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 4 Tue Jul 15 16:01:45 2008 MODEL 4 PARENT 2i38_A 2i2y_A 1ibx_B 1pn5_A 2cwb_A REMARK 7 REMARK 7 ALLPARENTS 2i38_A 2i2y_A 1ibx_B 1pn5_A 2cwb_A 1pgx_A 2igg_A REMARK 7 ALLPARENTS 1pgb_A 2igd_A 2igh_A 2qmt_A ATOM 1 N THR 1 13.967 8.956 16.312 1.00 0.00 ATOM 2 CA THR 1 14.472 9.281 17.648 1.00 0.00 ATOM 3 CB THR 1 16.010 9.346 17.670 1.00 0.00 ATOM 4 CG2 THR 1 16.509 9.702 19.062 1.00 0.00 ATOM 5 OG1 THR 1 16.550 8.076 17.283 1.00 0.00 ATOM 6 O THR 1 13.622 11.476 17.237 1.00 0.00 ATOM 7 C THR 1 13.870 10.611 18.069 1.00 0.00 ATOM 8 N THR 2 13.688 10.726 19.382 1.00 0.00 ATOM 9 CA THR 2 13.233 11.991 19.960 1.00 0.00 ATOM 10 CB THR 2 12.466 11.743 21.245 1.00 0.00 ATOM 11 CG2 THR 2 12.005 13.045 21.901 1.00 0.00 ATOM 12 OG1 THR 2 11.343 10.974 20.856 1.00 0.00 ATOM 13 O THR 2 15.485 12.536 20.637 1.00 0.00 ATOM 14 C THR 2 14.404 12.929 20.211 1.00 0.00 ATOM 15 N TYR 3 14.160 14.174 19.843 1.00 0.00 ATOM 16 CA TYR 3 15.144 15.236 20.087 1.00 0.00 ATOM 17 CB TYR 3 15.755 15.712 18.768 1.00 0.00 ATOM 18 CG TYR 3 16.528 14.642 18.028 1.00 0.00 ATOM 19 CD1 TYR 3 15.898 13.815 17.110 1.00 0.00 ATOM 20 CD2 TYR 3 17.885 14.466 18.249 1.00 0.00 ATOM 21 CE1 TYR 3 16.599 12.836 16.433 1.00 0.00 ATOM 22 CE2 TYR 3 18.597 13.490 17.577 1.00 0.00 ATOM 23 CZ TYR 3 17.950 12.677 16.668 1.00 0.00 ATOM 24 OH TYR 3 18.653 11.704 15.996 1.00 0.00 ATOM 25 O TYR 3 13.275 16.629 20.669 1.00 0.00 ATOM 26 C TYR 3 14.474 16.387 20.826 1.00 0.00 ATOM 27 N LYS 4 15.294 17.065 21.611 1.00 0.00 ATOM 28 CA LYS 4 14.838 18.223 22.391 1.00 0.00 ATOM 29 CB LYS 4 15.132 18.017 23.878 1.00 0.00 ATOM 30 CG LYS 4 14.634 19.139 24.779 1.00 0.00 ATOM 31 CD LYS 4 14.983 18.874 26.236 1.00 0.00 ATOM 32 CE LYS 4 14.142 17.743 26.811 1.00 0.00 ATOM 33 NZ LYS 4 14.476 17.470 28.235 1.00 0.00 ATOM 34 O LYS 4 16.620 19.461 21.342 1.00 0.00 ATOM 35 C LYS 4 15.512 19.497 21.874 1.00 0.00 ATOM 36 N LEU 5 14.752 20.585 21.931 1.00 0.00 ATOM 37 CA LEU 5 15.232 21.933 21.618 1.00 0.00 ATOM 38 CB LEU 5 14.514 22.477 20.376 1.00 0.00 ATOM 39 CG LEU 5 15.042 23.818 19.852 1.00 0.00 ATOM 40 CD1 LEU 5 16.465 23.653 19.335 1.00 0.00 ATOM 41 CD2 LEU 5 14.125 24.331 18.751 1.00 0.00 ATOM 42 O LEU 5 13.895 22.894 23.361 1.00 0.00 ATOM 43 C LEU 5 15.007 22.822 22.839 1.00 0.00 ATOM 44 N ILE 6 16.085 23.472 23.243 1.00 0.00 ATOM 45 CA ILE 6 16.026 24.473 24.319 1.00 0.00 ATOM 46 CB ILE 6 17.066 24.185 25.417 1.00 0.00 ATOM 47 CG1 ILE 6 16.811 22.813 26.047 1.00 0.00 ATOM 48 CG2 ILE 6 17.037 25.274 26.477 1.00 0.00 ATOM 49 CD1 ILE 6 17.907 22.358 26.984 1.00 0.00 ATOM 50 O ILE 6 17.258 26.093 23.001 1.00 0.00 ATOM 51 C ILE 6 16.262 25.842 23.671 1.00 0.00 ATOM 52 N LEU 7 15.230 26.662 23.809 1.00 0.00 ATOM 53 CA LEU 7 15.229 28.029 23.269 1.00 0.00 ATOM 54 CB