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 3 Tue Jul 15 13:37:25 2008 MODEL 3 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 13.511 8.796 15.295 1.00 0.00 ATOM 2 CA THR 1 13.925 8.959 16.677 1.00 0.00 ATOM 3 CB THR 1 15.465 8.990 16.798 1.00 0.00 ATOM 4 CG2 THR 1 15.951 9.039 18.224 1.00 0.00 ATOM 5 OG1 THR 1 16.008 7.751 16.291 1.00 0.00 ATOM 6 O THR 1 13.399 11.287 16.433 1.00 0.00 ATOM 7 C THR 1 13.422 10.309 17.181 1.00 0.00 ATOM 8 N THR 2 13.008 10.354 18.443 1.00 0.00 ATOM 9 CA THR 2 12.515 11.557 18.996 1.00 0.00 ATOM 10 CB THR 2 11.600 11.246 20.182 1.00 0.00 ATOM 11 CG2 THR 2 11.021 12.514 20.833 1.00 0.00 ATOM 12 OG1 THR 2 10.527 10.434 19.700 1.00 0.00 ATOM 13 O THR 2 14.614 11.939 20.094 1.00 0.00 ATOM 14 C THR 2 13.686 12.424 19.446 1.00 0.00 ATOM 15 N TYR 3 13.637 13.709 19.108 1.00 0.00 ATOM 16 CA TYR 3 14.690 14.623 19.493 1.00 0.00 ATOM 17 CB TYR 3 15.394 15.097 18.240 1.00 0.00 ATOM 18 CG TYR 3 16.245 14.055 17.546 1.00 0.00 ATOM 19 CD1 TYR 3 15.697 13.352 16.496 1.00 0.00 ATOM 20 CD2 TYR 3 17.549 13.832 17.954 1.00 0.00 ATOM 21 CE1 TYR 3 16.456 12.417 15.821 1.00 0.00 ATOM 22 CE2 TYR 3 18.297 12.874 17.284 1.00 0.00 ATOM 23 CZ TYR 3 17.756 12.182 16.213 1.00 0.00 ATOM 24 OH TYR 3 18.448 11.192 15.587 1.00 0.00 ATOM 25 O TYR 3 12.990 16.275 19.862 1.00 0.00 ATOM 26 C TYR 3 14.097 15.844 20.188 1.00 0.00 ATOM 27 N LYS 4 14.833 16.401 21.145 1.00 0.00 ATOM 28 CA LYS 4 14.364 17.574 21.877 1.00 0.00 ATOM 29 CB LYS 4 14.555 17.362 23.377 1.00 0.00 ATOM 30 CG LYS 4 13.604 16.308 23.931 1.00 0.00 ATOM 31 CD LYS 4 13.881 16.049 25.407 1.00 0.00 ATOM 32 CE LYS 4 12.963 14.924 25.881 1.00 0.00 ATOM 33 NZ LYS 4 13.123 14.736 27.311 1.00 0.00 ATOM 34 O LYS 4 16.357 18.698 21.107 1.00 0.00 ATOM 35 C LYS 4 15.180 18.796 21.472 1.00 0.00 ATOM 36 N LEU 5 14.523 19.936 21.519 1.00 0.00 ATOM 37 CA LEU 5 15.173 21.246 21.375 1.00 0.00 ATOM 38 CB LEU 5 14.690 21.945 20.118 1.00 0.00 ATOM 39 CG LEU 5 15.218 23.376 20.020 1.00 0.00 ATOM 40 CD1 LEU 5 16.737 23.457 19.801 1.00 0.00 ATOM 41 CD2 LEU 5 14.373 24.067 18.971 1.00 0.00 ATOM 42 O LEU 5 13.691 22.226 22.947 1.00 0.00 ATOM 43 C LEU 5 14.858 22.104 22.572 1.00 0.00 ATOM 44 N ILE 6 15.914 22.661 23.178 1.00 0.00 ATOM 45 CA ILE 6 15.771 23.583 24.289 1.00 0.00 ATOM 46 CB ILE 6 16.691 23.216 25.500 1.00 0.00 ATOM 47 CG1 ILE 6 16.314 21.809 26.044 1.00 0.00 ATOM 48 CG2 ILE 6 16.577 24.314 26.618 1.00 0.00 ATOM 49 CD1 ILE 6 17.429 21.308 26.996 1.00 0.00 ATOM 50 O ILE 6 17.197 25.195 23.259 1.00 0.00 ATOM 51 C ILE 6 16.108 24.962 23.785 1.00 0.00 ATOM 52 N LEU 7 15.172 25.892 23.943 1.00 0.00 ATOM 53 CA LEU 7 15.385 27.263 23.497 1.00 0.00 ATOM 54 CB LEU 7 14.108 27.826 22.873 1.00 0.00 ATOM 55 CG LEU 7 13.600 27.059 21.671 1.00 0.00 ATOM 