From mailer@bialko.llnl.gov Tue Jun 4 12:47:30 2002 Date: Tue, 4 Jun 2002 12:47:23 -0700 (PDT) From: Automatic Reply To: karplus@soe.ucsc.edu Subject: T0130 TS samt99.pdb 5 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 12:21:15 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_325546_10459 # (PIN number is not an ACCESSION CODE) # Thank you for your submission. Your prediction has been accepted with an ACCESSION CODE: T0130TS007_5 Current information on models submitted in prediction T0130TS007 MODEL_INDEX PIN CODE DATE E-mail T0130TS007_5 PIN_325546_10459 6269-7633-6117 06/04/02 12:21:15 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 T0130TS007_5 PIN_325546_10459 6269-7633-6117 06/04/02 12:21:15 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 6269-7633-6117 # Reading MODEL 5 PARENT 1KNY_B # Loading PARENT structure: 1kny (chain: B) # Number of residues in PARENT structure: 253 # Reading prediction format TS (DONE) # Checking the TS prediction MODEL 5 # 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 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 # Checking the TS prediction MODEL 5 (DONE) # MODEL index: 5 # Target name: T0130 # Total number of residues in target: 114 # Total number of residues in model: 45 # Total number of atoms in model: 45 # Number of atoms with 1.0 occupancy: 45 # Number of fragments in model: 1 # Number of METHOD records: 1 # No errors. # Number of Warnings: 45 ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT TS TARGET T0130 AUTHOR 6269-7633-6117 METHOD CAFASP MODEL 5 PARENT 1KNY_B ATOM 7 CA MET 1 51.543 41.948 23.146 1.00 1.00 ATOM 8 CA THR 2 54.369 42.579 25.634 1.00 1.00 ATOM 9 CA SER 3 54.972 45.101 28.293 1.00 1.00 ATOM 10 CA PHE 4 57.263 46.947 25.860 1.00 1.00 ATOM 11 CA ALA 5 54.644 47.241 23.224 1.00 1.00 ATOM 12 CA GLN 6 52.055 48.254 25.799 1.00 1.00 ATOM 13 CA LEU 7 54.373 50.669 27.468 1.00 1.00 ATOM 14 CA ASP 8 55.141 52.169 24.132 1.00 1.00 ATOM 15 CA ILE 9 51.502 53.251 23.589 1.00 1.00 ATOM 16 CA LYS 10 51.099 54.365 27.048 1.00 1.00 ATOM 17 CA SER 11 53.790 56.924 26.355 1.00 1.00 ATOM 18 CA GLU 12 52.370 57.803 22.991 1.00 1.00 ATOM 19 CA GLU 13 49.040 58.286 24.777 1.00 1.00 ATOM 20 CA LEU 14 50.829 60.161 27.426 1.00 1.00 ATOM 21 CA ALA 15 52.008 62.566 24.833 1.00 1.00 ATOM 22 CA ILE 16 48.692 63.310 23.111 1.00 1.00 ATOM 23 CA VAL 17 47.238 64.040 26.502 1.00 1.00 ATOM 24 CA LYS 18 50.061 66.397 27.263 1.00 1.00 ATOM 25 CA THR 19 49.890 68.087 23.873 1.00 1.00 ATOM 26 CA ILE 20 46.107 67.924 24.021 1.00 1.00 ATOM 27 CA LEU 21 45.291 69.134 27.483 1.00 1.00 ATOM 28 CA GLN 22 48.733 70.399 28.490 1.00 1.00 ATOM 29 CA GLN 23 48.668 72.296 31.836 1.00 1.00 ATOM 30 CA PRO 26 45.140 71.102 32.533 1.00 1.00 ATOM 31 CA ASP 27 46.759 67.636 33.120 1.00 1.00 ATOM 32 CA TYR 28 47.589 67.177 36.706 1.00 1.00 ATOM 33 CA THR 29 48.507 63.511 36.604 1.00 1.00 ATOM 34 CA VAL 30 48.519 60.587 34.255 1.00 1.00 ATOM 35 CA TRP 31 48.872 57.055 35.443 1.00 1.00 ATOM 36 CA ALA 32 48.416 53.452 34.540 1.00 1.00 ATOM 37 CA PHE 33 46.405 50.799 36.158 1.00 1.00 ATOM 38 CA GLY 34 45.358 47.305 35.551 1.00 1.00 ATOM 39 CA SER 35 47.475 44.305 34.904 1.00 1.00 ATOM 40 CA ARG 36 49.915 46.589 33.249 1.00 1.00 ATOM 41 CA VAL 37 50.125 48.972 36.253 1.00 1.00 ATOM 42 CA LYS 38 51.307 46.129 38.483 1.00 1.00 ATOM 43 CA GLY 39 53.134 44.573 35.633 1.00 1.00 ATOM 44 CA LYS 40 51.189 41.424 36.058 1.00 1.00 ATOM 45 CA ALA 41 50.130 41.960 32.453 1.00 1.00 ATOM 46 CA LYS 42 49.610 39.105 29.987 1.00 1.00 ATOM 47 CA LYS 43 49.951 38.419 26.252 1.00 1.00 ATOM 48 CA TYR 44 46.373 39.415 25.508 1.00 1.00 ATOM 49 CA SER 45 45.954 42.025 28.337 1.00 1.00 ATOM 50 CA ASP 46 44.666 45.570 27.764 1.00 1.00 ATOM 51 CA LEU 47 45.612 49.144 28.621 1.00 1.00 TER END ################################ # # # END # # # ################################ From mailer@bialko.llnl.gov Tue Jun 4 12:47:42 2002 Date: Tue, 4 Jun 2002 12:47:33 -0700 (PDT) From: Automatic Reply To: karplus@soe.ucsc.edu Subject: T0130 TS samt99.