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 3 Thu Aug 14 14:48:22 2008 MODEL 3 PARENT N/A ATOM 1 N GLN 3 11.921 7.871 25.049 1.00 0.00 ATOM 2 CA GLN 3 11.387 6.665 24.395 1.00 0.00 ATOM 3 CB GLN 3 10.003 6.410 24.965 1.00 0.00 ATOM 4 CG GLN 3 10.182 6.101 26.447 1.00 0.00 ATOM 5 CD GLN 3 8.870 6.052 27.214 1.00 0.00 ATOM 6 OE1 GLN 3 8.023 6.916 27.296 1.00 0.00 ATOM 7 NE2 GLN 3 8.591 4.947 27.821 1.00 0.00 ATOM 8 O GLN 3 11.498 5.743 22.176 1.00 0.00 ATOM 9 C GLN 3 11.336 6.756 22.867 1.00 0.00 ATOM 10 N LYS 4 11.103 7.953 22.340 1.00 0.00 ATOM 11 CA LYS 4 10.947 8.150 20.895 1.00 0.00 ATOM 12 CB LYS 4 9.469 8.264 20.474 1.00 0.00 ATOM 13 CG LYS 4 8.603 7.101 20.866 1.00 0.00 ATOM 14 CD LYS 4 9.051 5.831 20.140 1.00 0.00 ATOM 15 CE LYS 4 8.220 4.620 20.417 1.00 0.00 ATOM 16 NZ LYS 4 8.547 3.979 21.729 1.00 0.00 ATOM 17 O LYS 4 12.064 9.374 19.111 1.00 0.00 ATOM 18 C LYS 4 12.122 8.996 20.281 1.00 0.00 ATOM 19 N PHE 5 13.150 9.273 21.077 1.00 0.00 ATOM 20 CA PHE 5 14.286 10.053 20.600 1.00 0.00 ATOM 21 CB PHE 5 14.346 11.349 21.411 1.00 0.00 ATOM 22 CG PHE 5 15.562 12.222 21.111 1.00 0.00 ATOM 23 CD1 PHE 5 15.481 13.227 20.157 1.00 0.00 ATOM 24 CD2 PHE 5 16.749 12.006 21.775 1.00 0.00 ATOM 25 CE1 PHE 5 16.605 13.983 19.882 1.00 0.00 ATOM 26 CE2 PHE 5 17.853 12.774 21.482 1.00 0.00 ATOM 27 CZ PHE 5 17.782 13.763 20.557 1.00 0.00 ATOM 28 O PHE 5 15.952 8.699 21.770 1.00 0.00 ATOM 29 C PHE 5 15.571 9.236 20.723 1.00 0.00 ATOM 30 N THR 6 16.287 9.270 19.584 1.00 0.00 ATOM 31 CA THR 6 17.629 8.674 19.519 1.00 0.00 ATOM 32 CB THR 6 17.717 7.650 18.378 1.00 0.00 ATOM 33 CG2 THR 6 19.112 7.033 18.252 1.00 0.00 ATOM 34 OG1 THR 6 16.785 6.607 18.687 1.00 0.00 ATOM 35 O THR 6 18.510 10.704 18.592 1.00 0.00 ATOM 36 C THR 6 18.633 9.821 19.440 1.00 0.00 ATOM 37 N LYS 7 19.626 9.802 20.324 1.00 0.00 ATOM 38 CA LYS 7 20.640 10.843 20.338 1.00 0.00 ATOM 39 CB LYS 7 21.717 9.996 21.436 1.00 0.00 ATOM 40 CG LYS 7 21.156 8.874 22.232 1.00 0.00 ATOM 41 CD LYS 7 22.262 7.949 22.708 1.00 0.00 ATOM 42 CE LYS 7 23.287 7.622 21.616 1.00 0.00 ATOM 43 NZ LYS 7 24.356 6.683 22.095 1.00 0.00 ATOM 44 O LYS 7 22.010 12.049 18.744 1.00 0.00 ATOM 45 C LYS 7 21.445 10.998 19.030 1.00 0.00 ATOM 46 N ASP 8 21.408 9.953 18.220 1.00 0.00 ATOM 47 CA ASP 8 22.133 9.894 16.943 1.00 0.00 ATOM 48 CB ASP 8 22.053 8.462 16.455 1.00 0.00 ATOM 49 CG ASP 8 22.903 7.501 17.269 1.00 0.00 ATOM 50 OD1 ASP 8 23.696 7.924 18.137 1.00 0.00 ATOM 51 OD2 ASP 8 22.506 6.328 17.192 1.00 0.00 ATOM 52 O ASP 8 22.337 11.191 14.902 1.00 0.00 ATOM 53 C ASP 8 21.623 10.824 15.834 1.00 0.00 ATOM 54 N MET 9 20.344 11.171 15.945 1.00 0.00 ATOM 55 CA MET 9 19.687 12.028 14.954 1.00 0.00 ATOM 56 CB MET 9 18.195 12.133 15.250 1.00 0.00 ATOM 57 CG MET 9 17.464 10.795 15.076 1.00 0.00 ATOM 58 SD MET 9 15.660 11.054 14.935 1.00 0.00 ATOM 59 CE MET 9 15.304 11.431 16.630 1.00 0.00 ATOM 60 O MET 9 