PFRMAT TS TARGET T0499 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 METHOD All the models, whether native SAM+undertaker models or metaserver METHOD models, were very similar. I added some constraints to keep the OH METHOD atoms of Y3 and Y45 close together (as seen in the template 2igdA) and METHOD to keep W43 buried. METHOD METHOD The first model is the best scoring with my constrained cost function. METHOD The second is the same model followed by energy minimization by METHOD gromacs and repacking the sidechains by rosetta. Although many of the METHOD solvent-exposed residues have been changed to more canonical rotamers, METHOD I don't really like the way rosetta moved Y29, so I ranked this model METHOD lower. METHOD METHOD The third model is a meta-server model, optimized by undertaker using METHOD the same constrained cost function used to generate the first model, METHOD but starting from non-SAM server models. METHOD METHOD The fourth model is from an earlier metaserver run, without the METHOD constraints on Y45, so it ended up kicked out of position. METHOD METHOD The fifth model is the fully automatic one, with no human intervention METHOD other than choosing the gromacs-minimized version of the model to METHOD minimize clashes. METHOD METHOD Model METHOD 1 T0499.try4-opt3.pdb # < try3-gromacs0.repack-nonPC < try2-opt3 < align(2igdA) METHOD METHOD 2 T0499.try4-opt3.gromacs0.repack-nonPC.pdb # < try3-gromacs0.repack-nonPC < try2-opt3 < align(2igdA) METHOD # best rosetta energy METHOD METHOD 3 T0499.MQAX4-opt3.pdb # < pipe_int_TS1 METHOD METHOD 4 T0499.MQAC1-opt3.gromacs0.repack-nonPC.pdb # < SAM-T08-server_TS1 METHOD METHOD 5 T0499.try1-opt3.gromacs0.pdb # < align(2gi9A) REMARK 6 REMARK 6 T0499 model 1 Tue Jul 15 16:01:45 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 2igd_A 2igh_A 2qmt_A ATOM 1 N THR 1 15.513 9.566 17.156 1.00 0.00 ATOM 2 CA THR 1 14.388 9.306 18.100 1.00 0.00 ATOM 3 CB THR 1 14.923 8.567 19.342 1.00 0.00 ATOM 4 CG2 THR 1 13.784 7.885 20.118 1.00 0.00 ATOM 5 OG1 THR 1 15.875 7.587 18.906 1.00 0.00 ATOM 6 O THR 1 13.495 11.464 17.618 1.00 0.00 ATOM 7 C THR 1 13.805 10.655 18.490 1.00 0.00 ATOM 8 N THR 2 13.601 10.880 19.767 1.00 0.00 ATOM 9 CA THR 2 13.034 12.166 20.235 1.00 0.00 ATOM 10 CB THR 2 12.386 11.904 21.588 1.00 0.00 ATOM 11 CG2 THR 2 11.674 13.161 22.054 1.00 0.00 ATOM 12 OG1 THR 2 11.365 10.902 21.439 1.00 0.00 ATOM 13 O THR 2 15.005 12.896 21.419 1.00 0.00 ATOM 14 C THR 2 14.204 13.115 20.516 1.00 0.00 ATOM 15 N TYR 3 14.184 14.241 19.820 1.00 0.00 ATOM 16 CA TYR 3 15.185 15.292 20.030 1.00 0.00 ATOM 17 CB TYR 3 15.728 15.774 18.681 1.00 0.00 ATOM 18 CG TYR 3 16.499 14.663 17.951 1.00 0.00 ATOM 19 CD1 TYR 3 15.822 13.761 17.152 1.00 0.00 ATOM 20 CD2 TYR 3 17.880 14.580 18.072 1.00 0.00 ATOM 21 CE1 TYR 3 16.514 12.775 16.473 1.00 0.00 ATOM 22 CE2 TYR 3 18.576 13.586 17.404 1.00 0.00 ATOM 23 CZ TYR 3 17.888 12.672 16.596 1.00 0.00 ATOM 24 OH TYR 3 18.529 11.617 16.047 1.00 0.00 ATOM 