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 5 Tue Jul 15 16:01:45 2008 MODEL 5 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 14.149 9.164 16.246 1.00 0.00 ATOM 2 CA THR 1 14.638 9.439 17.607 1.00 0.00 ATOM 3 CB THR 1 16.167 9.574 17.587 1.00 0.00 ATOM 4 CG2 THR 1 16.834 9.933 18.914 1.00 0.00 ATOM 5 OG1 THR 1 16.658 8.307 17.193 1.00 0.00 ATOM 6 O THR 1 13.765 11.599 17.207 1.00 0.00 ATOM 7 C THR 1 13.973 10.727 18.046 1.00 0.00 ATOM 8 N THR 2 13.719 10.814 19.341 1.00 0.00 ATOM 9 CA THR 2 13.146 12.036 19.927 1.00 0.00 ATOM 10 CB THR 2 12.351 11.739 21.205 1.00 0.00 ATOM 11 CG2 THR 2 11.714 12.980 21.821 1.00 0.00 ATOM 12 OG1 THR 2 11.352 10.775 20.872 1.00 0.00 ATOM 13 O THR 2 15.210 12.629 20.984 1.00 0.00 ATOM 14 C THR 2 14.299 12.988 20.253 1.00 0.00 ATOM 15 N TYR 3 14.175 14.206 19.760 1.00 0.00 ATOM 16 CA TYR 3 15.151 15.272 20.051 1.00 0.00 ATOM 17 CB TYR 3 15.742 15.832 18.752 1.00 0.00 ATOM 18 CG TYR 3 16.518 14.773 17.967 1.00 0.00 ATOM 19 CD1 TYR 3 15.880 14.012 16.997 1.00 0.00 ATOM 20 CD2 TYR 3 17.872 14.596 18.206 1.00 0.00 ATOM 21 CE1 TYR 3 16.605 13.083 16.258 1.00 0.00 ATOM 22 CE2 TYR 3 18.595 13.676 17.462 1.00 0.00 ATOM 23 CZ TYR 3 17.968 12.915 16.489 1.00 0.00 ATOM 24 OH TYR 3 18.665 11.930 15.874 1.00 0.00 ATOM 25 O TYR 3 13.277 16.602 20.736 1.00 0.00 ATOM 26 C TYR 3 14.488 16.399 20.831 1.00 0.00 ATOM 27 N LYS 4 15.317 17.094 21.594 1.00 0.00 ATOM 28 CA LYS 4 14.860 18.257 22.369 1.00 0.00 ATOM 29 CB LYS 4 15.101 18.016 23.868 1.00 0.00 ATOM 30 CG LYS 4 14.187 16.890 24.361 1.00 0.00 ATOM 31 CD LYS 4 14.428 16.526 25.822 1.00 0.00 ATOM 32 CE LYS 4 13.412 15.459 26.213 1.00 0.00 ATOM 33 NZ LYS 4 13.679 14.996 27.574 1.00 0.00 ATOM 34 O LYS 4 16.684 19.518 21.417 1.00 0.00 ATOM 35 C LYS 4 15.551 19.538 21.900 1.00 0.00 ATOM 36 N LEU 5 14.752 20.594 21.885 1.00 0.00 ATOM 37 CA LEU 5 15.228 21.956 21.580 1.00 0.00 ATOM 38 CB LEU 5 14.495 22.527 20.369 1.00 0.00 ATOM 39 CG LEU 5 14.869 23.970 19.995 1.00 0.00 ATOM 40 CD1 LEU 5 16.325 24.107 19.562 1.00 0.00 ATOM 41 CD2 LEU 5 13.935 24.446 18.882 1.00 0.00 ATOM 42 O LEU 5 13.879 22.901 23.323 1.00 0.00 ATOM 43 C LEU 5 14.990 22.838 22.801 1.00 0.00 ATOM 44 N ILE 6 16.061 23.508 23.201 1.00 0.00 ATOM 45 CA ILE 6 16.008 24.517 24.267 1.00 0.00 ATOM 46 CB ILE 6 17.127 24.355 25.305 1.00 0.00 ATOM 47 CG1 ILE 6 17.123 22.931 25.855 1.00 0.00 ATOM 48 CG2 ILE 6 16.928 25.400 26.411 1.00 0.00 ATOM 49 CD1 ILE 6 18.298 22.540 26.753 1.00 0.00 ATOM 50 O ILE 6 17.203 26.180 22.968 1.00 0.00 ATOM 51 C ILE 6 16.173 25.885 23.587 1.00 0.00 ATOM 52 N LEU 7 15.173 26.713 23.818 1.00 0.00 ATOM 53 CA LEU 7 15.183 28.090 23.287 1.00 0.00 ATOM 54 CB LEU 7 13.843 28.470 22.657 1.00 0.00 ATOM 55 CG LEU 7 13.331 27.474 21.609 1.00 0.00 ATOM 56 CD1 LEU 7 11.934 