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 1 Thu Aug 14 14:48:22 2008 MODEL 1 PARENT N/A ATOM 1 N GLN 3 8.699 11.559 21.774 1.00 0.00 ATOM 2 CA GLN 3 8.469 10.092 21.930 1.00 0.00 ATOM 3 CB GLN 3 7.552 9.583 20.811 1.00 0.00 ATOM 4 CG GLN 3 7.242 8.095 20.896 1.00 0.00 ATOM 5 CD GLN 3 6.483 7.585 19.687 1.00 0.00 ATOM 6 OE1 GLN 3 6.936 7.726 18.550 1.00 0.00 ATOM 7 NE2 GLN 3 5.324 6.981 19.927 1.00 0.00 ATOM 8 O GLN 3 10.533 9.313 22.879 1.00 0.00 ATOM 9 C GLN 3 9.804 9.347 21.890 1.00 0.00 ATOM 10 N LYS 4 10.113 8.683 20.711 1.00 0.00 ATOM 11 CA LYS 4 11.328 7.938 20.671 1.00 0.00 ATOM 12 CB LYS 4 11.172 6.626 19.877 1.00 0.00 ATOM 13 CG LYS 4 10.268 5.575 20.554 1.00 0.00 ATOM 14 CD LYS 4 10.193 4.316 19.747 1.00 0.00 ATOM 15 CE LYS 4 9.264 3.292 20.396 1.00 0.00 ATOM 16 NZ LYS 4 9.116 2.089 19.505 1.00 0.00 ATOM 17 O LYS 4 12.349 9.120 18.865 1.00 0.00 ATOM 18 C LYS 4 12.406 8.738 20.033 1.00 0.00 ATOM 19 N PHE 5 13.392 9.148 20.921 1.00 0.00 ATOM 20 CA PHE 5 14.510 9.902 20.370 1.00 0.00 ATOM 21 CB PHE 5 14.570 11.265 21.061 1.00 0.00 ATOM 22 CG PHE 5 15.763 12.126 20.633 1.00 0.00 ATOM 23 CD1 PHE 5 15.643 13.006 19.581 1.00 0.00 ATOM 24 CD2 PHE 5 16.988 12.019 21.263 1.00 0.00 ATOM 25 CE1 PHE 5 16.745 13.742 19.206 1.00 0.00 ATOM 26 CE2 PHE 5 18.071 12.768 20.869 1.00 0.00 ATOM 27 CZ PHE 5 17.970 13.656 19.829 1.00 0.00 ATOM 28 O PHE 5 16.276 8.825 21.667 1.00 0.00 ATOM 29 C PHE 5 15.813 9.117 20.570 1.00 0.00 ATOM 30 N THR 6 16.471 8.963 19.436 1.00 0.00 ATOM 31 CA THR 6 17.839 8.416 19.392 1.00 0.00 ATOM 32 CB THR 6 17.949 7.450 18.251 1.00 0.00 ATOM 33 CG2 THR 6 19.431 6.903 18.171 1.00 0.00 ATOM 34 OG1 THR 6 17.058 6.381 18.551 1.00 0.00 ATOM 35 O THR 6 18.668 10.427 18.379 1.00 0.00 ATOM 36 C THR 6 18.780 9.611 19.296 1.00 0.00 ATOM 37 N LYS 7 19.710 9.712 20.241 1.00 0.00 ATOM 38 CA LYS 7 20.663 10.813 20.246 1.00 0.00 ATOM 39 CB LYS 7 21.619 10.472 21.405 1.00 0.00 ATOM 40 CG LYS 7 20.963 9.725 22.570 1.00 0.00 ATOM 41 CD LYS 7 21.508 8.290 22.671 1.00 0.00 ATOM 42 CE LYS 7 20.437 7.216 22.861 1.00 0.00 ATOM 43 NZ LYS 7 19.777 7.340 24.157 1.00 0.00 ATOM 44 O LYS 7 22.071 11.978 18.638 1.00 0.00 ATOM 45 C LYS 7 21.483 10.933 18.910 1.00 0.00 ATOM 46 N ASP 8 21.500 9.868 18.112 1.00 0.00 ATOM 47 CA ASP 8 22.233 9.882 16.850 1.00 0.00 ATOM 48 CB ASP 8 22.245 8.466 16.283 1.00 0.00 ATOM 49 CG ASP 8 23.157 7.511 17.036 1.00 0.00 ATOM 50 OD1 ASP 8 23.945 7.968 17.902 1.00 0.00 ATOM 51 OD2 ASP 8 22.937 6.302 16.847 1.00 0.00 ATOM 52 O ASP 8 22.395 11.130 14.805 1.00 0.00 ATOM 53 C ASP 8 21.688 10.794 15.755 1.00 0.00 ATOM 54 N MET 9 20.416 11.159 15.905 1.00 0.00 ATOM 55 CA MET 9 19.732 12.008 14.915 1.00 0.00 ATOM 56 CB MET 9 18.219 12.079 15.127 1.00 0.00 ATOM 57 CG MET 9 17.525 10.762 14.849 1.00 0.00 ATOM 58 SD MET 9 15.711 11.020 14.893 1.00 0.00 ATOM 59 CE MET 9 15.417 11.296 16.624 1.00 0.00 ATOM 60 O MET 9 