25 O TYR 3 13.336 16.727 20.610 1.00 0.00 ATOM 26 C TYR 3 14.511 16.452 20.780 1.00 0.00 ATOM 27 N LYS 4 15.302 17.144 21.581 1.00 0.00 ATOM 28 CA LYS 4 14.846 18.279 22.368 1.00 0.00 ATOM 29 CB LYS 4 15.173 18.118 23.844 1.00 0.00 ATOM 30 CG LYS 4 14.421 16.953 24.462 1.00 0.00 ATOM 31 CD LYS 4 14.781 16.865 25.931 1.00 0.00 ATOM 32 CE LYS 4 14.028 15.689 26.519 1.00 0.00 ATOM 33 NZ LYS 4 14.419 15.623 27.914 1.00 0.00 ATOM 34 O LYS 4 16.671 19.540 21.484 1.00 0.00 ATOM 35 C LYS 4 15.496 19.544 21.879 1.00 0.00 ATOM 36 N LEU 5 14.758 20.645 21.928 1.00 0.00 ATOM 37 CA LEU 5 15.264 21.992 21.697 1.00 0.00 ATOM 38 CB LEU 5 14.580 22.611 20.472 1.00 0.00 ATOM 39 CG LEU 5 15.125 23.979 20.041 1.00 0.00 ATOM 40 CD1 LEU 5 16.569 23.843 19.580 1.00 0.00 ATOM 41 CD2 LEU 5 14.254 24.546 18.931 1.00 0.00 ATOM 42 O LEU 5 13.898 22.935 23.433 1.00 0.00 ATOM 43 C LEU 5 15.032 22.834 22.954 1.00 0.00 ATOM 44 N ILE 6 16.130 23.373 23.462 1.00 0.00 ATOM 45 CA ILE 6 16.132 24.353 24.561 1.00 0.00 ATOM 46 CB ILE 6 17.269 24.129 25.588 1.00 0.00 ATOM 47 CG1 ILE 6 17.288 22.684 26.070 1.00 0.00 ATOM 48 CG2 ILE 6 17.143 25.112 26.747 1.00 0.00 ATOM 49 CD1 ILE 6 18.452 22.283 26.976 1.00 0.00 ATOM 50 O ILE 6 17.281 26.033 23.230 1.00 0.00 ATOM 51 C ILE 6 16.300 25.740 23.918 1.00 0.00 ATOM 52 N LEU 7 15.286 26.569 24.119 1.00 0.00 ATOM 53 CA LEU 7 15.209 27.902 23.516 1.00 0.00 ATOM 54 CB LEU 7 13.862 28.059 22.801 1.00 0.00 ATOM 55 CG LEU 7 13.661 27.157 21.577 1.00 0.00 ATOM 56 CD1 LEU 7 13.121 25.802 22.011 1.00 0.00 ATOM 57 CD2 LEU 7 12.712 27.831 20.598 1.00 0.00 ATOM 58 O LEU 7 14.638 29.117 25.521 1.00 0.00 ATOM 59 C LEU 7 15.403 29.009 24.557 1.00 0.00 ATOM 60 N ASN 8 16.503 29.725 24.380 1.00 0.00 ATOM 61 CA ASN 8 16.765 30.943 25.158 1.00 0.00 ATOM 62 CB ASN 8 18.154 30.814 25.751 1.00 0.00 ATOM 63 CG ASN 8 18.485 32.057 26.556 1.00 0.00 ATOM 64 ND2 ASN 8 19.769 32.361 26.698 1.00 0.00 ATOM 65 OD1 ASN 8 17.564 32.735 27.006 1.00 0.00 ATOM 66 O ASN 8 17.762 32.463 23.592 1.00 0.00 ATOM 67 C ASN 8 16.730 32.087 24.150 1.00 0.00 ATOM 68 N LEU 9 15.543 32.638 23.919 1.00 0.00 ATOM 69 CA LEU 9 15.395 33.739 22.980 1.00 0.00 ATOM 70 CB LEU 9 14.363 33.425 21.881 1.00 0.00 ATOM 71 CG LEU 9 14.471 31.996 21.386 1.00 0.00 ATOM 72 CD1 LEU 9 13.273 31.698 20.512 1.00 0.00 ATOM 73 CD2 LEU 9 15.798 31.757 20.680 1.00 0.00 ATOM 74 O LEU 9 14.679 34.924 24.939 1.00 0.00 ATOM 75 C LEU 9 14.954 34.984 23.739 1.00 0.00 ATOM 76 N LYS 10 14.888 36.114 23.041 1.00 0.00 ATOM 77 CA LYS 10 14.479 37.356 23.664 1.00 0.00 ATOM 78 CB LYS 10 14.533 38.501 22.668 1.00 0.00 ATOM 79 CG LYS 10 14.279 39.852 23.279 1.00 0.00 ATOM 80 CD LYS 10 14.457 40.966 22.236 1.00 0.00 ATOM 81 CE LYS 10 13.461 40.830 21.045 1.00 0.00 ATOM 82 NZ LYS 10 13.708 41.719 19.870 1.00 0.00 ATOM 83 O LYS 10 12.759 37.700 25.336 1.00 0.00 ATOM 84 C LYS 10 13.046 37.267 24.220 1.00 0.00 ATOM 85 N GLN 11 12.167 36.744 23.375 1.00 0.00 ATOM 86 CA GLN 11 10.737 36.724 23.706 1.00 0.00 ATOM 87 CB GLN 11 