PFRMAT TS TARGET T0498 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 All my predictions, whether from SAM+undertaker or metaserver METHOD predictions, came out almost identical. There are some differences in METHOD placing F52 and some of the surface residues, but it is hard do METHOD distinguish among the models. METHOD METHOD The first two models are metaserver models, optimized by undertaker METHOD from YASARA_TS3. The first one is then energy-minimized by gromacs, METHOD and has the sidechains repacked by rosetta design. METHOD METHOD The third and fifth models is are optimized strictly from METHOD SAM+undertaker models. The 4th model is a meta-server model, but METHOD using our own SAM-T08 server. METHOD METHOD METHOD Model METHOD 1 T0498.MQAX4-opt3.gromacs0.repack-nonPC.pdb #< YASARA_TS3 METHOD # best rosetta energy METHOD METHOD 2 T0498.MQAX4-opt3.pdb #< YASARA_TS3 METHOD METHOD 3 T0498.try4-opt3.pdb #< try3-opt3.gromacs0 < align(2gi9A) METHOD METHOD 4 T0498.MQAC1-opt3.gromacs0.pdb # < SAM-T08-server_TS1 METHOD METHOD 5 T0498.try2-opt3.pdb # < try1-opt3 < align(2gi9A) METHOD METHOD METHOD METHOD REMARK 6 REMARK 6 T0498 model 1 Tue Jul 15 13:37:25 2008 MODEL 1 PARENT 2i38_A 2i2y_A 1ibx_B 1pn5_A 2cwb_A REMARK 7 REMARK 7 ALLPARENTS 2i38_A 2i2y_A 1ibx_B 1pn5_A 2cwb_A 1pgx_A 2igg_A REMARK 7 ALLPARENTS 1pgb_A 2igh_A 2igd_A 2qmt_A 1fcc_C ATOM 1 N THR 1 13.616 8.868 15.220 1.00 0.00 ATOM 2 CA THR 1 14.064 9.158 16.591 1.00 0.00 ATOM 3 CB THR 1 15.599 9.118 16.704 1.00 0.00 ATOM 4 CG2 THR 1 16.039 9.469 18.117 1.00 0.00 ATOM 5 OG1 THR 1 16.072 7.807 16.371 1.00 0.00 ATOM 6 O THR 1 13.526 11.448 16.149 1.00 0.00 ATOM 7 C THR 1 13.514 10.539 16.959 1.00 0.00 ATOM 8 N THR 2 13.032 10.629 18.189 1.00 0.00 ATOM 9 CA THR 2 12.582 11.910 18.758 1.00 0.00 ATOM 10 CB THR 2 11.629 11.695 19.948 1.00 0.00 ATOM 11 CG2 THR 2 11.182 13.032 20.521 1.00 0.00 ATOM 12 OG1 THR 2 10.479 10.956 19.515 1.00 0.00 ATOM 13 O THR 2 14.460 12.399 20.201 1.00 0.00 ATOM 14 C THR 2 13.822 12.699 19.189 1.00 0.00 ATOM 15 N TYR 3 13.983 13.859 18.590 1.00 0.00 ATOM 16 CA TYR 3 15.013 14.818 19.021 1.00 0.00 ATOM 17 CB TYR 3 15.845 15.288 17.832 1.00 0.00 ATOM 18 CG TYR 3 16.626 14.137 17.204 1.00 0.00 ATOM 19 CD1 TYR 3 16.047 13.347 16.223 1.00 0.00 ATOM 20 CD2 TYR 3 17.925 13.866 17.606 1.00 0.00 ATOM 21 CE1 TYR 3 16.737 12.297 15.634 1.00 0.00 ATOM 22 CE2 TYR 3 18.595 12.796 17.018 1.00 0.00 ATOM 23 CZ TYR 3 18.017 12.006 16.057 1.00 0.00 ATOM 24 OH TYR 3 18.667 10.876 15.658 1.00 0.00 ATOM 25 O TYR 3 13.143 16.289 19.378 1.00 0.00 ATOM 26 C TYR 3 14.313 16.019 19.650 1.00 0.00 ATOM 27 N LYS 4 15.001 16.639 20.601 1.00 0.00 ATOM 28 CA LYS 4 14.461 17.799 21.319 1.00 0.00 ATOM 29 CB LYS 4 14.451 17.538 22.827 1.00 0.00 ATOM 30 CG LYS 4 13.818 18.651 23.653 1.00 0.00 ATOM 31 CD LYS 4 13.858 18.326 25.139 1.00 0.00 ATOM 32 CE LYS 4 12.874 17.221 25.492 1.00 0.00 ATOM 33 NZ LYS 4 