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 2 Tue Jul 15 16:01:45 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 2igd_A 2igh_A 2qmt_A ATOM 1 N THR 1 15.511 9.579 17.141 1.00 0.00 ATOM 2 CA THR 1 14.400 9.318 18.070 1.00 0.00 ATOM 3 CB THR 1 14.878 8.556 19.320 1.00 0.00 ATOM 4 CG2 THR 1 15.425 7.190 18.936 1.00 0.00 ATOM 5 OG1 THR 1 15.903 9.309 19.980 1.00 0.00 ATOM 6 O THR 1 13.558 11.467 17.548 1.00 0.00 ATOM 7 C THR 1 13.778 10.667 18.459 1.00 0.00 ATOM 8 N THR 2 13.607 10.928 19.749 1.00 0.00 ATOM 9 CA THR 2 13.065 12.207 20.257 1.00 0.00 ATOM 10 CB THR 2 12.262 12.005 21.556 1.00 0.00 ATOM 11 CG2 THR 2 11.743 13.336 22.076 1.00 0.00 ATOM 12 OG1 THR 2 11.156 11.129 21.305 1.00 0.00 ATOM 13 O THR 2 15.083 12.961 21.348 1.00 0.00 ATOM 14 C THR 2 14.233 13.159 20.488 1.00 0.00 ATOM 15 N TYR 3 14.182 14.259 19.777 1.00 0.00 ATOM 16 CA TYR 3 15.170 15.330 19.987 1.00 0.00 ATOM 17 CB TYR 3 15.741 15.791 18.647 1.00 0.00 ATOM 18 CG TYR 3 16.503 14.671 17.949 1.00 0.00 ATOM 19 CD1 TYR 3 15.825 13.760 17.149 1.00 0.00 ATOM 20 CD2 TYR 3 17.883 14.573 18.070 1.00 0.00 ATOM 21 CE1 TYR 3 16.506 12.770 16.470 1.00 0.00 ATOM 22 CE2 TYR 3 18.575 13.584 17.391 1.00 0.00 ATOM 23 CZ TYR 3 17.887 12.673 16.601 1.00 0.00 ATOM 24 OH TYR 3 18.509 11.573 16.092 1.00 0.00 ATOM 25 O TYR 3 13.318 16.738 20.585 1.00 0.00 ATOM 26 C TYR 3 14.518 16.480 20.746 1.00 0.00 ATOM 27 N LYS 4 15.316 17.131 21.566 1.00 0.00 ATOM 28 CA LYS 4 14.854 18.291 22.345 1.00 0.00 ATOM 29 CB LYS 4 15.193 18.123 23.826 1.00 0.00 ATOM 30 CG LYS 4 14.425 16.962 24.436 1.00 0.00 ATOM 31 CD LYS 4 14.814 16.823 25.896 1.00 0.00 ATOM 32 CE LYS 4 14.045 15.652 26.506 1.00 0.00 ATOM 33 NZ LYS 4 14.424 15.524 27.917 1.00 0.00 ATOM 34 O LYS 4 16.693 19.553 21.466 1.00 0.00 ATOM 35 C LYS 4 15.533 19.562 21.865 1.00 0.00 ATOM 36 N LEU 5 14.761 20.631 21.924 1.00 0.00 ATOM 37 CA LEU 5 15.259 21.991 21.694 1.00 0.00 ATOM 38 CB LEU 5 14.559 22.580 20.463 1.00 0.00 ATOM 39 CG LEU 5 15.117 23.950 20.083 1.00 0.00 ATOM 40 CD1 LEU 5 16.568 23.892 19.654 1.00 0.00 ATOM 41 CD2 LEU 5 14.287 24.509 18.952 1.00 0.00 ATOM 42 O LEU 5 13.907 22.920 23.432 1.00 0.00 ATOM 43 C LEU 5 15.027 22.862 22.933 1.00 0.00 ATOM 44 N ILE 6 16.136 23.374 23.444 1.00 0.00 ATOM 45 CA ILE 6 16.144 24.374 24.543 1.00 0.00 ATOM 46 CB ILE 6 17.266 24.091 25.557 1.00 0.00 ATOM 47 CG1 ILE 6 17.074 22.713 26.196 1.00 0.00 ATOM 48 CG2 ILE 6 17.306 25.174 26.624 1.00 0.00 ATOM 49 CD1 ILE 6 18.246 22.260 27.037 1.00 0.00 ATOM 50 O ILE 6 17.302 26.035 23.203 1.00 0.00 ATOM 51 C ILE 6 16.312 25.744 23.882 1.00 0.00 ATOM 52 N LEU 7 15.301 26.563 24.111 1.00 0.00 ATOM 53 CA LEU 7 15.179 27.892 23.500 1.00 0.00 ATOM 54 CB LEU 7 13.829 28.100 22.799 1.00 0.00 ATOM 55 CG LEU 7 13.612 27.169 21.600 1.00 0.00 ATOM 56 