20.652 13.974 15.928 1.00 0.00 ATOM 61 C MET 9 20.276 13.424 14.886 1.00 0.00 ATOM 62 N THR 10 20.154 14.019 13.719 1.00 0.00 ATOM 63 CA THR 10 20.401 15.469 13.596 1.00 0.00 ATOM 64 CB THR 10 20.326 15.939 12.098 1.00 0.00 ATOM 65 CG2 THR 10 21.223 15.106 11.199 1.00 0.00 ATOM 66 OG1 THR 10 18.953 15.820 11.685 1.00 0.00 ATOM 67 O THR 10 18.340 15.692 14.795 1.00 0.00 ATOM 68 C THR 10 19.422 16.202 14.500 1.00 0.00 ATOM 69 N PHE 11 19.766 17.366 14.992 1.00 0.00 ATOM 70 CA PHE 11 18.868 18.128 15.843 1.00 0.00 ATOM 71 CB PHE 11 19.621 19.311 16.404 1.00 0.00 ATOM 72 CG PHE 11 20.454 18.992 17.618 1.00 0.00 ATOM 73 CD1 PHE 11 21.790 19.326 17.597 1.00 0.00 ATOM 74 CD2 PHE 11 19.861 18.390 18.710 1.00 0.00 ATOM 75 CE1 PHE 11 22.573 19.024 18.683 1.00 0.00 ATOM 76 CE2 PHE 11 20.654 18.098 19.798 1.00 0.00 ATOM 77 CZ PHE 11 22.009 18.399 19.791 1.00 0.00 ATOM 78 O PHE 11 16.540 18.672 15.635 1.00 0.00 ATOM 79 C PHE 11 17.642 18.625 15.085 1.00 0.00 ATOM 80 N ALA 12 17.833 18.996 13.823 1.00 0.00 ATOM 81 CA ALA 12 16.728 19.487 13.001 1.00 0.00 ATOM 82 CB ALA 12 17.119 20.001 11.701 1.00 0.00 ATOM 83 O ALA 12 14.473 18.668 12.995 1.00 0.00 ATOM 84 C ALA 12 15.669 18.397 12.878 1.00 0.00 ATOM 85 N GLN 13 16.108 17.165 12.642 1.00 0.00 ATOM 86 CA GLN 13 15.172 16.021 12.506 1.00 0.00 ATOM 87 CB GLN 13 15.934 14.746 12.157 1.00 0.00 ATOM 88 CG GLN 13 16.359 14.818 10.694 1.00 0.00 ATOM 89 CD GLN 13 17.233 13.650 10.258 1.00 0.00 ATOM 90 OE1 GLN 13 18.194 13.196 10.886 1.00 0.00 ATOM 91 NE2 GLN 13 16.971 13.200 9.066 1.00 0.00 ATOM 92 O GLN 13 13.231 15.452 13.800 1.00 0.00 ATOM 93 C GLN 13 14.423 15.764 13.812 1.00 0.00 ATOM 94 N ALA 14 15.123 15.894 14.936 1.00 0.00 ATOM 95 CA ALA 14 14.507 15.674 16.239 1.00 0.00 ATOM 96 CB ALA 14 15.688 16.316 17.251 1.00 0.00 ATOM 97 O ALA 14 12.302 16.354 16.916 1.00 0.00 ATOM 98 C ALA 14 13.400 16.707 16.491 1.00 0.00 ATOM 99 N LEU 15 13.701 17.975 16.226 1.00 0.00 ATOM 100 CA LEU 15 12.723 19.040 16.430 1.00 0.00 ATOM 101 CB LEU 15 13.421 20.375 16.158 1.00 0.00 ATOM 102 CG LEU 15 12.453 21.563 16.125 1.00 0.00 ATOM 103 CD1 LEU 15 11.785 21.773 17.464 1.00 0.00 ATOM 104 CD2 LEU 15 13.186 22.839 15.706 1.00 0.00 ATOM 105 O LEU 15 10.378 19.055 15.921 1.00 0.00 ATOM 106 C LEU 15 11.521 18.845 15.512 1.00 0.00 ATOM 107 N GLN 16 11.779 18.445 14.271 1.00 0.00 ATOM 108 CA GLN 16 10.714 18.228 13.322 1.00 0.00 ATOM 109 CB GLN 16 11.290 18.000 11.942 1.00 0.00 ATOM 110 CG GLN 16 11.929 19.317 11.491 1.00 0.00 ATOM 111 CD GLN 16 12.557 19.176 10.122 1.00 0.00 ATOM 112 OE1 GLN 16 12.006 19.522 9.097 1.00 0.00 ATOM 113 NE2 GLN 16 13.784 18.714 10.126 1.00 0.00 ATOM 114 O GLN 16 8.605 17.118 13.597 1.00 0.00 ATOM 115 C GLN 16 9.822 17.075 13.773 1.00 0.00 ATOM 116 N THR 17 10.432 16.048 14.355 1.00 0.00 ATOM 117 CA THR 17 9.667 14.859 14.843 1.00 0.00 ATOM 118 CB THR 17 10.624 13.728 15.170 1.00 0.00 ATOM 119 