20.618 14.017 15.990 1.00 0.00 ATOM 61 C MET 9 20.257 13.453 14.954 1.00 0.00 ATOM 62 N THR 10 20.202 14.045 13.771 1.00 0.00 ATOM 63 CA THR 10 20.467 15.493 13.646 1.00 0.00 ATOM 64 CB THR 10 20.433 16.030 12.207 1.00 0.00 ATOM 65 CG2 THR 10 21.348 15.226 11.283 1.00 0.00 ATOM 66 OG1 THR 10 19.092 16.111 11.715 1.00 0.00 ATOM 67 O THR 10 18.339 15.721 14.729 1.00 0.00 ATOM 68 C THR 10 19.438 16.227 14.499 1.00 0.00 ATOM 69 N PHE 11 19.795 17.419 14.965 1.00 0.00 ATOM 70 CA PHE 11 18.884 18.219 15.796 1.00 0.00 ATOM 71 CB PHE 11 19.521 19.466 16.397 1.00 0.00 ATOM 72 CG PHE 11 20.435 19.093 17.538 1.00 0.00 ATOM 73 CD1 PHE 11 19.918 18.466 18.658 1.00 0.00 ATOM 74 CD2 PHE 11 21.793 19.361 17.496 1.00 0.00 ATOM 75 CE1 PHE 11 20.737 18.085 19.704 1.00 0.00 ATOM 76 CE2 PHE 11 22.616 18.990 18.550 1.00 0.00 ATOM 77 CZ PHE 11 22.089 18.361 19.653 1.00 0.00 ATOM 78 O PHE 11 16.536 18.655 15.564 1.00 0.00 ATOM 79 C PHE 11 17.642 18.647 15.021 1.00 0.00 ATOM 80 N ALA 12 17.823 19.001 13.753 1.00 0.00 ATOM 81 CA ALA 12 16.706 19.425 12.918 1.00 0.00 ATOM 82 CB ALA 12 17.187 19.969 11.583 1.00 0.00 ATOM 83 O ALA 12 14.481 18.448 12.980 1.00 0.00 ATOM 84 C ALA 12 15.694 18.253 12.832 1.00 0.00 ATOM 85 N GLN 13 16.186 17.035 12.613 1.00 0.00 ATOM 86 CA GLN 13 15.324 15.855 12.534 1.00 0.00 ATOM 87 CB GLN 13 16.156 14.609 12.231 1.00 0.00 ATOM 88 CG GLN 13 16.591 14.633 10.772 1.00 0.00 ATOM 89 CD GLN 13 17.580 13.529 10.416 1.00 0.00 ATOM 90 OE1 GLN 13 18.630 13.255 11.002 1.00 0.00 ATOM 91 NE2 GLN 13 17.334 12.999 9.260 1.00 0.00 ATOM 92 O GLN 13 13.424 15.253 13.906 1.00 0.00 ATOM 93 C GLN 13 14.579 15.599 13.851 1.00 0.00 ATOM 94 N ALA 14 15.291 15.862 14.955 1.00 0.00 ATOM 95 CA ALA 14 14.681 15.698 16.295 1.00 0.00 ATOM 96 CB ALA 14 15.670 15.989 17.372 1.00 0.00 ATOM 97 O ALA 14 12.446 16.337 16.884 1.00 0.00 ATOM 98 C ALA 14 13.557 16.698 16.474 1.00 0.00 ATOM 99 N LEU 15 13.826 17.958 16.153 1.00 0.00 ATOM 100 CA LEU 15 12.809 18.998 16.280 1.00 0.00 ATOM 101 CB LEU 15 13.532 20.280 15.894 1.00 0.00 ATOM 102 CG LEU 15 12.605 21.484 15.812 1.00 0.00 ATOM 103 CD1 LEU 15 11.950 21.750 17.150 1.00 0.00 ATOM 104 CD2 LEU 15 13.359 22.703 15.332 1.00 0.00 ATOM 105 O LEU 15 10.457 18.896 15.818 1.00 0.00 ATOM 106 C LEU 15 11.600 18.701 15.400 1.00 0.00 ATOM 107 N GLN 16 11.851 18.229 14.183 1.00 0.00 ATOM 108 CA GLN 16 10.763 17.905 13.248 1.00 0.00 ATOM 109 CB GLN 16 11.366 17.645 11.874 1.00 0.00 ATOM 110 CG GLN 16 11.932 18.960 11.366 1.00 0.00 ATOM 111 CD GLN 16 12.600 18.802 10.014 1.00 0.00 ATOM 112 OE1 GLN 16 12.073 19.096 8.954 1.00 0.00 ATOM 113 NE2 GLN 16 13.838 18.394 10.069 1.00 0.00 ATOM 114 O GLN 16 8.694 16.720 13.643 1.00 0.00 ATOM 115 C GLN 16 9.918 16.723 13.783 1.00 0.00 ATOM 116 N THR 17 10.576 15.740 14.387 1.00 0.00 ATOM 117 CA THR 17 9.875 14.581 14.929 1.00 0.00 ATOM 118 CB THR 17 10.888 13.484 15.300 1.00 0.00 ATOM 119 CG2 