CD1 LEU 7 13.023 25.828 22.050 1.00 0.00 ATOM 57 CD2 LEU 7 12.701 27.837 20.579 1.00 0.00 ATOM 58 O LEU 7 14.606 29.143 25.469 1.00 0.00 ATOM 59 C LEU 7 15.377 29.013 24.520 1.00 0.00 ATOM 60 N ASN 8 16.476 29.715 24.330 1.00 0.00 ATOM 61 CA ASN 8 16.794 30.946 25.060 1.00 0.00 ATOM 62 CB ASN 8 18.136 30.845 25.760 1.00 0.00 ATOM 63 CG ASN 8 18.435 32.007 26.667 1.00 0.00 ATOM 64 ND2 ASN 8 19.426 31.831 27.502 1.00 0.00 ATOM 65 OD1 ASN 8 17.824 33.077 26.560 1.00 0.00 ATOM 66 O ASN 8 17.782 32.486 23.510 1.00 0.00 ATOM 67 C ASN 8 16.763 32.125 24.109 1.00 0.00 ATOM 68 N LEU 9 15.572 32.643 23.918 1.00 0.00 ATOM 69 CA LEU 9 15.411 33.772 22.987 1.00 0.00 ATOM 70 CB LEU 9 14.382 33.450 21.897 1.00 0.00 ATOM 71 CG LEU 9 14.495 32.000 21.438 1.00 0.00 ATOM 72 CD1 LEU 9 13.256 31.668 20.627 1.00 0.00 ATOM 73 CD2 LEU 9 15.805 31.732 20.709 1.00 0.00 ATOM 74 O LEU 9 14.618 34.912 24.946 1.00 0.00 ATOM 75 C LEU 9 14.979 35.002 23.767 1.00 0.00 ATOM 76 N LYS 10 14.897 36.122 23.066 1.00 0.00 ATOM 77 CA LYS 10 14.475 37.391 23.695 1.00 0.00 ATOM 78 CB LYS 10 14.593 38.547 22.700 1.00 0.00 ATOM 79 CG LYS 10 16.025 38.935 22.353 1.00 0.00 ATOM 80 CD LYS 10 16.061 40.087 21.361 1.00 0.00 ATOM 81 CE LYS 10 17.490 40.456 20.991 1.00 0.00 ATOM 82 NZ LYS 10 17.540 41.562 19.998 1.00 0.00 ATOM 83 O LYS 10 12.753 37.690 25.353 1.00 0.00 ATOM 84 C LYS 10 13.045 37.300 24.224 1.00 0.00 ATOM 85 N GLN 11 12.166 36.748 23.394 1.00 0.00 ATOM 86 CA GLN 11 10.726 36.706 23.703 1.00 0.00 ATOM 87 CB GLN 11 9.925 37.442 22.626 1.00 0.00 ATOM 88 CG GLN 11 10.306 38.903 22.456 1.00 0.00 ATOM 89 CD GLN 11 9.958 39.737 23.673 1.00 0.00 ATOM 90 OE1 GLN 11 8.912 39.539 24.300 1.00 0.00 ATOM 91 NE2 GLN 11 10.830 40.678 24.015 1.00 0.00 ATOM 92 O GLN 11 9.178 35.114 24.602 1.00 0.00 ATOM 93 C GLN 11 10.128 35.305 23.843 1.00 0.00 ATOM 94 N ALA 12 10.750 34.336 23.184 1.00 0.00 ATOM 95 CA ALA 12 10.312 32.935 23.284 1.00 0.00 ATOM 96 CB ALA 12 10.004 32.344 21.914 1.00 0.00 ATOM 97 O ALA 12 12.563 32.179 23.696 1.00 0.00 ATOM 98 C ALA 12 11.383 32.107 24.006 1.00 0.00 ATOM 99 N LYS 13 10.993 31.507 25.116 1.00 0.00 ATOM 100 CA LYS 13 11.983 30.719 25.867 1.00 0.00 ATOM 101 CB LYS 13 12.781 31.621 26.810 1.00 0.00 ATOM 102 CG LYS 13 11.976 32.185 27.972 1.00 0.00 ATOM 103 CD LYS 13 12.838 33.063 28.868 1.00 0.00 ATOM 104 CE LYS 13 12.033 33.627 30.030 1.00 0.00 ATOM 105 NZ LYS 13 12.863 34.492 30.912 1.00 0.00 ATOM 106 O LYS 13 10.364 29.827 27.356 1.00 0.00 ATOM 107 C LYS 13 11.344 29.588 26.667 1.00 0.00 ATOM 108 N GLU 14 11.936 28.409 26.508 1.00 0.00 ATOM 109 CA GLU 14 11.488 27.109 27.078 1.00 0.00 ATOM 110 CB GLU 14 9.958 26.977 27.157 1.00 0.00 ATOM 111 CG GLU 14 9.289 26.995 25.777 1.00 0.00 ATOM 112 CD GLU 14 7.759 26.953 25.846 1.00 0.00 ATOM 113 OE1 GLU 14 