LEU 7 13.867 28.347 22.638 1.00 0.00 ATOM 55 CG LEU 7 13.548 27.577 21.350 1.00 0.00 ATOM 56 CD1 LEU 7 13.121 26.154 21.686 1.00 0.00 ATOM 57 CD2 LEU 7 12.453 28.301 20.582 1.00 0.00 ATOM 58 O LEU 7 14.939 29.040 25.441 1.00 0.00 ATOM 59 C LEU 7 15.567 29.015 24.382 1.00 0.00 ATOM 60 N ASN 8 16.608 29.777 24.099 1.00 0.00 ATOM 61 CA ASN 8 16.975 30.929 24.924 1.00 0.00 ATOM 62 CB ASN 8 18.307 30.713 25.620 1.00 0.00 ATOM 63 CG ASN 8 18.316 29.540 26.559 1.00 0.00 ATOM 64 ND2 ASN 8 19.090 28.544 26.212 1.00 0.00 ATOM 65 OD1 ASN 8 17.686 29.565 27.623 1.00 0.00 ATOM 66 O ASN 8 18.029 32.599 23.530 1.00 0.00 ATOM 67 C ASN 8 16.999 32.176 24.048 1.00 0.00 ATOM 68 N LEU 9 15.791 32.604 23.734 1.00 0.00 ATOM 69 CA LEU 9 15.618 33.793 22.877 1.00 0.00 ATOM 70 CB LEU 9 14.407 33.622 21.970 1.00 0.00 ATOM 71 CG LEU 9 14.460 32.223 21.424 1.00 0.00 ATOM 72 CD1 LEU 9 13.101 31.980 20.831 1.00 0.00 ATOM 73 CD2 LEU 9 15.731 31.944 20.638 1.00 0.00 ATOM 74 O LEU 9 14.700 34.846 24.777 1.00 0.00 ATOM 75 C LEU 9 15.305 34.993 23.717 1.00 0.00 ATOM 76 N LYS 10 15.425 36.129 23.064 1.00 0.00 ATOM 77 CA LYS 10 15.091 37.398 23.698 1.00 0.00 ATOM 78 CB LYS 10 15.362 38.562 22.744 1.00 0.00 ATOM 79 CG LYS 10 16.838 38.832 22.483 1.00 0.00 ATOM 80 CD LYS 10 17.027 40.001 21.528 1.00 0.00 ATOM 81 CE LYS 10 18.502 40.259 21.253 1.00 0.00 ATOM 82 NZ LYS 10 18.701 41.379 20.294 1.00 0.00 ATOM 83 O LYS 10 13.300 37.969 25.231 1.00 0.00 ATOM 84 C LYS 10 13.612 37.434 24.165 1.00 0.00 ATOM 85 N GLN 11 12.733 36.849 23.364 1.00 0.00 ATOM 86 CA GLN 11 11.283 36.845 23.662 1.00 0.00 ATOM 87 CB GLN 11 10.492 37.413 22.481 1.00 0.00 ATOM 88 CG GLN 11 10.859 38.840 22.114 1.00 0.00 ATOM 89 CD GLN 11 10.537 39.824 23.223 1.00 0.00 ATOM 90 OE1 GLN 11 9.455 39.782 23.815 1.00 0.00 ATOM 91 NE2 GLN 11 11.475 40.720 23.508 1.00 0.00 ATOM 92 O GLN 11 9.667 35.408 24.654 1.00 0.00 ATOM 93 C GLN 11 10.704 35.479 23.995 1.00 0.00 ATOM 94 N ALA 12 11.239 34.456 23.335 1.00 0.00 ATOM 95 CA ALA 12 10.724 33.092 23.512 1.00 0.00 ATOM 96 CB ALA 12 10.103 32.558 22.220 1.00 0.00 ATOM 97 O ALA 12 12.714 31.630 23.552 1.00 0.00 ATOM 98 C ALA 12 11.766 32.138 24.117 1.00 0.00 ATOM 99 N LYS 13 11.496 31.765 25.338 1.00 0.00 ATOM 100 CA LYS 13 12.372 30.817 26.043 1.00 0.00 ATOM 101 CB LYS 13 12.946 31.457 27.308 1.00 0.00 ATOM 102 CG LYS 13 13.886 32.627 27.050 1.00 0.00 ATOM 103 CD LYS 13 14.448 33.182 28.351 1.00 0.00 ATOM 104 CE LYS 13 15.405 34.336 28.093 1.00 0.00 ATOM 105 NZ LYS 13 15.984 34.871 29.354 1.00 0.00 ATOM 106 O LYS 13 10.343 29.726 26.441 1.00 0.00 ATOM 107 C LYS 13 11.560 29.567 26.362 1.00 0.00 ATOM 108 N GLU 14 12.243 28.418 26.436 1.00 0.00 ATOM 109 CA GLU 14 11.699 27.120 26.921 1.00 0.00 ATOM 110 CB GLU 14 10.174 27.100 26.800 1.00 0.00 ATOM 111 CG GLU 14 9.656 27.170 25.371 