THR 17 10.241 12.215 15.845 1.00 0.00 ATOM 120 OG1 THR 17 11.582 13.110 14.106 1.00 0.00 ATOM 121 O THR 17 7.970 14.328 16.365 1.00 0.00 ATOM 122 C THR 17 9.026 14.924 16.146 1.00 0.00 ATOM 123 N HIS 18 9.487 15.887 16.939 1.00 0.00 ATOM 124 CA HIS 18 8.755 16.300 18.131 1.00 0.00 ATOM 125 CB HIS 18 9.337 15.630 19.326 1.00 0.00 ATOM 126 CG HIS 18 9.015 14.174 19.372 1.00 0.00 ATOM 127 CD2 HIS 18 9.816 13.086 19.368 1.00 0.00 ATOM 128 ND1 HIS 18 7.721 13.705 19.456 1.00 0.00 ATOM 129 CE1 HIS 18 7.748 12.382 19.523 1.00 0.00 ATOM 130 NE2 HIS 18 9.001 11.979 19.458 1.00 0.00 ATOM 131 O HIS 18 9.945 18.244 18.905 1.00 0.00 ATOM 132 C HIS 18 8.885 17.783 18.464 1.00 0.00 ATOM 133 N PRO 19 7.727 18.414 18.583 1.00 0.00 ATOM 134 CA PRO 19 7.654 19.728 19.250 1.00 0.00 ATOM 135 CB PRO 19 6.260 20.213 18.977 1.00 0.00 ATOM 136 CG PRO 19 5.978 19.646 17.635 1.00 0.00 ATOM 137 CD PRO 19 6.495 18.236 17.766 1.00 0.00 ATOM 138 O PRO 19 8.645 20.559 21.307 1.00 0.00 ATOM 139 C PRO 19 7.978 19.667 20.782 1.00 0.00 ATOM 140 N GLY 20 7.506 18.625 21.460 1.00 0.00 ATOM 141 CA GLY 20 7.756 18.479 22.890 1.00 0.00 ATOM 142 O GLY 20 9.772 19.046 24.078 1.00 0.00 ATOM 143 C GLY 20 9.263 18.428 23.132 1.00 0.00 ATOM 144 N VAL 21 9.987 17.672 22.274 1.00 0.00 ATOM 145 CA VAL 21 11.453 17.547 22.350 1.00 0.00 ATOM 146 CB VAL 21 11.860 16.518 21.346 1.00 0.00 ATOM 147 CG1 VAL 21 13.330 16.638 21.104 1.00 0.00 ATOM 148 CG2 VAL 21 11.425 15.124 21.775 1.00 0.00 ATOM 149 O VAL 21 13.127 19.198 22.863 1.00 0.00 ATOM 150 C VAL 21 12.147 18.903 22.181 1.00 0.00 ATOM 151 N ALA 22 11.539 19.776 21.373 1.00 0.00 ATOM 152 CA ALA 22 12.043 21.141 21.125 1.00 0.00 ATOM 153 CB ALA 22 11.229 21.871 20.164 1.00 0.00 ATOM 154 O ALA 22 13.029 22.592 22.758 1.00 0.00 ATOM 155 C ALA 22 12.053 21.934 22.426 1.00 0.00 ATOM 156 N GLY 23 10.977 21.845 23.134 1.00 0.00 ATOM 157 CA GLY 23 10.929 22.492 24.424 1.00 0.00 ATOM 158 O GLY 23 12.617 22.793 26.059 1.00 0.00 ATOM 159 C GLY 23 11.931 22.007 25.405 1.00 0.00 ATOM 160 N VAL 24 12.036 20.687 25.525 1.00 0.00 ATOM 161 CA VAL 24 12.985 20.085 26.453 1.00 0.00 ATOM 162 CB VAL 24 12.939 18.554 26.397 1.00 0.00 ATOM 163 CG1 VAL 24 14.033 17.898 27.245 1.00 0.00 ATOM 164 CG2 VAL 24 11.644 18.123 27.060 1.00 0.00 ATOM 165 O VAL 24 15.201 20.820 27.035 1.00 0.00 ATOM 166 C VAL 24 14.414 20.520 26.132 1.00 0.00 ATOM 167 N LEU 25 14.735 20.542 24.856 1.00 0.00 ATOM 168 CA LEU 25 16.080 20.938 24.450 1.00 0.00 ATOM 169 CB LEU 25 16.312 20.798 22.951 1.00 0.00 ATOM 170 CG LEU 25 16.314 19.339 22.510 1.00 0.00 ATOM 171 CD1 LEU 25 16.545 19.277 20.972 1.00 0.00 ATOM 172 CD2 LEU 25 17.182 18.457 23.329 1.00 0.00 ATOM 173 O LEU 25 17.422 22.730 25.340 1.00 0.00 ATOM 174 C LEU 25 16.347 22.397 24.839 1.00 0.00 ATOM 175 N ARG 26 15.373 23.269 24.605 1.00 0.00 ATOM 176 CA ARG 26 15.533 24.680 24.957 1.00 0.00 ATOM 177 CB ARG 26 14.281 25.464 