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 4 Tue Jul 15 13:37:25 2008 MODEL 4 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 13.731 8.718 15.267 1.00 0.00 ATOM 2 CA THR 1 14.078 8.949 16.671 1.00 0.00 ATOM 3 CB THR 1 15.600 9.011 16.863 1.00 0.00 ATOM 4 CG2 THR 1 16.008 9.226 18.326 1.00 0.00 ATOM 5 OG1 THR 1 16.149 7.784 16.387 1.00 0.00 ATOM 6 O THR 1 13.487 11.211 16.201 1.00 0.00 ATOM 7 C THR 1 13.478 10.289 17.023 1.00 0.00 ATOM 8 N THR 2 13.039 10.361 18.264 1.00 0.00 ATOM 9 CA THR 2 12.566 11.630 18.827 1.00 0.00 ATOM 10 CB THR 2 11.588 11.364 19.983 1.00 0.00 ATOM 11 CG2 THR 2 10.907 12.647 20.456 1.00 0.00 ATOM 12 OG1 THR 2 10.607 10.439 19.511 1.00 0.00 ATOM 13 O THR 2 14.785 11.944 19.754 1.00 0.00 ATOM 14 C THR 2 13.770 12.458 19.300 1.00 0.00 ATOM 15 N TYR 3 13.692 13.738 19.013 1.00 0.00 ATOM 16 CA TYR 3 14.741 14.679 19.412 1.00 0.00 ATOM 17 CB TYR 3 15.561 15.152 18.197 1.00 0.00 ATOM 18 CG TYR 3 16.379 14.031 17.549 1.00 0.00 ATOM 19 CD1 TYR 3 15.828 13.266 16.529 1.00 0.00 ATOM 20 CD2 TYR 3 17.688 13.753 17.889 1.00 0.00 ATOM 21 CE1 TYR 3 16.528 12.298 15.847 1.00 0.00 ATOM 22 CE2 TYR 3 18.397 12.770 17.219 1.00 0.00 ATOM 23 CZ TYR 3 17.843 12.043 16.195 1.00 0.00 ATOM 24 OH TYR 3 18.536 10.991 15.687 1.00 0.00 ATOM 25 O TYR 3 13.013 16.308 19.756 1.00 0.00 ATOM 26 C TYR 3 14.116 15.886 20.110 1.00 0.00 ATOM 27 N LYS 4 14.836 16.391 21.089 1.00 0.00 ATOM 28 CA LYS 4 14.403 17.586 21.837 1.00 0.00 ATOM 29 CB LYS 4 14.604 17.385 23.342 1.00 0.00 ATOM 30 CG LYS 4 13.725 16.284 23.911 1.00 0.00 ATOM 31 CD LYS 4 13.945 16.185 25.406 1.00 0.00 ATOM 32 CE LYS 4 13.020 15.098 25.957 1.00 0.00 ATOM 33 NZ LYS 4 13.141 14.901 27.403 1.00 0.00 ATOM 34 O LYS 4 16.409 18.695 21.059 1.00 0.00 ATOM 35 C LYS 4 15.237 18.805 21.424 1.00 0.00 ATOM 36 N LEU 5 14.566 19.944 21.455 1.00 0.00 ATOM 37 CA LEU 5 15.221 21.250 21.343 1.00 0.00 ATOM 38 CB LEU 5 14.730 21.985 20.086 1.00 0.00 ATOM 39 CG LEU 5 15.227 23.432 20.033 1.00 0.00 ATOM 40 CD1 LEU 5 16.746 23.562 19.871 1.00 0.00 ATOM 41 CD2 LEU 5 14.421 24.163 18.973 1.00 0.00 ATOM 42 O LEU 5 13.712 22.202 22.929 1.00 0.00 ATOM 43 C LEU 5 14.883 22.075 22.579 1.00 0.00 ATOM 44 N ILE 6 15.938 22.606 23.170 1.00 0.00 ATOM 45 CA ILE 6 15.816 23.611 24.245 1.00 0.00 ATOM 46 CB ILE 6 16.616 23.230 25.499 1.00 0.00 ATOM 47 CG1 ILE 6 16.058 21.919 26.083 1.00 0.00 ATOM 48 CG2 ILE 6 16.531 24.336 26.550 1.00 0.00 ATOM 49 CD1 ILE 6 16.999 21.300 27.126 1.00 0.00 ATOM 50 O ILE 6 17.424 25.151 23.292 1.00 0.00 ATOM 51 C ILE 6 16.270 24.951 23.674 1.00 0.00 ATOM 52 N LEU 7 15.321 25.868 23.727 1.00 0.00 ATOM 53 CA LEU 7 15.512 27.243 23.290 1.00 0.00 ATOM 54 CB LEU 7 14.326 27.645 22.417 1.00 0.00 ATOM 55 CG LEU 7 14.257 29.131 22.063 1.00 0.00 ATOM 