CG2 THR 17 9.892 12.494 15.718 1.00 0.00 ATOM 120 OG1 THR 17 11.228 13.298 13.945 1.00 0.00 ATOM 121 O THR 17 7.685 14.710 16.173 1.00 0.00 ATOM 122 C THR 17 8.811 15.193 16.048 1.00 0.00 ATOM 123 N HIS 18 9.343 16.022 16.939 1.00 0.00 ATOM 124 CA HIS 18 8.612 16.414 18.138 1.00 0.00 ATOM 125 CB HIS 18 9.337 15.745 19.292 1.00 0.00 ATOM 126 CG HIS 18 8.995 14.277 19.292 1.00 0.00 ATOM 127 CD2 HIS 18 7.817 13.649 19.539 1.00 0.00 ATOM 128 ND1 HIS 18 9.889 13.302 18.927 1.00 0.00 ATOM 129 CE1 HIS 18 9.274 12.111 18.940 1.00 0.00 ATOM 130 NE2 HIS 18 8.031 12.293 19.295 1.00 0.00 ATOM 131 O HIS 18 9.824 18.330 18.949 1.00 0.00 ATOM 132 C HIS 18 8.762 17.897 18.505 1.00 0.00 ATOM 133 N PRO 19 7.597 18.537 18.655 1.00 0.00 ATOM 134 CA PRO 19 7.516 19.805 19.383 1.00 0.00 ATOM 135 CB PRO 19 6.084 20.302 19.097 1.00 0.00 ATOM 136 CG PRO 19 5.701 19.661 17.783 1.00 0.00 ATOM 137 CD PRO 19 6.392 18.291 17.832 1.00 0.00 ATOM 138 O PRO 19 8.477 20.573 21.459 1.00 0.00 ATOM 139 C PRO 19 7.852 19.680 20.885 1.00 0.00 ATOM 140 N GLY 20 7.437 18.579 21.503 1.00 0.00 ATOM 141 CA GLY 20 7.703 18.361 22.921 1.00 0.00 ATOM 142 O GLY 20 9.721 18.899 24.113 1.00 0.00 ATOM 143 C GLY 20 9.220 18.335 23.140 1.00 0.00 ATOM 144 N VAL 21 9.942 17.678 22.238 1.00 0.00 ATOM 145 CA VAL 21 11.394 17.592 22.348 1.00 0.00 ATOM 146 CB VAL 21 11.882 16.621 21.257 1.00 0.00 ATOM 147 CG1 VAL 21 13.391 16.589 21.073 1.00 0.00 ATOM 148 CG2 VAL 21 11.603 15.188 21.691 1.00 0.00 ATOM 149 O VAL 21 13.040 19.243 22.913 1.00 0.00 ATOM 150 C VAL 21 12.028 18.977 22.264 1.00 0.00 ATOM 151 N ALA 22 11.432 19.855 21.466 1.00 0.00 ATOM 152 CA ALA 22 11.958 21.263 21.295 1.00 0.00 ATOM 153 CB ALA 22 11.029 22.042 20.383 1.00 0.00 ATOM 154 O ALA 22 12.921 22.647 22.972 1.00 0.00 ATOM 155 C ALA 22 11.957 21.971 22.613 1.00 0.00 ATOM 156 N GLY 23 10.863 21.822 23.354 1.00 0.00 ATOM 157 CA GLY 23 10.744 22.462 24.660 1.00 0.00 ATOM 158 O GLY 23 12.424 22.781 26.295 1.00 0.00 ATOM 159 C GLY 23 11.786 21.991 25.598 1.00 0.00 ATOM 160 N VAL 24 11.983 20.677 25.633 1.00 0.00 ATOM 161 CA VAL 24 12.985 20.086 26.511 1.00 0.00 ATOM 162 CB VAL 24 13.055 18.578 26.404 1.00 0.00 ATOM 163 CG1 VAL 24 14.245 18.010 27.190 1.00 0.00 ATOM 164 CG2 VAL 24 11.761 18.000 26.935 1.00 0.00 ATOM 165 O VAL 24 15.173 20.942 27.093 1.00 0.00 ATOM 166 C VAL 24 14.402 20.571 26.184 1.00 0.00 ATOM 167 N LEU 25 14.736 20.607 24.889 1.00 0.00 ATOM 168 CA LEU 25 16.077 21.066 24.489 1.00 0.00 ATOM 169 CB LEU 25 16.284 20.833 22.992 1.00 0.00 ATOM 170 CG LEU 25 16.321 19.355 22.609 1.00 0.00 ATOM 171 CD1 LEU 25 16.573 19.285 21.101 1.00 0.00 ATOM 172 CD2 LEU 25 17.414 18.574 23.351 1.00 0.00 ATOM 173 O LEU 25 17.351 22.885 25.392 1.00 0.00 ATOM 174 C LEU 25 16.300 22.526 24.860 1.00 0.00 ATOM 175 N ARG 26 15.305 23.387 24.584 1.00 0.00 ATOM 176 CA ARG 26 15.415 24.797 24.931 1.00 0.00 ATOM 177 CB ARG 26 14.234 25.630 