1.00 0.00 ATOM 112 CD GLU 14 8.153 27.209 25.337 1.00 0.00 ATOM 113 OE1 GLU 14 7.553 27.215 26.385 1.00 0.00 ATOM 114 OE2 GLU 14 7.606 27.348 24.268 1.00 0.00 ATOM 115 O GLU 14 13.375 25.920 25.663 1.00 0.00 ATOM 116 C GLU 14 12.262 25.895 26.190 1.00 0.00 ATOM 117 N GLU 15 11.435 24.860 26.117 1.00 0.00 ATOM 118 CA GLU 15 11.787 23.561 25.563 1.00 0.00 ATOM 119 CB GLU 15 12.182 22.592 26.679 1.00 0.00 ATOM 120 CG GLU 15 11.064 22.275 27.662 1.00 0.00 ATOM 121 CD GLU 15 11.532 21.332 28.736 1.00 0.00 ATOM 122 OE1 GLU 15 12.692 20.997 28.741 1.00 0.00 ATOM 123 OE2 GLU 15 10.759 21.034 29.615 1.00 0.00 ATOM 124 O GLU 15 9.452 23.296 24.972 1.00 0.00 ATOM 125 C GLU 15 10.631 22.994 24.753 1.00 0.00 ATOM 126 N ALA 16 11.037 22.364 23.676 1.00 0.00 ATOM 127 CA ALA 16 10.137 21.642 22.788 1.00 0.00 ATOM 128 CB ALA 16 9.778 22.604 21.656 1.00 0.00 ATOM 129 O ALA 16 12.071 20.226 22.480 1.00 0.00 ATOM 130 C ALA 16 10.855 20.379 22.319 1.00 0.00 ATOM 131 N ILE 17 10.088 19.435 21.800 1.00 0.00 ATOM 132 CA ILE 17 10.645 18.155 21.304 1.00 0.00 ATOM 133 CB ILE 17 10.364 16.999 22.282 1.00 0.00 ATOM 134 CG1 ILE 17 8.856 16.816 22.473 1.00 0.00 ATOM 135 CG2 ILE 17 11.046 17.255 23.617 1.00 0.00 ATOM 136 CD1 ILE 17 8.486 15.581 23.262 1.00 0.00 ATOM 137 O ILE 17 9.005 18.243 19.565 1.00 0.00 ATOM 138 C ILE 17 10.087 17.782 19.932 1.00 0.00 ATOM 139 N LYS 18 10.841 16.986 19.192 1.00 0.00 ATOM 140 CA LYS 18 10.394 16.407 17.910 1.00 0.00 ATOM 141 CB LYS 18 10.518 17.436 16.785 1.00 0.00 ATOM 142 CG LYS 18 9.927 16.988 15.455 1.00 0.00 ATOM 143 CD LYS 18 8.406 17.000 15.492 1.00 0.00 ATOM 144 CE LYS 18 7.816 16.505 14.180 1.00 0.00 ATOM 145 NZ LYS 18 6.329 16.462 14.220 1.00 0.00 ATOM 146 O LYS 18 12.242 14.879 17.871 1.00 0.00 ATOM 147 C LYS 18 11.117 15.154 17.461 1.00 0.00 ATOM 148 N GLU 19 10.341 14.337 16.762 1.00 0.00 ATOM 149 CA GLU 19 10.800 13.016 16.296 1.00 0.00 ATOM 150 CB GLU 19 9.656 12.001 16.351 1.00 0.00 ATOM 151 CG GLU 19 9.167 11.681 17.757 1.00 0.00 ATOM 152 CD GLU 19 8.034 10.693 17.729 1.00 0.00 ATOM 153 OE1 GLU 19 7.642 10.297 16.657 1.00 0.00 ATOM 154 OE2 GLU 19 7.634 10.248 18.779 1.00 0.00 ATOM 155 O GLU 19 10.690 13.756 14.024 1.00 0.00 ATOM 156 C GLU 19 11.340 13.177 14.895 1.00 0.00 ATOM 157 N ALA 20 12.519 12.600 14.736 1.00 0.00 ATOM 158 CA ALA 20 13.224 12.633 13.455 1.00 0.00 ATOM 159 CB ALA 20 14.097 13.873 13.381 1.00 0.00 ATOM 160 O ALA 20 14.509 10.789 14.291 1.00 0.00 ATOM 161 C ALA 20 14.097 11.393 13.300 1.00 0.00 ATOM 162 N VAL 21 14.334 11.022 12.057 1.00 0.00 ATOM 163 CA VAL 21 15.158 9.845 11.766 1.00 0.00 ATOM 164 CB VAL 21 15.065 9.442 10.283 1.00 0.00 ATOM 165 CG1 VAL 21 16.057 8.331 9.969 1.00 0.00 ATOM 166 CG2 VAL 21 13.650 9.002 9.937 1.00 0.00 ATOM 167 O VAL 21 17.284 9.074 12.568 1.00 0.00 ATOM 168 C VAL 