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 2 Tue Jul 15 13:37:25 2008 MODEL 2 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 13.656 8.832 15.206 1.00 0.00 ATOM 2 CA THR 1 14.087 9.171 16.582 1.00 0.00 ATOM 3 CB THR 1 15.617 9.152 16.681 1.00 0.00 ATOM 4 CG2 THR 1 16.114 9.383 18.131 1.00 0.00 ATOM 5 OG1 THR 1 16.024 7.885 16.212 1.00 0.00 ATOM 6 O THR 1 13.472 11.446 16.216 1.00 0.00 ATOM 7 C THR 1 13.501 10.505 16.996 1.00 0.00 ATOM 8 N THR 2 13.001 10.616 18.215 1.00 0.00 ATOM 9 CA THR 2 12.558 11.913 18.713 1.00 0.00 ATOM 10 CB THR 2 11.743 11.647 19.972 1.00 0.00 ATOM 11 CG2 THR 2 11.164 12.956 20.479 1.00 0.00 ATOM 12 OG1 THR 2 10.617 10.821 19.632 1.00 0.00 ATOM 13 O THR 2 14.507 12.207 20.085 1.00 0.00 ATOM 14 C THR 2 13.784 12.675 19.194 1.00 0.00 ATOM 15 N TYR 3 13.981 13.848 18.660 1.00 0.00 ATOM 16 CA TYR 3 15.006 14.773 19.070 1.00 0.00 ATOM 17 CB TYR 3 15.837 15.245 17.877 1.00 0.00 ATOM 18 CG TYR 3 16.635 14.138 17.231 1.00 0.00 ATOM 19 CD1 TYR 3 16.077 13.345 16.237 1.00 0.00 ATOM 20 CD2 TYR 3 17.948 13.887 17.615 1.00 0.00 ATOM 21 CE1 TYR 3 16.793 12.314 15.669 1.00 0.00 ATOM 22 CE2 TYR 3 18.654 12.831 17.071 1.00 0.00 ATOM 23 CZ TYR 3 18.056 12.029 16.124 1.00 0.00 ATOM 24 OH TYR 3 18.693 10.923 15.625 1.00 0.00 ATOM 25 O TYR 3 13.187 16.282 19.366 1.00 0.00 ATOM 26 C TYR 3 14.327 15.966 19.707 1.00 0.00 ATOM 27 N LYS 4 15.014 16.636 20.617 1.00 0.00 ATOM 28 CA LYS 4 14.443 17.789 21.304 1.00 0.00 ATOM 29 CB LYS 4 14.419 17.521 22.827 1.00 0.00 ATOM 30 CG LYS 4 13.649 16.280 23.211 1.00 0.00 ATOM 31 CD LYS 4 13.951 15.840 24.647 1.00 0.00 ATOM 32 CE LYS 4 12.901 14.844 25.131 1.00 0.00 ATOM 33 NZ LYS 4 12.418 13.947 24.044 1.00 0.00 ATOM 34 O LYS 4 16.376 19.008 20.647 1.00 0.00 ATOM 35 C LYS 4 15.190 19.061 20.959 1.00 0.00 ATOM 36 N LEU 5 14.546 20.194 21.167 1.00 0.00 ATOM 37 CA LEU 5 15.208 21.487 21.231 1.00 0.00 ATOM 38 CB LEU 5 14.550 22.440 20.266 1.00 0.00 ATOM 39 CG LEU 5 15.119 23.857 20.276 1.00 0.00 ATOM 40 CD1 LEU 5 16.518 23.902 19.659 1.00 0.00 ATOM 41 CD2 LEU 5 14.148 24.846 19.572 1.00 0.00 ATOM 42 O LEU 5 13.736 22.209 22.948 1.00 0.00 ATOM 43 C LEU 5 14.904 22.095 22.587 1.00 0.00 ATOM 44 N ILE 6 15.925 22.544 23.295 1.00 0.00 ATOM 45 CA ILE 6 15.744 23.493 24.389 1.00 0.00 ATOM 46 CB ILE 6 16.628 23.167 25.621 1.00 0.00 ATOM 47 CG1 ILE 6 16.233 21.799 26.205 1.00 0.00 ATOM 48 CG2 ILE 6 16.466 24.263 26.689 1.00 0.00 ATOM 49 CD1 ILE 6 17.213 21.222 27.229 1.00 0.00 ATOM 50 O ILE 6 17.244 25.140 23.482 1.00 0.00 ATOM 51 C ILE 6 16.106 24.877 23.835 1.00 0.00 ATOM 52 N LEU 7 15.106 25.736 23.753 1.00 0.00 ATOM 53 CA LEU 7 15.335 27.092 23.231 1.00 0.00 ATOM 54 CB LEU 7 14.067 27.435 22.442 1.00 0.00 ATOM 55 CG LEU 7 13.982 28.816 21.790 1.00 0.00 ATOM 