PFRMAT TS TARGET T0498 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 All my predictions, whether from SAM+undertaker or metaserver METHOD predictions, came out almost identical. There are some differences in METHOD placing F52 and some of the surface residues, but it is hard do METHOD distinguish among the models. METHOD METHOD The first two models are metaserver models, optimized by undertaker METHOD from YASARA_TS3. The first one is then energy-minimized by gromacs, METHOD and has the sidechains repacked by rosetta design. METHOD METHOD The third and fifth models is are optimized strictly from METHOD SAM+undertaker models. The 4th model is a meta-server model, but METHOD using our own SAM-T08 server. METHOD METHOD METHOD Model METHOD 1 T0498.MQAX4-opt3.gromacs0.repack-nonPC.pdb #< YASARA_TS3 METHOD # best rosetta energy METHOD METHOD 2 T0498.MQAX4-opt3.pdb #< YASARA_TS3 METHOD METHOD 3 T0498.try4-opt3.pdb #< try3-opt3.gromacs0 < align(2gi9A) METHOD METHOD 4 T0498.MQAC1-opt3.gromacs0.pdb # < SAM-T08-server_TS1 METHOD METHOD 5 T0498.try2-opt3.pdb # < try1-opt3 < align(2gi9A) METHOD METHOD METHOD METHOD REMARK 6 REMARK 6 T0498 model 5 Tue Jul 15 13:37:25 2008 MODEL 5 PARENT 2i38_A 2i2y_A 1ibx_B 1pn5_A 2cwb_A REMARK 7 REMARK 7 ALLPARENTS 2i38_A 2i2y_A 1ibx_B 1pn5_A 2cwb_A 1pgx_A 2igg_A REMARK 7 ALLPARENTS 1pgb_A 2igh_A 2igd_A 2qmt_A 1fcc_C ATOM 1 N THR 1 13.758 8.704 15.227 1.00 0.00 ATOM 2 CA THR 1 14.070 8.941 16.626 1.00 0.00 ATOM 3 CB THR 1 15.590 9.032 16.856 1.00 0.00 ATOM 4 CG2 THR 1 15.893 9.263 18.329 1.00 0.00 ATOM 5 OG1 THR 1 16.212 7.808 16.441 1.00 0.00 ATOM 6 O THR 1 13.503 11.225 16.261 1.00 0.00 ATOM 7 C THR 1 13.522 10.291 17.057 1.00 0.00 ATOM 8 N THR 2 13.078 10.352 18.294 1.00 0.00 ATOM 9 CA THR 2 12.535 11.597 18.838 1.00 0.00 ATOM 10 CB THR 2 11.509 11.337 19.991 1.00 0.00 ATOM 11 CG2 THR 2 10.934 12.625 20.479 1.00 0.00 ATOM 12 OG1 THR 2 10.466 10.518 19.431 1.00 0.00 ATOM 13 O THR 2 14.482 11.974 20.197 1.00 0.00 ATOM 14 C THR 2 13.669 12.454 19.404 1.00 0.00 ATOM 15 N TYR 3 13.720 13.719 18.997 1.00 0.00 ATOM 16 CA TYR 3 14.757 14.626 19.476 1.00 0.00 ATOM 17 CB TYR 3 15.592 15.131 18.278 1.00 0.00 ATOM 18 CG TYR 3 16.366 14.068 17.609 1.00 0.00 ATOM 19 CD1 TYR 3 15.772 13.294 16.601 1.00 0.00 ATOM 20 CD2 TYR 3 17.668 13.767 17.957 1.00 0.00 ATOM 21 CE1 TYR 3 16.502 12.273 15.976 1.00 0.00 ATOM 22 CE2 TYR 3 18.389 12.726 17.337 1.00 0.00 ATOM 23 CZ TYR 3 17.752 11.989 16.341 1.00 0.00 ATOM 24 OH TYR 3 18.411 10.953 15.705 1.00 0.00 ATOM 25 O TYR 3 13.003 16.201 19.805 1.00 0.00 ATOM 26 C TYR 3 14.122 15.828 20.150 1.00 0.00 ATOM 27 N LYS 4 14.857 16.401 21.084 1.00 0.00 ATOM 28 CA LYS 4 14.397 17.572 21.834 1.00 0.00 ATOM 29 CB LYS 4 14.571 17.326 23.335 1.00 0.00 ATOM 30 CG LYS 4 13.703 16.206 23.884 1.00 0.00 ATOM 31 CD LYS 4 13.902 16.038 25.382 1.00 0.00 ATOM 32 CE LYS 4 13.029 14.923 25.933 1.00 0.00 ATOM 33 NZ LYS 4 