9.950 37.530 22.646 1.00 0.00 ATOM 88 CG GLN 11 10.298 39.033 22.699 1.00 0.00 ATOM 89 CD GLN 11 9.617 39.879 21.616 1.00 0.00 ATOM 90 OE1 GLN 11 9.757 41.128 21.583 1.00 0.00 ATOM 91 NE2 GLN 11 8.886 39.219 20.718 1.00 0.00 ATOM 92 O GLN 11 9.163 35.094 24.549 1.00 0.00 ATOM 93 C GLN 11 10.164 35.291 23.858 1.00 0.00 ATOM 94 N ALA 12 10.799 34.316 23.217 1.00 0.00 ATOM 95 CA ALA 12 10.342 32.934 23.297 1.00 0.00 ATOM 96 CB ALA 12 10.028 32.292 21.928 1.00 0.00 ATOM 97 O ALA 12 12.574 32.127 23.804 1.00 0.00 ATOM 98 C ALA 12 11.384 32.092 24.043 1.00 0.00 ATOM 99 N LYS 13 10.972 31.473 25.123 1.00 0.00 ATOM 100 CA LYS 13 11.948 30.701 25.932 1.00 0.00 ATOM 101 CB LYS 13 12.880 31.730 26.657 1.00 0.00 ATOM 102 CG LYS 13 12.278 32.261 27.955 1.00 0.00 ATOM 103 CD LYS 13 11.162 33.262 27.714 1.00 0.00 ATOM 104 CE LYS 13 10.543 33.711 29.033 1.00 0.00 ATOM 105 NZ LYS 13 9.616 34.875 28.860 1.00 0.00 ATOM 106 O LYS 13 10.206 29.753 27.153 1.00 0.00 ATOM 107 C LYS 13 11.263 29.522 26.574 1.00 0.00 ATOM 108 N GLU 14 11.930 28.379 26.518 1.00 0.00 ATOM 109 CA GLU 14 11.502 27.093 27.102 1.00 0.00 ATOM 110 CB GLU 14 9.976 26.993 27.116 1.00 0.00 ATOM 111 CG GLU 14 9.334 26.967 25.736 1.00 0.00 ATOM 112 CD GLU 14 7.834 26.931 25.831 1.00 0.00 ATOM 113 OE1 GLU 14 7.327 26.958 26.927 1.00 0.00 ATOM 114 OE2 GLU 14 7.192 26.988 24.810 1.00 0.00 ATOM 115 O GLU 14 13.210 25.998 25.820 1.00 0.00 ATOM 116 C GLU 14 12.084 25.922 26.317 1.00 0.00 ATOM 117 N GLU 15 11.319 24.841 26.208 1.00 0.00 ATOM 118 CA GLU 15 11.775 23.645 25.467 1.00 0.00 ATOM 119 CB GLU 15 12.097 22.467 26.409 1.00 0.00 ATOM 120 CG GLU 15 10.902 21.861 27.139 1.00 0.00 ATOM 121 CD GLU 15 10.607 22.476 28.520 1.00 0.00 ATOM 122 OE1 GLU 15 10.108 21.725 29.386 1.00 0.00 ATOM 123 OE2 GLU 15 10.838 23.696 28.747 1.00 0.00 ATOM 124 O GLU 15 9.491 23.605 24.656 1.00 0.00 ATOM 125 C GLU 15 10.649 23.193 24.549 1.00 0.00 ATOM 126 N ALA 16 11.087 22.453 23.543 1.00 0.00 ATOM 127 CA ALA 16 10.194 21.715 22.641 1.00 0.00 ATOM 128 CB ALA 16 9.930 22.525 21.387 1.00 0.00 ATOM 129 O ALA 16 12.028 20.184 22.582 1.00 0.00 ATOM 130 C ALA 16 10.872 20.427 22.233 1.00 0.00 ATOM 131 N ILE 17 10.155 19.591 21.488 1.00 0.00 ATOM 132 CA ILE 17 10.706 18.320 21.034 1.00 0.00 ATOM 133 CB ILE 17 10.264 17.177 21.961 1.00 0.00 ATOM 134 CG1 ILE 17 8.735 17.112 22.049 1.00 0.00 ATOM 135 CG2 ILE 17 10.934 17.304 23.322 1.00 0.00 ATOM 136 CD1 ILE 17 8.284 15.859 22.772 1.00 0.00 ATOM 137 O ILE 17 9.238 18.563 19.154 1.00 0.00 ATOM 138 C ILE 17 10.250 18.034 19.602 1.00 0.00 ATOM 139 N LYS 18 10.940 17.063 19.009 1.00 0.00 ATOM 140 CA LYS 18 10.491 16.464 17.742 1.00 0.00 ATOM 141 CB LYS 18 10.670 17.437 16.575 1.00 0.00 ATOM 142 CG LYS 18 10.110 16.937 15.250 1.00 0.00 ATOM 143 CD LYS 18 8.589 16.955 15.247 1.00 0.00 ATOM 144 CE LYS 18 8.030 16.435 13.932 1.00 0.00 ATOM 145 NZ LYS 18 6.542 16.402 13.934 1.00 0.00 ATOM 146 O LYS 18 12.324 14.919 17.827 1.00 0.00 ATOM 147 C LYS 18 11.158 15.118 17.483 1.00 0.00 ATOM 