From mailer@bialko.llnl.gov Tue Jun 4 12:48:10 2002 Date: Tue, 4 Jun 2002 12:48:02 -0700 (PDT) From: Automatic Reply To: karplus@soe.ucsc.edu Subject: T0130 TS samt02.pdb 2 X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK # # Protein Structure Prediction Center, LLNL, Livermore, CA # Verification system Tue Jun 4 12:21:43 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_329686_10461 # (PIN number is not an ACCESSION CODE) # Thank you for your submission. Your prediction has been accepted with an ACCESSION CODE: T0130TS189_2 Current information on models submitted in prediction T0130TS189 MODEL_INDEX PIN CODE DATE E-mail T0130TS189_2 PIN_329686_10461 5035-2079-5263 06/04/02 12:21:43 casp5@bialko.llnl.gov PLEASE NOTE: Submission of a duplicate prediction (same target, format, model index) will REPLACE an existing submission (ACCESSION CODE), provided it is received before the target has expired. The current status of models accepted for target T0130 MODEL_INDEX PIN CODE DATE E-mail T0130TS189_2 PIN_329686_10461 5035-2079-5263 06/04/02 12:21:43 casp5@bialko.llnl.gov For more information on accepted models submitted to CASP5 see: http://PredictionCenter.llnl.gov/casp5/models/casp5-models.html Please check below if the verified data of your submission is correct. # Reading prediction format TS PFRMAT TS TARGET T0130 AUTHOR 5035-2079-5263 # Reading MODEL 2 PARENT 1RPL # Loading PARENT structure: 1rpl (chain: ) # Number of residues in PARENT structure: 241 # Reading prediction format TS (DONE) # Checking the TS prediction MODEL 2 # IMPORTANT NOTE! Not complete main chain atoms for residue D 8 # !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! # # It is requested that coordinate data be supplied for at least # # all non-hydrogen main chain atoms, i.e. the N, CA, C and O # # atoms of every residue. Specifically, if only CA atoms are # # predicted by the method, predictors are encouraged to build # # the main chain atoms for every residue before submission to # # CASP. If only CA atoms were submitted it would not be possible # # to run most of the analysis software, which would severely # # limit the evaluation of that prediction. # # !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! # # IMPORTANT NOTE! Not complete main chain atoms for residue I 9 # IMPORTANT NOTE! Not complete main chain atoms for residue K 10 # IMPORTANT NOTE! Not complete main chain atoms for residue S 11 # IMPORTANT NOTE! Not complete main chain atoms for residue E 12 # IMPORTANT NOTE! Not complete main chain atoms for residue E 13 # IMPORTANT NOTE! Not complete main chain atoms for residue L 14 # IMPORTANT NOTE! Not complete main chain atoms for residue A 15 # IMPORTANT NOTE! Not complete main chain atoms for residue I 16 # IMPORTANT NOTE! Not complete main chain atoms for residue V 17 # IMPORTANT NOTE! Not complete main chain atoms for residue K 18 # IMPORTANT NOTE! Not complete main chain atoms for residue T 19 # IMPORTANT NOTE! Not complete main chain atoms for residue I 20 # IMPORTANT NOTE! Not complete main chain atoms for residue L 21 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 22 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 23 # IMPORTANT NOTE! Not complete main chain atoms for residue L 24 # IMPORTANT NOTE! Not complete main chain atoms for residue V 25 # IMPORTANT NOTE! Not complete main chain atoms for residue P 26 # IMPORTANT NOTE! Not complete main chain atoms for residue D 27 # IMPORTANT NOTE! Not complete main chain atoms for residue Y 28 # IMPORTANT NOTE! Not complete main chain atoms for residue T 29 # IMPORTANT NOTE! Not complete main chain atoms for residue V 30 # IMPORTANT NOTE! Not complete main chain atoms for residue W 31 # IMPORTANT NOTE! Not complete main chain atoms for residue A 32 # IMPORTANT NOTE! Not complete main chain atoms for residue F 33 # IMPORTANT NOTE! Not complete main chain atoms for residue G 34 # IMPORTANT NOTE! Not complete main chain atoms for residue S 35 # IMPORTANT NOTE! Not complete main chain atoms for residue R 36 # IMPORTANT NOTE! Not complete main chain atoms for residue V 37 # IMPORTANT NOTE! Not complete main chain atoms for residue K 38 # IMPORTANT NOTE! Not complete main chain atoms for residue G 39 # IMPORTANT NOTE! Not complete main chain atoms for residue A 41 # IMPORTANT NOTE! Not complete main chain atoms for residue K 42 # IMPORTANT NOTE! Not complete main chain atoms for residue K 43 # IMPORTANT NOTE! Not complete main chain atoms for residue Y 44 # IMPORTANT NOTE! Not complete main chain atoms for residue S 45 # IMPORTANT NOTE! Not complete main chain atoms for residue D 46 # IMPORTANT NOTE! Not complete main chain atoms for residue L 47 # IMPORTANT NOTE! Not complete main chain atoms for residue D 48 # IMPORTANT NOTE! Not complete main chain atoms for residue L 49 # IMPORTANT NOTE! Not complete main chain atoms for residue A 50 # IMPORTANT NOTE! Not complete main chain atoms for residue I 51 # IMPORTANT NOTE! Not complete main chain atoms for residue I 52 # IMPORTANT NOTE! Not complete main chain atoms for residue S 53 # IMPORTANT NOTE! Not complete main chain atoms for residue E 54 # IMPORTANT NOTE! Not complete main chain atoms for residue E 55 # IMPORTANT NOTE! Not complete main chain atoms for residue P 56 # IMPORTANT NOTE! Not complete main chain atoms for residue L 57 # IMPORTANT NOTE! Not complete main chain atoms for residue D 58 # IMPORTANT NOTE! Not complete main chain atoms for residue F 59 # IMPORTANT NOTE! Not complete main chain atoms for residue L 60 # IMPORTANT NOTE! Not complete main chain atoms for residue A 61 # IMPORTANT NOTE! Not complete main chain atoms for residue R 62 # IMPORTANT NOTE! Not complete main chain atoms for residue D 63 # IMPORTANT NOTE! Not complete main chain atoms for residue R 64 # IMPORTANT NOTE! Not complete main chain atoms for residue L 65 # IMPORTANT NOTE! Not complete main chain atoms for residue K 66 # IMPORTANT NOTE! Not complete main chain atoms for residue E 67 # IMPORTANT NOTE! Not complete main chain atoms for residue A 68 # IMPORTANT NOTE! Not complete main chain atoms for residue F 69 # IMPORTANT NOTE! Not complete main chain atoms for residue S 70 # IMPORTANT NOTE! Not complete main chain atoms for residue E 71 # IMPORTANT NOTE! Not complete main chain atoms for residue S 72 # IMPORTANT NOTE! Not complete main chain atoms for residue D 73 # Checking the TS prediction MODEL 2 (DONE) # MODEL index: 2 # Target name: T0130 # Total number of residues in target: 114 # Total number of residues in model: 65 # Total number of atoms in model: 65 # Number of atoms with 1.0 occupancy: 65 # Number of fragments in model: 1 # Number of METHOD records: 1 # No errors. # Number of Warnings: 65 ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT TS TARGET T0130 AUTHOR 5035-2079-5263 METHOD CAFASP MODEL 2 PARENT 1RPL ATOM 153 CA ASP 8 24.211 16.839 -16.287 1.00 1.00 ATOM 154 CA ILE 9 20.745 15.380 -15.471 1.00 1.00 ATOM 155 CA LYS 10 20.693 17.122 -12.019 1.00 1.00 ATOM 156 CA SER 11 20.962 20.546 -13.763 1.00 1.00 ATOM 157 CA GLU 12 17.981 19.716 -16.087 1.00 1.00 ATOM 158 CA GLU 13 15.890 18.467 -13.166 1.00 1.00 ATOM 159 CA LEU 14 16.816 21.677 -11.209 1.00 1.00 ATOM 160 CA ALA 15 15.624 23.687 -14.221 1.00 1.00 ATOM 161 CA ILE 16 12.218 21.998 -14.474 1.00 1.00 ATOM 162 CA VAL 17 11.635 22.598 -10.720 1.00 1.00 ATOM 163 CA LYS 18 12.712 26.237 -10.732 1.00 1.00 ATOM 164 CA THR 19 10.751 27.153 -13.919 1.00 1.00 ATOM 165 CA ILE 20 7.456 25.489 -12.674 1.00 1.00 ATOM 166 CA LEU 21 7.763 26.898 -9.194 1.00 1.00 ATOM 167 CA GLN 22 8.504 30.476 -10.564 1.00 1.00 ATOM 168 CA GLN 23 5.215 30.240 -12.597 1.00 1.00 ATOM 169 CA LEU 24 3.036 29.373 -9.624 1.00 1.00 ATOM 170 CA VAL 25 4.318 32.333 -7.616 1.00 1.00 ATOM 171 CA PRO 26 7.556 34.456 -8.063 1.00 1.00 ATOM 172 CA ASP 27 7.944 34.884 -4.280 1.00 1.00 ATOM 173 CA TYR 28 8.479 31.178 -3.751 1.00 1.00 ATOM 174 CA THR 29 12.234 30.586 -3.136 1.00 1.00 ATOM 175 CA VAL 30 13.499 27.166 -4.342 1.00 1.00 ATOM 176 CA TRP 31 17.017 25.833 -3.575 1.00 1.00 ATOM 177 CA ALA 32 18.316 22.401 -4.707 1.00 1.00 ATOM 178 CA PHE 33 20.761 21.586 -1.866 1.00 1.00 ATOM 179 CA GLY 34 23.097 18.511 -1.036 1.00 1.00 ATOM 180 CA SER 35 26.531 17.596 -2.559 1.00 1.00 ATOM 181 CA ARG 36 25.163 18.973 -5.917 1.00 1.00 ATOM 182 CA VAL 37 25.012 22.566 -4.670 1.00 1.00 ATOM 183 CA LYS 38 28.705 22.142 -3.663 1.00 1.00 ATOM 184 CA GLY 39 29.479 21.192 -7.278 1.00 1.00 ATOM 185 CA ALA 41 29.414 17.311 -7.114 1.00 1.00 ATOM 186 CA LYS 42 29.463 15.577 -10.469 1.00 1.00 ATOM 187 CA LYS 43 27.039 12.997 -9.292 1.00 1.00 ATOM 188 CA TYR 44 24.249 12.855 -6.749 1.00 1.00 ATOM 189 CA SER 45 22.121 10.049 -5.221 1.00 1.00 ATOM 190 CA ASP 46 18.926 12.091 -5.213 1.00 1.00 ATOM 191 CA LEU 47 17.521 15.712 -5.348 1.00 1.00 ATOM 192 CA ASP 48 16.814 17.700 -2.230 1.00 1.00 ATOM 193 CA LEU 49 14.827 20.896 -2.918 1.00 1.00 ATOM 194 CA ALA 50 14.385 23.275 0.118 1.00 1.00 ATOM 195 CA ILE 51 11.190 25.545 -0.391 1.00 1.00 ATOM 196 CA ILE 52 9.948 28.686 1.426 1.00 1.00 ATOM 197 CA SER 53 7.635 31.538 0.985 1.00 1.00 ATOM 198 CA GLU 54 7.363 34.860 2.711 1.00 1.00 ATOM 199 CA GLU 55 3.729 34.036 3.889 1.00 1.00 ATOM 200 CA PRO 56 5.104 31.110 5.787 1.00 1.00 ATOM 201 CA LEU 57 7.148 32.004 8.899 1.00 1.00 ATOM 202 CA ASP 58 7.578 29.940 12.207 1.00 1.00 ATOM 208 CA PHE 59 0.017 22.601 3.527 1.00 1.00 ATOM 209 CA LEU 60 -1.302 24.150 0.322 1.00 1.00 ATOM 210 CA ALA 61 2.044 26.070 -0.059 1.00 1.00 ATOM 211 CA ARG 62 4.004 22.782 -0.564 1.00 1.00 ATOM 212 CA ASP 63 1.088 20.754 -2.263 1.00 1.00 ATOM 213 CA ARG 64 0.449 23.229 -5.079 1.00 1.00 ATOM 214 CA LEU 65 4.080 22.749 -6.307 1.00 1.00 ATOM 215 CA LYS 66 3.867 18.864 -6.028 1.00 1.00 ATOM 216 CA GLU 67 0.608 18.954 -7.924 1.00 1.00 ATOM 217 CA ALA 68 2.122 21.252 -10.644 1.00 1.00 ATOM 218 CA PHE 69 5.223 18.894 -10.885 1.00 1.00 ATOM 219 CA SER 70 2.840 15.950 -11.193 1.00 1.00 ATOM 220 CA GLU 71 0.711 17.653 -13.912 1.00 1.00 ATOM 221 CA SER 72 3.777 18.523 -16.006 1.00 1.00 ATOM 222 CA ASP 73 4.708 14.716 -15.579 1.00 1.00 TER END ################################ # # # END # # # ################################ From mailer@bialko.llnl.gov Tue Jun 4 12:48:32 2002 Date: Tue, 4 Jun 2002 12:48:23 -0700 (PDT) From: Automatic Reply To: karplus@soe.ucsc.edu Subject: T0130 TS samt02.pdb 4 X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK # # Protein Structure Prediction Center, LLNL, Livermore, CA # Verification system Tue Jun 4 12:22:11 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_337361_10463 # (PIN number is not an ACCESSION CODE) # Thank you for your submission. Your prediction has been accepted with an ACCESSION CODE: T0130TS189_4 Current information on models submitted in prediction T0130TS189 MODEL_INDEX PIN CODE DATE E-mail T0130TS189_4 PIN_337361_10463 5035-2079-5263 06/04/02 12:22:11 casp5@bialko.llnl.gov T0130TS189_2 PIN_329686_10461 5035-2079-5263 06/04/02 12:21:43 casp5@bialko.llnl.gov PLEASE NOTE: Submission of a duplicate prediction (same target, format, model index) will REPLACE an existing submission (ACCESSION CODE), provided it is received before the target has expired. The current status of models accepted for target T0130 MODEL_INDEX PIN CODE DATE E-mail T0130TS189_2 PIN_329686_10461 5035-2079-5263 06/04/02 12:21:43 casp5@bialko.llnl.gov T0130TS189_4 PIN_337361_10463 5035-2079-5263 06/04/02 12:22:11 casp5@bialko.llnl.gov For more information on accepted models submitted to CASP5 see: http://PredictionCenter.llnl.gov/casp5/models/casp5-models.html Please check below if the verified data of your submission is correct. # Reading prediction format TS PFRMAT TS TARGET T0130 AUTHOR 5035-2079-5263 # Reading MODEL 4 PARENT 1JMS_A # Loading PARENT structure: 1jms (chain: A) # Number of residues in PARENT structure: 360 # Reading prediction format TS (DONE) # Checking the TS prediction MODEL 4 # IMPORTANT NOTE! Not complete main chain atoms for residue D 8 # !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! # # It is requested that coordinate data be supplied for at least # # all non-hydrogen main chain atoms, i.e. the N, CA, C and O # # atoms of every residue. Specifically, if only CA atoms are # # predicted by the method, predictors are encouraged to build # # the main chain atoms for every residue before submission to # # CASP. If only CA atoms were submitted it would not be possible # # to run most of the analysis software, which would severely # # limit the evaluation of that prediction. # # !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! # # IMPORTANT NOTE! Not complete main chain atoms for residue I 9 # IMPORTANT NOTE! Not complete main chain atoms for residue K 10 # IMPORTANT NOTE! Not complete main chain atoms for residue S 11 # IMPORTANT NOTE! Not complete main chain atoms for residue E 12 # IMPORTANT NOTE! Not complete main chain atoms for residue E 13 # IMPORTANT NOTE! Not complete main chain atoms for residue L 14 # IMPORTANT NOTE! Not complete main chain atoms for residue A 15 # IMPORTANT NOTE! Not complete main chain atoms for residue I 16 # IMPORTANT NOTE! Not complete main chain atoms for residue V 17 # IMPORTANT NOTE! Not complete main chain atoms for residue K 18 # IMPORTANT NOTE! Not complete main chain atoms for residue T 19 # IMPORTANT NOTE! Not complete main chain atoms for residue I 20 # IMPORTANT NOTE! Not complete main chain atoms for residue L 21 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 22 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 23 # IMPORTANT NOTE! Not complete main chain atoms for residue L 24 # IMPORTANT NOTE! Not complete main chain atoms for residue V 25 # IMPORTANT NOTE! Not complete main chain atoms for residue P 26 # IMPORTANT NOTE! Not complete main chain atoms for residue D 27 # IMPORTANT NOTE! Not complete main chain atoms for residue Y 28 # IMPORTANT NOTE! Not complete main chain atoms for residue T 29 # IMPORTANT NOTE! Not complete main chain atoms for residue V 30 # IMPORTANT NOTE! Not complete main chain atoms for residue W 31 # IMPORTANT NOTE! Not complete main chain atoms for residue A 32 # IMPORTANT NOTE! Not complete main chain atoms for residue F 33 # IMPORTANT NOTE! Not complete main chain atoms for residue G 34 # IMPORTANT NOTE! Not