13.198 14.762 27.404 1.00 0.00 ATOM 34 O LYS 4 16.366 18.671 21.047 1.00 0.00 ATOM 35 C LYS 4 15.187 18.781 21.416 1.00 0.00 ATOM 36 N LEU 5 14.573 19.952 21.507 1.00 0.00 ATOM 37 CA LEU 5 15.223 21.247 21.348 1.00 0.00 ATOM 38 CB LEU 5 14.708 21.974 20.098 1.00 0.00 ATOM 39 CG LEU 5 15.124 23.422 19.919 1.00 0.00 ATOM 40 CD1 LEU 5 16.574 23.487 19.549 1.00 0.00 ATOM 41 CD2 LEU 5 14.294 24.057 18.728 1.00 0.00 ATOM 42 O LEU 5 13.725 22.324 22.838 1.00 0.00 ATOM 43 C LEU 5 14.901 22.134 22.523 1.00 0.00 ATOM 44 N ILE 6 15.956 22.614 23.178 1.00 0.00 ATOM 45 CA ILE 6 15.813 23.553 24.276 1.00 0.00 ATOM 46 CB ILE 6 16.703 23.213 25.485 1.00 0.00 ATOM 47 CG1 ILE 6 16.333 21.840 26.051 1.00 0.00 ATOM 48 CG2 ILE 6 16.528 24.249 26.585 1.00 0.00 ATOM 49 CD1 ILE 6 17.298 21.330 27.098 1.00 0.00 ATOM 50 O ILE 6 17.318 25.139 23.288 1.00 0.00 ATOM 51 C ILE 6 16.201 24.936 23.764 1.00 0.00 ATOM 52 N LEU 7 15.277 25.886 23.861 1.00 0.00 ATOM 53 CA LEU 7 15.540 27.237 23.406 1.00 0.00 ATOM 54 CB LEU 7 14.763 27.507 22.038 1.00 0.00 ATOM 55 CG LEU 7 13.247 27.532 22.013 1.00 0.00 ATOM 56 CD1 LEU 7 12.782 28.066 20.616 1.00 0.00 ATOM 57 CD2 LEU 7 12.693 26.104 22.211 1.00 0.00 ATOM 58 O LEU 7 14.927 28.154 25.560 1.00 0.00 ATOM 59 C LEU 7 15.751 28.135 24.629 1.00 0.00 ATOM 60 N ASN 8 16.875 28.819 24.616 1.00 0.00 ATOM 61 CA ASN 8 17.142 29.869 25.570 1.00 0.00 ATOM 62 CB ASN 8 18.359 29.426 26.368 1.00 0.00 ATOM 63 CG ASN 8 18.611 30.379 27.516 1.00 0.00 ATOM 64 ND2 ASN 8 19.795 30.180 28.094 1.00 0.00 ATOM 65 OD1 ASN 8 17.773 31.223 27.860 1.00 0.00 ATOM 66 O ASN 8 18.509 31.572 24.578 1.00 0.00 ATOM 67 C ASN 8 17.373 31.124 24.735 1.00 0.00 ATOM 68 N LEU 9 16.295 31.688 24.201 1.00 0.00 ATOM 69 CA LEU 9 16.403 32.871 23.402 1.00 0.00 ATOM 70 CB LEU 9 15.395 32.866 22.259 1.00 0.00 ATOM 71 CG LEU 9 15.389 31.631 21.363 1.00 0.00 ATOM 72 CD1 LEU 9 14.220 31.635 20.369 1.00 0.00 ATOM 73 CD2 LEU 9 16.689 31.498 20.559 1.00 0.00 ATOM 74 O LEU 9 15.606 33.955 25.429 1.00 0.00 ATOM 75 C LEU 9 16.089 34.071 24.298 1.00 0.00 ATOM 76 N LYS 10 16.387 35.249 23.810 1.00 0.00 ATOM 77 CA LYS 10 16.076 36.481 24.506 1.00 0.00 ATOM 78 CB LYS 10 16.660 37.601 23.650 1.00 0.00 ATOM 79 CG LYS 10 16.565 38.976 24.232 1.00 0.00 ATOM 80 CD LYS 10 16.813 39.042 25.737 1.00 0.00 ATOM 81 CE LYS 10 17.935 39.971 26.081 1.00 0.00 ATOM 82 NZ LYS 10 17.936 40.271 27.534 1.00 0.00 ATOM 83 O LYS 10 14.132 37.265 25.680 1.00 0.00 ATOM 84 C LYS 10 14.571 36.686 24.685 1.00 0.00 ATOM 85 N GLN 11 13.787 36.211 23.723 1.00 0.00 ATOM 86 CA GLN 11 12.337 36.348 23.792 1.00 0.00 ATOM 87 CB GLN 11 11.991 36.674 22.098 1.00 0.00 ATOM 88 CG GLN 11 13.128 37.247 21.230 1.00 0.00 ATOM 89 CD GLN 11 13.508 38.710 21.532 1.00 0.00 ATOM 90 OE1 GLN 11 14.686 39.103 21.365 1.00 0.00 ATOM 91 NE2 GLN 11 12.547 39.511 21.947 1.00 0.00 ATOM 92 O GLN 11 10.699 34.890 24.766 1.00 0.00 ATOM 93 C GLN 11 11.628 35.009 23.965 