27.871 21.184 1.00 0.00 ATOM 57 CD2 LEU 7 14.035 27.594 20.294 1.00 0.00 ATOM 58 O LEU 7 14.890 28.987 25.511 1.00 0.00 ATOM 59 C LEU 7 15.484 29.064 24.435 1.00 0.00 ATOM 60 N ASN 8 16.524 29.851 24.202 1.00 0.00 ATOM 61 CA ASN 8 16.827 30.997 25.060 1.00 0.00 ATOM 62 CB ASN 8 18.167 30.818 25.772 1.00 0.00 ATOM 63 CG ASN 8 18.487 31.960 26.730 1.00 0.00 ATOM 64 ND2 ASN 8 19.761 32.135 26.952 1.00 0.00 ATOM 65 OD1 ASN 8 17.631 32.623 27.292 1.00 0.00 ATOM 66 O ASN 8 17.886 32.804 23.833 1.00 0.00 ATOM 67 C ASN 8 16.847 32.246 24.190 1.00 0.00 ATOM 68 N LEU 9 15.644 32.625 23.827 1.00 0.00 ATOM 69 CA LEU 9 15.525 33.812 22.976 1.00 0.00 ATOM 70 CB LEU 9 14.376 33.689 22.013 1.00 0.00 ATOM 71 CG LEU 9 14.267 32.293 21.472 1.00 0.00 ATOM 72 CD1 LEU 9 12.986 32.414 20.710 1.00 0.00 ATOM 73 CD2 LEU 9 15.522 31.744 20.820 1.00 0.00 ATOM 74 O LEU 9 14.922 34.896 25.023 1.00 0.00 ATOM 75 C LEU 9 15.248 35.009 23.842 1.00 0.00 ATOM 76 N LYS 10 15.272 36.137 23.172 1.00 0.00 ATOM 77 CA LYS 10 14.929 37.407 23.800 1.00 0.00 ATOM 78 CB LYS 10 15.148 38.522 22.783 1.00 0.00 ATOM 79 CG LYS 10 14.820 39.902 23.353 1.00 0.00 ATOM 80 CD LYS 10 15.386 40.079 24.764 1.00 0.00 ATOM 81 CE LYS 10 16.145 41.385 24.840 1.00 0.00 ATOM 82 NZ LYS 10 16.676 41.593 26.162 1.00 0.00 ATOM 83 O LYS 10 13.238 37.914 25.461 1.00 0.00 ATOM 84 C LYS 10 13.496 37.405 24.356 1.00 0.00 ATOM 85 N GLN 11 12.581 36.886 23.552 1.00 0.00 ATOM 86 CA GLN 11 11.150 36.886 23.891 1.00 0.00 ATOM 87 CB GLN 11 10.336 37.662 22.845 1.00 0.00 ATOM 88 CG GLN 11 10.835 39.096 22.658 1.00 0.00 ATOM 89 CD GLN 11 10.098 39.798 21.517 1.00 0.00 ATOM 90 OE1 GLN 11 9.827 39.262 20.450 1.00 0.00 ATOM 91 NE2 GLN 11 10.006 41.098 21.627 1.00 0.00 ATOM 92 O GLN 11 9.709 35.290 24.906 1.00 0.00 ATOM 93 C GLN 11 10.573 35.473 24.059 1.00 0.00 ATOM 94 N ALA 12 11.144 34.472 23.401 1.00 0.00 ATOM 95 CA ALA 12 10.684 33.074 23.539 1.00 0.00 ATOM 96 CB ALA 12 10.208 32.403 22.257 1.00 0.00 ATOM 97 O ALA 12 12.841 31.960 23.731 1.00 0.00 ATOM 98 C ALA 12 11.726 32.174 24.171 1.00 0.00 ATOM 99 N LYS 13 11.385 31.686 25.324 1.00 0.00 ATOM 100 CA LYS 13 12.313 30.777 25.993 1.00 0.00 ATOM 101 CB LYS 13 12.844 31.491 27.215 1.00 0.00 ATOM 102 CG LYS 13 11.747 31.811 28.243 1.00 0.00 ATOM 103 CD LYS 13 12.190 32.961 29.123 1.00 0.00 ATOM 104 CE LYS 13 13.484 32.637 29.851 1.00 0.00 ATOM 105 NZ LYS 13 13.891 33.791 30.637 1.00 0.00 ATOM 106 O LYS 13 10.375 29.723 26.650 1.00 0.00 ATOM 107 C LYS 13 11.539 29.526 26.350 1.00 0.00 ATOM 108 N GLU 14 12.200 28.387 26.424 1.00 0.00 ATOM 109 CA GLU 14 11.680 27.103 26.950 1.00 0.00 ATOM 110 CB GLU 14 10.162 27.001 27.197 1.00 0.00 ATOM 111 CG GLU 14 9.794 27.615 28.547 1.00 0.00 ATOM 112 CD GLU 14 8.282 27.664 28.746 1.00 0.00 ATOM 113 OE1 GLU 14 7.617 26.610 