7.198 27.082 26.945 1.00 0.00 ATOM 114 OE2 GLU 14 7.180 27.021 24.745 1.00 0.00 ATOM 115 O GLU 14 13.210 26.061 25.740 1.00 0.00 ATOM 116 C GLU 14 12.110 25.939 26.269 1.00 0.00 ATOM 117 N GLU 15 11.372 24.838 26.189 1.00 0.00 ATOM 118 CA GLU 15 11.754 23.638 25.450 1.00 0.00 ATOM 119 CB GLU 15 12.092 22.499 26.415 1.00 0.00 ATOM 120 CG GLU 15 13.304 22.762 27.298 1.00 0.00 ATOM 121 CD GLU 15 13.591 21.589 28.195 1.00 0.00 ATOM 122 OE1 GLU 15 12.851 20.636 28.150 1.00 0.00 ATOM 123 OE2 GLU 15 14.611 21.598 28.842 1.00 0.00 ATOM 124 O GLU 15 9.485 23.624 24.599 1.00 0.00 ATOM 125 C GLU 15 10.645 23.226 24.510 1.00 0.00 ATOM 126 N ALA 16 11.087 22.476 23.521 1.00 0.00 ATOM 127 CA ALA 16 10.219 21.744 22.590 1.00 0.00 ATOM 128 CB ALA 16 9.979 22.603 21.350 1.00 0.00 ATOM 129 O ALA 16 12.081 20.207 22.552 1.00 0.00 ATOM 130 C ALA 16 10.921 20.445 22.222 1.00 0.00 ATOM 131 N ILE 17 10.193 19.604 21.501 1.00 0.00 ATOM 132 CA ILE 17 10.725 18.304 21.063 1.00 0.00 ATOM 133 CB ILE 17 10.280 17.166 21.999 1.00 0.00 ATOM 134 CG1 ILE 17 8.752 17.068 22.031 1.00 0.00 ATOM 135 CG2 ILE 17 10.832 17.383 23.399 1.00 0.00 ATOM 136 CD1 ILE 17 8.235 15.851 22.762 1.00 0.00 ATOM 137 O ILE 17 9.226 18.401 19.221 1.00 0.00 ATOM 138 C ILE 17 10.287 17.973 19.632 1.00 0.00 ATOM 139 N LYS 18 10.978 17.044 19.003 1.00 0.00 ATOM 140 CA LYS 18 10.500 16.452 17.733 1.00 0.00 ATOM 141 CB LYS 18 10.753 17.410 16.568 1.00 0.00 ATOM 142 CG LYS 18 10.180 16.944 15.236 1.00 0.00 ATOM 143 CD LYS 18 8.664 17.061 15.214 1.00 0.00 ATOM 144 CE LYS 18 8.089 16.572 13.894 1.00 0.00 ATOM 145 NZ LYS 18 6.602 16.610 13.886 1.00 0.00 ATOM 146 O LYS 18 12.362 14.935 17.816 1.00 0.00 ATOM 147 C LYS 18 11.182 15.113 17.485 1.00 0.00 ATOM 148 N GLU 19 10.414 14.192 16.925 1.00 0.00 ATOM 149 CA GLU 19 10.936 12.862 16.566 1.00 0.00 ATOM 150 CB GLU 19 9.852 11.797 16.735 1.00 0.00 ATOM 151 CG GLU 19 9.359 11.624 18.165 1.00 0.00 ATOM 152 CD GLU 19 8.303 10.557 18.254 1.00 0.00 ATOM 153 OE1 GLU 19 7.951 10.010 17.237 1.00 0.00 ATOM 154 OE2 GLU 19 7.928 10.209 19.350 1.00 0.00 ATOM 155 O GLU 19 10.867 13.511 14.245 1.00 0.00 ATOM 156 C GLU 19 11.457 12.892 15.126 1.00 0.00 ATOM 157 N ALA 20 12.588 12.224 14.967 1.00 0.00 ATOM 158 CA ALA 20 13.239 12.094 13.658 1.00 0.00 ATOM 159 CB ALA 20 14.068 13.355 13.368 1.00 0.00 ATOM 160 O ALA 20 14.651 10.427 14.670 1.00 0.00 ATOM 161 C ALA 20 14.151 10.865 13.629 1.00 0.00 ATOM 162 N VAL 21 14.323 10.325 12.429 1.00 0.00 ATOM 163 CA VAL 21 15.215 9.156 12.211 1.00 0.00 ATOM 164 CB VAL 21 15.055 8.581 10.791 1.00 0.00 ATOM 165 CG1 VAL 21 16.103 7.511 10.529 1.00 0.00 ATOM 166 CG2 VAL 21 13.657 8.014 10.599 1.00 0.00 ATOM 167 O VAL 21 17.475 8.650 12.862 1.00 0.00 ATOM 168 C VAL 21 16.704 9.499 12.431 1.00 0.00 ATOM 169 N ASP 22 17.062 10.749 