56 CD1 LEU 7 15.157 29.109 20.914 1.00 0.00 ATOM 57 CD2 LEU 7 12.733 28.902 20.945 1.00 0.00 ATOM 58 O LEU 7 14.731 28.289 25.221 1.00 0.00 ATOM 59 C LEU 7 15.548 28.148 24.310 1.00 0.00 ATOM 60 N ASN 8 16.646 28.891 24.206 1.00 0.00 ATOM 61 CA ASN 8 16.955 29.939 25.188 1.00 0.00 ATOM 62 CB ASN 8 17.760 29.196 26.405 1.00 0.00 ATOM 63 CG ASN 8 17.657 27.690 26.509 1.00 0.00 ATOM 64 ND2 ASN 8 18.794 26.980 26.361 1.00 0.00 ATOM 65 OD1 ASN 8 16.592 27.125 26.772 1.00 0.00 ATOM 66 O ASN 8 18.429 31.765 24.560 1.00 0.00 ATOM 67 C ASN 8 17.333 31.221 24.434 1.00 0.00 ATOM 68 N LEU 9 16.406 31.687 23.613 1.00 0.00 ATOM 69 CA LEU 9 16.522 32.976 22.932 1.00 0.00 ATOM 70 CB LEU 9 15.407 33.172 21.938 1.00 0.00 ATOM 71 CG LEU 9 15.469 34.532 21.249 1.00 0.00 ATOM 72 CD1 LEU 9 16.618 34.649 20.241 1.00 0.00 ATOM 73 CD2 LEU 9 14.158 34.824 20.544 1.00 0.00 ATOM 74 O LEU 9 15.341 33.688 24.878 1.00 0.00 ATOM 75 C LEU 9 16.160 33.995 24.010 1.00 0.00 ATOM 76 N LYS 10 16.647 35.227 23.951 1.00 0.00 ATOM 77 CA LYS 10 16.229 36.228 24.940 1.00 0.00 ATOM 78 CB LYS 10 17.061 37.534 24.678 1.00 0.00 ATOM 79 CG LYS 10 16.644 38.702 25.555 1.00 0.00 ATOM 80 CD LYS 10 17.488 39.933 25.284 1.00 0.00 ATOM 81 CE LYS 10 17.116 41.075 26.218 1.00 0.00 ATOM 82 NZ LYS 10 17.985 42.272 26.001 1.00 0.00 ATOM 83 O LYS 10 14.134 36.708 25.994 1.00 0.00 ATOM 84 C LYS 10 14.719 36.438 24.952 1.00 0.00 ATOM 85 N GLN 11 14.080 36.252 23.806 1.00 0.00 ATOM 86 CA GLN 11 12.629 36.411 23.687 1.00 0.00 ATOM 87 CB GLN 11 12.348 37.530 22.558 1.00 0.00 ATOM 88 CG GLN 11 12.911 38.910 22.888 1.00 0.00 ATOM 89 CD GLN 11 14.334 39.099 22.472 1.00 0.00 ATOM 90 OE1 GLN 11 15.017 38.145 21.991 1.00 0.00 ATOM 91 NE2 GLN 11 14.894 40.275 22.542 1.00 0.00 ATOM 92 O GLN 11 10.591 35.142 23.737 1.00 0.00 ATOM 93 C GLN 11 11.824 35.105 23.749 1.00 0.00 ATOM 94 N ALA 12 12.469 33.946 23.773 1.00 0.00 ATOM 95 CA ALA 12 11.746 32.673 23.685 1.00 0.00 ATOM 96 CB ALA 12 11.605 32.241 22.220 1.00 0.00 ATOM 97 O ALA 12 13.627 31.310 24.261 1.00 0.00 ATOM 98 C ALA 12 12.456 31.594 24.494 1.00 0.00 ATOM 99 N LYS 13 11.765 31.041 25.483 1.00 0.00 ATOM 100 CA LYS 13 12.378 30.107 26.432 1.00 0.00 ATOM 101 CB LYS 13 13.276 30.993 27.410 1.00 0.00 ATOM 102 CG LYS 13 12.475 31.595 28.499 1.00 0.00 ATOM 103 CD LYS 13 13.274 31.655 29.805 1.00 0.00 ATOM 104 CE LYS 13 14.284 32.761 29.792 1.00 0.00 ATOM 105 NZ LYS 13 13.612 34.079 29.659 1.00 0.00 ATOM 106 O LYS 13 10.454 29.028 27.345 1.00 0.00 ATOM 107 C LYS 13 11.462 28.912 26.647 1.00 0.00 ATOM 108 N GLU 14 11.725 27.817 25.952 1.00 0.00 ATOM 109 CA GLU 14 10.787 26.695 25.871 1.00 0.00 ATOM 110 CB GLU 14 9.685 27.025 24.854 1.00 0.00 ATOM 111 CG GLU 14 10.160 27.176 23.420 1.00 0.00 ATOM 112 CD GLU 14 9.040 27.630 