00 0.00 ATOM 330 CA GLN 45 27.316 16.813 18.051 1.00 0.00 ATOM 331 CB GLN 45 27.238 16.755 16.529 1.00 0.00 ATOM 332 CG GLN 45 27.908 15.517 15.947 1.00 0.00 ATOM 333 CD GLN 45 27.480 15.322 14.488 1.00 0.00 ATOM 334 OE1 GLN 45 26.393 15.663 14.028 1.00 0.00 ATOM 335 NE2 GLN 45 28.314 14.654 13.749 1.00 0.00 ATOM 336 O GLN 45 27.829 18.971 18.992 1.00 0.00 ATOM 337 C GLN 45 26.964 18.229 18.538 1.00 0.00 ATOM 338 N GLY 46 25.651 18.489 18.577 1.00 0.00 ATOM 339 CA GLY 46 25.066 19.782 19.000 1.00 0.00 ATOM 340 O GLY 46 25.674 21.230 20.814 1.00 0.00 ATOM 341 C GLY 46 25.339 20.096 20.467 1.00 0.00 ATOM 342 N ALA 47 25.199 19.093 21.327 1.00 0.00 ATOM 343 CA ALA 47 25.439 19.279 22.765 1.00 0.00 ATOM 344 CB ALA 47 25.158 18.132 23.600 1.00 0.00 ATOM 345 O ALA 47 27.235 20.567 23.737 1.00 0.00 ATOM 346 C ALA 47 26.925 19.654 22.971 1.00 0.00 ATOM 347 N ASN 48 27.822 18.951 22.287 1.00 0.00 ATOM 348 CA ASN 48 29.249 19.227 22.406 1.00 0.00 ATOM 349 CB ASN 48 30.106 18.275 21.651 1.00 0.00 ATOM 350 CG ASN 48 30.220 16.955 22.376 1.00 0.00 ATOM 351 ND2 ASN 48 30.298 15.859 21.623 1.00 0.00 ATOM 352 OD1 ASN 48 30.248 16.923 23.608 1.00 0.00 ATOM 353 O ASN 48 30.362 21.352 22.450 1.00 0.00 ATOM 354 C ASN 48 29.518 20.641 21.904 1.00 0.00 ATOM 355 N ALA 49 28.800 21.049 20.863 1.00 0.00 ATOM 356 CA ALA 49 28.971 22.384 20.300 1.00 0.00 ATOM 357 CB ALA 49 28.117 22.507 19.020 1.00 0.00 ATOM 358 O ALA 49 29.390 24.452 21.460 1.00 0.00 ATOM 359 C ALA 49 28.648 23.479 21.329 1.00 0.00 ATOM 360 N HIS 50 27.546 23.309 22.053 1.00 0.00 ATOM 361 CA HIS 50 27.146 24.285 23.060 1.00 0.00 ATOM 362 CB HIS 50 25.671 24.536 22.782 1.00 0.00 ATOM 363 CG HIS 50 25.530 25.726 21.831 1.00 0.00 ATOM 364 CD2 HIS 50 25.338 25.667 20.529 1.00 0.00 ATOM 365 ND1 HIS 50 25.642 27.006 22.181 1.00 0.00 ATOM 366 CE1 HIS 50 25.505 27.755 21.096 1.00 0.00 ATOM 367 NE2 HIS 50 25.341 26.921 20.080 1.00 0.00 ATOM 368 O HIS 50 27.126 24.585 25.466 1.00 0.00 ATOM 369 C HIS 50 27.584 23.946 24.518 1.00 0.00 ATOM 370 N GLY 51 28.454 22.953 24.672 1.00 0.00 ATOM 371 CA GLY 51 28.927 22.561 25.994 1.00 0.00 ATOM 372 O GLY 51 28.121 21.960 28.172 1.00 0.00 ATOM 373 C GLY 51 27.921 21.942 26.958 1.00 0.00 ATOM 374 N LEU 52 26.839 21.392 26.414 1.00 0.00 ATOM 375 CA LEU 52 25.838 20.784 27.229 1.00 0.00 ATOM 376 CB LEU 52 24.518 21.025 26.516 1.00 0.00 ATOM 377 CG LEU 52 23.350 20.339 27.216 1.00 0.00 ATOM 378 CD1 LEU 52 23.135 20.876 28.626 1.00 0.00 ATOM 379 CD2 LEU 52 22.140 20.577 26.344 1.00 0.00 ATOM 380 O LEU 52 26.389 18.714 26.192 1.00 