1.00 0.00 ATOM 94 N ALA 12 12.066 34.004 23.216 1.00 0.00 ATOM 95 CA ALA 12 11.467 32.693 23.303 1.00 0.00 ATOM 96 CB ALA 12 11.245 32.098 21.879 1.00 0.00 ATOM 97 O ALA 12 13.449 31.416 23.673 1.00 0.00 ATOM 98 C ALA 12 12.302 31.675 24.038 1.00 0.00 ATOM 99 N LYS 13 11.728 31.086 25.082 1.00 0.00 ATOM 100 CA LYS 13 12.437 30.084 25.869 1.00 0.00 ATOM 101 CB LYS 13 12.938 30.729 27.164 1.00 0.00 ATOM 102 CG LYS 13 11.794 31.197 28.067 1.00 0.00 ATOM 103 CD LYS 13 12.295 31.812 29.366 1.00 0.00 ATOM 104 CE LYS 13 11.134 32.161 30.283 1.00 0.00 ATOM 105 NZ LYS 13 10.302 30.972 30.591 1.00 0.00 ATOM 106 O LYS 13 10.323 28.980 26.180 1.00 0.00 ATOM 107 C LYS 13 11.547 28.881 26.026 1.00 0.00 ATOM 108 N GLU 14 12.131 27.684 26.026 1.00 0.00 ATOM 109 CA GLU 14 11.342 26.500 26.381 1.00 0.00 ATOM 110 CB GLU 14 10.273 26.256 25.311 1.00 0.00 ATOM 111 CG GLU 14 9.067 27.160 25.438 1.00 0.00 ATOM 112 CD GLU 14 8.373 27.059 26.773 1.00 0.00 ATOM 113 OE1 GLU 14 8.308 25.954 27.378 1.00 0.00 ATOM 114 OE2 GLU 14 7.862 28.126 27.221 1.00 0.00 ATOM 115 O GLU 14 13.061 25.119 25.413 1.00 0.00 ATOM 116 C GLU 14 11.848 25.266 25.686 1.00 0.00 ATOM 117 N GLU 15 10.969 24.339 25.364 1.00 0.00 ATOM 118 CA GLU 15 11.340 23.034 24.851 1.00 0.00 ATOM 119 CB GLU 15 11.419 22.035 25.976 1.00 0.00 ATOM 120 CG GLU 15 11.174 20.597 25.582 1.00 0.00 ATOM 121 CD GLU 15 11.094 19.673 26.781 1.00 0.00 ATOM 122 OE1 GLU 15 10.178 19.854 27.614 1.00 0.00 ATOM 123 OE2 GLU 15 11.943 18.766 26.887 1.00 0.00 ATOM 124 O GLU 15 9.083 22.745 24.033 1.00 0.00 ATOM 125 C GLU 15 10.336 22.573 23.823 1.00 0.00 ATOM 126 N ALA 16 10.795 22.013 22.729 1.00 0.00 ATOM 127 CA ALA 16 9.977 21.406 21.669 1.00 0.00 ATOM 128 CB ALA 16 9.909 22.338 20.470 1.00 0.00 ATOM 129 O ALA 16 11.758 19.798 21.724 1.00 0.00 ATOM 130 C ALA 16 10.636 20.080 21.300 1.00 0.00 ATOM 131 N ILE 17 9.938 19.268 20.512 1.00 0.00 ATOM 132 CA ILE 17 10.471 17.978 20.096 1.00 0.00 ATOM 133 CB ILE 17 9.929 16.847 20.977 1.00 0.00 ATOM 134 CG1 ILE 17 8.397 16.878 20.976 1.00 0.00 ATOM 135 CG2 ILE 17 10.484 16.989 22.391 1.00 0.00 ATOM 136 CD1 ILE 17 7.740 15.760 21.750 1.00 0.00 ATOM 137 O ILE 17 9.189 18.344 18.092 1.00 0.00 ATOM 138 C ILE 17 10.097 17.710 18.631 1.00 0.00 ATOM 139 N LYS 18 10.798 16.775 17.997 1.00 0.00 ATOM 140 CA LYS 18 10.524 16.441 16.604 1.00 0.00 ATOM 141 CB LYS 18 11.238 17.330 15.584 1.00 0.00 ATOM 142 CG LYS 18 10.776 18.777 15.592 1.00 0.00 ATOM 143 CD LYS 18 9.351 18.904 15.075 1.00 0.00 ATOM 144 CE LYS 18 9.263 18.534 13.604 1.00 0.00 ATOM 145 NZ LYS 18 7.875 18.658 13.082 1.00 0.00 ATOM 146 O LYS 18 12.030 14.605 16.951 1.00 0.00 ATOM 147 C LYS 18 11.062 15.040 16.327 1.00 0.00 ATOM 148 N GLU 19 10.434 14.339 15.387 1.00 0.00 ATOM 149 CA GLU 19 10.865 12.984 15.034 1.00 0.00 ATOM 150 CB GLU 19 9.631 12.101 14.824 1.00 0.00 ATOM 151 CG GLU 19 9.945 10.705 14.288 1.00 0.00 ATOM 152 CD GLU 19 8.708 9.931 