21 16.653 10.037 12.111 1.00 0.00 ATOM 169 N ASP 22 17.123 11.270 12.118 1.00 0.00 ATOM 170 CA ASP 22 18.515 11.593 12.508 1.00 0.00 ATOM 171 CB ASP 22 19.482 11.260 11.370 1.00 0.00 ATOM 172 CG ASP 22 19.288 12.099 10.114 1.00 0.00 ATOM 173 OD1 ASP 22 18.620 13.103 10.191 1.00 0.00 ATOM 174 OD2 ASP 22 19.933 11.820 9.132 1.00 0.00 ATOM 175 O ASP 22 17.660 13.828 12.837 1.00 0.00 ATOM 176 C ASP 22 18.637 13.062 12.897 1.00 0.00 ATOM 177 N ALA 23 19.823 13.400 13.407 1.00 0.00 ATOM 178 CA ALA 23 20.074 14.746 13.943 1.00 0.00 ATOM 179 CB ALA 23 21.366 14.784 14.743 1.00 0.00 ATOM 180 O ALA 23 19.410 16.897 13.154 1.00 0.00 ATOM 181 C ALA 23 20.028 15.859 12.882 1.00 0.00 ATOM 182 N GLY 24 20.492 15.574 11.665 1.00 0.00 ATOM 183 CA GLY 24 20.419 16.520 10.538 1.00 0.00 ATOM 184 O GLY 24 18.605 18.070 10.120 1.00 0.00 ATOM 185 C GLY 24 18.967 16.895 10.207 1.00 0.00 ATOM 186 N THR 25 18.102 15.880 10.203 1.00 0.00 ATOM 187 CA THR 25 16.659 16.073 9.946 1.00 0.00 ATOM 188 CB THR 25 15.926 14.727 9.796 1.00 0.00 ATOM 189 CG2 THR 25 14.436 14.951 9.588 1.00 0.00 ATOM 190 OG1 THR 25 16.460 14.012 8.673 1.00 0.00 ATOM 191 O THR 25 15.275 17.838 10.806 1.00 0.00 ATOM 192 C THR 25 16.001 16.881 11.073 1.00 0.00 ATOM 193 N ALA 26 16.299 16.491 12.305 1.00 0.00 ATOM 194 CA ALA 26 15.789 17.201 13.502 1.00 0.00 ATOM 195 CB ALA 26 16.262 16.505 14.785 1.00 0.00 ATOM 196 O ALA 26 15.425 19.536 13.887 1.00 0.00 ATOM 197 C ALA 26 16.230 18.672 13.553 1.00 0.00 ATOM 198 N GLU 27 17.440 18.925 13.037 1.00 0.00 ATOM 199 CA GLU 27 17.995 20.289 12.938 1.00 0.00 ATOM 200 CB GLU 27 19.443 20.244 12.442 1.00 0.00 ATOM 201 CG GLU 27 20.121 21.603 12.360 1.00 0.00 ATOM 202 CD GLU 27 21.549 21.474 11.909 1.00 0.00 ATOM 203 OE1 GLU 27 21.984 20.371 11.683 1.00 0.00 ATOM 204 OE2 GLU 27 22.173 22.484 11.680 1.00 0.00 ATOM 205 O GLU 27 16.793 22.295 12.376 1.00 0.00 ATOM 206 C GLU 27 17.157 21.176 12.011 1.00 0.00 ATOM 207 N LYS 28 16.812 20.635 10.855 1.00 0.00 ATOM 208 CA LYS 28 15.997 21.371 9.859 1.00 0.00 ATOM 209 CB LYS 28 15.823 20.539 8.588 1.00 0.00 ATOM 210 CG LYS 28 15.033 21.231 7.485 1.00 0.00 ATOM 211 CD LYS 28 14.965 20.374 6.230 1.00 0.00 ATOM 212 CE LYS 28 14.140 21.047 5.143 1.00 0.00 ATOM 213 NZ LYS 28 14.045 20.208 3.917 1.00 0.00 ATOM 214 O LYS 28 14.213 22.903 10.372 1.00 0.00 ATOM 215 C LYS 28 14.628 21.746 10.439 1.00 0.00 ATOM 216 N TYR 29 13.993 20.749 11.062 1.00 0.00 ATOM 217 CA TYR 29 12.665 20.944 11.653 1.00 0.00 ATOM 218 CB TYR 29 12.127 19.623 12.208 1.00 0.00 ATOM 219 CG TYR 29 11.783 18.606 11.143 1.00 0.00 ATOM 220 CD1 TYR 29 11.660 18.980 9.812 1.00 0.00 ATOM 221 CD2 TYR 29 11.586 17.273 11.470 1.00 0.00 ATOM 222 CE1 TYR 29 11.346 18.055 8.835 1.00 0.00 ATOM 223 CE2 TYR 29 11.273 16.338 10.502 1.00 0.00 ATOM 224 CZ TYR 29 11.153 16.733 