24.466 1.00 0.00 ATOM 178 CG ARG 26 14.022 25.367 22.933 1.00 0.00 ATOM 179 CD ARG 26 12.567 25.733 22.565 1.00 0.00 ATOM 180 NE ARG 26 12.303 25.761 21.119 1.00 0.00 ATOM 181 CZ ARG 26 11.106 26.022 20.581 1.00 0.00 ATOM 182 NH1 ARG 26 10.049 26.270 21.369 1.00 0.00 ATOM 183 NH2 ARG 26 10.970 26.089 19.249 1.00 0.00 ATOM 184 O ARG 26 16.448 25.651 26.948 1.00 0.00 ATOM 185 C ARG 26 15.658 24.855 26.473 1.00 0.00 ATOM 186 N SER 27 14.902 24.036 27.188 1.00 0.00 ATOM 187 CA SER 27 14.853 24.073 28.653 1.00 0.00 ATOM 188 CB SER 27 13.508 23.456 29.083 1.00 0.00 ATOM 189 OG SER 27 13.282 22.170 28.525 1.00 0.00 ATOM 190 O SER 27 16.394 24.006 30.500 1.00 0.00 ATOM 191 C SER 27 16.150 23.664 29.340 1.00 0.00 ATOM 192 N TYR 28 16.999 22.894 28.645 1.00 0.00 ATOM 193 CA TYR 28 18.236 22.389 29.237 1.00 0.00 ATOM 194 CB TYR 28 18.320 20.865 29.086 1.00 0.00 ATOM 195 CG TYR 28 17.313 20.200 30.045 1.00 0.00 ATOM 196 CD1 TYR 28 17.601 20.174 31.390 1.00 0.00 ATOM 197 CD2 TYR 28 16.131 19.628 29.624 1.00 0.00 ATOM 198 CE1 TYR 28 16.729 19.596 32.298 1.00 0.00 ATOM 199 CE2 TYR 28 15.259 19.031 30.518 1.00 0.00 ATOM 200 CZ TYR 28 15.558 19.013 31.875 1.00 0.00 ATOM 201 OH TYR 28 14.715 18.473 32.799 1.00 0.00 ATOM 202 O TYR 28 20.568 22.614 28.638 1.00 0.00 ATOM 203 C TYR 28 19.482 23.168 28.791 1.00 0.00 ATOM 204 N ASN 29 19.298 24.471 28.635 1.00 0.00 ATOM 205 CA ASN 29 20.378 25.429 28.252 1.00 0.00 ATOM 206 CB ASN 29 21.474 25.445 29.315 1.00 0.00 ATOM 207 CG ASN 29 20.943 25.915 30.659 1.00 0.00 ATOM 208 ND2 ASN 29 21.163 25.116 31.668 1.00 0.00 ATOM 209 OD1 ASN 29 20.470 27.023 30.805 1.00 0.00 ATOM 210 O ASN 29 21.960 25.883 26.514 1.00 0.00 ATOM 211 C ASN 29 21.028 25.166 26.893 1.00 0.00 ATOM 212 N LEU 30 20.416 24.296 26.111 1.00 0.00 ATOM 213 CA LEU 30 20.800 24.178 24.693 1.00 0.00 ATOM 214 CB LEU 30 19.993 23.095 23.953 1.00 0.00 ATOM 215 CG LEU 30 19.969 21.711 24.602 1.00 0.00 ATOM 216 CD1 LEU 30 19.473 20.757 23.543 1.00 0.00 ATOM 217 CD2 LEU 30 21.331 21.164 24.940 1.00 0.00 ATOM 218 O LEU 30 21.379 25.907 23.108 1.00 0.00 ATOM 219 C LEU 30 20.611 25.529 23.994 1.00 0.00 ATOM 220 N GLY 31 19.577 26.256 24.450 1.00 0.00 ATOM 221 CA GLY 31 19.276 27.641 24.053 1.00 0.00 ATOM 222 O GLY 31 19.273 28.835 21.953 1.00 0.00 ATOM 223 C GLY 31 19.031 27.789 22.549 1.00 0.00 ATOM 224 N CYS 32 18.433 26.739 22.013 1.00 0.00 ATOM 225 CA CYS 32 18.265 26.594 20.571 1.00 0.00 ATOM 226 CB CYS 32 19.093 25.430 20.042 1.00 0.00 ATOM 227 SG CYS 32 20.869 25.548 20.314 1.00 0.00 ATOM 228 O CYS 32 16.185 25.529 21.037 1.00 0.00 ATOM 229 C CYS 32 16.834 26.224 20.252 1.00 0.00 ATOM 230 N ILE 33 16.392 26.552 19.039 1.00 0.00 ATOM 231 CA ILE 33 15.021 26.180 18.606 1.00 0.00 ATOM 232 CB ILE 33 14.708 26.787 17.225 1.00 0.00 ATOM 233 CG1 ILE 33 14.745 28.319 17.234 1.00 0.00 ATOM 234 CG2 ILE 33 13.403 26.247 16.652 1.00 0.00 ATOM 235 CD1 ILE 33 13.910 