28.564 1.00 0.00 ATOM 114 OE2 GLU 14 7.806 28.722 29.223 1.00 0.00 ATOM 115 O GLU 14 13.308 25.920 25.644 1.00 0.00 ATOM 116 C GLU 14 12.180 25.901 26.141 1.00 0.00 ATOM 117 N GLU 15 11.355 24.872 26.061 1.00 0.00 ATOM 118 CA GLU 15 11.730 23.573 25.507 1.00 0.00 ATOM 119 CB GLU 15 12.236 22.660 26.636 1.00 0.00 ATOM 120 CG GLU 15 11.370 22.442 27.888 1.00 0.00 ATOM 121 CD GLU 15 11.891 21.379 28.881 1.00 0.00 ATOM 122 OE1 GLU 15 11.169 21.008 29.826 1.00 0.00 ATOM 123 OE2 GLU 15 12.950 20.766 28.644 1.00 0.00 ATOM 124 O GLU 15 9.412 23.225 24.925 1.00 0.00 ATOM 125 C GLU 15 10.587 22.949 24.703 1.00 0.00 ATOM 126 N ALA 16 11.008 22.378 23.586 1.00 0.00 ATOM 127 CA ALA 16 10.140 21.630 22.682 1.00 0.00 ATOM 128 CB ALA 16 9.757 22.488 21.472 1.00 0.00 ATOM 129 O ALA 16 12.064 20.179 22.475 1.00 0.00 ATOM 130 C ALA 16 10.866 20.363 22.238 1.00 0.00 ATOM 131 N ILE 17 10.104 19.472 21.637 1.00 0.00 ATOM 132 CA ILE 17 10.603 18.176 21.161 1.00 0.00 ATOM 133 CB ILE 17 10.112 17.035 22.056 1.00 0.00 ATOM 134 CG1 ILE 17 8.578 17.012 22.098 1.00 0.00 ATOM 135 CG2 ILE 17 10.763 17.171 23.435 1.00 0.00 ATOM 136 CD1 ILE 17 8.105 15.717 22.721 1.00 0.00 ATOM 137 O ILE 17 9.078 18.413 19.333 1.00 0.00 ATOM 138 C ILE 17 10.126 17.905 19.730 1.00 0.00 ATOM 139 N LYS 18 10.796 16.961 19.093 1.00 0.00 ATOM 140 CA LYS 18 10.422 16.453 17.768 1.00 0.00 ATOM 141 CB LYS 18 10.988 17.385 16.687 1.00 0.00 ATOM 142 CG LYS 18 10.831 16.866 15.248 1.00 0.00 ATOM 143 CD LYS 18 9.363 16.794 14.853 1.00 0.00 ATOM 144 CE LYS 18 9.053 16.081 13.532 1.00 0.00 ATOM 145 NZ LYS 18 9.876 16.575 12.433 1.00 0.00 ATOM 146 O LYS 18 12.144 14.799 18.027 1.00 0.00 ATOM 147 C LYS 18 11.017 15.050 17.596 1.00 0.00 ATOM 148 N GLU 19 10.330 14.264 16.785 1.00 0.00 ATOM 149 CA GLU 19 10.844 12.980 16.322 1.00 0.00 ATOM 150 CB GLU 19 9.735 11.938 16.341 1.00 0.00 ATOM 151 CG GLU 19 10.289 10.596 15.871 1.00 0.00 ATOM 152 CD GLU 19 9.314 9.445 16.071 1.00 0.00 ATOM 153 OE1 GLU 19 8.275 9.672 16.708 1.00 0.00 ATOM 154 OE2 GLU 19 9.616 8.357 15.524 1.00 0.00 ATOM 155 O GLU 19 10.714 13.654 14.000 1.00 0.00 ATOM 156 C GLU 19 11.371 13.113 14.895 1.00 0.00 ATOM 157 N ALA 20 12.588 12.636 14.744 1.00 0.00 ATOM 158 CA ALA 20 13.277 12.631 13.448 1.00 0.00 ATOM 159 CB ALA 20 14.175 13.861 13.351 1.00 0.00 ATOM 160 O ALA 20 14.664 10.854 14.253 1.00 0.00 ATOM 161 C ALA 20 14.122 11.368 13.284 1.00 0.00 ATOM 162 N VAL 21 14.370 11.007 12.037 1.00 0.00 ATOM 163 CA VAL 21 15.220 9.837 11.704 1.00 0.00 ATOM 164 CB VAL 21 15.001 9.441 10.230 1.00 0.00 ATOM 165 CG1 VAL 21 15.901 8.290 9.781 1.00 0.00 ATOM 166 CG2 VAL 21 13.558 8.968 10.029 1.00 0.00 ATOM 167 O VAL 21 17.352 9.104 12.562 1.00 0.00 ATOM 168 C VAL 21 16.692 10.043 12.115 1.00 0.00 ATOM 169 N ASP 22 17.163 11.285 12.087 1.00 