13.859 1.00 0.00 ATOM 153 OE1 GLU 19 7.730 10.553 13.389 1.00 0.00 ATOM 154 OE2 GLU 19 8.724 8.687 13.974 1.00 0.00 ATOM 155 O GLU 19 11.281 13.768 12.789 1.00 0.00 ATOM 156 C GLU 19 11.669 13.069 13.726 1.00 0.00 ATOM 157 N LEU 20 12.762 12.389 13.670 1.00 0.00 ATOM 158 CA LEU 20 13.622 12.440 12.474 1.00 0.00 ATOM 159 CB LEU 20 14.286 13.416 12.008 1.00 0.00 ATOM 160 CG LEU 20 13.412 14.175 11.016 1.00 0.00 ATOM 161 CD1 LEU 20 14.204 15.328 10.406 1.00 0.00 ATOM 162 CD2 LEU 20 12.916 13.208 9.954 1.00 0.00 ATOM 163 O LEU 20 14.715 10.543 13.456 1.00 0.00 ATOM 164 C LEU 20 14.456 11.164 12.424 1.00 0.00 ATOM 165 N VAL 21 14.878 10.777 11.225 1.00 0.00 ATOM 166 CA VAL 21 15.687 9.571 11.060 1.00 0.00 ATOM 167 CB VAL 21 15.539 9.145 9.509 1.00 0.00 ATOM 168 CG1 VAL 21 16.431 7.972 9.219 1.00 0.00 ATOM 169 CG2 VAL 21 14.085 8.825 9.159 1.00 0.00 ATOM 170 O VAL 21 17.714 8.700 11.976 1.00 0.00 ATOM 171 C VAL 21 17.086 9.700 11.620 1.00 0.00 ATOM 172 N ASP 22 17.645 10.883 11.725 1.00 0.00 ATOM 173 CA ASP 22 18.995 11.076 12.204 1.00 0.00 ATOM 174 CB ASP 22 20.024 10.913 11.108 1.00 0.00 ATOM 175 CG ASP 22 19.729 11.716 9.862 1.00 0.00 ATOM 176 OD1 ASP 22 19.618 12.957 9.955 1.00 0.00 ATOM 177 OD2 ASP 22 19.617 11.106 8.778 1.00 0.00 ATOM 178 O ASP 22 18.207 13.301 12.566 1.00 0.00 ATOM 179 C ASP 22 19.109 12.482 12.743 1.00 0.00 ATOM 180 N ALA 23 20.225 12.771 13.407 1.00 0.00 ATOM 181 CA ALA 23 20.447 14.098 13.969 1.00 0.00 ATOM 182 CB ALA 23 21.615 13.975 15.017 1.00 0.00 ATOM 183 O ALA 23 20.200 16.308 13.115 1.00 0.00 ATOM 184 C ALA 23 20.645 15.176 12.924 1.00 0.00 ATOM 185 N GLY 24 21.329 14.855 11.785 1.00 0.00 ATOM 186 CA GLY 24 21.552 15.828 10.733 1.00 0.00 ATOM 187 O GLY 24 20.050 17.582 10.083 1.00 0.00 ATOM 188 C GLY 24 20.208 16.374 10.264 1.00 0.00 ATOM 189 N THR 25 19.240 15.483 10.069 1.00 0.00 ATOM 190 CA THR 25 17.928 15.893 9.629 1.00 0.00 ATOM 191 CB THR 25 17.034 14.702 9.275 1.00 0.00 ATOM 192 CG2 THR 25 17.577 14.002 8.034 1.00 0.00 ATOM 193 OG1 THR 25 16.983 13.788 10.379 1.00 0.00 ATOM 194 O THR 25 16.602 17.725 10.429 1.00 0.00 ATOM 195 C THR 25 17.211 16.692 10.711 1.00 0.00 ATOM 196 N ALA 26 17.283 16.214 11.949 1.00 0.00 ATOM 197 CA ALA 26 16.639 16.897 13.058 1.00 0.00 ATOM 198 CB ALA 26 16.852 16.081 14.427 1.00 0.00 ATOM 199 O ALA 26 16.457 19.227 13.527 1.00 0.00 ATOM 200 C ALA 26 17.188 18.290 13.206 1.00 0.00 ATOM 201 N GLU 27 18.488 18.436 12.970 1.00 0.00 ATOM 202 CA GLU 27 19.133 19.739 13.080 1.00 0.00 ATOM 203 CB GLU 27 20.637 19.645 12.812 1.00 0.00 ATOM 204 CG GLU 27 21.373 20.969 12.931 1.00 0.00 ATOM 205 CD GLU 27 22.867 20.828 12.719 1.00 0.00 ATOM 206 OE1 GLU 27 23.329 19.689 12.496 1.00 0.00 ATOM 207 OE2 GLU 27 23.575 21.855 12.773 1.00 0.00 ATOM 208 O GLU 27 18.268 21.886 12.433 1.00 0.00 ATOM 209 C GLU 27 18.533 20.735 12.084 1.00 0.00 ATOM 210 N LYS 28 18.322 20.288 10.850 1.00 0.00 ATOM 211 CA LYS 28 17.751 