PFRMAT TS TARGET TR469 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 This refinement started with two models: the provided Zhang-Server_TS3 METHOD model and SAM-T08-hand_TS1 (here called from-try13-opt3), which was METHOD very similar (closer to the Zhang model than the Zhang model is to the METHOD real structure). METHOD METHOD The main hand addition was to add clustering constraints for the C32, METHOD C35, and H50 residues, trying to create a metal-binding site. METHOD METHOD I don't think that the undertaker cost fcns are really fine tuend METHOD enough to refine a model that is this close to being correct. METHOD METHOD Model METHOD 1 TR469.try12-opt3.pdb # < try11-opt3 < chimera-try10-try7 METHOD chimera-try10-try7 METHOD mostly TR469.try7-opt3.pdb METHOD Q3 and K4 from try10-opt3. METHOD METHOD 2 TR469.try10-opt3.pdb # < try4-opt3 < try3-opt3 < try2-opt3 < TR469 METHOD METHOD 3 TR469.try9-opt3.pdb # < try8-opt3 < try7-opt3.gromacs0 < try6-opt3 < try5-opt3 < from-try13-opt3.pdb< try6-opt3 < try5-opt3 < from-try13-opt3 METHOD METHOD 4 TR469.try8-opt3.gromacs0.repack-nonPC.pdb # < try7-opt3.gromacs0 < try6-opt3 < try5-opt3 < from-try13-opt3 METHOD # best rosetta energy METHOD METHOD 5 TR469.try4-opt3.pdb # < try3-opt3 < try2-opt3 < TR469 REMARK 6 REMARK 6 TR469 model 4 Thu Aug 14 14:48:22 2008 MODEL 4 PARENT N/A ATOM 1 N GLN 3 11.849 7.759 24.976 1.00 0.00 ATOM 2 CA GLN 3 11.451 6.506 24.321 1.00 0.00 ATOM 3 CB GLN 3 10.087 6.041 24.836 1.00 0.00 ATOM 4 CG GLN 3 10.071 5.672 26.310 1.00 0.00 ATOM 5 CD GLN 3 8.683 5.305 26.799 1.00 0.00 ATOM 6 OE1 GLN 3 7.718 5.304 26.029 1.00 0.00 ATOM 7 NE2 GLN 3 8.573 4.995 28.086 1.00 0.00 ATOM 8 O GLN 3 11.552 5.604 22.076 1.00 0.00 ATOM 9 C GLN 3 11.378 6.591 22.791 1.00 0.00 ATOM 10 N LYS 4 11.148 7.803 22.300 1.00 0.00 ATOM 11 CA LYS 4 10.934 8.041 20.864 1.00 0.00 ATOM 12 CB LYS 4 9.579 8.711 20.627 1.00 0.00 ATOM 13 CG LYS 4 8.379 7.860 21.022 1.00 0.00 ATOM 14 CD LYS 4 7.071 8.567 20.703 1.00 0.00 ATOM 15 CE LYS 4 5.873 7.758 21.180 1.00 0.00 ATOM 16 NZ LYS 4 4.587 8.451 20.896 1.00 0.00 ATOM 17 O LYS 4 12.048 9.329 19.100 1.00 0.00 ATOM 18 C LYS 4 12.064 8.909 20.245 1.00 0.00 ATOM 19 N PHE 5 13.117 9.154 21.023 1.00 0.00 ATOM 20 CA PHE 5 14.265 9.920 20.536 1.00 0.00 ATOM 21 CB PHE 5 14.366 11.257 21.272 1.00 0.00 ATOM 22 CG PHE 5 15.374 12.201 20.679 1.00 0.00 ATOM 23 CD1 PHE 5 15.394 12.447 19.314 1.00 0.00 ATOM 24 CD2 PHE 5 16.303 12.844 21.483 1.00 0.00 ATOM 25 CE1 PHE 5 16.320 13.315 18.766 1.00 0.00 ATOM 26 CE2 PHE 5 17.228 13.713 20.939 1.00 0.00 ATOM 27 CZ PHE 5 17.236 13.948 19.578 1.00 0.00 ATOM 28 O PHE 5 15.917 8.644 21.759 1.00 0.00 ATOM 29 C PHE 5 15.570 9.149 20.688 1.00 0.00 ATOM 30 N THR 6 16.282 9.200 19.596 1.00 0.00 ATOM 31 CA THR 6 17.641 8.641 19.518 1.00 0.00 ATOM 32 CB THR 6 17.739 7.613 18.377 1.00 0.00 ATOM 33 CG2 THR 6 19.138 7.030 18.236 1.00 0.00 ATOM 34 OG1 THR 6 16.852 6.534 18.667 1.00 0.00 ATOM 35 O THR 6 18.490 10.672 18.514 1.00 0.00 ATOM 36 C THR 6 18.607 9.814 19.398 1.00 0.00 ATOM 37 N LYS 