22.512 1.00 0.00 ATOM 113 OE1 GLU 14 8.020 26.921 22.378 1.00 0.00 ATOM 114 OE2 GLU 14 9.165 28.709 21.894 1.00 0.00 ATOM 115 O GLU 14 12.705 25.474 25.113 1.00 0.00 ATOM 116 C GLU 14 11.518 25.443 25.418 1.00 0.00 ATOM 117 N GLU 15 10.831 24.332 25.396 1.00 0.00 ATOM 118 CA GLU 15 11.318 23.023 24.973 1.00 0.00 ATOM 119 CB GLU 15 11.348 22.061 26.154 1.00 0.00 ATOM 120 CG GLU 15 12.018 22.654 27.379 1.00 0.00 ATOM 121 CD GLU 15 12.119 21.673 28.529 1.00 0.00 ATOM 122 OE1 GLU 15 11.152 20.917 28.761 1.00 0.00 ATOM 123 OE2 GLU 15 13.167 21.670 29.209 1.00 0.00 ATOM 124 O GLU 15 9.110 22.677 24.116 1.00 0.00 ATOM 125 C GLU 15 10.317 22.476 23.956 1.00 0.00 ATOM 126 N ALA 16 10.791 21.827 22.902 1.00 0.00 ATOM 127 CA ALA 16 9.934 21.279 21.852 1.00 0.00 ATOM 128 CB ALA 16 9.781 22.302 20.731 1.00 0.00 ATOM 129 O ALA 16 11.781 19.827 21.487 1.00 0.00 ATOM 130 C ALA 16 10.577 19.998 21.327 1.00 0.00 ATOM 131 N ILE 17 9.808 19.103 20.721 1.00 0.00 ATOM 132 CA ILE 17 10.327 17.805 20.271 1.00 0.00 ATOM 133 CB ILE 17 9.870 16.662 21.235 1.00 0.00 ATOM 134 CG1 ILE 17 8.354 16.399 21.157 1.00 0.00 ATOM 135 CG2 ILE 17 10.262 17.010 22.679 1.00 0.00 ATOM 136 CD1 ILE 17 7.871 15.212 21.975 1.00 0.00 ATOM 137 O ILE 17 8.824 17.957 18.407 1.00 0.00 ATOM 138 C ILE 17 9.896 17.528 18.835 1.00 0.00 ATOM 139 N LYS 18 10.733 16.811 18.092 1.00 0.00 ATOM 140 CA LYS 18 10.424 16.465 16.653 1.00 0.00 ATOM 141 CB LYS 18 11.041 17.475 15.670 1.00 0.00 ATOM 142 CG LYS 18 10.551 18.921 15.776 1.00 0.00 ATOM 143 CD LYS 18 9.081 19.082 15.395 1.00 0.00 ATOM 144 CE LYS 18 8.648 20.531 15.596 1.00 0.00 ATOM 145 NZ LYS 18 7.188 20.747 15.351 1.00 0.00 ATOM 146 O LYS 18 12.096 14.715 16.654 1.00 0.00 ATOM 147 C LYS 18 10.972 15.058 16.286 1.00 0.00 ATOM 148 N GLU 19 10.176 14.270 15.570 1.00 0.00 ATOM 149 CA GLU 19 10.597 12.933 15.170 1.00 0.00 ATOM 150 CB GLU 19 9.380 11.982 15.124 1.00 0.00 ATOM 151 CG GLU 19 9.713 10.556 14.691 1.00 0.00 ATOM 152 CD GLU 19 8.481 9.717 14.380 1.00 0.00 ATOM 153 OE1 GLU 19 7.467 10.274 13.904 1.00 0.00 ATOM 154 OE2 GLU 19 8.539 8.487 14.596 1.00 0.00 ATOM 155 O GLU 19 10.809 13.368 12.827 1.00 0.00 ATOM 156 C GLU 19 11.377 12.991 13.853 1.00 0.00 ATOM 157 N LEU 20 12.645 12.604 13.828 1.00 0.00 ATOM 158 CA LEU 20 13.444 12.655 12.596 1.00 0.00 ATOM 159 CB LEU 20 14.336 13.903 12.515 1.00 0.00 ATOM 160 CG LEU 20 13.746 15.218 11.988 1.00 0.00 ATOM 161 CD1 LEU 20 12.907 15.051 10.753 1.00 0.00 ATOM 162 CD2 LEU 20 12.969 15.975 13.037 1.00 0.00 ATOM 163 O LEU 20 14.556 10.645 13.329 1.00 0.00 ATOM 164 C LEU 20 14.305 11.412 12.403 1.00 0.00 ATOM 165 N VAL 21 14.740 11.224 11.165 1.00 0.00 ATOM 166 CA VAL 21 15.504 10.049 10.752 1.00 0.00 ATOM 167 CB VAL 21 15.752 10.054 9.229 1.00 0.00 ATOM 168 CG1 VAL 21 