24.662 1.00 0.00 ATOM 178 CG ARG 26 14.207 25.977 23.173 1.00 0.00 ATOM 179 CD ARG 26 13.056 26.923 22.878 1.00 0.00 ATOM 180 NE ARG 26 11.824 26.220 22.727 1.00 0.00 ATOM 181 CZ ARG 26 11.359 25.458 21.767 1.00 0.00 ATOM 182 NH1 ARG 26 12.018 25.190 20.633 1.00 0.00 ATOM 183 NH2 ARG 26 10.150 24.951 21.948 1.00 0.00 ATOM 184 O ARG 26 16.262 25.856 26.946 1.00 0.00 ATOM 185 C ARG 26 15.563 24.954 26.481 1.00 0.00 ATOM 186 N SER 27 14.911 24.082 27.243 1.00 0.00 ATOM 187 CA SER 27 14.989 24.143 28.698 1.00 0.00 ATOM 188 CB SER 27 13.471 23.526 29.073 1.00 0.00 ATOM 189 OG SER 27 13.372 22.144 28.605 1.00 0.00 ATOM 190 O SER 27 16.611 24.164 30.475 1.00 0.00 ATOM 191 C SER 27 16.330 23.800 29.330 1.00 0.00 ATOM 192 N TYR 28 17.134 23.080 28.594 1.00 0.00 ATOM 193 CA TYR 28 18.418 22.638 29.133 1.00 0.00 ATOM 194 CB TYR 28 18.497 21.111 28.985 1.00 0.00 ATOM 195 CG TYR 28 17.564 20.452 30.011 1.00 0.00 ATOM 196 CD1 TYR 28 17.879 20.450 31.363 1.00 0.00 ATOM 197 CD2 TYR 28 16.393 19.820 29.600 1.00 0.00 ATOM 198 CE1 TYR 28 17.055 19.822 32.285 1.00 0.00 ATOM 199 CE2 TYR 28 15.568 19.191 30.520 1.00 0.00 ATOM 200 CZ TYR 28 15.895 19.192 31.862 1.00 0.00 ATOM 201 OH TYR 28 15.150 18.534 32.787 1.00 0.00 ATOM 202 O TYR 28 20.732 23.073 28.578 1.00 0.00 ATOM 203 C TYR 28 19.603 23.546 28.712 1.00 0.00 ATOM 204 N ASN 29 19.334 24.833 28.512 1.00 0.00 ATOM 205 CA ASN 29 20.377 25.771 28.117 1.00 0.00 ATOM 206 CB ASN 29 21.493 25.796 29.174 1.00 0.00 ATOM 207 CG ASN 29 20.988 26.243 30.533 1.00 0.00 ATOM 208 ND2 ASN 29 21.275 25.455 31.563 1.00 0.00 ATOM 209 OD1 ASN 29 20.350 27.290 30.657 1.00 0.00 ATOM 210 O ASN 29 21.996 26.124 26.348 1.00 0.00 ATOM 211 C ASN 29 21.023 25.476 26.751 1.00 0.00 ATOM 212 N LEU 30 20.394 24.606 25.961 1.00 0.00 ATOM 213 CA LEU 30 20.747 24.499 24.525 1.00 0.00 ATOM 214 CB LEU 30 19.971 23.368 23.832 1.00 0.00 ATOM 215 CG LEU 30 20.035 21.999 24.448 1.00 0.00 ATOM 216 CD1 LEU 30 19.366 20.996 23.506 1.00 0.00 ATOM 217 CD2 LEU 30 21.345 21.568 24.901 1.00 0.00 ATOM 218 O LEU 30 21.279 26.284 23.021 1.00 0.00 ATOM 219 C LEU 30 20.481 25.844 23.841 1.00 0.00 ATOM 220 N GLY 31 19.464 26.551 24.336 1.00 0.00 ATOM 221 CA GLY 31 19.101 27.914 23.906 1.00 0.00 ATOM 222 O GLY 31 18.965 29.027 21.801 1.00 0.00 ATOM 223 C GLY 31 18.803 27.978 22.422 1.00 0.00 ATOM 224 N CYS 32 18.363 26.862 21.878 1.00 0.00 ATOM 225 CA CYS 32 18.043 26.823 20.458 1.00 0.00 ATOM 226 CB CYS 32 19.120 25.887 19.938 1.00 0.00 ATOM 227 SG CYS 32 20.753 26.600 20.201 1.00 0.00 ATOM 228 O CYS 32 16.058 25.536 20.944 1.00 0.00 ATOM 229 C CYS 32 16.627 26.286 20.148 1.00 0.00 ATOM 230 N ILE 33 16.076 26.673 19.001 1.00 0.00 ATOM 231 CA ILE 33 14.746 26.221 18.613 1.00 0.00 ATOM 232 CB ILE 33 14.407 26.708 17.239 1.00 0.00 ATOM 233 CG1 ILE 33 14.447 28.239 17.163 1.00 0.00 ATOM 234 CG2 ILE 33 13.056 26.150 16.794 1.00 0.00 ATOM 235 CD1 ILE 33 13.707 