7 19.578 9.769 20.269 1.00 0.00 ATOM 38 CA LYS 7 20.710 10.715 20.431 1.00 0.00 ATOM 39 CB LYS 7 21.707 10.184 21.462 1.00 0.00 ATOM 40 CG LYS 7 22.447 8.926 21.032 1.00 0.00 ATOM 41 CD LYS 7 23.399 8.445 22.118 1.00 0.00 ATOM 42 CE LYS 7 24.008 7.097 21.764 1.00 0.00 ATOM 43 NZ LYS 7 24.880 7.177 20.560 1.00 0.00 ATOM 44 O LYS 7 21.972 12.068 18.835 1.00 0.00 ATOM 45 C LYS 7 21.445 10.990 19.099 1.00 0.00 ATOM 46 N ASP 8 21.420 9.985 18.250 1.00 0.00 ATOM 47 CA ASP 8 22.153 9.913 16.975 1.00 0.00 ATOM 48 CB ASP 8 22.134 8.484 16.426 1.00 0.00 ATOM 49 CG ASP 8 23.026 7.508 17.180 1.00 0.00 ATOM 50 OD1 ASP 8 23.833 7.952 17.961 1.00 0.00 ATOM 51 OD2 ASP 8 22.789 6.327 17.090 1.00 0.00 ATOM 52 O ASP 8 22.380 11.210 14.941 1.00 0.00 ATOM 53 C ASP 8 21.649 10.843 15.872 1.00 0.00 ATOM 54 N MET 9 20.359 11.151 15.948 1.00 0.00 ATOM 55 CA MET 9 19.693 12.019 14.968 1.00 0.00 ATOM 56 CB MET 9 18.193 12.078 15.249 1.00 0.00 ATOM 57 CG MET 9 17.440 10.795 14.927 1.00 0.00 ATOM 58 SD MET 9 15.664 10.942 15.202 1.00 0.00 ATOM 59 CE MET 9 15.110 9.308 14.720 1.00 0.00 ATOM 60 O MET 9 20.659 13.988 15.999 1.00 0.00 ATOM 61 C MET 9 20.278 13.433 14.968 1.00 0.00 ATOM 62 N THR 10 20.223 14.038 13.789 1.00 0.00 ATOM 63 CA THR 10 20.480 15.485 13.667 1.00 0.00 ATOM 64 CB THR 10 20.426 15.947 12.200 1.00 0.00 ATOM 65 CG2 THR 10 21.521 15.273 11.387 1.00 0.00 ATOM 66 OG1 THR 10 19.149 15.618 11.638 1.00 0.00 ATOM 67 O THR 10 18.310 15.744 14.713 1.00 0.00 ATOM 68 C THR 10 19.434 16.222 14.509 1.00 0.00 ATOM 69 N PHE 11 19.793 17.400 14.996 1.00 0.00 ATOM 70 CA PHE 11 18.858 18.168 15.822 1.00 0.00 ATOM 71 CB PHE 11 19.564 19.370 16.452 1.00 0.00 ATOM 72 CG PHE 11 20.252 19.057 17.750 1.00 0.00 ATOM 73 CD1 PHE 11 21.626 18.875 17.797 1.00 0.00 ATOM 74 CD2 PHE 11 19.527 18.943 18.927 1.00 0.00 ATOM 75 CE1 PHE 11 22.260 18.586 18.991 1.00 0.00 ATOM 76 CE2 PHE 11 20.158 18.656 20.122 1.00 0.00 ATOM 77 CZ PHE 11 21.526 18.477 20.153 1.00 0.00 ATOM 78 O PHE 11 16.522 18.648 15.601 1.00 0.00 ATOM 79 C PHE 11 17.628 18.666 15.062 1.00 0.00 ATOM 80 N ALA 12 17.822 19.005 13.801 1.00 0.00 ATOM 81 CA ALA 12 16.703 19.421 12.944 1.00 0.00 ATOM 82 CB ALA 12 17.199 19.911 11.579 1.00 0.00 ATOM 83 O ALA 12 14.499 18.479 12.991 1.00 0.00 ATOM 84 C ALA 12 15.690 18.274 12.784 1.00 0.00 ATOM 85 N GLN 13 16.197 17.053 12.614 1.00 0.00 ATOM 86 CA GLN 13 15.353 15.844 12.580 1.00 0.00 ATOM 87 CB GLN 13 16.197 14.609 12.256 1.00 0.00 ATOM 88 CG GLN 13 15.393 13.332 12.083 1.00 0.00 ATOM 89 CD GLN 13 14.438 13.404 10.907 1.00 0.00 ATOM 90 OE1 GLN 13 14.809 13.842 9.813 1.00 0.00 ATOM 91 NE2 GLN 13 13.199 12.978 11.124 1.00 0.00 ATOM 92 O GLN 13 13.407 15.366 13.870 1.00 0.00 ATOM 93 C GLN 13 14.608 15.592 13.884 1.00 0.00 ATOM 94 N ALA 14 15.287 15.836 15.000 1.00 0.00 ATOM 95 CA ALA 14 14.692 15.711 16.338 1.00 0.00 ATOM 96 CB ALA 14 15.753 16.083 17.359 1.00 0.00 ATOM 97 O ALA 14 12.419 16.299 16.881 1.00 0.00 ATOM 98 C ALA 14 13.534 16.689 16.538 1.00 0.00 ATOM 99 N LEU 15 13.812 17.936 16.197 1.00 0.00 ATOM 100 CA LEU 15 