56 CD1 LEU 7 12.253 27.660 21.288 1.00 0.00 ATOM 57 CD2 LEU 7 14.522 27.215 20.468 1.00 0.00 ATOM 58 O LEU 7 14.987 28.081 25.724 1.00 0.00 ATOM 59 C LEU 7 15.700 28.126 24.713 1.00 0.00 ATOM 60 N ASN 8 16.825 28.810 24.607 1.00 0.00 ATOM 61 CA ASN 8 17.152 29.884 25.547 1.00 0.00 ATOM 62 CB ASN 8 18.433 29.540 26.313 1.00 0.00 ATOM 63 CG ASN 8 18.214 28.310 27.177 1.00 0.00 ATOM 64 ND2 ASN 8 17.116 28.298 27.924 1.00 0.00 ATOM 65 OD1 ASN 8 19.057 27.377 27.194 1.00 0.00 ATOM 66 O ASN 8 18.522 31.610 24.598 1.00 0.00 ATOM 67 C ASN 8 17.385 31.157 24.741 1.00 0.00 ATOM 68 N LEU 9 16.309 31.733 24.216 1.00 0.00 ATOM 69 CA LEU 9 16.420 32.930 23.447 1.00 0.00 ATOM 70 CB LEU 9 15.476 32.910 22.282 1.00 0.00 ATOM 71 CG LEU 9 15.667 31.656 21.472 1.00 0.00 ATOM 72 CD1 LEU 9 14.473 31.599 20.562 1.00 0.00 ATOM 73 CD2 LEU 9 17.018 31.667 20.768 1.00 0.00 ATOM 74 O LEU 9 15.372 33.844 25.381 1.00 0.00 ATOM 75 C LEU 9 16.000 34.064 24.350 1.00 0.00 ATOM 76 N LYS 10 16.307 35.268 23.905 1.00 0.00 ATOM 77 CA LYS 10 15.961 36.476 24.676 1.00 0.00 ATOM 78 CB LYS 10 16.616 37.710 24.014 1.00 0.00 ATOM 79 CG LYS 10 16.359 39.021 24.747 1.00 0.00 ATOM 80 CD LYS 10 17.179 40.161 24.140 1.00 0.00 ATOM 81 CE LYS 10 16.976 41.466 24.904 1.00 0.00 ATOM 82 NZ LYS 10 17.816 42.568 24.346 1.00 0.00 ATOM 83 O LYS 10 13.924 37.187 25.725 1.00 0.00 ATOM 84 C LYS 10 14.448 36.654 24.746 1.00 0.00 ATOM 85 N GLN 11 13.748 36.205 23.709 1.00 0.00 ATOM 86 CA GLN 11 12.240 36.318 23.656 1.00 0.00 ATOM 87 CB GLN 11 11.780 36.897 22.311 1.00 0.00 ATOM 88 CG GLN 11 12.214 38.329 22.035 1.00 0.00 ATOM 89 CD GLN 11 11.504 39.217 23.034 1.00 0.00 ATOM 90 OE1 GLN 11 10.319 39.499 22.948 1.00 0.00 ATOM 91 NE2 GLN 11 12.230 39.674 24.018 1.00 0.00 ATOM 92 O GLN 11 10.409 34.863 24.329 1.00 0.00 ATOM 93 C GLN 11 11.488 34.940 23.740 1.00 0.00 ATOM 94 N ALA 12 12.066 33.896 23.155 1.00 0.00 ATOM 95 CA ALA 12 11.446 32.576 23.181 1.00 0.00 ATOM 96 CB ALA 12 11.315 32.018 21.758 1.00 0.00 ATOM 97 O ALA 12 13.448 31.325 23.657 1.00 0.00 ATOM 98 C ALA 12 12.298 31.595 23.968 1.00 0.00 ATOM 99 N LYS 13 11.718 31.090 25.041 1.00 0.00 ATOM 100 CA LYS 13 12.429 30.083 25.836 1.00 0.00 ATOM 101 CB LYS 13 13.046 30.710 27.093 1.00 0.00 ATOM 102 CG LYS 13 12.043 31.352 28.046 1.00 0.00 ATOM 103 CD LYS 13 12.781 31.946 29.243 1.00 0.00 ATOM 104 CE LYS 13 11.765 32.474 30.224 1.00 0.00 ATOM 105 NZ LYS 13 12.322 33.159 31.393 1.00 0.00 ATOM 106 O LYS 13 10.384 29.121 26.642 1.00 0.00 ATOM 107 C LYS 13 11.520 28.918 26.211 1.00 0.00 ATOM 108 N GLU 14 12.020 27.697 26.045 1.00 0.00 ATOM 109 CA GLU 14 11.232 26.487 26.377 1.00 0.00 ATOM 110 CB GLU 14 9.716 26.547 26.155 1.00 0.00 ATOM 111 CG GLU 14 9.063 26.811 27.505 1.00 0.00 ATOM 112 CD GLU 14 7.562 26.609 