complete main chain atoms for residue S 35 # IMPORTANT NOTE! Not complete main chain atoms for residue R 36 # IMPORTANT NOTE! Not complete main chain atoms for residue V 37 # IMPORTANT NOTE! Not complete main chain atoms for residue K 38 # IMPORTANT NOTE! Not complete main chain atoms for residue G 39 # IMPORTANT NOTE! Not complete main chain atoms for residue K 40 # IMPORTANT NOTE! Not complete main chain atoms for residue A 41 # IMPORTANT NOTE! Not complete main chain atoms for residue K 42 # IMPORTANT NOTE! Not complete main chain atoms for residue K 43 # IMPORTANT NOTE! Not complete main chain atoms for residue S 45 # IMPORTANT NOTE! Not complete main chain atoms for residue D 46 # IMPORTANT NOTE! Not complete main chain atoms for residue L 47 # IMPORTANT NOTE! Not complete main chain atoms for residue D 48 # IMPORTANT NOTE! Not complete main chain atoms for residue L 49 # IMPORTANT NOTE! Not complete main chain atoms for residue A 50 # IMPORTANT NOTE! Not complete main chain atoms for residue I 51 # IMPORTANT NOTE! Not complete main chain atoms for residue I 52 # IMPORTANT NOTE! Not complete main chain atoms for residue S 53 # IMPORTANT NOTE! Not complete main chain atoms for residue E 54 # IMPORTANT NOTE! Not complete main chain atoms for residue E 55 # IMPORTANT NOTE! Not complete main chain atoms for residue P 56 # IMPORTANT NOTE! Not complete main chain atoms for residue L 57 # IMPORTANT NOTE! Not complete main chain atoms for residue D 58 # IMPORTANT NOTE! Not complete main chain atoms for residue F 59 # IMPORTANT NOTE! Not complete main chain atoms for residue L 60 # IMPORTANT NOTE! Not complete main chain atoms for residue A 61 # IMPORTANT NOTE! Not complete main chain atoms for residue R 62 # IMPORTANT NOTE! Not complete main chain atoms for residue D 63 # IMPORTANT NOTE! Not complete main chain atoms for residue R 64 # IMPORTANT NOTE! Not complete main chain atoms for residue L 65 # IMPORTANT NOTE! Not complete main chain atoms for residue K 66 # IMPORTANT NOTE! Not complete main chain atoms for residue E 67 # IMPORTANT NOTE! Not complete main chain atoms for residue A 68 # IMPORTANT NOTE! Not complete main chain atoms for residue F 69 # IMPORTANT NOTE! Not complete main chain atoms for residue S 70 # IMPORTANT NOTE! Not complete main chain atoms for residue E 71 # IMPORTANT NOTE! Not complete main chain atoms for residue S 72 # IMPORTANT NOTE! Not complete main chain atoms for residue D 73 # IMPORTANT NOTE! Not complete main chain atoms for residue L 74 # IMPORTANT NOTE! Not complete main chain atoms for residue P 75 # IMPORTANT NOTE! Not complete main chain atoms for residue W 76 # IMPORTANT NOTE! Not complete main chain atoms for residue R 77 # IMPORTANT NOTE! Not complete main chain atoms for residue V 78 # IMPORTANT NOTE! Not complete main chain atoms for residue D 79 # IMPORTANT NOTE! Not complete main chain atoms for residue L 80 # IMPORTANT NOTE! Not complete main chain atoms for residue L 81 # IMPORTANT NOTE! Not complete main chain atoms for residue D 82 # IMPORTANT NOTE! Not complete main chain atoms for residue W 83 # IMPORTANT NOTE! Not complete main chain atoms for residue A 84 # IMPORTANT NOTE! Not complete main chain atoms for residue T 85 # IMPORTANT NOTE! Not complete main chain atoms for residue T 86 # Checking the TS prediction MODEL 4 (DONE) # MODEL index: 4 # Target name: T0130 # Total number of residues in target: 114 # Total number of residues in model: 78 # Total number of atoms in model: 78 # Number of atoms with 1.0 occupancy: 78 # Number of fragments in model: 1 # Number of METHOD records: 1 # No errors. # Number of Warnings: 78 ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT TS TARGET T0130 AUTHOR 5035-2079-5263 METHOD CAFASP MODEL 4 PARENT 1JMS_A ATOM 306 CA ASP 8 48.204 41.874 89.773 1.00 1.00 ATOM 307 CA ILE 9 46.003 44.876 90.627 1.00 1.00 ATOM 308 CA LYS 10 43.578 43.992 87.837 1.00 1.00 ATOM 309 CA SER 11 43.201 40.487 89.316 1.00 1.00 ATOM 310 CA GLU 12 42.639 41.791 92.840 1.00 1.00 ATOM 311 CA GLU 13 39.970 44.097 91.433 1.00 1.00 ATOM 312 CA LEU 14 38.546 41.064 89.640 1.00 1.00 ATOM 313 CA ALA 15 38.294 39.228 92.962 1.00 1.00 ATOM 314 CA ILE 16 36.417 42.159 94.549 1.00 1.00 ATOM 315 CA VAL 17 33.888 42.283 91.723 1.00 1.00 ATOM 316 CA LYS 18 33.283 38.530 91.941 1.00 1.00 ATOM 317 CA THR 19 32.825 38.579 95.724 1.00 1.00 ATOM 318 CA ILE 20 30.188 41.302 95.436 1.00 1.00 ATOM 319 CA LEU 21 28.344 40.023 92.362 1.00 1.00 ATOM 320 CA GLN 22 28.294 36.465 93.708 1.00 1.00 ATOM 321 CA GLN 23 26.476 37.817 96.757 1.00 1.00 ATOM 322 CA LEU 24 23.383 38.809 94.736 1.00 1.00 ATOM 323 CA VAL 25 23.582 36.401 91.781 1.00 1.00 ATOM 324 CA PRO 26 25.632 33.281 92.671 1.00 1.00 ATOM 325 CA ASP 27 25.339 32.134 89.056 1.00 1.00 ATOM 326 CA TYR 28 26.712 35.375 87.613 1.00 1.00 ATOM 327 CA THR 29 29.530 35.267 85.081 1.00 1.00 ATOM 328 CA VAL 30 32.219 37.938 85.406 1.00 1.00 ATOM 329 CA TRP 31 34.718 38.413 82.582 1.00 1.00 ATOM 330 CA ALA 32 37.613 40.857 82.487 1.00 1.00 ATOM 331 CA PHE 33 37.589 42.609 79.110 1.00 1.00 ATOM 332 CA GLY 34 39.485 45.424 77.416 1.00 1.00 ATOM 333 CA SER 35 43.262 45.617 77.195 1.00 1.00 ATOM 334 CA ARG 36 43.967 42.995 79.849 1.00 1.00 ATOM 335 CA VAL 37 41.876 40.382 78.037 1.00 1.00 ATOM 336 CA LYS 38 43.991 41.089 74.949 1.00 1.00 ATOM 337 CA GLY 39 47.110 40.270 76.954 1.00 1.00 ATOM 338 CA LYS 40 48.324 43.752 77.919 1.00 1.00 ATOM 339 CA ALA 41 50.478 44.191 81.042 1.00 1.00 ATOM 340 CA LYS 42 49.084 47.555 82.024 1.00 1.00 ATOM 341 CA LYS 43 46.021 49.697 81.533 1.00 1.00 ATOM 342 CA SER 45 44.474 52.930 82.751 1.00 1.00 ATOM 343 CA ASP 46 41.462 51.065 84.161 1.00 1.00 ATOM 344 CA LEU 47 39.932 47.595 84.498 1.00 1.00 ATOM 345 CA ASP 48 36.770 46.606 82.596 1.00 1.00 ATOM 346 CA LEU 49 34.330 43.787 83.238 1.00 1.00 ATOM 347 CA ALA 50 31.349 42.201 81.536 1.00 1.00 ATOM 348 CA ILE 51 28.702 40.731 83.837 1.00 1.00 ATOM 349 CA ILE 52 25.846 38.405 82.921 1.00 1.00 ATOM 350 CA SER 53 23.474 35.947 84.641 1.00 1.00 ATOM 351 CA GLU 54 21.886 32.843 83.034 1.00 1.00 ATOM 352 CA GLU 55 18.806 32.834 85.288 1.00 1.00 ATOM 353 CA PRO 56 18.469 36.521 86.161 1.00 1.00 ATOM 354 CA LEU 57 15.150 38.285 85.544 1.00 1.00 ATOM 355 CA ASP 58 14.919 41.620 83.727 1.00 1.00 ATOM 356 CA PHE 59 14.443 42.976 87.250 1.00 1.00 ATOM 357 CA LEU 60 17.410 41.227 88.844 1.00 1.00 ATOM 358 CA ALA 61 20.024 42.009 86.186 1.00 1.00 ATOM 359 CA ARG 62 18.883 45.625 86.273 1.00 1.00 ATOM 360 CA ASP 63 19.447 45.857 90.041 1.00 1.00 ATOM 361 CA ARG 64 22.728 43.978 90.483 1.00 1.00 ATOM 362 CA LEU 65 24.954 46.964 89.731 1.00 1.00 ATOM 363 CA LYS 66 23.025 49.149 92.191 1.00 1.00 ATOM 364 CA GLU 67 23.404 46.489 94.884 1.00 1.00 ATOM 365 CA ALA 68 27.076 45.773 94.230 1.00 1.00 ATOM 366 CA PHE 69 27.781 49.498 94.280 1.00 1.00 ATOM 367 CA SER 70 25.667 50.069 97.432 1.00 1.00 ATOM 368 CA GLU 71 27.530 47.193 99.048 1.00 1.00 ATOM 369 CA SER 72 30.916 48.790 98.321 1.00 1.00 ATOM 371 CA ASP 73 28.706 50.467 102.999 1.00 1.00 ATOM 372 CA LEU 74 32.305 49.276 103.304 1.00 1.00 ATOM 373 CA PRO 75 33.824 52.536 102.100 1.00 1.00 ATOM 374 CA TRP 76 35.402 