12.825 19.024 16.309 1.00 0.00 ATOM 101 CB LEU 15 13.545 20.316 15.897 1.00 0.00 ATOM 102 CG LEU 15 12.601 21.523 15.800 1.00 0.00 ATOM 103 CD1 LEU 15 11.928 21.821 17.137 1.00 0.00 ATOM 104 CD2 LEU 15 13.390 22.763 15.414 1.00 0.00 ATOM 105 O LEU 15 10.459 18.929 15.893 1.00 0.00 ATOM 106 C LEU 15 11.583 18.747 15.446 1.00 0.00 ATOM 107 N GLN 16 11.834 18.268 14.238 1.00 0.00 ATOM 108 CA GLN 16 10.743 17.928 13.300 1.00 0.00 ATOM 109 CB GLN 16 11.305 17.650 11.902 1.00 0.00 ATOM 110 CG GLN 16 11.843 18.879 11.192 1.00 0.00 ATOM 111 CD GLN 16 12.467 18.546 9.850 1.00 0.00 ATOM 112 OE1 GLN 16 12.562 17.376 9.468 1.00 0.00 ATOM 113 NE2 GLN 16 12.899 19.573 9.127 1.00 0.00 ATOM 114 O GLN 16 8.703 16.768 13.740 1.00 0.00 ATOM 115 C GLN 16 9.923 16.712 13.758 1.00 0.00 ATOM 116 N THR 17 10.583 15.757 14.388 1.00 0.00 ATOM 117 CA THR 17 9.892 14.571 14.941 1.00 0.00 ATOM 118 CB THR 17 10.924 13.488 15.312 1.00 0.00 ATOM 119 CG2 THR 17 10.274 12.215 15.838 1.00 0.00 ATOM 120 OG1 THR 17 11.625 13.126 14.130 1.00 0.00 ATOM 121 O THR 17 7.878 14.462 16.265 1.00 0.00 ATOM 122 C THR 17 9.001 14.953 16.133 1.00 0.00 ATOM 123 N HIS 18 9.506 15.879 16.950 1.00 0.00 ATOM 124 CA HIS 18 8.785 16.319 18.159 1.00 0.00 ATOM 125 CB HIS 18 9.242 15.518 19.383 1.00 0.00 ATOM 126 CG HIS 18 8.892 14.064 19.315 1.00 0.00 ATOM 127 CD2 HIS 18 9.670 12.965 19.181 1.00 0.00 ATOM 128 ND1 HIS 18 7.592 13.608 19.393 1.00 0.00 ATOM 129 CE1 HIS 18 7.587 12.289 19.306 1.00 0.00 ATOM 130 NE2 HIS 18 8.835 11.876 19.178 1.00 0.00 ATOM 131 O HIS 18 9.974 18.260 18.948 1.00 0.00 ATOM 132 C HIS 18 8.917 17.803 18.501 1.00 0.00 ATOM 133 N PRO 19 7.748 18.439 18.609 1.00 0.00 ATOM 134 CA PRO 19 7.687 19.754 19.255 1.00 0.00 ATOM 135 CB PRO 19 6.282 20.224 18.893 1.00 0.00 ATOM 136 CG PRO 19 5.974 19.579 17.552 1.00 0.00 ATOM 137 CD PRO 19 6.566 18.190 17.769 1.00 0.00 ATOM 138 O PRO 19 8.618 20.602 21.305 1.00 0.00 ATOM 139 C PRO 19 7.941 19.720 20.772 1.00 0.00 ATOM 140 N GLY 20 7.509 18.653 21.450 1.00 0.00 ATOM 141 CA GLY 20 7.773 18.444 22.899 1.00 0.00 ATOM 142 O GLY 20 9.773 19.077 24.106 1.00 0.00 ATOM 143 C GLY 20 9.269 18.389 23.222 1.00 0.00 ATOM 144 N VAL 21 9.986 17.698 22.331 1.00 0.00 ATOM 145 CA VAL 21 11.465 17.578 22.386 1.00 0.00 ATOM 146 CB VAL 21 11.995 16.620 21.302 1.00 0.00 ATOM 147 CG1 VAL 21 13.515 16.663 21.251 1.00 0.00 ATOM 148 CG2 VAL 21 11.513 15.202 21.562 1.00 0.00 ATOM 149 O VAL 21 13.116 19.230 22.922 1.00 0.00 ATOM 150 C VAL 21 12.152 18.938 22.221 1.00 0.00 ATOM 151 N ALA 22 11.565 19.782 21.380 1.00 0.00 ATOM 152 CA ALA 22 12.033 21.159 21.144 1.00 0.00 ATOM 153 CB ALA 22 11.055 21.949 20.264 1.00 0.00 ATOM 154 O ALA 22 13.111 22.548 22.784 1.00 0.00 ATOM 155 C ALA 22 12.092 21.928 22.463 1.00 0.00 ATOM 156 N GLY 23 10.974 21.874 23.179 1.00 0.00 ATOM 157 CA GLY 23 10.812 22.512 24.503 1.00 0.00 ATOM 158 O GLY 23 12.628 22.860 25.972 1.00 0.00 ATOM 159 C GLY 23 11.880 22.025 25.483 1.00 0.00 ATOM 160 N VAL 24 12.024 20.700 25.570 1.00 0.00 ATOM 161 CA VAL 24 13.012 20.059 26.475 1.00 0.00 ATOM 