148 N GLU 19 10.417 14.195 16.876 1.00 0.00 ATOM 149 CA GLU 19 10.948 12.920 16.592 1.00 0.00 ATOM 150 CB GLU 19 9.859 11.807 16.670 1.00 0.00 ATOM 151 CG GLU 19 10.336 10.377 16.353 1.00 0.00 ATOM 152 CD GLU 19 9.187 9.380 16.282 1.00 0.00 ATOM 153 OE1 GLU 19 8.209 9.681 15.572 1.00 0.00 ATOM 154 OE2 GLU 19 9.253 8.301 16.920 1.00 0.00 ATOM 155 O GLU 19 10.879 13.433 14.262 1.00 0.00 ATOM 156 C GLU 19 11.476 12.868 15.179 1.00 0.00 ATOM 157 N ALA 20 12.604 12.188 14.996 1.00 0.00 ATOM 158 CA ALA 20 13.209 12.071 13.674 1.00 0.00 ATOM 159 CB ALA 20 14.013 13.332 13.381 1.00 0.00 ATOM 160 O ALA 20 14.647 10.424 14.651 1.00 0.00 ATOM 161 C ALA 20 14.123 10.860 13.624 1.00 0.00 ATOM 162 N VAL 21 14.315 10.313 12.429 1.00 0.00 ATOM 163 CA VAL 21 15.175 9.148 12.261 1.00 0.00 ATOM 164 CB VAL 21 14.969 8.548 10.856 1.00 0.00 ATOM 165 CG1 VAL 21 15.977 7.437 10.599 1.00 0.00 ATOM 166 CG2 VAL 21 13.549 8.024 10.705 1.00 0.00 ATOM 167 O VAL 21 17.506 8.638 12.733 1.00 0.00 ATOM 168 C VAL 21 16.695 9.507 12.410 1.00 0.00 ATOM 169 N ASP 22 17.045 10.768 12.177 1.00 0.00 ATOM 170 CA ASP 22 18.433 11.201 12.293 1.00 0.00 ATOM 171 CB ASP 22 19.224 11.069 10.989 1.00 0.00 ATOM 172 CG ASP 22 18.744 11.980 9.867 1.00 0.00 ATOM 173 OD1 ASP 22 17.972 12.869 10.140 1.00 0.00 ATOM 174 OD2 ASP 22 19.271 11.883 8.784 1.00 0.00 ATOM 175 O ASP 22 17.586 13.419 12.861 1.00 0.00 ATOM 176 C ASP 22 18.556 12.648 12.776 1.00 0.00 ATOM 177 N ALA 23 19.799 13.011 13.118 1.00 0.00 ATOM 178 CA ALA 23 20.053 14.367 13.706 1.00 0.00 ATOM 179 CB ALA 23 21.476 14.463 14.193 1.00 0.00 ATOM 180 O ALA 23 19.251 16.515 13.003 1.00 0.00 ATOM 181 C ALA 23 19.802 15.463 12.677 1.00 0.00 ATOM 182 N GLY 24 20.206 15.216 11.435 1.00 0.00 ATOM 183 CA GLY 24 20.014 16.221 10.318 1.00 0.00 ATOM 184 O GLY 24 18.207 17.796 9.964 1.00 0.00 ATOM 185 C GLY 24 18.520 16.616 10.126 1.00 0.00 ATOM 186 N THR 25 17.628 15.632 10.149 1.00 0.00 ATOM 187 CA THR 25 16.204 15.897 9.982 1.00 0.00 ATOM 188 CB THR 25 15.449 14.557 9.910 1.00 0.00 ATOM 189 CG2 THR 25 13.953 14.795 9.770 1.00 0.00 ATOM 190 OG1 THR 25 15.917 13.802 8.785 1.00 0.00 ATOM 191 O THR 25 14.866 17.681 10.954 1.00 0.00 ATOM 192 C THR 25 15.641 16.718 11.152 1.00 0.00 ATOM 193 N ALA 26 16.046 16.376 12.378 1.00 0.00 ATOM 194 CA ALA 26 15.604 17.138 13.542 1.00 0.00 ATOM 195 CB ALA 26 16.170 16.443 14.779 1.00 0.00 ATOM 196 O ALA 26 15.369 19.502 13.879 1.00 0.00 ATOM 197 C ALA 26 16.085 18.584 13.477 1.00 0.00 ATOM 198 N GLU 27 17.298 18.785 12.973 1.00 0.00 ATOM 199 CA GLU 27 17.872 20.144 12.857 1.00 0.00 ATOM 200 CB GLU 27 19.257 20.060 12.286 1.00 0.00 ATOM 201 CG GLU 27 19.997 21.363 12.017 1.00 0.00 ATOM 202 CD GLU 27 21.468 21.099 11.638 1.00 0.00 ATOM 203 OE1 GLU 27 21.739 20.133 10.874 1.00 0.00 ATOM 204 OE2 GLU 27 22.358 21.850 12.088 1.00 0.00 ATOM 205 O GLU 27 16.704 22.167 12.230 1.00 0.00 ATOM 206 C GLU 27 17.029 21.027 11.900 1.00 0.00 ATOM 207 N LYS 28 16.687 20.490 10.732 1.00 0.00 ATOM 208 CA LYS 28 15.893 21.234 