27.451 1.00 0.00 ATOM 113 OE1 GLU 14 7.139 25.435 27.479 1.00 0.00 ATOM 114 OE2 GLU 14 6.839 27.606 27.296 1.00 0.00 ATOM 115 O GLU 14 12.979 25.138 25.398 1.00 0.00 ATOM 116 C GLU 14 11.794 25.201 25.727 1.00 0.00 ATOM 117 N GLU 15 10.942 24.197 25.552 1.00 0.00 ATOM 118 CA GLU 15 11.369 22.941 24.946 1.00 0.00 ATOM 119 CB GLU 15 11.501 21.891 26.032 1.00 0.00 ATOM 120 CG GLU 15 12.586 22.230 27.069 1.00 0.00 ATOM 121 CD GLU 15 12.689 21.132 28.120 1.00 0.00 ATOM 122 OE1 GLU 15 12.071 20.048 27.963 1.00 0.00 ATOM 123 OE2 GLU 15 13.549 21.316 29.014 1.00 0.00 ATOM 124 O GLU 15 9.186 22.987 23.912 1.00 0.00 ATOM 125 C GLU 15 10.316 22.514 23.925 1.00 0.00 ATOM 126 N ALA 16 10.814 21.881 22.892 1.00 0.00 ATOM 127 CA ALA 16 9.991 21.308 21.820 1.00 0.00 ATOM 128 CB ALA 16 9.934 22.242 20.611 1.00 0.00 ATOM 129 O ALA 16 11.727 19.651 21.781 1.00 0.00 ATOM 130 C ALA 16 10.600 19.972 21.402 1.00 0.00 ATOM 131 N ILE 17 9.854 19.197 20.621 1.00 0.00 ATOM 132 CA ILE 17 10.338 17.901 20.160 1.00 0.00 ATOM 133 CB ILE 17 9.624 16.764 20.922 1.00 0.00 ATOM 134 CG1 ILE 17 8.102 16.814 20.732 1.00 0.00 ATOM 135 CG2 ILE 17 10.034 16.809 22.397 1.00 0.00 ATOM 136 CD1 ILE 17 7.405 15.536 21.209 1.00 0.00 ATOM 137 O ILE 17 9.092 18.395 18.176 1.00 0.00 ATOM 138 C ILE 17 10.036 17.750 18.676 1.00 0.00 ATOM 139 N LYS 18 10.727 16.823 18.064 1.00 0.00 ATOM 140 CA LYS 18 10.480 16.422 16.666 1.00 0.00 ATOM 141 CB LYS 18 11.217 17.333 15.670 1.00 0.00 ATOM 142 CG LYS 18 10.720 18.788 15.650 1.00 0.00 ATOM 143 CD LYS 18 9.262 18.963 15.199 1.00 0.00 ATOM 144 CE LYS 18 9.142 18.657 13.713 1.00 0.00 ATOM 145 NZ LYS 18 7.773 18.756 13.209 1.00 0.00 ATOM 146 O LYS 18 11.939 14.558 17.114 1.00 0.00 ATOM 147 C LYS 18 11.002 15.006 16.434 1.00 0.00 ATOM 148 N GLU 19 10.373 14.311 15.513 1.00 0.00 ATOM 149 CA GLU 19 10.821 12.976 15.111 1.00 0.00 ATOM 150 CB GLU 19 9.598 12.064 14.979 1.00 0.00 ATOM 151 CG GLU 19 9.933 10.655 14.490 1.00 0.00 ATOM 152 CD GLU 19 8.704 9.836 14.124 1.00 0.00 ATOM 153 OE1 GLU 19 7.701 10.416 13.655 1.00 0.00 ATOM 154 OE2 GLU 19 8.753 8.598 14.291 1.00 0.00 ATOM 155 O GLU 19 11.087 13.618 12.814 1.00 0.00 ATOM 156 C GLU 19 11.573 13.038 13.786 1.00 0.00 ATOM 157 N LEU 20 12.759 12.439 13.748 1.00 0.00 ATOM 158 CA LEU 20 13.545 12.438 12.550 1.00 0.00 ATOM 159 CB LEU 20 14.480 13.613 12.252 1.00 0.00 ATOM 160 CG LEU 20 14.008 14.330 10.983 1.00 0.00 ATOM 161 CD1 LEU 20 13.571 13.414 9.821 1.00 0.00 ATOM 162 CD2 LEU 20 12.907 15.312 11.337 1.00 0.00 ATOM 163 O LEU 20 14.606 10.454 13.382 1.00 0.00 ATOM 164 C LEU 20 14.360 11.157 12.402 1.00 0.00 ATOM 165 N VAL 21 14.778 10.857 11.176 1.00 0.00 ATOM 166 CA VAL 21 15.556 9.673 10.927 1.00 0.00 ATOM 167 CB VAL 21 15.532 9.404 9.426 1.00 0.00 ATOM 168 CG1 VAL 21 