51.135 98.932 1.00 1.00 ATOM 375 CA ARG 77 33.381 53.343 96.568 1.00 1.00 ATOM 376 CA VAL 78 35.269 56.587 95.834 1.00 1.00 ATOM 377 CA ASP 79 33.181 57.477 92.769 1.00 1.00 ATOM 378 CA LEU 80 30.102 55.945 91.160 1.00 1.00 ATOM 379 CA LEU 81 27.985 56.771 88.120 1.00 1.00 ATOM 380 CA ASP 82 25.431 54.358 86.706 1.00 1.00 ATOM 381 CA TRP 83 23.934 54.784 83.241 1.00 1.00 ATOM 382 CA ALA 84 20.806 52.792 82.427 1.00 1.00 ATOM 383 CA THR 85 20.789 50.615 79.305 1.00 1.00 ATOM 384 CA THR 86 19.644 52.204 76.061 1.00 1.00 TER END ################################ # # # END # # # ################################ From mailer@bialko.llnl.gov Tue Jun 4 12:49:09 2002 Date: Tue, 4 Jun 2002 12:49:02 -0700 (PDT) From: Automatic Reply To: karplus@soe.ucsc.edu Subject: T0130 TS samt02.pdb 1 X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK # # Protein Structure Prediction Center, LLNL, Livermore, CA # Verification system Tue Jun 4 12:22:39 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_339761_10465 # (PIN number is not an ACCESSION CODE) # Thank you for your submission. Your prediction has been accepted with an ACCESSION CODE: T0130TS189_1 Current information on models submitted in prediction T0130TS189 MODEL_INDEX PIN CODE DATE E-mail T0130TS189_1 PIN_339761_10465 5035-2079-5263 06/04/02 12:22:39 casp5@bialko.llnl.gov T0130TS189_4 PIN_337361_10463 5035-2079-5263 06/04/02 12:22:11 casp5@bialko.llnl.gov T0130TS189_2 PIN_329686_10461 5035-2079-5263 06/04/02 12:21:43 casp5@bialko.llnl.gov PLEASE NOTE: Submission of a duplicate prediction (same target, format, model index) will REPLACE an existing submission (ACCESSION CODE), provided it is received before the target has expired. The current status of models accepted for target T0130 MODEL_INDEX PIN CODE DATE E-mail T0130TS189_1 PIN_339761_10465 5035-2079-5263 06/04/02 12:22:39 casp5@bialko.llnl.gov T0130TS189_2 PIN_329686_10461 5035-2079-5263 06/04/02 12:21:43 casp5@bialko.llnl.gov T0130TS189_4 PIN_337361_10463 5035-2079-5263 06/04/02 12:22:11 casp5@bialko.llnl.gov For more information on accepted models submitted to CASP5 see: http://PredictionCenter.llnl.gov/casp5/models/casp5-models.html Please check below if the verified data of your submission is correct. # Reading prediction format TS PFRMAT TS TARGET T0130 AUTHOR 5035-2079-5263 # Reading MODEL 1 PARENT 1FA0_A # Loading PARENT structure: 1fa0 (chain: A) # Number of residues in PARENT structure: 509 # Reading prediction format TS (DONE) # Checking the TS prediction MODEL 1 # IMPORTANT NOTE! Not complete main chain atoms for residue S 3 # !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! # # It is requested that coordinate data be supplied for at least # # all non-hydrogen main chain atoms, i.e. the N, CA, C and O # # atoms of every residue. Specifically, if only CA atoms are # # predicted by the method, predictors are encouraged to build # # the main chain atoms for every residue before submission to # # CASP. If only CA atoms were submitted it would not be possible # # to run most of the analysis software, which would severely # # limit the evaluation of that prediction. # # !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! # # IMPORTANT NOTE! Not complete main chain atoms for residue F 4 # IMPORTANT NOTE! Not complete main chain atoms for residue A 5 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 6 # IMPORTANT NOTE! Not complete main chain atoms for residue L 7 # IMPORTANT NOTE! Not complete main chain atoms for residue D 8 # IMPORTANT NOTE! Not complete main chain atoms for residue I 9 # IMPORTANT NOTE! Not complete main chain atoms for residue K 10 # IMPORTANT NOTE! Not complete main chain atoms for residue S 11 # IMPORTANT NOTE! Not complete main chain atoms for residue E 12 # IMPORTANT NOTE! Not complete main chain atoms for residue E 13 # IMPORTANT NOTE! Not complete main chain atoms for residue L 14 # IMPORTANT NOTE! Not complete main chain atoms for residue A 15 # IMPORTANT NOTE! Not complete main chain atoms for residue I 16 # IMPORTANT NOTE! Not complete main chain atoms for residue V 17 # IMPORTANT NOTE! Not complete main chain atoms for residue K 18 # IMPORTANT NOTE! Not complete main chain atoms for residue T 19 # IMPORTANT NOTE! Not complete main chain atoms for residue I 20 # IMPORTANT NOTE! Not complete main chain atoms for residue L 21 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 22 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 23 # IMPORTANT NOTE! Not complete main chain atoms for residue L 24 # IMPORTANT NOTE! Not complete main chain atoms for residue V 25 # IMPORTANT NOTE! Not complete main chain atoms for residue P 26 # IMPORTANT NOTE! Not complete main chain atoms for residue D 27 # IMPORTANT NOTE! Not complete main chain atoms for residue T 29 # IMPORTANT NOTE! Not complete main chain atoms for residue V 30 # IMPORTANT NOTE! Not complete main chain atoms for residue W 31 # IMPORTANT NOTE! Not complete main chain atoms for residue A 32 # IMPORTANT NOTE! Not complete main chain atoms for residue F 33 # IMPORTANT NOTE! Not complete main chain atoms for residue G 34 # IMPORTANT NOTE! Not complete main chain atoms for residue S 35 # IMPORTANT NOTE! Not complete main chain atoms for residue R 36 # IMPORTANT NOTE! Not complete main chain atoms for residue V 37 # IMPORTANT NOTE! Not complete main chain atoms for residue K 38 # IMPORTANT NOTE! Not complete main chain atoms for residue G 39 # IMPORTANT NOTE! Not complete main chain atoms for residue K 40 # IMPORTANT NOTE! Not complete main chain atoms for residue A 41 # IMPORTANT NOTE! Not complete main chain atoms for residue K 42 # IMPORTANT NOTE! Not complete main chain atoms for residue K 43 # IMPORTANT NOTE! Not complete main chain atoms for residue Y 44 # IMPORTANT NOTE! Not complete main chain atoms for residue S 45 # IMPORTANT NOTE! Not complete main chain atoms for residue D 46 # IMPORTANT NOTE! Not complete main chain atoms for residue L 47 # IMPORTANT NOTE! Not complete main chain atoms for residue D 48 # IMPORTANT NOTE! Not complete main chain atoms for residue L 49 # IMPORTANT NOTE! Not complete main chain atoms for residue A 50 # IMPORTANT NOTE! Not complete main chain atoms for residue I 51 # IMPORTANT NOTE! Not complete main chain atoms for residue I 52 # IMPORTANT NOTE! Not complete main chain atoms for residue S 53 # IMPORTANT NOTE! Not complete main chain atoms for residue E 54 # IMPORTANT NOTE! Not complete main chain atoms for residue E 55 # IMPORTANT NOTE! Not complete main chain atoms for residue P 56 # IMPORTANT NOTE! Not complete main chain atoms for residue L 57 # IMPORTANT NOTE! Not complete main chain atoms for residue D 58 # IMPORTANT NOTE! Not complete main chain atoms for residue F 59 # IMPORTANT NOTE! Not complete main chain atoms for residue L 60 # IMPORTANT NOTE! Not complete main chain atoms for residue A 61 # IMPORTANT NOTE! Not complete main chain atoms for residue R 62 # IMPORTANT NOTE! Not complete main chain atoms for residue D 63 # IMPORTANT NOTE! Not complete main chain atoms for residue R 64 # IMPORTANT NOTE! Not complete main chain atoms for residue L 65 # IMPORTANT