16.609 8.859 8.833 1.00 0.00 ATOM 169 CG2 VAL 21 14.417 10.005 8.496 1.00 0.00 ATOM 170 O VAL 21 17.227 8.874 11.936 1.00 0.00 ATOM 171 C VAL 21 16.841 9.953 11.488 1.00 0.00 ATOM 172 N ASP 22 17.557 11.061 11.606 1.00 0.00 ATOM 173 CA ASP 22 18.886 11.079 12.216 1.00 0.00 ATOM 174 CB ASP 22 19.963 10.714 11.223 1.00 0.00 ATOM 175 CG ASP 22 19.888 11.476 9.919 1.00 0.00 ATOM 176 OD1 ASP 22 19.944 12.722 9.946 1.00 0.00 ATOM 177 OD2 ASP 22 19.784 10.824 8.859 1.00 0.00 ATOM 178 O ASP 22 18.331 13.391 12.537 1.00 0.00 ATOM 179 C ASP 22 19.142 12.487 12.741 1.00 0.00 ATOM 180 N ALA 23 20.272 12.672 13.417 1.00 0.00 ATOM 181 CA ALA 23 20.630 13.994 13.973 1.00 0.00 ATOM 182 CB ALA 23 21.911 13.880 14.787 1.00 0.00 ATOM 183 O ALA 23 20.321 16.181 13.024 1.00 0.00 ATOM 184 C ALA 23 20.750 15.038 12.859 1.00 0.00 ATOM 185 N GLY 24 21.332 14.642 11.732 1.00 0.00 ATOM 186 CA GLY 24 21.497 15.553 10.605 1.00 0.00 ATOM 187 O GLY 24 20.047 17.381 10.010 1.00 0.00 ATOM 188 C GLY 24 20.186 16.157 10.133 1.00 0.00 ATOM 189 N THR 25 19.197 15.305 9.894 1.00 0.00 ATOM 190 CA THR 25 17.862 15.745 9.495 1.00 0.00 ATOM 191 CB THR 25 17.066 14.507 8.954 1.00 0.00 ATOM 192 CG2 THR 25 15.641 14.917 8.595 1.00 0.00 ATOM 193 OG1 THR 25 17.741 13.982 7.783 1.00 0.00 ATOM 194 O THR 25 16.450 17.503 10.322 1.00 0.00 ATOM 195 C THR 25 17.169 16.537 10.597 1.00 0.00 ATOM 196 N ALA 26 17.407 16.150 11.843 1.00 0.00 ATOM 197 CA ALA 26 16.814 16.832 12.987 1.00 0.00 ATOM 198 CB ALA 26 17.128 16.043 14.270 1.00 0.00 ATOM 199 O ALA 26 16.554 19.158 13.358 1.00 0.00 ATOM 200 C ALA 26 17.333 18.245 13.126 1.00 0.00 ATOM 201 N GLU 27 18.630 18.431 12.944 1.00 0.00 ATOM 202 CA GLU 27 19.233 19.746 13.085 1.00 0.00 ATOM 203 CB GLU 27 20.730 19.655 12.804 1.00 0.00 ATOM 204 CG GLU 27 21.498 20.940 13.075 1.00 0.00 ATOM 205 CD GLU 27 22.984 20.764 12.825 1.00 0.00 ATOM 206 OE1 GLU 27 23.381 19.784 12.167 1.00 0.00 ATOM 207 OE2 GLU 27 23.796 21.592 13.289 1.00 0.00 ATOM 208 O GLU 27 18.229 21.883 12.477 1.00 0.00 ATOM 209 C GLU 27 18.606 20.752 12.120 1.00 0.00 ATOM 210 N LYS 28 18.434 20.308 10.876 1.00 0.00 ATOM 211 CA LYS 28 17.864 21.184 9.850 1.00 0.00 ATOM 212 CB LYS 28 17.617 20.142 8.529 1.00 0.00 ATOM 213 CG LYS 28 17.525 20.699 7.110 1.00 0.00 ATOM 214 CD LYS 28 17.307 19.582 6.052 1.00 0.00 ATOM 215 CE LYS 28 18.038 19.848 4.703 1.00 0.00 ATOM 216 NZ LYS 28 19.199 18.923 4.364 1.00 0.00 ATOM 217 O LYS 28 15.956 22.629 10.010 1.00 0.00 ATOM 218 C LYS 28 16.396 21.485 10.130 1.00 0.00 ATOM 219 N TYR 29 15.639 20.458 10.502 1.00 0.00 ATOM 220 CA TYR 29 14.229 20.632 10.796 1.00 0.00 ATOM 221 CB TYR 29 13.587 19.296 11.187 1.00 0.00 ATOM 222 CG TYR 29 12.072 19.326 11.230 1.00 0.00 ATOM 223 CD1 TYR 29 11.320 18.660 10.265 1.00 0.00 ATOM 