0.00 ATOM 170 CA ASP 22 18.539 11.625 12.490 1.00 0.00 ATOM 171 CB ASP 22 19.544 11.214 11.388 1.00 0.00 ATOM 172 CG ASP 22 19.543 12.093 10.135 1.00 0.00 ATOM 173 OD1 ASP 22 18.651 12.957 10.006 1.00 0.00 ATOM 174 OD2 ASP 22 20.476 11.934 9.339 1.00 0.00 ATOM 175 O ASP 22 17.680 13.871 12.705 1.00 0.00 ATOM 176 C ASP 22 18.646 13.111 12.840 1.00 0.00 ATOM 177 N ALA 23 19.806 13.454 13.400 1.00 0.00 ATOM 178 CA ALA 23 20.088 14.823 13.889 1.00 0.00 ATOM 179 CB ALA 23 21.453 14.883 14.586 1.00 0.00 ATOM 180 O ALA 23 19.328 16.907 13.032 1.00 0.00 ATOM 181 C ALA 23 20.007 15.906 12.799 1.00 0.00 ATOM 182 N GLY 24 20.437 15.570 11.573 1.00 0.00 ATOM 183 CA GLY 24 20.325 16.460 10.405 1.00 0.00 ATOM 184 O GLY 24 18.528 18.064 9.950 1.00 0.00 ATOM 185 C GLY 24 18.897 16.889 10.092 1.00 0.00 ATOM 186 N THR 25 18.061 15.871 10.158 1.00 0.00 ATOM 187 CA THR 25 16.630 16.047 9.941 1.00 0.00 ATOM 188 CB THR 25 15.964 14.705 9.676 1.00 0.00 ATOM 189 CG2 THR 25 14.470 14.920 9.498 1.00 0.00 ATOM 190 OG1 THR 25 16.466 14.159 8.444 1.00 0.00 ATOM 191 O THR 25 15.212 17.743 10.895 1.00 0.00 ATOM 192 C THR 25 15.996 16.824 11.118 1.00 0.00 ATOM 193 N ALA 26 16.376 16.454 12.331 1.00 0.00 ATOM 194 CA ALA 26 15.918 17.153 13.542 1.00 0.00 ATOM 195 CB ALA 26 16.477 16.489 14.792 1.00 0.00 ATOM 196 O ALA 26 15.458 19.489 13.812 1.00 0.00 ATOM 197 C ALA 26 16.311 18.639 13.536 1.00 0.00 ATOM 198 N GLU 27 17.499 18.921 12.997 1.00 0.00 ATOM 199 CA GLU 27 18.026 20.292 12.873 1.00 0.00 ATOM 200 CB GLU 27 19.488 20.246 12.420 1.00 0.00 ATOM 201 CG GLU 27 20.128 21.650 12.330 1.00 0.00 ATOM 202 CD GLU 27 21.575 21.636 11.821 1.00 0.00 ATOM 203 OE1 GLU 27 22.303 20.711 12.177 1.00 0.00 ATOM 204 OE2 GLU 27 21.943 22.598 11.113 1.00 0.00 ATOM 205 O GLU 27 16.720 22.221 12.252 1.00 0.00 ATOM 206 C GLU 27 17.180 21.136 11.900 1.00 0.00 ATOM 207 N LYS 28 16.791 20.520 10.783 1.00 0.00 ATOM 208 CA LYS 28 15.908 21.168 9.785 1.00 0.00 ATOM 209 CB LYS 28 15.682 20.225 8.607 1.00 0.00 ATOM 210 CG LYS 28 14.748 20.802 7.535 1.00 0.00 ATOM 211 CD LYS 28 14.623 19.814 6.388 1.00 0.00 ATOM 212 CE LYS 28 13.375 20.017 5.558 1.00 0.00 ATOM 213 NZ LYS 28 13.361 19.176 4.362 1.00 0.00 ATOM 214 O LYS 28 14.123 22.709 10.269 1.00 0.00 ATOM 215 C LYS 28 14.564 21.560 10.411 1.00 0.00 ATOM 216 N TYR 29 13.969 20.606 11.123 1.00 0.00 ATOM 217 CA TYR 29 12.680 20.844 11.794 1.00 0.00 ATOM 218 CB TYR 29 12.137 19.580 12.464 1.00 0.00 ATOM 219 CG TYR 29 10.756 19.877 13.068 1.00 0.00 ATOM 220 CD1 TYR 29 9.643 19.959 12.237 1.00 0.00 ATOM 221 CD2 TYR 29 10.605 20.069 14.435 1.00 0.00 ATOM 222 CE1 TYR 29 8.398 20.234 12.769 1.00 0.00 ATOM 223 CE2 TYR 29 9.351 20.322 14.973 1.00 0.00 ATOM 224 CZ TYR 29 8.248 20.405 14.140 1.00 0.00 ATOM 225 OH TYR 29 7.028 20.719 14.649 1.00 