9.761 1.00 0.00 ATOM 209 CB LYS 28 15.680 20.398 8.497 1.00 0.00 ATOM 210 CG LYS 28 14.877 21.099 7.410 1.00 0.00 ATOM 211 CD LYS 28 14.770 20.237 6.160 1.00 0.00 ATOM 212 CE LYS 28 13.936 20.920 5.085 1.00 0.00 ATOM 213 NZ LYS 28 13.809 20.082 3.863 1.00 0.00 ATOM 214 O LYS 28 14.063 22.742 10.120 1.00 0.00 ATOM 215 C LYS 28 14.540 21.629 10.341 1.00 0.00 ATOM 216 N TYR 29 13.922 20.716 11.084 1.00 0.00 ATOM 217 CA TYR 29 12.600 20.984 11.704 1.00 0.00 ATOM 218 CB TYR 29 12.070 19.735 12.389 1.00 0.00 ATOM 219 CG TYR 29 10.602 19.739 12.747 1.00 0.00 ATOM 220 CD1 TYR 29 9.630 19.390 11.808 1.00 0.00 ATOM 221 CD2 TYR 29 10.160 20.070 14.019 1.00 0.00 ATOM 222 CE1 TYR 29 8.283 19.383 12.120 1.00 0.00 ATOM 223 CE2 TYR 29 8.807 20.070 14.354 1.00 0.00 ATOM 224 CZ TYR 29 7.874 19.724 13.391 1.00 0.00 ATOM 225 OH TYR 29 6.533 19.713 13.696 1.00 0.00 ATOM 226 O TYR 29 11.872 23.008 12.787 1.00 0.00 ATOM 227 C TYR 29 12.695 22.093 12.765 1.00 0.00 ATOM 228 N PHE 30 13.697 22.004 13.634 1.00 0.00 ATOM 229 CA PHE 30 13.882 23.003 14.679 1.00 0.00 ATOM 230 CB PHE 30 14.975 22.547 15.648 1.00 0.00 ATOM 231 CG PHE 30 14.575 21.386 16.511 1.00 0.00 ATOM 232 CD1 PHE 30 13.240 21.030 16.645 1.00 0.00 ATOM 233 CD2 PHE 30 15.530 20.646 17.191 1.00 0.00 ATOM 234 CE1 PHE 30 12.871 19.962 17.441 1.00 0.00 ATOM 235 CE2 PHE 30 15.163 19.576 17.985 1.00 0.00 ATOM 236 CZ PHE 30 13.831 19.235 18.110 1.00 0.00 ATOM 237 O PHE 30 13.811 25.404 14.558 1.00 0.00 ATOM 238 C PHE 30 14.276 24.363 14.088 1.00 0.00 ATOM 239 N LYS 31 15.119 24.357 13.066 1.00 0.00 ATOM 240 CA LYS 31 15.457 25.622 12.413 1.00 0.00 ATOM 241 CB LYS 31 16.372 25.357 11.255 1.00 0.00 ATOM 242 CG LYS 31 16.981 26.612 10.636 1.00 0.00 ATOM 243 CD LYS 31 17.545 26.348 9.243 1.00 0.00 ATOM 244 CE LYS 31 18.382 27.524 8.751 1.00 0.00 ATOM 245 NZ LYS 31 17.625 28.806 8.760 1.00 0.00 ATOM 246 O LYS 31 14.013 27.469 11.942 1.00 0.00 ATOM 247 C LYS 31 14.214 26.265 11.804 1.00 0.00 ATOM 248 N LEU 32 13.386 25.458 11.147 1.00 0.00 ATOM 249 CA LEU 32 12.136 25.940 10.536 1.00 0.00 ATOM 250 CB LEU 32 11.377 24.809 9.874 1.00 0.00 ATOM 251 CG LEU 32 9.975 25.171 9.364 1.00 0.00 ATOM 252 CD1 LEU 32 10.075 26.279 8.326 1.00 0.00 ATOM 253 CD2 LEU 32 9.307 23.933 8.770 1.00 0.00 ATOM 254 O LEU 32 10.758 27.655 11.485 1.00 0.00 ATOM 255 C LEU 32 11.225 26.528 11.628 1.00 0.00 ATOM 256 N ILE 33 11.146 25.847 12.769 1.00 0.00 ATOM 257 CA ILE 33 10.341 26.317 13.915 1.00 0.00 ATOM 258 CB ILE 33 10.341 25.263 15.044 1.00 0.00 ATOM 259 CG1 ILE 33 9.641 23.993 14.550 1.00 0.00 ATOM 260 CG2 ILE 33 9.630 25.819 16.274 1.00 0.00 ATOM 261 CD1 ILE 33 9.465 22.937 15.597 1.00 0.00 ATOM 262 O ILE 33 10.098 28.560 14.745 1.00 0.00 ATOM 263 C ILE 33 10.873 27.652 14.445 1.00 0.00 ATOM 264 N ALA 34 12.193 27.766 14.554 1.00 0.00 ATOM 265 CA ALA 34 12.807 28.994 15.045 1.00 0.00 ATOM 266 CB ALA 34 14.290 28.935 15.061 1.00 0.00 ATOM 267 O ALA 34 11.926 31.154 14.485 1.00 0.00 ATOM 268 C ALA 34 12.507 30.151 14.081 1.00 0.00 