28.928 18.311 1.00 0.00 ATOM 236 O ILE 33 14.160 24.013 19.469 1.00 0.00 ATOM 237 C ILE 33 14.777 24.686 18.645 1.00 0.00 ATOM 238 N GLY 34 15.670 24.340 17.795 1.00 0.00 ATOM 239 CA GLY 34 16.239 23.001 17.753 1.00 0.00 ATOM 240 O GLY 34 18.177 22.164 16.720 1.00 0.00 ATOM 241 C GLY 34 17.668 23.140 17.232 1.00 0.00 ATOM 242 N CYS 35 18.213 24.296 17.432 1.00 0.00 ATOM 243 CA CYS 35 19.472 24.775 16.824 1.00 0.00 ATOM 244 CB CYS 35 20.635 23.822 17.145 1.00 0.00 ATOM 245 SG CYS 35 21.037 23.645 18.903 1.00 0.00 ATOM 246 O CYS 35 18.400 24.351 14.723 1.00 0.00 ATOM 247 C CYS 35 19.242 25.019 15.301 1.00 0.00 ATOM 248 N MET 36 19.752 26.109 14.687 1.00 0.00 ATOM 249 CA MET 36 19.771 26.224 13.199 1.00 0.00 ATOM 250 CB MET 36 20.527 27.676 12.913 1.00 0.00 ATOM 251 CG MET 36 20.574 28.656 14.077 1.00 0.00 ATOM 252 SD MET 36 18.966 29.355 14.516 1.00 0.00 ATOM 253 CE MET 36 19.462 30.678 15.602 1.00 0.00 ATOM 254 O MET 36 20.802 24.676 11.698 1.00 0.00 ATOM 255 C MET 36 20.924 25.379 12.703 1.00 0.00 ATOM 256 N GLY 37 22.040 25.414 13.425 1.00 0.00 ATOM 257 CA GLY 37 23.200 24.606 13.067 1.00 0.00 ATOM 258 O GLY 37 23.709 22.279 13.159 1.00 0.00 ATOM 259 C GLY 37 22.926 23.171 13.460 1.00 0.00 ATOM 260 N ALA 38 21.741 22.952 14.120 1.00 0.00 ATOM 261 CA ALA 38 21.266 21.595 14.371 1.00 0.00 ATOM 262 CB ALA 38 19.589 21.844 14.246 1.00 0.00 ATOM 263 O ALA 38 21.387 19.387 13.528 1.00 0.00 ATOM 264 C ALA 38 21.345 20.590 13.242 1.00 0.00 ATOM 265 N GLN 39 21.077 21.088 12.040 1.00 0.00 ATOM 266 CA GLN 39 20.944 20.303 10.787 1.00 0.00 ATOM 267 CB GLN 39 20.830 21.135 9.561 1.00 0.00 ATOM 268 CG GLN 39 19.508 21.914 9.529 1.00 0.00 ATOM 269 CD GLN 39 19.464 22.795 8.295 1.00 0.00 ATOM 270 OE1 GLN 39 18.754 22.517 7.312 1.00 0.00 ATOM 271 NE2 GLN 39 20.239 23.900 8.346 1.00 0.00 ATOM 272 O GLN 39 21.960 18.161 10.384 1.00 0.00 ATOM 273 C GLN 39 22.114 19.316 10.741 1.00 0.00 ATOM 274 N ASN 40 23.259 19.846 11.140 1.00 0.00 ATOM 275 CA ASN 40 24.542 19.136 11.056 1.00 0.00 ATOM 276 CB ASN 40 25.652 20.197 10.783 1.00 0.00 ATOM 277 CG ASN 40 25.485 20.913 9.461 1.00 0.00 ATOM 278 ND2 ASN 40 25.975 22.150 9.385 1.00 0.00 ATOM 279 OD1 ASN 40 24.900 20.365 8.518 1.00 0.00 ATOM 280 O ASN 40 25.901 17.498 12.087 1.00 0.00 ATOM 281 C ASN 40 24.970 18.282 12.249 1.00 0.00 ATOM 282 N GLU 41 24.307 18.421 13.384 1.00 0.00 ATOM 283 CA GLU 41 24.826 17.819 14.621 1.00 0.00 ATOM 284 CB GLU 41 25.287 18.815 15.682 1.00 0.00 ATOM 285 CG GLU 41 26.563 19.558 15.290 1.00 0.00 ATOM 286 CD GLU 41 27.112 20.394 16.455 1.00 0.00 ATOM 287 OE1 GLU 41 26.465 20.451 17.537 1.00 0.00 ATOM 288 OE2 GLU 41 28.145 21.038 16.226 1.00 0.00 ATOM 289 O GLU 41 22.612 17.148 15.323 1.00 0.00 ATOM 290 C GLU 41 23.826 16.888 15.289 1.00 0.00 ATOM 291 N SER 42 24.395 15.847 15.930 1.00 0.00 ATOM 292 CA SER 42 23.590 14.909 16.698 1.00 0.00 ATOM 293 CB SER 42 24.235 13.516 16.727 