56 CD1 LEU 7 15.538 29.676 21.460 1.00 0.00 ATOM 57 CD2 LEU 7 13.079 29.367 21.130 1.00 0.00 ATOM 58 O LEU 7 14.865 28.220 25.412 1.00 0.00 ATOM 59 C LEU 7 15.682 28.166 24.500 1.00 0.00 ATOM 60 N ASN 8 16.828 28.827 24.480 1.00 0.00 ATOM 61 CA ASN 8 17.101 29.921 25.407 1.00 0.00 ATOM 62 CB ASN 8 18.295 29.534 26.254 1.00 0.00 ATOM 63 CG ASN 8 18.393 30.479 27.442 1.00 0.00 ATOM 64 ND2 ASN 8 19.593 30.595 27.915 1.00 0.00 ATOM 65 OD1 ASN 8 17.422 31.021 27.961 1.00 0.00 ATOM 66 O ASN 8 18.498 31.672 24.463 1.00 0.00 ATOM 67 C ASN 8 17.374 31.203 24.608 1.00 0.00 ATOM 68 N LEU 9 16.291 31.705 24.029 1.00 0.00 ATOM 69 CA LEU 9 16.336 32.974 23.269 1.00 0.00 ATOM 70 CB LEU 9 15.240 33.009 22.205 1.00 0.00 ATOM 71 CG LEU 9 15.211 34.244 21.313 1.00 0.00 ATOM 72 CD1 LEU 9 16.418 34.254 20.390 1.00 0.00 ATOM 73 CD2 LEU 9 13.883 34.378 20.572 1.00 0.00 ATOM 74 O LEU 9 15.482 33.999 25.274 1.00 0.00 ATOM 75 C LEU 9 16.119 34.143 24.234 1.00 0.00 ATOM 76 N LYS 10 16.431 35.320 23.711 1.00 0.00 ATOM 77 CA LYS 10 16.062 36.596 24.346 1.00 0.00 ATOM 78 CB LYS 10 16.580 37.762 23.508 1.00 0.00 ATOM 79 CG LYS 10 16.289 39.105 24.169 1.00 0.00 ATOM 80 CD LYS 10 17.103 40.198 23.511 1.00 0.00 ATOM 81 CE LYS 10 16.719 41.580 24.022 1.00 0.00 ATOM 82 NZ LYS 10 17.534 42.612 23.375 1.00 0.00 ATOM 83 O LYS 10 14.084 37.283 25.570 1.00 0.00 ATOM 84 C LYS 10 14.545 36.731 24.563 1.00 0.00 ATOM 85 N GLN 11 13.777 36.249 23.597 1.00 0.00 ATOM 86 CA GLN 11 12.307 36.381 23.642 1.00 0.00 ATOM 87 CB GLN 11 11.806 37.146 22.413 1.00 0.00 ATOM 88 CG GLN 11 12.275 38.595 22.350 1.00 0.00 ATOM 89 CD GLN 11 11.814 39.399 23.565 1.00 0.00 ATOM 90 OE1 GLN 11 10.656 39.431 23.927 1.00 0.00 ATOM 91 NE2 GLN 11 12.770 40.039 24.197 1.00 0.00 ATOM 92 O GLN 11 10.647 34.977 24.633 1.00 0.00 ATOM 93 C GLN 11 11.556 35.057 23.807 1.00 0.00 ATOM 94 N ALA 12 12.083 33.997 23.183 1.00 0.00 ATOM 95 CA ALA 12 11.472 32.662 23.236 1.00 0.00 ATOM 96 CB ALA 12 11.125 32.115 21.856 1.00 0.00 ATOM 97 O ALA 12 13.489 31.357 23.592 1.00 0.00 ATOM 98 C ALA 12 12.357 31.622 23.928 1.00 0.00 ATOM 99 N LYS 13 11.809 31.084 24.982 1.00 0.00 ATOM 100 CA LYS 13 12.509 30.146 25.887 1.00 0.00 ATOM 101 CB LYS 13 12.719 30.816 27.248 1.00 0.00 ATOM 102 CG LYS 13 11.449 31.130 28.080 1.00 0.00 ATOM 103 CD LYS 13 10.379 31.869 27.267 1.00 0.00 ATOM 104 CE LYS 13 8.972 31.382 27.565 1.00 0.00 ATOM 105 NZ LYS 13 8.493 32.092 28.744 1.00 0.00 ATOM 106 O LYS 13 10.442 29.123 26.290 1.00 0.00 ATOM 107 C LYS 13 11.622 28.917 26.068 1.00 0.00 ATOM 108 N GLU 14 12.185 27.719 26.086 1.00 0.00 ATOM 109 CA GLU 14 11.316 26.519 25.994 1.00 0.00 ATOM 110 CB GLU 14 10.514 26.642 24.692 1.00 0.00 ATOM 111 CG GLU 14 9.060 27.087 24.751 1.00 0.00 ATOM 112 CD GLU 14 8.396 27.005 