12.914 16.881 26.940 1.00 0.00 ATOM 34 O LYS 4 16.433 18.998 20.643 1.00 0.00 ATOM 35 C LYS 4 15.262 19.069 21.011 1.00 0.00 ATOM 36 N LEU 5 14.562 20.189 21.159 1.00 0.00 ATOM 37 CA LEU 5 15.173 21.519 21.230 1.00 0.00 ATOM 38 CB LEU 5 14.575 22.439 20.159 1.00 0.00 ATOM 39 CG LEU 5 15.126 23.878 20.239 1.00 0.00 ATOM 40 CD1 LEU 5 16.567 23.918 19.732 1.00 0.00 ATOM 41 CD2 LEU 5 14.278 24.879 19.448 1.00 0.00 ATOM 42 O LEU 5 13.690 22.180 22.987 1.00 0.00 ATOM 43 C LEU 5 14.861 22.119 22.609 1.00 0.00 ATOM 44 N ILE 6 15.910 22.559 23.281 1.00 0.00 ATOM 45 CA ILE 6 15.779 23.519 24.390 1.00 0.00 ATOM 46 CB ILE 6 16.671 23.130 25.583 1.00 0.00 ATOM 47 CG1 ILE 6 16.282 21.746 26.112 1.00 0.00 ATOM 48 CG2 ILE 6 16.569 24.172 26.686 1.00 0.00 ATOM 49 CD1 ILE 6 17.241 21.194 27.141 1.00 0.00 ATOM 50 O ILE 6 17.301 25.138 23.433 1.00 0.00 ATOM 51 C ILE 6 16.161 24.899 23.821 1.00 0.00 ATOM 52 N LEU 7 15.141 25.739 23.729 1.00 0.00 ATOM 53 CA LEU 7 15.283 27.099 23.199 1.00 0.00 ATOM 54 CB LEU 7 14.047 27.478 22.373 1.00 0.00 ATOM 55 CG LEU 7 13.962 28.953 21.963 1.00 0.00 ATOM 56 CD1 LEU 7 15.188 29.340 21.146 1.00 0.00 ATOM 57 CD2 LEU 7 12.687 29.187 21.167 1.00 0.00 ATOM 58 O LEU 7 14.650 28.320 25.188 1.00 0.00 ATOM 59 C LEU 7 15.502 28.129 24.309 1.00 0.00 ATOM 60 N ASN 8 16.592 28.869 24.181 1.00 0.00 ATOM 61 CA ASN 8 16.911 29.889 25.181 1.00 0.00 ATOM 62 CB ASN 8 17.975 29.404 26.148 1.00 0.00 ATOM 63 CG ASN 8 18.170 30.305 27.336 1.00 0.00 ATOM 64 ND2 ASN 8 19.379 30.327 27.836 1.00 0.00 ATOM 65 OD1 ASN 8 17.256 31.029 27.747 1.00 0.00 ATOM 66 O ASN 8 18.453 31.718 24.653 1.00 0.00 ATOM 67 C ASN 8 17.353 31.188 24.481 1.00 0.00 ATOM 68 N LEU 9 16.465 31.638 23.600 1.00 0.00 ATOM 69 CA LEU 9 16.536 32.988 22.990 1.00 0.00 ATOM 70 CB LEU 9 15.589 33.078 21.787 1.00 0.00 ATOM 71 CG LEU 9 15.724 34.350 20.942 1.00 0.00 ATOM 72 CD1 LEU 9 17.097 34.398 20.285 1.00 0.00 ATOM 73 CD2 LEU 9 14.622 34.385 19.893 1.00 0.00 ATOM 74 O LEU 9 15.334 33.699 24.938 1.00 0.00 ATOM 75 C LEU 9 16.185 33.999 24.099 1.00 0.00 ATOM 76 N LYS 10 16.686 35.228 23.999 1.00 0.00 ATOM 77 CA LYS 10 16.275 36.269 24.959 1.00 0.00 ATOM 78 CB LYS 10 17.001 37.583 24.666 1.00 0.00 ATOM 79 CG LYS 10 16.687 38.706 25.647 1.00 0.00 ATOM 80 CD LYS 10 17.516 39.946 25.351 1.00 0.00 ATOM 81 CE LYS 10 17.209 41.067 26.334 1.00 0.00 ATOM 82 NZ LYS 10 18.019 42.284 26.061 1.00 0.00 ATOM 83 O LYS 10 14.163 36.740 26.005 1.00 0.00 ATOM 84 C LYS 10 14.745 36.510 24.946 1.00 0.00 ATOM 85 N GLN 11 14.097 36.230 23.825 1.00 0.00 ATOM 86 CA GLN 11 12.647 36.441 23.752 1.00 0.00 ATOM 87 CB GLN 11 12.293 37.323 22.552 1.00 0.00 ATOM 88 CG GLN 11 12.864 38.728 22.622 1.00 0.00 ATOM 89 CD GLN 11 12.496 39.563 21.410 1.00 0.00 ATOM 90 OE1 GLN 11 11.728 39.127 20.548 1.00 0.00 ATOM 91 NE2 GLN 11 13.045 40.771 21.336 1.00 0.00 ATOM 92 O GLN 11 10.626 35.222 23.919 1.00 0.00 ATOM 93 C GLN 11 11.817 35.151 23.651 