ATOM 269 N ASN 35 12.569 29.843 12.799 1.00 0.00 ATOM 270 CA ASN 35 12.206 30.819 11.762 1.00 0.00 ATOM 271 CB ASN 35 12.517 30.295 10.372 1.00 0.00 ATOM 272 CG ASN 35 13.987 30.265 10.053 1.00 0.00 ATOM 273 ND2 ASN 35 14.326 29.532 9.023 1.00 0.00 ATOM 274 OD1 ASN 35 14.794 30.957 10.684 1.00 0.00 ATOM 275 O ASN 35 10.395 32.391 11.859 1.00 0.00 ATOM 276 C ASN 35 10.736 31.208 11.892 1.00 0.00 ATOM 277 N ALA 36 9.869 30.212 12.039 1.00 0.00 ATOM 278 CA ALA 36 8.423 30.466 12.178 1.00 0.00 ATOM 279 CB ALA 36 7.656 29.150 12.125 1.00 0.00 ATOM 280 O ALA 36 7.062 31.966 13.461 1.00 0.00 ATOM 281 C ALA 36 8.096 31.297 13.410 1.00 0.00 ATOM 282 N LYS 37 8.978 31.258 14.405 1.00 0.00 ATOM 283 CA LYS 37 8.767 32.015 15.632 1.00 0.00 ATOM 284 CB LYS 37 8.385 31.107 16.826 1.00 0.00 ATOM 285 CG LYS 37 7.050 30.383 16.621 1.00 0.00 ATOM 286 CD LYS 37 5.963 31.247 16.013 1.00 0.00 ATOM 287 CE LYS 37 5.580 32.460 16.846 1.00 0.00 ATOM 288 NZ LYS 37 5.212 33.624 15.968 1.00 0.00 ATOM 289 O LYS 37 9.769 33.818 16.900 1.00 0.00 ATOM 290 C LYS 37 9.729 33.213 15.824 1.00 0.00 ATOM 291 N THR 38 10.294 33.654 14.699 1.00 0.00 ATOM 292 CA THR 38 11.165 34.837 14.599 1.00 0.00 ATOM 293 CB THR 38 10.396 36.134 14.911 1.00 0.00 ATOM 294 CG2 THR 38 11.252 37.351 14.600 1.00 0.00 ATOM 295 OG1 THR 38 9.198 36.183 14.124 1.00 0.00 ATOM 296 O THR 38 12.768 35.634 16.195 1.00 0.00 ATOM 297 C THR 38 12.381 34.691 15.505 1.00 0.00 ATOM 298 N VAL 39 12.985 33.505 15.503 1.00 0.00 ATOM 299 CA VAL 39 14.174 33.246 16.338 1.00 0.00 ATOM 300 CB VAL 39 14.223 31.757 16.717 1.00 0.00 ATOM 301 CG1 VAL 39 15.537 31.357 17.398 1.00 0.00 ATOM 302 CG2 VAL 39 12.983 31.346 17.505 1.00 0.00 ATOM 303 O VAL 39 15.550 32.706 14.477 1.00 0.00 ATOM 304 C VAL 39 15.407 33.372 15.504 1.00 0.00 ATOM 305 N GLU 40 16.321 34.235 15.937 1.00 0.00 ATOM 306 CA GLU 40 17.568 34.443 15.209 1.00 0.00 ATOM 307 CB GLU 40 17.556 35.809 14.599 1.00 0.00 ATOM 308 CG GLU 40 18.031 35.704 13.155 1.00 0.00 ATOM 309 CD GLU 40 17.845 36.995 12.363 1.00 0.00 ATOM 310 OE1 GLU 40 18.839 37.482 11.776 1.00 0.00 ATOM 311 OE2 GLU 40 16.707 37.530 12.321 1.00 0.00 ATOM 312 O GLU 40 19.267 35.347 16.591 1.00 0.00 ATOM 313 C GLU 40 18.715 34.340 16.147 1.00 0.00 ATOM 314 N GLY 41 19.098 33.108 16.465 1.00 0.00 ATOM 315 CA GLY 41 20.214 32.875 17.374 1.00 0.00 ATOM 316 O GLY 41 21.448 31.552 15.735 1.00 0.00 ATOM 317 C GLY 41 21.341 31.972 16.883 1.00 0.00 ATOM 318 N VAL 42 22.155 31.641 17.865 1.00 0.00 ATOM 319 CA VAL 42 23.258 30.688 17.701 1.00 0.00 ATOM 320 CB VAL 42 24.557 31.209 18.343 1.00 0.00 ATOM 321 CG1 VAL 42 25.009 32.492 17.664 1.00 0.00 ATOM 322 CG2 VAL 42 24.361 31.438 19.834 1.00 0.00 ATOM 323 O VAL 42 21.961 29.276 19.200 1.00 0.00 ATOM 324 C VAL 42 22.820 29.352 18.312 1.00 0.00 ATOM 325 N TRP 43 23.412 28.303 17.786 1.00 0.00 ATOM 326 CA TRP 43 22.981 26.920 17.978 1.00 0.00 ATOM 327 CB TRP 43 22.451 26.352 16.666 1.00 0.00 ATOM 328 CG TRP 43 21.274 27.057 16.117 1.00 0.00 ATOM 329 CD1 TRP 43 