26.121 1.00 0.00 ATOM 113 OE1 GLU 14 8.337 25.886 26.682 1.00 0.00 ATOM 114 OE2 GLU 14 7.891 28.068 26.545 1.00 0.00 ATOM 115 O GLU 14 13.126 25.215 25.179 1.00 0.00 ATOM 116 C GLU 14 12.017 25.194 25.709 1.00 0.00 ATOM 117 N GLU 15 11.122 24.213 25.558 1.00 0.00 ATOM 118 CA GLU 15 11.413 22.943 24.901 1.00 0.00 ATOM 119 CB GLU 15 11.560 21.838 25.946 1.00 0.00 ATOM 120 CG GLU 15 10.303 21.669 26.809 1.00 0.00 ATOM 121 CD GLU 15 10.587 20.786 28.019 1.00 0.00 ATOM 122 OE1 GLU 15 11.367 21.214 28.884 1.00 0.00 ATOM 123 OE2 GLU 15 10.005 19.678 28.076 1.00 0.00 ATOM 124 O GLU 15 9.148 22.882 23.980 1.00 0.00 ATOM 125 C GLU 15 10.339 22.594 23.863 1.00 0.00 ATOM 126 N ALA 16 10.842 22.006 22.790 1.00 0.00 ATOM 127 CA ALA 16 10.045 21.386 21.720 1.00 0.00 ATOM 128 CB ALA 16 10.001 22.279 20.474 1.00 0.00 ATOM 129 O ALA 16 11.802 19.737 21.754 1.00 0.00 ATOM 130 C ALA 16 10.689 20.055 21.343 1.00 0.00 ATOM 131 N ILE 17 9.951 19.283 20.560 1.00 0.00 ATOM 132 CA ILE 17 10.390 17.944 20.137 1.00 0.00 ATOM 133 CB ILE 17 9.823 16.848 21.053 1.00 0.00 ATOM 134 CG1 ILE 17 8.283 16.805 20.977 1.00 0.00 ATOM 135 CG2 ILE 17 10.310 17.065 22.491 1.00 0.00 ATOM 136 CD1 ILE 17 7.661 15.596 21.655 1.00 0.00 ATOM 137 O ILE 17 9.036 18.214 18.145 1.00 0.00 ATOM 138 C ILE 17 10.018 17.680 18.671 1.00 0.00 ATOM 139 N LYS 18 10.820 16.874 18.013 1.00 0.00 ATOM 140 CA LYS 18 10.543 16.433 16.641 1.00 0.00 ATOM 141 CB LYS 18 11.310 17.322 15.637 1.00 0.00 ATOM 142 CG LYS 18 10.844 18.792 15.605 1.00 0.00 ATOM 143 CD LYS 18 9.413 18.981 15.079 1.00 0.00 ATOM 144 CE LYS 18 9.286 18.605 13.597 1.00 0.00 ATOM 145 NZ LYS 18 7.905 18.756 13.109 1.00 0.00 ATOM 146 O LYS 18 11.557 14.397 17.382 1.00 0.00 ATOM 147 C LYS 18 10.893 14.947 16.505 1.00 0.00 ATOM 148 N GLU 19 10.445 14.315 15.429 1.00 0.00 ATOM 149 CA GLU 19 10.853 12.946 15.047 1.00 0.00 ATOM 150 CB GLU 19 9.626 12.077 14.740 1.00 0.00 ATOM 151 CG GLU 19 9.957 10.630 14.354 1.00 0.00 ATOM 152 CD GLU 19 8.759 9.821 13.826 1.00 0.00 ATOM 153 OE1 GLU 19 7.595 10.245 14.010 1.00 0.00 ATOM 154 OE2 GLU 19 9.039 8.734 13.293 1.00 0.00 ATOM 155 O GLU 19 11.150 13.630 12.774 1.00 0.00 ATOM 156 C GLU 19 11.624 13.038 13.734 1.00 0.00 ATOM 157 N LEU 20 12.788 12.413 13.728 1.00 0.00 ATOM 158 CA LEU 20 13.693 12.447 12.563 1.00 0.00 ATOM 159 CB LEU 20 14.763 13.525 12.756 1.00 0.00 ATOM 160 CG LEU 20 14.429 14.936 12.238 1.00 0.00 ATOM 161 CD1 LEU 20 13.976 14.829 10.808 1.00 0.00 ATOM 162 CD2 LEU 20 13.271 15.732 12.804 1.00 0.00 ATOM 163 O LEU 20 14.710 10.451 13.374 1.00 0.00 ATOM 164 C LEU 20 14.414 11.122 12.392 1.00 0.00 ATOM 165 N VAL 21 14.837 10.867 11.161 1.00 0.00 ATOM 166 CA VAL 21 15.638 9.659 10.858 1.00 0.00 ATOM 167 CB VAL 21 15.644 9.382 9.344 1.00 0.00 ATOM 168 CG1 VAL 