28.974 18.319 1.00 0.00 ATOM 236 O ILE 33 14.677 24.046 19.619 1.00 0.00 ATOM 237 C ILE 33 15.059 24.657 18.626 1.00 0.00 ATOM 238 N GLY 34 15.890 24.249 17.652 1.00 0.00 ATOM 239 CA GLY 34 16.482 22.926 17.651 1.00 0.00 ATOM 240 O GLY 34 18.612 22.275 16.758 1.00 0.00 ATOM 241 C GLY 34 17.903 23.195 17.165 1.00 0.00 ATOM 242 N CYS 35 18.316 24.458 17.211 1.00 0.00 ATOM 243 CA CYS 35 19.619 24.807 16.784 1.00 0.00 ATOM 244 CB CYS 35 20.799 23.843 17.047 1.00 0.00 ATOM 245 SG CYS 35 21.229 23.645 18.815 1.00 0.00 ATOM 246 O CYS 35 19.344 23.963 14.542 1.00 0.00 ATOM 247 C CYS 35 19.636 24.930 15.249 1.00 0.00 ATOM 248 N MET 36 19.977 26.112 14.747 1.00 0.00 ATOM 249 CA MET 36 20.027 26.337 13.306 1.00 0.00 ATOM 250 CB MET 36 20.566 27.729 12.913 1.00 0.00 ATOM 251 CG MET 36 20.699 28.794 14.005 1.00 0.00 ATOM 252 SD MET 36 19.070 29.429 14.523 1.00 0.00 ATOM 253 CE MET 36 19.477 30.854 15.514 1.00 0.00 ATOM 254 O MET 36 20.900 24.694 11.747 1.00 0.00 ATOM 255 C MET 36 21.086 25.379 12.755 1.00 0.00 ATOM 256 N GLY 37 22.219 25.437 13.460 1.00 0.00 ATOM 257 CA GLY 37 23.394 24.592 13.239 1.00 0.00 ATOM 258 O GLY 37 23.842 22.230 13.221 1.00 0.00 ATOM 259 C GLY 37 23.088 23.118 13.561 1.00 0.00 ATOM 260 N ALA 38 21.895 22.920 14.128 1.00 0.00 ATOM 261 CA ALA 38 21.221 21.627 14.364 1.00 0.00 ATOM 262 CB ALA 38 19.563 21.955 14.064 1.00 0.00 ATOM 263 O ALA 38 21.396 19.381 13.525 1.00 0.00 ATOM 264 C ALA 38 21.389 20.587 13.269 1.00 0.00 ATOM 265 N GLN 39 21.216 21.096 12.060 1.00 0.00 ATOM 266 CA GLN 39 21.091 20.286 10.833 1.00 0.00 ATOM 267 CB GLN 39 21.022 21.179 9.597 1.00 0.00 ATOM 268 CG GLN 39 19.706 21.963 9.564 1.00 0.00 ATOM 269 CD GLN 39 19.668 22.829 8.316 1.00 0.00 ATOM 270 OE1 GLN 39 19.095 22.485 7.294 1.00 0.00 ATOM 271 NE2 GLN 39 20.398 23.919 8.376 1.00 0.00 ATOM 272 O GLN 39 22.157 18.279 10.113 1.00 0.00 ATOM 273 C GLN 39 22.297 19.387 10.611 1.00 0.00 ATOM 274 N ASN 40 23.395 19.799 11.237 1.00 0.00 ATOM 275 CA ASN 40 24.690 19.123 11.119 1.00 0.00 ATOM 276 CB ASN 40 25.812 20.117 10.960 1.00 0.00 ATOM 277 CG ASN 40 25.685 20.886 9.666 1.00 0.00 ATOM 278 ND2 ASN 40 26.490 21.887 9.657 1.00 0.00 ATOM 279 OD1 ASN 40 24.908 20.648 8.741 1.00 0.00 ATOM 280 O ASN 40 26.034 17.483 12.186 1.00 0.00 ATOM 281 C ASN 40 25.088 18.253 12.313 1.00 0.00 ATOM 282 N GLU 41 24.411 18.426 13.443 1.00 0.00 ATOM 283 CA GLU 41 24.866 17.795 14.685 1.00 0.00 ATOM 284 CB GLU 41 25.269 18.805 15.758 1.00 0.00 ATOM 285 CG GLU 41 26.570 19.540 15.452 1.00 0.00 ATOM 286 CD GLU 41 27.081 20.364 16.648 1.00 0.00 ATOM 287 OE1 GLU 41 26.402 20.375 17.700 1.00 0.00 ATOM 288 OE2 GLU 41 28.065 21.095 16.479 1.00 0.00 ATOM 289 O GLU 41 22.639 17.103 15.327 1.00 0.00 ATOM 290 C GLU 41 23.856 16.852 15.322 1.00 0.00 ATOM 291 N SER 42 24.418 15.801 15.962 1.00 0.00 ATOM 292 CA SER 42 23.601 14.851 16.702 1.00 0.00 ATOM 293 CB SER 42 24.259 13.469 16.766 