0.00 ATOM 226 O TYR 29 12.020 22.938 12.761 1.00 0.00 ATOM 227 C TYR 29 12.781 21.969 12.824 1.00 0.00 ATOM 228 N PHE 30 13.780 21.877 13.692 1.00 0.00 ATOM 229 CA PHE 30 13.966 22.876 14.765 1.00 0.00 ATOM 230 CB PHE 30 14.974 22.402 15.806 1.00 0.00 ATOM 231 CG PHE 30 14.420 21.322 16.737 1.00 0.00 ATOM 232 CD1 PHE 30 13.099 21.301 17.175 1.00 0.00 ATOM 233 CD2 PHE 30 15.316 20.376 17.214 1.00 0.00 ATOM 234 CE1 PHE 30 12.691 20.350 18.112 1.00 0.00 ATOM 235 CE2 PHE 30 14.904 19.428 18.138 1.00 0.00 ATOM 236 CZ PHE 30 13.599 19.410 18.595 1.00 0.00 ATOM 237 O PHE 30 13.768 25.251 14.782 1.00 0.00 ATOM 238 C PHE 30 14.329 24.275 14.274 1.00 0.00 ATOM 239 N LYS 31 15.126 24.353 13.217 1.00 0.00 ATOM 240 CA LYS 31 15.444 25.647 12.600 1.00 0.00 ATOM 241 CB LYS 31 16.559 25.486 11.566 1.00 0.00 ATOM 242 CG LYS 31 17.019 26.797 10.935 1.00 0.00 ATOM 243 CD LYS 31 17.636 27.767 11.950 1.00 0.00 ATOM 244 CE LYS 31 18.149 28.965 11.171 1.00 0.00 ATOM 245 NZ LYS 31 18.877 29.858 12.059 1.00 0.00 ATOM 246 O LYS 31 13.985 27.519 12.175 1.00 0.00 ATOM 247 C LYS 31 14.195 26.312 12.005 1.00 0.00 ATOM 248 N LEU 32 13.307 25.492 11.437 1.00 0.00 ATOM 249 CA LEU 32 11.996 25.961 10.949 1.00 0.00 ATOM 250 CB LEU 32 11.325 24.821 10.186 1.00 0.00 ATOM 251 CG LEU 32 9.923 25.142 9.667 1.00 0.00 ATOM 252 CD1 LEU 32 9.917 26.322 8.701 1.00 0.00 ATOM 253 CD2 LEU 32 9.387 23.891 8.973 1.00 0.00 ATOM 254 O LEU 32 10.575 27.540 12.039 1.00 0.00 ATOM 255 C LEU 32 11.093 26.440 12.087 1.00 0.00 ATOM 256 N ILE 33 11.070 25.669 13.181 1.00 0.00 ATOM 257 CA ILE 33 10.279 26.040 14.379 1.00 0.00 ATOM 258 CB ILE 33 10.352 24.962 15.479 1.00 0.00 ATOM 259 CG1 ILE 33 9.776 23.637 14.976 1.00 0.00 ATOM 260 CG2 ILE 33 9.697 25.414 16.796 1.00 0.00 ATOM 261 CD1 ILE 33 8.372 23.714 14.368 1.00 0.00 ATOM 262 O ILE 33 9.908 28.257 15.228 1.00 0.00 ATOM 263 C ILE 33 10.731 27.392 14.921 1.00 0.00 ATOM 264 N ALA 34 12.054 27.530 15.055 1.00 0.00 ATOM 265 CA ALA 34 12.655 28.759 15.570 1.00 0.00 ATOM 266 CB ALA 34 14.163 28.555 15.724 1.00 0.00 ATOM 267 O ALA 34 11.755 30.945 15.107 1.00 0.00 ATOM 268 C ALA 34 12.354 29.970 14.663 1.00 0.00 ATOM 269 N ASN 35 12.493 29.745 13.360 1.00 0.00 ATOM 270 CA ASN 35 12.118 30.766 12.371 1.00 0.00 ATOM 271 CB ASN 35 12.482 30.389 10.940 1.00 0.00 ATOM 272 CG ASN 35 13.984 30.461 10.707 1.00 0.00 ATOM 273 ND2 ASN 35 14.437 29.487 9.960 1.00 0.00 ATOM 274 OD1 ASN 35 14.770 31.275 11.168 1.00 0.00 ATOM 275 O ASN 35 10.259 32.297 12.516 1.00 0.00 ATOM 276 C ASN 35 10.635 31.134 12.382 1.00 0.00 ATOM 277 N ALA 36 9.807 30.111 12.476 1.00 0.00 ATOM 278 CA ALA 36 8.350 30.289 12.541 1.00 0.00 ATOM 279 CB ALA 36 7.664 28.923 12.502 1.00 0.00 ATOM 280 O ALA 36 6.855 31.667 13.809 1.00 0.00 ATOM 281 C ALA 36 7.922 31.067 13.789 1.00 0.00 