12.171 1.00 0.00 ATOM 170 CA ASP 22 18.452 11.211 12.312 1.00 0.00 ATOM 171 CB ASP 22 19.233 11.052 10.992 1.00 0.00 ATOM 172 CG ASP 22 18.782 11.980 9.872 1.00 0.00 ATOM 173 OD1 ASP 22 18.051 12.929 10.181 1.00 0.00 ATOM 174 OD2 ASP 22 19.323 11.840 8.752 1.00 0.00 ATOM 175 O ASP 22 17.538 13.390 12.910 1.00 0.00 ATOM 176 C ASP 22 18.529 12.651 12.821 1.00 0.00 ATOM 177 N ALA 23 19.748 13.013 13.172 1.00 0.00 ATOM 178 CA ALA 23 19.996 14.354 13.721 1.00 0.00 ATOM 179 CB ALA 23 21.346 14.317 14.422 1.00 0.00 ATOM 180 O ALA 23 19.213 16.513 13.049 1.00 0.00 ATOM 181 C ALA 23 19.835 15.513 12.710 1.00 0.00 ATOM 182 N GLY 24 20.166 15.233 11.441 1.00 0.00 ATOM 183 CA GLY 24 19.996 16.182 10.330 1.00 0.00 ATOM 184 O GLY 24 18.204 17.810 10.028 1.00 0.00 ATOM 185 C GLY 24 18.535 16.620 10.109 1.00 0.00 ATOM 186 N THR 25 17.637 15.649 10.149 1.00 0.00 ATOM 187 CA THR 25 16.186 15.896 9.998 1.00 0.00 ATOM 188 CB THR 25 15.390 14.579 9.947 1.00 0.00 ATOM 189 CG2 THR 25 13.899 14.861 9.848 1.00 0.00 ATOM 190 OG1 THR 25 15.805 13.810 8.811 1.00 0.00 ATOM 191 O THR 25 14.873 17.695 10.916 1.00 0.00 ATOM 192 C THR 25 15.644 16.766 11.147 1.00 0.00 ATOM 193 N ALA 26 16.024 16.388 12.367 1.00 0.00 ATOM 194 CA ALA 26 15.632 17.138 13.567 1.00 0.00 ATOM 195 CB ALA 26 16.192 16.439 14.807 1.00 0.00 ATOM 196 O ALA 26 15.318 19.507 13.845 1.00 0.00 ATOM 197 C ALA 26 16.100 18.598 13.536 1.00 0.00 ATOM 198 N GLU 27 17.290 18.820 12.987 1.00 0.00 ATOM 199 CA GLU 27 17.888 20.161 12.827 1.00 0.00 ATOM 200 CB GLU 27 19.321 20.048 12.299 1.00 0.00 ATOM 201 CG GLU 27 20.041 21.381 12.149 1.00 0.00 ATOM 202 CD GLU 27 21.450 21.188 11.662 1.00 0.00 ATOM 203 OE1 GLU 27 21.840 20.063 11.461 1.00 0.00 ATOM 204 OE2 GLU 27 22.100 22.168 11.383 1.00 0.00 ATOM 205 O GLU 27 16.676 22.158 12.235 1.00 0.00 ATOM 206 C GLU 27 17.047 21.039 11.885 1.00 0.00 ATOM 207 N LYS 28 16.699 20.498 10.726 1.00 0.00 ATOM 208 CA LYS 28 15.879 21.226 9.745 1.00 0.00 ATOM 209 CB LYS 28 15.661 20.376 8.492 1.00 0.00 ATOM 210 CG LYS 28 14.856 21.063 7.397 1.00 0.00 ATOM 211 CD LYS 28 14.746 20.187 6.158 1.00 0.00 ATOM 212 CE LYS 28 13.912 20.859 5.076 1.00 0.00 ATOM 213 NZ LYS 28 13.786 20.008 3.863 1.00 0.00 ATOM 214 O LYS 28 14.076 22.773 10.102 1.00 0.00 ATOM 215 C LYS 28 14.518 21.644 10.333 1.00 0.00 ATOM 216 N TYR 29 13.898 20.724 11.073 1.00 0.00 ATOM 217 CA TYR 29 12.588 20.962 11.712 1.00 0.00 ATOM 218 CB TYR 29 12.063 19.676 12.354 1.00 0.00 ATOM 219 CG TYR 29 11.672 18.609 11.356 1.00 0.00 ATOM 220 CD1 TYR 29 11.497 18.917 10.015 1.00 0.00 ATOM 221 CD2 TYR 29 11.481 17.294 11.758 1.00 0.00 ATOM 222 CE1 TYR 29 11.139 17.946 9.099 1.00 0.00 ATOM 223 CE2 TYR 29 11.124 16.315 10.851 1.00 0.00 ATOM 224 CZ TYR 29 10.955 16.644 9.522 1.00 0.00 ATOM 225 OH TYR 29 10.600 15.673 