1.00 0.00 ATOM 294 OG SER 42 25.226 13.415 17.744 1.00 0.00 ATOM 295 O SER 42 23.999 16.379 18.549 1.00 0.00 ATOM 296 C SER 42 23.403 15.383 18.135 1.00 0.00 ATOM 297 N LEU 43 22.579 14.669 18.895 1.00 0.00 ATOM 298 CA LEU 43 22.327 15.030 20.293 1.00 0.00 ATOM 299 CB LEU 43 21.431 13.991 20.924 1.00 0.00 ATOM 300 CG LEU 43 21.226 14.192 22.429 1.00 0.00 ATOM 301 CD1 LEU 43 20.477 15.474 22.745 1.00 0.00 ATOM 302 CD2 LEU 43 20.508 12.986 23.005 1.00 0.00 ATOM 303 O LEU 43 23.865 15.934 21.875 1.00 0.00 ATOM 304 C LEU 43 23.621 15.031 21.089 1.00 0.00 ATOM 305 N GLU 44 24.500 14.017 20.891 1.00 0.00 ATOM 306 CA GLU 44 25.757 13.945 21.619 1.00 0.00 ATOM 307 CB GLU 44 26.475 12.635 21.371 1.00 0.00 ATOM 308 CG GLU 44 25.717 11.447 21.961 1.00 0.00 ATOM 309 CD GLU 44 26.474 10.141 21.755 1.00 0.00 ATOM 310 OE1 GLU 44 27.333 10.139 20.854 1.00 0.00 ATOM 311 OE2 GLU 44 26.102 9.151 22.411 1.00 0.00 ATOM 312 O GLU 44 27.350 15.698 22.098 1.00 0.00 ATOM 313 C GLU 44 26.681 15.125 21.236 1.00 0.00 ATOM 314 N GLN 45 26.708 15.475 19.953 1.00 0.00 ATOM 315 CA GLN 45 27.546 16.575 19.488 1.00 0.00 ATOM 316 CB GLN 45 27.471 16.738 17.976 1.00 0.00 ATOM 317 CG GLN 45 28.226 15.608 17.322 1.00 0.00 ATOM 318 CD GLN 45 28.085 15.646 15.819 1.00 0.00 ATOM 319 OE1 GLN 45 27.067 16.048 15.286 1.00 0.00 ATOM 320 NE2 GLN 45 29.002 14.987 15.162 1.00 0.00 ATOM 321 O GLN 45 27.857 18.628 20.674 1.00 0.00 ATOM 322 C GLN 45 27.065 17.896 20.087 1.00 0.00 ATOM 323 N GLY 46 25.742 18.021 20.149 1.00 0.00 ATOM 324 CA GLY 46 25.088 19.196 20.738 1.00 0.00 ATOM 325 O GLY 46 25.624 20.329 22.773 1.00 0.00 ATOM 326 C GLY 46 25.366 19.256 22.226 1.00 0.00 ATOM 327 N ALA 47 25.316 18.097 22.905 1.00 0.00 ATOM 328 CA ALA 47 25.565 18.035 24.342 1.00 0.00 ATOM 329 CB ALA 47 25.300 16.617 24.765 1.00 0.00 ATOM 330 O ALA 47 27.279 19.227 25.525 1.00 0.00 ATOM 331 C ALA 47 27.007 18.456 24.603 1.00 0.00 ATOM 332 N ASN 48 27.931 17.950 23.793 1.00 0.00 ATOM 333 CA ASN 48 29.356 18.289 23.948 1.00 0.00 ATOM 334 CB ASN 48 30.233 17.588 22.917 1.00 0.00 ATOM 335 CG ASN 48 30.407 16.119 23.288 1.00 0.00 ATOM 336 ND2 ASN 48 30.247 15.187 22.285 1.00 0.00 ATOM 337 OD1 ASN 48 30.711 15.815 24.464 1.00 0.00 ATOM 338 O ASN 48 30.228 20.440 24.552 1.00 0.00 ATOM 339 C ASN 48 29.551 19.788 23.755 1.00 0.00 ATOM 340 N ALA 49 28.956 20.334 22.700 1.00 0.00 ATOM 341 CA ALA 49 29.071 21.786 22.407 1.00 0.00 ATOM 342 CB ALA 49 28.490 22.079 21.031 1.00 0.00 ATOM 343 O ALA 49 28.794 23.829 23.668 1.00 0.00 ATOM 344 C ALA 49 28.354 22.705 23.426 1.00 0.00 ATOM 345 N HIS 50 27.260 22.219 24.006 1.00 0.00 ATOM 346 CA HIS 50 26.511 23.002 24.983 1.00 0.00 ATOM 347 CB HIS 50 25.034 22.815 24.786 1.00 0.00 ATOM 348 CG HIS 50 24.564 23.409 23.495 1.00 0.00 ATOM 349 CD2 HIS 50 24.157 22.826 22.341 1.00 0.00 ATOM 350 ND1 HIS 50 24.538 24.767 23.269 1.00 0.00 ATOM 351 CE1 HIS 50 24.135 24.999 22.031 