ATOM 282 N LYS 37 8.742 30.987 14.836 1.00 0.00 ATOM 283 CA LYS 37 8.453 31.701 16.092 1.00 0.00 ATOM 284 CB LYS 37 8.497 30.746 17.275 1.00 0.00 ATOM 285 CG LYS 37 7.473 29.646 17.110 1.00 0.00 ATOM 286 CD LYS 37 6.060 30.235 17.120 1.00 0.00 ATOM 287 CE LYS 37 4.973 29.162 17.105 1.00 0.00 ATOM 288 NZ LYS 37 5.310 28.053 17.992 1.00 0.00 ATOM 289 O LYS 37 9.281 33.459 17.477 1.00 0.00 ATOM 290 C LYS 37 9.331 32.909 16.370 1.00 0.00 ATOM 291 N THR 38 9.980 33.388 15.316 1.00 0.00 ATOM 292 CA THR 38 10.622 34.714 15.308 1.00 0.00 ATOM 293 CB THR 38 9.419 35.696 15.482 1.00 0.00 ATOM 294 CG2 THR 38 9.724 37.171 15.685 1.00 0.00 ATOM 295 OG1 THR 38 8.494 35.529 14.388 1.00 0.00 ATOM 296 O THR 38 12.269 35.712 16.816 1.00 0.00 ATOM 297 C THR 38 11.907 34.742 16.163 1.00 0.00 ATOM 298 N VAL 39 12.647 33.628 16.072 1.00 0.00 ATOM 299 CA VAL 39 13.956 33.342 16.705 1.00 0.00 ATOM 300 CB VAL 39 14.010 31.881 17.165 1.00 0.00 ATOM 301 CG1 VAL 39 15.367 31.394 17.704 1.00 0.00 ATOM 302 CG2 VAL 39 12.736 31.401 17.834 1.00 0.00 ATOM 303 O VAL 39 14.967 32.348 14.786 1.00 0.00 ATOM 304 C VAL 39 14.994 33.300 15.581 1.00 0.00 ATOM 305 N GLU 40 16.076 33.995 15.834 1.00 0.00 ATOM 306 CA GLU 40 17.280 33.844 15.008 1.00 0.00 ATOM 307 CB GLU 40 17.228 34.826 13.833 1.00 0.00 ATOM 308 CG GLU 40 16.110 34.423 12.861 1.00 0.00 ATOM 309 CD GLU 40 15.871 35.443 11.760 1.00 0.00 ATOM 310 OE1 GLU 40 14.826 35.272 11.132 1.00 0.00 ATOM 311 OE2 GLU 40 16.708 36.351 11.546 1.00 0.00 ATOM 312 O GLU 40 18.775 35.010 16.500 1.00 0.00 ATOM 313 C GLU 40 18.518 33.986 15.883 1.00 0.00 ATOM 314 N GLY 41 19.214 32.865 16.048 1.00 0.00 ATOM 315 CA GLY 41 20.331 32.832 17.006 1.00 0.00 ATOM 316 O GLY 41 21.457 31.290 15.527 1.00 0.00 ATOM 317 C GLY 41 21.409 31.831 16.640 1.00 0.00 ATOM 318 N VAL 42 22.215 31.591 17.668 1.00 0.00 ATOM 319 CA VAL 42 23.329 30.641 17.622 1.00 0.00 ATOM 320 CB VAL 42 24.509 31.153 18.484 1.00 0.00 ATOM 321 CG1 VAL 42 25.704 30.202 18.505 1.00 0.00 ATOM 322 CG2 VAL 42 24.982 32.514 17.979 1.00 0.00 ATOM 323 O VAL 42 22.041 29.176 19.044 1.00 0.00 ATOM 324 C VAL 42 22.819 29.270 18.107 1.00 0.00 ATOM 325 N TRP 43 23.353 28.247 17.463 1.00 0.00 ATOM 326 CA TRP 43 22.932 26.841 17.633 1.00 0.00 ATOM 327 CB TRP 43 22.462 26.281 16.296 1.00 0.00 ATOM 328 CG TRP 43 21.148 26.903 15.837 1.00 0.00 ATOM 329 CD1 TRP 43 20.999 28.081 15.254 1.00 0.00 ATOM 330 CD2 TRP 43 19.880 26.345 16.005 1.00 0.00 ATOM 331 CE2 TRP 43 18.998 27.265 15.466 1.00 0.00 ATOM 332 CE3 TRP 43 19.424 25.165 16.540 1.00 0.00 ATOM 333 NE1 TRP 43 19.702 28.295 15.036 1.00 0.00 ATOM 334 CZ2 TRP 43 17.634 26.974 15.479 1.00 0.00 ATOM 335 CZ3 TRP 43 18.060 24.888 16.555 1.00 0.00 ATOM 336 CH2 TRP 43 17.169 25.808 16.019 1.00 0.00 ATOM 337 O TRP 43 25.217 26.120 17.847 