0.00 ATOM 381 C LEU 52 26.135 19.284 27.249 1.00 0.00 ATOM 382 N ASN 53 26.246 18.705 28.431 1.00 0.00 ATOM 383 CA ASN 53 26.356 17.231 28.522 1.00 0.00 ATOM 384 CB ASN 53 26.539 16.763 29.974 1.00 0.00 ATOM 385 CG ASN 53 27.899 17.192 30.517 1.00 0.00 ATOM 386 ND2 ASN 53 27.988 17.289 31.818 1.00 0.00 ATOM 387 OD1 ASN 53 28.894 17.340 29.829 1.00 0.00 ATOM 388 O ASN 53 24.003 17.017 28.105 1.00 0.00 ATOM 389 C ASN 53 25.130 16.557 27.915 1.00 0.00 ATOM 390 N VAL 54 25.351 15.470 27.185 1.00 0.00 ATOM 391 CA VAL 54 24.239 14.730 26.547 1.00 0.00 ATOM 392 CB VAL 54 24.821 13.699 25.527 1.00 0.00 ATOM 393 CG1 VAL 54 23.724 12.796 24.994 1.00 0.00 ATOM 394 CG2 VAL 54 25.490 14.437 24.374 1.00 0.00 ATOM 395 O VAL 54 22.090 13.999 27.317 1.00 0.00 ATOM 396 C VAL 54 23.287 14.122 27.571 1.00 0.00 ATOM 397 N GLU 55 23.819 13.715 28.728 1.00 0.00 ATOM 398 CA GLU 55 22.984 13.143 29.774 1.00 0.00 ATOM 399 CB GLU 55 23.833 12.754 30.988 1.00 0.00 ATOM 400 CG GLU 55 24.715 11.534 30.726 1.00 0.00 ATOM 401 CD GLU 55 26.010 11.766 29.947 1.00 0.00 ATOM 402 OE1 GLU 55 26.407 12.944 29.784 1.00 0.00 ATOM 403 OE2 GLU 55 26.542 10.721 29.512 1.00 0.00 ATOM 404 O GLU 55 20.785 13.773 30.500 1.00 0.00 ATOM 405 C GLU 55 21.925 14.150 30.223 1.00 0.00 ATOM 406 N ASP 56 22.298 15.430 30.297 1.00 0.00 ATOM 407 CA ASP 56 21.357 16.481 30.691 1.00 0.00 ATOM 408 CB ASP 56 22.046 17.834 30.858 1.00 0.00 ATOM 409 CG ASP 56 23.010 17.902 32.043 1.00 0.00 ATOM 410 OD1 ASP 56 22.953 17.057 32.968 1.00 0.00 ATOM 411 OD2 ASP 56 23.826 18.827 32.041 1.00 0.00 ATOM 412 O ASP 56 19.070 16.691 29.995 1.00 0.00 ATOM 413 C ASP 56 20.247 16.568 29.650 1.00 0.00 ATOM 414 N ILE 57 20.620 16.503 28.376 1.00 0.00 ATOM 415 CA ILE 57 19.641 16.572 27.295 1.00 0.00 ATOM 416 CB ILE 57 20.263 16.412 25.915 1.00 0.00 ATOM 417 CG1 ILE 57 21.375 17.441 25.766 1.00 0.00 ATOM 418 CG2 ILE 57 19.166 16.649 24.863 1.00 0.00 ATOM 419 CD1 ILE 57 22.146 17.299 24.473 1.00 0.00 ATOM 420 O ILE 57 17.439 15.642 27.340 1.00 0.00 ATOM 421 C ILE 57 18.651 15.433 27.412 1.00 0.00 ATOM 422 N LEU 58 19.164 14.221 27.594 1.00 0.00 ATOM 423 CA LEU 58 18.306 13.048 27.723 1.00 0.00 ATOM 424 CB LEU 58 19.164 11.743 27.747 1.00 0.00 ATOM 425 CG LEU 58 19.967 11.461 26.503 1.00 0.00 ATOM 426 CD1 LEU 58 20.847 10.224 26.797 1.00 0.00 ATOM 427 CD2 LEU 58 19.070 11.293 25.277 1.00 0.00 ATOM 428 O LEU 58 16.220 12.734 28.863 1.00 0.00 ATOM 429 C LEU 58 17.380 13.144 28.929 1.00 0.00 ATOM 430 N ARG 59 17.891 13.688 30.029 1.00 0.00 ATOM 431 CA ARG 59 17.082 13.839 31.270 