1.00 0.00 ATOM 94 N ALA 12 12.466 33.991 23.703 1.00 0.00 ATOM 95 CA ALA 12 11.755 32.701 23.642 1.00 0.00 ATOM 96 CB ALA 12 11.587 32.251 22.191 1.00 0.00 ATOM 97 O ALA 12 13.673 31.340 24.215 1.00 0.00 ATOM 98 C ALA 12 12.483 31.611 24.433 1.00 0.00 ATOM 99 N LYS 13 11.811 31.121 25.462 1.00 0.00 ATOM 100 CA LYS 13 12.439 30.101 26.313 1.00 0.00 ATOM 101 CB LYS 13 12.976 30.733 27.599 1.00 0.00 ATOM 102 CG LYS 13 13.724 29.768 28.509 1.00 0.00 ATOM 103 CD LYS 13 14.366 30.496 29.681 1.00 0.00 ATOM 104 CE LYS 13 15.206 29.552 30.528 1.00 0.00 ATOM 105 NZ LYS 13 15.894 30.265 31.638 1.00 0.00 ATOM 106 O LYS 13 10.507 29.133 27.390 1.00 0.00 ATOM 107 C LYS 13 11.498 28.952 26.682 1.00 0.00 ATOM 108 N GLU 14 11.729 27.872 25.953 1.00 0.00 ATOM 109 CA GLU 14 10.818 26.722 25.851 1.00 0.00 ATOM 110 CB GLU 14 9.681 27.023 24.873 1.00 0.00 ATOM 111 CG GLU 14 10.134 27.280 23.442 1.00 0.00 ATOM 112 CD GLU 14 8.974 27.651 22.561 1.00 0.00 ATOM 113 OE1 GLU 14 7.867 27.676 23.045 1.00 0.00 ATOM 114 OE2 GLU 14 9.205 28.021 21.433 1.00 0.00 ATOM 115 O GLU 14 12.759 25.501 25.055 1.00 0.00 ATOM 116 C GLU 14 11.578 25.462 25.413 1.00 0.00 ATOM 117 N GLU 15 10.838 24.362 25.392 1.00 0.00 ATOM 118 CA GLU 15 11.308 23.042 24.943 1.00 0.00 ATOM 119 CB GLU 15 11.500 22.107 26.139 1.00 0.00 ATOM 120 CG GLU 15 12.578 22.550 27.118 1.00 0.00 ATOM 121 CD GLU 15 12.710 21.583 28.260 1.00 0.00 ATOM 122 OE1 GLU 15 11.977 20.624 28.291 1.00 0.00 ATOM 123 OE2 GLU 15 13.619 21.738 29.042 1.00 0.00 ATOM 124 O GLU 15 9.069 22.613 24.169 1.00 0.00 ATOM 125 C GLU 15 10.279 22.502 23.951 1.00 0.00 ATOM 126 N ALA 16 10.780 21.831 22.922 1.00 0.00 ATOM 127 CA ALA 16 9.962 21.202 21.881 1.00 0.00 ATOM 128 CB ALA 16 9.734 22.062 20.641 1.00 0.00 ATOM 129 O ALA 16 11.862 19.801 21.455 1.00 0.00 ATOM 130 C ALA 16 10.642 19.951 21.343 1.00 0.00 ATOM 131 N ILE 17 9.833 19.092 20.761 1.00 0.00 ATOM 132 CA ILE 17 10.313 17.781 20.272 1.00 0.00 ATOM 133 CB ILE 17 9.801 16.628 21.154 1.00 0.00 ATOM 134 CG1 ILE 17 8.270 16.597 21.158 1.00 0.00 ATOM 135 CG2 ILE 17 10.338 16.761 22.570 1.00 0.00 ATOM 136 CD1 ILE 17 7.685 15.390 21.854 1.00 0.00 ATOM 137 O ILE 17 8.836 18.062 18.420 1.00 0.00 ATOM 138 C ILE 17 9.875 17.541 18.822 1.00 0.00 ATOM 139 N LYS 18 10.716 16.840 18.063 1.00 0.00 ATOM 140 CA LYS 18 10.438 16.470 16.653 1.00 0.00 ATOM 141 CB LYS 18 11.030 17.510 15.700 1.00 0.00 ATOM 142 CG LYS 18 10.449 18.909 15.854 1.00 0.00 ATOM 143 CD LYS 18 9.019 18.974 15.341 1.00 0.00 ATOM 144 CE LYS 18 8.433 20.369 15.506 1.00 0.00 ATOM 145 NZ LYS 18 7.017 20.435 15.053 1.00 0.00 ATOM 146 O LYS 18 12.117 14.749 16.696 1.00 0.00 ATOM 147 C LYS 18 10.988 15.080 16.314 1.00 0.00 ATOM 148 N GLU 19 10.199 14.290 15.593 1.00 0.00 ATOM 149 CA GLU 19 10.609 12.940 15.164 1.00 0.00 ATOM 150 CB GLU 19 9.395 12.012 15.084 1.00 0.00 ATOM 151 CG GLU 19 9.725 10.575 14.702 1.00 0.00 ATOM 152 CD GLU 19 8.488 9.723 14.660 