NOTE! Not complete main chain atoms for residue K 66 # IMPORTANT NOTE! Not complete main chain atoms for residue E 67 # IMPORTANT NOTE! Not complete main chain atoms for residue A 68 # IMPORTANT NOTE! Not complete main chain atoms for residue F 69 # IMPORTANT NOTE! Not complete main chain atoms for residue S 70 # IMPORTANT NOTE! Not complete main chain atoms for residue E 71 # IMPORTANT NOTE! Not complete main chain atoms for residue S 72 # IMPORTANT NOTE! Not complete main chain atoms for residue D 73 # IMPORTANT NOTE! Not complete main chain atoms for residue L 74 # IMPORTANT NOTE! Not complete main chain atoms for residue P 75 # Checking the TS prediction MODEL 1 (DONE) # MODEL index: 1 # Target name: T0130 # Total number of residues in target: 114 # Total number of residues in model: 72 # Total number of atoms in model: 72 # Number of atoms with 1.0 occupancy: 72 # Number of fragments in model: 1 # Number of METHOD records: 1 # No errors. # Number of Warnings: 72 ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT TS TARGET T0130 AUTHOR 5035-2079-5263 METHOD CAFASP MODEL 1 PARENT 1FA0_A ATOM 48 CA SER 3 66.524 38.726 57.794 1.00 1.00 ATOM 49 CA PHE 4 64.441 41.826 58.577 1.00 1.00 ATOM 50 CA ALA 5 61.395 39.531 58.576 1.00 1.00 ATOM 51 CA GLN 6 62.830 36.836 60.842 1.00 1.00 ATOM 52 CA LEU 7 63.872 39.498 63.361 1.00 1.00 ATOM 53 CA ASP 8 60.402 41.057 63.182 1.00 1.00 ATOM 54 CA ILE 9 58.935 37.705 64.189 1.00 1.00 ATOM 55 CA LYS 10 61.570 37.164 66.910 1.00 1.00 ATOM 56 CA SER 11 60.650 40.529 68.434 1.00 1.00 ATOM 57 CA GLU 12 57.008 39.372 68.383 1.00 1.00 ATOM 58 CA GLU 13 58.147 36.216 70.186 1.00 1.00 ATOM 59 CA LEU 14 60.252 38.085 72.751 1.00 1.00 ATOM 60 CA ALA 15 57.266 40.189 73.759 1.00 1.00 ATOM 61 CA ILE 16 55.024 37.100 73.844 1.00 1.00 ATOM 62 CA VAL 17 57.691 35.393 75.957 1.00 1.00 ATOM 63 CA LYS 18 57.812 38.213 78.532 1.00 1.00 ATOM 64 CA THR 19 54.025 38.684 78.507 1.00 1.00 ATOM 65 CA ILE 20 53.415 35.014 79.162 1.00 1.00 ATOM 66 CA LEU 21 55.906 34.845 81.997 1.00 1.00 ATOM 67 CA GLN 22 54.541 38.068 83.509 1.00 1.00 ATOM 68 CA GLN 23 50.999 36.638 83.477 1.00 1.00 ATOM 69 CA LEU 24 52.146 33.520 85.293 1.00 1.00 ATOM 70 CA VAL 25 53.290 36.004 87.942 1.00 1.00 ATOM 71 CA PRO 26 49.705 37.202 88.381 1.00 1.00 ATOM 72 CA ASP 27 50.365 40.445 86.560 1.00 1.00 ATOM 83 CA THR 29 63.003 43.539 73.226 1.00 1.00 ATOM 84 CA VAL 30 65.375 42.126 70.612 1.00 1.00 ATOM 85 CA TRP 31 68.868 43.476 69.964 1.00 1.00 ATOM 86 CA ALA 32 71.515 42.381 67.509 1.00 1.00 ATOM 87 CA PHE 33 75.303 42.423 67.643 1.00 1.00 ATOM 88 CA GLY 34 78.005 40.838 65.569 1.00 1.00 ATOM 89 CA SER 35 78.311 40.897 61.814 1.00 1.00 ATOM 90 CA ARG 36 74.715 41.808 61.031 1.00 1.00 ATOM 91 CA VAL 37 74.616 44.636 63.573 1.00 1.00 ATOM 92 CA LYS 38 77.592 46.371 61.955 1.00 1.00 ATOM 93 CA GLY 39 76.150 45.895 58.469 1.00 1.00 ATOM 94 CA LYS 40 79.086 43.890 57.125 1.00 1.00 ATOM 95 CA ALA 41 77.468 40.462 57.183 1.00 1.00 ATOM 96 CA LYS 42 77.519 38.105 54.252 1.00 1.00 ATOM 97 CA LYS 43 75.108 35.775 52.401 1.00 1.00 ATOM 98 CA TYR 44 75.848 32.984 54.854 1.00 1.00 ATOM 99 CA SER 45 76.265 35.042 57.987 1.00 1.00 ATOM 100 CA ASP 46 74.115 34.131 60.980 1.00 1.00 ATOM 101 CA LEU 47 72.223 36.769 62.993 1.00 1.00 ATOM 102 CA ASP 48 73.527 37.288 66.524 1.00 1.00 ATOM 103 CA LEU 49 70.576 38.234 68.651 1.00 1.00 ATOM 104 CA ALA 50 70.225 39.455 72.235 1.00 1.00 ATOM 105 CA ILE 51 66.909 39.165 74.060 1.00 1.00 ATOM 106 CA ILE 52 66.360 41.634 76.913 1.00 1.00 ATOM 107 CA SER 53 63.799 40.955 79.640 1.00 1.00 ATOM 108 CA GLU 54 62.623 42.593 82.919 1.00 1.00 ATOM 109 CA GLU 55 63.641 41.508 86.427 1.00 1.00 ATOM 110 CA PRO 56 60.921 38.845 86.799 1.00 1.00 ATOM 111 CA LEU 57 61.914 36.924 83.681 1.00 1.00 ATOM 112 CA ASP 58 64.655 34.369 84.482 1.00 1.00 ATOM 113 CA PHE 59 67.073 32.469 82.279 1.00 1.00 ATOM 114 CA LEU 60 65.294 29.256 83.155 1.00 1.00 ATOM 115 CA ALA 61 62.167 30.963 81.792 1.00 1.00 ATOM 116 CA ARG 62 64.285 31.623 78.693 1.00 1.00 ATOM 117 CA ASP 63 65.100 27.978 77.917 1.00 1.00 ATOM 118 CA ARG 64 61.622 26.861 78.911 1.00 1.00 ATOM 119 CA LEU 65 58.996 29.327 77.781 1.00 1.00 ATOM 120 CA LYS 66 60.892 31.156 75.030 1.00 1.00 ATOM 121 CA GLU 67 62.120 27.858 73.633 1.00 1.00 ATOM 122 CA ALA 68 58.631 26.356 73.603 1.00 1.00 ATOM 123 CA PHE 69 57.404 29.510 71.870 1.00 1.00 ATOM 124 CA SER 70 60.031 28.948 69.181 1.00 1.00 ATOM 125 CA GLU 71 59.086 25.323 68.562 1.00 1.00 ATOM 126 CA SER 72 55.422 26.291 68.116 1.00 1.00 ATOM 127 CA ASP 73 56.458 27.649 64.681 1.00 1.00 ATOM 128 CA LEU 74 56.616 26.554 61.045 1.00 1.00 ATOM 129 CA PRO 75 59.732 28.578 60.184 1.00 1.00 TER END ################################ # # # END # # # ################################ From mailer@bialko.llnl.gov Tue Jun 4 12:49:19 2002 Date: Tue, 4 Jun 2002 12:49:12 -0700 (PDT) From: Automatic Reply To: karplus@soe.ucsc.edu Subject: T0130 TS samt02.pdb 3 X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK # # Protein Structure Prediction Center, LLNL, Livermore, CA # Verification system Tue Jun 4 12:22:54 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_340123_10466 # (PIN number is not an ACCESSION CODE) # Thank you for your submission. Your prediction has been accepted with an ACCESSION CODE: T0130TS189_3 Current information on models submitted in prediction T0130TS189 MODEL_INDEX PIN CODE DATE E-mail T0130TS189_3 PIN_340123_10466 5035-2079-5263 06/04/02 12:22:54 casp5@bialko.llnl.gov T0130TS189_1 PIN_339761_10465 5035-2079-5263 06/04/02 12:22:39 casp5@bialko.llnl.gov T0130TS189_4 PIN_337361_10463 5035-2079-5263 06/04/02 12:22:11 casp5@bialko.llnl.gov T0130TS189_2 PIN_329686_10461 5035-2079-5263 06/04/02 12:21:43 casp5@bialko.llnl.gov PLEASE NOTE: Submission of a duplicate prediction (same target, format, model index) will REPLACE an existing submission (ACCESSION CODE), provided it is received before the target has expired. The current status of models accepted for target T0130 MODEL_INDEX PIN CODE DATE E-mail T0130TS189_1 PIN_339761_10465 5035-2079-5263 06/04/02 12:22:39 casp5@bialko.llnl.gov T0130TS189_2 PIN_329686_10461 5035-2079-5263 06/04/02 12:21:43 casp5@bialko.llnl.gov T0130TS189_3 PIN_340123_10466 5035-2079-5263 06/04/02 12:22:54 casp5@bialko.llnl.gov T0130TS189_4 PIN_337361_10463 5035-2079-5263 06/04/02 12:22:11 casp5@bialko.llnl.gov For more information on accepted models submitted to CASP5 see: http://PredictionCenter.llnl.gov/casp5/models/casp5-models.html Please check below if the verified data of your submission is correct. # Reading prediction format TS PFRMAT TS TARGET T0130 AUTHOR 5035-2079-5263 # Reading MODEL 3 PARENT 1KAN_A # Loading PARENT structure: 1kan (chain: A) # Number of residues in PARENT structure: 253 # Reading prediction format TS (DONE) # Checking the TS prediction MODEL 3 # IMPORTANT NOTE! Not complete main chain atoms for residue M 1 # !