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 12:21:29 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_330900_10460 # (PIN number is not an ACCESSION CODE) # Thank you for your submission. Your prediction has been accepted with an ACCESSION CODE: T0130TS007_1 Current information on models submitted in prediction T0130TS007 MODEL_INDEX PIN CODE DATE E-mail T0130TS007_1 PIN_330900_10460 6269-7633-6117 06/04/02 12:21:29 casp5@bialko.llnl.gov T0130TS007_5 PIN_325546_10459 6269-7633-6117 06/04/02 12:21:15 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 T0130TS007_1 PIN_330900_10460 6269-7633-6117 06/04/02 12:21:29 casp5@bialko.llnl.gov T0130TS007_5 PIN_325546_10459 6269-7633-6117 06/04/02 12:21:15 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 6269-7633-6117 # Reading MODEL 1 PARENT 1FA0_B # Loading PARENT structure: 1fa0 (chain: B) # Number of residues in PARENT structure: 511 # Reading prediction format TS (DONE) # Checking the TS prediction MODEL 1 # IMPORTANT NOTE! Not complete main chain atoms for residue K 10 # !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! # # 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 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 # 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 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 # IMPORTANT NOTE! Not complete main chain atoms for residue S 87 # IMPORTANT NOTE! Not complete main chain atoms for residue E 88 # IMPORTANT NOTE! Not complete main chain atoms for residue D 89 # IMPORTANT NOTE! Not complete main chain atoms for residue F 90 # IMPORTANT NOTE! Not complete main chain atoms for residue R 91 # IMPORTANT NOTE! Not complete main chain atoms for residue E 92 # IMPORTANT NOTE! Not complete main chain atoms for residue I 93 # IMPORTANT NOTE! Not complete main chain atoms for residue I 94 # IMPORTANT NOTE! Not complete main chain atoms for residue R 95 # IMPORTANT NOTE! Not complete main chain atoms for residue K 96 # IMPORTANT NOTE! Not complete main chain atoms for residue V 97 # IMPORTANT NOTE! Not complete main chain atoms for residue Y 98 # IMPORTANT NOTE! Not complete main chain atoms for residue V 99 # IMPORTANT NOTE! Not complete main chain atoms for residue V 100 # IMPORTANT NOTE! Not complete main chain atoms for residue I 101 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 102 # IMPORTANT NOTE! Not complete main chain atoms for residue E 103 # IMPORTANT NOTE! Not complete main chain atoms for residue K 104 # IMPORTANT NOTE! Not complete main chain atoms for residue E 105 # IMPORTANT NOTE! Not complete main chain atoms for residue K 106 # IMPORTANT NOTE! Not complete main chain atoms for residue T 107 # IMPORTANT NOTE! Not complete main chain atoms for residue V 108 # IMPORTANT NOTE! Not complete main chain atoms for residue E 109 # IMPORTANT NOTE! Not complete main chain atoms for residue K 110 # IMPORTANT NOTE! Not complete main chain atoms for residue P 111 # IMPORTANT NOTE! Not complete main chain atoms for residue T 112 # IMPORTANT NOTE! Not complete main chain atoms for residue A 113 # IMPORTANT NOTE! Not complete main chain atoms for residue L 114 # 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: 104 # Total number of atoms in model: 104 # Number of atoms with 1.0 occupancy: 104 # Number of fragments in model: 1 # Number of METHOD records: 1 # No errors. # Number of Warnings: 104 ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT TS TARGET T0130 AUTHOR 6269-7633-6117 METHOD CAFASP MODEL 1 PARENT 1FA0_B ATOM 44 CA LYS 10 52.045 81.496 104.650 1.00 1.00 ATOM 45 CA SER 11 52.060 80.262 101.059 1.00 1.00 ATOM 46 CA GLU 12 55.756 79.382 101.128 1.00 1.00 ATOM 47 CA GLU 13 55.024 77.284 104.235 1.00 1.00 ATOM 48 CA LEU 14 52.406 75.213 102.425 1.00 1.00 ATOM 49 CA ALA 15 54.984 74.691 99.647 1.00 1.00 ATOM 50 CA ILE 16 57.576 73.614 102.216 1.00 1.00 ATOM 51 CA VAL 17 55.229 71.088 103.828 1.00 1.00 ATOM 52 CA LYS 18 54.597 69.571 100.404 1.00 1.00 ATOM 53 CA THR 19 58.352 69.243 99.751 1.00 1.00 ATOM 54 CA ILE 20 58.617 67.143 102.894 1.00 1.00 ATOM 55 CA LEU 21 55.462 65.219 102.063 1.00 1.00 ATOM 56 CA GLN 22 56.823 64.279 98.605 1.00 1.00 ATOM 57 CA GLN 23 60.062 63.015 100.241 1.00 1.00 ATOM 58 CA LEU 24 58.027 60.966 102.701 1.00 1.00 ATOM 59 CA VAL 25 55.847 59.583 99.897 1.00 1.00 ATOM 60 CA PRO 26 59.016 58.458 98.146 1.00 1.00 ATOM 81 CA ASP 27 59.114 56.251 92.965 1.00 1.00 ATOM 82 CA TYR 28 56.096 57.830 94.614 1.00 1.00 ATOM 83 CA THR 29 54.591 61.217 93.836 1.00 1.00 ATOM 84 CA VAL 30 52.247 63.769 95.423 1.00 1.00 ATOM 85 CA TRP 31 49.518 65.815 93.763 1.00 1.00 ATOM 86 CA ALA 32 46.947 68.289 95.043 1.00 1.00 ATOM 87 CA PHE 33 43.299 68.965 94.353 1.00 1.00 ATOM 88 CA GLY 34 40.734 71.186 96.025 1.00 1.00 ATOM 89 CA SER 35 41.118 74.898 96.728 1.00 1.00 ATOM 90 CA ARG 36 44.921 74.891 96.932 1.00 1.00 ATOM 91 CA VAL 37 45.400 73.321 93.499 1.00 1.00 ATOM 92 CA LYS 38 43.039 75.917 92.000 1.00 1.00 ATOM 93 CA GLY 39 44.839 78.734 93.798 1.00 1.00 ATOM 94 CA LYS 40 41.723 79.992 95.543 1.00 1.00 ATOM 95 CA ALA 41 42.500 78.742 99.056 1.00 1.00 ATOM 96 CA LYS 42 42.649 80.894 102.174 1.00 1.00 ATOM 97 CA LYS 43 44.852 80.890 105.290 1.00 1.00 ATOM 98 CA TYR 44 42.316 78.761 107.128 1.00 1.00 ATOM 99 CA SER 45 41.827 76.325 104.258 1.00 1.00 ATOM 100 CA ASP 46 43.770 73.050 104.213 1.00 1.00 ATOM 101 CA LEU 47 45.730 71.240 101.500 1.00 1.00 ATOM 102 CA ASP 48 43.915 68.172 100.111 1.00 1.00 ATOM 103 CA LEU 49 46.640 65.755 98.999 1.00 1.00 ATOM 104 CA ALA 50 46.795 62.736 96.682 1.00 1.00 ATOM 105 CA ILE 51 49.625 60.250 97.146 1.00 1.00 ATOM 106 CA ILE 52 50.218 57.957 94.157 1.00 1.00 ATOM 112 CA SER 53 48.747 48.449 99.181 1.00 1.00 ATOM 113 CA GLU 54 46.157 50.319 101.233 1.00 1.00 ATOM 114 CA GLU 55 47.445 48.549 104.343 1.00 1.00 ATOM 115 CA PRO 56 50.955 49.808 103.609 1.00 1.00 ATOM 116 CA LEU 57 49.460 53.311 103.525 1.00 1.00 ATOM 117 CA ASP 58 47.887 53.195 106.988 1.00 1.00 ATOM 118 CA PHE 59 50.975 51.423 108.314 1.00 1.00 ATOM 119 CA LEU 60 54.264 52.513 106.768 1.00 1.00 ATOM 120 CA ALA 61 53.237 55.997 105.640 1.00 1.00 ATOM 121 CA ARG 62 51.518 56.475 109.015 1.00 1.00 ATOM 122 CA ASP 63 54.735 55.696 110.888 1.00 1.00 ATOM 123 CA ARG 64 56.898 57.966 108.698 1.00 1.00 ATOM 124 CA LEU 65 54.631 60.910 109.528 1.00 1.00 ATOM 125 CA LYS 66 54.621 60.126 113.232 1.00 1.00 ATOM 126 CA GLU 67 58.404 60.247 113.239 1.00 1.00 ATOM 127 CA ALA 68 58.375 63.957 112.436 1.00 1.00 ATOM 128 CA PHE 69 58.493 66.986 114.703 1.00 1.00 ATOM 129 CA SER 70 56.351 69.074 112.332 1.00 1.00 ATOM 130 CA GLU 71 53.550 66.606 113.047 1.00 1.00 ATOM 131 CA SER 72 50.972 68.197 115.394 1.00 1.00 ATOM 132 CA ASP 73 47.943 65.912 115.065 1.00 1.00 ATOM 133 CA LEU 74 47.076 62.806 113.073 1.00 1.00 ATOM 134 CA TRP 76 43.759 61.001 112.649 1.00 1.00 ATOM 135 CA ARG 77 43.704 57.826 110.511 1.00 1.00 ATOM 136 CA VAL 78 40.358 57.048 108.852 1.00 1.00 ATOM 137 CA ASP 79 40.630 53.660 107.074 1.00 1.00 ATOM 197 CA LEU 80 39.284 