9.185 1.00 0.00 ATOM 225 OH TYR 29 10.842 15.807 8.216 1.00 0.00 ATOM 226 O TYR 29 11.959 22.980 12.711 1.00 0.00 ATOM 227 C TYR 29 12.700 22.007 12.765 1.00 0.00 ATOM 228 N PHE 30 13.674 21.874 13.671 1.00 0.00 ATOM 229 CA PHE 30 13.861 22.853 14.759 1.00 0.00 ATOM 230 CB PHE 30 14.937 22.371 15.733 1.00 0.00 ATOM 231 CG PHE 30 14.458 21.315 16.689 1.00 0.00 ATOM 232 CD1 PHE 30 15.301 20.289 17.090 1.00 0.00 ATOM 233 CD2 PHE 30 13.165 21.344 17.189 1.00 0.00 ATOM 234 CE1 PHE 30 14.861 19.316 17.969 1.00 0.00 ATOM 235 CE2 PHE 30 12.723 20.375 18.068 1.00 0.00 ATOM 236 CZ PHE 30 13.574 19.359 18.458 1.00 0.00 ATOM 237 O PHE 30 13.669 25.231 14.804 1.00 0.00 ATOM 238 C PHE 30 14.235 24.259 14.301 1.00 0.00 ATOM 239 N LYS 31 15.090 24.342 13.287 1.00 0.00 ATOM 240 CA LYS 31 15.375 25.654 12.690 1.00 0.00 ATOM 241 CB LYS 31 16.415 25.522 11.576 1.00 0.00 ATOM 242 CG LYS 31 17.846 25.349 12.069 1.00 0.00 ATOM 243 CD LYS 31 18.842 25.454 10.924 1.00 0.00 ATOM 244 CE LYS 31 20.270 25.260 11.411 1.00 0.00 ATOM 245 NZ LYS 31 21.253 25.325 10.296 1.00 0.00 ATOM 246 O LYS 31 13.850 27.484 12.424 1.00 0.00 ATOM 247 C LYS 31 14.097 26.306 12.144 1.00 0.00 ATOM 248 N LEU 32 13.299 25.526 11.417 1.00 0.00 ATOM 249 CA LEU 32 11.990 26.028 10.954 1.00 0.00 ATOM 250 CB LEU 32 11.289 24.968 10.096 1.00 0.00 ATOM 251 CG LEU 32 11.933 24.704 8.728 1.00 0.00 ATOM 252 CD1 LEU 32 11.262 23.514 8.056 1.00 0.00 ATOM 253 CD2 LEU 32 11.817 25.949 7.863 1.00 0.00 ATOM 254 O LEU 32 10.471 27.500 12.033 1.00 0.00 ATOM 255 C LEU 32 11.069 26.442 12.109 1.00 0.00 ATOM 256 N ILE 33 11.056 25.674 13.194 1.00 0.00 ATOM 257 CA ILE 33 10.248 26.022 14.381 1.00 0.00 ATOM 258 CB ILE 33 10.339 24.933 15.466 1.00 0.00 ATOM 259 CG1 ILE 33 9.660 23.647 14.989 1.00 0.00 ATOM 260 CG2 ILE 33 9.711 25.420 16.763 1.00 0.00 ATOM 261 CD1 ILE 33 9.931 22.449 15.871 1.00 0.00 ATOM 262 O ILE 33 9.882 28.249 15.203 1.00 0.00 ATOM 263 C ILE 33 10.714 27.374 14.959 1.00 0.00 ATOM 264 N ALA 34 12.014 27.524 15.103 1.00 0.00 ATOM 265 CA ALA 34 12.592 28.778 15.627 1.00 0.00 ATOM 266 CB ALA 34 14.099 28.654 15.725 1.00 0.00 ATOM 267 O ALA 34 11.693 30.948 15.153 1.00 0.00 ATOM 268 C ALA 34 12.276 29.969 14.719 1.00 0.00 ATOM 269 N ASN 35 12.450 29.755 13.415 1.00 0.00 ATOM 270 CA ASN 35 12.090 30.780 12.425 1.00 0.00 ATOM 271 CB ASN 35 12.399 30.340 11.017 1.00 0.00 ATOM 272 CG ASN 35 13.886 30.266 10.717 1.00 0.00 ATOM 273 ND2 ASN 35 14.177 29.473 9.724 1.00 0.00 ATOM 274 OD1 ASN 35 14.775 30.851 11.336 1.00 0.00 ATOM 275 O ASN 35 10.263 32.260 12.659 1.00 0.00 ATOM 276 C ASN 35 10.599 31.099 12.452 1.00 0.00 ATOM 277 N ALA 36 9.771 30.068 12.528 1.00 0.00 ATOM 278 CA ALA 36 8.307 30.218 12.599 1.00 0.00 ATOM 279 CB ALA 36 7.628 28.854 12.574 1.00 0.00 ATOM 280 O ALA 36 6.721 31.523 13.889 1.00 0.00 