8.615 1.00 0.00 ATOM 226 O TYR 29 11.914 23.032 12.711 1.00 0.00 ATOM 227 C TYR 29 12.675 22.073 12.762 1.00 0.00 ATOM 228 N PHE 30 13.705 21.995 13.603 1.00 0.00 ATOM 229 CA PHE 30 13.963 23.016 14.642 1.00 0.00 ATOM 230 CB PHE 30 15.101 22.568 15.560 1.00 0.00 ATOM 231 CG PHE 30 14.750 21.397 16.435 1.00 0.00 ATOM 232 CD1 PHE 30 13.426 21.028 16.624 1.00 0.00 ATOM 233 CD2 PHE 30 15.740 20.664 17.069 1.00 0.00 ATOM 234 CE1 PHE 30 13.102 19.951 17.428 1.00 0.00 ATOM 235 CE2 PHE 30 15.419 19.587 17.872 1.00 0.00 ATOM 236 CZ PHE 30 14.098 19.231 18.051 1.00 0.00 ATOM 237 O PHE 30 13.739 25.405 14.491 1.00 0.00 ATOM 238 C PHE 30 14.301 24.396 14.092 1.00 0.00 ATOM 239 N LYS 31 15.062 24.376 13.002 1.00 0.00 ATOM 240 CA LYS 31 15.450 25.627 12.332 1.00 0.00 ATOM 241 CB LYS 31 16.479 25.349 11.234 1.00 0.00 ATOM 242 CG LYS 31 16.980 26.593 10.512 1.00 0.00 ATOM 243 CD LYS 31 18.056 26.245 9.495 1.00 0.00 ATOM 244 CE LYS 31 18.534 27.483 8.750 1.00 0.00 ATOM 245 NZ LYS 31 19.566 27.154 7.729 1.00 0.00 ATOM 246 O LYS 31 14.018 27.514 11.920 1.00 0.00 ATOM 247 C LYS 31 14.210 26.305 11.761 1.00 0.00 ATOM 248 N LEU 32 13.391 25.483 11.111 1.00 0.00 ATOM 249 CA LEU 32 12.111 25.931 10.549 1.00 0.00 ATOM 250 CB LEU 32 11.398 24.762 9.858 1.00 0.00 ATOM 251 CG LEU 32 12.052 24.276 8.558 1.00 0.00 ATOM 252 CD1 LEU 32 11.365 23.007 8.071 1.00 0.00 ATOM 253 CD2 LEU 32 11.968 25.372 7.506 1.00 0.00 ATOM 254 O LEU 32 10.768 27.679 11.478 1.00 0.00 ATOM 255 C LEU 32 11.209 26.540 11.638 1.00 0.00 ATOM 256 N ILE 33 11.140 25.861 12.779 1.00 0.00 ATOM 257 CA ILE 33 10.348 26.340 13.928 1.00 0.00 ATOM 258 CB ILE 33 10.355 25.322 15.082 1.00 0.00 ATOM 259 CG1 ILE 33 9.593 24.055 14.683 1.00 0.00 ATOM 260 CG2 ILE 33 9.752 25.936 16.337 1.00 0.00 ATOM 261 CD1 ILE 33 9.773 22.905 15.646 1.00 0.00 ATOM 262 O ILE 33 10.094 28.590 14.717 1.00 0.00 ATOM 263 C ILE 33 10.876 27.681 14.438 1.00 0.00 ATOM 264 N ALA 34 12.196 27.773 14.558 1.00 0.00 ATOM 265 CA ALA 34 12.873 29.014 14.988 1.00 0.00 ATOM 266 CB ALA 34 14.394 28.877 14.919 1.00 0.00 ATOM 267 O ALA 34 11.881 31.153 14.496 1.00 0.00 ATOM 268 C ALA 34 12.492 30.173 14.067 1.00 0.00 ATOM 269 N ASN 35 12.574 29.873 12.788 1.00 0.00 ATOM 270 CA ASN 35 12.193 30.842 11.747 1.00 0.00 ATOM 271 CB ASN 35 12.485 30.251 10.377 1.00 0.00 ATOM 272 CG ASN 35 13.985 30.233 10.098 1.00 0.00 ATOM 273 ND2 ASN 35 14.307 29.503 9.079 1.00 0.00 ATOM 274 OD1 ASN 35 14.854 30.885 10.649 1.00 0.00 ATOM 275 O ASN 35 10.421 32.439 11.855 1.00 0.00 ATOM 276 C ASN 35 10.722 31.249 11.816 1.00 0.00 ATOM 277 N ALA 36 9.874 30.248 11.996 1.00 0.00 ATOM 278 CA ALA 36 8.423 30.426 12.154 1.00 0.00 ATOM 279 CB ALA 36 7.765 29.055 12.265 1.00 0.00 ATOM 280 O ALA 36 7.050 31.935 13.433 1.00 0.00 ATOM 281 C ALA 36 8.081 31.266 13.384 1.00 