1.00 0.00 ATOM 153 OE1 GLU 19 7.423 10.244 14.889 1.00 0.00 ATOM 154 OE2 GLU 19 8.593 8.577 14.291 1.00 0.00 ATOM 155 O GLU 19 10.753 13.439 12.814 1.00 0.00 ATOM 156 C GLU 19 11.331 12.989 13.805 1.00 0.00 ATOM 157 N LEU 20 12.621 12.678 13.827 1.00 0.00 ATOM 158 CA LEU 20 13.453 12.698 12.619 1.00 0.00 ATOM 159 CB LEU 20 14.374 13.927 12.530 1.00 0.00 ATOM 160 CG LEU 20 13.755 15.237 12.019 1.00 0.00 ATOM 161 CD1 LEU 20 12.867 15.038 10.787 1.00 0.00 ATOM 162 CD2 LEU 20 12.984 15.988 13.097 1.00 0.00 ATOM 163 O LEU 20 14.560 10.687 13.371 1.00 0.00 ATOM 164 C LEU 20 14.282 11.427 12.421 1.00 0.00 ATOM 165 N VAL 21 14.724 11.257 11.191 1.00 0.00 ATOM 166 CA VAL 21 15.494 10.066 10.793 1.00 0.00 ATOM 167 CB VAL 21 15.795 10.067 9.282 1.00 0.00 ATOM 168 CG1 VAL 21 16.752 8.938 8.929 1.00 0.00 ATOM 169 CG2 VAL 21 14.506 9.940 8.483 1.00 0.00 ATOM 170 O VAL 21 17.202 8.876 12.026 1.00 0.00 ATOM 171 C VAL 21 16.833 9.946 11.555 1.00 0.00 ATOM 172 N ASP 22 17.554 11.055 11.616 1.00 0.00 ATOM 173 CA ASP 22 18.893 11.115 12.218 1.00 0.00 ATOM 174 CB ASP 22 19.958 10.704 11.199 1.00 0.00 ATOM 175 CG ASP 22 19.974 11.548 9.931 1.00 0.00 ATOM 176 OD1 ASP 22 20.047 12.749 10.041 1.00 0.00 ATOM 177 OD2 ASP 22 20.071 10.983 8.867 1.00 0.00 ATOM 178 O ASP 22 18.303 13.425 12.547 1.00 0.00 ATOM 179 C ASP 22 19.132 12.535 12.738 1.00 0.00 ATOM 180 N ALA 23 20.251 12.694 13.440 1.00 0.00 ATOM 181 CA ALA 23 20.641 14.004 14.011 1.00 0.00 ATOM 182 CB ALA 23 21.940 13.864 14.803 1.00 0.00 ATOM 183 O ALA 23 20.254 16.184 13.100 1.00 0.00 ATOM 184 C ALA 23 20.804 15.094 12.941 1.00 0.00 ATOM 185 N GLY 24 21.305 14.693 11.782 1.00 0.00 ATOM 186 CA GLY 24 21.448 15.603 10.642 1.00 0.00 ATOM 187 O GLY 24 19.970 17.434 10.089 1.00 0.00 ATOM 188 C GLY 24 20.149 16.214 10.119 1.00 0.00 ATOM 189 N THR 25 19.189 15.334 9.878 1.00 0.00 ATOM 190 CA THR 25 17.830 15.755 9.466 1.00 0.00 ATOM 191 CB THR 25 17.030 14.545 8.964 1.00 0.00 ATOM 192 CG2 THR 25 15.611 14.896 8.532 1.00 0.00 ATOM 193 OG1 THR 25 17.692 14.064 7.796 1.00 0.00 ATOM 194 O THR 25 16.469 17.546 10.303 1.00 0.00 ATOM 195 C THR 25 17.118 16.535 10.574 1.00 0.00 ATOM 196 N ALA 26 17.376 16.145 11.825 1.00 0.00 ATOM 197 CA ALA 26 16.814 16.816 13.014 1.00 0.00 ATOM 198 CB ALA 26 17.142 16.026 14.274 1.00 0.00 ATOM 199 O ALA 26 16.505 19.166 13.313 1.00 0.00 ATOM 200 C ALA 26 17.315 18.256 13.174 1.00 0.00 ATOM 201 N GLU 27 18.605 18.455 12.946 1.00 0.00 ATOM 202 CA GLU 27 19.226 19.785 13.067 1.00 0.00 ATOM 203 CB GLU 27 20.706 19.604 12.790 1.00 0.00 ATOM 204 CG GLU 27 21.517 20.863 13.061 1.00 0.00 ATOM 205 CD GLU 27 22.987 20.682 12.693 1.00 0.00 ATOM 206 OE1 GLU 27 23.318 19.732 11.954 1.00 0.00 ATOM 207 OE2 GLU 27 23.717 21.672 12.884 1.00 0.00 ATOM 208 O GLU 27 18.208 21.875 12.455 1.00 0.00 ATOM 209 C GLU 27 18.608 20.785 12.066 1.00 0.00 ATOM 210 N LYS 28 18.420 20.315 10.836 1.00 0.00 ATOM 211 CA LYS 28 17.812 