16.425 8.219 9.064 1.00 0.00 ATOM 169 CG2 VAL 21 14.106 9.084 8.978 1.00 0.00 ATOM 170 O VAL 21 17.476 8.700 12.018 1.00 0.00 ATOM 171 C VAL 21 16.958 9.722 11.548 1.00 0.00 ATOM 172 N ASP 22 17.541 10.908 11.625 1.00 0.00 ATOM 173 CA ASP 22 18.873 11.079 12.220 1.00 0.00 ATOM 174 CB ASP 22 19.978 10.773 11.184 1.00 0.00 ATOM 175 CG ASP 22 20.025 11.775 10.021 1.00 0.00 ATOM 176 OD1 ASP 22 19.531 12.888 10.230 1.00 0.00 ATOM 177 OD2 ASP 22 20.623 11.483 8.977 1.00 0.00 ATOM 178 O ASP 22 18.108 13.340 12.695 1.00 0.00 ATOM 179 C ASP 22 19.011 12.492 12.802 1.00 0.00 ATOM 180 N ALA 23 20.165 12.710 13.413 1.00 0.00 ATOM 181 CA ALA 23 20.492 14.011 14.005 1.00 0.00 ATOM 182 CB ALA 23 21.731 13.853 14.854 1.00 0.00 ATOM 183 O ALA 23 20.278 16.252 13.228 1.00 0.00 ATOM 184 C ALA 23 20.704 15.121 12.998 1.00 0.00 ATOM 185 N GLY 24 21.378 14.848 11.847 1.00 0.00 ATOM 186 CA GLY 24 21.614 15.852 10.828 1.00 0.00 ATOM 187 O GLY 24 20.098 17.634 10.298 1.00 0.00 ATOM 188 C GLY 24 20.272 16.418 10.375 1.00 0.00 ATOM 189 N THR 25 19.325 15.534 10.075 1.00 0.00 ATOM 190 CA THR 25 17.974 15.963 9.624 1.00 0.00 ATOM 191 CB THR 25 17.193 14.777 9.102 1.00 0.00 ATOM 192 CG2 THR 25 15.774 15.184 8.686 1.00 0.00 ATOM 193 OG1 THR 25 17.811 14.340 7.891 1.00 0.00 ATOM 194 O THR 25 16.613 17.774 10.472 1.00 0.00 ATOM 195 C THR 25 17.229 16.742 10.741 1.00 0.00 ATOM 196 N ALA 26 17.298 16.243 11.971 1.00 0.00 ATOM 197 CA ALA 26 16.636 16.902 13.092 1.00 0.00 ATOM 198 CB ALA 26 16.828 16.091 14.380 1.00 0.00 ATOM 199 O ALA 26 16.407 19.269 13.456 1.00 0.00 ATOM 200 C ALA 26 17.181 18.323 13.299 1.00 0.00 ATOM 201 N GLU 27 18.484 18.480 13.038 1.00 0.00 ATOM 202 CA GLU 27 19.154 19.790 13.111 1.00 0.00 ATOM 203 CB GLU 27 20.645 19.609 12.857 1.00 0.00 ATOM 204 CG GLU 27 21.426 20.919 13.053 1.00 0.00 ATOM 205 CD GLU 27 22.938 20.768 12.848 1.00 0.00 ATOM 206 OE1 GLU 27 23.362 19.689 12.387 1.00 0.00 ATOM 207 OE2 GLU 27 23.673 21.740 13.107 1.00 0.00 ATOM 208 O GLU 27 18.328 21.941 12.367 1.00 0.00 ATOM 209 C GLU 27 18.567 20.773 12.058 1.00 0.00 ATOM 210 N LYS 28 18.346 20.288 10.841 1.00 0.00 ATOM 211 CA LYS 28 17.795 21.127 9.783 1.00 0.00 ATOM 212 CB LYS 28 17.718 20.344 8.490 1.00 0.00 ATOM 213 CG LYS 28 19.102 19.981 7.926 1.00 0.00 ATOM 214 CD LYS 28 18.998 19.191 6.663 1.00 0.00 ATOM 215 CE LYS 28 20.339 18.946 6.072 1.00 0.00 ATOM 216 NZ LYS 28 20.210 18.217 4.799 1.00 0.00 ATOM 217 O LYS 28 16.045 22.774 9.996 1.00 0.00 ATOM 218 C LYS 28 16.379 21.602 10.174 1.00 0.00 ATOM 219 N TYR 29 15.567 20.692 10.703 1.00 0.00 ATOM 220 CA TYR 29 14.210 21.037 11.111 1.00 0.00 ATOM 221 CB TYR 29 13.502 19.772 11.612 1.00 0.00 ATOM 222 CG TYR 29 12.681 19.113 10.510 1.00 0.00 ATOM 223 CD1 TYR 29 11.336 19.414 10.402 1.00 0.00 ATOM 