ATOM 281 C ALA 36 7.846 31.028 13.834 1.00 0.00 ATOM 282 N LYS 37 8.676 30.976 14.874 1.00 0.00 ATOM 283 CA LYS 37 8.398 31.669 16.139 1.00 0.00 ATOM 284 CB LYS 37 8.585 30.719 17.323 1.00 0.00 ATOM 285 CG LYS 37 7.613 29.546 17.348 1.00 0.00 ATOM 286 CD LYS 37 7.833 28.670 18.572 1.00 0.00 ATOM 287 CE LYS 37 6.889 27.477 18.577 1.00 0.00 ATOM 288 NZ LYS 37 7.085 26.618 19.776 1.00 0.00 ATOM 289 O LYS 37 9.381 33.395 17.501 1.00 0.00 ATOM 290 C LYS 37 9.269 32.917 16.365 1.00 0.00 ATOM 291 N THR 38 9.904 33.372 15.297 1.00 0.00 ATOM 292 CA THR 38 10.562 34.689 15.223 1.00 0.00 ATOM 293 CB THR 38 9.617 35.819 15.672 1.00 0.00 ATOM 294 CG2 THR 38 10.252 37.177 15.419 1.00 0.00 ATOM 295 OG1 THR 38 8.383 35.730 14.947 1.00 0.00 ATOM 296 O THR 38 12.285 35.826 16.527 1.00 0.00 ATOM 297 C THR 38 11.849 34.772 16.079 1.00 0.00 ATOM 298 N VAL 39 12.587 33.660 16.003 1.00 0.00 ATOM 299 CA VAL 39 13.872 33.401 16.674 1.00 0.00 ATOM 300 CB VAL 39 13.843 31.941 17.139 1.00 0.00 ATOM 301 CG1 VAL 39 15.175 31.342 17.608 1.00 0.00 ATOM 302 CG2 VAL 39 12.556 31.586 17.867 1.00 0.00 ATOM 303 O VAL 39 14.830 32.508 14.664 1.00 0.00 ATOM 304 C VAL 39 14.907 33.363 15.558 1.00 0.00 ATOM 305 N GLU 40 16.030 33.981 15.876 1.00 0.00 ATOM 306 CA GLU 40 17.234 33.866 15.053 1.00 0.00 ATOM 307 CB GLU 40 17.225 34.917 13.941 1.00 0.00 ATOM 308 CG GLU 40 18.440 34.873 13.024 1.00 0.00 ATOM 309 CD GLU 40 18.310 35.861 11.898 1.00 0.00 ATOM 310 OE1 GLU 40 17.305 36.526 11.830 1.00 0.00 ATOM 311 OE2 GLU 40 19.261 36.030 11.172 1.00 0.00 ATOM 312 O GLU 40 18.836 35.126 16.319 1.00 0.00 ATOM 313 C GLU 40 18.453 34.017 15.967 1.00 0.00 ATOM 314 N GLY 41 19.041 32.872 16.268 1.00 0.00 ATOM 315 CA GLY 41 20.172 32.837 17.199 1.00 0.00 ATOM 316 O GLY 41 21.317 31.303 15.695 1.00 0.00 ATOM 317 C GLY 41 21.282 31.857 16.802 1.00 0.00 ATOM 318 N VAL 42 22.140 31.649 17.779 1.00 0.00 ATOM 319 CA VAL 42 23.218 30.659 17.673 1.00 0.00 ATOM 320 CB VAL 42 24.450 31.029 18.515 1.00 0.00 ATOM 321 CG1 VAL 42 25.043 32.374 18.083 1.00 0.00 ATOM 322 CG2 VAL 42 24.101 31.032 20.003 1.00 0.00 ATOM 323 O VAL 42 21.673 29.174 18.783 1.00 0.00 ATOM 324 C VAL 42 22.661 29.287 18.059 1.00 0.00 ATOM 325 N TRP 43 23.325 28.259 17.561 1.00 0.00 ATOM 326 CA TRP 43 22.850 26.878 17.711 1.00 0.00 ATOM 327 CB TRP 43 22.346 26.360 16.356 1.00 0.00 ATOM 328 CG TRP 43 21.273 27.258 15.738 1.00 0.00 ATOM 329 CD1 TRP 43 21.453 28.329 14.977 1.00 0.00 ATOM 330 CD2 TRP 43 19.913 27.073 15.881 1.00 0.00 ATOM 331 CE2 TRP 43 19.315 28.091 15.173 1.00 0.00 ATOM 332 CE3 TRP 43 19.184 26.105 16.547 1.00 0.00 ATOM 333 NE1 TRP 43 20.268 28.832 14.638 1.00 0.00 ATOM 334 CZ2 TRP 43 17.933 28.162 15.123 1.00 0.00 ATOM 335 CZ3 TRP 43 17.802 26.168 16.491 1.00 0.00 ATOM 336 CH2 TRP 43 17.190 27.197 15.785 1.00 0.00 ATOM 337 