21 16.525 8.179 8.963 1.00 0.00 ATOM 169 CG2 VAL 21 14.219 9.115 8.853 1.00 0.00 ATOM 170 O VAL 21 17.567 8.680 11.893 1.00 0.00 ATOM 171 C VAL 21 17.059 9.711 11.474 1.00 0.00 ATOM 172 N ASP 22 17.603 10.888 11.637 1.00 0.00 ATOM 173 CA ASP 22 18.948 11.060 12.215 1.00 0.00 ATOM 174 CB ASP 22 20.034 10.762 11.183 1.00 0.00 ATOM 175 CG ASP 22 19.886 11.602 9.915 1.00 0.00 ATOM 176 OD1 ASP 22 19.895 12.838 10.017 1.00 0.00 ATOM 177 OD2 ASP 22 19.692 10.996 8.851 1.00 0.00 ATOM 178 O ASP 22 18.175 13.315 12.538 1.00 0.00 ATOM 179 C ASP 22 19.067 12.496 12.738 1.00 0.00 ATOM 180 N ALA 23 20.165 12.728 13.452 1.00 0.00 ATOM 181 CA ALA 23 20.442 14.054 14.033 1.00 0.00 ATOM 182 CB ALA 23 21.621 13.947 14.990 1.00 0.00 ATOM 183 O ALA 23 20.209 16.295 13.223 1.00 0.00 ATOM 184 C ALA 23 20.679 15.173 13.008 1.00 0.00 ATOM 185 N GLY 24 21.295 14.878 11.863 1.00 0.00 ATOM 186 CA GLY 24 21.535 15.871 10.798 1.00 0.00 ATOM 187 O GLY 24 20.026 17.651 10.158 1.00 0.00 ATOM 188 C GLY 24 20.212 16.438 10.260 1.00 0.00 ATOM 189 N THR 25 19.273 15.529 10.056 1.00 0.00 ATOM 190 CA THR 25 17.928 15.910 9.622 1.00 0.00 ATOM 191 CB THR 25 17.163 14.695 9.088 1.00 0.00 ATOM 192 CG2 THR 25 15.927 15.158 8.339 1.00 0.00 ATOM 193 OG1 THR 25 17.870 14.052 8.035 1.00 0.00 ATOM 194 O THR 25 16.690 17.735 10.497 1.00 0.00 ATOM 195 C THR 25 17.196 16.645 10.745 1.00 0.00 ATOM 196 N ALA 26 17.344 16.194 11.993 1.00 0.00 ATOM 197 CA ALA 26 16.766 16.893 13.166 1.00 0.00 ATOM 198 CB ALA 26 17.034 16.138 14.467 1.00 0.00 ATOM 199 O ALA 26 16.485 19.259 13.494 1.00 0.00 ATOM 200 C ALA 26 17.276 18.331 13.314 1.00 0.00 ATOM 201 N GLU 27 18.552 18.494 12.986 1.00 0.00 ATOM 202 CA GLU 27 19.218 19.806 13.024 1.00 0.00 ATOM 203 CB GLU 27 20.697 19.604 12.710 1.00 0.00 ATOM 204 CG GLU 27 21.462 20.921 12.692 1.00 0.00 ATOM 205 CD GLU 27 22.968 20.775 12.525 1.00 0.00 ATOM 206 OE1 GLU 27 23.361 19.680 12.075 1.00 0.00 ATOM 207 OE2 GLU 27 23.696 21.759 12.798 1.00 0.00 ATOM 208 O GLU 27 18.273 21.917 12.381 1.00 0.00 ATOM 209 C GLU 27 18.572 20.781 12.029 1.00 0.00 ATOM 210 N LYS 28 18.304 20.300 10.820 1.00 0.00 ATOM 211 CA LYS 28 17.686 21.128 9.774 1.00 0.00 ATOM 212 CB LYS 28 17.599 20.389 8.443 1.00 0.00 ATOM 213 CG LYS 28 18.975 20.186 7.804 1.00 0.00 ATOM 214 CD LYS 28 18.812 19.442 6.473 1.00 0.00 ATOM 215 CE LYS 28 20.170 19.218 5.802 1.00 0.00 ATOM 216 NZ LYS 28 20.035 18.476 4.544 1.00 0.00 ATOM 217 O LYS 28 15.985 22.821 10.126 1.00 0.00 ATOM 218 C LYS 28 16.290 21.626 10.173 1.00 0.00 ATOM 219 N TYR 29 15.464 20.695 10.648 1.00 0.00 ATOM 220 CA TYR 29 14.103 21.027 11.113 1.00 0.00 ATOM 221 CB TYR 29 13.279 19.807 11.552 1.00 0.00 ATOM 222 CG TYR 29 12.764 19.024 10.348 1.00 0.00 ATOM 223 CD1 TYR 29 13.585 18.072 9.794 1.00 0.00 ATOM 