162 CB VAL 24 12.916 18.525 26.449 1.00 0.00 ATOM 163 CG1 VAL 24 14.025 17.814 27.238 1.00 0.00 ATOM 164 CG2 VAL 24 11.598 18.097 27.087 1.00 0.00 ATOM 165 O VAL 24 15.190 20.975 27.027 1.00 0.00 ATOM 166 C VAL 24 14.447 20.526 26.163 1.00 0.00 ATOM 167 N LEU 25 14.761 20.536 24.882 1.00 0.00 ATOM 168 CA LEU 25 16.097 20.956 24.444 1.00 0.00 ATOM 169 CB LEU 25 16.232 20.676 22.942 1.00 0.00 ATOM 170 CG LEU 25 16.260 19.184 22.570 1.00 0.00 ATOM 171 CD1 LEU 25 16.565 19.073 21.076 1.00 0.00 ATOM 172 CD2 LEU 25 17.259 18.315 23.333 1.00 0.00 ATOM 173 O LEU 25 17.383 22.709 25.508 1.00 0.00 ATOM 174 C LEU 25 16.409 22.427 24.808 1.00 0.00 ATOM 175 N ARG 26 15.425 23.285 24.577 1.00 0.00 ATOM 176 CA ARG 26 15.517 24.728 24.935 1.00 0.00 ATOM 177 CB ARG 26 14.354 25.533 24.376 1.00 0.00 ATOM 178 CG ARG 26 14.409 27.024 24.668 1.00 0.00 ATOM 179 CD ARG 26 13.328 27.816 24.026 1.00 0.00 ATOM 180 NE ARG 26 13.363 29.238 24.325 1.00 0.00 ATOM 181 CZ ARG 26 12.453 30.133 23.894 1.00 0.00 ATOM 182 NH1 ARG 26 11.459 29.767 23.114 1.00 0.00 ATOM 183 NH2 ARG 26 12.600 31.396 24.254 1.00 0.00 ATOM 184 O ARG 26 16.529 25.609 26.948 1.00 0.00 ATOM 185 C ARG 26 15.651 24.894 26.459 1.00 0.00 ATOM 186 N SER 27 14.900 24.094 27.189 1.00 0.00 ATOM 187 CA SER 27 14.855 24.126 28.658 1.00 0.00 ATOM 188 CB SER 27 13.679 23.312 29.162 1.00 0.00 ATOM 189 OG SER 27 12.451 23.855 28.760 1.00 0.00 ATOM 190 O SER 27 16.487 24.186 30.410 1.00 0.00 ATOM 191 C SER 27 16.125 23.622 29.378 1.00 0.00 ATOM 192 N TYR 28 16.960 22.874 28.663 1.00 0.00 ATOM 193 CA TYR 28 18.212 22.351 29.260 1.00 0.00 ATOM 194 CB TYR 28 18.257 20.831 29.087 1.00 0.00 ATOM 195 CG TYR 28 17.265 20.170 30.048 1.00 0.00 ATOM 196 CD1 TYR 28 17.540 20.142 31.394 1.00 0.00 ATOM 197 CD2 TYR 28 16.067 19.621 29.631 1.00 0.00 ATOM 198 CE1 TYR 28 16.649 19.597 32.297 1.00 0.00 ATOM 199 CE2 TYR 28 15.175 19.047 30.521 1.00 0.00 ATOM 200 CZ TYR 28 15.471 19.029 31.869 1.00 0.00 ATOM 201 OH TYR 28 14.679 18.432 32.788 1.00 0.00 ATOM 202 O TYR 28 20.559 22.515 28.628 1.00 0.00 ATOM 203 C TYR 28 19.479 23.082 28.821 1.00 0.00 ATOM 204 N ASN 29 19.326 24.395 28.652 1.00 0.00 ATOM 205 CA ASN 29 20.404 25.341 28.282 1.00 0.00 ATOM 206 CB ASN 29 21.505 25.364 29.325 1.00 0.00 ATOM 207 CG ASN 29 21.084 25.971 30.636 1.00 0.00 ATOM 208 ND2 ASN 29 21.751 25.563 31.685 1.00 0.00 ATOM 209 OD1 ASN 29 20.218 26.850 30.686 1.00 0.00 ATOM 210 O ASN 29 22.014 25.781 26.553 1.00 0.00 ATOM 211 C ASN 29 21.057 25.096 26.919 1.00 0.00 ATOM 212 N LEU 30 20.422 24.250 26.119 1.00 0.00 ATOM 213 CA LEU 30 20.827 24.121 24.705 1.00 0.00 ATOM 214 CB LEU 30 20.012 23.017 24.019 1.00 0.00 ATOM 215 CG LEU 30 20.785 21.728 23.716 1.00 0.00 ATOM 216 CD1 LEU 30 21.266 21.091 25.012 1.00 0.00 ATOM 217 CD2 LEU 30 19.892 20.770 22.941 1.00 0.00 ATOM 218 O LEU 30 21.420 25.853 23.158 1.00 0.00 ATOM 219 C LEU 30 20.640 25.473 24.017 1.00 0.00 ATOM 220 N GLY 31 19.618 26.197 24.466 1.00 0.00 ATOM 221 CA GLY 31 19.337 27.599 24.094 1.00 0.00 ATOM 222 O GLY 31 19.494 28.772 21.987 1.00 0.00 