224 CD2 TYR 29 11.389 20.010 12.230 1.00 0.00 ATOM 225 CE1 TYR 29 9.930 18.673 10.307 1.00 0.00 ATOM 226 CE2 TYR 29 10.008 20.055 12.242 1.00 0.00 ATOM 227 CZ TYR 29 9.286 19.362 11.308 1.00 0.00 ATOM 228 OH TYR 29 7.919 19.384 11.413 1.00 0.00 ATOM 229 O TYR 29 13.323 22.568 11.867 1.00 0.00 ATOM 230 C TYR 29 14.078 21.600 11.951 1.00 0.00 ATOM 231 N ILE 30 14.801 21.341 13.037 1.00 0.00 ATOM 232 CA ILE 30 14.738 22.205 14.209 1.00 0.00 ATOM 233 CB ILE 30 15.487 21.505 15.398 1.00 0.00 ATOM 234 CG1 ILE 30 14.818 20.161 15.698 1.00 0.00 ATOM 235 CG2 ILE 30 15.463 22.389 16.644 1.00 0.00 ATOM 236 CD1 ILE 30 15.423 19.402 16.879 1.00 0.00 ATOM 237 O ILE 30 14.760 24.593 14.460 1.00 0.00 ATOM 238 C ILE 30 15.264 23.610 13.916 1.00 0.00 ATOM 239 N LYS 31 16.273 23.745 13.037 1.00 0.00 ATOM 240 CA LYS 31 16.799 25.056 12.674 1.00 0.00 ATOM 241 CB LYS 31 18.086 24.946 11.820 1.00 0.00 ATOM 242 CG LYS 31 18.647 26.279 11.259 1.00 0.00 ATOM 243 CD LYS 31 19.048 27.295 12.345 1.00 0.00 ATOM 244 CE LYS 31 19.751 28.526 11.747 1.00 0.00 ATOM 245 NZ LYS 31 19.982 29.653 12.737 1.00 0.00 ATOM 246 O LYS 31 15.612 27.054 12.146 1.00 0.00 ATOM 247 C LYS 31 15.736 25.857 11.931 1.00 0.00 ATOM 248 N LEU 32 14.963 25.201 11.068 1.00 0.00 ATOM 249 CA LEU 32 13.875 25.887 10.377 1.00 0.00 ATOM 250 CB LEU 32 13.323 24.919 9.281 1.00 0.00 ATOM 251 CG LEU 32 12.108 25.404 8.455 1.00 0.00 ATOM 252 CD1 LEU 32 12.294 26.713 7.816 1.00 0.00 ATOM 253 CD2 LEU 32 11.834 24.344 7.410 1.00 0.00 ATOM 254 O LEU 32 12.376 27.511 11.316 1.00 0.00 ATOM 255 C LEU 32 12.828 26.364 11.379 1.00 0.00 ATOM 256 N ILE 33 12.465 25.521 12.334 1.00 0.00 ATOM 257 CA ILE 33 11.548 25.933 13.404 1.00 0.00 ATOM 258 CB ILE 33 11.242 24.838 14.386 1.00 0.00 ATOM 259 CG1 ILE 33 10.287 23.840 13.708 1.00 0.00 ATOM 260 CG2 ILE 33 10.643 25.395 15.685 1.00 0.00 ATOM 261 CD1 ILE 33 10.232 22.461 14.342 1.00 0.00 ATOM 262 O ILE 33 11.432 28.107 14.447 1.00 0.00 ATOM 263 C ILE 33 12.126 27.130 14.165 1.00 0.00 ATOM 264 N ALA 34 13.416 27.081 14.470 1.00 0.00 ATOM 265 CA ALA 34 14.074 28.162 15.187 1.00 0.00 ATOM 266 CB ALA 34 15.502 27.824 15.522 1.00 0.00 ATOM 267 O ALA 34 13.781 30.546 14.919 1.00 0.00 ATOM 268 C ALA 34 14.059 29.479 14.371 1.00 0.00 ATOM 269 N ASN 35 14.359 29.385 13.082 1.00 0.00 ATOM 270 CA ASN 35 14.373 30.563 12.222 1.00 0.00 ATOM 271 CB ASN 35 14.919 30.233 10.814 1.00 0.00 ATOM 272 CG ASN 35 16.414 30.200 10.734 1.00 0.00 ATOM 273 ND2 ASN 35 16.928 29.428 9.799 1.00 0.00 ATOM 274 OD1 ASN 35 17.094 30.851 11.494 1.00 0.00 ATOM 275 O ASN 35 12.840 32.419 12.172 1.00 0.00 ATOM 276 C ASN 35 12.987 31.195 12.132 1.00 0.00 ATOM 277 N ALA 36 11.955 30.367 12.050 1.00 0.00 ATOM 278 CA ALA 36 10.589 30.877 11.993 1.00 0.00 ATOM 279 CB ALA 36 9.635 