21.045 9.704 1.00 0.00 ATOM 212 CB LYS 28 17.814 20.177 8.445 1.00 0.00 ATOM 213 CG LYS 28 19.196 19.926 7.856 1.00 0.00 ATOM 214 CD LYS 28 19.115 19.067 6.602 1.00 0.00 ATOM 215 CE LYS 28 20.498 18.778 6.038 1.00 0.00 ATOM 216 NZ LYS 28 20.436 17.937 4.813 1.00 0.00 ATOM 217 O LYS 28 16.043 22.666 10.101 1.00 0.00 ATOM 218 C LYS 28 16.382 21.476 10.072 1.00 0.00 ATOM 219 N TYR 29 15.611 20.476 10.481 1.00 0.00 ATOM 220 CA TYR 29 14.190 20.637 10.798 1.00 0.00 ATOM 221 CB TYR 29 13.589 19.277 11.168 1.00 0.00 ATOM 222 CG TYR 29 12.059 19.318 11.235 1.00 0.00 ATOM 223 CD1 TYR 29 11.320 18.638 10.264 1.00 0.00 ATOM 224 CD2 TYR 29 11.397 20.009 12.224 1.00 0.00 ATOM 225 CE1 TYR 29 9.930 18.649 10.302 1.00 0.00 ATOM 226 CE2 TYR 29 10.017 20.040 12.241 1.00 0.00 ATOM 227 CZ TYR 29 9.289 19.360 11.290 1.00 0.00 ATOM 228 OH TYR 29 7.938 19.341 11.418 1.00 0.00 ATOM 229 O TYR 29 13.310 22.628 11.856 1.00 0.00 ATOM 230 C TYR 29 14.019 21.627 11.968 1.00 0.00 ATOM 231 N ILE 30 14.787 21.377 13.029 1.00 0.00 ATOM 232 CA ILE 30 14.765 22.217 14.239 1.00 0.00 ATOM 233 CB ILE 30 15.596 21.594 15.375 1.00 0.00 ATOM 234 CG1 ILE 30 14.932 20.310 15.880 1.00 0.00 ATOM 235 CG2 ILE 30 15.773 22.587 16.513 1.00 0.00 ATOM 236 CD1 ILE 30 15.805 19.494 16.806 1.00 0.00 ATOM 237 O ILE 30 14.716 24.607 14.438 1.00 0.00 ATOM 238 C ILE 30 15.297 23.637 13.950 1.00 0.00 ATOM 239 N LYS 31 16.288 23.766 13.061 1.00 0.00 ATOM 240 CA LYS 31 16.820 25.086 12.652 1.00 0.00 ATOM 241 CB LYS 31 18.061 24.915 11.774 1.00 0.00 ATOM 242 CG LYS 31 18.713 26.223 11.346 1.00 0.00 ATOM 243 CD LYS 31 19.986 25.972 10.550 1.00 0.00 ATOM 244 CE LYS 31 20.624 27.277 10.100 1.00 0.00 ATOM 245 NZ LYS 31 21.861 27.046 9.305 1.00 0.00 ATOM 246 O LYS 31 15.621 27.096 12.159 1.00 0.00 ATOM 247 C LYS 31 15.761 25.906 11.910 1.00 0.00 ATOM 248 N LEU 32 14.982 25.237 11.059 1.00 0.00 ATOM 249 CA LEU 32 13.864 25.887 10.347 1.00 0.00 ATOM 250 CB LEU 32 13.254 24.921 9.323 1.00 0.00 ATOM 251 CG LEU 32 14.145 24.600 8.116 1.00 0.00 ATOM 252 CD1 LEU 32 13.511 23.501 7.276 1.00 0.00 ATOM 253 CD2 LEU 32 14.353 25.860 7.289 1.00 0.00 ATOM 254 O LEU 32 12.413 27.548 11.284 1.00 0.00 ATOM 255 C LEU 32 12.783 26.378 11.315 1.00 0.00 ATOM 256 N ILE 33 12.470 25.558 12.314 1.00 0.00 ATOM 257 CA ILE 33 11.569 26.009 13.403 1.00 0.00 ATOM 258 CB ILE 33 11.298 24.881 14.416 1.00 0.00 ATOM 259 CG1 ILE 33 10.552 23.727 13.743 1.00 0.00 ATOM 260 CG2 ILE 33 10.508 25.411 15.602 1.00 0.00 ATOM 261 CD1 ILE 33 9.195 24.111 13.198 1.00 0.00 ATOM 262 O ILE 33 11.418 28.189 14.402 1.00 0.00 ATOM 263 C ILE 33 12.138 27.219 14.154 1.00 0.00 ATOM 264 N ALA 34 13.428 27.128 14.476 1.00 0.00 ATOM 265 CA ALA 34 14.117 28.208 15.207 1.00 0.00 ATOM 266 CB ALA 34 15.556 27.787 15.539 1.00 0.00 ATOM 267 O ALA 34 13.749 30.558 14.936 1.00 0.00 ATOM 268 C ALA 34 14.129 29.518 14.416 1.00 0.00 ATOM 269 N ASN 35 14.381 29.407 13.107 1.00 0.00 ATOM 