1.00 0.00 ATOM 294 OG SER 42 25.400 13.437 17.631 1.00 0.00 ATOM 295 O SER 42 24.029 16.395 18.488 1.00 0.00 ATOM 296 C SER 42 23.422 15.389 18.117 1.00 0.00 ATOM 297 N LEU 43 22.588 14.718 18.906 1.00 0.00 ATOM 298 CA LEU 43 22.339 15.142 20.291 1.00 0.00 ATOM 299 CB LEU 43 21.344 14.208 20.967 1.00 0.00 ATOM 300 CG LEU 43 21.200 14.538 22.450 1.00 0.00 ATOM 301 CD1 LEU 43 20.490 15.886 22.562 1.00 0.00 ATOM 302 CD2 LEU 43 20.544 13.425 23.261 1.00 0.00 ATOM 303 O LEU 43 23.877 16.031 21.905 1.00 0.00 ATOM 304 C LEU 43 23.623 15.122 21.113 1.00 0.00 ATOM 305 N GLU 44 24.433 14.084 20.923 1.00 0.00 ATOM 306 CA GLU 44 25.704 13.959 21.660 1.00 0.00 ATOM 307 CB GLU 44 26.407 12.634 21.449 1.00 0.00 ATOM 308 CG GLU 44 25.595 11.499 22.058 1.00 0.00 ATOM 309 CD GLU 44 26.278 10.164 21.834 1.00 0.00 ATOM 310 OE1 GLU 44 27.164 10.095 20.945 1.00 0.00 ATOM 311 OE2 GLU 44 25.756 9.189 22.401 1.00 0.00 ATOM 312 O GLU 44 27.303 15.720 22.096 1.00 0.00 ATOM 313 C GLU 44 26.634 15.129 21.248 1.00 0.00 ATOM 314 N GLN 45 26.664 15.447 19.957 1.00 0.00 ATOM 315 CA GLN 45 27.504 16.534 19.466 1.00 0.00 ATOM 316 CB GLN 45 27.453 16.641 17.956 1.00 0.00 ATOM 317 CG GLN 45 28.176 15.458 17.342 1.00 0.00 ATOM 318 CD GLN 45 28.046 15.495 15.832 1.00 0.00 ATOM 319 OE1 GLN 45 27.050 15.853 15.226 1.00 0.00 ATOM 320 NE2 GLN 45 28.980 14.841 15.203 1.00 0.00 ATOM 321 O GLN 45 27.822 18.596 20.631 1.00 0.00 ATOM 322 C GLN 45 27.039 17.875 20.018 1.00 0.00 ATOM 323 N GLY 46 25.714 17.988 20.098 1.00 0.00 ATOM 324 CA GLY 46 25.062 19.184 20.655 1.00 0.00 ATOM 325 O GLY 46 25.603 20.372 22.684 1.00 0.00 ATOM 326 C GLY 46 25.328 19.286 22.171 1.00 0.00 ATOM 327 N ALA 47 25.244 18.159 22.872 1.00 0.00 ATOM 328 CA ALA 47 25.479 18.145 24.311 1.00 0.00 ATOM 329 CB ALA 47 25.209 16.719 24.764 1.00 0.00 ATOM 330 O ALA 47 27.188 19.333 25.504 1.00 0.00 ATOM 331 C ALA 47 26.923 18.545 24.596 1.00 0.00 ATOM 332 N ASN 48 27.855 18.001 23.818 1.00 0.00 ATOM 333 CA ASN 48 29.290 18.315 23.996 1.00 0.00 ATOM 334 CB ASN 48 30.197 17.567 23.034 1.00 0.00 ATOM 335 CG ASN 48 30.395 16.132 23.515 1.00 0.00 ATOM 336 ND2 ASN 48 30.323 15.221 22.587 1.00 0.00 ATOM 337 OD1 ASN 48 30.659 15.871 24.677 1.00 0.00 ATOM 338 O ASN 48 30.175 20.477 24.544 1.00 0.00 ATOM 339 C ASN 48 29.509 19.805 23.755 1.00 0.00 ATOM 340 N ALA 49 28.946 20.320 22.666 1.00 0.00 ATOM 341 CA ALA 49 29.087 21.770 22.321 1.00 0.00 ATOM 342 CB ALA 49 28.606 22.060 20.903 1.00 0.00 ATOM 343 O ALA 49 28.786 23.842 23.529 1.00 0.00 ATOM 344 C ALA 49 28.370 22.699 23.334 1.00 0.00 ATOM 345 N HIS 50 27.310 22.200 23.962 1.00 0.00 ATOM 346 CA HIS 50 26.567 22.991 24.936 1.00 0.00 ATOM 347 CB HIS 50 25.078 22.799 24.679 1.00 0.00 ATOM 348 CG HIS 50 24.648 23.486 23.387 1.00 0.00 ATOM 349 CD2 HIS 50 24.286 22.924 22.247 1.00 0.00 ATOM 350 ND1 HIS 50 24.632 24.786 23.213 1.00 0.00 ATOM 351 CE1 HIS 50 24.295 25.044 21.963 