21.150 9.822 1.00 0.00 ATOM 212 CB LYS 28 17.687 20.408 8.489 1.00 0.00 ATOM 213 CG LYS 28 19.074 20.059 7.926 1.00 0.00 ATOM 214 CD LYS 28 18.979 19.307 6.640 1.00 0.00 ATOM 215 CE LYS 28 20.325 19.079 6.050 1.00 0.00 ATOM 216 NZ LYS 28 20.204 18.389 4.755 1.00 0.00 ATOM 217 O LYS 28 16.010 22.783 10.055 1.00 0.00 ATOM 218 C LYS 28 16.346 21.608 10.199 1.00 0.00 ATOM 219 N TYR 29 15.528 20.678 10.682 1.00 0.00 ATOM 220 CA TYR 29 14.170 21.004 11.076 1.00 0.00 ATOM 221 CB TYR 29 13.425 19.770 11.518 1.00 0.00 ATOM 222 CG TYR 29 12.824 18.972 10.407 1.00 0.00 ATOM 223 CD1 TYR 29 11.518 18.584 10.508 1.00 0.00 ATOM 224 CD2 TYR 29 13.535 18.603 9.287 1.00 0.00 ATOM 225 CE1 TYR 29 10.925 17.835 9.522 1.00 0.00 ATOM 226 CE2 TYR 29 12.957 17.850 8.309 1.00 0.00 ATOM 227 CZ TYR 29 11.654 17.458 8.439 1.00 0.00 ATOM 228 OH TYR 29 11.141 16.704 7.454 1.00 0.00 ATOM 229 O TYR 29 13.415 22.988 12.203 1.00 0.00 ATOM 230 C TYR 29 14.162 22.009 12.231 1.00 0.00 ATOM 231 N ILE 30 14.995 21.765 13.238 1.00 0.00 ATOM 232 CA ILE 30 15.074 22.659 14.386 1.00 0.00 ATOM 233 CB ILE 30 15.930 21.994 15.511 1.00 0.00 ATOM 234 CG1 ILE 30 15.222 20.735 16.020 1.00 0.00 ATOM 235 CG2 ILE 30 16.141 22.973 16.661 1.00 0.00 ATOM 236 CD1 ILE 30 16.009 19.935 17.043 1.00 0.00 ATOM 237 O ILE 30 15.130 25.021 14.518 1.00 0.00 ATOM 238 C ILE 30 15.628 24.001 13.998 1.00 0.00 ATOM 239 N LYS 31 16.641 24.060 13.141 1.00 0.00 ATOM 240 CA LYS 31 17.126 25.355 12.707 1.00 0.00 ATOM 241 CB LYS 31 18.334 25.192 11.782 1.00 0.00 ATOM 242 CG LYS 31 19.587 24.689 12.482 1.00 0.00 ATOM 243 CD LYS 31 20.747 24.555 11.506 1.00 0.00 ATOM 244 CE LYS 31 21.989 24.019 12.200 1.00 0.00 ATOM 245 NZ LYS 31 23.127 23.861 11.252 1.00 0.00 ATOM 246 O LYS 31 15.935 27.325 12.118 1.00 0.00 ATOM 247 C LYS 31 16.033 26.109 11.954 1.00 0.00 ATOM 248 N LEU 32 15.237 25.426 11.149 1.00 0.00 ATOM 249 CA LEU 32 14.080 26.117 10.553 1.00 0.00 ATOM 250 CB LEU 32 13.428 25.121 9.538 1.00 0.00 ATOM 251 CG LEU 32 12.145 25.652 8.900 1.00 0.00 ATOM 252 CD1 LEU 32 12.419 26.954 8.138 1.00 0.00 ATOM 253 CD2 LEU 32 11.514 24.590 8.031 1.00 0.00 ATOM 254 O LEU 32 12.573 27.721 11.520 1.00 0.00 ATOM 255 C LEU 32 13.078 26.600 11.601 1.00 0.00 ATOM 256 N ILE 33 12.778 25.750 12.598 1.00 0.00 ATOM 257 CA ILE 33 11.855 26.129 13.656 1.00 0.00 ATOM 258 CB ILE 33 11.711 25.021 14.717 1.00 0.00 ATOM 259 CG1 ILE 33 11.014 23.798 14.119 1.00 0.00 ATOM 260 CG2 ILE 33 10.886 25.518 15.895 1.00 0.00 ATOM 261 CD1 ILE 33 11.068 22.571 15.003 1.00 0.00 ATOM 262 O ILE 33 11.581 28.330 14.569 1.00 0.00 ATOM 263 C ILE 33 12.351 27.396 14.345 1.00 0.00 ATOM 264 N ALA 34 13.638 27.427 14.676 1.00 0.00 ATOM 265 CA ALA 34 14.228 28.597 15.341 1.00 0.00 ATOM 266 CB ALA 34 15.692 28.363 15.683 1.00 0.00 ATOM 267 O ALA 34 13.656 30.863 14.906 1.00 0.00 ATOM 268 C ALA 34 14.127 29.808 14.448 1.00 0.00 ATOM 269 N ASN 35 14.497 29.667 13.192 1.00 0.00 ATOM 