0.00 ATOM 282 N LYS 37 8.961 31.238 14.384 1.00 0.00 ATOM 283 CA LYS 37 8.739 32.039 15.584 1.00 0.00 ATOM 284 CB LYS 37 8.741 31.150 16.828 1.00 0.00 ATOM 285 CG LYS 37 7.578 30.170 16.904 1.00 0.00 ATOM 286 CD LYS 37 7.638 29.336 18.175 1.00 0.00 ATOM 287 CE LYS 37 6.523 28.301 18.213 1.00 0.00 ATOM 288 NZ LYS 37 6.567 27.481 19.455 1.00 0.00 ATOM 289 O LYS 37 9.705 33.791 16.883 1.00 0.00 ATOM 290 C LYS 37 9.737 33.170 15.824 1.00 0.00 ATOM 291 N THR 38 10.277 33.640 14.704 1.00 0.00 ATOM 292 CA THR 38 11.175 34.822 14.614 1.00 0.00 ATOM 293 CB THR 38 10.432 36.125 14.961 1.00 0.00 ATOM 294 CG2 THR 38 11.303 37.334 14.657 1.00 0.00 ATOM 295 OG1 THR 38 9.223 36.206 14.194 1.00 0.00 ATOM 296 O THR 38 12.753 35.615 16.305 1.00 0.00 ATOM 297 C THR 38 12.405 34.714 15.535 1.00 0.00 ATOM 298 N VAL 39 12.986 33.525 15.516 1.00 0.00 ATOM 299 CA VAL 39 14.186 33.227 16.317 1.00 0.00 ATOM 300 CB VAL 39 14.188 31.737 16.698 1.00 0.00 ATOM 301 CG1 VAL 39 15.468 31.319 17.419 1.00 0.00 ATOM 302 CG2 VAL 39 12.918 31.326 17.437 1.00 0.00 ATOM 303 O VAL 39 15.528 32.738 14.418 1.00 0.00 ATOM 304 C VAL 39 15.387 33.458 15.408 1.00 0.00 ATOM 305 N GLU 40 16.315 34.250 15.918 1.00 0.00 ATOM 306 CA GLU 40 17.585 34.491 15.219 1.00 0.00 ATOM 307 CB GLU 40 17.575 35.867 14.548 1.00 0.00 ATOM 308 CG GLU 40 16.588 35.997 13.395 1.00 0.00 ATOM 309 CD GLU 40 16.631 37.374 12.793 1.00 0.00 ATOM 310 OE1 GLU 40 17.417 38.173 13.240 1.00 0.00 ATOM 311 OE2 GLU 40 15.956 37.593 11.815 1.00 0.00 ATOM 312 O GLU 40 19.343 35.375 16.619 1.00 0.00 ATOM 313 C GLU 40 18.765 34.384 16.169 1.00 0.00 ATOM 314 N GLY 41 19.106 33.124 16.440 1.00 0.00 ATOM 315 CA GLY 41 20.196 32.846 17.381 1.00 0.00 ATOM 316 O GLY 41 21.419 31.527 15.723 1.00 0.00 ATOM 317 C GLY 41 21.338 31.988 16.863 1.00 0.00 ATOM 318 N VAL 42 22.138 31.650 17.853 1.00 0.00 ATOM 319 CA VAL 42 23.239 30.681 17.725 1.00 0.00 ATOM 320 CB VAL 42 24.548 31.173 18.365 1.00 0.00 ATOM 321 CG1 VAL 42 24.987 32.434 17.635 1.00 0.00 ATOM 322 CG2 VAL 42 24.436 31.484 19.855 1.00 0.00 ATOM 323 O VAL 42 21.950 29.260 19.184 1.00 0.00 ATOM 324 C VAL 42 22.801 29.341 18.305 1.00 0.00 ATOM 325 N TRP 43 23.423 28.311 17.746 1.00 0.00 ATOM 326 CA TRP 43 22.995 26.921 17.956 1.00 0.00 ATOM 327 CB TRP 43 22.476 26.329 16.646 1.00 0.00 ATOM 328 CG TRP 43 21.256 27.057 16.115 1.00 0.00 ATOM 329 CD1 TRP 43 21.275 28.147 15.355 1.00 0.00 ATOM 330 CD2 TRP 43 19.926 26.695 16.304 1.00 0.00 ATOM 331 CE2 TRP 43 19.175 27.624 15.603 1.00 0.00 ATOM 332 CE3 TRP 43 19.317 25.685 16.995 1.00 0.00 ATOM 333 NE1 TRP 43 20.024 28.465 15.064 1.00 0.00 ATOM 334 CZ2 TRP 43 17.785 27.532 15.582 1.00 0.00 ATOM 335 CZ3 TRP 43 17.937 25.593 16.974 1.00 0.00 ATOM 336 CH2 TRP 43 17.186 26.521 16.273 1.00 0.00 ATOM 337 O TRP 43 25.295 26.204 