ATOM 223 C GLY 31 19.124 27.762 22.590 1.00 0.00 ATOM 224 N CYS 32 18.445 26.771 22.047 1.00 0.00 ATOM 225 CA CYS 32 18.260 26.677 20.599 1.00 0.00 ATOM 226 CB CYS 32 19.191 25.597 20.096 1.00 0.00 ATOM 227 SG CYS 32 20.940 25.994 20.413 1.00 0.00 ATOM 228 O CYS 32 16.201 25.575 21.055 1.00 0.00 ATOM 229 C CYS 32 16.832 26.289 20.286 1.00 0.00 ATOM 230 N ILE 33 16.396 26.616 19.076 1.00 0.00 ATOM 231 CA ILE 33 15.039 26.229 18.643 1.00 0.00 ATOM 232 CB ILE 33 14.695 26.824 17.265 1.00 0.00 ATOM 233 CG1 ILE 33 14.620 28.351 17.347 1.00 0.00 ATOM 234 CG2 ILE 33 13.383 26.250 16.752 1.00 0.00 ATOM 235 CD1 ILE 33 14.532 29.030 16.000 1.00 0.00 ATOM 236 O ILE 33 14.452 24.032 19.483 1.00 0.00 ATOM 237 C ILE 33 15.033 24.694 18.628 1.00 0.00 ATOM 238 N GLY 34 15.802 24.251 17.661 1.00 0.00 ATOM 239 CA GLY 34 16.427 22.938 17.613 1.00 0.00 ATOM 240 O GLY 34 18.561 22.170 16.951 1.00 0.00 ATOM 241 C GLY 34 17.892 23.153 17.208 1.00 0.00 ATOM 242 N CYS 35 18.377 24.403 17.251 1.00 0.00 ATOM 243 CA CYS 35 19.704 24.875 16.778 1.00 0.00 ATOM 244 CB CYS 35 20.897 23.951 17.065 1.00 0.00 ATOM 245 SG CYS 35 21.047 23.424 18.805 1.00 0.00 ATOM 246 O CYS 35 19.045 24.286 14.535 1.00 0.00 ATOM 247 C CYS 35 19.621 25.069 15.269 1.00 0.00 ATOM 248 N MET 36 20.020 26.229 14.780 1.00 0.00 ATOM 249 CA MET 36 20.107 26.448 13.315 1.00 0.00 ATOM 250 CB MET 36 20.480 27.899 13.020 1.00 0.00 ATOM 251 CG MET 36 19.392 28.910 13.350 1.00 0.00 ATOM 252 SD MET 36 19.925 30.615 13.096 1.00 0.00 ATOM 253 CE MET 36 20.058 30.664 11.311 1.00 0.00 ATOM 254 O MET 36 20.886 24.713 11.773 1.00 0.00 ATOM 255 C MET 36 21.139 25.466 12.731 1.00 0.00 ATOM 256 N GLY 37 22.252 25.457 13.426 1.00 0.00 ATOM 257 CA GLY 37 23.400 24.549 13.222 1.00 0.00 ATOM 258 O GLY 37 23.841 22.188 13.214 1.00 0.00 ATOM 259 C GLY 37 23.091 23.098 13.593 1.00 0.00 ATOM 260 N ALA 38 21.894 22.892 14.113 1.00 0.00 ATOM 261 CA ALA 38 21.236 21.583 14.374 1.00 0.00 ATOM 262 CB ALA 38 19.717 21.683 14.316 1.00 0.00 ATOM 263 O ALA 38 21.487 19.374 13.514 1.00 0.00 ATOM 264 C ALA 38 21.434 20.573 13.256 1.00 0.00 ATOM 265 N GLN 39 21.229 21.099 12.057 1.00 0.00 ATOM 266 CA GLN 39 21.109 20.292 10.825 1.00 0.00 ATOM 267 CB GLN 39 20.963 21.201 9.601 1.00 0.00 ATOM 268 CG GLN 39 19.616 21.895 9.497 1.00 0.00 ATOM 269 CD GLN 39 19.541 22.842 8.315 1.00 0.00 ATOM 270 OE1 GLN 39 20.505 22.988 7.558 1.00 0.00 ATOM 271 NE2 GLN 39 18.397 23.494 8.152 1.00 0.00 ATOM 272 O GLN 39 22.179 18.290 10.084 1.00 0.00 ATOM 273 C GLN 39 22.317 19.372 10.640 1.00 0.00 ATOM 274 N ASN 40 23.413 19.793 11.255 1.00 0.00 ATOM 275 CA ASN 40 24.711 19.106 11.153 1.00 0.00 ATOM 276 CB ASN 40 25.837 20.085 10.877 1.00 0.00 ATOM 277 CG ASN 40 25.744 20.751 9.533 1.00 0.00 ATOM 278 ND2 ASN 40 26.306 21.929 9.445 1.00 0.00 ATOM 279 OD1 ASN 40 25.233 20.174 8.565 1.00 0.00 ATOM 280 O ASN 40 26.023 17.473 12.229 1.00 0.00 ATOM 281 C ASN 40 25.105 18.277 12.355 1.00 0.00 ATOM 282 N GLU 41 24.434 18.464 13.480 1.00 0.00 ATOM 283 CA GLU 41 24.858 17.832 14.731 1.00 0.00 ATOM 284 CB GLU 41 