270 CA ASN 35 14.410 30.797 12.285 1.00 0.00 ATOM 271 CB ASN 35 14.929 30.444 10.907 1.00 0.00 ATOM 272 CG ASN 35 16.447 30.525 10.819 1.00 0.00 ATOM 273 ND2 ASN 35 17.031 29.791 9.855 1.00 0.00 ATOM 274 OD1 ASN 35 17.091 31.268 11.585 1.00 0.00 ATOM 275 O ASN 35 12.719 32.493 12.144 1.00 0.00 ATOM 276 C ASN 35 12.976 31.289 12.127 1.00 0.00 ATOM 277 N ALA 36 12.042 30.353 11.975 1.00 0.00 ATOM 278 CA ALA 36 10.632 30.709 11.814 1.00 0.00 ATOM 279 CB ALA 36 9.815 29.447 11.586 1.00 0.00 ATOM 280 O ALA 36 9.112 32.206 12.911 1.00 0.00 ATOM 281 C ALA 36 10.080 31.453 13.026 1.00 0.00 ATOM 282 N LYS 37 10.697 31.243 14.185 1.00 0.00 ATOM 283 CA LYS 37 10.258 31.899 15.393 1.00 0.00 ATOM 284 CB LYS 37 9.668 30.789 16.376 1.00 0.00 ATOM 285 CG LYS 37 8.374 30.105 15.916 1.00 0.00 ATOM 286 CD LYS 37 7.367 29.934 17.066 1.00 0.00 ATOM 287 CE LYS 37 7.844 28.962 18.155 1.00 0.00 ATOM 288 NZ LYS 37 7.787 27.525 17.734 1.00 0.00 ATOM 289 O LYS 37 10.956 33.688 16.842 1.00 0.00 ATOM 290 C LYS 37 11.122 33.085 15.775 1.00 0.00 ATOM 291 N THR 38 12.075 33.458 14.916 1.00 0.00 ATOM 292 CA THR 38 12.812 34.694 15.141 1.00 0.00 ATOM 293 CB THR 38 11.679 35.884 15.171 1.00 0.00 ATOM 294 CG2 THR 38 12.339 37.256 15.139 1.00 0.00 ATOM 295 OG1 THR 38 10.775 35.777 14.061 1.00 0.00 ATOM 296 O THR 38 14.362 35.428 16.841 1.00 0.00 ATOM 297 C THR 38 13.992 34.499 16.122 1.00 0.00 ATOM 298 N VAL 39 14.567 33.300 16.140 1.00 0.00 ATOM 299 CA VAL 39 15.690 33.014 17.026 1.00 0.00 ATOM 300 CB VAL 39 15.477 31.638 17.653 1.00 0.00 ATOM 301 CG1 VAL 39 16.726 31.300 18.464 1.00 0.00 ATOM 302 CG2 VAL 39 14.253 31.734 18.572 1.00 0.00 ATOM 303 O VAL 39 16.834 31.972 15.244 1.00 0.00 ATOM 304 C VAL 39 16.917 32.779 16.175 1.00 0.00 ATOM 305 N GLU 40 18.008 33.434 16.447 1.00 0.00 ATOM 306 CA GLU 40 19.282 33.232 15.804 1.00 0.00 ATOM 307 CB GLU 40 19.337 34.100 14.508 1.00 0.00 ATOM 308 CG GLU 40 19.354 35.588 14.807 1.00 0.00 ATOM 309 CD GLU 40 19.411 36.435 13.548 1.00 0.00 ATOM 310 OE1 GLU 40 19.457 37.678 13.668 1.00 0.00 ATOM 311 OE2 GLU 40 19.410 35.860 12.438 1.00 0.00 ATOM 312 O GLU 40 20.652 34.190 17.517 1.00 0.00 ATOM 313 C GLU 40 20.372 33.190 16.868 1.00 0.00 ATOM 314 N GLY 41 20.975 32.019 17.053 1.00 0.00 ATOM 315 CA GLY 41 21.862 31.892 18.192 1.00 0.00 ATOM 316 O GLY 41 23.153 30.380 16.843 1.00 0.00 ATOM 317 C GLY 41 22.909 30.826 17.969 1.00 0.00 ATOM 318 N VAL 42 23.508 30.394 19.060 1.00 0.00 ATOM 319 CA VAL 42 24.533 29.389 19.107 1.00 0.00 ATOM 320 CB VAL 42 25.580 29.656 20.230 1.00 0.00 ATOM 321 CG1 VAL 42 26.664 28.553 20.224 1.00 0.00 ATOM 322 CG2 VAL 42 26.236 31.034 20.004 1.00 0.00 ATOM 323 O VAL 42 22.927 27.982 20.213 1.00 0.00 ATOM 324 C VAL 42 23.885 28.019 19.439 1.00 0.00 ATOM 325 N TRP 43 24.439 26.965 18.855 1.00 0.00 ATOM 326 CA TRP 43 23.842 25.642 18.895 1.00 0.00 ATOM 327 CB TRP 43 23.548 25.106 17.491 1.00 0.00 ATOM 328 CG TRP 43 22.532 25.912 