224 CD2 TYR 29 13.246 18.219 9.625 1.00 0.00 ATOM 225 CE1 TYR 29 10.577 18.832 9.409 1.00 0.00 ATOM 226 CE2 TYR 29 12.467 17.608 8.640 1.00 0.00 ATOM 227 CZ TYR 29 11.122 17.916 8.528 1.00 0.00 ATOM 228 OH TYR 29 10.349 17.265 7.613 1.00 0.00 ATOM 229 O TYR 29 13.393 22.973 12.278 1.00 0.00 ATOM 230 C TYR 29 14.199 22.041 12.267 1.00 0.00 ATOM 231 N ILE 30 15.090 21.849 13.232 1.00 0.00 ATOM 232 CA ILE 30 15.169 22.748 14.379 1.00 0.00 ATOM 233 CB ILE 30 15.999 22.130 15.541 1.00 0.00 ATOM 234 CG1 ILE 30 15.297 20.856 16.066 1.00 0.00 ATOM 235 CG2 ILE 30 16.065 23.126 16.711 1.00 0.00 ATOM 236 CD1 ILE 30 16.063 20.002 17.061 1.00 0.00 ATOM 237 O ILE 30 15.245 25.161 14.463 1.00 0.00 ATOM 238 C ILE 30 15.743 24.120 14.003 1.00 0.00 ATOM 239 N LYS 31 16.767 24.140 13.156 1.00 0.00 ATOM 240 CA LYS 31 17.270 25.418 12.635 1.00 0.00 ATOM 241 CB LYS 31 18.461 25.199 11.712 1.00 0.00 ATOM 242 CG LYS 31 19.718 24.744 12.472 1.00 0.00 ATOM 243 CD LYS 31 20.846 24.573 11.460 1.00 0.00 ATOM 244 CE LYS 31 22.136 24.157 12.166 1.00 0.00 ATOM 245 NZ LYS 31 23.218 23.880 11.216 1.00 0.00 ATOM 246 O LYS 31 15.922 27.362 12.213 1.00 0.00 ATOM 247 C LYS 31 16.157 26.190 11.899 1.00 0.00 ATOM 248 N LEU 32 15.329 25.464 11.151 1.00 0.00 ATOM 249 CA LEU 32 14.181 26.064 10.445 1.00 0.00 ATOM 250 CB LEU 32 13.546 25.004 9.509 1.00 0.00 ATOM 251 CG LEU 32 12.267 25.475 8.802 1.00 0.00 ATOM 252 CD1 LEU 32 12.632 26.571 7.813 1.00 0.00 ATOM 253 CD2 LEU 32 11.584 24.316 8.084 1.00 0.00 ATOM 254 O LEU 32 12.640 27.710 11.267 1.00 0.00 ATOM 255 C LEU 32 13.153 26.602 11.435 1.00 0.00 ATOM 256 N ILE 33 12.850 25.816 12.464 1.00 0.00 ATOM 257 CA ILE 33 11.863 26.231 13.494 1.00 0.00 ATOM 258 CB ILE 33 11.609 25.093 14.496 1.00 0.00 ATOM 259 CG1 ILE 33 10.850 23.945 13.815 1.00 0.00 ATOM 260 CG2 ILE 33 10.798 25.610 15.685 1.00 0.00 ATOM 261 CD1 ILE 33 10.821 22.635 14.611 1.00 0.00 ATOM 262 O ILE 33 11.569 28.458 14.336 1.00 0.00 ATOM 263 C ILE 33 12.332 27.503 14.191 1.00 0.00 ATOM 264 N ALA 34 13.590 27.515 14.621 1.00 0.00 ATOM 265 CA ALA 34 14.157 28.692 15.307 1.00 0.00 ATOM 266 CB ALA 34 15.588 28.436 15.722 1.00 0.00 ATOM 267 O ALA 34 13.640 30.982 14.807 1.00 0.00 ATOM 268 C ALA 34 14.089 29.912 14.394 1.00 0.00 ATOM 269 N ASN 35 14.533 29.749 13.152 1.00 0.00 ATOM 270 CA ASN 35 14.512 30.842 12.197 1.00 0.00 ATOM 271 CB ASN 35 15.074 30.433 10.839 1.00 0.00 ATOM 272 CG ASN 35 16.580 30.226 10.874 1.00 0.00 ATOM 273 ND2 ASN 35 17.028 29.489 9.898 1.00 0.00 ATOM 274 OD1 ASN 35 17.337 30.704 11.708 1.00 0.00 ATOM 275 O ASN 35 12.848 32.560 11.998 1.00 0.00 ATOM 276 C ASN 35 13.087 31.352 12.002 1.00 0.00 ATOM 277 N ALA 36 12.143 30.429 11.843 1.00 0.00 ATOM 278 CA ALA 36 10.747 30.802 11.653 1.00 0.00 ATOM 279 CB ALA 36 9.895 