25.197 18.894 15.780 1.00 0.00 ATOM 285 CG GLU 41 26.403 19.756 15.436 1.00 0.00 ATOM 286 CD GLU 41 26.709 20.733 16.536 1.00 0.00 ATOM 287 OE1 GLU 41 25.988 20.751 17.505 1.00 0.00 ATOM 288 OE2 GLU 41 27.724 21.383 16.461 1.00 0.00 ATOM 289 O GLU 41 22.629 17.130 15.323 1.00 0.00 ATOM 290 C GLU 41 23.848 16.873 15.343 1.00 0.00 ATOM 291 N SER 42 24.378 15.822 15.922 1.00 0.00 ATOM 292 CA SER 42 23.595 14.865 16.717 1.00 0.00 ATOM 293 CB SER 42 24.259 13.479 16.804 1.00 0.00 ATOM 294 OG SER 42 25.410 13.465 17.659 1.00 0.00 ATOM 295 O SER 42 24.062 16.368 18.552 1.00 0.00 ATOM 296 C SER 42 23.383 15.426 18.124 1.00 0.00 ATOM 297 N LEU 43 22.562 14.732 18.903 1.00 0.00 ATOM 298 CA LEU 43 22.338 15.091 20.310 1.00 0.00 ATOM 299 CB LEU 43 21.335 14.124 20.951 1.00 0.00 ATOM 300 CG LEU 43 21.059 14.363 22.441 1.00 0.00 ATOM 301 CD1 LEU 43 20.411 13.130 23.057 1.00 0.00 ATOM 302 CD2 LEU 43 22.361 14.700 23.153 1.00 0.00 ATOM 303 O LEU 43 23.885 16.022 21.892 1.00 0.00 ATOM 304 C LEU 43 23.640 15.101 21.119 1.00 0.00 ATOM 305 N GLU 44 24.458 14.071 20.940 1.00 0.00 ATOM 306 CA GLU 44 25.740 13.980 21.649 1.00 0.00 ATOM 307 CB GLU 44 26.403 12.627 21.383 1.00 0.00 ATOM 308 CG GLU 44 27.713 12.412 22.130 1.00 0.00 ATOM 309 CD GLU 44 28.272 11.042 21.868 1.00 0.00 ATOM 310 OE1 GLU 44 27.653 10.295 21.147 1.00 0.00 ATOM 311 OE2 GLU 44 29.373 10.779 22.293 1.00 0.00 ATOM 312 O GLU 44 27.242 15.769 22.126 1.00 0.00 ATOM 313 C GLU 44 26.699 15.110 21.254 1.00 0.00 ATOM 314 N GLN 45 26.703 15.442 19.970 1.00 0.00 ATOM 315 CA GLN 45 27.513 16.582 19.474 1.00 0.00 ATOM 316 CB GLN 45 27.463 16.650 17.945 1.00 0.00 ATOM 317 CG GLN 45 28.201 15.521 17.246 1.00 0.00 ATOM 318 CD GLN 45 28.117 15.622 15.735 1.00 0.00 ATOM 319 OE1 GLN 45 27.067 15.367 15.139 1.00 0.00 ATOM 320 NE2 GLN 45 29.226 15.993 15.106 1.00 0.00 ATOM 321 O GLN 45 27.838 18.614 20.704 1.00 0.00 ATOM 322 C GLN 45 27.052 17.925 20.048 1.00 0.00 ATOM 323 N GLY 46 25.742 18.042 20.125 1.00 0.00 ATOM 324 CA GLY 46 25.091 19.236 20.693 1.00 0.00 ATOM 325 O GLY 46 25.654 20.367 22.725 1.00 0.00 ATOM 326 C GLY 46 25.305 19.323 22.200 1.00 0.00 ATOM 327 N ALA 47 25.234 18.186 22.855 1.00 0.00 ATOM 328 CA ALA 47 25.488 18.079 24.304 1.00 0.00 ATOM 329 CB ALA 47 25.228 16.636 24.697 1.00 0.00 ATOM 330 O ALA 47 27.160 19.307 25.494 1.00 0.00 ATOM 331 C ALA 47 26.936 18.476 24.629 1.00 0.00 ATOM 332 N ASN 48 27.863 17.988 23.810 1.00 0.00 ATOM 333 CA ASN 48 29.293 18.342 23.949 1.00 0.00 ATOM 334 CB ASN 48 30.160 17.535 23.001 1.00 0.00 ATOM 335 CG ASN 48 30.314 16.093 23.402 1.00 0.00 ATOM 336 ND2 ASN 48 30.767 15.294 22.470 1.00 0.00 ATOM 337 OD1 ASN 48 30.096 15.723 24.562 1.00 0.00 ATOM 338 O ASN 48 30.134 20.436 24.619 1.00 0.00 ATOM 339 C ASN 48 29.551 19.829 23.731 1.00 0.00 ATOM 340 N ALA 49 28.974 20.384 22.662 1.00 0.00 ATOM 341 CA ALA 49 29.104 21.810 22.337 1.00 0.00 ATOM 342 CB ALA 49 28.610 22.077 20.910 1.00 0.00 ATOM 343 O ALA 49 28.878 23.828 23.630 1.00 0.00 ATOM 344 C ALA 49 28.387 22.744 23.321 1.00 0.00 ATOM 345 N HIS 50 27.348 