224 CD2 TYR 29 11.484 19.193 9.819 1.00 0.00 ATOM 225 CE1 TYR 29 13.144 17.288 8.750 1.00 0.00 ATOM 226 CE2 TYR 29 11.056 18.422 8.764 1.00 0.00 ATOM 227 CZ TYR 29 11.878 17.459 8.231 1.00 0.00 ATOM 228 OH TYR 29 11.422 16.573 7.325 1.00 0.00 ATOM 229 O TYR 29 13.423 23.054 12.210 1.00 0.00 ATOM 230 C TYR 29 14.108 22.037 12.259 1.00 0.00 ATOM 231 N ILE 30 14.937 21.751 13.262 1.00 0.00 ATOM 232 CA ILE 30 15.067 22.648 14.433 1.00 0.00 ATOM 233 CB ILE 30 15.983 22.027 15.494 1.00 0.00 ATOM 234 CG1 ILE 30 15.290 20.828 16.172 1.00 0.00 ATOM 235 CG2 ILE 30 16.405 23.074 16.533 1.00 0.00 ATOM 236 CD1 ILE 30 16.220 20.028 17.092 1.00 0.00 ATOM 237 O ILE 30 15.068 25.038 14.526 1.00 0.00 ATOM 238 C ILE 30 15.562 24.040 14.011 1.00 0.00 ATOM 239 N LYS 31 16.587 24.074 13.157 1.00 0.00 ATOM 240 CA LYS 31 17.100 25.372 12.705 1.00 0.00 ATOM 241 CB LYS 31 18.316 25.211 11.805 1.00 0.00 ATOM 242 CG LYS 31 19.567 24.734 12.524 1.00 0.00 ATOM 243 CD LYS 31 20.662 24.597 11.476 1.00 0.00 ATOM 244 CE LYS 31 21.973 24.213 12.138 1.00 0.00 ATOM 245 NZ LYS 31 23.021 23.997 11.135 1.00 0.00 ATOM 246 O LYS 31 15.841 27.356 12.244 1.00 0.00 ATOM 247 C LYS 31 16.017 26.175 11.970 1.00 0.00 ATOM 248 N LEU 32 15.202 25.482 11.170 1.00 0.00 ATOM 249 CA LEU 32 14.021 26.101 10.547 1.00 0.00 ATOM 250 CB LEU 32 13.373 25.120 9.560 1.00 0.00 ATOM 251 CG LEU 32 12.039 25.577 8.958 1.00 0.00 ATOM 252 CD1 LEU 32 12.118 26.900 8.188 1.00 0.00 ATOM 253 CD2 LEU 32 11.548 24.509 7.985 1.00 0.00 ATOM 254 O LEU 32 12.487 27.695 11.505 1.00 0.00 ATOM 255 C LEU 32 13.007 26.583 11.600 1.00 0.00 ATOM 256 N ILE 33 12.772 25.775 12.630 1.00 0.00 ATOM 257 CA ILE 33 11.881 26.154 13.740 1.00 0.00 ATOM 258 CB ILE 33 11.663 25.014 14.740 1.00 0.00 ATOM 259 CG1 ILE 33 11.022 23.797 14.063 1.00 0.00 ATOM 260 CG2 ILE 33 10.702 25.512 15.826 1.00 0.00 ATOM 261 CD1 ILE 33 11.046 22.531 14.917 1.00 0.00 ATOM 262 O ILE 33 11.575 28.376 14.605 1.00 0.00 ATOM 263 C ILE 33 12.361 27.438 14.434 1.00 0.00 ATOM 264 N ALA 34 13.631 27.443 14.794 1.00 0.00 ATOM 265 CA ALA 34 14.234 28.595 15.490 1.00 0.00 ATOM 266 CB ALA 34 15.688 28.331 15.841 1.00 0.00 ATOM 267 O ALA 34 13.574 30.852 15.070 1.00 0.00 ATOM 268 C ALA 34 14.155 29.855 14.635 1.00 0.00 ATOM 269 N ASN 35 14.478 29.709 13.352 1.00 0.00 ATOM 270 CA ASN 35 14.424 30.859 12.441 1.00 0.00 ATOM 271 CB ASN 35 15.020 30.472 11.114 1.00 0.00 ATOM 272 CG ASN 35 16.523 30.481 11.066 1.00 0.00 ATOM 273 ND2 ASN 35 17.005 29.673 10.162 1.00 0.00 ATOM 274 OD1 ASN 35 17.260 31.063 11.836 1.00 0.00 ATOM 275 O ASN 35 12.752 32.585 12.347 1.00 0.00 ATOM 276 C ASN 35 13.008 31.387 12.207 1.00 0.00 ATOM 277 N ALA 36 12.056 30.475 12.084 1.00 0.00 ATOM 278 CA ALA 36 10.669 30.884 11.853 1.00 0.00 ATOM 279 CB ALA 36 