29.578 11.373 1.00 0.00 ATOM 280 O ALA 36 9.138 32.223 12.688 1.00 0.00 ATOM 281 C ALA 36 10.135 31.513 12.827 1.00 0.00 ATOM 282 N LYS 37 10.732 31.330 14.000 1.00 0.00 ATOM 283 CA LYS 37 10.231 31.971 15.211 1.00 0.00 ATOM 284 CB LYS 37 9.706 30.929 16.209 1.00 0.00 ATOM 285 CG LYS 37 8.192 30.800 15.978 1.00 0.00 ATOM 286 CD LYS 37 7.514 29.633 16.689 1.00 0.00 ATOM 287 CE LYS 37 7.878 28.283 16.076 1.00 0.00 ATOM 288 NZ LYS 37 7.098 27.214 16.708 1.00 0.00 ATOM 289 O LYS 37 11.012 33.576 16.834 1.00 0.00 ATOM 290 C LYS 37 11.176 33.068 15.743 1.00 0.00 ATOM 291 N THR 38 11.973 33.584 14.782 1.00 0.00 ATOM 292 CA THR 38 12.831 34.768 14.937 1.00 0.00 ATOM 293 CB THR 38 11.856 35.977 14.883 1.00 0.00 ATOM 294 CG2 THR 38 12.434 37.371 15.112 1.00 0.00 ATOM 295 OG1 THR 38 11.196 35.948 13.595 1.00 0.00 ATOM 296 O THR 38 14.009 35.272 17.044 1.00 0.00 ATOM 297 C THR 38 13.866 34.524 16.076 1.00 0.00 ATOM 298 N VAL 39 14.570 33.400 15.907 1.00 0.00 ATOM 299 CA VAL 39 15.702 32.906 16.732 1.00 0.00 ATOM 300 CB VAL 39 15.533 31.412 17.049 1.00 0.00 ATOM 301 CG1 VAL 39 16.688 30.753 17.813 1.00 0.00 ATOM 302 CG2 VAL 39 14.175 31.178 17.667 1.00 0.00 ATOM 303 O VAL 39 17.113 32.170 14.947 1.00 0.00 ATOM 304 C VAL 39 16.979 32.950 15.898 1.00 0.00 ATOM 305 N GLU 40 18.004 33.470 16.555 1.00 0.00 ATOM 306 CA GLU 40 19.349 33.459 15.963 1.00 0.00 ATOM 307 CB GLU 40 19.474 34.678 15.008 1.00 0.00 ATOM 308 CG GLU 40 18.427 34.756 13.927 1.00 0.00 ATOM 309 CD GLU 40 18.957 35.543 12.752 1.00 0.00 ATOM 310 OE1 GLU 40 19.118 36.763 12.961 1.00 0.00 ATOM 311 OE2 GLU 40 19.293 34.917 11.718 1.00 0.00 ATOM 312 O GLU 40 20.748 34.377 17.682 1.00 0.00 ATOM 313 C GLU 40 20.392 33.368 17.071 1.00 0.00 ATOM 314 N GLY 41 20.881 32.159 17.328 1.00 0.00 ATOM 315 CA GLY 41 21.867 31.968 18.347 1.00 0.00 ATOM 316 O GLY 41 23.083 30.412 16.951 1.00 0.00 ATOM 317 C GLY 41 22.900 30.881 18.070 1.00 0.00 ATOM 318 N VAL 42 23.539 30.529 19.171 1.00 0.00 ATOM 319 CA VAL 42 24.537 29.448 19.189 1.00 0.00 ATOM 320 CB VAL 42 25.671 29.733 20.209 1.00 0.00 ATOM 321 CG1 VAL 42 26.353 31.065 19.903 1.00 0.00 ATOM 322 CG2 VAL 42 25.115 29.717 21.624 1.00 0.00 ATOM 323 O VAL 42 22.716 28.106 19.945 1.00 0.00 ATOM 324 C VAL 42 23.792 28.131 19.380 1.00 0.00 ATOM 325 N TRP 43 24.450 27.077 18.910 1.00 0.00 ATOM 326 CA TRP 43 23.837 25.738 18.898 1.00 0.00 ATOM 327 CB TRP 43 23.587 25.326 17.435 1.00 0.00 ATOM 328 CG TRP 43 22.828 26.321 16.644 1.00 0.00 ATOM 329 CD1 TRP 43 23.351 27.316 15.870 1.00 0.00 ATOM 330 CD2 TRP 43 21.403 26.428 16.542 1.00 0.00 ATOM 331 CE2 TRP 43 21.129 27.513 15.675 1.00 0.00 ATOM 332 CE3 TRP 43 20.321 25.687 17.077 1.00 0.00 ATOM 333 NE1 TRP 43 22.332 28.063 15.305 1.00 0.00 ATOM 334 CZ2 TRP 43 19.828 27.909 15.354 