16.741 1.00 0.00 ATOM 329 CD1 TRP 43 22.774 26.967 15.910 1.00 0.00 ATOM 330 CD2 TRP 43 21.112 25.730 16.754 1.00 0.00 ATOM 331 CE2 TRP 43 20.558 26.710 15.907 1.00 0.00 ATOM 332 CE3 TRP 43 20.254 24.833 17.398 1.00 0.00 ATOM 333 NE1 TRP 43 21.595 27.454 15.404 1.00 0.00 ATOM 334 CZ2 TRP 43 19.185 26.818 15.688 1.00 0.00 ATOM 335 CZ3 TRP 43 18.894 24.944 17.178 1.00 0.00 ATOM 336 CH2 TRP 43 18.370 25.928 16.331 1.00 0.00 ATOM 337 O TRP 43 25.965 24.633 19.383 1.00 0.00 ATOM 338 C TRP 43 24.738 24.618 19.572 1.00 0.00 ATOM 339 N THR 44 24.094 23.698 20.264 1.00 0.00 ATOM 340 CA THR 44 24.737 22.452 20.675 1.00 0.00 ATOM 341 CB THR 44 25.022 22.415 22.170 1.00 0.00 ATOM 342 CG2 THR 44 26.000 23.524 22.568 1.00 0.00 ATOM 343 OG1 THR 44 23.785 22.516 22.887 1.00 0.00 ATOM 344 O THR 44 22.578 21.412 20.331 1.00 0.00 ATOM 345 C THR 44 23.821 21.267 20.379 1.00 0.00 ATOM 346 N LEU 45 24.426 20.122 20.176 1.00 0.00 ATOM 347 CA LEU 45 23.769 18.835 20.102 1.00 0.00 ATOM 348 CB LEU 45 23.867 18.289 18.677 1.00 0.00 ATOM 349 CG LEU 45 23.396 16.839 18.496 1.00 0.00 ATOM 350 CD1 LEU 45 21.958 16.699 18.986 1.00 0.00 ATOM 351 CD2 LEU 45 23.501 16.444 17.034 1.00 0.00 ATOM 352 O LEU 45 25.612 17.489 20.837 1.00 0.00 ATOM 353 C LEU 45 24.415 17.754 20.957 1.00 0.00 ATOM 354 N LYS 46 23.621 17.129 21.821 1.00 0.00 ATOM 355 CA LYS 46 24.131 16.074 22.688 1.00 0.00 ATOM 356 CB LYS 46 24.055 16.487 24.155 1.00 0.00 ATOM 357 CG LYS 46 24.751 15.528 25.096 1.00 0.00 ATOM 358 CD LYS 46 24.967 16.099 26.477 1.00 0.00 ATOM 359 CE LYS 46 25.571 15.062 27.418 1.00 0.00 ATOM 360 NZ LYS 46 26.804 14.468 26.874 1.00 0.00 ATOM 361 O LYS 46 22.262 14.578 22.531 1.00 0.00 ATOM 362 C LYS 46 23.450 14.774 22.271 1.00 0.00 ATOM 363 N ASP 47 24.203 13.890 21.625 1.00 0.00 ATOM 364 CA ASP 47 23.659 12.632 21.192 1.00 0.00 ATOM 365 CB ASP 47 24.646 11.811 20.361 1.00 0.00 ATOM 366 CG ASP 47 24.872 12.395 18.980 1.00 0.00 ATOM 367 OD1 ASP 47 24.104 13.295 18.582 1.00 0.00 ATOM 368 OD2 ASP 47 25.818 11.950 18.295 1.00 0.00 ATOM 369 O ASP 47 22.147 11.040 22.118 1.00 0.00 ATOM 370 C ASP 47 23.126 11.754 22.309 1.00 0.00 ATOM 371 N GLU 48 23.798 11.786 23.465 1.00 0.00 ATOM 372 CA GLU 48 23.446 10.962 24.600 1.00 0.00 ATOM 373 CB GLU 48 24.492 11.091 25.708 1.00 0.00 ATOM 374 CG GLU 48 25.859 10.536 25.339 1.00 0.00 ATOM 375 CD GLU 48 26.888 10.747 26.431 1.00 0.00 ATOM 376 OE1 GLU 48 26.544 11.364 27.462 1.00 0.00 ATOM 377 OE2 GLU 48 28.040 10.296 26.258 1.00 0.00 ATOM 378 O GLU 48 21.366 10.295 25.611 1.00 0.00 ATOM 379 C GLU 48 22.013 11.207 25.093 1.00 0.00 ATOM 380 N ILE 49 21.526 12.432 24.928 1.00 0.00 ATOM 381 CA ILE 49 20.174 12.772 25.358 1.00 0.00 ATOM 382 CB ILE 49 20.240 13.916 26.391 1.00 0.00 ATOM 383 CG1 ILE 49 20.874 15.180 25.850 1.00 0.00 ATOM 384 CG2 ILE 49 20.934 13.433 27.653 1.00 0.00 ATOM 385 CD1 ILE 49 20.798 16.364 26.822 1.00 0.00 ATOM 386 O ILE 49 18.159 13.618 24.390 