22.224 23.964 1.00 0.00 ATOM 346 CA HIS 50 26.560 22.976 24.951 1.00 0.00 ATOM 347 CB HIS 50 25.062 22.753 24.702 1.00 0.00 ATOM 348 CG HIS 50 24.608 23.430 23.405 1.00 0.00 ATOM 349 CD2 HIS 50 24.279 22.889 22.235 1.00 0.00 ATOM 350 ND1 HIS 50 24.565 24.731 23.247 1.00 0.00 ATOM 351 CE1 HIS 50 24.249 25.012 21.984 1.00 0.00 ATOM 352 NE2 HIS 50 24.062 23.866 21.361 1.00 0.00 ATOM 353 O HIS 50 26.316 23.176 27.308 1.00 0.00 ATOM 354 C HIS 50 26.894 22.617 26.397 1.00 0.00 ATOM 355 N GLY 51 27.888 21.760 26.618 1.00 0.00 ATOM 356 CA GLY 51 28.302 21.329 27.978 1.00 0.00 ATOM 357 O GLY 51 27.247 20.655 30.032 1.00 0.00 ATOM 358 C GLY 51 27.210 20.631 28.804 1.00 0.00 ATOM 359 N LEU 52 26.315 19.925 28.115 1.00 0.00 ATOM 360 CA LEU 52 25.245 19.145 28.752 1.00 0.00 ATOM 361 CB LEU 52 23.885 19.519 28.150 1.00 0.00 ATOM 362 CG LEU 52 22.669 18.887 28.839 1.00 0.00 ATOM 363 CD1 LEU 52 22.636 19.285 30.309 1.00 0.00 ATOM 364 CD2 LEU 52 21.396 19.327 28.133 1.00 0.00 ATOM 365 O LEU 52 25.881 17.204 27.481 1.00 0.00 ATOM 366 C LEU 52 25.551 17.664 28.575 1.00 0.00 ATOM 367 N ASN 53 25.596 16.955 29.694 1.00 0.00 ATOM 368 CA ASN 53 25.881 15.513 29.641 1.00 0.00 ATOM 369 CB ASN 53 26.028 14.925 31.032 1.00 0.00 ATOM 370 CG ASN 53 27.274 15.367 31.748 1.00 0.00 ATOM 371 ND2 ASN 53 27.264 15.213 33.047 1.00 0.00 ATOM 372 OD1 ASN 53 28.262 15.773 31.124 1.00 0.00 ATOM 373 O ASN 53 23.606 15.071 28.971 1.00 0.00 ATOM 374 C ASN 53 24.787 14.777 28.856 1.00 0.00 ATOM 375 N VAL 54 25.242 13.828 28.038 1.00 0.00 ATOM 376 CA VAL 54 24.317 13.014 27.227 1.00 0.00 ATOM 377 CB VAL 54 25.078 12.017 26.333 1.00 0.00 ATOM 378 CG1 VAL 54 24.107 11.059 25.659 1.00 0.00 ATOM 379 CG2 VAL 54 25.902 12.759 25.290 1.00 0.00 ATOM 380 O VAL 54 22.137 12.201 27.820 1.00 0.00 ATOM 381 C VAL 54 23.344 12.249 28.119 1.00 0.00 ATOM 382 N GLU 55 23.841 11.778 29.255 1.00 0.00 ATOM 383 CA GLU 55 23.007 11.065 30.243 1.00 0.00 ATOM 384 CB GLU 55 23.855 10.618 31.437 1.00 0.00 ATOM 385 CG GLU 55 24.826 9.486 31.129 1.00 0.00 ATOM 386 CD GLU 55 25.703 9.184 32.312 1.00 0.00 ATOM 387 OE1 GLU 55 25.607 9.880 33.294 1.00 0.00 ATOM 388 OE2 GLU 55 26.391 8.190 32.277 1.00 0.00 ATOM 389 O GLU 55 20.703 11.422 30.784 1.00 0.00 ATOM 390 C GLU 55 21.835 11.894 30.751 1.00 0.00 ATOM 391 N ASP 56 22.127 13.164 31.015 1.00 0.00 ATOM 392 CA ASP 56 21.116 14.149 31.459 1.00 0.00 ATOM 393 CB ASP 56 21.788 15.470 31.842 1.00 0.00 ATOM 394 CG ASP 56 22.564 15.425 33.151 1.00 0.00 ATOM 395 OD1 ASP 56 22.404 14.474 33.881 1.00 0.00 ATOM 396 OD2 ASP 56 23.422 16.253 33.340 1.00 0.00 ATOM 397 O ASP 56 18.885 14.162 30.652 1.00 0.00 ATOM 398 C ASP 56 20.049 14.414 30.397 1.00 0.00 ATOM 399 N ILE 57 20.502 14.550 29.149 1.00 0.00 ATOM 400 CA ILE 57 19.575 14.760 28.024 1.00 0.00 ATOM 401 CB ILE 57 20.290 15.063 26.714 1.00 0.00 ATOM 402 CG1 ILE 57 21.034 16.383 26.858 1.00 0.00 ATOM 403 CG2 ILE 57 19.242 15.241 25.615 1.00 0.00 ATOM 404 CD1 ILE 57 22.056 16.634 25.767 1.00 0.00 ATOM 405 O ILE 57 17.425 13.751 27.613 1.00 0.00 ATOM 406 C ILE 57 18.622 