1.00 0.00 ATOM 335 CZ3 TRP 43 19.009 26.072 16.740 1.00 0.00 ATOM 336 CH2 TRP 43 18.781 27.172 15.882 1.00 0.00 ATOM 337 O TRP 43 25.991 24.763 19.390 1.00 0.00 ATOM 338 C TRP 43 24.763 24.702 19.529 1.00 0.00 ATOM 339 N THR 44 24.124 23.802 20.232 1.00 0.00 ATOM 340 CA THR 44 24.756 22.556 20.684 1.00 0.00 ATOM 341 CB THR 44 24.992 22.606 22.183 1.00 0.00 ATOM 342 CG2 THR 44 25.730 21.371 22.629 1.00 0.00 ATOM 343 OG1 THR 44 25.800 23.751 22.469 1.00 0.00 ATOM 344 O THR 44 22.650 21.366 20.518 1.00 0.00 ATOM 345 C THR 44 23.879 21.314 20.423 1.00 0.00 ATOM 346 N LEU 45 24.522 20.168 20.186 1.00 0.00 ATOM 347 CA LEU 45 23.805 18.913 20.092 1.00 0.00 ATOM 348 CB LEU 45 23.808 18.460 18.628 1.00 0.00 ATOM 349 CG LEU 45 23.297 17.024 18.445 1.00 0.00 ATOM 350 CD1 LEU 45 21.805 17.030 18.739 1.00 0.00 ATOM 351 CD2 LEU 45 23.592 16.488 17.046 1.00 0.00 ATOM 352 O LEU 45 25.698 17.537 20.803 1.00 0.00 ATOM 353 C LEU 45 24.504 17.861 20.944 1.00 0.00 ATOM 354 N LYS 46 23.738 17.291 21.851 1.00 0.00 ATOM 355 CA LYS 46 24.203 16.186 22.691 1.00 0.00 ATOM 356 CB LYS 46 23.878 16.485 24.148 1.00 0.00 ATOM 357 CG LYS 46 24.516 17.776 24.636 1.00 0.00 ATOM 358 CD LYS 46 24.178 17.964 26.105 1.00 0.00 ATOM 359 CE LYS 46 24.995 19.143 26.604 1.00 0.00 ATOM 360 NZ LYS 46 24.904 19.312 28.036 1.00 0.00 ATOM 361 O LYS 46 22.304 14.734 22.492 1.00 0.00 ATOM 362 C LYS 46 23.501 14.904 22.256 1.00 0.00 ATOM 363 N ASP 47 24.246 14.003 21.623 1.00 0.00 ATOM 364 CA ASP 47 23.681 12.752 21.170 1.00 0.00 ATOM 365 CB ASP 47 24.683 11.908 20.305 1.00 0.00 ATOM 366 CG ASP 47 24.963 12.545 18.948 1.00 0.00 ATOM 367 OD1 ASP 47 24.186 13.417 18.473 1.00 0.00 ATOM 368 OD2 ASP 47 25.995 12.147 18.362 1.00 0.00 ATOM 369 O ASP 47 22.235 11.131 22.191 1.00 0.00 ATOM 370 C ASP 47 23.219 11.862 22.320 1.00 0.00 ATOM 371 N GLU 48 23.928 11.926 23.443 1.00 0.00 ATOM 372 CA GLU 48 23.573 11.112 24.626 1.00 0.00 ATOM 373 CB GLU 48 24.687 11.271 25.720 1.00 0.00 ATOM 374 CG GLU 48 26.103 10.998 25.208 1.00 0.00 ATOM 375 CD GLU 48 26.825 12.276 24.823 1.00 0.00 ATOM 376 OE1 GLU 48 26.312 13.035 23.975 1.00 0.00 ATOM 377 OE2 GLU 48 27.910 12.532 25.383 1.00 0.00 ATOM 378 O GLU 48 21.494 10.411 25.631 1.00 0.00 ATOM 379 C GLU 48 22.112 11.323 25.081 1.00 0.00 ATOM 380 N ILE 49 21.578 12.517 24.847 1.00 0.00 ATOM 381 CA ILE 49 20.204 12.821 25.234 1.00 0.00 ATOM 382 CB ILE 49 20.185 13.918 26.319 1.00 0.00 ATOM 383 CG1 ILE 49 20.769 15.237 25.828 1.00 0.00 ATOM 384 CG2 ILE 49 20.896 13.404 27.579 1.00 0.00 ATOM 385 CD1 ILE 49 20.498 16.397 26.791 1.00 0.00 ATOM 386 O ILE 49 18.116 13.433 24.210 1.00 0.00 ATOM 387 C ILE 49 19.297 13.194 24.051 1.00 0.00 ATOM 388 N LYS 50 19.865 13.085 22.841 1.00 0.00 ATOM 389 CA LYS 50 19.158 13.428 21.592 1.00 