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! # # It is requested that coordinate data be supplied for at least # # all non-hydrogen main chain atoms, i.e. the N, CA, C and O # # atoms of every residue. Specifically, if only CA atoms are # # predicted by the method, predictors are encouraged to build # # the main chain atoms for every residue before submission to # # CASP. If only CA atoms were submitted it would not be possible # # to run most of the analysis software, which would severely # # limit the evaluation of that prediction. # # !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! # # IMPORTANT NOTE! Not complete main chain atoms for residue T 2 # IMPORTANT NOTE! Not complete main chain atoms for residue S 3 # IMPORTANT NOTE! Not complete main chain atoms for residue F 4 # IMPORTANT NOTE! Not complete main chain atoms for residue A 5 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 6 # IMPORTANT NOTE! Not complete main chain atoms for residue L 7 # IMPORTANT NOTE! Not complete main chain atoms for residue D 8 # IMPORTANT NOTE! Not complete main chain atoms for residue I 9 # IMPORTANT NOTE! Not complete main chain atoms for residue K 10 # IMPORTANT NOTE! Not complete main chain atoms for residue S 11 # IMPORTANT NOTE! Not complete main chain atoms for residue E 12 # IMPORTANT NOTE! Not complete main chain atoms for residue E 13 # IMPORTANT NOTE! Not complete main chain atoms for residue L 14 # IMPORTANT NOTE! Not complete main chain atoms for residue A 15 # IMPORTANT NOTE! Not complete main chain atoms for residue I 16 # IMPORTANT NOTE! Not complete main chain atoms for residue V 17 # IMPORTANT NOTE! Not complete main chain atoms for residue K 18 # IMPORTANT NOTE! Not complete main chain atoms for residue T 19 # IMPORTANT NOTE! Not complete main chain atoms for residue I 20 # IMPORTANT NOTE! Not complete main chain atoms for residue L 21 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 22 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 23 # IMPORTANT NOTE! Not complete main chain atoms for residue L 24 # IMPORTANT NOTE! Not complete main chain atoms for residue V 25 # IMPORTANT NOTE! Not complete main chain atoms for residue P 26 # IMPORTANT NOTE! Not complete main chain atoms for residue D 27 # IMPORTANT NOTE! Not complete main chain atoms for residue Y 28 # IMPORTANT NOTE! Not complete main chain atoms for residue T 29 # IMPORTANT NOTE! Not complete main chain atoms for residue V 30 # IMPORTANT NOTE! Not complete main chain atoms for residue W 31 # IMPORTANT NOTE! Not complete main chain atoms for residue A 32 # IMPORTANT NOTE! Not complete main chain atoms for residue F 33 # IMPORTANT NOTE! Not complete main chain atoms for residue G 34 # IMPORTANT NOTE! Not complete main chain atoms for residue S 35 # IMPORTANT NOTE! Not complete main chain atoms for residue R 36 # IMPORTANT NOTE! Not complete main chain atoms for residue V 37 # IMPORTANT NOTE! Not complete main chain atoms for residue K 38 # IMPORTANT NOTE! Not complete main chain atoms for residue G 39 # IMPORTANT NOTE! Not complete main chain atoms for residue K 40 # IMPORTANT NOTE! Not complete main chain atoms for residue A 41 # IMPORTANT NOTE! Not complete main chain atoms for residue K 42 # IMPORTANT NOTE! Not complete main chain atoms for residue K 43 # IMPORTANT NOTE! Not complete main chain atoms for residue Y 44 # IMPORTANT NOTE! Not complete main chain atoms for residue S 45 # IMPORTANT NOTE! Not complete main chain atoms for residue D 46 # IMPORTANT NOTE! Not complete main chain atoms for residue L 47 # IMPORTANT NOTE! Not complete main chain atoms for residue D 48 # IMPORTANT NOTE! Not complete main chain atoms for residue L 49 # IMPORTANT NOTE! Not complete main chain atoms for residue A 50 # IMPORTANT NOTE! Not complete main chain atoms for residue I 51 # IMPORTANT NOTE! Not complete main chain atoms for residue I 52 # IMPORTANT NOTE! Not complete main chain atoms for residue S 53 # IMPORTANT NOTE! Not complete main chain atoms for residue E 54 # IMPORTANT NOTE! Not complete main chain atoms for residue E 55 # Checking the TS prediction MODEL 3 (DONE) # MODEL index: 3 # Target name: T0130 # Total number of residues in target: 114 # Total number of residues in model: 55 # Total number of atoms in model: 55 # Number of atoms with 1.0 occupancy: 55 # Number of fragments in model: 1 # Number of METHOD records: 1 # No errors. # Number of Warnings: 55 ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT TS TARGET T0130 AUTHOR 5035-2079-5263 METHOD CAFASP MODEL 3 PARENT 1KAN_A ATOM 4 CA MET 1 43.722 19.113 31.783 1.00 1.00 ATOM 5 CA THR 2 45.075 22.623 31.994 1.00 1.00 ATOM 6 CA SER 3 46.237 24.594 34.950 1.00 1.00 ATOM 7 CA PHE 4 43.729 26.747 36.690 1.00 1.00 ATOM 8 CA ALA 5 43.219 28.893 39.729 1.00 1.00 ATOM 9 CA GLN 6 40.838 28.363 42.576 1.00 1.00 ATOM 10 CA LEU 7 39.266 31.454 41.547 1.00 1.00 ATOM 11 CA ASP 8 39.079 30.424 37.877 1.00 1.00 ATOM 12 CA ILE 9 37.192 27.371 39.008 1.00 1.00 ATOM 13 CA LYS 10 34.687 29.001 41.164 1.00 1.00 ATOM 14 CA SER 11 33.839 31.070 38.148 1.00 1.00 ATOM 15 CA GLU 12 32.836 28.232 36.048 1.00 1.00 ATOM 16 CA GLU 13 31.191 26.769 39.057 1.00 1.00 ATOM 17 CA LEU 14 29.186 29.821 39.281 1.00 1.00 ATOM 18 CA ALA 15 28.360 30.012 35.667 1.00 1.00 ATOM 19 CA ILE 16 27.278 26.454 36.169 1.00 1.00 ATOM 20 CA VAL 17 24.918 27.297 38.910 1.00 1.00 ATOM 21 CA LYS 18 23.527 30.041 36.684 1.00 1.00 ATOM 22 CA THR 19 22.330 27.730 33.990 1.00 1.00 ATOM 23 CA ILE 20 21.320 25.162 36.564 1.00 1.00 ATOM 24 CA LEU 21 18.754 27.556 37.651 1.00 1.00 ATOM 25 CA GLN 22 18.216 29.015 34.263 1.00 1.00 ATOM 26 CA GLN 23 16.992 25.614 33.003 1.00 1.00 ATOM 27 CA LEU 24 15.899 24.098 36.244 1.00 1.00 ATOM 29 CA VAL 25 12.465 25.869 41.650 1.00 1.00 ATOM 30 CA PRO 26 13.021 22.055 41.303 1.00 1.00 ATOM 31 CA ASP 27 16.546 22.930 42.500 1.00 1.00 ATOM 32 CA TYR 28 16.483 22.673 46.291 1.00 1.00 ATOM 33 CA THR 29 20.353 22.825 46.371 1.00 1.00 ATOM 34 CA VAL 30 23.667 23.165 44.614 1.00 1.00 ATOM 35 CA TRP 31 27.077 22.332 46.067 1.00 1.00 ATOM 36 CA ALA 32 30.773 21.816 45.296 1.00 1.00 ATOM 37 CA PHE 33 32.562 18.774 46.574 1.00 1.00 ATOM 38 CA GLY 34 35.878 16.954 46.405 1.00 1.00 ATOM 39 CA SER 35 39.072 19.022 46.065 1.00 1.00 ATOM 40 CA ARG 36 37.475 22.431 45.529 1.00 1.00 ATOM 41 CA VAL 37 35.270 21.721 48.549 1.00 1.00 ATOM 42 CA LYS 38 38.131 20.959 50.935 1.00 1.00 ATOM 43 CA GLY 39 40.049 23.655 49.172 1.00 1.00 ATOM 44 CA LYS 40 42.846 21.235 48.341 1.00 1.00 ATOM 45 CA ALA 41 42.694 22.282 44.770 1.00 1.00 ATOM 46 CA LYS 42 45.490 20.759 42.695 1.00 1.00 ATOM 47 CA LYS 43 46.532 22.682 39.570 1.00 1.00 ATOM 48 CA TYR 44 45.192 20.087 37.120 1.00 1.00 ATOM 49 CA SER 45 42.141 19.319 39.324 1.00 1.00 ATOM 50 CA ASP 46 38.430 18.819 38.520 1.00 1.00 ATOM 51 CA LEU 47 35.121 20.409 38.828 1.00 1.00 ATOM 52 CA ASP 48 32.891 18.255 40.835 1.00 1.00 ATOM 53 CA LEU 49 29.475 19.348 41.865 1.00 1.00 ATOM 54 CA ALA 50 26.113 18.052 42.653 1.00 1.00 ATOM 55 CA ILE 51 22.690 19.297 43.123 1.00 1.00 ATOM 56 CA ILE 52 19.570 18.311 45.017 1.00 1.00 ATOM 57 CA SER 53 16.479 18.462 42.737 1.00 1.00 ATOM 58 CA GLU 54 12.775 18.331 43.600 1.00 1.00 ATOM 59 CA GLU 55 11.932 15.860 40.989 1.00 1.00 TER END ################################ # # # END # # # ################################ From mailer@bialko.llnl.gov Sat Jun 15 15:28:05 2002 Date: Sat, 