13.575 27.841 1.00 0.00 ATOM 407 N LEU 58 19.209 12.398 27.736 1.00 0.00 ATOM 408 CA LEU 58 18.407 11.188 27.492 1.00 0.00 ATOM 409 CB LEU 58 19.321 9.963 27.360 1.00 0.00 ATOM 410 CG LEU 58 20.183 9.926 26.091 1.00 0.00 ATOM 411 CD1 LEU 58 21.170 8.770 26.165 1.00 0.00 ATOM 412 CD2 LEU 58 19.285 9.791 24.870 1.00 0.00 ATOM 413 O LEU 58 16.206 10.665 28.302 1.00 0.00 ATOM 414 C LEU 58 17.374 10.946 28.593 1.00 0.00 ATOM 415 N ARG 59 17.792 11.148 29.842 1.00 0.00 ATOM 416 CA ARG 59 16.869 11.082 30.991 1.00 0.00 ATOM 417 CB ARG 59 17.592 11.258 32.319 1.00 0.00 ATOM 418 CG ARG 59 18.471 10.088 32.729 1.00 0.00 ATOM 419 CD ARG 59 19.222 10.301 33.993 1.00 0.00 ATOM 420 NE ARG 59 20.088 9.195 34.372 1.00 0.00 ATOM 421 CZ ARG 59 20.922 9.205 35.429 1.00 0.00 ATOM 422 NH1 ARG 59 21.035 10.270 36.193 1.00 0.00 ATOM 423 NH2 ARG 59 21.643 8.123 35.666 1.00 0.00 ATOM 424 O ARG 59 14.552 11.672 30.881 1.00 0.00 ATOM 425 C ARG 59 15.714 12.083 30.852 1.00 0.00 ATOM 426 N ASP 60 16.084 13.255 30.344 1.00 0.00 ATOM 427 CA ASP 60 15.151 14.381 30.150 1.00 0.00 ATOM 428 CB ASP 60 15.909 15.674 29.838 1.00 0.00 ATOM 429 CG ASP 60 16.819 16.157 30.969 1.00 0.00 ATOM 430 OD1 ASP 60 16.575 15.806 32.138 1.00 0.00 ATOM 431 OD2 ASP 60 17.776 16.890 30.627 1.00 0.00 ATOM 432 O ASP 60 12.950 14.226 29.197 1.00 0.00 ATOM 433 C ASP 60 14.161 14.098 29.027 1.00 0.00 ATOM 434 N LEU 61 14.691 13.546 27.946 1.00 0.00 ATOM 435 CA LEU 61 13.881 13.155 26.795 1.00 0.00 ATOM 436 CB LEU 61 14.772 12.690 25.636 1.00 0.00 ATOM 437 CG LEU 61 14.025 12.455 24.319 1.00 0.00 ATOM 438 CD1 LEU 61 13.170 11.183 24.310 1.00 0.00 ATOM 439 CD2 LEU 61 13.183 13.683 24.005 1.00 0.00 ATOM 440 O LEU 61 11.707 12.147 26.796 1.00 0.00 ATOM 441 C LEU 61 12.873 12.076 27.194 1.00 0.00 ATOM 442 N ASN 62 13.382 11.057 27.857 1.00 0.00 ATOM 443 CA ASN 62 12.533 9.952 28.315 1.00 0.00 ATOM 444 CB ASN 62 13.361 8.815 28.887 1.00 0.00 ATOM 445 CG ASN 62 14.102 8.024 27.845 1.00 0.00 ATOM 446 ND2 ASN 62 15.071 7.267 28.295 1.00 0.00 ATOM 447 OD1 ASN 62 13.753 8.040 26.660 1.00 0.00 ATOM 448 O ASN 62 10.401 9.864 29.419 1.00 0.00 ATOM 449 C ASN 62 11.493 10.389 29.350 1.00 0.00 ATOM 450 N ALA 63 11.868 11.310 30.225 1.00 0.00 ATOM 451 CA ALA 63 10.880 11.845 31.178 1.00 0.00 ATOM 452 CB ALA 63 11.562 12.751 32.196 1.00 0.00 ATOM 453 O ALA 63 8.585 12.528 30.937 1.00 0.00 ATOM 454 C ALA 63 9.720 12.577 30.482 1.00 0.00 ATOM 455 N LEU 64 10.054 13.244 29.373 1.00 0.00 ATOM 456 CA LEU 64 9.056 13.873 28.488 1.00 0.00 ATOM 457 CB LEU 64 9.791 14.630 27.372 1.00 0.00 ATOM 458 CG LEU 64 8.794 15.209 26.371 1.00 0.00 ATOM 459 CD1 LEU 64 8.030 16.287 27.108 1.00 0.00 ATOM 460 CD2 LEU 64 9.459 15.720 25.101 1.00 0.00 ATOM 461 O LEU 64 6.914 12.813 28.293 1.00 0.00 ATOM 462 C LEU 64 8.098 12.813 27.935 1.00 0.00 ATOM 463 N ALA 65 8.634 11.993 27.029 1.00 0.00 ATOM 464 CA ALA 65 7.965 10.814 26.458 1.00 0.00 ATOM 465 CB ALA 65 7.642 11.056 24.971 1.00 0.00 ATOM 466 O ALA 65 10.088 9.734 26.761 1.00 0.00 ATOM 467 C ALA 65 8.870 9.558 26.540 1.00 0.00 TER END