270 CA ASN 35 14.363 30.567 12.207 1.00 0.00 ATOM 271 CB ASN 35 14.842 30.197 10.814 1.00 0.00 ATOM 272 CG ASN 35 16.323 29.954 10.729 1.00 0.00 ATOM 273 ND2 ASN 35 16.731 29.322 9.658 1.00 0.00 ATOM 274 OD1 ASN 35 17.096 30.398 11.586 1.00 0.00 ATOM 275 O ASN 35 12.905 32.458 12.134 1.00 0.00 ATOM 276 C ASN 35 12.994 31.238 12.094 1.00 0.00 ATOM 277 N ALA 36 11.964 30.398 12.013 1.00 0.00 ATOM 278 CA ALA 36 10.574 30.879 11.970 1.00 0.00 ATOM 279 CB ALA 36 9.624 29.710 11.689 1.00 0.00 ATOM 280 O ALA 36 9.533 32.630 13.248 1.00 0.00 ATOM 281 C ALA 36 10.182 31.590 13.269 1.00 0.00 ATOM 282 N LYS 37 10.700 31.080 14.380 1.00 0.00 ATOM 283 CA LYS 37 10.508 31.700 15.700 1.00 0.00 ATOM 284 CB LYS 37 10.500 30.634 16.797 1.00 0.00 ATOM 285 CG LYS 37 9.263 29.745 16.801 1.00 0.00 ATOM 286 CD LYS 37 9.273 28.790 17.985 1.00 0.00 ATOM 287 CE LYS 37 8.039 27.899 17.988 1.00 0.00 ATOM 288 NZ LYS 37 8.057 26.929 19.117 1.00 0.00 ATOM 289 O LYS 37 11.806 33.090 17.182 1.00 0.00 ATOM 290 C LYS 37 11.578 32.750 16.021 1.00 0.00 ATOM 291 N THR 38 12.240 33.259 14.982 1.00 0.00 ATOM 292 CA THR 38 13.131 34.438 15.034 1.00 0.00 ATOM 293 CB THR 38 12.367 35.705 15.463 1.00 0.00 ATOM 294 CG2 THR 38 13.246 36.936 15.304 1.00 0.00 ATOM 295 OG1 THR 38 11.192 35.853 14.656 1.00 0.00 ATOM 296 O THR 38 14.748 35.148 16.736 1.00 0.00 ATOM 297 C THR 38 14.319 34.258 15.986 1.00 0.00 ATOM 298 N VAL 39 14.818 33.038 15.977 1.00 0.00 ATOM 299 CA VAL 39 15.947 32.637 16.829 1.00 0.00 ATOM 300 CB VAL 39 15.745 31.208 17.349 1.00 0.00 ATOM 301 CG1 VAL 39 16.913 30.747 18.221 1.00 0.00 ATOM 302 CG2 VAL 39 14.444 31.088 18.137 1.00 0.00 ATOM 303 O VAL 39 17.300 32.166 14.901 1.00 0.00 ATOM 304 C VAL 39 17.228 32.736 15.991 1.00 0.00 ATOM 305 N GLU 40 18.217 33.386 16.592 1.00 0.00 ATOM 306 CA GLU 40 19.628 33.305 16.165 1.00 0.00 ATOM 307 CB GLU 40 20.014 34.544 15.353 1.00 0.00 ATOM 308 CG GLU 40 21.449 34.542 14.847 1.00 0.00 ATOM 309 CD GLU 40 21.743 35.770 14.033 1.00 0.00 ATOM 310 OE1 GLU 40 20.859 36.576 13.867 1.00 0.00 ATOM 311 OE2 GLU 40 22.880 35.961 13.670 1.00 0.00 ATOM 312 O GLU 40 20.515 34.055 18.246 1.00 0.00 ATOM 313 C GLU 40 20.486 33.155 17.416 1.00 0.00 ATOM 314 N GLY 41 21.135 32.005 17.558 1.00 0.00 ATOM 315 CA GLY 41 21.993 31.784 18.729 1.00 0.00 ATOM 316 O GLY 41 23.134 30.103 17.431 1.00 0.00 ATOM 317 C GLY 41 23.033 30.704 18.501 1.00 0.00 ATOM 318 N VAL 42 23.781 30.474 19.572 1.00 0.00 ATOM 319 CA VAL 42 24.770 29.383 19.654 1.00 0.00 ATOM 320 CB VAL 42 25.681 29.538 20.887 1.00 0.00 ATOM 321 CG1 VAL 42 26.629 28.353 21.000 1.00 0.00 ATOM 322 CG2 VAL 42 26.464 30.839 20.810 1.00 0.00 ATOM 323 O VAL 42 23.188 27.834 20.612 1.00 0.00 ATOM 324 C VAL 42 23.989 28.063 19.703 1.00 0.00 ATOM 325 N TRP 43 24.310 27.193 18.764 1.00 0.00 ATOM 326 CA TRP 43 23.790 25.813 18.763 1.00 0.00 ATOM 327 CB TRP 43 23.652 25.353 17.323 1.00 0.00 ATOM 328 CG TRP 43 22.463 25.964 