1.00 0.00 ATOM 352 NE2 HIS 50 23.898 23.838 21.446 1.00 0.00 ATOM 353 O HIS 50 26.272 23.188 27.389 1.00 0.00 ATOM 354 C HIS 50 26.868 22.644 26.459 1.00 0.00 ATOM 355 N GLY 51 27.826 21.742 26.647 1.00 0.00 ATOM 356 CA GLY 51 28.236 21.342 27.989 1.00 0.00 ATOM 357 O GLY 51 27.121 20.634 29.991 1.00 0.00 ATOM 358 C GLY 51 27.160 20.587 28.761 1.00 0.00 ATOM 359 N LEU 52 26.288 19.890 28.038 1.00 0.00 ATOM 360 CA LEU 52 25.243 19.146 28.666 1.00 0.00 ATOM 361 CB LEU 52 23.906 19.557 28.045 1.00 0.00 ATOM 362 CG LEU 52 22.686 18.706 28.371 1.00 0.00 ATOM 363 CD1 LEU 52 22.367 18.714 29.808 1.00 0.00 ATOM 364 CD2 LEU 52 21.607 19.406 27.568 1.00 0.00 ATOM 365 O LEU 52 25.817 17.148 27.503 1.00 0.00 ATOM 366 C LEU 52 25.582 17.685 28.586 1.00 0.00 ATOM 367 N ASN 53 25.608 17.024 29.739 1.00 0.00 ATOM 368 CA ASN 53 25.925 15.601 29.788 1.00 0.00 ATOM 369 CB ASN 53 26.006 15.064 31.207 1.00 0.00 ATOM 370 CG ASN 53 27.234 15.505 31.977 1.00 0.00 ATOM 371 ND2 ASN 53 27.125 15.405 33.274 1.00 0.00 ATOM 372 OD1 ASN 53 28.187 16.054 31.447 1.00 0.00 ATOM 373 O ASN 53 23.703 15.096 29.035 1.00 0.00 ATOM 374 C ASN 53 24.901 14.817 28.975 1.00 0.00 ATOM 375 N VAL 54 25.372 13.832 28.219 1.00 0.00 ATOM 376 CA VAL 54 24.483 13.016 27.404 1.00 0.00 ATOM 377 CB VAL 54 25.311 12.036 26.504 1.00 0.00 ATOM 378 CG1 VAL 54 24.397 10.978 25.880 1.00 0.00 ATOM 379 CG2 VAL 54 26.014 12.828 25.385 1.00 0.00 ATOM 380 O VAL 54 22.305 12.113 27.912 1.00 0.00 ATOM 381 C VAL 54 23.481 12.235 28.287 1.00 0.00 ATOM 382 N GLU 55 23.933 11.759 29.435 1.00 0.00 ATOM 383 CA GLU 55 23.049 11.041 30.366 1.00 0.00 ATOM 384 CB GLU 55 23.793 10.423 31.547 1.00 0.00 ATOM 385 CG GLU 55 24.880 9.410 31.211 1.00 0.00 ATOM 386 CD GLU 55 26.265 9.995 30.914 1.00 0.00 ATOM 387 OE1 GLU 55 26.408 11.205 30.638 1.00 0.00 ATOM 388 OE2 GLU 55 27.185 9.144 30.951 1.00 0.00 ATOM 389 O GLU 55 20.739 11.483 30.844 1.00 0.00 ATOM 390 C GLU 55 21.886 11.930 30.794 1.00 0.00 ATOM 391 N ASP 56 22.182 13.189 31.100 1.00 0.00 ATOM 392 CA ASP 56 21.125 14.166 31.534 1.00 0.00 ATOM 393 CB ASP 56 21.759 15.486 31.965 1.00 0.00 ATOM 394 CG ASP 56 22.639 15.387 33.212 1.00 0.00 ATOM 395 OD1 ASP 56 22.403 14.535 34.097 1.00 0.00 ATOM 396 OD2 ASP 56 23.621 16.158 33.222 1.00 0.00 ATOM 397 O ASP 56 18.881 14.384 30.707 1.00 0.00 ATOM 398 C ASP 56 20.082 14.369 30.439 1.00 0.00 ATOM 399 N ILE 57 20.542 14.517 29.187 1.00 0.00 ATOM 400 CA ILE 57 19.650 14.723 28.055 1.00 0.00 ATOM 401 CB ILE 57 20.449 15.022 26.778 1.00 0.00 ATOM 402 CG1 ILE 57 21.034 16.427 26.847 1.00 0.00 ATOM 403 CG2 ILE 57 19.528 14.964 25.563 1.00 0.00 ATOM 404 CD1 ILE 57 22.086 16.737 25.771 1.00 0.00 ATOM 405 O ILE 57 17.558 13.649 27.580 1.00 0.00 ATOM 406 C ILE 57 18.762 13.509 27.803 1.00 0.00 ATOM 407 N LEU 58 19.355 12.321 27.842 1.00 0.00 ATOM 408 CA LEU 58 18.597 11.076 27.616 1.00 0.00 ATOM 409 CB LEU 58 19.588 9.898 27.574 