O TRP 43 25.116 25.980 17.786 1.00 0.00 ATOM 338 C TRP 43 23.964 25.938 18.193 1.00 0.00 ATOM 339 N THR 44 23.533 25.061 19.079 1.00 0.00 ATOM 340 CA THR 44 24.362 23.895 19.438 1.00 0.00 ATOM 341 CB THR 44 24.931 24.024 20.864 1.00 0.00 ATOM 342 CG2 THR 44 25.767 25.288 20.992 1.00 0.00 ATOM 343 OG1 THR 44 23.854 24.069 21.809 1.00 0.00 ATOM 344 O THR 44 22.304 22.634 19.463 1.00 0.00 ATOM 345 C THR 44 23.531 22.619 19.324 1.00 0.00 ATOM 346 N TYR 45 24.247 21.519 19.141 1.00 0.00 ATOM 347 CA TYR 45 23.642 20.199 19.266 1.00 0.00 ATOM 348 CB TYR 45 23.084 19.700 17.934 1.00 0.00 ATOM 349 CG TYR 45 24.115 19.370 16.851 1.00 0.00 ATOM 350 CD1 TYR 45 24.474 18.040 16.705 1.00 0.00 ATOM 351 CD2 TYR 45 24.760 20.353 16.121 1.00 0.00 ATOM 352 CE1 TYR 45 25.482 17.685 15.836 1.00 0.00 ATOM 353 CE2 TYR 45 25.773 20.007 15.242 1.00 0.00 ATOM 354 CZ TYR 45 26.136 18.670 15.102 1.00 0.00 ATOM 355 OH TYR 45 27.006 18.275 14.157 1.00 0.00 ATOM 356 O TYR 45 25.738 19.010 19.557 1.00 0.00 ATOM 357 C TYR 45 24.576 19.188 19.922 1.00 0.00 ATOM 358 N LYS 46 24.088 18.717 21.071 1.00 0.00 ATOM 359 CA LYS 46 24.772 17.683 21.843 1.00 0.00 ATOM 360 CB LYS 46 24.774 18.040 23.331 1.00 0.00 ATOM 361 CG LYS 46 25.512 17.044 24.215 1.00 0.00 ATOM 362 CD LYS 46 25.527 17.497 25.667 1.00 0.00 ATOM 363 CE LYS 46 26.270 16.505 26.550 1.00 0.00 ATOM 364 NZ LYS 46 27.704 16.392 26.175 1.00 0.00 ATOM 365 O LYS 46 22.960 16.093 22.057 1.00 0.00 ATOM 366 C LYS 46 24.076 16.345 21.588 1.00 0.00 ATOM 367 N ASP 47 24.847 15.469 20.973 1.00 0.00 ATOM 368 CA ASP 47 24.384 14.117 20.612 1.00 0.00 ATOM 369 CB ASP 47 25.371 13.451 19.649 1.00 0.00 ATOM 370 CG ASP 47 25.341 14.011 18.234 1.00 0.00 ATOM 371 OD1 ASP 47 24.424 14.730 17.918 1.00 0.00 ATOM 372 OD2 ASP 47 26.311 13.846 17.531 1.00 0.00 ATOM 373 O ASP 47 23.156 12.550 21.930 1.00 0.00 ATOM 374 C ASP 47 24.183 13.215 21.823 1.00 0.00 ATOM 375 N GLU 48 24.995 13.462 22.836 1.00 0.00 ATOM 376 CA GLU 48 24.892 12.676 24.081 1.00 0.00 ATOM 377 CB GLU 48 26.057 13.048 24.983 1.00 0.00 ATOM 378 CG GLU 48 27.421 12.554 24.496 1.00 0.00 ATOM 379 CD GLU 48 28.518 12.979 25.472 1.00 0.00 ATOM 380 OE1 GLU 48 28.184 13.654 26.481 1.00 0.00 ATOM 381 OE2 GLU 48 29.689 12.701 25.133 1.00 0.00 ATOM 382 O GLU 48 23.000 11.856 25.380 1.00 0.00 ATOM 383 C GLU 48 23.514 12.797 24.773 1.00 0.00 ATOM 384 N ILE 49 22.876 13.943 24.579 1.00 0.00 ATOM 385 CA ILE 49 21.548 14.190 25.185 1.00 0.00 ATOM 386 CB ILE 49 21.552 15.395 26.130 1.00 0.00 ATOM 387 CG1 ILE 49 21.959 16.701 25.434 1.00 0.00 ATOM 388 CG2 ILE 49 22.512 15.152 27.288 1.00 0.00 ATOM 389 CD1 ILE 49 21.828 17.942 26.321 1.00 0.00 ATOM 390 O ILE 49 19.261 14.574 24.542 1.00 0.00 ATOM 391 C ILE 49 20.418 14.350 24.154 1.00 0.00 ATOM 392 N LYS 50 20.792 14.242 22.882 1.00 0.00 ATOM 393 