72.875 84.832 1.00 1.00 ATOM 198 CA LEU 81 42.464 74.930 84.946 1.00 1.00 ATOM 199 CA ASP 82 43.221 73.986 81.333 1.00 1.00 ATOM 200 CA TRP 83 39.712 74.888 80.243 1.00 1.00 ATOM 201 CA ALA 84 39.543 78.562 81.172 1.00 1.00 ATOM 202 CA THR 85 40.808 81.655 79.276 1.00 1.00 ATOM 203 CA THR 86 42.690 83.444 82.085 1.00 1.00 ATOM 204 CA SER 87 43.461 81.340 85.176 1.00 1.00 ATOM 205 CA GLU 88 43.876 84.313 87.538 1.00 1.00 ATOM 206 CA ASP 89 40.694 86.101 86.362 1.00 1.00 ATOM 207 CA PHE 90 38.994 82.771 87.108 1.00 1.00 ATOM 208 CA ARG 91 40.584 82.490 90.564 1.00 1.00 ATOM 209 CA GLU 92 39.238 85.885 91.631 1.00 1.00 ATOM 210 CA ILE 93 35.707 85.292 90.363 1.00 1.00 ATOM 211 CA ILE 94 35.784 81.860 92.026 1.00 1.00 ATOM 212 CA ARG 95 36.859 83.505 95.287 1.00 1.00 ATOM 213 CA LYS 96 33.958 85.955 95.032 1.00 1.00 ATOM 214 CA VAL 97 31.422 83.221 94.177 1.00 1.00 ATOM 421 CA TYR 98 19.171 62.467 129.315 1.00 1.00 ATOM 422 CA VAL 99 15.386 62.080 129.033 1.00 1.00 ATOM 423 CA VAL 100 15.152 65.758 130.010 1.00 1.00 ATOM 424 CA ILE 101 17.599 67.058 127.400 1.00 1.00 ATOM 425 CA GLN 102 15.296 65.455 124.838 1.00 1.00 ATOM 426 CA GLU 103 12.044 67.158 125.856 1.00 1.00 ATOM 427 CA LYS 104 13.542 70.493 126.923 1.00 1.00 ATOM 428 CA GLU 105 15.760 71.034 123.869 1.00 1.00 ATOM 429 CA LYS 106 14.147 72.471 120.755 1.00 1.00 ATOM 430 CA THR 107 12.030 75.475 121.712 1.00 1.00 ATOM 431 CA VAL 108 12.927 78.673 123.556 1.00 1.00 ATOM 432 CA GLU 109 10.179 78.094 126.143 1.00 1.00 ATOM 433 CA LYS 110 11.836 74.993 127.605 1.00 1.00 ATOM 434 CA PRO 111 15.371 75.588 126.239 1.00 1.00 ATOM 435 CA THR 112 16.643 77.233 129.445 1.00 1.00 ATOM 436 CA ALA 113 15.881 73.976 131.285 1.00 1.00 ATOM 437 CA LEU 114 19.096 72.500 129.853 1.00 1.00 TER END ################################ # # # END # # # ################################ From mailer@bialko.llnl.gov Tue Jun 4 12:48:42 2002 Date: Tue, 4 Jun 2002 12:48:34 -0700 (PDT) From: Automatic Reply To: karplus@soe.ucsc.edu Subject: T0130 TS samt99.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 12:22:25 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_336685_10464 # (PIN number is not an ACCESSION CODE) # Thank you for your submission. Your prediction has been accepted with an ACCESSION CODE: T0130TS007_2 Current information on models submitted in prediction T0130TS007 MODEL_INDEX PIN CODE DATE E-mail T0130TS007_2 PIN_336685_10464 6269-7633-6117 06/04/02 12:22:25 casp5@bialko.llnl.gov T0130TS007_1 PIN_330900_10460 6269-7633-6117 06/04/02 12:21:29 casp5@bialko.llnl.gov T0130TS007_5 PIN_325546_10459 6269-7633-6117 06/04/02 12:21:15 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 T0130TS007_1 PIN_330900_10460 6269-7633-6117 06/04/02 12:21:29 casp5@bialko.llnl.gov T0130TS007_2 PIN_336685_10464 6269-7633-6117 06/04/02 12:22:25 casp5@bialko.llnl.gov T0130TS007_5 PIN_325546_10459 6269-7633-6117 06/04/02 12:21:15 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 6269-7633-6117 # Reading MODEL 2 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 2 # IMPORTANT NOTE! Not complete main chain atoms for residue E 12 # !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! # # 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 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 # 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 # 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: 47 # Total number of atoms in model: 47 # Number of atoms with 1.0 occupancy: 47 # Number of fragments in model: 1 # Number of METHOD records: 1 # No errors. # Number of Warnings: 47 ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT TS TARGET T0130 AUTHOR 6269-7633-6117 METHOD