16.601 1.00 0.00 ATOM 329 CD1 TRP 43 22.575 26.903 15.681 1.00 0.00 ATOM 330 CD2 TRP 43 21.123 25.604 16.709 1.00 0.00 ATOM 331 CE2 TRP 43 20.455 26.415 15.808 1.00 0.00 ATOM 332 CE3 TRP 43 20.421 24.695 17.488 1.00 0.00 ATOM 333 NE1 TRP 43 21.366 27.174 15.199 1.00 0.00 ATOM 334 CZ2 TRP 43 19.075 26.335 15.675 1.00 0.00 ATOM 335 CZ3 TRP 43 19.041 24.616 17.346 1.00 0.00 ATOM 336 CH2 TRP 43 18.373 25.426 16.454 1.00 0.00 ATOM 337 O TRP 43 25.878 24.642 19.097 1.00 0.00 ATOM 338 C TRP 43 24.738 24.843 19.475 1.00 0.00 ATOM 339 N THR 44 24.166 24.034 20.355 1.00 0.00 ATOM 340 CA THR 44 24.864 22.833 20.846 1.00 0.00 ATOM 341 CB THR 44 25.292 22.973 22.307 1.00 0.00 ATOM 342 CG2 THR 44 26.021 21.723 22.808 1.00 0.00 ATOM 343 OG1 THR 44 26.193 24.083 22.418 1.00 0.00 ATOM 344 O THR 44 22.754 21.724 20.763 1.00 0.00 ATOM 345 C THR 44 23.974 21.604 20.665 1.00 0.00 ATOM 346 N LEU 45 24.584 20.483 20.336 1.00 0.00 ATOM 347 CA LEU 45 23.863 19.204 20.285 1.00 0.00 ATOM 348 CB LEU 45 23.832 18.670 18.847 1.00 0.00 ATOM 349 CG LEU 45 23.378 17.213 18.702 1.00 0.00 ATOM 350 CD1 LEU 45 21.914 17.078 19.098 1.00 0.00 ATOM 351 CD2 LEU 45 23.592 16.753 17.267 1.00 0.00 ATOM 352 O LEU 45 25.711 17.913 21.158 1.00 0.00 ATOM 353 C LEU 45 24.521 18.203 21.226 1.00 0.00 ATOM 354 N LYS 46 23.700 17.584 22.055 1.00 0.00 ATOM 355 CA LYS 46 24.118 16.434 22.856 1.00 0.00 ATOM 356 CB LYS 46 23.816 16.675 24.337 1.00 0.00 ATOM 357 CG LYS 46 24.616 17.807 24.966 1.00 0.00 ATOM 358 CD LYS 46 24.302 17.949 26.447 1.00 0.00 ATOM 359 CE LYS 46 25.111 19.072 27.080 1.00 0.00 ATOM 360 NZ LYS 46 24.911 19.141 28.553 1.00 0.00 ATOM 361 O LYS 46 22.267 14.915 22.713 1.00 0.00 ATOM 362 C LYS 46 23.408 15.174 22.345 1.00 0.00 ATOM 363 N ASP 47 24.159 14.384 21.587 1.00 0.00 ATOM 364 CA ASP 47 23.709 13.094 21.036 1.00 0.00 ATOM 365 CB ASP 47 24.838 12.423 20.249 1.00 0.00 ATOM 366 CG ASP 47 25.148 13.080 18.911 1.00 0.00 ATOM 367 OD1 ASP 47 24.374 13.902 18.481 1.00 0.00 ATOM 368 OD2 ASP 47 26.226 12.874 18.407 1.00 0.00 ATOM 369 O ASP 47 22.096 11.695 22.094 1.00 0.00 ATOM 370 C ASP 47 23.216 12.174 22.175 1.00 0.00 ATOM 371 N GLU 48 23.814 12.304 23.366 1.00 0.00 ATOM 372 CA GLU 48 23.522 11.395 24.506 1.00 0.00 ATOM 373 CB GLU 48 24.500 11.645 25.656 1.00 0.00 ATOM 374 CG GLU 48 25.926 11.194 25.377 1.00 0.00 ATOM 375 CD GLU 48 26.846 11.553 26.512 1.00 0.00 ATOM 376 OE1 GLU 48 26.395 12.184 27.438 1.00 0.00 ATOM 377 OE2 GLU 48 27.967 11.104 26.507 1.00 0.00 ATOM 378 O GLU 48 21.460 10.606 25.533 1.00 0.00 ATOM 379 C GLU 48 22.091 11.526 25.034 1.00 0.00 ATOM 380 N ILE 49 21.582 12.736 24.863 1.00 0.00 ATOM 381 CA ILE 49 20.182 13.047 25.210 1.00 0.00 ATOM 382 CB ILE 49 20.100 14.117 26.300 1.00 0.00 ATOM 383 CG1 ILE 49 20.892 15.377 25.921 1.00 0.00 ATOM 384 CG2 ILE 49 20.538 13.507 27.641 1.00 0.00 ATOM 385 CD1 ILE 49 20.671 16.577 26.840 1.00 0.00 ATOM 386 O ILE 49 18.224 13.848 24.137 