1.00 0.00 ATOM 338 C TRP 43 24.039 25.943 18.158 1.00 0.00 ATOM 339 N THR 44 23.611 25.041 19.027 1.00 0.00 ATOM 340 CA THR 44 24.433 23.876 19.417 1.00 0.00 ATOM 341 CB THR 44 25.003 23.915 20.839 1.00 0.00 ATOM 342 CG2 THR 44 25.739 25.228 21.168 1.00 0.00 ATOM 343 OG1 THR 44 23.982 23.612 21.790 1.00 0.00 ATOM 344 O THR 44 22.371 22.616 19.512 1.00 0.00 ATOM 345 C THR 44 23.587 22.604 19.291 1.00 0.00 ATOM 346 N TYR 45 24.301 21.521 19.070 1.00 0.00 ATOM 347 CA TYR 45 23.723 20.179 19.162 1.00 0.00 ATOM 348 CB TYR 45 23.370 19.675 17.765 1.00 0.00 ATOM 349 CG TYR 45 24.543 19.353 16.857 1.00 0.00 ATOM 350 CD1 TYR 45 25.054 20.374 16.069 1.00 0.00 ATOM 351 CD2 TYR 45 25.015 18.056 16.769 1.00 0.00 ATOM 352 CE1 TYR 45 26.064 20.078 15.173 1.00 0.00 ATOM 353 CE2 TYR 45 26.052 17.769 15.898 1.00 0.00 ATOM 354 CZ TYR 45 26.563 18.790 15.109 1.00 0.00 ATOM 355 OH TYR 45 27.524 18.529 14.189 1.00 0.00 ATOM 356 O TYR 45 25.827 19.131 19.649 1.00 0.00 ATOM 357 C TYR 45 24.636 19.219 19.923 1.00 0.00 ATOM 358 N LYS 46 24.103 18.706 21.020 1.00 0.00 ATOM 359 CA LYS 46 24.774 17.680 21.844 1.00 0.00 ATOM 360 CB LYS 46 24.697 18.006 23.334 1.00 0.00 ATOM 361 CG LYS 46 25.360 19.330 23.663 1.00 0.00 ATOM 362 CD LYS 46 25.199 19.524 25.146 1.00 0.00 ATOM 363 CE LYS 46 25.763 20.877 25.493 1.00 0.00 ATOM 364 NZ LYS 46 25.943 21.072 26.933 1.00 0.00 ATOM 365 O LYS 46 23.069 16.006 22.128 1.00 0.00 ATOM 366 C LYS 46 24.145 16.312 21.601 1.00 0.00 ATOM 367 N ASP 47 24.908 15.457 20.925 1.00 0.00 ATOM 368 CA ASP 47 24.404 14.110 20.607 1.00 0.00 ATOM 369 CB ASP 47 25.274 13.392 19.576 1.00 0.00 ATOM 370 CG ASP 47 25.255 14.009 18.174 1.00 0.00 ATOM 371 OD1 ASP 47 24.317 14.775 17.877 1.00 0.00 ATOM 372 OD2 ASP 47 26.104 13.597 17.370 1.00 0.00 ATOM 373 O ASP 47 23.272 12.400 21.873 1.00 0.00 ATOM 374 C ASP 47 24.201 13.201 21.837 1.00 0.00 ATOM 375 N GLU 48 24.979 13.474 22.894 1.00 0.00 ATOM 376 CA GLU 48 24.889 12.719 24.159 1.00 0.00 ATOM 377 CB GLU 48 25.993 13.139 25.122 1.00 0.00 ATOM 378 CG GLU 48 27.373 12.765 24.587 1.00 0.00 ATOM 379 CD GLU 48 28.499 13.104 25.551 1.00 0.00 ATOM 380 OE1 GLU 48 28.244 13.802 26.557 1.00 0.00 ATOM 381 OE2 GLU 48 29.592 12.552 25.286 1.00 0.00 ATOM 382 O GLU 48 23.046 11.887 25.464 1.00 0.00 ATOM 383 C GLU 48 23.539 12.839 24.870 1.00 0.00 ATOM 384 N ILE 49 22.889 13.967 24.648 1.00 0.00 ATOM 385 CA ILE 49 21.562 14.218 25.258 1.00 0.00 ATOM 386 CB ILE 49 21.583 15.442 26.187 1.00 0.00 ATOM 387 CG1 ILE 49 21.938 16.705 25.405 1.00 0.00 ATOM 388 CG2 ILE 49 22.560 15.214 27.349 1.00 0.00 ATOM 389 CD1 ILE 49 21.726 17.969 26.242 1.00 0.00 ATOM 390 O ILE 49 19.292 14.511 24.565 1.00 0.00 ATOM 391 C ILE 49 20.451 14.352 24.213 1.00 0.00 ATOM 392 N LYS 50 20.836 14.305 22.941 1.00 0.00 ATOM 393 CA LYS 50 19.927 