1.00 0.00 ATOM 410 CG LEU 58 18.946 8.503 27.441 1.00 0.00 ATOM 411 CD1 LEU 58 18.055 8.408 26.195 1.00 0.00 ATOM 412 CD2 LEU 58 20.035 7.454 27.439 1.00 0.00 ATOM 413 O LEU 58 16.394 10.573 28.334 1.00 0.00 ATOM 414 C LEU 58 17.542 10.888 28.647 1.00 0.00 ATOM 415 N ARG 59 17.919 11.079 29.906 1.00 0.00 ATOM 416 CA ARG 59 16.975 10.927 31.008 1.00 0.00 ATOM 417 CB ARG 59 17.618 11.280 32.321 1.00 0.00 ATOM 418 CG ARG 59 18.277 10.176 32.982 1.00 0.00 ATOM 419 CD ARG 59 18.735 10.574 34.384 1.00 0.00 ATOM 420 NE ARG 59 20.171 10.671 34.371 1.00 0.00 ATOM 421 CZ ARG 59 20.876 11.734 34.693 1.00 0.00 ATOM 422 NH1 ARG 59 20.311 12.866 35.120 1.00 0.00 ATOM 423 NH2 ARG 59 22.182 11.638 34.592 1.00 0.00 ATOM 424 O ARG 59 14.680 11.603 31.058 1.00 0.00 ATOM 425 C ARG 59 15.839 11.971 30.886 1.00 0.00 ATOM 426 N ASP 60 16.183 13.164 30.409 1.00 0.00 ATOM 427 CA ASP 60 15.208 14.249 30.226 1.00 0.00 ATOM 428 CB ASP 60 15.895 15.584 29.908 1.00 0.00 ATOM 429 CG ASP 60 16.661 16.108 31.123 1.00 0.00 ATOM 430 OD1 ASP 60 16.254 15.715 32.232 1.00 0.00 ATOM 431 OD2 ASP 60 17.657 16.820 30.924 1.00 0.00 ATOM 432 O ASP 60 13.020 14.103 29.217 1.00 0.00 ATOM 433 C ASP 60 14.223 13.914 29.096 1.00 0.00 ATOM 434 N LEU 61 14.765 13.428 28.001 1.00 0.00 ATOM 435 CA LEU 61 13.936 13.040 26.869 1.00 0.00 ATOM 436 CB LEU 61 14.817 12.629 25.685 1.00 0.00 ATOM 437 CG LEU 61 14.117 12.388 24.344 1.00 0.00 ATOM 438 CD1 LEU 61 13.310 11.116 24.403 1.00 0.00 ATOM 439 CD2 LEU 61 13.223 13.571 24.008 1.00 0.00 ATOM 440 O LEU 61 11.803 11.934 26.945 1.00 0.00 ATOM 441 C LEU 61 12.995 11.907 27.272 1.00 0.00 ATOM 442 N ASN 62 13.538 10.930 27.977 1.00 0.00 ATOM 443 CA ASN 62 12.726 9.798 28.444 1.00 0.00 ATOM 444 CB ASN 62 13.573 8.711 29.095 1.00 0.00 ATOM 445 CG ASN 62 14.412 7.932 28.071 1.00 0.00 ATOM 446 ND2 ASN 62 15.427 7.241 28.555 1.00 0.00 ATOM 447 OD1 ASN 62 14.143 7.945 26.869 1.00 0.00 ATOM 448 O ASN 62 10.467 9.846 29.263 1.00 0.00 ATOM 449 C ASN 62 11.614 10.282 29.376 1.00 0.00 ATOM 450 N ALA 63 11.956 11.181 30.294 1.00 0.00 ATOM 451 CA ALA 63 10.977 11.714 31.234 1.00 0.00 ATOM 452 CB ALA 63 11.617 12.621 32.254 1.00 0.00 ATOM 453 O ALA 63 8.690 12.374 30.891 1.00 0.00 ATOM 454 C ALA 63 9.858 12.453 30.505 1.00 0.00 ATOM 455 N LEU 64 10.220 13.179 29.446 1.00 0.00 ATOM 456 CA LEU 64 9.256 13.936 28.659 1.00 0.00 ATOM 457 CB LEU 64 9.947 14.742 27.581 1.00 0.00 ATOM 458 CG LEU 64 9.053 15.461 26.569 1.00 0.00 ATOM 459 CD1 LEU 64 8.149 16.469 27.244 1.00 0.00 ATOM 460 CD2 LEU 64 9.910 16.136 25.511 1.00 0.00 ATOM 461 O LEU 64 7.115 12.989 28.284 1.00 0.00 ATOM 462 C LEU 64 8.302 12.920 27.979 1.00 0.00 ATOM 463 N ALA 65 8.905 12.155 27.072 1.00 0.00 ATOM 464 CA ALA 65 8.138 11.087 26.447 1.00 0.00 ATOM 465 CB ALA 65 7.922 11.368 24.996 1.00 0.00 ATOM 466 O ALA 65 10.113 9.752 26.214 1.00 0.00 ATOM 467 C ALA 65 8.928 9.796 26.560 1.00 0.00 TER END