1.00 0.00 ATOM 387 C ILE 49 19.384 13.467 23.979 1.00 0.00 ATOM 388 N LYS 50 19.916 13.236 22.780 1.00 0.00 ATOM 389 CA LYS 50 19.278 13.556 21.489 1.00 0.00 ATOM 390 CB LYS 50 18.261 12.478 21.112 1.00 0.00 ATOM 391 CG LYS 50 18.838 11.072 21.028 1.00 0.00 ATOM 392 CD LYS 50 19.858 10.957 19.906 1.00 0.00 ATOM 393 CE LYS 50 20.394 9.537 19.786 1.00 0.00 ATOM 394 NZ LYS 50 21.487 9.439 18.781 1.00 0.00 ATOM 395 O LYS 50 17.420 15.137 21.255 1.00 0.00 ATOM 396 C LYS 50 18.599 14.957 21.567 1.00 0.00 ATOM 397 N THR 51 19.338 15.877 22.198 1.00 0.00 ATOM 398 CA THR 51 18.869 17.247 22.527 1.00 0.00 ATOM 399 CB THR 51 18.736 17.457 24.057 1.00 0.00 ATOM 400 CG2 THR 51 18.296 18.868 24.466 1.00 0.00 ATOM 401 OG1 THR 51 17.825 16.518 24.615 1.00 0.00 ATOM 402 O THR 51 21.030 18.246 22.170 1.00 0.00 ATOM 403 C THR 51 19.820 18.286 21.938 1.00 0.00 ATOM 404 N PHE 52 19.212 19.166 21.167 1.00 0.00 ATOM 405 CA PHE 52 19.803 20.436 20.708 1.00 0.00 ATOM 406 CB PHE 52 19.186 20.876 19.377 1.00 0.00 ATOM 407 CG PHE 52 19.767 20.135 18.188 1.00 0.00 ATOM 408 CD1 PHE 52 19.078 19.076 17.607 1.00 0.00 ATOM 409 CD2 PHE 52 20.999 20.535 17.700 1.00 0.00 ATOM 410 CE1 PHE 52 19.639 18.415 16.518 1.00 0.00 ATOM 411 CE2 PHE 52 21.560 19.884 16.611 1.00 0.00 ATOM 412 CZ PHE 52 20.880 18.814 16.030 1.00 0.00 ATOM 413 O PHE 52 18.282 21.667 22.105 1.00 0.00 ATOM 414 C PHE 52 19.432 21.526 21.707 1.00 0.00 ATOM 415 N THR 53 20.422 22.356 22.009 1.00 0.00 ATOM 416 CA THR 53 20.222 23.566 22.828 1.00 0.00 ATOM 417 CB THR 53 20.984 23.478 24.163 1.00 0.00 ATOM 418 CG2 THR 53 20.771 24.740 24.984 1.00 0.00 ATOM 419 OG1 THR 53 20.520 22.343 24.907 1.00 0.00 ATOM 420 O THR 53 21.864 24.825 21.630 1.00 0.00 ATOM 421 C THR 53 20.694 24.776 22.008 1.00 0.00 ATOM 422 N VAL 54 19.794 25.726 21.807 1.00 0.00 ATOM 423 CA VAL 54 20.126 26.996 21.127 1.00 0.00 ATOM 424 CB VAL 54 19.243 27.220 19.886 1.00 0.00 ATOM 425 CG1 VAL 54 17.794 27.442 20.297 1.00 0.00 ATOM 426 CG2 VAL 54 19.752 28.403 19.076 1.00 0.00 ATOM 427 O VAL 54 18.845 28.437 22.585 1.00 0.00 ATOM 428 C VAL 54 19.955 28.156 22.117 1.00 0.00 ATOM 429 N THR 55 21.055 28.856 22.318 1.00 0.00 ATOM 430 CA THR 55 21.084 29.976 23.268 1.00 0.00 ATOM 431 CB THR 55 21.945 29.649 24.503 1.00 0.00 ATOM 432 CG2 THR 55 21.964 30.825 25.466 1.00 0.00 ATOM 433 OG1 THR 55 21.411 28.497 25.169 1.00 0.00 ATOM 434 O THR 55 22.697 31.135 21.951 1.00 0.00 ATOM 435 C THR 55 21.626 31.215 22.559 1.00 0.00 ATOM 436 N GLU 56 20.927 32.316 22.737 1.00 0.00 ATOM 437 CA GLU 56 21.418 33.625 22.268 1.00 0.00 ATOM 438 CB GLU 56 20.328 34.676 22.476 1.00 0.00 ATOM 439 CG GLU 56 20.630 35.966 21.686 1.00 0.00 ATOM 440 CD GLU 56 19.660 37.106 21.984 1.00 0.00 ATOM 441 OE1 GLU 56 18.520 36.807 22.392 1.00 0.00 ATOM 442 OE2 GLU 56 20.032 38.276 21.724 1.00 0.00 ATOM 443 O GLU 56 23.245 33.285 23.851 1.00 0.00 ATOM 444 C GLU 56 22.747 34.025 22.960 1.00 0.00 TER END