9.888 29.669 11.425 1.00 0.00 ATOM 280 O ALA 36 9.118 32.351 13.008 1.00 0.00 ATOM 281 C ALA 36 10.056 31.550 13.083 1.00 0.00 ATOM 282 N LYS 37 10.619 31.222 14.231 1.00 0.00 ATOM 283 CA LYS 37 10.149 31.900 15.434 1.00 0.00 ATOM 284 CB LYS 37 9.495 30.857 16.344 1.00 0.00 ATOM 285 CG LYS 37 8.278 30.248 15.615 1.00 0.00 ATOM 286 CD LYS 37 7.166 31.265 15.358 1.00 0.00 ATOM 287 CE LYS 37 6.096 30.739 14.414 1.00 0.00 ATOM 288 NZ LYS 37 5.513 29.439 14.771 1.00 0.00 ATOM 289 O LYS 37 11.040 33.415 17.032 1.00 0.00 ATOM 290 C LYS 37 11.170 32.919 15.942 1.00 0.00 ATOM 291 N THR 38 12.013 33.405 15.025 1.00 0.00 ATOM 292 CA THR 38 12.837 34.624 15.106 1.00 0.00 ATOM 293 CB THR 38 11.821 35.777 14.896 1.00 0.00 ATOM 294 CG2 THR 38 12.293 37.201 15.020 1.00 0.00 ATOM 295 OG1 THR 38 11.379 35.690 13.540 1.00 0.00 ATOM 296 O THR 38 14.277 35.513 16.904 1.00 0.00 ATOM 297 C THR 38 13.908 34.558 16.225 1.00 0.00 ATOM 298 N VAL 39 14.528 33.379 16.259 1.00 0.00 ATOM 299 CA VAL 39 15.638 32.979 17.140 1.00 0.00 ATOM 300 CB VAL 39 15.343 31.603 17.773 1.00 0.00 ATOM 301 CG1 VAL 39 16.527 31.044 18.567 1.00 0.00 ATOM 302 CG2 VAL 39 14.070 31.633 18.618 1.00 0.00 ATOM 303 O VAL 39 16.842 31.891 15.379 1.00 0.00 ATOM 304 C VAL 39 16.864 32.778 16.233 1.00 0.00 ATOM 305 N GLU 40 17.952 33.436 16.613 1.00 0.00 ATOM 306 CA GLU 40 19.230 33.256 15.916 1.00 0.00 ATOM 307 CB GLU 40 19.399 34.366 14.881 1.00 0.00 ATOM 308 CG GLU 40 18.293 34.308 13.829 1.00 0.00 ATOM 309 CD GLU 40 18.385 35.452 12.827 1.00 0.00 ATOM 310 OE1 GLU 40 18.548 35.085 11.641 1.00 0.00 ATOM 311 OE2 GLU 40 18.422 36.622 13.266 1.00 0.00 ATOM 312 O GLU 40 20.684 34.268 17.533 1.00 0.00 ATOM 313 C GLU 40 20.336 33.241 16.963 1.00 0.00 ATOM 314 N GLY 41 20.896 32.051 17.182 1.00 0.00 ATOM 315 CA GLY 41 21.794 31.849 18.316 1.00 0.00 ATOM 316 O GLY 41 23.082 30.375 16.939 1.00 0.00 ATOM 317 C GLY 41 22.898 30.837 18.063 1.00 0.00 ATOM 318 N VAL 42 23.478 30.403 19.167 1.00 0.00 ATOM 319 CA VAL 42 24.518 29.363 19.191 1.00 0.00 ATOM 320 CB VAL 42 25.603 29.738 20.219 1.00 0.00 ATOM 321 CG1 VAL 42 26.694 28.697 20.199 1.00 0.00 ATOM 322 CG2 VAL 42 26.338 31.025 19.867 1.00 0.00 ATOM 323 O VAL 42 22.753 27.978 20.127 1.00 0.00 ATOM 324 C VAL 42 23.805 28.037 19.509 1.00 0.00 ATOM 325 N TRP 43 24.388 26.977 18.969 1.00 0.00 ATOM 326 CA TRP 43 23.807 25.632 18.948 1.00 0.00 ATOM 327 CB TRP 43 23.648 25.237 17.485 1.00 0.00 ATOM 328 CG TRP 43 22.784 26.122 16.605 1.00 0.00 ATOM 329 CD1 TRP 43 23.303 27.029 15.811 1.00 0.00 ATOM 330 CD2 TRP 43 21.407 26.141 16.420 1.00 0.00 ATOM 331 CE2 TRP 43 21.174 27.155 15.512 1.00 0.00 ATOM 332 CE3 TRP 43 20.349 25.411 16.927 1.00 0.00 ATOM 333 NE1 TRP 43 22.339 27.658 15.153 1.00 0.00 ATOM 334 CZ2 TRP 43 19.883 27.491 