29.710 11.647 1.00 0.00 ATOM 280 O ALA 36 9.565 32.627 13.280 1.00 0.00 ATOM 281 C ALA 36 10.233 31.594 13.296 1.00 0.00 ATOM 282 N LYS 37 10.729 31.082 14.416 1.00 0.00 ATOM 283 CA LYS 37 10.554 31.722 15.725 1.00 0.00 ATOM 284 CB LYS 37 10.339 30.647 16.805 1.00 0.00 ATOM 285 CG LYS 37 9.152 29.718 16.579 1.00 0.00 ATOM 286 CD LYS 37 7.828 30.458 16.663 1.00 0.00 ATOM 287 CE LYS 37 6.657 29.494 16.536 1.00 0.00 ATOM 288 NZ LYS 37 5.346 30.195 16.608 1.00 0.00 ATOM 289 O LYS 37 11.790 33.175 17.178 1.00 0.00 ATOM 290 C LYS 37 11.613 32.782 16.028 1.00 0.00 ATOM 291 N THR 38 12.251 33.283 14.980 1.00 0.00 ATOM 292 CA THR 38 13.132 34.451 15.051 1.00 0.00 ATOM 293 CB THR 38 12.283 35.702 15.389 1.00 0.00 ATOM 294 CG2 THR 38 12.929 36.988 14.921 1.00 0.00 ATOM 295 OG1 THR 38 11.044 35.588 14.677 1.00 0.00 ATOM 296 O THR 38 14.790 35.108 16.701 1.00 0.00 ATOM 297 C THR 38 14.316 34.223 15.987 1.00 0.00 ATOM 298 N VAL 39 14.799 32.993 15.979 1.00 0.00 ATOM 299 CA VAL 39 15.938 32.605 16.796 1.00 0.00 ATOM 300 CB VAL 39 15.777 31.165 17.384 1.00 0.00 ATOM 301 CG1 VAL 39 16.955 30.791 18.237 1.00 0.00 ATOM 302 CG2 VAL 39 14.401 31.041 18.174 1.00 0.00 ATOM 303 O VAL 39 17.320 32.249 14.878 1.00 0.00 ATOM 304 C VAL 39 17.216 32.760 15.989 1.00 0.00 ATOM 305 N GLU 40 18.213 33.379 16.592 1.00 0.00 ATOM 306 CA GLU 40 19.589 33.255 16.140 1.00 0.00 ATOM 307 CB GLU 40 20.067 34.525 15.431 1.00 0.00 ATOM 308 CG GLU 40 21.518 34.456 14.983 1.00 0.00 ATOM 309 CD GLU 40 21.775 33.266 14.084 1.00 0.00 ATOM 310 OE1 GLU 40 21.408 33.307 12.892 1.00 0.00 ATOM 311 OE2 GLU 40 22.330 32.251 14.565 1.00 0.00 ATOM 312 O GLU 40 20.559 34.061 18.164 1.00 0.00 ATOM 313 C GLU 40 20.500 33.131 17.353 1.00 0.00 ATOM 314 N GLY 41 21.167 32.001 17.532 1.00 0.00 ATOM 315 CA GLY 41 21.973 31.803 18.722 1.00 0.00 ATOM 316 O GLY 41 23.136 30.134 17.463 1.00 0.00 ATOM 317 C GLY 41 23.002 30.711 18.544 1.00 0.00 ATOM 318 N VAL 42 23.737 30.425 19.606 1.00 0.00 ATOM 319 CA VAL 42 24.761 29.388 19.614 1.00 0.00 ATOM 320 CB VAL 42 25.623 29.523 20.879 1.00 0.00 ATOM 321 CG1 VAL 42 26.610 28.354 20.957 1.00 0.00 ATOM 322 CG2 VAL 42 26.372 30.862 20.900 1.00 0.00 ATOM 323 O VAL 42 23.247 27.828 20.587 1.00 0.00 ATOM 324 C VAL 42 24.042 28.051 19.676 1.00 0.00 ATOM 325 N TRP 43 24.318 27.157 18.742 1.00 0.00 ATOM 326 CA TRP 43 23.743 25.814 18.783 1.00 0.00 ATOM 327 CB TRP 43 23.612 25.261 17.365 1.00 0.00 ATOM 328 CG TRP 43 22.514 25.883 16.616 1.00 0.00 ATOM 329 CD1 TRP 43 22.595 26.861 15.680 1.00 0.00 ATOM 330 CD2 TRP 43 21.136 25.567 16.740 1.00 0.00 ATOM 331 CE2 TRP 43 20.432 26.393 15.832 1.00 0.00 ATOM 332 CE3 TRP 43 20.419 24.650 17.518 1.00 0.00 ATOM 333 NE1 TRP 43 21.363 27.156 15.185 1.00 0.00 ATOM 334 CZ2 TRP 43 19.040 26.326 15.660 