1.00 0.00 ATOM 432 CB ARG 59 17.909 14.424 32.395 1.00 0.00 ATOM 433 CG ARG 59 18.911 13.456 32.983 1.00 0.00 ATOM 434 CD ARG 59 19.246 13.845 34.414 1.00 0.00 ATOM 435 NE ARG 59 19.718 15.221 34.523 1.00 0.00 ATOM 436 CZ ARG 59 20.963 15.560 34.839 1.00 0.00 ATOM 437 NH1 ARG 59 21.867 14.621 35.077 1.00 0.00 ATOM 438 NH2 ARG 59 21.300 16.840 34.925 1.00 0.00 ATOM 439 O ARG 59 14.783 14.512 31.379 1.00 0.00 ATOM 440 C ARG 59 15.927 14.806 31.033 1.00 0.00 ATOM 441 N ASP 60 16.229 15.959 30.442 1.00 0.00 ATOM 442 CA ASP 60 15.208 16.947 30.167 1.00 0.00 ATOM 443 CB ASP 60 15.734 18.336 29.822 1.00 0.00 ATOM 444 CG ASP 60 14.565 19.320 29.936 1.00 0.00 ATOM 445 OD1 ASP 60 13.766 19.185 30.885 1.00 0.00 ATOM 446 OD2 ASP 60 14.356 20.095 28.978 1.00 0.00 ATOM 447 O ASP 60 13.005 16.687 29.239 1.00 0.00 ATOM 448 C ASP 60 14.204 16.431 29.130 1.00 0.00 ATOM 449 N LEU 61 14.697 15.707 28.130 1.00 0.00 ATOM 450 CA LEU 61 13.831 15.164 27.091 1.00 0.00 ATOM 451 CB LEU 61 14.645 14.409 26.044 1.00 0.00 ATOM 452 CG LEU 61 15.506 15.286 25.153 1.00 0.00 ATOM 453 CD1 LEU 61 16.322 14.385 24.233 1.00 0.00 ATOM 454 CD2 LEU 61 14.666 16.235 24.295 1.00 0.00 ATOM 455 O LEU 61 11.626 14.310 27.537 1.00 0.00 ATOM 456 C LEU 61 12.835 14.203 27.752 1.00 0.00 ATOM 457 N ASN 62 13.344 13.271 28.551 1.00 0.00 ATOM 458 CA ASN 62 12.486 12.306 29.230 1.00 0.00 ATOM 459 CB ASN 62 13.330 11.259 29.955 1.00 0.00 ATOM 460 CG ASN 62 13.801 10.165 29.002 1.00 0.00 ATOM 461 ND2 ASN 62 14.967 9.637 29.291 1.00 0.00 ATOM 462 OD1 ASN 62 13.179 9.836 27.990 1.00 0.00 ATOM 463 O ASN 62 10.374 12.565 30.371 1.00 0.00 ATOM 464 C ASN 62 11.525 12.984 30.212 1.00 0.00 ATOM 465 N ALA 63 11.960 14.065 30.860 1.00 0.00 ATOM 466 CA ALA 63 11.111 14.768 31.817 1.00 0.00 ATOM 467 CB ALA 63 11.922 15.808 32.555 1.00 0.00 ATOM 468 O ALA 63 8.771 15.363 31.739 1.00 0.00 ATOM 469 C ALA 63 9.847 15.311 31.132 1.00 0.00 ATOM 470 N LEU 64 10.009 15.718 29.873 1.00 0.00 ATOM 471 CA LEU 64 8.900 16.228 29.060 1.00 0.00 ATOM 472 CB LEU 64 9.444 16.885 27.787 1.00 0.00 ATOM 473 CG LEU 64 8.370 17.402 26.799 1.00 0.00 ATOM 474 CD1 LEU 64 7.488 18.494 27.415 1.00 0.00 ATOM 475 CD2 LEU 64 9.023 17.944 25.528 1.00 0.00 ATOM 476 O LEU 64 6.672 15.258 29.027 1.00 0.00 ATOM 477 C LEU 64 7.869 15.078 28.796 1.00 0.00 ATOM 478 N ALA 65 8.347 13.931 28.322 1.00 0.00 ATOM 479 CA ALA 65 7.466 12.802 28.046 1.00 0.00 ATOM 480 CB ALA 65 6.808 13.085 26.694 1.00 0.00 ATOM 481 O ALA 65 9.420 11.419 28.095 1.00 0.00 ATOM 482 C ALA 65 8.195 11.452 27.890 1.00 0.00 TER END