15.122 1.00 0.00 ATOM 335 CZ3 TRP 43 19.052 25.724 16.530 1.00 0.00 ATOM 336 CH2 TRP 43 18.831 26.760 15.642 1.00 0.00 ATOM 337 O TRP 43 25.968 24.579 19.392 1.00 0.00 ATOM 338 C TRP 43 24.748 24.601 19.587 1.00 0.00 ATOM 339 N THR 44 24.101 23.655 20.248 1.00 0.00 ATOM 340 CA THR 44 24.744 22.404 20.689 1.00 0.00 ATOM 341 CB THR 44 25.073 22.392 22.192 1.00 0.00 ATOM 342 CG2 THR 44 25.909 21.167 22.601 1.00 0.00 ATOM 343 OG1 THR 44 25.825 23.560 22.506 1.00 0.00 ATOM 344 O THR 44 22.625 21.302 20.748 1.00 0.00 ATOM 345 C THR 44 23.805 21.227 20.405 1.00 0.00 ATOM 346 N LEU 45 24.442 20.106 20.129 1.00 0.00 ATOM 347 CA LEU 45 23.794 18.790 20.015 1.00 0.00 ATOM 348 CB LEU 45 23.839 18.334 18.565 1.00 0.00 ATOM 349 CG LEU 45 23.219 16.946 18.350 1.00 0.00 ATOM 350 CD1 LEU 45 21.712 16.971 18.617 1.00 0.00 ATOM 351 CD2 LEU 45 23.521 16.485 16.924 1.00 0.00 ATOM 352 O LEU 45 25.681 17.464 20.768 1.00 0.00 ATOM 353 C LEU 45 24.495 17.752 20.898 1.00 0.00 ATOM 354 N LYS 46 23.701 17.200 21.799 1.00 0.00 ATOM 355 CA LYS 46 24.166 16.124 22.676 1.00 0.00 ATOM 356 CB LYS 46 24.004 16.648 24.111 1.00 0.00 ATOM 357 CG LYS 46 25.135 17.593 24.523 1.00 0.00 ATOM 358 CD LYS 46 25.123 17.787 26.041 1.00 0.00 ATOM 359 CE LYS 46 26.074 18.923 26.409 1.00 0.00 ATOM 360 NZ LYS 46 25.515 19.704 27.526 1.00 0.00 ATOM 361 O LYS 46 22.239 14.665 22.640 1.00 0.00 ATOM 362 C LYS 46 23.431 14.815 22.346 1.00 0.00 ATOM 363 N ASP 47 24.136 13.930 21.660 1.00 0.00 ATOM 364 CA ASP 47 23.647 12.610 21.205 1.00 0.00 ATOM 365 CB ASP 47 24.711 11.871 20.382 1.00 0.00 ATOM 366 CG ASP 47 24.862 12.430 18.957 1.00 0.00 ATOM 367 OD1 ASP 47 24.026 13.273 18.575 1.00 0.00 ATOM 368 OD2 ASP 47 25.776 11.939 18.274 1.00 0.00 ATOM 369 O ASP 47 22.155 11.015 22.176 1.00 0.00 ATOM 370 C ASP 47 23.193 11.666 22.307 1.00 0.00 ATOM 371 N GLU 48 23.859 11.749 23.457 1.00 0.00 ATOM 372 CA GLU 48 23.511 10.948 24.663 1.00 0.00 ATOM 373 CB GLU 48 24.400 11.242 25.873 1.00 0.00 ATOM 374 CG GLU 48 25.881 10.951 25.606 1.00 0.00 ATOM 375 CD GLU 48 26.073 9.443 25.533 1.00 0.00 ATOM 376 OE1 GLU 48 25.506 8.785 26.441 1.00 0.00 ATOM 377 OE2 GLU 48 26.760 8.997 24.594 1.00 0.00 ATOM 378 O GLU 48 21.328 10.278 25.466 1.00 0.00 ATOM 379 C GLU 48 22.065 11.190 25.096 1.00 0.00 ATOM 380 N ILE 49 21.594 12.424 24.882 1.00 0.00 ATOM 381 CA ILE 49 20.240 12.787 25.308 1.00 0.00 ATOM 382 CB ILE 49 20.273 13.892 26.372 1.00 0.00 ATOM 383 CG1 ILE 49 20.786 15.178 25.736 1.00 0.00 ATOM 384 CG2 ILE 49 21.240 13.508 27.504 1.00 0.00 ATOM 385 CD1 ILE 49 20.468 16.402 26.576 1.00 0.00 ATOM 386 O ILE 49 18.173 13.559 24.408 1.00 0.00 ATOM 387 C ILE 49 19.313 13.186 24.145 1.00 0.00 ATOM 388 N LYS 50 19.810 13.046 22.914 1.00 0.00 ATOM 389 CA LYS 50 19.091 13.407 21.679 1.00 0.00 