15 Jun 2002 15:28:01 -0700 (PDT) From: Automatic Reply To: karplus@soe.ucsc.edu X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK # # Protein Structure Prediction Center, LLNL, Livermore, CA # Verification system Sat Jun 15 15:01:35 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_126525_10758 # (PIN number is not an ACCESSION CODE) # YOUR SUBMISSION CANNOT BE ACCEPTED THE FORMAT OF YOUR PREDICTION IS NOT CORRECT The following is an error report generated by the CASP prediction verifier for one of your server submissions. The attached file is the version of your prediction that was processed. This has been preprocessed by CAFASP, adding the required CASP records, and in some cases, co-ordinates generated from alignments, using the standard CAFASP procedure. Please address the errors, add the following record to your model REMARK Corrected submission: PIN_number and submit the corrected file to submit@predictioncenter.llnl.gov Please ONLY change the records indicated as an ERROR. The returned file will be checked for consistency with the original (current PIN_number). A gentle reminder is that your prediction is not considered accepted as part of CAFASP until it has passed this verification process and a CASP server prediction accession number is issued. Any queries should be sent to casp5@predictioncenter.llnl.gov Please check the format required for submissions of CASP5 predictions: http://PredictionCenter.llnl.gov/casp5/doc/casp5-format.html ################################################################# # # # Each submission may contain only one model, beginning with # # the MODEL record, ending with END, and no target residue # # repetitions. # # # # All submissions should contain the records described below: # # # # PFRMAT Format specification # TS , AL , SS , DR or RR # # TARGET Target identifier from the CASP5 target table # # AUTHOR XXXX-XXXX-XXXX The Group Leader registration code # # REMARK Comment record (may appear anywhere, optional) # # METHOD Records describing the methods used # # MODEL Beginning of the data section for the submitted model # # PARENT Structure template used to generate the TS/AL model # # ------ data submitted as a model ------ # # TER Terminates independent segments of the TS/AL model # # END End of the submitted model # # # # In all submissions the standard keywords # # must begin in the first column of a record. # # # # Sometimes an error may arise due to a # # TAB separator used instead of a SPACE! # # # ################################################################# PLEASE CHECK THE OUTPUT FROM THE VERIFICATION SERVER BELOW # Reading prediction format SS PFRMAT SS TARGET T0130 AUTHOR 2491-6940-1261 # Reading MODEL 1 L T 0.264 # ERROR! Check the line NB = 24 in the MODEL section. # Check the SS format description. # Number of Warnings: 0 # Number of Errors: 1 ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT SS TARGET T0130 AUTHOR 2491-6940-1261 METHOD CAFASP METHOD samt02_dssp METHOD Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net METHOD This is a 4-layer network, with METHOD window units METHOD 5 15 METHOD 7 15 METHOD 9 15 METHOD 13 7 (1 EBGHSTL ) METHOD The input amino acid frequencies were determined from METHOD alignment T0130.t2k-thin90.a2m.gz METHOD with weighted counts, using HenikoffWeight(-1 bits/column, 1) METHOD Counts were regularized to probabilities using METHOD /projects/compbio/lib/recode3.20comp METHOD Total sequence weight for alignment was 82 METHOD MODEL 1 M C 0.998 T C 0.886 S C 0.628 F H 0.737 A H 0.748 Q H 0.880 L H 0.933 D H 0.938 I H 0.948 K H 0.975 S H 0.984 E H 0.989 E H 0.995 L H 0.995 A H 0.994 I H 0.993 V H 0.994 K H 0.993 T H 0.988 I H 0.981 L H 0.956 Q H 0.846 Q H 0.633 L T 0.264 V C 0.504 P C 0.343 D C 0.405 Y E 0.684 T E 0.957 V E 0.988 W E 0.991 A E 0.973 F E 0.891 G E 0.786 S E 0.589 R E 0.555 V E 0.495 K E 0.366 G T 0.311 K C 0.324 A C 0.378 K C 0.497 K C 0.330 Y C 0.416 S C 0.529 D C 0.439 L E 0.715 D E 0.899 L E 0.980 A E 0.988 I E 0.975 I E 0.899 S E 0.539 E C 0.351 E C 0.380 P C 0.519 L C 0.360 D C 0.473 F H 0.687 L H 0.820 A H 0.884 R H 0.967 D H 0.973 R H 0.977 L H 0.980 K H 0.982 E H 0.977 A H 0.975 F H 0.954 S H 0.887 E H 0.760 S H 0.446 D T 0.441 L C 0.453 P C 0.461 W C 0.333 R C 0.493 V C 0.675 D E 0.516 L E 0.917 L E 0.949 D E 0.913 W E 0.803 A E 0.601 T E 0.332 T C 0.441 S C 0.718 E H 0.644 D H 0.664 F H 0.763 R H 0.853 E H 0.812 I H 0.794 I H 0.795 R H 0.754 K H 0.743 V H 0.758 Y H 0.740 V H 0.718 V H 0.672 I H 0.587 Q H 0.572 E H 0.564 K H 0.394 E H 0.337 K H 0.340 T H 0.364 V C 0.416 E C 0.530 K C 0.704 P C 0.765 T C 0.467 A C 0.719 L C 0.999 END ################################ # # # END # # # ################################ From mailer@bialko.llnl.gov Sat Jun 15 15:28:17 2002 Date: Sat, 15 Jun 2002 15:28:12 -0700 (PDT) From: Automatic Reply To: karplus@soe.ucsc.edu X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK # # Protein Structure Prediction Center, LLNL, Livermore, CA # Verification system Sat Jun 15 15:01:48 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_127826_10759 # (PIN number is not an ACCESSION CODE) # YOUR SUBMISSION CANNOT BE ACCEPTED THE FORMAT OF YOUR PREDICTION IS NOT CORRECT The following is an error report generated by the CASP prediction verifier for one of your server submissions. The attached file is the version of your prediction that was processed. This has been preprocessed by CAFASP, adding the required CASP records, and in some cases, co-ordinates generated from alignments, using the standard CAFASP procedure. Please address the errors, add the following record to your model REMARK Corrected submission: PIN_number and submit the corrected file to submit@predictioncenter.llnl.gov Please ONLY change the records indicated as an ERROR. The returned file will be checked for consistency with the original (current PIN_number). A gentle reminder is that your prediction is not considered accepted as part of CAFASP until it has passed this verification process and a CASP server prediction accession number is issued. Any queries should be sent to casp5@predictioncenter.llnl.gov Please check the format required for submissions of CASP5 predictions: http://PredictionCenter.llnl.gov/casp5/doc/casp5-format.html ################################################################# # # # Each submission may contain only one model, beginning with # # the MODEL record, ending with END, and no target residue # # repetitions. # # # # All submissions should contain the records described below: # # # # PFRMAT Format specification # TS , AL , SS , DR or RR # # TARGET Target identifier from the CASP5 target table # # AUTHOR XXXX-XXXX-XXXX The Group Leader registration code # # REMARK Comment record (may appear anywhere, optional) # # METHOD Records describing the methods used # # MODEL Beginning of the data section for the submitted model # # PARENT Structure template used to generate the TS/AL model # # ------ data submitted as a model ------ # # TER Terminates independent segments of the TS/AL model # # END End of the submitted model # # # # In all submissions the standard