CAFASP MODEL 2 PARENT 1FA0_A ATOM 50 CA GLU 12 61.395 39.531 58.576 1.00 1.00 ATOM 51 CA GLU 13 62.830 36.836 60.842 1.00 1.00 ATOM 52 CA LEU 14 63.872 39.498 63.361 1.00 1.00 ATOM 53 CA ALA 15 60.402 41.057 63.182 1.00 1.00 ATOM 54 CA ILE 16 58.935 37.705 64.189 1.00 1.00 ATOM 55 CA VAL 17 61.570 37.164 66.910 1.00 1.00 ATOM 56 CA LYS 18 60.650 40.529 68.434 1.00 1.00 ATOM 57 CA THR 19 57.008 39.372 68.383 1.00 1.00 ATOM 58 CA ILE 20 58.147 36.216 70.186 1.00 1.00 ATOM 59 CA LEU 21 60.252 38.085 72.751 1.00 1.00 ATOM 60 CA GLN 22 57.266 40.189 73.759 1.00 1.00 ATOM 61 CA GLN 23 55.024 37.100 73.844 1.00 1.00 ATOM 78 CA LEU 24 51.978 43.836 78.119 1.00 1.00 ATOM 79 CA VAL 25 53.864 46.808 79.549 1.00 1.00 ATOM 80 CA PRO 26 56.620 44.554 80.925 1.00 1.00 ATOM 81 CA ASP 27 57.667 44.527 77.276 1.00 1.00 ATOM 82 CA TYR 28 60.670 42.575 76.067 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 TER END ################################ # # # END # # # ################################ From mailer@bialko.llnl.gov Tue Jun 4 12:49:30 2002 Date: Tue, 4 Jun 2002 12:49:23 -0700 (PDT) From: Automatic Reply To: karplus@soe.ucsc.edu Subject: T0130 TS samt99.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 12:23:08 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_345457_10467 # (PIN number is not an ACCESSION CODE) # Thank you for your submission. Your prediction has been accepted with an ACCESSION CODE: T0130TS007_3 Current information on models submitted in prediction T0130TS007 MODEL_INDEX PIN CODE DATE E-mail T0130TS007_3 PIN_345457_10467 6269-7633-6117 06/04/02 12:23:08 casp5@bialko.llnl.gov T0130TS007_2 PIN_336685_10464 6269-7633-6117 06/04/02 12:22:25 casp5@bialko.llnl.gov T0130TS007_1 PIN_330900_10460 6269-7633-6117 06/04/02 12:21:29 casp5@bialko.llnl.gov T0130TS007_5 PIN_325546_10459 6269-7633-6117 06/04/02 12:21:15 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 T0130TS007_1 PIN_330900_10460 6269-7633-6117 06/04/02 12:21:29 casp5@bialko.llnl.gov T0130TS007_2 PIN_336685_10464 6269-7633-6117 06/04/02 12:22:25 casp5@bialko.llnl.gov T0130TS007_3 PIN_345457_10467 6269-7633-6117 06/04/02 12:23:08 casp5@bialko.llnl.gov T0130TS007_5 PIN_325546_10459 6269-7633-6117 06/04/02 12:21:15 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 6269-7633-6117 # Reading MODEL 3 PARENT 1F5A_A # Loading PARENT structure: 1f5a (chain: A) # Number of residues in PARENT structure: 455 # Reading prediction format TS (DONE) # Checking the TS prediction MODEL 3 # IMPORTANT NOTE! Not complete main chain atoms for residue A 5 # !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! # # 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 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 # 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 # 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: 54 # Total number of atoms in model: 54 # Number of atoms with 1.0 occupancy: 54 # Number of fragments in model: 1 # Number of METHOD records: 1 # No errors. # Number of Warnings: 54 ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT TS TARGET T0130 AUTHOR 6269-7633-6117 METHOD CAFASP MODEL 3 PARENT 1F5A_A ATOM 56 CA ALA 5 40.608 38.588 -0.111 1.00 1.00 ATOM 57 CA GLN 6 40.688 38.532 -3.887 1.00 1.00 ATOM 58 CA LEU 7 38.788 41.792 -4.135 1.00 1.00 ATOM 59 CA ASP 8 41.373 43.351 -1.810 1.00 1.00 ATOM 60 CA ILE 9 44.164 41.865 -3.875 1.00 1.00 ATOM 61 CA LYS 10 42.683 43.252 -7.122 1.00 1.00 ATOM 62 CA SER 11 42.307 46.653 -5.470 1.00 1.00 ATOM 63 CA GLU 12 45.986 46.707 -4.509 1.00 1.00 ATOM 64 CA GLU 13 47.010 45.634 -7.988 1.00 1.00 ATOM 65 CA LEU 14 45.015 48.417 -9.614 1.00 1.00 ATOM 66 CA ALA 15 46.596 50.925 -7.243 1.00 1.00 