CA LYS 50 19.904 14.427 21.715 1.00 0.00 ATOM 394 CB LYS 50 18.902 13.276 21.617 1.00 0.00 ATOM 395 CG LYS 50 19.536 11.893 21.561 1.00 0.00 ATOM 396 CD LYS 50 20.365 11.714 20.298 1.00 0.00 ATOM 397 CE LYS 50 20.985 10.326 20.234 1.00 0.00 ATOM 398 NZ LYS 50 21.913 10.184 19.079 1.00 0.00 ATOM 399 O LYS 50 17.953 15.906 21.795 1.00 0.00 ATOM 400 C LYS 50 19.179 15.798 21.841 1.00 0.00 ATOM 401 N THR 51 19.974 16.814 22.199 1.00 0.00 ATOM 402 CA THR 51 19.453 18.169 22.500 1.00 0.00 ATOM 403 CB THR 51 19.528 18.472 24.010 1.00 0.00 ATOM 404 CG2 THR 51 19.029 19.860 24.428 1.00 0.00 ATOM 405 OG1 THR 51 18.825 17.471 24.747 1.00 0.00 ATOM 406 O THR 51 21.412 19.347 21.723 1.00 0.00 ATOM 407 C THR 51 20.183 19.238 21.685 1.00 0.00 ATOM 408 N PHE 52 19.334 20.063 21.094 1.00 0.00 ATOM 409 CA PHE 52 19.714 21.292 20.380 1.00 0.00 ATOM 410 CB PHE 52 18.894 21.445 19.097 1.00 0.00 ATOM 411 CG PHE 52 19.396 20.563 17.964 1.00 0.00 ATOM 412 CD1 PHE 52 19.047 19.220 17.918 1.00 0.00 ATOM 413 CD2 PHE 52 20.191 21.118 16.966 1.00 0.00 ATOM 414 CE1 PHE 52 19.534 18.410 16.900 1.00 0.00 ATOM 415 CE2 PHE 52 20.665 20.311 15.944 1.00 0.00 ATOM 416 CZ PHE 52 20.348 18.957 15.911 1.00 0.00 ATOM 417 O PHE 52 18.412 22.471 22.021 1.00 0.00 ATOM 418 C PHE 52 19.378 22.493 21.249 1.00 0.00 ATOM 419 N THR 53 20.203 23.514 21.123 1.00 0.00 ATOM 420 CA THR 53 19.949 24.804 21.781 1.00 0.00 ATOM 421 CB THR 53 20.926 25.047 22.946 1.00 0.00 ATOM 422 CG2 THR 53 20.639 26.383 23.614 1.00 0.00 ATOM 423 OG1 THR 53 20.793 23.996 23.912 1.00 0.00 ATOM 424 O THR 53 20.971 25.936 19.923 1.00 0.00 ATOM 425 C THR 53 20.067 25.930 20.754 1.00 0.00 ATOM 426 N VAL 54 19.182 26.897 20.906 1.00 0.00 ATOM 427 CA VAL 54 19.343 28.156 20.170 1.00 0.00 ATOM 428 CB VAL 54 18.292 28.296 19.053 1.00 0.00 ATOM 429 CG1 VAL 54 16.887 28.249 19.635 1.00 0.00 ATOM 430 CG2 VAL 54 18.503 29.590 18.282 1.00 0.00 ATOM 431 O VAL 54 18.357 29.371 22.002 1.00 0.00 ATOM 432 C VAL 54 19.235 29.324 21.142 1.00 0.00 ATOM 433 N THR 55 20.194 30.225 20.973 1.00 0.00 ATOM 434 CA THR 55 20.382 31.335 21.908 1.00 0.00 ATOM 435 CB THR 55 21.603 31.091 22.808 1.00 0.00 ATOM 436 CG2 THR 55 21.722 32.152 23.907 1.00 0.00 ATOM 437 OG1 THR 55 21.491 29.816 23.454 1.00 0.00 ATOM 438 O THR 55 21.366 32.706 20.217 1.00 0.00 ATOM 439 C THR 55 20.547 32.648 21.140 1.00 0.00 ATOM 440 N GLU 56 19.772 33.629 21.569 1.00 0.00 ATOM 441 CA GLU 56 19.909 35.021 21.093 1.00 0.00 ATOM 442 CB GLU 56 18.531 35.645 20.858 1.00 0.00 ATOM 443 CG GLU 56 17.743 35.017 19.718 1.00 0.00 ATOM 444 CD GLU 56 16.386 35.649 19.578 1.00 0.00 ATOM 445 OE1 GLU 56 16.075 36.521 20.355 1.00 0.00 ATOM 446 OE2 GLU 56 15.705 35.343 18.628 1.00 0.00 ATOM 447 O GLU 56 21.242 35.358 23.100 1.00 0.00 ATOM 448 C GLU 56 20.718 35.902 22.087 1.00 0.00 TER END