keywords # # must begin in the first column of a record. # # # # Sometimes an error may arise due to a # # TAB separator used instead of a SPACE! # # # ################################################################# PLEASE CHECK THE OUTPUT FROM THE VERIFICATION SERVER BELOW # Reading prediction format SS PFRMAT SS TARGET T0130 AUTHOR 5144-8387-2760 # Reading MODEL 1 L T 0.374 # ERROR! Check the line NB = 24 in the MODEL section. # Check the SS format description. # Number of Warnings: 0 # Number of Errors: 1 ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT SS TARGET T0130 AUTHOR 5144-8387-2760 METHOD CAFASP METHOD samt02_stride METHOD Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net METHOD This is a 4-layer network, with METHOD window units METHOD 5 15 METHOD 7 15 METHOD 9 15 METHOD 13 6 (1 EBGHTL ) METHOD The input amino acid frequencies were determined from METHOD alignment T0130.t2k-thin90.a2m.gz METHOD with weighted counts, using HenikoffWeight(-1 bits/column, 1) METHOD Counts were regularized to probabilities using METHOD /projects/compbio/lib/recode3.20comp METHOD Total sequence weight for alignment was 82 METHOD MODEL 1 M C 0.754 T C 0.588 S H 0.451 F H 0.662 A H 0.749 Q H 0.851 L H 0.892 D H 0.870 I H 0.866 K H 0.945 S H 0.967 E H 0.978 E H 0.980 L H 0.992 A H 0.991 I H 0.995 V H 0.993 K H 0.991 T H 0.984 I H 0.986 L H 0.977 Q H 0.937 Q H 0.764 L T 0.374 V T 0.523 P T 0.521 D T 0.439 Y E 0.615 T E 0.953 V E 0.992 W E 0.994 A E 0.982 F E 0.826 G C 0.381 S T 0.468 R E 0.363 V E 0.315 K C 0.447 G C 0.397 K C 0.456 A C 0.522 K C 0.484 K T 0.442 Y T 0.569 S T 0.598 D C 0.396 L E 0.453 D E 0.737 L E 0.964 A E 0.990 I E 0.983 I E 0.958 S E 0.664 E C 0.517 E C 0.554 P T 0.494 L T 0.516 D C 0.421 F H 0.731 L H 0.842 A H 0.888 R H 0.931 D H 0.954 R H 0.968 L H 0.968 K H 0.974 E H 0.974 A H 0.969 F H 0.962 S H 0.929 E H 0.849 S H 0.659 D C 0.468 L C 0.456 P C 0.499 W C 0.463 R C 0.473 V E 0.565 D E 0.595 L E 0.778 L E 0.863 D E 0.848 W E 0.655 A E 0.532 T C 0.380 T C 0.671 S C 0.452 E H 0.570 D H 0.649 F H 0.704 R H 0.688 E H 0.637 I H 0.559 I H 0.570 R H 0.681 K H 0.671 V H 0.675 Y H 0.708 V H 0.617 V H 0.610 I H 0.500 Q H 0.461 E H 0.451 K H 0.474 E H 0.415 K C 0.318 T C 0.361 V E 0.305 E E 0.369 K T 0.353 P C 0.370 T C 0.419 A C 0.592 L C 0.952 END ################################ # # # END # # # ################################ From mailer@bialko.llnl.gov Tue Jul 16 19:00:18 2002 Date: Tue, 16 Jul 2002 19:00:13 -0700 (PDT) From: Automatic Reply To: karplus@soe.ucsc.edu X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK # # Protein Structure Prediction Center, LLNL, Livermore, CA # Verification system Tue Jul 16 18:33:20 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_447762_12186 # (PIN number is not an ACCESSION CODE) # Thank you for your submission. Your prediction has been accepted with an ACCESSION CODE: T0130SS389_1 Current information on models submitted in prediction T0130SS389 MODEL_INDEX PIN CODE DATE E-mail T0130SS389_1 PIN_447762_12186 1549-8716-6404 07/16/02 18:33:20 casp5@bialko.llnl.gov PLEASE NOTE: Submission of a duplicate prediction (same target, format, model index) will REPLACE an existing submission (ACCESSION CODE), provided it is received before the target has expired. The current status of models accepted for target T0130 MODEL_INDEX PIN CODE DATE E-mail T0130SS389_1 PIN_447762_12186 1549-8716-6404 07/16/02 18:33:20 casp5@bialko.llnl.gov For more information on accepted models submitted to CASP5 see: http://PredictionCenter.llnl.gov/casp5/models/casp5-models.html Please check below if the verified data of your submission is correct. # Reading prediction format SS PFRMAT SS TARGET T0130 AUTHOR 1549-8716-6404 # Reading MODEL 1 # Reading prediction format SS (DONE) # Checking the SS prediction MODEL 1 # Checking the SS prediction MODEL 1 (DONE) # MODEL index: 1 # Total number of residues in model: 114 # Number of residues with nonzero confidence: 114 # Number of METHOD records: 46 # No errors. ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT SS TARGET T0130 AUTHOR 1549-8716-6404 METHOD CAFASP METHOD samt02_dssp_ehl METHOD This file is the result of combining several RDB files, specifically METHOD preds/T0130.t2k.dssp-ebghstl.rdb (weight 1.53986) METHOD preds/T0130.t2k.stride-ebghtl.rdb (weight 1.24869) METHOD These files were combined by translating their predictions into EHL METHOD predictions with tables generated by compare-real, and then combining METHOD those predictions with weights proportional to their mutual information METHOD with the EHL alphabet. The comments from the individual files follow. METHOD METHOD Comments from preds/T0130.t2k.dssp-ebghstl.rdb METHOD ============================================ METHOD TARGET T0130 METHOD Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net METHOD This is a 4-layer network, with METHOD window units METHOD 5 15 METHOD 7 15 METHOD 9 15 METHOD 13 7 (1 EBGHSTL ) METHOD The input amino acid frequencies were determined from METHOD alignment T0130.t2k-thin90.a2m.gz METHOD with weighted counts, using HenikoffWeight(-1 bits/column, 1) METHOD Counts were regularized to probabilities using METHOD /projects/compbio/lib/recode3.20comp METHOD Total sequence weight for alignment was 82 METHOD METHOD ============================================ METHOD Comments from preds/T0130.t2k.stride-ebghtl.rdb METHOD ============================================ METHOD TARGET T0130 METHOD Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net METHOD This is a 4-layer network, with METHOD window units METHOD 5 15 METHOD 7 15 METHOD 9 15 METHOD 13 6 (1 EBGHTL ) METHOD The input amino acid frequencies were determined from METHOD alignment T0130.t2k-thin90.a2m.gz METHOD with weighted counts, using HenikoffWeight(-1 bits/column, 1) METHOD Counts were regularized to probabilities using METHOD /projects/compbio/lib/recode3.20comp METHOD Total sequence weight for alignment was 82 METHOD METHOD ============================================ MODEL 1 M C 0.95 T C 0.81 S C 0.67 F H 0.73 A H 0.78 Q H 0.88 L H 0.91 D H 0.90 I H 0.90 K H 0.94 S H 0.95 E H 0.96 E H 0.96 L H 0.97 A H 0.97 I H 0.97 V H 0.97 K H 0.97 T H 0.96 I H 0.96 L H 0.95 Q H 0.88 Q H 0.70 L C 0.69 V C 0.91 P C 0.90 D C 0.75 Y E 0.65 T E 0.94 V E 0.97 W E 0.97 A E 0.96 F E 0.85 G E 0.57 S C 0.52 R E 0.50 V C 0.45 K C 0.63 G C 0.78 K C 0.79 A C 0.71 K C 0.84 K C 0.84 Y C 0.83 S C 0.88 D C 0.74 L E 0.61 D E 0.82 L E 0.96 A E 0.97 I E 0.96 I E 0.91 S E 0.59 E C 0.78 E C 0.90 P C 0.90 L C 0.89 D C 0.86 F H 0.74 L H 0.84 A H 0.88 R H 0.93 D H 0.94 R H 0.95 L H 0.95 K H 0.95 E H 0.95 A H 0.95 F H 0.94 S H 0.90 E H 0.80 S H 0.55 D C 0.80 L C 0.84 P C 0.88 W C 0.83 R C 0.73 V C 0.61 D E 0.55 L E 0.85 L E 0.90 D E 0.87 W E 0.73 A E 0.57 T C 0.56 T C 0.80 S C 0.82 E H 0.75 D H 0.78 F H 0.83 R H 0.81 E H 0.80 I H 0.76 I H 0.73 R H 0.74 K H 0.72 V H 0.73 Y H 0.73 V H 0.68 V H 0.65 I H 0.55 Q H 0.54 E H 0.55 K H 0.49 E C 0.46 K C 0.52 T C 0.48 V C 0.55 E C 0.66 K C 0.80 P C 0.81 T C 0.76 A C 0.83 L C 0.98 END ################################ # # # END # # # ################################