1.00 0.00 ATOM 335 CZ3 TRP 43 19.037 24.618 17.349 1.00 0.00 ATOM 336 CH2 TRP 43 18.372 25.437 16.438 1.00 0.00 ATOM 337 O TRP 43 25.887 24.797 19.089 1.00 0.00 ATOM 338 C TRP 43 24.703 24.832 19.428 1.00 0.00 ATOM 339 N THR 44 24.185 23.995 20.308 1.00 0.00 ATOM 340 CA THR 44 24.902 22.829 20.805 1.00 0.00 ATOM 341 CB THR 44 25.277 22.974 22.278 1.00 0.00 ATOM 342 CG2 THR 44 25.989 21.725 22.771 1.00 0.00 ATOM 343 OG1 THR 44 26.152 24.097 22.431 1.00 0.00 ATOM 344 O THR 44 22.767 21.684 20.697 1.00 0.00 ATOM 345 C THR 44 23.994 21.600 20.598 1.00 0.00 ATOM 346 N LEU 45 24.586 20.452 20.349 1.00 0.00 ATOM 347 CA LEU 45 23.838 19.213 20.307 1.00 0.00 ATOM 348 CB LEU 45 23.957 18.623 18.940 1.00 0.00 ATOM 349 CG LEU 45 23.289 17.267 18.773 1.00 0.00 ATOM 350 CD1 LEU 45 21.744 17.306 19.036 1.00 0.00 ATOM 351 CD2 LEU 45 23.583 16.708 17.427 1.00 0.00 ATOM 352 O LEU 45 25.729 17.989 21.106 1.00 0.00 ATOM 353 C LEU 45 24.520 18.203 21.204 1.00 0.00 ATOM 354 N LYS 46 23.742 17.562 22.058 1.00 0.00 ATOM 355 CA LYS 46 24.214 16.450 22.872 1.00 0.00 ATOM 356 CB LYS 46 23.737 16.668 24.265 1.00 0.00 ATOM 357 CG LYS 46 24.812 17.475 24.978 1.00 0.00 ATOM 358 CD LYS 46 24.667 17.406 26.494 1.00 0.00 ATOM 359 CE LYS 46 25.039 16.032 27.034 1.00 0.00 ATOM 360 NZ LYS 46 24.999 15.987 28.524 1.00 0.00 ATOM 361 O LYS 46 22.326 14.974 22.752 1.00 0.00 ATOM 362 C LYS 46 23.487 15.194 22.405 1.00 0.00 ATOM 363 N ASP 47 24.170 14.370 21.616 1.00 0.00 ATOM 364 CA ASP 47 23.573 13.132 21.109 1.00 0.00 ATOM 365 CB ASP 47 24.965 12.407 20.342 1.00 0.00 ATOM 366 CG ASP 47 24.961 11.967 18.876 1.00 0.00 ATOM 367 OD1 ASP 47 24.271 10.998 18.537 1.00 0.00 ATOM 368 OD2 ASP 47 25.657 12.608 18.055 1.00 0.00 ATOM 369 O ASP 47 22.219 11.385 22.067 1.00 0.00 ATOM 370 C ASP 47 23.156 12.168 22.231 1.00 0.00 ATOM 371 N GLU 48 23.853 12.229 23.362 1.00 0.00 ATOM 372 CA GLU 48 23.541 11.361 24.492 1.00 0.00 ATOM 373 CB GLU 48 24.519 11.564 25.628 1.00 0.00 ATOM 374 CG GLU 48 25.762 10.700 25.465 1.00 0.00 ATOM 375 CD GLU 48 26.706 10.832 26.646 1.00 0.00 ATOM 376 OE1 GLU 48 26.215 11.074 27.776 1.00 0.00 ATOM 377 OE2 GLU 48 27.922 10.692 26.449 1.00 0.00 ATOM 378 O GLU 48 21.494 10.629 25.541 1.00 0.00 ATOM 379 C GLU 48 22.113 11.557 25.024 1.00 0.00 ATOM 380 N ILE 49 21.541 12.733 24.799 1.00 0.00 ATOM 381 CA ILE 49 20.154 13.021 25.166 1.00 0.00 ATOM 382 CB ILE 49 20.062 14.105 26.274 1.00 0.00 ATOM 383 CG1 ILE 49 20.876 15.347 25.883 1.00 0.00 ATOM 384 CG2 ILE 49 20.551 13.532 27.603 1.00 0.00 ATOM 385 CD1 ILE 49 20.662 16.550 26.767 1.00 0.00 ATOM 386 O ILE 49 18.217 13.930 24.113 1.00 0.00 ATOM 387 C ILE 49 19.336 13.434 23.971 1.00 0.00 ATOM 388 N LYS 50 19.890 13.234 22.780 1.00 0.00 ATOM 389 CA LYS 50 19.192 13.592 21.552 1.00 0.00 