21.252 28.174 15.328 1.00 0.00 ATOM 330 CD2 TRP 43 19.897 26.695 16.313 1.00 0.00 ATOM 331 CE2 TRP 43 19.100 27.620 15.608 1.00 0.00 ATOM 332 CE3 TRP 43 19.269 25.658 17.014 1.00 0.00 ATOM 333 NE1 TRP 43 19.959 28.524 15.022 1.00 0.00 ATOM 334 CZ2 TRP 43 17.726 27.531 15.594 1.00 0.00 ATOM 335 CZ3 TRP 43 17.914 25.588 16.979 1.00 0.00 ATOM 336 CH2 TRP 43 17.137 26.515 16.289 1.00 0.00 ATOM 337 O TRP 43 25.298 26.161 18.219 1.00 0.00 ATOM 338 C TRP 43 24.113 26.014 18.488 1.00 0.00 ATOM 339 N THR 44 23.696 25.044 19.265 1.00 0.00 ATOM 340 CA THR 44 24.581 23.922 19.582 1.00 0.00 ATOM 341 CB THR 44 25.257 24.068 20.957 1.00 0.00 ATOM 342 CG2 THR 44 26.080 25.346 21.014 1.00 0.00 ATOM 343 OG1 THR 44 24.257 24.104 21.984 1.00 0.00 ATOM 344 O THR 44 22.622 22.541 19.682 1.00 0.00 ATOM 345 C THR 44 23.840 22.590 19.510 1.00 0.00 ATOM 346 N TYR 45 24.578 21.514 19.257 1.00 0.00 ATOM 347 CA TYR 45 23.970 20.161 19.167 1.00 0.00 ATOM 348 CB TYR 45 23.813 19.694 17.718 1.00 0.00 ATOM 349 CG TYR 45 23.471 18.226 17.580 1.00 0.00 ATOM 350 CD1 TYR 45 22.304 17.712 18.126 1.00 0.00 ATOM 351 CD2 TYR 45 24.316 17.360 16.904 1.00 0.00 ATOM 352 CE1 TYR 45 21.986 16.374 18.005 1.00 0.00 ATOM 353 CE2 TYR 45 24.010 16.018 16.776 1.00 0.00 ATOM 354 CZ TYR 45 22.842 15.530 17.327 1.00 0.00 ATOM 355 OH TYR 45 22.532 14.195 17.201 1.00 0.00 ATOM 356 O TYR 45 25.994 18.965 19.645 1.00 0.00 ATOM 357 C TYR 45 24.812 19.150 19.937 1.00 0.00 ATOM 358 N LYS 46 24.202 18.496 20.921 1.00 0.00 ATOM 359 CA LYS 46 24.915 17.492 21.733 1.00 0.00 ATOM 360 CB LYS 46 25.254 18.116 23.114 1.00 0.00 ATOM 361 CG LYS 46 25.715 19.567 23.017 1.00 0.00 ATOM 362 CD LYS 46 26.886 19.867 23.926 1.00 0.00 ATOM 363 CE LYS 46 28.105 19.025 23.543 1.00 0.00 ATOM 364 NZ LYS 46 29.283 19.316 24.412 1.00 0.00 ATOM 365 O LYS 46 23.148 15.867 21.907 1.00 0.00 ATOM 366 C LYS 46 24.265 16.147 21.477 1.00 0.00 ATOM 367 N ASP 47 24.993 15.355 20.728 1.00 0.00 ATOM 368 CA ASP 47 24.546 14.023 20.359 1.00 0.00 ATOM 369 CB ASP 47 25.958 13.266 19.839 1.00 0.00 ATOM 370 CG ASP 47 27.092 14.201 19.474 1.00 0.00 ATOM 371 OD1 ASP 47 27.034 14.816 18.387 1.00 0.00 ATOM 372 OD2 ASP 47 28.041 14.321 20.275 1.00 0.00 ATOM 373 O ASP 47 23.522 12.251 21.611 1.00 0.00 ATOM 374 C ASP 47 24.397 13.118 21.577 1.00 0.00 ATOM 375 N GLU 48 25.250 13.321 22.575 1.00 0.00 ATOM 376 CA GLU 48 25.192 12.528 23.765 1.00 0.00 ATOM 377 CB GLU 48 26.294 12.913 24.757 1.00 0.00 ATOM 378 CG GLU 48 27.687 12.449 24.354 1.00 0.00 ATOM 379 CD GLU 48 28.770 12.891 25.327 1.00 0.00 ATOM 380 OE1 GLU 48 29.700 12.093 25.578 1.00 0.00 ATOM 381 OE2 GLU 48 28.701 14.033 25.838 1.00 0.00 ATOM 382 O GLU 48 23.256 11.658 24.931 1.00 0.00 ATOM 383 C GLU 48 23.796 12.651 24.439 1.00 0.00 ATOM 384 N ILE 49 23.236 13.856 24.451 1.00 0.00 ATOM 385 CA ILE 49 21.929 14.076 25.060 1.00 0.00 ATOM 386 CB ILE 49 22.407 15.330 26.276 1.00 0.00 ATOM 387 CG1 ILE 49 22.081 16.549 25.391 1.00 0.00 ATOM 388 CG2 ILE 49 23.845 15.366 26.697 1.00 0.00 ATOM 389 