1.00 0.00 ATOM 352 NE2 HIS 50 24.058 23.885 21.359 1.00 0.00 ATOM 353 O HIS 50 26.317 23.247 27.319 1.00 0.00 ATOM 354 C HIS 50 26.904 22.662 26.396 1.00 0.00 ATOM 355 N GLY 51 27.828 21.748 26.632 1.00 0.00 ATOM 356 CA GLY 51 28.231 21.362 27.983 1.00 0.00 ATOM 357 O GLY 51 27.182 20.606 30.008 1.00 0.00 ATOM 358 C GLY 51 27.179 20.587 28.776 1.00 0.00 ATOM 359 N LEU 52 26.282 19.907 28.070 1.00 0.00 ATOM 360 CA LEU 52 25.234 19.131 28.723 1.00 0.00 ATOM 361 CB LEU 52 23.909 19.526 28.094 1.00 0.00 ATOM 362 CG LEU 52 22.634 18.803 28.529 1.00 0.00 ATOM 363 CD1 LEU 52 22.385 18.764 30.038 1.00 0.00 ATOM 364 CD2 LEU 52 21.491 19.555 27.871 1.00 0.00 ATOM 365 O LEU 52 25.794 17.166 27.465 1.00 0.00 ATOM 366 C LEU 52 25.560 17.648 28.573 1.00 0.00 ATOM 367 N ASN 53 25.574 16.927 29.690 1.00 0.00 ATOM 368 CA ASN 53 25.865 15.535 29.655 1.00 0.00 ATOM 369 CB ASN 53 25.707 14.858 31.021 1.00 0.00 ATOM 370 CG ASN 53 26.930 15.084 31.892 1.00 0.00 ATOM 371 ND2 ASN 53 26.740 15.831 32.995 1.00 0.00 ATOM 372 OD1 ASN 53 28.022 14.567 31.608 1.00 0.00 ATOM 373 O ASN 53 23.615 15.110 28.928 1.00 0.00 ATOM 374 C ASN 53 24.802 14.794 28.841 1.00 0.00 ATOM 375 N VAL 54 25.233 13.812 28.055 1.00 0.00 ATOM 376 CA VAL 54 24.306 13.038 27.237 1.00 0.00 ATOM 377 CB VAL 54 25.071 12.100 26.279 1.00 0.00 ATOM 378 CG1 VAL 54 24.179 11.066 25.587 1.00 0.00 ATOM 379 CG2 VAL 54 25.740 12.931 25.183 1.00 0.00 ATOM 380 O VAL 54 22.130 12.196 27.797 1.00 0.00 ATOM 381 C VAL 54 23.314 12.292 28.123 1.00 0.00 ATOM 382 N GLU 55 23.798 11.765 29.243 1.00 0.00 ATOM 383 CA GLU 55 22.926 11.014 30.194 1.00 0.00 ATOM 384 CB GLU 55 23.684 10.401 31.375 1.00 0.00 ATOM 385 CG GLU 55 24.724 9.338 30.951 1.00 0.00 ATOM 386 CD GLU 55 26.132 9.875 30.655 1.00 0.00 ATOM 387 OE1 GLU 55 26.284 11.104 30.434 1.00 0.00 ATOM 388 OE2 GLU 55 27.035 9.019 30.727 1.00 0.00 ATOM 389 O GLU 55 20.634 11.495 30.826 1.00 0.00 ATOM 390 C GLU 55 21.775 11.941 30.696 1.00 0.00 ATOM 391 N ASP 56 22.090 13.204 30.966 1.00 0.00 ATOM 392 CA ASP 56 21.085 14.150 31.439 1.00 0.00 ATOM 393 CB ASP 56 21.706 15.479 31.854 1.00 0.00 ATOM 394 CG ASP 56 22.633 15.396 33.072 1.00 0.00 ATOM 395 OD1 ASP 56 22.374 14.568 33.963 1.00 0.00 ATOM 396 OD2 ASP 56 23.616 16.155 33.084 1.00 0.00 ATOM 397 O ASP 56 18.828 14.348 30.650 1.00 0.00 ATOM 398 C ASP 56 20.026 14.376 30.365 1.00 0.00 ATOM 399 N ILE 57 20.469 14.603 29.132 1.00 0.00 ATOM 400 CA ILE 57 19.543 14.833 28.023 1.00 0.00 ATOM 401 CB ILE 57 20.308 15.102 26.699 1.00 0.00 ATOM 402 CG1 ILE 57 21.003 16.467 26.785 1.00 0.00 ATOM 403 CG2 ILE 57 19.332 15.044 25.490 1.00 0.00 ATOM 404 CD1 ILE 57 22.049 16.685 25.708 1.00 0.00 ATOM 405 O ILE 57 17.385 13.828 27.566 1.00 0.00 ATOM 406 C ILE 57 18.573 13.649 27.813 1.00 0.00 ATOM 407 N LEU 58 19.150 12.454 27.720 1.00 0.00 ATOM 408 CA LEU 58 18.374 11.236 27.453 1.00 0.00 ATOM 409 CB LEU 58 19.317 10.003 27.297 