14.462 21.799 1.00 0.00 ATOM 394 CB LYS 50 19.043 13.203 21.648 1.00 0.00 ATOM 395 CG LYS 50 19.784 11.904 22.044 1.00 0.00 ATOM 396 CD LYS 50 18.993 10.612 21.854 1.00 0.00 ATOM 397 CE LYS 50 19.755 9.422 22.405 1.00 0.00 ATOM 398 NZ LYS 50 21.011 9.122 21.724 1.00 0.00 ATOM 399 O LYS 50 18.018 15.980 21.576 1.00 0.00 ATOM 400 C LYS 50 19.207 15.826 21.894 1.00 0.00 ATOM 401 N THR 51 19.989 16.849 22.269 1.00 0.00 ATOM 402 CA THR 51 19.440 18.198 22.530 1.00 0.00 ATOM 403 CB THR 51 19.408 18.492 24.032 1.00 0.00 ATOM 404 CG2 THR 51 18.781 19.828 24.424 1.00 0.00 ATOM 405 OG1 THR 51 18.714 17.430 24.685 1.00 0.00 ATOM 406 O THR 51 21.456 19.279 21.781 1.00 0.00 ATOM 407 C THR 51 20.223 19.278 21.788 1.00 0.00 ATOM 408 N PHE 52 19.426 20.106 21.142 1.00 0.00 ATOM 409 CA PHE 52 19.827 21.338 20.446 1.00 0.00 ATOM 410 CB PHE 52 19.022 21.552 19.159 1.00 0.00 ATOM 411 CG PHE 52 19.329 20.550 18.068 1.00 0.00 ATOM 412 CD1 PHE 52 18.662 19.335 18.029 1.00 0.00 ATOM 413 CD2 PHE 52 20.256 20.871 17.079 1.00 0.00 ATOM 414 CE1 PHE 52 18.939 18.421 17.022 1.00 0.00 ATOM 415 CE2 PHE 52 20.524 19.957 16.074 1.00 0.00 ATOM 416 CZ PHE 52 19.882 18.731 16.049 1.00 0.00 ATOM 417 O PHE 52 18.481 22.550 22.059 1.00 0.00 ATOM 418 C PHE 52 19.485 22.540 21.338 1.00 0.00 ATOM 419 N THR 53 20.313 23.563 21.207 1.00 0.00 ATOM 420 CA THR 53 20.035 24.864 21.846 1.00 0.00 ATOM 421 CB THR 53 20.966 25.271 23.004 1.00 0.00 ATOM 422 CG2 THR 53 21.013 24.213 24.085 1.00 0.00 ATOM 423 OG1 THR 53 22.283 25.567 22.558 1.00 0.00 ATOM 424 O THR 53 21.006 25.973 19.947 1.00 0.00 ATOM 425 C THR 53 20.127 25.973 20.818 1.00 0.00 ATOM 426 N VAL 54 19.215 26.927 20.958 1.00 0.00 ATOM 427 CA VAL 54 19.357 28.197 20.229 1.00 0.00 ATOM 428 CB VAL 54 18.400 28.266 19.024 1.00 0.00 ATOM 429 CG1 VAL 54 16.974 28.272 19.497 1.00 0.00 ATOM 430 CG2 VAL 54 18.582 29.526 18.178 1.00 0.00 ATOM 431 O VAL 54 18.275 29.476 21.975 1.00 0.00 ATOM 432 C VAL 54 19.238 29.360 21.215 1.00 0.00 ATOM 433 N THR 55 20.197 30.259 21.063 1.00 0.00 ATOM 434 CA THR 55 20.383 31.390 21.988 1.00 0.00 ATOM 435 CB THR 55 21.632 31.152 22.857 1.00 0.00 ATOM 436 CG2 THR 55 21.784 32.212 23.957 1.00 0.00 ATOM 437 OG1 THR 55 21.564 29.847 23.439 1.00 0.00 ATOM 438 O THR 55 21.301 32.748 20.240 1.00 0.00 ATOM 439 C THR 55 20.530 32.684 21.203 1.00 0.00 ATOM 440 N GLU 56 19.726 33.651 21.620 1.00 0.00 ATOM 441 CA GLU 56 19.857 35.033 21.117 1.00 0.00 ATOM 442 CB GLU 56 18.463 35.625 20.854 1.00 0.00 ATOM 443 CG GLU 56 17.686 34.885 19.755 1.00 0.00 ATOM 444 CD GLU 56 16.344 35.537 19.422 1.00 0.00 ATOM 445 OE1 GLU 56 15.564 35.808 20.360 1.00 0.00 ATOM 446 OE2 GLU 56 16.067 35.653 18.201 1.00 0.00 ATOM 447 O GLU 56 21.029 35.423 23.181 1.00 0.00 ATOM 448 C GLU 56 20.681 35.915 22.087 1.00 0.00 TER END