CD1 ILE 49 21.920 17.804 26.207 1.00 0.00 ATOM 390 O ILE 49 19.616 14.469 24.441 1.00 0.00 ATOM 391 C ILE 49 20.767 14.293 24.039 1.00 0.00 ATOM 392 N LYS 50 21.085 14.277 22.748 1.00 0.00 ATOM 393 CA LYS 50 20.072 14.468 21.718 1.00 0.00 ATOM 394 CB LYS 50 19.470 12.933 21.389 1.00 0.00 ATOM 395 CG LYS 50 20.424 11.778 21.121 1.00 0.00 ATOM 396 CD LYS 50 20.270 10.681 22.164 1.00 0.00 ATOM 397 CE LYS 50 21.613 10.058 22.509 1.00 0.00 ATOM 398 NZ LYS 50 21.952 8.934 21.594 1.00 0.00 ATOM 399 O LYS 50 18.087 15.878 21.935 1.00 0.00 ATOM 400 C LYS 50 19.317 15.791 21.952 1.00 0.00 ATOM 401 N THR 51 20.126 16.814 22.219 1.00 0.00 ATOM 402 CA THR 51 19.572 18.134 22.539 1.00 0.00 ATOM 403 CB THR 51 19.743 18.493 24.027 1.00 0.00 ATOM 404 CG2 THR 51 19.165 19.870 24.313 1.00 0.00 ATOM 405 OG1 THR 51 19.071 17.518 24.836 1.00 0.00 ATOM 406 O THR 51 21.480 19.214 21.543 1.00 0.00 ATOM 407 C THR 51 20.252 19.176 21.656 1.00 0.00 ATOM 408 N PHE 52 19.382 20.033 21.152 1.00 0.00 ATOM 409 CA PHE 52 19.738 21.274 20.457 1.00 0.00 ATOM 410 CB PHE 52 18.893 21.500 19.208 1.00 0.00 ATOM 411 CG PHE 52 19.467 20.888 17.970 1.00 0.00 ATOM 412 CD1 PHE 52 19.101 19.609 17.570 1.00 0.00 ATOM 413 CD2 PHE 52 20.391 21.588 17.209 1.00 0.00 ATOM 414 CE1 PHE 52 19.650 19.040 16.427 1.00 0.00 ATOM 415 CE2 PHE 52 20.945 21.029 16.070 1.00 0.00 ATOM 416 CZ PHE 52 20.573 19.750 15.676 1.00 0.00 ATOM 417 O PHE 52 18.495 22.433 22.134 1.00 0.00 ATOM 418 C PHE 52 19.481 22.461 21.383 1.00 0.00 ATOM 419 N THR 53 20.302 23.462 21.267 1.00 0.00 ATOM 420 CA THR 53 20.091 24.716 22.032 1.00 0.00 ATOM 421 CB THR 53 21.146 24.891 23.138 1.00 0.00 ATOM 422 CG2 THR 53 20.926 26.198 23.883 1.00 0.00 ATOM 423 OG1 THR 53 21.059 23.798 24.063 1.00 0.00 ATOM 424 O THR 53 21.144 26.035 20.327 1.00 0.00 ATOM 425 C THR 53 20.218 25.942 21.134 1.00 0.00 ATOM 426 N VAL 54 19.289 26.882 21.276 1.00 0.00 ATOM 427 CA VAL 54 19.315 28.092 20.475 1.00 0.00 ATOM 428 CB VAL 54 18.032 28.190 19.681 1.00 0.00 ATOM 429 CG1 VAL 54 16.804 28.163 20.588 1.00 0.00 ATOM 430 CG2 VAL 54 18.035 29.492 18.899 1.00 0.00 ATOM 431 O VAL 54 18.600 29.268 22.434 1.00 0.00 ATOM 432 C VAL 54 19.326 29.265 21.439 1.00 0.00 ATOM 433 N THR 55 20.152 30.265 21.147 1.00 0.00 ATOM 434 CA THR 55 20.245 31.443 22.002 1.00 0.00 ATOM 435 CB THR 55 21.429 31.325 23.040 1.00 0.00 ATOM 436 CG2 THR 55 21.436 29.982 23.780 1.00 0.00 ATOM 437 OG1 THR 55 22.668 31.480 22.333 1.00 0.00 ATOM 438 O THR 55 21.028 32.815 20.199 1.00 0.00 ATOM 439 C THR 55 20.260 32.695 21.156 1.00 0.00 ATOM 440 N GLU 56 19.354 33.578 21.532 1.00 0.00 ATOM 441 CA GLU 56 19.407 34.957 21.051 1.00 0.00 ATOM 442 CB GLU 56 17.992 35.500 20.835 1.00 0.00 ATOM 443 CG GLU 56 17.220 34.816 19.717 1.00 0.00 ATOM 444 CD GLU 56 15.834 35.385 19.583 1.00 0.00 ATOM 445 OE1 GLU 56 15.498 36.263 20.342 1.00 0.00 ATOM 446 OE2 GLU 56 15.152 35.021 18.655 1.00 0.00 ATOM 447 O GLU 56 20.634 35.311 23.107 1.00 0.00 ATOM 448 C GLU 56 20.184 35.813 22.052 1.00 0.00 TER END