ATOM 390 CB LYS 50 18.433 12.181 20.983 1.00 0.00 ATOM 391 CG LYS 50 18.963 10.831 21.484 1.00 0.00 ATOM 392 CD LYS 50 17.901 10.074 22.283 1.00 0.00 ATOM 393 CE LYS 50 18.449 9.638 23.645 1.00 0.00 ATOM 394 NZ LYS 50 17.803 10.318 24.808 1.00 0.00 ATOM 395 O LYS 50 17.448 15.203 21.291 1.00 0.00 ATOM 396 C LYS 50 18.591 14.966 21.700 1.00 0.00 ATOM 397 N THR 51 19.353 15.902 22.263 1.00 0.00 ATOM 398 CA THR 51 18.875 17.249 22.562 1.00 0.00 ATOM 399 CB THR 51 18.764 17.429 24.088 1.00 0.00 ATOM 400 CG2 THR 51 18.348 18.849 24.468 1.00 0.00 ATOM 401 OG1 THR 51 17.837 16.478 24.621 1.00 0.00 ATOM 402 O THR 51 21.027 18.274 22.233 1.00 0.00 ATOM 403 C THR 51 19.816 18.286 21.969 1.00 0.00 ATOM 404 N PHE 52 19.218 19.185 21.187 1.00 0.00 ATOM 405 CA PHE 52 19.849 20.388 20.705 1.00 0.00 ATOM 406 CB PHE 52 19.191 20.855 19.407 1.00 0.00 ATOM 407 CG PHE 52 19.756 20.121 18.219 1.00 0.00 ATOM 408 CD1 PHE 52 19.084 19.069 17.615 1.00 0.00 ATOM 409 CD2 PHE 52 20.994 20.505 17.721 1.00 0.00 ATOM 410 CE1 PHE 52 19.652 18.420 16.529 1.00 0.00 ATOM 411 CE2 PHE 52 21.548 19.854 16.636 1.00 0.00 ATOM 412 CZ PHE 52 20.881 18.810 16.033 1.00 0.00 ATOM 413 O PHE 52 18.304 21.629 22.045 1.00 0.00 ATOM 414 C PHE 52 19.462 21.513 21.647 1.00 0.00 ATOM 415 N THR 53 20.436 22.340 22.020 1.00 0.00 ATOM 416 CA THR 53 20.181 23.515 22.842 1.00 0.00 ATOM 417 CB THR 53 21.023 23.469 24.097 1.00 0.00 ATOM 418 CG2 THR 53 20.679 24.653 25.005 1.00 0.00 ATOM 419 OG1 THR 53 20.739 22.237 24.773 1.00 0.00 ATOM 420 O THR 53 21.841 24.829 21.668 1.00 0.00 ATOM 421 C THR 53 20.677 24.767 22.068 1.00 0.00 ATOM 422 N VAL 54 19.795 25.742 21.870 1.00 0.00 ATOM 423 CA VAL 54 20.161 26.961 21.158 1.00 0.00 ATOM 424 CB VAL 54 19.293 27.244 19.819 1.00 0.00 ATOM 425 CG1 VAL 54 17.778 27.200 20.033 1.00 0.00 ATOM 426 CG2 VAL 54 19.745 28.551 19.078 1.00 0.00 ATOM 427 O VAL 54 18.894 28.389 22.550 1.00 0.00 ATOM 428 C VAL 54 19.984 28.137 22.087 1.00 0.00 ATOM 429 N THR 55 21.064 28.882 22.343 1.00 0.00 ATOM 430 CA THR 55 21.100 29.958 23.298 1.00 0.00 ATOM 431 CB THR 55 22.008 29.581 24.429 1.00 0.00 ATOM 432 CG2 THR 55 22.124 30.706 25.455 1.00 0.00 ATOM 433 OG1 THR 55 21.427 28.481 25.154 1.00 0.00 ATOM 434 O THR 55 22.674 31.200 22.022 1.00 0.00 ATOM 435 C THR 55 21.618 31.219 22.643 1.00 0.00 ATOM 436 N GLU 56 20.886 32.309 22.772 1.00 0.00 ATOM 437 CA GLU 56 21.345 33.584 22.221 1.00 0.00 ATOM 438 CB GLU 56 20.293 34.658 22.454 1.00 0.00 ATOM 439 CG GLU 56 20.691 35.910 21.750 1.00 0.00 ATOM 440 CD GLU 56 19.737 37.063 21.985 1.00 0.00 ATOM 441 OE1 GLU 56 18.622 36.783 22.473 1.00 0.00 ATOM 442 OE2 GLU 56 20.100 38.254 21.684 1.00 0.00 ATOM 443 O GLU 56 22.779 33.957 24.116 1.00 0.00 ATOM 444 C GLU 56 22.652 34.024 22.869 1.00 0.00 TER END