0.00 ATOM 390 CB LYS 50 18.385 12.051 21.089 1.00 0.00 ATOM 391 CG LYS 50 18.988 10.730 21.560 1.00 0.00 ATOM 392 CD LYS 50 18.223 9.533 21.067 1.00 0.00 ATOM 393 CE LYS 50 18.911 8.264 21.548 1.00 0.00 ATOM 394 NZ LYS 50 20.268 8.023 20.947 1.00 0.00 ATOM 395 O LYS 50 17.379 15.094 21.412 1.00 0.00 ATOM 396 C LYS 50 18.554 14.851 21.721 1.00 0.00 ATOM 397 N THR 51 19.371 15.770 22.223 1.00 0.00 ATOM 398 CA THR 51 18.954 17.153 22.555 1.00 0.00 ATOM 399 CB THR 51 18.931 17.365 24.075 1.00 0.00 ATOM 400 CG2 THR 51 18.407 18.760 24.398 1.00 0.00 ATOM 401 OG1 THR 51 18.067 16.391 24.677 1.00 0.00 ATOM 402 O THR 51 21.082 18.148 22.026 1.00 0.00 ATOM 403 C THR 51 19.850 18.188 21.890 1.00 0.00 ATOM 404 N PHE 52 19.193 19.158 21.252 1.00 0.00 ATOM 405 CA PHE 52 19.795 20.359 20.731 1.00 0.00 ATOM 406 CB PHE 52 19.185 20.745 19.388 1.00 0.00 ATOM 407 CG PHE 52 19.600 19.848 18.246 1.00 0.00 ATOM 408 CD1 PHE 52 20.578 20.257 17.365 1.00 0.00 ATOM 409 CD2 PHE 52 18.921 18.657 18.055 1.00 0.00 ATOM 410 CE1 PHE 52 20.903 19.464 16.269 1.00 0.00 ATOM 411 CE2 PHE 52 19.214 17.892 16.949 1.00 0.00 ATOM 412 CZ PHE 52 20.210 18.272 16.057 1.00 0.00 ATOM 413 O PHE 52 18.327 21.581 22.184 1.00 0.00 ATOM 414 C PHE 52 19.448 21.511 21.678 1.00 0.00 ATOM 415 N THR 53 20.363 22.463 21.750 1.00 0.00 ATOM 416 CA THR 53 20.129 23.731 22.469 1.00 0.00 ATOM 417 CB THR 53 20.956 23.872 23.750 1.00 0.00 ATOM 418 CG2 THR 53 20.604 25.141 24.555 1.00 0.00 ATOM 419 OG1 THR 53 20.752 22.731 24.572 1.00 0.00 ATOM 420 O THR 53 21.593 24.914 21.028 1.00 0.00 ATOM 421 C THR 53 20.526 24.929 21.645 1.00 0.00 ATOM 422 N VAL 54 19.676 25.915 21.627 1.00 0.00 ATOM 423 CA VAL 54 20.045 27.196 20.983 1.00 0.00 ATOM 424 CB VAL 54 19.094 27.601 19.838 1.00 0.00 ATOM 425 CG1 VAL 54 17.650 27.634 20.320 1.00 0.00 ATOM 426 CG2 VAL 54 19.502 28.962 19.281 1.00 0.00 ATOM 427 O VAL 54 19.103 28.270 22.930 1.00 0.00 ATOM 428 C VAL 54 20.006 28.272 22.076 1.00 0.00 ATOM 429 N THR 55 21.047 29.087 22.096 1.00 0.00 ATOM 430 CA THR 55 21.209 30.134 23.121 1.00 0.00 ATOM 431 CB THR 55 22.458 29.868 23.946 1.00 0.00 ATOM 432 CG2 THR 55 22.592 30.943 25.015 1.00 0.00 ATOM 433 OG1 THR 55 22.319 28.591 24.584 1.00 0.00 ATOM 434 O THR 55 22.434 31.479 21.556 1.00 0.00 ATOM 435 C THR 55 21.577 31.460 22.441 1.00 0.00 ATOM 436 N GLU 56 20.925 32.511 22.920 1.00 0.00 ATOM 437 CA GLU 56 21.239 33.878 22.467 1.00 0.00 ATOM 438 CB GLU 56 19.953 34.654 22.145 1.00 0.00 ATOM 439 CG GLU 56 19.228 34.119 20.899 1.00 0.00 ATOM 440 CD GLU 56 17.954 34.912 20.528 1.00 0.00 ATOM 441 OE1 GLU 56 17.120 35.181 21.427 1.00 0.00 ATOM 442 OE2 GLU 56 17.763 35.115 19.305 1.00 0.00 ATOM 443 O GLU 56 22.297 34.019 24.612 1.00 0.00 ATOM 444 C GLU 56 22.076 34.618 23.541 1.00 0.00 TER END