1.00 0.00 ATOM 387 C ILE 49 19.277 13.173 24.183 1.00 0.00 ATOM 388 N LYS 50 19.762 13.052 22.965 1.00 0.00 ATOM 389 CA LYS 50 19.040 13.466 21.769 1.00 0.00 ATOM 390 CB LYS 50 18.100 12.136 21.357 1.00 0.00 ATOM 391 CG LYS 50 18.728 10.771 21.562 1.00 0.00 ATOM 392 CD LYS 50 17.749 9.625 21.441 1.00 0.00 ATOM 393 CE LYS 50 18.386 8.316 21.878 1.00 0.00 ATOM 394 NZ LYS 50 19.323 7.709 20.904 1.00 0.00 ATOM 395 O LYS 50 17.352 15.148 21.640 1.00 0.00 ATOM 396 C LYS 50 18.524 14.886 21.948 1.00 0.00 ATOM 397 N THR 51 19.400 15.795 22.386 1.00 0.00 ATOM 398 CA THR 51 18.952 17.146 22.729 1.00 0.00 ATOM 399 CB THR 51 18.917 17.326 24.258 1.00 0.00 ATOM 400 CG2 THR 51 18.568 18.763 24.649 1.00 0.00 ATOM 401 OG1 THR 51 17.942 16.442 24.817 1.00 0.00 ATOM 402 O THR 51 21.083 18.140 22.216 1.00 0.00 ATOM 403 C THR 51 19.856 18.163 22.047 1.00 0.00 ATOM 404 N PHE 52 19.206 19.084 21.361 1.00 0.00 ATOM 405 CA PHE 52 19.811 20.272 20.811 1.00 0.00 ATOM 406 CB PHE 52 19.173 20.629 19.460 1.00 0.00 ATOM 407 CG PHE 52 19.401 19.567 18.375 1.00 0.00 ATOM 408 CD1 PHE 52 20.499 19.680 17.493 1.00 0.00 ATOM 409 CD2 PHE 52 18.596 18.435 18.324 1.00 0.00 ATOM 410 CE1 PHE 52 20.762 18.716 16.484 1.00 0.00 ATOM 411 CE2 PHE 52 18.835 17.449 17.360 1.00 0.00 ATOM 412 CZ PHE 52 19.896 17.615 16.392 1.00 0.00 ATOM 413 O PHE 52 18.362 21.564 22.201 1.00 0.00 ATOM 414 C PHE 52 19.478 21.492 21.666 1.00 0.00 ATOM 415 N THR 53 20.386 22.408 21.693 1.00 0.00 ATOM 416 CA THR 53 20.141 23.686 22.406 1.00 0.00 ATOM 417 CB THR 53 20.936 23.827 23.693 1.00 0.00 ATOM 418 CG2 THR 53 20.647 25.139 24.350 1.00 0.00 ATOM 419 OG1 THR 53 20.571 22.735 24.579 1.00 0.00 ATOM 420 O THR 53 21.497 24.774 20.795 1.00 0.00 ATOM 421 C THR 53 20.484 24.833 21.495 1.00 0.00 ATOM 422 N VAL 54 19.681 25.902 21.545 1.00 0.00 ATOM 423 CA VAL 54 20.054 27.147 20.882 1.00 0.00 ATOM 424 CB VAL 54 19.159 27.399 19.653 1.00 0.00 ATOM 425 CG1 VAL 54 17.667 27.504 19.967 1.00 0.00 ATOM 426 CG2 VAL 54 19.676 28.632 18.924 1.00 0.00 ATOM 427 O VAL 54 18.973 28.450 22.554 1.00 0.00 ATOM 428 C VAL 54 19.999 28.282 21.894 1.00 0.00 ATOM 429 N THR 55 21.060 29.073 21.987 1.00 0.00 ATOM 430 CA THR 55 21.194 30.109 22.997 1.00 0.00 ATOM 431 CB THR 55 22.257 29.738 24.034 1.00 0.00 ATOM 432 CG2 THR 55 22.350 30.777 25.128 1.00 0.00 ATOM 433 OG1 THR 55 21.880 28.491 24.621 1.00 0.00 ATOM 434 O THR 55 22.438 31.491 21.477 1.00 0.00 ATOM 435 C THR 55 21.556 31.415 22.331 1.00 0.00 ATOM 436 N GLU 56 20.855 32.476 22.721 1.00 0.00 ATOM 437 CA GLU 56 21.158 33.825 22.247 1.00 0.00 ATOM 438 CB GLU 56 20.094 34.789 22.753 1.00 0.00 ATOM 439 CG GLU 56 18.805 34.637 22.004 1.00 0.00 ATOM 440 CD GLU 56 18.915 35.124 20.565 1.00 0.00 ATOM 441 OE1 GLU 56 20.042 35.390 20.084 1.00 0.00 ATOM 442 OE2 GLU 56 17.875 35.248 19.902 1.00 0.00 ATOM 443 O GLU 56 23.352 34.830 21.960 1.00 0.00 ATOM 444 C GLU 56 22.532 34.286 22.725 1.00 0.00 TER END