ATOM 390 CB LYS 50 17.971 12.380 21.371 1.00 0.00 ATOM 391 CG LYS 50 18.389 10.914 21.224 1.00 0.00 ATOM 392 CD LYS 50 18.926 10.206 22.480 1.00 0.00 ATOM 393 CE LYS 50 17.910 10.067 23.614 1.00 0.00 ATOM 394 NZ LYS 50 18.545 9.437 24.781 1.00 0.00 ATOM 395 O LYS 50 17.320 15.078 21.629 1.00 0.00 ATOM 396 C LYS 50 18.518 14.833 21.826 1.00 0.00 ATOM 397 N THR 51 19.360 15.734 22.323 1.00 0.00 ATOM 398 CA THR 51 18.924 17.112 22.610 1.00 0.00 ATOM 399 CB THR 51 18.808 17.376 24.122 1.00 0.00 ATOM 400 CG2 THR 51 18.462 18.813 24.544 1.00 0.00 ATOM 401 OG1 THR 51 17.881 16.464 24.723 1.00 0.00 ATOM 402 O THR 51 21.070 18.062 22.062 1.00 0.00 ATOM 403 C THR 51 19.839 18.121 21.943 1.00 0.00 ATOM 404 N PHE 52 19.173 19.041 21.282 1.00 0.00 ATOM 405 CA PHE 52 19.773 20.261 20.728 1.00 0.00 ATOM 406 CB PHE 52 19.188 20.506 19.338 1.00 0.00 ATOM 407 CG PHE 52 20.267 20.870 18.323 1.00 0.00 ATOM 408 CD1 PHE 52 20.996 22.038 18.433 1.00 0.00 ATOM 409 CD2 PHE 52 20.571 19.968 17.311 1.00 0.00 ATOM 410 CE1 PHE 52 22.030 22.249 17.549 1.00 0.00 ATOM 411 CE2 PHE 52 21.620 20.205 16.430 1.00 0.00 ATOM 412 CZ PHE 52 22.366 21.361 16.547 1.00 0.00 ATOM 413 O PHE 52 18.334 21.483 22.227 1.00 0.00 ATOM 414 C PHE 52 19.412 21.442 21.622 1.00 0.00 ATOM 415 N THR 53 20.336 22.391 21.706 1.00 0.00 ATOM 416 CA THR 53 20.120 23.675 22.394 1.00 0.00 ATOM 417 CB THR 53 20.994 23.841 23.632 1.00 0.00 ATOM 418 CG2 THR 53 20.691 25.132 24.363 1.00 0.00 ATOM 419 OG1 THR 53 20.709 22.765 24.510 1.00 0.00 ATOM 420 O THR 53 21.562 24.765 20.842 1.00 0.00 ATOM 421 C THR 53 20.483 24.799 21.440 1.00 0.00 ATOM 422 N VAL 54 19.658 25.821 21.495 1.00 0.00 ATOM 423 CA VAL 54 19.963 27.123 20.884 1.00 0.00 ATOM 424 CB VAL 54 19.059 27.388 19.672 1.00 0.00 ATOM 425 CG1 VAL 54 17.566 27.403 20.024 1.00 0.00 ATOM 426 CG2 VAL 54 19.477 28.655 18.919 1.00 0.00 ATOM 427 O VAL 54 19.062 28.156 22.861 1.00 0.00 ATOM 428 C VAL 54 19.909 28.203 21.966 1.00 0.00 ATOM 429 N THR 55 20.936 29.031 21.954 1.00 0.00 ATOM 430 CA THR 55 21.105 30.058 22.987 1.00 0.00 ATOM 431 CB THR 55 22.241 29.686 23.959 1.00 0.00 ATOM 432 CG2 THR 55 21.960 28.366 24.674 1.00 0.00 ATOM 433 OG1 THR 55 23.512 29.572 23.300 1.00 0.00 ATOM 434 O THR 55 22.127 31.428 21.336 1.00 0.00 ATOM 435 C THR 55 21.377 31.398 22.323 1.00 0.00 ATOM 436 N GLU 56 20.635 32.405 22.756 1.00 0.00 ATOM 437 CA GLU 56 20.947 33.799 22.355 1.00 0.00 ATOM 438 CB GLU 56 19.950 34.750 23.034 1.00 0.00 ATOM 439 CG GLU 56 20.096 36.213 22.583 1.00 0.00 ATOM 440 CD GLU 56 20.031 36.362 21.065 1.00 0.00 ATOM 441 OE1 GLU 56 21.023 36.819 20.452 1.00 0.00 ATOM 442 OE2 GLU 56 18.895 36.122 20.596 1.00 0.00 ATOM 443 O GLU 56 23.103 33.229 23.248 1.00 0.00 ATOM 444 C GLU 56 22.418 34.128 22.724 1.00 0.00 TER END