ATOM 67 CA ILE 16 50.054 49.798 -8.276 1.00 1.00 ATOM 68 CA VAL 17 49.035 50.093 -11.939 1.00 1.00 ATOM 69 CA LYS 18 47.623 53.558 -11.430 1.00 1.00 ATOM 70 CA THR 19 50.901 54.578 -9.849 1.00 1.00 ATOM 71 CA ILE 20 52.745 53.082 -12.815 1.00 1.00 ATOM 72 CA LEU 21 50.598 55.214 -15.094 1.00 1.00 ATOM 73 CA GLN 22 51.265 58.383 -13.100 1.00 1.00 ATOM 74 CA GLN 23 54.981 57.581 -12.986 1.00 1.00 ATOM 75 CA LEU 24 55.076 57.013 -16.758 1.00 1.00 ATOM 92 CA VAL 25 50.093 68.810 -11.710 1.00 1.00 ATOM 93 CA PRO 26 49.800 66.724 -14.871 1.00 1.00 ATOM 94 CA ASP 27 47.560 63.878 -13.871 1.00 1.00 ATOM 95 CA TYR 28 47.142 60.433 -15.289 1.00 1.00 ATOM 96 CA THR 29 44.738 57.837 -14.056 1.00 1.00 ATOM 97 CA VAL 30 43.526 54.345 -14.808 1.00 1.00 ATOM 98 CA TRP 31 39.713 53.887 -14.975 1.00 1.00 ATOM 99 CA ALA 32 38.142 50.444 -14.565 1.00 1.00 ATOM 100 CA PHE 33 34.952 49.754 -16.493 1.00 1.00 ATOM 101 CA GLY 34 32.639 46.933 -17.435 1.00 1.00 ATOM 102 CA SER 35 31.802 44.119 -15.014 1.00 1.00 ATOM 103 CA ARG 36 34.486 44.669 -12.420 1.00 1.00 ATOM 104 CA VAL 37 33.330 48.292 -12.260 1.00 1.00 ATOM 105 CA LYS 38 29.671 47.285 -11.914 1.00 1.00 ATOM 106 CA GLY 39 30.641 45.122 -8.983 1.00 1.00 ATOM 107 CA LYS 40 29.586 41.862 -10.643 1.00 1.00 ATOM 108 CA ALA 41 32.934 40.637 -11.978 1.00 1.00 ATOM 109 CA LYS 42 32.844 37.131 -13.411 1.00 1.00 ATOM 110 CA LYS 43 35.407 35.020 -11.490 1.00 1.00 ATOM 111 CA TYR 44 37.930 33.894 -14.100 1.00 1.00 ATOM 112 CA SER 45 37.470 36.971 -16.283 1.00 1.00 ATOM 113 CA ASP 46 39.948 39.813 -16.709 1.00 1.00 ATOM 114 CA LEU 47 39.730 43.355 -15.377 1.00 1.00 ATOM 115 CA ASP 48 39.086 45.934 -18.083 1.00 1.00 ATOM 116 CA LEU 49 40.690 49.330 -17.635 1.00 1.00 ATOM 117 CA ALA 50 41.259 52.594 -19.481 1.00 1.00 ATOM 118 CA ILE 51 44.492 54.549 -19.122 1.00 1.00 ATOM 119 CA ILE 52 43.605 58.240 -19.370 1.00 1.00 ATOM 120 CA SER 53 46.500 60.557 -20.168 1.00 1.00 ATOM 121 CA GLU 54 46.809 64.311 -21.005 1.00 1.00 ATOM 122 CA GLU 55 47.441 65.909 -24.454 1.00 1.00 ATOM 123 CA PRO 56 51.252 65.664 -24.533 1.00 1.00 ATOM 124 CA LEU 57 51.168 61.865 -24.387 1.00 1.00 ATOM 125 CA ASP 58 50.799 60.009 -27.704 1.00 1.00 TER END ################################ # # # END # # # ################################ From mailer@bialko.llnl.gov Tue Jun 4 12:49:40 2002 Date: Tue, 4 Jun 2002 12:49:33 -0700 (PDT) From: Automatic Reply To: karplus@soe.ucsc.edu Subject: T0130 TS samt99.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 12:23:22 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_346255_10468 # (PIN number is not an ACCESSION CODE) # Thank you for your submission. Your prediction has been accepted with an ACCESSION CODE: T0130TS007_4 Current information on models submitted in prediction T0130TS007 MODEL_INDEX PIN CODE DATE E-mail T0130TS007_4 PIN_346255_10468 6269-7633-6117 06/04/02 12:23:22 casp5@bialko.llnl.gov T0130TS007_3 PIN_345457_10467 6269-7633-6117 06/04/02 12:23:08 casp5@bialko.llnl.gov T0130TS007_2 PIN_336685_10464 6269-7633-6117 06/04/02 12:22:25 casp5@bialko.llnl.gov T0130TS007_1 PIN_330900_10460 6269-7633-6117 06/04/02 12:21:29 casp5@bialko.llnl.gov T0130TS007_5 PIN_325546_10459 6269-7633-6117 06/04/02 12:21:15 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 T0130TS007_1 PIN_330900_10460 6269-7633-6117 06/04/02 12:21:29 casp5@bialko.llnl.gov T0130TS007_2 PIN_336685_10464 6269-7633-6117 06/04/02 12:22:25 casp5@bialko.llnl.gov T0130TS007_3 PIN_345457_10467 6269-7633-6117 06/04/02 12:23:08 casp5@bialko.llnl.gov T0130TS007_4 PIN_346255_10468 6269-7633-6117 06/04/02 12:23:22 casp5@bialko.llnl.gov T0130TS007_5 PIN_325546_10459 6269-7633-6117 06/04/02 12:21:15 