18.158 1.00 0.00 ATOM 338 C TRP 43 24.115 26.023 18.468 1.00 0.00 ATOM 339 N THR 44 23.696 25.053 19.248 1.00 0.00 ATOM 340 CA THR 44 24.558 23.914 19.609 1.00 0.00 ATOM 341 CB THR 44 25.187 24.016 21.000 1.00 0.00 ATOM 342 CG2 THR 44 26.065 25.247 21.159 1.00 0.00 ATOM 343 OG1 THR 44 24.186 24.055 22.009 1.00 0.00 ATOM 344 O THR 44 22.580 22.571 19.639 1.00 0.00 ATOM 345 C THR 44 23.800 22.593 19.499 1.00 0.00 ATOM 346 N TYR 45 24.552 21.524 19.230 1.00 0.00 ATOM 347 CA TYR 45 23.964 20.173 19.171 1.00 0.00 ATOM 348 CB TYR 45 23.815 19.692 17.721 1.00 0.00 ATOM 349 CG TYR 45 23.448 18.221 17.591 1.00 0.00 ATOM 350 CD1 TYR 45 22.268 17.710 18.131 1.00 0.00 ATOM 351 CD2 TYR 45 24.319 17.352 16.953 1.00 0.00 ATOM 352 CE1 TYR 45 21.970 16.369 18.011 1.00 0.00 ATOM 353 CE2 TYR 45 24.011 16.012 16.813 1.00 0.00 ATOM 354 CZ TYR 45 22.832 15.510 17.342 1.00 0.00 ATOM 355 OH TYR 45 22.554 14.180 17.253 1.00 0.00 ATOM 356 O TYR 45 25.975 18.946 19.723 1.00 0.00 ATOM 357 C TYR 45 24.795 19.155 19.952 1.00 0.00 ATOM 358 N LYS 46 24.155 18.514 20.902 1.00 0.00 ATOM 359 CA LYS 46 24.906 17.546 21.703 1.00 0.00 ATOM 360 CB LYS 46 24.935 17.974 23.171 1.00 0.00 ATOM 361 CG LYS 46 25.672 19.281 23.431 1.00 0.00 ATOM 362 CD LYS 46 25.721 19.603 24.917 1.00 0.00 ATOM 363 CE LYS 46 26.467 20.902 25.179 1.00 0.00 ATOM 364 NZ LYS 46 26.604 21.182 26.634 1.00 0.00 ATOM 365 O LYS 46 23.148 15.903 21.952 1.00 0.00 ATOM 366 C LYS 46 24.288 16.165 21.553 1.00 0.00 ATOM 367 N ASP 47 24.990 15.375 20.764 1.00 0.00 ATOM 368 CA ASP 47 24.692 13.975 20.365 1.00 0.00 ATOM 369 CB ASP 47 25.860 13.382 19.574 1.00 0.00 ATOM 370 CG ASP 47 25.602 11.988 19.018 1.00 0.00 ATOM 371 OD1 ASP 47 24.694 11.842 18.236 1.00 0.00 ATOM 372 OD2 ASP 47 26.406 11.119 19.254 1.00 0.00 ATOM 373 O ASP 47 23.484 12.294 21.555 1.00 0.00 ATOM 374 C ASP 47 24.392 13.115 21.575 1.00 0.00 ATOM 375 N GLU 48 25.231 13.307 22.585 1.00 0.00 ATOM 376 CA GLU 48 25.172 12.497 23.816 1.00 0.00 ATOM 377 CB GLU 48 26.282 12.911 24.784 1.00 0.00 ATOM 378 CG GLU 48 27.682 12.513 24.342 1.00 0.00 ATOM 379 CD GLU 48 28.725 13.043 25.287 1.00 0.00 ATOM 380 OE1 GLU 48 28.368 13.748 26.200 1.00 0.00 ATOM 381 OE2 GLU 48 29.863 12.654 25.164 1.00 0.00 ATOM 382 O GLU 48 23.222 11.615 24.915 1.00 0.00 ATOM 383 C GLU 48 23.811 12.616 24.505 1.00 0.00 ATOM 384 N ILE 49 23.249 13.805 24.394 1.00 0.00 ATOM 385 CA ILE 49 22.008 14.113 25.113 1.00 0.00 ATOM 386 CB ILE 49 22.155 15.380 25.975 1.00 0.00 ATOM 387 CG1 ILE 49 22.459 16.594 25.094 1.00 0.00 ATOM 388 CG2 ILE 49 23.246 15.189 27.018 1.00 0.00 ATOM 389 CD1 ILE 49 22.385 17.914 25.827 1.00 0.00 ATOM 390 O ILE 49 19.678 14.470 24.531 1.00 0.00 ATOM 391 C ILE 49 20.829 14.301 24.122 1.00 0.00 ATOM 392 N LYS 50 21.120 14.241 22.822 1.00 0.00 ATOM 393 CA LYS 50 