1.00 0.00 ATOM 410 CG LEU 58 19.994 9.941 25.917 1.00 0.00 ATOM 411 CD1 LEU 58 21.256 9.044 25.964 1.00 0.00 ATOM 412 CD2 LEU 58 18.951 9.439 24.895 1.00 0.00 ATOM 413 O LEU 58 16.198 10.640 28.303 1.00 0.00 ATOM 414 C LEU 58 17.345 11.000 28.574 1.00 0.00 ATOM 415 N ARG 59 17.761 11.203 29.820 1.00 0.00 ATOM 416 CA ARG 59 16.866 11.011 30.956 1.00 0.00 ATOM 417 CB ARG 59 17.546 11.359 32.271 1.00 0.00 ATOM 418 CG ARG 59 18.164 10.125 32.893 1.00 0.00 ATOM 419 CD ARG 59 18.620 10.485 34.296 1.00 0.00 ATOM 420 NE ARG 59 20.079 10.598 34.257 1.00 0.00 ATOM 421 CZ ARG 59 20.801 11.680 34.572 1.00 0.00 ATOM 422 NH1 ARG 59 20.257 12.810 34.968 1.00 0.00 ATOM 423 NH2 ARG 59 22.115 11.622 34.493 1.00 0.00 ATOM 424 O ARG 59 14.558 11.598 30.980 1.00 0.00 ATOM 425 C ARG 59 15.702 12.007 30.855 1.00 0.00 ATOM 426 N ASP 60 16.052 13.198 30.362 1.00 0.00 ATOM 427 CA ASP 60 15.076 14.296 30.220 1.00 0.00 ATOM 428 CB ASP 60 15.780 15.637 29.939 1.00 0.00 ATOM 429 CG ASP 60 16.664 16.113 31.081 1.00 0.00 ATOM 430 OD1 ASP 60 16.425 15.736 32.248 1.00 0.00 ATOM 431 OD2 ASP 60 17.597 16.895 30.801 1.00 0.00 ATOM 432 O ASP 60 12.896 14.155 29.195 1.00 0.00 ATOM 433 C ASP 60 14.102 13.990 29.073 1.00 0.00 ATOM 434 N LEU 61 14.652 13.560 27.960 1.00 0.00 ATOM 435 CA LEU 61 13.833 13.203 26.811 1.00 0.00 ATOM 436 CB LEU 61 14.736 12.840 25.627 1.00 0.00 ATOM 437 CG LEU 61 14.019 12.623 24.281 1.00 0.00 ATOM 438 CD1 LEU 61 13.227 11.309 24.194 1.00 0.00 ATOM 439 CD2 LEU 61 13.105 13.811 23.987 1.00 0.00 ATOM 440 O LEU 61 11.719 12.100 26.833 1.00 0.00 ATOM 441 C LEU 61 12.905 12.057 27.157 1.00 0.00 ATOM 442 N ASN 62 13.418 11.055 27.865 1.00 0.00 ATOM 443 CA ASN 62 12.600 9.902 28.252 1.00 0.00 ATOM 444 CB ASN 62 13.412 8.750 28.829 1.00 0.00 ATOM 445 CG ASN 62 14.275 8.076 27.760 1.00 0.00 ATOM 446 ND2 ASN 62 15.282 7.402 28.229 1.00 0.00 ATOM 447 OD1 ASN 62 14.047 8.067 26.564 1.00 0.00 ATOM 448 O ASN 62 10.394 9.794 29.200 1.00 0.00 ATOM 449 C ASN 62 11.506 10.297 29.246 1.00 0.00 ATOM 450 N ALA 63 11.854 11.192 30.161 1.00 0.00 ATOM 451 CA ALA 63 10.841 11.709 31.108 1.00 0.00 ATOM 452 CB ALA 63 11.502 12.609 32.146 1.00 0.00 ATOM 453 O ALA 63 8.552 12.379 30.798 1.00 0.00 ATOM 454 C ALA 63 9.706 12.450 30.394 1.00 0.00 ATOM 455 N LEU 64 10.070 13.179 29.336 1.00 0.00 ATOM 456 CA LEU 64 9.091 13.887 28.482 1.00 0.00 ATOM 457 CB LEU 64 9.743 14.578 27.324 1.00 0.00 ATOM 458 CG LEU 64 8.772 15.176 26.302 1.00 0.00 ATOM 459 CD1 LEU 64 7.965 16.306 26.923 1.00 0.00 ATOM 460 CD2 LEU 64 9.573 15.685 25.110 1.00 0.00 ATOM 461 O LEU 64 6.945 12.920 28.022 1.00 0.00 ATOM 462 C LEU 64 8.154 12.858 27.826 1.00 0.00 ATOM 463 N ALA 65 8.771 12.051 26.952 1.00 0.00 ATOM 464 CA ALA 65 8.060 10.995 26.246 1.00 0.00 ATOM 465 CB ALA 65 7.864 11.413 24.796 1.00 0.00 ATOM 466 O ALA 65 10.075 9.746 26.063 1.00 0.00 ATOM 467 C ALA 65 8.862 9.708 26.353 1.00 0.00 TER END