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 6269-7633-6117 # Reading MODEL 4 PARENT 1KNY_A # Loading PARENT structure: 1kny (chain: A) # Number of residues in PARENT structure: 253 # Reading prediction format TS (DONE) # Checking the TS prediction MODEL 4 # 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 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 # 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: 45 # Total number of atoms in model: 45 # Number of atoms with 1.0 occupancy: 45 # Number of fragments in model: 1 # Number of METHOD records: 1 # No errors. # Number of Warnings: 45 ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT TS TARGET T0130 AUTHOR 6269-7633-6117 METHOD CAFASP MODEL 4 PARENT 1KNY_A ATOM 7 CA MET 1 3.159 34.969 49.071 1.00 1.00 ATOM 8 CA THR 2 0.378 35.578 46.765 1.00 1.00 ATOM 9 CA SER 3 -0.220 38.111 44.174 1.00 1.00 ATOM 10 CA PHE 4 -3.094 39.144 46.384 1.00 1.00 ATOM 11 CA ALA 5 -0.777 39.577 49.368 1.00 1.00 ATOM 12 CA GLN 6 1.688 41.320 47.269 1.00 1.00 ATOM 13 CA LEU 7 -0.804 43.694 45.975 1.00 1.00 ATOM 14 CA ASP 8 -2.041 44.740 49.468 1.00 1.00 ATOM 15 CA ILE 9 1.533 45.659 50.182 1.00 1.00 ATOM 16 CA LYS 10 1.576 47.706 46.961 1.00 1.00 ATOM 17 CA SER 11 -1.488 49.515 48.179 1.00 1.00 ATOM 18 CA GLU 12 -0.162 49.896 51.671 1.00 1.00 ATOM 19 CA GLU 13 2.966 51.532 50.311 1.00 1.00 ATOM 20 CA LEU 14 1.037 53.592 47.881 1.00 1.00 ATOM 21 CA ALA 15 -0.978 55.116 50.752 1.00 1.00 ATOM 22 CA ILE 16 2.213 55.887 52.559 1.00 1.00 ATOM 23 CA VAL 17 3.825 57.635 49.628 1.00 1.00 ATOM 24 CA LYS 18 0.863 59.981 49.387 1.00 1.00 ATOM 25 CA THR 19 0.502 60.703 53.071 1.00 1.00 ATOM 26 CA ILE 20 4.257 61.649 53.061 1.00 1.00 ATOM 27 CA LEU 21 4.686 63.554 49.784 1.00 1.00 ATOM 28 CA GLN 22 1.129 64.336 48.809 1.00 1.00 ATOM 29 CA GLN 23 1.067 66.946 46.023 1.00 1.00 ATOM 30 CA PRO 26 4.670 66.084 45.163 1.00 1.00 ATOM 31 CA ASP 27 3.571 62.670 43.755 1.00 1.00 ATOM 32 CA TYR 28 2.632 62.648 40.125 1.00 1.00 ATOM 33 CA THR 29 2.053 58.978 39.552 1.00 1.00 ATOM 34 CA VAL 30 3.011 55.561 41.029 1.00 1.00 ATOM 35 CA TRP 31 3.586 52.243 39.244 1.00 1.00 ATOM 36 CA ALA 32 4.318 48.523 39.728 1.00 1.00 ATOM 37 CA PHE 33 6.908 47.085 37.507 1.00 1.00 ATOM 38 CA GLY 34 8.444 43.617 37.297 1.00 1.00 ATOM 39 CA SER 35 6.727 40.265 37.601 1.00 1.00 ATOM 40 CA ARG 36 4.016 41.844 39.627 1.00 1.00 ATOM 41 CA VAL 37 3.366 44.648 37.129 1.00 1.00 ATOM 42 CA LYS 38 3.353 41.853 34.526 1.00 1.00 ATOM 43 CA GLY 39 1.102 39.774 36.804 1.00 1.00 ATOM 44 CA LYS 40 3.461 36.846 36.326 1.00 1.00 ATOM 45 CA ALA 41 4.803 37.108 39.851 1.00 1.00 ATOM 46 CA LYS 42 5.939 33.940 41.433 1.00 1.00 ATOM 47 CA LYS 43 5.835 32.649 44.892 1.00 1.00 ATOM 48 CA TYR 44 9.206 34.117 46.038 1.00 1.00 ATOM 49 CA SER 45 8.848 37.287 44.028 1.00 1.00 ATOM 50 CA ASP 46 9.706 40.818 45.139 1.00 1.00 ATOM 51 CA LEU 47 7.998 44.085 44.771 1.00 1.00 TER END ################################ # # # END # # # ################################ From mailer@bialko.llnl.gov Sat Jun 15 15:28:28 2002 Date: Sat, 15 Jun 2002 15:28:22 -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 15:02:01 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_134830_10760 # (PIN number is not an ACCESSION CODE) # Thank you for your submission. Your prediction has been accepted with an ACCESSION CODE: T0130SS007_1 Current information on models submitted in prediction T0130SS007 MODEL_INDEX PIN CODE DATE E-mail T0130SS007_1 PIN_134830_10760 6269-7633-6117 06/15/02 15:02:01 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 T0130TS007_1 PIN_330900_10460 6269-7633-6117 06/04/02 12:21:29 casp5@bialko.llnl.gov T0130TS007_2 PIN_336685_10464 6269-7633-6117 06/04/02 12:22:25 casp5@bialko.llnl.gov T0130TS007_3 PIN_345457_10467 6269-7633-6117 06/04/02 12:23:08 casp5@bialko.llnl.gov T0130TS007_4 PIN_346255_10468 6269-7633-6117 06/04/02 12:23:22 casp5@bialko.llnl.gov T0130TS007_5 PIN_325546_10459 6269-7633-6117 06/04/02 12:21:15 casp5@bialko.llnl.gov T0130SS007_1 PIN_134830_10760 6269-7633-6117 06/15/02 15:02:01 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 6269-7633-6117 # 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: 42 # No errors. ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT SS TARGET T0130 AUTHOR 6269-7633-6117 METHOD CAFASP METHOD samt99 METHOD This prediction was derived from the following methods METHOD by averaging the corresponding probabilities: METHOD Method 0: METHOD TARGET seed-seqs-24065.a2m(1) METHOD Using neural net overrep-2500-IDaa13-5-9-7-10-5-9-11-ehl2-seeded2-stride-trained.net METHOD This is a 4-layer network, with METHOD window units METHOD 5 9 METHOD 7 10 METHOD 5 9 METHOD 11 3 (1 EHL2 ) METHOD The input amino acid frequencies were determined from METHOD alignment /var/tmp/hmm-target99-work-23837//target-align-23837.a2m METHOD with weighted counts, using EntropyWeight(1.4 bits/column, 10) METHOD The weighting was determined by the posterior distribution METHOD after regularizing with /projects/compbio/lib/recode3.20comp. METHOD Counts were regularized to probabilities using METHOD /projects/compbio/lib/recode3.20comp METHOD Total sequence weight for alignment was 84.862 METHOD METHOD CHAIN 1 METHOD Method 1: METHOD Prediction using SAM HMM nearest-neighbor METHOD sequence: seed-seqs-24065.a2m(1) METHOD model_file: /projects/compbio/tmp/sam-nn-tmp.cc44.30505/model.mod METHOD database_files: /projects/compbio/programs/hmm-server-2.0/src/pcc/data/overrep-2260.verify.mixed.seq /projects/compbio/programs/hmm-server-2.0/src/pcc/data/overrep-2260.verify.mixed.2d METHOD scoring_mode: local METHOD null_model: reverse METHOD scoring_algorithm: EM METHOD adjust_score: 2 METHOD date: Wed May 29 21:07:15 2002 METHOD Method 2: METHOD ###begin 0 METHOD METHOD Protein secondary structure prediction by universal HMM METHOD HMM file: /projects/compbio/programs/hmm-server-2.0/src/pcc/scripts/gdac.test.initreest.38state.abb.isites.gd.updated.ghmm-128reest-1-128-105-0.07gd METHOD Alignment file: /var/tmp/hmm-target99-work-23837//target-align-23837.a2m METHOD METHOD guide seq name: seed-seqs-24065.a2m(1), 114 bases, D420CC5B checksum. METHOD ###end 0 MODEL 1 M C 0.555 T C 0.476 S H 0.584 F H 0.688 A H 0.688 Q H 0.722 L H 0.771 D H 0.777 I H 0.78 K H 0.812 S H 0.832 E H 0.835 E H 0.829 L H 0.841 A H 0.848 I H 0.839 V H 0.835 K H 0.836 T H 0.836 I H 0.814 L H 0.784 Q H 0.71 Q H 0.615 L C 0.514 V C 0.62 P C 0.604 D C 0.471 Y E 0.441 T E 0.585 V E 0.658 W E 0.683 A E 0.676 F E 0.645 G E 0.515 S E 0.428 R E 0.412 V C 0.443 K C 0.538 G C 0.646 K C 0.636 A C 0.595 K C 0.628 K C 0.602 Y C 0.606 S C 0.684 D C 0.584 L C 0.421 D E 0.422 L E 0.67 A E 0.706 I E 0.718 I E 0.664 S E 0.455 E C 0.538 E C 0.622 P C 0.638 L C 0.593 D C 0.542 F H 0.512 L H 0.59 A H 0.661 R H 0.714 D H 0.732 R H 0.734 L H 0.74 K H 0.742 E H 0.74 A H 0.728 F H 0.706 S H 0.659 E H 0.604 S H 0.436 D C 0.622 L C 0.628 P C 0.664 W C 0.62 R C 0.513 V C 0.437 D C 0.433 L E 0.529 L E 0.558 D E 0.573 W E 0.571 A E 0.506 T C 0.4 T C 0.597 S H 0.527 E H 0.67 D H 0.686 F H 0.686 R H 0.682 E H 0.69 I H 0.69 I H 0.675 R H 0.67 K H 0.675 V H 0.67 Y H 0.646 V H 0.654 V H 0.663 I H 0.665 Q H 0.682 E H 0.693 K H 0.695 E H 0.678 K H 0.647 T H 0.523 V C 0.516 E C 0.441 K C 0.389 P C 0.483 T C 0.691 A C 0.824 L C 0.845 END ################################ # # # END # # # ################################