20.180 14.439 21.701 1.00 0.00 ATOM 394 CB LYS 50 19.272 13.218 21.541 1.00 0.00 ATOM 395 CG LYS 50 20.010 11.917 21.255 1.00 0.00 ATOM 396 CD LYS 50 19.040 10.766 21.040 1.00 0.00 ATOM 397 CE LYS 50 19.773 9.485 20.675 1.00 0.00 ATOM 398 NZ LYS 50 20.642 9.003 21.782 1.00 0.00 ATOM 399 O LYS 50 18.098 15.776 21.859 1.00 0.00 ATOM 400 C LYS 50 19.328 15.718 21.910 1.00 0.00 ATOM 401 N THR 51 20.087 16.769 22.210 1.00 0.00 ATOM 402 CA THR 51 19.524 18.108 22.479 1.00 0.00 ATOM 403 CB THR 51 19.623 18.499 23.969 1.00 0.00 ATOM 404 CG2 THR 51 19.090 19.889 24.318 1.00 0.00 ATOM 405 OG1 THR 51 18.984 17.529 24.809 1.00 0.00 ATOM 406 O THR 51 21.434 19.090 21.330 1.00 0.00 ATOM 407 C THR 51 20.233 19.149 21.609 1.00 0.00 ATOM 408 N PHE 52 19.373 20.027 21.118 1.00 0.00 ATOM 409 CA PHE 52 19.731 21.287 20.457 1.00 0.00 ATOM 410 CB PHE 52 18.971 21.435 19.138 1.00 0.00 ATOM 411 CG PHE 52 19.364 20.427 18.095 1.00 0.00 ATOM 412 CD1 PHE 52 18.886 19.126 18.153 1.00 0.00 ATOM 413 CD2 PHE 52 20.213 20.777 17.057 1.00 0.00 ATOM 414 CE1 PHE 52 19.248 18.198 17.195 1.00 0.00 ATOM 415 CE2 PHE 52 20.576 19.852 16.098 1.00 0.00 ATOM 416 CZ PHE 52 20.092 18.561 16.167 1.00 0.00 ATOM 417 O PHE 52 18.468 22.456 22.146 1.00 0.00 ATOM 418 C PHE 52 19.439 22.467 21.386 1.00 0.00 ATOM 419 N THR 53 20.277 23.479 21.276 1.00 0.00 ATOM 420 CA THR 53 20.115 24.739 22.026 1.00 0.00 ATOM 421 CB THR 53 21.144 24.901 23.156 1.00 0.00 ATOM 422 CG2 THR 53 20.951 26.181 23.975 1.00 0.00 ATOM 423 OG1 THR 53 21.075 23.781 24.037 1.00 0.00 ATOM 424 O THR 53 21.174 25.989 20.286 1.00 0.00 ATOM 425 C THR 53 20.224 25.918 21.065 1.00 0.00 ATOM 426 N VAL 54 19.292 26.837 21.244 1.00 0.00 ATOM 427 CA VAL 54 19.271 28.107 20.493 1.00 0.00 ATOM 428 CB VAL 54 18.011 28.184 19.622 1.00 0.00 ATOM 429 CG1 VAL 54 16.711 28.113 20.421 1.00 0.00 ATOM 430 CG2 VAL 54 18.050 29.454 18.762 1.00 0.00 ATOM 431 O VAL 54 18.608 29.267 22.492 1.00 0.00 ATOM 432 C VAL 54 19.329 29.257 21.493 1.00 0.00 ATOM 433 N THR 55 20.137 30.248 21.143 1.00 0.00 ATOM 434 CA THR 55 20.215 31.439 22.002 1.00 0.00 ATOM 435 CB THR 55 21.419 31.368 22.959 1.00 0.00 ATOM 436 CG2 THR 55 21.462 32.596 23.854 1.00 0.00 ATOM 437 OG1 THR 55 21.320 30.192 23.772 1.00 0.00 ATOM 438 O THR 55 21.074 32.799 20.212 1.00 0.00 ATOM 439 C THR 55 20.314 32.719 21.181 1.00 0.00 ATOM 440 N GLU 56 19.362 33.577 21.490 1.00 0.00 ATOM 441 CA GLU 56 19.420 34.977 21.050 1.00 0.00 ATOM 442 CB GLU 56 18.010 35.529 20.831 1.00 0.00 ATOM 443 CG GLU 56 17.255 34.886 19.677 1.00 0.00 ATOM 444 CD GLU 56 15.883 35.481 19.524 1.00 0.00 ATOM 445 OE1 GLU 56 15.541 36.347 20.294 1.00 0.00 ATOM 446 OE2 GLU 56 15.217 35.153 18.570 1.00 0.00 ATOM 447 O GLU 56 20.689 35.270 23.070 1.00 0.00 ATOM 448 C GLU 56 20.178 35.839 22.070 1.00 0.00 TER END